title: Sample Q001S0002B0010R1S

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)


title: MC_glutamate_rep4, mast cells

status: Public on Mar 23 2021

type: SRA

city: Pittsburgh

first: Daniel

middle: H

last: Kaplan

state: PA

address: 200 Lothrop Street

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
RNA-sB68eq:  Paired-end reads were aligned using STAR aligner to mm9 genome assmebly. Cufflinks was used to measure transcripts abundance and report it as FPKM values.
Software used:  STAR aligner,  Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq data as cufflink reported FPKM values

molecule: total RNA

organism: Mus musculus

growth_protocol: peritoneal-derived mast cells (PCMC) were cultured for 48 hours with vehicle or NS102; or PCMC cultured for 6 hours in glutamate-free Tyrode’s buffer supplemented with vehicle or 4 mM glutamate.

extract_protocol:
The whole skin tissues or sorted mast cells were homogenized using a homogenizer, and mRNA was processed using the Qiagen RNeasy Kit following the manufacturer’s instructions.
Illumina single and paired end libraries, RNA-seq and DNA-seq
Adapter ligation to fragements followed by pcr amplification using indexed primers for Illumnia HiSeq-2500

treatment_protocol: MrgprdDTR mice and control MrgprdCre mice were treated with DT for 3-4 weeks. Ear of WT mice were treated with 50 mM β-ala or vehicle once daily for two days.

tag: cell type

value: Mast Cells

tag: sample derived from

value: Peritoneal

tag: strain

tag: treatment


title: FGMF24_4 [RNA-Seq]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
Sample_135309
FGF2.24hr

data_processing:
Alignment with STAR
Raw counts with featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

organism: Homo sapiens

source_name: normal adult human lung fibroblasts

growth_protocol: Cell culture was performed in low glucose Dulbecco’s modified Eagle’s medium (DMEM; Gibco Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS, Hyclone, Logan, UT), 100 Units/mL penicillin, and 100 µg/mL streptomycin (Invitrogen, Carlsbad, CA).  Cells were then serum-starved in FBS-free DMEM overnight and differentiation to myofibroblasts was induced by treatment with TGFβ for 48 h.

extract_protocol:
RNA extraction was performed using the Qiagen miRNeasy Mini kit per the manufacturer’s instructions to extract all RNA moieties >18nt. Genomic DNA was digested on-column per the manufacturer’s instructions using the RNase-Free DNase Set (New England Biolabs). Samples were split between total RNA and small RNA library preps.
NEBNext rRNA ultra II

treatment_protocol: CCL210 human adult lung fibroblasts were treated with PGE2, FGF2, or left untreated

tag: cell line

value: CCL210 (ATCC)

tag: time point


title: J1721_m1

city: Uppsala

first: Frauke

last: Augstein

address: Almas Allé 5

department: IOB

country: Sweden

institute: Uppsala University

data_processing:
Mapping to Arabidopsis thaliana reference genome with Hisat2
Generating of Count files with HTSeq
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Seeds were surface sterilized with ethanol, plated on 1/2MS+MES+bactoagar plates on mesh and stratified for 2 days. Seedlings were grown for 5 days in long day conditions, 16h light (22 C) and 8h darkness (20 C) at light intensity of 110µE/m2/s. Per sample 50-100 seedlings were pooled.

extract_protocol:
RNA was extracted using RNAeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using NEBNext®UltraTM RNA Library Prep Kit for Illumina® for paired-end sequencing with read length 150

treatment_protocol: Seedlings were transferred to plates containing 1µM ABA or mock and treated for 8h.

tag: tissue

value: root

tag: age

value: 5 days

tag: genotype

value: mock


title: Sample Q001S0002B0010R1N

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

data_processing:
Library strategy: Amplicon-seq
Adapter Trimming - Each sample was processed using Trimmomatic to trim off adapters. Fastqc analysis revealed that most of the reads are of high quality. Hence, no quality trimming was performed.
Alignment - Reads from each sample were aligned to the genome of barley, Blumeria and vector sequences using STAR (dobin et. Al 2013).
Fusion read recognition - Custom python scripts were used to recognize fusion reads based on the partial alignment to the genomes and vector sequences. Vector portions were trimmed off from fusion reads.
Differential expression analysis - Salmon (Patro 2017) was used to obtain gene counts. Samples were size normalized and differential expression analysis was carried out using DESeq2 (Love 2014).
In-frame fusion reads  - Fusion reads expressed in-frame with the protein were recognized by translating the entire sequence and comparing with the protein.
Genome_build: Barley (Mascher 2017) and Blumeria (Ensembl Fungi Assembly EF 2) (Spanu 2018).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew.

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: Yeast were grown at 28C shaking at 225rpm. Cells were subcultured once they reached saturation (OD600 >2.5).

extract_protocol:
Yeast cells were treated with lyticase to digest cell walls and Y2H plasmids were extracted using alkaline lysis and precipitation.
Libraries were constructed using the Nugen Ultralow System V2 with Custom AnyDeplete to reduce the abundance of an amplicon common to all libraries using the manufacturer's instructions.

treatment_protocol: Yeast were incubated in SC-Leu-Trp (no selection) or SC-Leu-Trp-His (reporter selection) liquid media. Two rounds of growth selection were performed.

tag: plant genotype

tag: fungal isolate

value: Bgh isolate 5874 (AVRa6)

value: Non-selected

tag: replication


title: MC_glutamate_rep2, mast cells


title: Sample Q001S0002B0009R3N


title: MF24_3 [RNA-Seq]

description:
Sample_135308
MF24hr.Control

value: Control


title: E2MF6_2 [RNA-Seq]

description:
Sample_135307
PGE2.6hr


title: MF6_1 [RNA-Seq]

description:
Sample_135306
MF6hr.Control


title: Sample Q001S0002B0009R1N


title: MC_glutamate_rep3, mast cells


title: MC_glutamate_rep1, mast cells


title: Sample Q001S0002B0009R3S

value: Selected


title: J1721_A2

value: 1µM ABA


title: FGMF24_12

description:
Sample_135329
FGF2.24hr

data_processing:
CAPmir-seq pipeline with Mayo clinic provided MiRBase and Gencode references
MIRDEEP2_PARAMS=-P -t Human
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

extract_protocol:
RNA extraction was performed using the Qiagen miRNeasy Mini kit per the manufacturer’s instructions to extract all RNA moieties >18nt. Genomic DNA was digested on-column per the manufacturer’s instructions using the RNase-Free DNase Set (New England Biolabs). Samples were split between total RNA and small RNA library preps.
NEB small RNA


title: MC_vehicle_rep4, mast cells


title: J0571_m3


title: J1721_A3


title: Sample Q001S0002B0009R2S


title: MF24_11

description:
Sample_135328
MF24hr.Control


title: MC_vehicle_rep3, mast cells


title: MC_vehicle_rep2, mast cells


title: Sample Q001S0002B0009R1S


title: E2MF6_10

description:
Sample_135327
PGE2.6hr


title: Sample Q001S0002B0009R2N


title: J0571_m1


title: MC_vehicle_rep1, mast cells


title: J0571_A3


title: A549-IFN-1

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw sequencing reads were aligned to the human hg38 genome with STAR
Read counts per gene were calculated using FeatureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited raw read counts per gene

source_name: A549 cell line

extract_protocol:
8 hours after stimulation, cell extracts were collected with Trizol and total RNA was extracted using RNeasy Mini Kit (Qiagen).
Strand-specific rRNA-depleted sequencing libraries were produced according to standard Illumina protocols.

treatment_protocol: Samples were stimulated with 100 IU/ml universal type I interferon or a mock treatment. After 1 hour, cells were washed and then incubated with medium at 37 °C.

value: A549 cell line

value: Interferon

tag: replicate


title: Sample 56: Q001S0002B0012R2N

source_name: Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)

value: Barley infected first leaf (PO:0007094)


title: J1721_A1


title: FGMF24_8

description:
Sample_135325
FGF2.24hr


title: Sample 44: Q001S0002B0012R1N


title: Main1.010819.l2

city: Philadelphia

first: Kiya

middle: W

last: Govek

address: 3700 Hamilton Walk

department: Genetics

institute: University of Pennsylvania

data_processing:
Library strategy: CITE-seq
Basecalling with Illumina bcl2fastq
Read alignment, cell barcode demultiplexing, and UMI demultiplexing using cellranger 3.0.2
Cell barcodes were filtered out if they contained less than 1200 UMIs or >10% mitochondrial mRNA content.
Count matrices between mice were concatenated, discarding genes expressed in fewer than 15 cells
Genome_build: mm10
Supplementary_files_format_and_content: gene_matrix_all_new.csv is a csv file of a genes x cells count matrix for all samples; protein_expr_all.csv is a csv file of a cells x proteins count matrix for all samples

molecule: polyA RNA

extract_protocol:
Spleens were removed from mice and mechanically dissociated with a syringe plunger over a 40 um strainer while being washed with 5 ml of PBS + 10% fetal calf serum. Suspensions were centrifuged briefly to pellet cells. Red blood cells were lysed with an RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA) for 5 minutes and centrifuged again. 2 million cells from the resulting pellet were re-suspended in staining buffer (2% BSA, 0.01% Tween in PBS), and subsequently incubated with the antibody panel
cDNA libraries were prepared following the standard CITE-seq and 10x protocols

value: BALB/cJ

tag: Sex

value: Female

value: 9 months

value: spleen


title: J0571_A2


title: β-ala_rep3, skin

source_name: β-ala

value: skin

value: Epidermal

value: β-ala


title: MF24_7

description:
Sample_135324
MF24hr.Control

value: CCL210 (ATCC)


title: J0571_A1

value: root

value: 5 days


title: β-ala_rep4, skin


title: E2MF6_6

description:
Sample_135323
PGE2.6hr


title: Sample 50: Q001S0002B0012R1S

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Bgh isolate 5874 (AVRa6)


