title: Candida albicans, CRISPRa non-targeting control, rep3

city: Guelph

first: Rebecca

middle: S

last: Shapiro

state: ON

address: 50 Stone Road East

department: Molecular and Cellular Biology

institute: University of Guelph

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the candida_albicans reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the control and experimental groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Candida albicans SC5314 (assembly ASM18296v3).
Supplementary files format and content: Tab-delimited text files including transcript hit counts .

organism: Candida albicans

source_name: Total

growth_protocol: All strains were grown in YPD at 30°C.

extract_protocol:
RNA extraction and sample QC was conducted at GENEWIZ, LLC./Azenta US, Inc (South Plainfield, NJ, USA) as follows:  Total RNA was extracted using Qiagen RNeasy Plus Universal kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
Library preparations and sequencing reactions were conducted at GENEWIZ, LLC./Azenta US, Inc (South Plainfield, NJ, USA) as follows: ERCC RNA Spike-In Mix kit (cat. 4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq 4000 or equivalent instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Illumina Control Software. Raw sequence data (.bcl files) generated from the Illumina instrument was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

value: Total

tag: cell line

value: CRISPRa Control (WT with Non-Targeting CRISPRa Construct)


title: Candida albicans, CRISPRa targeting ALS1, rep1

status: Public on May 03 2022

type: SRA

country: Canada

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: M2_8_DMSO_ctrl

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

data_processing:
Base-calling was performed with Illumina NovaSeq 6000 Sequencing System.
Alignment was performed with Bowtie2 (2.3.5)
Quantification of amplicon-mapping reads was performed with BEDtools (2.29.2)
QC and filtering was performed with BioQC (1.20.0), ribiosExpression (1.1.9), and ribiosNGS (1.1.30), as well as custom software.
Factor analysis was performed with R (4.0.1) and the psych package (2.1.6)
Differential gene expression was performed with edgeR (3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements are tab-delimited files, containing genes and number of reads mapped to the pre-defined amplicons; raw counts are in the GCT (version 1.2) file, a tab-delimited format of aggregated gene counts.

organism: Homo sapiens

source_name: Human induced pluripotent-stem-cell derived embryoid body

growth_protocol: The cells were passaged twice a week with a defined cell number of 2.4 × 104 cells/cm2 (three-day culture) or 1.2 × 104 cells/cm2 (four-day culture) to achieve a maximum confluence of 80%. The medium was removed and the cells were detached with StemPro Accutase™ Cell Dissociation Reagent (Thermo Fisher Scientific) for five minutes at 37°C/ 5% CO2. Cell detachment was stopped by adding StemFlex™ Medium (Thermo Fisher Scientific) to the detached cells, followed by centrifugation for five minutes at 240 × g. Afterwards, the cell pellet was gently suspended in culture medium and the cells were seeded into Geltrex™ coated culture flasks with complete StemFlex™ (containing 10% StemFlex™ Supplement and 1% RevitaCell™). StemFlex™ w/o RevitaCell™ replaced the medium completely the day after cell propagation. The cells were cultured throughout in a humidified incubator (Binder, Germany) at 37°C and 5% CO2.

extract_protocol:
Differentiated EBs were lysed after 7 days of differentiation in 350 μl MagNA Pure LC RNA Buffer (Roche Diagnostics) and purified by using the automated MagNA Pure 96 system (Roche Diagnostics).
The total RNA was quantified using the Qubit RNA Assay Kit (Thermo Fisher) on the Fluorometer Glomax (Promega). Total RNA with a maximum of 10 ng from each biological replicate was reverse transcribed to cDNA using Superscript IV Vilo (Thermo Fisher). Libraries were generated with the AmpliSeq Library Plus Kit (Illumina) according to the reference guide. Pipetting steps for target amplification, primer digestion, and adapter ligation were done with the mosquito automatic pipettor (SPT Labtech) in miniaturization. For the purifications before and after final library amplification, solid phase reversible immobilization magnetic bead purification (Clean NGS, LABGENE Scientific SA) was performed on the multidrop automated pipetting station (Thermo Fisher). We measured both amplicon sizes and cDNA concentrations using an Agilent High Sensitivity DNA Kit (Agilent Technologies) according to the manufacturer’s recommendation. Prior to sequencing, cDNA contents of the samples were normalized and pooled to 2 nM final concentration on Biomek FXP workstation.
RNA-Seq (Amplicon-based molecular phenotyping)

treatment_protocol: To start, human induced pluripotent stem cells (hiPSC) are seeded at a density of 120000 cells per well in 96-well microwell plates. They form homogenous embryoid bodies (EBs) which are spontaneously differentiated over 7 days. Compounds are added as six-point concentration range on day 0, day 3 and day 5. Single wells containing about 70 differentiated EBs are lysed to generate one sample for the viability assay and gene expression profiling.

tag: cell type

tag: run

tag: plate

value: DMSO

tag: usedforfactoranalysis

value: TRUE

tag: usedformodelbuilding

tag: contrast

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity


title: M2_9_DMSO_ctrl

value: Human induced pluripotent-stem-cell derived embryoid body


title: Candida albicans, CRISPRa non-targeting control, rep2


title: WGBS_US_SLOS_#6_sire_Blood

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

country: USA

institute: University of Missouri, Columbia

library_source: genomic

data_processing:
Duplicated reads generated during PCR and sequencing were removed from raw sequencing reads using the clumpify function of BBMap (version 38.90). The remaining raw reads were trimmed for adapter sequences and low quality bases using trimmomatic (version 0.39) with parameters ‘ILLUMINACLIP:adapter_seq:2:30:10:1:true LEADING:20 TRAILING:20 AVGQUAL:20 MAXINFO:0:0.5’. Trimmed reads were aligned to the bovine genome using bismark (version 0.23.0) with parameters ‘-X 900 --unmapped --ambiguous --non_bs_mm’. Trimmed reads were also aligned to lambda phage genome to determine bisulfite conversion rates. Samtools (version 1.13) was used to convert, sort, filter, and index bam files. MarkDuplicates function of picard (version 2.25.5) was used to further remove duplicated reads after alignment. Read groups were added for each samples using AddOrReplaceReadGroups function of picard. The dataset of known variants in bovine, namely ARS1.2PlusY_BQSR_v3.vcf.gz, was acquired from the 1000 bull genome project and served as reference to identify genomic variants in WGBS data. Indel realignment was performed using RealignerTargetCreator and IndelRealigner functions of BisSNP (version 1.0.1). Base quality recalibration was carried out using BisulfiteCountCovariates and BisulfiteTableRecalibration functions of BisSNP (version 0.82.2) since these functions are missing in version 1.0.0 and 1.0.1. Parameters used for BisulfiteCountCovariates were ‘-cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -baqGOP 30’. Genomic variants were identified using BisSNP (version 1.0.1) with default setting expect that ‘-bsRate’ was changed to bisulfite conversion rate observed from lambda phage genome alignment for each sample. BisSNP identified variants were filtered by its VCFpostprocess function with parameter ‘-windSizeForSNPfilter 0’. Additionally, genomic variants were identified using BS-SNPer (version 1.0) with parameters ‘-minhetfreq 0.1 --minhomfreq 0.85 --minquali 15 --mincover 5 --maxcover 1000 --minread2 2 --errorate 0.02 --mapvalue 20’. M-bias plots were generated using bismark and the first 3 bases of R1 reads and the first 4 bases of R2 reads showed biased CpG methylation level, thus these bases were excluded from downstream analyses. CpG methylation information were extracted from the bam files using bismark_methylation_extractor function of bismark with parameters ‘-p --ignore 3 --ignore_r2 4 --comprehensive --no_header –gzip --bedGraph --buffer_size 50% --cytosine_report’. Statistical analyses were conducted using R package hummingbird (version 1.2.0) with parameter ‘minCpGs = 10, minLength = 100, maxGap = 300’ to identify differentially methylated regions (DMRs) in various comparisons. DMRs with at least 15% difference in methylation level (both gain and loss of methylation) and at least 4 mean read coverage at CpG sites were reported. The sex chromosomes were not analyzed to circumvent confounding created by X chromosome inactivation associated DNA methylation.
Assembly: ARS-UCD1.2
Supplementary files format and content: Read coverage and DNA methylation percentage for CpG sites in BEDGRAPH format.

molecule: genomic DNA

organism: Bos taurus

source_name: Blood

growth_protocol: US_Control animals were purchased from the University of Missouri Foremost Dairy Research Center and used as tissue donors. Tissue samples of stillborn US_SLOS animals were collected by their owners, veterinarians, or our collaborators and shipped to us. Animals from Spain were generated as described previously (PMID: 32781545) and used as tissue donors.

extract_protocol:
Blood cells and tissues were lysed in lysis buffer (0.05 M Tris-HCl (pH 8.0), 0.1 M EDTA, and 0.5% (w/v) SDS) with proteinase K (Fisher BioReagents, BP1700) at 55°C for four hours (for blood cells) or overnight (for tissues). Genomic DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol (SIGMA, P3803) following the manufacturer’s instructions. The concentration of DNA was measured by using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific) and DNA integrity was confirmed by electrophoresis on a 0.7% agarose gel. Genomic DNA samples were stored at -20°C.
This WGBS was conducted by CD Genomics (Shirley, NY, USA). Information on library preparation and sequencing obtained from the company is as follows: For WGBS library preparation, 1 ug of genomic DNA was fragmented by sonication to a mean size of approximately 200-400 bp. Fragmented DNA was end-repaired, 5'-phosphorylated, 3'-dA-tailed and then ligated to methylated adapters. The methylated adapter-ligated DNAs were purified using 0.8× Agencourt AMPure XP magnetic beads and subjected to bisulfite conversion by ZYMO EZ DNA Methylation-Gold Kit (zymo). The converted DNAs were then amplified using 25 μl KAPA HiFi HotStart Uracil+ ReadyMix (2X) and 8-bp index primers with a final concentration of 1 μM each. The constructed WGBS libraries were then analyzed by Agilent 2100 Bioanalyzer and quantified by a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen), and finally sequenced on Illumina Hiseq X ten sequencer. 0.1-1% lambda DNA were added during the library preparation to monitor bisulfite conversion rate.

