title: ICR 4-cell embryos, 1 mg/mL Nanoplastic treated, replication 2

city: Jeongeup-si

first: Hyeongju

last: you

state: Jeongeup-si

address: Primate resource center

country: South Korea

institute: KRIBB

description: Library name: 1 mg/mL NP_Rep2

data_processing:
Raw sequencing data were assessed using FastQC (v0.10.1) to evaluate general quality metrics such as per-base sequence quality and GC content.
Adapter sequences and low-quality reads were trimmed using Trimmomatic (v0.39), and short reads were filtered. Post-trimming quality was reassessed using FastQC.
High-quality reads were mapped to the Mus musculus reference genome (GRCm39) using STAR aligner (v2.7.9a).
Transcript assembly and quantification were performed using StringTie (v2.2.1) to generate gene- and transcript-level abundance estimates.
Assembly: mm39
Supplementary files format and content: Tab-delimited files include raw read counts, TPM values, and transcript abundance estimates for each sample.

growth_protocol: Female ICR mice were superovulated and used for in vitro fertilization (IVF) with sperm collected from ICR males. Fertilized embryos were cultured in KSOM medium, and 4-cell stage embryos were collected at 48 hours af

extract_protocol:
Total RNA was extracted from pools of 40 embryos per group using Rneasy Micro Kit ((Qiagen) following the manufacturer’s protocol. RNA integrity was assessed using an Agilent 4200 TapeStation.
Total RNA was used to construct sequencing libraries with the Discover-sc WTA Kit V2 (Vazyme, N711) and TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504) following the manufacturer’s instructions. Briefly, cDNA was synthesized via reverse transcription, amplified, fragmented, and ligated with sequencing adapters. Index PCR was performed using the TruePrep Index Kit V2 for Illumina (Vazyme, TD202). Final libraries were quantified using qPCR and assessed with Agilent 4200 TapeStation. Sequencing was performed on the NovaSeq 6000 platform (Illumina).

treatment_protocol: Embryos were treated with 0, 0.1, or 1 mg/mL of PMMA nanoplastics in KSOM medium for 48 hours before RNA extraction

value: 4-cell embryo

value: WT

value: 1 mg/mL


title: miRNA-729 - base

status: Public on Aug 18 2025

type: SRA

city: Winston-Salem

first: Carl

last: Langefeld

state: NC

address: 525 Vine

country: USA

institute: Wake Forest University School of Medicine

description:
Library name: miCB31
column name in Normalized_miRNA_counts_v1: 729 - base

library_source: transcriptomic

data_processing:
The adapter for each miRNA sample was trimmed using Cutadapt (part of miRge3.0) pipeline. MiRNA sample data quality were evaluated using fastqc (html report) and the miRNA peak (at around 22 bp) was filtered for each sample. Samples with filtered miRNA peak were put into miRge3.0 pipeline to generate summary data files including miRNA read count, reads per million (RPM), etc.
Differentially expressed (DE) mRNA and miRNA were tested between 3 time points: 72hr vs. baseline, 7days vs. 72hrs and 7days vs. baseline. The DE mRNA and miRNA were tested for pathway enrichment via Ingenuity Pathway Analysis, Cytoscape, STRING and Reactome.
Principal component analysis (PCA) was computed on the differences in the expression for the timeframe.
Spearman’s correlation coefficient were computed between DE mRNA and DE miRNA for each timeframe comparison. The miRNA/mRNA with statistically significant correlation pairs were analyzed using TargetScan (version 8.0) and MirTarBase (9.0) to explore whether the pairs are reported as miRNA/mRNA targets.
Assembly: Human (Homo Sapiens) hg38
Supplementary files format and content: Normalized_miRNA_counts_v1.csv
Supplementary files format and content: Normalized_mRNA_counts_v1.csv

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
miRNA: The first round of sequencing was performed on NextSeq 2000 sequencer (Illumina, San Diego, CA) to generate a few million reads to quantify the relative concentration of each library. The volume of each library was then adjusted to generate about 5M read clusters from each sample under the same PE 2x61 bp setting for the final data analysis. mRNA: Directional globin mRNA/rRNA depletion RNA-seq was performed using NEBNext Globin & rRNA Depletion Kit (NEB) with 50 to 100 ng whole blood RNA was globin mRNA/rRNA depleted according to the protocol.
miRNA: NEBNext Small RNA Sample Library Preparation kit (NEB, Ipswich, MA) was used with modified approach for precise miRNA library size selection; this makes it possible for the kit to process low input and low-quality RNA with better library recovery and miRNA reads alignment.  mRNA: NEBNext Ultra II Directional RNA Library Prep kit (NEB) was used for library preparation under PCR cycle number of 14.

tag: tissue

value: whole blood

tag: treatment

value: baseline

tag: batch


title: A673,EWSR1-FLI1,R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

library_source: genomic

data_processing:
ChIP-seq, alignment: Sequence reads of the samples without spike-in were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3).
ChIP-seq, genome profiles: SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each ChIP-seq experiment. Height of the profiles is normalized by the total number of reads mapped over the human genome for samples without spike/in material, and by the number of fly spike-in genome reads in the case of samples with spike-in.
ChIP-seq, peak calling: Peak detection of every sample against its corresponding Input was performed with MACS (PubMed ID: 18798982).
ChIP-seq, replicate peaks: DiffBind (PubMed ID 22217937) was used to generate a consensus set of peaks for each pair of replicates.
RNA-seq, alignment: Sequence reads were mapped against the hg19 human genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
RNA-seq, differential analysis: DeSeq2 (PubMed ID 25516281) was run to identify differentially expressed genes.
Assembly: hg19
Supplementary files format and content: Bedgraph format for genome-wide profiles.
Supplementary files format and content: BED format for MACS and DiffBind peaks.
Supplementary files format and content: DESeq2 format column descriptions: Ensembl gene id, baseMean, log2FC, lfcSE, stat, pvalue, padj, gene symbol id, gene entrez id, RPKMs in control, RPKMs in first KD, RPKMs in second KD. Filenames indicate which KD is performed in that comparison against the control condition.

molecule: genomic DNA

growth_protocol: A673 cells were cultured in RPMI 1640 media (Gibco) and supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. Cells were maintained in a humidified chamber at 37ºC and 5% CO2, and split every 2-3 days when reaching confluence.

extract_protocol:
(ChIP-seq) Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. (RNA-seq) Total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions.
(ChIP-seq) ChIP-seq libraries were prepared using 2-5 ng of input and ChIP samples and the kit NEBNext Ultra DNA Library Prep for Illumina (New England Biolabs) following manufacturer’s protocol. (RNA-seq) Illumina Stranded Total RNA Prep kit (Illumina) was used according to manufacturer’s instructions.

treatment_protocol: EwS cell lines were seeded in 6-well plates at 0.25 x 10^6 cells/mL and transfected with Lipofectamine RNAiMAX (Invitrogene) using 30 pmol of siRNA in OptiMEM media (Gibco) following manufacturer’s instructions. For knock-downs, distinct target sequences for small interfering RNA and the SMARTvector inducible Tet-On shRNA system (Dharmacon) act over KDM6A or KDM6B. Empty and EWSR1-FLI1-pLIV vector was kindly provided by Dr Nicolo Riggi and published in Boulay et al., 2017. For KDM6A knockout cells, the Gene Knockout Kit v2 (Synthego) was used with a pool of three validated sgRNA and exogenous Cas9 following manufacturer's guidelines. CRISPR-edited cell pools were isolated by limit dilution in 96-well plates. Isolated clones were expanded and cells were collected for subsequent validation by Sanger sequencing of the PCR product.

tag: cell line

tag: cell type

value: Ewing sarcoma

tag: chip antibody

value: FLI1 (Abcam ab15289)


title: ICR 4-cell embryos, 1 mg/mL Nanoplastic treated, replication 1

description: Library name: 1 mg/mL NP_Rep1

organism: Mus musculus

tag: genotype


title: miRNA-175 - base

description:
Library name: miCB28
column name in Normalized_miRNA_counts_v1: 175 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_025, ME/CFS patient

city: Ithaca

first: Anne

middle: E

last: Gardella

state: NY

address: 237 Tower Rd

department: Molecular Biology and Genetics

institute: Cornell University

description:
Library name: cfs_cfrna_025
Column name in raw_counts_all.csv: cfs_cfrna_25

data_processing:
Sequencing results were processed using a custom bioinformatics pipeline.
First, samples were quality filtered and trimmed using BBDuk (v38.90) and aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR29 (v2.7.8a, default parameters), and features quantified using featureCounts30 (v2.0.0). Samples were also deduplicated using Picard MarkDuplicates (v2.19.2).
Ribosomal, mitochondrial ribosomal, X and Y chromosome genes were bioinformatically removed prior to analysis. Samples were filtered based on total read counts, alignment rate, total feature counts, DNA contamination, and RNA degradation
DNA contamination was determined based on the ratio of reads mapping to introns and exons. RNA degradation was estimated by calculating the 5’-3’ read alignment ratio bias using Qualimap31 (v2.2.1).
Samples which passed the quality filter all had greater than 5 million reads, greater than 100,000 feature counts, greater than 10% alignment rate, less than 1-fold intron to exon ratio, less than 3 standard deviations from the mean of the 5’-3’ bias, and less than 95% duplication rate.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: .csv file includes the gene counts for each sample

source_name: Plasma, extracted cell-free RNA

extract_protocol:
Plasma was stored at -8-˚C and then thawed at room temperature. Then ~500 μL samples were aliquoted and centrifuged at 3000 x g for 8 minutes at 4˚C. cfRNA was extracted using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000).  Extracted RNA was DNase treated with a combination of 10 µl DNase Turbo Buffer (Invitrogen, AM2238), 3 µl DNase Turbo (Invitrogen, AM2238), and 1 µl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37 °C, then concentrated into 12 µl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using the Illumina NovaSeq 6000 platform (paired-end, 150 bp).

value: Plasma, extracted cell-free RNA

tag: phenotype

value: case

tag: Sex

value: female

tag: test site

value: Los Angeles, CA

tag: age bin


title: ICR 4-cell embryos, Nanoplastics untreated compared with 1 mg/mL group, replication 2

description: Library name: Control_2_Rep2

value: 0 mg/mL


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_024, healthy control

description:
Library name: cfs_cfrna_024
Column name in raw_counts_all.csv: cfs_cfrna_24

value: control

value: Ithaca, NY


title: miRNA-454 - base

description:
Library name: miCB25
column name in Normalized_miRNA_counts_v1: 454 - base


title: ICR 4-cell embryos, Nanoplastics untreated compared with 1 mg/mL group, replication 1

description: Library name: Control_2_Rep1


title: miRNA-650 - base

description:
Library name: miCB22
column name in Normalized_miRNA_counts_v1: 650 - base


title: A673,EWSR1-FLI1,R1


title: A673,KDM6B,R2

value: KDM6B (Abcam ab169197)


