title: miRNASeq_CAD14_T0

status: Public on Jul 26 2025

type: SRA

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

library_source: transcriptomic

data_processing:
Genome-wide methylation study: for the quality trimming of paired end reads it is used Trimgalore v0.4.1, the reads were mapped using Bismark v0.16.1 with Bowtie2.
Genome-wide methylatio study: Bismark_deduplicate (Bismark v0.16.1) was used in order to remove PCR duplication artifacts.
Genome-wide methyylation study: The methylation status was extracted with Bismark_methylation_extractor (Bismark v0.16.1).
Genome-wide methylation study: The differentially methylated analysis was performed using the rn-beads R packages for gene, promoter, CpG island and site levels. Clusterings and Heat Maps  analysis have been performed using “dist” and “hclust” functions in R, Euclidean distance and Ward agglomeration method.
miRNA-seq: miRNAs data analysis and sequencing data quality was performed using FastQC.
miRNA-seq: Sequences were trimmed by cutadapt (v0.9.5) before analysis.
miRNA-seq: MiRNAs proportion in the sequences was evaluated using Bowtie (v0.12.7)
miRNA-seq:  HTSeq was used to count reads per gene on GeneCode v19 annotations.
miRNA-seq: MicroRNAs expression was obtained by mapping and quantifying sequences with mirDeep2 on mirbase v21.
miRNA-seq: Normalization and differential miRNA expression were performed using edgeR  on R on samples paired by patient. Only miRNAs with at least 5 mapped reads were considered as expressed. Results were considered statistically significant for p-values ≤ 0.05 and fold-changes ≥ ±1.5.
MiRNA data integration analysis was conducted by using miRTarBase v6.0.
Assembly: hg19
Supplementary files format and content: Genome-wide methylation: Tab-delimited text file includes rn-beads R packages normalizated expression values for gene, promoter, CpG island and site levels.
Supplementary files format and content: miRNASeq: Tab-delimited text file includes mirdeep2 normalized expression values for each miR and for each sample. Annotations from mirBase v21.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral whole blood

growth_protocol: We analyzed a total of 4 patients  including 2 control subjects (CTR group) and 2 patients with stable coronary artery disease (CAD group). A peripheral blood sample (8mL) has been collected within 24 hours from the coronary angiography. CTR group includes subjects without angiographically significant coronary artery stenosis. CAD group includes patients with chronic stable angiographically documented coronary artery disease, admitted to the hospital for provocative cardiac testing positive for inducible myocardial ischemia. Inclusion criteria were (a) gender (especially male); (b) age > 70 years; (c) dyslipidemia (total cholesterol ≥ 240 mg/dl, LDL-c ≥ 160 mg/dl, HDL-c < 40 mg/dl, Triglycerides ≥ 200 mg/dl); (d) hypertension, systolic blood pressure (BP) values ≥ 140 mmHg and/or di-astolic BP values ≥ 90 mmHg; (e) diabetes (only for one CAD patients), fasting plasma glucose ≥ 126 mg/dl (7.0 mmol/L) or 2-hour plasma glucose during 75 mg oral glucose tolerance test ≥ 200 mg/dl (11.1 mmol/L) or Hb1Ac ≥ 6,5% (48 mmol/mol); (f) smoking history for CAD patients.

extract_protocol:
isolated from 1ml of whole blood using miRNeasy Mini Kit (QIAGEN) and Buffer EL (QIAGEN) according to manufacturer instructions. miRNeasy Mini Kit allowed the extraction both of total RNA and a separated miRNA-enriched fraction.
SMARTer smRNA-Seq Kit NEB
polyAdenylation, polyA selection, RT, library prep
Genomic DNA has been manually extracted from whole blood samples (300µl) using FlexiGene DNA Kit (QIAGEN) according to the manufacturer’s instructions. The concentration of the isolated DNA was evaluated by using a NanoDrop ND-1000 Spectrophotometer (Euro-Clone).  Then, to converts all unmethylated cytosines to uracil, bisuphite treatment was performed on genomic DNA (2 µg/µl) using EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructions. The genomic DNA treated was quantified by the Qubit®2.0 Fluorometer (ThermoFisher Scientific, Massachusetts, USA).   Total RNA extraction from PBMCs was performed using Trizol® (Ambion, Waltham, MA, USA) reagent according to manufacturer instructions. RNA concentration was evaluated by using a NanoDrop ND-1000 Spectrophotometer (Euro-Clone), whereas RNA quality was checked on agarose gel 1%. To isolate miRNAs fraction, 50ng of RNA has been reverse transcribed into cDNA using the miScript II RT kit (QIAGEN) following the manufacturer’s instruction.
Genome-wide methylation study: for library preparation, Kapa ROCHE together with CpGiant ROCHE Nimblegen has been used. MiRNA sequencing: sequencing libraries were generated using SMARTer small RNA CLONTECH for Illumina following the manufacturer's recommendations (New England BioLabs, Ipswich, MA, USA).
Genome-wide methylation and miRNA-sequencing has been performed using NextSeq 500 ILLUMINA platform. All samples passed quality control analysis.

treatment_protocol: PBMCs have been isolated by whole blood (8mL) using Ficoll® Paque Plus (GE Healthcare, Little Chalfont, UK) according to manufacturer instructions. Isolated PBMCs have been suspended in 1mL of Trizol® (Invitrogen™) and stored at -80°C until further analysis.

tag: disease

value: patient with coronary artery diseases

tag: gender

value: male

tag: age

value: over 65

tag: recruitment time

value: recruitment at the hospitalization time


title: MethylSeq_CAD9_T0

library_source: genomic

molecule: genomic DNA

extract_protocol:
from whole blood sample (300µl) using FlexiGene DNA Kit (QIAGEN) according to manufacturer instructions.
SeqCap Epi Enrichment Kit ROCHE + Epi CpGiant capture ROCHE
library prep, bisulfite, capture
Genomic DNA has been manually extracted from whole blood samples (300µl) using FlexiGene DNA Kit (QIAGEN) according to the manufacturer’s instructions. The concentration of the isolated DNA was evaluated by using a NanoDrop ND-1000 Spectrophotometer (Euro-Clone).  Then, to converts all unmethylated cytosines to uracil, bisuphite treatment was performed on genomic DNA (2 µg/µl) using EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructions. The genomic DNA treated was quantified by the Qubit®2.0 Fluorometer (ThermoFisher Scientific, Massachusetts, USA).   Total RNA extraction from PBMCs was performed using Trizol® (Ambion, Waltham, MA, USA) reagent according to manufacturer instructions. RNA concentration was evaluated by using a NanoDrop ND-1000 Spectrophotometer (Euro-Clone), whereas RNA quality was checked on agarose gel 1%. To isolate miRNAs fraction, 50ng of RNA has been reverse transcribed into cDNA using the miScript II RT kit (QIAGEN) following the manufacturer’s instruction.
Genome-wide methylation study: for library preparation, Kapa ROCHE together with CpGiant ROCHE Nimblegen has been used. MiRNA sequencing: sequencing libraries were generated using SMARTer small RNA CLONTECH for Illumina following the manufacturer's recommendations (New England BioLabs, Ipswich, MA, USA).
Genome-wide methylation and miRNA-sequencing has been performed using NextSeq 500 ILLUMINA platform. All samples passed quality control analysis.


title: MethylSeq_CAD14_T0


title: miRNASeq_CTR4

value: patient with healthy coronary arteries


title: GD251

status: Public on Jul 31 2022

city: Beijing

first: Changying

last: Li

address: Panjiayuan Street 17, Chaoyang District

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: with arachidonic acid

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: Hepatic TCRγδ double negative T cells

extract_protocol:
TCRαβ+7-AAD-CD45+CD3+NK1.1-CD4-CD8- cells and TCRγδ+7-AAD-CD45+CD3+NK1.1-CD4-CD8- cells were sorted using FACS Aria II before arachidonic acid stimulation for 48 hours in mouse liver. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: liver

tag: developmental stage

value: adult


title: MethylSeq_CTR4


title: GD253

description: with arachidonic acid


title: GD03

description: without arachidonic acid


title: MethylSeq_CTR2


title: AB252

description: with arachidonic acid

source_name: Hepatic TCRαβ double negative T cells


title: AB251

description: with arachidonic acid


title: AB253

description: with arachidonic acid


title: miRNASeq_CTR2


title: AB03

description: without arachidonic acid


title: GD252

description: with arachidonic acid


title: GD01

description: without arachidonic acid


title: miRNASeq_CAD9_T0


title: AB01

description: without arachidonic acid


title: AB02

description: without arachidonic acid


title: soil.shoot.rhd6.rsl1_1.2.brep3

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

data_processing:
PE reads were mered and imported into GalaxyEurope. Samon was used to aling the sequence reads to the A. Thaliana genome and quantifiy the number of fragments. Exported tabular data were imported into 3DRNAseq app (Guo et al., 2018)
Reads were quality corrected for batch effects of which there were none. Read counts and transcripts per million reads (TPMs) were generated using the scaledTPM method. Since a 3' kit was used for the library generation the length of the gene was not unequal and therefore not taken into account.
Low expressed genes were filtered based on analying the mean-variance trend. Values were retained if equal or larger 6 of the 90 samples had a count of larger or equal 2 counts per million.
The TTM method was used to normalize expression to log2-CPM.
Only differentially expressed genes (DE) were analysed since splice variants cannot be accounted for with only a 3' library. The log2 fold chage of gene/transcript abundance was calucalted and a t-test used to calcuate a p-value. The Benjamin Hochberg method was used for multiple testing correction of the p-values. DEGs were defined as adjusted p-value < 0.05 and L_2 FC ≥ 0.5.
Genome_build: https://www.arabidopsis.org/download/index-auto.jsp%3Fdir%3D%252Fdownload_files%252FGenes%252FTAIR10_genome_release
Supplementary_files_format_and_content: The processed data file contains the name of each sample and the scaled TPM values using the LimmaVoom method (Gene TPM.csv). The tabular data file contains raw counts as output by Salmon. The orginal sequencing data can be found in the fastq data file. There are 2-4 sequence files per sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Plate grown plants were grown for 2 weeks on 1/2 MS medium solidifid with 1% Agar and containing 1% Sucrose. Soil grown plants were grown on peat soil for 5 weeks in short day conditions. Once a week plants were watered with 1l 1/10 Hoagland to ensure good nutrient supply. More information to be found in Fischer et al. DOI to be added.

extract_protocol:
RNA was extracted from frozen tissues using the method from Paredes et al., 2018. More information to be found in Fischer et al. DOI to be added.
Librarys were generated from mRNA by Deep Seq Nottingham using the QuantSeq 3’ mRNA-Seq library kit. More information to be found in Fischer et al. DOI to be added.

treatment_protocol: Plants were grown on control medium and on soil. More information to be found in Fischer et al. DOI to be added.

