title: BMDMs, treated with supernatants from apoptotic (+ LeTox) Nlrp1bTg/Casp1/11KO cells, rep 3

value: M0 Macrophages

value: 4 hrs with supernatants from apoptotic(+LeTox) C57BL/6 Nlrp1bTg+/-/Casp1/11KO cells


title: BMDMs, treated with supernatants from apoptotic (+ LeTox) Nlrp1bTg/Casp1/11KO cells, rep 4

status: Public on Apr 07 2024

type: SRA

city: Ghent

first: Parul

last: Mehrotra

address: Zwijnaarde Technology Lab

department: Center for Inflammation Research

country: Belgium

institute: VIB - UGhent

library_source: transcriptomic

data_processing:
Low quality reads (N > 10 or base quality < 20) and reads containing adaptors were removed (Performed by Novogene), levaing  above 90% of reads in all samples
HISAT2 was used to align reads to Mouse genome GRCm38/mm10 with an alignment rate above 93% in all samples (Performed by Novogene)
Aligned files' features were counted using featureCounts from the Rsubread (v.2.10.3) package
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file containing raw counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: cell culture

growth_protocol: Mouse  bone  marrow  cells were cultured in  Gibco  RPMI  1640,  supplemented  with  50ng/ml  of  murine MCSF,   10%   fetal   bovine   serum   (FBS),   and   1% penicillin-streptomycin   for   6 days   in   a humidified atmosphere containing 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the Quiagen® RNAeasy kit and protocols. 1ug per sample was used to construct the sequencing libraries
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), and index codes were added to attribute sequences to each sample (Performed by Novogene)

treatment_protocol:
Cells were treated with supernatants coming from media with Apoptotic (Casp), Pyroptotic (Nalp) or Alive cells (WT):
Apoptotic supernatants were obtained by treating C57BL/6 Nlrp1bTg+/-/Casp1/11KO  Mouse derived BMDMs with LeTox for 180 mins (Casp180). Controls (Casp0) had the same genotype but were not treated with LeTox.
Pyroptotic supernatants were obtained by treating C57BL/6 Nlrp1bTg+/- mouse derived BMDMs with LeTox for 120 mins (Nalp120). Controls (Nalp0) had the same genotype but were not treated with LeTox.
Alive cells supernatants were obtained by treating C57BL/6 cells with LeTox for 180 mins (WT180). Controls (WT0) had the same genotype but were not treated with LeTox.

tag: tissue

value: cell culture

tag: cell line

value: Primary Mouse bone marrow derived macrophages(BMDMs)

tag: cell type

tag: genotype

tag: treatment

value: 4 hrs with supernatants from apoptotic (+LeTox) C57BL/6 Nlrp1bTg+/-/Casp1/11KO cells


title: DD037G_distal_RNA

type: RNA

city: Chapel Hill

first: Scott

middle: H.

last: Randell

state: North Carolina

address: CB 7248, Room 1117 Marsico Hall, 125 Mason Farm Rd.

country: USA

institute: UNC Chapel Hill

hyb_protocol: Microarrays were hybridized in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% Triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.

scan_protocol: Microarrays were scanned with Agilent Scanner and intensity was recorded using Agilent Feature Extraction Software.

data_processing:
Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma.
Normalized_normalLung.txt file includes normalized log2 ratios (normal/reference).

organism: Homo sapiens

source_name: Normal lung

label_protocol: The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all reagents volumes were reduced by one half.

extract_protocol: Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.

value: Normal lung

tag: airway size

value: small

source_name: Stratagene Human Universal Reference

tag: sample type

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: DD010H_distal_RNA


title: Primary human macrophages, siALOX15B, rep2

city: Frankfurt

first: Yvonne

last: Benatzy

address: Theodor-Stern-Kai 7, building 74

department: Institute of Biochemistry I

country: Germany

institute: Goethe-University Frankfurt

data_processing:
Processing of sequencing data was performed within the Lexogen QuantSeq 3´ mRNA-Seq integrated data analysis pipeline on the BlueBee on-line platform (BlueBee Holding BV, Rijswijk, The Netherlands).
FASTQ reads were trimmed (bbduk v35.92), mapped to the hg38 human genome assembly (STAR Aligner v2.5.2a with modified ENCODE settings), and gene-specific read counts were determined (HTSeq-count v0.6.0).
Differential gene expression analysis of read counts was conducted by DESeq2.
Assembly: hg38
Supplementary files format and content: counts file, siC vs siALOX15B_DE analysis

source_name: primary macrophages

extract_protocol:
Total RNA of control and ALOX15B-silenced macrophages was isolated using RNeasy Mini Kit (Qiagen, cat. no. 74104) and RNA was purified by precipitation. RNA quality was determined using an Agilent High Sensitivity RNA ScreenTape (cat. no. 5067-5579) with an Agilent TapeStation 4150 (Agilent Technologies, Waldbronn, Germany) and RNA concentration was quantified using a Qubit HS RNA Assay Kit (cat. no. Q32852) and Qubit 3 fluorometer (Thermo Fisher Scientific).
Library preparation of 500 ng RNA was performed using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH, Vienna, Austria, cat. no. 015.24). Library quality and quantity was controlled by Qubit 3 fluorometer and Agilent D1000 DNA ScreenTape (cat. no. 5067-5582).
High Output Kit v2.5 (cat. no. 20024906)

treatment_protocol: Human monocytes derived from five individual donors were differentiated into naïve macrophages with RPMI 1640 medium containing 5% AB-positive human serum for 7 days. Subsequently, macrophages were transfected with non-targeting or ALOX15B-specific siRNA and after 5 days total RNA was isolated for next-generation sequencing.

tag: individual

value: primary macrophages

value: ALOX15B siRNA

value: ALOX15B silenced


title: BMDMs, treated with supernatants from apoptotic (+ LeTox) Nlrp1bTg/Casp1/11KO cells, rep 1

value: 4 hrs with supernatants from apoptotic (+ LeTox) C57BL/6 Nlrp1bTg+/-/Casp1/11KO cells


title: Primary human macrophages, siControl, rep3

value: control siRNA

value: control


title: DD010H_middle_RNA

value: medium


title: Resting T cells, PATIENT_#7

city: Nantes

first: Frédéric

last: Ebstein

address: IRS-UN - 8 quai Moncousu - BP 70721

department: L'unité de recherche de l'institut du thorax, Inserm UMR 1087

country: France

institute: French Institute of Health and Medical Research (Inserm)

hyb_protocol: One hundred nanograms total RNA was hybridized with the nCounter Autoimmune Profiling panel CodeSets for 16 hours at 65°C.

scan_protocol: Hybridized probes were immobilized on streptavidin-coated cartridges for digital counting by a nCounter™ Digital Analyzer.

data_processing: RCC files were analysed using nSolver 4.0. Normalization of RNA loading was performed using the geometric mean of a unique housekeeping gene.

label: biotin

source_name: Stimulated T cells

label_protocol: Labelling was performed using gene-specific biotin-tagged molecular barcodes (CodeSets) designed and provided by the manufacturer.

growth_protocol: PBMC were cultured in U-bottom 96-well plates together with irradiated feeder cells using RPMI 1640 medium supplemented with 10% human AB serum.

extract_protocol: Total RNA was isolated from resting T cells using the kit from Analytic Jena AG following the manufacturer’s instructions.

treatment_protocol: PBMC were stimulated with 1 µg/µl L-PHA (Sigma) and 150 U/ml IL-2 (Miltenyi Biotec) for three weeks to expand naive T cells following the procedure of Fonteneau et al.

value: blood

tag: gender

value: female

tag: phenotype

value: Neurodevelomental disorder


title: Resting T cells, PATIENT_#4

value: PSMD11 +/c.612dup


title: BMDMs, treated with supernatants from alive (No LeTox) Nlrp1bTg/Casp1/11KO cells, rep4

value: cell culture

value: M0 Macrophages

value: 4 hrs with supernatants from alive (No LeTox) C57BL/6 Nlrp1bTg+/-/Casp1/11KO cells


title: Primary human macrophages, siControl, rep2


title: DD010H_proximal_RNA

value: Normal lung

value: large


title: Resting T cells, HD_#3

value: PSMD11 +/+ (wild-type)

value: Clinically healthy


title: Kelly transfected piR-Ctrl 1

city: Regensburg

first: Tilman

last: Heise

address: Franz Josef Strauss Allee 11

institute: Uniklinik Regensburg

description: S513 1

data_processing:
Quality filtering of reads using cutadapt with parameters --minimum-length 25 --cut 5 -q 20
Read mapping to the human reference genome (Gencode, GRCh38, v43) using STAR with default parameters
Using featureCounts to gather final read counts per gene
Assembly: GRCh38, Gencode v43
Supplementary files format and content: count table of each sample

source_name: Kelly

growth_protocol: Kelly cells were maintained in RPMI1640 supplemented with 10% fetal calf serum (FCS), 1% L-Glutamine and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested 48 h after transfection with the Rneasy mini kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
Library preparation and RNAseq were carried out as described in the Illumina “Stranded mRNA Prep Ligation” Reference Guide, the Illumina NextSeq 2000 Sequencing System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA).

treatment_protocol: Kelly cells were reverse transient transfected with the lipofectamine RNAiMAX (Thermo Fisher) with piR-1254 or piR-Ctrl as control on a 6-well plate with 1.0 million cells per well and a final RNA concentration of 25 nM.

value: Kelly

value: Neuroblastoma

value: transient transfection sncRNACtrl


title: Primary human macrophages, siALOX15B, rep1

value: primary macrophages

value: ALOX15B siRNA

value: ALOX15B silenced


title: DD006H_proximal_RNA

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: WT BY4741 rep2

city: Paris

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

institute: Institute Pasteur

library_source: genomic

data_processing:
Fastq files were demiltiplexed using Je demultiplex suite (Girardot et al., 2016).
Paired-end reads were mapped to sacCer3 R64-1-1 genome using Bowtie2 ((Langmead and Salzberg, 2012) with default setting except -X 500, --no-discordant, --no-mixed options.
Bam files were generated using samtools (Li et al., 2009).
Nucleosome dyad coverage and bigWig files were generated using 140-160 bp reads and resizing to 50 bp at the dyad center for MNase-Seq.
Assembly: R64-1-1 (sacCer3)
Supplementary files format and content: Signal intensity in bigWig file format

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: Yeast strains were grown in YPAD media to OD 1.0-2.0.