treatment_protocol: For Spain animals, the control group (ES_Control) were conceived by artificial insemination using frozen-thawed semen from one bull among synchronized cows on the day of presumptive estrus. In vitro produced animals were generated using slaughterhouse oocytes and semen from the same bull as controls. Following fertilization, embryos were separated in two different groups: one culture group (ES_ART) composed of synthetic oviductal fluid (SOF) media supplemented with bovine serum albumin during the 7-8 days of culture and another group (ES_RF) composed of SOF media supplemented with bovine oviductal fluid (NaturARTs-BOF-EL, Embryocloud, Spain) for the first 4 days and bovine uterine fluid (NaturARTs-BUF-ML, Embryocloud) for the following days. Embryos (blastocysts and expanded blastocysts) were vitrified on day 7 or 8 of culture and stored until use. Recipients were synchronized and on day 6 to 8 after presumptive estrus, each cow received one thawed embryo.

value: Calf blood

tag: breed

value: Charolais

tag: Sex

value: Male

tag: country

value: United States (US)

tag: conception method

value: Artificial insemination/natural mating

tag: disease status

value: Healthy

value: Blood


title: CHIP_LBC21_024_Wave3

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description:
DNA (Targeted Myeloid Panel)
LBC_ARCHER.1PCT_VAF.Feb22.non-synonymous.tsv
LBC_ARCHER.1PCT_VAF.Feb22.synonymous.tsv
LBC_ARCHER.2PCT_VAF.Feb22.non-synonymous.tsv
LBC_ARCHER.2PCT_VAF.Feb22.synonymous.tsv

data_processing:
Reads were filtered for phred ≥30 and adapters removed using Trimmomatic (Bolger et al., 2014) before undergoing guided alignment to human genome assembly hg19 using bwa-mem and bowtie2.
Unique molecular barcodes (ligated prior to PCR amplification) were utilised for read deduplication to support quantitative multiplexed analysis and confident mutation detection. Within targeted regions, variants were called using three tools (Lofreq (Wilm et al., 2012), Freebayes (Garrison and Marth, 2012) and Vision (ArcherDX, unpublished) – building a consensus from the output of all callers
All filtered variants at 0.02 VAF met the following criteria: 1) the number of reads supporting the alternative allele surpasses the coverage criteria while exhibiting no directional biases (AO ≥ 5, UAO ≥ 3); 2) variants are significantly underrepresented within the Genome Aggregation Database (gnomAD; p ≤ 0.05); 3) variants are not obviously germline variants (stable VAF across all waves ~0.5 or ~1) that may have been underrepresented in the gnomAD database due to the narrow geographical origin of the Lothian Birth Cohort participants; 4) contain events that are overrepresented across the dataset - generally frameshift duplications and deletions - whose reads share some sequence homology to target regions yet are likely misaligned artefact from the capture method. In addition, we manually curated this list checking for variants that were previously reported, as per Jaiswal et al. (Jaiswal et al., 2014b), in the COSMIC (Catalogue of Somatic Mutations in Cancer) database or within the published literature (Table 4).
For any variant that surpassed the above criteria at, or above, 0.02 VAF across the measured time period, we endeavored to include all other participant matched data points regardless of VAF level
Genome_build: hg19
Supplementary_files_format_and_content: Extended MAF Format (Mutation Annotation Format)

source_name: Human Blood (PBMCs)

growth_protocol: DNA was extracted from EDTA whole blood using the Nucleon BACC3 kit, following the manufacturer’s instructions. Libraries were prepared from 200ng of each DNA sample using the Archer VariantPlex 75 Myeloid gene panel and VariantPlex Somatic Protocol for Illumina Sequencing (Invitae, Table 2), including modifications for detecting low allele frequencies.

extract_protocol: Sequencing of each pool was performed using the NextSeq 500/550 High-Output v2.5 (300 cycle) kit on the NextSeq 550 platform. To inform reproducibility, background model for error and batch correction, we sequenced “genome in a bottle” DNA in each batch of samples (DNA NA12878 Coriell Institute).

tag: wave

tag: cohort

tag: sequencing batch

tag: tissue

value: PBMCs


title: WGBS_US_Control_#2_Blood

value: Holstein

value: Artificial insemination


title: M2_10_DMSO_ctrl

tag: cell type

tag: run

tag: plate


title: WGBS_US_Control_#1_Blood


title: M2_5_DMSO_ctrl

tag: usedforfactoranalysis

tag: usedformodelbuilding

tag: contrast


title: CK_At-2

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Assembly: TAIR10;IRGSP-1.0; SL3.0
Supplementary files format and content: tab-delimited text files include count for each Sample

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
10 μg/mg doxycycline treated and  control check leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

tag: genotype

value: WT

tag: treatment

value: CK


title: M1_84_RO-12_DoseF

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity

value: Negative


title: Candida albicans, CRISPRa targeting ALS1, rep3

value: Total

tag: cell line


title: Dox_Sl-3

organism: Solanum lycopersicum

value: 10 μg/mg doxycycline


title: M2_3_DMSO_ctrl

value: Human induced pluripotent-stem-cell derived embryoid body

value: DMSO

value: TRUE


title: CHIP_LBC21_015_Wave3

tag: wave


title: Candida albicans, CRISPRa targeting ALS1, rep2


title: Arabidopsis root, suvh5, H.schachtii infected_RNA_rep 3

city: Knoxville

first: Morgan

last: Bennett

email: mmbennet@vols.utk.edu, thewezi@utk.edu

state: TN

address: 2505 E J Chapman Drive

department: Plant Sciences

institute: University of Tennessee

data_processing:
Quality assessment was performed on fastq raw data files using FastQC.
Paired-end RNA-seq reads were mapped to the Arabidopsis thaliana reference genome with STAR (v2.5) using default settings.
Uniquely mapped paired-end reads were counted using Htseq (v0.10.0).
The mapping output files of the three replicates for each genotype/ condition were merged. Then, read counts of uniquely mapped reads were analyzed for their differential expression between mutant versus wild-type plants and infected versus noninfected plants using DESeq in the R environment.
Genome_build: Arabidopsis thaliana TAIR10.28
Supplementary_files_format_and_content: Read count text files were generated using Htseq.

source_name: root tissue

growth_protocol: Mutant and wild-type seeds were germinated on modified Knop's medium in large petri plates and grown at 22°C under long day conditions.

extract_protocol:
Root tissues of 15-day-old (noninfected) or 5 dpi (H. schachtii infected) plants were collected and frozen immediately in liquid nitrogen. Total RNA was extracted using Trizol reagent (Invitrogen) using the Zymo Direct-zol RNA Miniprep Plus kit (R2071). RNA quality was assessed using an RNA nano bioanalyzer chip (Agilent 2100).
For the costrucion of a non-stranded, non-directional mRNA library, mature mRNAs were processed and captured using olido(dT) beads following the addition of a 3' poly(A) tail.

treatment_protocol: Replicates of each genotype were inoculated with 100 freshly-hatched J2 H. schachtii per plant at 10-days-old. Inoculated replicates were incubated in the dark at 26°C for 24 hours to facillitate nematode infection. Following incubation, inoculates replicates were grown in light conditions as previously described until 5 days post inoculation (dpi).

tag: developmental stage

value: 5 days post inoculation

value: inoculated with 100 J2 H. schachtii per plant at 10 days old


title: Arabidopsis root, suvh6, noninfected_RNA_rep 1

value: 15 days old

value: untreated


title: CHIP_LBC21_005_Wave3

tag: cohort

tag: sequencing batch

value: Blood


title: Arabidopsis root, suvh6, H.schachtii infected_RNA_rep 2


title: Candida albicans, CRISPRa non-targeting control, rep1

tag: tissue

value: CRISPRa Control (WT with Non-Targeting CRISPRa Construct)


title: CHIP_LBC21_010_Wave3

tag: cell type

value: PBMCs


title: M2_2_DMSO_ctrl

tag: run

tag: plate


title: Arabidopsis root, suvh5, H.schachtii infected_RNA_rep 2


title: M2_1_DMSO_ctrl

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: CHIP_LBC21_001_Wave3


title: Arabidopsis root, suvh5, H.schachtii infected_RNA_rep 1

tag: genotype


title: CK_Sl-2

tag: treatment


title: CHIP_LBC36_031_Wave2


title: CHIP_LBC21_008_Wave3


title: M1_80_RO-8_DoseF

tag: contrast

tag: concentration

value: Positive


title: Dox_Sl-2

value: leaf


title: M1_79_RO-7_DoseF

tag: conclabel

tag: concstr


title: CHIP_LBC36_001_Wave2


title: CHIP_LBC21_003_Wave3


title: Arabidopsis root, Col-0, H.schachtii infected_RNA_rep 2

value: Col-0 wild type


title: M1_82_RO-10_DoseF

tag: teratogenicity


title: CK_Sl-3

value: WT

value: CK


title: CHIP_LBC21_007_Wave3

tag: wave


title: Arabidopsis root, suvh5, noninfected_RNA_rep 2

tag: developmental stage


title: Arabidopsis root, suvh5, noninfected_RNA_rep 3


title: WL4_leaf_AV_24h

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

country: Germany

institute: University Bayreuth

data_processing:
Fastq files were used for transcript quantification by use of kallisto (Bray et al. 2016), with 30 bootstrap samples. The reference genome built v5 from Genoscope was used (http://www.genoscope.cns.fr/brassicanapus/). This genome built included 101 040 transcripts.
Differential expression analysis was performed with the edgeR and limma Bioconductor packages in R. Log2 Fold Changes and Benjamini-Hochberg-corrected P-values were calculated fitting a negative binomial generalized log-linear model with a full factorial design matrix of treatment and tissue.
Genome_build: AST_PRJEB5043_v1
Supplementary_files_format_and_content: tab-separated text files include length of transcript, est_counts and tpm for each sample

organism: Brassica napus

source_name: first true leaf of 16-day-old seedlings

growth_protocol: Sterilized seeds were germinated in small tubes containing 1:10 Hoagland solution (0.28 mm Ca(NO3)2, 0.1 mm (NH4)H2PO4, 0.2 mm MgSO4, 0.6 mm KNO3, 5 μm of a complex of Fe(III) and N,N′-di-(2-hydroxybenzoyl)-ethylenediamine-N,N′-diacetate, pH 5.7). Plants were grown in a short-day chamber (8 h illumination with ca. 100 µmol photons * m-2 * s-1) with 23 °C. After 4 days, the tubes were transferred into large buckets (4.5 l of volume) by use of place holders. The buckets were filled with KNOP nutrient solution, which was continuously bubbled with air. The nutrient solution was replaced twice a week.

