title: clp3

city: wenzhou

first: hui

last: wang

address: wenzhou medical university

institute: wenzhou medical university

description:
Library name: clp3
10x Genomics

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version 2.20). Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger, version 5.0.1) and scRNA-seq data were aligned to Ensembl genome Rnor 6.0 reference genome, a total of 63,747 single cell captured from three sham group and three CLP group were processed using 10× Genomics Chromium Single Cell 3’Solution. The Cell Ranger output was loaded into Seurat (version 5.1.0) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data. Potential doublets were detected and filtered using DoubletFinder based on the expression proximity of each cell to artificial doublets.
Assembly: rattus_norvegicus Ensembl v110
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: lymph fluid

extract_protocol:
For the droplet-encapsulation scRNA-seq experiments, approximately 1000 μL lymph fluid per rat was collected and centrifuged at 300g for 5 min at 4 ℃. The cell pellet was resuspended in 100 uL calcium-free and magnesium-free 1× PBS (0.04% BSA) and added with 1 mL 10× red blood cell lysis buffer (MACS 130-094-18) and incubated at room temperature for 5 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300 g for 5 min at room temperature. The suspension was resuspended and remove dead cells using Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1×PBS and centrifuged at 300 g for 3 min at 4 °C (repeat twice). The cell pellet was resuspended in 50 μL of 1×PBS. For each sample, cell viability was confirmed by trypan blue exclusion, which needed to be above 90%, single cell suspensions were counted using a Countess II Automated Cell Counter (Invitrogen, USA) and concentration adjusted to 700-1200 cells/uL.
For the droplet-encapsulation scRNA-seq experiments, approximately 1000 μL lymph fluid per rat was collected and centrifuged at 300g for 5 min at 4 ℃. The cell pellet was resuspended in 100 uL calcium-free and magnesium-free 1× PBS (0.04% BSA) and added with 1 mL 10× red blood cell lysis buffer (MACS 130-094-18) and incubated at room temperature for 5 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300 g for 5 min at room temperature. The suspension was resuspended and remove dead cells using Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1×PBS and centrifuged at 300 g for 3 min at 4 °C (repeat twice). The cell pellet was resuspended in 50 μL of 1×PBS. For each sample, cell viability was confirmed by trypan blue exclusion, which needed to be above 90%, single cell suspensions were counted using a Countess II Automated Cell Counter (Invitrogen, USA) and concentration adjusted to 700-1200 cells/uL.

value: lymph fluid

value: immune cell


title: TN_CE_KO_1

status: Public on Jun 06 2026

type: SRA

city: hangzhou city

first: qiang

last: chen

address: No. 1369, Wenyi West Road, Yuhang District

country: China

institute: Liangzhu Laboratory

description: Library name: Sample3

library_source: transcriptomic

data_processing:
Trimmomatic (v0.39) – Raw sequencing reads were processed to remove adapters and low-quality reads (quality limit: 0.05).
STAR (v2.7.10a) – Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using parameters: mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.8.
featureCounts (v2.0.3) – Gene-level raw counts were quantified based on Ensembl annotation (release 102).
DESeq2 (v1.36.0) – Differential expression analysis between control and experimental groups. Genes with absolute log2 fold change > 1 and adjusted p-value (Benjamini-Hochberg) < 0.05 were considered significantly differentially expressed.
Assembly: GRCm38/mm10
Supplementary files format and content: CSV file  including FPKM for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brown  adipose tissue

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Thermo Fisher Scientific, #15596018) according to manufacturer's protocol. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Kit.
Sequencing libraries were constructed using NEBNext Ultra II RNA Library Prep Kit (NEB, #E7770) following manufacturer's instructions. mRNA was enriched using oligo(dT) beads.

tag: tissue

value: Brown  adipose tissue

tag: genotype

value: Setdb1 AKO (Setdb1 fl/fl; Adipoq-Cre+)


title: clp2

description:
Library name: clp2
10x Genomics

library_source: transcriptomic single cell

tag: cell line

tag: cell type


title: whole larval P. promelas, Fipronil amide, sample3

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

country: USA

institute: United States Environmental Protection Agency

description:
Chem10_A_D3_C03
Chem10_counts_matrix.txt

data_processing:
*library strategy: TempO-Seq (Templated Oligo-Sequencing)
Sample-specific TempO-Seq libraries were pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2 × 50 bp, single-end reads, NovaSeq X 10B reagent kits.
Sequence reads were then demultiplexed based on sample-specific barcodes, and a FASTQ file was generated for each sample using Illumina's bcl2fastq conversion software. Resulting TempO-Seq data were analyzed by Biospyder using TempO-SeqR software implemented in R.
The FASTQ files were aligned to the known transcript composition of the reduced transcriptome, and a count table (columns = samples, genes = rows) was generated.
Assembly: GCA_016745375.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

organism: Pimephales promelas

source_name: whole body

growth_protocol: not applicable

extract_protocol:
Samples were prepared for transcriptomics analysis by homogenization in a protease lysis buffer as directed by BioSpyder Technologies, Inc. Pimephales promelas were homogenized in 75 µL/well with a 2.3 mm stainless steel bead (BioSpec) at 30 Hz for 2 min using a well plate homogenizer (Bead Ruptor 96, OMNI International). Plates were centrifuged for 3 min at 1000 rpm. Homogenates were pooled (excluding any mortalities) by treatment concentration within each plate, resulting in n=3 replicates per treatment, each containing five pooled organisms (Supplementary Figure 2B). The final plates containing pool homogenates were stored at -80ºC until shipped on dry ice to BioSpyder Technologies, Inc. (Carlsbad, CA) for TempO-seq analysis. Test acceptability criteria were met if control survival was >90 %.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification were performed with a DeNovix UV-visible spectrophotometer (DeNovix). Ligated transcripts were subjected to polymerase chain reaction amplification, which also introduces adaptors for sequencing and a sample-specific barcode.

treatment_protocol: High-throughput in vivo exposures were conducted in 1 mL 96-well deep well plates (NEST, Catalog #502162) for 24 h. Each exposure consisted of two chemicals tested in a 1/2 log dilution series with five replicates per treatment concentration on each of three plates (15 organisms exposed per concentration). Final exposure concentrations ranged from 66.67 – 0.021 µM for all data poor chemicals, except fipronil amide (56.43- 0.018 µM) and fexofenadine hydrochloride (32.2 – 0.011 µM). All chemical stocks were prepared in DMSO and had purities > 95%. For each exposure, a Tecan D300e Bioprinter (Corvallis, OR, USA) was used to prepare an initial chemical dosing plate containing 1800 µL/well of test solution diluted in UV-treated, filtered Lake Superior Water in a 2 mL 96-well deep well plate (NEST, Catalog #503162). The concentration of DMSO was normalized across all wells to match those of the highest % DMSO obtained with the chemical delivery (i.e., the highest exposure concentration; generally 0.34% DMSO). Using the bioprinter, the dosing solutions were arranged to evenly distribute replicate exposure groups along the edges of the plate to avoid confounding any edge effects, if present, with treatment. For each exposure, one organism was loaded with 150 µL of control water (UV-treated, filtered Lake Superior Water) to each well of the three 96-well plates. A multi-channel pipette was used to deliver 550 µL of dosing solution to each well for a final volume of 700 µL per well. Each assay included DMSO controls, with final in-well DMSO concentrations never exceeding 0.34% in the exposure plate wells.

value: whole body

tag: developmental stage

value: larval

tag: treatment

value: Fipronil amide


title: Nudt15KO_LSC2

city: Shanghai

first: Zhonghui

last: Zhang

state: Shanghai

address: 381 Nanchen Rd

department: School of Life Sciences

institute: Shanghai University

data_processing:
CASACVA software v 1.8
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low quality sequence using fastp v 0.19.5; mRNA-seq reads were aligned to the m38 genome assembly by using Hisat v 2.1.0.
Gene abundance measurements were generated and normalized by using Stringtie; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression was analyzed using edgeR package in R program v 3.4.3.
Assembly: GRCm38.102
Supplementary files format and content: tab-delimited file includes raw fragment counts for each sample

source_name: bone marrow

extract_protocol:
HSCs (Lin-Sca-1+c-Kit+CD150+CD48-) or LSCs (Linlowc-KithighGFP+CD34+CD16/32+) were isolated by FACS and the total RNAs were extracted by Qiagen RNeasy Micro Kit for the construction of sequencing libraries.
The RNA libraries for RNA-seq were prepared using a SMART-seq HT Kit (TAKARA, USA) following manufacturer's protocols.

value: bone marrow

value: primary cells

value: leukemic stem cells


title: snATACseq, In vivo control, donor IVS_7

city: Los Angeles

first: Genevieve

last: Konopka

state: CA

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

description:
Library name: IVS_CTRL_7_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

library_source: genomic single cell

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v7.0.0)
The “mkfastq” command was used to generate FASTQ files and the “cellranger-arc count” command was used to generate raw gene-cell expression matrices
Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters
Human Genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates
Seurat and Signac was used for downstream analysis
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz' contains barcodes, 'features.tsv.gz' containts gene symbols for RNA and chromatin regions for ATAC, 'matrix.mtx.gz' contains raw counts for RNA and ATAC respectively.

molecule: genomic DNA

organism: Homo sapiens

source_name: brain

growth_protocol: MEA stimulation: Using the Maxwell Biosystems MaxOne microelectrode array, stimulation was delivered at configurations of 32 randomly selected electrodes across the entire MEA chip. Stimulation occurred for 15 minutes at 300mv, with new electrode configurations being chosen after 5 bursts of stimulation pulses (bipolar square waves, positive first, 200us phase length, 50ms inter-pulse interval, 5s inter-burst interval). Stimulated slices were flash frozen 10-15 minutes after stimulation. Control samples did not receive stimulation and were instead resting in oxygenated normal artificial CSF (123mM NaCl, 4mM KCl, 25mM NaHCO3, 1.2mM NaH2PO4, 10mM D-Glucose, 1mM CaCl2, 1mM MgSO4, pH 7.3-7.4, 290-310 mOsm). Slices on the MEA were being bathed in oxygenated normal aCSF at 37 degrees Celsius.

