title: 24wk dnOGAh-Tg #5 [dnOGAh-F25-39]

city: Birmingham

first: Chae-Myeong

last: Ha

state: Alabama

institute: University of Alabama at Birmingham

data_processing:
Adapaters and low-quality sequences (PHRED < 20) were trimmed using Trim Galore (0.6.6) and CutAdapt (2.6)
Trimmed reads were aligned to the mouse genome (GRCm39) via STAR (2.7.3a)
Using R software (v4.0.3), DESeq2 perform differential gene expression based on a negative binomial generalized linear model.
Assembly: GRCm39
Supplementary files format and content: The Normalized_Count spreadsheet (.xlsx) contains the normalized counts, as given by DESeq2 for each sample and each Ensembl ID.

source_name: Left Ventricle

extract_protocol: RNA was extracted usinhg RNAeasy Fibrous Tissue Minikit (Qiagen) according to manufacturer protocol

treatment_protocol: Left Ventricle tissue was harvested from Control or dnOGAh mice following 2 weeks or 24 weeks of dnOGA-Tg using Doxycyclin food treatment.

value: Left Ventricle

value: dnOGAh-Tg


title: A549 cells, SEMA5A_Full, rep1

status: Public on Aug 19 2023

type: RNA

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description:
SAMPLE 7
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: A549 cells

label_protocol: Biotinylated cRNA were prepared with the Invitrogen Illumina™ TotalPrep™ RNA Amplification Kit

growth_protocol: A549 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (GIBCO; Thermo Fisher, Waltham, MA, USA) with 10% fetal bovine serum (FBS) (Millipore, US Origin, Korea Eligible) and 1% penicillin-streptomycin (GIBCO)

extract_protocol: Total RNA was extracted from cultured cells using NucleoZOL reagent (Machery-Nagel, Düren, Germany) according to the manufacturer’s protocol

treatment_protocol: Cells were transfected with different domains of SEMA5A expressing plasmids and control plasmid by jetPRIME transfection reagent (Polyplus-transfection, Illkirch, France) according to the manufacturer’s protocol.

tag: cell line

value: A549 non-small cell lung cancer cell line

tag: transfection


title: 24wk dnOGAh-Tg #2 [dnOGAh-F19-41]

type: SRA

country: USA

library_source: transcriptomic

organism: Mus musculus

tag: tissue

tag: treatment

tag: time


title: aco sinus venosus_1

city: Cincinnati

first: Joshua

last: Waxman

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology Division

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Zebrafish RNA-seq reads were aligned to the UCSC zebrafish genome, danRer11, using STAR aligner after trimming the Illumina adapter using cutadapt
These libraries were prepped across multiple batches with different library types in terms of RNA strand and sequencing mode (single-end or paired-end). Therefore, we treated them as single-end libraries by choosing read1 or read2 to match the strand as much as possible, and batch correction was applied as described below. Only uniquely aligned reads were retained for downstream analysis.
Gene expression levels were quantified as raw read counts using FeatureCounts in the subread package with an option, “-O --fracOverlap 0.8”, and with a proper strand option (-s).
Given the mixed sequencing batches and library types, we incorporated RUVseq batch correction (RUVs, k=1) in DESeq2 differential analysis.
Differentially expressed genes were identified by FDR < 0.05. Hierarchical clustering was performed using the Pearson correlation coefficient as a similarity measure under Ward’s criterion, and a heatmap was visualized in z-score.
Assembly: GRCz10/danRer10
Supplementary files format and content: text of DESeq2 data with LogFC, P-value, FDR, normalized expression, and raw counts

organism: Danio rerio

source_name: isolated WT sinus venosus

extract_protocol:
The heart chambers, bulbous arteriosus, and sinus venosus were removed from the adult fish and then separated into their respective tissues. Heart tissues from 20 fish were pooled and then placed in TRIZOL. RNA was harvested using phenol-chloroform separation and a PureLink RNA Micro Kit (Invitrogen).  The RNA was submitted to the CCHMC core for library generation and sequencing. Singles and paired-end sequencing was performed.
RNA libraries prepared for sequencing using standard protocols

value: isolated WT sinus venosus

tag: cell type

value: mixed

tag: genotype

value: aco (AB/TU)

value: adult (6 months-1.5 years)


title: 24wk dnOGAh-Tg #3 [dnOGAh-F23-23]


title: cardiac tube_2

data_processing:
Ciona paired-end RNA-seq reads were aligned to the UCSC Ciona genome, ci3, using STAR aligner after trimming the Illumina adapter using cutadapt
Gene expression levels were quantified as raw read counts using FeatureCounts in the subread package with an option, “-O --fracOverlap 0.8”, and with a proper strand option (-s).
Given the mixed sequencing batches and library types, we incorporated RUVseq batch correction (RUVs, k=1) in DESeq2 differential analysis.
Differentially expressed genes were identified by FDR < 0.05. Hierarchical clustering was performed using the Pearson correlation coefficient as a similarity measure under Ward’s criterion, and a heatmap was visualized in z-score.
Assembly: Ciona robusta (Ciona intestinalis A) version KH (ci3)
Supplementary files format and content: text of DESeq2 data with LogFC, P-value, FDR, normalized expression, and raw counts

organism: Ciona robusta

source_name: isolated cardiac tube

extract_protocol:
Hearts from adult Ciona robusta were dissected and placed into RNAlater. The different sections of the heart – pharyngeal blood sinus, stomach blood sinus, and cardiac region were then dissected in RNAlater and in RNeasy lysis buffer. The pooled sections of the heart were sonicated and the RNA was collected using the RNeasy kit.
RNA libraries were prepared for sequencing using standard protocols

value: isolated cardiac tube

value: wild caught

value: adult


title: aco sinus venosus_2


title: A549 cells, SEMA5A_ECD, rep1

description:
SAMPLE 4
replicate 1


title: cardiac tube_1


title: 24wk dnOGAh-Tg #4 [dnOGAh-F24-25]


title: A549 cells, SEMA5A_ECD, rep2

description:
SAMPLE 5
replicate 2


title: 24wk dnOGAh-Tg #1 [dnOGAh-F17-39]


title: aco mutant ventricle_2

source_name: isolated WT ventricle

value: isolated WT ventricle


title: TIS11B_iKO_WCL

city: New York

first: Christine

last: Mayr

state: NY

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: MSKCC

data_processing:
Raw reads were trimmed by Trimmomatic (version: 0.39; average quality per base < 15, 4 bp window)
Trimmed reads were mapped to human genome (hg19) using hisat2 (version: 2.1.0)
Reads mapped to each gene were counted by featureCounts (version: 1.6.4)
FPKM value for each gene was calculated by a custom Perl script
Assembly: hg19
Supplementary files format and content: Supplementary files format and content: TXT file; Raw read counts for each gene.
Supplementary files format and content: Supplementary files format and content: TSV file; computed FPKM or TPM per transcript.
Supplementary files format and content: Supplementary files format and content: XLSX file; TPMs per gene and transcript.

molecule: polyA RNA

source_name: Embryonic Kidney

growth_protocol: HEK293T cells were plated in six 10 cm dishes at 80% confluency in antibiotic free media

extract_protocol:
20 hours after transfection cells were rinsed once with ice cold PBS then scraped in 10 mL ice cold PBS and pelleted at 300g. Pellets from two 10 cm plates were resuspended in 1 mL ice cold hypotonic isolation buffer (225 mM mannitol, 75 mM sucrose, 20 mM Tris-HCl pH 7.4, 0.1 mM EDTA). Cells were lysed with 50 strokes in a 1 mL dounce homogenizer with pestle on ice in order to shear the nuclei from the cytoplasm. Nuclei were pelleted with a two-minute spin at 600g. Subcellular organelles were then pelleted from the supernatant with a 15-minute spin at 7000g and resuspended in ice cold PBS for fluorescence activated particle sorting. Particles were sorted on a BD FACSAria III cell sorter equipped with 70 um nozzle size. mCherry-TIS11B and GFP-SEC61B particles were first detected by fluorescence using the 594 nm and 488 nm excitation lasers respectively, and 405 nm excitation laser for DAPI. A particle gate was drawn to include mCherry-positive or GFP-positive events and DAPI-negative events in order to exclude any remaining nuclei. Particles were then selected for sorting by size and granularity using forward-scattered light (FSC) and side-scattered light (SSC) respectively. The FSC threshold was decreased from 5,000 to 800 in order to visualize subcellular particles. Sorting was performed on purity mode with an average of sorting speed of 150 particles/second. Particles were sorted directly into 1 mL of TRIzol solution in Eppenforf tubes, holding 180,000 particles per tube. RNA-extraction was then performed for each tube separately. Total RNA yield was combined before for library prep. For each replicate about 1.5 million TIS11B granule particles were collected and 2.0 million ER particles. For cytosolic extraction, 20 hours post transfection cells were rinsed once in the dish with ice cold PBS. After aspirating PBS, 400 ul ice cold digitonin solution (40 ug/mL digitonin, 150 mM NaCl, 20 mM HEPES pH 7.4, 0.2 mM EDTA, 2 mM DTT, 2 mM MgCl2) was added and incubated on a shaker at four degrees for ten minutes. After incubation, the digitonin solution now containing the cytosolic extract was pipetted from the plate and spun at 20,000g for one minute to pellet any floating cells. 200 ul of cytosolic extract was added to 1 mL TRIzol solution for RNA extraction.
Library preparation and Illumina sequencing were performed by the MSKCC Integrated Genomics Operations core facility. mRNA libraries were prepared by poly-A selection.The libraries were multiplexed and after paired-end 50 bp sequencing 10-20 million reads per sample were acquired.

treatment_protocol: For WT cells,  cells were transfected 24 hours after seeding by calcium phosphate with either 3ug mCherry-TIS11B or 3 ug GFP-SEC61B per plate. For ctrl and TIS11B iKO cells, cells were treated with 100ng/mL doxycycline for five days. Cells were seeded for transfection on D3 of dox treatment, transfected on D4 of dox treatment, and harvest on D5.

