title: ARC2 WT Rep 01

city: Toronto

first: Vanessa

last: Yoon Calvelo

state: ON

address: 661 University Avenue

department: Biochemistry

country: Canada

institute: University of Toronto

data_processing:
The first six bases were trimmed off the 5' end of each sequencing read using Trimmomatic v0.32.3
Illumina TruSeq adaptor sequence was trimmed off the 3' end of each sequencing read using Trimmomatic v0.32.3
Sequencing reads were aligned to Streptomyces coelicolor A3(2) reference genome (GenBank accession: NC_003888.3) using Bowtie2 v2.2.6.2
Mapped reads were counted using HTSeq v0.6
Differential gene expression analysis of the count data was performed using DESeq2 v2.11.38
Genome_build: Streptomyces coelicolor A3(2) - GenBank accession: NC_003888.3
Supplementary_files_format_and_content: htseq-count tabular files containg aligned read counts
Supplementary_files_format_and_content: DESeq2 tabular file containing differentially expressed features from count tables

organism: Streptomyces coelicolor

source_name: Bacterial cells

growth_protocol: Starter cultures of Streptomyces coelicolor M145 were grown for 8 hours, then exposed either treatment or control conditions. The cells were then grown for 10 hours prior to RNA extraction.

extract_protocol:
Total RNA was extracted from Streptomyces coelicolor cells using a modified version of the Kirby procedure (Kirby et al., 1967), using phenol:chloroform:isoamyl alcohol.
RNA library was constructed by the Farncome Metagenomics Facility, McMaster University.

treatment_protocol: Two biological replicate cultures of Streptomyces coelicolor were treated with the control solvent DMSO and two biological replicate cultures of Streptomyces coelicolor were treated with the ARC2 small molecule.

tag: treatment

value: ARC2 small molecule


title: ARC2 WT Rep 02

status: Public on Feb 26 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: strain


title: DMSO WT Rep 02

value: DMSO solvent control


title: CUcovID_0091

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

country: USA

description:
globin-depleted, poly(A)+ RNA from whole blood
Counts_for_GEO.txt.gz
FPKMs_for_GEO.txt.gz

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Universal Plus mRNA-Seq with NuQuant, Human Globin AnyDeplete (Tecan). Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the Genomics Shared Resource at the University of Colorado Anschutz Medical Campus.

tag: tissue

value: whole blood

tag: Sex

value: Male

tag: age

tag: sars-cov2 status

value: Negative

tag: library type

value: strand-specific


title: ChIPseq_H4K20me1_TX1072_8h_Dox_Rep2

city: Leuven

first: Aurélie

last: Bousard

address: Herestraat 49, bus 912

country: Belgium

institute: VIB/KULeuven

library_source: genomic

data_processing:
Adapters and low quality bases (< Q20) have been removed with TrimGalore (v0.4.4; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and Cutadapt (1.12) {Martin et al, 2011}. Moreover, for PE150 samples, last 50 pb were trimmed to allow unbiased comparison of the data with PE100 samples.
An ‘N-masked” genome has been generated with SNPSplit (0.3.2) {Krueger, 2016 #2319} which is a version of the mouse reference genome mm10 where all the polymorphic sites for the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 are masked by ambiguity nucleobase ‘N’. For all samples, reads were then mapped to the ‘N-masked” genome with STAR (2.5.3a) with options [--outFilterMultimapNmax 1 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.03 --alignIntronMax 1 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD] (Dobin et al., 2013)}.
Duplicates were discarded with Picard MarkDuplicates (1.65) with options [REMOVE_DUPLICATES = true] (https://broadinstitute.github.io/picard/) and reads mapped on blacklisted regions from Encode Consortium were discarded.
SNPSplit (0.3.2) {Krueger et al, 2016} was then used to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST and B6) based on SNPs information downloaded from Sanger.
Bigwig files were created with bedtools genome CoverageBed (2.27.1) {Quinlan et al, 2010}, using a scale factor calculated on the total library (10.000.000/total reads) for both allele specific bigwigs, and loaded on UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: TX1072 ESC lines were cultured on gelatine-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% foetal bovine serum, 2-mercaptoethanol (0.1mM), LIF(1000u/mL) and 2i (PD0325901 [0.4 mM], CHIR99021 [3 mM]). Cells were incubated at 37°C with 8% CO2. After 24hrs of culture in DMEM/15%FCS+LIF+2i the medium was supplemented with doxycycline (1ug/ml).

extract_protocol:
Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted.
Native ChIP-seq was performed as previously described {Zylicz, 2019}. Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted. Typically, 10 mln cells were used per immunoprecipitation (IP). A fraction of cells was always used for RNA/FISH verification of Xist induction. Cell pellet was resuspended in 90 μL (per 10 mln cells) of Lysis Buffer (50 mM Tris-HCl, pH7.5; 150mM NaCl; 0.1% sodium deoxycholate; 1% Triton X-100; 5mM CaCl2; Protease Inhibitor Cocktail; 5 mM sodium butyrate). After lysing cells on ice for 10 min we added 62 μL (per 10 mln cells) of Lysis Buffer with MNase (500 μL buffer + 0.5 μL MNase). Chromatin was digested for exactly 8 min at 37°C and reaction was stopped by the addition of 20 mM EGTA. To remove undigested debris the lysates were centrifuged at 13000 rpm for 5 min at 4°C. Supernatant was transferred to a fresh tube, an equal volume of STOP Buffer (50 mM Tris-HCl, pH7.5; 150mM NaCl; 0.1% sodium deoxycholate; 1% Triton X-100; 30 mM EGTA; 30 mM EDTA; Protease Inhibitor Cocktail; 5 mM sodium butyrate) was added, samples were stored on ice. 5 μL of lysate was digested in 45 μL of ProtK Digestion Buffer (20 mM HEPES; 1 mM EDTA; 0.5% SDS) for 30 min at 56°C. 50 μL of AMPure XP beads were added to the digested lysate together with 60 μL of 20% PEG8000 1.25M NaCl. After mixing the samples were incubated for 15 min at RT. Beads were separated on a magnet and washed twice with 80% Ethanol for 30sec. DNA was eluted in 12 μL of Low-EDTA TE. DNA isolated in this step was used as the input sample. The volume of each undigested lysate was adjusted to obtain 1mL per IP using a 1:1 mix of Lysis Buffer and STOP Buffer. Anti-mouse Dynabeads (25ul/IP) were washed twice in Blocking Buffer (0.5% BSA; 0.5% Tween in PBS). Beads were then resuspended in Blocking buffer and coated with antibodies for 4hrs at 4°C (H4K20me1 [0.5ug/IP], Active Motif cat. 39727). Once coated beads were magnet-separated and resuspended in 1mL of lysate. Samples were left rotating overnight at 4°C. Following day beads were magnet-separated and washed quickly with ice-cold washing buffers. IPs were washed 4-times with Low Salt Buffer, 2-times with High Salt Buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.1; 360 mM NaCl; 0.1% sodium deoxycholate) and 2-times with LiCl buffer (0.25 M LiCl; 1% NP40;1.1% sodium deoxycholate; 1 mM EDTA; 10 mM Tris-HCl pH 8.1). Prior to elution all samples were rinsed once in TE. ChIP-DNA was eluted in ProtK-Digestion buffer for 15 min at 56°C. Beads were separated and the supernatant was further digested for another 2 hr at 56°C. DNA was isolated using AMPure XP beads as described for the input sample.  For each nChIP-seq, 0.5 μL of each sample was used for qPCR validation of enrichment at control regions. 0.5 μL of input samples were also used to verify the digestion efficiency using D1000 tapestation. Remaining DNA concentration was adjusted and used for library preparation using Ovation® Ultralow Library System V2 following suppliers protocol. Amplified libraries were size-selected for dinucleotide fraction (350-600bp fragments) using agarose gel-separation and MinElute Gel Extraction Kit (QIAGEN). Sample quality was inspected using D1000 tapestation. S

value: CAST / C57BL/6

tag: cell line

tag: genotype

value: WT

tag: condition

value: 8h Dox

tag: replicate

tag: antibody


title: CUcovID_0083

institute: University of Colorado Anschutz Medical Campus


title: DMSO WT Rep 01


title: Sample_Plate11_B4

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: rawcounts_dengue_samples.txt and filtered_normalized_counts_dengue_samples.txt

data_processing:
Sequencing and mapping were controlled for quality using standard tools provided in the FastQC software.
Raw reads were mapped to the reference human genome (hg19_ens_GRCh37) using tophat 2.0.11. Read counts per gene were calculated for each sample using HTseq version 0.6.1 (only genes with the “gene_biotype” type “protein coding” were considered for quantification).
Lowly expressed genes were removed, and genes with a total number of less than 5 counts across all samples were discarded (the total number of remaining genes was 10,238). Read counts per gene were further normalised across all samples using the “trimmed mean of M-value” (TMM) approach.
Genome_build: hg19_ens_GRCh37
Supplementary_files_format_and_content: rawcounts_dengue_samples.txt: abundance measurements at the gene level for protein coding genes (HTSeq output gene counts)
filtered_normalized_counts_dengue_samples.txt: library size normalized and low expression filtered abundance measurements
metadata_dengue_samples.txt: technical covariates

source_name: dendritic cell

growth_protocol: CD14+ cells were isolated by positive selection from PBMCs using MACS CD14 microbeads (Miltenyi Biotec). PBMCs were centrifuged at 1500 rpm for 5 minutes and cell pellet. Primary human DCs or monocytes were collected in 50 ml falcon tubes, centrifuged and infected with DENV at a MOI of 1 or 5 FFU/cell, as determined based on the viral titre and number of cells, for 2 hours at 37 °C at 5% CO2. Excess DENV was washed off three times with RPMI 1640. Cells were then resuspended in R10 (5x10^5 cells/ml) and plated in 24 or 48 well plate at 37 °C, for an overnight period.  The antibody dependent enhancement assay was performed using a monoclonal antibody against the DENV precursor membrane protein prM (1H10; produced in house as described in [17]). Anti-prM antibody was diluted to a final concentration of 0.2 μg/ml in R10 in a volume of 100 μl. DENV, at (MOI 1 or 5 FFU/cell), was then mixed with the diluted antibody in a final volume of 200 μl for 1 hour at 37 °C to allow immune complex formation. After incubation, the antibody-virus mixture was added to human monocyte-derived macrophages and incubated for 2 hours at 37 °C at 5% CO2. To remove residual ICs, supernatants were discarded from the monolayer and cells were carefully rinsed 3 times with RPMI 1640 before incubating cells in R10 at 37 °C, overnight. The infection rates in macrophages and DCs were measured by flow cytometry using an antibody against DENV protein NS3, 24 hours following infection. was resuspended in 80 μl of MACS buffer with the addition of 10 μl CD14 microbeads per 107 cells. After incubation at 4 °C for 30 minutes, labelled cells were resuspended in 12 ml MACS buffer and applied onto a LS column (Miltenyi Biotec). Cells were flushed out mechanically by adding 5 ml of R10, centrifuged and resuspended in R10. The purity of CD14+ cells was determined with an anti CD14-APC antibody (BD Biosciences) by flow cytometry.  To generate monocyte derived macrophages, 7x10^6 CD14+ cells were plated in a 60mm dish and cultured in 5 ml R10 with 100 ng/ml recombinant human M-CSF (Peprotech). After 5 days, adherent cells were gently washed with RPMI 1640 and detached with cell dissociation solution non-enzymatic (Sigma-Aldrich). Cells were then resuspended in R10 and cultured at 5x10^5 cells/ml in 24 or 48 well plate for additional 24 hours at 37 °C in a 5% CO2 incubator. Monocyte-derived dendritic cells (DCs) were generated by culturing CD14+ cells in R10 (5x10^5 cells/ml) with 20 ng/ml human recombinant GM-CSF (First Link) and 25 ng/ml human recombinant IL-4 (eBioscience) for 5 to 6 days at 37 °C in a 5% CO2 incubator. On day 3, half of the culture media was carefully replaced with fresh media containing 40 ng/ml human recombinant GM-CSF and 50 ng/ml human recombinant IL-4. Immature DCs were harvested and confirmed with anti CD14-APC (BD Biosciences) and anti CD209-PE (Miltenyi Biotec) by flow cytometry.

