title: HCC827H

city: 上海

first: 港

last: 郭

address: 上海市闵行区浦江镇联航路1188号25号楼

institute: 上海欧易生物医学科技有限公司

description: Library name: Sample 4

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Human non-small cell lung cancer cells

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Human non-small cell lung cancer cells


title: Mix4_1_R4_P4_H_pool1

status: Public on Jun 30 2025

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: other

data_processing:
The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.422. The FASTQ files were were processed using the R-ODAF pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada). Briefly:
Reads were trimmed and filtered with fastp (--cut_front_window_size 1, --cut_front_mean_quality 3, --cut_tail_window_size 1, --cut_tail_mean_quality 3, --cut_right_window_size 4, --cut_right_mean_quality 15, --length_required 50). Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2). Quantification was performed in R using the qAlign function from the QuasR package.
Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2).
Quantification was performed in R using the qAlign function from the QuasR package.
Assembly: GTF file generated from probe sequences in Biospyder manifest file
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

molecule: other

organism: Homo sapiens

growth_protocol: MCF-7 cells were maintained in complete media (phenol red DMEM + 10% FBS + 1% P/S) in 10 cm culture dishes at 37°C in a humidified atmosphere (5% CO2). Cells were depleted of estrogen for 96h in phenol red-free DMEM supplemented with CS 5% FBS + 1% P/S. 48h into the estrogen depletion cells were plated in 96-well plates prior to chemical exposure.

extract_protocol:
Cells were lysed and RNA was extracted according to BioSpyder's protocol
Total RNA input of 100 ng was used to build whole transcriptome Templated Oligo-Sequencing libraries using the TempO-Seq Human Whole Transcriptome 2.1 kit (BioSpyder, Carlsbad, CA); RNA was diluted to 50 ng/ul in 1 x TempO-Seq lysis buffer and 2 ul of this mixture was used as input. Briefly, detector oligos (DO) targeting whole transcriptome were annealed to mRNA. Each transcript is targeted by a pair of DOs. Bound DOs were ligated to form one contiguous sequence, while unbound DOs were eliminated by nuclease digestion. The ligated DOs were indexed and amplified by PCR, after which 96 [?] individual libraries were pooled to create a single pool for sequencing on the [instrument] (Illumina).
A 96-sample Human Whole Transcriptome Template Oligo-Sequencing (TempO-Seq) kit, which contains 50 nt detector oligos that target mRNA transcripts, was used to generate sequencing libraries.

treatment_protocol: After estrogen depletion, cells were exposed to chemicals (dissolved in DMSO, final DMSO concentration 0.1%) under serum free conditions (phenol red-free DMEM + 2% BSA + 1%) for 48h.

tag: cell line

tag: plate

tag: chemical

value: Mix 4

tag: dose


title: Mix4_0-5_R4_P4_H_pool1


title: Pulmonary cells, Microplastics 1um, 0.1 g/L (A) 1

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description: Library name: MA1_1

library_source: transcriptomic

data_processing:
trimming and filtering was performed using Flexbar software (3.5.0)
Cleaned, good quality reads were mapped to the Mouse GRC39 assembly with STAR aligner (2.7.5c)
Htseq-count (1.99.2) was used for reads counting
Assembly: Mouse GRC39 annotation MM109
Supplementary files format and content: raw counts from Htseq-count

molecule: polyA RNA

source_name: pulmonary fibroblast

extract_protocol:
3'mRNA-Seq
Library was prepared from 50 ng of total RNA with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Austria)

treatment_protocol: Treated and control cells were trypsinized, transferred to 1.5 mL Eppendorf-type tubes, and centrifuged at 500xg for 7 minutes. Obtained supernatants were instantly removed, and pelleted cells were snap-frozen at −80 °C pending RNA isolation. TRI Reagent™ Solution (ThermoFisher Scientific, USA) was used to purify total RNA according to a standard procedure. RNA was assessed for quality using the TapeStation 4150 System (Agilent, USA). RNA quantification was performed using the Qubit RNA BR assay (ThermoFisher Scientific, USA).

tag: tissue

value: pulmonary fibroblast

tag: treatment

value: Microplastics 1um, 0.1 g/L (A) 1


title: HCC827C

address: 上海市闵行区浦江镇联航路1188号25号楼

country: China

institute: 上海欧易生物医学科技有限公司

description: Library name: Sample 3

molecule: total RNA

tag: cell type


title: Mix4_0-1_R4_P4_H_pool1


title: H3K27ac_mg_GrnKO_rep2

city: South San Francisco

first: Leon

last: Tejwani

address: 161 Oyster Point Blv.

country: USA

institute: Denali Therapeutics

library_source: genomic

data_processing:
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert reads aligning to a single genomic location into “tag directories” for subsequent analysis using the command makeTagDirectory (Heinz et al., 2010). To annotate raw and normalized H3K27ac signal around ATAC-seq peaks,  the annotatePeaks command was used with the parameters -raw for raw counts or default for normalized counts, along with -size 800 for the annotation region. DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal with > 2 fold-change and p-adj < 0.05. To identify motifs enriched in differential peak regions over background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. Background sequences were comprised of random GC-matched genomic sequences or experimental unchanged backgrounds as defined in the text.
Assembly: mm10
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for microglia. Microglia ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.

molecule: genomic DNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Brain nuclei were isolated as previously described (Nott et al., 2019,2021), with initial homogenization and crosslinking performed with 1% formaldehyde in Dulbecco’s PBS for 10 minutes at room temperature. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099), and NEUN-AF488 (Millipore MAB 377X). Nuclei were stained with DAPI (BioLegend 422801) the next day then sorted with a BD Influx Cell Sorter. Nuclei were sorted as DAPI positive, singlets, PU.1+, OLIG2-, and NEUN-. Chromatin immunoprecipitation sequencing was performed as previously described (Heinz et al, 2010, Texari et al, 2021). For H3K27ac ChIP-seq, ~500,000 fixed nuclei were quickly thawed on ice and resuspended in ice-cold LB3 buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and 1x protease inhibitor cocktail. Nuclei / chromatin was sheared by sonication using the PIXUL Multi-Sample Sonicator (Active Motif) in low bind 96 well plates following the manufacturer’s instructions. Samples were sonicated with the following settings: Pulse (N): 50, PRF [kHz]: 1.00, Process time: 60 min, Burst Rate [Hz]: 20.00. Samples were pulse spun to 600xg at 4°C in the 96-well plate, transferred to low-bind tubes, and chromatin recovered by retaining the supernatant following a spin at 21,000xg at 4°C for 10 minutes. The supernatant was then diluted 1.1-fold with ice-cold 10% Triton X-100. Two percent of the lysate was kept as ChIP input control. 10 μL of Dynabead Protein A and 10 μL of Protein G were added per sample, in addition to 2 μg of a specific antibody for H3K27ac (Active Motif 39685). The samples were rotated overnight at 4°C and were washed as follows the next day: 3x with Wash Buffer I (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) + 1x protease inhibitor cocktail, 3x with Wash Buffer III (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1% Triton X-100, 1 mM EDTA, 0.7% Sodium Deoxycholate) + 1x protease inhibitor cocktail, 2x with TET (0.2% Tween-20/TE) + 1/3x protease inhibitor cocktail, and 1x with IDTET (0.2% Tween-20, 10 mM Tris pH 8, 0.1 mM EDTA). Samples were finally resuspended in 25 μL TT buffer (10 mM Tris pH 8 + 0.05% Tween 20) prior to on-bead library preparation.
Sequencing libraries for H3K27ac ChIP and input samples were prepared with NEBNext Ultra II DNA library prep kit (NEB, E7645) reagents according to the manufacturer’s protocol on beads suspended in 25 μL TT (10 mM Tris/HCl pH 7.5, 0.05% Tween-20), with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 μL 10% SDS, 4.5 μL 5 M NaCl, 3 μL EDTA, 4 μL EGTA, 1 μL proteinase K (20 mg/ml), 16 μL water, incubating for 1 h at 55°C, then 30 minutes to overnight at 65°C. DNA was purified using 2 μL of SpeedBeads (Cytiva GE45152105050250) in a 20% PEG8000 / 1.5M NaCl solution to final concentration of 12% PEG, then eluted with 25 μL TT. DNA contained in the eluate was then amplified for 12-14 cycles in 25 μL PCR reactions using NEBNext High-Fidelity Q5 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. Resulting libraries were size selected by gel excision to 200-500 bp, purified, and paired-end sequenced using an Illumina NovaSeq instrument.

value: Brain

tag: strain

value: PU.1+ nuclei

tag: genotype

value: GrnKO

tag: chip antibody

value: ActiveMotif #39685


title: A549H

address: 上海市闵行区浦江镇联航路1188号25号楼

institute: 上海欧易生物医学科技有限公司

description: Library name: Sample 2


title: H3K27ac_mg_WT_rep2

value: WT


title: H3K27ac_mg_WT_rep1


title: Mix4_0-01_R4_P4_H_pool1


title: Pulmonary cells, control, 1

description: Library name: CTR_1

value: control


title: Mix3_5_R4_P4_H_pool1

value: Mix 3


title: Mix3_50_R4_P4_H_pool1


title: Med13L KO3_cortex_E13.5, bulk RNA

city: SHanghai

first: Yulan

last: Zhao

address: North Zhongshan Rd 3663#

institute: East China Normal University

data_processing:
For bulk RNA-seq, quality control of the RNA-seq data was performed using FastQC (version 0.11.9). Paired-end reads were trimmed to remove adapters and low-quality reads using skewer (version 0.2.2). Clean reads were aligned to UCSC mm10 mouse genome using STAR (version 25.2b) with default parameters. The number of mapped reads was counted using stringtie (version 2.2.1). For scRNA-seq, CellRanger 6.6.1 was applied for preliminary data analysis. Raw data from single-cell RNA-seq libraries were first trimmed to remove the template switch oligo (TSO) sequence and poly(A) tail sequence. Reads with adaptor contaminants and low-quality bases were removed. Clean reads were aligned to the reference genome. Gene expression levels were quantified as transcripts per million (TPM). Valid barcodes and Unique Molecular Identifiers (UMIs) were used to generate the gene-barcode matrix for single cells. Seurat was used for quality control and data analysis in R.
Assembly: mm10
Supplementary files format and content: Tab includes raw counts for each sample
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: embryonic brain cortex

growth_protocol: Med13L Het mice were inbred and E13.5 embryonic cortex were isolated after genotyping.

