title: GL2_WT3

city: Chengdu

first: Linrui

last: Peng

state: Sichuan

address: No37 Guoxue Alley Wuhou District

institute: West China Hospital

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of  Mus musculus GRCm38 using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Primary pancreatic stellate cell

growth_protocol: Primary PSCs were cultured in DMEM/F12 medium containing 10% FBS, 100 U/mL penicillin, 100 µg/mL streptomycin, and 4 mM L-glutamine, with media changes every 2 days.

extract_protocol:
Total RNAs were extracted from primary PSCs using TRIzol Reagent (Invitrogen, cat. NO 15596026. DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: The Gli2△PSC and Gli2fl/fl micegenetically modified mice were intraperitoneally injected with tamoxifen at a dose of 100 mg/kg body weight for 5 consecutive days to induce Gli2 deletion in PSCs. After a 1-week interval, PSCs were isolated and then cultured in vitro for 4 days

value: Primary pancreatic stellate cell

tag: genotype

value: WT

value: Cuture-activated


title: Neuron derived from CTRL2-iPSC,Div35 [snRNA-seq]

status: Public on Nov 13 2024

type: SRA

city: Ota-ku

first: Taro

last: Sato

state: Tokyo

address: 2-1-1 Kitasenzoku

department: Prosthodontics

country: Japan

institute: Showa University School of Dentistry

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggression were made using the Cell Ranger software v7.1.0 .
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: All neurons were cultured on dishes coated with poly-L-lysine (Sigma-Aldrich) and fibronectin (Corning, Corning, NY, USA) in 5% CO2 at a density of 2 ×106 cells/well in 6-well plates. The medium was changed to Neurobasal Plus Medium (Thermo Fisher Scientific) supplemented with 1 ×B-27 Plus supplement,0.5% penicillin/streptomycin, 20 ng/mL brain-derived neurotrophic factor (BDNF; BioLegend, San Diego, CA, USA), 20 ng/mL glial cell-derived neurotrophic factor (GDNF; Alomone Labs, Jerusalem BioPark, Israel), 0.2 mM ascorbic acid (Sigma-Aldrich), 0.5 mM dbcAMP (Nacalai Tesque), 1 ng/mL transforming growth factor-β (TGF-β; BioLegend), 10 μM DAPT (Sigma-Aldrich), and 3 μM CHIR99021. Half of the medium volume was replaced with fresh medium (including all supplements except CHIR99021) every three or four days.

extract_protocol:
Nuclei isolation was performed by referring to the protocol provided by 10x Genomics (Nuclei Isolation for Single Cell Multisome ATAC + Gene Expression Sequencing CG000365 RevC).
cDNA synthesis and gene expression libraries were performed according to the protocol provided by 10x Genomics (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) CG000315 Rev E). The quality of cDNA and libraries was evaluated by electrophoresis.

tag: cell line

tag: cell type

value: neuron

tag: time


title: G16262-2-T105

city: Belmont

first: Shu

last: Dan

state: MA

address: 115 Mill St

department: Basic Neuroscience

country: USA

institute: McLean Hospital, Harvard Medical School

library_source: transcriptomic

data_processing:
The obtained RNAseq data were processed through the bulk RNA-seq pipeline in bcbio (v1.2.8, Chapman et al 2021).
Reads were aligned using STAR against transcriptome references of the human genome (build 94, Dobin et al. 2013) and quantified with Salmon (Patro et al. 2017).
N/A
N/A
N/A
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: blood

extract_protocol:
Total RNA was extracted using the Norgen Total RNA Purification Kit (Cat. 17200, Norgen Biotek Corp, Thorold, ON, Canada) and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc., Waltham, MA).
RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina. The sequencing libraries were multiplexed and clustered on seven lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

tag: tissue

value: blood

tag: mdd phenotype

value: Hyper

tag: visit

tag: condition

value: NS

tag: time point


title: TC 009

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
GeoMx_NGS_Pipeline_ 2.0.0
Counts from barcodes corresponding to RNA probes were normalized with internal positive and negative controls and then normalized to ROI area.
The FastQ files generated by the Illumina sequencing were converted into digital count conversion (dcc) files, then loaded into the GeoMx DSP analysis suite as raw counts. The GeoMx DSP software captures the number of SYTO13 positive nuclei in each segment as well as the surface area of each segment, which were exported for data calibrations. From the software, the counts for oligonucleotides per segment were also exported into a package for quality control and data normalization protocols. Biological probe quality control was performed using default settings. A total of 112 AOIs were all carefully reviewed for segments with sequencing saturation of less than 45%, nuclei of fewer than 160, negative probe counts of less than 8, or a surface area of less than 12,000 squared microns. All 112 AOIs were included for further analysis following the NanoString user’s manual recommendations. Background correction and scaling were performed using geometric means and normalization was performed using Q3 averages of housekeeping genes. Genes with expression levels at or lower than the limit of quantification (LOQ) in at least 5% of segments were filtered out. A total of 1,223 genes passed quality control and were analyzed. Eight patients with four sporadic EOCC and four sporadic LOCC were processed. Per patient, a total of six ROIs with tumor invasive margin (TIM, three ROIs) and tumor center (TC, three ROIs), were selected, respectively.
Assembly: GRCh38.p13
Supplementary files format and content: Nanostring GeoMx normalized data, annotation, and probe data files as xlsx format
Library strategy: Spatial Transcriptomics

source_name: Melanoma liver metastasis

extract_protocol:
FFPE tissue sections of 5 µm thickness was prepared according to vendor's protocol with slight modifications. Sections baked at 60°C for 30 min, and incubated sequentially 3x 5 min in xylene, then 2x 5 min each in 100% EtOH, 95% EtOH, and H2O. Antigen retrieved by placing in EDTA at 100°C 20 min, followed by PBS 5 min. Slides then placed in staining jar of 1mg/mL Proteinase K at 37°C 15 min. This was followed by washing in 10% NBF 10 min, 2x washes in NBP stop buffer, and 1x PBS. RNA probe mix was added to tissue slides with a hybridization coverslip at 37°C overnight. Then, slides were washed 2x with SSC buffer and formamide at 37°C, then 2x with SSC buffer. Slides stained for morphology markers SYTO13, PanCK+, VIM, and FAP. Slides were loaded onto NanoString GeoMx DSP for imaging/barcode acquisition, following the manufacturer's protocol. Manual selection of 600-650 µm ROIs and AOIs were performed based on pathology defined areas and morphological markers.
Libraries constructed using NanoString NGS readout protocol. Dried aspirates in the collection plate were resuspended with 10 μL of nuclease-free water for 10 min, and 4 μL were transferred to a polymerase chain reaction (PCR) plate. Two μL of 5X PCR Master Mix (NanoString Technologies, Inc., Seattle, WA) and 4 μL of 17 a unique primer mix (NanoString) assigned by their position on the collection plate were added to each well. Contents were mixed by pipetting and the sealed PCR plate was transferred to a thermal cycler for an amplification for 18 cycles. PCR products were pooled in equal amounts. Pooled library was purified twice with a 1.2X magnetic beads-to-sample ratio with KAPA Pure Beads (Roche, Basel, Switzerland), each followed by two 80% ethanol washes, then eluted with Elution Buffer (Nanostring). The quality and quantity of the purified pooled library were assessed with High Sensitivity D1000 ScreenTape System (Agilent, Santa Clara, CA) and Qubit dsDNA High Sensitivity assay (Invitrogen, Waltham, MA), respectively. The library was denatured following Illumina’s recommendations and sequenced on NextSeq 550 (Illumina, San Diego, CA) with 27 paired-end cycles, achieving the minimum read depth (30 reads per μm2) or higher determined by the selected AOI’s sizes.
RNA (amplified oligo nucleotide probes)

value: Melanoma liver metastasis

tag: tissue type

value: MLiM

tag: segment tag

value: T HMB45 D

tag: scan id

tag: roi id


title: GL2_WT2

country: China

organism: Mus musculus

tag: treatment


title: G16262-2-T0


title: Neuron derived from SB3-iPSC,Div35

data_processing:
Quality control measurements were performed using FastQC v0.11.7.
Sequence reads were trimmed using Trimmomatic v.0.38 and mapped to the human reference genome (GRCh38) using HISAT2 v2.1.0 alignment tool.
BAM files were prepared using SAMtools v1.11.
featureCounts v1.6.3 was used to calculate the number of raw reads mapped to known exon regions.
Raw read counts were normalized to transcripts per million (TPM).
Assembly: hg38
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 TPM values for each sample

extract_protocol:
Total RNA was extracted from DIV35 neurons using TRIZOL Reagent (Thermo Fisher Scientific), according to the manufacturer's protocol. The extracted RNA was further purified and enriched using NucleoSpin RNA Clean-up XS (Macherey-Nagel) according to the manufacturer's protocol. Each RNA sample was evaluated for purity and concentration using BioDrop µLite (BioDrop), and the A260∶A280 ratio was 1.8~2.2, A260∶A230 ratio was 1.8 or higher, and the concentration was 50ng/µl.
Sequences of each sample were obtained after library preparation by the poly-A selection method using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext® UltraTMII Directional RNA Library Prep Kit (New England Biolabs) following manufacturer`s protocol.


title: CC15L

type: RNA

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

hyb_protocol: According to NanoString nCounter® XT Assay user manual

data_processing:
The raw data was analysed by ROSALIND® (https://rosalind.bio/). The normalization, fold changes and p values for the data were calculated using the nCounter® Advanced Analysis protocol. In brief, the counts within a lane are divided by the geometric mean of the normalizer probes from the same lane. For normalization genes, housekeeping probes are selected based on the geNorm algorithm as implemented in the NormqPCR R library 29. Fold changes and p values are calculated using the fast method and Generalized Linear Model (GLM) as described in the nCounter® Advanced Analysis 2.0 User Manual. P value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Downstream analyses were done using R.
Data collection is performed using epifluorescence microscopy and CCD capture technology on an nCounter instrument to yield hundreds of thousands of target molecule counts. Digital images are processed within the nCounter instrument, and the Reporter Probe counts are tabulated in a comma separated value (CSV) format for convenient data analysis with NanoString’s free nSolver™ Analysis Software or the application of your choice.