extract_protocol:
The cDNA synthesis, labelling and subsequent hybridization were performed according to the manufacturer’s protocol using the TruSeq® Stranded mRNA Low Sample Preparation Guide (Illumina). Briefly, 500 ng total RNA was purified to obtain polyA containing mRNA using poly-T oligo attached magnetic beads. PolyA RNA was fragmented and primed with random hexamers for cDNA synthesis. After synthesis of the first strand cDNA, remaining RNA was removed and a second strand cDNA was synthesised to obtain blunt-ended double stranded cDNA.
RNA sequencing was performed using an ultra-high-throughput sequencing system HiSeq 2500 (Illumina).

treatment_protocol: Primary human DCs and macrophages were infected with DENV or IC for 6 or 24 hours. As a control, cells were treated with medium only (DCs) or anti-prM only (macrophages). After incubation time, cells were washed with warm PBS before adding 500 µl TRIzol® reagent (Invitrogen) and RNA was isolated using the RNeasy mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quantification and quality were assessed using NanoDrop 2000 and stored at -80 °C until further use.

tag: infection

value: dengue

tag: cell type

value: dendritic cell

tag: infection time (hours)

tag: treated with

tag: biological replicate


title: ChIPseq_H4K20me1_TX1072_4h_Dox_Rep2

value: 4h Dox


title: tumor - HSF1-303-7

city: New York

first: Kathryn

middle: Grace

last: Hockemeyer

state: New York

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

data_processing:
The Cell Ranger Single-Cell Software Suite (v3.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting
The cDNA insert was aligned to the mm10/GRCm38 reference genome. Only confidently mapped, non-PCR duplicates with valid barcodes and unique molecular identifiers were used to generate the gene-barcode matrix that contained 7847 and 5289 cells for HSF1-WT and HSF1-S303/7A, respectively.
Further analysis—including quality filtering, the identification of highly variable genes, dimensionality reduction, standard unsupervised clustering algorithms and the discovery of differentially expressed genes—was performed using the Seurat R package v3.0.
To exclude low-quality cells, we removed 2% cells that expressed the lowest number of genes. To exclude cells that were extreme outliers in terms of library complexity and that might possibly include multiple cells or doublets, we first calculated the distribution of genes detected per cell and removed any cells in the top 2% quantile and then calculated a doublet score per cell using doubletCells from the scran Bioconductor package (v1.12.0).
After quality filtering, 6654 and 4802 cells for HSF1WT and HSF1S303/7A, respectively, remained. After removing unwanted cells from the dataset, we normalized cell expression by the library size, multiplied by a scale factor of 10,000 and log-transformed the result.
Genome_build: mm10
Supplementary_files_format_and_content: counts-HSF1-303-7.tar.gz and counts-HSF1-WT.tar.gz are the counts for each sample produced by Cell Ranger. The counts.normalized.csv.gz consists of integrated and normalized counts after all quality filtering steps. The metadata.csv consists of the metadata, including clusters and cell types.

source_name: tumor

extract_protocol:
Tumors from HSF1S303/7A and WT mice were dissected, manually dissociated, and digested enzymatically with 0.04 U/mL Liberase TM (Sigma) and 0.15 mg/ml Dnase I (Roche) in Hank’s Balanced Salt Solution (Life Technologies) for 30 min at 37 °C with agitation. Tumors were homogenized by briefly vortexing and filtered through a 70-μm nylon filter. Single-cell suspensions were washed with 1 × PBS-4% FBS before incubation 20 min on ice at 5 × 107 cells/ml with 500 ng/ml Fc block (2.4G2, BD Pharmingen) to prevent nonspecific antibody binding. Cells were then incubated 1 h on ice with PE-eFluor610-conjugated CD45 monoclonal antibody (30-F11, eBioscience). For scRNAseq libraries, DAPI- (live) CD45+ and CD45− cells were sorted using a SY3200 flow cytometer. Sorted cells were counted, and live CD45+ and CD45− cells were mixed 5:1.
The libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v2, 10x Genomics): Single Cell 3′ Library & Gel Bead Kit v2 (PN-120237), Single Cell 3′ Chip Kit v2 (PN-120236) and i7 Multiplex Kit (PN-120262) and following the Single Cell 3′ Reagent Kits (v2) User Guide (manual part no. CG00052 Rev A).
single-cell RNA-seq


title: tumor - HSF1-WT

value: wild-type


title: Sample_Plate11_B3


title: RNA-Seq splenic NK - MUT 7

data_processing:
Reads were trimmed for adapter sequences and low-quality score bases using Trimmomatic; reads that were properly paired and had a unique alignment (mapping quality > 30) were retained
Trimmed reads were aligned to the Mus musculus genome (mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was used to to generate counts for each gene based on how many aligned reads overlapped the exons of that gene
These counts were then normalized and used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: counts.raw.csv consist of counts for each gene based on aligned reads; counts.normalized.csv consists of raw counts that have been normalized to library size

source_name: splenic NK cells

extract_protocol:
Single-cell suspension of splenocytes was enriched for NK using DX5 Microbeads (Miltenyi) before sort purification for NK cells (CD49b+,CD3e-). Each mouse served as a biological replicate. 3-5 x 10^5 NK cells from each mouse were used for isolation of total RNA using the RNeasy Plus Micro Kit (Qiagen)
Libraries were generated with the SMART-seq HT Kit (Takara Bio no. 634438)

treatment_protocol: Spleens were isolated from mice wild-type (WT) for HSF1 or those bearing serine to alanine mutations in amino acids 303 and 307 (S303/7A or MUT) under steady state conditions


title: Sample_Plate11_B2


title: ChIPseq_H4K20me1_TX1072_0h_Dox_Rep2

value: 0h Dox


title: CUcovID_0105


title: ChIPseq_H4K20me1_TX1072_24h_Dox_Rep1

value: 24h Dox


title: RNA-Seq splenic NK - MUT 6


title: Sample_Plate11_B1

source_name: macrophage

value: macrophage

value: dengue+antibody against dengue


title: CUcovID_0028

value: Female


title: ChIPseq_H4K20me1_TX1072_12h_Dox_Rep2

value: 12h Dox


title: Sample_Plate11_B5


title: Sample_Plate11_B12


title: ChIPseq_H4K20me1_TX1072_8h_Dox_Rep1


title: Sample_Plate11_B11


title: RNA-Seq splenic NK - MUT 5


title: CUcovID_0069

value: whole blood

value: Positive


title: CUcovID_0072

value: Male

value: Negative


title: CUcovID_0022

value: strand-specific


title: RNA-Seq splenic NK - WT 2


title: ChIPseq_H4K20me1_TX1072_12h_Dox_Rep1

value: CAST / C57BL/6

value: WT


title: RNA-Seq splenic NK - WT 1


title: ChIPseq_H4K20me1_TX1072_0h_Dox_Rep1


title: ChIPseq_H4K20me1_TX1072_4h_Dox_Rep1


title: Sample_Plate11_A8

value: dengue


title: CUcovID_0040


title: RNA-Seq splenic NK - WT 3


title: ATAC-Seq splenic NK - MUT 29

data_processing:
Reads were trimmed for adapter sequences and low-quality score bases using Trimmomatic; reads that were properly paired and had a unique alignment (mapping quality > 30) were retained
Trimmed reads were aligned to the Mus musculus genome (mm10/GRCm38) using the Bowtie2 aligner (v2.3.4.1)
Duplicate reads were removed using sambamba markdup.
Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm (v1.4.2) with q < 0.05
Differential peaks were called using negative binomial generalized linear models implemented by the DESeq2 analysis in the DiffBind (v3.0.12) package
Genome_build: mm10
Supplementary_files_format_and_content: Preprocessed bed files for all biological replicates consist of peaks determined algorithmicaly using MACS 2 with q < 0.05

extract_protocol:
Single-cell suspension of splenocytes was enriched for NK using DX5 Microbeads (Miltenyi) before sort purification for NK cells (CD49b+,CD3e-). Each mouse served as a biological replicate. 2 x 10^5 NK cells from each mouse were used for the ATAC-seq protocol
Assay for transposase-accessible chromatin (ATAC) and library preparation was performed as previously described (Buenrostro J.D. et al, Curr Protoc Mol Biol, 2015)


title: CUcovID_0041


title: Sample_Plate11_A7


title: ATAC-Seq splenic NK - MUT 28


title: CUcovID_0063


title: RNAseq_AGHMT_TTF

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

data_processing:
Basecalls performed using CASAVA version 1.8.2
For RNA-seq analysis,reads were aligned to the mouse reference genome  GRCm38 (mm10) using the Hisat (version 2.0.0) aligner using default settings. Aligned reads were counted using featureCounts (version 1.4.6) per gene ID. Differential gene expression analysis was done using the R package edgeR (version 3.8.6). Cutoff values of fold change >2 and FDR <0.01 were used to select for differentially expressed genes.
For ChIP-seq analysis, raw sequencing reads with > 30% nucleotide with phred quality scores < 20 were filtered. Single-end sequencing reads were then aligned to the mouse reference genome GRCm38 (mm10) using bowtie2 aligner (v 2.3.4.3) with default parameters. For transcription factor ChIP-seq data, peaks were called using HOMER software package (version 4.9) findpeaks command, with parameter ‘-style factor’, peaks were called with >2 fold enrichment over input controls and > 4 fold enrichment over local tag counts and FDR threshold was set to 10-3. For histone marker ChIP-Seq data, peaks were called by findpeaks command with parameter ‘–style histone’, peaks were called with >2 fold enrichment over input controls and > 4 fold enrichment over local tag counts and FDR threshold set to 10-3. ChIP-seq peaks within a 1000 bp range were stitched together to form broad regions. To identify differential peaks between two samples, called peaks were merged from each sample and raw read count within each peak region were calculated. Then differential peaks were identified using R package DEseq version 3.8. PHF7 peaks with > 2 fold change were designated as DE peaks.
For ATAC-Seq analysis, Paired-end raw reads were trimmed 30 bps from 3’end to remove possible adaptor sequences and mapped to the mouse reference genome (GRCh38/mm10) using bowtie2 (version 2.3.4.3) with parameter ‘–very-sensitive’ enabled. Read duplication and reads that mapped to chrM were removed from downstream analysis. For peak calling, we adopt ENCODE IDR pipeline. In brief, macs2 was used to call peaks and IDR procedure were performed to identify peaks with IDR < 0.05 as final peaks
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: Genome tracks in .bigwig format

source_name: iCLM TTFs

growth_protocol: MEFs and TTFs were isolated as previously described by Song, et al (Nature, 2012) and maintained in DMEM with 10% FBS and 1% pen-strep.