title: Sample 25: Q001S0001B0012R3N

value: Non-selected


title: MF6_5

description:
Sample_135322
MF6hr.Control

value: Control


title: β-ala_rep2, skin


title: MF6_9

description:
Sample_135326
MF6hr.Control


title: WT rep 1

city: Aurora

first: James

middle: T

last: Nichols

state: Colorado

address: 12700 East 19th Avenue

department: Craniofacial Biology

institute: University of Colorado - Anschutz Medical Campus

data_processing:
make ref / make fastq files / aggr command / count command; CellRanger 2.2.0
merge WT and mut data; Seurat v2; e10x <- MergeSeurat(object1 = wt, object2 = mut, project = "n10x", min.cells = 5, min.genes = 100)
filter for <250 genes per cell and for any mitochondrial UMIs at less than or equal to 2.5% per cell; Seurat v2; e10x <- FilterCells(object = e10x, subset.names = c("nGene", "percent.mito"), low.thresholds = c(250, -Inf), high.thresholds = c(Inf, 0.025))
cluster projection/dim red. Via PCA/UMAP after WT subset; Seurat v2; nichols_TSNE <- RunTSNE(nichols_dr_seurat_WT, dims.use = 1:10, do.fast= TRUE, seed.use = 123)/nichols_umap_clusters <- FindClusters(object = nichols_TSNE, reduction.type = "pca", dims.use = 1:15, resolution = 0.2, save.SNN = TRUE, n.start = 10, nn.eps = 0.5, print.output = FALSE, force.recalc = TRUE)/nichols_umap_clusters <- FindClusters(object = nichols_TSNE, reduction.type = "pca", dims.use = 1:15, resolution = 0.2, save.SNN = TRUE, n.start = 10, nn.eps = 0.5, print.output = FALSE, force.recalc = TRUE)
main dim reduction plot; Seurat v2; DimPlot(object = nichols_umap_clusters, reduction.use = "umap", do.return = TRUE, pt.size = 1.3)
differential expression marker gene ID/localization of expression; Seurat v2; nichols_umap.markers1 <- FindAllMarkers(nichols_umap_clusters, only.pos = TRUE, min.pct = 0.1, thresh.use = 0.25)/FeaturePlot
organizing genes by descending ascending pct.2; Seurat v2; subset based on ascending pct.2
visualize distribution of alx genes across each cluster; Seurat v2; VlnPlot(nichols_umap_clusters, features.plot = <each alx gene>), single.legend = TRUE, y.max = 2) + ggplot2::theme_classic() + ylab("Expression Level (log TPM)")
pseudotemporal and lineage tracing analyses; mnonocle3 v3; Follows from pseudotime and lineage trajectory mapping vignette for Monocle 3 (Trapnell et al., 2014)
seurat /featureplot app; Seurat v2, RShiny; FeaturePlot(nichols_umap_clusters_diet, features = input$gene_name, reduction = "umap", cols = c("grey","blue"), label = TRUE,label.size = 4.5, pt.size = 1.5, ncol = 3) + xlim(-10, 10) + ylim(-10, 15); used the diet seurat function native to seurat to generate the "skiny" object used here
lineage tracing/trajectory analysis app; monocle3 v3, Rshiny; plot_cells(Nichols_cds_subset, genes = input$gene_name, cell_size = 1.5, graph_label_size = 3, group_label_size = 4) + theme(plot.title = element_text(size = 25); uses the main cell data set object as in our pseudotemporal and lineage tracing analyses
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: counts.csv
Supplementary_files_format_and_content: raw UMI counts per gene per cell

organism: Danio rerio

source_name: Nerual crest cells

growth_protocol: Animals were maintained and staged according to established protocols (Westerfield, 1993, Kimmel et al., 1995).

extract_protocol:
32 double transgenic flia:EGFP;sox10:mRFP embryos were dissociated into single cell suspension using cold-active protease from Bacillus licheniformis, DNase, EDTA, and trituration (Adam et al., 2017)
10X Genomics libraries

treatment_protocol: Crispr/cas9 mutagenesis of alx3 gene (Jao et al., 2013, Barske et al., 2016)

tag: tissue source

value: neuroectoderm

value: AB strain

value: 24 hpf


title: C24_m1

value: mock


title: Sample 05: Q001S0001B0012R1N

value: Barley infected first leaf (PO:0007094)


title: Sample 15: Q001S0001B0012R2N


title: MF24_3

description:
Sample_135320
MF24hr.Control


title: β-ala_rep1, skin


title: J0571_m2


title: PBS_rep3, skin

source_name: PBS

value: PBS


title: C24_m3


title: C24_m2


title: C24_A3

value: 1µM ABA


title: KO rep1

city: Turku

first: Sina

last: Tadayon

address: Tykistökatu 6A, 4 floor

country: Finland

institute: Turku University

data_processing:
Single-end 50 bp reads were aligned to the mm10 mouse genome with STAR version 2.5.2b. Read counting was performed with subreads package.
Read counts were normalized and TPM were calculated.
The Bioconductor package Limma was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited csv files include TPM values for each Sample ...

source_name: lymph node's lymphatic endothelial cells

extract_protocol:
Popliteal & brachial Lymph Node from WT and KO mice were removed, digested with collagenase and Live lymphatic endothelial cells (CD45- CD31+ Podoplanin+)  were sorted and RNA was extracted. cDNA was synthesized with SMART-Seq v4 ultra low input RNA kit.
Sequencing libraries were generated from the amplified cDNA using Nextera XT (Illumina)

value: Popliteal & brachial Lymph Node

value: Lymphatic endothelial cells

value: Steady State


title: E2MF6_2

description:
Sample_135319
PGE2.6hr

value: CCL210 (ATCC)


title: Sample 30: Q001S0001B0012R3S

value: Selected


title: PBS_rep4, skin

value: skin

value: Epidermal


title: PBS_rep2, skin


title: Sample 62: Q001S0002B0012R2S

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Bgh isolate 5874 (AVRa6)


title: C24_A2

value: root

value: 5 days


title: PBS_rep1, skin


title: Sample 20: Q001S0001B0012R2S


title: C24_A1


title: MF6_1

description:
Sample_135318
MF6hr.Control

value: Control


title: MrgprdDTR_rep4, skin

source_name: MrgprdDTR

value: DT (IP) + Acetone:Olive oil (4:1)


title: Sample 10: Q001S0001B0012R1S


title: BLEO-ML324 H3K36 02

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

country: China

institute: Chinese Academy of Sciences

description:
Sample 10 (L02)
Illumina NovaSeq 6000 PE150 high-throughout data

library_source: genomic

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 mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata. ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the specified configurations.
Data were filtered using predetermined specifications.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bw: bigWig; Peak files. Scores represent the abundance of genomic DNA fragments.

molecule: genomic DNA

source_name: Human stromal cell

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 10,000,000 was reached in each flask (T182) and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or ML324, the latter a small molecular inhibitor against the demethylase activity of human KDM4.

extract_protocol:
Cells were lysed for RNA preparation 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.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a epigenetic-specific mechanism, the agent ML324 was applied to the media at a final concentration of 20 μM.

value: Normal human prostate-derived primary stromal cells

tag: passage

tag: chip antibody


title: MrgprdDTR_rep3, skin


title: DNA from seed produced at 27°C_Mature stage, T28_M2

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
fastQC was used to perform fastq (short reads) quality check
Methypy software (Schultz et al. 2015) was used to mapped reads againt the Arabidopsis genome (TAIR 10) using the paired-end-pipeline (chloroplastic genome was used as negative control then remove duplicated reads, and finally call methylation state for all cytosine (allc files). Bigwig files were generated using Methylpy
Genome_build: TAIR 10
Supplementary_files_format_and_content: bw

growth_protocol: Plants were grown in a culture room in trays containing a sterile  soil at 20°C/18°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².

extract_protocol:
Total DNA were extracted from the frozen grinded tissues lots using the Macherey-Nagel NucleoSpin® DNA Food kit following manufacturer’s instructions
DNA samples were sent to to the BGI and library construction, bisulfite treatment using a ZYMO EZ DNA Methylation-Gold kit and paired-end sequencing using an Illumina Hiseq 2500 (PE100 20M)
Library Construction (MGIEasy Whole Genome Bisulfite Sequencing Library Prep Kit) details:  Fragment genome DNA to 100-300 bp by Sonication  DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors.  1) Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit. (Unmethylated Lambda DNA, Promega as control)    2) PCR amplification and purification    3) Denaturation    4) ssDNA circularization    5) Enzymatic Digestion and purification    6) Qualified library for sequencing.

treatment_protocol: After bolting and first flowers, control plants were grown at the same temperature condition 24°C/22°C (23°C) but stressed plants were transferred to another culture room with mild stress conditions 26°C/24°C (25°C) and severe stress conditions 28°C/26°C (27°C)

tag: ecotype

tag: developmental stage

value: seed Mature stage

value: growing severe heat stress conditions 27°C

value: entire seed


title: FGMF24_4

description:
Sample_135321
FGF2.24hr


title: BLEO-ML324 H3K36 01

description:
Sample 10 (L01)
Illumina NovaSeq 6000 PE150 high-throughout data

tag: cell type


title: DNA from seed produced at 27°C_Mature stage, T28_M1

tag: treatment


title: BLEO-ML324 input 04

description:
Sample 10 (K02)
Illumina NovaSeq 6000 PE150 high-throughout data

tag: cell line


title: MrgprdDTR_rep2, skin

tag: sample derived from

tag: strain


title: DNA from seed produced at 27°C_Bent stage, T28_B2

value: seed Bent stage

tag: tissue


title: MrgprdDTR_rep1, skin


title: BLEO-ML324 input 03

description:
Sample 10 (K01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: BLEO-ML324 H3K9 02

description:
Sample 10 (J02)
Illumina NovaSeq 6000 PE150 high-throughout data


title: DNA from seed produced at 27°C_Bent stage, T28_B1


title: B10_1

city: Yangzhou

first: Dongping

last: Zhang

address: 12 East Wenhui Avenue

institute: Yangzhou University

data_processing:
The raw reads were filtered by removing reads with adapters, reads in which unknown bases were > 5%, and low-quality reads.
The FASTQC program was used to assess the quality of the clean reads, which were then aligned to the rice reference genome Release 7 of the MSU Rice Genome Annotation Project using TOPHAT v.2.1.0
CUFFLINKS v.2.1.1 was then used to normalize and estimate the gene expression level according to fragments per kilobase of transcript per million reads
The differentially expressed genes (DEGs) were also calculated using CUFFLINKS v.2.1.1 at a significance level of q < 0.05 and the absolute value of log2 ratio ≥ 1.
Genome_build: MSU Rice Genome Annotation Project
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Oryza sativa

source_name: developing grain

growth_protocol: The experiment was carried out at the farm of Yangzhou University (32°30’N, 119°25’E) during the rice (Oryza sativa) growing season, and in Hainan in winter seasons.

extract_protocol:
Total RNA was extracted from the grains at 5 and 10 DAF, using the RNAprep Pure Plant kit (Tiangen). RNA integrity and quantity were determined with an Agilent 2100 Bioanalyzer according to the manufacturer’s protocol.
Enrichment of mRNA from total RNA, complementary DNA synthesis, and construction of the library were performed at Vazyme Biotech.