label: biotin

source_name: B16F10 murine melanoma cell line

growth_protocol: The B16-F10 melanoma cells were obtained from the American Type Culture Collection (ATCC). The cells were cultured in complete Dulbecco's Modified Eagle's Medium (DMEM, high glucose) supplemented with 10% (v/v) Fetal Bovine Serum (FBS), and maintained at 37°C in a humidified incubator with 5% CO2. 120'000 tumor cells were implanted with a microsurgery in the mice ear pinnae in a mixture of thrombin and fibrinogen. Melanomas were left growing for 10 days prior to irradiation treatment.

extract_protocol: Exctraction was performed according to the protocols of the company Canopy Biosciences (a Bruker company) from whom we purchsed the Nanostring assay.

treatment_protocol: The following irradiations were delivered at the European Synchrotron Radiation Facility (France): MRT (400 Gy peak-dose, 6.2 Gy valley-dose, 50 µm beam width, 200 µm spacing) and uniform RT (6.2 Gy). The control group received no treatment (0 Gy).

tag: group

value: CTR_2 days

tag: strain

tag: Sex

value: female


title: CC9L

scan_protocol: According to NanoString nCounter® XT Assay user manual


title: G86L

label_protocol: According to NanoString nCounter® XT Assay user manual

value: BB_2 days


title: G4L

value: BB_7 days


title: G25L


title: CC23R


title: G41R


title: G35R

value: MRT_2 days


title: G81R


title: G23L


title: G71L


title: CC1L


title: G82L


title: G10L


title: G68L


title: G42R


title: G16262-1-T105

value: S


title: GLI2_KO3

tag: genotype

value: GLI2 Knockout


title: TC 007


title: Neuron derived from SB1-iPSC,Div35

tag: cell line


title: G16262-1-T0


title: GLI2_KO2

tag: cell type

value: Primary pancreatic stellate cell


title: GL2_WT1

value: WT


title: G16260-2-T105

value: Hypo


title: Neuron derived from CTRL3-iPSC,Div35

value: neuron

tag: time


title: TC 006

tag: tissue


title: Neuron derived from SB2-iPSC,Div35


title: TC 008


title: GLI2_KO1

value: Cuture-activated


title: G16260-2-T0

value: blood

tag: mdd phenotype


title: G16260-1-T105

tag: visit

value: NS


title: Neuron derived from CTRL1-iPSC,Div35


title: Neuron derived from CTRL2-iPSC,Div35


title: G16260-1-T0

tag: condition


title: G16256-2-T105

tag: time point


title: TC 004

value: Melanoma liver metastasis

tag: tissue type


title: TC 005

value: MLiM

tag: segment tag


title: G16256-2-T0


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 16

city: Palo Alto

first: Rebecca

last: Hamlin

address: 1291 Welch Road

department: Medicine

institute: Stanford University

data_processing:
ParseBiosciences-Pipeline.1.0.3p was used to identify barcodes, align sequencing reads, assign transcript counts to genes, and generate a cell-by-gene count matrix
After running each sublibrary through the pipeline, the outputs of each sublibrary were combined into a single dataset
Assembly: Custom genome containing the human genome (HG38) and the annotated Wuhan-Hu-1 SARS-CoV-2 reference sequence (NC_045512.2)
Supplementary files format and content: .rds file is a Seurat object containing all samples and associated cell metadata. Genes expressed in fewer than 100 cells have been removed. Cells with >20% mitrochondrial genes, >7500 unique genes, and >30000 transcripts have been removed. A cluster of cells with 22% mitochondrial/ribosomal RNA genes, thought to represent dead/dying cells, were also removed.

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
PBMCs were fixed using Parse fixation reagents, frozen at -80°C for less than 6 months, and prepped according to Parse Evercode WT Mega v2 protocol. In this combinatorial split pool barcoding process, samples were first loaded into a 96-well plate and underwent reverse transcription with barcoded primers, pooled, split and barcoded again, followed by cell lysis using Parse reagents.
According to Parse Evercode WT Mega v2 protocol. First, cDNA was amplified, then underwent fragmentation, adaptor ligation, sublibrary index PCR, and double-sided size selection. Sequencing was performed on a NovaSeq S4 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with i7 index, i5 index, and the 4th barcode (6bp) that tags each sublibrary acting as a standard Illumina index.

value: Peripheral blood

value: Cryopreserved PBMCs


title: ANH 004

value: AN HepPar1

tag: scan id


title: ANH 003

tag: roi id


title: DNH 006

value: IN HepPar1


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 13


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 14


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 15


title: Saline1_snRNA

city: Iowa City

first: Snehajyoti

last: Chatterjee

state: IA

address: 169 Newton Road

department: Neuroscience & Pharmacology

institute: University of Iowa

data_processing:
Multiomic raw files were processed with cellranger-arc-2.0.2.
Outputs required for downstrean analyses with Seurat/Signac packages for each samples are provided in tar.gz files. Compressed directory containing cell-ranger-arc outpus required to perform downstream analyses with Seurat/Signac packages. filtered_feature_bc.matrix.h5 contains gene expression data. atac_fragments.tsv.gz contains the fragments file related to open chromatin. atac_fragments.tsv.gz.tbi contains a tabix index of the fragment intervals facilitating random access to records from an arbitrary genomic interval. per_barcode_metrics.csv contains the metadata
Assembly: mm10
Supplementary files format and content: Processed_Saline1.tar.gz
Supplementary files format and content: Processed_Saline2.tar.gz
Supplementary files format and content: Processed_Crotonate1.tar.gz
Supplementary files format and content: Processed_Crotonate2.tar.gz

source_name: Dorsal Hippocampus

extract_protocol:
Nuclei were isolated from dorsal hippocampus using the Chromium Nuclei Isolation Kit. Nuclei were directly processed for droplet capture for single cell multiome ATAC + gene expression using a chromium controller.
Chromium Next GEM Single Cell Multiome ATAC + Gene v1 chemistry was used to create single nuclei ATAC and RNA libraries from the same cell. Two saline and two crotonate treated samples were used for independent replicates. Libraries were sequenced on an Illumina Novaseq 6000 with a 150 bp paired end read setup.

value: Dorsal Hippocampus

value: Male

value: Saline


title: Saline2_snRNA


title: Saline2_ATAC


title: Saline1_ATAC


title: G16256-1-T105

value: S


title: Crotonate2_snRNA

value: Crotonate


title: DNH 005


title: Crotonate1_ATAC


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 11


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 10


title: G16255-2-T0


title: TM 003

value: T HMB45 P


title: DNH 004


title: G16255-1-T105

value: Hypo


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 9


title: Crotonate1_snRNA


title: TM 004


title: Crotonate2_ATAC


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 8


title: Antibody Capture

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

library_source: other

data_processing:
*library strategy: TotalSeq-C
Cell Ranger v. 7.1.0 (10x Genomics, Pleasanton, CA, USA) was used to process raw sequencing data following the 10x instructions (https://www.10xgenomics.com/analysis-guides/demultiplexing-and-analyzing-5’-immune-profiling-libraries-pooled-with-hashtags). Briefly, gene expression and T-cell receptor data were demultiplexed with ‘cellranger multi’ and organ-specific data were aggregated using ‘cellranger aggr’.  Gene expression data analysis was performed using Seurat v.5.0.1 R package following the standard workflow for visualization and clustering ("Seurat - Guided Clustering Tutorial” vignette). Clustering resolution (“resolution” parameter in the FindClusters function) was set to 0.5 to obtain biologically expected number of clusters. Cluster-specific conserved markers were detected using the FindConservedMarkers function. Clusters were annotated using scTyper v.0.1.0, singleR v.2.4.1, clustermole v.1.1.1 and manually annotated based on cluster-specific differentially expressed genes. Selected clusters were merged to represent major cell types (for kidney data, two clusters were merged into "Activated naïve CD4+ T cells" and three clusters were merged into "Effector CD4+ T cells"; for spleen, two clusters were merged into "Memory CD4+ T cells"). Immune receptor sequencing data for each condition were annotated with cluster-specific barcodes defined at the RNA-seq analysis step and analyzed using the scRepertoire v.1.12.0 R package. Plots were made using Seurat’s visualization functions or the ggplot2 v3.4.4 R package. All computations were performed in R/Bioconductor v.4.3.2.
Assembly: mm10, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: CellRanger output files: kidney_barcodes.tsv.gz, spleen_barcodes.tsv.gz. Each cell barcode is prefixed with 'WT_' or 'KO_' prefixes
Supplementary files format and content: CellRanger output files: kidney_features.tsv.gz, spleen_features.tsv.gz
Supplementary files format and content: CellRanger output files: kidney_matrix.mtx.gz, spleen_matrix.mtx.gz

molecule: protein

source_name: mixed sample (kidney, spleen)

growth_protocol: Female B6(129X1)-Tg(Cd4-cre/ERT2)11Gnri/J mice from the Jackson Laboratory were backcrossed to MRL/lpr male mice. A speed congenic method was used by selecting the top two out of 15-20 male pups with the highest MRL/lpr genetic background from each generation for subsequent backcrossing. After 6 generations, a mouse reached 99.8% MRL/lpr background and was crossed with female EZH2fl/fl MRL/lpr mice we recently generated, to get Ezh2fl/fl and CD4-Cre/ERT2 Ezh2fl/fl (abbreviated as iCD4-Cre Ezh2fl/fl) mice. Both groups of mice received oral gavage administration of tamoxifen (300 mg/Kg) dissolved in corn oil 3 days a week (on Mondays, Wednesdays and Fridays), every other week starting from 10 weeks of age in the preventative model and 14 weeks of age in the therapeutic model until mice reached 24 weeks of age. The Ezh2fl/fl and littermate iCD4-Cre Ezh2fl/fl mice were housed together in a pathogen-free environment. Upon euthanasia, we isolated superficial and deep cervical lymph nodes, spleens, and kidneys.