extract_protocol:
Libraries were constructed using the 10x Genomics multiome kit and protocol (revision F) with the goal of targeting 10,000 nuclei per sample.
10X multiome

treatment_protocol:
In vivo stimulation: Intraoperative cortical mapping procedures of the premotor area (BA6/8) were completed according to clinical need. Stimulation was delivered for 2 minutes in 30s 60Hz bursts (bipolar square waves, positive first, 200us phase length) with current amplitudes from 2 to 10 mA according to clinical need. Control samples were adjacent (~2cm away) cortex that did not receive direct stimulation. Samples were flash frozen immediately after resection, within 10 to 20 minutes of stimulation.
Nuclei were extracted using a modified version of the 10x Genomics Nuclei Isolation from Complex Tissues demonstrated protocol (CG000375). A sucrose density gradient was used in place of nuclei sorting.

value: brain

value: In vivo control

tag: batch

tag: brain region

value: premotor cortex

tag: sample id

tag: age

tag: Sex

value: female

tag: hemisphere

value: L

tag: epilepsy duration_years


title: snATACseq, In vivo control, donor IVS_6

description:
Library name: IVS_CTRL_6_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: male


title: Nudt15KO_LSC1


title: whole larval P. promelas, Fipronil amide, sample2

description:
Chem10_A_D2_B03
Chem10_counts_matrix.txt


title: clp

description:
Library name: clp1
10x Genomics


title: snATACseq, In vivo control, donor IVS_5

description:
Library name: IVS_CTRL_5_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: R


title: WT_LSC2

value: Wild-type


title: whole larval P. promelas, Fipronil amide, sample4

description:
Chem10_A_D4_D03
Chem10_counts_matrix.txt


title: sham3

description:
Library name: sham3
10x Genomics

value: lymph fluid

value: immune cell


title: whole larval P. promelas, Fipronil amide, sample1

description:
Chem10_A_D1_A03
Chem10_counts_matrix.txt


title: snATACseq, In vivo control, donor IVS_4

description:
Library name: IVS_CTRL_4_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz


title: WT_LSC1


title: Sham2

description:
Library name: sham2
10x Genomics


title: whole larval P. promelas, Metolachlor OA, sample24

description:
Chem1_C_D8_H02
Chem1_counts_matrix.txt

value: Metolachlor OA


title: snATACseq, In vivo control, donor IVS_3

description:
Library name: IVS_CTRL_3_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz


title: sham

description:
Library name: sham1
10x Genomics


title: Nudt15KO_HSC2

value: hematopoietic stem cells


title: whole larval P. promelas, Metolachlor OA, sample23

description:
Chem1_C_D7_G02
Chem1_counts_matrix.txt

value: whole body

value: larval


title: snATACseq, In vivo control, donor IVS_2

description:
Library name: IVS_CTRL_2_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz


title: Nudt15KO_HSC1

value: bone marrow


title: WT_HSC2

value: primary cells


title: snATACseq, In vivo control, donor IVS_1

description:
Library name: IVS_CTRL_1_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz


title: tibias, Ovx_RE_5

city: Nanjing

first: Qing

last: Wang

address: No.138 Xianlin Street

institute: Nanjing University of Chinese Medicine

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads. Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
The result of alignment with the reference genome was stored in a binary file, called a bam file. Using the Stringtie software to assemble the reads, the new transcript was spliced. Aligning the sequencing reads of each sample with the sequence of mRNA transcript sequences by bowtie2, and using eXpress to make gene quantitative analysis, the FPKM value and counts value(the number of reads for each gene in each sample) were obtained.
Using the estimateSizeFactors function of the DESeq (2012) R package to normalize the counts, and using nbinomTest function to calculate pvalue and flodchange values for the difference comparison. Selecting differential transcripts with p-values <= 0.05 and flodchange >= 2，and analysising differential mRNA GO and KEGG enrichment by Hypergeometric Distribution Test.
Assembly: Rnor_6.0
Supplementary files format and content: the FPKM value and counts value(the number of reads for each gene in each sample).

source_name: tibias

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: tibias

value: resistance exercise


title: whole larval P. promelas, Metolachlor OA, sample21

description:
Chem1_C_D5_E02
Chem1_counts_matrix.txt


title: snRNAseq, In vivo control, donor IVS_9

description:
Library name: IVS_CTRL_9_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

molecule: polyA RNA

value: brain

value: In vivo control


title: tibias, Ovx_RE_8


title: WT_HSC1


title: whole larval P. promelas, Metolachlor OA, sample20

description:
Chem1_C_D4_D02
Chem1_counts_matrix.txt


title: Female, MSCs, TAC 4w, hashtag

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

description:
Library name: Hashtag250918_2
10x Genomics. Female samples demultiplexed using TotalSeq-B0301 (F_3), TotalSeq-B0311 (F_1), TotalSeq-B0312 (F_2).

library_source: other

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics) and aligned to the mouse reference genome (GRCm39). Downstream analyses were performed primarily using Seurat (v4) and SCALA. For MSC datasets, cells with fewer than 586 UMIs or mitochondrial gene content >5% were excluded. To remove potential doublets, cells with high  unique molecular identifiers (UMIs) counts (>3,500) were also excluded. After filtering, 5,063 control cells and 2,956 TAC cells were retained. Datasets were integrated using the fastMNN algorithm to correct for batch effects. Clustering was performed using a graph-based approach with the Louvain modularity optimization algorithm. Uniform Manifold Approximation and Projection (UMAP) was used for dimensionality reduction and visualization.
Assembly: Mouse GRCm39
Supplementary files format and content: AnnData h5ad file (MSC.h5ad) containing gene expression count matrix, cell-level metadata (sample identity, cluster assignment, sex), and dimensionality reduction results (UMAP) for female MSCs (control and TAC).

molecule: protein

source_name: Mesenchymal stromal cells

extract_protocol:
Tibiae, femurs, and pelvis were harvested from mice (3 sham-operated and 3 TAC mice) and processed separately for isolation of HSPCs and MSCs. Bone marrow was first collected by flushing with cell suspension medium (PBS containing 2% FBS) and digested with collagenase type II (1 mg/mL) and DNase I (25 U/mL) in HBSS for 30 min at 37 °C. Remaining bone fragments were then crushed and further digested with collagenase type I (2.5 mg/mL) and DNase I (25 U/mL) in HBSS for 45 min at 37 °C. Cell suspensions were washed, filtered through a 100 µm strainer, and subjected to red blood cell lysis using PharmLyse solution. Cells were depleted of hematopoietic and endothelial populations using Mouse CD45 MicroBeads, CD31 MicroBeads, and Lineage Cell Depletion Kit (Miltenyi Biotec) via autoMACS separation. The negatively selected cells were washed and maintained in FACS buffer supplemented with actinomycin D (2 µM). Three biological replicates in each group were labeled with TotalSeq-B0301, B0311, B0312 (anti-mouse Hashtag 1,11,12). Cells were stained with antibodies against lineage markers (Ter119, CD45, CD71, CD144, CD31, CD41, CD61, CD11b, Gr1, CD45R, CD5) and Leptin receptor (Lepr). Lin-Lepr+ cells were sorted as MSCs. Hashtag-labeled cells were pooled within each experimental group.
Single-cell suspensions were processed using the 10x Genomics Chromium platform with the Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index) according to the manufacturer’s instructions. Feature Barcoding technology was used for cell hashing with oligonucleotide-labeled antibodies to enable sample multiplexing.

treatment_protocol: Transverse aortic constriction (TAC) surgery was performed to induce cardiac stress. Sham-operated mice underwent identical surgical procedures without aortic constriction.

value: Mesenchymal stromal cells

value: TAC


title: tibias, Ovx_RE_3


title: whole larval P. promelas, Metolachlor OA, sample22

description:
Chem1_C_D6_F02
Chem1_counts_matrix.txt


title: snRNAseq, In vivo control, donor IVS_8

description:
Library name: IVS_CTRL_8_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: premotor cortex

value: female


title: tibias, Ovx_NE_9

value: non-exercise


title: whole larval P. promelas, Metolachlor OA, sample19

description:
Chem1_C_D3_C02
Chem1_counts_matrix.txt


title: snRNAseq, In vivo control, donor IVS_7

description:
Library name: IVS_CTRL_7_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: L


title: RNA-seq of HCASMC: IL-1b treatment, replicate 3

city: Guangzhou

first: Fengfeng

last: Li

address: 253 Gongye Dadao Zhong, Haizhu District

department: Department of Cardiovascular Medicine

institute: ZhuJiang Hospital, Southern Medical University

description: Library name: sample 15

data_processing:
Raw Data Filtering: Use SOAPnuke to remove adapter-contaminated, low-quality (≥20% Q≤15 bases), and high-N-content (≥5%) reads, generating clean FASTQ data.
Genome Alignment: Align clean reads to the reference genome using HISAT2 with sensitive mode and strand-specific parameters
Transcript Assembly & Quantification: Assemble transcripts and quantify gene expression (FPKM) via RSEM after mapping clean reads to the reference gene set with Bowtie2.
Differential Expression Analysis: Identify differentially expressed genes using DESeq2 (or DEGseq/PoissonDis) with a threshold of Q value ≤0.05 or FDR ≤0.001.
Functional Enrichment: Perform GO and KEGG enrichment analysis on differentially expressed genes using Phyper with hypergeometric testing (Q value ≤0.05).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: Homo sapiens coronary artery smooth muscle cell (HCASMC)

growth_protocol: Human coronary artery smooth muscle cells (HCASMCs, ATCC PCS-100-021) were cultured in Vascular Cell Basal Medium (ATCC PCS-100-030) supplemented with Vascular Smooth Muscle Cell Growth Kit (ATCC PCS-100-042) at 37°C in a humidified 5% CO₂ atmosphere.

extract_protocol:
Total RNA was isolated from HCASMCs using a combined TRIzol-RNeasy Micro Kit method. Cells were lysed in TRIzol reagent (Invitrogen, 15596026) and stored at -80°C until processing. Thawed lysates were mixed with 0.2 volumes of chloroform/iso-amyl alcohol (24:1), followed by centrifugation at 12,000×g for 10 min. The aqueous phase was collected and combined with an equal volume of 75% ethanol. This mixture was then applied to an RNeasy MinElute spin column (QIAGEN, Germany). Subsequent steps included membrane washing with RW1 and RPE buffers, and on-column DNase I digestion using Buffer RDD for 15 min at room temperature to remove genomic DNA contamination. Purified RNA was eluted in 20 µL RNase-free water and assessed for integrity and concentration using Fragment Analyzer, Agilent 2100 Bioanalyzer, or Qseq-400 systems with fluorescent dye-based quantification.
RNA libraries were prepared from total RNA using the Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) according to the manufacturer's instructions. mRNA was enriched through polyA selection and subsequently fragmented. First-strand cDNA synthesis was carried out using random hexamer primers, followed by second-strand synthesis to generate double-stranded cDNA. The cDNA then underwent end repair, A-tailing, and adapter ligation. Finally, the libraries were amplified by PCR, assessed for quality, and sequenced on the BGISEQ-500 platform.