value: Embryonic Kidney

value: CaPO4 transfection


title: A549 cells, SEMA5A_Full, rep2

description:
SAMPLE 8
replicate 2


title: A549 cells, SEMA5A_Empty, rep1

description:
SAMPLE 10
replicate 1


title: A549 cells, SEMA5A_ECD, rep3

description:
SAMPLE 6
replicate 3


title: A549 cells, SEMA5A_ICD, rep3

description:
SAMPLE 3
replicate 3


title: A549 cells, SEMA5A_ICD, rep1

description:
SAMPLE 1
replicate 1


title: 24wk Control #5 [dnOGAh-F25-38]

value: Control


title: aco mutant ventricle_1


title: A549 cells, SEMA5A_ICD, rep2

description:
SAMPLE 2
replicate 2


title: CTRL_iKO_WCL

value: Control (WT):Flag-iCas9-P2A-GFP/Control (intergenic) gRNA 1st sgRNA target:Chr7:10,195,223-10,195,242 2nd sgRNA target:Chr7:10,195,281-10,195,300 (Hg38)


title: WT sinus venosus_2

value: WT (AB/TU)


title: 24wk Control #4 [dnOGAh-F24-26]


title: TIS11B_iKO_ER_rep3


title: 24wk Control #2 [dnOGAh-F19-42]


title: 24wk Control #3 [dnOGAh-F23-24]


title: WT sinus venosus_1


title: TIS11B_iKO_ER_rep2


title: WT atrium_1

source_name: isolated WT atrium

value: isolated WT atrium


title: WT ventricle_2


title: TIS11B_iKO_ER_rep1


title: TIS11B_iKO_cyto_rep3


title: 2wk dnOGAh-Tg #5 [dnOGAh-F14-24]

value: Left Ventricle


title: WT ventricle_1


title: TIS11B_iKO_cyto_rep2


title: 2wk dnOGAh-Tg #4 [dnOGAh-F14-21]

value: dnOGAh-Tg


title: TIS11B_iKO_cyto_rep1


title: WT bulbous arteriosus_2

source_name: isolated WT bulbous arteriosus

value: isolated WT bulbous arteriosus


title: 2wk dnOGAh-Tg #3 [dnOGAh-F13-31]


title: ctrl_iKO_ER_rep3


title: 2wk dnOGAh-Tg #2 [dnOGAh-F11-31]


title: ctrl_iKO_ER_rep2


title: WT bulbous arteriosus_1


title: 2wk dnOGAh-Tg #1 [dnOGAh-F11-30]


title: 24wk Control #1 [dnOGAh-F17-40]


title: ctrl_iKO_ER_rep1


title: circRNA HA45T

city: huai’an

first: haixiao

last: wang

state: Jiangsu

address: No 1,  The Yellow River West Road

department: Department of General Surgery

country: China

institute: The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to human reference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively.
Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads, bwa mem mapping) to quantify every circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values and counts for each Sample

source_name: Gastric cancer tissues

growth_protocol: no

extract_protocol:
Total RNA was extracted with TRlzol reagent (Invitrogen, CA, USA). The ribosomal RNAs were removed from total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA), then RNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp for the preparation of cDNA synthesis with random hexamer primers. dUTPs were used for second-strand cDNA synthesis. The ligated double-stranded cDNA products were purified and treated with uracil DNA glycosylase (UDG). Later, the purified first-strand cDNA was subjected to PCR amplification and sequenced on a HiSeq 3000 system (Illumina, San Diego, CA, USA) with 2 × 150 bp mode.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no

value: stomach

tag: age

value: 60 years old

tag: gender

value: female

tag: tnm


title: circRNA HA45N

source_name: Gastric cancer adjacent normal tissues


title: WT atrium_2

value: mixed

value: adult (6 months-1.5 years)


title: ctrl_iKO_cytosol_rep3


title: 2wk Control #5 [dnOGAh-F14-23]


title: circRNA HA43T

value: 55 years old

value: male


title: ctrl_iKO_cytosol_rep2


title: 2wk Control #4 [dnOGAh-F14-22]


title: circRNA HA43N


title: 2wk Control #3 [dnOGAh-F14-19]


title: circRNA HA42T

value: 62 years old


title: 2wk Control #2 [dnOGAh-F11-29]


title: Gene expression in Atg7::Keap1-Alb 1

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

country: Japan

institute: Tohoku University

description: Gene expression in Atg7::Keap1-Alb

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Data was obtained using the Agilent Feature Extraction software (v10.1), using default for all parameters.  The data were analyzed using GeneSpring GX software (v11.5) (Agilent).

source_name: Atg7 flox/flox::Keap1 flox/flox::Albumin-Cre (Female) liver

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA from mouse whole livers was extracted.

tag: tag


title: Creb-ff

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

hyb_protocol: Arrays were prepared according to Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit

scan_protocol: Scanner 3000 7G

data_processing: Expression console software and Transcriptome console software 3.0 from Affymetrix. Normalization and summarization performed with RMA algorithm

source_name: murine lung treated with ethyl-carbamate (1g/kg)

label_protocol: Arrays were prepared according to Affymetrix specifications with GeneChip™ WT Pico Reagent Kit

growth_protocol: cells were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 1 mM pyruvate, 100 U/ml penicillin, and 100 mg/ml streptomycin

extract_protocol: Total RNA from the cells was extracted with the Trizol protocol followed by Qiagen RNeasy Mini Kit

treatment_protocol: Subculturing of plasmid expressing cell lines is done in DMEM + 10% FBS + 4-6 µM puromycin

tag: genotype/variation

value: Creb1-deficient mice

value: plasmid encoding luciferase


title: Creb-cre

value: plasmid encoding CRE recombinase


title: Gene expression in Atg7::Keap1-Alb 2

description: Gene expression in Atg7::Keap1-Alb


title: 2wk Control #1 [dnOGAh-F11-28]

value: Control


title: circRNA HA42N


title: Cytosol_transfected_rep3

value: Embryonic Kidney

value: WT

value: CaPO4 transfection


title: Gene expression in Keap1-Alb 2

description: Gene expression in Keap1-Alb

source_name: Keap1 flox/flox::Albumin-Cre (Male) liver


title: ER_transfected_SEC61B_rep3


title: Gene expression in Atg7-Alb 2

description: Gene expression in Atg7-Alb

source_name: Atg7 flox/flox::Albumin-Cre (Male) liver


title: Gene expression in Atg7-Alb 1

description: Gene expression in Atg7-Alb


title: postnatal hypothalamus of CRH-IRESCre (CRH-Cre) mice

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

country: South Korea

institute: Ajou University School of Medicine

library_source: transcriptomic single cell

data_processing:
For FASTQ generation and alignments, Illumina basecall files (*.bcl) were converted to FASTQs using Cell Ranger v.1.3 (10× Genomics), which uses bcl2fastq v.2.17.1.14. FASTQ files were then aligned to mm10 genome and transcriptome using the Cell Ranger v.1.3 pipeline, which generates a ‘gene vs cell’ expression matrix.
For filtering out of the cells and QC, the Seurat package in R (v. 4.2.1) was used. For cell clustering, resolution was set as 0.25, and 8 cell clusters were identified using specific marker genes, such as Agt, Pecam1, Itm2a, Mki67, C1qa, Mog, Syp, and Pdgfra.
Assembly: mm10 genome
Supplementary files format and content: raw_counts.txt: Raw count of QC-passed cells of Seurat object
Supplementary files format and content: normalized_data.txt: Normalized expression of QC-passed cells of Seurat object (normalized data)

source_name: brain - hypothalamus

extract_protocol:
Connect-seq experiments were performed as previously described with modifications for nuclei isolations, Adult 8-week-old CRH-Cre mice were injected with PRVB180. After 3 days, mice were euthanized by cervical dislocation, and the brain was quickly removed. The hypothalamus was carefully microdissected under a microscope and immediately placed into a nuclei isolation medium (sucrose 0.25 M, KCl 25 mM, MgCl2 5 mM, TrisCl 10 mM, dithiothreitol, 0.1 % Triton). Tissue was Dounce homogenized, allowing for mechanical separation of nuclei from cells. The nucleic acid stain Hoechst 33342 (5 μM, Life Technologies) was included in the media to facilitate visualization of the nuclei. Samples were washed, resuspended in nuclei storage buffer (sucrose, MgCl2 5 mM, and TrisCl 10 mM) and filtered. Solutions and samples were kept cold throughout the protocol. Then, PRV-infected single nuclei were isolated based on the fluorescence emitted by TK-GFP using flow cytometry (FACSAria II; BD Biosciences) according to methods described previously.
FACS-sorted single nuclei were loaded onto an independent single channel of a Chromium Controller (10× Genomics) single-cell platform. Briefly, 10,000 single nuclei were loaded for capture using a Chromium Single Cell 3 ′ Reagent kit, v2 Chemistry (10× Genomics).
Following capture and lysis, complementary DNA was synthesized and amplified (14 cycles) as per the manufacturer’s protocol (10× Genomics). The amplified cDNA was used to construct an Illumina sequencing library and sequenced on a single lane of a NovaSeq 6000 (Illumina).

tag: strain

value: CRH-IRESCre (CRH-Cre)

value: brain - hypothalamus


title: ctrl_iKO_cytosol_rep1

value: Control (WT):Flag-iCas9-P2A-GFP/Control (intergenic) gRNA 1st sgRNA target:Chr7:10,195,223-10,195,242 2nd sgRNA target:Chr7:10,195,281-10,195,300 (Hg38)


title: liver;FGF21 treated 4

city: wenzhou

first: chuanren

last: zhou

address: chashan road

institute: wenzhou meidical 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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Liver

