title: Control iPSC EKA03, 2wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: Control iPSC EKA03, 2wks

value: FUSWT/WT


title: dG-2

status: Public on Apr 19 2021

type: SRA

city: State College

first: Paul

last: Babitzke

state: PA

address: 203 Althouse Laboratory

country: USA

institute: Pennsylvania State University

description: nusG deletion

library_source: transcriptomic

data_processing:
base calling and quality scoring conducted via BaseSpace
adaptor trimming and low quality read removal via Trimmomatic v. 0.38 for RNA-seq .fastq dataset
all reads containing custom oligo were extracted via Cutadapt v. 1.16 for Term-seq .fastq dataset
both RNA-seq and Term-seq .fastq files were mapped to B. subtilis genome using bwa-mem v.0.7.12-r1034
sam -> bam, and bam files split by strand via samtools v. 0.1.19-44428cd
coverage files (.cov) for 3' end mapping and .bedgraph files to illustrate coverage were generated using bedtools v. 2.26.0
2 custom python (python v. 3.8.3) scripts were used to identify 3' ends from Term-seq .fastq derived .cov files (located at: https://github.com/zfmandell/Term-seq)
RNA-seq coverage files generated using bedtools v. 2.26.0
Genome_build: Refseq : NC_000964.3
Supplementary_files_format_and_content: .bedgraph files, containing either RNA-seq coverage information, and list of called 3' ends with associated Cv values

molecule: total RNA

organism: Bacillus subtilis

source_name: nusG deletion

growth_protocol: cells were plated on LB plates at 37°C +2 mM IPTG +20 µg/ml chloramphenicol -> single colonies isolated and grown O/N at 37°C standing culture in +0.4 mM IPTG +20 µg/ml chloramphenicol -> next day, cells were grown at in 25 mL of LB at 37°C +20 µg/ml chloramphenicol and +2 mM IPTG in cases where NusA production was to be sustained

extract_protocol:
Total RNA was extracted from collected cell paste via RNeasy mini-kit (Qiagen, cat # 74104)
total RNA was dephosphorylated using CIP (NEB, discontinued), rRNA was depleted via ribo-zero Gram-positive rRNA depletion kits (Illumina, discontinued), remaining RNA was ligated to custom unique 2', 3’ dideoxy RNA oligonucleotide (IDT), Illumina sequencing libraries were generated from ligation products using TruSeq Stranded mRNA kit (Illumina, cat # 20020594)
Term-seq

tag: genotype

value: rpoC-10His nusG::kan amyE::Physpank-nusA lacIq nusA::Spr

tag: iptg

value: 2 mM


title: Control iPSC 201B7, 2wks, biological rep3

type: RNA

city: Fujisawa

first: MASAHIRO

last: NOGAMI

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Research

country: Japan

institute: Takeda Pharmaceutical Company Limited

description: Gene expression data from iPSC-MN

hyb_protocol: Following fragmentation, 5μg of Single-Stranded cDNA was hybridized for 16 hr at 45˚C on GeneChip Human Transcriptome Array 2.0. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: Biotin

organism: Homo sapiens

source_name: Control iPSC 201B7, 2wks

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit（Thermo Fisher Scientific) following the manufacturer's instructions.

extract_protocol: Total RNA were extracted by miRNeasy Kit with QIAzol (QIAGEN)

tag: cell type

value: iPSC-MN

tag: time (differentiation from motor neuron precursor)

value: 2 weeks


title: Control iPSC EKA03, 2wks, biological rep1

description: Gene expression data from iPSC-MN


title: 30_E3_10_C05

city: San Francisco

first: Kelly

last: Zalocusky

state: CA

address: 1650 Owens Street, Gladstone Center for Translational Advancement

institute: Gladstone Institutes

description: single nucleus RNA sequencing

data_processing:
Demultiplexed fastq files were aligned to a custom reference genome built from mm10-1.2.0 that includes introns, using the Cellranger v2.0.1 counts function with default parameters, as described in the Cellranger documentation.
UMI counts were also determined using the Cellranger counts function, and count matrices from different samples were aggregated into a single count matrix using Cellranger’s aggr function with default parameters. This function filters barcodes (potential cells) according to a UMI count threshold.
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: h5

organism: Mus musculus

source_name: hippocampus

growth_protocol: All protocols and procedures followed the guidelines of the Laboratory Animal Resource Center at the University of California, San Francisco (UCSF). Experimental and control mice had identical housing conditions from birth through sacrifice (12 h light/dark cycle, housed 5 animals/cage, PicoLab Rodent Diet 20). ApoE3-KI and apoE4-KI homozygous mouse lines (Taconic)51 were born and aged under normal conditions at the Gladstone Institute/UCSF animal facility. ApoE4-KI/Syn-Cre and apoE3-KI/Syn-Cre mice were generated by cross-breeding apoE-floxed-KI mice, which was generated in our lab52, with Syn-Cre mice11.

extract_protocol:
To isolate single nuclei from adult mouse brains, we combined and adapted the 10x Genomics demonstrated protocol for nuclei isolation from adult mouse brain55 and the Allen Brain Institute protocol for FACS sorting of single nuclei56 as follows. Hippocampi were acutely dissected on ice. Dissected hippocampi were placed in 2mL Hibernate A®/B27®/GlutaMAX™ (HEB) medium in a 5mL tube. The HEB medium was removed to a 15mL conical and kept on ice. 2mL of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Nonidet™ P40 Substitute in Nuclease-Free Water) were added to the tissue, and the hippocampi were homogenized by suctioning 10 times through a 21G needle. After homogenization, the tissue was lysed on ice for 15min, swirling 2–3 times during this incubation period. The reserved chilled HEB media was then returned to the lysed tissue solution, and the tissue was further triturated with 5–7 passes through a 1mL pipette. A 30µm cell strainer (MACS SmartStrainer; Miltenyi Biotech 130-110-915) was washed with 1mL of PBS, and the lysed tissue solution was filtered through the strainer to remove debris and clumps. Filtered nuclei were centrifuged at 500 rcf for 5min at 4°C. The supernatant was removed, and nuclei were washed in 1mL of Nuclei Wash and Resuspension Buffer (1X PBS with 1.0% BSA and 0.2U/µl RNase Inhibitor). Nuclei were again centrifuged at 500 rcf for 5min at 4°C and resuspended in 400µL of Nuclei Wash and Resuspension Buffer. DAPI was added to a final concentration of 0.1ug/mL, and the nuclei were filtered through a 35µm cell strainer. DAPI-positive nuclei were sorted by gating on DAPI-positive events, excluding debris and doublets, using the BD FACSAria-II at the Gladstone Institutes’ Flow Cytometry Core.
cDNA libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead kit v2 (10x Genomics: 120267) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.

tag: age (months)


title: fALS-e48, 2wks, biological rep1

description: Gene expression data from iPSC-MN

source_name: fALS-e48, 2wks


title: dA-1

description: NusA depletion

source_name: NusA depletion

value: rpoC-10His amyE::Physpank-nusA lacIq nusA::Spr

value: 0 mM


title: fALS-e46, 2wks, biological rep2

description: Gene expression data from iPSC-MN

source_name: fALS-e46, 2wks


title: Control iPSC 409B2, 2wks, biological rep2

description: Gene expression data from iPSC-MN

source_name: Control iPSC 409B2, 2wks


title: Control iPSC 409B2, 2wks, biological rep1

description: Gene expression data from iPSC-MN


title: WT_ACF-S5

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
subread-1.6.1, featurecounts, -s 2 -t exon -g gene_name
Differential expression analysis was performed using DESeq2-1.16.1
Genome_build: GRCm38 + M17 Annotation
Supplementary_files_format_and_content: Raw counts

source_name: Heart

growth_protocol: Primary cardiac fibroblasts were isolated from three pairs of P60 wild type and Fam114a1-/- mice

extract_protocol:
The RNA extraction and purification from the isolated cardiac fibroblasts from WT vs Fam114a1-/- mouse hearts were performed using regular TRIzol reagent (ThermoFisher) according to the instructions in the manual. Then the extracted totoal RNA were treated with DNase I to remove potential genomic DNA followed by purification using phenol:chloroform:isoamyl alcohol for RNA-Seq.
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100-nt are generated for each sample and aligned to the organism specific reference genome.

tag: strain

tag: tissue

value: Cardiac cells

value: WT


title: Control iPSC 409B2, 2wks, biological rep3

description: Gene expression data from iPSC-MN


title: Fam114a1-/-_ACF-S1


title: WT_ACF-S2


title: fALS-e46, 2wks, biological rep3

description: Gene expression data from iPSC-MN


title: pericytes, co-culture, E2, rep 3

city: Schlieren

first: Lisa

middle: Maria

last: Kurmann

address: Wagistrasse 14

department: Reproductive endocrinology

country: Switzerland

institute: University Hospital Zurich

description: gene expression data from pericytes co-cultured with endothelial cells and treated with estradiol (E2)

hyb_protocol: 15 ug of cRNA were subjected to 2nd-cylce ss-cDNA synthesis. 5.5 ug of the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin. Hybridization to Clariom S Assay, human (Applied Biosystems, 902927) is performed for 16 hr at 45°C with rotation at 60 rpm in the GeneChip Hybridization Oven 645 (00-0331, 110/220V). GeneChips were washed and stained in the CheneChip Fluidics Station 450 (00-079).