treatment_protocol: Following 24 hours of serum starvation, HCASMCs were maintained in low-serum medium (2% FBS) and treated for 48 hours with one of the following: 20 ng/mL PDGF-BB, 10 ng/mL IL-1β, 25 μM Repsox, or vehicle control (0.5% BSA). All treatments were performed under standard culture conditions (37°C, 5% CO₂).

value: 10 ng/mL IL-1b for 48 hours


title: tibias, Ovx_NE_8


title: RNA-seq of HCASMC: IL-1b treatment, replicate 2

description: Library name: sample 14

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)


title: whole larval P. promelas, Metolachlor OA, sample18

description:
Chem1_C_D2_B02
Chem1_counts_matrix.txt

value: Metolachlor OA


title: snRNAseq, In vivo control, donor IVS_6

description:
Library name: IVS_CTRL_6_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: male


title: tibias, Ovx_NE_6


title: RNA-seq of HCASMC: IL-1b treatment, replicate 1

description: Library name: sample 13


title: snRNAseq, In vivo control, donor IVS_5

description:
Library name: IVS_CTRL_5_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: R


title: whole larval P. promelas, Metolachlor OA, sample17

description:
Chem1_C_D1_A02
Chem1_counts_matrix.txt

value: whole body

value: larval


title: RNA-seq of HCASMC: control for IL-1b treatment, replicate 3

description: Library name: sample 12

value: vehicle control (0.5% BSA) for 48 hours


title: RNA-seq of HCASMC: control for IL-1b treatment, replicate 2

description: Library name: sample 11


title: whole larval P. promelas, Metolachlor OA, sample16

description:
Chem1_B_D8_H02
Chem1_counts_matrix.txt


title: tibias, Sham_8

value: tibias

value: sham-operated


title: tibias, Sham_7


title: whole larval P. promelas, Metolachlor OA, sample15

description:
Chem1_B_D7_G02
Chem1_counts_matrix.txt


title: snRNAseq, In vivo control, donor IVS_3

description:
Library name: IVS_CTRL_3_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: brain

value: In vivo control


title: RNA-seq of HCASMC: control for IL-1b treatment, replicate 1

description: Library name: sample 10


title: tibias, Sham_12


title: RNA-seq of HCASMC: Repsox treatment, replicate 3

description: Library name: sample 9

value: 25 μM Repsox for 48 hours


title: whole larval P. promelas, Metolachlor OA, sample14

description:
Chem1_B_D6_F02
Chem1_counts_matrix.txt


title: iMGL-iNSpheroids, iPSC IMR90-4 cell line

city: Oeiras

first: Catarina

middle: Monteiro

last: Gomes

state: Lisboa

address: Av. República, Qta. do Marquês

country: Portugal

institute: iBET

description: Library name: IMR-Ctrl

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the geneID feature in the annotation file. Only unique reads that fell within exon regions were counted. After the extraction of gene hit counts, the gene hit counts table was used for downstream analysis. TPM values for microglia gene targets were used and represent the number of a given transcript over one million full-length transcripts.
Supplementary files format and content: TPM (Transcripts Per Million) values, normalization method used in RNA-seq to quantify gene expression. Values obtained after read count, lenght normalization and scaling. TPM value is obtained by multiplying the normalized value by one million.
Assembly: Homo sapiens GRCh38 reference genome

source_name: Brain

growth_protocol: Prior to inoculation, the vessels of the Ambr® 15 Cell Culture Bioreactor (from here onwards referred to as microbioreactor) were loaded onto the platform, and stabilized for pH (7.4), temperature (37 °C) and pO2 (15%), as described previously26. The working volume range was 11-15 mL, and the impeller speed was set to 300 rpm, in down-pumping mode. The iNSpheroids were collected from the software-controlled stirred-tank DASGIP Bioblock bioreactor system (Eppendorf), sedimented and resuspended in fresh medium prior to the microbioreactor inoculum. iNSpheroids were inoculated at 1.0 x 106 cell/mL. An iMGL suspension at 0.1 x 106 cell/mL was added subsequently to the co-culture vessels. Cells were co-cultured for three days prior to downstream analysis or inflammatory challenge. The culture medium was composed of a 1:1 mixture of DMEM/F-12 without phenol red with 0.1X Glutamax and Neurobasal™ Medium (Gibco™, cat. no. 21103049), 1% B27 supplement, 1.6 μg/mL glucose, 10 μg/mL insulin, 10 μg/mL putrescin, 63 ng/mL progesterone, 50 μg/mL apotransferrin, 50 ng/mL sodium selenium (all from Sigma-Aldrich), 200 mM ascorbic acid (Wako), recombinant human M-CSF, IL-34 and TGF-𝛽 (all 10 ng/mL, Peprotech, 300-25, 200-34, 100-21, respectively).

extract_protocol:
The RNA sequencing workflow after RNA isolation included initial Poly-A selection-based mRNA enrichment, mRNA fragmentation, and random priming with subsequent first- and second-strand complementary cDNA synthesis. End-repair 5’ phosphorylation and adenine nucleotide (dA)–tailing was performed.
Adaptor ligation, polymerase chain reaction (PCR) enrichment, and Illumina NovaSeq technology–based sequencing with 2× 150–base pair (bp) read length were carried out.

treatment_protocol: iMGL-iNSpheroids from both cell lines were harvested after three days of co-culture and sedimented by centrifugation at 300 xg, for 5 min. Cells were cryopreserved in a cell freezing medium, Cryostor CS10 (100-1061, STEMCELLTechnologies) and stored at -80 °C. The frozen samples were shipped on dry ice to Genewiz (Leipzig, Germany) for RNA sequencing analysis.

value: Brain

value: iPSC IMR90-4

value: hiPSC-derived CNS cells


title: snRNAseq, In vivo control, donor IVS_4

description:
Library name: IVS_CTRL_4_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: premotor cortex

value: female

value: L


title: whole larval P. promelas, Metolachlor OA, sample13

description:
Chem1_B_D5_E02
Chem1_counts_matrix.txt

value: Metolachlor OA


title: RNA-seq of HCASMC: Repsox treatment, replicate 2

description: Library name: sample 8

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)


title: iMGL-iNSpheroids, iPSC DF6-9-9T.B cell line

description: Library name: DF6-Ctrl

value: iPSC DF6-9-9T.B


title: WT3

city: Wuhan

first: Zhensheng

last: Qiao

address: School of Life Sciences, Hubei University, Wuhan, China

institute: Hubei University

description:
Library name: sample 12
WT3

data_processing:
Raw reads were filtered using fastp to remove adapters and low-quality reads (Q < 20). Clean reads were aligned to the Oryza sativa Nipponbare reference genome (IRGSP-1.0) using HISAT2.
Gene expression levels were quantified using featureCounts, and read counts were normalized to FPKM.
Differential expression analysis between mock and inoculated groups was performed using DESeq2. Genes with |log2FC| ≥ 1 and FDR < 0.05 were considered significantly differentially expressed.
Assembly: Oryza sativa (japonica cultivar-group) reference genome assembly IRGSP Build 1.0 (GCA_000005425.2)
Supplementary files format and content: gene.counts.matrix.xls

organism: Oryza sativa

source_name: leaf

extract_protocol:
Total RNA was extracted from rice leaf tissues using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and purity were assessed using agarose gel electrophoresis, NanoDrop spectrophotometer and Agilent 2100 Bioanalyzer. Only high-quality RNA samples (RIN ≥ 7.0, 260/280 ratio ≥ 1.8) were used for library construction.
Strand-specific RNA-seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and reverse transcribed into cDNA. After end repair, A-tailing and adapter ligation, the library fragments were PCR-amplified and purified. Library quality and concentration were verified using the Agilent 2100 Bioanalyzer and qPCR.

value: leaf

value: WT

value: Before Magnaporthe oryzae inoculation


title: RNA-seq of HCASMC: Repsox treatment, replicate 1

description: Library name: sample 7


title: snATACseq, MEA stimulation, donor MEA_5

description:
Library name: MEA_STIM_5_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: MEA stimulation

value: temporal cortex

value: R


title: WT2

description:
Library name: sample 11
WT2


title: RNA-seq of HCASMC: PDGF-BB treatment, replicate 3

description: Library name: sample 6

value: 20 ng/mL PDGF-BB for 48 hours


title: whole larval P. promelas, Metolachlor OA, sample10

description:
Chem1_B_D2_B02
Chem1_counts_matrix.txt

value: whole body

value: larval


title: WT1

description:
Library name: sample 10
WT1


title: RNA-seq of HCASMC: PDGF-BB treatment, replicate 2

description: Library name: sample 5


title: snATACseq, MEA stimulation, donor MEA_4

description:
Library name: MEA_STIM_4_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: brain

value: male


title: whole larval P. promelas, Metolachlor OA, sample9

description:
Chem1_B_D1_A02
Chem1_counts_matrix.txt


title: RNA-seq of HCASMC: PDGF-BB treatment, replicate 1

description: Library name: sample 4


title: P3

description:
Library name: sample 9
P3

value: Magnaporthe oryzae inoculation


title: snATACseq, MEA stimulation, donor MEA_3

description:
Library name: MEA_STIM_3_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz


title: whole larval P. promelas, Metolachlor OA, sample8

description:
Chem1_A_D8_H02
Chem1_counts_matrix.txt


title: snATACseq, MEA stimulation, donor MEA_2

description:
Library name: MEA_STIM_2_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: female


title: P2

description:
Library name: sample 8
P2


title: whole larval P. promelas, Metolachlor OA, sample7

description:
Chem1_A_D7_G02
Chem1_counts_matrix.txt


title: P1

description:
Library name: sample 7
P1


title: whole larval P. promelas, Metolachlor OA, sample6

description:
Chem1_A_D6_F02
Chem1_counts_matrix.txt


title: snATACseq, MEA stimulation, donor MEA_1

description:
Library name: MEA_STIM_1_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: L


title: snRNAseq, MEA stimulation, donor MEA_6

description:
Library name: MEA_STIM_6_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz


title: RNA-seq of HCASMC: control, replicate 1

description: Library name: sample 1

value: vehicle control (0.5% BSA) for 48 hours


title: F3

description:
Library name: sample 6
F3


title: snRNAseq, MEA stimulation, donor MEA_5

description:
Library name: MEA_STIM_5_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz


title: RNA-seq of HCASMC: DDIT4 knockdown, replicate 2

description: Library name: sample 8

treatment_protocol: HCASMCs were infected with recombinant adenoviruses at a multiplicity of infection (MOI) of 100 for 48 hours to achieve genetic manipulation. The specific viruses used included:Empty adenoviral vector (serving as negative control); Adenovirus encoding full-length human DDIT4 (for overexpression); Adenovirus encoding a non-targeting shRNA (for knockdown control); Adenovirus encoding a DDIT4-targeting shRNA (for knockdown).