extract_protocol:
RNA was extracted from the ground plant tissue by use of the ISOLATE II RNA plant kit according to the manual, including a DNAse treatment (Bioline, Luckenwalde, Germany).
RNA was further processed by Eurofins Genomics Europe Shared Services GmbH (Ebersberg, Germany). Integrity and quantity of the RNA was determined by appropriate methods, i.e., measurement of volume and quantity, gel electrophoresis and fluorimeter measurements. Library preparation incorporated adaptor sequences and indexing compatible for Illumina sequencing technology, using proprietary methods of Eurofins Genomics Europe Shared Services GmbH. The cDNA library preparation was performed following optimized protocols. After first strand synthesis, the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next, the sequencing adapters were ligated to the DNA fragments, and the dUTP containing second strand was removed. Determination of size distribution and quantification of the sequencing library was accomplished with appropriate methods according to optimized protocols. Sequencing was performed on the Illumina HiSeq 4000 platform.

treatment_protocol: When plants were 15 days old, the stress treatment was applied 2 h after the start of the photoperiod by bubbling the nutrient solution with nitrogen gas. The shoot tissues remained in air. For controls, the nutrient solution was bubbled with air. After 4 and 24 h of stress treatment, the first true leaf and the root system was harvested.

value: hypoxic nutrient solution

tag: treatment duration

tag: cultivar

value: Brassica napus cv. Avatar


title: M1_83_RO-11_DoseF

value: Human induced pluripotent-stem-cell derived embryoid body

value: Negative


title: Arabidopsis root, Col-0, noninfected_RNA_rep 3


title: Arabidopsis root, Col-0, H.schachtii infected_RNA_rep 3


title: M1_81_RO-9_DoseF

value: TRUE


title: CK_Sl-1

tag: tissue


title: M1_76_RO-4_DoseF

tag: cell type


title: M1_75_RO-3_DoseF

tag: run


title: CHIP_LBC36_002_Wave2

tag: cohort

tag: sequencing batch


title: Dox_Sl-1

value: 10 μg/mg doxycycline


title: Arabidopsis root, Col-0, noninfected_RNA_rep 1


title: M1_77_RO-5_DoseF

tag: plate

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: WL4_leaf_ZS9_24h

tag: treatment

value: Brassica napus cv. Zhongshuang 9


title: CHIP_LBC36_042_Wave2


title: WL4_root_ZS9_24h

source_name: roots of 16-day-old seedlings


title: M1_78_RO-6_DoseF

tag: contrast

tag: concentration


title: Arabidopsis root, suvh5, noninfected_RNA_rep 1

tag: genotype

value: 15 days old


title: Arabidopsis root, Col-0, H.schachtii infected_RNA_rep 1

value: 5 days post inoculation

value: inoculated with 100 J2 H. schachtii per plant at 10 days old


title: Arabidopsis root, suvh6, H.schachtii infected_H3K9me2_rep 2

data_processing:
Quality assessment was performed on fastq raw data files using FastQC.
Trimmomatic (v0.39) was used to trim adapter sequences and overrepresented sequences from raw reads.
Additional quality assessment was performed on trimmed data files using FastQC.
Paired-end ChIP-seq reads were mapped to the Arabidopsis thaliana reference genome with Bowtie2 (v2.2.9) using the very sensitive mapping parameter.
Mapping depth and coverage were determined using Samtools (v1.3.1) and IGV (v2.7.2), respectively.
The mapping output files of the three replicates for each genotype/ condition were used to call H3K9me2 peaks using the broad peak function of MACS2 for paired-end reads.
Peaks were then annotated using the closest function of Bedtools2 (v2.29.2).
Genome_build: Arabidopsis thaliana TAIR10.28
Supplementary_files_format_and_content: Bed files were generated from sam files output by Bowtie2

extract_protocol:
Root tissues of 15-day-old (noninfected) or 5 dpi (H. schachtii infected) plants were collected and frozen immediately in liquid nitrogen. ChIP DNA was extracted following the manufactur's instructions (Abcam).
Libraries were prepared according to the manufacturer's insutrctiuons using NEBNext Ultra II DNA Library Prep Kit (NEB E7645).

tag: chip antibody

value: Anti-Histone H3 (di methyl K9) antibody [mAbcam 1220] - ChIP Grade (ab1220)


title: CHIP_LBC36_041_Wave2

tag: wave

value: Blood

value: PBMCs


title: WL4_root_ZS9_4h

source_name: roots of 15-day-old seedlings

value: 4 h


title: CHIP_LBC36_037_Wave2


title: Arabidopsis root, suvh6, H.schachtii infected_H3K9me2_rep 1

tag: developmental stage


title: CHIP_LBC36_038_Wave2


title: Arabidopsis root, Col-0, noninfected_RNA_rep 2

value: Col-0 wild type

value: untreated


title: M1_72_RO-12_DoseE

tag: conclabel

tag: concstr

tag: teratogenicity


title: CHIP_LBC36_040_Wave2

tag: tissue

tag: cell type


title: M1_74_RO-2_DoseF

tag: run


title: WL4_root_AV_4h

tag: treatment duration

tag: cultivar


title: Arabidopsis root, suvh6, H.schachtii infected_H3K9me2_rep 3


title: Arabidopsis root, suvh6, noninfected_H3K9me2_rep 3


title: M1_70_RO-10_DoseE

tag: plate

tag: usedforfactoranalysis

value: Positive


title: CHIP_LBC36_039_Wave2

tag: cohort

tag: sequencing batch


title: M1_73_RO-1_DoseF

tag: usedformodelbuilding

tag: contrast

tag: concentration


title: WL3_leaf_ZS9_24h

tag: treatment

value: hypoxic nutrient solution


title: WL4_root_AV_24h

value: Brassica napus cv. Avatar


title: WL3_root_AV_4h


title: CHIP_LBC36_033_Wave2

tag: wave


title: WL3_root_ZS9_4h


title: Arabidopsis root, suvh5, H.schachtii infected_H3K9me2_rep 3

tag: genotype

tag: developmental stage

tag: chip antibody


title: Arabidopsis root, suvh6, noninfected_H3K9me2_rep 2


title: M1_67_RO-7_DoseE

value: Human induced pluripotent-stem-cell derived embryoid body

tag: conclabel

tag: concstr

tag: teratogenicity


title: Arabidopsis root, suvh5, H.schachtii infected_H3K9me2_rep 2


title: CHIP_LBC36_035_Wave2

tag: tissue

tag: cell type


title: WL3_leaf_AV_24h

tag: treatment duration

tag: cultivar


title: M1_69_RO-9_DoseE

tag: run

tag: plate

tag: usedforfactoranalysis


title: M1_66_RO-6_DoseE

tag: usedformodelbuilding

tag: contrast

value: Negative


title: CHIP_LBC36_036_Wave2

tag: cohort

tag: sequencing batch


title: CHIP_LBC36_032_Wave2

tag: wave


title: Arabidopsis root, suvh6, noninfected_H3K9me2_rep 1

tag: genotype

tag: developmental stage

tag: treatment


title: WL3_root_ZS9_24h


title: Arabidopsis root, suvh5, noninfected_H3K9me2_rep 2

tag: chip antibody


title: M1_64_RO-4_DoseE

value: TRUE

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity


title: WL1_root_ZS9_4h

tag: treatment duration

tag: cultivar


title: M1_71_RO-11_DoseE

tag: cell type

tag: run

tag: plate


title: M1_68_RO-8_DoseE

tag: usedforfactoranalysis

tag: usedformodelbuilding

tag: contrast


title: CHIP_LBC36_034_Wave2

tag: wave

tag: cohort

tag: sequencing batch

tag: tissue


title: Arabidopsis root, suvh5, H.schachtii infected_H3K9me2_rep 1

tag: genotype

tag: developmental stage

tag: chip antibody

tag: treatment


title: WL1_leaf_ZS9_24h


title: WL1_leaf_AV_24h


title: M1_61_RO-1_DoseE

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity


title: WL1_root_AV_24h

tag: treatment duration

tag: cultivar


title: WL1_root_ZS9_24h


title: M1_65_RO-5_DoseE

tag: cell type

tag: run

tag: plate

tag: usedforfactoranalysis


title: Arabidopsis root, suvh5, noninfected_H3K9me2_rep 3


title: CHIP_LBC36_029_Wave2

tag: wave

tag: cohort


title: WL3_root_AV_24h


title: Arabidopsis root, suvh5, noninfected_H3K9me2_rep 1


title: CHIP_LBC36_027_Wave2

tag: sequencing batch

tag: tissue


title: M1_62_RO-2_DoseE

tag: usedformodelbuilding

tag: contrast


title: CHIP_LBC36_026_Wave2


title: CHIP_LBC36_023_Wave2


title: KL5_leaf_ZS9_24h

tag: treatment

value: aerated nutrient solution


title: Arabidopsis root, Col-0, H.schachtii infected_H3K9me2_rep 2

tag: genotype

tag: developmental stage

tag: chip antibody


title: CHIP_LBC36_028_Wave2


title: M1_63_RO-3_DoseE

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity


title: WL1_root_AV_4h

tag: treatment duration

tag: cultivar


title: Arabidopsis root, Col-0, H.schachtii infected_H3K9me2_rep 3


title: KL5_leaf_AV_24h


title: CHIP_LBC36_025_Wave2

tag: cell type


title: CHIP_LBC36_021_Wave2

tag: wave


title: Arabidopsis root, Col-0, H.schachtii infected_H3K9me2_rep 1


title: Arabidopsis root, Col-0, noninfected_H3K9me2_rep 2


title: M1_60_RO-12_DoseD

tag: run

tag: plate

tag: usedforfactoranalysis


title: M1_57_RO-9_DoseD

tag: usedformodelbuilding


title: M1_58_RO-10_DoseD

tag: contrast


title: KL5_root_ZS9_24h

tag: treatment

value: Brassica napus cv. Zhongshuang 9


title: KL5_root_AV_24h


title: CHIP_LBC36_022_Wave2

tag: cohort

tag: sequencing batch

tag: tissue


title: Arabidopsis root, Col-0, noninfected_H3K9me2_rep 3

tag: genotype

tag: developmental stage

value: 15 days old

tag: chip antibody


title: M1_54_RO-6_DoseD

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity


title: KL3_leaf_ZS9_24h

tag: treatment duration

tag: cultivar


title: CHIP_LBC36_043_Wave2

tag: wave

tag: cell type


title: M1_53_RO-5_DoseD

tag: run

tag: plate

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: CHIP_LBC36_015_Wave2

tag: cohort

tag: sequencing batch


title: CHIP_LBC36_018_Wave2

tag: tissue


title: CHIP_LBC36_020_Wave2


title: CD20_post_donor3_rep1

type: RNA

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

country: Spain

institute: CSIC

description: Gene expression in PBMC after IVIg infusion

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at room temperature in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Human peripheral blood B cell (CD20+) from Common Variable Immunodeficiency patients were isolated before and after IVIg infusion