extract_protocol: For ChIP-Seq, cross-linked and fragmented genomic DNA was extracted using the ChIP-IT Highsensitivity Kit from Active Motif. For ATAC-Seq, Omni-Seq protocol was followed for 50,000 cells per sample without adaptation. For RNA Seq, extraction and isolation was performed using Trizol.

treatment_protocol: Cells were retrovirally infected with epitope tagged PHF7-3xTY1 and/or AGHMT (Akt1, Gata4, Hand2, Mef2c, and Tbx5) reprogramming cocktail and induced with cardiac reprogramming induction media as previously described in Song, et al (Nature, 2012).

value: 6-8wk tail-tip fibroblast

value: alpha-MHC-GFP+/-

tag: cell culture medium

value: Cardiac induction media

tag: treatment


title: CUcovID_0012

tag: tissue


title: ChIPseq_Day2_MEFS_AGHMT, Input

source_name: iCLM MEFs

value: E13.5-14.5 embryonic fibroblast

tag: chip antibody


title: CUcovID_0065

tag: Sex

tag: age


title: ChIPseq_Day2_5F+PHF7_3xTy1

value: anti-Ty1 antibody (Diagenode, C15200054)


title: ATAC-Seq splenic NK - MUT 27


title: ATAC-Seq splenic NK - MUT 26


title: CUcovID_0075

tag: sars-cov2 status

tag: library type


title: ATAC-Seq splenic NK - WT 7

tag: genotype

value: wild-type


title: Sample_Plate11_A5

value: macrophage

value: dengue+antibody against dengue


title: Sample_Plate11_A9


title: CUcovID_0077

value: Female


title: Sample_Plate11_A4


title: ATAC-Seq splenic NK - WT 6


title: Sample_Plate11_B10

value: dendritic cell


title: ChIPseq_Day2_PHF7


title: Sample_Plate11_A3


title: Sample_Plate11_A2


title: ATAC-Seq splenic NK - WT 5


title: RNAseq_AGHMT_PHF7_TTF


title: WT.TC_rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
CellRanger software (v3.0.2) (10X Genomics) (default parameters) mm10 genome complemented with complemented with the transgene sequences of the Ires-Gfp, Yfp, Cre.
Hashtag count matrices were obtained from CITE-Seq-Count package (https://zenodo.org/record/2590196) (default parameters).
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file with cell x genes count matrix
Supplementary_files_format_and_content: count matrix for all cells from all samples in matrix.mtx. Cell ID in barcodes.tsv. Genes in genes.tsv. Metadata (including in particular the hastag counts for each cell ID) in metadata.tsv

source_name: CD4 Tconv cell

extract_protocol:
A single cell suspension was obtained of murine splenocytes after mechanical dissociation and red blood cell lysis. Cells were stained with fluorophore-conjugated +- DNA-conjugated antibodies for cell sorting by flow cytometry and sample pooling for single cell RNAseq library construction (10x Genomics, Single Cell 3′ Reagent Kit (V2 or V3 chemistry)
RNA libraries were prepared for sequencing using standard 10X Genomics Single Cell 3′ Reagent Kit (V2 or V3 chemistry)

tag: strain

value: B6 Foxp3-IRES-GFP x CD45.1

value: Spleen

tag: groups

value: WT CD4+ Tconv cells

value: male

tag: hashid

value: Single Cell 3′ Reagent Kit (V3 chemistry)


title: WT.CD4_rep2

source_name: CD4 T cell

value: WT CD4+ T cells


title: CUcovID_0018

value: whole blood

value: Positive

value: strand-specific


title: CUcovID_0059

value: Male


title: ATAC-Seq splenic NK - WT 4


title: Sample_Plate11_A1

tag: infection

value: dengue


title: Sample_Plate11_A12

tag: cell type


title: CUcovID_0029


title: BMC.WT.CD4_rep1

value: BMC WT (B6 Foxp3-IRES-GFP x CD45.1) / deltaFoxp3 (B6 Foxp3DeltaEGFPiCre x ROSA-YFP x CD45.1/2)

value: WT CD4+ T cells in BMC

value: 16w-10w post-HSCT


title: Sample_Plate11_A6

value: macrophage

tag: infection time (hours)

value: dengue+antibody against dengue


title: CUcovID_0009

value: Female


title: BMC.WT.CD4_rep3


title: deltaFoxp3.CD4_rep2

value: B6 Foxp3DeltaEGFPiCre x ROSA-YFP

value: deltaFoxp3 CD4+ T cells


title: BMC.deltaFoxp3.CD4_rep2

value: Spleen

value: deltaFoxp3 CD4+ T cells in BMC


title: CUcovID_0071


title: CUcovID_0046


title: YKO MEF 2

city: Cologne

first: Thomas

last: MacVicar

address: Joseph-Stelzmann Str 9B

country: Germany

institute: Max Planck Institute for Biology of Ageing

data_processing:
raw reads were mapped using HISAT version 2.0.4
transcripts were assembled using StringTie version 1.3.3
differential gene expression was analyzed using cufflinks/cuffdiff version 2.2.1
Genome_build: BUILD_GRCm38_RELEASE_91
Supplementary_files_format_and_content: Tab-separated differential gene expression results

source_name: Yme1l-/- MEF

extract_protocol:
Total RNA was extracted from cells using NucleoSpin RNA (Macherey-Nagel)
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1µg  total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and Rnase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

value: SV40 immortalized mouse embryonic fibroblast


title: Sample_Plate11_A11

tag: treated with


title: Sample_Plate11_A10

tag: biological replicate


title: WT MEF 3

source_name: WT MEF

value: Yme1l fl/fl


title: YKO MEF 1


title: CUcovID_0080

value: whole blood


title: WT.TR_rep2

source_name: CD4 Treg cell

value: B6 Foxp3-IRES-GFP x CD45.1

value: WT CD4+ Treg cells

value: male

value: Single Cell 3′ Reagent Kit (V3 chemistry)


title: CUcovID_0011

value: Male

value: Positive

value: strand-specific


title: WT.TR_rep1


title: WT.TC_rep1

value: WT CD4+ Tconv cells


title: WT MEF 2


title: YKO MEF 3


title: BMC.WT.CD4_rep2

value: BMC WT (B6 Foxp3-IRES-GFP x CD45.1) / deltaFoxp3 (B6 Foxp3DeltaEGFPiCre x ROSA-YFP x CD45.1/2)

value: WT CD4+ T cells in BMC

value: 16w-10w post-HSCT


title: CUcovID_0096


title: WT MEF + Yme1l siRNA 2

extract_protocol:
Total RNA was extracted from cells using NucleoSpin RNA (Macherey-Nagel).
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1µg  total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and Rnase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

treatment_protocol: Cells were collected 72 h after transfection with the indicated siRNA.

value: 3T3 immortalized mouse embryonic fibroblast

value: WT MEF

tag: sirna


title: CUcovID_0003

value: Female


title: WT5 (16483-R2)

type: RNA

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
WT5_16483_R2

hyb_protocol: 50 ng of total RNA from each sample was hybridized for 20 hours at 65C to the CodeSet nCounter PanCancer Immune Profiling Panel, Mouse

scan_protocol: The scannning was processed on the NanoString Technologies nCounter Sprint Profiler for about 6 hours.

data_processing: We used the nSolver 4.0 software normalization module (NanoString Technologies) and NanoSstring Advanced Analysis Module 2.0

source_name: mT3-2D sc WT tumor

extract_protocol: RNA extraction was done using the PureLink RNA Mini Kit (Ambion). RNA concentration and quality were assessed using the Agilent BioAnalyzer

tag: type

value: Immunocompetent

value: mT3-2D subcutaneous WT tumor


title: BMC.deltaFoxp3.CD4_rep3

tag: tissue

value: Spleen

value: deltaFoxp3 CD4+ T cells in BMC


title: WT MEF + Yme1l siRNA 1


title: CUcovID_0045

value: whole blood


title: BMC.deltaFoxp3.CD4_rep1

value: male


title: CUcovID_0019


title: WT MEF + Scr 2

value: Scr


title: WT1 (16482-R1)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
WT1_16482 R1

source_name: mT3-2D subcutaneous (sc) WT tumor


title: deltaFoxp3.CD4_rep1

value: B6 Foxp3DeltaEGFPiCre x ROSA-YFP

value: deltaFoxp3 CD4+ T cells

value: Single Cell 3′ Reagent Kit (V3 chemistry)


title: WT MEF 1

value: SV40 immortalized mouse embryonic fibroblast

value: Yme1l fl/fl


title: WT MEF + Scr 3


title: CUcovID_0090

value: Positive

value: strand-specific


title: WT.CD4_repB

value: B6 Foxp3-IRES-GFP

value: WT CD4+ T cells

value: Single Cell 3′ Reagent Kit (V2 chemistry)


title: mT3-2D cell line 2nd replicate

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
mT3 2D_02

source_name: Murine KPC mT3-2D cell line

value: Cell line

tag: cell line


title: CUcovID_0095

tag: Sex

value: Female

value: Negative


title: WT.CD4_rep1

value: B6 Foxp3-IRES-GFP x CD45.1

value: Spleen

tag: age


title: WT MEF + Yme1l siRNA 3

value: 3T3 immortalized mouse embryonic fibroblast

value: WT MEF


title: WT3 (16483-R1)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
WT3_16483_R1