extract_protocol:
For bulk RNA sequencing, total mRNA from mouse cortical tissues was isolated using the RNAiso Plus kit (Takara, #9109) on ice. For scRNA sequencing, cortex from 5 embryos of the same genotype from 3 litters were pooled into 5 ml tissue storage solution (Miltenyi Biotec, Inc, MD, USA) on ice and carefully cut into small pieces of 1-3 mm. Tissue samples were subjected to enzymatic digestion with 0.25% Trypsin-EDTA (Thermo Fisher Scientific) at 37°C in an atmosphere of 5% CO2 for up to 30 min. Cell suspensions were centrifuged at 300 × g for 5 min at 4℃. The pellets were further digested in basal media supplemented with 0.2% type II collagenase (Sigma-Aldrich) at 37°C for up to 4 h. Isolated cells were filtered through 70 mm nylon filters (BD), washed twice with sterile PBS. Samples with a cell density of 700-1200 cells/ml and a viability higher than 85% were proceeded for scRNA-seq.
For bulk RNA sequencing, RNA-seq libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version, NR616). For scRNA sequencing, Droplet-based scRNA-seq was performed using the 10x Genomics Chromium Single Cell 3′ Reagents Kit (v3.1). The single cell samples were passed through a 40 μm cell strainer and counted using a hemocytometer with trypan blue. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell A chip. After droplet generation, samples were transferred into PCR tubes and reverse transcription was performed using a T100 Thermal Cycler (Bio-Rad). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide. Before clean-up using SPRIselect beads, cDNA was amplified for 10 cycles. Libraries were submitted to 150 bp paired-end sequencing on an Illumina Novaseq 6000 platform, yielding 150 G of sequencing data per sample.

value: embryonic brain cortex

value: Med13L KO


title: Med13L KO2_cortex_E13.5, bulk RNA


title: Med13L KO1_cortex_E13.5, bulk RNA


title: Mix3_0-01_R4_P4_H_pool1


title: Mix3_0-001_R4_P4_H_pool1


title: hiPSC cardiomyocytes, monoculture with TGF-Beta inhibitor, rep 2

city: MINNEAPOLIS

first: Sophie

middle: E

last: Givens

state: MN

address: 312 Church Street SE, Room 7-256

department: Biomedical Engineering

institute: University of Minnesota

description:
Library name: CM_SB_2
10X Genomics protocols

library_source: transcriptomic single cell

data_processing:
Reads were preprocessed (demultiplexed, aligned to the GRCh38 genome and counted) with cellranger v7.1.0.
Fastq files per sample were generated with bamtofastqs v1.4.1 using the cellranger count sample_alignments.bam as input
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix contents: lists of barcodes, features and counts matrix after cellranger filtering
Supplementary files format and content: cell_num.txt contains the cellranger estimated cell numbers per sample to use with the --force-cells since not aligned reads are not included in the bamtofastq output.

growth_protocol: CM and EPC co-cultures were seeded in a layered fashion to allow for maximum and consistent CM attachment. First, the plates (12 and 48 well-plates) were coated overnight at 37°C with 17.36 microg/cm2 of Cultrex-RGF. On day 26 of CM differentiation the CM were washed with 0.5 mL of DPBS without calcium or magnesium and 0.5 mL 37°C 0.25% trypsin-EDTA solution was added to each well and incubated at 37°C for 20 minutes. The CM was singularized by pipetting with a P1000 micro pipettor and then quenched with 1mL of RPMI/B27(+ins) with 20% FBS and 5 microM Rock Inhibitor. The cell suspension was transferred to a conical tube and counted with a hemocytometer with a 1:1 dilution of 0.4% trypan blue. The cells were centrifuged at 200g for 5 minutes and plated at a density of 75,000 cells/cm2 in LASR media containing 10 mM Rock Inhibitor. On day 27, after the CM had fully attached, the epicardial cells were seeded on top of the CM at a density of 25,000 cells/cm2 in LASR containing 5 microM Rock Inhibitor (CM + EPC->DC) and 2 microM SB431542 (For the CM + EPC(+SB) condition only). On day 27 the CM-only conditions were given LASR containing 5mM Rock Inhibitor (CM) and 2mM SB431542 (For the CM(+SB) condition only). The media was changed to fresh LASR with or without 2microM SB431542 on day 28 and every 2 days until day 35 of CM differentiation (8 days of co-culture total). On day 35, the CM-only controls and co-cultures were singularized and scRNA-sequencing was completed.

extract_protocol:
Single-cell RNA sequencing was done following the supplier’s manual for the Chromium Next GEM Single Cell Sequencing Kits. The 2D co-cultures were singularized using 0.25% trypsin-EDTA for 20 minutes at 37°C. The viability of the cells was determined via propidium iodide on the BD Accuri C6 flow analyzer and then the cells were prepped for fixed single-cell sequencing according to the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics 1000414).
Libraries for single-cell sequencing were created using the Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 4 BC (10X Genomics 1000475) by following the manual for probe hybridization and library creation. The samples were sequenced according to the 10X genomics FLEX single-cell sequencing workflow at the University of Minnesota Genomics Center (UMGC).

treatment_protocol: Detailed in growth protocol

value: hiPSC cardiomyocytes

value: Monoculture, Basal Media

tag: batch


title: H3K27ac_mg_WT_rep1_input


title: Mix4_0-001_R4_P4_H_pool1


title: Mix2_50_R4_P4_H_pool1

value: Mix 2


title: hiPSC cardiomyocytes, monoculture with TGF-Beta inhibitor, rep 1

description:
Library name: CM_SB_1
10X Genomics protocols


title: Mix2_10_R4_P4_H_pool1


title: Mix2_1_R4_P4_H_pool1


title: Mix2_0-5_R4_P4_H_pool1


title: Med13L Het2_cortex_E13.5, bulk RNA

value: Med13L Het


title: hiPSC cardiomyocytes, monoculture without TGF-Beta inhibitor, rep 2

description:
Library name: CM_2
10X Genomics protocols

value: Monoculture, TGF-Beta inhibitor (SB431542)


title: A549C

address: 上海市闵行区浦江镇联航路1188号25号楼

institute: 上海欧易生物医学科技有限公司

description: Library name: Sample 1

value: Human non-small cell lung cancer cells


title: Med13L Het1_cortex_E13.5, bulk RNA


title: Mix2_5_R4_P4_H_pool1


title: Mix3_1_R4_P4_H_pool1


title: hiPSC cardiomyocytes, monoculture without TGF-Beta inhibitor, rep 1

description:
Library name: CM_1
10X Genomics protocols


title: Med13L WT3_cortex_E13.5, bulk RNA

value: Med13L WT


title: Mix3_10_R4_P4_H_pool1


title: Mix3_0-1_R4_P4_H_pool1


title: Mix3_0-5_R4_P4_H_pool1


title: Mix2_0-001_R4_P4_H_pool1


title: hHO_Torin1

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: Library name: ChRN0573

data_processing:
The pooled libraries were sequenced on an Illumina NovaSeq 6000 (Illumina) using the 10x Genomics standard 28-10-10-90 cycle configuration (Standard Workflow).
bcl2fastq (v2.20.0.422) and cellranger (v7.1.0) were used to generate FASTQ files. The cellranger mkfastq pipeline was executed with default parameters.
Cellranger(v9.0.0) with GRCh38-2024-A as the transcriptome dataset was used to generate processed data files.
Assembly: GRCh38
Supplementary files format and content: tab-separated values and matrix files

extract_protocol:
Heart organoids were dissociated into single cells using 0.25% Trypsin-EDTA. Cells were washed and resuspended with PBS, and filtered through a 70-µm strainer. After centrifugation, the cells were resuspended in 0.04% BSA-PBS and counted using trypan blue. Only samples with at least 90% viability were used for library preparation.
Libraries were prepared using the Chromium GEM-X Single Cell 3’ Kit v4 (10x Genomics), following the manufacturer's standard protocol.

value: heart organoid


title: Mix1_50_R4_P4_H_pool1

value: Mix 1


title: Med13L Het3_cortex_E13.5, bulk RNA


title: Mix1_10_R4_P4_H_pool1


title: Med13L WT1_cortex_E13.5, bulk RNA


title: hiPSC cardiomyocytes and epicardial cells, coculture without TGF-Beta inhibitor, rep 1

description:
Library name: CM_EPC_1
10X Genomics protocols

value: Coculture, Basal Media


title: Mix1_5_R4_P4_H_pool1


title: Mix1_0-5_R4_P4_H_pool1


title: hHO_Control

description: Library name: ChRN0572

value: untreated


title: hiPSC cardiomyocytes and epicardial cells, coculture with TGF-Beta inhibitor, rep 2

description:
Library name: CM_EPC_SB_2
10X Genomics protocols

value: Coculture, TGF-Beta inhibitor (SB431542)


title: Mix2_0-01_R4_P4_H_pool1


title: Mix2_0-1_R4_P4_H_pool1


title: PC_B_R3_P3_G_pool1

value: No cells; Brain positive control


title: PC_UH_R3_P3_G_pool1

value: No cells; Universal human positive control


title: hiPSC cardiomyocytes and epicardial cells, coculture with TGF-Beta inhibitor, rep 1

description:
Library name: CM_EPC_SB_1
10X Genomics protocols

value: WT


title: hiPSC cardiomyocytes and epicardial cells, coculture without TGF-Beta inhibitor, rep 2

description:
Library name: CM_EPC_2
10X Genomics protocols


title: Med13L WT2_cortex_E13.5, bulk RNA

value: embryonic brain cortex


title: Mix1_0-01_R4_P4_H_pool1


title: FA-STV-2day-4

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description:
Library name: Sample 8
Read legnth: 100

data_processing:
The adapter sequences were trimmed using TrimGalore (https://www.bioinformatics.babraham.ac.uk/).
Trimmed sequence reads were aligned to the Mus musculus reference genome (GRCm39) using the STAR aligner (v. 2.7.9a)
Transcript quantification was performed using RSEM (v. 1.3.3)
Assembly: Mus musculus (GRCm39)
Supplementary files format and content: Tab-deliminated text file includes raw counts for each sample
Supplementary files format and content: Tab-deliminated text file includes TPM values for each sample

source_name: kidney

growth_protocol: All animal experiments were conducted in accordance with Pusan National University (PNU) animal experimentation guidelines and were approved by the PNU Institutional Animal Care Committee (PNU-IACUC approval No. 2023-0238).

extract_protocol:
Total RNA was isolated from tissue using Maxwell (Promega) based method. One 1 µg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
RNA libraries were prepared using MGIEasy RNA Directional Library Prep Kit (MGI)

treatment_protocol: To investigate the effects of starvation on kidney function under normal and impaired conditions, starvation was induced by withholding food, with water available ad libitum. For the renal injury model, mice were intraperitoneally administered 250 mg/kg of folic acid (FA) and observed for one week before undergoing 3 days of starvation.