value: shoot

tag: growth medium

value: peat soil

tag: ploidy

value: tetraploid

tag: condition

value: control

tag: replicate

tag: genotype

value: rhd6-3/rsl1-1 mutant


title: soil.shoot.X10.brep2

value: diploid

value: sos3-2 mutant


title: soil.shoot.rhd6.rsl1_1.2.brep2


title: soil.shoot.X10.brep1


title: soil.shoot.esb1.1.brep3

value: esb1-1 mutant


title: soil.shoot.esb1.1.brep1


title: soil.shoot.rhd6.rsl1.brep2


title: soil.shoot.rhd6.rsl1.brep1


title: soil.shoot.rhd6.rsl1.brep3


title: GD02

description: without arachidonic acid


title: soil.shoot.Col.04x.brep2

value: wild type


title: soil.shoot.X25.brep1

value: chx25-3 mutant


title: soil.shoot.X25.2.1.brep3


title: soil.shoot.esb1.1_7.1.brep3


title: soil.shoot.esb1.1.brep2


title: soil.shoot.Col.04x.brep3


title: soil.shoot.esb1.1_7.1.brep2


title: soil.shoot.X10.brep3


title: soil.shoot.esb1.1_7.1.brep1


title: soil.shoot.Col.02x.brep1


title: soil.shoot.X25.brep2


title: soil.shoot.X10.9.1.brep2


title: soil.root.X10.brep2

source_name: root

value: root


title: soil.shoot.rhd6.rsl1_1.2.brep1


title: soil.shoot.X25.brep3


title: soil.shoot.Col.02x.brep2


title: soil.shoot.Col.04x.brep1


title: soil.root.rhd6.rsl1.brep2


title: soil.shoot.Col.02x.brep3


title: soil.root.rhd6.rsl1.brep3


title: soil.shoot.X10.9.1.brep1


title: soil.root.rhd6.rsl1_1.2.brep2


title: soil.root.rhd6.rsl1_1.2.brep1


title: soil.root.esb1.1.brep3


title: soil.root.esb1.1.brep2


title: soil.shoot.X25.2.1.brep2


title: soil.shoot.X25.2.1.brep1


title: soil.root.X10.brep1


title: soil.root.rhd6.rsl1_1.2.brep3


title: soil.root.esb1.1_7.1.brep3


title: soil.root.Col.02x.brep3


title: soil.root.esb1.1_7.1.brep1


title: soil.root.X10.brep3


title: soil.shoot.X10.9.1.brep3


title: soil.root.Col.02x.brep2


title: soil.root.Col.02x.brep1


title: soil.root.rhd6.rsl1.brep1


title: soil.root.X25.brep1


title: soil.root.esb1.1.brep1


title: soil.root.X25.2.1.brep3


title: soil.root.esb1.1_7.1.brep2


title: soil.root.Col.04x.brep2


title: plate.root.X25.2.1.brep3

value: plate


title: soil.root.X10.9.1.brep3


title: soil.root.X10.9.1.brep2


title: plate.root.X25.2.1.brep1


title: soil.root.Col.04x.brep1


title: soil.root.X25.brep3


title: soil.root.Col.04x.brep3


title: soil.root.X10.9.1.brep1


title: plate.root.X25.brep3


title: soil.root.X25.2.1.brep1


title: plate.root.rhd6.rsl1_1.2.brep2


title: plate.root.rhd6.rsl1_1.2.brep3


title: plate.root.X25.brep1


title: plate.root.X25.brep2


title: soil.root.X25.2.1.brep2


title: plate.root.X25.2.1.brep2


title: plate.root.X10.9.1.brep2


title: plate.root.rhd6.rsl1_1.2.brep1


title: plate.root.rhd6.rsl1.brep2


title: plate.root.X10.brep1


title: plate.root.X10.9.1.brep1


title: plate.root.rhd6.rsl1.brep1


title: plate.root.X10.brep2


title: plate.root.esb1.1.brep3


title: plate.root.esb1.1.brep2


title: plate.root.X10.9.1.brep3


title: soil.root.X25.brep2


title: plate.root.esb1.1_7.1.brep1


title: plate.root.esb1.1_7.1.brep3


title: plate.root.Col.02x.brep1


title: plate.root.Col.04x.brep1


title: plate.root.Col.04x.brep3


title: plate.root.esb1.1.brep1


title: plate.root.Col.02x.brep2


title: plate.root.Col.02x.brep3


title: plate.root.esb1.1_7.1.brep2


title: EPN_non-enriched_n3

city: Philadelphia

first: Jay

middle: S

last: Schneider

state: PA

address: 1020 Locust St

department: Anatomy,Pathology and Cell biology

country: USA

institute: Thomas Jefferson University

data_processing:
Raw paired-end FASTQ sequencing reads were mapped to the rat reference genome (rn6) using STAR (Spliced Transcripts Alignment to a Reference) aligner followed by read trimming using trimmomatic to remove adaptors and low-quality reads.
FeatureCounts calculated how many reads map to each gene/feature with parameters ‘-M’ (with multi-mapped reads) and ‘-t exon’ (within exon region).
Genome_build: rn6
Supplementary_files_format_and_content: Normalized abundance measurements, Matrix table for normalized gene count for every gene and sample

organism: Rattus norvegicus

source_name: Hippocampus CA1

extract_protocol:
At postnatal day 55, animals (N=3 per group) were euthanized by decapitation, brains removed fresh, sliced in a rat brain tissue matrix over ice, and CA1 of the hippocampus was quickly dissected from brain slices, frozen, and stored at -80ºC until used.  RNA was extracted manually using Qiagen RNeasy kits.
Next generation sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit with ribosomal RNA depletion, following the manufacturer’s protocol.

treatment_protocol: Dams were fed RMH 1000 chow with no added Pb during gestation and were fed chow with or without added Pb acetate (150ppm) beginning at day of birth (postnatal day 1) and pups continued to receive this exposure to Pb through weaning at postnatal day 21. Post-weaning, rats were housed 3 to a standard cage (47.6 cm x 25.9 cm) with no added stimuli (non-enriched) or 6 to a cage (61 cm x 43.5 cm) containing a variety of toys, climbing and nesting materials, and tunnels that were changed twice per week (enriched group).

value: Long Evans

value: Brain

value: postnatal day 55

tag: treatment

value: Pb and no stimuli


title: EPN_non-enriched_n1


title: EPN_non-enriched_n2


title: EPN_enriched_n3

value: Pb and stimuli


title: plate.root.Col.04x.brep2


title: EPN_enriched_n1


title: EPN_enriched_n2


title: Control_non-enriched_n1

value: no Pb and no stimuli


title: Control_enriched_n2

value: no Pb but stimuli


title: Control_non-enriched_n2


title: Control_enriched_n3


title: Control_enriched_n1


title: Control_non-enriched_n3


title: 48hpf-STX-3

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Base calling: Sanger/Illumina 1.9
FASTQC: Pre-processing
STAR aligner 2.5 for mapping
Htseq count for obtaining the read counts
Assembly: Danio_rerio.GRCz10 version 84
Supplementary files format and content: Format - text; content - read counts per gene

organism: Danio rerio

source_name: Embryos

extract_protocol:
DNase free total RNA was isolated using BioRad Aurum kit following manufacturer’s instructions. Total RNA was quantified using Nanodrop spectrophotometer and quality checked using Agilent Technology Tape Station. All the samples had RIN numbers between 9.2-10.
RNAsequencing library preparation and sequencing were done at Tufts University Core Facility. Unstranded RNA seq libraries were prepared using TruSeq kit and sequenced on HiSeq 2000 platform.

treatment_protocol: Zebrafish embryos were injected with either saxitoxin or weak solution of hydrochloric acid (3mM) at 6 hpf (early gastrula stage) directly into the yolk. Embryos were reared in clean 0.3X danieu’s solution until sampling. Embryos were sampled at 24, 36 and 48 hpf for quantifying gene expression patterns.

value: Embryos

tag: time

value: Saxitoxin


title: 48hpf-STX-2


title: 48hpf-Control-1

value: Control


title: 48hpf-Control-3


title: 36hpf-STX-2


title: 48hpf-Control-2


title: 48hpf-STX-1


title: 36hpf-STX-3


title: 36hpf-STX-1


title: 24hpf-STX-3


title: 24hpf-STX-1


title: 24hpf-STX-2


title: 36hpf-Control-1


title: 36hpf-Control-2


title: 24hpf-Control-2


title: 24hpf-Control-1


title: 24hpf-Control-3


title: 36hpf-Control-3


title: CD14cells, patient27

type: RNA

city: Madrid

first: María Isabel

last: Delgado Dolset

address: Urb. Montepríncipe s/n

department: Instituto de Medicina Molecular Aplicada Nemesio Díez

country: Spain

institute: Universidad CEU-San Pablo

description: Gene Expression data from CD14+ cells from non-allergic patient

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 20 hr at 48ºC on GeneChip™ Human Gene 2.1 ST Array Strip. GeneChips were washed and stained in the GeneAtlas™ System for Academic Customers, 230V (Applied Biosystems™)

scan_protocol: GeneChips were scanned using the GeneAtlas™ System for Academic Customers, 230V (Applied Biosystems™)

data_processing: The data was RMA-normalized (.chp files) using Expression Console (Affymetrix). Gene expression analysis of .chp files was performed with Transcriptome Analysis Console 3.0 (TAC) (Affymetrix).

label: biotin

source_name: CD14+ cells isolated by magnetic beads from human PBMCs

label_protocol: Single-stranded cDNA was biotinylated according to Affymetrix protocols

extract_protocol: RNA was extracted using Rneasy® Mini Kit (Qiagen) with Dnase treatment following manufacturer procedure. RNA concentration was determined using a NanoDrop™ 2000/2000c Spectrophotometer, and its integrity was assessed with Experion RNA StdSens analysis kit (Bio‐Rad Laboratories Inc.), establishing an RNA quality indicator (RQI) ≥ 7 as a requisite for transcriptomic analysis.

tag: cell type

value: CD14+ cells

value: F

tag: individual

tag: allergy

value: control


title: Platelets, patient24

description: Gene Expression data from platelets from non-allergic patient

source_name: Platelets isolated by plateletpheresis

extract_protocol: For RNA isolation, samples frozen in 1ml of TRIzol were thawed and maintained at RT for 5 minutes. Then, 200 µL of cold chloroform were added to each tube. After mixing by inverting the tubes 5 times, they were left to rest for 3 minutes at RT and later centrifuged for 15 minutes, 14000g at 4ºC. Approximately 400µl of supernatant were transferred to new tubes containing 10 µg of ultra-pure glycogen. 500µl of cold isopropanol were added to each tube and mixed by inversion. Samples were stored overnight at -20ºC. Next, samples were centrifuged for 15 minutes, 14000g at 4ºC. Supernatant was discarded and pellets of the same study subject were pooled and resuspended in 1 mL of ethanol 70%. After 10 minutes of 5500g centrifugation at 4ºC, supernatant was discarded. Pellets were dried out at 35-37ºC in a thermoblock for 2 minutes with open tube lids. RNA pellets were resuspended in 30 µl of water, mixed by vortex, and frozen at -80ºC. Finally, RNA isolation was performed following MinElute Cleanup (Qiagen) kit instructions