treatment_protocol: At the heading stage, 200 uniformly growing and headed panicles (1-2 panicles per plant) were chosen, and spikelets on the selected panicles with the same flowering date were labeled for each cultivar/line. The flowering date and position of each spikelet on the labeled panicles were recorded. Approximately 30 labeled panicles were sampled each time from flowering to maturity. Half of the sampled grains were frozen in liquid nitrogen for at least 2 min and then stored at -80°C for further analyses. The other half of the grains were dried at 80°C for approximately 72 h to a constant weight and used for starch analyses.

tag: genotype

value: RGB1 RNAi line

value: grain

value: 10 days after flowering


title: DNA from seed produced at 25°C_Mature stage, T26_M2

value: growing mild heat stress conditions 25°C


title: B10_2


title: MrgprdCre_rep4, skin

source_name: MrgprdCre

value: skin

value: Acetone:Olive oil (4:1)


title: W10_2

value: Wuyujing 8


title: W10_3


title: BLEO-ML324 H3K9 01

description:
Sample 10 (J01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: DNA from seed produced at 25°C_Mature stage, T26_M1


title: MrgprdCre_rep3, skin

value: Epidermal


title: BLEO-ML324 input 02

description:
Sample 10 (I02)
Illumina NovaSeq 6000 PE150 high-throughout data


title: W10_1


title: MrgprdCre_rep2, skin


title: MrgprdCre_rep1, skin


title: DNA from seed produced at 25°C_Bent stage, T26_B2


title: B5_3

value: 5 days after flowering


title: B10_3


title: DNA from seed produced at 25°C_Bent stage, T26_B1


title: BLEO H3K36 02

description:
Sample 10 (H02)
Illumina NovaSeq 6000 PE150 high-throughout data

value: BLEO


title: BLEO-ML324 input 01

description:
Sample 10 (I01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: B5_2


title: DNA from seed produced at 23°C_Mature stage, T24_M2

value: growing control conditions 23°C


title: DDDA-LT LT3409

city: pittsburgh

first: Edward

middle: V.

last: Prochownik

address: 4401 Penn Avenue

department: Section of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh

description: DDDA-LT

data_processing:
CLC Genomics Workbench v12.0
Genome_build: Reference sequence = Mus_musculus_ensembl_v80_Sequence Gene track = mus_musculus_refseq_GRCm38.p6_Genes  mRNA track = mus_musculus_refseq_GRCm38.p6_mRNA
Supplementary_files_format_and_content: counts

source_name: Tumor

extract_protocol:
RNA purification from five representative tumors of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

tag: gender

value: M

value: FVB

value: SB_Del90+xloc+SB_YAP S127A

tag: diet

value: 10% DDDA long term


title: BLEO H3K36 01

description:
Sample 10 (H01)
Illumina NovaSeq 6000 PE150 high-throughout data

value: Normal human prostate-derived primary stromal cells


title: B5_1


title: DDDA-LT LT3158

description: DDDA-LT

value: F


title: DNA from seed produced at 23°C_Mature stage, T24_M1

value: seed Mature stage

value: entire seed


title: W5_3

value: grain


title: BLEO input 04

description:
Sample 10 (G02)
Illumina NovaSeq 6000 PE150 high-throughout data


title: DNA from seed produced at 23°C_Bent stage, T24_B2

value: seed Bent stage


title: DDDA-LT LT3176

description: DDDA-LT


title: BLEO input 03

description:
Sample 10 (G01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: DDDA-LT LT3161

description: DDDA-LT


title: BLEO H3K9 02

description:
Sample 10 (F02)
Illumina NovaSeq 6000 PE150 high-throughout data


title: DNA from seed produced at 23°C_Bent stage, T24_B1


title: W5_1


title: DDDA-Tumor DT2264

description: DDDA-Tumor

value: 10% DDDA 3-4 weeks


title: BLEO H3K9 01

description:
Sample 10 (F01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: RNAs from seed produced at 23°C_germination IV stage, ros_2

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Genome mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm
Clean reads were mapped to the reference transcriptome araport v11  and quantified using Salmon algorithm to calculate gene expression level in counts
Genome_build: Araport11_genes.201606.cdna.fasta downlaoded from arabidopsis.org
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

extract_protocol:
Total RNAs were extracted from the frozen grinded tissues lots using the Macherey-Nagel NucleoSpin RNA Plus kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. 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. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample

value: seed germination IV stage


title: W5_2

value: Wuyujing 8


title: DDDA-Tumor DT2277

description: DDDA-Tumor


title: DDDA-LT LT3155

description: DDDA-LT


title: RNAs from seed produced at 23°C_germination IV stage, ros_1


title: BLEO input 02

description:
Sample 10 (E02)
Illumina NovaSeq 6000 PE150 high-throughout data


title: DDDA-Tumor DT2270

description: DDDA-Tumor


title: BLEO input 01

description:
Sample 10 (E01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: NRCM_hypoxia_4n_rep3

city: Chongqing

first: Yun-Han

last: Jiang

address: No. 183 Xinqiao Street

institute: Xinqiao Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor_6.0.81 whole genome using Hisat2(version:2.0.4).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after Hisat2 alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Genome_build: Rnor_6.0.81
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Rattus rattus

growth_protocol: neonatal rat crdiomyocytes (NRCMs) were cultured for 24h after differential adherence supplemented with 0.2 mM AraC and 1X Insulin-Transferrin-Selenium (100X) (Gibco, Waltham, USA).

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
According to the experimental instructions, the purified total RNA was subjected to mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, terminal repair, 3' end plus A, ligation linker, enrichment and other steps to complete the library construction of the samples.

treatment_protocol: After cultured for 24h, NRCMs were were effectively synchronized at G0/ G1 stages of the cell cycle by serum starvation. Subsequently, hypoxia condition (1% oxygen) was used to induce polyploid multi-nucleated NRCMs for 48h. For cell sorting, NRCMs were stained with 2 ug/mL Hoechst 33342 and then sorted into two subpopulation including diploid (2n) and tetraploid (4n).

tag: stress

value: hypoxia

value: NRCM

tag: ploidy subpopulation

value: tetraploid NRCM (4n)

tag: age

value: 1-3 day after birth

value: SD


title: NRCM_hypoxia_4n_rep4


title: CTRL H3K36 02

description:
Sample 10 (D02)
Illumina NovaSeq 6000 PE150 high-throughout data

value: CTRL


title: RNAs from seed produced at 23°C_germination II stage, ros_3

value: seed germination II stage

value: growing control conditions 23°C


title: NRCM_hypoxia_2n_rep4

value: diploid NRCM (2n)


title: NRCM_hypoxia_4n_rep2


title: NRCM_hypoxia_2n_rep3


title: DDDA-Tumor DT3168

description: DDDA-Tumor

value: F

value: FVB

value: SB_Del90+xloc+SB_YAP S127A


title: RNAs from seed produced at 23°C_germination II stage, ros_2

value: entire seed


title: NRCM_hypoxia_2n_rep2


title: CTRL input 04

description:
Sample 8 (C02)
Illumina NovaSeq 6000 PE150 high-throughout data

value: Normal human prostate-derived primary stromal cells


title: RNAs from seed produced at 23°C_germination II stage, ros_1


title: RNAs from seed produced at 23°C_germination IV stage, ros_3


title: DDDA-Liver DL05

description: DDDA-Liver

source_name: Liver

value: M

value: no injection

value: 10% DDDA 3-4 weeks


title: DDDA-Tumor DT3167

description: DDDA-Tumor


title: CTRL input 03

description:
Sample 7 (C01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: RNAs from seed produced at 23°C_mature stage, ros_3

value: seed mature stage


title: NRCM_hypoxia_4n_rep1

value: hypoxia

value: NRCM


title: DDDA-Liver DL04

description: DDDA-Liver


title: DDDA-Liver DL03

description: DDDA-Liver


title: RNAs from seed produced at 23°C_mature stage, ros_2


title: NRCM_hypoxia_2n_rep1

value: 1-3 day after birth


title: CTRL H3K9 02

description:
Sample 5 (B02)
Illumina NovaSeq 6000 PE150 high-throughout data


title: CTRL H3K9 01

description:
Sample 4 (B01)
Illumina NovaSeq 6000 PE150 high-throughout data


title: DDDA-Liver DL02

description: DDDA-Liver


title: RNAs from seed produced at 23°C_mature stage, ros_1


title: RNAs from seed produced at 23°C_germination IV stage, Col_3

value: control

value: seed germination IV stage


title: HC#2 H3K4me3

city: Lodz

first: Przemyslaw

last: Lewkowicz

address: Pomorska 251/A4

department: Department of Neurology, Laboratory of Neuroimmunology

country: Poland

institute: Medical University of Lodz, Poland,

description:
MACS2 results: GO (biocyc.txt; bilogical_process.txt; cellular_component.txt; molecular_function.txt; pathwayInteractionDB.txt)
HOMER results: motif1-45.motif

data_processing:
Basecalls performed using CASAVA version 1.4
Quality of the raw sequence reads was checked using the FASTQC software (version: 0.11.8).
All reads were subjected to the adapter and quality filtering (minimum quality (-q 25), minimum length (-m 15)) using the Cutadapt tool (version: 1.18) in NextSeq reads mode
Trimmed reads were aligned to the reference genome (GRCh38) using the Bowtie2 (version: 2.2.9) in the single-end mode.
Duplicated reads were located and tagged using the Picard MarkDuplicates tool (version: 2.18.4). Reads with low mapping quality score (MAPQ <10) were removed from downstream analysis with the Samtools software (version: 1.6).
Protein binding sites identification in the previously prepared BAM files was performed with the MACS2 (Model-based Analysis of ChIP-seq) software (version: 2.1.0) in narrow peak mode (Feng, 2012). Subsequently, identified peaks were annotated using annotatePeaks.pl from Homer software (version: 4.11.1, hg38 annotation library). Additionally, a functional enrichment analysis for various categories (e.g. gene function, biological pathways, domain structure, etc.) was executed (Schaefer, 2009). To find enriched motifs in ChIPseq peaks the findMotifsGenome.pl program from Homer software (version: 4.11.1) was used.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: cells isolated from peripheral blood of healthy volunteer