value: kidney

value: C57BL/6 WT(wid type)

value: Folic acid (250 mg/kg) + Starvation


title: Donor6, bronchial epitheial cells, UNC, filtered air exposure

city: Chapel Hill

first: Sarah

middle: A

last: Lester

state: North Carolina

address: 120 Mason Farm Rd

department: Department of Genetics

institute: University of North Carolina at Chapel Hill

description:
Library name: Donor6_U_FA_2hr
Column name in raw_counts.csv: Donor6_U_FA_2hr

data_processing:
Raw read quality was checked using FastQC (v0.12.1). Residual adapter sequences were trimmed using cutadapt (v4.1). Reads were aligned to the human transcriptome (GRch38.p14, release 44) using Star (v2.7.11a) and quantified using Salmon (v1.10.2).
All downstream analyses were performed using R (v4.3.1). Salmon counts were imported using tximport. Genes without at least 10 counts across 6 samples were filtered out. Differential expression analysis was performed using DESeq2; genes were considered differentially expressed with an adj.p.val < 0.05 and an absolute log2FC > 0.58.
Assembly: GRCh38.p14
Supplementary files format and content: comma-delimited text file includes metadata necessary for constructing DESeq2 models
Supplementary files format and content: csv file includes raw counts for each sample

source_name: human bronchial epithelial cells

growth_protocol: Primary human bronchial epithelial cells from 6 donors were grown in parallel in the PneumaCult media system and the UNC media system. Cryopreserved P1 cells were expanded in each system's expansion media (PneumaCult -EX Plus or UNC BEGM) until desired confluence, then differentiated in each system's air-liquid interface (ALI) media (PneumaCult ALI or UNC ALI) for 28-35 days until well-differentiated. Cells were maintained in an incubator with a humid atmosphere and 5% CO2 at 37C.

extract_protocol:
RNA was harvested using the RNeasy Mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using KAPA stranded mRNA-seq kit according to the manufacturer's instructions.

treatment_protocol: Pairs of well-differentiated bronchial epithelial cells were exposed to 0.5 PPM ozone or filtered air in an atmosphere with > 80% humidity and 5% CO2 at 37C for 2 hours.

tag: individual

tag: media

value: UNC

value: human bronchial epithelial cells

value: filtered air


title: Donor6, bronchial epitheial cells, PneumaCult, ozone exposure

description:
Library name: Donor6_P_O3_2hr
Column name in raw_counts.csv: Donor6_P_O3_2hr

value: PneumaCult

value: ozone


title: STV-2day-4

description:
Library name: Sample 11
Read legnth: 100

value: Starvation


title: TMBPF_50_R3_P3_G_pool1

value: Tetramethyl bisphenol F


title: Mix1_0-001_R4_P4_H_pool1

value: Mix 1


title: STV-2day-6

description:
Library name: Sample 12
Read legnth: 100


title: STV-2day-2

description:
Library name: Sample 10
Read legnth: 100


title: FA-STV-2day-5

description:
Library name: Sample 9
Read legnth: 100


title: Donor6, bronchial epitheial cells, UNC, ozone exposure

description:
Library name: Donor6_U_O3_2hr
Column name in raw_counts.csv: Donor6_U_O3_2hr


title: Donor6, bronchial epitheial cells, PneumaCult, filtered air exposure

description:
Library name: Donor6_P_FA_2hr
Column name in raw_counts.csv: Donor6_P_FA_2hr


title: TMBPF_5_R3_P3_G_pool1


title: TMBPF_1_R3_P3_G_pool1


title: TMBPF_0-01_R3_P3_G_pool1


title: FA-STV-2day-3

description:
Library name: Sample 7
Read legnth: 100


title: Mix1_1_R4_P4_H_pool1


title: Mix1_0-1_R4_P4_H_pool1


title: TMBPF_0-1_R3_P3_G_pool1


title: 44BPF_50_R3_P3_G_pool1

value: 4,4'-Bisphenol F


title: 44BPF_10_R3_P3_G_pool1


title: Donor5, bronchial epitheial cells, PneumaCult, ozone exposure

description:
Library name: Donor5_P_O3_2hr
Column name in raw_counts.csv: Donor5_P_O3_2hr


title: FA-3

description:
Library name: Sample 5
Read legnth: 100

value: Folic acid (250 mg/kg)


title: 44BPF_5_R3_P3_G_pool1


title: Donor5, bronchial epitheial cells, UNC, filtered air exposure

description:
Library name: Donor5_U_FA_2hr
Column name in raw_counts.csv: Donor5_U_FA_2hr


title: FA-6

description:
Library name: Sample 6
Read legnth: 100


title: TMBPF_10_R3_P3_G_pool1


title: FA-1

description:
Library name: Sample 4
Read legnth: 100


title: 44BPF_1_R3_P3_G_pool1


title: 44BPF_0-5_R3_P3_G_pool1


title: 44BPF_0-001_R3_P3_G_pool1


title: Control-3

description:
Library name: Sample 3
Read legnth: 100

value: non


title: 44BPF_0-01_R3_P3_G_pool1


title: Control-2

description:
Library name: Sample 2
Read legnth: 100


title: 44BPF_0-1_R3_P3_G_pool1


title: BPC_5_R3_P3_G_pool1

value: Bisphenol C


title: Donor5, bronchial epitheial cells, PneumaCult, filtered air exposure

description:
Library name: Donor5_P_FA_2hr
Column name in raw_counts.csv: Donor5_P_FA_2hr


title: Control-1

description:
Library name: Sample 1
Read legnth: 100


title: Donor4, bronchial epitheial cells, UNC, filtered air exposure

description:
Library name: Donor4_U_FA_2hr
Column name in raw_counts.csv: Donor4_U_FA_2hr


title: BPC_0-5_R3_P3_G_pool1


title: BPC_10_R3_P3_G_pool1


title: Donor4, bronchial epitheial cells, UNC, ozone exposure

description:
Library name: Donor4_U_O3_2hr
Column name in raw_counts.csv: Donor4_U_O3_2hr


title: Donor4, bronchial epitheial cells, PneumaCult, ozone exposure

description:
Library name: Donor4_P_O3_2hr
Column name in raw_counts.csv: Donor4_P_O3_2hr


title: HFrST3, High fructose diet, Stress

city: Hyderabad

first: Arvind

last: Kumar

state: Telangana

address: CSIR-CCMB, Habsiguda, Near habsiguda metro station

country: India

institute: Center for Cellular and Molecular Biology

data_processing:
The sample quality was checked with FastQC. MGI adapters and low-quality reads were removed from raw sequencing reads using cutadapt. Reads with quality scores less than 20 and smaller than 36 bp were discarded. The processed reads were then mapped to the mouse genome mm10 using hisat2 with default parameters. Uniquely aligned reads were counted using the featureCounts of Subread package. There were 55487 genes in the gtf file, downloaded from Ensembl, for which we had count information. Genes with a total read count of 10 across all the samples were removed resulting in 31299 genes for further analysis. DEGs analysis was carried out using DESeq2. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 0.5 were considered differentially expressed. For the PCA plot and heat map, the raw read counts were log normalized, available with the DESeq2 package.
Assembly: mm10
Supplementary files format and content: tab delimited file contains raw read count for each sample

source_name: Pre frontal cortex

extract_protocol:
RNA was isolated using a mirVanaTM isolation kit as per protocol (Catalog number: #AM1560; Thermo Fisher Scientific). To prepare the RNA samples, we added 10x DNase I buffer and one unit of DNase I enzyme (New England Biolabs) to a maximum of 5 μg RNA for DNase treatment. The samples were incubated at 37°C for 15 minutes and then the enzyme was inactivated at 70°C for 15 minutes. After that, we quantified the DNase-treated RNA by measuring the absorption at 260 nm using a NanoDrop 2000 spectrophotometer.
The MGIEasy RNA Library Prep Set (MGI) was usedfor library preparation following the manufacturer’s instructions. Initially, 500 ng of total RNAwas used, and the rRNAwas depletedusing an MGIEasy rRNAdepletion kit. Following rRNA depletion, samples were fragmented and reverse transcribed. The second strand was then synthesized and converted into cDNA. The kit provided DNA Clean Beads for DNA purification, followed by end repair and A-tailing. The samples were then barcoded, adaptor-ligated, and subjected to purification. Adaptor-specific primers were used for amplification, and quantification was done using a Qubit dsDNA high-sensitivity kit from (Thermo Scientific). The size of the sample fragments was determined using a 4200 TapeStation (Agilent). Denaturation and circularization of 1pMol dsDNAwere performedto generate single-stranded circular DNA, followed by the creation of DNA Nano Balls using Rolling cycleamplification. The DNBs were sequenced on an MGISEQ-2000 sequencer (MGI) using the PE100 recipe, after being placed on a patterned flow cell.

value: Pre frontal cortex

value: C57bl/6 Ncrl

value: High Fructose + Stress


title: BPC_1_R3_P3_G_pool1


title: Donor4, bronchial epitheial cells, PneumaCult, filtered air exposure

description:
Library name: Donor4_P_FA_2hr
Column name in raw_counts.csv: Donor4_P_FA_2hr


title: BPC_0-01_R3_P3_G_pool1


title: Donor3, bronchial epitheial cells, UNC, ozone exposure

description:
Library name: Donor3_U_O3_2hr
Column name in raw_counts.csv: Donor3_U_O3_2hr


title: HFrST1, High fructose diet, Stress


title: BPAF_50_R3_P3_G_pool1

value: Bisphenol AF


title: HFrUST3, High fructose diet, No stress

value: High Fructose


title: BPC_0-1_R3_P3_G_pool1


title: BPC_50_R3_P3_G_pool1


title: BPC_0-001_R3_P3_G_pool1


title: HFrST2, High fructose diet, Stress


title: BPAF_5_R3_P3_G_pool1


title: BPAF_1_R3_P3_G_pool1


title: Donor3, bronchial epitheial cells, PneumaCult, ozone exposure

description:
Library name: Donor3_P_O3_2hr
Column name in raw_counts.csv: Donor3_P_O3_2hr


title: BPAF_0-5_R3_P3_G_pool1


title: Donor5, bronchial epitheial cells, UNC, ozone exposure

description:
Library name: Donor5_U_O3_2hr
Column name in raw_counts.csv: Donor5_U_O3_2hr

value: UNC


title: Donor2, bronchial epitheial cells, PneumaCult, ozone exposure

description:
Library name: Donor2_P_O3_2hr
Column name in raw_counts.csv: Donor2_P_O3_2hr

value: human bronchial epithelial cells


title: Donor3, bronchial epitheial cells, UNC, filtered air exposure

description:
Library name: Donor3_U_FA_2hr
Column name in raw_counts.csv: Donor3_U_FA_2hr

value: filtered air


title: Donor2, bronchial epitheial cells, UNC, ozone exposure

description:
Library name: Donor2_U_O3_2hr
Column name in raw_counts.csv: Donor2_U_O3_2hr


title: BPAF_10_R3_P3_G_pool1


title: HFrUST2, High fructose diet, No stress


title: Donor3, bronchial epitheial cells, PneumaCult, filtered air exposure

description:
Library name: Donor3_P_FA_2hr
Column name in raw_counts.csv: Donor3_P_FA_2hr

value: PneumaCult


title: BPAF_0-1_R3_P3_G_pool1


title: Donor2, bronchial epitheial cells, UNC, filtered air exposure

description:
Library name: Donor2_U_FA_2hr
Column name in raw_counts.csv: Donor2_U_FA_2hr


