title: SLn_3_mRNA

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN negative nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

value: negative


title: eS7_4KR.4hr.Ribo-seq_rep1

status: Public on Nov 12 2020

type: SRA

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

country: Japan

institute: The University of Tokyo,

description: Ribosome Profiling

library_source: transcriptomic

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.0.6
Alignment with TopHat v2.0.7 to Genome
Read quantitation using custom scripts
Genome_build: sacCer3
Supplementary_files_format_and_content: text files contain following columns: 1.gene name 2.length (codon) 3.reads counts

molecule: total RNA

organism: Saccharomyces cerevisiae

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
The lysate was treated with RNase I and then subjected to ultracentrifugation for ribosome profiling. Total RNA was extracted by TRIzol reagent from the lysate (RNA-seq) or ribosome pellet (Ribosome profiling).
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129 . RNA-seq libraries were generated from rRNA-depleted total RNA using an Illumina TruSeq stranded total RNA kit.

tag: treatment

value: Tm treatment for 4hr

tag: genetic background

value: MATa ade2 his3 leu2 trp1 ura3 can1 RPS7a::HisMX6 RPS7b::natNT2 pRS315-RPS7a-4KR-3HA

tag: cell line


title: Committed Progenitors: Lineage Committed Progenitors sorted on day 0

city: Barcelona

first: Karthik

last: Arumugam

state: Barcelona

address: C/Dr.Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

data_processing:
The sequenced reads from the Illumina sequencer, were processed through the Cell Ranger (v 2.0.0) pipeline.
Demultiplexed FASTQ files (CellRanger v 2.0.0)
BAM files (Cell Ranger v 2.0.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: The cellranger count program also generated the HDF5  gene barcode matrix files that contain only the detected barcodes. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

organism: Homo sapiens

extract_protocol:
Single cells were sorted in a BD Influx cytometer and  were pelleted by centrifugation followed by resuspension in DMEM at approximately 500cells/µl. Cell viability and concentration was verified.
Each sample was loaded into one well of a Chromium chip (10X Genomics, #120236), following manufacturer’s instructions, and aiming for a recovery of 5,000 cells per sample. Library construction was carried out according to the manufacturer’s instructions and were sequenced on Illumina Hiseq 2000.

tag: tissue

value: Umbilical cord blood

tag: surface markers


title: MOLM13_IFNg_6hr_R1

city: Cambridge

first: Tony

last: D'Alessio

state: MA

address: 250 Massachusetts Avenue

country: USA

institute: Novartis Institutes for BioMedical Research

data_processing:
FASTQ files were created using bcl2fastq version 2.17.1.
Transcript and gene abundances from RNAseq libraries were estimated using salmon (Patro et al., Nature Methods 2017) version 0.8.2, run with default parameters plus --seqBias, --gcBias, and –useVBOpt, against the Gencode v25 transcriptome.
TMM scaling of the TPM values was performed as described in Robinson and Oshlack (Genome Biology, 2010).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. Last 6 columns contain gene metadata.
Supplementary_files_format_and_content: Matrix table with TPM (transripts per million) counts for every gene and every sample. Last 6 columns contain gene metadata.
Supplementary_files_format_and_content: Matrix table with trimmed mean of M values (TMM)-scaled TPM counts for every gene and every sample. Last 6 columns contain gene metadata.

source_name: cancer cell line

growth_protocol: MOLM13, SEM, HCC827 cells were cultured in RPMI with 10% FBS. Cells were expanded and maintained in 0.5-1 million cells/ml. For each cell line, 10 million cells were collected for IFNg treatment

extract_protocol:
The total RNA for each sample was extracted using the PureLink™ RNA Mini Kit (Invitrogen Catalog #12183018A). The RNA quality was assessed using the Bioanalyzer 2100 (Agilent) to ensure RIN scores for all samples were above 9.0. RNA samples were diluted to 4ng/μl for RNA sequencing.
Total RNA was quantified using the Agilent RNA 6000 Nano Kit (catalog number 5067-1511) on the Agilent 2100 BioAnalyzer. Two hundred nanograms of high purity RNA (RNA Integrity Number 7.0 or greater) was used as input to the Illumina TruSeq Stranded mRNA Library Prep Kit, High Throughput (catalog number RS-122-2103), and the sample libraries were generated per manufacturer’s specifications on the Hamilton STAR robotics platform. The PCR amplified RNA-Seq library products were then quantified using the Advanced Analytical Fragment Analyzer Standard Sensitivity NGS Fragment Analysis Kit (catalog number DNF-473).

treatment_protocol: MOLM13, SEM, HCC827 cells were treated with 100ng/ml human IFNg (Peprotech Catalog #300-02). Cell lysates were collected at 0hr, 6hrs, 24hrs post IFNg treatment. Samples were prepared in triplicates.

value: 100 ng/ml interferon gamma

tag: time

value: 6 hours


title: KLp_3_mRNA

city: Oslo

first: Magnus

middle: D.

last: Vigeland

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

description: processed data file: counts_gencode.M16_LEFT.txt

data_processing:
Trimming of fastq files with Trim Galore! (v0.4.3; default parameters).
RRBS alignment to mm10, by Bismark v0.20, powered by bowtie2.
RRBS analysis of methylated/unmethylated read counts, by R package edgeR.
RNA-Seq alignment and feature counts, by R package Rsubread.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bismark coverage file: Tab-delimited file with one row for each covered cytosine position in the experiment, and the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
Supplementary_files_format_and_content: counts_gencode.M16_LEFT.txt: Feature counts: Tab-delimited file with one row per gene. The first column has Gene ID (Ensembl), followed by one column per sample, with unnormalised counts.

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN positive nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

value: Hippocampus

value: Kainate

tag: neun

value: positive

tag: biol. repl.


title: MLPs: Multi-Lymphoid progenitors sorted on day 0


title: MOLM13_IFNg_24hr_R3

value: 24 hours


title: MPPs: Multipotent progenitors sorted on day 0

source_name: Multipotent progenitors sorted on day 0


title: WT.4hr.Ribo-seq

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1


title: KLn_3_mRNA


title: SEM_IFNg_0hr_R2

value: SEM

value: 0 hours


title: SLp_2_mRNA

value: Sham


title: MOLM13_IFNg_24hr_R2


title: HSCs: Hematopoietic Stem cells sorted on day 0


title: WT.2hr.Ribo-seq

description: Ribosome Profiling

value: Tm treatment for 2hr


title: KLp_2_mRNA


title: WT.1hr.Ribo-seq

description: Ribosome Profiling

value: Tm treatment for 1hr


title: MOLM13_IFNg_24hr_R1


title: Bcells_TreatedwithPEG_Sample_2

description: B-cells treated with PEG

data_processing:
Alignment of the FASTQ Files were performed using bowtie2 (version 2.2.6) aligner. Alignment was done using using  --no-mixed --no-discordant flags to eliminate ambiguous read pairs and only counting reads where both pairs were mapped. PE data was directly converted to sorted BAM format using the samtools API.
BAM files were converted into EntrezGene count files using the summarizeOverlaps function in the GenomicAlignments package (v 1.8.4) using "union" mode, dropping reads mapped to multiple features. Reads were counted using the MM10 and HG19 genomes downloaded from the UCSD Genome Browser database.
Multi-mapping reads were corrected in 2 steps. First, reads that mapped to both genomes but aligned within a gene boundary for only one genome were assigned to aligned gene boundary and genome. Second, reads that mapped gene boundaries for both human and mouse genomes were evenly split between both genes. For example if a read mapped to Human Gene A that already had 4 reads mapped to it, and Mouse Gene B that already had 6 reads assigned to it, then Gene A would receive 0.4 reads, and Gene B would receive 0.6 reads.   Additional details for the correctly algorithm can be found in the associated publication.  Uploaded count files have been aligned, mapped, and corrected using these methods.
Genome_build: Human (HG19) and Mouse (MM10) genomes were downloaded from the Illumina igenome database (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) for indexing and aligment with bowtie2. For generation of count files, MM10 and HG19 genomes were downloaded from the USCD Genome Browser database (http://hgdownload.soe.ucsc.edu/downloads.html)
Supplementary_files_format_and_content: Count Files contain the corrected count values for Human and Mouse genes.

source_name: Human B cell line

growth_protocol: Tcf3-/- mouse embryonic stem cells were cultured in DMEM media supplemented with 10% foetal bovineserum and murine LIF. Human B lymphocytes were cultured in RPMI media supplemented with 20% foetal bovine serum

extract_protocol:
The cells were processed using the Qiagen RNA extraction kit for isolating the RNA
RNA Samples isolated from the heterokaryons were further processed to generate sequencing libraries using a Truseq RNA library Prep Kit.
The libraries were then analyzed on an Illumina HiSeq 2000 sequencer using 100 bp paired-end sequencing.

treatment_protocol: Tc3-/- mouse embryonic stem cells were labeled with Vybrant DiD and Human B lymphocytes were labeled with Vybrant DiO. Both labeled cells were mixed and treated withpolyethylene glycol (PEG) at 37 deg for a maximum period of 2.5 mins. Cells were then resuspended and washed with DMEM and plated in DMEM media supplemented with 10% foetal bovine serum and mouse LIF. Finally at specific timepoints the cells labeled with both dyes were sorted by flow cytometry for RNA extraction.

value: Human B cell line

tag: strain


title: MOLM13_IFNg_0hr_R3


title: WT.0hr.Ribo-seq_rep2

description: Ribosome Profiling


title: KLn_2_mRNA

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN negative nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify approximately 0.05 ng mRNA from total RNA, with 15 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

value: negative


title: MOLM13_IFNg_0hr_R2


title: Bcells_TreatedwithPEG_Sample_3

description: B-cells treated with PEG


title: WT.0hr.Ribo-seq_rep1

description: Ribosome Profiling


title: Bcells_TreatedwithPEG_Sample_1

description: B-cells treated with PEG


title: MOLM13_IFNg_0hr_R1


title: eS7_WT.0hr.Ribo-seq_rep1

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1 RPS7a::HisMX6 RPS7b::natNT2 pRS315-RPS7a-3HA


title: pH7_3

city: La Plata

first: Gonzalo

middle: A

last: Torres Tejerizo

state: Buenos Aires

address: Calle 49 y 115

country: Argentina

institute: Instituto de Biotecnología y Biología Molecular

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence with Trimmomatic, then mapped to whole genome using bowtie2
The resulting bam files were loaded in ReadXplorer 2 (Hilker R 2016 https://doi.org/10.1093/bioinformatics/btw541), and the raw data file was exported.
ReadXplorer 2 (Hilker R 2016 https://doi.org/10.1093/bioinformatics/btw541) predicted also TSS and operons. It also performed the DESEQ2 analyses
Genome_build: GCA_000577275.2
Supplementary_files_format_and_content: Nilsson_raw_count_data.xls; 2019-10-10_operones.xls;20191010_TSS.xls;2019_10_11_deseq.xls (raw counts data, operons detections, TSS detection and DESEQ2 analyses, respectevely)

organism: Rhizobium favelukesii

source_name: Batch culture pH 7

growth_protocol: R. favelukesii LPU83 was cultivated (SG medium) at pH 4.6 and pH 7.0.

extract_protocol:
RNA Protect (Qiagen) reagent was added and cells harvested, the pellet was frozen in liquid nitrogen. The commercial kit RNeasy® Protect Bacteria Mini Kit (Qiagen) was used to the RNA extraction and DNA removed with DNase I (Qiagen). The depletion of the ribosomal RNA was performed with a commercial kit (Ribo-Zero rRNA removal kit, Illumina Inc.).
The cDNA library was made with the commercial kit TruSeq® mRNA Sample Preparation (stranded) (Illumina Inc., San Diego, U.S.A.).