growth_protocol: 20 mL of the whole blood on lithium heparin anticoagulant was collected form HIV-infected individuals and HC. Neutrophils were purified by negative selection by microbeads, which allowed the removal of DCs, B cells, monocytes, macrophages, activated T cells, and activated NK cells (MACSxpress Whole Blood Neutrophil Isolation Kit; cat. 130-104-434). Residual erythrocytes were lysed with the use of 2mL ammonium chloride Lysing Reagent (BD cat. 555899) for 5 minutes. 2x106 neutrophils were incubated without stimulation, in RPMI 1640 for 6 h (5%CO2, 20C, humid atmosphere). For DNA isolation, samples of isolated neutrophils were frozen and kept at -80C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Double-stranded DNA was generated from single-stranded fraction of ChIPed DNA using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module (E6111S,New England Biolabs). Reaction was carried out in the presence of random primers from NEBNext® RNA First Strand Synthesis Module (E7525, New England Biolabs). Libraries for sequencing were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645L, New England Biolabs). Single-end sequencing with read length of 75 bases (SE75) was performed with NextSeq550 (Illumina) in order to obtain at least 20 million of reads per sample that could be mapped to human genome

treatment_protocol: ChIP was carried out in neutrophils according to manual of Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Merck Millipore, cat.17-1010). Briefly, cells were fixed with 1%  formaldehyde in RPMI solution for 10 min. at RT and lysed by Lysis and Nuclear Lysis Buffer. Sonication (10 cycles; 30sec. “ON” 30sec. “OFF”) was done using Bioruptor® Pico Sonicator (Diagenode, Belgium). Chromatin immunoprecipitation was performed with the use of set of antibodies: Normal mouse IgG (negative control), anti-RNA Polymerase II (clone CTD4H8) as positive control and anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745) mAbs. Both antibodies were recommended for the use in ChIP-seq technique (Egelhofer, 2011)

value: highly purified peripheral blood neutrophils

tag: disease state

value: healthy

value: 2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere)


title: CTRL input 01

description:
Sample 1 (A01)
Illumina NovaSeq 6000 PE150 high-throughout data

tag: passage

value: CTRL


title: CTRL H3K36 01

description:
Sample 12 (D01)
Illumina NovaSeq 6000 PE150 high-throughout data

tag: chip antibody


title: CTRL input 02

description:
Sample 2 (A02)
Illumina NovaSeq 6000 PE150 high-throughout data


title: HC#1 input

value: none (input)


title: DDDA-Liver DL01

description: DDDA-Liver

value: F

value: FVB


title: NFD-Tumor s2139

description: NFD-Tumor

value: SB_Del90+xloc+SB_YAP S127A

value: Normal Diet


title: HC#1 H3K4me3

value: anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745


title: RNAs from seed produced at 23°C_germination IV stage, Col_1

tag: ecotype

value: growing control conditions 23°C

value: entire seed


title: NFD-Tumor s2138

description: NFD-Tumor

value: M


title: NET-seq HEK293 wt technical R2

city: Berlin

first: Andreas

last: Mayer

address: Ihnestraße 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Data processing of nested NET-seq data sets was performed similar as described in Mayer et al., 2015.
Pre-processing: The ten 5' end nucleotides corresponding to the molecular barcode, are trimmed from the reads, but remain associated with the read using a custom Python script.
Mapping: eads were aligned to the human reference genome (GRCh38.p12) using the STAR aligner (v2.4.0) (Dobin et al., 2013) with the following parameters: –clip3pAdapterSeq ATCTCGTATGCCGTCTTCTGCTTG –clip3pAdapterMMp 0.21 –clip3pAfterAdapterNbases 1 –outFilterMultimapNmax 1 –outSJfilterOverhangMin 3 1 1 1 –outSJfilterDistToOtherSJmin 0 0 0 0 –alignIntronMin 11 –alignEndsType EndToEnd. The alignment was performed with the GENCODE annotation v28.
Filtering: We removed putative contaminations such as reverse transcription mispriming events (barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read), PCR duplicates (reads that align to the same genomic position and contain identical barcode) and splicing intermediates (exact single bp 3' ends of introns and exons).
Normalization: For uniquely mapped reads, the position corresponding to the 3′-end of the nascent RNA fragment (the 5′-end of the sequencing reads after removal of the barcode) was recorded with a custom Python script using the HTSeq package (Anders et al., 2014).
Genome_build: Human (hg38/GRCh38)
Supplementary_files_format_and_content: BigWig files - NET-seq coverage

growth_protocol: Cells were cultured in RPMI containing 10% FBS, 5% penicillin-streptomycin. Cells were seeded at 5 x 10^5 cells/ml, NIH/3T3 were seeded at 2 x 10^6 cells/T75 flask every two days.

extract_protocol:
Nascent RNA was extracted as described by Mayer and Churchman (2016).
Libraries were constructed as described by Mayer and Churchman (2016), with the following modifications: After purification of the nascent RNA, a DNA linker containing a random decamer sequence was ligated to the 3'-end of the transcripts. Ligated RNA was fragmented by incubation with NEBNext RNA fragmentation solution at 95°C for 10 min. To improve read mapping and take the increased linker length into account, all size selection steps were adapted.

value: embryonic kidney

value: untreated

value: wild type


title: NET-seq HEK293 wt technical R1


title: RNAs from seed produced at 23°C_germination II stage, Col_3

value: control

tag: developmental stage

value: seed germination II stage


title: HC#17 H3K4me3

tag: cell type

value: highly purified peripheral blood neutrophils

value: healthy


title: NFD-Tumor s1800

description: NFD-Tumor

tag: treatment


title: HIV#6 H3K4me3

source_name: cells isolated from peripheral blood HIV infected individuls

value: HIV infected

value: 2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere)


title: RNAs from seed produced at 23°C_germination II stage, Col_2


title: HIV#11 H3K4me3


title: NFD-Tumor s1799

description: NFD-Tumor

value: F


title: nested NET-seq HeLa wt biological R1

source_name: HeLa

value: cervix


title: NFD-Tumor s1758

description: NFD-Tumor

value: FVB

value: SB_Del90+xloc+SB_YAP S127A


title: RNAs from seed produced at 23°C_germination II stage, Col_1


title: RNAs from seed produced at 23°C_germination IV stage, Col_2

value: seed germination IV stage


title: nested NET-seq HeLa wt biological R2


title: HIV#4 H3K4me3

value: anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745


title: RNAs from seed produced at 23°C_mature stage, Col_3

value: seed mature stage

value: growing control conditions 23°C

value: entire seed


title: NFD-Liver c7

description: NFD-Liver

value: no injection

value: Normal Diet


title: HIV#4 input

value: none (input)


title: OphaCfkbU

city: Tianjin

first: Pan

last: Wang

address: Peiyang Park Campus: No.135 Yaguan Road, Haihe Education Park

institute: Tianjin university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Streptomyces hygroscopicus var. ascomyceticus FS35 using bowtie 2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to genes. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time (Trapnell, Cole, et al., 2010).
Genome_build: whole genome of Streptomyces hygroscopicus var. ascomyceticus FS35 that had been sequenced but not public
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Streptomyces hygroscopicus subsp. ascomyceticus

source_name: hyphae

extract_protocol:
Fermentation broth were collected at 50 h of fermentation. After centrifugation at 8000 r for 10 minutes, the wet hyphae were rapidly frozen in liquid nitrogen. The total RNA was extracted from frozen hyphae with the Trizol reagent (Invitrogen, USA).
The cDNA libraries were generated using NEBNext® UltraTM Directional RNA Library Prep Kit for Ιllumina® (NEB, USA) following manufacturer’s recommendations. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). After terminal repair and PCR amplification, the quality of cDNA libraries were assessed on the Agilent Bioanalyzer 2100 systerm.

value: OphaCfkbU

tag: fermentation time

tag: passages


title: RNAs from seed produced at 23°C_mature stage, Col_2

value: control


title: Uninfected HUVEC, Replicate 2

city: Hoersholm

first: Christian

last: Garde

address: Dr Neergaards Vej 5F

country: Denmark

institute: Evaxion Biotech

description:
4988
HUVEC.tsv.gz

data_processing:
Fastq files were preprocessed using cutadapt and base qualities checked using fastqc.
The reads were mapped against the human reference genome hg38 using STAR. Unmapped reads were mapped to the NC_007795.1 reference genome using bwa mem.
Gene read coverages were computed using featureCounts.
Differential gene expression analysis was conducted using the DESeq2 workflow with the BH corrected Wald test and log2FC skrinkage
Genome_build: hg38, NC_007795.1
Supplementary_files_format_and_content: Tab separated text files with gene read coverages.

source_name: HUVEC

growth_protocol: The Staphylococcus aureus ATCC29213 reference strain and primary human umbilical cord endothelial cells (HUVEC from pooled donors, passage 2-3, PromoCell) were used for all experiments. Prior to experiments, the bacteria were grown until exponential growth phase in tryptic soy broth (2½h at 37°C), and bacterial stock solution could then be prepared by centrifugation and resuspension of pellet in phosphate buffered saline (PBS) followed by adjustment to OD600=0.1. HUVECs were grown until confluence in basal medium (Endothelial Cell Growth Medium 2, PromoCell) with fetal bovine serum (FBS) and penicillin-streptomycin (PS) and then split into microtiter plates. Prior to experiments, the confluent HUVEC microtiter plates were washed 3 times in PBS and filled with 0.5 ml basal medium+FBS without PS.

extract_protocol:
Pellets were resuspended in 700 μl acetate buffer (20 mM NaOAc, 1 mM EDTA, 0.5% SDS, pH 4.5) and transferred to FastPrep tubes containing lysing matrix B. Cells were lysed in a Thermo Savant FastPrep FP120 Cell Homogenizer at 6.0 m/sec for 3 x 40 sec with 1 min pause on ice in between runs, and then centrifuged for 5 min at 20,000 g. Lysate was transferred to tubes containing 500 μl phenol solution (2:1 phenol in water adjusted to pH 4.5 with NaOAc) and 100 μl chloroform followed by incubation at 65 °C at 1100 rpm in a thermomixer for 15 min with vortexing every 2 min. After centrifugation, the aqueous phase was transferred into tubes containing 500 μl chloroform followed by vortexing, centrifugation, and transferring to new tubes. The RNA was precipitated using 96% EtOH and 10vol% 3M NaOAc on ice for ≥1 hour. Tubes were centrifuged for 60 min at 4°C, and pellets were washed in ice cold 70% EtOH followed by centrifugation for 10 min. Supernatant was removed and pellets were then air-dried and dissolved in sterile ddH2O. RNA quantity was measured using Nanodrop spectrophotometer, and RNA quality was then verified by fragment analysis using a Fragment Analyzer (Agilent), followed by RiboZero Gold (MRZE724, Epidemiology/Illumina) treatment on the 3 samples from each group to remove both human and bacterial rRNA.
After DNase treatment, library preparation was performed using the NebNext® UltraTM Library prep kit (NEB) followed by quality assessment by the fragment analyzer

treatment_protocol: Microtiter plates were inoculated with 20 μl of bacterial stock suspension corresponding to a multiplicity of infection (MOI) of 16, followed by centrifugation at 300g for 5 min to sediment the bacteria. After 1½ hours post-infection (hpi), wells were supplemented with lysostaphin (10 μg/ml) + gentamicin (100 μg/ml). HUVEC samples were collected by washing 3 times in PBS followed by trypsination for 10 min, centrifugation, and washing the pellet followed by centrifugation and resuspension of the pellet in 100 μl PBS. Samples were then snap-frozen in liquid nitrogen and kept at -80°C until RNA isolation.