value: Immunocompetent

value: mT3-2D subcutaneous WT tumor


title: WT4 (16483-L1)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
WT4_16483_L1


title: WT MEF + Scr 1

value: Scr


title: SCID5 (11880-N)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
SCID5_11880_N

source_name: mT3-2D sc SCID tumor

value: Immunodeficient

value: mT3-2D subcutaneous subcutaneousID tumor


title: mT3-2D cell line 1st replicate

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
mT3 2D_01


title: WT.CD4_repA

value: male


title: WT2 (11878-N)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
WT2_11878_N


title: CUcovID_0031

value: whole blood

value: Male

tag: sars-cov2 status

value: strand-specific


title: deltaFoxp3.CD4_repB

value: B6 Foxp3DeltaEGFPiCre x ROSA-YFP

value: deltaFoxp3 CD4+ T cells

value: Single Cell 3′ Reagent Kit (V2 chemistry)


title: SCID3 (16487-R1)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
SCID3_16487_R1


title: SCID4 (16487-R2)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
SCID4_16487_R2


title: CUcovID_0102

value: Female

value: Positive

tag: library type


title: lepr-expressing POMC pulldown #5

first: Nasim

last: Biglari

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

description: 3 males and 3 females pooled

data_processing:
Illumina TruSeq mRNA stranded protocol and the HiSeq 4000 sequencer with a PE75 read length run
Data was processed using the nf-core/rnaseq v1.4.2 pipeline
Alignment to reference genome was done using STAR vSTAR_2.6.1d
Gene abundance estimation was done using Salmon 0.14.1
Differential gene expression analysis of IP/Input normalised gene counts was carried out using DESeq2 1.26.0
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel sheet of DESeq2 contrasts glp1r and lepr

source_name: arcuate nucleus (ARC)

extract_protocol:
Samples were homogenized in Trizol LS, extracted with Chloroform, precipitated with isopropranol, washed with 80% Ethanol, resuspende din Nuclease free water and treated with DNAse I. The TRAP technique was performed using a modified version of (Heiman et al., 2008) on hypothalami of mice described under “Study design of bacTRAP (EGFPL10a) mice”. Concentration was analyzed using QuBit/Bioanalyzer and remaining samples were stored at -80°C until sequencing.
Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input. After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System) all 24 transcriptome libraries were pooled. The pool was quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on a Illumna NovaSeq S2 flowcell with a PE100 protocol. The RNA sequencing pipeline utilizes the GRCm38 assembly of the mouse genome as gene sets from Ensembl release 96 (Yates et al., 2015).

treatment_protocol: All mice were rapidly decapitated and tissue was taken between 11-13h

tag: genotype

value: pooled male and female

value: hypothalami

tag: feeding

value: Random-fed


title: CUcovID_0086

source_name: whole blood

value: Negative


title: deltaFoxp3.CD4_repA

tag: strain

value: Spleen

tag: groups


title: lepr-expressing POMC pulldown #4

description: 3 males and 3 females pooled


title: CUcovID_0081


title: CUcovID_0082


title: Forskolin [150_6]

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Florida

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

source_name: Forskolin_Primary Hippocampal neurons

growth_protocol: Hippocampi were cultured from P0 mice for generating RNA at DIV 16.

extract_protocol:
RNA was extracted using traditional Trizol/chloroform extraction method
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD-1 IGS

value: DIV 16 neurons from P0 pups

tag: tissue/cell type

value: Primary Hippocampal neurons

tag: treatment

value: 50uM Forskolin


title: lepr-expressing POMC pulldown #2

description: 3 males and 3 females pooled


title: SCID1 (16486-R1)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
SCID1_16486_R1

value: Immunodeficient

value: mT3-2D subcutaneous subcutaneousID tumor


title: SCID2 (16486-R2)

description:
Total RNA was obtained and gene expression was measured on the NanoString nCounter Analysis System (NanoString Technologies)
SCID2_16486_R2


title: CUcovID_0056

value: whole blood

value: Male

value: strand-specific


title: lepr-expressing POMC input #5

description: 3 males and 3 females pooled


title: 9311-HS-3:  RNA-seq

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

country: China

institute: Chinese Academy of Agricultrual Sciences

data_processing:
After removing the adapter and primer sequences, low-quality reads with more than 20% low-quality bases (quality <20) were filtered out. The clean reads were mapped to reference genome by HISAT2 v 2.0.4. The gene expression level (FPKM) was calculated by StringTie v1.3.4d using default parameters. The genes that have expression values greater than 0.1 were considered as expressed. Differently expressed genes (DEGs) between mock and heat shock treatment were identified by DEseq2 package.
Genome_build: Nip-BRI, 93-11-BRI (The genome assembly and annotation could be download from the public database http://www.elabcaas.cn/rice/downloads.html <http://www.elabcaas.cn/rice/downloads.html>, which was built for Nip and 93-11.  And following link is the reference: https://www.ncbi.nlm.nih.gov/pubmed/30448535)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Oryza sativa

source_name: 3-week-old seedling

growth_protocol: Rice plants were grown on Yoshida solution in a growth chamber under short-day (SD) conditions (10 h light/14 h dark) with a light intensity of 800 μmol m-2 s-1. To test heat response, we incubated 3-week-old Nip and 93-11 seedlings grown in culture solution 45°C for 36 h in a growth chamber with high relative humidity (>80%) and low light intensity (60–80 μmol m-2 s-1).

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies). Samples were then subjected to poly(A) purification using oligo-dT beads (Life Technologies) followed by rRNA removal using Ribo-Zero Kit (Epicenter) according to the manufacturer’s instructions. RNA integrity was measured using 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).
All transcriptome libraries were constructed using the Illumina TruSeq library Stranded mRNA Prep Kit and then sequenced on the Illumina HiSeq X-ten platform.

tag: cultivar


title: lepr-expressing POMC input #4

description: 3 males and 3 females pooled


title: CUcovID_0024


title: Forskolin [150_4]


title: 9311-HS-2:  RNA-seq


title: 9311-Normal-3:  RNA-seq


title: 9311-HS-1:  RNA-seq


title: 9311-Normal-2:  RNA-seq


title: CUcovID_0088


title: lepr-expressing POMC input #2

description: 3 males and 3 females pooled


title: lepr-expressing POMC input #3

description: 3 males and 3 females pooled


title: lepr-expressing POMC pulldown #3

description: 3 males and 3 females pooled


title: CUcovID_0084


title: CUcovID_0035


title: 9311-Normal-1:  RNA-seq


title: DMSO [150_1]

source_name: DMSO_Primary Hippocampal neurons

value: DMSO


title: ATACseq_5F

tag: cell type

value: E13.5-14.5 embryonic fibroblast

value: alpha-MHC-GFP+/-

tag: cell culture medium

value: Cardiac induction media


title: Forskolin [150_5]


title: DMSO [150_3]


title: glp1r-expressing POMC pulldown #2

description: 6 males and 6 females pooled

value: pooled male and female

value: hypothalami


title: CUcovID_0002

value: Female

value: Positive


title: Nip-HS-2:  RNA-seq

value: Nipponbare


title: glp1r-expressing POMC pulldown #3

description: 6 males and 6 females pooled

value: Random-fed


title: Nip-HS-1:  RNA-seq


title: CUcovID_0070


title: glp1r-expressing POMC input #3

description: 6 males and 6 females pooled


title: CUcovID_0047


title: 67-2_S30

city: IRVINE

first: Shan

last: Jiang

address: 2300E Biological Sciences III

institute: UNIVERSITY OF CALIFORNIA, IRVINE

data_processing:
Pair-end RNA-seq reads were aligned using STAR v.2.5.1b with parameters ‘--outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.07 --outFilterMultimapNmax 10’ to the reference genome GRCm38/mm10. We used STAR to then convert to transcriptome-based mapping with gene annotation Gencode v.M8. Gene expression was measured using RSEM v.1.2.22 with expression values normalized into transcripts per million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: TXT table format; gene expression profile normalized to TPM.

source_name: Hippocampus

extract_protocol:
AUP-17-38
Total RNAs from the hippocampus were extracted by using RNeasy Mini Kit (Qiagen). RNA integrity number (RIN) was measured by Agilent 2100 Bioanalyzer and samples with RIN >= 8.0 were kept for cDNA synthesis.  cDNA synthesis and amplification were performed followed by Smart-seq2 (1) standard protocol.  Libraries were constructed by using the Nextera DNA Sample Preparation Kit (Illumina). Libraries were base-pair selected based on Agilent 2100 Bioanalyzer profiles and normalized determined by KAPA Library Quantification Kit (Illumina). The libraries were sequenced using paired-end 43bp mode on Illumina NextSeq500 platform with around 10 million reads per sample.

tag: Stage

value: F

value: hAbKI


title: glp1r-expressing POMC input #2

description: 6 males and 6 females pooled


title: Nip-Normal-3:  RNA-seq


title: 67-0_S29


title: Nip-Normal-2:  RNA-seq


title: CUcovID_0087


title: glp1r-expressing POMC input #1

description: 6 males and 6 females pooled


title: 66-2_S26

value: M


title: Nip-Normal-1:  RNA-seq


title: ATACseq_5F_PHF7


title: CUcovID_0039

value: Negative


title: CUcovID_0089

value: whole blood


title: 85A-7_S31


title: 66-0_S25


title: CUcovID_0049

value: Male


title: glp1r-expressing POMC pulldown #1

description: 6 males and 6 females pooled


title: HS_Rep2 93-11 HiC

data_processing:
Mapping of Hi-C reads and assignment to restriction fragments were performed as previous described (Burton et al., 2013). Briefly, adapter sequences of raw reads were trimmed with cutadapt v1.0, and low-quality paired-end (PE) reads were removed for raw data processing. The clean Hi-C reads were mapped to reference genome using bwa align v0.7.10 (Li and Durbin, 2009) with default parameters. For each rice cultivar, the unique mapping data were retained to identify valid chromatin interactions by filtering reads from dangling-end and self-ligation products. Duplicate removal, sorting, and quality assessment were performed with HiC-Pro v2.8.1(Servant et al., 2015) with command of “mapped_2hic_fragments.py -v -S -s 100 -l 1000 -a -f -r -o”. Raw counts of Hi-C links were aggregated in 10-kb bins and normalized separately for intra- and inter- chromosomal contacts using HiC-Pro v2.8.1 with default settings.
Genome_build: Nip-BRI, 93-11-BRI (The genome assembly and annotation could be download from the public database http://www.elabcaas.cn/rice/downloads.html <http://www.elabcaas.cn/rice/downloads.html>, which was built for Nip and 93-11.  And following link is the reference: https://www.ncbi.nlm.nih.gov/pubmed/30448535)
Supplementary_files_format_and_content: Bed files include Hi-C cotact position information

extract_protocol: 2 g aerial parts of the rice seedlings were fixed with formaldehyde, and lysed and grounded into powder in liquid nitrogen. The procedure for the Hi-C experiment, including chromatin digestion, labelling of DNA ends, DNA ligation, purification and fragmentation, was as described previously (Xie et al., 2015). The cross-linked DNA were digested with Dpn II restriction enzyme by incubating overnight at 37 °C. DNA ends were labeled with biotin and incubated at 37 °C for 45 min, and the enzyme was inactivated with 20% SDS solution. DNA ligation as performed by the addition of T4 DNA ligase (Fermentas) and incubation at 4 °C for 1 h followed by 22 °C for 4 h. After ligation, proteinase K was added to reverse cross-linking during incubation at 65 °C overnight. DNA fragments were purified and dissolved in 86 µl of water. Unligated ends were then removed. Purified DNA was fragmented to a size of 300 - 700 bp using a sonicator (Covaris S220), and DNA ends were then repaired. DNA fragments labeled by biotin were finally separated on Streptavidin C1 beads (Life Technologies). Chimeric fragments representing the original cross-linked long-distance physical interactions were then processed into paired-end sequencing libraries. Hi-C libraries were constructed with an Illumina TruSeq DNA Sample Prep Kit and sequenced on an Illumina HiSeq X-ten platform (Illumina, USA) with 2 x 150-bp reads.