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_023, ME/CFS patient

description:
Library name: cfs_cfrna_023
Column name in raw_counts_all.csv: cfs_cfrna_23


title: A673,KDM6B,R1


title: miRNA-649 - base

description:
Library name: miCB37
column name in Normalized_miRNA_counts_v1: 649 - base


title: ICR 4-cell embryos, 0.1 mg/mL Nanoplastic treated, replication 1

description: Library name: 0.1 mg/mL NP_Rep1

value: 0.1 mg/mL


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_022, healthy control

description:
Library name: cfs_cfrna_022
Column name in raw_counts_all.csv: cfs_cfrna_22

value: male


title: A673,KDM6A,R2

value: KDM6A (UTX) (Cell Signaling 33510)


title: ICR 4-cell embryos, 0.1 mg/mL Nanoplastic treated, replication 2

description: Library name: 0.1 mg/mL NP_Rep2

value: 4-cell embryo

value: WT


title: miRNA-100 - base

description:
Library name: miCB19
column name in Normalized_miRNA_counts_v1: 100 - base

value: whole blood


title: ICR 4-cell embryos, Nanoplastics untreated compared with 0.1 mg/mL group, replication 2

description: Library name: Control_1_Rep2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_021, healthy control

description:
Library name: cfs_cfrna_021
Column name in raw_counts_all.csv: cfs_cfrna_21


title: Naïve YFP-1

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

description: Library name: N1-

data_processing:
Raw FASTQ sequencing reads were mapped against the mm10 reference genome using the DRAGEN genome pipeline.
BAM files were used to generate a feature/gene counts matrix using the R/Bioconductor package Rsubread.
The DESeq2 library was used for secondary analysis and differential gene expression between experimental groups
Assembly: mm10
Supplementary files format and content: tab delimited text file of gene counts per sample

source_name: GM-CSF reporter/fate reporter transgenic mice

growth_protocol: YFP+, YFP− naïve (CD62L+CD44−), and TEM (CD62L−CD44hi) CD4+ T cells from the spleens of Gr/fr mice were FACS sorted.

extract_protocol:
Then, RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions
Libraries were prepared using 200 ng of total RNA and the Illumina TruSeq Stranded Total RNA library preparation kit. Libraries’ qualities were evaluated using the PerkinElmer Labchip GX and qPCR using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries at a concentration of 2nM were sequenced on the Illumina HiSeq2500 using the High Output v4 chemistry. Raw FASTQ sequencing reads were mapped against the mm10 reference genome using the DRAGEN genome pipeline.

tag: strain

value: CD4+ T cell


title: miRNA-788 - base

description:
Library name: miCB16
column name in Normalized_miRNA_counts_v1: 788 - base

value: baseline


title: A673,KDM6A,R1

value: Ewing sarcoma


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_027, ME/CFS patient

description:
Library name: cfs_cfrna_027
Column name in raw_counts_all.csv: cfs_cfrna_27

value: Plasma, extracted cell-free RNA

value: New York City, NY


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_018, ME/CFS patient

description:
Library name: cfs_cfrna_018
Column name in raw_counts_all.csv: cfs_cfrna_18

value: case

value: female


title: miRNA-914 - base

description:
Library name: miCB13
column name in Normalized_miRNA_counts_v1: 914 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_017, healthy control

description:
Library name: cfs_cfrna_017
Column name in raw_counts_all.csv: cfs_cfrna_17


title: ICR 4-cell embryos, Nanoplastics untreated compared with 0.1 mg/mL group, replication 1

description: Library name: Control_1_Rep1

value: 0 mg/mL


title: Voracious feeding

city: South San Francisco

first: Kimberle

last: Shen

state: CA

address: 1 Dna way

institute: Genentech

description: Library name: Sample 2

library_source: transcriptomic single cell

data_processing:
The dataset was aligned to the zebrafish reference genome GRCz11 (v104) on PartekFlow using 10X Genomics CellRanger. Quality filtering was performed using the following parameters: 200 < Number of expressed genes < 4000; maximum mitochondrial reads percent = 15. Quality filtering resulted in a total of 9031 cells (Food-deprived: 4412; Voraciously feeding: 4619).
Assembly: GRCz11(v104)
Supplementary files format and content: matrix files and tab seperated value files

molecule: polyA RNA

organism: Danio rerio

source_name: Brain

extract_protocol:
Dissociation was carried out with a Papain Dissociation System (Worthington Biochemical Corporation) but with a shorter papain incubation time to avoid cell death. Larval brains were initially incubated in papain mixture for 10 minutes at 34°C, followed by gentle trituration with a p1000 pipette to ensure uniform dissociation and a final incubation for 5 minutes. To avoid dissociation-induced activity and preserve hunger/feeding based neuronal activity patterns, actinomycin D was added at a concentration of 0.1 𝜇g/ml to the papain mixture to inhibit transcription. The cell suspension was filtered using a 40 μm cell strainer to avoid cell clumps. DAPI (1:1000) was added to the cell samples prior to sorting in a BD FACSAria II SORP cell sorter.GCaMP6s positive (LH) and negative (cells from all other brain regions, which we refer to as non-LH cells) cells were collected in Neurobasal medium with B27 supplementation and 10% FBS as they were prone to cell death. The proportion of GCaMP6s-positive LH cells is very low as compared to non-LH cells in the brain. Out of 100% live cells, 97% of cells were GCaMP6s-negative (non-LH cells) with only 3% being GCaMP6s- positive. Since the ratio of LH to non-LH cells is roughly 1:323, positive and negative populations were mixed at 50:50 ratio in both samples to ensure we captured a sufficient number of LH cells. Overall cell viability after mixing the positive and negative populations was 70-75%.
Single cell 3’ Gene Expression libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 and Chromium Dual Index Plate TT Set A Sample Index following the manufacturer's instructions (10X Genomics, Pleasanton, CA, USA). The libraries were sequenced on an Illumina NovaSeq 6000 system (Illumina, San Diego, CA, USA) using indexed paired-end reads (2 × 151 bp), targeting a depth of approximately 50,000 reads per cell.

treatment_protocol: Transgenic Tg(76A:Gal4FF:UAS GCaMP6s) zebrafish larvae were obtained from a mass cross of three female and three male adults. They were pre-screened for GCaMP6s fluorescence in the lateral hypothalamus and fed with paramecia from 5 dpf onwards. At 7 dpf, larval zebrafish were randomly sorted into two treatment groups with 50 larvae per group: 1) “Food deprived” - starved for four hours 2) “Voraciously feeding” - starved for four hours and fed excess paramecia for 30 minutes. At the endpoint, larvae were rapidly euthanised in ice-cold E3 and brains were dissected.

value: Brain

value: Food deprived for 4 hours and fed paramecia for 30 minutes


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_016, ME/CFS patient

description:
Library name: cfs_cfrna_016
Column name in raw_counts_all.csv: cfs_cfrna_16


title: scATAC-seq of WT mouse cochlea, lysed for 10 min

city: Tarrytown

first: Artur

last: Rego-Costa

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals Inc.

description: Library name: sc-0077_coch_atac_10min

library_source: genomic single cell

data_processing:
For scATAC-seq, raw sequencing data was processed using the 10X Genomics CellRanger ATAC pipeline (10X Genomics, Pleasanton, CA, USA) with default parameters. The reference genome used was GRCm38 mm10. All further filtering and downstream analysis of the data described in subsequent sections was performed with the Signac v1 R package,29 using default parameters unless specified. A joint reference was first generated by selecting peaks common across biological replicates using the UnifyPeaks function. New count matrices for the common peak reference were then obtained using the GetFragments function. Quality control metrics were computed, and cells with a TSS enrichment score <2, nucleosome signal score <5, percentage of reads within peaks >25% and number of unique peaks >500 were selected for downstream analysis. Normalization was performed using term frequency-inverse document frequency (RunTFIDF), followed by feature selection (FindTopFeatures), and dimensionality reduction by single value deconvolution (RunSVD). Components 2:30 were used for clustering and 2D UMAP projection. Gene activity matrices were computed using reads within the gene body coordinates and up to 2,000 bases upstream of the transcriptional start site. For cluster annotation, the gene activity scores of individual cells were compared to mean expression profiles from an adult mouse cochlea reference dataset using Spearman correlation, using the highest correlation value as the tentative cell label. We then labeled clusters based on the majority label across individual cells. Genome browser tracks for specific cell types were obtained by generating pseudo-bulk ATAC-seq profiles using the cluster cell type labels, combining reads across clusters based on individual cell barcodes.
For scRNA-seq, reads were demultiplexed, aligned to a GRCm38 mm10 reference genome to which the OTOF transgene sequence was added, and filtered. Cell barcodes and UMIs were quantified using the 10X Genomics CellRanger pipeline (10x Genomics, Pleasanton, CA, USA) with default parameters (software.10xgenomics.com/single-cell/overview/welcome). CellRanger uses STAR for alignment and manufacturer’s software for all other steps . All further filtering and downstream analysis of single-cell data described in subsequent sections was performed with the Seurat v3 R package, using default parameters unless specified. To limit the influence of low-complexity cells and genes, cells with fewer than 100 expressed genes and genes with detectable expression in 10 or fewer cells were removed. Red blood cell contamination is a concern when dissociating cells from the adult cochlea, since there is a large niche of erythroid cells near the bony apex. Red blood cells are highly enriched for hemoglobin transcripts, and hemoglobin protein occupies up to 98% of the red blood cell cytosol. Therefore, we analyzed the fraction of total transcript counts from each single cell that were comprised of transcripts from the hemoglobin genes (Hba-a1, Hba-a2, Hbb-bh1, Hbb-bs, Hbb-bt). We removed any cell with >5% contamination. Cells with >25% mitochondrial or >40% ribosomal transcripts fractions were removed, as well as cells with >50,000 unique molecular identifiers (UMIs) detected. Full descriptions of Seurat’s clustering procedure can be found at satijalab.org/seurat/. Principal component analysis (PCA) was used for dimensionality reduction and calculated from z-scored residuals of the regressed gene expression matrix. PCA was computed for the top 2,000 most variable genes, and the first 25 components were used for clustering and UMAP 2D projection. For cluster annotation, the expression profiles of individual cells were compared to mean expression profiles from an adult mouse cochlea reference dataset using Spearman correlation, using the highest correlation value as the tentative cell label. We then labeled clusters based on the majority label across individual cells. Scrublet software was used to identify putative doublets in the dataset. Clusters with high median doublet scores were filtered out. Immune cells were further taken out as a subset from the full dataset, re-clustered and re-labeled for further granularity, using the same workflow and parameters as for the full dataset. Differential expression analysis between AAV-smCBA and AAV-Myo15 macrophages was performed using Seurat’s FindMarkers function. Gene set enrichment analysis was performed using the fgsea R package (https://bioconductor.org/packages/release/bioc/html/fgsea.html).
Assembly: GRCm38 mm10
Supplementary files format and content: For scATAC-seq, files include: fragments.tsv.gz, detailing DNA fragments with positional and barcode information; and filtered_peak_bc_matrix.h5, an HDF5 file storing a peak-by-cell matrix that indicates chromatin accessibility for specific genomic regions across cells. For scRNA-seq, processed files include: barcodes.tsv.gz, listing unique cell barcodes to identify individual cells; features.tsv.gz, containing detected genes or transcripts; and matrix.mtx.gz, a sparse matrix of gene expression levels for each cell.