value: Peripheral blood monocytes

tag: treatment

value: IVIg treatment


title: CD20_pre_donor3_rep1

description: Gene expression in PBMC


title: M1_56_RO-8_DoseD

tag: contrast


title: KL5_root_ZS9_4h


title: M1_59_RO-11_DoseD

tag: concentration


title: M1_50_RO-2_DoseD

tag: conclabel


title: KL5_root_AV_4h


title: CHIP_LBC36_016_Wave2


title: CHIP_LBC36_017_Wave2


title: M1_52_RO-4_DoseD

tag: concstr


title: Arabidopsis root, Col-0, noninfected_H3K9me2_rep 1

tag: genotype

tag: developmental stage

tag: chip antibody

value: Anti-Histone H3 (di methyl K9) antibody [mAbcam 1220] - ChIP Grade (ab1220)


title: CD20_pre_donor2_rep1

description: Gene expression in PBMC


title: CD3_post_donor3_rep1

treatment_protocol: Human peripheral blood T cells (CD3+) from Common Variable Immunodeficiency patients were isolated before and after IVIg infusion

value: after IVIg infusion


title: M1_48_RO-12_DoseC

tag: teratogenicity


title: CHIP_LBC36_013_Wave2

tag: wave

value: Blood

tag: cell type

value: PBMCs


title: CD20_post_donor1_rep1


title: KL1_leaf_ZS9_24h

tag: treatment duration

tag: cultivar


title: M1_47_RO-11_DoseC

tag: run

tag: plate

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: M1_55_RO-7_DoseD


title: M1_51_RO-3_DoseD


title: KL3_root_ZS9_24h

tag: treatment

value: 4 h


title: KL1_leaf_AV_24h


title: KL3_root_ZS9_4h


title: CD20_post_donor2_rep1

tag: tissue


title: CHIP_LBC36_009_Wave2

tag: cohort

tag: sequencing batch


title: CHIP_LBC36_014_Wave2


title: CD3_pre_donor2_rep1

description: Gene expression in PBMC


title: KL3_leaf_AV_24h


title: KL3_root_AV_4h


title: M1_44_RO-8_DoseC

tag: contrast

tag: concentration

tag: conclabel

tag: concstr


title: CD20_pre_donor1_rep1

description: Gene expression in PBMC


title: M1_49_RO-1_DoseD

tag: teratogenicity


title: CHIP_LBC36_012_Wave2

tag: wave


title: KL3_root_AV_24h


title: M1_46_RO-10_DoseC

tag: cell type


title: CHIP_LBC36_005_Wave2


title: CHIP_LBC36_010_Wave2


title: KL1_root_ZS9_4h

tag: treatment duration


title: CHIP_LBC36_008_Wave2


title: M1_45_RO-9_DoseC


title: CD14_post_donor3_rep1

treatment_protocol: Human peripheral blood monocytes (CD14+) from Common Variable Immunodeficiency patients were isolated before and after IVIg infusion


title: CHIP_LBC36_011_Wave2


title: KL1_root_ZS9_24h

tag: cultivar


title: CHIP_LBC36_007_Wave2


title: CD3_pre_donor3_rep1

description: Gene expression in PBMC


title: KL1_root_AV_4h


title: CD3_post_donor2_rep1


title: M1_43_RO-7_DoseC

tag: run


title: CHIP_LBC36_006_Wave2


title: M1_39_RO-3_DoseC

tag: plate


title: CHIP_LBC36_041_Wave1


title: M1_42_RO-6_DoseC

tag: usedforfactoranalysis


title: CHIP_LBC36_040_Wave1


title: CD3_post_donor1_rep1


title: CD3_pre_donor1_rep1

description: Gene expression in PBMC


title: CHIP_LBC36_039_Wave1


title: M1_37_RO-1_DoseC

tag: usedformodelbuilding


title: CHIP_LBC36_003_Wave2


title: M1_41_RO-5_DoseC


title: KL1_root_AV_24h

tag: treatment


title: H2

city: Hangzhou

first: Luoyi

last: Zhu

state: Zhejiang

address: 866 Yuhang Tang Road

institute: Zhejiang University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm39
Supplementary files format and content: Processed_data_files-colon.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Mus musculus

source_name: colon

extract_protocol:
RNA extracted from mouse colon tissue using Trizol reagent. Total amount and integrity of RNA were accurately detected with an Agilent RNA 6000 Nano Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: colon

tag: age

value: post natal day 98

value: high-fat diet


title: HB4

value: high-fat diet with gavage of Papillibacter cinnamivorans


title: HB3


title: CHIP_LBC36_038_Wave1

tag: cohort

tag: sequencing batch


title: CD14_post_donor2_rep1


title: CHIP_LBC36_042_Wave1


title: HB1


title: H4


title: M1_35_RO-11_DoseB

value: Human induced pluripotent-stem-cell derived embryoid body

tag: contrast

tag: concentration

tag: conclabel


title: CHIP_LBC36_036_Wave1

tag: wave


title: H1


title: M1_40_RO-4_DoseC

tag: cell type

tag: concstr

tag: teratogenicity

value: Negative


title: M1_38_RO-2_DoseC

tag: run

value: TRUE


title: C2

value: control


title: CD14_post_donor1_rep1


title: CD14_pre_donor1_rep1

description: Gene expression in PBMC


title: CD14_pre_donor3_rep1

description: Gene expression in PBMC


title: CHIP_LBC36_035_Wave1


title: CHIP_LBC36_033_Wave1


title: HBL4

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm39
Supplementary files format and content: Processed_data_files-liver.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: liver

extract_protocol:
RNA extracted from mouse liver tissue using Trizol reagent. Total amount and integrity of RNA were accurately detected with an Agilent RNA 6000 Nano Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver


title: CHIP_LBC36_037_Wave1


title: C3


title: HBL1


title: PBMC_pre_donor3_rep1

description: Gene expression in PBMC

treatment_protocol: Human peripheral blood mononuclear cells from Common Variable Immunodeficiency patients were isolated before and after IVIg infusion

value: Peripheral blood mononuclear cells


title: M1_32_RO-8_DoseB

tag: plate

value: Positive


title: PBMC_pre_donor4_rep1

description: Gene expression in PBMC


title: CD14_pre_donor2_rep1

description: Gene expression in PBMC

value: Peripheral blood monocytes


title: PBMC_post_donor1_rep1


title: M1_33_RO-9_DoseB

tag: usedforfactoranalysis


title: CHIP_LBC36_032_Wave1


title: M1_34_RO-10_DoseB

tag: usedformodelbuilding


title: PBMC_post_donor3_rep1


title: CHIP_LBC36_034_Wave1


title: PBMC_post_donor2_rep1


title: M1_29_RO-5_DoseB


title: HBL3

tag: treatment


title: HL2

tag: strain


title: PBMC_post_donor4_rep1

tag: tissue


title: C1

tag: age


title: M1_36_RO-12_DoseB


title: PBMC_pre_donor2_rep1

description: Gene expression in PBMC


title: HL1


title: CHIP_LBC36_028_Wave1

tag: cohort


title: CHIP_LBC36_027_Wave1

tag: sequencing batch


title: M1_30_RO-6_DoseB

tag: contrast


title: M1_26_RO-2_DoseB

tag: concentration


title: E6

city: Natong

first: Xi'an

last: Ni

address: Qixiu Road No.19

institute: Nantong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw BCL files were converted to FASTQ files and then individual samples were aligned and quantified using the 10X Genomics Cell Ranger software (version 3.1.0). Briefly, reads with low  quality barcodes and UMIs were filtered out and then mapped to the reference genome. Quality control ( QC ) filters were applied using the following parameters, similar to what has been reported. Firstly, at least 50 % reads mapping to the transcriptome and intersecting an exon were considered. Secondly, cells with unusually high numbers of UMIs (≥ 8,000) or mitochondrial gene percent (≥ 10%) were filtered out. Thirdly, we excluded cells with less than 500 or more than 4,000 genes detected.
Assembly: Ensembl_release100
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: kidney

extract_protocol:
1 mL filtered tissue homogenate was then mixed with 1 mL 50% iodixanol (DKSC). The tissue mixture was added slowly into 3 mL 33 % DKSC in a 15 mL centrifuge tube for gradient centrifugation. After centrifuging at 4 °C, 3, 234 g for 20 minutes, 3.5 mL of the upper layer of the centrifuge solution was removed to a new 15 mL centrifuge tube. 1 mL cell nucleus layer at the interface of gradient centrifugation was transferred into a new 15 mL centrifuge tube, and then we added 2 mL of nuclear cleaning solution   to resuspend Buffer. Finally, we used a microscope cytometry plate stain with 0.4 % trypan blue to   detect the concentration, viability, and integrity of the nuclei.
Cellular suspensions were loaded on the 10X Genomics GemCode Single-cell instrument and   performed following the manufacturer’s protocol that produced single-cell Gel Bead-In-EMlusion   (GEMs). According to the manufacturer instructions, we constructed the sequencing libraries with   Chromium Next GEM Single Cell 3’ Reagent Kits v3.1, which contain read sequencing primer, 10x barcode, unique molecular identifier (UMI), and poly-dT primer   sequence. Cell lysis, RNA extraction, cDNA synthesis, and amplification were automatically   completed on the Illumina sequencing platform.