title: BPAF_0-001_R3_P3_G_pool1


title: BPAF_0-01_R3_P3_G_pool1


title: CoST3, Control diet, Stress

value: Control + Stress


title: BPA_0-5_R3_P3_G_pool1

value: Bisphenol A


title: BPA_50_R3_P3_G_pool1


title: BPA_10_R3_P3_G_pool1


title: CoST2, Control diet, Stress


title: BPA_5_R3_P3_G_pool1


title: CoST1, Control diet, Stress


title: BPA_1_R3_P3_G_pool1


title: Donor2, bronchial epitheial cells, PneumaCult, filtered air exposure

description:
Library name: Donor2_P_FA_2hr
Column name in raw_counts.csv: Donor2_P_FA_2hr


title: BPA_0-1_R3_P3_G_pool1


title: BPA_0-01_R3_P3_G_pool1


title: CoUST2, Control Diet, No stress

value: Control


title: Donor1, bronchial epitheial cells, UNC, ozone exposure

description:
Library name: Donor1_U_O3_2hr
Column name in raw_counts.csv: Donor1_U_O3_2hr

value: ozone


title: Mix6_50_R3_P3_G_pool1

value: Mix 6


title: CoUST3, Control Diet, No stress


title: Donor1, bronchial epitheial cells, PneumaCult, ozone exposure

description:
Library name: Donor1_P_O3_2hr
Column name in raw_counts.csv: Donor1_P_O3_2hr


title: BPA_0-001_R3_P3_G_pool1


title: Mix6_10_R3_P3_G_pool1


title: CoUST1, Control Diet, No stress


title: Mix6_5_R3_P3_G_pool1


title: Mix6_1_R3_P3_G_pool1


title: Mix6_0-1_R3_P3_G_pool1


title: N2AFOXF1-3

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

description:
Library name: Sample 9
F3

data_processing:
Library preparation and sequencing were performed by Beijing Genomics Institute. A BGIseq500 platform was used to generate 150 bp paired-end reads.
Assembly: mm10 and KOS
Supplementary files format and content: geneID_symbol_readcount.txt

extract_protocol:
Neuro-2a cells overexpressed FOXK1 and FOXF1 for 36 hours and then infected with ICP0-null virus for 5 h (MOI = 2) before being harvested for RNA extraction using a total RNA extraction kit (Vazyme RC112-01)
DNA libraries were constructed and sequenced by Tianjin Novogene Bioin_x0002_formatic Technology Co., Ltd. Briefly, an NEBNext® Ultra™ II DNA Library Prep kit (catalogue no. E7645L; NEB) was used for library preparation.

treatment_protocol: For infection, cells were infected with ICP0-null HSV-1 (strain 7134) for 5hpi (MOI = 2) before RNAseq

value: Brain

value: overexpressing FOXF1

value: Infect cells with HSV-1 virus for five hours


title: HFrUST1, High fructose diet, No stress

value: Pre frontal cortex


title: Mix6_0-5_R3_P3_G_pool1


title: Donor1, bronchial epitheial cells, PneumaCult, filtered air exposure

description:
Library name: Donor1_P_FA_2hr
Column name in raw_counts.csv: Donor1_P_FA_2hr


title: N2AFOXF1-2

description:
Library name: Sample 8
F2


title: Mix6_0-01_R3_P3_G_pool1


title: COVAX_015R_VDJ-B

city: Darlinghurst

first: Wunna

last: Kyaw

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description:
Library name: COVAX_015R_S49
VDJ

data_processing:
The 10X Genomics Cell Ranger (July 7, 2020, release) multi pipeline, processing both the GEX and V(D)J library data, was used to align the sequencing data against the human reference genome (hg38), with default parameters.
Assembly: hg38
Supplementary files format and content: Cellranger output files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: consensus.fasta and filtered_contig_annotations.csv

source_name: lymph node fine needle biopsy

extract_protocol:
FNB lymph node samples (n=12, which includes samples for both LNs for each of 6 participants) were washed with DPBS by centrifugation at 550 x g for 5 mins. The supernatant was discarded, and the cell pellet was resuspended in 100µl PBS. To confirm the presence of lymphocytes, cells were stained with CD45-AF700 (clone HI100) (BD Pharmingen) for 15 mins at RT in the dark, RBCs were lysed with 2.4mL RBC Lysis Solution (16.52g NH4Cl + 2g KHCO3 + 0.74g disodium EDTA in 2L dH2O, pH7.2-7.4) for 10 mins at RT in the dark, with intermittent agitation. Samples were then centrifuged at 550 x g for 5 mins. The supernatant was discarded, and the cells were resuspended in 100µl Iscove’s Modified Dulbecco’s Medium (IMDM) + 2% FCS.
Prior to sorting, the cells were stained with DAPI (0.1μg/ml) (Sigma Aldrich) for 15mins in the dark and live-sorted on a FACSAriaIII cell sorter (BD Biosciences). Single cell libraries were generated using the 10X Genomics 5’v2 Gene Expression and Immune Profiling at the Garvan Cellular Genomics Platform, according to manufacturer’s instructions. cDNA and BCR libraries were then sequenced using the Illumina NovaSeq S4 Flow Cell according to manufacturer’s instructions at Read 1 = 28, i7 index = 10 and Read 2 = 90 cycles.

value: lymph node fine needle biopsy

value: B Cells


title: Mix5_50_R3_P3_G_pool1

value: Mix 5


title: Mix6_0-001_R3_P3_G_pool1


title: COVAX_015R_GEX

description:
Library name: COVAX_015R_S28
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: N2AFOXF1-1

description:
Library name: Sample 7
F1


title: Mix5_10_R3_P3_G_pool1


title: COVAX_015L_VDJ-B

description:
Library name: COVAX_015L_S47
VDJ


title: N2AFOXK1-3

description:
Library name: Sample 6
K3

value: overexpressing FOXK1


title: Mix5_5_R3_P3_G_pool1


title: Donor1, bronchial epitheial cells, UNC, filtered air exposure

description:
Library name: Donor1_U_FA_2hr
Column name in raw_counts.csv: Donor1_U_FA_2hr

value: UNC


title: COVAX_015L_GEX

description:
Library name: COVAX_015L_S27
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: Mix5_0-1_R3_P3_G_pool1


title: N2AFOXK1-2

description:
Library name: Sample 5
K2


title: Mix5_0-5_R3_P3_G_pool1


title: Mix5_1_R3_P3_G_pool1


title: N2AEmpty-3

description:
Library name: Sample 3
P3

value: control


title: N2AFOXK1-1

description:
Library name: Sample 4
K1


title: Mix5_0-01_R3_P3_G_pool1


title: COVAX_012R_VDJ-B

description:
Library name: COVAX_012R_S41
VDJ


title: NC_R5_P3_G_pool1

value: No cells; 1X Lysis buffer


title: NC_R6_P3_G_pool1


title: DMSO_0-1_R12_P3_G_pool1

value: Dimethyl sulfoxide


title: COVAX_012L_VDJ-B

description:
Library name: COVAX_012L_S39
VDJ


title: N2AEmpty-2

description:
Library name: Sample 2
P2


title: DMSO_0-1_R10_P3_G_pool1


title: Mix5_0-001_R3_P3_G_pool1


title: COVAX_012L_GEX

description:
Library name: COVAX_012L_S23
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: COVAX_012R_GEX

description:
Library name: COVAX_012R_S24
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: N2AEmpty-1

description:
Library name: Sample 1
P1


title: DMSO_0-1_R9_P3_G_pool1


title: E2_0-1_R3_P3_G_pool1


title: DMSO_0-1_R11_P3_G_pool1


title: Mix4_50_R3_P3_G_pool1

value: Mix 4


title: COVAX_011R_VDJ-B

description:
Library name: COVAX_011R_S37
VDJ


title: E2_1_R3_P3_G_pool1


title: COVAX_011R_GEX

description:
Library name: COVAX_011R_S22
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: M_N_3

city: Chongqing

first: Hongsheng

last: Zhang

address: 1 Yixueyuan Road

institute: Chongqing Medical University

data_processing:
Sample quality was assessed by using FastQC. Samples were aligned to the mouse reference genome GRCm38 by using HISAT2. Mapped sequencing reads were assigned to genomic features by using the featureCounts function
Normalized by DESeq2 with rlogTransformed.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample.

source_name: hippocampus

growth_protocol: Primary neurons were maintained in Neurobasal supplemented with 10%B27 and 1%GlutaMAX in humidified atmosphere with 5%CO2 at 37℃.

extract_protocol:
Primary neuron treated astrocytic apoE particles and microglial apoE particles were harvested. Isolated RNA was subsequently used for RNA-seq analysis. cDNA library construction and sequencing were performed by the BGI using BGI platform.
RNA libraries were prepared by BGI for sequencing using standard DNBSEQ protocols

treatment_protocol: Primary neurons were treated with 6ug/mL A-apoE or M-apoE at day10 for 24h.

value: hippocampus

value: Primary neuron

value: WT

value: Microglial apoE particles


title: M_N_2


title: Mix4_5_R3_P3_G_pool1


title: Mix4_10_R3_P3_G_pool1


title: COVAX_011L_VDJ-B

description:
Library name: COVAX_011L_S35
VDJ


title: Mix4_1_R3_P3_G_pool1


title: A_N_3

value: Astrocytic apoE particles


title: Mix4_0-5_R3_P3_G_pool1


title: M_N_1


title: COVAX_011L_GEX

description:
Library name: COVAX_011L_S21
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: A_N_2


title: COVAX_010R_VDJ-B

description:
Library name: COVAX_010R_S33
VDJ


title: Mix4_0-001_R3_P3_G_pool1


title: Mix4_0-01_R3_P3_G_pool1


title: A_N_1


title: Mix3_50_R3_P3_G_pool1

value: Mix 3


title: Mix3_10_R3_P3_G_pool1


title: peripheral blood, Con-5

city: Harbin

first: li

last: jia

state: Asia

address: No. 157, Health Care Road, Nangang District

institute: Harbin Medical University

description: Con-5 FPKM

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)  by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5)  .The expression level of genes was calculated by RSEM (v1.3.1)
Between-group differential gene analysis was performed using DEseq2/DEGSeq under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001 (Depends on projects). PoissonDis was performed between-sample differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001 (Depends on projects). Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters.
Assembly: GCF_000001405.39_GRCh.p13
Supplementary files format and content: tab-delimited text file includes FPKM values for each samples

source_name: whole blood

extract_protocol:
Trizol extracted total RNA from peripheral blood of total ten samples. The RNA concentration was measured on NanoDrop 2000/2000C (Thermo Fisher Scientific, Waltham, MA, USA). These RNA samples were subsequently subjected to RNA-seq on the DNBSEQ platform following standard procedures (Bgi Genomics Co., Ltd, Shenzhen, China).
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

value: whole blood

tag: condition

value: Con

value: normal

value: no


title: Mix3_5_R3_P3_G_pool1


title: COVAX_010L_VDJ-B

description:
Library name: COVAX_010L_S31
VDJ

value: lymph node fine needle biopsy

value: B Cells


title: COVAX_010R_GEX

description:
Library name: COVAX_010R_S20
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: Mix3_1_R3_P3_G_pool1