extract_protocol:
Yeast nuclei was prepared according to (Almer and Horz, 1986). Cells were harvested  and incubated in 2 volume of preincubation solution (0.7 M ß-mercaptoethanol, 28 mM EDTA) for 25-30 mins. After washing with 1M sorbitol, cell wall was digested with Zymolyase. Spheroplasts were washed with 1M sorbitol and lysed with Ficoll buffer (18 % Ficoll, 20 mM KH2PO4 pH 6.8, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA). Nuclei was centrifuged and stored at -80 ̊C before use. For MNase digestion, nuclei was washed and dissolved in MNase digestion buffer (15 mM Tris-Cl pH 7.5, 50 mM NaCl, 1.4 mM CaCl2, 0.2 mM EGTA, 0.2 mM EDTA, 5 mM ß-mercaptoethanol). Equal volume of nuclei was digested with increasing amount of MNase for 20 mins at 37 ̊C. Reaction was stopped with 10 mM EDTA, 1% SDS and 50 mM Tris-Cl pH 8.5, followed by Proteinase K incubation for 30 mins at 37 ̊C. DNA was isolated by Phenol:Chloroform extraction and precipitation with 100% ethanol. Pellet was dissolved in TE buffer and RNA was removed with RNAse A incubation at 37 ̊C for 60 mins. DNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50 μl TE. 25 μl DNA was loaded on 1.7% agarose gel and resolved for 4 hours at 2 V/cm. Appopriately digested sample with 70% mono-, 20% di- and 10% tri-nucleosome bands were used for library preparation without cutting mononucleosome band.
Libraries were prepared from whole MNase digested DNA. DNA fragments longer than 500 bp were removed using ampure size selection. 50 ng of size-selected DNA was used for library preparation with NEBNext Ultra II DNA Library Prep Kit, according to the manufacturer’s protocol. For PCR amplification step, 3 or 4 cycles were performed. Quality control on final libraries was performed using DNA 1000 Bioanalyzer and fragment length of ~270-280 bp was consistently observed, corresponding to ~150-160 bp insert length.

treatment_protocol: No treatment.

tag: strain background


title: BMDMs, treated with supernatants from alive (No LeTox) Nlrp1bTg/Casp1/11KO cells, rep3

value: Primary Mouse bone marrow derived macrophages(BMDMs)


title: DD006H_middle_RNA

value: medium


title: BMDMs, treated with supernatants from alive (No LeTox) Nlrp1bTg/Casp1/11KO cells, rep1


title: BMDMs, treated with supernatants from alive (No LeTox) Nlrp1bTg/Casp1/11KO cells, rep2


title: NGFR_tumor

city: Philadelphia

first: Katherine

middle: Paige

last: Mueller

state: Pennsylvania

address: 3501 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

description: Filtered feature barcode matrices from 10X 3' scRNA-seq

library_source: transcriptomic single cell

data_processing:
FASTQ files were generated and aligned to the genome with Cellranger version 7.1.0, using a custom GRCh38 reference genome containing the Her2.BBζ CAR sequence.
Low quality cells with <300 or >7500 genes or >10% mitochondrial reads were removed using Seurat version 4.3.0 in R. Doublets were identified using DoubletFinder v2.0.3 and removed.
Filtered samples were normalized using SCTransform prior to integration. The integrated dataset was scaled, and uniform manifold approximation and projection (UMAP) dimensionality reduction was performed using the top 30 principal components. Unsupervised Louvain clustering was performed on a Shared Nearest Neighbor (SSN) graph at a final resolution of 0.6.
FindAllMarkers (Seurat) was used to identify differentially expressed (DE) genes in each cluster, and gene ontology (GO) analyses were performed for each cluster using ClusterProfiler version 4.6.2.
DE genes and GO processes were used to manually annotate each cluster, and contaminating CD3- tumor cells were removed. Differential gene analyses between samples were performed using FindMarkers (Seurat) using the Wilcoxon rank sum test with Bonferroni correction.
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

molecule: polyA RNA

source_name: tumor-infiltrating primary human CAR T cells

growth_protocol: Primary human T cells were grown in RPMI media supplemented with 10% FBS, 10mM HEPES, 1x Penicillin-Streptomycin-Glutamate, and 100U/mL recombinant human IL-2. T cells were activated with anti-CD3/CD28 beads immediately after thawing from liquid nitrogen. At 48 and 72 hours post-activation, cells were transduced with retroviruses containing CARs and transcription factors of interest. 96 hours post-activation, beads were removed; subsequently, T cells were resuspended at a concentration of 0.5e6 cells/mL every 2-3 days in the above described media. NGFR+ cells were isolated using the StemCell EasySep magnetic sorting system prior to infusion into 143B-bearing mice.

extract_protocol:
Polyadenylated RNA was captured using the 10X Chromium Next GEM Single Cell 3’ v. 3.1 kit (10X Genomics). Approximately 17,000 cells per sample were loaded onto the 10X chip for barcoding.
3’ libraries were generated using the 10X Genomics Next GEM Single Cell 3’ v. 3.1 kit according to the manufacturer’s instructions. Libraries were sequenced at the CHOP High Throughput Sequencing Core on an Illumina NovaSeq 6000 with an average read depth of 50,000 reads per cell.

treatment_protocol: Cells were treated the same, the only difference being which viruses they were transduced with (CAR/transcription factor). Tumor infiltrating CAR T cells (CAR TILs) were isolated from Her2+ 143B tumors on Day 29 after infusion into mice. Tumors were harvested from 5 mice per condition. Human CD45+ cells were isolated from tumors using StemCell EasySep magnetic selection, and CD3+ TILs were sorted from dissociated tumors using a Cytek Aurora Sorter. 20,000 cells were sorted from each tumor, for a total of 100,000 cells per condition distributed across five mice prior to cell barcoding.


title: Resting T cells, HD_#2

value: blood

value: male


title: FOXO1_tumor

value: tumor-infiltrating primary human CAR T cells


title: BMDMs, treated with supernatants from apoptotic (+ LeTox) Nlrp1bTg/Casp1/11KO cells, rep 2

value: cell culture

value: M0 Macrophages

value: 4 hrs with supernatants from apoptotic(+ LeTox) C57BL/6 Nlrp1bTg+/-/Casp1/11KO cells


title: DD006H_distal_RNA

value: Normal lung

value: small


title: Resting T cells, HD_#1

value: PSMD11 +/+ (wild-type)

value: Clinically healthy


title: TCPOBOP_8wk_Male_replicate3_LowCornOil [G186-M16]

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Liver nuclear RNA_polyA-selected, stranded library

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Custom GTF files previously used to count sequence reads mapping to 24,195 RefSeq genes and 15,558 liver-expressed lncRNA genes (Melia et al., 2019; PMID: 30840070) were combined into single GTF file, after removing 852 non-coding RefSeq genes that significantly matched one of the 15,558 lncRNA structures (combined total of 38,901 genes). The GTF file entry for each gene is comprised of the union of all exonic regions for all isoforms of each gene ('Exon Collapsed' counting).
Reads were mapped using TopHat (v2.0.13), and multi-mapped reads were removed from the BAM files, leaving only singly mapped reads, which were counted by featureCounts (1.4.6-p5) using the MultiOverlap funtion (-O).
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Assembly: mm9
Supplementary files format and content: Microsoft Excel file with differential expression data (fold-change, sample 1 intensity (FPKM), sample-2 intensity (FPKM), adjusted p-value) for 5 different pairwise comparisons: MaleLiver_2weekTCPO-LowCornOil vs. MaleLiver_2weekControl-LowCornOil; FemaleLiver_2weekTCPO-LowCornOil vs. FemaleLiver_2weekControl-LowCornOil; MaleLiver_8weekTCPO-HighCornOil vs. MaleLiver_8weekControl-HighCornOil; MaleLiver_8weekTCPO-LowCornOil vs. MaleLiver_Control-LowCornOil; and MaleLiver_8weekTCPO-HighCornOil vs. MaleLiver_8weekTCPO-LowCornOil.

source_name: liver

extract_protocol:
Frozen mouse liver (~250 mg) was placed on dry ice and minced into small pieces, which were transferred to 1 mL of Lysis buffer (100 mM Tris (pH 7.4), 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.1% NP40) in a Dounce homogenizer on wet ice. The tissue was dounced on ice (10 strokes with pestle A, then 10 strokes with pestle B) until the sample was fully homogenized. Nuclei wash buffer (1 ml of 100 mM Tris Cl (pH 7.4), 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.01% BSA, 80 U/ml Protector RNase inhibitor (Millipore Sigma #3335402001)) was added to the homogenizer, followed by gentle mixing. The sample was then passed through a 40 micron cell strainer (Sigma #Z742102-50EA) placed on top of a 50 mL centrifuge tube on ice. The homogenizer tube was rinsed with 1 ml of wash buffer, which was passed through the same 40 micron cell strainer and combined with the first strained homogenate. Each sample was kept on ice until samples from all livers were ready to proceed to the next step. Lysed cells were pelleted at 500 g for 5 min at 4°C in a swinging bucket rotor. The crude nuclei were resuspended in 1000 microliter of Staining Buffer (PBS, 2% BSA (Sigma #SRE0036-500ML), 80 U/ml Protector RNase Inhibitor). Samples were centrifuged at 500 g for 5 min at 4°C in a swinging bucket rotor. The pelleted nuclei were resuspended in 1000 microliter of Staining Buffer and passed through a 20 micron filter (PluriSelect #43-50020-50) then centrifuged at 500 g for 5 min at 4°C in a swinging bucket rotor. The purified nuclei were resuspended in 250 microliter nuclease-free water, followed by the immediate addition of 750 microliter of Trizol-LS, pipetting up and down thoroughly to mix, followed by RNA isolation using the manufacturer’s protocol (Life Technologies).
Illumina sequencing libraries were prepared by poly(A) selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat #E7490L) using 0.5 µg of input RNA, followed by cDNA synthesis and library preparation using the NEBNext Ultra Directional RNA Sequencing for Illumina kit (Cat #E7420L).

treatment_protocol: TCPOBOP (1,4-bis(2-(3,5-dichloropyridyloxy))benzene) (Santa Cruz Biotechnology; Chem Cruze, Cat. #SC-203291) was delivered to mice using one of two different regimens, termed Low Corn Oil regimen and High Corn Oil regimen, respectively. Low Corn Oil regimen: TCPOBOP was dissolved in DMSO at 7.5 mg/ml, and then diluted 10-fold into corn oil, followed by IP injection at 4 µl per g body weight (final dose: 3 mg TCPOBOP and 4 µl of 10% DMSO in corn oil, per kg body weight). Mice were euthanized 2 weeks later for the groups labeled '2wk'. For the Low Corn Oil groups labeled '8wk', mice were given additional injections of TCPOBOP at 1.5 mg/kg using the same vehicle. High Corn Oil Regimen: The TCPOBOP stock solution dissolved in DMSO at 7.5 mg/ml (as above) was diluted 50-fold in corn oil to give a working solution of 0.15 mg TCPOBOP/ml of 2% DMSO/98% corn oil. Mice were injected with 20 µl of this working TCPOBOP solution per g body weight on day 0 (TCPOBOP dose: 3 mg/kg), followed by additional weekly injections at one-third that dose (1 mg TCPOBOP/kg) beginning on day 7, by injecting of 20 µl of 0.05 mg TCPOBOP/ml of 0.67% DMSO/99.3% corn oil. This weekly dosing schedule was designed to minimize the bioaccumulation of TCPOBOP by taking into account its 14 day biological half-life in mice. For both regimens, TCPOBOP or Vehicle injections were performed in the morning, and mice were euthanized between 10:30 AM and 12 noon under CO2 followed by cervical dislocation (Boston University animal facility light cycle: 7:30 AM to 7:30 PM). Livers were excised and flash frozen in liquid nitrogen then stored at -80° C.