value: kidney

value: MRL/lpr

tag: time

value: 6 weeks old

tag: Sex

value: female


title: CHIP_LBC36_026_Wave1

tag: wave

value: Blood

tag: cell type

value: PBMCs


title: M1_28_RO-4_DoseB

tag: conclabel

tag: concstr

tag: teratogenicity


title: CL1

value: post natal day 98


title: NC6

description: 10x Genomics


title: CL4


title: NC10

description: 10x Genomics

value: 10 weeks old


title: CHIP_LBC36_030_Wave1


title: E10

description: 10x Genomics


title: gz_Fibroblast_p7_rep3

city: Kyoto Sakyo

first: Yoshinori

last: Endo

state: Kyoto

address: 2-24 Tanaka Sekidencho

country: Japan

institute: Kyoto University

description: Grevy's zebra iPSCs at passage 7, replicate 3

data_processing:
Sequenced reads were basecalled and demultiplexed by using the ONT EPI2ME software.
Adapter sequences were trimmed from the reads using Porechop (v 0.2.4).
Low-quality reads were filtered using Nanofilt included in the NanoPack (v 2.7.1).
The filtered reads were mapped to the horse transcriptome using Minimap2 (v 2.17).
The mapped reads were then counted using Salmon (v 1.3.0).
The transcript reads were converted to gene-level abundance using tximport (v 3.13) and annotated with human orthologous using the Biomart tool of Ensembl (http://www.ensembl.org/biomart/martview/). The differentially expressed genes (DEGs) were identified using DESeq2 (v 1.28.1) with FDR-adjusted p value of 0.1 and | log2FoldChange | > 1 with default settings.
Genome_build: EquCab3.0
Supplementary_files_format_and_content: tsv file including output from Salmon (v 1.3.0). Measurements in TPM and number of reads for transcripts.

organism: Equus grevyi

source_name: fibroblasts, skin

growth_protocol: Grevy’s zebra fibroblasts were cultured in Dulbecco's modified Eagle medium (DMEM; Sigma) supplemented with 10 % (v/v) fetal bovine serum (FBS; CCB Japan), 100 units/mL penicillin/streptomycin (Wako), and 100 µM non-essential amino acids (NEAA; Sigma-Aldrich) on gelatin coated dish. The generated gz-iPSCs were cultured in mTeSR-1 (STEMCELL) with 10 µM Rho-associated coiled-coil forming kinase (ROCK) inhibitor Y-27632 (Wako) on Matrigel (Corning) coated dish. All cellular samples were cultured in a humidified incubator at 37 °C with 5 % (v/v) CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit 50 (Qiagen) according to the manufacturer's instructions. DNA was eliminated with RNase-Free DNase Set (Qiagen) in solution followed by RNA cleanup. The RNA solution was quantified using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).
RNA (40 ng) was used for library preparation for Oxford Nanopore Technologies (ONT) long-read cDNA sequencing. The cDNA was generated using the PCR-cDNA Barcoding kit (SQK-PCB109) by ONT according to the manufactures protocol. For sequencing, libraries were applied to the Nanopore Flow Cell (v 9.4.1) and ran for up to 72 h.

treatment_protocol: Skin tissue sample was obtained from a female Grevy’s zebra, which had died of natural cause at Kyoto City Zoo (Japan). Primary fibroblast cells were established from the skin tissue as previously described (Glenn, V. L., Schell, J. P. & Fakunle, E. S. Isolation of human dermal fibroblasts from biopsies. Hum Stem Cell Manual, A Lab Guid 129–141 (2012)). gz-iPSCs were generated by transducing the primary fibroblasts with retroviral vectors carrying OCT3/4, SOX2, KLF4, and c-MYC (Takahashi, K. & Yamanaka, S. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell 126, 663–676 (2006), Takahashi, K. et al. Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors. Cell 131, 861–872 (2007)). Colonies with typical PSC morphology were isolated and propagated. The generated iPSCs were tested for the criteria for PSCs by qRT-PCR for pluripotency marker expressions, immunocytochemistry, and embryoid body (EB) formation.

value: Fibroblasts

value: primary fibroblasts


title: M1_27_RO-3_DoseB

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run

tag: plate

tag: usedforfactoranalysis


title: M1_23_RO-11_DoseA

value: TRUE

tag: usedformodelbuilding

value: Negative


title: PBMC_pre_donor1_rep1

description: Gene expression in PBMC

tag: tissue


title: CHIP_LBC36_029_Wave1


title: M1_22_RO-10_DoseA


title: gz_Fibroblast_p6_rep2

description: Grevy's zebra iPSCs at passage 6, replicate 2

tag: treatment


title: gz_Fibroblast_p3_rep1

description: Grevy's zebra fibroblasts at passage 3, replicate 1


title: CL2

tag: strain

value: liver

tag: age

value: control


title: CHIP_LBC36_025_Wave1

tag: cohort

tag: sequencing batch


title: Sample 8A Ubc-CreERT2; Csf1fl/fl, Ly6Clow monocytes

city: Toronto

first: Clinton

middle: S.

last: Robbins

state: Ontario

address: 101 College Street

institute: University Health Network

data_processing:
Read mapping to the mouse reference genome (GRCm38) was done using hisat2 (v2.1.0)
SAM file to BAM file conversion and BAM file indexing was done using samtools (v1.9)
stringtie (v1.3.4d) was used for transcript assembly
Mapping quality control metrics were determined using picard (v2.10.9) and analyzed using multiqc (v1.6)
Gene-level read quantification was done using HTSeq (v0.10.0)
Assembly: GRCm38 (mm10)
Supplementary files format and content: Gene-level quantified raw reads from HTSeq (.tsv – tab separated) for each sample

source_name: Bone Marrow

extract_protocol:
RNA was extracted from sorted cells using PicoPure RNA Isolation Kit (Arcturus, cat #KIT0202)
Takara Smarter Stranded Total RNA-seq kit v2 pico Input Mammalian

treatment_protocol:
Single cell suspensions from bone marrows were obtained from pooled femurs, tibias and pelvises
Sorting was performed on an Aria Fusion cell sorter (BD Biosciences)

value: Bone Marrow

value: Sorted monocytes

tag: genotype

value: Ubc-CreERT2; Csf1fl/fl,

value: Tamoxyfen for  4 weeks


title: M1_21_RO-9_DoseA

tag: contrast

tag: concentration

value: Positive


title: Sample 5E Ubc-CreERT2; Csf1fl/fl, Ly6Clow monocytes

tag: cell type


title: Sample 4A Control, Ly6Clow monocytes

value: Csf1fl/fl mice,


title: M1_25_RO-1_DoseB

tag: conclabel


title: low6

city: Milwaukee

middle: D

last: Klaper

state: WI

address: 600 E Greenfield Ave

department: School of Freshwater Sciences

institute: University of Wisconsin - Milwaukee

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed for adapters with Ctuadapt v. 1.1.18, and a reference transcriptome assembled with Trinity v. 2.8.3 using standard parameters
Estimated counts were determined by mapping reads to the reference transcriptome assembly with Kalisto 0.45.0 using parameters --rf-stranded -t 4
Genome_build: assembled transcriptome
Supplementary_files_format_and_content: estimated counts, tsv text

organism: Daphnia magna

source_name: daphnids

growth_protocol: Cultures were maintained at 20° C with a 16 h:8 h light:dark photoperiod, 20 adult daphnids per liter. Cultures were fed 3 times weekly with 25 mL Raphidocelis subcapitata (~500,000 algal cells/mL) and 10 mL alfalfa solution (8 g Medigo sativa in 1 L of 18 MΩ ultrapure water). Media was changed 100% and neonates removed 3 times per week. Cultures were maintained using only third or fourth brood neonates less than 24 hr old. Each replicate consisted of ten 5-day-old daphnids, which were then exposed for 48 hr.

extract_protocol:
Flash-frozen Daphnia were homogenized in TRIzol and RNA-purified using the Direct-zol RNA MiniPrep (Zymo Research, R2051).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 48 h exposure in moderately hard water control, 1 or 10 mg/L LCO, or ion control of 66 μg/L Li as LiCl and 15 μg/L Co as CoCl2. Animals were fed alfalfa solution immediately after exposure setup and again after 24 hr. After 48 hr, animals were collected, pooled by replicate (i.e. 5 replicates per condition, each replicate containing 10 pooled daphnia), and flash frozen in liquid nitrogen.