tag: culture condition

value: Batch culture pH 7


title: pH7_2


title: WT L4 worms fed Sphingomonas_rep4

city: Los Angeles

first: Sean

last: Curran

state: CA

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

description:
Y3_4
fpkm.txt
ReadCounts.txt
Yellow_DESeq2.txt

data_processing:
Raw reads were first cleaned by removing reads containing adapter, reads contraining ploy-N , and low quality reads. Base quality and phred score relationship with CASAVA v1.8 software from Illumina was used for QC.
Index of reference genome was built using Bowtie v2.2.3 on files available publicly and paired-end clean reads were aligned to reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count reads numbers mapped to each gene. FPKM of each gene was calculated based on length of gene and reads count mapped. FPKM is most commonly used currently (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups was performed using DESeq2 R package (1.18.0). Resulting p-values were adjusted using Benjamini and Hochberg's approach.
Genome_build: ce11
Supplementary_files_format_and_content: txt file contains fpkm/read counts for all samples and DESeq results with normalized read counts comparing WT on OP50 and WT on other diets at L4 stage.

organism: Caenorhabditis elegans

source_name: L4 WT C elegans - whole animal

growth_protocol: Grew N2 wildtype worms on each bacterial diet for 30+ generations before egg prep synchronization and collection at the L4 larval stage

extract_protocol:
Animals are homogenized in Trizol and RNA extraction is performed following protocol in Zymo Direct-zol RNA Isolation Kit. 1ug of RNA was used per sample for library construction using NEBNext® UltraTM RNA Library Prep Kit  for Illumina® (NEB, USA).
Sequencing libraries were generated following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: N2 wildtype worms were fed to one of the six bacterial diets for 30+ generations

value: whole animal

value: N2 Bristol

tag: genotype

value: wildtype

value: Sphingomonas


title: WT L4 worms fed Sphingomonas_rep3

description:
Y3_3
fpkm.txt
ReadCounts.txt
Yellow_DESeq2.txt


title: HCC827_IFNg_6hr_R2

value: 100 ng/ml interferon gamma

value: 6 hours


title: HCC827_IFNg_6hr_R3


title: WT L4 worms fed Sphingomonas_rep2

description:
Y3_2
fpkm.txt
ReadCounts.txt
Yellow_DESeq2.txt


title: SEM_IFNg_0hr_R3


title: pH4_3

source_name: Batch culture pH 4.6

value: Batch culture pH 4.6


title: pH4_2


title: B67_2008

city: Cardiff

first: Matthew

middle: John

last: Smalley

state: Cardiff

address: Hadyn Ellis Building, Maindy Road

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description: MS 1166.1

data_processing:
Raw FASTQ sequence files were quality control checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
To estimate gene expression, reads were aligned to the mouse genome (build 38) using StarAlign with no more than three mismatches, and only uniquely mapped reads permitted. Reads whose ratio of mismatches to mapped length was greater than 0.10 were also discarded. All other parameters were set to their defaults for un-stranded alignment.
Read counts across each gene were calculated by HTSeq-count (B67_xxxx_normcounts.txt)
The expression level, based on Fragments Per Kilobase per Million fragments mapped (FPKM), of each gene present in the mouse GTF annotation (build 38) file downloaded from Ensembl [14] was estimated using Cufflinks [15] with library type defined as “fr-unstranded”. All other parameters were set to defaults.
FPKMs from multiple samples were merged to generate a gene-by-sample matrix using a custom Perl script for input into downstream signature scoring algorithms.
Non-negative matrix factorization (NMF) was used to cluster tumor gene expression data. Only the most highly expressed and variable genes were chosen for clustering according to the following criteria: (mean FPKM+SD)>1.00 and CV>0.10, where CV = coefficient of variation. The underlying principle of NMF is dimensionality reduction in which a small number of meta-genes, each defined as a positive linear combination of the genes in the expression data, are identified and then used to group samples into clusters based on the gene expression pattern of the samples as positive linear combinations of these meta-genes. Using the R package NMF [18], factorization rank k was chosen by computing the clustering for k = 2–6 against 50 random initializations of both the actual and a permuted gene expression matrix, and selecting the k value achieving the largest difference between cophenetic correlation coefficients calculated from the actual and permutated data. For further visual confirmation of a sensible choice of k, consensus matrices were generated corresponding to different k values. To achieve stability, the NMF algorithm was then run against 200 perturbations of each gene expression matrix at the chosen value of k = 3.
Read count normalistion was repeated excluding B67_1006 (Sample_B67_xxxx_norm2.txt)
Read counts were input to DESeq2 to detect differential expression between high amplification and non/low-amplification samples excluding B67_1006
Genome_build: Mouse genome build 38
Supplementary_files_format_and_content: .txt files each containing normalised read counts for a single sample across each gene. First set of normalization in files format B67_xxxx_normcounts.txt. Rerun normalization exluding B67_1006 in files format Sample_B67_xxxx_norm2.txt.

source_name: Mammary tumor

growth_protocol: N/A - RNA harvested from snap frozen tumor material from a euthanased genetically modified mouse.

extract_protocol:
Total RNA was isolated from tissues using Trizol (Life Technologies, Paisley, UK) or the RNeasy kit (QIAGEN, Manchester, UK) according to manufacturer’s protocol. Genomic DNA was removed from 500ng of total RNA using the genomic DNA eliminator column from RNeasy Plus Micro Kit (QIAGEN) and rRNA removed using RiboZero (Epicentre, Wisconsin, USA) following manufacturer’s instructions.
Strand-specific libraries were created using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Hitchin, Herts, UK) and 20ng of the rRNA depleted RNA. Final libraries were quantified using qPCR and clustered at a molarity of 14.5 pM, sequencing was performed on an Illumina HiSeq 2500 using 2x76 cycles of version 3 SBS chemistry.

tag: reproductive history

value: Parous

tag: tumor diagnosis

value: Adenocarcinoma (No Special Type)

tag: amplification status of erbb2/neu locus

value: Non / low amplification


title: B67_1006

description: MS 1156.1

value: Mammary Sarcoma


title: HCC827_IFNg_6hr_R1


title: B67_1010

description: MS 1210.1

value: Metaplastic Adenosquamous Carcinoma


title: WT L4 worms fed Methylobacterium_rep4

description:
R3_4
fpkm.txt
ReadCounts.txt
Red_DESeq2.txt

value: Methylobacterium


title: B67_2007

description: MS 1349.1


title: HCC827_IFNg_24hr_R3

value: 24 hours


title: WT L4 worms fed Sphingomonas_rep1

description:
Y3_1
fpkm.txt
ReadCounts.txt
Yellow_DESeq2.txt


title: HCC827_IFNg_24hr_R2


title: pH4_1


title: B67_1005

description: MS 1155.3

value: High Amplification


title: WT L4 worms fed Methylobacterium_rep3

description:
R3_3
fpkm.txt
ReadCounts.txt
Red_DESeq2.txt


title: HNHx_ABE8e_Rep3

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Raw reads were trimmed and filtered using fastp version version 0.20.0
Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
variants were called using HaplotypeCaller (GATK version 4.1.2.0)
Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
Supplementary_files_format_and_content: vcf files and Tab delimited text file containing transcript level normalized counts (TPM)

source_name: HEK cells

growth_protocol: DMEM grwoth medium supplemented with 10% FBS and 1% P/S

extract_protocol:
Detachment with TryplE, wash with PBS, lysis in RLT buffer and RNA isolation following RNAeasy protocol
total RNA

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000

value: HEK

tag: treatment method

value: Lipofection

tag: treatment type


title: HCC827_IFNg_24hr_R1


title: B67_1003

description: MS 1218.2


title: B67_1002

description: MS 1163.2

value: Virgin


title: WT L4 worms fed Methylobacterium_rep2

description:
R3_2
fpkm.txt
ReadCounts.txt
Red_DESeq2.txt

value: whole animal

value: N2 Bristol


title: HNHx_ABE8e_Rep2


title: WT L4 worms fed Methylobacterium_rep1

description:
R3_1
fpkm.txt
ReadCounts.txt
Red_DESeq2.txt
R1 fastq unavailable. Only the R2 fastq is available.

value: wildtype


title: HCC827_IFNg_0hr_R3

value: 0 hours


title: HCC827_IFNg_0hr_R2


title: HNHx_ABE8e_Rep1


title: B67_1001

description: MS 1163.1


title: WT L4 worms fed Xanthomonas_rep4

description:
Oran_4
fpkm.txt
ReadCounts.txt
Orange_DESeq2.txt

value: Xanthomonas


title: B67_0004

description: MS 1213.1


title: HNHx_ABEmax7.10_Rep3


title: WT L4 worms fed Xanthomonas_rep3

description:
Oran_3
fpkm.txt
ReadCounts.txt
Orange_DESeq2.txt


title: HNHx_ABEmax7.10_Rep2


title: HCC827_IFNg_0hr_R1


title: UT_1385

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

description:
FLS cells from Healthy Donor untreated control.
FLS cells from Healthy Donor.

library_source: genomic

data_processing:
Merging of fastq files for each sample, followed by QC with FASTQC and adaptor trimming.
Alignment with bowtie2 using -X 2000 for large inserts followed by removal of PCR duplicates and low quality mapped reads.
Combine bam files from technical replicates followed by peak calling using MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: bigWig enriched for chromatin occupancy over controls.

molecule: genomic DNA

source_name: Fibroblast like Synoviocytes

growth_protocol: RA-FLS (3 RA and 3 healthy donors) were seeded at 300,000 cells/well in 6-well plates and incubated overnight.

extract_protocol:
See Buenrostro et. al (2013).
Illumina Library Construction.

treatment_protocol: Cells were treated with JQ1+ (1µM) or along with 1 ng/ml IL-1β and continued incubation for another 24 hrs. FLS were trypsinized, washed, counted for viability and aliquoted at 7500 cells/vial in 1 ml freezing media and frozen at -80oC, and then in liquid N2 according to vendor’s protocol (Epinomics, CA, USA).

tag: diagnosis

value: Healthy

tag: cell type

value: Fibroblast like Synoviocytes

value: Untreated control

tag: donor


title: pH7_1

value: Batch culture pH 7


title: HNHx_ABEmax7.10_Rep1

tag: cell line


title: UT_1359

description:
RA FLS cells untreated control.
RA FLS cells.

value: Rheumatoid arthritis

tag: treatment


title: WT L4 worms fed Xanthomonas_rep2

description:
Oran_2
fpkm.txt
ReadCounts.txt
Orange_DESeq2.txt

tag: tissue


title: WT L4 worms fed Xanthomonas_rep1

description:
Oran_1
fpkm.txt
ReadCounts.txt
Orange_DESeq2.txt


title: ABE8e_Rep3


title: JQ1_IL1b_1399

description:
RA FLS cells treated with JQ1 and IL1b.
RA FLS cells.