value: platelets


title: CD3cells, patient27

description: Gene Expression data from CD3+ cells from non-allergic patient

source_name: CD3+ cells isolated by magnetic beads from human PBMCs

value: CD3+ cells


title: CD3cells, patient22

description: Gene Expression data from CD3+ cells from mild allergic patient

value: mild


title: CD14cells, patient22

description: Gene Expression data from CD14+ cells from mild allergic patient


title: Platelets, patient21

description: Gene Expression data from platelets from severe allergic patient

value: severe


title: CD3cells, patient24


title: Platelets, patient20


title: CD3cells, patient19

value: M


title: Platelets, patient27


title: Platelets, patient18


title: Platelets, patient22

description: Gene Expression data from platelets from mild allergic patient


title: Platelets, patient19


title: CD14cells, patient19


title: CD14cells, patient23


title: CD3cells, patient20

description: Gene Expression data from CD3+ cells from severe allergic patient


title: Platelets, patient23


title: CD14cells, patient17

description: Gene Expression data from CD14+ cells from severe allergic patient


title: CD3cells, patient17


title: CD3cells, patient21


title: CD14cells, patient21


title: CD3cells, patient18


title: CD14cells, patient20


title: CD3cells, patient23


title: CD14cells, patient18


title: Platelets, patient17


title: CD14cells, patient24


title: CD3cells, patient16


title: Platelets, patient16


title: SCCVII/SF cells, GFP+

city: Los Angeles

first: Yi-Ling

last: Lin

state: California

address: 10833 Le Conte Ave, CHS 53-058

department: School of Dentistry

institute: University of California, Los Angeles

description:
RNA-Seq differential expression analysis
SCC-mOc-D2_vs_SCC-VII-SF-GFP-control_all_detectable_genes.txt
SCC-mOc-D2_vs_SCC-VII-SF-GFP-control_atfc1.5p0.05_1208_genes.txt
SCC-mOc-D3_vs_SCC-VII-SF-GFP-control_all_detectable_genes.txt
SCC-mOc-D3_vs_SCC-VII-SF-GFP-control_atfc1.5p0.05_1957_genes.txt
SCC-VII-SF-GFP-control

data_processing:
The data was sequenced on Illumina HiSeq 3000 for a single read 50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0  and the gene expression level was estimated using RSEM v1.2.15.  TMM (trimmed mean of M-values) was used to normalize the gene expression.
TMM (trimmed mean of M-values) were used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files

source_name: SCCVII/SF

growth_protocol: SCCVII/SF and SCC-macrophage hybrid clones were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit.
The workflow consisted of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: SCC-macrophage hybrid clones were generated by coculturing  SCCVII/SF and GFP-expressing macrophages  in MEM-a/10% FBS containing RANKL and M-CSF. Antibiotic selection was used to enrich the hybrid cells, which were later cloned.

tag: strain background

value: cell line, C3H strain

tag: cell line

value: SCCVII/SF

value: squamous cell carcinoma

value: Wt


title: SCCVII/SF fused with GFP+ macrophages, clone D2-4B

description:
RNA-Seq differential expression analysis
SCC-mOc-D2_vs_SCC-VII-SF-GFP-control_all_detectable_genes.txt
SCC-mOc-D2_vs_SCC-VII-SF-GFP-control_atfc1.5p0.05_1208_genes.txt
SCC-mOc-D2-4_vs_SCC-mOc-D3-1_all_detectable_genes.txt
SCC-mOc-D2-4_vs_SCC-mOc-D3-1_atfc1.5p0.05_3911_genes.txt
SCC-mOc-D2

source_name: SCCVII/SF-macrophage D2

value: SCCVII/SF-macrophage D2

value: squamous cell carcinoma-macrophage hybrid

value: SCCVII/SF fused with GFP+ macrophages in the presence of RANKL


title: SCCVII/SF fused with GFP+ macrophages, clone D3-1A

description:
RNA-Seq differential expression analysis
SCC-mOc-D3_vs_SCC-VII-SF-GFP-control_all_detectable_genes.txt
SCC-mOc-D3_vs_SCC-VII-SF-GFP-control_atfc1.5p0.05_1957_genes.txt
SCC-mOc-D2-4_vs_SCC-mOc-D3-1_all_detectable_genes.txt
SCC-mOc-D2-4_vs_SCC-mOc-D3-1_atfc1.5p0.05_3911_genes.txt
SCC-mOc-D3

source_name: SCCVII/SF-macrophage D3

value: SCCVII/SF-macrophage D3


title: CD14cells, patient16

tag: gender

tag: age


title: 3930402G23Rik-KO Male + Vehicle_pool3

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: poly-A selected, stranded library

data_processing:
Data were analyzed using a custom RNA-seq analysis pipeline (PMID: 28323953, Connerney, 2017) as described elsewhere (PMID: 28903501, Lodato, 2017). Briefly, paired  sequence reads were analzyed using FastQC (Andrews, 2016) for quality control and were mapped to the mouse genome (release mm9) using TopHat2 (v2.1.1) (Kim et al, PMID: 23618408). Reads were counted for each RefSeq or LncRNA gene in each sample, and were converted to RPKM. LncRNA genes are based on a set of 15,558 liver-expressed lncRNA genes whose gene and isoform structures are described in Melia et al, 2019 (PMID: 30840070).
QUANTIFICATION: FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq and long noncoding genes (Lodato et al 2017). Transcripts were quantified by counting sequence reads that map to a the gene body of a gene.
DIFFERENTIAL EXPRESSION: Differential expression analysis for RefSeq genes and long noncoding genes was conducted using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel workbook containing gene expression data and results of differential expression analysis for 24,197 mouse RefSeq  genes on one sheet, and for 15,558 liver-expressed lncRNA genes on a second sheet, with the latter gene set and their annotations described in Melia et al, 2019 (PMID: 30840070) and in Lodato et al, 2017 (PMID: 28903501).

source_name: liver tissue

growth_protocol: lncRNA 3930402G23Rik-knockout mice were constructed using CRISPR/Cas gene targetting technology; homozygous mice were then backcrossed into the C57BL/6J background.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA) was used to extract total RNA from individual livers, followed by quality assessment of RNA by TapeStation 4200 (Agilent, Santa Clara, CA, USA), to identify high quality RNA samples (RIN>9.0) for pooling, with each pool comprised of RNA obtained from n=3-5 individual livers.
Stranded RNA-seq libraries were prepared from polyA-selected total liver RNA using an Illumina stranded TruSeq mRNA Prep Kit (Illumina, San Diego, CA, USA). Three independent RNA pools were prepared for each of the 4 treatment groups, with each pool comprised of n = 3-5 individual liver RNA samples.
RNA-seq libraries were subjected to 150 cycle paired-end sequencing using an Illumina HiSeq 2500 instrument (Illumina) for each of the 12 RNA-seq libraries.

treatment_protocol: Mice were housed in light and temperature-controlled rooms and were provided with water and pelleted chow ad libitum. Mice were provided a grain-based control diet (NIH-31) or matched diet containing 0.1% Wy-14643 for 48 hours.

tag: strain

tag: Sex

value: male

value: 12 weeks old


title: Wild-type Male + Wy14,643_pool1

description: poly-A selected, stranded library


title: Wild-type Male + Wy14,643_pool2

description: poly-A selected, stranded library


title: 3930402G23Rik-KO Male + Vehicle_pool1

description: poly-A selected, stranded library


title: 3930402G23Rik-KO Male + Wy-14643_pool2

description: poly-A selected, stranded library


title: 3930402G23Rik-KO Male + Wy-14643_pool1

description: poly-A selected, stranded library


title: 3930402G23Rik-KO Male + Wy-14643_pool3

description: poly-A selected, stranded library


title: Wild-type Male + Vehicle_pool2

description: poly-A selected, stranded library


title: Callus, D91, rep1

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

data_processing:
NGSQC toolkit (SQIT); tool used for QC
Alignment and mapping of reads was performed using STAR pipeline (Dobin et al., 2013; https://github.com/alexdobin/STAR) and Trinity platform (genome-guided mode) (Hass et al., 2013; https://github.com/trinityrnaseq/trinityrnaseq).
Abundance estimation was calculated  using RSEM (RNA-Seq by Expectation-Maximization) method (Li and Dewey, 2011) and differential gene expression analysis was  performed using DESeq2 (Mi et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: http://ftp.ensemblgenomes.org/pub/plants/release-53/fasta/hordeum_vulgare/
Supplementary files format and content: tab-delimited text files include COUNT matrix for each Sample
Supplementary files format and content: tab-delimited text files include TMM.EXPR matrix for each Sample

organism: Hordeum vulgare

source_name: Callus

extract_protocol:
Total RNA was isolated from 31-day-old calli sample (28 days BCIM dark + 3 days BRM indirect light) of GP and D91  using RNeasy plant RNA isolation kit with on column DNase digestion (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: Callus


title: Callus, GP, rep2

value: GP


title: Callus, D91, rep2


title: Callus, GP, rep1


title: Wild-type Male + Vehicle_pool1

description: poly-A selected, stranded library


title: 203869580092_R08C01

type: genomic

city: Wellington

first: Aarib

middle: John

last: Stevens

address: 23a Mein Street

department: Pathology and Molecular Medicine

country: New Zealand

institute: University of Otago Wellington

description: Replicate 6 S-Phase Control 4 hrs

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850KEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: minfi/limma in R

label: Cy3, Cy5

source_name: Control 4 hrs

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Jurakt T cell samples using Qiagen DNeasy Kit according to standard instructions

value: Male

value: Jurkat T-Lymphoma cell

value: PBS control

tag: treatment time

value: 4 hrs

tag: exposure

value: S-Phase


title: 203869580093_R06C01

description: Replicate 5 S-Phase Control 72 hrs

source_name: Control 72 hrs

value: 72 hrs


title: Wild-type Male + Wy14,643_pool3

description: poly-A selected, stranded library


title: 203869580092_R03C01

description: Replicate 7 S-Phase Treatment 4 hrs

source_name: Treatment 4 hrs

value: Glycine chloramine


title: 203869580093_R07C01

description: Replicate 7 S-Phase Treatment 72 hrs

source_name: Treatment 72 hrs


title: 203869580093_R02C01

description: Replicate 5 S-Phase Treatment 4 hrs


title: Wild-type Male + Vehicle_pool3

description: poly-A selected, stranded library


title: 203869580092_R05C01

description: Replicate 6 S-Phase Treatment 4 hrs


title: 3930402G23Rik-KO Male + Vehicle_pool2

description: poly-A selected, stranded library


title: 203869580093_R05C01

description: Replicate 6 S-Phase Treatment 72 hrs


title: 203869580092_R04C01

description: Replicate 7 S-Phase Control 72 hrs


title: 203869580092_R02C01

description: Replicate 5 S-Phase Treatment 72 hrs


title: 203869580093_R03C01

description: Replicate 7 S-Phase Control 4 hrs


title: 204234160103_R05C01

description: Replicate 3 Pre Replication Treatment 72 hrs

value: Pre Replication


title: 204234160103_R07C01


title: 204234160090_R06C01

description: Replicate 3 Pre Replication Control 72 hrs


title: 204234160103_R06C01

description: Replicate 1 Pre Replication Control 72 hrs


title: DMMMSU rep4

city: Quezon City

first: Ma. Anita

last: Bautista

address: Ma. Regidor St., National Science Complex

department: National Institute of Molecular Biology and Biotechnology

country: Philippines

institute: University of the Philippines Diliman

data_processing:
BCL to FASTQ conversion: Illumina bcl2fastq (v. 2.2.0)
Adaptor trimming and quality filtering was performed using Trimmomatic (0.39) with the parameters: ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36. Poly G sequences was filtered using fastp (0.20.0) with parameters -g -A.
Read alignment: reads were aligned to the B. mori reference genome GCF_000151625.1 using HISAT (2.1.0) with parameters -p 8 --dta
Gene-level quantification was performed using featureCounts (1.4.6-p5) under the R Subread package (2.4.3) with the following parameters: GTF.featureType="exon", GTF.attrType="gene_id", isPairedEnd=TRUE.
Normalization: Size-factor normalization implemented in DESeq2 (1.30.1)
Genome_build: GCF_000151625.1
Supplementary_files_format_and_content: gene-level read counts in csv format
Supplementary_files_format_and_content: matrix table of normalized log gene counts for every gene and every sample

organism: Bombyx mori

source_name: silk gland

extract_protocol:
Silk glands were dissected, flash frozen on dry ice, total RNA extracted from 100 µg tissue with TRIzol reagent. RNA purified with Turbo DNAse (Ambion) and RNA Clean and Concentrator (Zymo Research).
RNA libraries were constructed using the TruSeq Stranded RNA Library Prep Kit (Illumina) following the manufacturer protocols.