source_name: cochlea

extract_protocol:
For scATAC-seq, 1X lysis and wash buffers were prepared according to 10x Genomics' Demonstrated Protocol CG000212. One live cochlea was placed into a 1.5 mL Eppendorf tube on ice and 100 uL 1X lysis buffer was added. The cochlea was broken up with spring scissors and then incubated in the lysis buffer for either 5 min or 10 min. 1 mL chilled wash buffer was added to the lysed cells and the nuclei suspension was filtered with a 20 µm pluristrainer (Pluriselect-USA, El Cajon, CA, USA) to remove debris. For scRNA-seq, micro-dissected tissue from each mouse was pooled in a solution of DMEM/F-12 medium containing 200 units/mL collagenase IV (Thermo Fisher Scientific, Waltham, MA) and 10 kunitz/mL DNase I (STEMCELL Technologies, Cambridge, MA) and incubated for 30 min at 37 °C to digest extracellular matrix. The collagenase IV solution was then replaced with EBSS containing 20 units of papain (Worthington Biochemical, Lakewood, NJ, USA), 1 mM L-cysteine, 0.5 mM EDTA, 15 mM HEPES, and 15 kunitz/mL DNase I and incubated for an additional 30 min at 37 °C, triturating with a 1000 µL pipette every 10 min to generate a single cell suspension. An equal volume of DMEM/F-12 medium containing 20% ovomucoid protease inhibitor (Worthington Biochemical, Lakewood, NJ, USA) was added, and the dissociated cells were passed through a 40 µm filter (PluriSelect-USA, El Cajon, CA) to remove large debris. The cells were pelleted at 350g for 5 min, washed twice, and then pelleted and resuspended in DMEM/F-12 containing 0.08 % BSA. Finally, a 10 µL sample of the cell suspension was counted on a Luna-FL automated counter using AO/PI cell viability staining (Logos Biosystems, Annandale, VA, USA).
For scATAC-seq, the nuclei were centrifuged at 500 xg for 5 minutes, resuspended in diluted nuclei buffer, and counted with the Luna-FL. Transposition, nuclei capture, and library preparation were performed according to the 10x Genomics protocol using ATAC v1 reagents. For scRNA-seq, cells were captured, lysed, and primed for reverse transcription (RT) using the high-throughput, droplet microfluidics Gemcode platform (10x Genomics, Pleasanton, CA, USA) with v3 chemistry.

treatment_protocol: For scATAC-seq, whole cochleae were dissected from 7-week-old, male, CBA/CaJ mice. For scRNA-seq, WT FVB mice were treated with either AAV1-smCBA-OTOF-v5 or AAV1-1.0kb-mMyo15-OTOF-v5 at a dose of 1e11 vg/ear via round window membrane injection. After 4 weeks, temporal bones from injected mice were dissected and isolated in ice-cold DMEM/F-12 medium, and the vestibular system was removed, leaving just the cochlea. To allow the dissociation enzymes better access to the cochlea tissue, the bone overlying the apical portion of the cochlea was removed.

value: cochlea

value: CBA/CaJ


title: miRNA-784 - base

description:
Library name: miCB1
column name in Normalized_miRNA_counts_v1: 784 - base


title: chic_OUD8882-old-nucli-k4me1-L

city: Utrecht

first: Vivek

last: Bhardwaj

address: Padualaan 8

country: Netherlands

institute: Utrecht University

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
4-12hpf_merged_samples_genelevel_counts.h5ad

data_processing:
The first-in-pair reads from the T-ChIC protocol contain an RNA or ChIC barcode in the following format “RNA: 6N7X, ChIC: 3N8X”; where N=UMI nucleotide and X=Cell barcode nucleotide. We used a custom Python script to split the raw .fastq files into the ChIC and RNA fractions based on which one of the 2 barcode patterns is observed at the start. The two fractions are then independently mapped to the GRCz11/danRer11 genome.
A complete processing workflow with all parameters is available at: https://github.com/bhardwaj-lab/scChICflow
Assembly: GRCz11/danRer11
Supplementary files format and content: .h5 files (anndata object) containing gene-level raw counts for chromatin (chic) and RNA fraction per single-cell. The files can be loaded in python with scanpy (sc.read_h5ad) or in R with the LoomExperiment (import) package. The adata objects for TChIC samples contain "spliced", "unsplliced" and "chic" layers. The annotation for celltype, timepoints, and histone marks, are available as metadata columns in the same object.
Library strategy: tChIC

source_name: whole embryo

growth_protocol: Zebrafish (TL strain) were maintained at 27.5°C in a 14/10 h light/dark cycle, according to standard laboratory conditions (Aleström et al., 2020). Embryos were collected and staged according to Kimmel et al. (1995). Animal experiments were approved by the Animal Experimentation Committee (DEC) of the Royal Netherlands Academy of Arts and Sciences (KNAW).

extract_protocol:
For early time points (4, 6, and 8 hpf), cells were dissociated with the addition of 200 µL of pre-warmed FACSmax cell dissociation solution (Genlantis T200100) for 5 minutes resuspending gently up and down at RT. For later time points (10, 12 and 24 hpf) cells were dissociated with the addition of 200 µL of pre-warmed Protease solution (100 µL Trypsin-EDTA (0.5%), no phenol red, Thermofisher 15400054, 20 µL 10X PBS0, 80 µL H2O) for 6 minutes on a shaker (Eppendorf Thermomixer Comfort) at 28°C and 400 rpm, resuspending vigorously every 2 minutes.
The detailed, step-by-step scT-ChIC protocol is available at: https://www.protocols.io/private/714FFF81809D11EE958A0A58A9FEAC02

treatment_protocol: Wild-type TL embryos were collected 20 minutes after fertilization in a petri dish with E3 medium (13.3 mg NaCl, 0.63 mg KCl, 2.4 mg CaCl2, 4.0 mg MgSO4, diluted in a final volume of 1 L of H2O) and kept at 28.5°C in an incubator. They were dechorionated by incubation in 5mL of 1 mg/mL of pronase solution at 28.5°C for 3 to 5 minutes, and deyolked using Ca2+-free Ringer’s solution for 5 min at RT.

value: whole embryo

value: Tupfel long-fin (TL)


title: scATAC-seq of WT mouse cochlea, lysed for 5 min

description: Library name: sc-0077_coch_atac_5min


title: miRNA-323 - base

description:
Library name: miCB10
column name in Normalized_miRNA_counts_v1: 323 - base


title: STMN.PIP.8.10

city: Maebashi

first: Ryohei

last: Yoshikawa

state: Gunma

address: 3-39-22, showamachi,

department: Department of General Surgical Science

country: Japan

institute: Gunma University, Graduate School of Medicine

data_processing:
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500/NextSeq 2000 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the human hg38※  genome using STAR (version 2.7.9a).
CAGE tag count data were clustered using the CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default parameters. Clusters with count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools:　AMD, GLAM2, DREME and Weeder. The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the  motifs in database JASPAR CORE 2016 vertebrates※ were evaluated by Tomtom.
The list of differentially expressed genes detected by CAGEr (CPM > 1 and fold-change < 0.25, or CPM > 1 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes cpm values for each sample

growth_protocol: The human SCLC cell lines H446 were ultured in RPMI1640 containing 100 units/mL penicillin, 100 units/mL streptomycin, and 10% FBS in a humidified 5% CO2 incubator at 37 °C.

extract_protocol:
Total RNA was extracted from H446  using the miRNeasy Kit (Qiagen, Hilden, Germany), and the quantity of isolated RNA was measured with an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

treatment_protocol: H446 cells were treated with the PIP compound (6 μM) and Control for 48 h.

value: Lung tumor

value: Wild type

value: Chb-STMN1 PIP


title: chic_OUD8882-old-nucli-k4me1-K


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_015, healthy control

description:
Library name: cfs_cfrna_015
Column name in raw_counts_all.csv: cfs_cfrna_15

value: control

value: male

value: Ithaca, NY


title: STMN.PIP.


title: scRNA-seq of mouse cochlea transduced with AAV1-1.0kb-mMyo15-OTOF-v5, biol. rep. 3

description: Library name: C8_WT_Myo15_hOTOF

value: FVB WT


title: scRNA-seq of mouse cochlea transduced with AAV1-1.0kb-smCBA-OTOF-v5, biol. rep. 3

description: Library name: C7_WT_smCBA_hOTOF


title: chic_OUD8882-old-nucli-k4me1-J


title: scRNA-seq of mouse cochlea transduced with AAV1-1.0kb-smCBA-OTOF-v5, biol. rep. 2

description: Library name: C5_WT_smCBA_hOTOF


title: chic_OUD8882-old-nucli-k4me1-I


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_013, ME/CFS patient

description:
Library name: cfs_cfrna_013
Column name in raw_counts_all.csv: cfs_cfrna_13

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_014, ME/CFS patient

description:
Library name: cfs_cfrna_014
Column name in raw_counts_all.csv: cfs_cfrna_14

value: case

value: Los Angeles, CA


title: scRNA-seq of mouse cochlea transduced with AAV1-1.0kb-smCBA-OTOF-v5, biol. rep. 1

description: Library name: C4_WT_smCBA_hOTOF


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_012, ME/CFS patient

description:
Library name: cfs_cfrna_012
Column name in raw_counts_all.csv: cfs_cfrna_12

value: female


title: chic_OUD8882-old-nucli-k4me1-H


title: Control.8.10.

value: Control


title: Control.


title: NCI-H1299_3D-4

type: RNA

city: North Chicago

first: Vivian

last: Park

state: ILLINOIS

address: 1 North Waukegan Road

institute: AbbVie Inc.

description:
Gene expression data from 3D cell culture.
3D, biological rep4

hyb_protocol: DNA target was hybridized on the Clariom D, human array according to manufacturer’s instructions.

scan_protocol: not provided

data_processing: The Transcriptome Analysis Console software (TAC, Applied Biosystem) was used for expression analysis.

label: biotin

source_name: 3D cell culture

label_protocol: For sense-strand complementary DNA synthesis, fragmentation and labeling GeneChipTM WT PLUS Reagent Kit was used according to manufacturer’s instructions.

growth_protocol: For 2D and 3D conditions, cells were cultured in RPMI 1640 medium and supplemented with 10% fetal bovine serum and 1% sodium pyruvate. For 2D culture, cells were seeded then harvested at approximately 80% confluency. For 3D culture, 2,000 cells were seeded in 96-well ultra-low attachment microplates, spun at 1,200 rpm for 2 min for spheroid formation, then pooled and harvested 48 h post-seeding.

extract_protocol: Total RNA was extracted using Qiagen's miRNAeasy Mini Kit according to manufacturer's instructions.

treatment_protocol: For 2D culture, cells were harvested at approximately 80% confluency. For 3D culture, spheroids were pooled and harvested 48 h post-seeding.