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G System (00-0213).

data_processing:
The data were analyzed with GeneChip Command Console Software (GCC) v5.0. The obtained CEL files were up-loaded to the Transcriptome Analysis Console (TAC, applied biosystems) and analysis was performed by the software (Limma-based, eBayes).
LOG2 TAC signal (software produces only avg normalized values for each triplicate)

label: biotin

source_name: human brain pericytes, co-culture, E2

label_protocol: Biotinylation was prepared according to the protocol (GeneChipTM WT PLUS Reagent Kit) from 5.5 ug total RNA.

growth_protocol: Pericytes were plated on the basolateral side (Poly-L-Lysine-coated) of permeable transparent PET transwell insert (6-wellplate format, 0.4um pore-size). After attaching (2-3h), endothelial cells were seeded onto the apical side (collagen-coated) and the cells were cultured for a total of 7 days. Media in the basolateral chamber consisted of pericyte growing media (DMEM/F12 +Glutamax (1x)+ Antibiotics/Antimicotics (1x)+ 5% FBS). In the apical chamber, endothelial cell media was used (EndoGRO Basal Medium supplemented with 0.2 % EndoGRO-LS Supplement, 5 ng/ml rh EGF, 4 mM L-Glutamine, 0.75 U/ml Heparin Sulfate, 50 ug/ml Ascorbic Acid, 1 ng/ml bFGF, antibiotic-antimycotic (1x) + 5% FBS). After 3 days, media was changed to 2 % steroid-free FCS (charcoal-stripped) and hydrocortisone was added (1 ug/ml).

extract_protocol: Total RNA was extracted by using the Quick-RNA MiniPrep Kit (ZymoResearch) according to the manufacture’s protocol. RNA integrity was checked by determinig the ratio of absorbance at 260 nm and 280 nm / 230 nm respectively. The samples were frozen at -80 °C and shipped to the Gene expression Affymetrix facility in dry ice.

treatment_protocol: Cells were treated either with estradiol (10 nM) or DMSO in the apical and basolateral chamber for 48h before cell lysis.

tag: origin

value: brain


title: Control iPSC EKA03, 2wks, biological rep2

description: Gene expression data from iPSC-MN


title: WT-1

description: Wild Type

source_name: Wild Type


title: 28_E3_5_C03

description: single nucleus RNA sequencing


title: 29_E4_5_C04

description: single nucleus RNA sequencing


title: pericytes, co-culture, E2, rep 2


title: pericytes, co-culture, E2, rep 1


title: 27_E4_20_C02

description: single nucleus RNA sequencing


title: Control iPSC 201B7, 2wks, biological rep2

description: Gene expression data from iPSC-MN


title: 26_E3_20_C01

description: single nucleus RNA sequencing


title: pericytes, co-culture, DMSO, rep 3

description: gene expression data from pericytes co-cultured with endothelial cells and treated with vehicle (DMSO)

source_name: human brain pericytes, co-culture, DMSO


title: Sample_41_no training_Vehicle

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Quality control was performed using FastQC and MultiQC
Reads were alligned to rn6 using STAR aligner (version 2.7.0b) settings: --runThreadN' '8' '--outSAMunmapped' 'Within' '--twopassMode' 'Basic’
Gene-read quantification was perfromed using HTSeq-count (version 0.6.1) settings: --format' 'bam' '--order' 'name' '--stranded' 'reverse'
HTSeq-count output files were merged into the raw_gene_count_matrix.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every feature according to Ensembl97 for each sample.

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
From the snap-frozen, dissected hippocampi, total RNA was isolated using TriPure (Roche) according to manufacturer's protcol after homogenization of the tissue by shaking the tissue with ceramic beads in a FastPrep-24 5G instrument (MP Biomedicals.
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.

value: Sprague-Dawley

tag: training

value: no training

tag: treatment

value: Vehicle

value: Hippocampus


title: 25_E4_20_B08

description: single nucleus RNA sequencing


title: Sample_39_no training_Corticosterone

value: Corticosterone


title: 23_E4_5_B06

description: single nucleus RNA sequencing


title: Sample_40_training_Corticosterone

value: training


title: Sample_35_training_Vehicle


title: 22_E3_5_B05

description: single nucleus RNA sequencing


title: Sample_33_training_Corticosterone


title: Liver_Dscr-1;ApoE-DKO_rep2

city: Kumamoto

first: Takashi

last: Minami

institute: Kumamoto University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430.2.0 Array.

scan_protocol: GeneChips Scanner 3000 (Affymetrix)

data_processing: The data were analyzed with GeneSpringGX (Version12.5)  using Affymetrix default analysis settings and global scaling as normalization method, and Transcriptome Analysis Console (TAC) software. For global normalization, the average signal in the array was set to 100

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Maintain mice in normal circumstance (temperature and humidity). For aortic endothelial cell, primary endothalial cells were isolated from aorta of each mice, and cultured for several days.

extract_protocol: For liver sample, total RNA was extracted using RNeasy (QIAGEN) according to the manufacturer's instructions. For aorta sample, Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For liver samples, mice were feeded with HFD or 12 weeks.

value: Dscr-1;ApoE-DKO mouse liver with HFD

tag: age

value: adult


title: Aorta_Dscr-1;ApoE-KO_rep1

value: Dscr-1; ApoE-KO mouse aorta


title: Aorta_ApoE-KO_rep1

value: ApoE-KO mouse aorta


title: Sample_32_no training_Vehicle


title: Control iPSC 201B7, 2wks, biological rep1

description: Gene expression data from iPSC-MN

value: iPSC-MN

value: FUSWT/WT


title: 21_E4_5_B04

description: single nucleus RNA sequencing


title: 20_E3_5_B03

description: single nucleus RNA sequencing


title: pericytes, co-culture, DMSO, rep 2


title: pericytes, mono-culture, E2, rep 3

description: gene expression data from pericytes cultured alone and treated with estradiol (E2)

source_name: human brain pericytes, mono-culture, E2


title: Liver_ApoE-KO_rep2

value: ApoE-KO mouse liver with HFD


title: pericytes, co-culture, DMSO, rep 1


title: Aorta_Dscr-1;ApoE-KO_rep2


title: pericytes, mono-culture, E2, rep 1


title: Sample_29_no training_Corticosterone


title: 24_E3_20_B07

description: single nucleus RNA sequencing


title: Sample_28_training_Corticosterone


title: pericytes, mono-culture, DMSO, rep 3

description: gene expression data from pericytes cultured alone and treated with vehicle (DMSO)

source_name: human brain pericytes, mono-culture, DMSO


title: 18_E3_15_B01

description: single nucleus RNA sequencing


title: pericytes, mono-culture, E2, rep 2


title: Liver_ApoE-KO_rep1


title: Aorta_ApoE-KO_rep2


title: Liver_Dscr-1-KO_rep2

value: Dscr-1-KO mouse liver with HFD


title: pericytes, mono-culture, DMSO, rep 1


title: 17_E4_15_A12

description: single nucleus RNA sequencing


title: Liver_Dscr-1;ApoE-DKO_rep1


title: Liver_Dscr-1-KO_rep1


title: Liver_WT_rep2

value: WT mouse liver with HFD


title: Sample_22_no training_Vehicle


title: endothelial cells, co-culture, E2, rep 3

description: gene expression data from endothelial cells co-cultured with pericytes and treated with estradiol (E2)

source_name: human endothelial cell line, co-culture, E2


title: endothelial cells, co-culture, E2, rep 2


title: 16_E3_15_A11

description: single nucleus RNA sequencing


title: Sample_25_training_Vehicle


title: Sample_20_training_Vehicle


title: Sample_27_no training_Vehicle


title: endothelial cells, co-culture, E2, rep 1


title: iMB tumor 2

city: Baltimore

first: Mingyao

last: Ying

state: MD

address: 733 N Broadway

department: Department of Neurology

institute: Johns Hopkins School of Medicine

data_processing:
The raw reads were aligned to reference human genome build hg19 using HISAT2 with default parameters. For each gene, the number of reads aligned to its exons were counted and summarized into gene level counts by StringTie the R Bioconductor package GenomicFeatures based on the GENCODE hg19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix of genes for all samples in csv

source_name: iMB xenograft from the mouse brain

extract_protocol:
the RNeasy kit from Qiagen
Illumina TrueSeq RNA Sample Preparation kit v2

value: tumor xenograft


title: 15_E4_20_A10

description: single nucleus RNA sequencing


title: endothelial cells, co-culture, DMSO, rep 3

description: gene expression data from endothelial cells co-cultured with pericytes and treated with vehicle (DMSO)

source_name: human endothelial cell line, co-culture, DMSO

value: brain


title: iMB tumor 3


title: pericytes, mono-culture, DMSO, rep 2


title: Sample_19_no training_Corticosterone

value: Sprague-Dawley


title: Sample_18_training_Corticosterone


title: 13_E4_20_A08

description: single nucleus RNA sequencing


title: endothelial cells, co-culture, DMSO, rep 2


title: Liver_WT_rep1


title: iMB tumor 1


title: Sample_17_no training_Vehicle

value: no training


title: 12_E3_20_A07

description: single nucleus RNA sequencing


title: endothelial cells, co-culture, DMSO, rep 1


title: 19_E4_15_B02

description: single nucleus RNA sequencing


title: iMB tumor 4


title: GBM1B_EGF_24h_rep2

description: GBM1B cells depleted of growth factors for 16 hours followed by EGF stimulation for 24 hours and sent for RNA sequencing

source_name: GBM cells

extract_protocol:
RNeasy kit (Qiagen)
Illumina TrueSeq RNA Sample Preparation kit v2

value: GBM stem-like cells


title: 14_E3_20_A09

description: single nucleus RNA sequencing


title: Sample_14_no training_Corticosterone

value: Hippocampus


title: GBM1B_EGF_4h_rep2

description: GBM1B cells depleted of growth factors for 16 hours followed by EGF stimulation for 4 hours and sent for RNA sequencing


title: endothelial cells, mono-culture, E2, rep 3

description: gene expression data from endothelial cells cultured alone and treated with estradiol (E2)

source_name: human endothelial cell line, mono-culture, E2


title: Sample_10_training_Vehicle

value: Vehicle


title: GBM1B_untreated_rep2

description: GBM1B cells depleted of growth factors for 16 hours and sent for RNA sequencing


title: 09_E4_10_A04

description: single nucleus RNA sequencing

source_name: hippocampus


title: 10_E3_10_A05

description: single nucleus RNA sequencing


title: GBM1B_EGF_24h_rep1


title: Sample_9_no training_Corticosterone

value: Corticosterone


title: 08_E3_10_A03

description: single nucleus RNA sequencing


title: endothelial cells, mono-culture, DMSO, rep 3

description: gene expression data from endothelial cells cultured alone and treated with vehicle (DMSO)

source_name: human endothelial cell line, mono-culture, DMSO


title: Sample_7_no training_Vehicle


title: GBM1B_EGF_4h_rep1


title: endothelial cells, mono-culture, E2, rep 2


title: endothelial cells, mono-culture, E2, rep 1


title: GBM1B_untreated_rep1


title: 07_E4_5_A02

description: single nucleus RNA sequencing


title: 06_E3_5_A01

description: single nucleus RNA sequencing


title: endothelial cells, mono-culture, DMSO, rep 2


title: 11_E4_10_A06

description: single nucleus RNA sequencing


title: Genemic DNA enriched by TAZ ChIP rep2

description: Biological replicate 2

library_source: genomic

data_processing:
The raw TAZ ChIP-Seq reads were aligned to the reference human genome build hg19 using Bowtie2 allowing at most two mismatches. TAZ binding sites were called using MACS with default settings by comparing the two TAZ ChIP-Seq samples against the two control samples and filtered by FDR<0.05.
Genome_build: hg19

molecule: genomic DNA

extract_protocol: MAGnify ChIP system (Invitrogen)

tag: chip antibody

value: anti-TAZ antibody (Cell Signaling)