extract_protocol:
Spleens were mashed through 70-µm cell strainers with a syringe plunger and rinsed with PBS to prepare into single-cell suspensions. For kidney dissociation, we followed the protocol for mouse kidney dissociation using the Multi Tissue Dissociation Kit 2 from Miltenyi Biotec. To preserve cell surface epitopes, we decreased the volume of Enzyme P in the dissociation buffer and the kit’s components for each kidney was as follows: 4.8 mL of Buffer X, 5 µL Enzyme P, 50 µL Buffer Y, 100 µL Enzyme D, and 20 µL Enzyme A. Kidney capsules were removed, and kidneys were placed into gentleMACS C tubes (Miltenyi Biotec) with dissociation buffer and quartered. GentleMACS Octo Dissociator with heating function (Miltenyi Biotec) was used and the program ‘37C_Multi_E’ was run to dissociate kidneys. Cell suspension went through a 70-µm cell strainer and was rinsed with PBS. Red blood cells (RBCs) in spleen and kidneys were lysed with RBC lysis buffer (Invitrogen). Cells were resuspended in PBS and stained with LIVE/DEAD fixable near-IR dead cells stain kit (Invitrogen). Then cells were blocked with anti-mouse CD16/CD32 (BD Biosciences) followed by staining with the following antibodies: anti-CD3 epsilon-VioBlue (Clone 17A2, Miltenyi Biotec), anti-TCR β-Alexa Fluor 488 (Clone H57-597, BioLegend), anti-CD4-V500 (Clone RM4-5, BD Biosciences), and anti-CD8a-PE-Cyanine5 (Clone 53-6.7, BioLegend) in PBS with 1% fetal bovine serum (FBS). CD4+ T cells from a total of 10 Ezh2fl/fl mice and 9 iCD4-Cre Ezh2fl/fl mice were sorted by FACSAria cell sorter in the Unified Flow Core at the Department of Immunology in the University of Pittsburgh.
CD4+ T cells isolated from a single organ in each mouse were individually incubated with unique TotalSeq-C anti-mouse antibodies from BioLegend. All CD4+ T cells were barcoded in the above manner to distinguish between different organs and mice before pooling cells together. Sequencing libraries of cell surface protein feature barcoding, single cell 5’ gene expression, and paired single-cell T-cell receptor (TCR) were prepared according to instructions provided by10X Genomics in the Single Cell Core at the University of Pittsburgh.  These libraries were sequenced at the UPMC Genome Center. In total, 10,271 splenic CD4+ T cells from Ezh2fl/fl mice were sequenced, with a mean of 26,854 reads per cell, and 7,704 splenic CD4+ T cells from iCD4-Cre Ezh2fl/fl mice were sequenced with a mean of 22,603 reads per cell.  In the kidneys, 8,850 kidney-infiltrating CD4+ T cells from Ezh2fl/fl mice were sequenced, with a mean of 24,796 reads per cell, and 4,066 kidney-infiltrating CD4+ T cells from iCD4-Cre Ezh2fl/fl mice were sequenced with a mean of 25,649 reads per cell.

value: mixed sample (kidney, spleen)

value: mixed sample (WT, KO)


title: G16252-2-T105

value: blood

value: Hyper


title: VDJ-T

molecule: other


title: mRNA expression


title: TM 002

value: Melanoma liver metastasis


title: DNH 002

value: MLiM


title: G16252-2-T0


title: DNH 001


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 7

value: Peripheral blood


title: G16256-1-T0


title: G16255-1-T0


title: LYVE-1+ intestinal B cell, EAE 7 DPI, rep6

city: Epalinges

first: Caroline

last: Pot

address: Chemin des Boveresses 155

department: Department of Clinical Neurosciences

institute: Lausanne University Hospital

data_processing:
Data processing was performed by the Lausanne Genomic Technologies Facility (GTF) as follows:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al.2013). Reads were aligned against the Mus_musculus.GRCm38.102 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al.2014) using Mus_musculus.GRCm38.102 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al.2012).
Assembly: GRCm38.102
Supplementary files format and content: Tab-delimited text file containing in the first column Ensembl Gene ID, and raw count values in columns 2 for each sample

source_name: Jejunum (small intestine)

growth_protocol: Wild-type mice were obtained from Charles-River Laboratories or bred in the animal facility. All mouse strains were on a pureC57BL/6Jbackground. 8-12 weeks-old-mice were used for all experiments. Animals were kept in a specific pathogen-free (SPF) facility at Lausanne University. All experiments were carried out in respect with guidelines from the Cantonal Veterinary Service of the state of Vaud.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNAseq libraries were prepared from 10 ng of total RNA for all but sample 2B_LY_neg (4.02 ng) and 2B_LY_pos (6.9 ng).
RNA libraries for RNA-seq were prepared using Takara SMART-seq v4 PLUS Kit following the manufacturer's protocols.

treatment_protocol: EAE: Wild-type mice were immunized with the antigen myelin oligodendrocyte glycoprotein 35-55 (MOG35–55) emulsified with complete Freund's adjuvant (CFA) subcutaneously into flanks. Pertussis toxin was injected intravenously (IV) at days 0 and 2. Small intestinal B cells were extracted at 7 days post-immunization to perform the analysis.

value: Jejunum (small intestine)

value: B cell

value: WT

tag: phenotype

value: LYVE-1+ B cell

tag: treatment

value: EAE


title: ANH 002

value: AN HepPar1


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 5

value: Cryopreserved PBMCs


title: LYVE-1- intestinal B cell, EAE 7 DPI, rep6

value: LYVE-1- B cell


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 4


title: G16252-1-T0

value: NS


title: DNH 003

value: IN HepPar1


title: LYVE-1+ intestinal B cell, EAE 7 DPI, rep5


title: ANH 001


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 3


title: G16245-2-T105

value: S


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 2


title: LYVE-1- intestinal B cell, EAE 7 DPI, rep5


title: TC 003

value: T HMB45 D


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 6


title: G16245-2-T0

value: blood


title: LYVE-1+ intestinal B cell, EAE 7 DPI, rep4


title: TC 002


title: G16245-1-T105

value: Hyper


title: G16252-1-T105


title: TC 001

value: Melanoma liver metastasis


title: RNA-Seq of Homo sapiens: Long COVID cohort, sublibrary 1


title: G16245-1-T0


title: LYVE-1+ intestinal B cell, EAE 7 DPI, rep3


title: HES1-IGG1_2

city: Wuhan

first: Chengcheng

last: Li

state: hubei

address: Jiefang Road

department: Department of Hand Surgery, Union Hospital

institute: Huazhong University of Science and Technology

library_source: genomic

data_processing:
*library strategy: Cut&Tag
Raw sequencing data was first filtered by fastp (version 0.23.1), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The initial data underwent filtration to acquire clean data, which was subsequently aligned to the reference genome utilizing bowtie2 (version 2.2.6) with default settings
Sambamba (version 0.7.1) is used for sam/bam format conversion and PCR duplicate reads removal. The RSeQC（version 2.6）was used for reads distribution analysis. The insert length was counted by Collect Insert Size Metrics tools from picard software (version 2.8.2). DeepTools (version 2.4.1) was used to visualize the distribution of reads on upstream and downstream of TSS. The MACS2 software（Version 2.2.7.1）was used for peak calling
The bedtools（version 2.30.0）was used for peaks annotation and peak distribution analysis. The different peaks were identified by csaw (version 1.24.3). The Homer（version 4.10）was used for motifs analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: genomic DNA

source_name: adipose tissue

extract_protocol:
In summary, 60,000 ADSCs were collected, rinsed, and subsequently exposed to Concanavalin A-coated magnetic beads. Subsequently, the cells were treated with either an anti-flag antibody (Cat. 14793S, Cell Signaling Technology, USA) or an isotype control antibody (Cat. 2729S, Cell Signaling Technology, USA) for a duration of 2 hours, followed by an additional hour with a secondary antibody at ambient temperature. The hyperactive pG-Tn5 transposonase was then introduced to facilitate tagmentation. The reaction was terminated, and DNA fragments were extracted by PCI.
DNA fragments were extracted by PCI, followed by PCR amplification using indexed P5 and P7 primers. The library products were enriched, quantified and finally sequenced on a Novaseq 6000 sequencer (Illumina) with PE150 model.

value: adipose tissue

value: adipose stem cells

value: stem cells

tag: chip antibody


title: HES1-IGG1_1


title: G16240-2-T105

value: Hypo


title: TM 001

value: MLiM

value: T HMB45 P


title: IP_WT_2

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

data_processing:
For RNA-seq data analysis, the raw paired-end reads were checked using the FastaQC Package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). By using Cutadapt, adaptor sequences, low-quality sequence reads, and the short reads (<25 bp) were removed from the data sets. These clean reads were mapped to the reference genome of A. flavus by Hisat2 tools (version 2.0.4) . For ChIP-seq, the clean reads were mapped to the reference genome of A. flavus by Burrows-Wheeler Alignment tool (BWA, version 0.7.15) [41]. MACS2 (v2.1.1) was used for peak calling. Bedtools (v2.25.0) was used for peak annotation and peak distribution analysis. Differential binding peaks were identified using python script with Fisher’s test (q value <0.05). Homer (v4.10) was used for motif analysis. Genes less than 2000 bp away were associated to the corresponding peak.
Supplementary files format and content: tab-delimited text files include SNTB_HA_vs_WT.peak_annotation
Supplementary files format and content: tab-delimited text files include gene fpkm for each sample

organism: Aspergillus flavus

source_name: mycelia

growth_protocol: For RNA-seq, the conidia (104/ml) for each strain were inoculated in 100 mL PDB shaking at 180 rpm under 29°C for 72 h. ChIP-seq analysis was carried out on the WT and sntB-HA strains. The conidia (104/ml) for each strain were inoculated in 100 mL PDB shaking at 180 rpm under 29°C for 72h, and subjected to ChIP -seq

extract_protocol:
For RNA-seq, total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al. For ChiP-seq, the mycelium were cross-linked with 1% formaldehyde for 10 min at room temperature, after which 0.125 mol/L glycine was added, and the mixture was rested for 5 min to terminate the cross-linking reaction. Nuclei were collected by centrifuging the samples at 2,000 g for 5 min at 4 °C after being treated with lysis buffer (ECOTOP, ES-8523-500). To fragment chromatin DNA, nuclei were treated with nucleus lysis buffer and sonicated. For the lysis-sonicated chromatin, 10% was stored as “Input”, 90% was used in IP reactions with specific anti-HA magnetic beads (Beyotime, P2121, China). The Input DNA and IP DNA were extracted using the phenol-chloroform method.
For ChiP-seq, high-throughput DNA sequencing libraries were prepared using a NEXTFLEX® ChIP Seq Kit (NOVA-514120, Bioo Scientific). The library products corresponding to 200-500 bp were enriched, quantified, and sequenced on a NovaSeq 6000 sequencer (Illumina, USA) using the PE150 model.