title: scRNA-seq of mouse cochlea transduced with AAV1-1.0kb-mMyo15-OTOF-v5, biol. rep. 2

description: Library name: C3_WT_Myo15_hOTOF


title: NCI-H1299_3D-3

description:
Gene expression data from 3D cell culture.
3D, biological rep3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_011, ME/CFS patient

description:
Library name: cfs_cfrna_011
Column name in raw_counts_all.csv: cfs_cfrna_11


title: Starved

description: Library name: Sample 1

value: Brain

value: Food deprived for 4 hours


title: chic_OUD8882-old-nucli-k4me1-G


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_008, healthy control

description:
Library name: cfs_cfrna_008
Column name in raw_counts_all.csv: cfs_cfrna_8

value: New York City, NY


title: NCI-H1299_3D-2

description:
Gene expression data from 3D cell culture.
3D, biological rep2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_007, healthy control

description:
Library name: cfs_cfrna_007
Column name in raw_counts_all.csv: cfs_cfrna_7


title: chic_OUD8882-old-nucli-k4me1-F

value: whole embryo


title: scRNA-seq of mouse cochlea transduced with AAV1-1.0kb-mMyo15-OTOF-v5, biol. rep. 1

description: Library name: C1_WT_Myo15_hOTOF

value: cochlea


title: chic_OUD8882-old-nucli-k4me1-E

value: Tupfel long-fin (TL)


title: Double Heterzygous (+/delmcs9.7;+/CFP) Replicate 2

city: New York

first: Sumantra

last: Chatterjee

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Grossman School of Medicine

description: Library name: 3RE-194

data_processing:
Fastq files were analyzed using 10X genomics custom pipeline CellRanger to generate barcodes.tsv.gz, /features.tsv.gz and matrix.mtx.gz which were then run through our custom pipeline using Seurat ( PMID: 31178118 )
Assembly: mm10
Supplementary files format and content: Outs files from 10X cell ranger pipeline containing features.tsv.gz, barcodes.tsv.gz and matrix.mtx.gz

source_name: GI tract

growth_protocol: Mouse of various genotypes were bred to generate embryos at relevant developmental time points

extract_protocol:
GI tract was dssociated into single cell using accumax
scRNA-seq

value: GI tract

value: All cells of the GI tract


title: Double Heterzygous (+/delmcs9.7;+/CFP) Replicate 1

description: Library name: 3RE-188


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_006, ME/CFS patient

description:
Library name: cfs_cfrna_006
Column name in raw_counts_all.csv: cfs_cfrna_6


title: NCI-H1299_3D-1

description:
Gene expression data from 3D cell culture.
3D, biological rep1


title: chic_OUD8882-old-nucli-k4me1-D


title: NCI-H1299_2D-3

description:
Gene expression data from 2D cell culture.
2D, biological rep3

source_name: 2D cell culture, 80% confluency


title: Ret mcs9.7 Enhancer null Replicate 2

description: Library name: 3RE-212


title: NCI-H1299_2D-2

description:
Gene expression data from 2D cell culture.
2D, biological rep2


title: chic_OUD8882-old-nucli-k4me1-C


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_004, ME/CFS patient

description:
Library name: cfs_cfrna_004
Column name in raw_counts_all.csv: cfs_cfrna_4


title: chic_OUD8882-old-nucli-k4me1-B

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
4-12hpf_merged_samples_genelevel_counts.h5ad


title: Ret mcs9.7 Enhancer null Replicate 1

description: Library name: 3RE-208


title: chic_OUD8882-old-nucli-k4me1-A


title: WT_Replicate 2

description: Library name: 3RE-167

value: WT


title: NCI-H1299_2D-1

description:
Gene expression data from 2D cell culture.
2D, biological rep1


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_003, healthy control

description:
Library name: cfs_cfrna_003
Column name in raw_counts_all.csv: cfs_cfrna_3

value: control


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_002, healthy control

description:
Library name: cfs_cfrna_002
Column name in raw_counts_all.csv: cfs_cfrna_2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_001, healthy control

description:
Library name: cfs_cfrna_001
Column name in raw_counts_all.csv: cfs_cfrna_1


title: HT-1080_3D-4


title: WT_Replicate 1

description: Library name: 225_S27


title: HT-1080_3D-2


title: Lung_wt_e15.5_Input_rep2

city: Québec

first: Lucie

last: Jeannotte

state: QC

address: 2260, boulevard Henri Bourassa

department: Biologie moléculaire, Biochimie médicale & Pathologie

country: Canada

institute: Université Laval

description: Library name: Lung_wt_e15.5_Input_rep2

data_processing:
Quality of sequencing reads was evaluated using FastQC software (v0.12.1). Reads were trimmed and filtered using Trim Galore with default parameters  (v0.6.10).
Reads were mapped with Bowtie2 aligner (v2.5.2), with the following parameters :  --end-to-end -q --sensitive -X 2000
Duplicates were removed using the markdup command from Samtools package (v1.18),  Exclusion regions were removed with BEDTools (v2.31.0), using the ENCODE exclusion list.
Peaks were called using MACS3 (v3.0.1) with the callpeak module with a cut-off of False Discovery Rate (FDR) value of 0.01.
Coverage tracks were generated with the BamCompare command from deepTools and the number of reads was normalized with the signal extraction scaling algorithm (SES).
Assembly: mm10
Supplementary files format and content: BigWig, narrrowpeak (except for input samples)

source_name: Lung

extract_protocol:
Lungs from E15.5 mouse embryos were cross-linked in 1% formaldehyde prepared in phosphate-buffered saline (PBS) for 10 min at room temperature and stopped by adding glycine to a final concentration of 125 mM. Samples were then washed once with PBS, snap-frozen in liquid nitrogen and kept at −80 °C until use. Lungs were disrupted with a Dounce homogenizer in Nucleus Isolation Buffer (20 mM HEPES, 250 mM sucrose, 3 mM MgCl2, 0.25% Nonidet P-40, 3 mM ß-mercaptoethanol and protease inhibitors), equilibrated on ice for 20 min, and filtered on cell strainer (70 μm) to eliminate debris. Nuclei were lysed in 50 mM Tris–HCl pH8.0, 10 mM EDTA, 1% SDS and protease inhibitors for 10 min on ice. Chromatin was then fragmented by sonication in a Covaris M220 Focused Ultrasonicator to obtain an average DNA size of 200–500 bp. Fragmented chromatin (20 μg) was incubated overnight at 4°C with 5 μl of antibody: FLAG (Sigma-Aldrich, F1804). Immunoprecipitation products were isolated with Dynabeads protein G (ThermoFisher), washed in successive saline buffers, and reverse cross-linked in 200 mM NaCl overnight at 65 °C. Samples were then digested with Proteinase K (0.12 mg/ml) and RNaseA (0.04 mg/ml) in 40 mM Tris–HCl pH8.0, 10 mM EDTA for 2 h at 50 °C.
The NEBNext Ultra II DNA library prep kit from Illumina (New England Biolabs) was used to prepare DNA libraries, according to manufacturer’s instructions, from 2 ng of fragmented ChIP DNA, followed by the addition of NEBNext adaptors and purification with AxyPrep Mag PCR Clean-up kit (Axygen).

value: Lung


title: HT-1080_3D-3


title: chic_OUD8882-new-nucli-k4me1-J


title: chic_OUD8882-new-nucli-k4me1-K


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_005, healthy control

description:
Library name: cfs_cfrna_005
Column name in raw_counts_all.csv: cfs_cfrna_5

value: Ithaca, NY


title: HT-1080_3D-1


title: chic_OUD8882-new-nucli-k4me1-H


title: AJAI-Zhen-DCM4_1720

city: Saint Louis

first: Zhen

last: Guo

state: MO

address: 4939 Children's Place

department: Medicine

institute: Washington University in St. Louis

description:
Library name: sample25
10x Genomics

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference.
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Assembly: hg18
Supplementary files format and content: txt files of doublet prediction

molecule: nuclear RNA

source_name: heart

extract_protocol:
Frozen heart tissues from Donor, DoxCM and NICM were minced with a razor blade, then homogenized gently with 5 strokes in a 5 mL Dounce homogenizer containing 1-2 mL of chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 in nuclease-free water). Lysates were gently filtered through a 40 μm filter after a 15-minutes incubation on ice. Nuclei were resuspended in 1 mL Nuclei Wash Buffer (1x PBS with 2% BSA and 0.2 U/μL RNase inhibitor after centrifuging at 500 x g for 5 min at 4°C, and filtered through a 20 μm pluristrainer into a fresh 15 mL conical tube. Nuclei were resuspended in 300 μL Nuclei Wash Buffer after a second wash with Nuclei Wash Buffer and transferred to 5 mL FACS tube for flow sorting. 1 μL DRAQ5 (5 mM solution) was added and gently mixed before sorting. DRAQ5+ nuclei were sorted into Nuclei Wash Buffer on BD FACS Melody (BD Biosciences) using a 100 µm nozzle. After centrifuging at 500 x g for 5 min at 4°C, nuclei were gently resuspended in Nuclei Wash Buffer to a target concentration of 1,000 nuclei/μL after counting with a hemocytometer.
10X Genomics Chromium Single Cell 5’ Reagent V2

value: heart

value: DRAQ5+DAPI- alive cells

value: Male

tag: disease state

value: non-ischemia cardiomyopathy (NICM)


title: AJAI-Zhen-DCM4_1668

description:
Library name: sample23
10x Genomics

value: Female


title: Lung_wt_e15.5_Input_rep1

description: Library name: Lung_wt_e15.5_Input_rep1


title: AJAI-Zhen-DCM4_1686

description:
Library name: sample24
10x Genomics


title: chic_OUD8882-new-nucli-k4me1-G


title: HT-1080_2D-4

description:
Gene expression data from 2D cell culture.
2D, biological rep4


title: AJAI-Zhen-DCM4_1658

description:
Library name: sample22
10x Genomics


title: Lung_wt_e15.5_IP_HOXA5FLAG_rep1

description: Library name: Lung_wt_e15.5_IP_HOXA5FLAG_rep1


title: chic_OUD8882-new-nucli-k4me1-F


title: HT-1080_2D-3


title: chic_OUD8882-new-nucli-k4me1-E


title: Lung_wt_e15.5_ATAC_seq_rep3

description: Library name: Lung_wt_e15.5_ATAC_seq_rep3

data_processing:
Quality of sequencing reads was evaluated using FastQC software (v0.12.1). Reads were trimmed and filtered using Trim Galore with default parameters  (v0.6.10).
Reads were mapped with Bowtie2 aligner (v2.5.2), with the following parameters :  ---local -q --very-sensitive -X 2000.
Duplicates were removed using the markdup command from Samtools package (v1.18). Exclusion regions were removed with BEDTools (v2.31.0), using the ENCODE exclusion list. Reads mapping to the mitochondrial genome were also removed.
Reads were then adjusted for Tn5 offset using ATACseqQC package from R.
Peaks were called using MACS3 (v3.0.1) using callpeak module with the following parameters: -q 0.05 --shift 37, --extsize 73, --nomodel and --nolambda.
Coverage tracks were generated with the BamCoverage command from deepTools and the number of reads was normalized in bin by million (BPM) with bin size of 10.
Assembly: mm10
Supplementary files format and content: BigWig, narrrowpeak

extract_protocol:
Lungs from E15.5 mouse embryos were isolated, snap-frozen in liquid nitrogen and kept at -80oC until use. Nucleus extraction and tagmentation were performed as described (Grandi et al., 2022). Tagmentation with Tn5 transposase (Diagenode, C01070012) was done on 60,000 nuclei.
The NEBNext Ultra II DNA library prep kit from Illumina (New England Biolabs) was used to prepare DNA libraries, according to manufacturer’s instructions, from 2 ng of fragmented ChIP DNA, followed by the addition of NEBNext adaptors and purification with AxyPrep Mag PCR Clean-up kit (Axygen).