value: JQ1 and IL1b


title: ISF0985_aNSCS

city: Planegg

first: Jovica

last: Ninkovic

address: Grosshaderner strasse 9

country: Germany

institute: LMU Munich

description: FACS based purification

data_processing:
FASTQ files were used for the transcript counting using kallisto pipeline (the reference transcriptome was Muss musculus full transcriptome (mm10))
Sleuth pipeline was used for statistical analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: prospectively isolated adult neural stem cells

growth_protocol: cells are isolated from gfap:GFP transgenic animals using FACS protocol as previously described (Fischer et al., 2011)

extract_protocol:
RNA is isolated using PicoPure RNA isolation Kit (ThermoFisher; KIT0204) and cDNA was made using SMART-Seq v4 Ultra Low Input RNA Kit (Takara, Cat. No. 634888).
MicroPlex Library Preparation Kit v2 and processed according to the manufacturer ́s instruction. Deep sequencing was performed on Illumina HiSeq system with 100bp paired-end reads

treatment_protocol: no treatment

tag: background

value: CD1/C57BL/6 mixed background

value: neural stem cells

tag: cell  subtype

value: activated EGFR+ cells

tag: cell  markers

value: Prom1+, EGFR+, GFAP+

tag: age

value: 3 months old animals


title: ISF0984_aNSCS

description: FACS based purification


title: ABE8e_Rep2

value: HEK

value: Lipofection


title: JQ1_IL1b_1387


title: WT L4 worms fed OP50_rep3

description:
OP50_3
fpkm.txt
ReadCounts.txt

value: whole animal

tag: strain

value: N2 Bristol

value: OP50 (control)


title: ISF0982_aNSCS

description: FACS based purification


title: WT L4 worms fed OP50_rep4

description:
OP50_4
fpkm.txt
ReadCounts.txt
R1 fastq unavailable. Only the R2 fastq is available.

tag: genotype

value: wildtype


title: ABE8e_Rep1


title: JQ1_IL1b_1385

description:
FLS cells from Healthy Donor treated with JQ1 and IL1b.
FLS cells from Healthy Donor.

value: Healthy


title: WT L4 worms fed OP50_rep1

description:
OP50_1
fpkm.txt
ReadCounts.txt


title: JQ1_IL1b_1359

value: Fibroblast like Synoviocytes


title: JQ1_IL1b_1305


title: ABEmax_Rep2


title: ABEmax_Rep3


title: WT L4 worms fed OP50_rep2

description:
OP50_2
fpkm.txt
ReadCounts.txt


title: KO male BM donor_50

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: Isolated CD68+ cells from atherosclerotic lesions from bone marrow transplanted Bco1-/- (KO) mice

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (bw), count table (txt)

source_name: Mouse atherosclerotic plaque CD68+ cells

extract_protocol:
Cells isolated by laser capture microdissection were pooled in a tube. Rna was isolated and purified using the PicoPure kit. DNAse was used. RNA samples with an RNA integrity number above six were amplified using the Automated Nugen Ovation Trio Low Input RNA kit (Nugen, Manchester, UK). Samples were sequenced using the Illumina HiSeq2500 Single-end (Illumina, San Diego, CA) and the results were analyzed using Gene Set Enrichment Analysis (GSEA, Broad Institute Inc., MIT, Cambridge, MA).
The NYU Genome Technology Center constructed the libraries followed their standard protocol

treatment_protocol: Recipient mice were irradiated and transplanted with bone marrow from either WT or KO mice

value: CD68+ myeloid cells

tag: cells isolated from


title: KO female BM donor_46

value: atherosclerotic lesions from bone marrow transplanted Bco1-/- (KO) mice


title: ISF0983_aNSCS

description: FACS based purification


title: WT male BM donor_47

description: Isolated CD68+ cells from atherosclerotic lesions from bone marrow transplanted Wild-type mice


title: WT female BM donor_44

value: atherosclerotic lesions from bone marrow transplanted Wild-type mice


title: WT L4 worms fed HT115_rep4

description:
HT115_4
fpkm.txt
ReadCounts.txt
HT115_DESeq2.txt


title: ABEmax_Rep1


title: JQ1_IL1b_1303

value: JQ1 and IL1b


title: JQ1_1399

description:
RA FLS cells treated with JQ1.
RA FLS cells.

value: Rheumatoid arthritis


title: Day 6 - mixed samples

city: San Francisco

first: Todd

last: McDevitt

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

description:
mixed samples:
Unencapsulated WT Aggregates at Day 6
Unencapsulated CDH1 KD Aggregates at Day 6
Unencapsulated Mixed 25% WT:75 % CDH1 Aggregates at Day 6
Encapsulated WT Aggregates at Day 6
Encapsulated CDH1 KD Aggregates at Day 6
Encapsulated Mixed 25% WT:75 % CDH1 Aggregates at Day 6

data_processing:
Demultiplexing sample reads with cellranger demux v1.2.0
Align samples to GRCh38 and generate counts with cellranger count v1.2.0
Demultiplex MultiSeq barcodes with bcl2fastq v2.20.0
Assign barcodes to individual UMIs with deMULTIplex v1.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix market formatted counts, tab separated value formatted barcodes, features, sample barcodes

source_name: mixed samples (day6_unencap_wt, day6_unenap_cdh1, day6_unencap_mixed, day6_encap_wt, day6_encap_cdh1, day6_encap_mixed)

growth_protocol: Aggregates were grown in mTeSR1 in suspenion culture for 6 days

extract_protocol:
Aggregates were unencapsulated from agarose by washing in sodium citrate, then all aggregates were dissociated in Accutase for 30 minutes. Cells for each condition were barcoded using the MuliSeq protocol (Mcginnis et al 2018).
Individual GEMs were then generated using the 10x genomics V2 library construction kit with additional anchor specific primers for Multi-Seq. Barcode libraries were generated with KAPA HiFi Hotstart protocol to functionalize with the P5 sequencing adapter and library-specific RPIX barcode. Sample libraries were sequenced on an Illumina NovaSeq 6000 to a depth of >30k reads/cell. Barcode libraries were sequenced on an Illumina NextSeq 500 to an average depth of ~10k reads/barcode.

treatment_protocol: DOX inducible CRISPRi CDH1-KD cells were pre-treated with DOX for 5 days prior to aggregation and then force aggregated with WT cells

value: hiPSC

tag: time

value: day 6

value: mixed samples (wild type, knockdown, mixed)

value: mixed samples (2D, unencapsulated, encapsulated)


title: WT L4 worms fed HT115_rep2

description:
HT115_2
fpkm.txt
ReadCounts.txt
HT115_DESeq2.txt


title: KO male BM donor_42


title: WT female BM donor_39


title: Day 3 - mixed samples

description:
mixed samples:
Unencapsulated WT Aggregates at Day 3
Unencapsulated CDH1 KD Aggregates at Day 3
Unencapsulated Mixed 25% WT:75 % CDH1 Aggregates at Day 3
Encapsulated WT Aggregates at Day 3
Encapsulated CDH1 KD Aggregates at Day 3
Encapsulated Mixed 25% WT:75 % CDH1 Aggregates at Day 3

source_name: mixed samples (day3_unencap_wt, day3_unenap_cdh1, day3_unencap_mixed, day3_encap_wt, day3_encap_cdh1, day3_encap_mixed)

value: day 3


title: WT L4 worms fed HT115_rep1

description:
HT115_1
fpkm.txt
ReadCounts.txt
HT115_DESeq2.txt


title: JQ1_1387


title: Day 1 - mixed samples

description:
mixed samples:
2D WT hiPSCs at day 1
2D DOX-inducible CRISPRi CDH1 KD hiPSCs at Day 1
Unencapsulated WT Aggregates at Day 1
Unencapsulated CDH1 KD Aggregates at Day 1
Unencapsulated Mixed 25% WT:75 % CDH1 Aggregates at Day 1
Encapsulated WT Aggregates at Day 1
Encapsulated CDH1 KD Aggregates at Day 1
Encapsulated Mixed 25% WT:75 % CDH1 Aggregates at Day 1

source_name: mixed samples (day1_2d_wt, day1_2d_cdh1, day1_unencap_wt, day1_unenap_cdh1, day1_unencap_mixed, day1_encap_wt, day1_encap_cdh1, day1_encap_mixed)

value: day 1


title: JQ1_1385

description:
FLS cells from Healthy Donor treated with JQ1.
FLS cells from Healthy Donor.


title: WT female Bone Marrow (BM) donor_27


title: Bco1-/- (KO) Female BM donor_38


title: 12d-TNFa treatment+withdraw-10d+12h TNFa, ATAC-seq, rep2

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
ATAC-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ATAC-seq reads were mapped to UCSC hg38 genome by Bowtie2 (2.3.4.2)
ATAC-seq data were filtered using samtools rmdup to remove potential PCR duplicates
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension of average fragments size.

source_name: 12d-TNFa treated HEK 293 cells+withdraw-10d+12h-TNFa

extract_protocol:
45,000 cells were collected and resuspended in 50 μL cold ATAC-Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in sterile water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Then the cells were incubated on ice for 3 minutes. The nuclei were washed with 1 mL cold ATAC-Resuspension Buffer containing 0.1% Tween-20 and centrifuged at 500 g and 4 ℃ for 10 minutes. The cell pellet were resuspended in 50 μL transposition mix (10 μL 5×TTBL, 5 μL TTE Mix V50, 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, 17.5 μL ddH2O) with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501) and incubated at 37 ℃ for 30 minutes with shaking in a thermomixer. The reactions were cleaned up with DNA Clean & Concentrator-5 (Zymo Research D4014).
The ATAC-seq libraries are prepared as previously described (Corces et al., 2017) with minor modifications. After transposition reaction, the libraries were constructed through PCR amplification with TruePrep Index Kit V2 for Illumina (Vazyme TD202) to barcode samples.

treatment_protocol:
The final concentration of TNF (high, default) is 50 ng/mL.
The final concentration of TNF (low, specified) is 0.4 ng/mL.

value: HEK 293 transfected with reporter construct

value: somatic cell

tag: tissue source

value: embryonic kidney

value: TNF-α treatment 12 days, then withdraw to recover 10 days, and add TNF-α 12 hours


title: JQ1_1359


title: WT L4 worms fed HB101_rep3

description:
HB101_3
fpkm.txt
ReadCounts.txt
HB101_DESeq2.txt

value: whole animal

value: N2 Bristol

value: wildtype


title: SLp_3_RRBS

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). DNA was extracted from NeuN positive nuclei with MasterPure Complete DNA and RNA Purification Kit (Epicentre cat.no. MC85200), following the DNA purification protocol for cell samples.
100ng DNA was digested with MspI (New England Biolabs cat.no. R0106S), followed by gap filling and A-tailing using Klenow fragment (NEB cat.no. M0212S) and dCTP, dGTP, and dATP (NEB cat.no. N0446S). Clean-up was performed using 3 volumes of AMPure XP beads (Beckman Coulter cat.no. A63880). 1 µL of a 1:10 dilution of adaptors from Illumina kit FC-121-3001/2 or FC-121-4001/2 was used for indexing of samples, with ligation performed by T4 ligase (NEB cat.no. M0202S). A two-sided size selection using AMPure XP beads was performed to recover ligation products between approximately 200 and 400 bp. Size selected fragments were bisulfite converted with the EpiTect Bisulfite Kit (Qiagen cat.no. 59104) using the procedure for FFPE samples and two consecutive rounds of the incubations given in the protocol. Bisulfite converted samples were amplified using TruSeq forward and reverse primers and PfuTurbo Cx hotstart DNA polymerase (Agilent cat.no. 600412), followed by AMPure XP clean-up.

value: Hippocampus

value: Sham

tag: neun

value: positive

tag: biol. repl.