value: liver

tag: strain

tag: age at_euthanasia

value: 15-16 weeks

tag: Sex

value: Male

value: TCPOBOP (3 mg/kg, i.p.), 8 wk

tag: dosing regimen

value: Low Corn Oil


title: NTGP3

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

description: NOMe-seq data

data_processing:
Library strategy: NOMe-seq
Nucleosome occupancy and methylome sequencing (NOMe-seq) raw sequencing data were processed by removing the first nine bases random primer in reads, and discarding reads with adaptors and low-quality bases using trim_galore (version: 0.1.3) with parameters ‘--quality 20 --stringency 3 --length 50 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33’. Under a paired-end and non-directional aligned mode, clean reads were mapped against the mouse genome (UCSC mm10) using Bismark (version: 0.7.6) with parameters ‘--fastq --non_directional --unmapped --phred33-quals’1. Then, under a single-end aligned mode, unmapped reads were furtherly re-aligned against the same reference genome in order to gather more mapped reads from the raw data. PCR duplicated reads were then discarded using SAMtools (version: 0.1.18) with default parameters2, and the processed BAM format file was finally transformed to indicate the methylation level in each cytosine site as the number of methylated reads ‘C’ dividing the number of methylated and unmethylated reads (‘C+T’). DNA methylation analysis was performed with WCG (‘ACG’ and ‘TCG’ trinucleotides), and chromatin accessibility analysis was performed with GCH (‘GCA’, ‘GCT’ and ‘GCC’ trinucleotides).
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: In the BED format files, each column indicates 'chr, start, end, methylated C reads, unmethylated C reads'.

source_name: heart

extract_protocol:
The NOMe-seq protocol was modified based on previous studies. In brief, the myocardial cells  from Ddx7-TG and WT mice was lysed in lysis buffer (10 mM Tris·HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, and 0.5% NP-40) with PMSF and Protease Inhibitor Cocktail (Active Motif) for 60 min. The released nuclei were washed twice with ice-cold DPBS (Corning) and incubated in M.CviPI GpC Methyltransferase (NEB) for 2 h with unmodified lambda DNA (Thermo Fisher). Then the reactions were  stopped by EDTA and proteinase K at 55 °C overnight. Genomic DNAs were purified by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. Bisulfite conversion of genomic DNAs was operated using EZ-96 DNA Methylation-Direct™ MagPrep (Zymo Research). The first strand and the second strand were synthesized using random primers Oligo1 (5′-biotin- CTACACGACGCTCTTCCGATCTNNNNNNNNN-3′) and Oligo2 (5′-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3′), respectively.
The final NOMe-seq libraries were amplified with 12 cycles of PCR in KAPA HiFi Hot Start Ready Mix (KAPA Biosystems) and sequenced on the HiSeq 4000 platform (sequenced by Novogene).

value: heart

tag: background strain

tag: group

value: TG-plus (Ddx-17 TG)

tag: biology replication

value: Replication 3


title: TCPOBOP_8wk_Male_replicate2_LowCornOil [G186-M15]

tag: tissue


title: NTGP2

description: NOMe-seq data

value: male

value: Replication 2


title: RNA-seq-E7.5ExE-WT-2

first: Liping

last: Wang

address: 1239 Siping Road

institute: Tongji University

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC mm10) using Hisat2 (v2.1.0) with the parameters: --dta-cufflinks --no-unal(Kim et al., 2015).
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20(Li et al., 2009).
The retained reads were subsequently assembled into transcripts guided by the UCSC gtf annotation files using Stringtie (v1.3.4)(Pertea et al., 2015).
The expression level of each gene was quantified as FPKM (fragments per kilobase per million mapped reads).
Assembly: mm10
Supplementary files format and content: tab-delimited Excel files include log2(FPKM+1) values for each Sample.

source_name: extraembryonic ectoderm

extract_protocol:
Pre-implantation embryos were obtained by in vitro fertilization (IVF). MII-stage oocytes were collected from 7-week-old superovulated C57BL/6N female mice by intraperitoneally injecting with 6 IU of pregnant mare’s serum gonadotropin (PMSG) and 6 IU of human chorionic gonadotrophin (hCG) (San-Sheng Pharmaceutical). MII oocytes were then transferred into G-IVF PLUS medium (Vitrolife) and inseminated with activated spermatozoa obtained from the caudal epididymides of adult PWK/PhJ male mice. The zona pellucida of each MII oocyte was punched to make a small hole using a Piezo-drill micromanipulator, and the spermatozoa capacitation was attained by 20-30 minutes incubation in G-IVF PLUS medium. At 4 hours post-insemination (hpi), fertilized oocytes were transferred and cultured in G-1 PLUS medium (Vitrolife) at 37°C under 5% CO2. The morula and blastocyst stage IVF embryos were harvested at 78 and 96 hpi, respectively. To obtain post-implantation embryos, female mice at 6.5 days post-coitum (dpc) were executed and the uteri were dissected and transferred into Dulbecco's phosphate-buffered saline (DPBS). Next, each decidua was carefully freed from the uterine muscle layers using properly sharpened forceps. 6.5 dpc embryos were carefully separated from deciduas. Reichart's membrane and the ectoplacental cone were also removed from the embryos.
Embryos with zona pellucida and polar bodies removed were disrupted in TRIzol Reagent (Invitrogen) and total RNAs were isolated by chloroform extraction, coupled with isopropanol precipitation with 1/10 volume of 3M NaAc and 1 μL glycogen added to the aqueous phase of each sample. RNAs were washed twice with 75% ethanol before they were eluted with nuclease-free water. Purified RNAs were then subjected to library generation using SMARTer Stranded Total RNA-Seq Kit (Takara) following the manufacturer’s instructions. Briefly, random primers were used for reverse transcription, and the amplified cDNA was then subjected to ribosomal RNA depletion. Prepared RNA-seq libraries were sequenced on the Illumina NovaSeq 6000 platform with paired ends and 150-bp read lengths at Novogene Co., Ltd.

treatment_protocol: The Cas9 mRNA and sgRNAs were produced as previously reported (Zhang et al., 2020). Cas9 mRNA was in vitro transcribed using mMESSAGE mMACHINE T7 ultra transcription kit. The integrity of manufactured mRNA was confirmed by electrophoresis. Meanwhile, sgRNAs which targeted mouse Suv39h2 or Prdm2 were in vitro transcribed using MEGA shortscript T7 kit. Both Cas9 mRNA and specific sgRNA were purified according to the standard protocol by phenol:chloroform extraction and ethanol precipitation, and then dissolved in nuclease-free water (Thermo). For microinjection, the Cas9 mRNA was diluted to 100ng/μL and each sgRNA mix was diluted to a final concentration of 50ng/μL. Zygotes were injected with approximately 10pL of Cas9 mRNA and sgRNAs using a Piezo-driven micromanipulator. Embryos were then transferred into the oviduct of E2.5 pseudo-pregnant female ICR mice. Cesarean section was carried out at day E6.5 or E7.5, and the separated extraembryonic ectoderm were harvested for total-RNA seq. The genome targeting efficiency has been verified by PCR and Sanger sequencing. Primers for sgRNA are listed in supplementary table S1.

value: extraembryonic ectoderm

tag: developmental stage

value: wild type


title: UNG CTRL

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

description:
Read1 contains cell barcode and UMI, Read2 covers the gene sequences
preprocessed_data.txt
processed_data_CER.txt
metadata_CER.csv

data_processing:
Reads containing gene sequences were trimmed to uniform length 50 bp by TrimmomaticSE (0.36). Quality control was performed using FastQ Screen (0.11.1). STARsolo (STAR 2.7.9a) was used for alignment to reference genome.
EmptyDrops (DropletUtils R package 1.16.0) with a threshold of 1000 UMIs and FDR <= 0.01 was used to filter out empty droplets.
R language (4.2.2) and Seurat package (4.3.0) were used for downstream analysis. Samples were SCTransformed and integrated, excluding mitochondrial genes prefixed by MT-. Doublets were identified and filtered out using DoubletFinder (2.0.3). Cells with percentage of mitochondrial reads > 15 % were filtered out.
Unguided and cortical samples were further analyzed separately using Seurat. The unguided samples were normalized, scaled, SCTransformed, and clustered. Analysis of cortical samples included one extra integration step due to great difference of the control and AxD samples. Clusters in both datasets were annotated based on expression of marker genes.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: preprocessed_data.txt contains count matrix generated after initial integration step. Only EmptyDrops filtering was applied. These data are not normalized and were extracted from the RNA assay, counts slot of the Seurat object. Genes in rows, individual cells named by specific barcode and sample name in columns. Comma separated. All samples are included in one file.
Supplementary files format and content: processed_data.txt files contain normalized data from the RNA assay, data slot of the Seurat object. Unguided and cortical samples were analyzed separately, therefore, we provide two separate preprocessed_data files. This is the dataset after filtering and QC. Genes in rows, individual cells named by specific barcode and sample name in columns. Comma separated.
Supplementary files format and content: metadata.csv was extracted from the Seurat objects and contain additional information about individual cells including the transcript numbers, cluster and sample classification, or cell cycle phase score. Cell identificators are in rows, names of variables are in columns. Unguided (metadata_CER.csv) and cortical (metadata_Ctx.csv) metadata are provided in separate files.

source_name: corrected AxD (GFAP (R239C)

growth_protocol: Briefly, the culture of unguided organoids was started from single-cell suspensions of iPSCs (approx. 9000 cells/well) loaded into 96-well plates. At day 6 of cultivation, the medium was changed to neural induction medium. At day 13, the organoids were embedded in Matrigel and were further grown in culture dishes. At day 17, the organoids were transferred to orbital shaker. The medium was regularly changed and its components differed according to respective phases of cultivation. This protocol was inspired by Ormel et al. 2018 and Lancaster et al. 2013. The cortical organoids were cultivated according to the protocol of Yoon et al. 2019. In this case, the cells (approx. 3.5 x 106) were seeded into AggrewellTM800 plates. The embryoid bodies were tranferred to 96-well plates at day 2. From day 2 to day 6, the medium contained two SMAD inhibitors to allow for cortical specification.