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)

value: adenovirus carrying DDIT4-targeting shRNA


title: F2

description:
Library name: sample 5
F2

value: leaf


title: whole larval P. promelas, Metolachlor OA, sample4

description:
Chem1_A_D4_D02
Chem1_counts_matrix.txt

value: Metolachlor OA


title: snRNAseq, MEA stimulation, donor MEA_4

description:
Library name: MEA_STIM_4_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz


title: RNA-seq of HCASMC: DDIT4 knockdown, replicate 1

description: Library name: sample 7


title: whole larval P. promelas, Metolachlor OA, sample3

description:
Chem1_A_D3_C02
Chem1_counts_matrix.txt


title: F1

description:
Library name: sample 4
F1


title: snRNAseq, MEA stimulation, donor MEA_3

description:
Library name: MEA_STIM_3_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz


title: RNA-seq of HCASMC: non-targeting shRNA control, replicate 2

description: Library name: sample 6

value: adenovirus carrying non-targeting shRNA


title: M3

description:
Library name: sample 3
M3

value: WT


title: whole larval P. promelas, Metolachlor OA, sample2

description:
Chem1_A_D2_B02
Chem1_counts_matrix.txt


title: snRNAseq, MEA stimulation, donor MEA_2

description:
Library name: MEA_STIM_2_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz

value: MEA stimulation

value: temporal cortex


title: M2

description:
Library name: sample 2
M2


title: RNA-seq of HCASMC: DDIT4 overexpression, replicate 2

description: Library name: sample 4


title: snRNAseq, MEA stimulation, donor MEA_1

description:
Library name: MEA_STIM_1_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz


title: M1

description:
Library name: sample 1
M1


title: KG-1a, shNYNRIN4

city: Chongqing

first: Jianming

state: Chongqing

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing medical university

description: Library name: shNYNRIN-4

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample …

source_name: Bone marrow

extract_protocol:
About 1000000 KG-1a cells transfected with lentivirus were isolated by FACS and the mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction RNA libraries were prepared for sequencing using standard Illumina protocols
The mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction.RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Leukemia stem cell

value: NYNRIN-knockdown


title: snATACseq, MEA control, donor MEA_6

description:
Library name: MEA_CTRL_6_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: brain

value: MEA control

value: R


title: B.sub_TST3

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

description: Library name: TST_3

data_processing:
read trimming with Trimmomatic
read alignment with STAR
read couning with featureCounts
Assembly: Drosophila melanogaster BDGP6.54
Supplementary files format and content: Tab-separated files, with 1st column – Flybase gene identifier, and 2nd – number of reads spanning into exonic regions of genome

organism: Drosophila melanogaster

growth_protocol: D.melanogaster flies were maintained on standard yeast-agar medium, at 24 Celsius temperature, with 12/12 light/dark incubator.

extract_protocol:
Total RNA was isolated using RNAzol RT reagent (Molecular Research Center, USA). Briefly, 10–20 flies were homogenized in 200 μL of RNAzol reagent, after which 80 μL of dH₂O was added, and the mixture was incubated on ice for 10 minutes. The homogenate was then centrifuged at 15,000×g for 10 minutes at 4°C. The resulting supernatant was collected and transferred to a new sterile 1.5-mL tube. An additional purification step was performed by adding 1 μL of 4-bromoanisole (MRC, BN 191). The mixture was incubated at room temperature for 3 minutes and centrifuged again at 15,000×g for 10 minutes at +4°C. The supernatant was transferred to a new sterile tube, and 200 μL of isopropyl alcohol was added to precipitate the RNA. The mixture was incubated on ice for 30 min and then centrifuged at 20,000×g for 20 min at +4°C. The RNA pellet was washed twice with chilled 75% ethanol and dissolved in RNase-free water.
RNA-seq libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (cat# NR605-01, Vazyme Biotech, China) according to the manufacturer’s protocol. Sequencing was performed on an Illumina NextSeq 500 platform

treatment_protocol: 5 day old flies were infected with bacteria (Bacillus subtilis) by needle pricking method. Gram-positive bacterium Bacillus Subtilis with a (DAP)-type peptidoglycan  at a concentration of 5 OD was used.

value: whole body

value: TST1 deletion

value: B.subtilis inoculated


title: KG-1a, shNYNRIN3

description: Library name: shNYNRIN-3


title: snATACseq, MEA control, donor MEA_5

description:
Library name: MEA_CTRL_5_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: female


title: RNA-seq of HCASMC: negative control, replicate 2

description: Library name: sample 2

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)

value: empty adenoviral vector


title: KG-1a, Control4

description: Library name: shCTL-2


title: whole larval P. promelas, Metolachlor OA, sample11

description:
Chem1_B_D3_C02
Chem1_counts_matrix.txt

value: larval

value: Metolachlor OA


title: snATACseq, MEA control, donor MEA_4

description:
Library name: MEA_CTRL_4_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: male

value: L


title: B.sub_TST1

description: Library name: TST_1


title: RNA-seq of HCASMC: negative control, replicate 1

description: Library name: sample 1


title: KG-1a, Control3

description: Library name: shCTL-1

value: WT


title: snATACseq, MEA control, donor MEA_3

description:
Library name: MEA_CTRL_3_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: temporal cortex


title: SUR 3

city: Ningbo

first: Yuhui

last: Zhu

address: No. 59 Liuting Street, Haishu District

department: Anesthesiology

institute: The First Affiliated Hospital of Ningbo University

data_processing:
DNBSEG
Sequence reads were tirmmed for adaptor sequence/lpw-quality sequence using SOAPnuke v1.5.2.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 v2.0.4.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw count for each sample
Supplementary files format and content: tab-delimited text files includes FPKM for each sample

source_name: alveoli

growth_protocol: MH-S AM cells were cultured in 1640 medium containing 10% fetal bovine serum (FBS), 0.05 mM - Mercaptoethanol and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
RNA was harvested using Trizol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
MGIEasy RNA Library Prep Kit

treatment_protocol: MH-S AM cells were incubated at a final concentration of 1 μg/ml LPS for 4h as LPS group; cells were stimulated by 200 μM suramin  and 1 μg/ml LPS for 4h as SUR+LPS group;1640 medium was added as CON group.

value: alveoli

value: MH-S

value: alveolar macrophage

value: Suramin


title: KG-1a, shNYNRIN2

description: Library name: shNYNRIN-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Assembly: hg38
Supplementary files format and content: RPKM values for each Sample

value: Bone marrow

value: Leukemia stem cell

value: NYNRIN-knockdown


title: snATACseq, MEA control, donor MEA_2

description:
Library name: MEA_CTRL_2_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: brain

value: MEA control

value: R


title: SUR 2


title: B.sub_CBS/CSE/TST2

description: Library name: MCC_2

value: whole body

value: CBS/CSE/TST1 deletion

value: B.subtilis inoculated


title: snATACseq, MEA control, donor MEA_1

description:
Library name: MEA_CTRL_1_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: female


title: B.sub_CBS/CSE/TST1

description: Library name: MCC_1


title: SUR 1


title: LPS 3

value: lipopolysaccharide (LPS)


title: B.sub_CBS/CSE3

description: Library name: BE_3

value: CBS/CSE deletion


title: snRNAseq, MEA control, donor MEA_5

description:
Library name: MEA_CTRL_5_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz

value: temporal cortex


title: LPS 2

value: alveoli


title: BY4741_CRISPR_mutant2_MNase_replicate_2

city: Kansas City

first: Melanie

last: Weilert

state: MO

institute: Stowers Institute for Medical Research

description: Library name: sc_cover2_crispr_mutant_fixed_mnase_100U_2

library_source: genomic

data_processing:
Paired-end reads were aligned against the sacCer3 genome using bowtie2 (--very-sensitive -X 1000).
For all paired reads, we created coverage tracks of the 3′ endpoints of each fragment, 5′ endpoints of each fragment, and fragment midpoints (midpoints are provided as supplemental tracks). 3′ and 5′ in this context are with respect to the genome. Fragment midpoints represent the centers of each nucleosomal fragment, thus act as proxy dyad coverage.
Assembly: UCSC sacCer3
Supplementary files format and content: BigWig coverage of MNase-seq fragment midpoints

organism: Saccharomyces cerevisiae

source_name: S288C-derivative laboratory strain

growth_protocol: BY4741 yeast cultures were grown at 30°C in YPD to OD600 0.8-1.

extract_protocol:
BY4741 yeast cultures were first crosslinked with 1% formaldehyde for 15 minutes at room temperature. 125mM Glycine was added to quench the reaction. Cell pellets were resuspended in spheroplasting buffer (1M Sorbitol, 5 mM fi-mercaptoethanol, 50mM Tris pH 7.5, 2 mg/ml zymolyase (AMS Bio cat no: 120493-1); 1 mL of buffer per 20 mL of cell culture) and incubated for 15 min. at room temperature. The derived spheroplasts were treated with 100U MNase (NEB cat no: M0247S) for 30-40 min at 37°C. The reactions were stopped by the addition of EDTA pH 8.0 (50 mM final conc.) and EGTA pH 8.0 (50 mM final conc.). Samples were then incubated with RNase A (Thermo Scientific, EN0531, final conc. 0.2 mg/ml) at 42°C for 30 min to digest RNA. The crosslinks were reversed by adding SDS and proteinase K (Invitrogen cat no: 25530049, 1mg/ml final concentration) and incubation at 65°C for 45 min.
DNA was extracted using the Monarch PCR & DNA cleanup kit. Samples were resolved on 1% agarose gel to evaluate the digestion. Mononucleosome-sized bands were extracted and libraries were constructed from 10ng purified DNA using the Watchmaker Genomics according to the manufacturer's instructions. Paired-end sequencing was performed on AVITI (2x 75bp cycles).