value: mycelia

value: HA tag fused to snt2 strain ChiP


title: G16240-2-T0


title: LYVE-1+ intestinal B cell, EAE 7 DPI, rep2

value: Jejunum (small intestine)

value: B cell

value: WT

value: LYVE-1+ B cell

value: EAE


title: HES1-FLAG1_2


title: IP_WT_1


title: G16240-1-T105

value: NS


title: LYVE-1- intestinal B cell, EAE 7 DPI, rep2

value: LYVE-1- B cell


title: G16240-1-T0

value: blood


title: oe_NC_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.


title: LYVE-1+ intestinal B cell, EAE 7 DPI, rep1


title: IP_SNTB_HA_1

value: WT ChiP


title: oe_NC_2

value: adipose tissue


title: LYVE-1- intestinal B cell, EAE 7 DPI, rep1


title: G16239-2-T105


title: IN_WT_2

value: HA tag fused to snt2 strain


title: G16239-2-T0


title: IN_WT_1


title: LYVE-1- intestinal B cell, EAE 7 DPI, rep3


title: WT_rep3

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Aligned and quantified using Bowtie2 + RSEM
Assembly: mm10
Supplementary files format and content: Tab-delimitted raw counts
Supplementary files format and content: Tab-delimitted TPM

source_name: colon spheroids

extract_protocol:
Followed Invitrogen’s Purelink RNA Mini kit according to manufacturer's directions
Followed Illumina Stranded mRNA Prep protocol

value: colon spheroids

tag: strain background

value: mixed; mostly C57Bl6 with some FVB


title: oe_HES1_2

value: adipose stem cells

value: stem cells

tag: genotype

value: HES1 overexpression


title: oe_HES1_3

tag: cell line


title: G16239-1-T0

value: Hypo

value: S


title: IN_SNTB_HA_2

value: mycelia


title: HES1-FLAG1_1

tag: cell type


title: WT_rep1

value: WT


title: IP_SNTB_HA_2


title: IN_SNTB_HA_1


title: G16237-2-T105


title: oe_HES1_1


title: MB361-dCas9-KRAB+NC_Rep3__

city: Dallas

first: Yihan

last: Wang

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern

data_processing:
custom pipeline
Mapped with cellranger count and combined the counts for each library.
Genome_build: hg38

source_name: MDA-MB-361 Cell line

growth_protocol: Cells were cultured in alpha modified MEM plus 10% FBS, 1mM sodium pyruvate, 10mM HEPES, 1X Glutamax supplement, 1X MEM non-essential amino acid, 1 mg/mL insulin, 1ng/mL hydrocortisone, 25 ug/mL EGF and pen/strep at 37C and 5% CO2.

extract_protocol:
Cells were collected, washed once with PBS and extracted the RNA with Zymo Quick-RNA miniprep kit.
100 ng of RNA was used to build an RNA-seq library with the chemistry of 10x Chromium Next GEM Single-cell 3’ Reagent Kit. 10 uL of beads were used in each reaction. The remaining steps of cDNA library preparation were identical to the 10x protocol with 0.25 fold of the reaction volume.

treatment_protocol: Cells were infected with lenti-dCas9-KRAB-blast (Addgene:89567) to stablly express dCas9-KRAB with two weeks of blasticidin selection.


title: Y_ADSC5

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

tag: group

value: Y-ADSCs


title: G16237-2-T0

tag: tissue


title: LYVE-1- intestinal B cell, EAE 7 DPI, rep4

value: Jejunum (small intestine)

value: B cell

value: EAE


title: MB361-dCas9-KRAB+NC_Rep2__


title: G16237-1-T105

value: blood

tag: mdd phenotype


title: MB361-dCas9-KRAB+NC_Rep1__


title: Y_ADSC3


title: G16237-1-T0

tag: visit


title: G16239-1-T105

tag: condition


title: KO2_2

city: shenzhen

first: TINGTING

last: DENG

address: 3002 Sungang West Road

institute: Shenzhen Second People's Hospital

description: Toe1 konckout

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readcount values for each Sample …

source_name: cell line

growth_protocol: For differentiation studies, the C17.2 cells were seeded in a routine culture medium. Twenty-four hours after seeding, the medium was replaced with DMEM/F-12 medium (11330032, Thermo Fisher Scientific)  supplemented with 1 mM L-glutamine, 1% penicillin/streptomycin, modified N2 supplements (17502048, Thermo Fisher Scientific), 10 ng/mL NGF (1156-NG-100, R&D Systems), and 10 ng/mL BDNF (248-BDB-010, R&D Systems). The differentiation medium was changed every third day for the duration of differentiation.

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

value: cell line

value: differentiated C17.2

value: neural stem cells

value: Toe1 konckout


title: Y_ADSC4

value: adipose tissue


title: MB361-dCas9-KRAB+chr13:32639465-32639967_Rep3__


title: Y_ADSC2


title: MB361-dCas9-KRAB+chr13:32639465-32639967_Rep2__


title: KO2_1

description: Toe1 konckout


title: Y_ADSC1


title: G16233-2-T0

value: Hyper

tag: time point


title: G16233-2-T105


title: MB361-dCas9-KRAB+chr13:32639465-32639967_Rep1__


title: RA_rep2

value: colon spheroids

value: mixed; mostly C57Bl6 with some FVB

value: expressing Notch dimerization-deficient (DD) alleles Notch1DD and Notch2DD (NDD)


title: G16233-1-T105

value: NS


title: NC3

description: control


title: O_ADSC5

value: O-ADSCs

value: stem cells


title: G16233-1-T0


title: O_ADSC6


title: NC2

description: control

value: WT


title: NC1

description: control


title: KO2_3

description: Toe1 konckout


title: RA_rep1


title: MB361-dCas9-KRAB+NFYC_pro_Rep2__


title: MB361-dCas9-KRAB+NFYC_pro_Rep3__


title: G16222-2-T105

value: Hypo

value: S


title: MB361-dCas9-KRAB+NFYC_pro_Rep1__


title: O_ADSC4


title: G16222-2-T0


title: KO_3

description: Toe1 konckout

growth_protocol: C17.2 cells were cultured in Dulbecco's modified Eagle's medium (DMEM, SH30243.01, Hyclone) containing 10% fetal bovine serum (10099141, Gibco), 5% horse serum (SH30074.03, Hyclone), 2 mM L-glutamine (25030081, Life Technologies), and 1% penicillin/streptomycin (15070063, Gibco)

value: undifferentiated C17.2


title: O_ADSC3


title: KO_1

description: Toe1 konckout


title: G16222-1-T105

value: blood


title: primary mouse chondrocytes, siPKM2_3

city: Shanghai

first: Liu

last: Bo

address: 180 Fenglin Road

department: 1Department of Orthopedic Surgery

institute: Zhongshan Hospital, Fudan University

data_processing:
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Neonatal mouse knee joints

growth_protocol: chondrocytes were cultured in DMEM/F12 medium containing 10% FBS.

extract_protocol:
RNA was first extracted from the cells using Trizol(Sigma). After quantification and quality control with ND 2000 (NanoDrop Technologies, Waltham, USA), 1 μg of highquality total RNA sample was used for the transcriptome library construction by Shanghai Majorbio Biopharm Technology (Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neonatal mouse knee joints

value: primary mouse chondrocytes

value: chondrocyte

value: PKM4 knockdown


title: O_ADSC2

value: adipose tissue


title: NC_3

description: control

value: cell line

value: neural stem cells


title: primary mouse chondrocytes, siPKM2_2

value: PKM3 knockdown


title: G16222-1-T0


title: O_ADSC1


title: NC_1

description: control


title: Endometrial Cancer_T9

city: Bengaluru

first: Prathibha

last: Ranganathan

state: Karnataka

address: Electronic City Phase I

country: India

institute: Centre for Human Genetics

data_processing:
Single end sequencing data was checked for phred score.   The reads were trimmed using the adapter sequence (AGATCGGAAGAGCACACGTCT). Reads that mapped to rRNA sequences were removed using Bowtie.
Reads were size-selected for 18-25bp long reads using BBTools . Obtained sequences were then collapsed using the mapper tool from miRDeep2 and used for identification and quantification of miRNA.
Differentially expressed miRNAs were identified at FDR<0.001
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
Supplementary files format and content: .xlx file of raw read values for all samples  (miRNA_Counts_for_DE)

source_name: Endometrium

extract_protocol:
Total RNA was isolated using Rneasy mini kit (Qiagen). 1 microgram of total RNA was used for making the libraries.
NEB NextR Multiplex Small RNA Library Prep Set was used for making libraries

value: Endometrium

tag: disease

value: Endometrial Cancer


title: APAP_MSC-3

city: Guangzhou

first: Rukang

last: Liang

state: Guangdong

address: Shipai Street, Tianhe district

department: Biotherapy Center

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
fastp (version 0.18.0)
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Assembly: Ensembl release107
Supplementary files format and content: tab-delimited text fle includes raw counts and FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA).
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.     The ligation reaction was purified with the AMPure XP Beads(1.0X).

treatment_protocol: C57 mice were injected intraperitoneally with 400 mg/kg APAP and with or without MSCs injection via tail vein after 4 hours. Liver tissue was collected 24 hours after successful modeling.