tag: group

value: Uninfected

tag: s. aureus strain


title: NFD-Liver c4

description: NFD-Liver

value: M

tag: strain


title: FS35


title: Uninfected HUVEC, Replicate 1

description:
4987
HUVEC.tsv.gz


title: Uninfected HUVEC, Replicate 3

description:
4989
HUVEC.tsv.gz


title: NFD-Liver c17

description: NFD-Liver

tag: gender


title: HA-Ash2L E14 cell line HA-tag Cut & Run rep1

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

data_processing:
Cut&Run sequencing reads were mapped to the mm10 genome for mouse by using Bowtie2 (v2-2.2.4) with parameters “-q --phred33  --very-sensitive -p 10”.
Then, we removed duplicated reads using SAMtools (v1.5) . BAM files of mapping results were merged for the same sample using SAMtools and converted to BED format by using BEDTools.
Peaks regions were called for each sample by using MACS (v 1.4) from cutRun mapped reads with parameters "macs -t mapped.bed  -n sample_id -w -S -g mm -p 0.00001".
Homer v4.10 was employed to perform gene annotation of peaks and differential peaks.
Genome_build: mm10
Supplementary_files_format_and_content: peaks in text format

source_name: E14 cell line

growth_protocol: Parental E14 cells or HA-Ash2L E14 cells are maintained in standard knock-out DMEM with serum and LIF condition

extract_protocol:
Cut & Run experiments were performed using 1X10^6 cells or 1X10^5 cells for HA-tag (Cell Signaling Co. #3724) or H3K4me3 (Millipore #07-473) antibody, respectively, according to Cut & Run protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: Doxcycline was added to induce the expression of HA-Ash2L transgene for 48hrs.

tag: cell line

tag: genotype

value: HA-Ash2L knock-in

tag: protocol

value: Cut&Run

value: anti-HA-tag (Cell Signaling Co. #3724)


title: NFD-Liver c1

description: NFD-Liver

value: FVB

tag: diet


title: 3--3: BLEO/ML324 03

description: ATAC-Seq library prepared from an Illumina Nextera DNA Flex Library Preparation kit

data_processing:
We used a publically available ATAC-Seq pipeline based on the official pipeline specification of ENCODE (https://github.com/kundajelab/atac-seq-pipeline).
Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 was used to call peaks and an initial threshold q-value of 0.1 was set as cutoff, using the Benjamini-Hochberg procedure for multiple-hypothesis correction.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized (per million reads) bigWig files were generated using the pipelines' MACS2 output.

source_name: Prostate stromal cell

growth_protocol: Normal prostate-derived stromal cells were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 50,000 was reached in each flask.

extract_protocol:
Following an Omni-ATAC protocol, cells were trypsinized and resuspended in 1 ml cold ATAC-Seq resuspension buffer, and centrigued at 500 rcf for 5 min in a pre-chilled fixed-angle centrifuge. After centrifugation, 900 ul of supernatant was aspirated, the remaining 100 ul of supernant was carefully taken to avoid the cell pellet. Pellets were then suspended in 50 ul ATAC-Seq RSB containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin, with cell lysis incubated on ice for 3 min. After lysis, 1 ml of ATAC-Seq RSB containing 0.1% Tween-20 was added. Nuclei were then centrifuged for 10 min at 500 rcf at 4 C, with supernant removed and nuclei resuspended in 50 ul transposition mix.
Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Flex Library Prep Kit (FC-121-1030; Part# 1000000025416 v04). Briefly, nuclear pellets were subject to tagmentation by Bead-linked Transposomes (RLT), which were designed to tagment DNA with adapter sequences. Upon completion, tagmented products were cleaned up, and a pre-optimized PCR procedure was followed to amplify tagmented DNA. The resultant library of barcoded and amplified DNA was purified with a double-sided bead purification procedure. The library pool was quantified using a Bioanalyzer 2200 (Agilent) to assess size range of amplified DNA fragments and with a dsDNA fluorescent dye method, Quant-iT PicoGreen dsDNA Assay kit to quantify DNA fragments generated. ATAC libraries were pooled at equimolar concentrations and were sequenced multiplexed on the Illumina NovaSeq 6000 with 50-bp paired-ends.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To minimize the senescence-associated secretory phenotype (SASP) by a mechanism of reversing H3K36me3 decline in these senescent cells, the JMJD2 inhibitor ML324 was applied at 10 μM.

value: Normal human prostate derived primary stromal cells


title: 30 °C_rep2

city: Yangling

first: Wu

middle: bing

last: jin

state: Shaanxi

address: Litai street

institute: Northwest A&F University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to whole genome.
Raw counts and Fragments Per Kilobase Million(FPKM) were calculated by edgeR  3.24.3
Genome_build: IWGSC v1.0
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

organism: Triticum aestivum

source_name: Grains

growth_protocol: Common wheat (T. aestivum cv. Chinese Spring) were grown in a greenhouse, daily care to avoid stress. The main stem of the plant was labeled when the first flower appeared on the spike. After flowering 12 days, plants were transferred to growth chambers with a temperature regime of 20 °C (14/10 h) day/night cycle for three days adaptation, which has the same anthesis and in good condition.

extract_protocol:
After collected, the ovarian granulosa cells were put in liquid nitrogen quickly, and preserved in low temperature environment. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from granulosa cells following a manufacturer’s protocol. Total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running an 1% agarose gel electrophoresis, stained with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All plants were divided into three groups (about 50 plants), two groups were quickly shifted to the incubators which pre-heated to 30 °C and 40 °C respectively, the other one remained 20 °C as control. The grains on the main stem were collected at the same time after been exposed to three temperature environments for 1 h (in light), immediately frozen in liquid N2 and stored at -80 °C freezer for transcriptomic and proteomic analysis.

tag: tissue

value: Grains

tag: cultivar

value: Chinese Spring

value: filling stage

value: 30 °C heat stress


title: 3--1: BLEO/ML324 01

tag: passage


title: mESC_Sall4_ChIPSeq

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using deeptools; Scores is calculated as the number of reads per bin, where bins are short consecutive counting windows of a defined size.

source_name: mES cells

growth_protocol: mESCs were maintained feeder free with N2B27+2i medium (Knockout/DMEM, DMEM, N2, B27, NEAA, GlutaMAX, β-ME, PD0325901, Chir99021, LIF).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: mouse embryonic stem (mES) cells

tag: chip antibody

value: SALL4 (abcam, ab29112)


title: 1--3: CTRL 03


title: 20 °C_rep3

tag: developmental stage


title: 1--2: CTRL 02

tag: cell type


title: Isl_braLan_15hpf_4C-seq

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

institute: Max Delbrück Center for Molecular Medicine (MDC)

description: 4C-seq experiments performed using as bait the specified promoter

data_processing:
Library strategy: 4C-Seq
Demultiplexing: Different samples were demultiplexed using the primer sequences
Mapping: Reads were mapped to the Branchiostoma lanceolatum (Bl71nemr assembly) or Danio rerio (danRer7 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: Only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Data visualization: Data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7/Bl71nemr(http://amphiencode.github.io/Data/)
Supplementary_files_format_and_content: BEDGRAPH

organism: Branchiostoma lanceolatum

source_name: 15 hpf amphioxus embryos

growth_protocol: Embryos were cultivated at 19°C in filtered seawater until desired developmental stage

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

tag: 4c-seq bait

value: Isl promoter

value: whole embryos

tag: Stage

value: 15 hpf


title: 20 °C_rep2

tag: treatment

value: control


title: NFD-Liver c12

description: NFD-Liver

value: F

value: no injection

value: Normal Diet


title: 2--1: BLEO 01


title: HA-Ash2L E14 cell line HA-tag Cut & Run rep2

city: Ann Arbor

institute: University of Michigan

value: HA-Ash2L knock-in

value: Cut&Run


title: 30 °C_rep1


title: 30 °C_rep3


title: 40 °C_rep3

value: 40 °C heat stress


title: HA-Ash2L E14 cell line H3K4me3 Cut & Run rep1

value: anti-H3K4me3 (Millipore #07-473)


title: 40 °C_rep2

value: Grains


title: 3--2: BLEO/ML324 02

value: Normal human prostate derived primary stromal cells


title: parental E14 cell line HA-tag Cut & Run rep2

value: WT


title: 2--2: BLEO 02


title: HuH-7-M exosome

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: HuH-7-M derived exosome by ultracentrifugation

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: HuH-7 was cultured and maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS) and 500 µg/ml penicillin streptomycin.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: After medium was replaced with advanced DMEM medium, exosome is cllected from supernatant. The supernatant was filtered with a 0.22-mm Stericup and ultracentrifuged at 110,000g for 70 min at 4 ℃. The pellets were resuspended in PBS after ultracentrifugation.

value: hepatocellular carcinoma (HCC) cell line


title: 2--3: BLEO 03


title: Otx_braLan_15hpf_4C-seq

value: Otx promoter


title: HA-Ash2L E14 cell line H3K4me3 Cut & Run rep2


title: HuH-7-P exosome

source_name: HuH-7-P derived exosome by ultracentrifugation


title: RNAs from seed produced at 23°C_mature stage, Col_1

tag: ecotype

value: seed mature stage

value: growing control conditions 23°C

value: entire seed


title: 20 °C_rep1

value: Chinese Spring

value: filling stage


title: 1--1: CTRL 01


title: HEK293T_output1

status: Public on Mar 22 2021

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

data_processing:
Adapter seqeucnes were trimmed by using trim_galore
Clean reads were mapped to genome by using Bowtie2
dU sites calling was performed by VarScan.v2.4.4.jar
Supplementary_files_format_and_content: dU sites

source_name: cell line

growth_protocol: HEK293T cells were cultured in DMEM medium without sodium pyruvate (Dulbecco’s Modified Eagle Medium, HyClone) supplemented with 10% FBS (Cegrogen) and 1% penicillin/streptomycin (Genview). The cells were maintained at 37 ℃ under a humidified atmosphere containing 5% CO2.