treatment_protocol: For the CRISPR experiments, derived from BY4741 strains, a mutant strain with three point mutations was created using CRISPR Cas9-based genome editing technique. A 20 bp gRNA close to the mutation site was designed with BsaI overhangs and ordered as oligonucleotides. The gRNA-encoding oligonucleotides were annealed and cloned into the pCASB plasmid (Addgene 190175) using BsaIHF-v2 enzyme and T4 DNA ligase. The cloning reaction was transformed into E. coli and plated on Kanamycin selection plates. The plasmids were then isolated and verified by Sanger sequencing. A 160 bp homology-directed repair (HDR) template was designed to contain the desired mutant sequence, synthesized by Genescript and amplified by PCR.Yeast cells were then co-transformed with the cloned plasmid encoding Cas9 and gRNA, along with the HDR template. Transformants containing pCASB were selected on G418-containing media. Colonies were streaked twice, and isolates were screened for loss of the gRNA plasmid via replica plating to G418. For each isolate, genomic DNA was extracted, and the region of interest was amplified by PCR, purified and validated by Sanger sequencing.

tag: strain

value: S288C-derivative laboratory strain

value: CRISPR Pho5 upstream mutant


title: snRNAseq, MEA control, donor MEA_4

description:
Library name: MEA_CTRL_4_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz

value: male

value: L


title: KG-1a, shNYNRIN1

description: Library name: shNYNRIN-1

value: Bone marrow

value: Leukemia stem cell


title: KG-1a, Control2

description: Library name: shCTL-4

value: WT


title: LPS 1

value: MH-S

value: alveolar macrophage


title: B.sub_CBS/CSE1

description: Library name: BE_1

value: whole body


title: snRNAseq, MEA control, donor MEA_6

description:
Library name: MEA_CTRL_6_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz

value: brain

value: MEA control

value: R


title: KG-1a, Control1

description: Library name: shCTL-3


title: BY4741_CRISPR_mutant2_MNase_replicate_1

description: Library name: sc_cover2_crispr_mutant_fixed_mnase_100U_1


title: CON 3

value: Control


title: B.sub_Control3

description: Library name: 58492_3

value: B.subtilis inoculated


title: snRNAseq, MEA control, donor MEA_3

description:
Library name: MEA_CTRL_3_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz

value: temporal cortex


title: snRNAseq, In vivo control, donor IVS_2

description:
Library name: IVS_CTRL_2_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: In vivo control

value: premotor cortex


title: snRNAseq, MEA control, donor MEA_2

description:
Library name: MEA_CTRL_2_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz

value: female


title: BY4741_CRISPR_mutant3_MNase_replicate_2

description: Library name: sc_cover1_crispr_mutant_fixed_mnase_100U_2

value: S288C-derivative laboratory strain

value: CRISPR Pho5 upstream mutant


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample10

description:
Chem8_B_D2_B09
Chem8_counts_matrix.txt

value: larval

value: 4-Chlorophenyl methyl sulfoxide


title: snRNAseq, In vivo control, donor IVS_1

description:
Library name: IVS_CTRL_1_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: male


title: CON 2

value: alveoli

value: MH-S


title: B.sub_Control2

description: Library name: 58492_2

value: whole body


title: B.sub_CBS/CSE2

description: Library name: BE_2

value: CBS/CSE deletion


title: snATACseq, MEA stimulation, donor MEA_6

description:
Library name: MEA_STIM_6_ATAC
mea_atac_barcodes.tsv.gz
mea_atac_features.tsv.gz
mea_atac_matrix.mtx.gz

value: brain

value: MEA stimulation


title: BY4741_CRISPR_mutant3_MNase_replicate_1

description: Library name: sc_cover1_crispr_mutant_fixed_mnase_100U_1


title: whole larval P. promelas, Metolachlor OA, sample12

description:
Chem1_B_D4_D02
Chem1_counts_matrix.txt

value: Metolachlor OA


title: snRNAseq, MEA control, donor MEA_1

description:
Library name: MEA_CTRL_1_RNA
mea_rna_barcodes.tsv.gz
mea_rna_features.tsv.gz
mea_rna_matrix.mtx.gz

value: MEA control

value: L


title: CON 1

value: alveolar macrophage

value: Control


title: B.sub_Control1

description: Library name: 58492_1

value: B.subtilis inoculated


title: MEP diploid Pgpd SAK1 overexpression, 48h, rep 4

status: Public on Jun 05 2026

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description: Library name: SAK1 7

data_processing:
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.48.1
Assembly: R64-1-1
Supplementary files format and content: Supplementary files format and content: Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.
Supplementary files format and content: tsv

source_name: Whole organism

growth_protocol: All cells were grown in YPD media (2% peptone, 1% yeast extract, 2% glucose) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPD then inoculated in 125 ml YPD at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 hours. An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.

extract_protocol:
Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C. Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit. 150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).
NEBNext Ultra II Direction RNA-seq kit

value: Whole organism

value: Pgpd SAK1 overexpression


title: MEP diploid wild type, log, rep 7

description: Library name: wt log 7

value: wild type

value: log


title: MEP diploid wild type, 48h, rep 7

description: Library name: wt 48h 7


title: MEP diploid wild type oleic acid, 48 h, rep 2

description: Library name: wt 48h oleic 2


title: MEP diploid wild type oleic acid, 48 h, rep 3

description: Library name: wt 48h oleic 3


title: MEP diploid wild type oleic acid, 48 h, rep 1

description: Library name: wt 48h oleic 1


title: MEP diploid wild type oleic acid, log, rep 1

description: Library name: wt log oleic 1

value: log + 0.04% oleic acid + 0.04% Tween 80


title: MEP diploid wild type oleic acid, log, rep 2

description: Library name: wt log oleic 2


title: RNA-seq of HCASMC: control, replicate 3

description: Library name: sample 3

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)

value: vehicle control (0.5% BSA) for 48 hours


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 48h, rep 4

description: Library name: A2A 48h 4


title: RNA-seq of HCASMC: control, replicate 2

description: Library name: sample 2


title: Baseline sample ADK023-pre (week 0)

city: Maribor

first: Martina

last: Krušič

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine

description:
Library name: ADK023-pre
Column name in RawCounts.txt: ADK023pre

data_processing:
A three-stage approach was employed for differential expression analysis, similar to that used in a previously published article by our group. In stage one, differentially expressed genes influenced by dupilumab therapy were identified. These genes were excluded prior to the second stage. Stage two consisted of two substages aimed at identifying differentially expressed genes associated with inflammation. The union of unique differentially expressed genes identified in both substages was considered to represent inflammation-related genes and was subsequently removed from the analysis prior to the third stage. In the final stage, differentially expressed genes that could serve as predictors of response to dupilumab were determined.
Blood transcriptome analysis for each stage was performed using a custom pipeline developed by the Center for Human Molecular Genetics and Pharmacogenomics in the environment R 4.5.2, employing various packages as described in previously published studies. In stage one, genes with an adjusted p-value < 0.05 were considered differentially expressed. In all subsequent stages, a p-value < 0.05 was used as the significance threshold.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file (RawCounts_StageThree.txt) include raw counts for samples included in the stage three analysis.

source_name: Blood

extract_protocol:
RNA samples were extracted from peripheral blood mononuclear cells using the innuPREP Micro RNA Kit (iST Innuscreen GmbH).
RNA samples were sequenced at BGI facilities using BGI Optimal Dual-mode mRNA Library Prep Kit PE150 on the DNBSEQ G400 (China). Raw data containing adapter sequences or low-quality reads were removed using the SOAPnuke tool by BGI.

value: Blood

value: F

value: Naïve to biological treatment


title: Follow-up sample ADK023-post (week 16-18)

description:
Library name: ADK023-post
Column name in RawCounts.txt: ADK023post

value: Responder to dupilumab


title: Follow-up sample ADK022-post (week 16-18)

description:
Library name: ADK022-post
Column name in RawCounts.txt: ADK022post

value: M


title: Baseline sample ADK022-pre (week 0)

description:
Library name: ADK022-pre
Column name in RawCounts.txt: ADK022pre


title: whole larval P. promelas, Metolachlor OA, sample5

description:
Chem1_A_D5_E02
Chem1_counts_matrix.txt

value: whole body

value: larval

value: Metolachlor OA


title: Baseline sample ADK020-pre (week 0)

description:
Library name: ADK020-pre
Column name in RawCounts.txt: ADK020pre


title: Follow-up sample ADK019-post (week 16-18)

description:
Library name: ADK019-post
Column name in RawCounts.txt: ADK019post


title: Baseline sample ADK019-pre (week 0)

description:
Library name: ADK019-pre
Column name in RawCounts.txt: ADK019pre


title: Baseline sample ADK018-pre (week 0)

description:
Library name: ADK018-pre
Column name in RawCounts.txt: ADK018pre


title: Follow-up sample ADK018-post (week 16-18)

description:
Library name: ADK018-post
Column name in RawCounts.txt: ADK018post


title: Follow-up sample ADK020-post (week 16-18)

description:
Library name: ADK020-post
Column name in RawCounts.txt: ADK020post


title: Follow-up sample ADK016-post (week 16-18)

description:
Library name: ADK016-post
Column name in RawCounts.txt: ADK016post

value: Non-responder to dupilumab


title: Follow-up sample ADK015-post (week 16-18)

description:
Library name: ADK015-post
Column name in RawCounts.txt: ADK015post


title: Baseline sample ADK016-pre (week 0)

description:
Library name: ADK016-pre
Column name in RawCounts.txt: ADK016pre


title: Baseline sample ADK015-pre (week 0)

description:
Library name: ADK015-pre
Column name in RawCounts.txt: ADK015pre


title: Baseline sample ADK014-pre (week 0)