value: liver

value: APAP+MSC


title: primary mouse chondrocytes, siNC_3

value: WT


title: G16220-2-T0

data_processing:
The obtained RNAseq data were processed through the bulk RNA-seq pipeline in bcbio (v1.2.8, Chapman et al 2021).
Reads were aligned using STAR against transcriptome references of the human genome (build 94, Dobin et al. 2013) and quantified with Salmon (Patro et al. 2017).
N/A
N/A
N/A
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using the Norgen Total RNA Purification Kit (Cat. 17200, Norgen Biotek Corp, Thorold, ON, Canada) and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc., Waltham, MA).
RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina. The sequencing libraries were multiplexed and clustered on seven lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: Hypo

value: NS


title: primary mouse chondrocytes, siNC_2


title: Endometrial Cancer_T84


title: Endometrial Cancer_T83


title: APAP_MSC-2


title: APAP_MSC-1


title: G16220-1-T105

value: S


title: primary mouse chondrocytes, siNC_1


title: Endometrial Cancer_T77


title: APAP_PBS-3

value: APAP+PBS


title: G16220-1-T0

value: blood


title: APAP_PBS-2


title: Endometrial Cancer_T5


title: TP17_M383

city: Boston

first: Fangyuan

last: Chen

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
For RNA-seq data, we used FastQC for FASTQ data quality control, trimmomatic for adapter trimming, Hisat2 for alignment to human genome 38 (hg38), and HTSeq for quantification, to generate normalized expression in transcripts per million (TPM).
Assembly: Human genome 38 (hg38)
Supplementary files format and content: csv format of transcripts per million (TPM).

source_name: ER+/HER2- primary invasive lobular breast cancer

extract_protocol:
Sample RNA was extracted with Qiagen tissue DNA/RNA kit from FFPE sections, assessed with High Sensitivity RNA TapeStation for quality and concentration.
Library was prepared with Illumina TruSeq RNA Library Preparation Kit.
Sequenced with Illumina Nextseq 500 75 bp pair-end in 150 cycles at University of Pittsburgh Health Sciences Sequencing Core.


title: TP17_M378

value: ER+/HER2- primary invasive lobular breast cancer


title: G16214-2-T105


title: primary mouse chondrocytes, siPKM2_1

value: Neonatal mouse knee joints

value: primary mouse chondrocytes

value: chondrocyte

value: PKM2 knockdown


title: G16214-2-T0


title: APAP_PBS-1


title: Endometrial Cancer_T4


title: G16214-1-T0


title: TP17_M510


title: Endometrial Cancer_T43


title: CTRL-2

value: control


title: TP17_M605


title: G16220-2-T105


title: G16211-2-T105

value: Hyper


title: Endometrial Cancer_T40

value: Endometrium


title: CTRL-1


title: G16211-2-T0


title: Endometrial Cancer_T38

value: Endometrial Cancer


title: Microbiota in mouse stool, sample MN99

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 274 --p-trunc-len-r 169 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x $BOWTIE2_DATABASE/INDEXED_mouse_GRCm39_BOWTIE2/GRCm39 -U dna-sequences.fasta --al eucar_contaminant_ASV_2.fasta -S eucar_contaminants_ASV/bowtie2_MICE_SAM_output.txt -f -p 4
qiime feature-classifier classify-consensus-vsearch --i-query clean_rep-seqs.qza --i-reference-reads ~/Scrivania/Tools/Database/silva-138-99-seqs.qza --i-reference-taxonomy ~/Scrivania/Tools/Database/silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza --o-search-results vsearch_hits.qza --verbose
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: feature_table.tsv: tab delimited text file containing the abundances of ASVs in each sample and the related taxonomic assignments
Supplementary files format and content: taxonomy.tsv: tab delimited text file containing the complete taxonomic classification of the reference sequence

organism: feces metagenome

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

tag: host

value: Mus musculus

value: Stool

tag: strain mutation

tag: time

value: SY

tag: sequencing batch

tag: sample id


title: TP17_M882


title: TP17_M802


title: G16211-1-T105

city: Belmont

first: Shu

last: Dan

address: 115 Mill St

institute: McLean Hospital, Harvard Medical School

source_name: blood


title: Endometrial Cancer_T37


title: Microbiota in mouse stool, sample MN98

description: 16s rRNA v3-v4 sequencing

value: OS


title: TP18_M95


title: G16211-1-T0


title: TP18_M121


title: Endometrial Cancer_T35


title: Endometrial Cancer_T34


title: G16210-2-T105

value: Hypo


title: Microbiota in mouse stool, sample MN96

description: 16s rRNA v3-v4 sequencing


title: Microbiota in mouse stool, sample MN97

description: 16s rRNA v3-v4 sequencing

value: PS


title: Endometrial Cancer_T33


title: G16210-2-T0

value: S


title: Microbiota in mouse stool, sample MN95

description: 16s rRNA v3-v4 sequencing


title: Endometrial Cancer_T32


title: G16210-1-T105

value: blood

value: NS


title: Microbiota in mouse stool, sample MN94

description: 16s rRNA v3-v4 sequencing


title: TP18_M278

value: ER+/HER2- primary invasive lobular breast cancer


title: TP18_M251


title: Endometrial Cancer_T31


title: Endometrial Cancer_T30


title: Microbiota in mouse stool, sample MN92

description: 16s rRNA v3-v4 sequencing

value: Ntg


title: TP18_M329


title: G16207-2-T105


title: Microbiota in mouse stool, sample MN93

description: 16s rRNA v3-v4 sequencing


title: G16210-1-T0


title: TP18_M302


title: Endometrial Cancer_T2


title: G16207-2-T0


title: Microbiota in mouse stool, sample MN91

description: 16s rRNA v3-v4 sequencing


title: TP18_M355


title: TP18_M202


title: Microbiota in mouse stool, sample MN90

description: 16s rRNA v3-v4 sequencing


title: TP18_M372


title: Microbiota in mouse stool, sample MN9

description: 16s rRNA v3-v4 sequencing


title: Endometrial Cancer_T28


title: Endometrial Cancer_T27


title: G16207-1-T0


title: G16207-1-T105


title: G16201-2-T105


title: TP17_M384


title: G16201-2-T0


title: Endometrial Cancer_T25


title: TP17_M559


title: Endometrial Cancer_T24


title: G16201-1-T105


title: TP17_M622


title: G16201-1-T0


title: Endometrial Cancer_T29


title: Microbiota in mouse stool, sample MN86

description: 16s rRNA v3-v4 sequencing


title: Microbiota in mouse stool, sample MN85

description: 16s rRNA v3-v4 sequencing


title: Endometrial Cancer_T22


title: G16196-2-T105


title: Microbiota in mouse stool, sample MN84

description: 16s rRNA v3-v4 sequencing


title: G16196-2-T0


title: Microbiota in mouse stool, sample MN89

description: 16s rRNA v3-v4 sequencing


title: TP17_M901


title: Endometrial Cancer_T20


title: 20230614-B136-HSC-PMN-0616HEF

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

description: HIVE scRNA-seq

data_processing:
scRNA-seq data were quantified using BeeNetPLUS (Honeycomb) with reference genome GRCh38. To remove low-quality and doublets cells, we excluded the following cells: (1) cells with fewer than 700 total UMI; (2) cells with more than 20% mitochondrial transcripts; (3) Scrublet scores above 0.4 using Scrublet (v0.2.3).
Assembly: GRCh38
Supplementary files format and content: count matrix incsv

source_name: Blood

growth_protocol: CD34+ Umbilical cord cells purchased from Lonza (Lonza, Cambridge, MA), CD34+ BM live cells isolated from BM filters (Massachusetts General Hospital Institutional Review Board-approved protocol 2019P003676), and cadaveric CD34+ BM purchased from Ossium Health (Ossium Health, San Francisco, CA), were all cultured in SFEMII (Stem Cell Technologies) supplemented with stem cell factor (SCF, 50ng/ml) (Peprotech, Cranbury, NJ), FMS-like tyrosine kinase 3 ligand (Flt-3L, 50ng/ml) (Peprotech), interleukin 3 (IL3, 5ng/ml) (Peprotech), and interleukin 6 (IL6, 50ng/ml) (Peprotech) with or without UM729 (1uM) (StemCell Technologies). Cells were seeded at 7.5x10^4 cells/mL in a 6-well plate and passed into equal parts fresh media every other day. HSCs cultured with UM729 were cryopreserved on day 10 of ex vivo culture, and HSCs cultured without UM729 were cryopreserved on Day 6 of ex vivo culture. Cells were cryopreserved in Cryostor CS10 (StemCell Technologies) and stored in liquid nitrogen.

extract_protocol: Single live cells were counted and processed using Honeycomb Single Cell RNA Sequencing platform HIVE. The samples were prepared for library preparation according to the manufacturer's protocol, and were then sequenced on an Illumina NextSeq500 sequencer.