value: EGF 4 hours


title: endothelial cells, mono-culture, DMSO, rep 1


title: Sample_4_no training_Corticosterone


title: 05_E3_15_H12

description: single nucleus RNA sequencing


title: Sample_5_training_Vehicle

value: training


title: Genemic DNA enriched by TAZ ChIP rep1

description: Biological replicate 1


title: 04_E4_10_H11

description: single nucleus RNA sequencing


title: Sample_3_training_Corticosterone


title: TH2

city: Little Rock

first: Zulema

last: Udaondo

state: AR

address: 501 Jack Stephens Drive

department: Biomedical Informatics

institute: UAMS

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts (Novogen, Hong Kong). In this step, clean data (clean reads) were obtained by removing reads containing adapters and reads in which uncertain nucleotides (N) were more than the 10% of the read length. Reads with low quality nucleotides (base quality <20) in more than 50% of the read length were also discarded
Paired-end clean reads were mapped to the reference genome (JABXWS000000000) using HISAT2 software v.0.6.1. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. HTSeq software was used to count the read mapped to each gene, including known and novel genes.
The RNA-seq reads were assembled according to the reference genomes using Rockhopper , and then compared to known gene structures, so that novel gene transcripts were predicted. The novel transcripts were aligned to sequences in the NCBI NR database using Blastx (cutoff: evalue < 1e-5). Novel transcripts with NR annotations were considered as novel potential protein coding transcripts. In total 1038 putative novel genes were identified.
The level of gene expression was measured by transcript abundance. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes. Read count is proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. To be comparable, the FPKM (fragments per kilobase of transcript sequence per millions of sequenced base pairs) is used. This method takes into account the effects of both sequencing depth and gene length on counting of fragments .
Supplementary_files_format_and_content: Level of gene expression (measured as FPKM) for both replicates. Functional annotation of the genes

organism: Novosphingobium sp. HR1a

source_name: cell culture

growth_protocol: Overnight cultures grown in M9 minimal medium plus glucose of Novosphingobium sp. HR1a were diluted in the gnotobiotic systems  to reach an initial O.D.660nm of 0.1.

extract_protocol:
Total RNA was extracted using the Trizol method (TRIzol RNA Isolation Reagents, Thermofisher Scientist), followed by further DNAse treatment and purification with the RNeasy Mini Kit (Qiagen).
One microgram of RNA per sample was used to prepare the sequencing libraries which were generated by Novogen (Hong Kong) using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Eight days after planting and inoculation, the liquid media of 4 pots were mixed and centrifuged (6000 rpm during 10 minutes). Pellets containing the cells were immediately frozen in liquid N2 and stored a -80ºC. Two independent experimental replicas were analyzed.

tag: source

value: clover roots and exudates


title: Input genomic DNA rep2

description: Biological replicate 2


title: TH1


title: Sample_2_no training_Vehicle


title: Input genomic DNA rep1

description: Biological replicate 1


title: Sample_8_training_Corticosterone


title: 03_E3_10_H10

description: single nucleus RNA sequencing


title: 02_E4_15_H09

description: single nucleus RNA sequencing


title: Total_SmallRNA_THP1_ML602178_2h_2_2

status: Public on Apr 18 2021

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

description:
small RNA
Total Small RNA-seq monocyte 2h ML-60218 technical rep 2 seq rep 2
Total_SmallRNA_THP1_ML602178_2h_2_abundance.txt

data_processing:
Biological replicates and experimental conditions (control, + 72h PMA, + 4h ML-60218) were sequenced together on an Illumina HiSeq4000 (paired-end, 100) for each experiment, and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed smallRNA sequencing reads were mapped to the GRCh38 genome using Bowtie v 2.2.4 with settings --sensitive
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed abundance files correpond to read counts extracted over a comprehensive RNAcentral database annotation of noncoding RNAs. Gene annotation set and corresponding GRCh38 coordinates were downloaded from the contemporaneous RNAcentral database [release version13: ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/releases/13.0/genome_coordinates/bed/homo_sapiens.GRCh38.bed.gz.]. RNAcentral coordinate IDs were mapped to Ensembl, Gencode, GtRNAdb, HGNC, Lncbase, Lncbook, Lncipedia, Lndcrnadb, miRbase, noncode, Refseq, and Rfam. To remove duplicate coordinate gene entries derived from multiple databases, genes with start and end coordinates within 50 bp of each other were merged into singular coordinate entries. Gene-specific raw small RNA signal counts were extracted and include the flanking 25 bp for each RNAcentral gene coordinate entry

source_name: THP-1 cells, + ML-60218 exposure (2h)

growth_protocol: THP-1 cells were obtained from ATCC (Lot # 62454382) and grown for multiple passages in T-75 flasks between 2-8 x 105 cells/mL in growth medium containing RPMI-1640 (Corning), 10% fetal bovine serum, and 1% penicillin streptomycin.

extract_protocol:
Nuclear and cytoplasmic THP-1 fractions were isolated using the NE-PER Nuclear and Cytoplasmic Extraction Reagents (ThermoFisher) according to instructions, with additional nuclear washes prior to nuclear extraction. Fractionation purities were assessed by b-tubulin and Lamin B2 contamination. THP-1 monocyte and THP-1 macrophage exosomes were isolated by differential centrifugation (10 min x 300 g, 10 min x 2000 g, 30 min x 10,000 g, 70min x 100,000 g all at 4°C), washed and resuspended in PBS for analysis. Exosome particle size distributions were assessed by nanoparticle tracking analysis (NanoSight). Small RNA was immediately isolated from subcellular fractionation experiments using the mirVana miRNA isolation kit according to instructions (AM1560, Invitrogen).
Small RNA libraries were generated using the NEBnext small RNA library preparation kit according to instructions (E7580S, New England BioLabs)

treatment_protocol: For differentiation of THP-1 cells, non-adherent cells were diluted to 2 x 105 cells/mL and grown overnight, and a final concentration of 100 nM PMA was added the following morning. THP-1 derived macrophages were collected after 72 hr exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 minutes followed by cell wash in phosphate buffer saline (PBS) buffer. ML-60218 treated THP-1 cells were exposed for 4 h at a final concentraion of 25 mM

value: 2 h ML-60218 exposure

tag: cell line


title: Total_SmallRNA_THP1_ML602178_2h_2_1

description:
small RNA
Total Small RNA-seq monocyte 2h ML-60218 technical rep 2 seq rep 1
Total_SmallRNA_THP1_ML602178_2h_2_abundance.txt


title: Total_SmallRNA_THP1_ML602178_1h_2_2

description:
small RNA
Total Small RNA-seq monocyte 1h ML-60218 technical rep 2 seq rep 2
Total_SmallRNA_THP1_ML602178_1h_2_abundance.txt

source_name: THP-1 cells, + ML-60218 exposure (1h)

value: 1 h ML-60218 exposure


title: Total_SmallRNA_THP1_ML602178_4h_2_2

description:
small RNA
Total Small RNA-seq monocyte 4h ML-60218 biological replicate 2 seq rep 2
Total_SmallRNA_THP1_ML602178_4h_2_abundance.txt

source_name: THP-1 cells, + ML-60218 exposure (4h)

value: 4 h ML-60218 exposure


title: Total_SmallRNA_THP1_ML602178_1h_1

description:
small RNA
Total Small RNA-seq monocyte 1h ML-60218 technical replicate 1
Total_SmallRNA_THP1_ML602178_1h_1_abundance.txt


title: Total_SmallRNA_THP1_ML602178_3h_1

description:
small RNA
Total Small RNA-seq monocyte 3h ML-60218 technical replicate 1
Total_SmallRNA_THP1_ML602178_3h_1_abundance.txt

source_name: THP-1 cells, + ML-60218 exposure (3h)

value: 3 h ML-60218 exposure


title: Total_SmallRNA_THP1_ML602178_3h_2_1

description:
small RNA
Total Small RNA-seq monocyte 3h ML-60218 technical rep 2 seq rep 1
Total_SmallRNA_THP1_ML602178_3h_2_abundance.txt


title: Total_SmallRNA_THP1_ML602178_4h_2_1

description:
small RNA
Total Small RNA-seq monocyte 4h ML-60218 biological replicate 2 seq rep 1
Total_SmallRNA_THP1_ML602178_4h_2_abundance.txt


title: Total_SmallRNA_THP1_ML602178_1h_2_1

description:
small RNA
Total Small RNA-seq monocyte 1h ML-60218 technical rep 2 seq rep 1
Total_SmallRNA_THP1_ML602178_1h_2_abundance.txt


title: Total_SmallRNA_THP1_ML602178_2h_1

description:
small RNA
Total Small RNA-seq monocyte 2h ML-60218 technical replicate 1
Total_SmallRNA_THP1_ML602178_2h_1_abundance.txt


title: Total_SmallRNA_THP1_ML602178_0h_1

description:
small RNA
Total Small RNA-seq monocyte 0h ML-60218 biological replicate 1
Total_SmallRNA_THP1_ML602178_0h_1_abundance.txt

source_name: THP-1 cells (control)

value: control ( - ML-60218)


title: Exosomal_SmallRNA_THP1_macrophage_2_1

description:
small RNA
Exosomal purified SmallRNA-seq macrophage 72 h PMA biological replicate 2 seq rep 1
Exosomal_SmallRNA_THP1_macrophage_2_abundance.txt

source_name: THP-1 cells, + PMA exposure (72h)

value: 72 h PMA exposure


title: Exosomal_SmallRNA_THP1_macrophage_3

description:
small RNA
Exosomal purified SmallRNA-seq macrophage 72 h PMA biological replicate 3
Exosomal_SmallRNA_THP1_macrophage_3_abundance.txt


title: Exosomal_SmallRNA_THP1_macrophage_2_2

description:
small RNA
Exosomal purified SmallRNA-seq macrophage 72 h PMA biological replicate 2 seq rep 2
Exosomal_SmallRNA_THP1_macrophage_2_abundance.txt


title: Exosomal_SmallRNA_THP1_macrophage_2_3

description:
small RNA
Exosomal purified SmallRNA-seq macrophage 72 h PMA biological replicate 2 seq rep 3
Exosomal_SmallRNA_THP1_macrophage_2_abundance.txt


title: Exosomal_SmallRNA_THP1_macrophage_1_2

description:
small RNA
Exosomal purified SmallRNA-seq macrophage 72 h PMA biological replicate 1 seq rep 2
Exosomal_SmallRNA_THP1_macrophage_1_abundance.txt


title: Exosomal_SmallRNA_THP1_macrophage_1_1

description:
small RNA
Exosomal purified SmallRNA-seq macrophage 72 h PMA biological replicate 1 seq rep 1
Exosomal_SmallRNA_THP1_macrophage_1_abundance.txt


title: Exosomal_SmallRNA_THP1_monocyte_3

description:
small RNA
Exosomal purified SmallRNA-seq monocyte 0h (control) biological replicate 3
Exosomal_SmallRNA_THP1_monocyte_3_abundance.txt

value: control ( - PMA)