value: 5th instar day 3

tag: site

value: TCMO (Misamis Oriental)

value: silk gland


title: 204234160090_R05C01

description: Replicate 2 Pre Replication Treatment 4 hrs


title: 204234160090_R02C01

description: Replicate 3 Pre Replication Treatment 4 hrs


title: 204234160103_R01C01

description: Replicate 2 Pre Replication Control 72 hrs


title: 203869580093_R01C01

description: Replicate 6 S-Phase Control 72 hrs


title: 204234160090_R01C01

description: Replicate 1 Pre Replication Control 4 hrs


title: DMMMSU rep2


title: 203869580092_R01C01

description: Replicate 5 S-Phase Control 4 hrs


title: LAT51 rep1

value: CAR (Benguet)


title: LAT51 rep2


title: 204234160090_R04C01

description: Replicate 1 Pre Replication Treatment 72 hrs


title: 204234160103_R02C01

description: Replicate 1 Pre Replication Treatment 4 hrs


title: 204234160103_R03C01

description: Replicate 3 Pre Replication Control 4 hrs


title: LAT51 rep4


title: MO204 rep4


title: PC9siEPHB2 rep1

city: Jinan

first: Jiajun

last: Du

address: 324 Jingwu Road

institute: Provincial Hospital Affiliated to Shandong University

data_processing:
Illumina Casava software used for basecalling.
Raw data filtering:（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
Data comparison:The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Gene Expression Calculation:Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.94.chr
Supplementary files format and content: FPKM: tab-delimited text files include FPKM values for Sample1、Sample2……
Supplementary files format and content: Read count: Matrix table with raw gene counts for every gene and every sample

growth_protocol: PC-9 was maintained in RPMI 1640 (Gibco) supplemented with 10% FBS and cultured at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Following manufacturer's protocol, the total RNA of EPHB2 knockdown or control treated PC-9 cells was extracted using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PC-9 cells were plated at a density of 3*105 per 60 mm dish. After 24 h culture, the medium was changed to fresh medium. The PC-9 cells were transfected with EPHB2-short interfering RNAs (siRNAs) or control-siRNA purchased from TransheepBio (Shanghai, China), accompanied by jetPRIME® transfection reagent (PolyPlus transfection, Illkirch, France). The transfected cells were cultured for 36 h in 10% FBS RPMI 1640 medium.

value: LUAD

value: EPHB2 knockdown


title: PC9NT rep3

value: control


title: PC9siEPHB2 rep2


title: 204234160090_R08C01

description: Replicate 2 Pre Replication Control 4 hrs


title: MO204 rep3


title: DMMMSU rep0


title: PC9NT rep2


title: PC9NT rep1


title: MO204 rep1


title: Cut&tag-seq RBPJK175R

city: HangZhou

first: Hua

last: Jiang

state: Zhejiang

address: Hangzhou, Zhejiang province, China

institute: Westlake University

data_processing:
Raw fastq files were trimmed using Trim Galore (length 20, e = .1) and aligned to the human genome (hg38) using Bowtie2.
Reads were sorted and converted to BAM format.
Peak calling through MACS2.
Deeptools was used to analyze peak strength in TSS regions.
Use igv2.13.0 to present peak in specific gene sites.
Assembly: hg38
Supplementary files format and content: bw file including peak strength for samples.
Supplementary files format and content: bed file including peak location for samples.
Library strategy: CUT&TAG

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Thermo Fisher Scientific). JURKAT cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Followed Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit for Illumina® (12598ES12) and Novoprotein Chromatin Profile Kit for Illumina (N248) instructions.
Cut&tag-seq and ATAC-seq

treatment_protocol: For KO experiments, CRISPR constructs were packaged into lentiviruses by cotransfecting them with the packaging plasmids pMD2.G (Addgene #12259) and psPAX2 (Addgene #12260) into HEK-293T cells. Forty-eight hours after transfection, the cell medium was collected and used to infect HEK293T or JURKAT cells. The cells were infected twice at an interval of 24 h to achieve maximal infection efficiency.

value: Renal epidermal cell

value: FBXO42 KO

tag: chip antibody

value: RBPJ antibody


title: ATAC-seq FBXO42 KO

data_processing:
Raw fastq files were trimmed using Trim Galore (length 20, e = .1) and aligned to the human genome (hg38) using Bowtie2.
Reads were sorted and converted to BAM format.
Peak calling through MACS2.
Deeptools was used to analyze peak strength in TSS regions.
Use igv2.13.0 to present peak in specific gene sites.
Assembly: hg38
Supplementary files format and content: bw file including peak strength for samples.
Supplementary files format and content: bed file including peak location for samples.

source_name: Jurkat

value: Jurkat

value: Leukemia cell

tag: genotype


title: ATAC-seq FBXO42WT

value: wild type


title: Cut&tag-seq FBXO42WT RBPJ


title: Cut&tag-seq FBXO42WT IgG

value: IgG


title: PDAC_NC2

city: shanghai

first: chang

last: liu

state: China

address: 上海瑞金二路瑞金医院7号楼4楼核医学科实验室

institute: Ruijin Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38.p13

source_name: Pancreatic ductal adenocarcinoma (PDAC)

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pancreatic ductal adenocarcinoma (PDAC)

value: WT


title: PDAC_sh_PC1

address: 上海瑞金二路瑞金医院7号楼4楼核医学科实验室

value: PC knockdown


title: PDAC_sh_PC3

address: 上海瑞金二路瑞金医院7号楼4楼核医学科实验室


title: PDAC_sh_PC2

address: 上海瑞金二路瑞金医院7号楼4楼核医学科实验室


title: PDAC_NC1

address: 上海瑞金二路瑞金医院7号楼4楼核医学科实验室


title: Cut&tag-seq FBXO42KO IgG


title: Cut&tag-seq RBPJ IgG


title: PDAC_NC3

address: 上海瑞金二路瑞金医院7号楼4楼核医学科实验室


title: Sample6 Macrophages, siNeg, day6

city: Yokohama-shi

first: Yukie

last: Yamaguchi

state: Kanagawa-Ken

address: 3-9 Fukuura Kanazawa-ku

country: Japan

institute: Yokohama City University Graduate School of Medicine

data_processing:
HISAT2 version 2.1.0, Bowtie2 2.3.4.1
Transcript is assembled by StringTie version 2.1.3b  with aligned reads.
DEG (Differentially Expressed Genes) analysis was performed on a comparison pair (Cav_vs_Neg) as  requested using DESeq2.

source_name: Healthy control

extract_protocol:
RNA was harvested using the IllustraTM RNAspin Mini RNA Isolation Kit. 1-2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Healthy control

value: macrophage

value: Control

tag: treatment

value: macrophage differentiation


title: Sample6 Macrophages, siCav1, day6

value: Cav-1 knockdown


title: Sample4 Macrophages, siCav1, day6


title: Sample4 Macrophages, siNeg, day6


title: PC9siEPHB2 rep3

value: LUAD

value: EPHB2 knockdown


title: Sample5 Macrophages, siNeg, day6


title: R3_T_T72

data_processing:
Quality control and filtering of sequence data was performed by the service provider according to their internal protocols. In brief, this utilised cutadapt for adapter and low quality read filtering from the raw data (Pass Filter Data), removal of primers and adapters sequences, removal of the end sequences with base quality less than 20, removal of sequences with N content greater than 10%, and removal of reads with lengths less than 75bp after filtering. BWA (v. 0.7.12) (90) was also used to filter out host sequences based on host genome sequence. Filtered fastq files were then processed and aligned to the human reference genome (Gencode release 29) based on the GRCh38.p12, using the STAR spliced read aligner (v. 2.7.8a) (91), and a two-pass alignment mode.
reads were aligned to theGRCHh39.p12 genome assembly using STAR, and genes were annotated using gencode.v29
A gene matrix was built from the resulting Sam sorted, BAM files using GenomicAlignments (v. 1.26.0) (92) package in R (v. 4.0.3) and summarizeoverlaps within edgeR (v. 3.32.1)  utilising the “union” mode for paired-end, stranded sequencing. This was performed by making a gene level transcription database against the same gencode v. 29 annotation gene transfer file used for alignments. Filtering was performed by filterByExpr within edgeR and resulted in 20,374 genes retained for further analysis. An average of 29 million (range: 23 - 31 million) read pairs were successfully assigned in each sample. Differentially expressed genes were called using DESeq2 package (v. 1.30.1) with adjusted p-value cut-off of 0.05, and an internal log2FC of 0.2.
Assembly: Hg39
Supplementary files format and content: Filtered expression count data
Supplementary files format and content: targets.csv: metadata file

source_name: Jurkat T cell line

growth_protocol: Jurkat E6.1 human suspension T-cell lymphoma cells were grown in RPMI 1640 medium  supplemented with 10% v/v heat-inactivated FBS, 100 U/mL penicillin and 100 µg/mL streptomycin at 37° C in a humidified incubator with 5% CO2. Cell concentrations were not permitted to exceed 1 x 106/mL and were not seeded at concentrations below 2.5 x 105/mL. A log phase of growth was maintained by sub-culturing the cells every two days.

extract_protocol:
Cell aliquots were pelleted and frozen at -80oC for RNA extraction using the NucleoSpin RNA plus kit (Macherey-Nagel, Duren, Germany) according to the manufacturer’s recommendations. RNA quality was checked using the Agilent RNA Screen Tape and sequencing was outsourced to Custom Science (Auckland, New Zealand) according to their protocol for LncRNA-seq. For shipping, RNA was treated using the RNAstable Tube Kit (Biomatrica).
Libraries were prepared according to Illumina's instructions by the service provider

treatment_protocol: Treatment with glycine chloramine (GlyCl) occurred immediately after release from the cell cycle block. Growth rate was determined by live cell counts and flow cytometry was used to determine cell viability at 24, 48 and 72 hours post release. At 4 and 72 hours post-release, 5 x 10^6 cells were harvested and stored for DNA and RNA extractions. All harvested cells underwent a slow centrifugation step (1000 x g for 5 min) to avoid harvesting late apoptotic or dead cells. Cell cycle arrest of Jurkat cells was performed by using an excess of thymidine as previously described (15, 78). Briefly, Jurkat cells (1 x 106/mL) were treated with 1 mM thymidine for 18 hours. Cells were washed twice in PBS, resuspended in fresh media supplemented with 50 µM cytidine to promote progression out of G1 into S-phase. The cells were then split into either a treatment or control flasks and the treatment flask received a single bolus of 200 µM GlyCl while the control received the volumetric equivalent of PBS.