title: WT L4 worms fed HB101_rep2

description:
HB101_2
fpkm.txt
ReadCounts.txt
HB101_DESeq2.txt


title: 12d-TNFa treatment+withdraw-10d+12h TNFa, ATAC-seq, rep1


title: SLn_3_RRBS

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). DNA was extracted from NeuN negative nuclei with MasterPure Complete DNA and RNA Purification Kit (Epicentre cat.no. MC85200), following the DNA purification protocol for cell samples.
100ng DNA was digested with MspI (New England Biolabs cat.no. R0106S), followed by gap filling and A-tailing using Klenow fragment (NEB cat.no. M0212S) and dCTP, dGTP, and dATP (NEB cat.no. N0446S). Clean-up was performed using 3 volumes of AMPure XP beads (Beckman Coulter cat.no. A63880). 1 µL of a 1:10 dilution of adaptors from Illumina kit FC-121-3001/2 or FC-121-4001/2 was used for indexing of samples, with ligation performed by T4 ligase (NEB cat.no. M0202S). A two-sided size selection using AMPure XP beads was performed to recover ligation products between approximately 200 and 400 bp. Size selected fragments were bisulfite converted with the EpiTect Bisulfite Kit (Qiagen cat.no. 59104) using the procedure for FFPE samples and two consecutive rounds of the incubations given in the protocol. Bisulfite converted samples were amplified using TruSeq forward and reverse primers and PfuTurbo Cx hotstart DNA polymerase (Agilent cat.no. 600412), followed by AMPure XP clean-up.

value: negative


title: JQ1_1305

tag: diagnosis

value: Healthy

value: Fibroblast like Synoviocytes


title: WT L4 worms fed HT115_rep3

description:
HT115_3
fpkm.txt
ReadCounts.txt
HT115_DESeq2.txt


title: 12d-TNFa treatment+withdraw-10d, ATAC-seq, rep2

source_name: 12d-TNFa treated HEK 293 cells+withdraw-10d

tag: cell type

value: TNF-α treatment 12 days, then withdraw to recover 10 days


title: KLp_3_RRBS

value: Kainate


title: DMSO_IL1b_1399

description:
RA FLS cells treated with DMSO and IL1b.
RA FLS cells.

value: Rheumatoid arthritis

value: DMSO and IL1b

tag: donor


title: JQ1_1303


title: WT L4 worms fed HB101_rep1

description:
HB101_1
fpkm.txt
ReadCounts.txt
HB101_DESeq2.txt


title: Roots_TG2R_2

first: Yongqiang

last: Liu

address: 1# West Beichen Road, Chaoyang Dist

department: Center for Genome Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Reads of raw data files were filtered in trimmomatic (v0.36) with parameter "ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50"
Filtered clean reads were mapped to reference genome using HISAT2 (v2.1.0) with parameter "--dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE）"
Clean reads were mapped to reference genes using bowtie2 (v2.2.5) with parameter "-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200"
normalized abundance of all the annotated genes were calculated by RSEM (v1.2.8) with parameter "default"
Genome_build: Oryza_sativa_Japonica (version_7.0_plantbiology_20181115)
Supplementary_files_format_and_content: Matrix table with normalized abundance for every gene with three repeats

organism: Oryza sativa Japonica Group

source_name: Rice roots

growth_protocol: Rice seedlings were grown in Kimura solution for hydroponic culture for 14 days and change the solution every day in a growth chamber with 12 h light (28°C) and 12 h dark (25°C) photoperiod, ~70% humidity and about 200 μmol m-2 s-1 photon density.

extract_protocol:
Rice seedling roots were ground in liquid nitrogen and RNA was extracted using Trizol reagent as the manufacturer's protocol.
Poly (A) RNA from 1 mg total RNA was purified with OligodT beads and then used to generate the cDNA libraries

value: roots

tag: developmental stage

value: 14 day after gemination

value: OsTCP19 overexpression line


title: KLn_3_RRBS

source_name: Hippocampus

tag: treatment


title: Roots_TG2R_3

tag: tissue


title: 12d-TNFa treatment+withdraw-10d, ATAC-seq, rep1

tag: cell line

value: HEK 293 transfected with reporter construct

value: somatic cell

value: embryonic kidney


title: 12h-TNFa treatment, ATAC-seq, rep2

source_name: 12h-TNFa treated HEK 293 cells

value: TNF-α treatment 12 hours


title: DMSO_IL1b_1387


title: SLp_2_RRBS

value: Hippocampus


title: DMSO_IL1b_1385

description:
FLS cells from Healthy Donor treated with DMSO and IL1b.
FLS cells from Healthy Donor.


title: 12h-TNFa treatment, ATAC-seq, rep1


title: non-treated control, ATAC-seq, rep2

source_name: non-treated HEK 293

value: no treatment


title: SLn_2_RRBS

value: Sham


title: Roots_TG2R_1


title: Roots_TG1R_3


title: KLp_2_RRBS

value: positive


title: non-treated control, ATAC-seq, rep1


title: DMSO_IL1b_1359


title: DMSO_IL1b_1305

value: Healthy


title: Roots_TG1R_2


title: SLp_1_RRBS


title: WT L4 worms fed HB101_rep4

description:
HB101_4
fpkm.txt
ReadCounts.txt
HB101_DESeq2.txt
R2 fastq unavailable. Only the R1 fastq is available.

value: whole animal

value: N2 Bristol

value: wildtype


title: DMSO_IL1b_1303

value: Fibroblast like Synoviocytes


title: Roots_TG1R_1


title: IP4_replicate2: SH-SY5Y LSM12 shRNA TRAP RNA

city: Ulsan

first: Chunghun

last: Lim

address: 50 UNIST-gil

country: South Korea

institute: UNIST

data_processing:
Clusters were generated in the flow cell on the cBot automated cluster-generation system (Illumina).
RNA sequencing was performed on a NovaSeq 6000 system (Illumina) with a 2x100-bp read length (DNA Link).
Sequence reads were first mapped to the reference genome (Human hg19) using Tophat (v2.0.13), yielding 50–75 million mapped reads per sample.
The aligned results were added to Cuffdiff (v2.2.0), and differentially expressed genes (DEGs) were identified using the Cuffdiff output file, “gene_exp.diff”.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Human neuroblastoma SH-SY5Y cell was cultured in Dulbecco’s Modified Eagle Medium (HyClone) supplemented with 10% fetal bovine serum and 1% antibiotics and maintained at 37C in a humidified incubator with 95% air and 5% CO2.

extract_protocol:
SH SY5Y cells stably expressing GFP-RPL10A were collected and lysed in a lysis buffer (20 mM HEPES-KOH pH 7.4, 150 mM KCl, 10 mM MgCl2, 1%(v/v) NP-40, 100 μg/ml cycloheximide, 1 mM dithiothreitol [DTT], 1 mM phenylmethylsulfonyl fluoride [PMSF], and 200 U/ml RNase inhibitor) at 4C for 15 minutes with gentle rocking. Lysates were first centrifuged at 2,000 x g for 5 minutes at 4C, and the supernatant was collected and further clarified by centrifugation at 20,000 x g for 10 minutes at 4C. After clarification by centrifugation, 30 ul of soluble extracts were retained as input, and the remaining soluble extract was incubated with anti-GFP antibody (NeuroMab) at 4C for 1.5 hours with gentle rocking. Pre-equilibrated Protein G magnetic beads (New England BioLabs) were added to the extracts and further incubated at 4C for 1.5 hours with gentle rocking. The beads were washed four times with a wash buffer (20 mM HEPES-KOH pH 7.4, 350 mM KCl, 5 mM MgCl2, 1%(v/v) NP-40, 100 μg/ml cycloheximide, 1 mM DTT, 1 mM PMSF, and 200 U/ml RNase inhibitor) prior to RNA extraction.
Input and translating ribosome-associated RNAs were purified using an RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from 50 ng of purified RNA samples using an rRNA depletion kit (New England BioLabs). cDNA libraries for RNA sequencing were generated using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions (New England BioLabs).

value: neuroblastoma

tag: genotype/variation

value: GFP-RPL10A stable cell

tag: molecule subtype

value: TRAP RNA


title: IP4_replicate1: SH-SY5Y LSM12 shRNA TRAP RNA


title: DMSO_1399

description:
RA FLS cells treated with DMSO.
RA FLS cells.

value: Rheumatoid arthritis

value: DMSO


title: Roots_WTR_3

value: roots

value: 14 day after gemination

value: wild-type


title: KLp_1_RRBS

value: Hippocampus

value: Kainate


title: KLn_1_RRBS

value: negative


title: DMSO_1387


title: DMSO_1385

description:
FLS cells from Healthy Donor treated with DMSO.
FLS cells from Healthy Donor.


title: Synovium_SIA

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

institute: University of Bern

data_processing:
Illumina RTA 1.18.66.3 was used for base calling
Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v3.0.1 (10x Genomics) mkfastq with standard parameters.
Cell Ranger v3.0.1 quant was used to map the demultiplexed reads to the reference genome (mm10, v3.0.0, 10x Genomics), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts per droplet and estimate the number of cells using standard parameters.
Seurat v3.1.0 was used under R v3.6.1 to first remove low quality cells expressing less than 300 genes or more than 20% mitochondrial genes or both. The filtered cells were clustered by similarity in gene expression and visualized. For the clusters marker genes were determined.
To compare between tissues, data sets were integrated follwing the recommended approach for SCT-transformed data in Seurat v3.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with UMI counts per gene per cell after filtering in Seurat (min.cells = 3, min.genes = 300)

source_name: Synovial eosinophil granulocytes

extract_protocol:
The  lungs of 3 mice were pooled for the sample Lung_OVA+SIA, 16 hind ankle joints (8 mice) were pooled for the sample Synovium_OVA+SIA and 24 hind ankle joints (12 mice) were pooled for the sample Synovium_SIA. Eosinophils were sorted via the markers CD45+ CD11b+ Siglec-F+. For each sample 8000 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) with Chromium Single Cell 3' v3 Gel Beads (10x Genomics) to generate single cell bead emulsions for reverse transcription and cell bar coding according to the manufacturers instructions
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v3 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v3 chemistry.

treatment_protocol: To trigger eosinophilic asthma, 6 weeks old Balb/c mice were sensitized twice with intraperitoneal injection of 100µg OVA/Alum mixture at day -20 and -13, and challenged three times with intranasal injection of 50µg OVA at day -2, -1 and 0. At day 0, mice were injected with 150µl K/BxN serum intraperitoneally for inducing SIA. Mice were challenged again at day 4, 5, 6 with intranasal injection of 50µg OVA and sacrificed at day 7.

value: Hind paw synovial tissue

value: Balb/c

value: CD45+CD11b+Siglec-F+ granulocytes

value: SIA

tag: time point

value: Day 7 post SIA


title: Input4_replicate2: SH-SY5Y LSM12 shRNA total RNA

value: total RNA


title: IP1_replicate1: SH-SY5Y control shRNA TRAP RNA

value: neuroblastoma


title: Input4_replicate1: SH-SY5Y LSM12 shRNA total RNA

value: GFP-RPL10A stable cell


title: Synovium_OVA+SIA

tag: strain

value: OVA+SIA


title: Input1_replicate2: SH-SY5Y control shRNA total RNA


title: Roots_WTR_2

tag: genotype


title: NOD_8_wks_untreated_2

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger pipeline
Genome_build: GRCm38
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Pancreatic islets

extract_protocol:
Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting cells were pelleted and resuspended in 10% FBS (HyClone) in PBS(pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics).
Samples were processed using the Chromium Single Cell 3’ Library & Gel Bead Kit following the manufacturer’s protocol.
10X Single Cell 3' v2

treatment_protocol: Mice at 6 weeks of age were treated intraperitoneally with 250μg anti-PD-1 (RMP1-14) on days 0, 3, and 6.