extract_protocol:
Single-cell suspension was prepared from organoids using combination of mechanical and enzymatic dissociation. The organoids were chopped to small pieces, treated with papain, and repeatedly resuspended by pipetting and subsequently incubated on an orbital shaker. The single-cell suspension was then fixed using 10x Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling, 10x Genomics protocol and kit, and the sequencing libraries were prepared using Chromium Fixed RNA Kit.
Chromium Fixed RNA Kit (10x Genomics, Pleasanton, CA)

value: unguided neural organoids

tag: age

value: 165 days

tag: cell line

value: corrected AxD (GFAP (R239C)

tag: genotype

value: GFAP corrected


title: RNA-seq-E7.5ExE-WT-1


title: CTX AxD

description:
Read1 contains cell barcode and UMI, Read2 covers the gene sequences
preprocessed_data.txt
processed_data_Ctx.txt
metadata_Ctx.csv

source_name: AxD (GFAP (R239C)

tag: sample type

value: cortical organoids

value: AxD (GFAP (R239C)


title: NTGP1

description: NOMe-seq data

value: Replication 1


title: TCPOBOP_8wk_Male_replicate1_LowCornOil [G186-M14]

value: liver

value: 15-16 weeks

value: Male

tag: treatment


title: RNA-seq-E7.5ExE-KO-3

value: Suv39h2 and Prdm2 double KO


title: NTGM3

description: NOMe-seq data

value: heart

value: WT

value: TG-minus (con)


title: Primary human macrophages, siControl, rep1

tag: individual

tag: cell type

value: primary macrophages

value: control siRNA

value: control


title: CTX CTRL


title: RNA-seq-E7.5ExE-KO-2

value: extraembryonic ectoderm


title: TCPOBOP_8wk_Male_replicate4_LowCornOil [G186-M17]

value: TCPOBOP (3 mg/kg, i.p.), 8 wk

value: Low Corn Oil


title: Vehicle_Male_replicate3_LowCornOil [G186-M3]

value: Vehicle control, 4-8 wk


title: NTGM2

description: NOMe-seq data

value: male

value: Replication 2


title: RNA-seq-E7.5ExE-WT-3

value: wild type


title: 90Sr 5 Gy×4, replicate 1, scRNAseq

city: Chengdu

first: Xiaoqian

last: Li

address: No.17 People's South Road

institute: Sichuan University

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Seurat v 3.1.2 was used for quality control, dimensionality reduction and clustering.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: keloid

extract_protocol:
Single-cell suspensions at 1 × 105 cells/mL in concentration in PBS were prepared and loaded onto microfluidic devices.
Libraries were constructed according to Singleron GEXSCOPE protocol by GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies), which included cell lysis, mRNA trapping, labeling cells (barcode) and mRNA (UMI), reverse transcription mRNA into cDNA and amplification, and finally fragment cDNA.

value: keloid

value: primary

value: fibroblast


title: Vehicle_Male_replicate2_LowCornOil [G186-M2]

value: liver

value: 11-12 weeks

value: Male


title: NTGM1

description: NOMe-seq data

value: heart

value: WT

value: TG-minus (con)

value: Replication 1


title: RNA-seq-E6.5ExE-WT-3

value: extraembryonic ectoderm


title: 90Sr 5 Gy×2, replicate 1, scRNAseq


title: Vehicle_Male_replicate1_LowCornOil [G186-M1]


title: Electron beam 5 Gy×4, replicate 1, scRNAseq


title: UNG AxD

value: unguided neural organoids

value: 165 days

value: AxD (GFAP (R239C)


title: TCPOBOP_8wk_Male_replicate3_HighCornOil [G184-M20]

value: 15-16 weeks

value: TCPOBOP (3 mg/kg, i.p.), 8 wk

value: High Corn Oil


title: Pss9644, control, KB, rep 2

city: Birmingham

first: Andrea

last: Vadillo Dieguez

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

description:
ribosomal depletion
RNA_14

data_processing:
The quality of the raw sequencing data was checked with FastQC version 0.11.9
Read adapters were trimmed using fastq-mcf version 1.04.807
Transcripts were aligned and counted and normalised using Salmon version 1.9.0
Assembly: GCF_023277945.1
Supplementary files format and content: Matrix table with raw transcript counts for every transcript and every sample
Supplementary files format and content: Matrix table with normalized transcript counts for every transcript and every sample

organism: Pseudomonas syringae pv. syringae

growth_protocol: King 's B media and Hrp inducing miminum media growth protocols performed according to  Moreno-Lopez et al. 2021 (https://doi.org/10.3390/microorganisms9071447)

extract_protocol:
Total RNA extraction protocol performed according to Moreno-Lopez et al. 2021 (https://doi.org/10.3390/microorganisms9071447)
RNA was converted atNovogeneinto sequencing-ready libraries for Illumina sequencing using Illumina Ribo-Zero Plus rRNA Depletion Kit andNovogeneNGS Stranded RNA Library Prep Set (PT044)*. cDNA libraries were subjected to RNASeq, using an Illumina Novaseq 6000 system with 150-bp pair-end reads.
Prokaryotic directional mRNA preparation (rRNA removal)

value: Kings B broth (KB)

tag: time

value: 5h post inoculation


title: Pss9644, control, KB, rep 3

description:
ribosomal depletion
RNA_9_2607

treatment_protocol: King 's B media and Hrp inducing miminum media growth protocols performed according to  Moreno-Lopez et al. 2021 (https://doi.org/10.3390/microorganisms9071447)

tag: strain


title: RNA-seq-E6.5ExE-WT-1

value: wild type


title: X-rays 5 Gy×4, replicate 1, scRNAseq

value: keloid

value: primary

value: fibroblast


title: Vehicle_Male_replicate4_LowCornOil [G186-M4]

value: liver

tag: age at_euthanasia

value: Male

value: Vehicle control, 4-8 wk

value: Low Corn Oil


title: Control, replicate 1, scRNAseq


title: Pss9644, control, KB, rep 1

description:
ribosomal depletion
RNA_18

value: WT


title: RNA-seq-E6.5ExE-KO-3

value: extraembryonic ectoderm

value: Suv39h2 and Prdm2 double KO


title: OGD astroAxD/neuroAxD

description: Read1 contains cell barcode and UMI, Read2 covers the gene sequences

data_processing:
Quality control of the sequencing data was performed using FastQ Screen (0.11.1). STARsolo (STAR 2.7.9a) was used for alignment to reference genome.
EmptyDrops (DropletUtils 1.16.0) with threshold of 2000 UMIs and FDR <= 0.01 was used to filter out empty droplets.
R programming language (4.1.1) and Seurat package (4.1.0) were used for the downstream analysis. Data were SCTransformed, integrated (excluding mitochondrial and ribosomal genes), and series of quality control and filtering steps were applied, including filtering for nFeature_RNA > 1500 and nCount_RNA > 2500, identification of doublets (DoubletFinder 2.0.3), and removal of MT- (mitochondrial genes) and MALAT1-high clusters.
SoupX package (1.5.2) was used to identify contaminating transcripts and correct expression values according to the estimated contamination fraction.
Following Seurat analysis pipeline, three cell groups (astrocytes, neurons, and less differentiated precursors) were identified in normalized, scaled, SCTransformed, and clustered dataset. These groups were then analyzed separately along with additional filtering steps, to keep only the high-quality data. Finally, they were merged again together into one Seurat object.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: preprocessed_data.txt contains count matrix generated after initial integration step. Only EmptyDrops filtering was applied. These data are not normalized and were extracted from RNA assay, counts slot of the Seurat object. Genes in rows, individual cells named by specific barcode and sample name in columns. Comma separated.
Supplementary files format and content: processed_data.txt file contains normalized data from RNA assay, data slot of the Seurat object. This is the dataset after multiple rounds of filtering, QC, and merging of individually analyzed cell populations (iA, iN, precursors). Genes in rows, individual cells named by specific barcode and sample name in columns. Comma separated.
Supplementary files format and content: metadata.csv was extracted from the Seurat object with processed data and contains additional information about individual cells including the total transcript numbers, cluster and sample classification, or cell cycle phase score. Cell identificators are in rows, names of variables are in columns.

source_name: AxD (GFAP(R239C))

growth_protocol: iPSCs were dissociated with accutase and plated on Matrigel-coated 6-well plates with mTeSR medium with ROCK inhibitor. Astrocyte differentiation was induced with Sox9 and Nfib carried by lentiviral vectors. Neurons were induced similarly using Ngn2. For co-culture, accutase-dissociated cultures of astrocytes and neurons were plated together: 3.9×104 iAs + 1.11×105 iNs and were maintained for 42 days before experiments.

extract_protocol:
Cells were dissociated by accutase with actinomycin D, resuspended with wide-bore pipette tips, and strained before centrifugation. The suspension was centrifuged and resuspended two times. Concentrations were normalized to target concentration, samples were strained and counted. Volumes of samples were adjusted to target concentration of 700-1200 cells/µL and target cell count of 10000 cells per sample.
Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, Pleasanton, CA)

treatment_protocol: For OGD (oxygen-glucose deprivation) challenge, the co-cultures were cultured in deoxygenated ischemic media, in 1 % O2, which was followed by a recovery period of 16 h in fresh media.

value: AxD (GFAP(R239C))

value: neurons and astrocytes derived from iPSCs

value: GFAP(R239C) neurons + GFAP(R239C) astrocytes

value: oxygen-glucose deprivation challenge


title: RNA-seq-E6.5ExE-KO-2


title: Vehicle_8wk_Male_replicate3_HighCornOil [G184-M17]

value: 15-16 weeks

tag: Sex

value: Vehicle control, 8 wk

value: High Corn Oil


title: TCPOBOP_8wk_Male_replicate1_HighCornOil [G184-M18]

value: TCPOBOP (3 mg/kg, i.p.), 8 wk

tag: dosing regimen


title: Pss9644, experimental, HMM, rep 3

description:
ribosomal depletion
RNA_19

value: hrp inducing minimum media (HMM)

value: 5h post inoculation


title: Pss9644, experimental, HMM, rep 2

description:
ribosomal depletion
RNA_16


title: OGD astroAxD/neuroC

source_name: AxD (GFAP(R239C)) + corrected AxD (GFAP(R239C))

value: corrected neurons + GFAP(R239C) astrocytes


title: Vehicle_8wk_Male_replicate2_HighCornOil [G184-M16]

value: liver

value: Male


title: RNA-seq-E7.5ExE-KO-1


title: RNA-seq-E6.5ExE-KO-1


title: Pss9644, experimental, HMM, rep 1

description:
ribosomal depletion
RNA_1


title: RNA-seq-E6.5ExE-WT-2

value: wild type


title: cir1 in Yeast Nitrogen Base rep3

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
illumina hiseq was used for basecalling
Sequenced reads were trimmed for adapter content using BBDuk and parameters ktrim=r k=23 mink=11
Trimmed sequences were then aligned (and genes counted) to the cryptococcus neoformans genome CNA3 via STAR version 2.7.6a with parameters   --runMode alignReads --twopassMode Basic --quantMode GeneCounts --outSAMtype BAM Unsorted --outSAMunmapped Within
Counts were normalized during differential expression analysis via DESeq2’s median of ratios from Anders, S., & Huber, W. (2010).
Assembly: CNA3
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with normalized expression (DESeq2) information for each gene and every sample

organism: Cryptococcus neoformans H99

source_name: fungal cell

growth_protocol: All strains were grown for 16 hours in YPD rich media at 30 degrees prior to a 6 hour treatment in YPD or YNB.