title: Exosomal_SmallRNA_THP1_macrophage_1_3

description:
small RNA
Exosomal purified SmallRNA-seq macrophage 72 h PMA biological replicate 1 seq rep 3
Exosomal_SmallRNA_THP1_macrophage_1_abundance.txt


title: Total_SmallRNA_THP1_ML602178_3h_2_2

description:
small RNA
Total Small RNA-seq monocyte 3h ML-60218 technical rep 2 seq rep 2
Total_SmallRNA_THP1_ML602178_3h_2_abundance.txt


title: Total_SmallRNA_THP1_ML602178_4h_1

description:
small RNA
Total Small RNA-seq monocyte 4h ML-60218 biological replicate 1
Total_SmallRNA_THP1_ML602178_4h_1_abundance.txt


title: Exosomal_SmallRNA_THP1_monocyte_2_1

description:
small RNA
Exosomal purified SmallRNA-seq monocyte 0h (control) biological replicate 2 seq rep 1
Exosomal_SmallRNA_THP1_monocyte_2_abundance.txt


title: Exosomal_SmallRNA_THP1_monocyte_1_2

description:
small RNA
Exosomal purified SmallRNA-seq monocyte 0h (control) biological replicate 1 seq rep 2
Exosomal_SmallRNA_THP1_monocyte_1_abundance.txt


title: Cytoplasm_SmallRNA_THP1_macrophage_72h

description:
small RNA
Cytoplasmic fraction SmallRNA-seq macrophage 72h PMA exposure
Cytoplasm_SmallRNA_THP1_72h_macrophage_abundance.txt


title: Exosomal_SmallRNA_THP1_monocyte_1_1

description:
small RNA
Exosomal purified SmallRNA-seq monocyte 0h (control) biological replicate 1 seq rep 1
Exosomal_SmallRNA_THP1_monocyte_1_abundance.txt


title: Exosomal_SmallRNA_THP1_monocyte_1_3

description:
small RNA
Exosomal purified SmallRNA-seq monocyte 0h (control) biological replicate 1 seq rep 3
Exosomal_SmallRNA_THP1_monocyte_1_abundance.txt


title: Cytoplasm_SmallRNA_THP1_monocyte_24h

description:
small RNA
Cytoplasmic fraction SmallRNA-seq monocyte 24h PMA exposure
Cytoplasm_SmallRNA_THP1_monocyte_24h_abundance.txt

source_name: THP-1 cells, + PMA exposure (24h)

value: 24 h PMA exposure


title: Exosomal_SmallRNA_THP1_monocyte_2_3

description:
small RNA
Exosomal purified SmallRNA-seq monocyte 0h (control) biological replicate 2 seq rep 3
Exosomal_SmallRNA_THP1_monocyte_2_abundance.txt


title: Exosomal_SmallRNA_THP1_monocyte_2_2

description:
small RNA
Exosomal purified SmallRNA-seq monocyte 0h (control) biological replicate 2 seq rep 2
Exosomal_SmallRNA_THP1_monocyte_2_abundance.txt


title: Total_SmallRNA_THP1_ML602178_0h_2

description:
small RNA
Total Small RNA-seq monocyte 0h ML-60218 biological replicate 2
Total_SmallRNA_THP1_ML602178_0h_2_abundance.txt


title: Cul30-3

city: Beijing

first: Xiulin

last: Zhang

address: No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing

country: China

institute: Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Hisat2
cufflink
cuffdiff
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

source_name: Gastric epithelial cells

extract_protocol:
After treatment with Helicobacter pylori,cells were collected and total mRNA of  cells extracted with TRIzol reagent (Vazyme, Piscataway, NJ, USA) were retrotranscribed to cDNA using 5×All-In-One RT MasterMix (ABM, Richmond, BC, Canada) following the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GES-1 cells co-cultured with 2 μg/mL Helicobacter pylori lysate for 1 to 30 generations.Wild type cells that never co-cultured with lysate were control groups.

value: GES-1 gastric epithelial cells

tag: tretment

value: Co-cultured with Helicobacter Pylori lysate for 30 generations.


title: Cul30-2


title: Cul1-3

value: Co-cultured with Helicobacter Pylori lysate for 1 generation.


title: Cul1-1


title: BGES-2

value: Wild type. Never co-cultured with Helicobacter Pylori lysate.


title: Cytoplasm_SmallRNA_THP1_monocyte_1h

description:
small RNA
Cytoplasmic fraction SmallRNA-seq monocyte 1h PMA exposure
Cytoplasm_SmallRNA_THP1_monocyte_1h_abundance.txt

source_name: THP-1 cells, + PMA exposure (1h)

value: 1 h PMA exposure


title: Cytoplasm_SmallRNA_THP1_monocyte_0h

description:
small RNA
Cytoplasmic fraction SmallRNA-seq monocyte 0h (control)
Cytoplasm_SmallRNA_THP1_monocyte_0h_abundance.txt


title: Nuclear_SmallRNA_THP1_monocyte_1h

description:
small RNA
Nuclear fraction SmallRNA-seq monocyte 1h PMA exposure
Nuclear_SmallRNA_THP1_monocyte_1h_abundance.txt


title: Nuclear_SmallRNA_THP1_monocyte_0h

description:
small RNA
Nuclear fraction SmallRNA-seq monocyte 0h (control)
Nuclear_SmallRNA_THP1_monocyte_0h_abundance.txt


title: Nuclear_SmallRNA_THP1_monocyte_24h

description:
small RNA
Nuclear fraction SmallRNA-seq monocyte 24h PMA exposure
Nuclear_SmallRNA_THP1_monocyte_24h_abundance.txt


title: Nuclear_SmallRNA_THP1_macrophage_72h

description:
small RNA
Nuclear fraction SmallRNA-seq macrophage 72h PMA exposure
Nuclear_SmallRNA_THP1_macrophage_72h_abundance.txt


title: Nuclear_SmallRNA_THP1_monocyte_4h

description:
small RNA
Nuclear fraction SmallRNA-seq monocyte 4h PMA exposure
Nuclear_SmallRNA_THP1_monocyte_4h_abundance.txt

source_name: THP-1 cells, + PMA exposure (4h)

value: 4 h PMA exposure


title: BGES-3


title: BGES-1


title: Total_SmallRNA_THP1_macrophage_2

description:
small RNA
Total Small RNA-seq macrophage biological replicate 1
Total_SmallRNA_THP1_macrophage_2_abundance.txt


title: Blood-experienced_10

city: Boston

first: Kimberly

middle: Alynn

last: Barker

state: MA

address: 72 E Concord St., R205

department: Pulmonary Center

institute: Boston University School of Medicine

data_processing:
FastQC and Trimmomatic 0.36 were used to quality-trim Illumina files with the following parameters: cutoff quality: 30, minimum length: 45
Reads were aligned to the GRCm38.p5 build of the mouse genome (https://www.gencodegenes.org/) using STAR 2.5.3a. Uniquely aligned reads were used for downstream analysis
Indexed bam files were converted to raw gene counts using HTSeq/0.61p1 and the GENCODE.vM15 gene annotation reference.
The Bioconductor package DESeq2 in R was used for statistical evaluations of expression differences between naïve and experienced mice.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Raw counts for every gene and every sample

source_name: whole blood (facial vein)

extract_protocol:
RNA was extracted from facial vein blood of 10 naïve and 10 experienced mice using the Mouse RiboPure-Blood RNA Isolation Kit (Thermo Fisher Scientific, AM1951) according to the manufacturer’s instructions.
RNA was purified and a cDNA library was generated using a TruSeq Stranded Total RNA Library Prep Globin (Illumina, 20020612). Single-end 50 base pair read length sequencing was performed on an Illumina HiSeq 2500.

value: S. pneumoniae infection


title: Total_SmallRNA_THP1_monocyte_2

description:
small RNA
Total Small RNA-seq monocyte biological replicate 2
Total_SmallRNA_THP1_monocyte_2_abundance.txt


title: Blood-experienced_9


title: Blood-experienced_8


title: Blood-experienced_7


title: Cul30-1


title: Cytoplasm_SmallRNA_THP1_monocyte_4h

description:
small RNA
Cytoplasmic fraction SmallRNA-seq monocyte 4h PMA exposure
Cytoplasm_SmallRNA_THP1_monocyte_4h_abundance.txt


title: Blood-naive_10

value: saline (vehicle control)


title: Blood-experienced_6


title: Cul1-2


title: POLR3GL_monocyte_ML60218_2

description: ChIP-seq monocyte biological replicate 2

data_processing:
Biological replicates and experimental conditions (control, + 72h PMA, + 4h ML-60218) were sequenced together on an Illumina HiSeq4000 (paired-end, 100) for each individual ChIP factor, and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed ChIP sequencing reads were mapped to the GRCh38 genome using Bowtie v 2.2.4 with settings --sensitive
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig track signal files were generated from mapped sequencing reads using DeepTools bamCoverage with settings --normalizeTo1x 2451960000 --binSize 100000 --smoothLength 300000

source_name: THP-1 cells, + ML60218 exposure (4h)

extract_protocol:
Equal numbers of THP-1 monocytes were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 x 106 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 minutes. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 minutes of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1x RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 seconds on, 60 seconds off; 15 additional cycles on a Bioruptor sonicator: 30 seconds on, 30 seconds off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled Dynabead protein G (ThermoFisher) magnetic beads. Anti-histone H3 (acetyl K27) antibody was obtained from Abcam (ab4729), POLR3D antibody was obtained from abcam (ab86786; Lot# GR267691-1). 3-5 ug of antibody per ChIP was coupled to 18 uL beads and rotated overnight with sheared chromatin at 40 C. Beads were then washed 5x in ChIP wash buffer (Santa Cruz), 1x in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 650 C overnight, followed by digestion of RNA (30 min RNase incubation at 370C) and digestion of protein (30 min proteinase K incubation at 450C). ChIP DNA was then purified on a minElute column (Qiagen)
libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: Novus Biologicals NBP1-79826

tag: pma, ml60218 exposure


title: POLR3G_monocyte_ML60218_2

value: Invitrogen PA5-51120 lot#UG2803044


title: Blood-naive_9


title: Blood-naive_6


title: Blood-experienced_4


title: Total_SmallRNA_THP1_macrophage_1

description:
small RNA
Total Small RNA-seq macrophage biological replicate 1
Total_SmallRNA_THP1_macrophage_1_abundance.txt