title: 41-2-4_S27


title: HS_Rep1 93-11 HiC


title: CUcovID_0098

value: strand-specific


title: Normal_Rep2 93-11 HiC


title: aME_10x_Genomics

first: Xi

middle: ze

last: Guo

state: Beijing

address: No. 1 Courtyard, Beichen West Road, Chaoyang District

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Science

description:
mRNA
scRNA-Seq

data_processing:
Sequencing was performed on an Illumina NovaSeq6000 platform
We used cellranger count pipeline 2.0.1 to check the quality of raw data,analyze single sequecing data and generate single cell information
Input NGS sequences are aligned against a reference genome using STAR2.7.1a and GRCm38 RefSeq annotations.The read counts are used as input for differential expression analysis between test and control groups using R and DESeq2
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: scRNA-seq:UMI counts matrix with gene and barcode annotations; RNA-seq:matrix

source_name: median eminance

growth_protocol: 2-month-old female mice.

extract_protocol:
Median eminances from 10 adult mice were removed. Single cells were isolated by papain and resuspended in DPBS for 10x Genomics instrument. In bulk RNAseq, ME tissue is kep in Trizol reagent.
10x Genomics instrument to generatea single-cell Gel bead in EMulsion(GEM) using Chromium Single Cell 3' Reagent Kits v2.
Bulk total RNA was prepared from adult ME tissue using Trizol reagent (Invitrogen) according to the supplier’s recommendations. Aliquots of the bulk prep were stored at −80 °C in nuclease-free water. RNA libraries are constructed by Smart seq2 methhod.

value: WT

value: median eminance

value: 2 months


title: CUcovID_0052

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Universal Plus mRNA-Seq with NuQuant, Human Globin AnyDeplete (Tecan). Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the Genomics Shared Resource at the University of Colorado Anschutz Medical Campus.


title: retinal microglia, OIR

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

description: single cell suspension

data_processing:
10X Genomics Cellranger 3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: These output files of each sample are in standard output file formats, created by the 10X Genomics Cellranger pipeline, compatible with any downstream single-cell RNA analysis pipeline

source_name: Retina

extract_protocol:
Retinas from 6 mice per group were pooled together and cut into small pieces before incubated in Ames’ Medium containing 15 U/mL papain (Worthington) and 0.1 mg/mL DNase I (Sigma) at 34 ℃.Then cell pellets were resuspended and incubated with CD11b MicroBeads (Miltenyi Biotec) .Magnetically labeled CD11b+ cells were selected and used for single cell RNA-sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OIR model was established according to a previously described method 34. Briefly, mouse pups and their nursing mother were exposed to 75% O2 from postnatal day 7 (P7) to P12 in an Oxy Cycler system (BioSpherix, Inc., NY, USA) and then returned to room air. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.

tag: disease state

value: oxygen-induced retinopathy

value: retina

value: retinal microglia

value: post natal day 17

value: wild type


title: microgila BV2 cells-cytoplasmic fraction_oxyhemoglobin-treated 24h_rep3

city: Luzhou

first: Zheng

last: Bao

state: Sichuan

address: No. 25, Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

description: BV2-Control-Cytoplasmic_vs_BV2-Hb-24h-Cytoplasmic.deseq2.txt

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using hisat2 v2.2.0 with parameters --dta -p 10
Counts were calculated using featurecounts with parameters -t exon -T 10 -p -g gene_id -f. Normalized counts were calculated using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include deseq2 output for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: cytoplasmic RNA

source_name: Microglia BV2 cells

growth_protocol: BV2 mouse microgial cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained under normal conditions with 37℃ and 5% CO2.

extract_protocol:
One 10cm2 dish of BV2 cells were digested by trypsin (0.25%) without ethylene diamine tetraacetic acid (EDTA) and phenolsulfonphthalein (PSP), and harvested cells were incubated for 10 min on ice with 380 μl of ice-cold hypotonic lysis buffer (HLB) (10mM Tris (pH 7.5), 3mM MgCl2, 10mM NaCl, 0.3% (vol/vol) NP-40 and 0.3% (vol/vol) glycerol) supplemented with 100 U of RNaseout. The nuclear pellet and supernate were centrifuged for 20 min at 8000×g at 4℃. The supernate, containing cytoplasmic RNA fraction, was mixed by 1 mL of RNA precipitation solution (0.5 mL of 3 M sodium acetate (pH 5.5)with 9.5 mL of ethanol) and stored at -20°C for 1 hours, then cytoplasmic pellet was centrifuged at 18000×g at 4℃ for 15 min. The nuclear pellet was washed three times with 1 mL of ice-cold HLB. The nuclear and cytoplasmic pellets were followed by extraction with RNAsimple Total RNA Kit (TIANGEN, Beijing CN) according to the manufacturer’s instructions, and nuclear and cytoplasmic RNA samples were experimented immediately or stored at -80℃.
The Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech Co., Ltd., Nanjing CN) was used for library preparation. Briefly, samples were normalized at a concentration of 500 ng/ml. Samples were first subjected to a tagmentation reaction, indexed, and PCR amplified. Libraries were then purified with magnetic beads (AMPure). QC checks for the library preparations included electrophoresis (Agilent Technologies 2100 Bioanalyzer) or library quantification. Samples were sequenced in the Novogene (Beijing CN) on an Illumina HiSeq 1500 highthroughput sequencing system.

treatment_protocol: One replicate was oxyhemoglobin treated for 12 hours or 24 hours.

value: Microglia BV2 cells

value: treated with oxyhemoglobin for 24 hours


title: retinal microglia, NOIR

description: single cell suspension

value: control

tag: tissue


title: 60-4_S24

value: hAbKI


title: Normal_Rep1 93-11 HiC


title: 56-4_S23

value: F


title: microgila BV2 cells-cytoplasmic fraction_oxyhemoglobin-treated 24h_rep2


title: 209-2_S20

value: M


title: CUcovID_0026

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

value: whole blood

value: Female

value: Positive


title: CUcovID_0057

value: Male

value: strand-specific


title: CUcovID_0085


title: 209-0_S19


title: HS_Rep2 Nipponbare HiC

value: Nipponbare


title: HS_Rep1 Nipponbare HiC


title: 176-2_S22


title: Nip-HS-3:  RNA-seq


title: microgila BV2 cells-nuclear fraction_oxyhemoglobin-treated 24h_rep3

description: BV2-Control-Nuclear_vs_BV2-Hb-24h-Nuclear.deseq2.txt

molecule: nuclear RNA


title: 176-0_S21


title: CUcovID_0092


title: microgila BV2 cells-nuclear fraction_oxyhemoglobin-treated 24h_rep2


title: Normal_Rep1 Nipponbare HiC


title: Normal_Rep2 Nipponbare HiC


title: CUcovID_0067


title: CUcovID_0043


title: microgila BV2 cells-nuclear fraction_oxyhemoglobin-treated 24h_rep1


title: 175-2_S18


title: microgila BV2 cells-cytoplasmic fraction_oxyhemoglobin-treated 12h_rep3

description: BV2-Control-Cytoplasmic_vs_BV2-Hb-12h-Cytoplasmic.deseq2.txt

value: treated with oxyhemoglobin for 12 hours


title: microgila BV2 cells-cytoplasmic fraction_oxyhemoglobin-treated 12h_rep1


title: microgila BV2 cells-cytoplasmic fraction_oxyhemoglobin-treated 24h_rep1


title: HS_Rep2 93-11 ATAC-seq

data_processing:
After quality control, sequencing reads were mapped to their corresponding genome of Nip and 93-11 using bwa mem (v0.7.10-r789) (Li and Durbin, 2009) with default parameters. Mapped reads were filtered using Samtools v0.1.19 to retain unique mapped reads with a mapping quality score > 30 (Samtools view command with option “-q 30”). ATAC-seq reads were further filtered with Samtools to remove those mapping to either the chloroplast or mitochondrial genomes. For normalization and visualization, the filtered, sorted .bam files were converted to bigwig format using the “bamcoverage” script in deepTools v2.0 (Ramirez et al., 2016) with a bin size of 1 bp and RPKM normalization. Heat maps and average plots displaying ATAC-seq data were also generated using the “computeMatrix” and “plotHeatmap” functions in the deepTools package. Peak calling on ATAC-seq data was performed using the MACS v2.1.1 (Zhang et al., 2008). The peaks called in this way (FDR < 0.05) were identified as transposase hypersensitive sites.
Genome_build: Nip-BRI, 93-11-BRI (The genome assembly and annotation could be download from the public database http://www.elabcaas.cn/rice/downloads.html <http://www.elabcaas.cn/rice/downloads.html>, which was built for Nip and 93-11.  And following link is the reference: https://www.ncbi.nlm.nih.gov/pubmed/30448535)
Supplementary_files_format_and_content: bed files include ATAC position information for each sample.