value: Blood

value: Primary neutrophil

tag: days

value: Day 0

tag: cells

value: PMN


title: TP18_M403


title: Microbiota in mouse stool, sample MN88

description: 16s rRNA v3-v4 sequencing

tag: genotype


title: Endometrial Cancer_T1

value: Endometrium


title: Endometrial Cancer_T19

value: Endometrial Cancer


title: G16196-1-T105

value: Hyper


title: WT_rep2

value: colon spheroids

tag: strain background

value: mixed; mostly C57Bl6 with some FVB

value: WT


title: 20230614-B136-HSC-UCB5-0616HEF

description: HIVE scRNA-seq

source_name: Umbilical cord blood

value: Umbilical cord blood

value: Day 10 UM729 diff

value: Day 10

value: CD34 cells


title: Microbiota in mouse stool, sample MN82

description: 16s rRNA v3-v4 sequencing

value: Mus musculus

value: Stool

value: PS


title: Microbiota in mouse stool, sample MN83

description: 16s rRNA v3-v4 sequencing

value: OS


title: Microbiota in mouse stool, sample MN87

description: 16s rRNA v3-v4 sequencing

value: Ntg

value: SY


title: G16196-1-T0

value: blood

value: S


title: Endometrial Cancer_T18

value: Endometrium

value: Endometrial Cancer


title: TP17_M899

value: ER+/HER2- primary invasive lobular breast cancer


title: 20230614-B136-HSC-UCB4-0616HEF

description: HIVE scRNA-seq

value: Day 10 reg diff


title: Microbiota in mouse stool, sample MN81

description: 16s rRNA v3-v4 sequencing


title: G16195-2-T105

value: Hypo

value: NS


title: Endometrial Cancer_T15


title: Endometrial Cancer_T23


title: 20230614-B136-HSC-UCB3-0616HEF

description: HIVE scRNA-seq

value: Umbilical cord blood

value: Day 10 reg exp


title: Microbiota in mouse stool, sample MN80

description: 16s rRNA v3-v4 sequencing


title: G16195-2-T0


title: 20230614-B136-HSC-UCB2-0616HEF

description: HIVE scRNA-seq

value: Day 6 reg exp

value: Day 6

value: CD34 cells


title: Microbiota in mouse stool, sample MN8

description: 16s rRNA v3-v4 sequencing

value: Mus musculus

value: Stool

value: PS


title: G16195-1-T105


title: 20230614-B136-HSC-UCB1-0616HEF

description: HIVE scRNA-seq

value: Day 0 Expansion

value: Day 0


title: G16195-1-T0

value: blood

value: S


title: Endometrial Cancer_T13

value: Endometrium

value: Endometrial Cancer


title: Microbiota in mouse stool, sample MN79

description: 16s rRNA v3-v4 sequencing


title: 20230614-B136-HSC-Oss5-0616HEF

description: HIVE scRNA-seq

source_name: OSS

value: OSS

value: Day 10 UM729 diff

value: Day 10


title: oe_NC_1

value: adipose tissue

tag: cell line

value: adipose stem cells

tag: cell type

value: stem cells

value: WT

tag: treatment


title: Endometrial Cancer_T10

tag: tissue


title: Microbiota in mouse stool, sample MN78

description: 16s rRNA v3-v4 sequencing

value: SY


title: 20230614-B136-HSC-Oss4-0616HEF

description: HIVE scRNA-seq

value: Day 10 reg diff

value: CD34 cells


title: Microbiota in mouse stool, sample MN77

description: 16s rRNA v3-v4 sequencing

value: Mus musculus

value: Stool

value: OS


title: Biol rep3 early ery HES6 knockdown 2

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

data_processing:
Reads were aligned to GRCh38 using STAR2.7.10b. RNA sequencing counts were analyzed using the DESeq2 packages in R and genes with adjusted P-values <0.05 were considered differentially expressed.
QC of fastq files was done with FastQC

source_name: Cord blood

growth_protocol: After transduction, cells were cultured for four days in homemade MEMa (ThermoFisher, #12000-014) with 20% FCS and cytokines (SCF and EPO 5 ng/ml, TPO 50 ng/ml), in 7% CO2, 37°C incubator.

extract_protocol:
RNA isolation using kit (Qiagen, #217084)
RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen) using different quantities of input RNA (mgk 9,35ng; CD34- 109,2ng; early ery 12,75ng; late ery 11,55ng)

treatment_protocol: Cells were stained for cell surface markers and sorted before RNA isolation

value: Cord blood

value: early erythroblast

value: HES6 shRNA2


title: Control_Endometrium_C7

value: Endometrium

value: normal


title: 20230614-B136-HSC-Oss2-0616HEF

description: HIVE scRNA-seq

value: OSS

value: Day 6 reg exp

value: Day 6


title: Microbiota in mouse stool, sample MN76

description: 16s rRNA v3-v4 sequencing

value: PS


title: Biol rep3 CD34- HES6 knockdown 2


title: Control_Endometrium_C9


title: 20230614-B136-HSC-Oss3-0616HEF

description: HIVE scRNA-seq

value: Day 10 reg exp

value: Day 10


title: Microbiota in mouse stool, sample MN75

description: 16s rRNA v3-v4 sequencing

value: Ntg

value: SY


title: Endometrial Cancer_T14

value: Endometrial Cancer


title: 20230614-B136-HSC-Oss1-0616HEF

description: HIVE scRNA-seq

value: Day 0 Expansion

value: Day 0

value: CD34 cells


title: Control_Endometrium_C5


title: Biol rep3 late ery HES6 knockdown 1

value: Cord blood

value: late erythroblast

value: HES6 shRNA1


title: 20230614-B136-HSC-BM5-0616HEF

description: HIVE scRNA-seq

source_name: Bone Marrow

value: Bone Marrow

value: Day 10 UM729 diff


title: Control_Endometrium_C4

value: Endometrium

value: normal


title: Microbiota in mouse stool, sample MN73

description: 16s rRNA v3-v4 sequencing

value: Mus musculus

value: Stool


title: Biol rep3 early ery HES6 knockdown 1

value: early erythroblast


title: 20230614-B136-HSC-BM4-0616HEF

description: HIVE scRNA-seq

value: Day 10 reg diff

value: Day 10


title: Biol rep3 late ery HES6 knockdown 2

value: HES6 shRNA2


title: Control_Endometrium_C3


title: Biol rep3 CD34- HES6 knockdown 1


title: Microbiota in mouse stool, sample MN72

description: 16s rRNA v3-v4 sequencing

value: Ntg

value: SY


title: 20230614-B136-HSC-BM3-0616HEF

description: HIVE scRNA-seq

value: Day 10 reg exp


title: Biol rep3 mgk HES6 knockdown 1

value: CD41+ Mgk


title: Control_Endometrium_C22


title: Microbiota in mouse stool, sample MN71

description: 16s rRNA v3-v4 sequencing

value: OS


title: Control_Endometrium_C6


title: Biol rep3 mgk HES6 knockdown 2

value: Cord blood


title: Control_Endometrium_C20


title: 20230614-B136-HSC-BM2-0616HEF

description: HIVE scRNA-seq

value: Day 6 reg exp

value: Day 6

value: CD34 cells


title: Biol rep3 late ery control

value: late erythroblast

value: shRNA control


title: Microbiota in mouse stool, sample MN74

description: 16s rRNA v3-v4 sequencing

value: Mus musculus


title: Control_Endometrium_C18

value: Endometrium

value: normal


title: Biol rep3 early ery control

value: early erythroblast


title: 20230614-B136-HSC-BM1-0616HEF

description: HIVE scRNA-seq

value: Bone Marrow

value: Day 0 Expansion

value: Day 0


title: Microbiota in mouse stool, sample MN69

description: 16s rRNA v3-v4 sequencing

value: Stool

value: Ntg

value: SY


title: JB_341, snRNAseq

city: La Jolla

first: David

last: Brenner

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys

description: MASH

data_processing:
For each sequenced snATAC-Seq libraries, we obtained four FASTQ files paired-end DNA reads as well as the combinatorial indexes for i5 (768 different PCR indices) and T7 (96 different tagmentation indices; Supplementary Table 8). We selected all reads with <= 2 mistakes per individual index (Hamming distance between each pair of indices is 4) and subsequently integrated the full barcode at the beginning of the read name in the FASTQ files (https://gitlab.com/Grouumf/ATACdemultiplex/).
Next, we used trim galore (v.0.4.4) to remove adapter sequences from reads prior to read alignment.
We aligned reads to the reference genome using bwa mem (v.0.7.17) 10 and subsequently used samtools to remove unmapped, low map quality (MAPQ<30), secondary, and mitochondrial reads.
Downstream analysis of snATACseq peaks were conducted with the Signac tool.
Sequencing reads were demultiplexed (cellranger mkfastq) and processed (cellranger count) using the Cell Ranger software package v3.0.2 (10x Genomics). Reads were aligned to the human reference hg38 (Cell Ranger software package v3.0.2). Reads mapping to intronic and exon sequences were retained. Resulting UMI feature-barcode count matrices were loaded into Seurat for downstream processing
Assembly: hg38
Supplementary files format and content: snATAC-seq: bed files containing regions of open chromatin (peaks), per sample
Supplementary files format and content: snRNA-seq: hLIVER_processed_files.tar.gz. Contains sparse matrix file containing raw counts (one file for all samples), csv files containing gene names and cell ids, and csv file containing cell metadata (including cluster ID, sample ID, condition, QC metrics).

extract_protocol:
Nuclei were isolated from frozen liver tissue using gentleMACS dissociation (Miltenyi). ~50-70 mg of frozen liver tissue was suspended in 1 ml of MACS dissociation buffer consisting of 5 mM CaCl2 (G-Biosciences, R040), 2 mM EDTA (Invitrogen, 15575-038), 1X protease inhibitor (Roche, 05-892-970-001), 3 mM MgAc (Grow Cells, MRGF-B40), 10 mM Tris-HCl pH 8 (Invitrogen, 15568-075), and 0.6 mM DTT (Sigma-Aldrich, D9779) in water (Corning, 46-000-CV) and placed on wet ice. Next, samples were homogenized using gentleMACS dissociator (Miltenyi) with gentleMACS M tubes (Miltenyi, 130-096-335) and the “protein_01” protocol. Suspension was filtered through a 30 µM CellTrics filter (Sysmex, 04-0042-2316). M tube and filters were washed with 1 ml of MACS dissociation buffer and combined with the suspension. Suspension was centrifuged in a swinging bucket centrifuge (Eppendorf, 5920R) at 500 rcf for 5 minutes (4°C, ramp speed 3/3). Supernatant was removed and pellet was resuspended in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X complete Protease inhibitor). Nuclei were rotated at 4 °C for 5 minutes before being pelleted again with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. For single nucleus RNA-seq, 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 ul of collection buffer consisting of 1 U/ul RNase inhibitor in 5% BSA; the FACS gating strategy sorted based on particle size and DRAQ7 fluorescence. Sorted nuclei were then centrifuged at 1000 rcf for 15 minutes (4°C, run speed 3/3) and supernatant was removed. For single nucleus ATAC-seq, unsorted nuclei were used as input for single nucleus ATAC-seq using combinatorial barcoding
For single nucleus ATAC-seq, unsorted nuclei were used as input for single nucleus ATAC-seq using combinatorial barcoding. Approximately 15,000 nuclei were loaded onto the Chromium controller (10x Genomics) for downstream single-nucleus RNA-seq processing with the Single Cell 3’ v3.1 GEM generation kit (10x Genomics).
single nucleus ATAC-seq, single nucleus RNA-seq

value: liver


title: Microbiota in mouse stool, sample MN7

description: 16s rRNA v3-v4 sequencing

value: PS


title: Microbiota in mouse stool, sample MN70

description: 16s rRNA v3-v4 sequencing


title: Control_Endometrium_C15


title: Control_Endometrium_C14


title: Biol rep3 CD34- control

value: Cord blood


title: Biol rep3 mgk control

value: CD41+ Mgk


title: Microbiota in mouse stool, sample MN68

description: 16s rRNA v3-v4 sequencing

value: OS


title: JB_340, snRNAseq

description: MASH


title: Control_Endometrium_C13


title: Biol rep2 late ery HES6 knockdown 2

value: late erythroblast

value: HES6 shRNA2


title: Microbiota in mouse stool, sample MN67

description: 16s rRNA v3-v4 sequencing

value: Mus musculus


title: JB_338, snRNAseq

description: MASH


title: UBE2S-KO3

city: xi'an

first: Renyu

last: Zhang

state: Shaanxi

address: 169 Changle West Road

institute: Fourth Military Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release104
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: hepatocellular carcinoma cells