value: NOD/ShiLtJ (NOD)

value: untreated

tag: Sex

value: female

value: Pancreatic islet-infiltrating cells

tag: age

value: 8 weeks


title: NOD_8_wks_aPD1


title: Input1_replicate1: SH-SY5Y control shRNA total RNA


title: DMSO_1303

value: Healthy

value: Fibroblast like Synoviocytes

value: DMSO


title: SLn_1_RRBS

value: Hippocampus

value: Sham

value: negative


title: Input rep1

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: input

data_processing:
fastq files were obtained from CCHMC DNA core.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with the following configurations: -S -m 1 --best
sam files were converted to bam files using samtools.
Reads were sorted and duplicates were removed using samtools.
Peaks were identified using HOMER with the following configurations: -style factor -L 10 -F 10
Genome_build: mm9
Supplementary_files_format_and_content: tdf files were generated using igvtools
Supplementary_files_format_and_content: xlsx file were generated using HOMER as peak callers

source_name: kidney

growth_protocol: not applicable

extract_protocol:
not applicable
Sequencing libraries were generated using Rubicon ThruPLEX DNA sequencing kit (Rubicon Genomics, Ann Arbor MI)

treatment_protocol: not applicable

value: kidney

tag: Stage

value: newborn P0

tag: chip antibody

value: input DNA


title: NOD_8_wks_untreated_1


title: MERS-HKU9-N

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

description:
UTR and flanking region
293_np_vivo.out

data_processing:
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to SARS-CoV2 genome or other virus UTR regions or human hg38 with STAR as default parameters
calculate rpkm as icshape pipeline
calulate reverse transcript stop sites as icshape pipeline
calculate icSHAPE score as icshape pipeline
Genome_build: SARS-CoV2, SARS2,SARS,MERS,HKU1,HKU5,HKU9,NL63 UTR regions, human hg38
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Ensemble ID, second is gene length, third is RPKM, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score.

organism: Middle East respiratory syndrome-related coronavirus

source_name: in vitro refolding

growth_protocol: Huh7.5.1 cells were provided by Dr. Yang (Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College), and were maintained at 37°C, 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, cat.C11965500BT) supplemented with 10% fetal bovine serum (FBS, HyClone, cat.SH30396.03) and penicillin-streptomycin (GENOM, cat.GNM15140). SARS-CoV-2, Isolate IPBCAMS-YL01/2020 was obtained from a clinical sample at Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, which was passaged thrice in Vero cells (ATCC, CCL-81) before use. Infectious titers of SARS-CoV-2 were determined by plaque assay in Vero cells. For SARS-CoV-2 infection, Huh7.5.1 cells were cultured in T-175 flasks at a density of 5×106 cells for 16 h. The cells were briefly washed with DMEM and incubated with SARS-CoV-2/IPBCAMS-YL01/2020 for 1 h at a multiplicity of infection (MOI) of 0.05, then supplemented with DMEM maintenance medium, which was supplemented with 1% BSA(Sigma-Aldrich, cat.B2064)and penicillin-streptomycin, and  then cultured at 37°C, 5% CO2 for additional 30 h. Cultured cells were washed twice with PBS before collecting by cell scraper. All experiments involving live SARS-CoV-2 in these studies were performed in a biosafety level 3 facility.

extract_protocol:
After probing, samples were transferred immediately to ice in order to stop the reaction. After which it was centrifuged for 5 min at 500 ×g (4 ℃) and discarded the supernatant, cell pellets were resuspended in 6 mL TRIzol (Invitrogen, cat.15596018) and supplemented with 1/5 volumes of chloroform. The sample was vigorously vortexed for 15 sec and then incubated for 5 min at room temperature, after centrifuged for 15 min at 12,000 ×g (4 ℃), the upper aqueous phase was transferred to a clean 15 mL tube, then supplemented with 2 volumes of 100% ethanol and mixed up and down,  followed by column purification according to the manufacturer’s instructions (Hipure RNA pure Micro Kit, Magen, cat.R2144-03).
We isolated poly(A) RNA with the DynabeadsTM mRNA DIRECT TM kit as the manufacturer’s instructions with the next modification. Wash the ploy-dT beads with washing buffer B for 2 times after the first round of ploy(A) purification. Then perform a second ploy(A) enrichment using the beads for the first-round enriched ploy(A) RNA. Usually, about 1% ploy(A) RNA of the DMSO treated samples and 5‰ ploy(A) RNA of the NAI-N3 treated samples were yield.icSHAPE library were constructed from in vivo modified, in vitro modified or DMSO treated control RNA as previously described with the following modification. We designed the new library linker, reverse transcription (RT) primer, P5 and P7 amplification primer as previous description to adapt to the Illumina hiseq X system.       To simplify the library construction of UTR regions of many virus types, we merged the in vitro transcription RNA of different virus into one group according to their sequence variability. i.e.  RNA of SARS-CoV-2 (SARS2-C mutation), human NL63 (hNL63) and human HKU1 (hHKU1) was merged into a group (SARS2-C-NL63-HKU1). RNA of SARS and bat HKU5 (bHKU5) was merged into a group (SARS-HKU5). RNA of MERS and bat HKU9 was merged into a group (MERS-HKU9). RNA of SARS-CoV-2 with T mutation (SARS2-T) was a group independently.   Libraries of virus infection (modification in vivo, refolding and modification in vitro) was sequenced on Hiseq X system to approximately 200 million reads per replicates while libraries of virus for UTR regions were sequenced about 10-30 million reads per replicates. Though the reads were pair-end sequencing, only the R1 reads (*_1.fastq) which include the reverse transcription stop (RT stop) site were used to for further analysis in this study.
icSHAPE

treatment_protocol: For in vivo probing of RNA, NAI-N3 was added to the cell pellet at a final concentration of 100mM and then incubated at 37 ℃ for 5 min with mixing gently. For preparing negative control samples, an equal amount of DMSO (25μl, Sigma-Aldrich, cat. D2650) was added to the cell pellet.

value: MERS-CoV BtCoV-HKU9


title: Input rep2

description: input


title: Knock_down4

city: Edison

first: Ashutosh

last: Dharap

state: NJ

address: 65 James st

department: Neuroscience

institute: HackensackMeridian Health JFK Medical Center

data_processing:
The sequencing reads were aligned to the mouse reference genome GRCm38 using HISAT2 (v2.0). StringTie (v1.3) was then used to assemble the transcripts of each sample independently using mouse transcript annotations from Ensembl 81 as a guide.StringTie and gffcompare was then used to merge all the assemblies to create a StringTie merged gtf. Finally, the mRNA profiling was done using StringTie and Differentially expressed mRNAs were identified using Rpackage Ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: gtf files

source_name: Cerebral cortex

extract_protocol:
Animals were euthanized and the infarcted ipsilateral cortical tissues were immediately harvested and snap-frozen in liquid nitrogen before storing in -80°C. Total RNA was then isolated from the tissues using the mirVana total RNA isolation kit, followed by Dnase I tratment. The RNA integrity was evaluated using Bioanalyzer.
For  Negative control and Knockdown samples Poly(A) RNA sequencing, the library was prepared following Illumina’s truseq-stranded-mRNA sample preparation protocols. RNA integrity of total RNA sample received was checked using an Agilent Technologies 2100 Bioanalyzer.  The polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads and using two rounds of purification.  After purification the polyA RNA was fragmented using divalent cation containing buffer and elevated temperature. Quality control analysis and quantification of the DNA library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.  Paired-end sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.For the Sham samples,previously generated data from our lab was used. Please refer to  GEO accession number GSE112348 for the relevant details regarding sham samples.

treatment_protocol: In order to understand the role of eRNAs in mediating the post-stroke pathophysiology in vivo, we knocked-down the expression of eRNA_06347 in the mouse brain using sequence-specific locked nucleic acid (LNA) antisense oligos delivered via the lateral ventricles. Cohorts of mice underwent either eRNA_06347 knockdown or  Negative control oligo treatment, followed by a 1 h  Middle cerebral arterey occlusion(MCAO) and 6 h of reperfusion (n=3/group). A sham cohort (n=3/group) receiving  undergoing sham surgery served as healthy controls.Transient focal ischemia was induced using the MCAO method. Mice were anesthetized with 5% isoflurane and a midline neck incision was made to expose the common  carotid artery (CCA). A nick was made in CCA and a 6-0 silicon-coated filament was inserted and advanced through the internal carotid artery up to the middle cerebral artery (MCA) and left in place for 1 h to occlude blood flow into the MCA. Cerebral blood flow and body tem- perature were continuously monitored. The incision was sutured and the animals were returned to warm cages for recovery. After 1 h of occlusion, the filament was removed, the incision was sutured, and the mice were returned to their cages. Reperfusion was allowed for 6 h. For the sham cohort, midline neck incision was similarly done to expose the ECA; however, no filament was inserted to occlude the MCA.

tag: gender

value: Male

value: 9-12 weeks

value: eRNA_06347 knockdown


title: WGBS of 12d-TNFa treated HEK 293 cells with TET2 KO

description:
embryonic kidney cells
somatic cell
WGBS

data_processing:
RNA-seq basecalls performed by BGI, Shenzhen.
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantified by Cuffdiff.
ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC hg38 genome by Bowtie2 (2.3.4.2).
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates.
Enzymatic Methyl-seq reads in PE150 were firstly assessed by FASTQC software and then trimmed by trim_galore to remove adapters and low-quality bases. The filtered reads were then mapped to human genome (hg38) using the Bismark software (v0.22.3). Duplicate reads were discarded, and methylation information were called by Bismark.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: FPKM values were calculated by Cuffdiff and stored as tab-separated texts.
Supplementary_files_format_and_content: bigWig files were generated using IGV tools with fragment extension of average fragments size.

extract_protocol:
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were synthesized using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT.
The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.
ChIP-seq were performed as previously described (Xiong et al., Molecular Cell 64, 913-925).
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB). DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).
The NEBNext Enzymatic Methyl-seq Conversion Module (NEB E7125L) was used for measuring genome-wide DNA methylation level. Purified genomic DNA containing 0.05% CpG methylated pUC19 control DNA and 1% unmethylated lambda DNA was sheared to a mean length of 450 bp with Covaris M220 Focused-ultrasonicator. End repair, A-tailing, methylated adaptor ligation and size selection were performed on 125 ng fragmented genomic DNA with Kapa hyper prep kit (Kapa Biosystems KK8504) according to the manufacturer’s instructions. The methylated adaptor ligated DNA fragments were then treated with oxidation of 5mC and 5hmC, clean-up of TET2 converted DNA, denaturation of DNA, deamination of cytosines and clean-up of deaminated DNA using the NEBNext Enzymatic Methyl-seq Conversion Module (NEB E7125L). The deaminated DNA was amplified with KAPA HiFi Hotstart Uracil+ ReadyMix PCR kit using primers from NEBNext multiplex oligos for Illumina (index primers set 1) (NEB E7335) (Kapa Biosystems KK2801) according to the manufacturer’s protocol. PCR cycling condition was as follows: 98℃ for 45 s, followed by 7 cycles of 98℃ for 15 s, 60℃ for 30 s, 72℃ for 30 s, and final extension 72℃ for 1 min, then hold at 4℃. Libraries were sequenced on an Illumina NovaSeq 6000 using 150-bp paired-end mode.