extract_protocol: Freshly purified nuclei to be used for ATAC-seq were kept on ice prior to the transposase integration reaction. Transposase integration reactions and sequencing library preparations were then performed as previously described (Bajic et al., 2018). In brief, 50 ng of genomic DNA was used in each 50 μl Tn5 transposase integration reaction for 30 min at 37°C using Nextera reagents. DNA fragments were purified using the Minelute PCR purification kit (Qiagen), eluted in 11 μl elution buffer, and the entirety of each sample was then amplified using High Fidelity PCR Mix (NEB) and barcode primers for 9-12 PCR cycles. These amplified ATAC-seq libraries were purified using AMPure XP beads (Beckman Coulter), quantified by qPCR with the NEBNext Library Quantification Kit (NEB), and analyzed on a Bioanalyzer High Sensitivity DNA Chip (Agilent) prior to pooling and sequencing. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration. DNA libraries were constructed using NEBNext DNA Library Prep Kit (Neb) and sequenced on an Illumina HiSeq X-ten platform with 150-bp paired-end reads.


title: HS_Rep1 93-11 ATAC-seq


title: Normal_Rep2 93-11 ATAC-seq


title: 175-0_S17


title: microgila BV2 cells-cytoplasmic fraction_oxyhemoglobin-treated 12h_rep2


title: REH cells, C_3

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

data_processing:
First 5 steps were carried out by Novogene UK. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Filter the raw reads and obtain the clean reads - (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
HISAT2 is selected to map the filtered sequenced reads to the reference genome.
Gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008)
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). It provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Therefore, if the readcount of the i-th gene in j-th sample is Kij, there is: Kij ～ NB(μij,σij2) And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
GO analysis with BinGO in Cytoscape and GSEA analysis with GSEA Software (Broad Institute)
Genome_build: ensembl_homo_sapiens_grch38_p12
Supplementary_files_format_and_content: AtovsControl_DEG.txt is in text format and reports counts and fpkms. DEG_1.3FC_0.05adj_FINAL.xlsx is in Excel format. This is the gene list used for GO and GSEA analysis. It contains rows with all differentially expressed genes at 1.3 FC and adj p-value<0.05 (Gene ID), columns with the respective log2FoldChange, padj, and gene_name, as well as columns with FPKM values for each sample - Ato_1_fpkm Ato_2_fpkm Ato_3_fpkm C_1_fpkm C_2_fpkm C_3_fpkm.

source_name: REH cells - childhood ALL

growth_protocol: RPMI 1640 with 10% FCS and 0.5% Pen/Strep

extract_protocol:
Rneasy kit (Qiagen)
Sequencing was outsourced to Novogene UK -  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used for library preparation with AMPure XP beads (Beckman Coulter, Beverly, USA) for size selection and PCR purification steps, both performed as instructed by the manufacturers.

treatment_protocol: 30uM of Atovaquone for 3 days

tag: cell line

value: REH

tag: tumor

value: B-cell ALL

tag: origin

value: Peripheral blood at first relapse


title: 71-7_S12

tag: Sex

value: Wildtype

tag: age


title: 71-4_S11

tag: genotype


title: REH cells, C_2


title: REH cells, C_1


title: 71-2_S10


title: microgila BV2 cells-nuclear fraction_oxyhemoglobin-treated 12h_rep3

description: BV2-Control-Nuclear_vs_BV2-Hb-12h-Nuclear.deseq2.txt

value: Microglia BV2 cells


title: Normal_Rep1 93-11 ATAC-seq


title: HS_Rep2 Nipponbare ATAC-seq


title: REH cells, Ato_3

value: Atovaquone


title: 71-0_S9


title: microgila BV2 cells-nuclear fraction_oxyhemoglobin-treated 12h_rep2


title: REH cells, Ato_2


title: 70-2_S16


title: HS_Rep1 Nipponbare ATAC-seq


title: microgila BV2 cells-nuclear fraction_oxyhemoglobin-treated 12h_rep1


title: 70-0_S15


title: Normal_Rep2 Nipponbare ATAC-seq


title: microgila BV2 cells-cytoplasmic fraction_control_rep3

value: untreated


title: HeLa CAD + ddC C

data_processing:
raw reads were mapped and qunatified using kallisto-quant version 0.45.0
differential gene expression was analyzed using DESeq2 version 1.22.2
Genome_build: BUILD_GRCh38_RELEASE_95
Supplementary_files_format_and_content: Tab-separated differential gene expression results

source_name: HeLa

treatment_protocol: Cells were treated with 20 µM ddC or water for 6 days. Knockdown was performed using esiRNA for 6 days.

tag: esirna

value: CAD

value: ddC

value: HeLa


title: Normal_Rep1 Nipponbare ATAC-seq


title: 69-2_S14

value: M

tag: strain


title: microgila BV2 cells-cytoplasmic fraction_control_rep1


title: microgila BV2 cells-cytoplasmic fraction_control_rep2


title: HeLa CAD + ddC A


title: 69-0_S13


title: 9311-HS-1 MeDIP-Seq

data_processing:
Raw data were trimmed with Skewer to remove adapters and low-quality bases. Reads with more than 15% N, more than 50% low-quality base or less than 18 nt were filtered out. BWA was used to align reads to reference genome. After alignment, 6mA enriched regions were called with MASC2 with the cutoffs FDR <0.05, fold change >2.
Genome_build: Nip-BRI, 93-11-BRI (The genome assembly and annotation could be download from the public database http://www.elabcaas.cn/rice/downloads.html <http://www.elabcaas.cn/rice/downloads.html>, which was built for Nip and 93-11.  And following link is the reference: https://www.ncbi.nlm.nih.gov/pubmed/30448535)
Supplementary_files_format_and_content: Wig files were generated using the MACS2

extract_protocol:
Genomic DNA was extracted from3-week-old wild-type Oryza sativa 93-11and sonicated to produce fragments of ~250 bp. Fragmented DNA was incubated for 2 h at 4 °C with anti-6mA polyclonal antibody (Synaptic Systems) in immunoprecipitation buffer (10 mM sodium phosphate, 2 mM potassium phosphate, 137 mM NaCl, 2.7 mM KCl, 0.05% Triton X-100, pH 7.4). The mixture was then immunoprecipitated by incubation with Protein A/G Plus-Agarose (Santa Cruz) that was pre-bound with bovine serum albumin (BSA) at 4 °C for additional 2 h. After extensive washing, bound DNA was eluted from the beads in elution buffer (50 mM Tris, pH 8.0, 1% SDS, 10 mM EDTA) at 65 °C, treated with proteinase K and purified using QIAquick PCR Purification Kit (Qiagen).
DNA quality was monitored on agarose gels and Qubit® DNA Assay in Qubit® 2.0Flurometer (Life Technologies). Two biological replicates for 6mA IP and one biological replicates for input were prepared with NEBNext DNA library prep kit (NEB) following manufacturer’s instructions, Size selection and gel purification, followed by PCR amplification. Library concentration was quantified by Qubit®2.0 Flurometer (Life Technologies) and the insert size was determined by Agilent Bioanalyzer 2100 system (Agilent).

tag: antibody


title: microgila BV2 cells-nuclear fraction_control_rep3


title: HS9_IN MeDIP-Seq


title: C57-51-4_S3

value: F


title: HeLa CAD + ddC B


title: 9311-HS-2 MeDIP-Seq


title: Nip-HS-2 MeDIP-Seq


title: HeLa Con + ddC B

value: Gfp


title: C57-50-4_S7


title: microgila BV2 cells-nuclear fraction_control_rep2


title: REH cells, Ato_1


title: HeLa Con + ddC C


title: HeLa Con + ddC A


title: 140-0_S4


title: microgila BV2 cells-nuclear fraction_control_rep1


title: aME_bulk RNA, mut-4

description:
adultME_matrix.csv
mouse-mut-4

data_processing:
Sequencing was performed on an Illumina NovaSeq6000 platform
We used cellranger count pipeline 2.0.1 to check the quality of raw data,analyze single sequecing data and generate single cell information
Input NGS sequences are aligned against a reference genome using STAR2.7.1a and GRCm38 RefSeq annotations.The read counts are used as input for differential expression analysis between test and control groups using R and DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-seq:UMI counts matrix with gene and barcode annotations; RNA-seq:matrix

growth_protocol: 2 month old mice

value: median eminance

value: 2 months

value: Rax::BrafV600E mutant


title: Nip-HS-1 MeDIP-Seq

value: Nipponbare


title: 120-2_S6


title: NHS_IN MeDIP-Seq


title: HeLa CAD C

value: Water


title: aME_bulk RNA, mut-3

description:
adultME_matrix.csv
mouse-mut-3


title: HeLa CAD B


title: 9311-normal-2 Bisultife-seq

data_processing:
The Trimmomatic (version 0.39) program (Bolger et al., 2014) was employed to clip adapters and filter low-quality reads. Clean data from Nip and 93-11 were mapped to their corresponding reference sequence using Bismark (version 0.22) with parameters of ‘-N 1, -L 30’. Then, methylated cytosines were extracted from aligned reads using the Bismark methylation extractor with default parameters (Krueger and Andrews, 2011). The binomial test was employed to determine whether the observed methylation frequency was above the background (FDR < 0.05). All the analyses were done using sites covered by a minimum of 10 reads. Only 5mC sites both supported by two biological replicates were considered for further analysis.
Genome_build: Nip-BRI, 93-11-BRI (The genome assembly and annotation could be download from the public database http://www.elabcaas.cn/rice/downloads.html <http://www.elabcaas.cn/rice/downloads.html>, which was built for Nip and 93-11.  And following link is the reference: https://www.ncbi.nlm.nih.gov/pubmed/30448535)
Supplementary_files_format_and_content: Bed files containing 5mC site position information

extract_protocol:
The genomic DNA was extracted for normal and heat shock seedlings using the DNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.
DNA libraries were constructed using the Illumina TruSeq DNA Sample Prep Kit according to the manufacturer’s instructions. Bisulfite-treated DNA libraries were sequenced on an Illumina HiSeq X-ten sequencing platform.


title: aME_bulk RNA, mut-2

description:
adultME_matrix.csv
mouse-mut-2


title: 119-2_S2


title: 9311-normal-1 Bisultife-seq


title: HeLa CAD A


title: aME_bulk RNA, wt-3

description:
adultME_matrix.csv
mouse-wt-3

value: WT


title: 119-0_S1


title: 9311-HS-2 Bisultife-seq


title: HeLa Con B


title: 9311-HS-1 Bisultife-seq


title: HeLa Con C


title: aME_bulk RNA, wt-1

description:
adultME_matrix.csv
mouse-wt-1


title: HeLa_A33_OE_DDC_REP3

treatment_protocol: Cells were treated with 40 µM ddC or water for 6 days.