value: WT

value: wild type

value: whole daphnids

value: LCO 1 mg/L

value: 5 days

tag: exposure


title: M1_19_RO-7_DoseA

tag: concstr

tag: teratogenicity


title: CHIP_LBC36_024_Wave1

tag: wave

value: Blood

value: PBMCs


title: M1_18_RO-6_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run

tag: plate

tag: usedforfactoranalysis

value: TRUE


title: low3

tag: tissue

tag: treatment


title: CHIP_LBC36_022_Wave1


title: M1_24_RO-12_DoseA

tag: usedformodelbuilding

value: Negative


title: CHIP_LBC36_018_Wave1

tag: cohort


title: Sample 8E Ubc-CreERT2; Csf1fl/fl, Ly6Clow monocytes


title: gz_iPS_cloneA_p25_rep2

description: Grevy's zebra iPSCs at passage 25, replicate 2

source_name: induced Pluripotent Stem Cells

value: iPSCs

value: retrovairal reprogramming


title: M1_17_RO-5_DoseA


title: M1_20_RO-8_DoseA


title: CHIP_LBC36_023_Wave1

tag: sequencing batch


title: gz_iPS_cloneA_p31_rep3

description: Grevy's zebra iPSCs at passage 31, replicate 3


title: Sample 3A Control, Ly6Clow monocytes

value: Bone Marrow

value: Sorted monocytes

tag: genotype


title: gz_iPS_cloneA_p16_rep1

description: Grevy's zebra iPSCs at passage 16, replicate 1


title: Sample 1A Control, Ly6Clow monocytes

value: Tamoxyfen for  4 weeks


title: Sample 2A Control, Ly6Clow monocytes


title: CHIP_LBC36_017_Wave1


title: CHIP_LBC36_021_Wave1


title: Sample 7E Control, Ly6Clow monocytes


title: CHIP_LBC36_020_Wave1


title: low5

tag: strain

tag: age


title: M1_16_RO-4_DoseA

tag: cell type

tag: contrast

tag: concentration


title: CHIP_LBC36_019_Wave1


title: CHIP_LBC36_016_Wave1


title: low1

tag: exposure


title: low2


title: Sample 8B Ubc-CreERT2; Csf1fl/fl, Ly6Chi monocytes

value: Ubc-CreERT2; Csf1fl/fl


title: Ion6

value: Ion


title: M1_15_RO-3_DoseA

tag: conclabel

tag: concstr

tag: teratogenicity

value: Positive


title: M1_14_RO-2_DoseA

tag: run

tag: plate


title: CHIP_LBC36_043_Wave1

tag: wave

tag: tissue


title: CHIP_LBC36_015_Wave1


title: Sample 6B Ubc-CreERT2; Csf1fl/fl, Ly6Chi monocytes

tag: treatment


title: Ion5

value: WT

value: wild type


title: Sample 5B Ubc-CreERT2; Csf1fl/fl, Ly6Chi monocytes


title: Ion4

value: whole daphnids


title: M1_13_RO-1_DoseA

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: Ion3

tag: genotype

value: 5 days


title: M1_12_DMSO_ctrl

value: DMSO


title: Sample 3E Control, Ly6Clow monocytes

value: Csf1fl/fl mice,


title: Sample 8C Ubc-CreERT2; Csf1fl/fl, Ly6Chi monocytes


title: M1_11_DMSO_ctrl

value: Human induced pluripotent-stem-cell derived embryoid body


title: CHIP_LBC36_012_Wave1

tag: cohort

tag: sequencing batch

value: Blood

value: PBMCs


title: Ion1

tag: strain

tag: age


title: high6

value: LCO 10 mg/L


title: Sample 4B Control, Ly6Chi monocytes

tag: cell type


title: M1_10_DMSO_ctrl

value: TRUE

tag: contrast

tag: concentration


title: CHIP_LBC36_014_Wave1


title: Sample 4C Ubc-CreERT2; Csf1fl/fl, Ly6Chi monocytes

value: Bone Marrow


title: high4

tag: exposure


title: M1_9_DMSO_ctrl

tag: conclabel

tag: concstr

tag: teratogenicity


title: CHIP_LBC36_010_Wave1

tag: wave


title: M1_8_DMSO_ctrl

tag: run

tag: plate


title: Sample 3B Control, Ly6Chi monocytes

tag: tissue

value: Sorted monocytes

tag: treatment


title: HL3

value: liver

value: post natal day 98

value: high-fat diet


title: CHIP_LBC36_011_Wave1


title: CHIP_LBC36_013_Wave1


title: high2

tag: genotype


title: Sample 1B Control, Ly6Chi monocytes

value: Tamoxyfen for  4 weeks


title: high5

value: WT


title: M1_7_DMSO_ctrl

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: CHIP_LBC36_008_Wave1

tag: cohort

tag: sequencing batch


title: M1_6_DMSO_ctrl

tag: cell type


title: Sample 3C Control, Ly6Chi monocytes


title: high1

tag: strain

value: wild type

value: untreated

tag: age


title: control6

value: whole daphnids

value: 5 days

tag: exposure


title: CHIP_LBC36_007_Wave1


title: M1_5_DMSO_ctrl

value: DMSO

tag: contrast

tag: concentration

tag: conclabel


title: M1_4_DMSO_ctrl

value: Human induced pluripotent-stem-cell derived embryoid body

tag: concstr

tag: teratogenicity


title: CD3+ CD4+ CD25+ regulatory T cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000 systems, with 101 bp single-end reads obtained.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: CD3+ CD4+ CD25+ regulatory T cells

extract_protocol:
Cells were digested in QIAZOL (Qiagen) to extract to total RNA, in accordance with the manufacturer’s instructions.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio). An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina) according to the SMARTer Kit instructions.

tag: cell line

value: T cells

value: CD3+ CD4+ CD25+ regulatory T cells


title: control4

tag: tissue


title: control5

tag: treatment


title: M1_3_DMSO_ctrl

tag: run

tag: plate


title: CHIP_LBC36_005_Wave1

tag: wave

value: Blood

value: PBMCs


title: CD3+ CD4+ CD25- CD62L- CD44+ effector T cells


title: Sample 2B Control, Ly6Chi monocytes

value: Bone Marrow

tag: genotype

value: Csf1fl/fl mice,


title: CHIP_LBC36_004_Wave1

tag: cohort

tag: sequencing batch


title: control1

tag: strain


title: CHIP_LBC36_003_Wave1

tag: cell type


title: CD3+CD4+ cells isolated from lamina propria lymphocytes of the colons: Wt2

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 or NovaSeq 6000 platforms in 75 or 101-base single-end mode, respectively.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10

extract_protocol:
Total RNA was purified using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Murine CD3+CD4+ cells were isolated from lamina propria lymphocytes of the colons with FACSAria. Cells were collected and library preparation was performed.


title: M1_1_DMSO_ctrl

tag: usedforfactoranalysis

value: TRUE

tag: usedformodelbuilding


title: control2

tag: age

tag: exposure


title: AmBS rep1

status: Public on May 02 2022

city: NEWARK

first: Neeraj

last: Chauhan

state: New Jersey

address: 225 Warren Street

department: Department of Microbiology, Biochemistry & Molecular Genetics

institute: NJMS-PHRI

data_processing:
Raw reads from RNA-seq libraries were filtered to remove the adaptor sequences, low-quality reads (the quality value of over 50% bases of the read is ≤ 20), and the reads containing N > 0.1% (N represents base that could not be determined).
C. auris B8441 reference genome was downloaded from Candida Genome Database (http://www.candidagenome.org) and mapped to the clean reads using HISAT2
HTSeq was used to count the read numbers mapped for each gene. The FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the gene read counts mapped.
Read count obtained from gene expression analysis was used to do differential expression analysis using the DESeq2 R package, while the significant criterion is false discovery rate (padj) <0.05 and log2 fold change ≥0.585.
For further downstream analysis, C. albicans orthologs were retrieved from the Candida Genome Database (http://www.candidagenome.org).
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: Fold change in gene expression in AmB resistant strains compared to susceptible strain
Genome_build: C. auris B8441 reference genome

organism: Candidozyma auris

source_name: Clinical isolate

growth_protocol: Overnight-grown C. auris cultures were inoculated into YPD (initial OD600 of 0.1) and grown at 30°C for 4h.

extract_protocol:
Total RNA was purified using the Genejet RNA purification kit (Thermo Scientific).
mRNA was enriched using oligo(dT) beads (NEB), and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

tag: phenotype

value: AmB-susceptible


title: CD3+CD4+ cells isolated from lamina propria lymphocytes of the colons: Wt1


title: AmBS rep3


title: AmBR1 rep3

value: AmB-resistant


title: CD3+ CD4+ CD25- CD44- CD62L+ naive T cells


title: AmBR2 rep3


title: AmBR2 rep1


title: AmBS rep2


title: CHIP_LBC36_006_Wave1


title: AmBR3 rep2


title: AmBR2 rep2


title: M1_2_DMSO_ctrl

data_processing:
Base-calling was performed with Illumina NovaSeq 6000 Sequencing System.
Alignment was performed with Bowtie2 (2.3.5)
Quantification of amplicon-mapping reads was performed with BEDtools (2.29.2)
QC and filtering was performed with BioQC (1.20.0), ribiosExpression (1.1.9), and ribiosNGS (1.1.30), as well as custom software.
Factor analysis was performed with R (4.0.1) and the psych package (2.1.6)
Differential gene expression was performed with edgeR (3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements are tab-delimited files, containing genes and number of reads mapped to the pre-defined amplicons; raw counts are in the GCT (version 1.2) file, a tab-delimited format of aggregated gene counts.

source_name: Human induced pluripotent-stem-cell derived embryoid body

extract_protocol:
Differentiated EBs were lysed after 7 days of differentiation in 350 μl MagNA Pure LC RNA Buffer (Roche Diagnostics) and purified by using the automated MagNA Pure 96 system (Roche Diagnostics).
The total RNA was quantified using the Qubit RNA Assay Kit (Thermo Fisher) on the Fluorometer Glomax (Promega). Total RNA with a maximum of 10 ng from each biological replicate was reverse transcribed to cDNA using Superscript IV Vilo (Thermo Fisher). Libraries were generated with the AmpliSeq Library Plus Kit (Illumina) according to the reference guide. Pipetting steps for target amplification, primer digestion, and adapter ligation were done with the mosquito automatic pipettor (SPT Labtech) in miniaturization. For the purifications before and after final library amplification, solid phase reversible immobilization magnetic bead purification (Clean NGS, LABGENE Scientific SA) was performed on the multidrop automated pipetting station (Thermo Fisher). We measured both amplicon sizes and cDNA concentrations using an Agilent High Sensitivity DNA Kit (Agilent Technologies) according to the manufacturer’s recommendation. Prior to sequencing, cDNA contents of the samples were normalized and pooled to 2 nM final concentration on Biomek FXP workstation.
RNA-Seq (Amplicon-based molecular phenotyping)

tag: contrast

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity


title: AmBR1 rep1


title: AmBR3 rep1


title: X35STRAPLATEOSROOT1

city: Riverside

first: Mauricio

last: Reynoso

state: CA

address: 4126 Genomics Bldg

department: Botany and Plant Sciences

institute: University of California Riverside

description:
TRAP RNA
Random primed libraries

data_processing:
Genome_build: Genome_build:  RICE: IRGSP-1.0-30 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Rice RNA-seq raw reads were aligned to the IGRSP-1.0-30, with the splice junction aware short read alignment suite Bowtie2/Tophat2, allowing unique alignments with 2 or less mismatches
Rice read count data for RNA-seq was generated for features of exons-by-genes using the summarize Overlaps function of the GenomicRanges package in R.
ATAC-seq raw reads were aligned to the 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<10.
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 proccessed with limma-voom to quantile normalize samples
For accurate visualization, all filtered ATAC-seq bigwig files were scaled with quantile normalization and combined per condition to create a single merged bigwig  file for a condition using a bin size resolution of 1 base pair.
Supplementary_files_format_and_content: Transcripts per per million reads (TPM) values for polyA RNA or TRAP RNA datasets were calculated from count data after quantile normalization
Supplementary_files_format_and_content: Read counts values for ATAC datasets were calculated for regions 2kb upstream of ATG

organism: Oryza sativa Japonica Group

source_name: 7 days-old seedling roots

growth_protocol: For plate experiments, 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 greenhouse experiments, seeds were imbibed for 2 d in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote consistent germination. The seeds were then rinsed with distilled water and returned to 28° C in darkness for 24 h. Germinated seeds (21) were transferred to pots (15 cm diameter and 18 cm height), filled with Profile® Greens GradeTM and placed in a greenhouse at the University of California, Riverside California during June and July 2016. Temperature was controlled at 28° C for 16 h per day and at 25° C for 8 h per night. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at solar midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). For the field experiments, seedlings were germinated in Magenta boxes on selective medium after sterilization, transferred to Profile®, and grown for 14 d in the greenhouse before before transplantation into a pre-fertilized paddy at the Agricultural Operations field at the University of California Riverside Agricultural Experiment Station. The paddy was maintained at 8-10 cm depth for 35 d. Planting of genotypes was based on a randomized design with ten plants per biological replicate.