title: peripheral blood, Con-4

description: Con-4 FPKM


title: Mix3_0-1_R3_P3_G_pool1


title: COVAX_010L_GEX

description:
Library name: COVAX_010L_S19
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: Mix4_0-1_R3_P3_G_pool1


title: Mix3_0-5_R3_P3_G_pool1


title: peripheral blood, Con-1

description: Con-1 FPKM


title: Mix2_10_R3_P3_G_pool1

value: Mix 2


title: Mix2_1_R3_P3_G_pool1


title: COVAX_008L_VDJ-B

description:
Library name: COVAX_008L_S24
VDJ


title: Mix3_0-01_R3_P3_G_pool1


title: COVAX_008R_VDJ-B

description:
Library name: COVAX_008R_S26
VDJ


title: Mix3_0-001_R3_P3_G_pool1


title: peripheral blood, AIT-5

description: AIT-5 FPKM

value: AIT


title: peripheral blood, Con-3

description: Con-3 FPKM


title: Mix2_5_R3_P3_G_pool1


title: Mix2_50_R3_P3_G_pool1


title: Mix2_0-5_R3_P3_G_pool1


title: peripheral blood, Con-2

description: Con-2 FPKM


title: Mix2_0-01_R3_P3_G_pool1


title: Mix1_50_R3_P3_G_pool1

value: Mix 1


title: COVAX_008R_GEX

description:
Library name: COVAX_008R_S16
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: COVAX_007R_GEX

description:
Library name: COVAX_007R_S14
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: peripheral blood, AIT-2

description: AIT-2 FPKM


title: peripheral blood, AIT-4

description: AIT-4 FPKM


title: COVAX_008L_GEX

description:
Library name: COVAX_008L_S15
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: Mix2_0-1_R3_P3_G_pool1


title: Mix1_10_R3_P3_G_pool1


title: peripheral blood, AIT-3

description: AIT-3 FPKM


title: COVAX_007R_VDJ-B

description:
Library name: COVAX_007R_S22
VDJ


title: Mix2_0-001_R3_P3_G_pool1


title: COVAX_007L_GEX

description:
Library name: COVAX_007L_S13
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript


title: Mix1_0-01_R3_P3_G_pool1


title: hOBLCs, siPiezo1_2_3

city: Wuhan

first: Pei

last: Huang

state: Hubei

address: 237 Luoyu Road

department: School and Hospital of Stomatology

institute: Wuhan University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.1.0). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.8).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: text files include FPKM, TPM and read counts for each gene in all samples

source_name: human odontoblast-like cells

growth_protocol: The human odontoblast-like cells were cultured in general medium: maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total mRNA from treated human odontoblast-like cells (DMSO, Yoda1, siNc, siPIEZO1-1 and siPIEZO1-2) was extracted using TRIzol reagent (Takara, Japan). A total of 15 RNA samples (3 samples each group, 5 groups in total) were subjected to RNA sequencing.
mRNA libraries were prepared for sequencing using the following protocols: 1. Sample QC: Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2: mRNA Isolation: A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3. mRNA Fragmentation: The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4. cDNA Synthesis: Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5. End Repair, Add A and Adaptor Ligation: After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6. PCR: The PCR reaction system and program are configured and set up to amplify the product. 7. Library QC: The corresponding library quality control protocol will be selected depending upon product requirements. 8. Circularization: Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9. Sequencing: Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: To explore the effect of PIEZO1 activation on human odontoblast-like cells, 2μM Yoda1 was used to treat the cells for 48 hours with DMSO serving as the negative control. For PIEZO1 knockdown groups, the cells were transfected with negative control (Nc), siPIEZO1-1 and siPIEZO1-2 sequences for 72 hours to ensure sufficient transfection efficiency.

value: human odontoblast-like cells

value: human odontoblasts induced from human dental pulp stem cells by odontogenic medium for 14 days

value: PIEZO1 knockdown

tag: time


title: hOBLCs, siPiezo1_2_2


title: Mix1_0-001_R3_P3_G_pool1


title: hOBLCs, siPiezo1_2_1


title: COVAX_007L_VDJ-B

description:
Library name: COVAX_007L_S20
VDJ


title: Mix1_0-1_R3_P3_G_pool1


title: Mix1_0-5_R3_P3_G_pool1


title: peripheral blood, AIT-1

description: AIT-1 FPKM


title: Mix1_5_R3_P3_G_pool1


title: L5042

city: Leiden, The Netherlands

first: Siddh

last: van Oost

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Library name: 104320-001-115

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Reads were aligned against hg38 with STAR and expression quantification was performed using HTseq-count
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

source_name: Myxofibrosarcoma

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

value: Myxofibrosarcoma

tag: tumor grade

value: low

tag: tumor depth

value: deep


title: TMBPF_10_R2_P2_F_pool1

tag: cell line

value: Tetramethyl bisphenol F


title: PC_B_R2_P2_F_pool1

tag: plate

value: No cells; Brain positive control


title: L4684

description: Library name: 104320-001-114


title: PC_UH_R2_P2_F_pool1

tag: chemical

value: No cells; Universal human positive control


title: L7291

description: Library name: 104320-001-112

source_name: USTS

value: USTS

value: high


title: hOBLCs, siPiezo1_1_2


title: TMBPF_0-01_R2_P2_F_pool1

tag: dose


title: TMBPF_5_R2_P2_F_pool1


title: L7289

description: Library name: 104320-001-111

tag: tissue


title: Mix1_1_R3_P3_G_pool1


title: TMBPF_0-1_R2_P2_F_pool1


title: L7284

description: Library name: 104320-001-110


title: L6497

description: Library name: 104320-001-102

value: superficial


title: 44BPF_10_R2_P2_F_pool1

value: 4,4'-Bisphenol F


title: 44BPF_5_R2_P2_F_pool1


title: 44BPF_50_R2_P2_F_pool1


title: hOBLCs, Nc_3

value: WT

tag: treatment

value: Nc


title: hOBLCs, siPiezo1_1_1

tag: cell type


title: hOBLCs, Nc_2


title: 44BPF_0-5_R2_P2_F_pool1


title: 44BPF_0-1_R2_P2_F_pool1


title: 44BPF_0-01_R2_P2_F_pool1


title: L2460

description: Library name: 104320-001-093R


title: 44BPF_0-001_R2_P2_F_pool1


title: TMBPF_50_R2_P2_F_pool1


title: L7305

description: Library name: 104320-001-087


title: hOBLCs, Nc_1


title: hOBLCs, siPiezo1_1_3


title: L7309

description: Library name: 104320-001-088


title: hOBLCs, Yoda1_3


title: BPC_10_R2_P2_F_pool1

value: Bisphenol C


title: TMBPF_1_R2_P2_F_pool1


title: BPC_50_R2_P2_F_pool1


title: hOBLCs, Yoda1_2


title: BPC_1_R2_P2_F_pool1


title: BPC_5_R2_P2_F_pool1


title: L7292

description: Library name: 104320-001-086


title: L7283

description: Library name: 104320-001-085


title: L4903

description: Library name: 104320-001-071


title: 44BPF_1_R2_P2_F_pool1


title: L7310

description: Library name: 104320-001-064


title: hOBLCs, con_3

value: DMSO


title: BPC_0-1_R2_P2_F_pool1


title: BPC_0-5_R2_P2_F_pool1


title: hOBLCs, Yoda1_1

value: human odontoblast-like cells


title: BPC_0-01_R2_P2_F_pool1


title: hOBLCs, con_2

value: human odontoblasts induced from human dental pulp stem cells by odontogenic medium for 14 days


title: L7300

description: Library name: 104320-001-063


title: hOBLCs, con_1


title: BPAF_10_R2_P2_F_pool1

value: Bisphenol AF


title: WYY 24h-2

city: Chengdu

first: Ben

last: Ma

address: Huimin Street 211

institute: Sichuan Agricultural University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insertion cost 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using Cl _C genomic benchwork
Assembly: Stuberosum_686_v6.1
Supplementary files format and content: Excel file includes fpkm for each Sample

organism: Solanum tuberosum

source_name: Potato leaf

growth_protocol: After being disinfected with carbendazim for 15 minutes, CLS and WYY varieties were planted in a greenhouse under 24℃ light culture for 16h and 20℃ dark culture for 8h.

extract_protocol:
RNA was extracted from the leaves of CLS and WYY by standard extraction methods.
The starting RNA for library construction is total RNA, which is enriched with polyA tailed mRNA using Oligo (dT) magnetic beads. Subsequently, the resulting mRNA is randomly interrupted with divalent cations in the Fragmentation Buffer. Using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system. Subsequently, the RNA strand was degraded using RNaseH, and the second strand of cDNA was synthesized using dNTPs as raw material in the DNA polymerase I system. The purified double stranded cDNA undergoes end repair, A-tailed addition, and sequencing connections. cDNA of approximately 370-420 bp was screened using AMPure XP beans, amplified by PCR, and the PCR product was purified again using AMPure XP beans, ultimately obtaining a library.

treatment_protocol: Under normal growth conditions, samples were taken after 0h and 24h infection with Phytophthora infestation.

value: Potato leaf

tag: cultivar

value: WYY

value: Potato leaf cells

value: 24h after infection with Phytophthora infestans


title: WYY 24h-1

tag: genotype


title: L7298

description: Library name: 104320-001-043

value: deep


title: L7287

description: Library name: 104320-001-042


title: BPAF_1_R2_P2_F_pool1


title: WYY 0h-2

value: 0h after infection with Phytophthora infestans


title: WYY 24h-3


title: L7312

description: Library name: 104320-001-022

value: Myxofibrosarcoma


title: Total RNA, 2year old EV_3

city: Augusta

first: Sang Ho

last: Kwon

state: Georgia

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta Univeristy

description:
Library name: Sample12
RJ-2018_S10

data_processing:
Adapters were trimmed from the FASTQ sequence files using Cutadapt (version 4.0)
sequence files were aligned to the mm10 mouse reference genome, and gene counts were obtained using STAR (version 2.7.10a). Counts from different lanes were summed.
Assembly: mm10
Supplementary files format and content: Comma separated Value (csv) file for the raw counts

source_name: plasma

extract_protocol:
Total RNA from young, mature, 1year and 2 year old mice EVs was extracted using the Total Exosome RNA Isolation Kit (Invitrogen, 4478545).
miRNA Library was prepared by using Illumina TruSeq stranded mRNA kit

value: plasma

tag: age

value: 2year old

value: plasma extracellular vesicles


title: Total RNA, 2year old EV_1

description:
Library name: Sample10
RJ-2020_S12


title: Total RNA, 1year old EV_3

description:
Library name: Sample9
RJ-3071_S6

value: 1year old


title: BPAF_0-5_R2_P2_F_pool1

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

data_processing:
The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.422. The FASTQ files were were processed using the R-ODAF pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada). Briefly:
Reads were trimmed and filtered with fastp (--cut_front_window_size 1, --cut_front_mean_quality 3, --cut_tail_window_size 1, --cut_tail_mean_quality 3, --cut_right_window_size 4, --cut_right_mean_quality 15, --length_required 50). Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2). Quantification was performed in R using the qAlign function from the QuasR package.
Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2).
Quantification was performed in R using the qAlign function from the QuasR package.
Assembly: GTF file generated from probe sequences in Biospyder manifest file
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

extract_protocol:
Cells were lysed and RNA was extracted according to BioSpyder's protocol
Total RNA input of 100 ng was used to build whole transcriptome Templated Oligo-Sequencing libraries using the TempO-Seq Human Whole Transcriptome 2.1 kit (BioSpyder, Carlsbad, CA); RNA was diluted to 50 ng/ul in 1 x TempO-Seq lysis buffer and 2 ul of this mixture was used as input. Briefly, detector oligos (DO) targeting whole transcriptome were annealed to mRNA. Each transcript is targeted by a pair of DOs. Bound DOs were ligated to form one contiguous sequence, while unbound DOs were eliminated by nuclease digestion. The ligated DOs were indexed and amplified by PCR, after which 96 [?] individual libraries were pooled to create a single pool for sequencing on the [instrument] (Illumina).
A 96-sample Human Whole Transcriptome Template Oligo-Sequencing (TempO-Seq) kit, which contains 50 nt detector oligos that target mRNA transcripts, was used to generate sequencing libraries.