description:
Library name: ADK014-pre
Column name in RawCounts.txt: ADK014pre


title: Follow-up sample ADK013-post (week 16-18)

description:
Library name: ADK013-post
Column name in RawCounts.txt: ADK013post


title: Baseline sample ADK013-pre (week 0)

description:
Library name: ADK013-pre
Column name in RawCounts.txt: ADK013pre


title: Follow-up sample ADK014-post (week 16-18)

description:
Library name: ADK014-post
Column name in RawCounts.txt: ADK014post


title: Baseline sample ADK011-pre (week 0)

description:
Library name: ADK011-pre
Column name in RawCounts.txt: ADK011pre


title: Follow-up sample ADK011-post (week 16-18)

description:
Library name: ADK011-post
Column name in RawCounts.txt: ADK011post


title: Follow-up sample ADK010-post (week 16-18)

description:
Library name: ADK010-post
Column name in RawCounts.txt: ADK010post


title: Baseline sample ADK010-pre (week 0)

description:
Library name: ADK010-pre
Column name in RawCounts.txt: ADK010pre


title: Follow-up sample ADK008-post (week 16-18)

description:
Library name: ADK008-post
Column name in RawCounts.txt: ADK008post


title: Baseline sample ADK008-pre (week 0)

description:
Library name: ADK008-pre
Column name in RawCounts.txt: ADK008pre


title: Follow-up sample ADK007-post (week 16-18)

description:
Library name: ADK007-post
Column name in RawCounts.txt: ADK007post


title: RNA-seq of HCASMC: non-targeting shRNA control, replicate 1

description: Library name: sample 5

value: adenovirus carrying non-targeting shRNA


title: whole larval P. promelas, Metolachlor OA, sample1

description:
Chem1_A_D1_A02
Chem1_counts_matrix.txt


title: Baseline sample ADK007-pre (week 0)

description:
Library name: ADK007-pre
Column name in RawCounts.txt: ADK007pre


title: Follow-up sample ADK006-post (week 16-18)

description:
Library name: ADK006-post
Column name in RawCounts.txt: ADK006post


title: Baseline sample ADK006-pre (week 0)

description:
Library name: ADK006-pre
Column name in RawCounts.txt: ADK006pre


title: Follow-up sample ADK003-post (week 16-18)

description:
Library name: ADK003-post
Column name in RawCounts.txt: ADK003post


title: Baseline sample ADK003-pre (week 0)

description:
Library name: ADK003-pre
Column name in RawCounts.txt: ADK003pre


title: Follow-up sample ADK002-post (week 16-18)

description:
Library name: ADK002-post
Column name in RawCounts.txt: ADK002post


title: Baseline sample ADK002-pre (week 0)

description:
Library name: ADK002-pre
Column name in RawCounts.txt: ADK002pre


title: Follow-up sample ADK001-post (week 16-18)

description:
Library name: ADK001-post
Column name in RawCounts.txt: ADK001post


title: Baseline sample ADK001-pre (week 0)

description:
Library name: ADK001-pre
Column name in RawCounts.txt: ADK001pre


title: H3K27ac_CD2_cntrl_rep2

city: Miami

first: Mustafa

last: Tekin

state: Florida

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

description: Library name: H3K27ac_CD2_cntrl_2

data_processing:
Sequence reads were mapped to hg38 reference genome with Bowtie 2.
Normalized ChIP-seq read densities were visualized using deepTools and/or Integrative Genomics Viewer (IGV).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: CD2 iPSCs

growth_protocol: The generation of inner ear organoids (IEOs) have been described in the Methods of this study (Zafeer et. al. 2026). About 200 organoids were pooled for the downstream ChIP-seq analysis.

extract_protocol:
Cells were lysed as described in Ortabozkoyun et al., 2022 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Covaris sonicator. ChIP was performed by using antibodies listed. Chromatin from Drosophila (1:100 ratio to CD2 cells chromatin), and Drosophila-specific H2Av antibody were used as spike-in control in each sample.
ChIP-seq Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).

value: CD2 iPSCs

value: CD2 iPSC-derived inner ear organoids (IEOs)

value: WT

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_CD2_166_patient_rep1

description: Library name: H3K27ac_CD2_166_patient

value: Patient-derived deletion


title: H3K27ac_CD2_cntrl_rep1

description: Library name: H3K27ac_CD2_cntrl_1


title: H3K4me1_CD2_166_patient_rep1

description: Library name: H3K4me1_CD2_166_patient

value: H3K4me1 (Abcam, ab8895)


title: H3K4me1_CD2_cntrl_rep1

description: Library name: H3K4me1_CD2_cntrl_1


title: H3K4me1_CD2_cntrl_rep2

description: Library name: H3K4me1_CD2_cntrl_2


title: CTCF_CD2_166_patient_rep1

description: Library name: CTCF_CD2_166_patient

value: CTCF (Abcam, ab128873)


title: CTCF_CD2_cntrl_rep2

description: Library name: CTCF_CD2_cntrl_2


title: CD2_input

description: Library name: CD2_input

value: Not Applicable


title: catID_29

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

description:
Library name: PAM73696__bc_3.fastq_catID_29
column 7 in Counts File

data_processing:
mapping against felCat9
base-calling using Guppy
pre-processing with fastP
allignment with Minimap2
FeatureCounts
Assembly: felCat9
Supplementary files format and content: tab-delimited file with counts per sample in each collumn

organism: Felis catus

source_name: cardiac biopsy left ventricle

extract_protocol:
RNEasy, Qiagen
SQK-RNA002, Oxford Nanopore

treatment_protocol: cardiac tissue collected post mortem

value: cardiac biopsy left ventricle


title: catID_37

description:
Library name: PAM73696__bc_1.fastq_catID_37
column 6 in Counts File


title: catID_36

description:
Library name: PAM73681_bc_4.fastq_catID_36
column 5 in Counts File


title: catID_15

description:
Library name: PAM73681_bc_2.fastq_catID_15
column 11 in Counts File


title: catID_10

description:
Library name: PAM73681_bc_1.fastq_catID_10
column 10 in Counts File


title: catID_30

description:
Library name: PAK20671_bc_3.fastq_catID_30
column 2 in Counts File


title: catID_31

description:
Library name: PAK20671_bc_4.fastq_catID_31
column 3 in Counts File


title: catID_11

description:
Library name: PAK20671_bc_1.fastq_catID_11
column 13 in Counts File


title: ICoVax_133_D30 (high reacto)

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: Amphipôle, Quartier UNIL-Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: Library name: ICoVax_133_D30

data_processing:
ATAC-seq libraries were processed with the nfcore atacseq pipeline (release 2.1.0)l. As part of the atacseq pipeline, adapter trimming was performed with Trim Garlore (0.6.7) and reads were mapped to the human genome (GRCh38.p13) from ensembl. Duplicate reads marked using MarkDuplicates from Picard (3.0.0). Reads were filtered with SAMtools (1.17) and broad peaks were called with MACS2 (2.2.7.1) and annotated with HOMER (4.11). A consensus peakset was created across all samples with BEDTools (2.30.0). The consensus peakset was filtered to keep peaks from primary chromosomes, remove peaks overlapping ENCODE blacklisted regions from the human genome, and keep peaks annotated to protein coding genes for downstream analyses. Peaks were classified according to their distance from the nearest gene transcription start site as: promoter (-2 kb to +500 bp), distal (-10 kb to + 10 kb, excluding the promoter region), and trans peaks (< -10 kb and > +10 kb).
Differential accessibility analysis and count matrix generation were performed using DiffBind (3.12.0) in R. Raw counts across the filtered consensus peakset were computed with dba.count() from DiffBind from the corresponding bam files.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw peak-level counts for each sample across the filtered consensus peak set.
Supplementary files format and content: The filtered consensus peak set annotation file is a tab-delimited text file which contains the annotation of consensus peaks obtained from the nfcore atacseq pipeline, annotated with HOMER and further classified into promoter, distal, and trans peaks.

source_name: Monocytes

growth_protocol: Venous blood was collected in CPT tubes (BD) for peripheral blood monocuclear cell (PBMC) isolation. PBMCs were isolated by density gradient centrifugation. Red blood cells were lysed (ACK lysis buffer, Lonza) and PBMCs were resuspended in FCS containing 10% DMSO and cryopreserved in liquid nitrogen. PBMCs were thawed and cell-surface stained for 30 minutes at 4ºC and draq7 (1:500, Invitrogen) was added to exclude dead cells. Classical monocytes were sorted with a FACSAria (BD) as CD3- CD19- CD15- CD56- HLA-DR+ CD14+ CD16- cells.

extract_protocol:
Classical monocytes were resuspended in PBS with 2% FCS and centrifuged 20 minutes at 4ºC. Cell pellets were resuspended in 50 µL of lysis buffer (10 mM TRIS-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged for 30 minutes at 600 g at 4ºC. Supernatants were removed and nuclei were resuspended in 50 µL of tagmentation buffer containing the Tn5 transposase (Illumina) and incubated 30 minutes at 37ºC. Tagmented DNA was purified using the miniElute PCR purification kit (Qiagen).
Libraries were amplified and indexed by PCR for 5 cycles using indexing primers and NEBNext Ultra II Q5 Master Mix (New England Biolabs). To reduce GC bias and to avoid amplification before saturation, qPCR was performed on an aliquot of pre-amplified libraries using Sybr Green (ThermoFisher). ATAC-seq libraries were amplified for a total of 10-12 cycles. Amplified libraries were then cleaned up by using AMPure XP magnetic beads (Agencourt) at a 1.5x ratio Library molarity and quality were assessed with a Qubit and Tapestation using a DNA High sensitivity chip (Agilent). Libraries were pooled at equimolar amounts and sequenced on an Illumina HiSeq 6000 sequencer for a minimum of 50 million paired-end 50 bp reads per sample.

treatment_protocol: Participants were vaccinated with the Spikevax or Comirnaty COVID-19 mRNA vaccine and blood samples were obtained approximately 30 days after the first vaccine dose.