value: wt


title: Lung_wt_e15.5_ATAC_seq_rep4

description: Library name: Lung_wt_e15.5_ATAC_seq_rep4


title: AJAI-Zhen-DCM4_1657

description:
Library name: sample21
10x Genomics


title: chic_OUD8882-new-nucli-k4me1-D


title: Lung_wt_e15.5_ATAC_seq_rep2

description: Library name: Lung_wt_e15.5_ATAC_seq_rep2


title: HT-1080_2D-1


title: Lung_wt_e15.5_IP_HOXA5FLAG_rep2

description: Library name: Lung_wt_e15.5_IP_HOXA5FLAG_rep2


title: chic_OUD8882-new-nucli-k4me1-I


title: HT-1080_2D-2


title: chic_OUD8882-new-nucli-k4me1-C


title: mutant cells, week 8 of differentiation, biol rep 4

city: Bruxelles

first: Miriam

last: Cnop

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: LC59482405

data_processing:
Raw RNA-seq data were assessed for sequencing quality using fastp 0.20.1 to trim adapters, correct low-quality bases, filter-out low-quality reads and infer sample contamination by recording the GC content for each read.
Gene expression was quantified using Salmon 1.4.0 setting parameters to correct for sequence-specific and fragment-level GC biases and to validate the produced mapping. GENCODE version 38 (GRCh38.p13) was selected as the reference human genome for the quasi-alignment and indexed with the default k-mer values.
Assembly: GRCh38.p13
Supplementary files format and content: csv file containing TPM counts across all samples (counted with Salmon)

extract_protocol:
Total RTotal RNA was extracted from 1.023, TMEM167A V59E.37 and V59E.48 iPSC-β cell differentiationstages S4, S5, S6, S7 and long-term culture (n=4 per stage and per iPSC line)using RNeasy Plus Micro Kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s recommendation. For the library preparation, all samples had at least 200 ng high-quality RNA with RNA integrity number (RIN) higher than 7, as calculated by Agilent Bioanalyzer.
RNA libraries for RNA-seq were prepared using the Abclonal strand-specific mRNA library prep kit following manifacturer's protocol

value: clone 48 mutation V59E in TMEM167A


title: AJAI-Zhen-DoxT2_1778

description:
Library name: sample19
10x Genomics

value: doxorubicin cardiomyopathy (DoxCM)


title: AJAI-Zhen-DCM4_1617

description:
Library name: sample20
10x Genomics


title: Lung_wt_e15.5_ATAC_seq_rep1

description: Library name: Lung_wt_e15.5_ATAC_seq_rep1


title: mutant cells, week 8 of differentiation, biol rep 3

description: Library name: LC59482404


title: chic_OUD8882-new-nucli-k4me1-B

value: whole embryo


title: Organoid, AH 72hr

city: TORONTO

first: Shawn

last: Goyal

state: ON

address: 1 King's College CirToronto, ON M5S 1A8

institute: University of Toronto

description: Library name: AH_72hr_scRNAseq

data_processing:
Alignment was performed using the BD Rhapsody Whole Transcriptome Analysis (WTA) pipeline.
Assembly: mm10/GRCm38
Supplementary files format and content: .csv contain counts per cell for scRNAseq samples

source_name: intestinal epithelial

extract_protocol:
RNA was isolation using the BD Rhapsody WTA analysis kit  following the manufacturer’s instructions (BD Rhapsody)
scRNAseq - An estimated 10,000 cells were collected for BD Rhapsody single-cell library preparation following the manufacturer’s instructions.

value: intestinal epithelial

value: wild-type

value: ADP Hep 72hr


title: AJAI-Zhen-DoxT2_1552

description:
Library name: sample17
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)


title: mutant cells, week 8 of differentiation, biol rep 2

description: Library name: LC59372408

value: clone 37 mutation V59E in TMEM167A


title: AJAI-Zhen-DoxT2_1777

description:
Library name: sample18
10x Genomics


title: mutant cells, week 8 of differentiation, biol rep 1

description: Library name: LC59372405


title: Organoid, No Treatment 72hr

description: Library name: NT_72hr_scRNAseq

value: no treatment 72hr


title: AJAI-Zhen-DoxT2_1541

description:
Library name: sample16
10x Genomics


title: chic_OUD8326-nucli-k27me3-X

value: Tupfel long-fin (TL)


title: Organoid, AH, 48hr

description: Library name: AH_48hr_scRNAseq

value: ADP Hep 48 hr


title: chic_OUD8882-new-nucli-k4me1-A


title: AJAI-Zhen-DoxT2_1438

description:
Library name: sample15
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)


title: Organoid, No Treatment, 48hr

description: Library name: NT_48hr_scRNAseq

value: no treatment 48 hr


title: chic_OUD8326-nucli-k27me3-W


title: AJAI-Zhen-DoxT2_1303

description:
Library name: sample14
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)

value: heart


title: Organoid, AH, 48hr, rep5

description:
Library name: AH_48_rep5_Bulk_RNAseq
F8

data_processing:
Alignment was performed using STAR software (v 2.6.1d).
Assembly: mm10/GRCm38
Supplementary files format and content: counts for Bulk RNAseq samples

extract_protocol:
RNA was isolated using the GeneJET RNA purification kit (Thermo).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.


title: wildtype cells, week 8 of differentiation, biol rep 3

description: Library name: LC1A_24_33

value: wildtype


title: AJAI-Zhen-DoxT2_1299

description:
Library name: sample13
10x Genomics

value: DRAQ5+DAPI- alive cells


title: chic_OUD8326-nucli-k27me3-V


title: wildtype cells, week 8 of differentiation, biol rep 2

description: Library name: LC1A_24_28


title: chic_OUD8326-nucli-k27me3-U


title: AJAI-Zhen-DoxT2_1283

description:
Library name: sample12
10x Genomics


title: wildtype cells, week 8 of differentiation, biol rep 1

description: Library name: LC1A_24_19


title: mutant cells, Day 31 of differentiation,  biol rep 4

description: Library name: S7482403


title: chic_OUD8326-nucli-k27me3-T


title: Organoid, AH, 24hr, rep5

description:
Library name: AH_24_rep5_Bulk_RNAseq
F5

value: ADP Hep 24 hr


title: Organoid, IFN, 24hr, rep5

description:
Library name: IFN_24_rep5_Bulk_RNAseq
F6

value: IFN  24 hr


title: AJAI-Zhen-DoxT2_1214

description:
Library name: sample11
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)

value: Male


title: mutant cells, Day 31 of differentiation,  biol rep 3

description: Library name: S7482308

value: clone 48 mutation V59E in TMEM167A


title: AJAI-Zhen-DoxT2_1201

description:
Library name: sample10
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)

value: Female

value: doxorubicin cardiomyopathy (DoxCM)


title: Organoid, No Treatment, 48hr, rep5

description:
Library name: NT_48_rep5_Bulk_RNAseq
F7

value: intestinal epithelial


title: Organoid, No Treatment, 24hr, rep5

description:
Library name: NT_24_rep5_Bulk_RNAseq
F4

value: wild-type

value: no treatment 24 hr


title: Organoid, IFN, 6hr, rep5

description:
Library name: IFN_6_rep5_Bulk_RNAseq
F3

value: IFN 6 hr


title: wildtype cells, week 8 of differentiation, biol rep 4

description: Library name: LC1A_24_46


title: chic_OUD8326-nucli-k27me3-Q

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
4-12hpf_merged_samples_genelevel_counts.h5ad

value: whole embryo


title: mutant cells, Day 31 of differentiation,  biol rep 2

description: Library name: S759372408

value: clone 37 mutation V59E in TMEM167A


title: AJAI-Zhen-DoxT2_1113

description:
Library name: sample9
10x Genomics


title: AJAI-Zhen-Ctrl1_1744

description:
Library name: sample8
10x Genomics

value: non-failing donor (Donor)


title: Organoid, AH, 6hr, rep5

description:
Library name: AH_6_rep5_Bulk_RNAseq
F2

value: ADP Hep 6 hr


title: mutant cells, Day 31 of differentiation,  biol rep 1

description: Library name: S7372402


title: chic_OUD8326-nucli-k27me3-P

value: Tupfel long-fin (TL)


title: wildtype cells, Day 31 of differentiation, biol rep 4

description: Library name: S71A2415

value: wildtype


title: AJAI-Zhen-Ctrl1_1739

description:
Library name: sample7
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)

value: heart

value: DRAQ5+DAPI- alive cells


title: wildtype cells, Day 31 of differentiation, biol rep 3

description: Library name: S71A2410


title: chic_OUD8326-nucli-k27me3-O


title: Organoid, No Treatment, 6hr, rep5

description:
Library name: NT_6_rep5_Bulk_RNAseq
F1

value: no treatment 6 hr


title: Organoid, AH, 48hr, rep4

description:
Library name: AH_48_rep4_Bulk_RNAseq
E8

value: ADP Hep 48 hr


title: AJAI-Zhen-Ctrl1_1698

description:
Library name: sample5
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)


title: chic_OUD8326-nucli-k27me3-N


title: wildtype cells, Day 31 of differentiation, biol rep 2

description: Library name: S71A2408


title: Organoid, No Treatment, 48hr, rep4

description:
Library name: NT_48_rep4_Bulk_RNAseq
E7

value: no treatment 48 hr


title: wildtype cells, Day 31 of differentiation, biol rep 1

description: Library name: S71A2403


title: AJAI-Zhen-Ctrl1_1690

description:
Library name: sample4
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)

value: Female


title: chic_OUD8326-nucli-k27me3-S


title: chic_OUD6112_K27me3_i48

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
wholecell_samples_genelevel_counts.h5ad


title: Organoid, AH, 24hr, rep4

description:
Library name: AH_24_rep4_Bulk_RNAseq
E5

value: ADP Hep 24 hr


title: mutant cells, Day 24 of differentiation,  biol rep 4

description: Library name: S6482404

value: clone 48 mutation V59E in TMEM167A


title: rna_OUD8882-old-nucli-k4me1-L

description:
multiplexed file from a 384-well plate, celseq2 barcodes
4-12hpf_merged_samples_genelevel_counts.h5ad


title: Organoid, IFN, 24hr, rep4

description:
Library name: IFN_24_rep4_Bulk_RNAseq
E6

value: intestinal epithelial

value: wild-type

value: IFN  24 hr


title: chic_OUD8326-nucli-k27me3-R

value: whole embryo


title: AJAI-Zhen-Ctrl1_1673

description:
Library name: sample3
10x Genomics

value: Male


title: mutant cells, Day 24 of differentiation,  biol rep 3

description: Library name: S6482401


title: rna_OUD8882-old-nucli-k4me1-K


title: AJAI-Zhen-Ctrl1_1666

description:
Library name: sample1
10x Genomics; raw data was not provided for this sample because the files were lost (deleted from server)

value: non-failing donor (Donor)


title: mutant cells, Day 24 of differentiation,  biol rep 2

description: Library name: S6372407

value: clone 37 mutation V59E in TMEM167A


title: rna_OUD8882-old-nucli-k4me1-J

value: Tupfel long-fin (TL)


title: Organoid, IFN, 6hr, rep4

description:
Library name: IFN_6_rep4_Bulk_RNAseq
E3

value: IFN 6 hr


title: AJAI-Zhen-Ctrl1_1708

description:
Library name: sample6
10x Genomics

value: heart


title: AJAI-Zhen-Ctrl1_1670

description:
Library name: sample2
10x Genomics

value: DRAQ5+DAPI- alive cells


title: Organoid, AH, 6hr, rep4

description:
Library name: AH_6_rep4_Bulk_RNAseq
E2

value: ADP Hep 6 hr


title: chic_OUD8326-nucli-k27me3-M


title: wildtype cells, Day 24 of differentiation, biol rep 4

description: Library name: S61A2415

value: wildtype


title: DIO3_delta33_Multiome_RNA

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

description:
Library name: DIO3_delta33_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

data_processing:
Single cell Multiome: Sequencing results were processed through the Cell Ranger ARC pipeline (10x Genomics) with default parameters. Seurat V4 was used to perform downstream analysis following the standard pipeline.
Assembly: GRCh38
Supplementary files format and content: Cell-by-gene count matrix for all the samples as csv
Supplementary files format and content: Cell-by-peak count matrix for all the samples as csv
Supplementary files format and content: Metadata for the cell-by-gene count matrix as csv

source_name: Retinal Organoid

extract_protocol:
0.01% Nonidet P40 lysis buffer to prepare single nuclei suspension
scATAC-Seq and scRNA-Seq following 10x multiome guideline

value: Retinal Organoid

value: H7 ESCs

tag: age

value: ~200 days

tag: library type

value: mRNA


title: Organoid, No Treatment, 6hr, rep4

description:
Library name: NT_6_rep4_Bulk_RNAseq
E1

value: intestinal epithelial

value: no treatment 6 hr


title: Wildtype_Multiome_ATAC

description:
Library name: Wildtype_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq