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: Sex

value: Male


title: liver;FGF21 treated 2


title: HLE cells, CYR61 stable expression#2

city: Nanchang

first: Xiaohua

last: Yan

address: No. 1299, Xuefu Avenue, Honggutan

institute: Nanchang University

data_processing:
Raw single end reads were firstly trimmed of the first 13 bp from each end and mapped to the human genome (hg38) with Tophat2 (v2.1.1).
Gene expression level was estimated and normalized with Cufflinks (v2.2.1) into an FPKM matrix using default parameters for the annotation GTF file downloaded from GENCODE (v24).
Differentially expressed genes (DEGs) were generated with Cuffdiff (v1.3.0) with p-value <0.05, and filtered by a Fold change ≥1.4 or ≤0.7.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: HLE cells

growth_protocol: HLE cell lines (Vector or CYR61 stable expression) were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method
RNA libraries were prepared for sequencing using standard IIIumina proticols

value: HLE cells

value: human hepatocellular carcinoma

value: CYR61 stable expression cell line


title: HLE cells, CYR61 stable expression#1


title: HLE cells, Vector stable expression#2

value: Vector stable expression cell line


title: female MEFs, HP1γ CUT & RUN, rep2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: genomic

data_processing:
Sequenced CUT & RUN reads were aligned to the mouse genome version mm9 using Bowtie2. For mapping the spike-in fragments, the --no-overlap --no-dovetail options were selected to avoid cross-mapping of the experimental genome to that of the yeast DNA.
Normalized bedgraphs were obtained after spike in calibration with SEACR tool (SEACR_1.0) and converted to Bigwigs using UCSC wigToBigWig program.
Assembly: mm9
Supplementary files format and content: Bigwig files of normalised data
Library strategy: CUT & RUN

molecule: genomic DNA

source_name: embryo body

growth_protocol: Culture medium: DMEM, 15% FBS, 1% Penicillin/Steptomycin. Cells were grown at 37 °C, 5% CO2

extract_protocol:
The CUT & RUN assay was performed as described in (Skene, Henikoff and Henikoff 2018), with minor adaptations. Briefly, 1 million MEFs were employed per condition and optimal digitonin (Enzo Life Sciences, UK) concentration for membrane  permeabilization was determined at 0.02 %. Primary antibodies (mouse anti-HP1γ and mouse anti-IgG included in the same set, Millipore #17-646; or mouse anti-H3K27me3, Abcam, #6002 were used at a 1:100 dilution and for spike-in purposes 100 pg of yeast DNA was employed
DNA libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s instructions

value: embryo body

value: CBA

value: female

value: E13.5 primary MEFs


title: female MEFs, IgG CUT & RUN, rep1


title: female MEFs, HP1γ CUT & RUN, rep1


title: HepG2-2-15-OE2

city: Chongqing

first: Ping

address: No. 1 Youyi Road, Yuzhong District

department: Department of Hepatobiliary Surgery

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated. Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. Featurecount was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: FileincludeFPKM/Countvaluesforeachsample

source_name: Hepatoma Cell

growth_protocol: HepG2.2.15 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from HepG2.2.15 using TRIzol (15596018, Invitrogen), RNA purity and concentration were then examined using NanoDrop 2000, RNA integrity and quantity were measured using the Agilent 2100 system.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Lentivirus-mediated overexpression of ADH4 or empty vector in HepG2.2.15.

value: Hepatoma Cell

value: Standard


title: male MEFs, HP1γ CUT & RUN, rep2

value: male

value: WT


title: HepG2-2-15-OE1


title: Gene expression in Keap1-Alb 1

description: Gene expression in Keap1-Alb


title: Gene expression in Control 1

description: Gene expression in Control

source_name: Atg7 flox/flox (Male) liver

value: Control


title: HepG2-2-15-OE3


title: HepG2-2-15-V3


title: liver;FGF21 treated 3


title: HepG2-2-15-V2


title: male MEFs, HP1γ CUT & RUN, rep1


title: liver;FGF21 treated 1


title: male MEFs, H3K27me3 CUT & RUN, rep1


title: miRNA HA45N

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the hg19 reference genome using the bwa aligner.The mapped reads were then compared to the Rfam database and  miRbase21.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

extract_protocol:
no
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stomach

value: 60 years old


title: miRNA HA45T


title: liver;control3

value: Liver

value: PBS


title: HLE cells, Vector stable expression#1

value: HLE cells


title: liver;control4

value: Male


title: liver;control1


title: miRNA HA43T

value: 55 years old


title: Caco cells treated with MEVs for 24 hours 2

city: Ottawa

first: Basit

last: Yousuf

state: ON

address: 2035, Othello Avenue, Ottawa

country: Canada

institute: University of Ottawa

data_processing:
Analysis was performed using Human GENCODE(Frankish et al. 2021)v43 annotations based on the GRCh38 genome assembly. Thenf-core/rnaseq(Ewels et al. 2020)pipeline version 3.11.2 was used to generate the quality assessment and read pseudocounts table.
The read counts are imported into a DESeq data object and from that we calculate variance stabilized log transformed normalized counts for PCA and clustering.
Fold change analyses TREATMENT vs CONTROL was calculated using thelfcShrink()function,
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes log2FoldChnage Treatment vs Control

source_name: Cell line

growth_protocol: Caco-2 cells at a density of 5×104 (P8) were seeded in 12 well plates onto ThinCert™ tissue culture inserts (12-well plates, 0.4 µm, 108 pores, 1.131 cm2) and then maintained in CCM. The culture media were refreshed every 2 days. Cells were allowed to grow and differentiate for 21 days.

extract_protocol:
RNA was extracted with Trizol methods followed by DNase treatment and RNA purification by RNeasy MinElute Cleanup Kit (Qiagen)
total RNA was quantified and its integrity was assessed using a LabChip GXII (PerkinElmer) instrument. Libraries were generated from 250 ng of total RNA using Illumina® Stranded mRNA Prep, Ligation kit (Illumina), as per the manufacturer’s recommendations. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GXII (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 175pM on an Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3.4.4. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.

treatment_protocol: After 21 days, in the treatment samples, MEVs labeled with fluorescein isothiocyanate (FITC) (equivalent to 5.95e+11) were suspended in CCM and added to the apical side of the tissue culture insert. Fresh CCM was added to the basolateral side. In control, only CCM media was added in both apical and basolateral.

value: Cell line

value: Epithelial cells


title: miRNA HA43N


title: Caco cells treated with MEVs for 24 hours 1


title: Caco cells without MEVs 2


title: Gene expression in Control 2

description: Gene expression in Control


title: Sample 2 VDJ

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description:
VDJ library: read1 file contains cell barcode and UMI; read2 file contains the constant region of the antibody chains
poly-A RNA

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation, and the TCR clonotype assembly were performed using the 10x Genomics Cell Ranger software v6.0.1
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz and airr_rearrangement.tsv

source_name: Spleen

extract_protocol:
Single cell suspensions were prepared from OVA immunized popliteal lymph nodes of SellCreERT2 ROSAtdT mice on day 17 post immunization and 7 days post tamoxifen delivery. Samples were indexed with TotalSeqC (BioLegend) cell surface antibodies and CD4 + , CD62 low , CD44 hi , PD1 hi , CXCR5 high , tdTomato+ and - Tfh cells were purified by flow cytometry, pooled and loaded onto a Chromium Controller (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences were added.
V(D)J libraries were generated with 350 the Chromium Single Cell 5′ Library & Gel Bead Kit and 351 Chromium Single Cell V(D)J Enrichment Kit

value: Spleen

value: T cell

tag: condition

value: NP-OVA immunization

tag: library type

value: VDJ

tag: hto


title: Sample 2 HTO

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein

value: HTO

value: TotalSeq-C0301 anti-mouse Hashtag 1, TotalSeq-C0302 anti-mouse Hashtag 2, TotalSeq-C0303 anti-mouse Hashtag 3, TotalSeq-C0304 anti-mouse Hashtag 4, TotalSeq-C0305 anti-mouse Hashtag 5, TotalSeq-C0306 anti-mouse Hashtag 6, TotalSeq-C0307 anti-mouse Hashtag 7, TotalSeq-C0308 anti-mouse Hashtag 8, TotalSeq-C0309 anti-mouse Hashtag 9, TotalSeq-C0310 anti-mouse Hashtag 10, TotalSeq-C0075 anti-mouse CD90.2, TotalSeq-C0157 anti-mouse CD45.2, TotalSeq-C0070 anti-mouse CD49f, TotalSeq-C0096 anti-mouse CD45


title: miRNA HA42T

value: 62 years old

value: male


title: Sample 2 GEX

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly-A RNA

value: mRNA


title: miRNA HA42N

value: stomach


title: Sample 1 HTO


title: Sample 1 VDJ


title: Sample 1 GEX


title: HepG2-2-15-V1

value: Hepatoma Cell

tag: cell line

value: Control

value: Standard


title: female MEFs, H3K27me3 CUT & RUN, rep1

value: embryo body

value: CBA

value: female

value: E13.5 primary MEFs

value: WT


title: liver;control2

value: Liver

value: Male

value: PBS


title: BF638R_WT Low Heme rep2

status: Public on Aug 18 2023

city: Greenville

first: Edson

middle: R

last: Rocha

state: NC

address: 600 Moye Blvd.

department: M

institute: East Carolina University Brody School of Medicine

description: This sample is of the Bacteroides fragilis 638R wild type second of two independent biological replicates from two separate cultures in low heme conditions.

hyb_protocol: Hybridization was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

scan_protocol: Scanning was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

data_processing: Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site. The RMA processed data was averaged and log2 transformed (see *.calls files).

organism: Bacteroides fragilis 638R

source_name: Bacteroides fragilis 638R Wild type

label_protocol: Labeling was peformed by at the FSU Nimblegen Microarray Facility using standard protocols as described previously (Sund et al., 2008, Mol Microbiol. 67:129-142).

growth_protocol: Overnight cultures of Bacteroides fragilis 638R wild type or mutant strains were diluted into minimal defined media supplemented with 5 microgram/ml protoporphyrin IX containing 100 micromolar iron sulfate, 50 micromomolar 2,2-bipyridyl, 5 microgram/ml hemin, or 0.1 microgram/ml hemin.

extract_protocol: Total RNA was isolated by the hot phenol method and treatd as described by Sund et al., 2008, Mol. Microbiol. 67:129-142.

treatment_protocol: Bacterial cultures were grown to mid-logarithmic phase (O.D. 550 nm of 0.3-0.4) and submitted to total RNA extract by the hot phenol method.

value: Wild type

tag: growth condition

value: low heme


title: BF638R_WT High Heme rep2

description: This sample is of the Bacteroides fragilis 638R wild type second of two independent biological replicates from two separate cultures in high heme conditions.

value: high heme


title: BF638R_WT High Heme rep1

description: This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in high heme conditions.