extract_protocol:
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: tissue samples were increased to isolate polysomes from low abundant cell populations; 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 libraries were prepared from poly(A)+ selected mRNA as described. (Townsley et al 2014, Reynoso et al. 2019)
Nuclei were purified from frozen and pulverized tissue as previously described for O. sativa (Reynoso et al., 2018) 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, Reynoso et al., 2019), with slight modifications. 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 polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least three biological replicates for each condition.

treatment_protocol:
For plate experiments, Oryza sativa cv. Nipponbare seeds from transgenic lines 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 greenhouse experiments, seeds were imbibed for 2 d in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote consistent germination. The seeds were then rinsed with distilled water and returned to 28° C in darkness for 24 h. Germinated seeds (21) were transferred to pots (15 cm diameter and 18 cm height), filled with Profile® Greens GradeTM and placed in a greenhouse at the University of California, Riverside California. Temperature was controlled at 28° C for 16 h per day and at 25° C for 8 h per night. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). For the field experiments, seedlings were germinated in Magenta boxes on selective medium after sterilization, transferred to Profile®, and grown for 14 d in the greenhouse before before transplantation into a pre-fertilized paddy at the Agricultural Operations field at the University of California Riverside Agricultural Experiment Station. The paddy was maintained at 8-10 cm depth for 35 d. Planting of genotypes was based on a randomized design with ten plants per biological replicate.
Five independent biological replicates were grown for each treatment. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at solar midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). A fiber optic oxygen meter (Neofox Sport, Ocean Optics, Dunedin, USA), in five replicates was used to determine the percentage of dissolved oxygen in the submergence tanks was measured at the start and end of the experiment. Oxygen content was stable a 18.90 ± 0.03% at the start (0 d) and end of the experiment.

tag: tissue

value: 7 days-old seedling roots

tag: cultivar

value: Nipponbarre

tag: line

tag: condition

value: Plate grown

tag: tag

value: previously uploaded as GSM4494459


title: SCRTRAPLATEOSROOT1

description:
TRAP RNA
Random primed libraries

value: pAtSCR:HF-GFP-OsRPL18 (Kajala et al., 2021)

value: previously uploaded as GSM4494464


title: M1_31_RO-7_DoseB

tag: run

tag: plate

value: Negative


title: SCRTRAPLATEOSROOT2

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494468


title: AmBR3 rep3


title: X35STRAPLATEOSROOT2

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494460


title: X35STRAPLATEOSROOT3

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494462


title: SHRTRAPLATEOSROOT1

description:
TRAP RNA
Random primed libraries

value: pSHR1:HF-GFP-OsRPL18 (Kajala et al., 2021)

value: previously uploaded as GSM4494461


title: SCRTRAPLATEOSROOT3

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494473


title: RSS1TRAPLATEOSROOT3

description:
TRAP RNA
Random primed libraries

value: pRSS1:HF-GFP-OsRPL18 (Kajala et al., 2021)

value: previously uploaded as GSM4494472


title: SHRTRAPLATEOSROOT2

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494465


title: X35STRAWATRECOSROOT3

description:
TRAP RNA
Random primed libraries

source_name: 27 days-old plant roots

value: 27 days-old plant roots

value: Waterlogged recovery in greenhouse


title: RSS1TRAPLATEOSROOT1

description:
TRAP RNA
Random primed libraries

value: 7 days-old seedling roots

value: Nipponbarre

value: previously uploaded as GSM4494463


title: X35STRAWATRECOSROOT1

description:
TRAP RNA
Random primed libraries


title: CMZTRAPLATEOSROOT1

description:
TRAP RNA
Random primed libraries

value: pCMZ:HF-GFP-OsRPL18 (Kajala et al., 2021)

value: Plate grown

value: previously uploaded as GSM4494466


title: SHRTRAPLATEOSROOT3

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494469


title: X35STRAWATRECOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRAPLATEOSROOT2

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494471


title: AmBR1 rep2

value: AmB-resistant


title: X35STRASUBRECOSROOT3

description:
TRAP RNA
Random primed libraries

value: Submergence recovery in greenhouse


title: X35STRAWATOSROOT1

description:
TRAP RNA
Random primed libraries

source_name: 26 days-old plant roots

value: 26 days-old plant roots

value: Waterlogged in greenhouse


title: X35STRAWATOSROOT2

description:
TRAP RNA
Random primed libraries


title: X35STRAWATOSROOT3

description:
TRAP RNA
Random primed libraries


title: X35STRASUBRECOSROOT2

description:
TRAP RNA
Random primed libraries


title: X35STRASUBOSROOT3

description:
TRAP RNA
Random primed libraries

value: Submergence in greenhouse


title: X35STRASUBRECOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRAPLATEOSROOT2

description:
TRAP RNA
Random primed libraries

value: pRSS1:HF-GFP-OsRPL18 (Kajala et al., 2021)

value: previously uploaded as GSM4494467


title: CMZTRAPLATEOSROOT3

description:
TRAP RNA
Random primed libraries

value: previously uploaded as GSM4494470


title: X35STRASUBOSROOT2

description:
TRAP RNA
Random primed libraries


title: X35STRADRORECOSROOT3

description:
TRAP RNA
Random primed libraries

value: 27 days-old plant roots

value: Water deficit recovery in greenhouse


title: X35STRADRORECOSROOT2

description:
TRAP RNA
Random primed libraries

value: Nipponbarre


title: X35STRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries

source_name: 49 days-old plant roots

value: 49 days-old plant roots

value: Field grown


title: CMZTRAPLATEOSROOT4

description:
TRAP RNA
Random primed libraries

value: 7 days-old seedling roots

value: pCMZ:HF-GFP-OsRPL18 (Kajala et al., 2021)

value: Plate grown

value: previously uploaded as GSM4494474


title: X35STRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries


title: X35STRASUBOSROOT1

description:
TRAP RNA
Random primed libraries


title: X35STRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: X35STRADROOSROOT2

description:
TRAP RNA
Random primed libraries

value: Water deficit in greenhouse


title: X35STRACONOSROOT1

description:
TRAP RNA
Random primed libraries

value: Control in greenhouse I


title: X35STRADROOSROOT1

description:
TRAP RNA
Random primed libraries

value: 26 days-old plant roots


title: X35STRADRORECOSROOT1

description:
TRAP RNA
Random primed libraries


title: X35STRACON2OSROOT3

description:
TRAP RNA
Random primed libraries

value: Control in greenhouse II


title: X35STRADROOSROOT3

description:
TRAP RNA
Random primed libraries


title: X35STOTWATRECOSROOT2

description:
PolyA RNA
Random primed libraries

value: Waterlogged recovery in greenhouse


title: X35STRACONOSROOT3

description:
TRAP RNA
Random primed libraries


title: X35STRACONOSROOT2

description:
TRAP RNA
Random primed libraries


title: X35STRACON2OSROOT2

description:
TRAP RNA
Random primed libraries


title: X35STOTWATRECOSROOT3

description:
PolyA RNA
Random primed libraries


title: X35STRACON2OSROOT1

description:
TRAP RNA
Random primed libraries


title: X35STOTWATOSROOT3

description:
PolyA RNA
Random primed libraries

value: Waterlogged in greenhouse


title: X35STOTWATOSROOT2

description:
PolyA RNA
Random primed libraries


title: X35STOTWATRECOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTWATOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTSUBRECOSROOT3

description:
PolyA RNA
Random primed libraries

value: Submergence recovery in greenhouse


title: X35STOTSUBOSROOT3

description:
PolyA RNA
Random primed libraries

value: Submergence in greenhouse


title: X35STOTSUBRECOSROOT2

description:
PolyA RNA
Random primed libraries

value: 27 days-old plant roots


title: X35STOTSUBRECOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTPLATEOSROOT3

description:
PolyA RNA
Random primed libraries


title: X35STOTFIELDOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTSUBOSROOT2

description:
PolyA RNA
Random primed libraries


title: X35STOTPLATEOSROOT2

description:
PolyA RNA
Random primed libraries


title: X35STOTDRORECOSROOT2

description:
PolyA RNA
Random primed libraries

value: Water deficit recovery in greenhouse


title: X35STOTFIELDOSROOT3

description:
PolyA RNA
Random primed libraries

value: Nipponbarre


title: X35STOTSUBOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTFIELDOSROOT2

description:
PolyA RNA
Random primed libraries

value: 49 days-old plant roots


title: X35STOTDROOSROOT3

description:
PolyA RNA
Random primed libraries


title: X35STOTPLATEOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTDRORECOSROOT3

description:
PolyA RNA
Random primed libraries


title: X35STOTDROOSROOT2

description:
PolyA RNA
Random primed libraries


title: X35STOTDRORECOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTDROOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTCONOSROOT3

description:
PolyA RNA
Random primed libraries


title: X35STOTCONOSROOT1

description:
PolyA RNA
Random primed libraries


title: X35STOTCONOSROOT2

description:
PolyA RNA
Random primed libraries


title: X35STOTCON2OSROOT3

description:
PolyA RNA
Random primed libraries


title: SHRTRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries

value: pSHR1:HF-GFP-OsRPL18 (Kajala et al., 2021)

value: Field grown


title: SHRTRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries


title: X35STOTCON2OSROOT2

description:
PolyA RNA
Random primed libraries


title: X35STOTCON2OSROOT1

description:
PolyA RNA
Random primed libraries


title: SHRTRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: SCRTRAWATRECOSROOT3