title: POLR3D_macrophage_1

description: ChIP-seq monocyte biological replicate 1

extract_protocol:
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 x 106 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 minutes. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 minutes of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1x RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 seconds on, 60 seconds off; 15 additional cycles on a Bioruptor sonicator: 30 seconds on, 30 seconds off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled Dynabead protein G (ThermoFisher) magnetic beads. Anti-histone H3 (acetyl K27) antibody was obtained from Abcam (ab4729), POLR3D antibody was obtained from abcam (ab86786; Lot# GR267691-1). 3-5 ug of antibody per ChIP was coupled to 18 uL beads and rotated overnight with sheared chromatin at 40 C. Beads were then washed 5x in ChIP wash buffer (Santa Cruz), 1x in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 650 C overnight, followed by digestion of RNA (30 min RNase incubation at 370C) and digestion of protein (30 min proteinase K incubation at 450C). ChIP DNA was then purified on a minElute column (Qiagen)
libraries were prepared for sequencing using standard Illumina protocols

value: Bethyl A302-295A


title: POLR3GL_macrophage_2


title: POLR3G_monocyte_ML60218_1

value: 4 h ML-60218 exposure


title: POLR3D_macrophage_2


title: Blood-naive_8


title: Blood-experienced_5


title: POLR3GL_macrophage_1


title: POLR3G_macrophage_1


title: Blood-experienced_3


title: POLR3G_macrophage_2


title: POLR3GL_monocyte_ML60218_1


title: Total_SmallRNA_THP1_monocyte_1

description:
small RNA
Total Small RNA-seq monocyte biological replicate 1
Total_SmallRNA_THP1_monocyte_1_abundance.txt


title: POLR1D_macrophage_2

value: Bethyl A304-847A


title: POLR1D_macrophage_1


title: Blood-experienced_1


title: Blood-experienced_2


title: Blood-naive_5


title: POLR3B_macrophage_2

value: Bethyl A301-855A


title: IgG_monocyte

value: NeoMarkers NC-100-P0


title: Blood-naive_4


title: POLR3B_macrophage_1

value: 72 h PMA exposure


title: Blood-naive_2


title: Blood-naive_3


title: BRF1_monocyte

value: Abcam ab74221

value: control ( - PMA)


title: Blood-naive_1


title: GTF3C1_monocyte

value: SigmaAldrich (PLA0180)


title: Blood-naive_7


title: POLR3E_monocyte_2

value: Bethyl A303-708A


title: POLR3E_monocyte_1


title: no6_ACE2_COV_1

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq500 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt ver 1.14. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR ver 2.5.3a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count ver 0.12.4 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM) with DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with TPM for every gene and every sample

source_name: SARS-CoV- infected ACE2-iPS cells

growth_protocol: The human iPS cells were maintained on 0.5 μg/cm2 recombinant human laminin 511 E8 fragments (iMatrix-511, Nippi) with StemFit AK02N medium (Ajinomoto) containing 10 μM Y-27632 (from day 0 to day 1, FUJIFILM Wako Pure Chemical). To passage human iPS cells, near-confluent human iPS cell colonies were treated with TrypLE Select Enzyme (Thermo Fisher Scientific) for 5 min at 37°C. After the centrifugation, human iPS cells were seeded at an appropriate cell density (1.3×104 cells/9 cm2) onto iMatrix-511. Human ES/iPS cells on iMatrix-511 were subcultured every 6 days.

extract_protocol:
Total RNA was isolated from uninfected or infected ACE2-iPS cells using ISOGENE (NIPPON GENE).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Undifferentiated human iPS cells (1383D6) were transduced with 600 VP/cells of LacZ-, ACE2-, or TMPRSS2-expressing Ad vectors (Ad-LacZ, Ad-ACE2, or Ad-TMPRSS2, respectively) for 2 hr, and then cultured with AK02 medium for 2 days. ACE2-expressing human iPS (ACE2-iPS) cells were infected with SARS-CoV-2 (5×104 TCID50/well) for 2 hr, and then cultured with AK02 medium.

value: iPS cells

tag: infection status

value: SARS-CoV-2 infected


title: POLR3D_monocyte_1


title: POLR3D_monocyte_2


title: no6_ACE2_COV_2


title: no6_ACE2_COV_3


title: POLR3G_monocyte_1


title: no6_ACE2_CNT_3

description: control

source_name: uninfected ACE2-iPS cells

value: uninfected


title: no6_ACE2_CNT_2

description: control


title: POLR3C_monocyte_2

value: Bethyl A303-063A


title: POLR3GL_monocyte_1


title: no6_ACE2_CNT_1

description: control


title: HG3, Low survivorship - timepoint 3 (ATAC-seq)

city: Austin

first: Amy

last: Brock

state: TX

address: 107 West Dean Keeton St.

institute: University of Texas at Austin

data_processing:
ATAC-Sequencing data was processed uniformly with the Cromwell-based pipeline employed by the ENCODE (https://github.com/ENCODE-DCC/atac-seq-pipeline) project to reproducibly align and call IDR-resolved peaks in our samples.
Relevant pipeline settings were as follows: Paired-end: true, auto_detect_adapter enabled, idr and xcor enabled with idr_threshold of 0.05.
Blacklist-filtered .narrowPeaks files from MACS2 were used for further analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-separated .narrowPeaks files from MACS2

source_name: HG3 cell line

extract_protocol:
50,000 HG3 cells were sorted into 1.5 mL microcentrifuge tubes and pelleted by centrifugation at 500 RCF for 5 minutes at 4°C in a pre-cooled fixed-angle centrifuge. All supernatant was removed and 50 µL of transposase mixture (25 µL TD Buffer, 2.5 µL TDE1, 0.5 µL Digitonin and 22 µL nuclease-free H20) (Illumina #15027866 and 15027864; Promega G9441) was added to the cells and mixed gently by pipetting. Transposition reactions were incubated at 37°C for 30 minutes and subsequently purified using a QIAgen MinElute Reaction Cleanup Kit (Qiagen #28204).
Transposed fragments were subsequently amplified for 6-8 cycles as needed per sample using Nextera i7 and i5 primers. Libraries were purified using double-sided bead purification (0.5x followed by 1.3x volume of AMPure XP beads) and eluted in nuclease-free H20. Library size and concentrations were confirmed on an Agilent High Sensitivity DNA Bioanalysis chip and by qPCR using a KAPA Library Quantification Kit (Roche #KK4824). All libraries were sequenced using paired-end, dual-index sequencing on a 75-cycle high output kit on an Illumina NextSeq 500 system.

value: B-cell chronic lymphocytic leukemia


title: POLR3GL_monocyte_2

value: Novus Biologicals NBP1-79826


title: HG3, Low survivorship - timepoint 2 (ATAC-seq)


title: POLR3G_monocyte_2

value: Invitrogen PA5-51120 lot#UG2803044


title: HG3, Low survivorship - timepoint 1 (ATAC-seq)


title: HG3, High survivorship - timepoint 2 (ATAC-seq)


title: POLR1D_monocyte_1


title: POLR1D_monocyte_2


title: HG3, High survivorship - timepoint 1 (ATAC-seq)


title: POLR3C_monocyte_1


title: Ardisia pusilla toluene treatment rep2

city: Wanju-gun

first: Su Young

last: Lee

state: Jeollabuk-do

address: 100, Nongsaengmyeong-ro, Iseo-myeon

department: Floriculture Research Division, National Institute of Horticultural and Herbal Science

country: South Korea

institute: Rural Development Administration

data_processing:
Basecalls performed using Sequencing Control Software
Trimmomatic program is used to remove adapter sequences and bases with base quality lower  than three from the ends. Also using sliding window method, bases of reads that does not qualify for  window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are  dropped to produce trimmed data.
Trimmed reads for every sample were merged into one file to construct combined reference. The de novo assembly of merged data was carried out using Trinity with default parameters; it can be assembled into transcript contigs.
For assembled genes, longest contigs of the assembled contigs are filtered and clustered into the  non-redundant transcripts using CD-HIT-EST program. We defined these transcripts as ‘unigenes’  which are used for predicting the ORFs (Open Reading Frames), annotating against several known  sequence databases, and analyzing differentially expressed genes (DEGs).
Genome_build: In this study, Other de novo transcriptome assembly was performed in order to reconstruct the  transcript sequences without reference genome sequence. To annotate the clustered unigenes, they were blasted against public databases with a blastx and  BLASTN and BLASTX, including Kyoto Encyclopedia of Genes and Genomes (KEGG), NCBI Nucleotide  (NT), Pfam, Gene ontology (GO), NCBI non-redundant Protein (NR), UniProt and EggNOG.
Supplementary_files_format_and_content: WT and Toluene treated Excel files include FPKM values for each Sample.
Supplementary_files_format_and_content: merge_Annotation_Result file include raw gene counts for every unigene

organism: Ardisia pusilla

source_name: Ardisia pusilla

growth_protocol: A. pusilla plants were kept in greenhouses.

extract_protocol:
A. pusilla leaf samples were ground into powder in a mortar with liquid nitrogen, and total RNA was extracted from the samples using TRIzol reagent (MRC, Cincinnati, OH, USA).Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A. pusilla plants (20 cm height) grown in a greenhouse were placed in a sealed chamber at room temperature (25±5 °C) under a pressure of 760 mm Hg with 12/12 h light/dark cycle. After that, toluene treatment was applied at a concentration of 1.5 ppm inside the chamber for 5 h. A. pusilla plants without toluene treatment were used as controls.

value: leaves

tag: size

value: 20 cm height

value: treated with 1.5ppm toluene for 5 hours


title: POLR3B_monocyte_2

value: Bethyl A301-855A


title: Ardisia pusilla toluene treatment rep1


title: Ardisia pusilla WT rep2

value: untreated


title: HG3, High survivorship - timepoint 3 (ATAC-seq)

tag: cell type


title: POLR3B_monocyte_1


title: HG3, Low survivorship - timepoint 3 (RNA-seq)

data_processing:
Bulk RNA-sequencing data was processed by trimming illumina sequencing adapters with cutadapt and aligned to human genome build GrCH38 with bowtie2.
Subread featurecounts was used to count exon-mapping reads in gene transcripts in the Ensemble human reference annotation version 77.
A sample-by-gene count matrix was derived from the “expected count” values in the RSEM outputs. Genes with fewer than 10 total counts across all samples were filtered out.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-separated text files of counts and TPM values produced by RSEM

molecule: polyA RNA

extract_protocol:
Forty million cells from the bulk TP0 and TP1 populations were co-stained using human CXCR4-APC (Thermo Fisher #FAB173A) and CD18-PE (BioLegend #302108) conjugated antibodies. CXCR4 and CD18 single-positive cells (representative of the high and low survivorship sub-populations) were isolated using a BD FACSAria II. Three biological replicates were collected in this manner over the course of two weeks. RNA was isolated from purified populations using a RNeasy Micro Kit (Qiagen #74004) and RNA quality was verified using an Agilent Bioanalyzer Pico Eukaryote chip.
400 ng of total RNA was used as input for library preparation using the KAPA stranded mRNA HyperPrep Kit (KAPA Biosystems #KK8580) per the manufacturer’s instructions. Library yields and sizes were confirmed using an Agilent High Sensitivity DNA kit (Agilent Technologies #5067-4626) on an Agilent 2100 bioanalyzer. Libraries were pooled in equimolar ratios and sequenced using a 75-cycle high output kit on an Illumina NextSeq 500 system.