extract_protocol:
Genomic DNA was extracted from the harvested HEK293T cells by a DNeasy® Blood & Tissue Kit according to the manufacturer’s instructions with minor change in the lysis buffer (included with kit) containing 50 µg/mL tetrahydrouridine.
The samples were performed with  NEBNext Ultra II DNA Library Prep Kit for Illumina following its manufacturer's instruction in parallel for Illumina sequencing.

treatment_protocol: Genomic DNA was extracted from the harvested HEK293T cells by a DNeasy® Blood & Tissue Kit according to the manufacturer’s instructions with minor change in the lysis buffer (included with kit) containing 50 µg/mL tetrahydrouridine. Firstly, the obtained genomic DNA was sonicated into small fragments (mainly 200-300 base pairs). Then, the fragmented DNA was subsequently annealed and treated with human apurinic/apyrimidinic (AP) endonuclease (APE 1) to remove the endogenous AP sites. The reaction mixture contained 20 µg fragmented DNA and 20 U APE 1 in 1×NEBuffer 4 containing 50 µg/mL tetrahydrouridine for 1 h at 37 °C, and APE 1 inactivation at 65°C for 20 min. Next, after purification with Micro Bio-Spin™ P-6 Gel Columns, the product was treated with 1 U Uracil DNA Glycosylase (UDG) for 1 h at 37 °C. Finally, the purified DNA and 10 mM N3-C (soluble in water, 5 µL) was added into 50 mM MES buffer (pH 6.0) at 37 °C for 6 h to yield azido-modified dU-containing genomic DNA, and labeled with DBCO-S-S-PEG3-biotin for the pull-down assay and next-generation sequencing (NGS).

value: labelling with N3-C


title: HEK293T_output2


title: HEK293T_input

treatment_protocol: Genomic DNA was extracted from the harvested HEK293T cells by a DNeasy Blood & Tissue Kit according to the manufacturer’s instructions with minor change in the lysis buffer (included with kit) containing 50 µg/mL tetrahydrouridine. Firstly, the obtained genomic DNA was sonicated into small fragments (mainly 200-300 base pairs). The fragmented DNA was subsequently annealed and treated with human apurinic/apyrimidinic (AP) endonuclease (APE 1) to remove the endogenous AP sites. Then the DNA was subjected to library construction (NEBNext Ultra II DNA Library Prep Kit for Illumina) for next-generation sequencing (NGS).


title: 40 °C_rep1


title: parental E14 cell line HA-tag Cut & Run rep1


title: BCT hColl + Dextran_RGD_1

city: Hannover

first: Monika

last: Szepes

address: Carl-Neuberg Str. 1

department: Department of Cardiac, Thoracic, Transplantation and Vascular Surgery

institute: Hannover Medical School

description:
N1631
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (version 1.3). Sequenced reads were trimmed for adaptor sequence (Trim Galore! 0.5.0), the reads were aligned (STAR2.6.1d) and RNA reads were assigned and counted (featureCounts1.6.4). Report was generated by MultiQC1.7.
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table” which was set to “Yes”.
Genome_build: Homo sapiens; Reference data coming from GENCODE (www.gencodegenes.org); Genome sequence (GRCh38.p12) - Release 29 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/GRCh38.primary_assembly.genome.fa.gz); Comprehensive gene annotation (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz).
Supplementary_files_format_and_content: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt: Tab-delimited text file includes RPKM values for each Sample.

source_name: hColl + Dextran_RGD

extract_protocol:
RNA was harvested using Trizol reagent and purified through sodium-acetate precipitation.
200 ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs).

tag: cell/tissue type

value: iPSC-CMs + human foreskin fibroblasts (ATCC-SCRC-1041) + RGD

tag: age

value: Tissue cultivation day 29

tag: batch number

tag: growth protocol

value: BCTs were prepared and cultivated as described (Dahlmann et al. 2013 Biomaterials; Halloin et al. 2019 Stem Cell Reports).


title: BCT hColl + Dextran_RGD_2

description:
N1632
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt


title: BCT hColl + Dextran_1

description:
N1628
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

source_name: hColl + Dextran

value: iPSC-CMs + human foreskin fibroblasts (ATCC-SCRC-1041)


title: BCT hColl + Dextran_RGD_3

description:
N1633
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt


title: iPSC-CM_3

description:
N1639
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

source_name: iPSC-CM

value: CMs differentiated from induced pluripotent stem cells

value: Differentiation day 27

value: CMs differentiated in suspension culture (Halloin et al. 2019 Stem Cell Reports).


title: BCT hColl + Dextran_3

description:
N1630
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt


title: WT-H4K5ac-Input

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files

organism: Arabidopsis

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
Two ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction.  Libraries were constructed by the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607), VAHTSTM DNA Adapters set3 - set6 for Illumina® (N805) and VAHTS® DNA Clean Beads (N411-02, Vazyme) according to the manufacturer’s protocol. protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

value: Young seedlings

tag: antibody

value: GFP (ab290, abcam)


title: brd1_2_13-H4K8ac-Input


title: brd1_2_13-H4K5ac-Input


title: iPSC-CM_2

description:
N1638
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

value: Differentiation day 29


title: BCT hColl + Dextran_2

description:
N1629
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt


title: WT-H4K8ac-IP-bio2


title: brd1_2_13-H4K8ac-IP-bio1


title: WT-H4K8ac-Input


title: WT-H4K5ac-IP-bio2


title: brd1_2_13-H4K5ac-IP-bio2


title: brd1_2_13-H4K8ac-IP-bio2


title: WT-H4K5ac-IP-bio1


title: WT-H4K8ac-IP-bio1


title: iPSC-CM_1

description:
N1634
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

value: Differentiation day 10


title: *AB wildtype zebrafish-M.marinum granuloma cells

city: Durham

first: David

middle: M

last: Tobin

state: NC

address: 304 Research Drive, 207A Jones Building

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
10X Cell Ranger was used to demultiplex raw base call (BCL) files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96, performed filtering, barcode and UMI counting.
Genome_build: GRCz11.96
Supplementary_files_format_and_content: WTGran.matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Mus musculus Uninjured Control & Injured(1d)  tibialis anterior muscle cells. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.

source_name: WT Zebrafish granuloma cels

growth_protocol: Adult, wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.

extract_protocol:
Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA
Library preparation was done using Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v3.

value: Granulomas

value: Granuloma cells

tag: zebrafish strain

value: *AB


title: brd1_2_13-H4K5ac-IP-bio1


title: iPSC_3

description:
N1637
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

source_name: iPSC

value: Undifferentiated iPSC (MHHi001-A)

value: passage 20 (on feeder) + 10 (monolayer)

value: Undifferentiated cells generated and cultivated as described (Haase et al. 2017 Stem Cell Res.)


title: iPSC_2

description:
N1636
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

value: passage 20 (on feeder) + 9 (monolayer)


title: RS Rb Hi-C

city: Cerdanyola del Vallès (Bellaterra)

first: Covadonga

last: Vara

state: Barcelona

address: Campus UAB

department: Biologia cel·lular, Fisiologia i Immunologia

country: Spain

institute: Universitat Autònoma de Barcelona

data_processing:
Reads were quality-checked and filtered using BBDuk version10/2015 and then aligned using TADbit version 0.2.0.23. Data was binned and normalised using an in-house script taht read the map files generated after filtering, obtaining matrix that were stored into a file in NPZ format (raw).
Genome_build: mm10
Supplementary_files_format_and_content: h5 format containing Hi-C matrix

organism: Mus musculus domesticus

source_name: Testis germ cells

extract_protocol:
Enriched cell populations were processed following the in situ Hi-C protocol described by Rao et. al 2014.
Hi-C libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Wild mice (domesticus)

tag: diploid number

value: Testis germ cells


title: PD Rb Hi-C

tag: tissue


title: Fibroblast Rb Hi-C

source_name: Fibroblasts

value: Fibroblasts


title: Cebpap30/p30 cells - RNA shRen rep2 [RNA_shCebpa_2]

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

description: processed data file: rna_expression_file_shRen_shCebpa.txt

data_processing:
ChIP-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Alignment against the mouse reference genome (mm10) with BWA (version 0.7.15-r1140) and further processing with SAMtools (version 1.4).
Peaks were called with MACS2 (version 2.1.0)
Differential ChIP-seq analysis with DiffBind (version 2.16.0)
Differential ChIP-seq analysis was performed with an in-house script applying a sliding window approach (available on request) using csaw (version 1.20.0) and edgeR
Peaks were annotated using HOMER (version 4.9.1)
Further characterization and visualization of called peaks was done with ChIPseeker (version 1.22.1) for the binding sites and with deepTools (version 3.0.2-1-ac19361)
ATAC-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Alignment against the mouse reference genome (mm10) with BWA (version 0.7.15-r1140) and further processing with SAMtools (version 1.4).
Peaks were called with MACS2 (version 2.1.0)
Further characterization and visualization of called peaks was done with ChIPseeker (version 1.22.1) for the binding sites and with deepTools (version 3.0.2-1-ac19361)
RNA-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Splicing aware alignment against the mouse reference genome (mm10) was done with STAR (version 2.5.0b)
Counts per gene were obtained with featureCounts (version 1.6.0)
Differential expression analysis was performed with DESeq2 (version 1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content:
ChIP-seq: bigWig files hold coverage information for the C/EBPa-ChIP with sh Cebpa knock-down, control (Ren) and respective input-controls (IN)
ChIP-seq: bigWig files hold coverage information for the H3K27ac-ChIP with sh Cebpa knock-down, control (Ren) and respective input-controls (IN)
ATAC-seq: bigWig files hold coverage information for the three p30/p30 replicates
SRNA-seq: The tab-delimited text file includes the normalized gene expression for the sh knock-down of Cebpa and control (shRen)

source_name: Cebpap30/p30 cells - RNA shRen

growth_protocol: Cells are grown in RPMI supplemented with 10 % FCS and 2 mM glutamine, 100 U/ml penicillin and   100 µg/ml streptomycin and IL-3 (5ng/ml).