title: BPC_0-001_R2_P2_F_pool1


title: L7297

description: Library name: 104320-001-021

value: USTS

value: high


title: BPAF_50_R2_P2_F_pool1


title: Total RNA, 1year old EV_2

description:
Library name: Sample8
RJ-3072_S7


title: BPAF_0-01_R2_P2_F_pool1


title: L7293

description: Library name: 104320-001-019


title: Total RNA, 1year old EV_1

description:
Library name: Sample7
RJ-3073_S8


title: CLS 24h-3

value: CLS

value: WT


title: L7299

description: Library name: 104320-001-062


title: CLS 24h-1


title: L7285

description: Library name: 104320-001-018


title: BPAF_5_R2_P2_F_pool1


title: WYY 0h-3


title: Total RNA, 2year old EV_2

description:
Library name: Sample11
RJ-2019_S11


title: Total RNA, Mature EV_3

description:
Library name: Sample6
RJ-3091_S3

value: Mature


title: Total RNA, Mature EV_2

description:
Library name: Sample5
RJ-3095_S4


title: BPAF_0-001_R2_P2_F_pool1

value: Bisphenol AF


title: CLS 0h-3

value: Potato leaf


title: BPA_10_R2_P2_F_pool1

value: Bisphenol A


title: CLS 0h-2

value: Potato leaf cells


city: Bengaluru

first: Dimple

last: Notani

state: Karnataka

address: GKVK

institute: National Centre for Biological Sciences

description: Library name: ChIP-seq_H3_S10D_Mit_Repeat_2_with-spike-in

data_processing:
For ChIP-seq analysis; fastq files were aligned to hg19 using Bowtie2 and read depth and input normalised using SAM tools, followed by processing the BAM files with MACS2 (default with broad mode) and bigwig conversion. The regions were called a using a method involving stitching of sliding window bins in genome based on H3S10p coverage. For ChIP-seq with S2 chromatin spike-in, in addition to the above, the fastq files were aligned to dm3 or dm6 using Bowtie2. This was followed by the above stated method for coverage file making along with spike-in normalisation in addition to depth normalisation.
For ATAC-seq analysis; fastq files were trimmed for adapter sequence and aligned to hg19 using Bowtie2 with read depth normalisation using SAM tools, followed by processing the BAM files with MACS2 and bigwig conversion.
For RNA-seq analysis; fastq files were subjected to Trimmomatic and FASTQC was done to check read quality. The reads were then aligned to hg19 using HISAT2. BAM files obtained were read depth normalised and FeatureCounts was used with default settings to get coverage at all GeneIDs. The fold changes between different lines were calculated using DeSeq2.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: bed, tabular

source_name: Cervix; Uterus

growth_protocol: HeLa and MCF7 cell lines were cultured in DMEM with 10% FBS and 1% Pen-Strep at 37℃ and 5% CO2 in a humidified incubator. The cells were passaged every 3-4 days.

extract_protocol:
For ChIP-seq, genomic DNA was isolated as per standard ChIP-seq protocol. For ATAC-seq, genomic DNA was isolated as per standard ATA-seq protocol, following viable nuclei isolation. For RNA-seq, total RNA was isolated using trizol as per the reagent manual.
ChIP-seq and ATAC-seq library was prepared using the NEBNext® Ultra™II DNA Library Prep kit with Sample Purification Beads (Catalogue-E7103L) following the manufacturer's protocol. For total RNA-seq, rRNA depletion was done using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads(Catalog no-E7405L) and library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads(Catalog no-E7765L).

treatment_protocol: HeLa and MCF-7 cells were treated with DMSO or Nocodazole(100ng/ml) for 24h for mitotic arrest and H3S10p ChIP-seq. HeLa stable lines: H3S10, H3S10A and H3S10D were treated with Thymidine(2mM) for 24h, followed by wash and Doxycycline(1ug/ml) for 8h and finally washed and treated with Nocodazole(100ng/ml) for mitotic arrest with induction and HA, H3, H3S10p ChIP-seq. For RNA-seq and ATAC-seq, the stables lines were subjected to mitotic arrest with induction as mentioned, and followed by a mitotic release into fresh media for 7h.

value: Cervix; Uterus

value: HeLa

value: epithelial cell

value: Thymidine 24h, wash and Doxycycline 8h, wash and Nocodazole 12h


title: BPAF_0-1_R2_P2_F_pool1

institute: Government of Canada


title: BPA_5_R2_P2_F_pool1


description: Library name: ChIP-seq_H3_S10A_Mit_Repeat_2_with-spike-in


title: CLS 0h-1

value: 0h after infection with Phytophthora infestans


title: Total RNA, Young EV_3

description:
Library name: Sample3
RJ-3013_S1

value: plasma

value: Young


title: BPA_0-5_R2_P2_F_pool1


title: BPA_1_R2_P2_F_pool1


title: ZBTB16-2, CUT&Tag

city: 咸阳市

first: YouJie

last: Cui

state: 陕西省

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院

data_processing:
Post-PCR cleanup was performed by adding NovoNGS DNA clean beads, and libraries were incubated with beads for 15 min at RT, washed twice gently in 80 % ethanol, and eluted in 20 μL TE buffer. The DNA fragments were used for   stranded DNA library preparation. Then, the library was detected by agarose electrophoresis, quantified using Qubit 2.0, and sequenced on an Illumina NovaSeq 6000 by the Wuhan frasergen Company.
Assembly: Genome assembly Sscrofa11.1
Supplementary files format and content: ZBTB16-1.peakAnno.tsv，ZBTB16-2.peakAnno.tsv
Library strategy: CUT&Tag

organism: Sus scrofa

source_name: Pigtesticles

extract_protocol:
In briefly, 100,000 cells were harvested and centrifuged for 3 min at 600×g at room temperature. Cells were washed twice in 300 μL Wash Buffer (20mM HEPES pH 7.5;150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. 10 μL of activated concanavalin A-coated magnetic beads were added per sample and incubated at RT for 10 min. The unbound supernatant was removed and bead-bound cells were resuspended in 50 μL Dig-wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2mM EDTA and a 1:50 dilution of the appropriate primary antibody. Primary antibody incubation was performed on a rotating platform for 2 h at room temperature (RT) . Then the liquid was removed on the magnet stand. An appropriate secondary antibody (Goat anti-Rabbit IgG, proteintech, B900210 or Rabbit Anti-Mouse IgG, abcam, ab46540) was diluted 1:50 in 50μL of Dig-Wash buffer and cells were incubated at RT for 1 h. For constructing negative control library (IgG), we only added secondary antibody without primary antibody. Cells were washed using the magnet stand twice for 1 min in 500 μL Dig-Wash buffer to remove unbound antibodies. A 1:200 dilution of pG-Tn5 adapter complex (~0.04 μM) was prepared in Dig-300 Buffer (0.01% Digitonin, 20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1× Protease inhibitor cocktail). After removing the liquid, 100 μL was added to the cells with gentle vortexing, which was incubated with pG-Tn5 at RT for 1 h. Cells were washed twice for 1 min in 500 μL Dig-300 Buffer to remove unbound pG-Tn5 protein. Next, cells were resuspended in 300 μL Tagmentation buffer (10mM MgCl2 in Dig-300 Buffer) and incubated at 37 °C for 1 h. To stop tagmentation, 10 μL of 0.5M EDTA, 3 μL of 10% SDS and 2.5 μL of 20 mg/mL Proteinase K was added to 300 μL of sample, which was incubated at 55 °C for 1h, purified using phenol–chloroform–isoamyl alcohol and ethanol, washed with 100% ethanol and suspended in water. The DNA was amplified by PCR reaction as follows: 3 min at 72 °C and 30 s at 98 °C followed by 16 cycles of 15 s at 98 °C and 30 s at 60 °C and 30 s at 72 °C, with a final extension at 72 °C for 3 min. Finally, the amplified DNA was purified using Ampure XP beads (Beckman Counter). Libraries were sequenced on illumina Nova-seq platform.
In CUT&Tag analysis pipeline. At the beginning, the interference information, containing adapter sequence, low-quality bases and undetected bases (indicated by N) were filtered using Trimmomatic (v0.39, with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:8).Paired-end raw data was performed quality assessment using FastQC(0.11.9). After obtaining clean data through quality control, we used the Bowtie2 to map clean reads to the reference genome (v2.3.5, with parameters: -- dovetail --no-unal --very-sensitive-local --no-mixed --no-discordant), and further screened out the low-quality mapping , PCR redundancy and organelle alignment by Samtools (V1.12, with default parameters) and Picard (v2.25.6, with default parameters), and thus to get the retained valid pairs for subsequent analysis. MACS3 (v3.0.0a6) software based on statistical  methods was used to call peaks (with parameters: -f BAMPE -B --SPMR --keep-dup all) with valid pairs data. For the sequencing experiments with biological replication, we got the overlapped peaks between replicates to assess the data reproducibility. After that, the R scripts with deepTools(3.5.1) software  were performed to illustrate the signal enrichment analysis of peak regions, gene body regions and the regions from transcription start site(TSS) with default parameters. We also use ChIPseeker to obtain gene annotations on peak regions at the same time. Finally, we randomly selected the enrichment regions on genome, and visualize the called peaks of all samples using Gviz .