title: BF638R_fur_mut Low iron rep2

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant second of two independent biological replicates from two separate cultures in low iron conditions.

value: fur deletion mutant

value: low iron


title: BF638R_WT Low Heme rep1

description: This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in low heme conditions.


title: UpperEpidermis_#3

city: Yokohama

first: Umi

last: Tahara

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences

description: Gene expression of upper epidermis

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: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The original dataset was normalized using the normexp background correction and quantile method implemented in the Limma R package, v3.52.4.

source_name: Epidermis, ETA treatment, human3

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: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: tissue

value: epidermis

tag: subject id


title: UpperEpidermis_#1

description: Gene expression of upper epidermis

source_name: Epidermis, ETA treatment, human1


title: WholeEpidermis_#3

description: Gene expression of whole epidermis

source_name: Epidermis, dispase treatment, human3


title: UpperEpidermis_#2

description: Gene expression of upper epidermis

source_name: Epidermis, ETA treatment, human2


title: BF638R_fur_mut Low iron rep1

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant first of two independent biological replicates from two separate cultures in low iron conditions.


title: Caco cells without MEVs 1

value: Cell line

value: Epithelial cells


title: BF638R_fur_mut High iron rep2

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant second of two independent biological replicates from two separate cultures in high iron conditions.

value: high iron


title: BF638R_fur_mut High iron Rep1

description: This sample is of the Bacteroides fragilis 638R fur deletion mutant first of two independent biological replicates from two separate cultures in high iron conditions.


title: BF638R_WT Low iron Rep1

description: This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in low iron conditions.

source_name: Bacteroides fragilis 638R wild type


title: BF638R_WT High iron Rep2

description: This sample is of the Bacteroides fragilis 638R wild type second of two independent biological replicates from two separate cultures in high iron conditions.


title: BF638R_WT High iron Rep1

description: This sample is of the Bacteroides fragilis 638R wild type first of two independent biological replicates from two separate cultures in high iron conditions.


title: BF638R_WT Low iron Rep2

description: This sample is of the Bacteroides fragilis 638R wild type swecond of two independent biological replicates from two separate cultures in low iron conditions.


title: NR8383, ZnO 16, rep1

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

description: Gene expression in NR8383 cells after 200 passages

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA were fragmented at 60°C for 30 min in a reaction volume of 25 µL following the manufacturer’s instructions. 25 µL of 2x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Rat GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent).

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 074036_D_F_20150914) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

organism: Rattus norvegicus

source_name: NR8383, ZnO

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (specific activity > 10 pmol Cy3 / µg cRNA, BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: NR8383 cell line were established from normal rat by lung lavage and was obtained from American Type Culture Collection (ATCC® CRL-2192™, Manassas, VA, USA). Cells, with a 50% adherent and 50% floating cell phenotype, were grown in DMEM medium supplemented with 15 % of heat-inactivated fetal bovine serum, 2 mM of L-glutamine, as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma Aldrich). Cells were incubated at 37°C in an atmosphere composed of 95 % air, 5 % CO2 and medium are changed every 2-3 days.

extract_protocol: The quality of the RNA extracted by RNA-Solv Reagent (Omega Bio-tek, USA) was determined by spectrophotometry (A260nm/A280nm, A260nm/A230nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 7.5, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: Cells were seeded in 25 cm2 flasks at a density of 3 x 105 cells / mL for 48 h.

tag: organ

value: lung

tag: treatment

value: (4 ug/mL or 16 ug/mL) of ZnO for 4 h


title: NR8383, ZnO 16, rep4


title: NR8383, Printex90, rep4

description: Gene expression in NR8383 cells after 20 passages

source_name: NR8383, Printex 90

value: (0.9 cm2/cm2) of carbon black (Printex 90) for 4 h


title: NR8383, ZnO 4, rep2


title: NR8383, ZnO 4, rep3


title: NR8383, ZnO 16, rep3


title: NR8383, ZnO 16, rep2


title: NR8383, ZnO 4, rep1


title: WholeEpidermis_#1

description: Gene expression of whole epidermis

source_name: Epidermis, dispase treatment, human1

value: female


title: WholeEpidermis_#2

description: Gene expression of whole epidermis

source_name: Epidermis, dispase treatment, human2


title: NR8383, Printex90, rep2


title: NR8383, Printex90, rep3


title: NR8383, ZnO 4, rep4


title: NR8383, NRCWE055, rep3

value: (11 cm2/cm2) of pristine single-walled carbon nanotubes


title: NR8383, NRCWE055, rep1


title: NR8383, NRCWE055, rep4


title: NR8383, NRCWE049, rep3

value: (1.2 cm2/cm2) of NH2-functionalized carbon nanotubes


title: NR8383, NRCWE049, rep4


title: NR8383, NRCWE055, rep2


title: NR8383, NRCWE049, rep1


title: NR8383, NRCWE021, rep1

value: (17 ug/mL) of zinc iron oxide


title: NR8383, NRCWE049, rep2


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.TCGACGTC_ACTCTAGG)

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The sample is aligned to GRCm38 transcriptome and quantified using Kallisto
Genome_build: GRCm38
Supplementary_files_format_and_content: gzipped abundance.tsv output from Kallisto

extract_protocol:
N/A
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

value: CNS

tag: cell type

value: DC

value: Itgax Cre HIF1a flox

value: Female

value: Adults

tag: genotype

value: D-LA producing bacteria


title: NR8383, NRCWE021, rep4


title: NR8383, NRCWE042, rep1

value: (6.8 cm2/cm2) of COOH-functionalized carbon nanotubes


title: NR8383, Printex90, rep1


title: NR8383, NRCWE042, rep2


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.TGCAGCTA_ACTCTAGG)

tag: age


title: NR8383, NRCWE021, rep2


title: NR8383, NRCWE021, rep3


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.CGATCAGT_ACTCTAGG)


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.CCTAAGAC_ACTCTAGG)


title: NR8383, NRCWE042, rep4


title: NR8383, NRCWE018, rep4

value: (2 ug/mL) of Fe2O3 (NRCWE018)


title: DCs from CNS from EcN treated mice (4KMQ.TAGCGCTC_ACTCTAGG)

source_name: DCs from CNS from EcN treated mice

value: WT

value: Parental Bacteria (E. coli-Nissle)


title: DCs from CNS from EcN treated mice (4KMQ.ATGCGCAG_ACTCTAGG)


title: NR8383, NRCWE018, rep2

value: lung


title: DCs from CNS from EcN treated mice (4KMQ.ACTGAGCG_ACTCTAGG)


title: NR8383, NRCWE018, rep3


title: NR8383, NRCWE018, rep1


title: NR8383, NiZnFe2O4, rep4

source_name: NR8383, NiZnFe2O4

value: (9.25 ug/mL) of NiZnFe2O4 for 4 h


title: NR8383, NiZnFe2O4, rep1


title: NR8383, NiZnFe2O4, rep2


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.GCGTAGTA_ACTCTAGG)


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.CGGAGCCT_ACTCTAGG)


title: NR8383, NiZnFe2O4, rep3


title: DCs from CNS from EcN treated mice (4KMQ.TACGCTGC_ACTCTAGG)


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.GGAGCTAC_ACTCTAGG)


title: DCs from CNS from EcN treated mice (4KMQ.TCGACGTC_AGCTAGAA)


title: DCs from CNS from D-LA producing EcN treated mice (4KMQ.ACTCGCTA_ACTCTAGG)


title: DCs from CNS from EcN treated mice (4KMQ.TGCAGCTA_AGCTAGAA)


title: NR8383, NRCWE006, rep2

value: (1 cm2/cm2) of multi-walled carbon nanotubes


title: NR8383, NRCWE006, rep3


title: DCs from CNS from EcN treated mice (4KMQ.CGATCAGT_AGCTAGAA)


title: DCs from CNS from EcN treated mice (4KMQ.CCTAAGAC_AGCTAGAA)


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.ACTGAGCG_AGCTAGAA)

value: Spleen


title: NR8383, NRCWE006, rep1


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.TAGCGCTC_AGCTAGAA)


title: NR8383, NRCWE001, rep1

value: (3 cm2/cm2) of TiO2


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.ATGCGCAG_AGCTAGAA)


title: NR8383, NRCWE001, rep2


title: NR8383, NRCWE001, rep4


title: NR8383, NRCWE006, rep4


title: NR8383, NRCWE001, rep3


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.TACGCTGC_AGCTAGAA)


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.CGGAGCCT_AGCTAGAA)


title: NR8383, NM403, rep3

value: (0.8 cm2/cm2) of NM403 for 4 h


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.GGAGCTAC_AGCTAGAA)


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.GCGTAGTA_AGCTAGAA)


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.ACTCGCTA_AGCTAGAA)