extract_protocol:
Cells were flash frozen with liquid nitrogen and RNA was extracted using the Qiagen Rneasy protocol for yeast (mechanical disruption) followed by treatment with Dnase I (TURBO DNA-free™ Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment was carried out over 6 hours in YPD with and without L-DOPA or in YNB with and without antimycin A. the cir1 knockout strain was only treated in YNB without antimycin A

value: fungal cell

value: cir1 knockout

value: 6 hours YNB


title: TCPOBOP_2wk_Female_replicate4_LowCornOil [G185-M14]

value: 9-10 weeks

value: Female

value: TCPOBOP (3 mg/kg, i.p.), 2 wk

value: Low Corn Oil


title: Vehicle_8wk_Male_replicate1_HighCornOil[G184-M15]

value: 15-16 weeks


title: CTRL astroAxD/neuroAxD

value: AxD (GFAP(R239C))

value: neurons and astrocytes derived from iPSCs

value: GFAP(R239C) neurons + GFAP(R239C) astrocytes

value: control


title: MD

city: Beijing

first: Honglei

last: Dang

address: 18 Life Science Parkway, Changping District

institute: National Engineering Research Center for Beijing Biochip Technology

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.8.2
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens(GRCh38) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the human genome were imported into StringTie(v1.3.3b) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq2(v1.28.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Genome_build: Homo sapiens
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample

source_name: LPS+MD treated

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions，Illumina TruSeq RNA Sample 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: Mouse monocyte macrophages

value: experimental group

value: LPS with MD for 24h


title: TCPOBOP_2wk_Female_replicate3_LowCornOil [G184-M13]

value: liver


title: DCE

source_name: LPS+DCE treated

value: LPS with DCE  for 24 h


title: cir1 in Yeast Nitrogen Base rep1

value: fungal cell


title: TCPOBOP_8wk_Male_replicate2_HighCornOil [G184-M19]

value: Male

value: TCPOBOP (3 mg/kg, i.p.), 8 wk

value: High Corn Oil


title: TCPOBOP_2wk_Female_replicate2_LowCornOil [G184-M12]

value: 9-10 weeks

value: Female


title: CTRL astroC/neuroC

source_name: corrected AxD (GFAP(R239C))

value: corrected AxD (GFAP(R239C))

value: corrected neurons + corrected astrocytes


title: WT with 0.5ug/ml Antimycin A in Yeast Nitrogen Base rep3

value: wildtype

value: 6 hours YNB with 0.5ug/ml antimycin A


title: YN3

source_name: LPS+YN3 treated

value: LPS with YN3  for 24 h


title: WT with 0.5ug/ml Antimycin A in Yeast Nitrogen Base rep2


title: 3 layer spheroid channel 2 [3-2-SBO_S5_L002]

city: Crawley

first: Jessica

last: King

state: WA

address: 35 Stirling Hwy

department: School of Molecular Sciences

country: Australia

institute: University of Western Australia

description:
3-2-SBO_S5_L002
Channel 3
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C3_barcodes.tsv.gz
C3_features.tsv.gz
C3_matrix.mtx.gz

data_processing:
Fastq files were generated with Illumina bcl2fastq v2.20.0.422, allowing 1 mismatch in each index.
Transcript alignment and generation of gene count and feature barcode matrices were performed using 10x Genomics Cell Ranger count v6.0.2. Output from four channels was combined either with Cell Ranger aggr (for data QC and initial exploration), or Seurat v4.1.0 in R for all further downstream analysis.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: 3 layer spheroid channel 2

extract_protocol:
Spheroids were dissociated with TryplE and resuspended in 0.04% w/v BSA. Cells from each sample were pooled together in equal numbers at a final concentration of 2,000 cells/μL.
Cells were loaded onto a 10x Genomics Chromium Controller, Chip K (PN  1000286) and libraries were prepared using the Chromium Next GEM single cell 5’ kit v2  (PN1000263/1000265). Libraries from SBOs were prepared using the 5’ Feature Barcode kit (PN 1000256) following  manufacturer guidelines. Illumina iSeq 100 platform was used for initial QC of the libraries and deeper sequencing was conducted on Illumina NovaSeq 6000 in the vendor recommended format to reach up to 50,000 reads per cell.

treatment_protocol: 10 samples were labelled with unique short barcoded oligonucleotides (SBOs) for multiplexing.

value: HeLa

value: Epithelial

tag: antibodies/tags

value: DNA barcoded oligonucleotides (SBOs)


title: Vehicle_2wk_Female_replicate3_LowCornOil [G184-M11]

value: Vehicle control, 2 wk

value: Low Corn Oil


title: 3 layer spheroid channel 2 [3-2-SBO_S5_L001]

description:
3-2-SBO_S5_L001
Channel 3
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C3_barcodes.tsv.gz
C3_features.tsv.gz
C3_matrix.mtx.gz


title: YN2

source_name: LPS+YN2 treated

value: Mouse monocyte macrophages

value: experimental group

value: LPS with YN2  for 24 h


title: OGD astroC/neuroC

value: neurons and astrocytes derived from iPSCs

value: oxygen-glucose deprivation challenge


title: YN1

source_name: LPS+YN1 treated

value: LPS with YN1 for 24 h


title: 3 layer spheroid channel 2 [3-2-GEX_S2_L002]

description:
3-2-GEX_S2_L002
Channel 3
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C3_barcodes.tsv.gz
C3_features.tsv.gz
C3_matrix.mtx.gz

tag: library type

value: mRNA


title: Vehicle_2wk_Female_replicate2_LowCornOil [G184-M9]

value: liver

value: 9-10 weeks

value: Female


title: WT with 0.5ug/ml Antimycin A in Yeast Nitrogen Base rep1

value: fungal cell

value: wildtype

value: 6 hours YNB with 0.5ug/ml antimycin A


title: WT in Yeast Nitrogen Base rep3

value: 6 hours YNB


title: CTRL astroAxD/neuroC

value: AxD (GFAP(R239C)) + corrected AxD (GFAP(R239C))

value: corrected neurons + GFAP(R239C) astrocytes

value: control


title: DMSO

source_name: DMSO treated

value: Mouse monocyte macrophages

value: control group

value: DMSO for 24 h


title: Vehicle_2wk_Female_replicate1_LowCornOil [G184-M8]

source_name: liver

value: Vehicle control, 2 wk

value: Low Corn Oil


title: LPS

source_name: LPS treated

value: model group

value: LPS for 24 h


title: WT in Yeast Nitrogen Base rep2


title: 3 layer spheroid channel 1 [3-1-SBO_S4_L002]

description:
3-1-SBO_S4_L002
Channel 2
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C2_barcodes.tsv.gz
C2_features.tsv.gz
C2_matrix.mtx.gz

source_name: 3 layer spheroid channel 1

value: HeLa

value: Epithelial

value: DNA barcoded oligonucleotides (SBOs)


title: 3 layer spheroid channel 2 [3-2-GEX_S2_L001]

description:
3-2-GEX_S2_L001
Channel 3
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C3_barcodes.tsv.gz
C3_features.tsv.gz
C3_matrix.mtx.gz

value: mRNA


title: 3 layer spheroid channel 1 [3-1-GEX_S1_L002]

description:
3-1-GEX_S1_L002
Channel 2
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C2_barcodes.tsv.gz
C2_features.tsv.gz
C2_matrix.mtx.gz


title: TCPOBOP_2wk_Male_replicate4_LowCornOil [G184-M7]

value: liver

value: 9-10 weeks

value: Male

value: TCPOBOP (3 mg/kg, i.p.), 2 wk


title: TCPOBOP_2wk_Male_replicate3_LowCornOil [G184-M6]


title: WT in Yeast Nitrogen Base rep1

value: fungal cell

value: wildtype

value: 6 hours YNB


title: TCPOBOP_2wk_Female_replicate1_LowCornOil [G184-M10]

value: Female


title: PS

source_name: LPS+PS treated

value: Mouse monocyte macrophages

value: experimental group

value: LPS with PS for 24h


title: TCPOBOP_2wk_Male_replicate2_LowCornOil [G184-M5]

value: Low Corn Oil


title: 3 layer spheroid channel 1 [3-1-SBO_S4_L001]

description:
3-1-SBO_S4_L001
Channel 2
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C2_barcodes.tsv.gz
C2_features.tsv.gz
C2_matrix.mtx.gz


title: WT in melanin induction medium without 0.7 mM L-DOPA rep2


title: 3 layer spheroid channel 1 [3-1-GEX_S1_L001]

description:
3-1-GEX_S1_L001
Channel 2
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C2_barcodes.tsv.gz
C2_features.tsv.gz
C2_matrix.mtx.gz


title: EVs from SEA treated LE/6, biological rep3

city: Wu Han

first: YUE

last: YUAN

institute: tongji medical college

description: Gene expresssion data in EVs from SEA treated LE/6

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: EVs from SEA treated LE/6 for 24hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Hepatic progenitor cell line, LE/6, were cultured in DMEM with Ham’s F-10 (1:1) supplemented with 1 μg/ml insulin and 0.5 μg/ml hydrocortisone.

extract_protocol: Cell culture medium was harvested every 24 hours from unstimulated or SEA-stimulated HPCs and stored at -80℃ until isolation of EVs. HPC-conditioned medium (CM) and serum were centrifuged for 10 minutes at 300g, 10minutes at 2000g and 30 minutes at 10000g at 4℃ to remove cell debris and aggregates. Supernatant was transferred into new tubes and ultracentrifuged at 120000g for 2.5 hours by Beckman. EVs were resuspended in PBS in equal volumes for miRNA array. Trizol extraction of total miRNA was performed according to the manufacturer's protocols.

treatment_protocol: LE/6 was treated with SEA (20ug/mL) or PBS for 24hours.

tag: agent

value: SEA


title: TCPOBOP_2wk_Male_replicate1_LowCornOil [G184-M4]

tag: tissue


title: WT in melanin induction medium without 0.7 mM L-DOPA rep1


title: 2 layer spheroid [1-SBO_S6_L002]

description:
1-SBO_S6_L002
Channel 1
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C1_barcodes.tsv.gz
C1_features.tsv.gz
C1_matrix.mtx.gz

source_name: 2 layer spheroid

value: HeLa


title: Vehicle_2wk_Male_replicate3_LowCornOil [G184-M3]

value: Vehicle control, 2 wk


title: 2 layer spheroid [1-GEX_S3_L002]

description:
1-GEX_S3_L002
Channel 1
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C1_barcodes.tsv.gz
C1_features.tsv.gz
C1_matrix.mtx.gz

value: Epithelial


title: WT in melanin induction medium with 0.7 mM L-DOPA rep3


title: Vehicle_2wk_Male_replicate2_LowCornOil [G184-M2]


title: cir1 in Yeast Nitrogen Base rep2

value: cir1 knockout


title: EVs from SEA treated LE/6, biological rep2


title: 2 layer spheroid [1-SBO_S6_L001]

description:
1-SBO_S6_L001
Channel 1
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C1_barcodes.tsv.gz
C1_features.tsv.gz
C1_matrix.mtx.gz

value: DNA barcoded oligonucleotides (SBOs)


title: WT in melanin induction medium with 0.7 mM L-DOPA rep2


title: IMPRINT1_S433

city: Wuerzburg

first: Chase

last: Beisel

address: Josef-Schneider-Str. 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

library_source: other

data_processing:
Paired-end reads were merged using BBMerge (version 38.69) with parameters “qtrim2=t, ecco, trimq=20, -Xmx1g”
Sequences with perfect matches of flanking sequences were extracted as potential RBS regions using a Python script
After filtering by 10 count per million in minimal 2 samples, differential abundance (log2FC) of potential RBS region sequences between time points was calculated using the quasi-likelihood F test after fitting in a generalized linear model.
Supplementary files format and content: TSV, counts of each RBS sequence in different samples
Supplementary files format and content: CSV, normalized differential abundance of each RBS sequence in different samples
Library strategy: DNA-seq

molecule: other

organism: Escherichia coli

source_name: bacteria

growth_protocol: Escherichia coli was grown in LB media supplemented with 100 µg/mL ampicillin; Bifidobacterium breve was grown on reinforced clostridial agar with 20 ug/mL tetracycline or in MRS liquid broth (BD CN# 288130) supplemented with 0.03% L-cysteine and 20 ug/mL tetracycline.