value: T lymphoblast

value: Clone E6-1

tag: biological replicate

value: Treatment

tag: sample time (hours post release from cell block)


title: R4_C_T48

value: Jurkat

tag: cell type


title: R4_C_T24


title: R3_C_T24


title: Cut&tag-seq RBPJ

value: Renal epidermal cell

value: FBXO42 KO

value: RBPJ antibody


title: R3_T_T4


title: R3_C_T48


title: R3_T_T24


title: Cut&tag-seq FBXO42KO RBPJ


title: R4_T_T24


title: R4_C_T72


title: Sample5 Macrophages, siCav1, day6


title: R3_C_T4


title: R2_C_T72


title: R2_T_T48


title: R2_T_T4


title: R2_C_T24


title: R1_C_T72


title: R2_C_T4


title: R3_C_T72


title: R1_T_T72


title: R1_T_T48


title: R1_C_T48


title: R1_C_T24


title: R1_T_T24


title: R1_T_T4


title: R1_C_T4


title: R2_T_T24


title: R2_C_T48


title: DB952_CD4_C7

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

description: single cell

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM with default parameters. Reads aligning to features were counted from the alignment bam files with the htseq-count script from HTSeq(17) with parameters: -r pos -m union -s no. Counts were aggregated accross the 2 lanes for each cell to give the raw counts matrix
Genome_build: hg38
Supplementary_files_format_and_content: Counts matrix with raw feature counts for each cell

source_name: single cell

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation and frozen in FCS containing 10% DMSO and stored at –80°C for later use. T cells were sorted on the FACS Aria fusion (BD, USA) using CD3-PERCPCy5.5 (Biolegend, clone HIT3A), CD4-APC/Cy7 (BD Biosciences, clone RPA-T4), and CD8-Viogreen (Miltneyi Biotec, clone BW135/80). CD56-FITC (Biolegend, clone 5.1H11) was used to gate out NK cells and propidium iodide to exclude dead cells (Miltenyi Biotec).
Single cells were sorted into a 96 well plate directly into 3ul of lysis buffer. Library preparation and sequencing was performed by Oxford Genomics Centre (Oxford University, United Kingdom)
Paired end single cell sequencing using Smartseq2

treatment_protocol: Single cell RNA sequencing was performed in 3 patients on T cells isolated from 30–50 ml peripheral blood collected at two weeks after transplantation