title: HG3, Low survivorship - timepoint 2 (RNA-seq)


title: Ardisia pusilla WT rep1


title: POLR3A_monocyte_2

value: Abcam ab96328 lot#GR318563


title: HG3, Low survivorship - timepoint 1 (RNA-seq)


title: HG3, High survivorship - timepoint 3 (RNA-seq)


title: POLR3A_monocyte_1


title: PBMC_CD4posIL17neg_TCRb

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

data_processing:
Library strategy: TCR-seq
Adapter trimming and quality filtering of sequencing data were performed by using PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. Filtered reads were aligned to reference mouse TCR V/D/J sequences and assembled into TCR clonotypes using "analyze amplicon" command with the following parameters:  -s hsa,  --starting-material rna,  --5-end no-v-primers,  --3-end c-primers,  --adapters no-adapters,  --receptor-type trb,  --region-of-interest CDR3,  --only-productive, --align "-OvParameters.geneFeatureToAlign=VTranscript", --align "-OvjAlignmentOrder=JThenV", --assemble "-ObadQualityThreshold=10", --assemble "-OseparateByV=true", --assemble "-OseparateByJ=true".
List of final clones were converted into VDJtools format and analyzed by VDJtools-1.2.1.
Genome_build: ImMunoGeneTics (IMGT) reference sequences of human TRB
Supplementary_files_format_and_content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

source_name: sorted IL-17-CD4+ T cells after M3R peptide stimulation for 9 days

extract_protocol:
Salivary gland biopsy sample was taken at the time of diagnosis, and stored in RNA later solution at -30℃. Peripheral blood mononuclear cells were collected from M3R reactive Th17 positive pSS patient, and cultured with M3R peptide for 8 days. After stimulating with M3R peptide for 12hrs, IL-17 secreting CD4+ T cells were identified by Flow cytometry, using MACS cytokine secretion detection kit. Detected CD4+ IL-17+ T cells were purified by cell sorting.
TCR sequencing libraries for next generation sequencing were prepared from the mRNA of FACS-sorted IL-17 producing or non-producing CD4+ T cells. PolyA RNAs were isolated and amplified from sorted T cells according to a previous report (Shichino, et al, JCI Insight 2019). Human TCR beta chain cDNAs are amplified and fragmented according to a previous report (Shitara et al J Immunother Cancer 2019). Final TCR libraries, whose lengths were 200–300 base pairs, were pooled and sequenced using an Ion 540 Chef kit, an Ion 540 Chip kit, and an Ion Genestudio S5 Sequencer (Thermo Fisher Scientific) according to the manufacturer’s instructions, except the input library concentration (65 pM) and flow number (500).

value: lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4+ CD8- T cells in PBL

value: pSS patient

value: peripheral blood


title: HG3, High survivorship - timepoint 2 (RNA-seq)


title: HG3, High survivorship - timepoint 1 (RNA-seq)


title: HG3, TP0.5

data_processing:
Sequencing data was aligned to the GRCh38 genome using Cell Ranger (v3.1.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered cell barcodes and gene expression counts produced by cellranger

extract_protocol:
Cryopreserved samples were thawed, pelleted and resuspended in cold PBS-0.04% BSA. 100,000 viable BFP+ cells were sorted into cold PBS-0.04% BSA, resuspended at 1x106 cells per mL, and barcoded with a 10X Chromium Controller (10X Genomics) by reverse transcription of RNA from individual cells.
Sequencing libraries were subsequently constructed using reagents from a Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions (10X Genomics, #PN-120267). Sequencing was performed on an Illumina NovaSeq platform (paired-end, Read 1: 26 cycles and Read 2: 98 cycles) according to the manufacturer’s instructions (Illumina).

treatment_protocol: Cells were treated with an LD95 dose of fludarabine+mafosfamide for 72 hours and then washed and resuspended in fresh media.

value: 12 days after FM treatment


title: HCC827GR

city: Shanghai

first: Zhang

last: Ke-Ren

address: Chongqing South Road, No. 227

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

source_name: lung adenocarcinoma cell

extract_protocol:
Cells were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

tag: response to egfr-tki

value: resistant to EGFR-TKI (gefitinib)

value: lung adenocarcinoma


title: H1975OR

value: resistant to EGFR-TKI (osimertinib)


title: Multiplexed sample

data_processing:
Sequencing data was aligned to the GRCh38 genome using Cell Ranger (v3.1.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: cell barcodes, demultiplexed sample assignment, and transcript counts

extract_protocol:
For assessment of sub-clonal transcriptional identity parental and daughter TP0 and TP1 clones were expanded, following which 0.5x106 cells from each population of interest were washed and incubated with 5ul of Trustain FcX for 10 minutes on ice (Biolegend, #422302). To minimize batch effect, all 12 samples were prepared in parallel and subjected to cell hashing. Each population was incubated with a unique combination of 2 TotalSeq-C antibodies for 3 minutes on ice (Biolegend). Cells were washed twice in cold PBS-0.04% BSA and normalized before being mixed in equimolar amounts and resuspended to 1x106/ml. 20,000 cells were loaded onto a single 10X channel using the Single Cell 5’ reagent kit.
Sequencing libraries were subsequently constructed using reagents from a Chromium Single Cell 5’ reagent kit according to the manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq platform (paired-end) according to the manufacturer’s instructions (Illumina).

treatment_protocol: TP1 samples had been treated with an LD95 dose of fludarabine+mafosfamide for 72 hours and then washed and resuspended in fresh media.

value: pre- and post-treatment (multiplexed sample)


title: HG3, TP0

value: B-cell chronic lymphocytic leukemia

value: pre-treatment


title: HCC827

value: sensitive to EGFR-TKI (gefitinib)


title: HG3, TP1, replicate 7

value: 21 days after FM treatment


title: SG_TCRb

source_name: pSS patient salivary gland biopsy sample at the onset of diagnosis

value: lineage-negative (CD11b, CD19, NK1.1 and Ter119) and CD4+CD8- T cells in salivary gland

value: salivary gland


title: H1975

value: sensitive to EGFR-TKI (osimertinib)


title: HG3, TP1, replicate 1


title: PBMC_CD4posIL17pos_TCRb

source_name: sorted IL-17+CD4+ T cells after M3R peptide stimulation for 8 days


title: N1

status: Public on Apr 17 2021

city: Nanjing

first: yueming

last: sun

state: jiangsu

address: Nanjing medical university

institute: The First Affiliated Hospital of Nanjing Medical University

description: circRNAs expression in paired adjacent normal tissue

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: adjacent normal tissue

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.

growth_protocol: The colorectal cancer tissue and adjacent tissue were obtained after surgery, respectively.

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

treatment_protocol: Fresh tissues were acquired after surgery and immediately frozen in -80℃.Total RNA containing small RNA was extracted by using  the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol.

value: adjacent normal tissue

tag: subject number


title: T5

description: circRNAs expression in colorectal cancer tissue

source_name: colorectal cancer tissues

value: colorectal cancer tissue


title: Joint_PTOA_untreated_rep2

city: Nashville

first: Sean

middle: K

last: Bedingfield

state: TN

address: 2301 Vanderbilt Place PMB 351826

department: Biomedical Engineering

institute: Vanderbilt University

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing: The raw Nanostring nCounter genes were normalized using nSolver 4.0 (NanoString Technologies Inc., Seattle, WA), adjusting for positive controls, housekeeping genes and background level.

source_name: No Treatment PTOA

extract_protocol: Equal mass of (1) synovial tissue and (2) articular cartilage and subchondral bone were stored in RNAlater Stabilization Solution (AM7020, Invitrogen) at -80°C until further processing. Samples were homogenized with the Tissuelyser 2 from Qiagen (Redwood City, CA) before total RNA from the was extracted using Qiagen RNeasy Kit for purification of total RNA according to the manufacturer's instructions. mRNA expression analysis with the NanoString nCounter® Mouse Inflammation v2 Panel was performed according to the manufacturer's protocol (NanoString Technologies Inc., Seattle, WA).

tag: disease state

value: post-traumatic osteoarthritis (PTOA)

value: Knee joint

value: 3 months

tag: gender

value: Male

tag: strain

value: untreated


title: Joint_PTOA_untreated_rep1

tag: tissue


title: Joint_PTOA_untreated_rep8

tag: treatment


title: Joint_PTOA_untreated_rep11

tag: age


title: Joint_PTOA_untreated_rep7


title: Joint_PTOA_untreated_rep10


title: N3


title: T2


title: Joint_PTOA_untreated_rep6


title: N4


title: Joint_PTOA_untreated_rep3


title: Joint_PTOA_untreated_rep12


title: Joint_PTOA_untreated_rep4


title: Joint_PTOA_untreated_rep5


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep11

source_name: Negative Ctrl siRNA

value: negative-ctrl-siRNA


title: Joint_PTOA_untreated_rep9


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep12


title: T1


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep10


title: N2


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep9


title: N5


title: T4


title: T3


title: 4T1_KO_rep1

city: Limoges

first: Justine

last: Pollet

address: 2, avenue Martin Luther King

country: France

institute: CBRS

description: Gene expression data from a mouse triple negative breast cancer cell line

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse or HumanGene2.0ST (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: Hybridized microarrays were scanned by a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Probes were normalized by robust multi-array averaging with rma function from oligo R package and mapped using clariomsmousetranscriptcluster.db from bioconductor as database.Statistical analyses were performed using the Linear Model for Series of Arrays (lmFit) from limma R package.

source_name: unstimulated breast cancer cells

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

growth_protocol: The 4T1 cell line was cultured in RPMI supplemented with 8% heat-inactivated FCS (v/v) and 2 mM L-glutamine at 37°C/5% CO2.

extract_protocol: Cells were dissociated with trypsin/EDTA (0.05% trypsin; Gibco) for 5 min. Dissociated cells were washed twice in PBS. RNA was extracted using the NucleoSpin RNA XS extraction kit (Macherey–Nagel), according to the manufacturer’s recommendations.