extract_protocol:
Total RNA for RNA-seq was isolated using the RNeasy Mini Kit (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Indicated samples were treated with Doxycyline (1µg/mL) 48 hrs prior to harvest for sequencing.

tag: cell line

value: myeloid progenitor cell model for p30-driven AML

tag: strain background

value: 48 hrs of Doxycycline-treatment


title: Cebpap30/p30 cells - RNA shRen rep3 [RNA_shCebpa_3]


title: Cebpap30/p30 cells - RNA shRen rep3 [RNA_shRen_3]


title: Cebpap30/p30 cells - RNA shRen rep2 [RNA_shRen_2]


title: Cebpap30/p30 cells - RNA shRen rep1 [RNA_shRen_1]


title: iPSC_1

description:
N1635
processed data file: N1628-N1639_AllTreated_vs_AllControls_DESeq2_result.txt

value: passage 20 (on feeder) + 7 (monolayer)


title: BSPCR_ZFSss_fwa_drm12

city: Haining

first: Wanlu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description:
BS-PCR over FWA in ZFSssI_in_fwa_drm1_drm2_region1to3
PCR amplified DNA

data_processing:
BS-PCR-seq analysis was conducted as previously described (Gallego-Bartolome et al., 2019). Briefly, raw sequencing reads with designed BS-PCR primers were first filtered and trimmed based on the primer sequence with customized scripts. Trimmed reads were then mapped to the reference TAIR10 genome with BSMAP (Xi et al., 2009) (v.2.74) by allowing maximal two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described 19. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were excluded for further analysis. To visualize the BS-PCR-seq data, only cytosines within amplified regions were kept and plotted with R (ggplot2 package, https://ggplot2.tidyverse.org/).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text

growth_protocol: Plant materials  All plants in this study were grown under long-day conditions (16 h light/8 h dark). The fwa-4 mutant has been described previously (Johnson et al.,2014), as have the fwa nrpd1, fwa drm1 drm2 and fwa nrpe1 lines (Gallego-Bartolome et al., 2019). The pMDC123-ZF-3xFLAG-SssI plasmid was transformed into Agrobacterium AGLO and transformed into the different backgrounds by Agrobacterium-mediated floral dipping. T1 transgenic plants were grown on 1/2 MS medium + Glufosinate 50 μg/mL (Goldbio) in growth chambers under long-day conditions and transplanted to soil. The selection of transgenic lines for experiments was based on i) early flowering T1 plants for the lines in the fwa backgrounds and  ii) protein expression by WB for the lines in the Col-0 background. Following transgenic generations were germinated directly on soil and presence of the transgene was done by genotyping. Plants were not selected for homozygocity except for the T4 populations used for the ChIP experiment. Controls in this study correspond to untransformed plants of the different backgrounds used coming from the same seed stock. Flowering time was scored by counting the total number  rosette and caulinar leaves. In the flowering time dot plots, each dot represents the flowering time of individual plants. Plants with 20 or fewer leaves were considered early flowering. The samples used for all our genomics data correspond to inflorescence tissue collected during the day.

extract_protocol:
BS-PCR-seq was performed as previously described (GallegoBartolome et al., 2019). Briefly, leaf tissues from adult plants of representative T2 lines containing the ZF-SssI transgene were collected and DNA was extracted following a CTAB-based method. Bisulfite conversion was done using the Epitect Bisulfite Conversion kit (QIAGEN). The following regions of FWA were analyzed: Region 1 (chr4: 13038143-13038272); Region 2 (chr4: 13038356-13038499); Region3 (chr4: 13038568-13038695), which cover fragments of the promoter and 5′ transcribed region of FWA. Pfu Turbo Cx (Agilent) was used to amplify bisulfite-treated DNA using primers containing Illumina adaptors. The primers used are listed in Table S1.
For each sample, individual PCR products from each of the three FWA regions were pooled and purified using AMPure beads (Beckman Coulter) before making the libraries. Libraries were made from purified PCR products using a TruSeq Nano DNA Library Prep kit for Neoprep automated library preparation machine (Illumina), a Kapa DNA hyper kit (Kapa Biosystems) with Illumina TruSeq DNA adapters or an Ovation Ultralow V2 kit (NuGEN). Libraries were sequenced on Illumina HiSeq 2000 or HiSeq 2500.

tag: library type

value: BSPCR-seq

value: inflorescence

tag: genotype

value: Columbia 0


title: BSPCR_ZFSssI_fwa_nrpe1

description:
BS-PCR over FWA in ZFSssI_in_fwa_nrpe1_region1to3
PCR amplified DNA


title: Cebpap30/p30 shCebpa cells - H3K27ac rep2 [H3K27ac_shCebpa_2]

source_name: Cebpap30/p30 shCebpa cells - H3K27ac

tag: cell type

tag: chip antibody

value: anti-H3K27ac (abcam, Cambridge, UK, ab4729)


title: Cebpap30/p30 shRen cells - C/EBPa rep1 [C/EBPa_shRen_1]

source_name: Cebpap30/p30 shRen cells - C/EBPa

tag: treatment

value: anti-C/EBPα (Santa Cruz, Dallas, Texas, USA, sc-9314)


title: Cebpap30/p30 shCebpa cells - C/EBPa rep1 [C/EBPa_shCebpa_1]

source_name: Cebpap30/p30 shCebpa cells - C/EBPa


title: Cebpap30/p30 shRen cells - C/EBPa rep1 input [C/EBPa_shRen_1_IN]


title: Cebpap30/p30 shRen cells - H3K27ac input [H3K27ac_shRen_IN]


title: Cebpap30/p30 shCebpa cells - H3K27ac  rep1 [H3K27ac_shCebpa_1]


title: Cebpap30/p30 shRen cells - C/EBPa rep2 [C/EBPa_shRen_2]


title: STIM1 KO_KO3 (Replicate3)

city: Bangalore

first: Gaiti

last: Hasan

state: Karnataka

address: GKVK Campus, Bellary Road

department: Laboratory of Intracellular calcium signaling

country: India

institute: National Centre for Biological Sciences

data_processing:
Basecalling was performed using Illumina Real-Time Analysis Software version 1.18.66.3
Reads (FASTQ sequences) obtained after sequencing were aligned to the annotated UCSC Mus musculus genome  (GRCm38/mm10) using Tophat (Version-2.0.13)
Read counts for each transcript were calculated using the Python based package HTSeq (Version 0.9.1)
Read counts obtained were then used as inputs for the differential analysis with DESeq and EdgeR.
Genome_build: UCSC Mus musculus genome  (GRCm38/mm10)
Supplementary_files_format_and_content: Raw read counts in .txt format for each sample. Differential Expression result by EdgeR and DESeq are given as supplementary files in .txt format.

source_name: Purkinje neurons

growth_protocol: Purkinje neurons (Purkinje neuron layer and molecular layer) were microdissected from the cerebellum of wild type and STIM1 knock out mice of 1 year old.

extract_protocol:
Total RNA was isolated from the purkinje neuronal layer alongwith with the molecular layer using TRIzol as per manufacturer’s instructions. The isolated RNA was run on a Bio-analyzer chip to ensure integrity.
Approximately 500 ng of total isolated RNA with an average RIN of 8.2 was used per sample to prepare libraries using TruSeq mRNA Library Prep Kit following manufacturer’s instructions. The prepared libraries were run on a DNA chip in the bio-analyzer to check for their size followed by its quantification using qPCR. The libraries were then run on an Illumina Hiseq 2500 platform using single end and 50 bp read protocol (NGS Facility, NCBS).

treatment_protocol: Microdissected Purkinje neurons (Purkinje neuron layer and molecular layer) from wild type and STIM1 knockout mice was used for RNA isolation.

value: Purkinje cells (Purkinje neuron layer + molecular layer)

value: cerebellum (Purkinje neuron layer + molecular layer)

value: STIM1 Knockout

value: 1 year


title: Cebpap30/p30 shRen cells - C/EBPa rep2 input [C/EBPa_shRen_2_IN]


title: Cebpap30/p30 shRen cells - H3K27ac rep1 [H3K27ac_shRen_1]

data_processing:
ChIP-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Alignment against the mouse reference genome (mm10) with BWA (version 0.7.15-r1140) and further processing with SAMtools (version 1.4).
Peaks were called with MACS2 (version 2.1.0)
Differential ChIP-seq analysis with DiffBind (version 2.16.0)
Differential ChIP-seq analysis was performed with an in-house script applying a sliding window approach (available on request) using csaw (version 1.20.0) and edgeR
Peaks were annotated using HOMER (version 4.9.1)
Further characterization and visualization of called peaks was done with ChIPseeker (version 1.22.1) for the binding sites and with deepTools (version 3.0.2-1-ac19361)
ATAC-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Alignment against the mouse reference genome (mm10) with BWA (version 0.7.15-r1140) and further processing with SAMtools (version 1.4).
Peaks were called with MACS2 (version 2.1.0)
Further characterization and visualization of called peaks was done with ChIPseeker (version 1.22.1) for the binding sites and with deepTools (version 3.0.2-1-ac19361)
RNA-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Splicing aware alignment against the mouse reference genome (mm10) was done with STAR (version 2.5.0b)
Counts per gene were obtained with featureCounts (version 1.6.0)
Differential expression analysis was performed with DESeq2 (version 1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content:
ChIP-seq: bigWig files hold coverage information for the C/EBPa-ChIP with sh Cebpa knock-down, control (Ren) and respective input-controls (IN)
ChIP-seq: bigWig files hold coverage information for the H3K27ac-ChIP with sh Cebpa knock-down, control (Ren) and respective input-controls (IN)
ATAC-seq: bigWig files hold coverage information for the three p30/p30 replicates
RNA-seq: The tab-delimited text file includes the normalized gene expression for the sh knock-down of Cebpa and control (shRen)

source_name: Cebpap30/p30 shRen cells - H3K27ac


title: Cebpap30/p30 shCebpa cells - C/EBPa rep1 input [C/EBPa_shCebpa_1_IN]


title: STIM1 KO_KO2 (Replicate2)


title: Cebpap30/p30 shRen cells - H3K27ac rep2 [H3K27ac_shRen_2]