title: Microbiota in mouse stool, sample MN66

description: 16s rRNA v3-v4 sequencing


title: JB_337, snRNAseq

description: MASL


title: UBE2S-KO2


title: Biol rep2 CD34- HES6 knockdown 2


title: Microbiota in mouse stool, sample MN65

description: 16s rRNA v3-v4 sequencing


title: JB_336, snRNAseq

description: NORMAL


title: UBE2S-KO1


title: Biol rep2 mgk HES6 knockdown 2


title: Biol rep2 late ery HES6 knockdown 1

value: HES6 shRNA1


title: JB_339, snRNAseq

description: MASH


title: JB_320, snRNAseq

description: NORMAL


title: WT2


title: Biol rep2 early ery HES6 knockdown 1

value: early erythroblast


title: Microbiota in mouse stool, sample MN61

description: 16s rRNA v3-v4 sequencing


title: JB_321, snRNAseq

description: MASH


title: JB_322, snRNAseq

description: MASH


title: Biol rep2 early ery HES6 knockdown 2


title: Biol rep2 mgk HES6 knockdown 1


title: Microbiota in mouse stool, sample MN63

description: 16s rRNA v3-v4 sequencing


title: Microbiota in mouse stool, sample MN60

description: 16s rRNA v3-v4 sequencing


title: JB_319, snRNAseq

description: MASH


title: JB_318, snRNAseq

description: MASL


title: Biol rep2 late ery control

value: shRNA control


title: Biol rep2 CD34- HES6 knockdown 1


title: Microbiota in mouse stool, sample MN62

description: 16s rRNA v3-v4 sequencing


title: Microbiota in mouse stool, sample MN6

description: 16s rRNA v3-v4 sequencing


title: WT1


title: HCF09, EF-1

city: Leuven

first: Llewelyn

last: Roderick

address: Herestraat 49

department: Department of Cardiovascular Sciences

institute: KU Leuven

data_processing:
Gene expression was quantified at the transcript level using Salmon, with the validatMappings and -gcBias parameters switched on, to the human transcriptome. Transcript level counts were aggregated to gene level count using the import in the tximport package, setting countsFromAbundance to ‘lengthScaledTPM’ in the R.
DESeq2 was used for differential gene expression between different conditions. The batch variability of different sequencing runs was accounted for by defining “batch” as a covariate in the linear model to analyze differential gene expression.
Differential gene expression heat maps were generated by using the pheatmap, and volcano plots by EnhancedVolcano.
The overlapping genes between different conditions were obtained by VennDiagram.
Functional enrichment of the differentially expressed genes was determined using a hypergeometric test against the Gene Ontology database by using the ClueGO module of Cytoscape with Benjamini–Hochberg adjusted (FDR) P < 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: heart atrium

growth_protocol: Human atrial cardiac fibroblasts (HCF) were cultured in a fibroblast medium supplemented with fetal bovine serum (FBS), fibroblast growth supplement (FGS), and penicillin/streptomycin solution.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq library were prepared with TruSeq RNA Sample Preparation Kit following manufacturer's manual

treatment_protocol: HCFs were seeded at a density of 150000 cells/well in an antibiotic-free medium in 12-well plates.

value: heart atrium

value: HCF

value: atrial cardiac fibroblasts

value: WT


title: JB_317, snRNAseq

description: NORMAL


title: WT3


title: Microbiota in mouse stool, sample MN59

description: 16s rRNA v3-v4 sequencing

value: Stool

value: Ntg

value: SY


title: Microbiota in mouse stool, sample MN64

description: 16s rRNA v3-v4 sequencing

value: PS


title: JB_305, snRNAseq

description: MASH

value: liver


title: Biol rep2 CD34- control

value: Cord blood


title: HCF06, NRG1


title: Microbiota in mouse stool, sample MN58

description: 16s rRNA v3-v4 sequencing


title: JB_304, snRNAseq

description: MASL


title: HCF05, NRG1


title: Biol rep2 mgk control

value: CD41+ Mgk


title: Microbiota in mouse stool, sample MN57

description: 16s rRNA v3-v4 sequencing


title: JB_303, snRNAseq

description: NORMAL


title: HCF04, NRG1


title: HCF08, EF-1


title: Biol rep1 late ery HES6 knockdown 2

value: late erythroblast

value: HES6 shRNA2


title: Biol rep1 early ery HES6 knockdown 2


title: HCF03, Control

value: PBS


title: JB_289, snRNAseq

description: MASL


title: Microbiota in mouse stool, sample MN56

description: 16s rRNA v3-v4 sequencing

value: Mus musculus


title: Microbiota in mouse stool, sample MN55

description: 16s rRNA v3-v4 sequencing


title: Biol rep1 CD34- HES6 knockdown 2


title: Biol rep2 early ery control

value: early erythroblast


title: HCF02, Control


title: JB_288, snRNAseq

description: NORMAL


title: Biol rep1 mgk HES6 knockdown 2


title: HCF01, Control


title: Microbiota in mouse stool, sample MN54

description: 16s rRNA v3-v4 sequencing


title: HCF07, EF-1


title: hESC(RUES2)-Cardiomyocyte  bio_rep3

city: Tainan City

first: Po-Hsien

middle: Joseph

last: Huang

address: 1 University Rd.

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Cheng Kung University

description:
m5C_loci.xlsx
DESeq2_DEGs.xlsx
HTseqCount_raw.txt

data_processing:
The raw fastq file were merge into one R1 and one R2 file by Concatenate datasets tool on Galaxy web platform.
Use Trim Galore! tool remove reads with Q score less than 20 and the adaptor seqeunces. With the followed arguments: for read 1 ‘-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’ and read 2 ‘-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT’
The trimmed and quality reads were aligned to human reference genome GRCh38 (Release-100 from Ensembl website) with gene transfer format (GTF) by meRanGh align, and with arguments of maximum mismatch ratio set at 0.1 (‘-mmr 0.1’).
The SAM files were then proceed to meRanCall with arguments ‘-rl 150 -md 5 -ei 0.1 -cr 99 -fdr 0.05 -mcov 10 -mr 0.05’ to identifiy  m5C sites
The gene annotaion of m5C sites were retrieved by meRanAnnotate with arguments of ‘-f 'gene' -g Homo_sapiens.GRCh38.100.gff3‘
Assembly: hg38
Supplementary files format and content: excel file with m5C sites commonly present in preplicates
Supplementary files format and content: excel file with differential gene expression data between groups
Supplementary files format and content: tab-delimited txt files of HTseq-count reads counts of each sample

source_name: embryonic tissue

growth_protocol: All hPSCs include hiPSCs and hESC were cultured on Matrigel matrix (Corning; 354230) pre-coated cell culture dish in Stemflex medium (Thermo; A3349401). Addition of ROCK inhibitor Y27632 (10uM; Cayman; 10005583) allows cells to attach.

extract_protocol:
Total RNA was purifed with Direct-zol RNA MiniPrep kit (Zymo) and treated with DNAse I followed manufactorers instruction. Purify the poly(A) RNA sample by Dynabeads mRNA DIRECT purification kit (Thermo) with twice purification process, followed by bisulfite conversion reaction with three cycles of 70℃ 10minutes and 64℃ 45 minutes by EZ RNA methylation kit (Zymo).
The bisulfite treated mRNA samples librarires were generated with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: The hPSCs were differentiated followed the well-established 14 days protocol by Burridge et al (2014). On day 0, the RPMI-1640 medium contains  B27 minus insulin supplement (Thermo; 1895201) and Wnt activator Chir99021 (5 µM; Stemcell Technology; 72054). On Day 2, medium was changed to RPMI-1640 supplemented with B27 minus insulin. On day 3, addition of Wnt inhibitor IWR-1 (5 µM; Sigma; I0161) to the medium. On day 7, addition of insulin (B27 supplement; Thermo; 17504044) to induce cardiomyocyte formation. The medium was changed every 2 days untill the completion of the 14 days protocol.

value: embryonic tissue

value: human embryonic stem cells derived cardiomyocyte

value: wild-type

value: Bisulfite-treated mRNA


title: hESC(RUES2)-Cardiomyocyte  bio_rep2


title: SW1463n3controle

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
The quality of raw data was assessed using FastQC (v.0.12.1) and MultiQC (v.1.12) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v3.5).
STAR (v.2.7.11a) was applied to align sequences to the human genome (GRCh38) and to determine counts per gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count for each Sample

growth_protocol: LS513 and SW1463 were maintained in DMEM/F12 supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37oC

extract_protocol:
RNA was harvested using NucleoSpin RNA isolation kit (Macherey Nagel). 1,25ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep following manufacturer’s protocol.

treatment_protocol: 135.000 cells LS513 and 300.000 cells SW1463 were plated in a 6 well plate. After they adhere the cells were treated for 3,5 days (ca. 84 hour) with 100uM H3B-120 (cat. SML3007, Sigma), refreshing the medium and drugs twice a day.