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.TGCAGCTA_CTAGTCGA)


title: NR8383, NRCWE042, rep3


title: DCs from spleen from EcN treated mice (4KMQ.CGATCAGT_CTAGTCGA)

source_name: DCs from spleen from EcN treated mice


title: NR8383, NM403, rep2


title: NR8383, NM105, rep2

value: (3 cm2/cm2) of TiO2 (NM105, p25 anatase/rutile) for 4 h


title: DCs from spleen from EcN treated mice (4KMQ.CCTAAGAC_CTAGTCGA)


title: DCs from spleen from EcN treated mice (4KMQ.TAGCGCTC_CTAGTCGA)


title: NR8383, NM403, rep4


title: DCs from spleen from EcN treated mice (4KMQ.ACTGAGCG_CTAGTCGA)


title: DCs from spleen from EcN treated mice (4KMQ.ATGCGCAG_CTAGTCGA)


title: NR8383, NM403, rep1


title: NR8383, Control_sub, rep4

source_name: NR8383, Ctrl_sub

value: submerge condition


title: DCs from spleen from D-LA producing EcN treated mice (4KMQ.TCGACGTC_CTAGTCGA)

value: DC


title: NR8383, NM105, rep3


title: DCs from spleen from EcN treated mice (4KMQ.CGGAGCCT_CTAGTCGA)


title: NR8383, Control_sub, rep2


title: DCs from spleen from EcN treated mice (4KMQ.TACGCTGC_CTAGTCGA)


title: NR8383, NM105, rep1


title: NR8383, Control_sub, rep3


title: NR8383, NM105, rep4


title: NR8383, H2O Control_ALI, rep2

source_name: NR8383, Ctrl_ALI_H2O

value: water (H2O)


title: NR8383, H2O Control_ALI, rep1


title: NR8383, FBS Control_ALI, rep3

source_name: NR8383, Ctrl_ALI_FBS

value: 10% FBS


title: DCs from Itgax Cre Xbp1 flox (ATCTCAGG_CTCCTTAC)

data_processing:
The sample is aligned to GRCm38 reference genome using STAR, and then quantified using RSEM
Genome_build: GRCm38
Supplementary_files_format_and_content: .isoforms.results files from RSEM

source_name: DCs from Itgax Cre Xbp1 flox

value: Female

value: Adults


title: DCs from spleen from EcN treated mice (4KMQ.GCGTAGTA_CTAGTCGA)


title: NR8383, FBS Control_ALI, rep2


title: NR8383, H2O Control_ALI, rep4


title: DCs from spleen from EcN treated mice (4KMQ.GGAGCTAC_CTAGTCGA)


title: DCs from WT (GTAGAGGA_CTCCTTAC)

source_name: DCs from WT


title: LY1

city: Zhongshan City

first: Fengyun

last: Zhao

address: 2 Sunwen East Road

department: Cancer Research Institute of Zhongshan City

institute: Zhongshan City People's Hospital

data_processing:
WriteFQ and FastQC and STAR and RSEM
Sequencing reads were constructed using WriteFQ
Sequence reads were cleaned for adaptor sequence/low-quality sequence using FastQC
Trimmed sequence reads were mapped to GRCm39 using STAR
Read count extraction and normalization were performed using RSEM
Differential gene analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Count values for each Sample

source_name: RBE

growth_protocol: RBE cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using GenJET RNA Purification Kit (thermo scientific). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by MGI DNBSEQ-T7 PE150

treatment_protocol: For lycorine hydrochloride treatment, RBE cells were treated for 24 hours with either DMSO, or lycorine hydrochloride (1 μM)

value: RBE

value: cholangiocarcinoma

value: treated with Lycorine hydrochloride


title: DCs from WT (AAGAGGCA_CTCCTTAC)

value: WT


title: Ctl2

value: control


title: NR8383, FBS Control_ALI, rep4

value: lung


title: DCs from spleen from EcN treated mice (4KMQ.ACTCGCTA_CTAGTCGA)

value: Parental Bacteria (E. coli-Nissle)


title: DCs from Itgax Cre Xbp1 flox (AGGCAGAA_TATGCAGT)

value: Spleen


title: NR8383, Control_sub, rep1


title: NR8383, FBS Control_ALI, rep1


title: NR8383, H2O Control_ALI, rep3


title: shSQLE-2

value: SQLE knockdown

value: Inhibition of SQLE by lentiviruses-mediated shRNA.


title: DCs from Itgax Cre Xbp1 flox (CGTACTAG_TATGCAGT)


title: NR8383, ALI_CB, rep1

source_name: NR8383, ALI_CB

value: (0.9 cm2/cm2) of Printex90


title: DCs from Itgax Cre Xbp1 flox (TAAGGCGA_TATGCAGT)


title: NR8383, ALI_CB, rep4


title: Ctl1


title: DCs from Itgax Cre Xbp1 flox (GCTCATGA_CTCCTTAC)


title: DCs from WT (CTCTCTAC_CTCCTTAC)


title: Ctl-2


title: NR8383, ALI_CB, rep2


title: shFDFT1-2

value: FDFT1 knockdown

value: Inhibition of FDFT1 by lentiviruses-mediated shRNA


title: NR8383, ALI_CB, rep3


title: shFDFT1-1


title: LY2


title: shSQLE-1


title: DCs from WT (CGAGGCTG_CTCCTTAC)

value: DC


title: DCs from Itgax Cre Xbp1 flox (AGGCAGAA_CTCCTTAC)

value: CNS


title: Ctl-1


title: DCs from Itgax Cre Xbp1 flox (GGACTCCT_CTCCTTAC)

value: Female


title: DCs from Itgax Cre Xbp1 flox (CGTACTAG_CTCCTTAC)

value: Adults


title: DCs from Itgax Cre Xbp1 flox (TAAGGCGA_CTCCTTAC)


title: DCs from WT (ATCTCAGG_AGAGGATA)


title: DCs from WT (AAGAGGCA_AGAGGATA)


title: DCs from WT (TAGGCATG_CTCCTTAC)


title: DCs from WT (GCTCATGA_AGAGGATA)


title: DCs from WT (GTAGAGGA_AGAGGATA)


title: DCs from Itgax Cre Xbp1 flox (CTCTCTAC_AGAGGATA)


title: DCs from Itgax Cre Xbp1 flox (TCCTGAGC_CTCCTTAC)


title: Library B3R

city: Detroit

first: Roger

last: Pique-Regi

state: Michigan

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

description: 10x Genomics scRNAseq

data_processing:
Raw data fastq.gz files and vcf files with genotypes  have been deposited in dbGaP (phs003260.v1.p1) due to donor privacy concerns.
We processed each scRNAseq library using cellranger (V7.0) count using the GRCh38 human reference genome and the default parameters except for the --include-introns option which is recommended for single nuclei preparations. The resulting aligned reads bam files were further processed with demuxlet(78) together with the genotype vcf files. Demuxlet assigns the most likely individual for each cell barcode based on the reads overlapping genetic variants. Based on the demuxlet assignments, we removed barcodes that were called doublets, ambiguous, or that could not be assigned to an individual that corresponded to the pool that was used to create the library. Any library that did not contain at least a case and a control individual was also excluded.
Assembly: GRCh38
Supplementary files format and content: Cellranger filtered gene expression counts and barcodes in h5 format

source_name: Ventral Midbrain

extract_protocol:
Sample processing for both brain cohorts, including purification of nuclei, RNA extraction, and generation of single nuclei RNA-seq libraries, was performed in New York. Brains were processed in pools of N=3-4 unique brains (donors). From each unique brain, a tissue aliquot, containing approximately 20mg of ventral midbrain from the area of the substantia nigra (A10) and portions of the adjacent ventral tegmental area (A9), was homogenized using a douncer at least 20x in 1ml lysis buffer (0.32M sucrose, 5mM CaCl2, 3mM Mg(Ace)2, 0.1mM EDTA, 10mM Tris pH8, 0.5mM DTT, 0.1% Triton X-100) with 400U RNase inhibitor (Takara Bio Recombinant RNase Inhibitor, Cat. 2313) added to it. Then, an additional 4ml of lysis buffer was added and the sample solution was dounced an additional 20x until homogenous. After douncing, each pool of 4 unique samples was transferred to an ultracentrifuge tube (Beckman Coulter Polypropylene Centrifuge Tubes ⅝ x 3 ¾ in., Ref. 361707) and underlaid with 9ml of sucrose buffer (1.8M sucrose, 3mM Mg(Ace)2, 0.5mM DTT, 10mM Tris-HCl pH8), then ultracentrifuged with 24,000rpm in a SureSpin 630 (17mL) Rotor (106,803x g) for 1hr at 4oC. After centrifugation, the supernatant was removed and each pellet of nuclei was carefully resuspended in 1ml of 1% BSA with 1,000U RRI added to it, transferred to a sterile tube, and 1 µl of the nucleophilic dye, DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride, Invitrogen Cat. D1306), was added. For FACS collection, sterile tubes were coated with 5% BSA. After residual BSA solution at bottom of tubes was removed, DAPI+ nuclei were sorted into the collection tubes using a BD FACSAria Cell Sorter, with approximately 300,000 DAPI+ nuclei for each pool of 4 unique midbrain samples collected
Pools were processed using  the 10x Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) Protocol (CG000315 Rev A) according to the  manufacturer’s instructions. The Agilent 2100 High Sensitivity DNA Bioanalyzer Kit was used as a quality control step at Step 2.4 and end of the library preparation, also as per 10x Genomics’ guidelines. To prepare samples for sequencing, sample concentration was determined using the KAPA Biosystems Library Quantification Kit  (ROX Low qPCR Master Mix, Cat. KK4873). Libraries were sequenced by the New York Genome Center using the Illumina NovaSeq platform aimed  at a sequencing depth of 50,000 read pairs per nucleus. Libraries consisted of paired-end reads with a read length of 100bp.

value: Ventral Midbrain


title: Library B5R

description: 10x Genomics scRNAseq


title: Library B12

description: 10x Genomics scRNAseq


title: Library B11

description: 10x Genomics scRNAseq


title: Library B7

description: 10x Genomics scRNAseq


title: Library B9

description: 10x Genomics scRNAseq


title: Library B2R

description: 10x Genomics scRNAseq


title: Library B6R

description: 10x Genomics scRNAseq


title: Library B1R

description: 10x Genomics scRNAseq


title: Library M13

description: 10x Genomics scRNAseq


title: Library B10

description: 10x Genomics scRNAseq


title: DCs from Itgax Cre Xbp1 flox (TAGGCATG_AGAGGATA)


title: Library M9

description: 10x Genomics scRNAseq


title: Library M7

description: 10x Genomics scRNAseq


title: DCs from Itgax Cre Xbp1 flox (TCCTGAGC_AGAGGATA)


title: DCs from WT (AGGCAGAA_AGAGGATA)


title: Library M5

description: 10x Genomics scRNAseq


title: Library M4

description: 10x Genomics scRNAseq


title: DCs from Itgax Cre Xbp1 flox (CGAGGCTG_AGAGGATA)


title: Library M3

description: 10x Genomics scRNAseq


title: DCs from WT (TAAGGCGA_AGAGGATA)


title: Library M20

description: 10x Genomics scRNAseq


title: DCs from WT (ATCTCAGG_ATAGAGAG)


title: DCs from WT (GCTCATGA_ATAGAGAG)


title: Library M2

description: 10x Genomics scRNAseq


title: Library M19

description: 10x Genomics scRNAseq


title: DCs from Itgax Cre Xbp1 flox (GTAGAGGA_ATAGAGAG)


title: DCs from Itgax Cre Xbp1 flox (AAGAGGCA_ATAGAGAG)