value: TET2 KO for HEK 293 transfected with reporter construct

value: TNF-alpha treatment 12 days


title: Roots_WTR_1

value: roots

value: 14 day after gemination

value: wild-type


title: Knock_down3


title: WGBS of non-treated HEK 293 with TET2 KO

source_name: non-treated HEK 293 with TET2 KO

value: no treatment


title: MERS-HKU9-D

description: UTR and flanking region


title: IP1_replicate2: SH-SY5Y control shRNA TRAP RNA

value: neuroblastoma

value: GFP-RPL10A stable cell

value: TRAP RNA


title: DMSO_1359

source_name: Fibroblast like Synoviocytes

tag: diagnosis

value: Rheumatoid arthritis

value: Fibroblast like Synoviocytes

value: DMSO


title: Hnf4a ChIP-seq rep2

description: Hnf4a ChIP-seq

tag: cell type

value: kidney

value: newborn P0

value: Hnf4a (abcam ab41898)


title: Hnf4a ChIP-seq rep1

description: Hnf4a ChIP-seq


title: DMSO_1305

value: Healthy

tag: donor


title: WGBS of 12d-TNFa treated HEK 293 cells with RELA KO

value: RELA-KO for HEK 293 transfected with reporter construct


title: Knock_down2

value: Male

value: 9-12 weeks

value: eRNA_06347 knockdown


title: Negative_control2

value: Negative control oligo treatment


title: Sample 65

type: RNA

city: Geneva

first: Thomas

last: Matthes

address: Rue Gabrielle Perret-Gentil

department: Hematology

institute: Geneva University Hospital

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: mRNA analysis and counting were performed with NanoString technologies, according to the manufacturer’s protocol (Nanostring H Technologies, Seattle, WA, USA). Each mRNA species was extracted, pre-processed, analyzed with the nCounter system

label: not applicable

source_name: normal B cells

label_protocol: not applicable

extract_protocol: No extraction protocol was used. Cells were lysed in RNA lysis buffer (Qiagen) and directly used for the hybridisation with the Nanostring CodeSet according to the manufacturer's instructions.

treatment_protocol: Fresh blood was collected and Lysis of Red blood cells was performed.Total white blood cells were stored in RNA lysis buffer (Qiagen)

tag: disease state

value: normal

value: Blood

value: not known


title: Lung_OVA+SIA

source_name: Lung eosinophil granulocytes

value: Lung tissue

value: Balb/c

value: CD45+CD11b+Siglec-F+ granulocytes

tag: treatment

value: OVA+SIA

value: Day 7 post SIA


title: Sample 64

tag: tissue


title: Sample 63


title: WGBS of 12d-TNFa treated HEK 293 cells

source_name: 12d-TNFa treated HEK 293 cells

tag: cell line

value: HEK 293 transfected with reporter construct

value: TNF-alpha treatment 12 days


title: Sample 74

source_name: normal mononuclear peripheral blood cells


title: 12d-TNFa treatment+withdraw-10d+12h TNFa, H3K27ac

description:
embryonic kidney cells
somatic cell

source_name: 12d-TNFa treated HEK 293 cells+withdraw-10d+12h-TNFa

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days, and add TNF-alpha 12 hours

value: H3K27ac (Active Motif; Cat# 39133; RRID:AB_2561016)


title: WGBS of non-treated HEK 293

value: no treatment


title: control.rep2

data_processing:
sequences (fastq files) were aligned to mm9 using Tophat (v2.0.11) and Bowtie (v1.0.0) with parameters --library-type fr-unstranded -p 3 --no-coverage-search.
BAM files were further processed for sorting and duplicate removal using Samtools (v0.1.19)
FPKM were calculated using cufflinks (v2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: excel file including FPKM values for each sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from mouse embryonic kidneys using Qiagen RNeasy Micro (Qiagen 74004). Afterwards, mRNA was isolated from total RNA using  NEBNext® Poly(A) mRNA Magnetic Isolation Module, 24 rxns (NEB, E7490)
Sequencing libraries were generated using ThruPLEX DNA-seq 12S (48) Kit (Rubicon Genomics, Ann Arbor, MI)

value: mixed

value: Kidney

value: Hnf4a c/+ ; Osr2Cre


title: control.rep1


title: Sample 78


title: 12d-TNFa treatment+withdraw-10d, H3K27ac

description:
embryonic kidney cells
somatic cell

source_name: 12d-TNFa treated HEK 293 cells+withdraw-10d

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days


title: 12h-TNFa treatment H3K27ac

description:
embryonic kidney cells
somatic cell

value: TNF-alpha treatment 12 hours


title: L2

city: Chengyang District, Qingdao City, Shandong Province

first: xianxun

last: liu

address: 700 Changcheng Road

institute: Qingdao Agricultural University

data_processing:
StringTie used to calculate read abundance
Genome_build: Bos_taurus.NCBI.795.1.gtf
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample

organism: Bos taurus

source_name: muscle

extract_protocol:
Remove the muscle tissue and harvest RNA using Trizol reagent. Illumina TruSeq RNA sample preparation kit (Cat#FC-122-1001) is used with 1 ug total RNA to construct a sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Luxi cattle

value: muscle

value: Eighteen months


title: L3


title: non-treated control H3K27ac

description:
embryonic kidney cells
somatic cell


title: Sample 80

value: normal

value: Blood

value: not known


title: Negative_control3

value: Male

value: 9-12 weeks

value: Negative control oligo treatment


title: L1


title: mutant.rep2

value: Hnf4a c/c ; Osr2Cre


title: B3

value: Shandong Black cattle


title: WGBS of non-treated HEK 293 with RELA KO

source_name: non-treated HEK 293 with RELA KO

value: RELA-KO for HEK 293 transfected with reporter construct

value: no treatment


title: mutant.rep1

value: mixed

value: Kidney


title: Sample 79


title: Sample 66


title: B2


title: Negative_control1


title: B1


title: Sample 75


title: p65-TNF-12d+withdraw-10d

description: embryonic kidney

data_processing:
RNA-seq basecalls performed by BGI, Shenzhen
ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC hg38 genome by Bowtie2 (2.3.4.2)
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantitified by Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension of average fragments size.
Supplementary_files_format_and_content: RPKM values were calculated by Cuffdiff and stored as tab separated texts.

extract_protocol:
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were sythesised using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT.
ChIP-seq were performed as previously described (Xiong et al, Molecular Cell 64, 913-925). P65 antibody (Cat# sc-372) was purchased from Santa Cruz.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).
The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.

treatment_protocol: The final concentration of TNF is 50 ng/mL.

value: HEK 293 transfected with reporter construct

value: somatic cell

value: TNF-α treatment 12 days, then withdraw to recover 10 days

tag: developmental stage

value: embryos

tag: library strategy

value: ChIP

tag: antibody

value: sc-372, Santa Cruz


title: Sample 77

value: normal

value: Blood


title: 3_3-OHBcP: 3-hydroxybenzo[c]phenanthrene (3-OHBcP)-treated

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: Scales were incubated with 3-OHBcP at 15°C for 6 h.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite (Expression Console)

label: biotin

organism: Danio rerio

source_name: zebrafish scales

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: Scales were collected from zebrafish under anesthesia.

extract_protocol: Total RNAs were prepared from zebrafish scales using a total RNA isolation kit for fibrous tissue (Qiagen GmbH, Hilden, Germany) and treated with DNase I (RNase-Free DNase kit, Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >8.5 were considered acceptable.

treatment_protocol: The scales were incubated at 15 °C for 6 h in Leibovitz's L-15 medium (Invitrogen, Grand Island, NY, USA) with benzo[c]phenanthrene (BcP: 1 nM) or 3-hydroxybenzo[c]phenanthrene (3-OHBcP: 1 nM).

value: scale


title: 2_BcP: benzo[c]phenanthrene (BcP)-treated

description: Scales were incubated with BcP at 15°C for 6 h.


title: Sample 62

value: not known


title: Sample 26

source_name: Hairy cell leukemia (classical)

value: Hairy cell leukemia (classical)

value: M


title: SARS2-T-N

description:
UTR and flanking region
mes_ch_vivo.out

organism: Severe acute respiratory syndrome coronavirus 2

tag: strain

value: SARS-CoV-2 with T mutation


title: Sample 25


title: HiC_replicate2

city: Johnston

first: John

middle: Anthony

last: Crow

state: Iowa

address: 7000 NW 62nd Ave

department: Applied Science and Technology

institute: Corteva Agriscience

description: Reports for all chromosomes except Chr0. HITADs file contains hierarchical TADs produced by runHIC followed by the hitad pipeline; default parameters. HIC file contains interaction matrices produced by Juicer from Juicer Tools 1.14.08 as inter.hic. HiC_replicate2-merged_loops.bedpe contains loops called by HICCUPS from Juicer Tools 1.14.08 based on HiC_replicate2-inter.hic.

data_processing:
Illumina CASAVA 1.8 software was used for basecalling.
Following quality score-based trimming , reads with adapter sequences or of low quality were removed.
Filtered reads were processed using the Juicer package versions 1.9.9 and 1.14.08, for replicates 1 and 2, respectively.
Hierarchical TADs were called for both Hi-C replicates using HiTAD from the TADLib package. Default parameters were used. The related runHiC pipeline was run for each replicate, also with defaults, to generate the .cool files needed for HiTAD analysis.
Chromatin loops were detected using the HICCUPS software package from the Juicer package versions 1.9.9 and 1.14.08, for replicates 1 and 2, respectively.
Genome_build: Zea_mays.AGPv4
Supplementary_files_format_and_content: Hi-C interaction matrices (.hic" files) containing paired-end Hi-C reads

organism: Zea mays

source_name: Leaf tissue

growth_protocol: Plants were grown under normal light and temperature conditions in a static greenhouse and tissue was collected when plants reached the v04 stage.

extract_protocol:
Leaf tissue was collected and grinded before storage at -80C. Lysates were recovered according to the Dovetail Hi-C Library Preparation Kit protocol. Since tissues had previously been grinded (in liquid nitrogen) before long-term storage at -80°C, 2ml 1X PBS and 81μl 37% formaldehyde were added directly to 250mg of frozen and grinded tissue in a 15-ml tube then incubated at room temperature for 15min, prior to completing the protocol.
Libraries were constructed with the Dovetail Hi-C Library preparation Kit (Dovetail), according to the manufacturer’s instructions, including protocol modifications recommended by Dovetail for plant tissue.

tag: genotype

value: leaf

tag: development stage


title: HiC_replicate1

description: Reports for all chromosomes except Chr0. HITADs file contains hierarchical TADs produced by runHIC followed by the hitad pipeline; default parameters. HIC file contains interaction matrices produced by Juicer from Juicer Tools 1.9.9 as inter.hic. HiC_replicate1-merged_loops.bedpe contains loops called by HICCUPS from Juicer Tools 1.9.9 based on HiC_replicate1-inter.hic.