treatment_protocol: no stimulation

tag: genotype/variation

value: KO


title: 4T1_WT_rep2

value: WT


title: 4T1_KO_rep2


title: 4T1_WT_rep1


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep8


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep6


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep7


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep1


title: Joint_PTOA_MMP13-siRNA-treated_rep12

source_name: MMP13 siRNA


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep5


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep4


title: Joint_PTOA_MMP13-siRNA-treated_rep11


title: Joint_PTOA_MMP13-siRNA-treated_rep9


title: Joint_PTOA_MMP13-siRNA-treated_rep10


title: Joint_PTOA_MMP13-siRNA-treated_rep6


title: Joint_PTOA_MMP13-siRNA-treated_rep1


title: Joint_PTOA_MMP13-siRNA-treated_rep2


title: Joint_PTOA_MMP13-siRNA-treated_rep7


title: Joint_PTOA_MMP13-siRNA-treated_rep3


title: Joint_PTOA_MMP13-siRNA-treated_rep5


title: Joint_PTOA_MMP13-siRNA-treated_rep4


title: Joint_healthy_untreated_rep12

source_name: Healthy

value: Healthy


title: Joint_healthy_untreated_rep11


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep2


title: Joint_healthy_untreated_rep9


title: Joint_healthy_untreated_rep8


title: Joint_PTOA_negative-ctrl-siRNA-treated_rep3


title: Joint_healthy_untreated_rep6


title: Joint_healthy_untreated_rep4


title: Joint_healthy_untreated_rep10


title: Joint_PTOA_MMP13-siRNA-treated_rep8


title: Joint_healthy_untreated_rep3


title: DIO DMSO-2

city: San Diego

first: Brian

middle: Patrick

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Differential transcript expression was determined using the Cufflinks Cuffdiff package (https://github.com/cole-trapnell-lab/cufflinks).
Genome_build: Mus musculus genome mm10
Supplementary_files_format_and_content: Read FPKM and Log2 fold differential expression, and FDR corrected Q-values

source_name: Liver

growth_protocol: 16 weeks old C57BL/6J DIO male mice (cat#380050)

extract_protocol:
Liver from DMSO or NCT treated mice was removed, flash frozen in liquid nitrogen, and RNA harvested using Trizol reagent.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: High fat diet mice treated with DMSO or NCT for 2 weeks with intraperitoneal injection.

value: 16weeks old

value: DMSO control


title: DIO DMSO-3


title: DIO NCT-2

value: NCT treated 200 mg/kg bid 14 days


title: DIO NCT-1


title: DIO DMSO-1


title: Joint_healthy_untreated_rep2


title: Joint_healthy_untreated_rep1


title: Joint_healthy_untreated_rep7


title: Joint_healthy_untreated_rep5


title: panc-1-siALDOA-1

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in NCBI were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Cell line

extract_protocol:
PDAC cells were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using polyA selection RNA-seq protocols

value: PDAC cell line

value: siALDOA


title: panc-1-nc


title: 90siAldoa1

value: siAldoa


title: 90siAldoa2


title: 90NC


title: DIO NCT-3


title: panc-1-siALDOA-2


title: Hepatocytes-like cells (iHep)

first: Chunyan

last: Liu

address: 163 Xianlin Avenue

institute: Nanjing University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 026655_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hepatocytes-like cells (iHep)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary mouse SiO2-remodelled spleen fibroblasts were transfected LV-NC or LV-3TF. After 14-day culture post-transduction, MF and iHeps were collected. Freshly isolated PH was a positive control.

value: Hepatocytes-like cells (iHep)

value: female


title: Primary mouse hepatocytes (PH)

source_name: Primary mouse hepatocytes (PH)

value: Primary mouse hepatocytes (PH)


title: GAS

first: Yusuke

last: Ono

state: Kumamoto

address: 2-2-1 Honjo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

hyb_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

scan_protocol: The data were analyzed with Expression Console v1.4(Affymetrix) and Transcriptome Analysis Console v3.1 (Affymetrix). RMA was used as summarization algorithm.

data_processing: log2 GC-RMA signal

source_name: Male, 12-week-old, C57BL/6J

label_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the GeneChip Mouse Gene 2.0 ST Array using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

extract_protocol: RNA was harvested from freshly frozen muscle tissue using IsogenII reagent.  The RNA was further purified with the Qiagen RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.

tag: Sex

tag: muscle tissue

value: gastrocnemius


title: Primary mouse SiO2-remodelled spleen fibroblasts (MF)


title: SOL

value: soleus


title: SiO2-treated spleen 9SiO2 spleen)

source_name: SiO2-treated spleen 9SiO2 spleen)

treatment_protocol: SiO2-treated spleen spleens and SiO2-3TF-3C-treated spleens were collected on day 82.Mouse normal liver tissues were as a positive control.

value: spleen tissue


title: TRI

value: Male

value: triceps


title: TA

value: tibialis anterior


title: Mouse normal liver tissue (Mouse liver)

source_name: Mouse normal liver tissue (Mouse liver)

value: liver tissue


title: MDAmammos-KO-rep1

description: Gene expression data from a human triple negative breast cancer cell line

data_processing: Probes were normalized by robust multi-array averaging with rma function from oligo R package and mapped using hugene20sttranscriptcluster.db as database.Statistical analyses were performed using the Linear Model for Series of Arrays (lmFit) from limma R package.

growth_protocol: cultured at 37°C/5% CO2 in DMEM supplemented with 8% heat-inactivated FCS and 2 mM L-glutamine

tag: cell line

value: KO


title: 1.5mg/kg_PrimHep_Rep1

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

institute: UZH Zurich

data_processing:
Library strategy: targeted amplicon sequencing
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: macFas5
Supplementary_files_format_and_content: CHANGE-seq: text files containing identified off-target sites

source_name: primary hepatocytes

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CHANGE-seq  library preparation

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus. For HepG2 cells, the base editor and sgRNA was inroduced by NEON electroporation. In vivo treatment was delivery by AAV or LNP mediated delivery via tail vein injection.

value: LNP-mediated delivery

value: tail vein

value: targeted amplicon sequencing

tag: genotype

value: base-edited PCSK9


title: 1.5mg/kg_PrimHep_Rep2


title: 1.5mg/kg_redose_PrimHep_Rep1


title: 1.5mg/kg_redose_PrimHep_Rep2


title: p53_treated_8

source_name: whole liver lysate

value: AAV-mediated delivery


title: p53_treated_7


title: 1.5mg/kg_PrimHep_Rep3


title: p53_treated_6


title: SiO2-3TF-3C-treated spleen (SiO2-3TF-3C spleen)


title: 1.5mg/kg_redose_PrimHep_Rep3


title: MAS

value: masseter


title: MDAmammos-KO-rep2


title: RF

value: rectus femoris


title: PBS-treated spleen (PBS)

source_name: PBS-treated spleen (PBS)

treatment_protocol: Spleens were treated with PBS or SiO2. Spleen samples were harvested 19 days after the first injection.

value: female


title: Skin Ikkb-deleted cKO rep3

city: Philadelphia

first: Kang

last: Ko

address: 240 S 40th St

department: Periodontics

institute: University of Pennsylvania

data_processing:
Gene expression libraries were aligned to the Cellranger version of the mm10 reference genome and count matrices were generated using the default Cell Ranger v1.3.0 workflow, using default filtering.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of genes corresponding to count matrix rows
Supplementary_files_format_and_content: tab-delimited text file of cell barcodes corresponding to count matrix columns
Supplementary_files_format_and_content: mtx format UMI count gene expression matrix

source_name: Ventral skin

extract_protocol:
Ventral skin from wildtype or Prx1Cre+Ikkbf/f mice (4 weeks old) was enzymatically digested at 37°C with constant agitation in DMEM media containing DNAse I (0.15mg/ml, Roche), collagenase type IV (3.2mg/ml, Gibco) and dispase (2.6mg/ml, Sigma) for 1 hr, with 10 sec of vortex every 15 min and immediately sorted on FACSAria II SORP instrument to exclude debris, dead cells (DAPI-positive) and aggregates.
A pool of two mice per group was used to generate a single library, for a total of 5 cDNA libraries (2 for wildtype and 3 for the Ikkb deletion group). Single cell barcode capture was performed on a GemCode instrument platform with the 10X single-cell 3’ v2 chemistry (10X Genomics). cDNA library was prepared and sequenced on a HiSeq 4000 instrument (Illumina). Single cell barcode capture, quality control using BioAnalyzer, cDNA amplification and RNA sequencing were performed at the University of Pennsylvania Next Generation Sequencing Core according to manufacturer protocols.

value: post natal day 28

value: ventral skin


title: SiO2-remodelled spleen (SiO2)

source_name: SiO2-remodelled spleen (SiO2)


title: SS

city: Kumamoto

value: supraspinatus


title: MDAmammos-WT-rep1

value: WT


title: DIG

value: Male

value: digastric


title: TRP

value: trapezius


title: p53_treated_5


title: Skin Ikkb-deleted cKO rep2


title: p53_treated_3


title: Skin WT rep2

value: wild type


title: Skin Ikkb-deleted cKO rep1


title: p53_treated_1


title: TxT+GW4869_5

city: Ulm

first: Tim

last: Eiseler

address: Albert-Einstein Allee 23

department: Internal Medicine 1

country: Germany

institute: Ulm University

data_processing:
Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-base-pair, single-end mode. Base calls, provided by the real-time analysis (RTA) software (Illumina, San Diego, CA, USA), were subsequently converted into multiplexed, unaligned BAM format before demultiplexing into sample-specific, unaligned BAM files. For raw data processing off the instruments, custom programs, based on Picard tools (https://broadinstitute.github.io/picard/), were used
NGS reads were mapped to the Genome Reference Consortium GRCm38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR) utilising the “basic” Ensembl transcript annotation from version e99 (January 2020) as reference transcriptome. Since the mm10 assembly flavour of the UCSC Genome Browser was preferred for downstream data processing with Bioconductor packages for entirely technical reasons, Ensembl transcript annotation had to be adjusted to UCSC Genome Browser sequence region names. STAR was run with options suggested by the ENCODE project. Aligned NGS reads overlapping Ensembl transcript features were counted with the Bioconductor GenomicAlignments::summarizeOverlaps() function, taking into account that the Illumina TruSeq stranded mRNA protocol leads to sequencing of the second strand so that all reads needed inverting before counting. Transcript-level counts were aggregated to gene-level counts and the Bioconductor DESeq2 package was used to test for differential expression based on a model using the negative binomial distribution
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV files, FPKMS all samples

source_name: Total lung

extract_protocol:
Total RNA was extracted from lung tissue using miRNAeasy mini kit (Qiagen)
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively

treatment_protocol: mice were subjected to blast-wave induced thorax trauma (TxT) under anesthesia. 10-15 minutes after the insult the sEV biogenesis inhibitor GW4869 (2µg/g body weight) or NaCl (vehicle) was injected intravenously.