value: WT

value: ATAC


title: wildtype cells, Day 24 of differentiation, biol rep 3

description: Library name: S61A2410


title: rna_OUD8882-old-nucli-k4me1-H

value: whole embryo


title: Wildtype_Multiome_RNA

description:
Library name: Wildtype_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: wildtype cells, Day 24 of differentiation, biol rep 2

description: Library name: S61A2408


title: rna_OUD8882-old-nucli-k4me1-F


title: Organoid, No Treatment, 48hr, rep3

description:
Library name: NT_48_rep3_Bulk_RNAseq
D7

value: wild-type

value: no treatment 48 hr


title: AA130985-8016_ontreatment

city: Lund

first: Peter

last: Ellmark

address: Scheelevägen 2, Medicon Village

country: Sweden

institute: Alligator Bioscience AB

description:
Library name: AA130985-8016
ENSG_as_rows_on_per_sample_basis

data_processing:
DRAGEN RNA pipeline (Illumina version 4.0)
Assembly: GRCh37
Supplementary files format and content: csv file with raw counts for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from FFPE slides using the AllPrep DNA/RNA FFPE Kit (Qiagen)
Kapa RNA HyperPrep kit with RiboErase(HMR) Globin (Roche)

value: Liver

value: On treatment


title: Organoid, IFN, 24hr, rep3

description:
Library name: IFN_24_rep3_Bulk_RNAseq
D6

value: IFN  24 hr


title: Organoid, No Treatment, 24hr, rep4

description:
Library name: NT_24_rep4_Bulk_RNAseq
E4

value: no treatment 24 hr


title: DIO3_delta33_Multiome_ATAC

description:
Library name: DIO3_delta33_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq


title: mutant cells, Day 16 of differentiation,  biol rep 4

description: Library name: S5482404

value: clone 48 mutation V59E in TMEM167A


title: wildtype cells, Day 24 of differentiation, biol rep 1

description: Library name: S61A2403

value: wildtype


title: mutant cells, Day 24 of differentiation,  biol rep 1

description: Library name: S6372402

value: clone 37 mutation V59E in TMEM167A


title: rna_OUD8882-old-nucli-k4me1-E

value: Tupfel long-fin (TL)


title: Organoid, No Treatment, 24hr, rep3

description:
Library name: NT_24_rep3_Bulk_RNAseq
D4


title: rna_OUD8882-old-nucli-k4me1-I


title: rna_OUD8882-old-nucli-k4me1-C


title: Organoid, AH, 48hr, rep3

description:
Library name: AH_48_rep3_Bulk_RNAseq
D8b

value: ADP Hep 48 hr


title: AA130939_ontreatment

description:
Library name: AA130939
ENSG_as_rows_on_per_sample_basis

source_name: Stomach

value: Stomach


title: Organoid, IFN, 6hr, rep3

description:
Library name: IFN_6_rep3_Bulk_RNAseq
D3

value: intestinal epithelial

value: IFN 6 hr


title: mutant cells, Day 16 of differentiation,  biol rep 2

description: Library name: S5372407


title: rna_OUD8882-old-nucli-k4me1-B


title: AA130982-8016_ontreatment

description:
Library name: AA130982-8016
ENSG_as_rows_on_per_sample_basis


title: mutant cells, Day 16 of differentiation,  biol rep 1

description: Library name: S5372402


title: AA130974-8016_baseline

description:
Library name: AA130974-8016
ENSG_as_rows_on_per_sample_basis

value: Naïve


title: rna_OUD8882-old-nucli-k4me1-A


title: Organoid, AH, 24hr, rep3

description:
Library name: AH_24_rep3_Bulk_RNAseq
D5

value: ADP Hep 24 hr


title: mutant cells, Day 16 of differentiation,  biol rep 3

description: Library name: S5482401


title: AA130983_ontreatment

description:
Library name: AA130983
ENSG_as_rows_on_per_sample_basis


title: AA130984-8016_ontreatment

description:
Library name: AA130984-8016
ENSG_as_rows_on_per_sample_basis


title: Organoid, No Treatment, 6hr, rep3

description:
Library name: NT_6_rep3_Bulk_RNAseq
D1

value: no treatment 6 hr


title: rna_OUD8882-new-nucli-k4me1-J

value: whole embryo


title: Organoid, AH, 48hr, rep2

description:
Library name: AH_48_rep2_Bulk_RNAseq
C8

value: wild-type


title: wildtype cells, Day 16 of differentiation,  biol rep 3

description: Library name: S51A2410


title: AA130152-R_baseline

description:
Library name: AA130152-R
ENSG_as_rows_on_per_sample_basis

source_name: Peritoneum

value: Peritoneum


title: Organoid, No Treatment, 48hr, rep2

description:
Library name: NT_48_rep2_Bulk_RNAseq
C7

value: no treatment 48 hr


title: wildtype cells, Day 16 of differentiation,  biol rep 2

description: Library name: S51A2408


title: rna_OUD8882-old-nucli-k4me1-G


title: rna_OUD8882-old-nucli-k4me1-D


title: AA130955-8020_baseline

description:
Library name: AA130955-8020
ENSG_as_rows_on_per_sample_basis

value: Liver


title: wildtype cells, Day 16 of differentiation, biol rep 4

description: Library name: S51A2415


title: Organoid, AH, 6hr, rep3

description:
Library name: AH_6_rep3_Bulk_RNAseq
D2

value: ADP Hep 6 hr


title: rna_OUD8882-new-nucli-k4me1-I

description:
multiplexed file from a 384-well plate, celseq2 barcodes
4-12hpf_merged_samples_genelevel_counts.h5ad


title: AA130980-8016_baseline

description:
Library name: AA130980-8016
ENSG_as_rows_on_per_sample_basis


title: Organoid, IFN, 24hr, rep2

description:
Library name: IFN_24_rep2_Bulk_RNAseq
C6

value: IFN  24 hr


title: wildtype cells, Day 16 of differentiation,  biol rep 1

description: Library name: S51A2403

value: wildtype


title: AA130979_baseline

description:
Library name: AA130979
ENSG_as_rows_on_per_sample_basis

source_name: Pancreas

value: Pancreas


title: rna_OUD8882-new-nucli-k4me1-H

value: Tupfel long-fin (TL)


title: Organoid, AH, 24hr, rep2

description:
Library name: AH_24_rep2_Bulk_RNAseq
C5


title: rna_OUD8882-new-nucli-k4me1-G


title: rna_OUD8882-new-nucli-k4me1-K


title: AA130976_baseline

description:
Library name: AA130976
ENSG_as_rows_on_per_sample_basis


title: Organoid, No Treatment, 24hr, rep2

description:
Library name: NT_24_rep2_Bulk_RNAseq
C4

value: no treatment 24 hr


title: AA130973_baseline

description:
Library name: AA130973
ENSG_as_rows_on_per_sample_basis


title: rna_OUD8882-new-nucli-k4me1-F


title: mutant cells, Day 12 of differentiation,  biol rep 3

description: Library name: S4482401

value: clone 48 mutation V59E in TMEM167A


title: rna_OUD8882-new-nucli-k4me1-E


title: mutant cells, Day 12 of differentiation,  biol rep 2

description: Library name: S4372407

value: clone 37 mutation V59E in TMEM167A


title: Organoid, AH, 6hr, rep2

description:
Library name: AH_6_rep2_Bulk_RNAseq
C2

value: intestinal epithelial


title: Organoid, No Treatment, 6hr, rep2

description:
Library name: NT_6_rep2_Bulk_RNAseq
C1


title: AA130969_baseline

description:
Library name: AA130969
ENSG_as_rows_on_per_sample_basis

value: Naïve


title: rna_OUD8882-new-nucli-k4me1-D


title: Organoid, IFN, 6hr, rep2

description:
Library name: IFN_6_rep2_Bulk_RNAseq
C3

value: IFN 6 hr


title: AA130970_baseline

description:
Library name: AA130970
ENSG_as_rows_on_per_sample_basis


title: mutant cells, Day 12 of differentiation,  biol rep 1

description: Library name: S4372402


title: wildtype cells, Day 12 of differentiation,  biol rep 4

description: Library name: S41A2415


title: AA130967_baseline

description:
Library name: AA130967
ENSG_as_rows_on_per_sample_basis


title: rna_OUD8882-new-nucli-k4me1-C


title: wildtype cells, Day 12 of differentiation,  biol rep 2

description: Library name: S41A2408


title: Organoid, AH, 48hr, rep1

description:
Library name: AH_48_rep1_Bulk_RNAseq
B8

value: ADP Hep 48 hr


title: AA130968_baseline

description:
Library name: AA130968
ENSG_as_rows_on_per_sample_basis


title: Organoid, No Treatment, 48hr, rep1

description:
Library name: NT_48_rep1_Bulk_RNAseq
B7


title: rna_OUD8882-new-nucli-k4me1-B

value: whole embryo


title: rna_OUD8882-new-nucli-k4me1-A


title: mutant cells, Day 12 of differentiation,  biol rep 4

description: Library name: S4482404


title: wildtype cells, Day 12 of differentiation,  biol rep 1

description: Library name: S41A2403


title: Organoid, IFN, 24hr, rep1

description:
Library name: IFN_24_rep1_Bulk_RNAseq
B6

value: wild-type


title: rna_OUD8326-nucli-k27me3-X


title: AA130965-8016_baseline

description:
Library name: AA130965-8016
ENSG_as_rows_on_per_sample_basis


title: LENG8-depletion,nucleus,replicate3

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

description:
Library name: P62
PAS-seq

data_processing:
For PAS-seq data processing, raw reads were trimmed using Cutadapt (v2.10) to remove (1) a 6-nucleotide linker sequence, (2) poly(A) tails, and (3) any reads that failed trimming. Cleaned reads were then aligned to a concatenated human (hg19) reference genome using STAR (v2.7.3a). For RNA-seq data processing,raw reads were trimmed using Cutadapt (v2.10). Cleaned reads were then aligned to a concatenated human (hg19) reference genome using STAR (v2.7.3a).
Assembly: hg19
Supplementary files format and content: BigWig files

source_name: Kidney

growth_protocol: HEK293T cell lines containing dTAG-Flag in LENG8 N-terninus were cultured in DMEM supplemented with 10% FBS

extract_protocol:
For fragnation analysis, 150 ŒºL of pre-chilled 0.7% NP-40 lysis buffer (10 mM Tris-HCl, 75 mM NaCl, 0.7% NP-40, pH 7.5, supplemented with fresh protease inhibitors) was added. The suspension was pipetted using a 200 ŒºL tip until homogeneous and incubated on ice for 30 seconds. Samples were then centrifuged at 13,300 rpm for 15 seconds to separate the cytoplasmic (supernatant) and nuclear (pellet) fractions. A total of 150 ŒºL of the cytoplasmic supernatant was collected into new tubes for cytoplasmic RNA extraction by TRIzol reagent. The nuclear pellet was washed three times with 1√ó PBS. 1 mL of TRIzol reagent was added to extract nuclear RNAs. For total RNA, total RNA was extracted from cells using TRIzol reagent
Polyadenylated RNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and then purified mRNA was fragmented at 94¬∞C for 3 minutes using the NEBNext Magnesium RNA Fragmentation Module. For PAS-seq analysis, only the 3'end of mRNA was used for library constrcution.All of library construction was followed illumina's protocol

treatment_protocol: The cells were treated with DMSO and dTAG-V1 for 24h seperately