value: Pigtesticles

value: Immature spermatogonia from the porcine


title: Total RNA, Young EV_1

description:
Library name: Sample1
RJ-3120_S2

value: plasma extracellular vesicles


title: ZBTB16-1, CUT&Tag

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院


title: BPA_0-1_R2_P2_F_pool1


title: BPA_0-01_R2_P2_F_pool1


description: Library name: ChIP-seq_H3S10p_Asyn_Repeat_4_with-spike-in

value: DMSO 24h


title: Monocyte-derived macrophage, exposure, rep6

city: Guelph

first: Heng

last: Kang

address: 50 Stone Rd E

department: Pathobiology

institute: University of Guelph

data_processing:
The quality of the raw data was assessed using FastQC (v.0.11.5).
Adaptors were trimmed using Trim Galore v. 0.5.0. (parameter: -q 25, --clip_R1 6, __clip_R2 6, --stringency 5, --length 40, --paired)
The raw trimmed reads were aligned to the reference genome (Ensembl EcuCab3.0) using the STAR aligner, v.2.6.0c.
Raw read counts for genes were extracted from STAR alignments using HTSeq v.0.6.1p2. (parameter: intersection_nonempty)
Normalized read counts (FPKMs) were generated using DESeq2 v.1.26.0s, using R v.3.6.1.
Assembly: EcuCab3.0
Supplementary files format and content: Tab-separated values (TSV) file containing FPKM values for each sample for the complete unfiltered gene set
Supplementary files format and content: Text files containg raw gene counts for each sample

organism: Equus caballus

source_name: Monocyte-derived macrophage

growth_protocol:
Alveolar macropahges were isolated from bronchoalveolar lavage fluid and cultured in completed RPMI containing 10% horse serum and antibiotics at 37 °C with 5% CO2
Monocyte-derived macrophges was derived from blood monocytes which was culture for 7 days at 37 °C with 5% CO2 with the same culture medium as alveolar macrophages.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen). Only RNA with an integrity number higher than 7 assessed by Agilent Bioanalyzer was used for library preparation.
The cDNA libraries were prepared using the NEBNExt Ultra II Directional RNA library preparation kit following manufacturer's instructions

treatment_protocol: For control group, AMs and MDMs were cultured with serum-free RPMI for 6 hours. For treatment groups, AMs and MDMs were culture with serum-free RPMI containing 106/mL Aspergillus fumigatus spores, 100 ng/mL LPS and 106/mL silica microspheres.

value: Monocyte-derived macrophage

value: Serum-free RPMI+FLS,6 hours


title: Total RNA, Mature EV_1

description:
Library name: Sample4
RJ-3098_S5

value: Mature


title: L6085

description: Library name: 104320-001-009

value: Myxofibrosarcoma

value: high

value: deep


title: CD45+-positive cells, Sham

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

description:
Library name: Sham
10x Genomics

data_processing:
The scRNA-seq raw data was aligned to the mm10 reference genome using Cell Ranger (version 7.1.0
Assembly: mm10
Supplementary files format and content: Matrix (h5)

source_name: Kidney

extract_protocol:
The right kidney was then harvested from each mouse,  and digested by incubation in collagenase D (5 mg/mL; Sigma-Aldrich) for 30 minutes at 37 °C. The digested tissue was  filtered through a 70-µm strainer (Corning), then centrifuged at room temperature (3000 RPM for 30 minutes, no acceleration, no brake) in a Percoll density gradient. After isolation, approximately 1 x 10^6 KMNCs per mouse were pooled within their experimental groups for CD45+ cell sorting and downstream scRNA-seq.
Flow-sorted CD45+ kidney cells were partitioned and barcoded using the 10X Chromium Controller, with approximately 10,000 cells loaded onto the NovaSeq 6000 S4 200-cycle flow cell. The library was constructed using the Chromium Next GEM Single Cell 5' HT v2 Kit and sequenced on the Illumina NovaSeq 6000 system.

value: Kidney

value: CD45+-positive cells


title: CD45+-positive cells, UNx, 1day

description:
Library name: Unx-1day
10x Genomics


title: GFP, DNL343, replicate 6

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Data was processed using nf-core/rnaseq v3.11.2 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020) using Gencode v42 gene annotations. Because the QuantSeq data only captures 3' tags from transcripts, the following custom parameters were supplied: extra_star_align_args: '--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA' and extra_salmon_quant_args: '--noLengthCorrection'. -
Assembly: GRCh38
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a microsoft excel file with three worksheets: 1. sample information 2. raw count table 3. normalized count table (log2 counts per million)

growth_protocol: HEK293 cells stably expressing EGFP or (G4C2)71-EGFP were generated as previously described (Naguib et al., 2019). Briefly, HEK293 cells were transfected with pcDNA3.1+ EGFP or (G4C2)71-EGFP with Lipofectamine 3000 (Invitrogen) and selected with G418 (Corning, #30234CI) to produce stable clones. Stable HEK293 cells were maintained in DMEM (Gibco, #11965-092), supplemented with 10% FBS (VWR, #97068-085), and 1X sodium pyruvate (Gibco, #11360-070) at 37°C in 5% CO2.

extract_protocol:
Total RNA was harvested from cells using the RNeasy Micro Kit (Qiagen), following the manufacturer’s protocol. RNA integrity (RIN) and concentration were measured by High Sensitivity RNA Screen Tape Analysis (Agilent) on a 4200 TapeStation System (Agilent).
RNA-Seq libraries were generated using the QuantSeq 3’ mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with high quality total RNA (RINe>8) as input template.  Briefly, total RNA was primed with oligo(dT) for reverse transcription, followed by RNA removal.  Lexogen’s UMI Second Strand Synthesis Module was added to introduce unique molecular identifiers to identify and remove PCR duplicates.  Amplified cDNA was purified using magnetic beads followed by 12 cycles of PCR with dual indexes and PCR purification.  Library quantity and quality were assessed with High Sensitivity D1000 ScreenTape (Agilent 5067-5584).  Libraries were pooled in equimolar ratios and the sequencing pool was purified with magnetic beads to remove residual adaptor dimers.  Sequencing reads were generated on an Illumina NovaSeq 6000 instrument (75 bp single end) by SeqMatic (Fremont, CA, USA).

treatment_protocol: Protein expression was induced in each cell line with 1 μg/mL doxycycline (Clontech, #NC0424034) and the cells were grown for 24 h. Afterwards, the cells were treated with either 1 μM DNL343 or DMSO for 2.5 h at 37°C in 5% CO2.

value: embryonic kidney

value: GFP

tag: batch


title: Total RNA, Young EV_2

description:
Library name: Sample2
RJ-3117_S9


description: Library name: ChIP-seq_H3_S10_Mit_Repeat_2_with-spike-in

value: Cervix; Uterus

value: HeLa

value: epithelial cell

value: Thymidine 24h, wash and Doxycycline 8h, wash and Nocodazole 12h


title: (G4C2)71-GFP, DMSO, replicate 6

value: DMSO


title: CD45+-positive cells, UNx, 1week

description:
Library name: UNx-1week
10x Genomics


title: Monocyte-derived macrophage, exposure, rep3


title: Mix6_10_R2_P2_F_pool1

value: Mix 6


description: Library name: ChIP-seq_H3S10p_Mit_Repeat_4_with-spike-in

value: Nocodazole 24h


title: CD45+-positive cells, UNx, 4week

description:
Library name: UNx-4week
10x Genomics


title: CD45+-positive cells, non-UNx

description:
Library name: Control
10x Genomics


title: Mix6_5_R2_P2_F_pool1


title: Monocyte-derived macrophage, exposure, rep2

value: Monocyte-derived macrophage


title: (G4C2)71-GFP, DNL343, replicate 5


title: Mix6_1_R2_P2_F_pool1


title: Monocyte-derived macrophage, exposure, rep1

value: Serum-free RPMI+FLS,6 hours


title: (G4C2)71-GFP, DNL343, replicate 6


title: Monocyte-derived macrophage, exposure, rep5


title: Monocyte-derived macrophage, control, rep6

value: Serum-free RPMI, 6 hours


title: T2

city: 郑州

first: yucheng

last: li

state: 河南省

address: 河南省郑州市金水区博学路街道金水东路156号

institute: Henan University of Chinese Medicine

description: Library name: T2

data_processing:
Transcriptome analysis process
Supplementary files format and content: 1_genes_fpkm_expression.xlsx

source_name: liver tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used forthe construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kitfollowing manufacturer's protocols.

value: liver tissue

value: crizotinib


title: T3

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: T3


title: Monocyte-derived macrophage, exposure, rep4


title: GFP, DNL343, replicate 5


title: BPA_0-001_R2_P2_F_pool1

value: Bisphenol A


title: Mix6_50_R2_P2_F_pool1


title: Monocyte-derived macrophage, control, rep5


title: T1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: T1


title: Mix6_0-1_R2_P2_F_pool1


title: (G4C2)71-GFP, DMSO, replicate 5


title: Monocyte-derived macrophage, control, rep4


title: C3

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: C3

value: control


title: GFP, DMSO, replicate 5


title: GFP, DMSO, replicate 6


title: Mix6_0-01_R2_P2_F_pool1


title: C2

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: C2


title: Monocyte-derived macrophage, control, rep3


title: Mix6_0-001_R2_P2_F_pool1


title: Monocyte-derived macrophage, control, rep2


title: GFP, DNL343, replicate 4


title: C1

address: 河南省郑州市金水区博学路街道金水东路156号

description: Library name: C1


title: Mix5_50_R2_P2_F_pool1

value: Mix 5


title: Kif13b-/- aorta scRNA-seq

city: 海淀区

first: YiRan

last: Liu

state: 北京市

department: Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, China

institute: PKU

description:
Library name: sample2
KO_mtx.gz contains for KO group

data_processing:
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
Assembly: mm10
Supplementary files format and content: WT_mtx.gz contains features.tsv.gz barcodes.tsv.gz and matrix.mtx.gz for WT group scRNA-seq data and KO_mtx.gz contains features.tsv.gz barcodes.tsv.gz and matrix.mtx.gz for KO group

source_name: aorta

growth_protocol: Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3.1(10x Genomics, 1000121) and Chromium Single Cell G Chip Kit (10x Genomics, 1000120), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: aorta

value: Kif13b knock down


title: GFP, DMSO, replicate 4

value: embryonic kidney

value: GFP


title: Mix5_10_R2_P2_F_pool1


title: WT aorta scRNA-seq

description:
Library name: sample1
WT_mtx.gz contains for WT group

value: WT


title: Mix6_0-5_R2_P2_F_pool1


title: Alveolar macrophage, exposure, rep6

source_name: Alveolar macrophage

value: Alveolar macrophage


title: (G4C2)71-GFP, DNL343, replicate 3


title: Alveolar macrophage, exposure, rep5


title: (G4C2)71-GFP, DMSO, replicate 3

value: DMSO


title: Mix5_5_R2_P2_F_pool1


title: Mix5_1_R2_P2_F_pool1


title: Alveolar macrophage, exposure, rep4


title: Mix5_0-5_R2_P2_F_pool1


title: KA_3

description:
Library name: sample12
KA3 in BMDMs_with_AC_rawcount.csv

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software and clean data with high quality were obtained.
Next, the clean reads were mapped with Mesocricetus auratus genome using Hisat2 v2.0.5. FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs) was used to estimate gene expression levels. Differential expression genes (DEGs) analysis was performed using DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: BMDMs_rawcount.csv,BMDMs_with_AC_rawcount.csv contains raw counts file in samples in each group, normal treatment in BMDMs_rawcount.csv and AC treatment in BMDMs_with_AC_rawcount.csv

source_name: tibial

growth_protocol: RNA was extracted from BMDMs from mouse tibial of WT and Kif13b-/- mouse with normal treatment(n=3/group) an AC treatment(n=3/group).