value: CD4 T


title: DB952_CD4_G7

description: single cell


title: DB952_CD8_D7

description: single cell

value: CD8 T


title: DB952_CD4_D7

description: single cell


title: DB952_CD4_H6

description: single cell


title: DB952_CD4_A7

description: single cell


title: DB952_CD8_G6

description: single cell


title: DB952_CD4_E7

description: single cell


title: P6_SClysatecontrol_F7

description: single cell

value: single cell lysate from non-control wells


title: DB952_CD8_B7

description: single cell


title: DB952_CD4_B7

description: single cell


title: DB952_CD4_F7

description: single cell


title: DB952_CD4_H7

description: single cell


title: DB952_CD8_C7

description: single cell


title: DB952_CD8_F6

description: single cell


title: DB952_CD4_G6

description: single cell


title: DB952_CD4_F6

description: single cell


title: DB952_CD8_E6

description: single cell


title: DB952_CD4_D6

description: single cell


title: DB952_CD4_C6

description: single cell


title: DB952_CD8_D6

description: single cell


title: DB952_CD8_C6

description: single cell


title: DB952_CD4_B6

description: single cell


title: DB952_CD8_A6

description: single cell


title: DB952_CD8_B6

description: single cell


title: DB952_CD8_A7

description: single cell


title: DB952_CD4_E6

description: single cell


title: DB952_CD8_H6

description: single cell


title: DB952_CD4_A6

description: single cell


title: DB952_CD4_G5

description: single cell


title: DB952_CD8_F5

description: single cell


title: DB952_CD4_H4

description: single cell


title: DB952_CD8_D5

description: single cell


title: DB952_CD4_B5

description: single cell


title: DB952_CD4_F4

description: single cell


title: DB952_CD4_C5

description: single cell


title: DB952_CD4_F5

description: single cell


title: DB952_CD8_B5

description: single cell


title: DB952_CD4_E5

description: single cell


title: DB952_CD8_G5

description: single cell


title: DB952_CD8_A5

description: single cell


title: DB952_CD4_G4

description: single cell


title: DB952_CD8_C5

description: single cell


title: DB952_CD8_E5

description: single cell


title: DB952_CD4_A5

description: single cell


title: DB952_CD8_H5

description: single cell


title: DB952_CD4_D5

description: single cell


title: DB952_CD8_F4

description: single cell


title: DB952_CD4_E4

description: single cell


title: DB952_CD8_E4

description: single cell


title: DB952_CD8_D4

description: single cell


title: DB952_CD8_G4

description: single cell


title: DB952_CD4_D4

description: single cell


title: DB952_CD4_C4

description: single cell


title: DB952_CD8_C4

description: single cell


title: DB952_CD4_B4

description: single cell


title: DB952_CD8_H4

description: single cell


title: DB952_CD8_B4

description: single cell


title: DB952_CD4_A4

description: single cell


title: DB952_CD4_F3

description: single cell


title: DB952_CD8_A4

description: single cell


title: DB952_CD4_G3

description: single cell


title: DB952_CD8_H3

description: single cell


title: DB952_CD8_F3

description: single cell


title: DB952_CD4_E3

description: single cell


title: DB952_CD4_C3

description: single cell


title: DB952_CD4_F2

description: single cell


title: DB952_CD4_H2

description: single cell


title: DB952_CD8_G2

description: single cell


title: DB952_CD4_A3

description: single cell


title: DB952_CD8_H2

description: single cell


title: DB952_CD4_E2

description: single cell


title: DB952_CD8_B3

description: single cell


title: DB952_CD4_B3

description: single cell


title: DB952_CD8_C3

description: single cell


title: DB952_CD8_A3

description: single cell


title: DB952_CD8_D3

description: single cell


title: DB952_CD8_F2

description: single cell


title: DB952_CD4_G2

description: single cell


title: DB952_CD8_D2

description: single cell


title: DB952_CD8_E3

description: single cell


title: DB952_CD4_H3

description: single cell


title: DB952_CD8_C2

description: single cell


title: DB952_CD8_A2

description: single cell


title: DB952_CD4_D2

description: single cell


title: DB952_CD4_H5

description: single cell


title: DB952_CD4_C2

description: single cell


title: DB952_CD4_B2

description: single cell


title: DB952_CD4_A2

description: single cell


title: DB952_CD4_H1

description: single cell


title: DB952_CD8_E2

description: single cell


title: DB952_CD8_B2

description: single cell


title: DB952_CD4_D3

description: single cell


title: DB952_CD8_H1

description: single cell


title: DB952_CD4_G1

description: single cell


title: DB952_CD8_G3

description: single cell


title: DB952_CD4_D1

description: single cell


title: DB952_CD4_F1

description: single cell


title: DB952_CD8_C1

description: single cell


title: DB952_CD4_C1

description: single cell


title: DB952_CD8_F1

description: single cell


title: DB952_CD4_H12

description: single cell


title: DB952_CD4_E1

description: single cell


title: DB952_CD8_A1

description: single cell


title: DB952_CD4_A1

description: single cell


title: DB952_CD4_B1

description: single cell


title: DB952_CD4_G12

description: single cell


title: DB952_CD8_G1

description: single cell


title: DB952_CD8_E1

description: single cell


title: DB952_CD8_H12

description: single cell


title: DB952_CD8_F12

description: single cell


title: DB952_CD8_G12

description: single cell


title: DB952_CD8_D1

description: single cell


title: DB952_CD8_B1

description: single cell


title: DB952_CD4_F12

description: single cell


title: DB952_CD8_E12

description: single cell


title: DB952_CD4_100_C12

description: single cell


title: DB952_CD4_E12

description: single cell


title: HD3_CD4_100_D12

description: single cell


title: HD3_CD8_100_D12

description: single cell


title: DB952_CD8_100_C12

description: single cell


title: DB952_CD8_B12

description: single cell


title: DB952_CD4_B12

description: single cell


title: DB952_CD4_H11

description: single cell


title: DB952_CD4_A12

description: single cell


title: DB952_CD8_H11

description: single cell


title: DB952_CD4_G11

description: single cell


title: DB952_CD8_G11

description: single cell


title: DB952_CD4_F11

description: single cell


title: DB952_CD4_E11

description: single cell


title: DB952_CD8_E11

description: single cell


title: DB952_CD8_F11

description: single cell


title: DB952_CD8_D11

description: single cell


title: DB952_CD4_B11

description: single cell


title: DB952_CD8_H10

description: single cell


title: DB952_CD8_B11

description: single cell


title: DB952_CD4_A11

description: single cell


title: DB952_CD8_F10

description: single cell


title: DB952_CD4_G10

description: single cell


title: DB952_CD4_D11

description: single cell


title: DB952_CD4_H10

description: single cell


title: DB952_CD4_F10

description: single cell


title: DB952_CD8_A11

description: single cell


title: DB952_CD8_A12

description: single cell


title: DB952_CD8_G10

description: single cell


title: DB952_CD8_C11

description: single cell


title: DB952_CD4_E10

description: single cell


title: DB952_CD4_C11

description: single cell


title: DB952_CD8_E10

description: single cell


title: DB952_CD8_C10

description: single cell


title: DB952_CD8_B10

description: single cell


title: DB952_CD4_B10

description: single cell


title: DB952_CD4_A10

description: single cell


title: DB952_CD8_D10

description: single cell


title: DB952_CD8_H9

description: single cell


title: DB952_CD8_G9

description: single cell


title: DB952_CD4_F9

description: single cell


title: DB952_CD4_C10

description: single cell


title: DB952_CD4_E9

description: single cell


title: DB952_CD4_D10

description: single cell


title: DB952_CD4_H9

description: single cell


title: DB952_CD8_F8

description: single cell


title: DB952_CD4_A9

description: single cell


title: DB952_CD8_B9

description: single cell


title: DB952_CD8_D9

description: single cell


title: DB952_CD8_E9

description: single cell


title: P5_SClysatecontrol_F8

description: single cell


title: DB952_CD8_E8

description: single cell


title: DB952_CD8_C9

description: single cell


title: DB952_CD8_D8

description: single cell


title: DB952_CD4_B8

description: single cell


title: DB952_CD8_H8

description: single cell


title: DB952_CD4_G9

description: single cell


title: DB952_CD8_A8

description: single cell


title: DB952_CD4_B9

description: single cell


title: DB952_CD8_A10

description: single cell


title: DR940_CD4_G6

description: single cell


title: DB952_CD4_D9

description: single cell


title: DB952_CD8_G8

description: single cell


title: DR940_CD4_F6

description: single cell


title: DB952_CD4_C9

description: single cell


title: DB952_CD8_C8

description: single cell


title: DB952_CD4_C8

description: single cell


title: DR940_CD4_E6

description: single cell


title: DR940_CD8_E6

description: single cell


title: DR940_CD8_D6

description: single cell


title: DB952_CD4_A8

description: single cell


title: DR940_CD4_D6

description: single cell


title: DR940_CD4_A6

description: single cell


title: DR940_CD4_C6

description: single cell


title: DR940_CD4_H5

description: single cell


title: DB952_CD8_F9

description: single cell


title: DB952_CD8_B8

description: single cell


title: DR940_CD4_H6

description: single cell


title: DB952_CD4_D8

description: single cell


title: DR940_CD4_G5

description: single cell


title: DR940_CD8_C6

description: single cell


title: DR940_CD8_F6

description: single cell


title: DR940_CD8_H6

description: single cell


title: DR940_CD8_B6

description: single cell


title: DR940_CD8_D5

description: single cell


title: DB952_CD8_A9

description: single cell


title: DR940_CD8_G6

description: single cell


title: DR940_CD8_A6

description: single cell


title: DR940_CD8_H5

description: single cell


title: DR940_CD4_F5

description: single cell


title: DR940_CD8_G5

description: single cell


title: DR940_CD8_B5

description: single cell


title: DR940_CD4_C5

description: single cell


title: DR940_CD4_A5

description: single cell


title: DR940_CD4_E5

description: single cell


title: DR940_CD8_A5

description: single cell


title: DR940_CD4_B6

description: single cell


title: DR940_CD8_C5

description: single cell


title: DR940_CD4_E4

description: single cell


title: DR940_CD8_H4

description: single cell


title: DR940_CD8_F4

description: single cell


title: DR940_CD4_D5

description: single cell


title: DR940_CD8_E5

description: single cell


title: DR940_CD8_E4

description: single cell


title: DR940_CD4_C4

description: single cell


title: DR940_CD8_F5

description: single cell


title: DR940_CD8_D4

description: single cell


title: DR940_CD8_G4

description: single cell


title: DR940_CD4_B4

description: single cell


title: DR940_CD4_B5

description: single cell


title: DR940_CD8_A4

description: single cell


title: DR940_CD4_A4

description: single cell


title: DR940_CD4_G3

description: single cell


title: DR940_CD4_G4

description: single cell


title: DR940_CD4_H3

description: single cell


title: DR940_CD4_H4

description: single cell


title: DR940_CD4_D3

description: single cell


title: DR940_CD4_D4

description: single cell


title: DR940_CD8_C4

description: single cell


title: DR940_CD8_A3

description: single cell


title: DR940_CD8_G3

description: single cell


title: DR940_CD4_B3

description: single cell


title: DR940_CD4_F4

description: single cell


title: DR940_CD4_A3

description: single cell


title: DR940_CD8_B4

description: single cell


title: DR940_CD8_H3

description: single cell


title: DR940_CD4_H2

description: single cell


title: DR940_CD8_E3

description: single cell


title: DR940_CD4_F3

description: single cell


title: DR940_CD4_C3

description: single cell


title: DR940_CD8_H2

description: single cell


title: DR940_CD8_D3

description: single cell


title: DR940_CD4_F2

description: single cell


title: DR940_CD8_C2

description: single cell


title: DR940_CD4_D2

description: single cell


title: DR940_CD4_E3

description: single cell


title: DR940_CD4_C2

description: single cell


title: DR940_CD8_B3

description: single cell


title: DR940_CD4_E2

description: single cell


title: DR940_CD8_B2

description: single cell


title: DR940_CD8_G2

description: single cell


title: DR940_CD4_B2

description: single cell


title: DR940_CD8_F3

description: single cell


title: DR940_CD8_D2

description: single cell


title: DR940_CD8_C3

description: single cell


title: DR940_CD8_A2

description: single cell


title: DR940_CD8_F1

description: single cell


title: DR940_CD8_G1

description: single cell


title: DR940_CD4_G1

description: single cell


title: DR940_CD8_E1

description: single cell


title: DR940_CD8_F2

description: single cell


title: DR940_CD8_E2

description: single cell


title: DR940_CD4_F1

description: single cell


title: DR940_CD4_D1

description: single cell


title: DR940_CD8_H1

description: single cell


title: DR940_CD8_C1

description: single cell


title: DR940_CD8_D1

description: single cell


title: DR940_CD4_E1

description: single cell


title: DR940_CD4_C1

description: single cell


title: DR940_CD8_B1

description: single cell


title: DR940_CD8_A1

description: single cell


title: DR940_CD8_H12

description: single cell


title: DR940_CD4_A2

description: single cell


title: DR940_CD4_A1

description: single cell


title: DR940_CD4_H12

description: single cell


title: DR940_CD4_F12

description: single cell


title: DR940_CD4_E12

description: single cell


title: DR940_CD8_F12

description: single cell


title: DR940_CD4_H1

description: single cell


title: HD2_CD8_100_D12

description: single cell


title: DR940_CD8_100_C12

description: single cell


title: DR940_CD4_100_C12

description: single cell


title: DR940_CD8_B12

description: single cell


title: DR940_CD4_B12

description: single cell


title: DR940_CD8_A12

description: single cell


title: DR940_CD4_A12

description: single cell


title: DR940_CD4_B1

description: single cell


title: DR940_CD8_H11

description: single cell


title: DR940_CD4_G11

description: single cell


title: DR940_CD8_G11

description: single cell


title: DR940_CD8_G12

description: single cell


title: RS1 4S

city: Beltsville

first: Wayne

last: Jurick II

state: MD

address: 10300 Baltimore Ave

department: Food Quality Lab

institute: USDA-ARS

description: Penicillium spp. Fungal sample

data_processing:
FAST-QC v. 0.11.9
Trinity de novo Alignment to reference (MD-8 genome) usegalaxy.org
Salmon transcriptome read counting usegalaxy.org
Assembly: GCA_000769745.1
Supplementary files format and content: gene count data from transcriptome as aligned to reference genome

organism: Penicillium polonicum

source_name: sample obtained from ungerminated conidia harvested from Penicillium spp. Grown on PDA plates

growth_protocol: Penicillium spp. Grown on PDA medium at 25C before harvesting conidia for apple inoculation or for direct RNA extraction. Apple tissue harvested at leading edge of lesion 5 days postinoculation for fungal RNA extraction.

extract_protocol:
Ungerminated conidia extracted using Trizol method by manufacterer (Invitrogen) using a bead mill. Apple tissue was ground with mortar/pestle in LN2 before using CTAB method followed by cleanup using RNA Extraction Kit (Qiagen).
BGISeq-500 library preparation performed by Beijing Genomics Institute (BGI, China)

treatment_protocol: ungerminated conidia vs ramifying hyphae extracted from apple tissue

tag: sample source

value: ungerminated conidia


title: DR940_CD8_E12

description: single cell


title: DR940_CD8_F11

description: single cell


title: DR940_CD4_F11

description: single cell


title: RS1 3A

description: Penicillium spp. Fungal sample

source_name: sample obtained from leading edge of apple infection lesion 5 days postinoculation

value: apple tissue infection


title: HD2_CD4_100_D12

description: single cell


title: DR940_CD4_G12

description: single cell


title: RS1 4A

description: Penicillium spp. Fungal sample


title: RS1 2A

description: Penicillium spp. Fungal sample


title: DR940_CD8_D11

description: single cell


title: DR940_CD8_E11

description: single cell


title: DR940_CD4_E11

description: single cell


title: DR940_CD4_D11

description: single cell


title: RS1 1A

description: Penicillium spp. Fungal sample


title: DR940_CD4_H11

description: single cell


title: RS1 3S

description: Penicillium spp. Fungal sample


title: R19 4S

description: Penicillium spp. Fungal sample

organism: Penicillium expansum


title: R19 5S

description: Penicillium spp. Fungal sample


title: DR940_CD8_B11

description: single cell


title: DR940_CD4_C11

description: single cell


title: R19 3S

description: Penicillium spp. Fungal sample


title: RS1 2S

description: Penicillium spp. Fungal sample


title: R19 2S

description: Penicillium spp. Fungal sample

source_name: sample obtained from ungerminated conidia washed from Penicillium spp. Grown on PDA plates


title: DR940_CD4_B11

description: single cell


title: R19 5A

description: Penicillium spp. Fungal sample


title: DR940_CD8_A11

description: single cell


title: R19 4A

description: Penicillium spp. Fungal sample


title: DR940_CD4_A11

description: single cell


title: RS1 1S

description: Penicillium spp. Fungal sample


title: DR940_CD8_H10

description: single cell


title: R19 3A

description: Penicillium spp. Fungal sample


title: DR940_CD8_G10

description: single cell


title: P3_SClysatecontrol_F10

description: single cell


title: DR940_CD8_F10

description: single cell


title: DR940_CD8_E10

description: single cell


title: R19 1A

description: Penicillium spp. Fungal sample


title: DR940_CD8_C11

description: single cell


title: d56-19s

city: Ames

first: James

last: Koltes

state: Iowa

address: 239A Kildee Hall

department: Animal Science

institute: Iowa State University

description:
miRNA
Control_07_d56-19s

data_processing:
Sequence read quality was evaluated with FastQC version0.11.3 (Andrews and Babraham Bioinformatics, 2010)
Adaptors and low-quality reads were trimmed using Trim Galore version 0.4.5 (Krueger, 2015).
Sequence reads from mRNA libraries were aligned to the Sscrofa 11.1 reference genome using the STAR alignment software version 2.5.4a  (Dobin et al., 2013). To determine miRNA expression levels, sequence reads were aligned to the Sscrofa11.1 reference genome using miRDeep2 (Friedländer et al., 2008).
The number of read counts for each transcript was quantified with FeatureCounts version 2.0.3 (Liao et al., 2014).
Assembly: Sscrofa 11.1
Supplementary files format and content: Matrix with gene counts

organism: Sus scrofa

source_name: PBMC

growth_protocol: All piglets were weaned and transferred to a nursery facility without soil at d 20.  Piglets were weighed and blood samples collected at 11, 20, and 56 days of age.

extract_protocol:
Whole blood samples (10 mL) were collected through venipuncture via jugular vena cava into EDTA tubes (BD Vacutainer® K2EDTA coated blood collection tube, Franklin lake, NJ) from piglets with median BW in each litter at days 11, 20 (weaning), and 56 (the end of nursery) of age. PBMCs were isolated using Histopaque®-1077 (MilliporeSigma, Burlington, MA) gradient centrifugation according to manufacturer’s protocol and stored at -80C until total RNA extraction. Total RNA was extracted with TRIzol® using the Direct-Zol RNA Isolation Kit (Zymo Research Corp.), according to manufacturer’s protocol. RNA quality was determined using an Experion RNA analysis kit (Biorad, Hurcules, CA) to determine RNA degradation using the RNA quality index (RQI) and RNA quantity was measured by fluorometer using a Qubit (ThermoFisher, Waltham, MA).
Total RNA samples that passed quantity (100 ng/uL) and quality criteria (RNA quality indicator, RQI= 5.1-9.8) were utilized for sequencing. The RNA-Seq analysis was conducted using Illumina HiSeq4000 chemistry at the Beijing Genomics Institute (BGI) Americas (BGI, Shenzhen, Guangdong, China). Small RNA and mRNA libraries were constructed from the total RNA samples for 50-bp single-end sequencing.

treatment_protocol: Control piglets (control group; n=6 for mRNA and n=8 for miRNA analysis) were reared conventionally in farrowing crates. Treatment piglets (topsoil group; n=6 for mRNA and n=5 for miRNA analysis) were exposed daily to fresh topsoil from day 4 postpartum until the end of lactation (d 20).