value: Kidney

value: Human embryonic kidney 293 cell line

tag: group

value: PAS-seq


title: Organoid, AH, 24hr, rep1

description:
Library name: AH_24_rep1_Bulk_RNAseq
B5b

value: ADP Hep 24 hr


title: AA130964-8016_baseline

description:
Library name: AA130964-8016
ENSG_as_rows_on_per_sample_basis

value: Liver


title: wildtype cells, Day 12 of differentiation,  biol rep 3

description: Library name: S41A2410

value: wildtype


title: rna_OUD8326-nucli-k27me3-W


title: LENG8-depletion,nucleus,replicate2

description:
Library name: P61
PAS-seq


title: AA130963_baseline

description:
Library name: AA130963
ENSG_as_rows_on_per_sample_basis


title: Organoid, No Treatment, 24hr, rep1

description:
Library name: NT_24_rep1_Bulk_RNAseq
B4


title: rna_OUD8326-nucli-k27me3-V


title: Organoid, IFN, 6hr, rep1

description:
Library name: IFN_6_rep1_Bulk_RNAseq
B3


title: AA130962-8016_baseline

description:
Library name: AA130962-8016
ENSG_as_rows_on_per_sample_basis


title: Organoid, AH, 6hr, rep1

description:
Library name: AH_6_rep1_Bulk_RNAseq
B2

value: ADP Hep 6 hr


title: LENG8-depletion,cytoplasm,replicate3

description:
Library name: P59
PAS-seq


title: rna_OUD8326-nucli-k27me3-T

value: Tupfel long-fin (TL)


title: AA130961_baseline

description:
Library name: AA130961
ENSG_as_rows_on_per_sample_basis


title: Organoid, No Treatment, 6hr, rep1

description:
Library name: NT_6_rep1_Bulk_RNAseq
B1

value: no treatment 6 hr


title: LENG8-depletion,nucleus,replicate1

description:
Library name: P60
PAS-seq


title: rna_OUD8326-nucli-k27me3-U

description:
multiplexed file from a 384-well plate, celseq2 barcodes
4-12hpf_merged_samples_genelevel_counts.h5ad


title: LENG8-depletion,cytoplasm,replicate2

description:
Library name: P58
PAS-seq


title: AA130960_baseline

description:
Library name: AA130960
ENSG_as_rows_on_per_sample_basis


title: LENG8-depletion,cytoplasm,replicate1

description:
Library name: P57
PAS-seq


title: rna_OUD8326-nucli-k27me3-R


title: AA130966_baseline

description:
Library name: AA130966
ENSG_as_rows_on_per_sample_basis


title: AA130958-8016_baseline

description:
Library name: AA130958-8016
ENSG_as_rows_on_per_sample_basis

value: Peritoneum


title: NK, hd15 condition, knock-out, replicate 2

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

description:
Library name: HD15_KO_rep2
HD15_KO_rep2

data_processing:
Basecalls and demultiplexing were performed with Illumina's bcl2fastq2 software.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: mm10
Supplementary files format and content: csv file including differential expression result
Supplementary files format and content: all.genes_counts_raw.tsv

source_name: Spleen

growth_protocol: Rosa YFP/YFP Ncr1 CRE-ERT2 or Acly fl/fl Rosa YFP/YFP Ncr1 CRE-ERT2 mice were treated with tamoxifen diet for 48 hours. 5 days after withdrawal of tamoxifen diet, YFP+ cells from splenic NK cells were sorted.

extract_protocol:
RNA was harvested with Rneasy kit (Qiagen)
Takara-Clontech SMARTer

treatment_protocol: Priming was induced by IL-15 (100ng/ml) for 72 hours. Primed NK cells were washed and stimulated with plate-bound NKG2D (20ug/ml) for 6 hours.

value: Spleen

value: NK cell


title: control,nucleus,replicate3

description:
Library name: P56
PAS-seq

value: WT

value: DMSO


title: AA130956_baseline

description:
Library name: AA130956
ENSG_as_rows_on_per_sample_basis

value: Naïve


title: control,nucleus,replicate2

description:
Library name: P55
PAS-seq


title: NK, hd15 condition, knock-out, replicate 1

description:
Library name: HD15_KO_rep1
HD15_KO_rep1


title: rna_OUD8326-nucli-k27me3-P

value: whole embryo


title: AA130954Block1_baseline

description:
Library name: AA130954Block1
ENSG_as_rows_on_per_sample_basis


title: AA130950_baseline

description:
Library name: AA130950
ENSG_as_rows_on_per_sample_basis

source_name: Skin

value: Skin


title: NK, hd15 condition, wild type, replicate 3

description:
Library name: HD15_WT_rep3
HD15_WT_rep3


title: control,cytoplasm,replicate3

description:
Library name: P54
PAS-seq

value: Kidney


title: control,cytoplasm,replicate1

description:
Library name: P53
PAS-seq

value: Human embryonic kidney 293 cell line


title: NK, hd15 condition, knock-out, replicate 3

description:
Library name: HD15_KO_rep3
HD15_KO_rep3


title: LENG8-depletion,total RNA,replicate2

description:
Library name: P52
PAS-seq

value: PAS-seq


title: rna_OUD8326-nucli-k27me3-S


title: AA130949_baseline

description:
Library name: AA130949
ENSG_as_rows_on_per_sample_basis

value: Pancreas


title: NK, hd15 condition, wild type, replicate 1

description:
Library name: HD15_WT_rep1
HD15_WT_rep1


title: rna_OUD8326-nucli-k27me3-O


title: rna_OUD8326-nucli-k27me3-M


title: AA130948-8016_baseline

description:
Library name: AA130948-8016
ENSG_as_rows_on_per_sample_basis


title: rna_OUD8326-nucli-k27me3-N


title: control,total RNA,replicate3

description:
Library name: P51
PAS-seq


title: NK, nkg2d condition, knock-out, replicate 3

description:
Library name: NKG2D_KO_rep3
NKG2D_KO_rep3


title: AA130947_baseline

description:
Library name: AA130947
ENSG_as_rows_on_per_sample_basis

value: Liver


title: NK, nkg2d condition, knock-out, replicate 2

description:
Library name: NKG2D_KO_rep2
NKG2D_KO_rep2


title: control,total RNA,replicate2

description:
Library name: P50
PAS-seq


title: AA130941_baseline

description:
Library name: AA130941
ENSG_as_rows_on_per_sample_basis


title: control,total RNA,replicate1

description:
Library name: P49
PAS-seq


title: NK, nkg2d condition, knock-out, replicate 1

description:
Library name: NKG2D_KO_rep1
NKG2D_KO_rep1


title: AA130938-8015_baseline

description:
Library name: AA130938-8015
ENSG_as_rows_on_per_sample_basis


title: control,nucleus,replicate1

description:
Library name: P19
PAS-seq


title: rna_OUD8326-nucli-k27me3-Q


title: NK, nkg2d condition, wild type, replicate 3

description:
Library name: NKG2D_WT_rep3
NKG2D_WT_rep3


title: NK, hd15 condition, wild type, replicate 2

description:
Library name: HD15_WT_rep2
HD15_WT_rep2


title: control,cytoplasm,replicate2

description:
Library name: P18
PAS-seq


title: NK, nkg2d condition, wild type, replicate 2

description:
Library name: NKG2D_WT_rep2
NKG2D_WT_rep2


title: NK, nkg2d condition, wild type, replicate 1

description:
Library name: NKG2D_WT_rep1
NKG2D_WT_rep1


title: LENG8-depletion, total RNA, replicate1

description:
Library name: P16
PAS-seq


title: NK, fresh condition, knock-out, replicate 3

description:
Library name: Fresh_KO_rep3
Fresh_KO_rep3

value: Fresh


title: AA130936-8015_baseline

description:
Library name: AA130936-8015
ENSG_as_rows_on_per_sample_basis


title: AA130934_baseline

description:
Library name: AA130934
ENSG_as_rows_on_per_sample_basis


title: AA130153_baseline

description:
Library name: AA130153
ENSG_as_rows_on_per_sample_basis


title: Sertraline hydrochloride exposure, replicate C, concentration 30623

city: Duluth

first: Phillip

last: Ankley

state: MN

address: 6201 Congdon Blvd

institute: U.S. EPA

description: Library name: sertraline_C_30623

data_processing:
Sequencing was performed in a 1x100bp single read format using Illumina NovaSeq SP flow cells (Illumina, Inc., San Diego, CA, USA). Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and the output of the RTA was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v2.20.0. The R. subcapitata reference genome (GCA_003203535.1) was indexed using STAR v2.7.10a (Dobin et al., 2012) using the following parameters: genomeSAindexNbases = 11, sjdbOverhang = 99, and sjdbGTFfeatureExon = gene. The raw, 1x100bp single end FASTQ sequence files were trimmed, quality filtered (Phred score <15), and had UMIs and adapter sequences removed after deduplication using fastp v0.23.2 (Chen 2023, Chen et al., 2018). Quality reads were aligned and mapped to the indexed reference genome using STAR. The resulting alignment files were sorted by coordinates and indexed by sample using Samtools v1.15.1 (Danecek et al., 2021). Aligned reads were quantified with respect to gene features using the “featureCounts” program (v2.0.6) of the subread package (Liao et al., 2014). A 1,400 bp extension was added to each read at the 5’ end as most reads aligned at unannotated 3’ untranslated regions (UTR) of the genome and gene features with the largest overlap were counted. The quantified reads were organized into a count matrix file where columns represented samples and rows represented genes.
Assembly: Raphidocelis subcapitata reference genome (GCA_003203535.1)
Supplementary files format and content: Three samples with low alignment (< 35 %) and assignment (< 10 %) rates were removed including an additional outlier sample, removing two samples from both treatment 12249 and 30623 (i.e. total 41 data columns in the Normalized_Sertraline_Microalgae_RNAseq.tsv). For additional quality control, genes that had 0 abundance in any of the controls or a mean count < 10 in treatment samples were removed prior to concentration-response modeling with DRomics. Data was then normalized with respect to library size and transfromed using the "rlog" method from DESeq2.

organism: Raphidocelis subcapitata

source_name: whole cell

growth_protocol: Reared in Woods Hole MBL media at 24°C with constant light (~250 µmol/m2/s)

extract_protocol:
RNA was extracted from pooled homogenates (Plant/Fungi Total RNA Purification kits, #31900, Norgen Biotek, Ontario, Canada) with a protocol slightly modified from the manufacturer’s instructions. First, the algae were centrifuged, and the supernatant was aspirated. Glass beads (0.5 mm) were added to each well and the plate went through five cycles of freezing with liquid nitrogen and bead milling for 2 minutes. Next, 400 µl of kit Buffer C was added to each well and then the manufacturer’s procedure was followed.
Libraries were prepared using the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Unique Dual Index) and QuantSeq UMI (Unique Molecular Identifier) module with PhiX spike-in making up ~5% of the total reads in each lane. The UMI module (https://faqs.lexogen.com/faq/quantseq-umi-module) added a random, 6nt sequence to the start of each read 1 (R1), followed by a constant, 4nt (TATA) spacer. Preparation followed manufacturer’s recommendations. Completed libraries were quality checked and quantified using Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. Libraries were pooled in equimolar amounts and quantified using the Invitrogen Collibri Quantification qPCR kit.