title: DCs from Itgax Cre Xbp1 flox (GGACTCCT_AGAGGATA)


title: DCs from Itgax Cre Xbp1 flox (CGAGGCTG_ATAGAGAG)


title: DCs from Itgax Cre Xbp1 flox (CTCTCTAC_ATAGAGAG)


title: Library M16

description: 10x Genomics scRNAseq


title: Library M15

description: 10x Genomics scRNAseq


title: Library M17

description: 10x Genomics scRNAseq


title: DCs from Itgax Cre Xbp1 flox (TAGGCATG_ATAGAGAG)


title: Library M18

description: 10x Genomics scRNAseq


title: DCs from WT (CGTACTAG_AGAGGATA)


title: Library M11

description: 10x Genomics scRNAseq


title: DCs from WT (AGGCAGAA_ATAGAGAG)


title: Library M10

description: 10x Genomics scRNAseq


title: DCs from WT (CGTACTAG_ATAGAGAG)


title: EC, replicate 3, scRNAseq

description: 10x Genomics

data_processing:
Gene counts were obtained by aligning reads to the 10 mm genome using Cell Ranger, v3.1.0 (10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ear epidermis

extract_protocol:
Ear skin of C57BL/6N mice was split into dorsal and ventral halves and placed with the dermal side facing downward in 10 mg/mL dispase II dissolved in 50 mM HEPES (pH 7.5) and 150 mM NaCl. After incubation (37 °C, 15 min), the epidermis was separated from the dermis. After rinsing with 1 mM EDTA in PBS, the epidermis was placed in 1 mL of Trypsin/EDTA solution in a 35-mm plastic dish and incubated for 5 min at 37°C. Then, epidermal cells were isolated with fine tweezers from the basal side of the epidermis; 1 mL of Trypsin Neutralizing solution was added to the cell suspension, which was then diluted with 8 mL HuMedia-KG2 without antibiotics and centrifuged. The supernatant was discarded, and the cell pellet was resuspended and cryopreserved in Bambanker until analysis.
Single-cell RNA-seq libraries were prepared according to the user guide of Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10X Genomics), except for the following modification. Modified protocol was commenced from post-cDNA Amplification Reaction Cleanup. After 0.6x size selection, the supernatant was not discarded, but processed for small fragments. 20 ul (0.8x) SPRIselect reagent was added to the supernatant and incubated for 5 min at room temperature. The beads were washed and eluted in 50 ul Buffer EB. Sample is referred to as No Fragmentation short size cDNA. The modifications were re-commenced from the adapter ligation. Adapter ligation mix was prepared according to manufacturer's instructions with the following change: Nuclease free water 7.5 uL/rxn. Add 40 uL adapter ligation mix to 50uL of sample. Add 10 uL of No Fragmentation short size cDNA to the mix. Return the sample to the thermocycler and resume the manufacturer's protocol. The libraries were sequenced using the HiseqX instrument (Illumina) with 150 bp paired-end read length.

value: Epidermal cells

value: Ear epidermis

value: 9 weeks old


title: DCs from WT (TCCTGAGC_ATAGAGAG)

value: WT


title: DCs from WT (TAAGGCGA_ATAGAGAG)


title: DCs from WT (GGACTCCT_ATAGAGAG)


title: Library M1

description: 10x Genomics scRNAseq


title: EC, replicate 2, scRNAseq

description: 10x Genomics


title: Carotid plaque donor 2 SARSCov2-72h [11-Donor-2plus-SARSCov2-72h_S11]

city: New York

first: Dr. Chiara

last: Giannarelli

address: 435 E 30th St

department: Cardiology

institute: NYU Langone Health

description: RNA bulk sequencing

data_processing:
Quality control of RNA-seq data was performed using FastQC2 v.0.11.7, a final report was generated for each FASTQ file to
assess general sequencing quality.
Following that the raw reads were aligned
using STAR v.2.6.1d with hg38 as the reference genome. The gene-level expression counts were
computed with featureCounts function in the Subread package (v.1.6.3; parameters: -g gene_id -s 2 )
using the human gene annotations from Gencode release 33.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample

source_name: carotid atherosclerotic plaque

growth_protocol: Human carotid plaque specimens were cultured in DMEM culture media supplemented with 10% FBS, 2 mM L-glutamine and 100 U ml−1 penicillin–streptomycin in a humidified 37°C, 5% CO2 incubator for 2 hours.

extract_protocol:
Total RNA from human atherosclerotic tissue was isolated using QIAzol Lysis Reagent and the gentleMACSTM Octo Dissociator (Miltenyi Biotec) homogenizer, combined with RNA clean-up using the RNAeasy Mini kit.
For human atherosclerotic plaqueex-vivoexperiments, libraries were prepared following the Revelo RNA-Seq High Sensitivity library preparation kit according to manufacturer’s instructions. Libraries were diluted and quantification was performed using KAPA library Quantification kit. Prepared libraries were pooled at2nMequimolar concentration and sequenced using the Illumina NovaSeq 6000 sequencer(100 cycles with S1 workflow).

treatment_protocol: Tissue specimens were infected with 105 PFU/mL of SARS-CoV-2 virus (USA-WA1/2020 strain). Non-infected tissues were used as controls.

tag: time point

value: carotid atherosclerotic plaque

value: SARS-CoV-2 infection


title: EAE sample D-LA treated (4ARP.TCCTGAGC_AGGCTTAG)

source_name: EAE sample D-LA treated

value: Spleen

tag: group

value: EAE

value: Free D-lactate


title: Library B4R

description: 10x Genomics scRNAseq


title: EAE sample D-LA treated (4ARP.ATCTCAGG_TACTCCTT)


title: EAE sample Control (4ARP.GCTCATGA_TACTCCTT)

source_name: EAE sample Control

value: Vehicle


title: Carotid plaque donor 2 not_infected [2-Donor-2-not-infected_S2]

description: RNA bulk sequencing


title: EAE sample Control (4ARP.GTAGAGGA_TACTCCTT)


title: EAE sample D-LA treated (4ARP.CGTACTAG_AGGCTTAG)


title: Naïve sample D-LA treated (4ARP.TAGGCATG_TACTCCTT)

source_name: Naïve sample D-LA treated

value: Naive


title: EAE sample D-LA treated (4ARP.TAAGGCGA_AGGCTTAG)


title: Carotid plaque donor 2 SARSCov2-24h [5-Donor-2plus-SARSCov2-24h_S5]

description: RNA bulk sequencing


title: βca3 Ele Pst rep2

city: Hangzhou

first: Zhangjian

last: Hu

state: Zhejiang province

address: yuhangtang road 886

institute: zhejiang 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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: ITAG3.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: toamto leaf

growth_protocol: Tomato were grown in trays and then transferred to pots with a mixture of peat and vermiculite (3:1, v/v) in a plant growth room, under 14/10 h (day/night) photoperiod, 500 μmol m-2 s-1 photosynthetic photon flux density (PPFD), 25 °C/20 °C day/night air temperature, and 88% relative humidity.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the experiments using a combined treatment of CO2 concentration and Pseudomonas syringae pv. tomato DC3000 (Pst) , 5-week-plants  were transferred to controlled environment cabinets, where the atmospheric CO2 was maintained at either 400 µmol mol-1 or 800 µmol mol-1, corresponding to the “ambient CO2” and “elevated CO2”, respectively. After 2 days, plants exposed to both ambient and elevated CO2 were subjected to Pst inoculation.

tag: genotype/variation

value: elevated CO2 + Pst


title: Naïve sample D-LA treated (4ARP.CTCTCTAC_TACTCCTT)

value: DC

tag: strain


title: EAE sample Control (4ARP.AAGAGGCA_TACTCCTT)

tag: Sex


title: Carotid plaque donor 2 SARSCov2-48h [8-Donor-2plus-SARSCov2-48h_S8]

description: RNA bulk sequencing


title: βca3 Ele Pst rep3


title: βca3 Amb Pst rep1

value: ambient CO2 + Pst


title: βca3 Amb Pst rep2


title: Carotid plaque donor 3 SARSCov2-72h [12-Donor-3plus-SARSCov2-72h_S12]

description: RNA bulk sequencing


title: Carotid plaque donor 3 not_infected [3-Donor-3-not-infected_S3]

description: RNA bulk sequencing


title: βca3 Amb Pst rep3


title: EAE sample Control (4ARP.CGAGGCTG_TACTCCTT)

value: Female


title: βca3 Ele Pst rep1


title: EC, replicate 1, scRNAseq

description: 10x Genomics


title: EAE sample D-LA treated (4ARP.AGGCAGAA_AGGCTTAG)

value: Adults


title: Naïve sample D-LA treated (4ARP.GGACTCCT_TACTCCTT)


title: βca3 Ele Mock rep3

value: elevated CO2 + mock


title: Carotid plaque donor 3 SARSCov2-24h [6-Donor-3plus-SARSCov2-24h_S6]

description: RNA bulk sequencing


title: Naïve sample D-LA treated (4ARP.TCCTGAGC_TACTCCTT)


title: Naïve sample D-LA treated (4ARP.AGGCAGAA_TACTCCTT)


title: Naïve sample Control (4ARP.CGTACTAG_TACTCCTT)

source_name: Naïve sample Control


title: Naïve sample Control (4ARP.ATCTCAGG_TATGCAGT)


title: Carotid plaque donor 3 SARSCov2-48h [9-Donor-3plus-SARSCov2-48h_S9]

description: RNA bulk sequencing


title: Naïve sample Control (4ARP.TAAGGCGA_TACTCCTT)


title: DCs from Itgax Cre HIF1a flox (3XHP.CGAGGCTG_AGCTAGAA)

source_name: DCs from Itgax Cre HIF1a flox

value: Itgax Cre HIF1a flox

value: HIF1 knockout


title: foam cells not infected timepoint 2 [13_S1_S4]

description: RNA bulk sequencing

data_processing:
Quality control of RNA-seq data was performed using FastQC2 v.0.11.7, a final report was generated for each FASTQ file to
assess general sequencing quality.
Following that the raw reads were aligned
using STAR v.2.6.1d with hg38 as the reference genome. The gene-level expression counts were
computed with featureCounts function in the Subread package (v.1.6.3; parameters: -g gene_id -s 2)
using the human gene annotations from Gencode release 33.
Assembly: hg38 concatenated with SARS-CoV-2 Washington isolate (WA1/2020) genome
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample

source_name: foam cell

growth_protocol: Human primary monocytes derived from peripheral blood mononuclear cells (PBMCs) were obtained (StemCell Technologies, Cat. #200-0167) and maintained in DMEM culture media (Corning, Cat. #10-013-CV) supplemented with 10% FBS, 2 mM L-glutamine, 100 U ml−1 penicillin–streptomycin in a humidified 37°C, 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent and Direct-zol RNA Microprep Kits following the manufacturer’s instructions.
For human primary macrophage and foam cellin-vitroexperiments, library preparation was performed byPolyA capture and ligation-based addition of adapters and indexeswith Illumina Stranded mRNA Preparation and Ligation.