value: PBMC

tag: group

value: Topsoil

value: M


title: d56-20s

description:
miRNA
Control_08_d56-20s

value: Control

value: F


title: DR940_CD8_D10

description: single cell


title: d56-15s

description:
miRNA
Control_06_d56-15s


title: d56-14s

description:
miRNA
Topsoil_05_d56-14s


title: DR940_CD4_D10

description: single cell


title: d56-13s

description:
miRNA
Control_05_d56-13s


title: d56-12s

description:
miRNA
Topsoil_04_d56-12s


title: DR940_CD8_C10

description: single cell


title: DR940_CD4_C10

description: single cell


title: DR940_CD8_B10

description: single cell


title: d56-10s

description:
miRNA
Topsoil_02_d56-10s


title: d56-11s

description:
miRNA
Topsoil_03_d56-11s


title: d56-08s

description:
miRNA
Control_04_d56-08s


title: DR940_CD4_B10

description: single cell


title: d56-05s

description:
miRNA
Topsoil_01_d56-05s


title: DR940_CD8_A10

description: single cell


title: d56-04s

description:
miRNA
Control_03_d56-04s


title: DR940_CD4_H9

description: single cell


title: d56-03s

description:
miRNA
Control_02_d56-03s


title: DR940_CD4_A10

description: single cell


title: DR940_CD4_G9

description: single cell


title: d20-20s

description:
miRNA
Control_08_d20-20s


title: d56-01s

description:
miRNA
Control_01_d56-01s


title: P4_SClysatecontrol_F9

description: single cell


title: DR940_CD4_F9

description: single cell


title: DR940_CD4_E9

description: single cell


title: d20-15s

description:
miRNA
Control_06_d20-15s


title: d20-19s

description:
miRNA
Control_07_d20-19s


title: d20-12s

description:
miRNA
Topsoil_04_d20-12s


title: DR940_CD8_D9

description: single cell


title: d20-11s

description:
miRNA
Topsoil_03_d20-11s


title: d20-14s

description:
miRNA
Topsoil_05_d20-14s


title: d20-13s

description:
miRNA
Control_05_d20-13s


title: DR940_CD4_C9

description: single cell


title: DR940_CD8_C9

description: single cell


title: d20-05s

description:
miRNA
Topsoil_01_d20-05s


title: d20-10s

description:
miRNA
Topsoil_02_d20-10s


title: DR940_CD8_A9

description: single cell


title: d20-04s

description:
miRNA
Control_03_d20-04s


title: d20-08s

description:
miRNA
Control_04_d20-08s


title: DR940_CD8_B9

description: single cell


title: DR940_CD8_H8

description: single cell


title: DR940_CD4_G8

description: single cell


title: DR940_CD4_B9

description: single cell


title: DR940_CD8_G8

description: single cell


title: d11-19s

description:
miRNA
Control_07_d11-19s


title: d11-20s

description:
miRNA
Control_08_d11-20s


title: d11-15s

description:
miRNA
Control_06_d11-15s


title: d20-01s

description:
miRNA
Control_01_d20-01s


title: DR940_CD4_D9

description: single cell


title: DR940_CD4_E8

description: single cell


title: d11-11s

description:
miRNA
Topsoil_03_d11-11s


title: d11-12s

description:
miRNA
Topsoil_04_d11-12s


title: DR940_CD8_F8

description: single cell


title: DR940_CD4_A9

description: single cell


title: DR940_CD4_D8

description: single cell


title: DR940_CD4_H8

description: single cell


title: d11-14s

description:
miRNA
Topsoil_05_d11-14s


title: DR940_CD8_C8

description: single cell


title: d11-04s

description:
miRNA
Control_03_d11-04s


title: DR940_CD8_D8

description: single cell


title: DR940_CD4_F8

description: single cell


title: d11-05s

description:
miRNA
Topsoil_01_d11-05s


title: d20-03s

description:
miRNA
Control_02_d20-03s


title: d11-10s

description:
miRNA
Topsoil_02_d11-10s


title: DR940_CD8_B8

description: single cell


title: DR940_CD4_C8

description: single cell


title: d11-01s

description:
miRNA
Control_01_d11-01s


title: DR940_CD8_E8

description: single cell


title: DR940_CD4_B8

description: single cell


title: DR940_CD8_A8

description: single cell


title: d56_19m

description:
mRNA
Control_06_d56_19m


title: DR940_CD4_A8

description: single cell


title: d56_17m

description:
mRNA
Topsoil_06_d56_17m


title: DR940_CD4_H7

description: single cell


title: d56_15m

description:
mRNA
Control_05_d56_15m


title: DR940_CD8_H7

description: single cell


title: DR940_CD4_G7

description: single cell


title: d11-13s

description:
miRNA
Control_05_d11-13s


title: DR940_CD8_G7

description: single cell


title: d56_13m

description:
mRNA
Control_04_d56_13m


title: d56_14m

description:
mRNA
Topsoil_05_d56_14m


title: d56_12m

description:
mRNA
Topsoil_04_d56_12m


title: d56_10m

description:
mRNA
Topsoil_02_d56_10m


title: d56_08m

description:
mRNA
Control_03_d56_08m


title: d11-03s

description:
miRNA
Control_02_d11-03s


title: DR940_CD4_F7

description: single cell


title: DR940_CD4_E7

description: single cell


title: DR940_CD8_E7

description: single cell


title: DR940_CD8_F7

description: single cell


title: d56_11m

description:
mRNA
Topsoil_03_d56_11m


title: d11-08s

description:
miRNA
Control_04_d11-08s


title: DR940_CD8_D7

description: single cell


title: d56_05m

description:
mRNA
Topsoil_01_d56_05m


title: d56_07m

description:
mRNA
Control_02_d56_07m


title: DR940_CD4_D7

description: single cell


title: DR940_CD8_C7

description: single cell


title: d56_03m

description:
mRNA
Control_01_d56_03m


title: DR940_CD4_C7

description: single cell


title: DR940_CD8_B7

description: single cell


title: d20_19m

description:
mRNA
Control_06_d20_19m


title: d20_15m

description:
mRNA
Control_05_d20_15m


title: DR940_CD4_B7

description: single cell


title: d20_14m

description:
mRNA
Topsoil_05_d20_14m


title: DR940_CD8_A7

description: single cell


title: d20_13m

description:
mRNA
Control_04_d20_13m


title: DR940_CD4_A7

description: single cell


title: d20_12m

description:
mRNA
Topsoil_04_d20_12m


title: KW939_CD4_H5

description: single cell


title: d20_11m

description:
mRNA
Topsoil_03_d20_11m


title: KW939_CD8_H5

description: single cell


title: KW939_CD4_G5

description: single cell


title: d20_10m

description:
mRNA
Topsoil_02_d20_10m


title: d20_07m

description:
mRNA
Control_02_d20_07m


title: KW939_CD8_F5

description: single cell


title: d20_08m

description:
mRNA
Control_03_d20_08m


title: KW939_CD4_F5

description: single cell


title: d20_05m

description:
mRNA
Topsoil_01_d20_05m


title: d11_19m

description:
mRNA
Control_06_d11_19m


title: d11_17m

description:
mRNA
Topsoil_06_d11_17m


title: d20_17m

description:
mRNA
Topsoil_06_d20_17m


title: KW939_CD4_E5

description: single cell


title: KW939_CD8_G5

description: single cell


title: d11_15m

description:
mRNA
Control_05_d11_15m


title: d20_03m

description:
mRNA
Control_01_d20_03m


title: d11_14m

description:
mRNA
Topsoil_05_d11_14m


title: KW939_CD4_D5

description: single cell


title: KW939_CD8_C5

description: single cell


title: KW939_CD8_D5

description: single cell


title: KW939_CD8_E5

description: single cell


title: d11_13m

description:
mRNA
Control_04_d11_13m


title: d11_12m

description:
mRNA
Topsoil_04_d11_12m


title: KW939_CD4_C5

description: single cell


title: KW939_CD8_A5

description: single cell


title: d11_10m

description:
mRNA
Topsoil_02_d11_10m


title: d11_05m

description:
mRNA
Topsoil_01_d11_05m


title: KW939_CD4_H4

description: single cell


title: KW939_CD4_A5

description: single cell


title: d11_07m

description:
mRNA
Control_02_d11_07m


title: d11_11m

description:
mRNA
Topsoil_03_d11_11m


title: d11_08m

description:
mRNA
Control_03_d11_08m


title: KW939_CD8_H4

description: single cell


title: KW939_CD4_F4

description: single cell


title: KW939_CD4_B5

description: single cell


title: d11_03m

description:
mRNA
Control_01_d11_03m


title: KW939_CD8_G4

description: single cell


title: KW939_CD8_F4

description: single cell


title: KW939_CD8_B5

description: single cell


title: KW939_CD4_G4

description: single cell


title: KW939_CD8_E4

description: single cell


title: KW939_CD8_D4

description: single cell


title: KW939_CD4_E4

description: single cell


title: KW939_CD8_C4

description: single cell


title: KW939_CD4_C4

description: single cell


title: KW939_CD8_B4

description: single cell


title: KW939_CD4_B4

description: single cell


title: DR940_CD4_G2

description: single cell


title: KW939_CD4_A4

description: single cell


title: KW939_CD8_A4

description: single cell


title: KW939_CD4_H3

description: single cell


title: Liver_J40

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

institute: INRA

hyb_protocol: 600ng of Cy3-cRNA was then fragmented with a specific buffer (30 minutes at 60°C) and hybridized on a sub-array. Hybridization was performed in a microarray hybridization oven (Agilent) for 17h at 65°C.

scan_protocol: After a washing step, slides were scanned (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3μm and 20bits). Data were then obtained with the Agilent Feature Extraction software (10.7.1.1).

data_processing: Data from microarray analysis were transformed with a logarithmic transformation, scale-normalized and analyzed using the package limma from R.

organism: Oncorhynchus mykiss

source_name: liver of NN offspring fed a complete plant-based diet

label_protocol: For each sample, 150 ng of total RNA was amplified and labelled using Cy3-CTP according to the manufacturer’s instructions (Agilent). cRNA were obtained by first reverse transcribed RNA, using a polyDT T7 primer (denaturation step: 10min at 65°C, reaction step: 2hr at 40°C, inactivation step: 5min at 70°C). cRNA were then labeled with Cy3-dye (2hr at 40°C). Excess dye was removed using a RNeasy kit (Qiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech)

extract_protocol: Total RNA was extracted from 6 liver of 6 fish per treatment, using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s recommendations.T he concentration of extracted RNA was analysed using a spectrophotometer (ND-1000, NanoDrop) by measuring absorbance at 260 nm. Quality of RNAs was checked with Bioanalyzer (Agilent Technologies, Kista, Sweden).

treatment_protocol: Offspring from 4 different conditions : NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the high carbohydrate/low protein (HC/LP) diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet) were fed during 6 months a commercial diet. Liver were sampled at the end of the trial.

tag: FISH identification

value: liver

tag: condition

value: NN


title: KW939_CD8_H3

description: single cell


title: Liver_J51

source_name: liver of NH offspring fed a complete plant-based diet

value: NH


title: KW939_CD4_D4

description: single cell


title: KW939_CD4_G3

description: single cell


title: Liver_J37


title: Liver_J57

source_name: liver of HN offspring fed a complete plant-based diet

value: HN


title: Liver_J58


title: Liver_J46


title: Liver_J65

source_name: liver of HH offspring fed a complete plant-based diet

value: HH


title: Liver_J69


title: Liver_J64


title: Liver_J55


title: Liver_J42


title: Liver_J38


title: Liver_J71


title: KW939_CD8_G3

description: single cell


title: Liver_J53


title: KW939_CD4_E3

description: single cell


title: KW939_CD8_F3

description: single cell


title: KW939_CD4_D3

description: single cell


title: KW939_CD8_E3

description: single cell


title: Liver_J70


title: KW939_CD4_C3

description: single cell


title: KW939_CD4_F3

description: single cell


title: Liver_J52


title: Liver_J62


title: BKO-CC-rep1

city: Nanjing

first: Hao

last: Huang

address: Dongnandaxue Road

department: Department of Bioinformatics

institute: Southeast University

data_processing:
RNA-seq raw reads for wild type and Bmal1 knockout experiments were mapped to the UCSC mouse reference genome (mm10) and calculation of gene counts using STAR (version 2.7.1a) with default parameters.
Only uniquely mapped reads were retained for the subsequent analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: corpus callosum

growth_protocol: Neurospheres: The SVZ was dissected from 8- to 10-week old wild-type and Bmal1-/-. Mechanically dissociated SVZ cells were cultured in Mouse Neural Stem Cell Expansion Medium containing 20 ng ml‒1 EGF and 2 ug ml‒1 heparin (all from Millipore) for one week to obtain primary neurospheres. Harvested primary neurospheres were processed for total RNA extraction.