extract_protocol:
After assessment of RNA integrity using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), the cDNA library was prepared following the Illumina protocol.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated before clustering of the index-coded samples via cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia).

value: tibial

value: primary bone marrow-derived macrophages

value: co-cultured with apoptotic Jurkat cells

value: 6-8 weeks


title: KA_2

description:
Library name: sample11
KA2 in BMDMs_with_AC_rawcount.csv


title: KA_1

description:
Library name: sample10
KA1 in BMDMs_with_AC_rawcount.csv


title: (G4C2)71-GFP, DNL343, replicate 4


title: Alveolar macrophage, exposure, rep3

value: Serum-free RPMI+FLS,6 hours


title: (G4C2)71-GFP, DNL343, replicate 2


title: Mix5_0-1_R2_P2_F_pool1


title: GFP, DMSO, replicate 3


title: WA_3

description:
Library name: sample9
WA3 in BMDMs_with_AC_rawcount.csv


title: Alveolar macrophage, exposure, rep2


title: Mix5_0-01_R2_P2_F_pool1


title: GFP, DNL343, replicate 2


title: WA_2

description:
Library name: sample8
WA2 in BMDMs_with_AC_rawcount.csv


title: WA_1

description:
Library name: sample7
WA1 in BMDMs_with_AC_rawcount.csv


title: Alveolar macrophage, control, rep6

value: Serum-free RPMI, 6 hours


title: Mix5_0-001_R2_P2_F_pool1


title: (G4C2)71-GFP, DMSO, replicate 2


title: GFP, DNL343, replicate 3


title: NC_R4_P2_F_pool1

value: No cells; 1X Lysis buffer


title: Monocyte-derived macrophage, control, rep1

value: Monocyte-derived macrophage


title: Alveolar macrophage, control, rep5


title: GFP, DMSO, replicate 2


title: Alveolar macrophage, exposure, rep1


title: KO_2

description:
Library name: sample5
KO2 in BMDMs_rawcount.csv

value: DMEM supplemented with 13% FBS


title: NC_R3_P2_F_pool1


title: (G4C2)71-GFP, DNL343, replicate 1


title: DMSO_0-1_R8_P2_F_pool1

value: Dimethyl sulfoxide


title: KO_1

description:
Library name: sample4
KO1 in BMDMs_rawcount.csv

value: DMEM supplemented with 12% FBS


title: Alveolar macrophage, control, rep4


title: (G4C2)71-GFP, DMSO, replicate 1


title: WT_3

description:
Library name: sample3
WT3 in BMDMs_rawcount.csv

value: DMEM supplemented with 11% FBS


title: DMSO_0-1_R7_P2_F_pool1


title: GFP, DNL343, replicate 1

value: embryonic kidney


title: DMSO_0-1_R6_P2_F_pool1


title: WT_2

description:
Library name: sample2
WT2 in BMDMs_rawcount.csv

value: DMEM supplemented with 10% FBS


title: Alveolar macrophage, control, rep2


title: DMSO_0-1_R5_P2_F_pool1


title: GFP, DMSO, replicate 1

value: GFP


title: Alveolar macrophage, control, rep3

value: Alveolar macrophage


title: TDP43-CYTO, DNL343, 8hr, replicate 4

data_processing:
Sequencing adapters were trimmed from the raw reads with skewer. Reads were aligned to the human genome version GRCh38_p126. A STAR index (version 2.7.1a) was built with the –sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M28) were provided via the –sjdbGTFfile argument. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6. Alignments sharing the same UMI and genomic coordinate were deduplicated using the collapse_UMI_bam tool (Lexogen). The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R. Gene symbols and biotype information were extracted from the Gencode GTF file. To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package.
Assembly: GRCh38
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a microsoft excel file with three worksheets: 1. sample information 2. raw count table 3. normalized count table (log2 counts per million)

growth_protocol: Lentiviruses encoding G3BP1-mCherry in a pLVX-CMV-IRES-Hygro vector (Clontech) and GFP-tagged RBPs [GFP-TDP-43(WT), GFP-TDP-43(86-414), GFP-TDP-43(86-414, M337V) in a pLVX-TetOne_IRES_Puro vector (Clontech) were first expressed in HEK293T-17 cells to produce virus using Lenti-x Single Shot (ClonTech, #631275). H4 cells, a human neuroglioma cell line, (ATCC HTB-148) were transduced with these viruses under the selection of hygromycin B (Invitrogen, #10687010) and puromycin (Gibco, #A1113803) to generate stable cell clones. All inducible cell lines were grown in DMEM (Gibco, #11965-092), supplemented with 10% FBS (Clontech, #631106) and 1X sodium pyruvate (Gibco, #11360-070), 1µg/mL puromycin and 150 µg/mL hygromycin B at 37°C in 5% CO2.

treatment_protocol: Protein expression was induced in each cell line with 1 μg/mL doxycycline (Clontech, #NC0424034) and the cells were grown for 8 or 24 h. Afterwards, the cells were treated with either 1 μM DNL343 or DMSO for 2.5 h at 37°C in 5% CO2.

value: neuroglioma cells

tag: induction duration

value: 8 hours


title: Ndufa4KO_IFNg_Rep3

city: Philadelphia

first: Megan

middle: Lynn

last: Clark

state: PA

address: 421 Curie Blvd, Room 320

institute: University of Pennsylvania

data_processing:
Transcripts were aligned to the mm10 reference genome using Kallisto, and differential gene analysis was performed using DESeq2 and EdgeR.
Assembly: GRCm39
Supplementary files format and content: transcripts per million

source_name: Bone marrow-derived macrophages

growth_protocol: Primary bone marrow cells were differentiated in complete DMEM supplemented with 30% L929 supernatant to differentiate cells for 7 days. On day 7, cells were plated for stimulation.

extract_protocol:
For RNA-seq from wild-type, Ndufa4-/-, and Ndufa4l3-miR-147-/- (AKA Nmes1-deficient) BMDMs, total RNA was isolated from stimulated BMDMs using the PureLink RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions. Isolated total RNA was quantified using a Nanodrop 8000 Spectrophotometer.  RNA integrity numbers were determined using a TapeStation instrument (Agilent), and all samples used for RNA-seq library preparation had RIN numbers greater than 9. Three technical replicates were generated and sequenced for each genotype
The RNA libraries were generated and sequenced externally by Genewiz/Azenta standard RNA sequencing protocols. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: BMDMs from WT, Ndufa4−/−, and Ndufa4l3-miR-147−/−  (AKA Nmes1-deficient) were stimulated with Interferon-gamma (40ng/mL) for 12 hours

value: Bone marrow-derived macrophages


title: KO_3

description:
Library name: sample6
KO3 in BMDMs_rawcount.csv

value: tibial

value: primary bone marrow-derived macrophages

value: Kif13b knock down

value: DMEM supplemented with 14% FBS


title: WT_1

description:
Library name: sample1
WT1 in BMDMs_rawcount.csv

value: WT

value: 6-8 weeks


title: E2_1_R2_P2_F_pool1


title: Ndufa4KO_IFNg_Rep2


title: Alveolar macrophage, control, rep1

value: Serum-free RPMI, 6 hours


title: E2_0-1_R2_P2_F_pool1


title: 3rd_Batch_GEX-4

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: Sample28

data_processing:
RNA data were filtered by mouse sample with the following thresholds: number of genes expressed > 1000 (between 800 and 1200 depending on the mouse sample), fraction of mitochondrial content < 20%, and total counts per cell > 1800 (between 1600 and 2400). The new single-cell gene expression profiles were normalized with the NormalizeData function using the "LogNormalize" normalization method and were scaled with the ScaleData function from Seurat package.
Assembly: mm10
Supplementary files format and content: tsv.gz count and mtrix files

source_name: CD11b and/or CD11c

extract_protocol:
Tumors were perfused with a solution containing DNase I and Liberase , cut in smaller pieces and incubated for 30 min at 37°C. The suspension was washed with RPMI, 5% FBS and 2 mM ethylenediaminetetraacetic acid , mashed and filtered through a 70 μm cell strainer, twice. Lymph nodes were mashed, filtered and washed in HBSS. Spleen were mashed and red blood cells were lysed by ACK lysing buffer (Ammonium-Chloride-Potassium, home-made). Suspension was neutralized by adding RPMI, 5% FBS and filtered before further manipulation.
Librairies were performed using Reagent Kits v3.1 (Dual Index) with surface protein from 10X according to manufactur's instruction

value: CD11b and/or CD11c


title: 3rd_Batch_GEX-3

description: Library name: Sample27


title: TDP43-FL, DNL343, 8hr, replicate 4


title: Ndufa4KO_IFNg_Rep1


title: GFP, DNL343, 8hr, replicate 4


title: Mix4_50_R2_P2_F_pool1

value: Mix 4


title: Nmes1-Ndufa4l3miR147KO_IFNg_Rep3


title: 3rd_Batch_GEX-2

description: Library name: Sample26


title: Mix4_10_R2_P2_F_pool1


title: TDP43-CYTO, DMSO, 8hr, replicate 4

value: DMSO


title: Nmes1-Ndufa4l3miR147KO_IFNg_Rep2


title: TDP43-FL, DMSO, 8hr, replicate 4


title: 2nd_Batch_cell-Hashing-8

description: Library name: Sample24


title: Mix4_5_R2_P2_F_pool1


title: TDP43-CYTO, DNL343, 24hr, replicate 4

value: 24 hours


title: Ndufa4l3miR147KO_IFNg_Rep1


title: Mix4_1_R2_P2_F_pool1


title: BPA_50_R2_P2_F_pool1

value: Bisphenol A


title: TDP43-FL, DNL343, 24hr, replicate 4


title: WT_IFNg_Rep3

value: Wild-type


title: 2nd_Batch_cell-Hashing-7

description: Library name: Sample23


title: 2nd_Batch_cell-Hashing-6

description: Library name: Sample22


title: WT_IFNg_Rep2


title: Mix4_0-5_R2_P2_F_pool1


title: 3rd_Batch_GEX-1

description: Library name: Sample25


title: WT_IFNg_Rep1


title: 2nd_Batch_cell-Hashing-4

description: Library name: Sample20


title: GFP, DNL343, 24hr, replicate 4

value: GFP


title: TDP43-CYTO, DMSO, 24hr, replicate 4

value: neuroglioma cells


title: Mix4_0-1_R2_P2_F_pool1


title: Mix4_0-01_R2_P2_F_pool1