value: Total lung

value: blast-wave induced thorax trauma + GW4869

value: 12 week-old

value: male


title: TxT+GW4869_3


title: p53control_scramble3

value: tail vein

value: targeted amplicon sequencing

value: base-edited PCSK9


title: p53control_scramble4

value: AAV-mediated delivery


title: TxT+GW4869_4


title: p53control_scramble5


title: p53control_scramble2


title: Skin WT rep1


title: TxT+vehicle_2

value: blast-wave induced thorax trauma + vehicle


title: TxT+vehicle_4


title: p53control_untreated1


title: p53control_scramble1


title: TxT+vehicle_5


title: 1.5mg/kg_redose_Liver_Rep2

value: LNP-mediated delivery


title: TxT+GW4869_1


title: SBW25_pQBR103_dgacS_CR10

city: Liverpool

first: James

last: Hall

address: Crown Street

country: United Kingdom

institute: University of Liverpool

description:
Sample 30
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
30-CR10

data_processing:
Trimmed using Cutadapt version 1.2.1 using the option -O 3
Trimmed using Sickle version 1.200 with a minimum window quality score of 20 and reads longer than 19 bp
Strand-specific alignment to the reference sequence(s) using HISAT 2.1.0 with options phred33, no-spliced-alignment, new-summary, and rna-strandness RF
Filtering using samtools to remove mapping with PHRED-scaled quality <10
Function featureCounts from Rsubread 1.30.9
Analysis using edgeR 3.22.5
Genome_build: Aligned to reference sequences AM181176, LN713926, AM235768
Supplementary_files_format_and_content: CountsMatrix.csv: raw counts for each feature for each sample. Output from Rsubread
Supplementary_files_format_and_content: CountsMatrix_stats.csv: statistics of the raw counts for each sample. Output from Rsubread
Supplementary_files_format_and_content: de_table_chr_vanc.csv: differential expression of chromosomal genes for each sample relative to the control. Output from edgeR
Supplementary_files_format_and_content: de_table_chr_comp.csv: differential expression of chromosomal genes for each sample relative to corresponding plasmid-bearing strains. Output from edgeR
Supplementary_files_format_and_content: de_table_pQ57.csv: differential expression for relevant samples relative to the wild-type pQBR57-bearer. Output from edgeR
Supplementary_files_format_and_content: de_table_pQ103.csv: differential expression for relevant samples relative to the wild-type pQBR103-bearer. Output from edgeR
Supplementary_files_format_and_content: edgeR_NormalizationFactors.csv: normalization factors for each sample. Output from edgeR
Supplementary_files_format_and_content: rpkm_*.csv: calculated RPKM values. Output from edgeR

organism: Pseudomonas [fluorescens] SBW25

source_name: Pseudomonas fluorescens SBW25

growth_protocol: Overnight cultures of bacteria were subcultured 1:50 into 6 ml prewarmed KB microcosms and grown at 28°C shaking at 180 rpm. Samples were harvested when cultures reached intermediate exponential phase (OD600 = 0.6, as assessed on a Tecan Spark plate reader).

extract_protocol:
Samples were harvested at 4.5 G for 10 minutes, resuspended in 1 ml TRI reagent, and incubated at room temperate for 5 minutes. Amylene-stabilised chloroform (400 µl, Sigma-Aldrich 34854-M) was added to each tube, and incubated for 2-15 minutes at room temperature. Samples were then transferred to 5Prime Phase Lock Gel 'Heavy' tubes (VWR 733-2478) and centrifuged at 17 G for 15 minutes at room temperature. The aqueous phase was collected into a fresh microfuge tube and 450 µl isopropanol was added to precipitate RNA. Samples were incubated at room temperature for 30 minutes before pelleting at 17 G for 30 minutes. The pellet was rinsed by gently adding 1 ml of 70% ethanol and pelleting at 7.5 G for 5 minutes. The supernatant was carefully removed and the pellet allowed to air dry before resuspension in RNase-free water at 65°C. To remove any residual contaminating DNA, RNA was diluted to ≤200 ng/µl and treated with TURBO DNA-free RNase-free DNase (Invitrogen AM1907) according to the manufacturer's instructions. Reaction products were purified with Agencourt RNAClean XP beads. Ribosomal RNA was removed using the Bacterial RiboZero rRNA depletion kit (Illumina).
NEBNext Ultra-Directional RNA library preparation kit (Illumina). Sequencing is 'reverse-stranded'.

treatment_protocol: 1 ml samples were added to 0.4 volumes of ice-cold 95% ethanol 5% phenol 'stop solution' [@Colgan2016-mu], mixed gently, and incubated on ice for at least 30 minutes. Each of the three replicates was processed separately as a block.

tag: taxid

tag: amelioration/genotype

value: dgacS

tag: plasmid


title: 1.5mg/kg_redose_Liver_Rep3


title: TxT+vehicle_1


title: mouseBrain

first: Qi

middle: Trinity

last: Peng

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

institute: Peking University

description: mBrain.uniq.sorted.bw

data_processing:
Library strategy: Iso-seq
ROI (Reads-Of-Insert) reads were extracted and primer sequences flanking ROI reads were then trimmed
Primer-trimmed reads were further processed to scan the PA tail and trimmed to get PA-trimmed reads which represents reads with a PA tail trimmed.
PA-trimmed reads were then mapped to the reference genome (rheMac8 for macaque; mm9 for mouse) by GMAP and the low-quality reads were filtered to get the final processed alignments.
Genome_build: rheMac8, mm9
Supplementary_files_format_and_content: bigWig files were generated using DeepTools (version 3.3.0) with default parameters; scores represented coverage of uniquely-mapped Iso-seq reads；

source_name: Brain

extract_protocol:
Total RNAs were extracted using the Trizol Reagent (Invitrogen, catalog #15596018) and analyzed on an Agilent 2100 Bioanalyzer to access the quality. The quantity of total RNA was measured by Qubit. cDNA was synthesized using the SMARTer PCR cDNA Synthesis Kit (Clotech, catalog #634925) and PrimeSTAR GXL DNA Polymerase (Clontech, catalog #R050B).
SMRT bell libraries were generated by using SMRTbellTM Template prep kit 1.0-SPv3 (PN 100-991-900)

value: Brain


title: p53_treated_4


title: p53_treated_2


title: sham+GW4869_5


title: TxT+GW4869_2


title: 1.5mg/kg_redose_Liver_Rep1


title: TxT+vehicle_3


title: sham+GW4869_4


title: SBW25_pQBR57_V100A_CR07

description:
Sample 27
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
27-CR07


title: 1.5mg/kg_Liver_Rep3


title: SBW25_pQBR57_d4242_CR04

description:
Sample 24
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
24-CR04


title: SBW25_pQBR103_d4242_CR06

description:
Sample 26
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
26-CR06


title: SBW25_pQBR103_wt_CR05

description:
Sample 25
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
25-CR05

value: wt


title: SBW25_pQBR57_wt_CR03

description:
Sample 23
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
23-CR03


title: sham+GW4869_3


title: 1.5mg/kg_Liver_Rep2


title: SBW25_noplasmid_wt_CR01

description:
Sample 21
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
21-CR01


title: sham+GW4869_2


title: SBW25_noplasmid_d4242_CR02

description:
Sample 22
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
22-CR02


title: 1.5mg/kg_Liver_Rep1


title: sham+GW4869_1


title: SBW25_pQBR57_dgacS_BR09

description:
Sample 19
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
19-BR09


title: sham+vehicle_5

value: sham+vehicle


title: SBW25_pQBR57_dgacS_CR09

description:
Sample 29
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
29-CR09


title: SBW25_pQBR57_V100A_BR07

description:
Sample 17
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
17-BR07


title: sham+vehicle_4


title: SBW25_pQBR103_d4242_BR06

description:
Sample 16
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
16-BR06


title: SBW25_noplasmid_dgacS_CR08

description:
Sample 28
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
28-CR08


title: SBW25_pQBR103_wt_BR05

description:
Sample 15
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
15-BR05


title: sham+vehicle_3


title: SBW25_pQBR57_d4242_BR04

description:
Sample 14
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
14-BR04


title: SBW25_pQBR57_wt_BR03

description:
Sample 13
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
13-BR03


title: SBW25_pQBR103_dgacS_BR10

description:
Sample 20
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
20-BR10


title: SBW25_noplasmid_d4242_BR02

description:
Sample 12
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
12-BR02


title: PBS 10ml/Kg [189747]

city: Frederick

first: RAJAA

last: EL MESKINI

address: 1050, Boyles Street

department: Center for Advanced Preclinical Research

institute: Leidos Biomedical Research, Inc

description:
Study#3
PBS 10ml/Kg [189747]

hyb_protocol: A total of 20 ug of biotinylated cRNA was then fragmented for hybridization on the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChip Operating Software Tool was used for data capture and quality

data_processing: Raw CEL files from the scan were analyzed using a microarray pipeline written in ‘R’.  Data were normalized using the Robust Multichip Average (RMA) method.  Linear modeling was performed using Limma’s lmFit function (LIMMA, RRID:SCR_010943, Limma powers differential expression analyses for RNA-sequencing and microarray studies), and differential gene expression was determined using the contrasts.fit and eBayes functions. Top pathways for each comparison (Non-responders, Responders, and Relapse;  normalized with control IgG treatment samples) were determined using (Gene Set Enrichment Analysis) GSEA (SeqGSEA, RRID:SCR_005724, http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Gsea_Citation). The top 10 up and down regulated pathways were generated from Reactome (Reactome diagram viewer: data structures and strategies to boost performance) based on NES scores if Q-value meets threshold of less than 0.1. The top genes from Reactome were then used to run GSVA (Gene Set Variation Analysis for microarray and RNA-seq data) to find enrichment for each sample. Heatmaps were generated for the GSVA analysis, columns (samples) were sorted by group and rows (pathways) were clustered by Euclidean distance. Individual sample differential expression heatmap was analyzed by computing the log fold-change between a sample against the mean expression of the IgG samples, upper and lower limits shown on the heat map are log values from -2 to 2. Gene expression data from this report is available through the Collaborative Bioinformatics Resource of NIH, Center for Cancer Research (CCR). https://zenodo.org/record/3770853#.X9PmhhNKg_N.

source_name: Subcutaneous tumor

label_protocol: A total input of 800ng of isolated RNA was applied to the Message Amp II-Biotin Enhanced aRNA Amplification Kit according to manufacture protocol for first and second Strand cDNA synthesis followed by in-vitro transcription (IVT) reaction to synthesize the complementary RNA (cRNA) for transcriptional amplification and biotin labeling.

growth_protocol: See publication Materials and Methods: Melanoma allograft model

extract_protocol: Tumor samples were lysed and homogenized for RNA isolation using the RNeasy Mini Kit following manufacturer’s protocol for purification of total RNA with on-column DNase digestion (Qiagen). RNA purity and concentration were determined spectrophotometrically, and RNA quality was assessed using the Agilent Technology Tape Station RNA Screen Tape.

treatment_protocol: See publication Materials and Methods: Immunotherapy treatment

tag: disease

value: Melanoma


title: SBW25_noplasmid_wt_BR01

description:
Sample 11
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
11-BR01