tag: expression


title: aME_bulk RNA, wt-2

description:
adultME_matrix.csv
mouse-wt-2


title: HeLa Con A

tag: treatment


title: Nip-normal-1 Bisultife-seq

tag: cultivar


title: Nip-normal-2 Bisultife-seq


title: HeLa_A33_OE_DDC_REP2


title: 120-0_S5


title: Nip-HS-1 Bisultife-seq


title: HeLa_A33_OE_DDC_REP1


title: HeLa_A33_OE_REP3


title: Nip-HS-2 Bisultife-seq


title: HeLa_A33_OE_REP2


title: aME_bulk RNA, mut-1

description:
adultME_matrix.csv
mouse-mut-1


title: HeLa_TWT_DDC_REP3

value: Empty


title: HeLa_TWT_DDC_REP2


title: HeLa_TWT_DDC_REP1


title: HeLa_TWT_REP3


title: S3_5038

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software.

data_processing: Probe cell intensity data were further analyzed in the Affymetrix Expression Console software using the Robust Multichip Analysis (RMA) algorithm.

label: Biotin

organism: Sus scrofa

source_name: Liver SINS high

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: The study was approved by the authorities in Stuttgart, Baden-Wurttemburg, Germany with file numbers 35–9185.81/0415 and 35–9185.64 / 0035. The animal experiment was carried out in the conventional stables of the State In-stitution for Swine Breeding (Landesanstalt für Schweinezucht, LSZ, Ba-den-Württemburg, Boxberg, Germany). 12 out of 120 piglets from 40 sows of a herd of Baden-Württemburg Genetics hybrid sows artificially inseminated with Pietrain se-men were used for the experiment. The complete experiment was described by Reiner et al. [2]. From all piglets scored for SINS in this experiment, six piglets with least (SINS low) and six piglets with highest (SINS high) SINS-Scores were selected for transcriptomics.

extract_protocol: Total RNA from liver aliquots (20 mg) of six suckling piglets each of the SINS low group (either no or only low-grade signs of SINS) and the SINS high group (high-grade signs of SINS) was extracted using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol. RNA quantity and quality were determined spectrophotometrically and by electrophoresis. The average RNA concentration and RNA integrity number (RIN) of all total RNA samples (n = 12, means ± SD) was 454 ± 34 ng/µL and 8.0 ± 0.6, respectively. For microarray hybridization, RNA samples were sent on dry-ice to the Center of Excellence for Fluorescent Bioanalytics (Regensburg, Germany) and, following a further RNA quality check using an Agilent 2100 Bioanalyzer (RIN of all samples: 7.7 ± 0.5), processed using an Affymetrix GeneChip Porcine Gene 1.0 Sense Target array.

tag: gender

value: mixed-sex

tag: condition

value: SINS high

value: Liver


title: S5_5118

treatment_protocol: From all piglets scored for SINS in this experiment, six piglets with least (SINS low) and six piglets with highest (SINS high) SINS-Scores were selected for transcriptomics.


title: S6_5145


title: DRIPc_seq_siDDX5_2

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description:
RNA-DNA
1

data_processing:
Library strategy: DRIPc-seq
All fastq files were trimmed with FASTQ Toolkit before mapping
Reads were aligned to the hg 38 genome using Bowtie2.
Peaks were called using MACS2 callpeak.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using bedtools bamcoverage

source_name: Erythromyeloblastoid leukemia cell line

extract_protocol:
DRIPc-seq: Genomic DNA from K562 cells enzimatically fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.  Monoclonal S9.6 antibody was used to immunoprecipitate RNA-DNA hybrids.
Libraries were prepared using TruSeq Stranded Total RNA Library Prep (Illumina) as determined by the company

tag: drip antibody

tag: sequenced molecule

value: RNA moiety from RNA-DNA hybrids


title: DRIPc_seq_siDDX5_1

description:
RNA-DNA
1


title: DRIPc_seq_siC_2 reanalysis

description:
RNA-DNA
1


title: S4_5114

tag: tissue


title: S2_5183


title: HeLa_TWT_REP2

extract_protocol:
Total RNA was extracted from cells using NucleoSpin RNA (Macherey-Nagel)
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1µg  total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and Rnase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

tag: cell line


title: hMADS_Control_rep5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from hMADS cells, controls, biological replicate 5

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

label: biotin

source_name: hMADS cells, controls, differentiated for 2 days, experiment 1, biological replicate 5

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

extract_protocol: RNA extraction was performed using the miRneasy kit (Qiagen)

treatment_protocol: As described in the paper. Briefly, hMADS cells were plated at a density of 5000-7000 cells/cm2 in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 10 mM Hepes, 2.5 ng/ml hFGF2, 50 mg/ml penicillin, and 50 mg/ml streptomycin. Once the cells reached confluence, FGF2 was removed (Day -2) and cells were transfected with siRNA for HAND2 (20nM). 48 hours later (Day 0) the differentiation was induced using DMEM/Ham’s F12 (volume to volume) supplemented with 10 mg/ml transferrin, 10 nM insulin, 0.2 nM triiodothyronine, 100nM Rosiglitazone (Rosi), 1 mM dexamethasone, 1mM IBMX. Cells were harvested two days later (Day 2).

tag: cell type

value: human multipotent adipose-derived stem (hMADS) cells

tag: knockdown

value: control


title: hMADS_Control_rep3

description: Gene expression data from hMADS cells, controls, biological replicate 3

source_name: hMADS cells, controls, differentiated for 2 days, experiment 1, biological replicate 3


title: DMSO [150_2]

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

value: CD-1 IGS

value: DIV 16 neurons from P0 pups

tag: tissue/cell type

value: Primary Hippocampal neurons

value: DMSO


title: hMADS_Control_rep4

description: Gene expression data from hMADS cells, controls, biological replicate 4

source_name: hMADS cells, controls, differentiated for 2 days, experiment 1, biological replicate 4


title: HeLa_TWT_REP1

value: HeLa


title: HeLa_A33_OE_REP1


title: S1_5039


title: C6_5474

source_name: Liver SINS low

value: SINS low


title: C3_5569


title: hMADS_siRNA_HAND2_rep4

description: Gene expression data from hMADS cells treated with siRNA for HAND2 for three days, biological replicate 4

source_name: hMADS cells treated with siRNA for HAND2, differentiated for 2 days, experiment 1, biological replicate 4


title: C4_5464


title: hMADS_Control_rep1

description: Gene expression data from hMADS cells, controls, biological replicate 1

source_name: hMADS cells, controls, differentiated for 2 days, experiment 2, biological replicate 1


title: C5_5549


title: DRIPc_seq_siC_1 reanalysis

description:
RNA-DNA
1


title: hMADS_siRNA_HAND2_rep2

description: Gene expression data from hMADS cells treated with siRNA for HAND2 for three days, biological replicate 2

source_name: hMADS cells treated with siRNA for HAND2, differentiated for 2 days, experiment 1, biological replicate 2


title: hMADS_siRNA_HAND2_rep3

description: Gene expression data from hMADS cells treated with siRNA for HAND2 for three days, biological replicate 3

source_name: hMADS cells treated with siRNA for HAND2, differentiated for 2 days, experiment 2, biological replicate 3


title: hMADS_Control_rep2

description: Gene expression data from hMADS cells, controls, biological replicate 2

source_name: hMADS cells, controls, differentiated for 2 days, experiment 2, biological replicate 2


title: C2_5538


title: C1_5544


title: CRC-32

status: Public on Feb 25 2021

city: Iruma-gun

first: Toshiaki

last: Miyazaki

state: Saitama

address: 38 Morohongo, Moroyama-machi

department: Social Medicine

country: Japan

institute: Saitama Medical University

data_processing:
Basecalls performed using Illumina BaseSpace v1.1.0
Sequenced reads were mapped to hg19 whole genome using TopHat
Cufflinks were used to procude aligned reads, variant calls and FPKM abundance estimates of reference genes and transcripts.
Genome_build: hg19

source_name: primary colon cancer

extract_protocol:
Human CRC spheroid cells (1x10^5), cultured in Spheroid buffer, were collected by centrifugation at 500 xg for 1min at 4C. Cells were then washed twice with PBS(-) and total RNAs were purified with RNAeasy kit (Qiagen) according to the manufacturers instruction. Indexed cDNA libraries were generated from each 500 ng of the purified RNA with TruSeq stranded mRNA kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: primary colon cancer

value: CRC spheroid cells


title: CRC-29M

source_name: Liver metastasis colon cancer

value: Liver metastasis colon cancer


title: CRC-20


title: CRC-26M


title: CRC-29


title: hMADS_siRNA_HAND2_rep1

description: Gene expression data from hMADS cells treated with siRNA for HAND2 for three days, biological replicate 1

source_name: hMADS cells treated with siRNA for HAND2, differentiated for 2 days, experiment 2, biological replicate 1


title: CRC-31M


title: CRC-6


title: CRC17


title: CRC-24M


title: Cd4CrePofut1_fl/fl_NICD 1

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: NICD expressing vector-transduced Pofut1-null P14 cells at day 7.5 post-infection from spleen

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: WT or Pofut1-null P14 cells with or without NICD co-expression were sorted from spleen after LCMV-Armstrong infection.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: transduction

value: NICD expressing vector

tag: genotype/variation


title: Cd4CrePofut1_WT_NICD 1

source_name: NICD expressing vector-transduced WT P14 cells at day 7.5 post-infection from spleen

tag: strain

value: WT


title: Cd4CrePofut1_fl/fl_NICD 4


title: CRC-9


title: Cd4CrePofut1_fl/fl 3

source_name: empty vector-transduced Pofut1-null P14 cells at day 7.5 post-infection from spleen

value: empty vector


title: Cd4CrePofut1_fl/fl_NICD 2


title: Cd4CrePofut1_WT_NICD 4


title: Cd4CrePofut1_fl/fl 4


title: Cd4CrePofut1_fl/fl 2


title: Cd4CrePofut1_fl/fl 1


title: Cd4CrePofut1_WT 4

source_name: empty vector-transduced WT P14 cells at day 7.5 post-infection from spleen


title: Cd4CrePofut1_WT_NICD 3


title: 14_Input DNA_Day5_mES_s_6_sequence

city: Barcelona

first: Ana

last: Sevilla

state: Barcelona

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

department: Departamento de Biologia Celular, Fisiologia e Inmunologia

institute: Universidad de Barcelona

description: Input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the Mouse July, 2007 (NCBI37/mm9) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Mouse ES

growth_protocol: Esrrb_R rescue clone was grown  under  under typical ES conditions; D-MEMâHigh Glucose (Dulbeccoâs modified Eagleâs medium-1X-High Glucose) (GibcoÂ®, Invitrogen), 15% FBS (Fetal bovine serum) (Hyclone, Thermo Scientific), 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-glutamine, Penicillin/Streptomycin (Gibco, Invitrogen) and 103 U ml-1 LIF (Chemicon, Millipore) on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes or Esrrb (TF)-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 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 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.