treatment_protocol: Using 96-well plates, sertraline exposure was serially diluted in algae media (Woods Hole MBL media) with a Biomek i5 liquid handler to final nominal exposure concentrations of 100, 40, 16, 6.4, 2.56, 1.024, 0.410, and 0.164 uM with five replicates per concentration. There were also five control replicates and two concentrations of CuSO4 (0.75 and 1.5 mM) with three replicates each as positive controls. All sertraline and control replicates were arranged on a 96-well plate in a predetermined systematic layout such that each concentration was distributed to equal numbers of edge and interior wells. All wells contained 0.33% solvent. Prior to exposure, the cells per ml of a R. subcapitata culture in exponential growth was adjusted to approximately 5 x 10^6 cells/ml. Each well of exposure plates was loaded with 800 µl of algal suspension. All assays were conducted in four replicate, 96-well plates using deep-well plates sealed with optically clear adhesive covers. Three of the replicate plates were randomly designated for transcriptomic analysis while the fourth plate was used for phenotypic measurements. Algae were kept in suspension during incubation by shaking using a temperature controlled orbital shaker.

value: whole cell

value: Carolina Biological

value: Sertraline (DTXSID6023577)

tag: concentration

tag: concentration units

value: µg/L

tag: exposure duration

value: 24 hour

tag: growth stage

value: Exponential Growth Stage


title: AA130157_baseline

description:
Library name: AA130156
ENSG_as_rows_on_per_sample_basis

tag: tissue

tag: treatment


title: TBM4_CSF

city: Ho Chi Minh

first: HongThai

last: LeNguyen

address: 764, Vo Van Kiet

department: Tuberculosis Group

country: Viet Nam

institute: Oxford University Clinical Research Unit

description:
Library name: Sc007
10x Genomics

data_processing:
Sequencing data was processed using Cell Ranger v7.1.0 (10x Genomics). Namely, reads were aligned to a GRCh38 reference genome (v3.0.0) and gene expression matrices generated using cellranger count. SoupX (v1.6.2) was used to remove ambient RNA contamination [38]. Doublets were removed using Scrublet (v0.0.4) with default parameters [39]. The data from all samples were combined using the merge function in Seurat v4.3.1 [40]. Low quality cells with < 500 genes detected or > 10% of reads aligned to the mitochondrial genome were removed. Genes expressed in fewer than five cells were removed. After quality control, data was analyzed using Seurat v4.3.1 [40]. Raw count data was normalized using sctransform [41] with percent mitochondrial reads and the number of unique molecular identifier (UMI) counts regressed out. Variance stabilizing transformation was performed to identify the 3,000 most variable genes, which were used for principal component analysis (PCA). Batch effects from different donors were removed using Harmony [42]. A shared nearest neighbor graph was constructed using the top 30 Harmony components, and clustering was performed with the Louvain algorithm (resolution 1.9). Data was visualized using UMAP of the top 30 Harmony PCs.
Assembly: 10x human reference (GRCh38)
Supplementary files format and content: h5: Matrix files

source_name: CSF

extract_protocol:
As part of routine hospital procedure, 5-10 ml of CSF and 1 ml heparinized blood were collected. 2-3 ml of CSF were sent to the hospital laboratory for routine tests for viral, bacterial, or fungal infection. The remaining CSF was concentrated by centrifugation at 300 × g for 10 min and re-suspended in 700 µl of CSF supernatant. This CSF deposit was used for TB diagnostic tests, including 100 μl for Ziehl-Neelsen smear, 200 μl for Xpert MTB/RIF, and 200 μl was stored at -80°C for future use. The remaining 200 μl of CSF was used for scRNA-seq if processed within four hours of collection, with ≥ 75 cells/µl deposit, and no artificial blood contamination (evidenced by > 200 RBCs/μl CSF total) [15]. After re-centrifugation (300 × g, 5 min), CSF pellets were resuspended in 50 μl PBS containing 0.04% bovine serum albumin (BSA, Sigma) and counted. Blood was processed alongside CSF, with PBMCs isolated using density gradient centrifugation with Histopaque 1077 (Sigma) following the manufacturer’s instructions.
Single-cell suspensions were loaded onto a 10x Genomics Chromium Controller. One patient sample was loaded per channel with a target capture rate of 4,000 cells, while the healthy control PBMCs had a target capture rate of 1,000 cells. Libraries were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s instructions. The library from the healthy control PBMCs was sequenced internally on an Illumina MiSeq to a mean depth of 20,922 reads per cell, with a sequencing saturation of 66.1%. Patient libraries were sequenced on an Illumina NovaSeq 6000 (BGI, Hong Kong) to a mean depth of 33,072-163,448 reads per cell, with a sequencing saturation of 54.0-91.6%.

value: CSF

tag: cell type

value: CSF cells

tag: disease

value: tuberculous meningitis

value: baseline

tag: batch


title: Sertraline hydrochloride exposure, replicate E, concentration 30623

description: Library name: sertraline_E_30623

tag: genotype


title: LENG8-depletion,total RNA,replicate3

description:
Library name: P17
PAS-seq

tag: cell line


title: NK, fresh condition, knock-out, replicate 1

description:
Library name: Fresh_KO_rep1
Fresh_KO_rep1

value: Spleen

value: NK cell


title: Sertraline hydrochloride exposure, replicate A, concentration 30623

description: Library name: sertraline_A_30623


title: TBM4_PBMCs

description:
Library name: Sc008
10x Genomics

source_name: blood

value: blood

value: PBMCs


title: NK, fresh condition, wild type, replicate 1

description:
Library name: Fresh_WT_rep1
Fresh_WT_rep1


title: Sertraline hydrochloride exposure, replicate B, concentration 30623

description: Library name: sertraline_B_30623


title: Sertraline hydrochloride exposure, replicate D, concentration 30623

description: Library name: sertraline_D_30623


title: NK, fresh condition, knock-out, replicate 2

description:
Library name: Fresh_KO_rep2
Fresh_KO_rep2


title: Sertraline hydrochloride exposure, replicate E, concentration 12249

description: Library name: sertraline_E_12249


title: TBM3_PBMCs

description:
Library name: Sc006
10x Genomics


title: AA130154_baseline

description:
Library name: AA130154
ENSG_as_rows_on_per_sample_basis

value: Pancreas

value: Naïve


title: NK, fresh condition, wild type, replicate 2

description:
Library name: Fresh_WT_rep2
Fresh_WT_rep2

value: Fresh


title: Wildtype mouse 3, no doxycycline, eye cup (RPE, choroid, sclera)

city: Dallas

first: Katherine

middle: J.

last: Wert

state: TX

address: 5323 Harry Hines Blvd. E7.138

department: Ophthalmology and Molecular Biology

institute: University of Texas Southwestern Medical Center

description:
WTnoDx_RPE3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

data_processing:
Samples were processed by Novogene Inc.
Original image data file is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).  Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Perform alignments with HISAT2 to the reference. Gene expression level is calculated by the number of mapped reads.
Assembly: GRCm39/mm39
Supplementary files format and content: file includes: Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

source_name: Eye cup (RPE, choroid, sclera)

growth_protocol: Animals were kept on a light–dark cycle (12 hour–12 hour). Food and water were available ad libitum throughout the experiment.

extract_protocol:
Eyes were dissected to harvest the neural retina and remaining eye cup (RPE, sclera, choroid), which were then flash frozen using liquid nitrogen. RNA was extracted from tissue samples following the standard protocol of the Qiagen RNeasy Mini Kit (Qiagen, 74106).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Mice were provided 2mg/mL doxycycline (Sigma-Aldrich, #D9891-100G) with 10% sucrose (Sigma-Aldrich, S0389-1KG) orally via drinking water. Doxycycline and sucrose treated water was provided ad libitum in red tinted water bottles for 72 hours.

value: Eye cup (RPE, choroid, sclera)

value: Wildtype


title: Preterm microbiome, 2 wks old, mouse 4

city: Chicago

first: Jing

last: Lu

state: Illinois

address: 900 E 57th St

institute: University of Chicago

description: Library name: ECZ-18

data_processing:
The processed data files were created using Cell Ranger’s (10x Genomics) count function to align sequencing reads to the GRCm38 (mm10) mouse reference genome. The uploaded files originate from the raw_feature_bc_matrix folder created by running the function for each sample.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz - Contains a sparse gene expression matrix (UMI counts). Each non-zero entry indicates the number of UMIs detected for a specific gene in a specific cell. Cells and genes are referenced by indices that correspond to entries in barcodes.tsv.gz and features.tsv.gz.
Supplementary files format and content: barcodes.tsv.gz - Provides cell barcode identifiers
Supplementary files format and content: features.tsv.gz - Provides gene names/IDs

source_name: brain

growth_protocol: All mice in this study were allowed ad libitum access to NIH-31 germ-free chow and water. We maintained germ-free C57BL/6J mice (Jackson Laboratory, ME, USA) at the Gnotobiotic Research Animal Facility at the University of Chicago, where animals are routinely tested for microbes and parasites to ensure they remain germ-free.

extract_protocol:
When the pups reached two weeks of age, we collected whole-brain samples from four of the full-term microbiome mice (three female, one male) and four of the preterm microbiome mice (two female, two male). To isolate brain cells, we used the Neural Tissue Dissociation Kit - Postnatal Neurons created by Miltenyi Biotec. We followed the protocol established by Miltenyi Biotec for use of the kit without small modifications: using a 40 µm strainer instead of a 70 µm one, incubation after addition of enzyme mix 1 for eight minutes instead of fifteen, and incubation after dissociation of tissue for six minutes instead of ten. The change in filter size was necessary to remove debris, and we shortened the incubation times to reduce potential cell stress and RNA degradation.
We prepared scRNA-seq libraries using Chromium Next GEM Single Cell 3′ v.3.1 reagent kit (10x Genomics, CA, USA). We barcoded cells using the Chromium Controller (10x Genomics). Eleven polymerase chain reaction cycles were applied to generate cDNA and thirteen cycles for final library generation. The final scRNA-seq libraries were sequenced with the Illumina NovaSeq X (Illumina, CA, USA).

treatment_protocol: We obtained patient fecal samples from 2015 to 2023 from the Center for the Science of Early Trajectories biorepository at the University of Chicago Comer Children’s Hospital, which operates a level IV NICU in Chicago, IL, USA. All infants enrolled were delivered between 24 and 40 weeks of gestation age (GA) and had no congenital anomalies. We thawed 100-mg aliquots of fecal samples from two full-term, healthy infants at GAs of 39 weeks and 40 weeks (MTerm) and a sample from an infant born from a mother with confirmed chorioamnionitis with GA of 24 weeks (MPreterm). Under anaerobic conditions, we resuspended the fecal samples in PBS, clarified the homogenates through 100 µm nylon filters (BD Falcon, NJ, USA), and stored them in in PBS containing glycerol (concentration of 15% v/v) at -80°C in 600 µL aliquots. We colonized germ-free mice by gavaging eight- to nine-week-old pregnant females (estimated embryonic day 15-17) with 250 µL aliquots of the prepared MTerm or MPreterm fecal supernatant. Pups were delivered spontaneously and kept with their mothers until weaning, allowing them to naturally acquire the transplanted patient-derived microbiota.

value: brain

tag: Sex

value: female

value: preterm microbiome


title: TBM3_CSF

description:
Library name: Sc005
10x Genomics


title: AA130937_baseline

description:
Library name: AA130937
ENSG_as_rows_on_per_sample_basis


title: Sertraline hydrochloride exposure, replicate D, concentration 12249

description: Library name: sertraline_D_12249

value: whole cell

value: Carolina Biological

value: Sertraline (DTXSID6023577)

value: µg/L

value: 24 hour

value: Exponential Growth Stage


title: Wildtype mouse 3, no doxycycline, neural retina

description:
WTnoDx_Ret3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

source_name: retina

value: retina


title: Preterm microbiome, 2 wks old, mouse 3

description: Library name: ECZ-17

tag: strain