extract_protocol:
Zyppy Plasmid Miniprep Kit
A plasmid library containing a stretch of nine randomized nucleotides was used. For NGS library preparation, adapters and unique dual indices based on Illumina TruSeq were added in a two-step amplification process using the KAPA HiFi HotStart Library Amplification Kit (KAPA Biosystems, KK2611), according to manufacturer's protocols. The samples were purified with Agencourt AMPure XP (Beckman Coulter, A63881).

treatment_protocol: Bifidobacterium breve was resuspend in 250uL of 30mg/mL lysozyme and incubate at 37°C for 30 minutes at 250 rpm, then removed lysozyme mix to harvest cells.

value: bacteria

value: Amplified in liquid culture

tag: biological replicate


title: WT in melanin induction medium without 0.7 mM L-DOPA rep3


title: WT in melanin induction medium with 0.7 mM L-DOPA rep1


title: CN_Arg3

status: Public on Apr 06 2024

city: Klong-luang

first: Pornpimon

last: Angkasekwinai

state: Patumthani

country: Thailand

institute: Thammasat University

data_processing:
All high-quality paired-end reads were aligned to the Mus musculus reference genome GRCm39 using Hisat2 (v 2.0.5).
NCBI BLAST v2.2.28 was used to annotate the reads based on known mouse genes with the expected value (e-value) of 1.0 x 10-10.
To estimate the abundance of the gene expression, the read numbers mapped of each gene from each transcript were counted and then normalized by fragment per kilobases per million mapped reads (FPKM) approach using HTSeq v0.6.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Lung

extract_protocol:
Lung of PBS-treated or C. neoformans-infected mice received PBS or nor-NOHA were extracted for total RNA by using TRIzolTM and Qiagen RNeasy® Plus Mini kit. 600 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA library prep kit for Illumina® following the manufacturer's protocols.

treatment_protocol: BALB/c mice were anesthetized and treated with PBS or C. neoformans H99 cell suspension at 5 × 104 cells/mouse by the intranasal route. The activity of the arginase enzyme was inhibited before and after infection by intraperitoneal injection of arginase inhibitor, nor-NOHA (N-hydroxy-nor-L-arginine) daily at 17 mg/kg /day (300 µg/100 µl PBS/mouse). At 14 days postinfection, mice were euthanized by inhalation of CO2, and lungs were aseptically collected. Total RNA was isolated and subjected to RNA sequencing analysis.

tag: background strain

value: BALB/c

value: Lung

tag: treatment time

value: 14 days


title: CN_Arg2


title: CN_Arg1


title: CN3


title: EVs from PBS treated LE/6, biological rep1

description: Gene expresssion data in EVs from PBS treated LE/6

source_name: EVs from PBS treated LE/6 for 24hours

tag: cell line

value: PBS


title: EVs from PBS treated LE/6, biological rep2


title: EVs from PBS treated LE/6, biological rep3


title: EVs from SEA treated LE/6, biological rep1


title: CN2


title: PBS3


title: CN1


title: PBS2


title: PBS1


title: gWAT, HFDSG1

city: Bunkyo-ku

first: Goro

last: Katsuumi

state: Tokyo

address: Hongo 2-1-1

country: Japan

institute: Juntendo University

data_processing:
Acquired read data was processed and analyzed by nf-core/rnaseq pipeline (version 3.12.0) as default setting on nextflow software (version 23.10.0). Z-score was calculated from transcript per million (tpm) data and its heatmap was generated in RStudio (version 2023.12.0+369) and R (version 4.3.2).
Assembly: GRCm38/mm10
Supplementary files format and content: salmon.merged.gene_tpm.xlsx

source_name: gWAT

growth_protocol: C57B6/N mice fed high-fat-diet32(Crea, Japan) for 2 months

extract_protocol:
Total RNA was extracted from mouse gWAT by using Maxwell® RSC 48 Instrument(Promega) and Maxwell® RSC simplyRNA Tissue Kit (Promega, AS1340) in accordance with manufacturer’s instruction.
The complemenary DNA libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina). The quality of total RNA and cDNA were assessed using the Agilent 2100 Bioanalyzer with the RNA6000 nano Kit and the DNA7500 kit (Agilent Technologies).
Sequencing was performed using the NovaSeq6000 system (Illumina) with a pair-end-read sequencing length of 150bp.

treatment_protocol: Canagliflozin was administerd by mixing food at 0.03% w/w for 7 days.

value: gWAT

tag: diet

value: high-fat-diet

value: 7-days canagliflozin(0.03% w/w mixed in food)


title: gWAT, HFDSG2

tag: treatment


title: Vehicle_2wk_Male_replicate1_LowCornOil [G184-M1]

description: Liver nuclear RNA_polyA-selected, stranded library

value: liver

value: 9-10 weeks

value: Male


title: Liver, BPS, Male-3

city: Fuyang

first: Qi

state: Anhui

address: 100 Qinghe West Road

institute: Fuyang Normal University

data_processing:
Paired-end 150-bp sequencing was performed on an Illumina Novaseq6000 system by OE Biotech Co., Ltd. (Shanghai, China).
Firstly, adaptor only reads and low-quality reads were filtered out using FASTQ preprocessor to obtain clean reads of all transcriptomes from the raw data for subsequent analysis.The clean reads were mapped to the reference genome using HISAT2.
Then, Fragments Per Kilobase Million (FPKM) of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.Principal component analysis (PCA) were performed using R (v 3.2.0) to evaluate the biological duplication of samples.q-value < 0.05 and foldchange (FC) > 2 or < 0.5 was set as the threshold for significantly DEGs. The expression patterns of genes in different groups and samples were demonstrated by performing a hierarchical cluster analysis of DEGs using R (v 3.2.0). In addition, based on the hypergeometric distribution, Wiki Pathways enrichment analysis of DEGs was performed to screen the significant enriched term using R (v 3.2.0). Identification of differentially expressed genes (DEGs) were conducted using DEseq2.
Gene Set Enrichment Analysis (GSEA) was used to investigate the pathways enriched in the cholesterol metabolism-associated DEGs that were annotated with known biological pathways curated from the Kyoto Encyclopedia of Genes and Genomes (KEGG).
The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Fisher’s exact test was applied to evaluate the significance of overlapping genes and pathways between DEG sets, and tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Supplementary files format and content: FPKMs and counts for allsamples

source_name: Liver

growth_protocol: Animals were housed in polypropylene cages under a constant cycle of 12 hours light alternated with dark at 22-24 °C with free access to standard water and pellet diet based on AIN 93.

extract_protocol:
Liver samples were obtained from offspring randomly selected from litters of different dams (n = 3/group/sex). Total RNA was isolated from each liver of offspring using the MiRneasy MiNi Kit (QIAGEN, Cat No. 74104) purchased from Qiagen Co. Ltd. (Hilden, Germany) in accordance with a protocol provided by the manufacturer.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Since 2,4-BPS, BPSIP, BPS and E2 are extremely insoluble in water, anhydrous ethanol was used as a solvent to dissolve each of these synthetic chemicals to prepare the corresponding mother liquor. First, 10 mg of a chemical was dissolved in 10 mL of anhydrous ethanol to prepare the mother liquor with the concentration of 1 mg/mL. And then, 1 mL of the mother liquor was added to 999 mL of ddH2O to make a stock solution at 1 μg/mL concentration of the chemical and 0.1% ethanol. In the end, drinking water for mice was obtained by further dilution of the stock solution. The drinking water at a chemical concentration of 10 ng/mL and 0.001% of ethanol was obtained by adding 2 mL of the stock solution to 198 mL of drinking water. The control group also received a treat with the same amount of ethanol (0.001%) as the other treatment groups.
Dams were divided into five groups (n = 8 per group) and exposed to variable concentrations of either 2,4-BPS, BPSIP, BPS or E2 through drinking water from the first day after pregnancy was determined until the end of weaning of the pups, which lasted for approximately 40 days. Considering the body mass gain and changes in water consumption of dams, the amount of chemicals dissolved in drinking water was adjusted every 5 days to maintain the oral exposure within the expected range (5ug/kg bw/day).

value: ICR

value: Liver

value: BPS

value: 10 week


title: Liver, E2, Male-3


title: gWAT, HFD1

value: control


title: Liver, BPS, Male-2


title: Liver, E2, Male-1


title: gWAT, HFD2


title: 2 layer spheroid [1-GEX_S3_L001]

description:
1-GEX_S3_L001
Channel 1
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C1_barcodes.tsv.gz
C1_features.tsv.gz
C1_matrix.mtx.gz

value: HeLa

value: Epithelial

value: mRNA


title: Liver, BPSIP, Male-2

value: BPSIP


title: Liver, BPS, Male-1


title: Liver, E2, Male-2


title: Liver, 2,4-BPS, Male-2


title: Liver, 2,4-BPS, Male-1


title: Liver, CK, Male-3


title: Liver, CK, Male-2


title: Liver, CK, Male-1


title: Liver, BPS, Female-3

value: Female


title: Liver, BPS, Female-1


title: Liver, 2,4-BPS, Male-3


title: Liver, BPS, Female-2


title: Liver, BPSIP, Female-3


title: Liver, BPSIP, Female-2


title: Liver, BPSIP, Male-3


title: LKS-M-1

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

data_processing:
Low quality 3’ ends of reads were trimmed (cutoff q=30), and remaining adapter sequences were removed using cutadapt. Reads were aligned to the mm10 genome build using bowtie2 with default parameters except --very-sensitive and --non-deterministic options.
Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. Duplicated reads were removed using Picard MarkDuplicates.
MACS3 was used to identify peaks for each sample with FDR < 0.01. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary.
Assembly: mm10
Supplementary files format and content: counts_v2.tab, where rows are peaks identified by MACS3 and columns are raw read counts per sample

source_name: LKS derived macrophage

growth_protocol: Bone marrow was isolated from C57Bl/6 mice.  HSPC populations were defined using lineage markers cocktail of biotinylated antibodies against CD5, CD11b, CD45R (B220), Gr- 1, 7-4, and Ter-119 and anti-biotin from Miltenyi Biotec; anti-c-Kit (CD117; clone 2B8), and anti-CD34 (clone RAM34) from BD Biosciences; anti-Sca-1 (clone D7), and anti-CD16/32 (clone 93) from BioLegend.

extract_protocol:
100,000 macrophages derived from either LKS+ or LKS– CD34+ FcγR+ cells were collected in ice-cold PBS, lysed in ATAC lysis buffer for 10 minutes and then tagmented with TN5 transposase (ActiveMotif) for 30 minutes
Six samples were uniquely barcoded and the sequencing library was prepared using NEBNext DNA Ultra II kit (NEB)

treatment_protocol: Cells were treated with murine GM-CSF (50 ng/mL) and/or M-CSF (50 ng/mL) for 24 h, washed and differentiated into macrophages with M-CSF for 6 or 8 days, respectively

value: LKS derived macrophage

tag: genotype

value: WT

value: M-CSF


title: Liver, E2, Female-2


title: Liver, E2, Female-1


title: LKS-M-3

tag: cell type


title: LKS-M-2


title: Liver, 2,4-BPS, Female-2

tag: time


title: Liver, 2,4-BPS, Female-1

tag: strain


title: Liver, BPSIP, Male-1


title: Liver, CK, Female-3


title: LKS-GM-3

value: GM-CSF + M-CSF


title: LKS-GM-1


title: LKS-GM-2


title: Liver, CK, Female-2


title: Sarcopenia patients

city: Suzhou

first: Ling

address: 899 Pinghai Road

institute: Department of General Medicine, The First Affiliated Hospital of Soochow University

description:
microRNA
Serum from sarcopenia was isolated and RNA was collected for detection.