title: SARS2-T-D

description: UTR and flanking region


title: p65-TNF-12d+withdraw-10d+TNF12h

description: embryonic kidney

value: TNF-α treatment 12 days, then withdraw to recover 10 days, and add TNF-α 12 hours


title: Sample 22

source_name: Hairy cell leukemia (variant)

value: Hairy cell leukemia (variant)

tag: age


title: Sample 21

value: F


title: Sample 29


title: SARS2-C_NL63-KHU1-N

description:
UTR and flanking region
293_cy_vitro.out

source_name: in vitro refolding

value: SARS-CoV-2 HCoV-NL63 HCoV-HKU1


title: dorsal root ganglia tissues 9 days after injecting CFA into the rat knee

city: Zheng zhou

first: Qian

last: Bai

state: Henan

address: NO.2 Jingba Road

institute: The second afficated hospital of zhengzhou University

description: LncRNA expression data from Rat sapiens hepar

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Rat LncRNA Microarray V1.0, and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

organism: Rattus norvegicus

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Male inbred Wistar rats (200 g) were were housed in the central facility at Zhengzhou University School of Medicine under a standard 12 h light/12 h dark cycle, with water and food available adlibitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from dorsal root ganglia  and propmptly frozen in the liquid nitrogen

value: dorsal root ganglia

value: male

tag: time point

value: 9 days

value: CFA


title: WT_i

city: Oulu

first: Nadiya

last: Byts

address: Aapistie 7C

department: FBMM

country: Finland

institute: Biocenter Oulu

description: gene expression data fromipsilateral cortex of wild-type mice 24h after onset of pMCAO

hyb_protocol: Biotinylated cRNA was cleaned with a GeneChip Sample Cleanup Module (Qiagen), fragmented to 35 to 200 nt, and hybridized to Affymetrix Mouse Genome 430_ 2.0 arrays according to manufacturer's instructions.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip Scanner 3000

data_processing: Data were normalized using RMA algorithm with variance stabilization in Chipster software.

source_name: cortical tissue 24h after pMCAO

label_protocol: biotin-labeled cRNA was produced using an IVT labeling kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: 3 months old mice

extract_protocol: Total RNA was isolated using TriPure isolation reagent (Roche Applied Science) and further purified with an EZNA total RNA kit (Omega Biotek)

treatment_protocol: 24h of permanent occlusion on left midle cerebral artery

value: wild-type

value: ipsilateral cortex


title: Sample 20

value: Blood

tag: gender


title: dorsal root ganglia tissues 8 days after injecting CFA into the rat knee

value: 8 days


title: 1_Ctr: Control

description: Scales were incubated at 15°C for 6 h.

value: scale


title: KO_i

description: gene expression data from ipsilateral cortex of P4H-TM deficient mice 24h after onset of pMCAO

value: P4H-TM deficient


title: Sample 30

value: Hairy cell leukemia (classical)

value: M


title: WT_c

description: gene expression data from contralateral cortex of wild-type mice 24h after onset of pMCAO

value: contralateral cortex


title: dorsal root ganglia tissues 8 days after injecting Saline into the rat knee

value: saline


title: dorsal root ganglia tissues 7 days after injecting Saline into the rat knee

value: 7 days


title: dorsal root ganglia tissues 7 days after injecting CFA into the rat knee


title: dorsal root ganglia tissues 9 days after injecting Saline into the rat knee


title: DTGA5650

first: li

last: bu

address: NO.2 yuanmingyuan

institute: China Agricultural University

description: Gene expression

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: whole skin

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: DTG mouse skin


title: SARS2-C_NL63-KHU1-D

description:
UTR and flanking region
293_cy_vivo.out

value: SARS-CoV-2 HCoV-NL63 HCoV-HKU1


title: A42323

description: Gene expression

value: Extramammary paget disease scrotum


title: SARS-HKU5-N

description: UTR and flanking region

value: SARS-CoV BtCoV-HKU5


title: SARS-HKU5-D

description:
UTR and flanking region
293_np_vitro.out


title: Sample 16


title: Sample 15


title: SARS2-huh7-T

description:
whole genome
293_ch_vitro.out

source_name: Huh7 cells


title: Sample 03


title: SARS2-huh7-N

description:
whole genome
293_ch_vivo.out


title: SARS2-huh7-D

description: whole genome


title: C84EPD

description: Gene expression

value: male


title: Sample 19

value: Hairy cell leukemia (variant)


title: A0421202

description: Gene expression


title: DTGA5648

description: Gene expression


title: DTGA5643

description: Gene expression


title: KA5652

description: Gene expression

value: Control mouse skin


title: Sample 01


title: DTGA5645

description: Gene expression


title: KO_c

description: gene expression data from contralateral cortex of P4H-TM deficient mice 24h after onset of pMCAO


title: KA5646

description: Gene expression


title: A42537

description: Gene expression

value: Normal skin


title: A42211

description: Gene expression


title: A42333

description: Gene expression


title: MesAur_Lung_day4_CoV2_1000pfu_2

status: Public on Nov 11 2020

city: New York

first: Rasmus

last: Moeller

address: 1 Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
IAV_vs_CoV2.csv
26

data_processing:
automated base-calling performed with bcl2fastq (Illumina)
fastq files were aligned using RNA-Seq Alignment application (Basespace, Illumina).
total counts were extracted and comiled in .csv files for each tissue
Genome_build: Ensembl MesAur1.0
Supplementary_files_format_and_content: All processed data files are .csv files containining total counts of each gene after alignment. Each file contains counts from one tissue.

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: whole lung

extract_protocol:
Tissues were homogenized in 1ml TRIzol reagent (invitrogen) and RNA total RNA was extracted my phenol/chloroform extraction following manufacturer's protocol.
All libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Starting material: 1µg total RNA

treatment_protocol: Syrian golden hamsters were infected with SARS-CoV-2 or IAV intranasally with 100µl of inoculum (virus in PBS) under anaesthesia with ketamine/xylazine at doses indicated and organs were collected at the times indicated. All hamsters were perfused before the collection of organs.

value: 3-5 weks old

tag: Sex

value: lung

tag: virus

value: SARS-CoV-2, USA-WA1/2020 strain

tag: dosage

value: 4 days


title: MesAur_Lung_day4_IAV_1000pfu_3

description:
IAV_vs_CoV2.csv
7

value: Inflenza A virus, H1N1, A/California/04/2009


title: MesAur_Lung_day4_IAV_1000pfu_4

description:
IAV_vs_CoV2.csv
8


title: MesAur_Lung_day4_CoV2_1000pfu_4

description:
IAV_vs_CoV2.csv
28


title: MesAur_Lung_day4_IAV_1000pfu_2

description:
IAV_vs_CoV2.csv
6


title: MesAur_Lung_day4_IAV_1000pfu_1

description:
IAV_vs_CoV2.csv
5


title: A42345

description: Gene expression


title: A41785

description: Gene expression


title: MesAur_Lung_day4_CoV2_1000pfu_3

description:
IAV_vs_CoV2.csv
27


title: MesAur_Lung_day4_CoV2_1000pfu_1

description:
IAV_vs_CoV2.csv
25


title: MesAur_Sm_int_day14_CoV2_10000pfu_2

description:
HAG_smint_count_matrix.csv
HAG35_day14high_sm_int

source_name: proximal small intestine

value: small intestine

value: 14 days


title: KA5651

description: Gene expression


title: MesAur_Sm_int_day8_CoV2_10000pfu_2

description:
HAG_smint_count_matrix.csv
HAG32_d8high_smint_r

value: 8 days


title: MesAur_Sm_int_day14_CoV2_10000pfu_1

description:
HAG_smint_count_matrix.csv
HAG34_day14high_sm_int


title: MesAur_Sm_int_day6_CoV2_10000pfu_3

description:
HAG_smint_count_matrix.csv
HAG30_d6high_sm_int

value: 6 days


title: MesAur_Sm_int_day6_CoV2_10000pfu_2

description:
HAG_smint_count_matrix.csv
HAG29_d6high_sm_int


title: Sample 02

tag: disease state

value: Hairy cell leukemia (classical)