value: Monocytes

value: Classical monocytes (CD14+ CD16-)

value: Time point:D30

tag: reactogenicity group

value: high


title: ICoVax_126_D30 (low reacto)

description: Library name: ICoVax_126_D30

value: low


title: ICoVax_123_D30 (low reacto)

description: Library name: ICoVax_123_D30


title: ICoVax_131_D30 (high reacto)

description: Library name: ICoVax_131_D30


title: ICoVax_119_D30 (high reacto)

description: Library name: ICoVax_119_D30


title: ICoVax_46_D30 (low reacto)

description: Library name: ICoVax_46_D30


title: ICoVax_37_D30 (high reacto)

description: Library name: ICoVax_37_D30


title: HDLEC, ZEB1 siRNA knockdown, biological replicate 2

city: Nottingham

first: Alan

last: McIntyre

address: Biodiscovery Institute

department: Centre for Cancer Sciences

institute: University of Nottingham

description:
Library name: ZEB1_16
HDLEC_ZEB1KD_2

data_processing:
Read quality and adapter content were assessed with FASTQC.
Reads were trimmed of adapters and quality filtered using cutadapt to a minimum quality 20 (-q 20) and a minimum read length of 1 in a paired-end manner.
Subsequent alignment of trimmed, paired-end reads was performed using STAR to the reference genome GRCh38 (primary assembly, release 107, https://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/). Alignment files were output from STAR in sorted BAM format.
Aligned reads were quantified using featureCounts.
Read normalisation and identification of significantly (Benjamini-Hochberg adjusted p-value <0.05) differentially expressed genes (DEGs) was carried out with DESeq2.
DEGs were imported to WEB-based GEne SeT AnaLysis Toolkit and Qiagen Ingenuity Pathway Analysis to identify the most significant enriched biological processes, cellular components and molecular functions in ZEB1 knockdown cells.
Assembly: GRCh38 (primary assembly, release 107
Supplementary files format and content: raw_counts.csv: raw gene-level read counts produced by featureCounts. Rows are Ensembl gene IDs, columns are samples (HDLEC_control_1, HDLEC_control_2, HDLEC_control_3, HDLEC_ZEB1KD_1, HDLEC_ZEB1KD_2, HDLEC_ZEB1KD_3).

source_name: HDLEC

growth_protocol: Pooled Primary Human Dermal Lymphatic Endothelial Cells (HDLECs, Promocell®,  Heidelberg, Germany) were cultured in endothelial cell growth medium MV2 (Promocell®,  Heidelberg, Germany) supplemented with MV2 supplements (Promocell®,  Heidelberg, Germany) in a humidified environment with 5% CO2 at 37°C. Cells were passaged at 80-90% confluency and cells were reseeded or pelleted at an appropriate density for each experiment, and used between P1-5.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Cat No. 74104, QIAGEN). RNA concentration was quantified using Nanodrop and all samples were deemed pure if  280/260 ratio > 1.75.
RNA samples were diluted to 5µg using RNAase free water.  First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA were converted into blunt ends via exonuclease/polymerase. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated for hybridisation. cDNA fragments of 150-200bp in length were generated by PCR and purified using the AMPure XP system (Beckman Coulter, USA). Transcriptomes were read by Illumina HiSeq platforms by Novogene Inc (Hong Kong, China) in a paired-end manner to a depth of 20M reads.

treatment_protocol: RNAi using 20nmol ON-TARGETplus (SMARTpool Dharmacon®) to ZEB1 (6935, L-006564-01-0020, target sequences: CUGUAAGAGAGAAGCGGAA, CUGAAAUCCUCUCGAAUGA, GCGCAAUAACGUUACAAAU, GCAACAGGGAGAAUUAUUA).   YAP1, L-012200-00-0020, ON-TARGETplus Human YAP1 (10413) siRNA – SMARTpool Dharmacon® GCACCUAUCACUCUCGAGA, UGAGAACAAUGACGACCAA, GGUCAGAGAUACUUCUUAA, CCACCAAGCUAGAUAAAGA And  siControl (ON-TARGETplus non-targeting pool) (D-001810-10-20, Dharmacon® UGGUUUACAUGUCGACUAA, UGGUUUACAUGUUGUGUGA, UGGUUUACAUGUUUUCUGA, UGGUUUACAUGUUUUCCUA. 1*106 HDLECs per 60mm dish and left to adhere overnight. Cells were transfected with 20nM of siRNA human ZEB1 and YAP1 (denoted as ZEB1 KD and YAP1 KD respectively) and control cells with non-targeted siControl (denoted as NS) using Lipofectamine RNAimax (Thermo Fisher Scientific) for 6 hours. The transfection reagent complex was then aspirated and replaced with MV2. Cellular material was  extracted after 48 (RNA) or 72 (protein) hours.

value: HDLEC

value: Human dermal lymphatic endothelial cells

value: ZEB1 siRNA knockdown


title: HDLEC, non-silencing siRNA control, biological replicate 3

description:
Library name: NS_21
HDLEC_control_3

value: non-silencing siRNA control


title: HDLEC, ZEB1 siRNA knockdown, biological replicate 3

description:
Library name: ZEB1_22
HDLEC_ZEB1KD_3


title: HDLEC, ZEB1 siRNA knockdown, biological replicate 1

description:
Library name: ZEB1_15
HDLEC_ZEB1KD_1


title: HDLEC, non-silencing siRNA control, biological replicate 2

description:
Library name: NS_20
HDLEC_control_2


title: HDLEC, non-silencing siRNA control, biological replicate 1

description:
Library name: NS_19
HDLEC_control_1


title: Multiome, iPSC-derived otic progenitors, patient (166-101), GEX

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

description:
Library name: 166P0426_RNA
10X Genomics Multiome GEX (snRNA-seq) library: R1 contains cell barcode and UMI; R2 contains transcript sequence; I1/I2 are sample index reads.
166P0426_filtered_feature_bc_matrix.h5

data_processing:
Raw BCL files were demultiplexed into FASTQs using Cell Ranger ARC mkfastq (10X Genomics).
Paired GEX and ATAC FASTQs for each sample were processed using the Cell Ranger ARC count pipeline (10X Genomics) against the GRCh38 (refdata-cellranger-arc-GRCh38-2020-A) joint reference.
Per-sample Cell Ranger ARC outputs (filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz) were loaded into R for downstream analysis using Seurat and Signac.
ArchR was used to compare scATAC-seq peaks between patient and control samples at the GDF6 locus.
Assembly: GRCh38 (refdata-cellranger-arc-GRCh38-2020-A)
Supplementary files format and content: Cell Ranger ARC HDF5 output: filtered_feature_bc_matrix.h5 — contains both Gene Expression and Peaks assays per sample.
Supplementary files format and content: Cell Ranger ARC ATAC fragments file: atac_fragments.tsv.gz — per-sample tabix-indexed fragments for scATAC-seq downstream analysis.

source_name: 166-101 (patient iPSC line)

growth_protocol: Not applicable - cells were not exposed to a drug treatment. The biological condition (control vs. patient with homozygous ~200 Kb deletion downstream of GDF6) was the variable of interest.

extract_protocol:
On the day of collection, iPSC-derived otic progenitor cells were dissociated into a single-cell suspension using Accutase. Cells were then subjected to negative selection for TRA-1-81 (pluripotency marker) followed by positive selection for CD271/p75 (early otic progenitor marker) using CD271 magnetic beads (Miltenyi Biotec). The CD271-enriched population was used for single-nuclei isolation following the 10X Genomics Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing demonstrated protocol (CG000365).
Joint snRNA-seq and scATAC-seq libraries were prepared from the same nuclei using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit (10X Genomics, PN-1000283) following the manufacturer's user guide (CG000338). Transposed nuclei were partitioned into Gel Beads-in-emulsion (GEMs) on the Chromium Controller (Chromium-X). Gene expression (GEX) and ATAC libraries were prepared in parallel and sequenced at the Center for Genome Technology DNA Sequencing Core, John P. Hussman Institute for Human Genomics, University of Miami, on an Illumina NovaSeq 6000.

value: iPSC-derived otic progenitor cells

value: 166-101 (patient iPSC line)

value: CD271+ otic progenitor (nuclei)

value: homozygous ~200 Kb deletion Chr8:96,596,661-96,803,788 (hg19), downstream of GDF6

tag: source subject_status

value: patient


title: Multiome, iPSC-derived otic progenitors, patient (166-101), ATAC

description:
Library name: 166P0426_ATAC
10X Genomics Multiome ATAC (scATAC-seq) library: R1 and R3 contain genomic DNA sequences; R2 contains cell barcode; I1 is the sample index read.
166P0426_filtered_feature_bc_matrix.h5


title: Multiome, iPSC-derived otic progenitors, control (CA-26), ATAC

description:
Library name: CKR0426_ATAC
10X Genomics Multiome ATAC (scATAC-seq) library: R1 and R3 contain genomic DNA sequences; R2 contains cell barcode; I1 is the sample index read.
CKR0426_filtered_feature_bc_matrix.h5

source_name: CA-26 (control iPSC line)

value: CA-26 (control iPSC line)

value: wild-type (no GDF6 downstream deletion)

value: control


title: Multiome, iPSC-derived otic progenitors, control (CA-26), GEX

description:
Library name: CKR0426_RNA
10X Genomics Multiome GEX (snRNA-seq) library: R1 contains cell barcode and UMI; R2 contains transcript sequence; I1/I2 are sample index reads.
CKR0426_filtered_feature_bc_matrix.h5


title: CD2 iPSC-derived IEO, ATAC-seq, Day 13

description:
Library name: day13-cd2
Chromatin accessibility profiling at GDF6 cis-regulatory locus in control CD2 iPSC-derived inner ear organoids at Day 13 of differentiation. ~200 organoids were pooled per replicate.

data_processing:
Raw sequencing reads were assessed for quality using FastQC, followed by adapter trimming and removal of low-quality bases using Trimmomatic v0.38.
Cleaned reads were aligned to the hg38 reference genome using Bowtie2 with default parameters.
Post-processing: aligned reads filtered with SAMtools v1.9 (minimum mapping quality of 30, primary alignments only). PCR and optical duplicates and mitochondrial DNA reads were removed using Picard v2.18.26. Unplaced contigs were discarded.
Open chromatin regions were identified using MACS2 v2.1.2, excluding ENCODE blacklisted genomic regions.
Peaks detected in at least 66% of samples for a given condition were retained for downstream analysis.
Assembly: hg38
Supplementary files format and content: BED format: MACS2-called peak files containing genomic coordinates and peak statistics for open chromatin regions.