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Serum

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: Serum

tag: diagnosis

value: sarcopenia


title: Liver, BPSIP, Female-1

tag: Sex


title: CD34-M-3

source_name: CD34+ derived macrophage

value: CD34+ derived macrophage


title: CD34-M-2


title: Healthy control

value: healthy control


title: young-sham 4

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University

data_processing:
Macrogen NGS service analysis workflow
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2
Transcript is assembled by StringTie with aligned reads.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage.
Assembly: mm10
Supplementary files format and content: Excel file includes Read_Count, FPKM, TPM values for all Samples

source_name: lung

extract_protocol:
RNA was harvested using the ReliaPrep RNA MiniprReliaPrep RNA Miniprep Systems (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Reference Guide Document # 1000000040498 v00

value: lung

tag: age

value: young

value: wild-type

value: sham operation


title: CD34-M-1


title: young-sham 3


title: Liver, E2, Female-3

value: ICR

value: Liver

value: 10 week


title: young-sham 2


title: young-sham 1


title: CD34-GM-2


title: Liver, 2,4-BPS, Female-3


title: CD34-GM-1


title: young-1h 4

value: 1 hour after ischemia reperfusion


title: young-1h 3


title: shH3f3b_input_2

first: li

last: wang

institute: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital

data_processing:
The reads were aligned to the mm10 genome using BWA, and the peaks were called with SICER.
For differential analysis of ChIP-seq data, the SICER-df.sh script of SICER package (V1.1) was used with the parameters: window size 200bp, gap size 600bp and FDR q value 0.01
ChIP-Seq peakswere evaluated and normalized by the function of annotatePeaks.pl in HOMER
For visualizing individual samples, the BAM file was converted to BIGWIG format using the bamCoverage function of deepTools.
Assembly: mm10
Supplementary files format and content: bigWig(except for Input sample)

source_name: aorta

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
DNA libraries for ChIP-seq were prepared using Nextera XT DNA Library Preparation Kit following manufacturer's protocols.

value: aorta

value: primary mouse vascular smooth muscle cells

tag: chip antibody

value: input


title: shNT_input_1

value: shNT


title: young-1d 4

value: 1 day after ischemia reperfusion


title: shNT_input_2


title: young-1h 1


title: shH3f3b_H3.3_2

value: ab176840, Abcam


title: young-1d 3


title: young-1h 2


title: shNT_H3.3_2


title: shNT_H3.3_1


title: shH3f3b_input_1


title: young-1d 2


title: old-sham 3

value: old


title: Liver, CK, Female-1

value: Female

value: control


title: primary mouse VSMCs,shH3.3,rep3

data_processing:
Paired-end reads were mapped to the mm10 transcriptome and genome by STAR.
The featureCounts function of the Rsubread package was used to counts the reads for each gene.
The genes reads count table was normalized and the differentially expressed genes were identified by DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include genes reads count  for each Sample

extract_protocol:
RNA was harvested 1  ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kits following manufacturer's protocols.

value: H3f3b knockdown


title: young-1d 1

value: lung

value: young


title: old-sham 2

value: wild-type

value: sham operation


title: shH3f3b_H3.3_1


title: primary mouse VSMCs,shH3.3,rep2


title: CD34-GM-3

value: CD34+ derived macrophage

value: WT

value: GM-CSF + M-CSF


title: old-sham 4


title: old-sham 1


title: primary mouse VSMCs,shH3.3,rep1

value: aorta


title: primary mouse VSMCs,shNT,rep3

value: primary mouse vascular smooth muscle cells


title: primary mouse VSMCs,shNT,rep2


title: old-1h 3

value: 1 hour after ischemia reperfusion


title: old-1h 2


title: primary mouse VSMCs,shNT,rep1


title: old-1d 4


title: WT_1_24h_2

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 24 hours after LPS treatment, replicate 2

data_processing:
Possible poly-A tails and low sequence quality bases were trimmed by Cutadapt version 1.15 with `-m 20 -q 20,20 -a "A{100}"` parameters.
After the trimming, all the remaining reads were aligned to the mm9 reference genome using STAR version 2.5.3a with the primary genome annotation in GENCODE Release M1.
Cuffquant and Cuffnorm softwares, part of Cufflinks suite version 2.2.142, were used to calculate an FPKM value for each gene.
Cumulative FPKM (AUC values) were calculated by using R version 4.0.5. The AUC value for a gene was calculated as the area under the curve of LPS time-course FPKM values, i.e. AUC = (0h+2h)*2/2 + (2h+4h)*2/2 + (4h+8h)*4/2 + (8h+12h)*4/2 + (12h+24h)*12/2. Before the AUC calculation, replicates were merged as mean.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene.
Supplementary_files_format_and_content: oxygen_AUC.tab: Tab-delimited text file includes AUC values for every gene and every treatment.

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were obtained in the DMEM supplemented with 40 ng/ml M-CSF (PeproTech), 10% FBS and penicillin/streptomycin. The cells were cultured at 37oC under 5% CO2 and saturated humidity in 1% or 20% oxygen. After 1 week, the culture medium was replaced with fresh DMEM supplemented with 10% FBS and penicillin/streptomycin without M-CSF. 20%>1%BMDM were obtained by incubation of 20%-BMDM at 1% O2 for 12h and stimulated with LPS at 1% O2.

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen).
Total RNA from the BMDMs was used to prepare cDNA sequencing libraries using the SureSelect Strand-Specific RNA library preparation kit (Agilent Technologies) after the polyA selection step.

treatment_protocol: BMDM were treated with LPS for 0, 2, 4, 8, 12, 24h and the cells were harvested for RNA purification.

value: Bone marrow-derived macrophages

tag: time point


title: WT_1_24h_1

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 24 hours after LPS treatment, replicate 1


title: WT_1_12h_2

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 12 hours after LPS treatment, replicate 2


title: old-1h 1


title: old-1d 2

value: 1 day after ischemia reperfusion


title: WT_1_12h_1

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 12 hours after LPS treatment, replicate 1


title: WT_1_8h_2

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 8 hours after LPS treatment, replicate 2


title: old-1d 3


title: old-1d 1


title: WT_1_4h_2

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 4 hours after LPS treatment, replicate 2


title: WT_1_8h_1

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 8 hours after LPS treatment, replicate 1


title: TIGAR KO BMDM + LPS 3

city: Nanjing

first: dong

middle: dong

state: jiangsu

address: 101Longmian Avenue, Jiangning District,

institute: Nanjing Medical University

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text file includes FPKM values for each Sample

source_name: primary culture cell

growth_protocol: Cells were maintained for 7 days in RPMI 1640 medium supplemented with 10 ng ml−1 mMCSFr, 10% FBS, and 1% Penicilin-Streptomycin and allowed to differentiate into mature macrophages.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China).

treatment_protocol: Cells were incubated with 100 ng ml−1 lipopolysaccharide (LPS, Sigma-Aldrich)  for 8 hours for analysis.BMDMS from WT and TIGAR KO mice were treated or untreated with LPS (100 ng/ml, Sigma-Aldrich) for 8 h were used for RNA-seq analysis.

value: macrophage

value: TIGAR knockdown

value: with LPS

value: 8 hours


title: TIGAR KO BMDM - 2

value: without LPS


title: WT_1_2h_2

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 2 hours after LPS treatment, replicate 2


title: CS-3

city: Anseong-si

first: Dasom

last: Choi

state: Gyeonggi-do

address: 4726, Seodong-daero

country: South Korea

institute: Chung-Ang University

description: replicate 3

data_processing:
Quality of raw reads were pre-checked using the FastQC software.
Trimmed reads of each sample were aligned to the Arabidopsis TAIR10 genome using STAR aligner with default parameters.
Mapped reads were converted to digital counts using FeatureCounts and were analyzed using edgeR.
DEGs were identified based on an adjusted p-value <0.05 and an absolute log2 fold change ≥ 1.
Assembly: Arabidopsis thaliana reference genome (TAIR10) was downloaded via the TAIR database (https://www.arabidopsis.org/)
Supplementary files format and content: Aligned reads were converted to digital counts using FeatureCounts.

organism: Arabidopsis thaliana

source_name: Whole plants

growth_protocol: Sterilized seeds were grown in a growth chamber at 22℃ under long day condition (16 h light/8 h dark) for 10 days.

extract_protocol:
Total RNAs were isolated using the RNeasy Plant Mini Kit (QIAGEN, Valencia, CA) and treated with DNase I (NEB, USA).
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA).

treatment_protocol: For control, Col-0 seeds were grown on half-strength MS medium alone. For Cs-treated plants, Col-0 seeds were grown on half-strength MS media supplemented with 1.5mM CsCl.

value: Whole plants

tag: ecotype

value: 1.5mM CsCl


title: WT_1_4h_1

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 4 hours after LPS treatment, replicate 1


title: TIGAR KO BMDM - 3


title: TIGAR KO BMDM + LPS 1


title: WT_1_2h_1

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously) 2 hours after LPS treatment, replicate 1


title: WT BMDM + LPS 3


title: TIGAR KO BMDM + LPS 2


title: old-1h 4

tag: tissue

value: lung

value: old

value: wild-type


title: CS-2

description: replicate 2


title: CS-1

description: replicate 1


title: TIGAR KO BMDM - 1


title: WT BMDM + LPS 2

value: WT


title: WT_1_0h_2

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously), no LPS treatment, replicate 2


title: WT BMDM + LPS 1


title: MS-3

description: replicate 3

value: Mock


title: WT BMDM - 3


title: WT BMDM - 2


title: WT_1_0h_1

description: BMDM continuous hypoxia (differentiated and cultured in 1% oxygen continuously), no LPS treatment, replicate 1


title: WT_H_24h_2

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 24hours after LPS treatment, replicate 2

value: Differentiation in 20% O2 followed by 1% O2 for 12hours before and during LPS stimulation


title: WT BMDM - 1


title: MS-2

description: replicate 2


title: DMSO-24h-2

description: Vehicle (DMSO) treated control BMDM harvested 24 hours after LPS treatment, replicate 2

data_processing:
Possible poly-A tails and low sequence quality bases were trimmed by Cutadapt version 1.15 with `-m 20 -q 20,20 -a "A{100}"` parameters.
After the trimming, all the remaining reads were aligned to the mm9 reference genome using STAR version 2.5.3a with the primary genome annotation in GENCODE Release M1.
Cuffquant and Cuffnorm softwares, part of Cufflinks suite version 2.2.142, were used to calculate an FPKM value for each gene.
Cumulative FPKM (AUC values) were calculated by using R version 4.0.5. The AUC value for a gene was calculated as the area under the curve of LPS time-course FPKM values, i.e. AUC = (0h+2h)*2/2 + (2h+4h)*2/2 + (4h+8h)*4/2 + (8h+12h)*4/2 + (12h+24h)*12/2. Before the AUC calculation, replicates were merged as mean.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene.
Supplementary_files_format_and_content: lysosome_AUC.tab: Tab-delimited text file includes AUC values for every gene and every treatment.

growth_protocol: Bone marrow cells were obtained in the DMEM supplemented with 40 ng/ml M-CSF (PeproTech), 10% FBS and penicillin/streptomycin. The cells were cultured at 37oC under 5% CO2 and saturated humidity in 20% oxygen. After 1 week, the culture medium was replaced with fresh DMEM supplemented with 10% FBS and penicillin/streptomycin without M-CSF and treated with DMSO, 10nM ConcanamycinA or 100nM Bafilomycin a1 for 16h.