treatment_protocol:
Monocytes were plated and differentiated to macrophages in the presence of 20 nM human macrophage-colony stimulating factor (M-CSF) for 5 days. Macrophages were first treated with ox-LDL at final concentration of 10 μg/mL for 1 hour before infection
Cells were cultured with SARS-CoV-2 virus (USA-WA1/2020 strain) at MOI 0.1 in infection media with 2% FBS.  Mock infected cells were used as controls.

value: foam cell

value: not infected


title: βca3 Ele Mock rep2


title: Naïve sample Control (4ARP.GCTCATGA_TATGCAGT)


title: DCs from Itgax Cre HIF1a flox (3XHP.TAGGCATG_AGCTAGAA)


title: DCs from Itgax Cre HIF1a flox (3XHP.TCCTGAGC_AGCTAGAA)


title: foam cells not infected timepoint 2 [15_S6]

description: RNA bulk sequencing


title: foam cells not infected timepoint 2 [14_S2_S5]

description: RNA bulk sequencing


title: βca3 Ele Mock rep1


title: DCs from WT (3XHP.CGTACTAG_AGCTAGAA)

value: WT


title: βca3 Amb Mock rep2

value: ambient CO2 + mock


title: DCs from Itgax Cre HIF1a flox (3XHP.GGACTCCT_AGCTAGAA)

value: Spleen


title: βca3 Amb Mock rep3


title: Macrophage not infected timepoint 8 [19_S3_S7]

description: RNA bulk sequencing

source_name: macrophage

value: macrophage

value: SARS-CoV-2 infection


title: DCs from WT (3XHP.AGGCAGAA_AGCTAGAA)


title: Macrophage not infected timepoint 8 [20_S8]

description: RNA bulk sequencing


title: DCs from WT (3XHP.GCTCATGA_CTAGTCGA)


title: βca3 Amb Mock rep1


title: DCs from WT (3XHP.TAAGGCGA_AGCTAGAA)


title: WT Ele Pst rep3


title: Macrophage not infected timepoint 8 [21_S9]

description: RNA bulk sequencing


title: DCs from Itgax Cre HIF1a flox (3XHP.AAGAGGCA_CTAGTCGA)

value: CNS


title: foam cells not infected timepoint 8 [25_S10]

description: RNA bulk sequencing


title: DCs from Itgax Cre HIF1a flox (3XHP.CGAGGCTG_CTAGTCGA)


title: DCs from Itgax Cre HIF1a flox (3XHP.CTCTCTAC_AGCTAGAA)


title: WT Ele Pst rep2


title: foam cells not infected timepoint 8 [26_S11_S4]

description: RNA bulk sequencing


title: DCs from Itgax Cre HIF1a flox (3XHP.TAGGCATG_CTAGTCGA)


title: DCs from Itgax Cre HIF1a flox (3XHP.CTCTCTAC_CTAGTCGA)


title: WT Ele Pst rep1


title: DCs from WT (3XHP.ATCTCAGG_CTAGTCGA)


title: DCs from WT (3XHP.GGACTCCT_CTAGTCGA)


title: DCs from WT (3XHP.TCCTGAGC_CTAGTCGA)


title: foam cells not infected timepoint 8 [27_S12]

description: RNA bulk sequencing


title: DCs from WT (3XHP.AGGCAGAA_CTAGTCGA)


title: WT Amb Pst rep3


title: Macrophage not infected timepoint 24 [31_S13]

description: RNA bulk sequencing


title: WT Amb Pst rep2


title: WT Amb Pst rep1


title: DCs from Itgax Cre HIF1a flox (3XHP.GTAGAGGA_CTAGTCGA)


title: DCs from WT (3XHP.CGTACTAG_CTAGTCGA)


title: P007_RNA_S16

city: Bethesda

first: Uma

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

data_processing:
fastq files were prepared according to ccbrpipeliner module (https://github.com/CCBR/Pipeliner) in Biowulf cluster. Reads were aligned using hg38 humna genome reference. Read counts obtatined from the pipeline were normalized with edgeR analysis in R stastistical package. Before normalization, counts were filtered to keep raw counts >0.5 in greater than 3 samples.
Assembly: hg38
Supplementary files format and content: normalized counts saved as txt format

source_name: lymphoblastoid cell lines

extract_protocol:
Total RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturer’s protocol.
Total RNA-seq libraries were then prepared using 800ng of resulting RNA from each sample and NEBNext Ultra II RNA Library Prep Kit for Illumina with Poly(A) mRNA Magnetic Isolation Module (NEB #E7760, E7490 and E6440) according to the manufacturer’s protocol with 11 amplification cycles. Libraries were sequenced on a NextSeq550 with paired-end reads of 75 base pairs, with a read depth of 60 million fragments / library. Two libraries from two corresponding biological replicates were prepared for each sample.

value: lymphoblastoid cell lines

value: PRO


title: Macrophage not infected timepoint 24 [33_S15]

description: RNA bulk sequencing


title: P006_RNA_S14

value: SIB


title: P007_RNA_S15


title: Macrophage not infected timepoint 24 [32_S14]

description: RNA bulk sequencing


title: DCs from WT (3XHP.TAAGGCGA_CTAGTCGA)

value: DC


title: P006_RNA_S13


title: WT Ele Mock rep3


title: WT Ele Mock rep2


title: foam cells not infected timepoint 24 [38_S17]

description: RNA bulk sequencing


title: scRNA-seq of thyroid tumor

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

description: 10x Genomics

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Reads with low-quality barcodes and UMIs were filtered out and then mapped to the reference genome. Reads uniquely mapped to the transcriptome and intersecting an exon at least 50% were considered for UMI counting.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thyroid tumor

extract_protocol:
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction.
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: thyroid tumor

value: female

value: 17 years old

tag: disease state

value: papillary thyroid carcinoma (PTC)


title: WT Ele Mock rep1

value: elevated CO2 + mock


title: scRNA-seq of lymph node metastasized tumor

description: 10x Genomics

source_name: lymph node metastasized tumor

value: lymph node metastasized tumor


title: WT Amb Mock rep3


title: Macrophage not infected timepoint 48 [43_S19_S7]

description: RNA bulk sequencing


title: Wt represents ARP-1 cells,EV_2

city: Shanghai

first: Jumei

last: Shi

address: 150 Jimo Road

department: Department of Hematology

institute: Shanghai East Hospital

data_processing:
Sequenced reads were irimmed for adaptor sequence,and masked for low-complexity or low-quality sequence,than mapped hg19 whole genemocies
Cufflinks are used for assemble transcripts and remap and quanity gene-expression level,which is estimate by FPKM value
Supplementary files format and content: tab-delimited text dile includes raw counts for each Sample
Supplementary files format and content: tab-delimited text dile includes FPKM value for each Sample

source_name: myeloma cells

extract_protocol: RNA libraries were prepared for sequencing using standard IIIumina protocols

value: myeloma cells

value: multiple myeloma cells


title: Wt represents ARP-1 cells,EV_3


title: Macrophage not infected timepoint 48 [44_S20_S8]

description: RNA bulk sequencing


title: WT Amb Mock rep1

value: WT

value: ambient CO2 + mock


title: PG7 Week 0

type: protein

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

country: Australia

institute: Liverpool Hospital

description: Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.

data_processing: 5mL of serum was drawn from patients at baseline and after 12 weeks of Tildrakizumab 200mg q4weekly

label: OLINK PEA

source_name: Serum

extract_protocol: serum

tag: condition

value: Baseline


title: PG5 Week 0


title: WT Amb Mock rep2


title: Macrophage not infected timepoint 48 [45_S21_S9]

description: RNA bulk sequencing

value: macrophage

value: SARS-CoV-2 infection


title: PG4 Week 0


title: PG6 Week 0


title: Case represents ARP-1 cells,TRIP13-OE_2


title: foam cells not infected timepoint 48 [49_S10_S22]

description: RNA bulk sequencing

value: foam cell

value: not infected


title: Control_midbrain_4

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined, aligned, and quantitated with Illumina's DRAGEN Bio-IT system version 3.9.3-8
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with TPM in tab-delimitted text format

source_name: dissected midbrain

extract_protocol:
Frozen brain samples extracted in Trizol, RNA isolated using Invitrogen PureLink kit.
oligo-dT

value: dissected midbrain


title: Bmal1KO_midbrain_3


title: foam cells not infected timepoint 24 [37_S16_S5]

description: RNA bulk sequencing


title: PG3 Week 0


title: PG2 Week 0


title: scRNA-seq of adjacent normal thyroid

description: 10x Genomics

source_name: adjacent normal thyroid

value: adjacent normal thyroid


title: Case represents ARP-1 cells,TRIP13-OE_1


title: foam cells not infected timepoint 48 [50_S23]

description: RNA bulk sequencing


title: PG1 Week 0


title: foam cells not infected timepoint 48 [51_S24]

description: RNA bulk sequencing


title: Control_midbrain_3


title: foam cells not infected timepoint 24 [39_S18_S6]

description: RNA bulk sequencing


title: Control_midbrain_2


title: Wt represents ARP-1 cells,EV_1


title: Carotid_plaque_3_scRNAseq

description: 10x Genomics

data_processing:
scRNA-seq used the Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) to quality control the single-cell expression data.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human plaque isolated cells

extract_protocol:
The Chromium Single Cell 3′ v2 Reagent (10X Genomics, 120237) kit was used to prepare single-cell RNA libraries according to the manufacturer’s instructions.
The single-cell suspensions of scRNA-seq samples were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit, and Chip Kit (10X Genomics)73,74.