value: Blood

value: M


title: MesAur_Sm_int_day4_CoV2_10000pfu_2

description:
HAG_smint_count_matrix.csv
HAG26_d4high_sm_int


title: MesAur_Sm_int_day2_CoV2_10000pfu_3

description:
HAG_smint_count_matrix.csv
HAG24_d2high_smint_r

value: 2 days


title: MesAur_Sm_int_day4_CoV2_10000pfu_1

description:
HAG_smint_count_matrix.csv
HAG25_d4high_sm_int

value: male


title: MesAur_Sm_int_day4_CoV2_10000pfu_3

description:
HAG_smint_count_matrix.csv
HAG27_d4high_sm_int


title: MesAur_Sm_int_day8_CoV2_10000pfu_1

description:
HAG_smint_count_matrix.csv
HAG31_day8high_sm_int


title: KA5649

description: Gene expression


title: MesAur_Sm_int_day2_CoV2_10000pfu_2

description:
HAG_smint_count_matrix.csv
HAG23_smintestine


title: MesAur_Sm_int_day1_CoV2_10000pfu_2

description:
HAG_smint_count_matrix.csv
HAG20_day1high_sm_int

value: 1 day


title: MesAur_Sm_int_day1_CoV2_10000pfu_3

description:
HAG_smint_count_matrix.csv
HAG21_day1high_sm_int


title: MesAur_Sm_int_day14_CoV2_100pfu_2

description:
HAG_smint_count_matrix.csv
HAG17_day14low_sm_int

value: 100 pfu


title: MesAur_Sm_int_day14_CoV2_100pfu_3

description:
HAG_smint_count_matrix.csv
HAG18_day14low_sm_int


title: MesAur_Sm_int_day14_CoV2_100pfu_1

description:
HAG_smint_count_matrix.csv
HAG16_day14low_sm_int


title: MesAur_Sm_int_day6_CoV2_100pfu_3

description:
HAG_smint_count_matrix.csv
HAG12_d6low_sm_int


title: MesAur_Sm_int_day8_CoV2_100pfu_1

description:
HAG_smint_count_matrix.csv
HAG13_d8low_smint_r


title: MesAur_Sm_int_day8_CoV2_100pfu_2

description:
HAG_smint_count_matrix.csv
HAG14_day8low_sm_int


title: MesAur_Sm_int_day14_CoV2_10000pfu_3

description:
HAG_smint_count_matrix.csv
HAG36_day14high_sm_int


title: MesAur_Sm_int_day2_CoV2_10000pfu_1

description:
HAG_smint_count_matrix.csv
HAG22_d2high_sm_int


title: MesAur_Sm_int_day4_CoV2_100pfu_2

description:
HAG_smint_count_matrix.csv
HAG08_d4low_sm_int


title: MesAur_Sm_int_day6_CoV2_100pfu_1

description:
HAG_smint_count_matrix.csv
HAG10_d6low_sm_int


title: MesAur_Sm_int_day6_CoV2_100pfu_2

description:
HAG_smint_count_matrix.csv
HAG11_d6low_sm_int


title: MesAur_Sm_int_day1_CoV2_10000pfu_1

description:
HAG_smint_count_matrix.csv
HAG19_day1high_sm_int


title: MesAur_Sm_int_day4_CoV2_100pfu_3

description:
HAG_smint_count_matrix.csv
HAG09_d4low_sm_int


title: MesAur_Sm_int_day4_CoV2_100pfu_1

description:
HAG_smint_count_matrix.csv
HAG07_d4low_sm_int


title: MesAur_Sm_int_day2_CoV2_100pfu_3

description:
HAG_smint_count_matrix.csv
HAG06_d2low_sm_int


title: MesAur_Sm_int_day2_CoV2_100pfu_2

description:
HAG_smint_count_matrix.csv
HAG05_d2low_sm_int


title: MesAur_Sm_int_day1_CoV2_100pfu_3

description:
HAG_smint_count_matrix.csv
HAG03_day1low_sm_int


title: MesAur_Sm_int_day1_CoV2_100pfu_2

description:
HAG_smint_count_matrix.csv
HAG02_day1low_sm_int


title: MesAur_Sm_int_day2_CoV2_100pfu_1

description:
HAG_smint_count_matrix.csv
HAG04_d2low_sm_int


title: MesAur_Sm_int_day1_CoV2_100pfu_1

description:
HAG_smint_count_matrix.csv
HAG01_day1low_sm_int


title: MesAur_Sm_int_mock_3

description:
HAG_smint_count_matrix.csv
HAB18_day7_PBS_sm_int


title: MesAur_Olf_bulb_day14_CoV2_10000pfu_3

description:
HAG_olf_count_matrix.csv
HAG36_day14high_olf_bulb

source_name: olfactory bulb

value: olfactory bulb


title: MesAur_Olf_bulb_day14_CoV2_10000pfu_1

description:
HAG_olf_count_matrix.csv
HAG34_day14high_olf_bulb

value: 3-5 weks old


title: MesAur_Olf_bulb_day14_CoV2_10000pfu_2

description:
HAG_olf_count_matrix.csv
HAG35_d14high_olfb_r


title: MesAur_Sm_int_mock_1

description:
HAG_smint_count_matrix.csv
HAB16_day7_sm_int


title: MesAur_Sm_int_mock_2

description:
HAG_smint_count_matrix.csv
HAB17_day7_PBS_sm_int


title: MesAur_Olf_bulb_day8_CoV2_10000pfu_1

description:
HAG_olf_count_matrix.csv
HAG31_day8high_olf_bulb


title: MesAur_Olf_bulb_day8_CoV2_10000pfu_3

description:
HAG_olf_count_matrix.csv
HAG33_day8high_olf_bulb


title: MesAur_Olf_bulb_day4_CoV2_10000pfu_3

description:
HAG_olf_count_matrix.csv
HAG27_d4high_olf_bulb


title: MesAur_Olf_bulb_day4_CoV2_10000pfu_2

description:
HAG_olf_count_matrix.csv
HAG26_d4high_olf_bulb


title: MesAur_Olf_bulb_day2_CoV2_10000pfu_3

description:
HAG_olf_count_matrix.csv
HAG24_d2high_olf_bulb


title: MesAur_Olf_bulb_day4_CoV2_10000pfu_1

description:
HAG_olf_count_matrix.csv
HAG25_d4high_olf_bulb


title: MesAur_Olf_bulb_day6_CoV2_10000pfu_1

description:
HAG_olf_count_matrix.csv
HAG28_d6high_olfb_r


title: MesAur_Olf_bulb_day2_CoV2_10000pfu_1

description:
HAG_olf_count_matrix.csv
HAG22_d2high_olf_bulb


title: MesAur_Olf_bulb_day1_CoV2_10000pfu_2

description:
HAG_olf_count_matrix.csv
HAG20_day1high_olf_bulb


title: MesAur_Olf_bulb_day2_CoV2_10000pfu_2

description:
HAG_olf_count_matrix.csv
HAG23_olfactorybulb


title: MesAur_Olf_bulb_day1_CoV2_10000pfu_1

description:
HAG_olf_count_matrix.csv
HAG19_day1high_olf_bulb


title: MesAur_Sm_int_mock_6

description:
HAG_smint_count_matrix.csv
HAJ03_mock_sm_int


title: MesAur_Olf_bulb_day14_CoV2_100pfu_3

description:
HAG_olf_count_matrix.csv
HAG18_day14low_olf_bulb


title: MesAur_Olf_bulb_day1_CoV2_10000pfu_3

description:
HAG_olf_count_matrix.csv
HAG21_d1high_olfb_r


title: MesAur_Olf_bulb_day14_CoV2_100pfu_1

description:
HAG_olf_count_matrix.csv
HAG16_day14low_olf_bulb


title: MesAur_Olf_bulb_day14_CoV2_100pfu_2

description:
HAG_olf_count_matrix.csv
HAG17_day14low_olf_bulb


title: MesAur_Olf_bulb_day8_CoV2_100pfu_3

description:
HAG_olf_count_matrix.csv
HAG15_day8low_olf_bulb


title: MesAur_Olf_bulb_day8_CoV2_10000pfu_2

description:
HAG_olf_count_matrix.csv
HAG32_d8high_olfb_r


title: MesAur_Olf_bulb_day8_CoV2_100pfu_2

description:
HAG_olf_count_matrix.csv
HAG14_day8low_olf_bulb


title: MesAur_Olf_bulb_day8_CoV2_100pfu_1

description:
HAG_olf_count_matrix.csv
HAG13_day8low_olf_bulb


title: MesAur_Olf_bulb_day6_CoV2_100pfu_3

description:
HAG_olf_count_matrix.csv
HAG12_d6low_olf_bulb


title: MesAur_Olf_bulb_day4_CoV2_100pfu_3

description:
HAG_olf_count_matrix.csv
HAG09_d4low_olf_bulb


title: MesAur_Olf_bulb_day6_CoV2_100pfu_2

description:
HAG_olf_count_matrix.csv
HAG11_d6low_olfb_r


title: MesAur_Olf_bulb_day4_CoV2_100pfu_1

description:
HAG_olf_count_matrix.csv
HAG07_d4low_olf_bulb


title: MesAur_Olf_bulb_day2_CoV2_100pfu_3

description:
HAG_olf_count_matrix.csv
HAG06_d2low_olf_bulb


title: MesAur_Olf_bulb_day2_CoV2_100pfu_2

description:
HAG_olf_count_matrix.csv
HAG05_olfactorybulb


title: MesAur_Olf_bulb_day6_CoV2_100pfu_1

description:
HAG_olf_count_matrix.csv
HAG10_d6low_olf_bulb


title: MesAur_Olf_bulb_day2_CoV2_100pfu_1

description:
HAG_olf_count_matrix.csv
HAG04_d2low_olf_bulb


title: MesAur_Olf_bulb_day1_CoV2_100pfu_3

description:
HAG_olf_count_matrix.csv
HAG03_day1low_olf_bulb


title: MesAur_Olf_bulb_day4_CoV2_100pfu_2

description:
HAG_olf_count_matrix.csv
HAG08_d4low_olf_bulb


title: MesAur_Olf_bulb_day1_CoV2_100pfu_2

description:
HAG_olf_count_matrix.csv
HAG02_day1low_olf_bulb


title: MesAur_Olf_bulb_mock_4

description:
HAG_olf_count_matrix.csv
HAJ01_olfactorybulb


title: MesAur_Olf_bulb_mock_5

description:
HAG_olf_count_matrix.csv
HAJ02_mock_olf_bulb


title: MesAur_Olf_bulb_mock_1

description:
HAG_olf_count_matrix.csv
HAB16_day7_PBS_olf_bulb


title: MesAur_Olf_bulb_mock_3

description:
HAG_olf_count_matrix.csv
HAB18_day7_PBS_olf_bulb


title: MesAur_Olf_bulb_day1_CoV2_100pfu_1

description:
HAG_olf_count_matrix.csv
HAG01_d1low_olfb_r


title: MesAur_Brain_day14_CoV2_10000pfu_3

description:
HAG_brain_count_matrix.csv
HAG36_d14high_brain_r

source_name: brain without olfactory bulb

value: brain


title: MesAur_Brain_day14_CoV2_10000pfu_2

description:
HAG_brain_count_matrix.csv
HAG35_day14high_brain

value: SARS-CoV-2, USA-WA1/2020 strain


title: MesAur_Olf_bulb_mock_2

description:
HAG_olf_count_matrix.csv
HAB17_day7_PBS_olf_bulb


title: MesAur_Brain_day14_CoV2_10000pfu_1

description:
HAG_brain_count_matrix.csv
HAG34_day14high_brain


title: MesAur_Brain_day8_CoV2_10000pfu_3

description:
HAG_brain_count_matrix.csv
HAG33_day8high_brain


title: MesAur_Brain_day8_CoV2_10000pfu_1

description:
HAG_brain_count_matrix.csv
HAG31_day8high_brain


title: MesAur_Brain_day8_CoV2_10000pfu_2

description:
HAG_brain_count_matrix.csv
HAG32_d8high_brain_r


title: MesAur_Brain_day6_CoV2_10000pfu_3

description:
HAG_brain_count_matrix.csv
HAG30_day6high_brain


title: MesAur_Brain_day6_CoV2_10000pfu_2

description:
HAG_brain_count_matrix.csv
HAG29_d6high_brain


title: MesAur_Brain_day6_CoV2_10000pfu_1

description:
HAG_brain_count_matrix.csv
HAG28_d6high_brain


title: MesAur_Brain_day4_CoV2_10000pfu_3

description:
HAG_brain_count_matrix.csv
HAG27_d4high_brain

value: 4 days


title: MesAur_Brain_day4_CoV2_10000pfu_1

description:
HAG_brain_count_matrix.csv
HAG25_d4high_brain


title: MesAur_Brain_day2_CoV2_10000pfu_3

description:
HAG_brain_count_matrix.csv
HAG24_brain


title: MesAur_Brain_day4_CoV2_10000pfu_2

description:
HAG_brain_count_matrix.csv
HAG26_d4high_brain


title: MesAur_Brain_day1_CoV2_10000pfu_3

description:
HAG_brain_count_matrix.csv
HAG21_day1high_brain


title: MesAur_Brain_day2_CoV2_10000pfu_2

description:
HAG_brain_count_matrix.csv
HAG23_d2high_brain_r


title: MesAur_Brain_day2_CoV2_10000pfu_1

description:
HAG_brain_count_matrix.csv
HAG22_brain


title: MesAur_Brain_day1_CoV2_10000pfu_2

description:
HAG_brain_count_matrix.csv
HAG20_d1high_brain_r


title: MesAur_Brain_day1_CoV2_10000pfu_1

description:
HAG_brain_count_matrix.csv
HAG19_day1high_brain


title: MesAur_Brain_day14_CoV2_100pfu_2

description:
HAG_brain_count_matrix.csv
HAG17_day14low_brain


title: MesAur_Brain_day14_CoV2_100pfu_1

description:
HAG_brain_count_matrix.csv
HAG16_day14low_brain


title: MesAur_Brain_day6_CoV2_100pfu_3

description:
HAG_brain_count_matrix.csv
HAG12_d6low_brain


title: MesAur_Brain_day8_CoV2_100pfu_1

description:
HAG_brain_count_matrix.csv
HAG13_day8low_brain


title: MesAur_Brain_day6_CoV2_100pfu_2

description:
HAG_brain_count_matrix.csv
HAG11_d6low_brain


title: MesAur_Brain_day14_CoV2_100pfu_3

description:
HAG_brain_count_matrix.csv
HAG18_day14low_brain


title: MesAur_Brain_day8_CoV2_100pfu_3

description:
HAG_brain_count_matrix.csv
HAG15_day8low_brain


title: MesAur_Brain_day8_CoV2_100pfu_2

description:
HAG_brain_count_matrix.csv
HAG14_d14low_brain_r


title: MesAur_Sm_int_mock_4

description:
HAG_smint_count_matrix.csv
HAJ01_smintestine


title: MesAur_Sm_int_mock_5

description:
HAG_smint_count_matrix.csv
HAJ02_mock_sm_int


title: MesAur_Brain_day4_CoV2_100pfu_3

description:
HAG_brain_count_matrix.csv
HAG09_d4low_brain


title: MesAur_Brain_day6_CoV2_100pfu_1

description:
HAG_brain_count_matrix.csv
HAG10_d6low_brain


title: MesAur_Brain_day4_CoV2_100pfu_2

description:
HAG_brain_count_matrix.csv
HAG08_d4low_brain_r


title: MesAur_Brain_day4_CoV2_100pfu_1

description:
HAG_brain_count_matrix.csv
HAG07_d4low_brain