title: BSPCR_ZFSssI_fwa

description:
PCR amplified DNA
BS-PCR over FWA in ZFSssI_in_fwa_region1to3

data_processing:
Library strategy: BSPCR-seq
BS-PCR-seq analysis was conducted as previously described (Gallego-Bartolome et al., 2019). Briefly, raw sequencing reads with designed BS-PCR primers were first filtered and trimmed based on the primer sequence with customized scripts. Trimmed reads were then mapped to the reference TAIR10 genome with BSMAP (Xi et al., 2009) (v.2.74) by allowing maximal two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described 19. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were excluded for further analysis. To visualize the BS-PCR-seq data, only cytosines within amplified regions were kept and plotted with R (ggplot2 package, https://ggplot2.tidyverse.org/).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
WGBS analysis was performed as previously described (Gallego-Bartolome et al.,2019). Raw reads were first aligned to the reference TAIR10 genome using BSMAP (Xi  et al., 2009) (v2.74) by allowing up to two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described (Cokus  et al.,2008). Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between ZF-SssI and Col-0 were defined similar to before using the R package DMRcaller (Gallego-Bartolome et al.,2019). To increase coverage for DMR analysis, biological replicates were merged for each genotype (ZF-SssI + and ZF-SssI -), each generation (T2 to T5) and each transgenic lines (line 1 and line 2). In general, the whole TAIR10 genome was divided into 200 bp bins, and only bins with at least four cytosines, with each cytosine covered at least four times, more than 10% more methylation in ZF-SssI than Col-0, and a significance level of less than 0.05 were kept. To define hCG DMRs for T2 and T3, the intersect hCG DMRs of two transgenic lines in each generation were first calculated, then the union set of T2 and T3 in the same genotype (either ZF-SssI + or ZF-SssI -) were kept. DMRs overlapping with 200 bp bins in each cluster were considered as DMRs specific for certain clusters. Genomic location for DMRs and mCG equivalent control were annotated using the Homer (Heinz  et al.,2010) ‘annotatePeaks’ function with default parameters. For T4 and T5, two transgenic lines were separated in order to trace the heritable hCG DMRs. To define heritable hCG DMRs, T2 ZF-SssI – were compared with T2 ZF-SssI + and the shared hCG DMRs were considered as heritable hCG DMRs in T2 ZF-SssI –. For T3 ZF-SssI + and ZF-SssI -, hCG DMRs were overlapped with T2 ZF-SssI +. For T4 ZF-SssI – heritable hCG sites, DMRs were first intersected with T3 ZF-SssI + and then intersected with T2 ZF-SssI + while T5 ZF-SssI – heritable hCG sites were further intersected with T4 ZF-SssI – hCG DMRs.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al., 2019, Buenrostro et al., 2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmead et al., 2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al., 2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al., 2014) or deepTools (Ramirez et al., 2014).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
For ChIP-seq data, raw reads were first mapped to the reference TAIR10 genome with Bowtie (Langmead et al.,2009) (v0.12.8) by allowing uniquely mapped reads and maximal two mismatches. PCR-duplicated reads were then filtered with SAMTools (Li  et al.,2009) (v 1.19) . To call ZF-SssI FLAG peaks, the MACS2 calldiff function (Zhang et al.,2008) (v 2.1.2) was used to compare ZF-SssI FLAG ChIP-seq and Col-0 FLAG ChIP-seq data with default parameters. Genomic location and enriched motifs of ZF-SssI FLAG-specific peaks were then annotated with Homer (Heinz et al.,2010) ‘annotatePeaks’ and ‘findMotifGenome’ functions using 100 bp flanking the summit of the peaks. Promoter regions were defined as default in homer (upstream 1kb and downstream 100bp of TSS). ChIP-seq data visualizations were performed using ngs.plot (Shen  et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al.,2019, Buenrostro et al.,2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmeadet al.,2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al.,2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

tag: ecotype


title: Wild type_WT1 (Replicate1)

value: Wild type


title: Wild type_WT2 (Replicate2)


title: STIM1 KO_KO1 (Replicate1)


title: Cebpap30/p30 cells - RNA shRen rep1 [RNA_shCebpa_1]


title: Cebpap30/p30 shCebpa cells - C/EBPa rep2 input [C/EBPa_shCebpa_2_IN]


title: Cebpap30/p30 shCebpa cells - H3K27ac input [H3K27ac_shCebpa_IN]


title: Cebpap30/p30 shCebpa cells - C/EBPa rep2 [C/EBPa_shCebpa_2]


title: Vehicle_SWR_J

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description: PolyA RNA

data_processing:
Reads were quantified against mouse transcriptome reference from GRCm38.p6 (Ensembl release 97) with 100 bootstrap replicates using kallisto v0.46.
Differential expression was performed using sleuth (v 0.30).
Gene counts and TPM values were tabulated with tximport.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *.txt files are tab-delimited text containing either gene counts or gene TPMs.
Supplementary_files_format_and_content: *.h5 files are HDF5 files generated by kallisto containing pseudo alignment counts and bootstrapping estimates for analysis with sleuth R package.

source_name: liver

extract_protocol:
Total RNA from mouse liver samples (one mouse per strain) was purified using the Qiagen miRNeasy kit (Qiagen cat#217004) per the manufacturer’s instructions.
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation protocol.
Paired-end mode to a length of 2x76 base pairs using the Illumina HiSeq2500 platform.

treatment_protocol: CCl4 was administered intraperitoneally at a dose of 5 microliters of 10% solution in olive oil (both CCl4 and olive oil from Sigma-Aldrich, St. Louis, MO) per gram of body weight. CCl4 injections were started at 10-12 weeks age and given twice weekly for 6 weeks. Olive oil was used for vehicle-injected mice. Mice were sacrificed 72 hours after the final injection and their livers were harvested for RNA (snap-frozen) and histology (formalin-fixed and paraffin-embedded).

value: SWR/J

value: Liver

value: Vehicle


title: CCl4_SM_J

description: PolyA RNA

value: SM/J


title: Vehicle_SJL_J

description: PolyA RNA

value: SJL/J


title: Vehicle_SM_J

description: PolyA RNA


title: CCl4_SWR_J

description: PolyA RNA


title: Wild type_WT3 (Replicate3)


title: Vehicle_SEA_GnJ

description: PolyA RNA

value: SEA/GnJ


title: CCl4_SJL_J

description: PolyA RNA


title: Vehicle_RIIIS_J

description: PolyA RNA

value: RIIIS/J


title: CCl4_NZB_BlNJ

description: PolyA RNA

value: NZB/BlNJ


title: Vehicle_NZW_LacJ

description: PolyA RNA

value: NZW/LacJ


title: CCl4_NZW_LacJ

description: PolyA RNA


title: CCl4_NON_ShiLtJ

description: PolyA RNA

value: NON/ShiLtJ


title: Vehicle_NOD_ShiLtJ

description: PolyA RNA

value: NOD/ShiLtJ


title: Vehicle_PL_J

description: PolyA RNA

value: PL/J


title: Vehicle_MA_MyJ

description: PolyA RNA

value: MA/MyJ


title: CCl4_RIIIS_J

description: PolyA RNA


title: CCl4_MA_MyJ

description: PolyA RNA


title: Vehicle_KK_HlJ

description: PolyA RNA

value: KK/HlJ


title: CCl4_LG_J

description: PolyA RNA

value: LG/J


title: CCl4_PL_J

description: PolyA RNA


title: CCl4_KK_HlJ

description: PolyA RNA


title: Vehicle_I_LnJ

description: PolyA RNA

value: I/LnJ


title: CCl4_NOD_ShiLtJ

description: PolyA RNA


title: Vehicle_NON_ShiLtJ

description: PolyA RNA


title: Vehicle_FVB_NJ

description: PolyA RNA

value: FVB/NJ


title: Vehicle_LG_J

description: PolyA RNA


title: CCl4_SEA_GnJ

description: PolyA RNA


title: CCl4_I_LnJ

description: PolyA RNA


title: Vehicle_NZB_BlNJ

description: PolyA RNA


title: CCl4_DBA_2J

description: PolyA RNA


title: CCl4_FVB_NJ

description: PolyA RNA


title: Vehicle_DBA_2J

description: PolyA RNA


title: Vehicle_CXB8_HiAJ

description: PolyA RNA


title: CCl4_LP_J

description: PolyA RNA

value: LP/J


title: Vehicle_CXB7_ByJ

description: PolyA RNA

value: Liver


title: Vehicle_CXB9_HiAJ

description: PolyA RNA

value: Vehicle


title: CCl4_CXB7_ByJ

description: PolyA RNA


title: Vehicle_CXB6_ByJ

description: PolyA RNA


title: CCl4_CXB4_ByJ

description: PolyA RNA


title: Vehicle_CXB4_ByJ

description: PolyA RNA


title: Vehicle_CXB3_ByJ

description: PolyA RNA


title: Vehicle_CXB13_HiAJ

description: PolyA RNA


title: CCl4_CXB3_ByJ

description: PolyA RNA


title: Vehicle_CXB2_ByJ

description: PolyA RNA


title: CCl4_CXB2_ByJ

description: PolyA RNA


title: CCl4_CXB11_HiAJ

description: PolyA RNA


title: CCl4_CXB6_ByJ

description: PolyA RNA


title: CCl4_CXB12_HiAJ

description: PolyA RNA


title: Vehicle_LP_J

description: PolyA RNA


title: Vehicle_CXB1_ByJ

description: PolyA RNA


title: Vehicle_CXB12_HiAJ

description: PolyA RNA


title: Vehicle_CXB11_HiAJ

description: PolyA RNA


title: CCl4_CXB1_ByJ

description: PolyA RNA


title: Vehicle_CE_J

description: PolyA RNA

value: CE/J


title: CCl4_CXB8_HiAJ

description: PolyA RNA


title: CCl4_CE_J

description: PolyA RNA


title: Vehicle_CBA_J

description: PolyA RNA

value: CBA/J


title: CCl4_CBA_J

description: PolyA RNA


title: CCl4_C58_J

description: PolyA RNA


title: Vehicle_C57L_J

description: PolyA RNA


title: CCl4_C57L_J

description: PolyA RNA


title: Vehicle_C57BLKS_J

description: PolyA RNA


title: CCl4_CXB13_HiAJ

description: PolyA RNA


title: Vehicle_C57BL_6J

description: PolyA RNA


title: CCl4_CXB9_HiAJ

description: PolyA RNA


title: CCl4_C57BLKS_J

description: PolyA RNA


title: Vehicle_C3H_HeJ

description: PolyA RNA


title: CCl4_BXH6_TyJ

description: PolyA RNA


title: CCl4_C3H_HeJ

description: PolyA RNA


title: Vehicle_BXH6_TyJ

description: PolyA RNA


title: Vehicle_BXH22_KccJ

description: PolyA RNA