description:
TRAP RNA
Random primed libraries

value: pAtSCR:HF-GFP-OsRPL18 (Kajala et al., 2021)


title: SCRTRAWATOSROOT3

description:
TRAP RNA
Random primed libraries


title: SCRTRAWATOSROOT2

description:
TRAP RNA
Random primed libraries


title: SCRTRAWATRECOSROOT1

description:
TRAP RNA
Random primed libraries


title: SCRTRAWATOSROOT1

description:
TRAP RNA
Random primed libraries


title: SCRTRADRORECOSROOT3

description:
TRAP RNA
Random primed libraries


title: SCRTRADROOSROOT1

description:
TRAP RNA
Random primed libraries


title: SCRTRADROOSROOT3

description:
TRAP RNA
Random primed libraries


title: SCRTRADROOSROOT2

description:
TRAP RNA
Random primed libraries


title: SCRTRADRORECOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRAWATRECOSROOT2

description:
TRAP RNA
Random primed libraries

value: pRSS1:HF-GFP-OsRPL18 (Kajala et al., 2021)


title: SCRTRACONOSROOT1

description:
TRAP RNA
Random primed libraries


title: SCRTRADRORECOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRAWATRECOSROOT3

description:
TRAP RNA
Random primed libraries


title: RSS1TRAWATOSROOT3

description:
TRAP RNA
Random primed libraries


title: SCRTRACONOSROOT3

description:
TRAP RNA
Random primed libraries


title: SCRTRACONOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRAWATRECOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRAWATOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRASUBRECOSROOT3

description:
TRAP RNA
Random primed libraries


title: SCRTRAWATRECOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRAWATOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRASUBRECOSROOT2

description:
TRAP RNA
Random primed libraries


title: CHIP_LBC36_009_Wave1

data_processing:
Reads were filtered for phred ≥30 and adapters removed using Trimmomatic (Bolger et al., 2014) before undergoing guided alignment to human genome assembly hg19 using bwa-mem and bowtie2.
Unique molecular barcodes (ligated prior to PCR amplification) were utilised for read deduplication to support quantitative multiplexed analysis and confident mutation detection. Within targeted regions, variants were called using three tools (Lofreq (Wilm et al., 2012), Freebayes (Garrison and Marth, 2012) and Vision (ArcherDX, unpublished) – building a consensus from the output of all callers
All filtered variants at 0.02 VAF met the following criteria: 1) the number of reads supporting the alternative allele surpasses the coverage criteria while exhibiting no directional biases (AO ≥ 5, UAO ≥ 3); 2) variants are significantly underrepresented within the Genome Aggregation Database (gnomAD; p ≤ 0.05); 3) variants are not obviously germline variants (stable VAF across all waves ~0.5 or ~1) that may have been underrepresented in the gnomAD database due to the narrow geographical origin of the Lothian Birth Cohort participants; 4) contain events that are overrepresented across the dataset - generally frameshift duplications and deletions - whose reads share some sequence homology to target regions yet are likely misaligned artefact from the capture method. In addition, we manually curated this list checking for variants that were previously reported, as per Jaiswal et al. (Jaiswal et al., 2014b), in the COSMIC (Catalogue of Somatic Mutations in Cancer) database or within the published literature (Table 4).
For any variant that surpassed the above criteria at, or above, 0.02 VAF across the measured time period, we endeavored to include all other participant matched data points regardless of VAF level
Genome_build: hg19
Supplementary_files_format_and_content: Extended MAF Format (Mutation Annotation Format)

source_name: Human Blood (PBMCs)

extract_protocol: Sequencing of each pool was performed using the NextSeq 500/550 High-Output v2.5 (300 cycle) kit on the NextSeq 550 platform. To inform reproducibility, background model for error and batch correction, we sequenced “genome in a bottle” DNA in each batch of samples (DNA NA12878 Coriell Institute).

tag: wave

tag: cohort

tag: sequencing batch

value: Blood

tag: cell type

value: PBMCs


title: RSS1TRASUBOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries


title: RSS1TRASUBOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRASUBOSROOT3

description:
TRAP RNA
Random primed libraries


title: RSS1TRADRORECOSROOT3

description:
TRAP RNA
Random primed libraries


title: RSS1TRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRADRORECOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRADRORECOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRADROOSROOT3

description:
TRAP RNA
Random primed libraries

value: Water deficit in greenhouse


title: RSS1TRACONOSROOT3

description:
TRAP RNA
Random primed libraries

value: 26 days-old plant roots

value: Control in greenhouse I


title: RSS1TRASUBRECOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRADROOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRACONOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRADROOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRACONOSROOT1

description:
TRAP RNA
Random primed libraries


title: RSS1TRACON2OSROOT3

description:
TRAP RNA
Random primed libraries

value: Control in greenhouse II


title: QHBTRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries


title: RSS1TRACON2OSROOT1

description:
TRAP RNA
Random primed libraries


title: QHBTRAPLATEOSROOT1

description:
TRAP RNA
Random primed libraries

value: 7 days-old seedling roots

value: Plate grown


title: QHBTRADROOSROOT1

description:
TRAP RNA
Random primed libraries


title: QHBTRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: QHBTRADROOSROOT2

description:
TRAP RNA
Random primed libraries


title: QHBTRADROOSROOT3

description:
TRAP RNA
Random primed libraries


title: QHBTRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries


title: NRAMPTRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries


title: QHBTRACONOSROOT2

description:
TRAP RNA
Random primed libraries


title: NRAMPTRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries


title: QHBTRACONOSROOT3

description:
TRAP RNA
Random primed libraries


title: QHBTRACONOSROOT1

description:
TRAP RNA
Random primed libraries


title: LSI1TRAWATRECOSROOT2

description:
TRAP RNA
Random primed libraries

value: Waterlogged recovery in greenhouse


title: NRAMPTRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: LSI1TRAWATRECOSROOT1

description:
TRAP RNA
Random primed libraries

value: 27 days-old plant roots


title: LSI1TRAWATOSROOT3

description:
TRAP RNA
Random primed libraries

value: Waterlogged in greenhouse


title: RSS1TRACON2OSROOT2

description:
TRAP RNA
Random primed libraries

value: Nipponbarre


title: LSI1TRAWATOSROOT2

description:
TRAP RNA
Random primed libraries


title: LSI1TRAWATOSROOT1

description:
TRAP RNA
Random primed libraries


title: QHBTRAPLATEOSROOT2

description:
TRAP RNA
Random primed libraries


title: QHBTRAPLATEOSROOT3

description:
TRAP RNA
Random primed libraries


title: LSI1TRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries

value: 49 days-old plant roots


title: LSI1TRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries


title: LSI1TRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: LSI1TRADRORECOSROOT2

description:
TRAP RNA
Random primed libraries

value: Water deficit recovery in greenhouse


title: LSI1TRAWATRECOSROOT3

description:
TRAP RNA
Random primed libraries


title: LSI1TRADRORECOSROOT1

description:
TRAP RNA
Random primed libraries


title: LSI1TRADROOSROOT1

description:
TRAP RNA
Random primed libraries


title: CMZTRAWATRECOSROOT2

description:
TRAP RNA
Random primed libraries

value: pCMZ:HF-GFP-OsRPL18 (Kajala et al., 2021)


title: LSI1TRADROOSROOT3

description:
TRAP RNA
Random primed libraries


title: LSI1TRACONOSROOT1

description:
TRAP RNA
Random primed libraries


title: LSI1TRACONOSROOT3

description:
TRAP RNA
Random primed libraries


title: CMZTRAWATRECOSROOT1

description:
TRAP RNA
Random primed libraries


title: CMZTRAWATOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRAWATOSROOT3

description:
TRAP RNA
Random primed libraries


title: CMZTRAWATRECOSROOT3

description:
TRAP RNA
Random primed libraries


title: HMATRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries

value: Field grown


title: HMATRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: LSI1TRACONOSROOT2

description:
TRAP RNA
Random primed libraries


title: EXPTRAFIELDOSROOT1

description:
TRAP RNA
Random primed libraries


title: LSI1TRADROOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRAWATOSROOT1

description:
TRAP RNA
Random primed libraries


title: EXPTRAFIELDOSROOT3

description:
TRAP RNA
Random primed libraries


title: LSI1TRADRORECOSROOT3

description:
TRAP RNA
Random primed libraries


title: HMATRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries


title: EXPTRAFIELDOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRADROOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRADRORECOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRADROOSROOT1

description:
TRAP RNA
Random primed libraries


title: CMZTRADRORECOSROOT3

description:
TRAP RNA
Random primed libraries


title: CMZTRADROOSROOT3

description:
TRAP RNA
Random primed libraries


title: CMZTRACONOSROOT1

description:
TRAP RNA
Random primed libraries


title: CMZTRACONOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRACONOSROOT3

description:
TRAP RNA
Random primed libraries


title: CASPTRAWATRECOSROOT3

description:
TRAP RNA
Random primed libraries


title: CASPTRADROOSROOT1

description:
TRAP RNA
Random primed libraries


title: CASPTRADROOSROOT3

description:
TRAP RNA
Random primed libraries


title: CASPTRADROOSROOT2

description:
TRAP RNA
Random primed libraries


title: CMZTRADRORECOSROOT1

description:
TRAP RNA
Random primed libraries


title: CASPTRAWATRECOSROOT1

description:
TRAP RNA
Random primed libraries


title: 35S_FLAG-BD rep A

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
Shortstack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with a fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

growth_protocol: Plants were grown under 16-hour day conditions at 22°C in a growth chamber. All tissue was leaf harvested at the time of the plant's first flower opening.

extract_protocol:
Total RNA was isolated with Trizol reagent (Invitrogen) and enriched for small RNAs using the mirVana microRNA Isolation Kit (Ambion).
Size-enriched small RNAs were used in the Illumina TruSeq Small RNA Library Preparation Kit.
Multiplexed libraries were sequenced on Illumina HiSeq 3000 or HiSeq X Ten or NextSeq 550 or NovaSeq 6000

tag: ecotype

value: Columbia

tag: genotype/variation


title: CASPTRAWATOSROOT3

description:
TRAP RNA
Random primed libraries