treatment_protocol: Esrrb_R rescue clone was grown in +Dox (1ug/ml) media_Day0; Dox withdrawal was performed for 5 days performing  H3K4me3 and H3K27me3 ChIP-Seq at the respective days: Day0 ( Esrrb expressed) and days  1,3 and 5 ( Esrrb non expressed)

value: Esrrb_Rescue Clone

tag: time point

tag: fraction

value: Input DNA


title: Cd4CrePofut1_fl/fl_NICD 3


title: Cd4CrePofut1_WT_NICD 2


title: CRC-19


title: 13_Input DNA_Day3_mES_s_5_sequence

description: Input DNA


title: 11_Input DNA_Day0_mES_s_4_sequence

description: Input DNA


title: 12_Input DNA_Day1_mES_s_4_sequence

description: Input DNA


title: 9_H3K27me3_ChIP_Seq_Day3_mES_s_5_sequence

description: Chromatin IP against H3K27me3. Upstate Cat#07-449. Lot# DAM1387952

value: Chromatin IP

tag: antibody

tag: antibody vendor

value: Upstate

tag: antibody catalog#

tag: antibody lot#


title: 6_H3K4me3_ChIP_Seq_Day5_mES_s_6_sequence

description: Chromatin IP against H3K4me3. Abcam (ab 8580). Lot #1016899

value: Abcam


title: Cd4CrePofut1_WT 2


title: 5_H3K4me3_ChIP_Seq_Day3_mES_s_4_sequence


title: 8_H3K27me3_ChIP_Seq_Day1_mES_s_3_sequence


title: 7_H3K27me3_ChIP_Seq_Day0_mES_s_8_sequence


title: 3_H3K4me3_ChIP_Seq_Day0_mES_s_8_sequence


title: 4_H3K4me3_ChIP_Seq_Day1_mES_s_1_sequence


title: 2_Input DNA_mES_sequence

description: Input DNA


title: 10_H3K27me3_ChIP_Seq_Day5_mES_s_8_sequence


title: NICD_day 7.5 1

source_name: NICD expressing vector-transduced P14 cells at day 7.5 post-infection from spleen

growth_protocol: P14 cells transduced with indicated sgRNAs were sorted from spleen after LCMV-Armstrong infection.


title: NICD_day 7.5 4


title: Cd4CrePofut1_WT 1


title: spike for NICD_day 7.5 1

source_name: empty vector-transduced P14 cells at day 7.5 post-infection from spleen


title: spike for NICD_day 7.5 2


title: 1_Esrrb ChIP-Seq_mES_sequence

description: Chromatin IP against Esrrb. R&D systems. PP-H6707-00. Clone H6707.Lot# A-1

value: Esrrb

value: R&D systems


title: NICD_day 7.5 2


title: NICD_day 7.5 3


title: MP HWT027

description: MP

source_name: sgNTC-transduced P14 cells at day 7.5 post-infection from spleen

growth_protocol: P14 cells transduced with indicatd sgRNAs were sorted from spleen after LCMV-Armstrong infection.

tag: sample type


title: MP HWT026

description: MP

value: sgNTC-transduced P14 cells at day 7.5 post-infection from spleen


title: TE' HWT022

description: TE'


title: spike for NICD_day 7.5 4


title: spike for NICD_day 7.5 3


title: TE' HWT023

description: TE'


title: MP HWT025

description: MP


title: MP HWT028

description: MP


title: TE' HWT021

description: TE'


title: TE' HWT024

description: TE'


title: HTHuGene11_050911K_MT225_Fetal-Cb-8

city: Toronto

first: Michael

middle: David

last: Taylor

state: Ontario

address: 555 University Avenue

department: Division of Neurosurgery

institute: SickKids

hyb_protocol: As directed by affimetrix

scan_protocol: As directed by affimetrix

data_processing: Data were processed using software packages from R/Bioconductor. CEL files were read using functions from the oligo package. Quality control was performed using the arrayQualityMetrics package. Background correction, normalisation and summarisation was performed using RMA. Feature were then annotated with their gene symbols and Entrez IDs and probes mapping to multiple gene symbols were filtered out.

source_name: cerebellum

label_protocol: As directed by affimetrix

extract_protocol: RNA has been obtained from the Biochain company

value: cerebellum

tag: developmental stage

value: fetal


title: HTHuGene11_050911K_MT231_Adult-Cb-4

tag: tissue

value: adult


title: Col-0 infected by Fo47 96HPI R2

city: Xi'an

first: Li

state: Shaanxi

address: 28 Xianning West Road

institute: Xi'an Jiao Tong University

description: 96 HOURS post inoculation

data_processing:
Illumina Casava1.7 software used for basecalling.
DATA FILTERING: java -jar trimmomatic-0.32.jar PE -phred33 control_a.fq control_b.fq control_aPaired.fq control_aUnpaired.fq control_bPaired.fq control_bUnpaired.fq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36
Mapping using Tophat and bowtie
Transcript assembly using Cufflinks
Differential gene expression called using Cuffdiff
Genome_build: Arabidopsis thaliana TAIR10, Fusarium oxysporum 5176 genome, F. oxysporum 47 genome

organism: Arabidopsis thaliana

source_name: plant roots

growth_protocol: Arabidopsis thaliana Col-0 seeds (ARBC Ohio State University) were germinated on autoclaved MetroMix360® potting mix and allowed to grow in growth chamber with a photoperiod of 14-hour light and 10-hour dark at 24 C.

extract_protocol:
Total RNAs were extracted from leaves of healthy and infected basil plants using Trizol reagent (Thermo Fisher Scientific, MA) following manufacturer’s protocol. After removal of genomic DNA by DNase I (New England Biolabs, MA) treatment, RNA samples were quantified using NanoDrop 1000 (Thermo Fisher Scientific, MA) and assessed for integrity using Agilent Bioanalyzer 2100 (Agilent, MA).
Library construction was conducted using Illumina TruSeq mRNA library preparation kit (Illumina, CA)

treatment_protocol: For F. oxysporum infection, Arabidopsis plants of 14 days old were root-dipped for 30 seconds in 1x106 spores/ml fungal spore suspension of FO5176 or FO47 and sterile dH2O for control. Inoculated plants were planted in autoclaved potting mix and incubated in 28C growth chamber of the same photoperiod as above.

value: roots

tag: ecotype

tag: pathogen

value: Fusarium oxysporum 47


title: Col-0 infected by Fo47 96HPI R3

description: 96 HOURS post inoculation


title: Col-0 infected by Fo47 96HPI R1

description: 96 HOURS post inoculation


title: HTHuGene11_050911K_MT226_Fetal-Cb-9


title: HTHuGene11_050911K_MT233_Adult-Cb-6


title: TINT HWT019

description: TINT


title: TINT HWT017

description: TINT


title: sgPofut1_day 7.5 HWT013

description: sgPofut1_day 7.5

source_name: sgRNA-transduced P14 cells from the dual-color transfer system at day 7.5 post-infection from spleen


title: HTHuGene11_050911K_MT227_Fetal-Cb-10


title: TINT HWT018

description: TINT


title: HTHuGene11_050911K_MT224_Fetal-Cb-7


title: HTHuGene11_050911K_MT228_Adult-Cb-1


title: HTHuGene11_050911K_MT229_Adult-Cb-2


title: HTHuGene11_050911K_MT223_Fetal-Cb-6


title: spike for sgPofut1_ day 7.5 HWT016

description: spike for sgPofut1_ day 7.5

value: sgRNA-transduced P14 cells from the dual-color transfer system at day 7.5 post-infection from spleen


title: HTHuGene11_050911K_MT222_Fetal-Cb-5


title: TINT HWT020

description: TINT


title: sgPofut1_day 7.5 HWT015

description: sgPofut1_day 7.5


title: sgPofut1_day 7.5 HWT011

description: sgPofut1_day 7.5


title: HTHuGene11_050911K_MT221_Fetal-Cb-4


title: spike for sgPofut1_ day 7.5 HWT012

description: spike for sgPofut1_ day 7.5


title: spike for sgPofut1_ day 5 HWT008

description: spike for sgPofut1_ day 5

source_name: sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen


title: spike for sgPofut1_ day 7.5 HWT010

description: spike for sgPofut1_ day 7.5


title: spike for sgPofut1_ day 7.5 HWT014

description: spike for sgPofut1_ day 7.5


title: HTHuGene11_050911K_MT220_Fetal-Cb-3


title: Col-0 infected by Fo47 48HPI R2

description: 48 HOURS post inoculation


title: Col-0 infected by Fo47 48HPI R1

description: 48 HOURS post inoculation


title: sgPofut1_day 7.5 HWT009

description: sgPofut1_day 7.5


title: Col-0 infected by Fo47 24HPI R1

description: 24 HOURS post inoculation


title: Col-0 infected by Fo47 24HPI R2

description: 24 HOURS post inoculation


title: Col-0 infected by Fo47 12HPI R3

description: 12 HOURS post inoculation


title: Col-0 infected by Fo47 12HPI R2

description: 12 HOURS post inoculation


title: YJ56 grown under 13℃

city: Seoul

first: SON

last: YONGJUN

address: 145, Anam-ro, Seongbuk-gu

country: South Korea

institute: Korea University

data_processing:
RNA sequencing was performed on an Illumina HiSeq 2500 platform using single end 50-bp sequencing
The reference genome sequence was retrieved from the NCBI database.
Quality-filtered reads were aligned to the reference genome sequence using Bowtie2.
The relative abundance of transcripts is presented as RPKM, defined as the total exon reads/(mapped reads in millions × exon length in kilobases).

organism: Pseudarthrobacter psychrotolerans

source_name: Bacteria cells

growth_protocol: Exponential phase on R2A at 13℃ or R2A at 13℃

extract_protocol:
Using an RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
Illumina sequencing library was constructed by the TruSeq Stranded mRNA Library Prep Lit (Illumina, San Diego, CA, USA) following the manufacturer's protocol

tag: cell type

value: Mid-exponential phase (OD=1.0-1.1)


title: YJ56 grown under 25℃


title: Col-0 infected by Fo5176 96HPI R2

description: 96 HOURS post inoculation

value: Fusarium oxysporum 5176


title: sgPofut1_day 5 HWT007

description: sgPofut1_day 5

value: sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen


title: Col-0 infected by Fo5176 96HPI R1

description: 96 HOURS post inoculation


title: sgPofut1_day 5 HWT005

description: sgPofut1_day 5


title: spike for sgPofut1_ day 5 HWT006

description: spike for sgPofut1_ day 5


title: Col-0 infected by Fo47 48HPI R3

description: 48 HOURS post inoculation


title: Col-0 infected by Fo5176 48HPI R2

description: 48 HOURS post inoculation


title: sgPofut1_day 5 HWT001

description: sgPofut1_day 5


title: Col-0 infected by Fo5176 48HPI R3

description: 48 HOURS post inoculation