value: human plaque isolated cells


title: Macrophage not infected timepoint 2 [7_S1]

description: RNA bulk sequencing


title: Bmal1KO_midbrain_2


title: Case represents ARP-1 cells,TRIP13-OE_3


title: Carotid_plaque_2_scRNAseq

description: 10x Genomics


title: Macrophage not infected timepoint 2 [8_S2]

description: RNA bulk sequencing


title: Bmal1KO_midbrain_1


title: RiboTag, DRG, Injured

city: Daegu

first: Eunsu

last: Jang

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

institute: DGIST

description: HA-IP product, RNA

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts

source_name: Dorsal root ganglion(DRG)

extract_protocol:
For total RNA sequencing, freshly collected DRGs were lysed, and their RNA was extracted using RNeasy mini kit(Qiagen, 74104). For HA-IP sequencing, lysate from the freshly collected DRGs of RiboTag mice were immunoprecipitated with an anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using the same kit.
Both libraries for total RNA sequencing and HA-IP sequencing were prepared following the instrcutions from the manufacture. (Total RNA sequencing: direct RNA sequencing kit(SQK-RNA002), HA-IP sequencing: cDNA-PCR barcoding kit(SQK-PCB109))

value: Dorsal root ganglion(DRG)

tag: developmental stage

value: adult

value: Sciatic nerve injury, 72hr

tag: ip antibody

value: Anti-HA tag(abcam, #ab9110)


title: Macrophage not infected timepoint 2 [9_S3]

description: RNA bulk sequencing


title: foam cells not infected timepoint 0 [Foam-cells-Donor-1-0hpi_S4]

description: RNA bulk sequencing


title: RiboTag, DRG, Uninjured

description: HA-IP product, RNA

value: Uninjury


title: Control_midbrain_1


title: Bulk, DRG, Uninjured

value: Wild type


title: Carotid_plaque_4_scRNAseq

description: 10x Genomics


title: Thbs1-/- HFD 2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCm38/m10 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCm38
Supplementary files format and content: gene_expected_count.annot.txt
Supplementary files format and content: tab-delimited text files include expected counts values for each Sample

source_name: Diaphragm

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) after mechanical homogenization of the tissues
Lexogen QuantSeq 3‘ mRNA-Seq Library Prep (single end)

value: Diaphragm

value: Tissue

value: High fat diet (x 6 months)


title: Thbs1-/- HFD 3


title: Ribotag, shGpr151, DRG

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

department: Department of Brain Sciences

extract_protocol:
For CSDE1-IP or HA-IP sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-CSDE1 or anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using Rneasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB109))

value: Cultured adult doral root ganglion neurons

value: Sciatic nerve injury, 24hr

tag: in vivo_viral_gene_delivery

tag: in vitro_viral_gene_delivery

tag: molecule subtype

value: HA-IP product, RNA


title: Carotid_plaque_1_scRNAseq

description: 10x Genomics


title: foam cells SARSCov2 infected timepoint 24 [Foam-cells-Donor-1-1-dpi_S22]

description: RNA bulk sequencing

value: foam cell

value: SARS-CoV-2 infection


title: foam cells SARSCov2 infected timepoint 2 [Foam-cells-Donor-1-2-hpi_S7]

description: RNA bulk sequencing


title: WT HFD 3

tag: tissue


title: Ribotag, control, DRG

tag: treatment

value: AAV-control


title: 5'UTRm+shGpr151, DRG

tag: cell type

value: CSDE1-IP product, RNA


title: KO MA

first: Ziyan

last: Lin

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Downstream analysis was performed using the Seurat package in R utilizing their integrated pipeline analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone and bone marrow

extract_protocol:
Cells were isolated from the tibia and femur and crushed once, using mortar and pestle, then cut into small pieces with scissors. The tissue was subjected to three rounds of enzymatic digestion with 0.2%collagenaseat 37°C under agitation for 30min each. Cells were filtered through a 70-μm strainer and centrifuged at 1500 rpm for 5 minutes at 4°C.  Red blood cells were lysed using NH4Cl (StemCell Technologies, Vancouver, Canada) for 10 min on ice, washed with staining media (HBSS (Thermo Fisher Scientific, Waltham, MA, USA) containing 2% fetal bovine serum (Life Technologies: 10437-028), 1% HEPES (10 mM) (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Thermo Fisher Scientific) and resuspended in HBSS for subsequent analyses
Libraries were prepared using the Chromium single cell 3ʹ reagent v2 protocol (10x Genomics) per the manufacturer’s recommendations. Sequencing was performed by the Illumina NovaSeq 6000

value: Bone and bone marrow

value: mouse bone and bone marrow

tag: genotype

value: LeprCre; Ncstnfl/fl


title: WT MA

description: 10x Genomics

value: Ncstnfl/fl


title: Young

description: 10x Genomics


title: foam cells SARSCov2 infected timepoint 8 [Foam-cells-Donor-1-8-hpi_S16]

description: RNA bulk sequencing


title: WT HFD 2


title: 5'UTRm, embryonic DRG

value: Cultured primary dorsal root ganglion neurons

value: embryonic stage E13


title: Bulk, DRG, Injured

value: Dorsal root ganglion(DRG)

value: Wild type

value: adult

value: Sciatic nerve injury, 72hr


title: Thbs1-/- HFD 1

value: Diaphragm

value: Tissue

value: High fat diet (x 6 months)


title: foam cells not infected timepoint 0 [Foam-cells-Donor-2-0-hpi-1_S5]

description: RNA bulk sequencing

value: foam cell

value: not infected


title: foam cells SARSCov2 infected timepoint 48 [Foam-cells-Donor-1-2-dpi_S28]

description: RNA bulk sequencing

value: SARS-CoV-2 infection


title: WT HFD1


title: cKO 3

data_processing:
NovaSeq 6000 System (RTA Version 3.4.4)
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Cells were isolated from the tibia and femur and crushed once, using mortar and pestle, then cut into small pieces with scissors. The tissue was subjected to three rounds of enzymatic digestion with 0.2%collagenaseat 37°C under agitation for 30min each. Cells were filtered through a 70-μm strainer and centrifuged at 1500 rpm for 5 minutes at 4°C.  Red blood cells were lysed using NH4Cl (StemCell Technologies, Vancouver, Canada) for 10 min on ice, washed with staining media (HBSS (Thermo Fisher Scientific, Waltham, MA, USA) containing 2% fetal bovine serum (Life Technologies: 10437-028), 1% HEPES (10 mM) (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Thermo Fisher Scientific) and resuspended in HBSS for subsequent analyses
RNA was isolated from cells using RNeasy Kit (Qiagen, Germantown, MD, USA) according to manufacturer’s instruction
RNA-seq, Low input RNA (10 pg) library prep (SMARTer or Nugen method)

value: LEPR+CD45-CD31-TER-119- skeletal stem cells


title: cKO 4

value: Bone and bone marrow


title: Control, embryonic DRG

value: LV-control

value: CSDE1-IP product, RNA


title: cKO 2

value: LeprCre; Ncstnfl/fl


title: foam cells not infected timepoint 0 [Foam-cells-Donor-2-0-hpi-2_S6]

description: RNA bulk sequencing


title: shGpr151, DRG, Injured


title: foam cells SARSCov2 infected timepoint 24 [Foam-cells-Donor-2-1-dpi-2_S24]

description: RNA bulk sequencing


title: shGpr151, DRG, Uninjured

value: Uninjury


title: foam cells SARSCov2 infected timepoint 24 [Foam-cells-Donor-2-1-dpi-1_S23]

description: RNA bulk sequencing


title: cKO 1


title: control 4

value: Ncstnfl/fl


title: Wildtype, DRG, Uninjured

value: Dorsal root ganglion(DRG)


title: control 1


title: foam cells SARSCov2 infected timepoint 48 [Foam-cells-Donor-2-2-dpi-2_S30]

description: RNA bulk sequencing


title: foam cells SARSCov2 infected timepoint 48 [Foam-cells-Donor-2-2-dpi-1_S29]

description: RNA bulk sequencing


title: ovary_H_RNA2_rep3

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

institute: University of East Anglia

data_processing:
Sequencing reads were pseudoaligned to the Drosophila melanogaster transcriptome using Kallisto v0.46.1 with parameter --rf-stranded
Estimated transcript counts were summarised per gene in R v4.0.1 using the tximport package v1.16.1 with parameter type="kallisto"
Differential expression analysis was conducted in R v4.0.1 using the DESeq2 package v1.28.1
Genome_build: Drosophila_melanogaster.BDGP6.22.cdna.all.fa
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in head
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in fat body
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in ovary

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Drosophila melanogaster were maintained under standard conditions. See the publication for further details.

extract_protocol:
Drosophila melanogaster females were flash-frozen in liquid nitrogen and stored at -80oC. Females were then defrosted and the head, fat body (abdomen minus gut and ovaries) and ovaries were dissected out (over dry ice), pooled into groups of 11 or 12 within each treatment and sub-group, then flash-frozen in liquid nitrogen, and stored at -80oC. Each sample (tissue pooled from 11 or 12 individuals) was then ground in liquid nitrogen using a micropestle with the resulting powder resuspended in Tri-reagent (Sigma-Aldrich, UK). RNA was extracted using the Direct-zolTM RNA extraction kit (Zymo Research, USA) according to the manufacturer's protocol. An additional DNase treatment was performed using TurboTM DNA-free kit (Thermo Fisher Scientific, UK), according to the manufacturer's protocol.
Illumina TruSeq stranded mRNA-seq libraries constructed by Edinburgh Genomics (Edinburgh, UK)

treatment_protocol: Drosophila melanogaster larvae were reared on either 100% sugar-yeast-agar (SYA) (medium-quality diet (M) treatment) or 120% SYA (high-quality diet (H) treatment).

value: ovary

value: high (H), larval diet of 120% sugar-yeast-agar (SYA)

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died

tag: biological replicate

value: biological replicate 3


title: control 3