extract_protocol:
Total RNAs were extracted from the corpus callosum dissected from 8- to 10-week old wild-type and Bmal1-/- mice as well as primary neurospheres cultured from  8- to 10-week old wild-type and Bmal1-/- mice using TRIzol.
1) mRNA enrichment: Oligo dT Selection or rRNA depletion; 2) RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer; 3) End repair, add A tailing and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments; 4) PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) Sequencing on BGISEQ-500 platform.


title: Liver_J67


title: Liver_J41


title: KW939_CD8_B3

description: single cell


title: WT-CC-rep2

value: wild type


title: WT-CC-rep1


title: KW939_CD4_B3

description: single cell


title: KW939_CD4_A3

description: single cell


title: KW939_CD8_A3

description: single cell


title: KW939_CD4_H2

description: single cell


title: BKO-NSP-rep3

source_name: neurosphere


title: KW939_CD8_H2

description: single cell


title: Liver_J47


title: WT-CC-rep3


title: KW939_CD8_D3

description: single cell


title: BKO-CC-rep2


title: WT-NSP-rep2


title: KW939_CD8_C3

description: single cell


title: KW939_CD4_G2

description: single cell


title: BKO-NSP-rep2


title: BKO-NSP-rep1


title: Liver_J39


title: Liver_J61


title: KW939_CD8_G2

description: single cell


title: T10

first: xiaolei

last: cheng

state: jiangsu

address: 321 Zhongshan Road

department: Department of Anesthesiology

institute: Affiliated Drum Tower Hospital of Medical School of Nanjing University

description: small RNA

data_processing:
The raw sequencing data are called raw tags. The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants;remove tags without 3 primer; remove tags without insertion; remove tags with poly A; ; remove tags shorter than 18 nt.
The clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2
cmsearch was performed for Rfam mapping.The software miRDeep2 was used to predict novel miRNA by exploring the secondary structure, and Piano was used to predict piRNAs.RNAhybrid miRanda and TargetScan were used to predict target genes of miRNAs.
The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers.Differential expression analysis was performed using the DEGseq, Q value≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default hreshold to judge the significance of expression difference.
all target genes were aligned against the Kyoto Encyclopedia of Genes (KEGG) and Gene Ontology (GO) database. GO enrichment analysis and KEGG enrichment analysis of target genes were performed using phyper, a function of R.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: plasma

value: plasma

tag: disease state

value: dilated cardiomyopathy


title: KW939_CD8_F2

description: single cell

value: CD8 T


title: T11

description: small RNA


title: KW939_CD8_E2

description: single cell


title: KW939_CD4_E2

description: single cell

value: CD4 T


title: Liver_J48


title: WT-NSP-rep3


title: T9

description: small RNA


title: KW939_CD4_C2

description: single cell


title: T4

description: small RNA


title: T5

description: small RNA


title: KW939_CD4_F2

description: single cell


title: KW939_CD8_B2

description: single cell


title: T6

description: small RNA


title: KW939_CD8_C2

description: single cell


title: KW939_CD4_D2

description: single cell


title: T7

description: small RNA


title: WT-NSP-rep1


title: KW939_CD4_B2

description: single cell


title: N10

description: small RNA

value: control


title: T13

description: small RNA


title: T3

description: small RNA


title: KW939_CD4_H1

description: single cell


title: KW939_CD8_D2

description: single cell


title: KW939_CD8_A2

description: single cell


title: N9

description: small RNA


title: N8

description: small RNA


title: KW939_CD8_H1

description: single cell


title: KW939_CD8_G1

description: single cell


title: N6

description: small RNA


title: KW939_CD4_F1

description: single cell


title: N5

description: small RNA


title: N4

description: small RNA


title: aPSM- HiC

city: Bethsda

first: Vittorio

last: Sartorelli

address: 50 South Dr.

department: NIAMS

institute: NIH

description: Hi-C

data_processing:
ChIP-seq reads were mapped to the mm10 genome assembly using Bowtie version 1.1.1,allowing two mismatches, after adapter sequences were removed using trimgalore version0.6.6.
RNA-seq reads were mapped to the mm10 genome assembly using TopHat version 2.1.1 with the default configurations after adapter sequences were removed using trimgalore version 0.6.6.
peaks were called using MACS 1.4.2 (Zhang et al., 2008)  with the following setting: a p value (1.0E-05).
Gene expression values (RPKM: Reads Per Kilobase exon per Million mapped reads) were calculated using Partek Genomics Suite 7.18.
scRNA-seq reads were processed with CellRanger ver. 3.1.0  and bcl2fastq/2.20.0 to generate fastq files with default parameters.
scATAC-seq reads were processed with Cellranger-atac ver. 1.1.0  and bcl2fastq/2.20.0 to generate fastq files with default parameters.
omics reads were processed with cellranger-arc/2.0.0 and bcl2fastq/2.20.0 to generate fastq files with default parameters.
For clustering, filtering, variable gene selection, dimensionality reduction of scRNA(single cell RNA) are performed using the Seurat ver.4.1.0 (Butler et al., 2018).
For clustering, filtering, variable gene selection, dimensionality reduction of scATAC(single cell ATAC) are performed using the Signac ver.1.5.0 (Stuart et al., 2019).
The pseudotemporal Analyses of scRNA(single cell RNA) was performed using Monocle v.3.0.0, Slingshot(ver 2.2.0) (Street et al., 2018)  and tradeSeq(ver 1.8.0) (Van den Berge et al., 2020).
Hi-C  reads were mapped to the mm10 genome assembly using BWA (Li and Durbin, 2010),filtering reads that aligned to more than two places in the genome and low mapping quality score (MAPQ <30).
Hi-C downstream analysis was performed with HOMER (Heinz et al., 2010)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include barcodes,gene names, and UMI counts  for each Sample.

source_name: aPSM

growth_protocol: ESCs were plated on 0.1% gelatin and cultured in DMEM supplemented with 15% FBS, 1% penicillin-streptomycin,2 mM L-glutamine, 0.1 mM non-essential amino acids, 0.1% β-mercaptoethanol, 1,500 U/ml LIF and 2i inhibitors. Somites were dissected from embryoes, sorted and processed for RNAseq and ATACseq assays.

extract_protocol:
RNA was extracted using Trizol. For ChIP cells were  lysed in RIPA buffer as described in Mousavi et al., 2012. ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013)
For RNA-seq, poly (A)+ mRNA libraries were generated  using NEBNext Ultra II RNA library preparation kit for Illumina (NEB #E7490). Single-cell RNA-seq libraries were prepared using a Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (P/N 1000121, 10x Genomics) and scATAC seq performed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x genomics, 1000175). Single Cell Multiome ATAC+ Gene Expression (10x Genomics kit, CG000338). Hi-C experiments were performed using the Arima-HiC kit (A510008GFP)
Bulk RNAseq, Bulk ATAC seq, ChIPseq, scRNA, scATAC, snRNA and scATAC from the same cell (multiomeic) and HiC

treatment_protocol: ESCs differentiation was induced as described inChalet al., 2015. ESC were plated on gelatin-coated plates in serum-free N2B27 medium and BMP4 10ng/ml for 2 days. cells were shifted to MEM, 1%FBS, 14% KSR,10ng/ml Rspo3, 0.5% DMSO and 0.1 μM LDN19318 for 4 days. Subsequently, medium was changed to DMEM, 1%FBS, 14% KSR,  10 ng/ml Rspo3, 10 ng/ml HGF,2 ng/ml IGF-1,20 ng/ml FGF-2  and 0.1 μM LDN193189 for additional 2 days..

tag: sample type

value: Differentiated ESC


title: HIFLR-scATAC (omics)

description: Multiomics

source_name: HIFLR


title: aPSM- scATACseq_rep1

description: scATACseq


title: HIFLR- HiC

description: Hi-C


title: N3

description: small RNA


title: T1

description: small RNA


title: KW939_CD4_A2

description: single cell


title: Naïve ESC- scATAC_rep1

description: scATACseq

source_name: Naïve ESC

value: ESC-Naive


title: Instructed ESC- scATAC_rep1

description: scATACseq

source_name: Instructed ESC


title: KW939_CD8_E1

description: single cell


title: N2

description: small RNA


title: RC3

city: Toledo

first: Carolina

last: Escobar

address: Avenida Carlos III, s/n

institute: University of Castilla-La Mancha

description: Control (non-infected roots)

data_processing:
The reads were firstly checked for quality using FastQC (version 0.11.8). Trimming was then performed using BBDuk (version 38.39).
Trimmed reads were mapped to the combined A. thaliana (TAIR10) and M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017) using STAR (version 2.7.0d; Dobin et al., 2013) and the following parameters: --outFilterMismatchNmax 7, --outFilterMultimapNmax 5.
The BAM files produced with STAR where then used by HTSeq (version 0.11.2), in order to produce the count tables used for the differentially expressed analysis.
The normalized count tables and the posterior differentially expression analysis were performed with DESeq2 (version 1.20.0; Love et al., 2014) using R (version 3.5.2) and RStudio (version 1.1.463).
Genome_build: A. thaliana (TAIR10) and M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017)
Supplementary_files_format_and_content: Matrix table with normalized counts for each A. thaliana gene and sample
Supplementary_files_format_and_content: Text file including pvalue and padjusted value for each A.thaliana gene
Supplementary_files_format_and_content: normalized counts (.txt)
Supplementary_files_format_and_content: DEseq analysis output (.txt)

source_name: Roots

growth_protocol: Arabidopsis thaliana plants were were grown in controlled environment chambers under 16 h/8 h of light/dark at 23ºC

extract_protocol:
Galls and control roots were collected at 3 days post infection and frozen on liquid nitrogen. Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657)
Illumina's TruSeq Stranded mRNA Library Prep Kit was used to prepare the libraries, strictly following the manufacturer's instructions. The fragment size distribution of the libraries were checked in the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit. The libraries were then sequenced in a fraction of an Illumina HiSeq X PE150. Both steps were performed by the company AllGenetics & Biology SL.

treatment_protocol: Arabidopsis plants were inoculated at 5 days post germination at the root tip with approximately 20 freshly-hatched Meloidogyne J2 each plant. The inoculated and non-inoculated plants were then kept in the dark for 2 days. During the first 48 hours, the infections and control roots growth were accessed. After 2 days, the plates containing both inoculated and non-inoculated plants were maintained in the light, covered by a gauze. For more details concerning this protocol please see Olmo et al. (2017; doi: 10.1007/978-1-4939-6831-2_5).

tag: ecotype

tag: developmental stage

value: Aprox. 9-days-old plants (3 days post infection)

tag: agent

value: Non-infected


title: N1

description: small RNA

tag: tissue


title: N7

description: small RNA


title: RC1

description: Control (non-infected roots)


title: KW939_CD4_G1

description: single cell

source_name: single cell


title: KW939_CD8_D1

description: single cell


title: G3

description: Treatment (infected roots)

value: Infected with Meloidogyne javanica


title: G2

description: Treatment (infected roots)


title: KW939_CD4_D1

description: single cell


title: KW939_CD4_E1

description: single cell


title: KW939_CD8_F1

description: single cell


title: G1

description: Treatment (infected roots)


title: RC2

description: Control (non-infected roots)