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen).
Total RNA from the BMDMs was used to prepare cDNA sequencing libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: DMSO


title: WT_H_24h_1

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 24hours after LPS treatment, replicate 1


title: DMSO-24h-1

description: Vehicle (DMSO) treated control BMDM harvested 24 hours after LPS treatment, replicate 1


title: DMSO-12h-2

description: Vehicle (DMSO) treated control BMDM harvested 12 hours after LPS treatment, replicate 2


title: WT_H_12h_2

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 12hours after LPS treatment, replicate 2


title: DMSO-8h-2

description: Vehicle (DMSO) treated control BMDM harvested 8 hours after LPS treatment, replicate 2


title: DMSO-4h-2

description: Vehicle (DMSO) treated control BMDM harvested 4 hours after LPS treatment, replicate 2


title: DMSO-4h-1

description: Vehicle (DMSO) treated control BMDM harvested 4 hours after LPS treatment, replicate 1


title: DMSO-8h-1

description: Vehicle (DMSO) treated control BMDM harvested 8 hours after LPS treatment, replicate 1


title: Hippocampus

first: Haruya

last: Yagishita

state: Miyagi

address: 6-3 Aoba, Aramaki, Aoba-ku

department: Graduate School of Pharmaceutical Sciences

data_processing:
The Cell Ranger Software Suite v7.1.0 (10x Genomics, Pleasanton, CA, USA) was used to perform sample de-multiplexing, barcode processing, single-cell 3' unique molecular identifier (UMI) counting and generating the gene-barcode expression matrix. The matrix was imported into Seurat v4 (Hao et al., 2021) for quality control and downstream analyses. Except in certain situations, default parameters were used in all operations.
Assembly: mm10
Supplementary files format and content: comma-separated value and matrix

source_name: Hippocampus

extract_protocol:
The cryopreserved single-cell lysate was used to construct a sequence library in accordance with the methods described in the original Quartz-Seq2 study (Sasagawa et al., 2018).
The library was sequenced using an Illumina HiSeq X sequencer (Illumina, San Diego, CA, USA). The sequence specifications of the Quartz-Seq2 library were as follows: Read1, 23 bp (15-bp cell barcode + 8-bp UMI); index1, 6 bp; Read2, 91 bp.

value: Hippocampus

value: Neuron

value: 3-5 weeks old


title: DMSO-0h-2

description: Vehicle (DMSO) treated control BMDM harvested before LPS treatment, replicate 2

value: Bone marrow-derived macrophages


title: WT_H_8h_1

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 8hours after LPS treatment, replicate 1


title: WT_H_8h_2

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 8hours after LPS treatment, replicate 2


title: WT_H_12h_1

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 12hours after LPS treatment, replicate 1


title: DMSO-2h-2

description: Vehicle (DMSO) treated control BMDM harvested 2 hours after LPS treatment, replicate 2


title: WT_H_4h_2

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 4hours after LPS treatment, replicate 2


title: Baf-24h-1

description: BMDM treated with Bafilomycin A1 and harvested 24 hours after LPS treatment, replicate 1

value: Bafilomycin A1


title: wing disc_etomoxir_2h_rep2

city: Heidelberg

first: Philipp

last: Willnow

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum (DKFZ)

data_processing:
analysis performed on galaxy server
adapter trimming: Trim Galore! (version 0.6.3)
alignment: Bowtie2 (version 2.4.2), settings  adjusted according to Skene et al, Nature Protocols 2018: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
remove duplicates: MarkDuplicates  (version 2.18.2.2)
peak calling: MACS2 callpeak (version 2.1.1.20160309.6)
differential binding: DiffBind (version 2.10.0)
annotation: ChIPseeker (version 1.18.0)
Assembly: dm6
Supplementary files format and content: ChIPseeker: tabular

organism: Drosophila melanogaster

source_name: wing disc (third instar)

extract_protocol:
according to Ahmand und Spens, PLoS Genet 2019 (https://protocols.io/private/D6B0AD2DC1431A513994A2A05AC59CDA)
KAPA Hyper Prep Kit (Roche 7962312001), deviation from protocol: AmpureXP beads instead of KAPA Pure Beads, adapter ligation for3 h, rapid PCR cycle (10 s at 60C) according to Skene et al, Nature Protocols 2018

treatment_protocol: untreated or explant culture according to Strassburger et al, Development 2017; 2 h ±etomoxir (500 uM)

value: wing disc (third instar)

value: male and female

tag: antibody

value: 2 h explant culture, etomoxir (500uM)


title: DMSO-0h-1

description: Vehicle (DMSO) treated control BMDM harvested before LPS treatment, replicate 1


title: Baf-12h-2

description: BMDM treated with Bafilomycin A1 and harvested 12 hours after LPS treatment, replicate 2


title: wing disc_etomoxir_2h_rep1


title: MS-1

description: replicate 1

value: Whole plants


title: WT_H_2h_2

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 2hours after LPS treatment, replicate 2


title: Baf-8h-2

description: BMDM treated with Bafilomycin A1 and harvested 8 hours after LPS treatment, replicate 2


title: wing disc_control_2h_rep2

value: 2 h explant culture


title: Baf-12h-1

description: BMDM treated with Bafilomycin A1 and harvested 12 hours after LPS treatment, replicate 1


title: Baf-8h-1

description: BMDM treated with Bafilomycin A1 and harvested 8 hours after LPS treatment, replicate 1


title: DMSO-12h-1

description: Vehicle (DMSO) treated control BMDM harvested 12 hours after LPS treatment, replicate 1


title: WT_H_2h_1

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 2hours after LPS treatment, replicate 1


title: Baf-4h-2

description: BMDM treated with Bafilomycin A1 and harvested 4 hours after LPS treatment, replicate 2


title: DMSO-2h-1

description: Vehicle (DMSO) treated control BMDM harvested 2 hours after LPS treatment, replicate 1


title: WT_H_0h_2

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) harvested before LPS stimulation, replicate 2

value: Differentiation in 20% O2 followed by 1% O2 for 12hours


title: wing disc_control_2h_rep1


title: Baf-24h-2

description: BMDM treated with Bafilomycin A1 and harvested 24 hours after LPS treatment, replicate 2


title: wing disc_control

value: untreated


title: Baf-2h-2

description: BMDM treated with Bafilomycin A1 and harvested 2 hours after LPS treatment, replicate 2


title: WT_H_0h_1

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) harvested before LPS stimulation, replicate 1


title: conA-24h-2

description: BMDM treated with concanamycin A and harvested 24 hours after LPS treatment, replicate 2

value: Concanamycin A


title: WT_N_24h_2

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 24 hours after LPS treatment, replicate 2


title: Baf-0h-1

description: BMDM treated with Bafilomycin A1 and harvested before LPS treatment, replicate 1


title: Baf-0h-2

description: BMDM treated with Bafilomycin A1 and harvested before LPS treatment, replicate 2


title: ControlBuffer_22-3 5DPT biol rep 4

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

data_processing:
STAR v2.7.5c, mapping to reference CPB genome using " --outFilterMultimapNmax 1" to disregard multimapped reads.
R version 4.1.1 with package edgeR_3.36.0, filtering genes with raw counts below 50 in less than 4 samples
R version 4.1.1 with package edgeR_3.36.0, TMM normalization
R version 4.1.1 with package limma_3.50.0, voom transformation, linear model fit, adj.p.val calculation (BH correction)with eBayes function, DE table export
Assembly: Ldec_2.0
Supplementary files format and content: TMM_RPMs_allsamples.txt - a tab-delimited text file with TMM-normalized CPM values for all samples
Supplementary files format and content: DGE_results.xlsx - a MS Excel file containing a data matrix that aggreates the results of differential gene expression analysis (logFC and adj.p.val) for the comparisons between treated and control larvae in both time points and corresponding normalized counts

organism: Leptinotarsa decemlineata

source_name: whole larva

growth_protocol: The CPB larvae were obtained from laboratory colony established from adults collected from untreated potato fields in Central Slovenia in June 2021. The beetle colony was kept on potato foliage diet.

extract_protocol:
RNA extraction from individual larvae was performed using TRIzol reagent (Invitrogen) and Direct-zol RNA Microprep kit (Zymo Research) followed by DNase treatment and cleaning using RNeasy MinElute columns (QIAGEN).
Illumina library prep without retaining read strand specificity was performed by Novogene Ltd.

treatment_protocol: Four fresh potato leaves were soaked in PlyA2/PlyB solution and another four in the corresponding Control Buffer. One 2nd instar larva (4 days old) was placed on each leaf disk.  After 1 and 5 days of feeding , whole larvae were collected and rapidly frozen in liquid nitrogen, yielding four biological replicates per group at both time points.

value: whole larva

tag: larval instar_sampled

tag: days post_treatment

value: ControlBuffer


title: ControlBuffer_22-2 5DPT biol rep 3


title: WT_H_4h_1

description: BMDM hypoxia (differentiated in 20% oxygen and incubated in 1% oxygen for 12 hours before LPS stimulation) 4hours after LPS treatment, replicate 1

value: Differentiation in 20% O2 followed by 1% O2 for 12hours before and during LPS stimulation


title: conA-24h-1

description: BMDM treated with concanamycin A and harvested 24 hours after LPS treatment, replicate 1


title: conA-12h-2

description: BMDM treated with concanamycin A and harvested 12 hours after LPS treatment, replicate 2


title: ControlBuffer_18-4 5DPT biol rep 2


title: WT_N_12h_2

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 12 hours after LPS treatment, replicate 2


title: WT_N_24h_1

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 24 hours after LPS treatment, replicate 1


title: conA-12h-1

description: BMDM treated with concanamycin A and harvested 12 hours after LPS treatment, replicate 1


title: conA-8h-2

description: BMDM treated with concanamycin A and harvested 8 hours after LPS treatment, replicate 2


title: conA-8h-1

description: BMDM treated with concanamycin A and harvested 8 hours after LPS treatment, replicate 1


title: WT_N_12h_1

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 12 hours after LPS treatment, replicate 1


title: OlyA_PlyB_8-3 5DPT biol rep 4


title: Baf-4h-1

description: BMDM treated with Bafilomycin A1 and harvested 4 hours after LPS treatment, replicate 1