source_name: inner ear organoid

growth_protocol: Human iPSCs (CD2 healthy donor line) were differentiated into inner ear organoids (IEOs) following the protocol of Koehler et al. (Nat Biotechnol, 2017) with modifications by van der Valk et al. (Cell Rep, 2023), as described in detail in the Methods section of the associated manuscript. Approximately 200 Day-8 or Day-13 organoids were pooled per sample to meet ATAC-seq input requirements.

extract_protocol:
ATAC-seq libraries were prepared by Azenta Life Sciences. Nuclei were isolated from pooled IEOs and tagmented using the Tn5 transposase. Sample quality and quantity were assessed before library preparation. Libraries were sequenced using the Illumina 2x150 bp paired-end configuration.
ATAC-seq libraries were prepared and sequenced by Azenta Life Sciences using standard ATAC-seq library preparation followed by Illumina 2x150 bp paired-end sequencing (Azenta Quote 30-978196434).

tag: tissue

value: inner ear organoid

value: iPSC-derived inner ear organoid (IEO)

value: WT (healthy control donor)

value: Day 13 of IEO differentiation


title: CD2 iPSC-derived IEO, ATAC-seq, Day 8

description:
Library name: day8-cd2
Chromatin accessibility profiling at GDF6 cis-regulatory locus in control CD2 iPSC-derived inner ear organoids at Day 8 of differentiation. ~200 organoids were pooled per replicate.

tag: genotype

value: Day 8 of IEO differentiation


title: IBI351_3

first: Shuangli

state: - Select -

address: Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description: Library name: Sample 6

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:hisat2-2.2.1) 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.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) 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: mm10
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: cell

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
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. 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 NovaseqTM 6000 following the vendor's recommended protocol.

value: cell

tag: cell line

value: KRAS G17C mutant NSCLC


title: IBI351_2

description: Library name: Sample 5

tag: cell type

value: KRAS G16C mutant NSCLC


title: IBI351_1

description: Library name: Sample 4

value: KRAS G15C mutant NSCLC


title: CTL3

description: Library name: Sample 3

value: KRAS G14C mutant NSCLC

value: DMSO


title: catID_38

description:
Library name: PAM73696__bc_2.fastq_catID_38
column 9 in Counts File

value: cardiac biopsy left ventricle


title: CTL1

description: Library name: Sample 1

value: KRAS G12C mutant NSCLC


title: CTL2

description: Library name: Sample 2

value: KRAS G13C mutant NSCLC


title: huSCC, human cutaneous squamous cell carcinoma, replicate 5

city: Salzburg

first: Giorgia

last: Nasi

address: Hellbrunner strasse 34

country: Austria

institute: University of Salzburg

description: Library name: S_34_SCC_RNA_S141434

data_processing:
Reads were mapped to the Genome Reference Consortium GRCh38 using STAR (v2.7.11b) with GENCODE annotations. Further downstream analysis were conducted using statistical software R (v4.5.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited (tsv) textfile containing raw count data for each sample.

source_name: human cSCC

extract_protocol:
Total RNA was extracted from biopsies of HD skin, huSCC, ES and xSCC using the Monarch Total RNA Miniprep Kit (NEB, Cat# TS2010).
RNA quantity and integrity were assessed with Qubit 2.0 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (RNA 6000 Pico Kit, Cat# 5067-1513). Libraries were prepared with the NEBNext® Poly(A) mRNA Magnetic Isolation Module, Ultra™ II Directional RNA kit, and Multiplex Oligos for Illumina (New England Biolabs), quantified with Qubit 2.0 assay and assessed on the 2100 Bioanalyzer (High Sensitivity DNA Kit, Cat.# 5067-4626). Sample-specific libraries were pooled equimolarly

value: human cSCC


title: huSCC, human cutaneous squamous cell carcinoma, replicate 4

description: Library name: S_31_SCC_RNA_S141435


title: huSCC, human cutaneous squamous cell carcinoma, replicate 3

description: Library name: S_29_SCC_RNA_S141432


title: ICoVax_122_D30 (low reacto)

description: Library name: ICoVax_122_D30

value: Monocytes

value: Classical monocytes (CD14+ CD16-)

value: Time point:D30

value: low


title: huSCC, human cutaneous squamous cell carcinoma, replicate 2

description: Library name: S_28_SCC_RNA_S141433


title: huSCC, human cutaneous squamous cell carcinoma, replicate 1

description: Library name: S_27_SCC_RNA_S141430


title: xSCC, tumor xenograft, replicate 5

description: Library name: S_2003_SCC_HC_70_S141444

source_name: xenograft SCC

value: xenograft SCC


title: ES, human engineered skin, xenograft, replicate 5

description: Library name: S_1962_ES_S141436

source_name: Enginereed skin

value: Enginereed skin


title: ICoVax_100_D30 (high reacto)

description: Library name: ICoVax_100_D30

value: high


title: xSCC, tumor xenograft, replicate 4

description: Library name: S_1961_SCC_2_S141443


title: ES, human engineered skin, xenograft, replicate 4

description: Library name: S_1922_ES_HC_70_S141441


title: xSCC, tumor xenograft, replicate 3

description: Library name: S_1921_SCC_S141445


title: ES, human engineered skin, xenograft, replicate 3

description: Library name: S_1919_ES_S141438


title: ES, human engineered skin, xenograft, replicate 2

description: Library name: S_1866_ES_S141439


title: xSCC, tumor xenograft, replicate 2

description: Library name: S_1865_tumor_S141440


title: ES, human engineered skin, xenograft, replicate 1

description: Library name: S_1863_ES_S141437


title: HD, skin, replicate 5

description: Library name: P94B_HD_skin_S141429

source_name: Healthy human skin

value: Healthy human skin


title: xSCC, tumor xenograft, replicate 1

description: Library name: S_1778_SCC_S141442


title: HD, skin, replicate 4

description: Library name: P69B_HD_skin_S141431


title: Intermediate monocytes RNA-seq from control participants with reported reactogenicity

description: Library name: ICoVax_control_reacto_monocytes_intermediate

data_processing:
nfcore rnaseq pipeline (release 3.17.0) using a modified version of the human genome (GRCh38.p13) from ensembl where the sequences corresponding to the BioNTech/Pfizer BNT-162b2 and Moderna mRNA-1273 SARS-CoV-2 spike-encoding mRNA vaccine transcripts were added.
Pseudoalignment and quantification was performed with Salmon (1.10.3). Gene-level quantification was obtained with the tximport R package (1.20.1).
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw gene-level counts for each sample.

growth_protocol: Venous blood was collected in PAXgene Blood RNA Tubes (BD) for transcriptomic analysis. Blood samples were processed less than 3 hours after collection. PAXgene tubes were stored at -80ºC until RNA extraction.  Venous blood was collected in CPT tubes (BD) for peripheral blood monocuclear cell (PBMC) isolation. PBMCs were isolated by density gradient centrifugation. Red blood cells were lysed (ACK lysis buffer, Lonza) and PBMCs were resuspended in FCS containing 10% DMSO and cryopreserved in liquid nitrogen. PBMCs were thawed and cell-surface stained for 30 minutes at 4ºC and draq7 (1:500, Invitrogen) was added to exclude dead cells. Classical monocytes were sorted with a FACSAria (BD) as CD3- CD19- CD15- CD56- HLA-DR+ CD14+ CD16- cells, wheras intermediate monocytes were sorted as CD3- CD19- CD15- CD56- HLA-DR+ CD14+ CD16+.

extract_protocol:
Whole blood RNA extraction was performed with the PAXgene Blood miRNA Kit (PreAnalytix) on a QIAcube instrument following the manufacturer's instructions.  RNA extraction for sorted monocyte samples was performed with the Rneasy kit (Qiagen) following the manufacturer's instructions.  After extraction, RNA concentration and quality were assessed with a Qubit (Invitrogen) and 2100 Bioanalyzer (Agilent) respectively.
RNA libraries for whole blood samples were prepared with the Stranded Total RNA Ribo-Zero Plus kit (Illumina) with 250 ng of total RNA as input.  RNA libraries for sorted monocytes were prepared with the SMARTer + Nextera XT kit (Illumina) with 1 to 5 ng of total RNA as input.  Library molarity and quality were assessed with a Qubit and Tapestation using a DNA High sensitivity chip (Agilent). Libraries from the same biological source were pooled at equimolar amounts and sequenced on an Illumina HiSeq 4000 sequencer (whole blood) or NovaSeq 6000 (sorted monocytes) for a minimum of 30 million single-end reads per sample.

treatment_protocol: Participants were vaccinated with the Spikevax or Comirnaty COVID-19 mRNA vaccine.

value: Intermediate monocytes

value: Time points:D0, D30


title: Classical monocytes RNA-seq from control participants with reported reactogenicity

description: Library name: ICoVax_control_reacto_monocytes_classical

value: Classical monocytes


title: HD, skin, replicate 2

description: Library name: P63B_HD_skin_S141446


title: HD, skin, replicate 1

description: Library name: P62B_HD_skin_S141447


title: HD, skin, replicate 3

description: Library name: P68B_HD_skin_S141428


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 11

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description:
Library name: CSS27_ATAC
BS1322

data_processing:
The fastq files were processed using Cell Ranger ARC 2.0 with default parameters
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: HDF5 10X Genomics file containing features, barcodes and sparse matrix of gene expression counts
Supplementary files format and content: Gzipped BED-like tabular file created by cellranger-atac count, where each line represents a unique ATAC-seq fragment captured by the assay.

source_name: lung tumor, NSCLC

extract_protocol:
CD56⁺ NK and T cells were sorted from non-small cell lung cancer (NSCLC) tumor single-cell suspensions. Nuclei were isolated according to protocol and processed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338, Rev C), following the manufacturer’s instructions.
The libraries were constructed according to 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338, Rev C), following the manufacturer’s instructions.

value: lung tumor, NSCLC

value: CD56⁺ NK and T cell


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 11

description:
Library name: CSS27_GEX
BS1322

molecule: nuclear RNA


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 10

description:
Library name: CSS25_ATAC
BS1318


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 10

description:
Library name: CSS25_GEX
BS1318


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, ATAC, rep 9

description:
Library name: CSS23_ATAC
BS1319


title: CD56⁺ NK and T cells sorted from treatment-naive NSCLC, GEX, rep 9

description:
Library name: CSS23_GEX
BS1319