value: control


title: Microbiota in mouse stool, sample MN53

description: 16s rRNA v3-v4 sequencing

value: Stool


title: Microbiota in mouse stool, sample MN52

description: 16s rRNA v3-v4 sequencing


title: SW1463n3plus100umH3B120


title: Biol rep1 early ery HES6 knockdown 1

value: HES6 shRNA1


title: Microbiota in mouse stool, sample MN51

description: 16s rRNA v3-v4 sequencing

value: SY


title: JB_290, snRNAseq

description: MASH


title: SW1463n2plus100umH3B120


title: Biol rep1 CD34- HES6 knockdown 1


title: Microbiota in mouse stool, sample MN50

description: 16s rRNA v3-v4 sequencing

value: Ntg


title: Biol rep1 mgk HES6 knockdown 1


title: SW1463n2controle


title: Biol rep1 late ery HES6 knockdown 1


title: hESC(RUES2) bio_rep4

value: human embryonic stem cells


title: hESC(RUES2) bio_rep3


title: Biol rep1 late ery control

value: Cord blood

value: shRNA control


title: SW1463n1plus100umH3B120


title: Microbiota in mouse stool, sample MN49

description: 16s rRNA v3-v4 sequencing


title: hESC(RUES2) bio_rep2


title: Biol rep1 early ery control


title: Microbiota in mouse stool, sample MN5

description: 16s rRNA v3-v4 sequencing

value: PS


title: SW1463n1controle


title: Microbiota in mouse stool, sample MN48

description: 16s rRNA v3-v4 sequencing


title: Biol rep1 CD34- control


title: Microbiota in mouse stool, sample MN47

description: 16s rRNA v3-v4 sequencing


title: hESC(RUES2) bio_rep1


title: hAFSC-iPSC-Cardiomyocyte  bio_rep3

source_name: Amniotic fluid stem cell

value: Amniotic fluid stem cell

value: AFSC-iPSC

value: AFSC-iPSC derived cardiomyocyte


title: LS513n3controle


title: Microbiota in mouse stool, sample MN46

description: 16s rRNA v3-v4 sequencing

value: Mus musculus


title: hESC(RUES2)-Cardiomyocyte  bio_rep1

value: embryonic tissue


title: LS513n2plus100umH3B120


title: hAFSC-iPSC-Cardiomyocyte  bio_rep2


title: Liver_PHx_11dpi

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

institute: Shiv Nadar Institution of Eminence

description: 10x Genomics

data_processing:
A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger (options: ‘—attribute = gene_biotype:lincRNA –attribute = gene_biotype:antisense), as well as the pseudo mTagBFP2, H2B-mGL, mCherry-NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software (v.7.1.0) provided by 10x Genomics with the option “–include- introns” set to False (all other options were used as per default).
Assembly: GRCz11
Supplementary files format and content: Count Matrix as h5ad file
Supplementary files format and content: Metadata listing the cell annotations as csv file

organism: Danio rerio

source_name: Liver

extract_protocol:
Zebrafish were euthanized in 500 mg/l solution of tricaine (MS-222) (Sigma-Aldrich, E10521). The entire liver was dissected out of the body using Dumont #5 forceps (Fine Science Tools, 11295-10). All steps for making the single-cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly, the liver was dissociated into single cells by incubation it in TrypLE (Thermo Fisher, 12563029) at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation, TrypLE was inactivated with goat serum. To remove undissociated chunks and debris, the solution was passed through a 40 μm cell strainer (Miltenyi Biotec, 130-041-407). Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft-stop setting. The supernatant was carefully discarded and the pellet re-suspended in 500 μl of PBS. To remove dead cells, Calcein violet (Thermo Fisher, C34858) or Draq7 (Thermo Fisher, D15105) was added at a final concentration of 1 µM and 3 µM, respectively, and the cell suspension was incubated at room temperature for 20 min. The single-cell preparation was sorted using appropriate gates, including excitation with UV (405 nm) or a 633 nm laser for identifying live cells with Calcein+ or Draq7-, respectively. FACS was performed  using a 100 µm nozzle, and a minimum of ~15,000 live cells per condition were collected into BSA-coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min.
For single-cell RNA sequencing using the 10x Genomics platform, the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease-free water according to the manufacturer’s instructions to yield 7,000 cells. Subsequently, the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system (Single Cell 3’ v3). After the gel emulsion bead suspension underwent the reverse transcription reaction, emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles, following the guidelines of the 10x Genomics user manual. The 10x Genomics single-cell RNA-seq library preparation—involving fragmentation, dA tailing, adapter ligation, and indexing PCR—was performed based on the manufacturer’s protocol. After quantification, the libraries were sequenced on an Illumina NextSeq 550 machine.

value: Liver

tag: transgene

value: Partial Hepatectomy


title: Microbiota in mouse stool, sample MN45

description: 16s rRNA v3-v4 sequencing


title: hAFSC-iPSC-Cardiomyocyte  bio_rep1

value: wild-type

value: Bisulfite-treated mRNA


title: Liver_PHx_4dpi

description: 10x Genomics


title: hAFSC-iPSC bio_rep4

value: Amniotic fluid stem cell-induced pluripotent stem cell


title: LS513n1plus100umH3B120


title: Liver_MTZ_9dppa

description: 10x Genomics

value: Partial Ablation


title: Microbiota in mouse stool, sample MN43

description: 16s rRNA v3-v4 sequencing

value: Stool

value: SY


title: hAFSC-iPSC bio_rep2


title: hAFSC-iPSC bio_rep3


title: Liver_MTZ_1dppa

description: 10x Genomics


title: LS513n3plus100umH3B120


title: Liver_MTZ_0dppa

description: 10x Genomics


title: MM_481, snATACseq

description: MASH

value: liver


title: LS513n1controle

value: control


title: Microbiota in mouse stool, sample MN41

description: 16s rRNA v3-v4 sequencing


title: hAFSC-iPSC bio_rep1


title: Biol rep1 mgk control

value: Cord blood

value: CD41+ Mgk

value: shRNA control


title: Liver_Control2

description: 10x Genomics

value: Control – No 4-OHT


title: Microbiota in mouse stool, sample MN40

description: 16s rRNA v3-v4 sequencing

value: Ntg

value: OS


title: MM_480, snATACseq

description: MASH


title: hiPSCs(1103)-Cardiomyocyte bio_rep3

source_name: Peripheral blood mononuclear cell

value: Peripheral blood mononuclear cell

value: human induced pluripotent stem cell derived cardiomyocyte


title: MM_479, snATACseq

description: NORMAL


title: Liver_Control1

description: 10x Genomics

value: Liver


title: Microbiota in mouse stool, sample MN4

description: 16s rRNA v3-v4 sequencing

value: Mus musculus

value: PS


title: hiPSCs(1103)-Cardiomyocyte bio_rep2

value: wild-type

value: Bisulfite-treated mRNA


title: LS513n2controle


title: MM_478, snATACseq

description: MASH


title: hiPSCs(1103)-Cardiomyocyte bio_rep1


title: Microbiota in mouse stool, sample MN39

description: 16s rRNA v3-v4 sequencing

value: Stool


title: iAM12, EF-1

description: Immortalized atrial cardiomyocytes - iAM12

data_processing:
Gene expression was quantified at the transcript level using Salmon, with the validatMappings and -gcBias parameters switched on, to the Rnor transcriptome. Transcript level counts were aggregated to gene level count using the import in the tximport package, setting countsFromAbundance to ‘lengthScaledTPM’ in the R.
DESeq2 was used for differential gene expression between different conditions. The batch variability of different sequencing runs was accounted for by defining “batch” as a covariate in the linear model to analyze differential gene expression.
Differential gene expression heat maps were generated by using the pheatmap, and volcano plots by EnhancedVolcano.
The overlapping genes between different conditions were obtained by VennDiagram.
Functional enrichment of the differentially expressed genes was determined using a hypergeometric test against the Gene Ontology database by using the ClueGO module of Cytoscape with Benjamini–Hochberg adjusted (FDR) P < 0.05.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Rattus norvegicus

source_name: iAM

growth_protocol: Immortalized rat atrial cardiomyocytes (iAM) were cultured in Advanced DMEM F-12 supplemented with 2% heat-inactivated FBS, 1% penicillin/streptomycin, 1X GlutaMAX, and 100 ng/mL doxycycline for proliferation. To induce differentiation, iAM were transferred to medium without doxycycline.

treatment_protocol: iAM were seeded at a density of 6x106 cells/mL in a differentiation medium in T75-flasks and incubated for 9 days. Then, cells were treated with either compound EF-1 (32 µM), PBS, or NRG1 (0.1 µM), and cells were incubated for 16 h at 37 °C.

tag: genetic modification

value: Freshly isolated neonatal rat atrial cardiomyocytes (AMs) were transduced with a lentiviral vector conferring doxycycline (dox)-controlled expression of simian virus 40 large T antigen and stable cell lines generated through selection using puromycin

value: iAM

value: atrial myocytes

value: WT


title: iAM11, EF-1

description: Immortalized atrial cardiomyocytes - iAM11


title: Microbiota in mouse stool, sample MN44

description: 16s rRNA v3-v4 sequencing

value: SY


title: Microbiota in mouse stool, sample MN38

description: 16s rRNA v3-v4 sequencing


title: Microbiota in mouse stool, sample MN42

description: 16s rRNA v3-v4 sequencing


title: hiPSCs(1103) bio_rep3

value: human induced pluripotent stem cell


title: MM_476, snATACseq

description: NORMAL

value: liver


title: Microbiota in mouse stool, sample MN37

description: 16s rRNA v3-v4 sequencing

value: Ntg


title: Microbiota in mouse stool, sample MN36

description: 16s rRNA v3-v4 sequencing

value: OS


title: hiPSCs(1103) bio_rep1

value: Peripheral blood mononuclear cell


title: MM_475, snATACseq

description: MASH


title: iAM10, EF-1

description: Immortalized atrial cardiomyocytes - iAM10


title: hiPSCs(1103) bio_rep2


title: Microbiota in mouse stool, sample MN35

description: 16s rRNA v3-v4 sequencing


title: iAM08, NRG1

description: Immortalized atrial cardiomyocytes - iAM08


title: iAM09, EF-1

description: Immortalized atrial cardiomyocytes - iAM09


title: MM_474, snATACseq

description: MASL


title: YW83_HTO

data_processing:
Basecalls performed 10x Cellranger v6 and fba v0.0.6
Mapping and combining the libraries with 10x Cellranger
Genome_build: hg38
processed_data_files_format_and_content: single cell process h5

source_name: MDAMB231 Cell line

extract_protocol:
Cells were collected, washed once with PBS and stained with Cell Hashing antibodies ot CellPlex followed by manuffacturer manual. Cells were resuspended in PBS containing 0.05% of BSA to the desired concentration and immediately load on the 10x Chromium controller for single-cell RNA-seq preparation.
For single-cell library preparation, we followed the standard protocol of 10x Genomics. After the cDNA amplification, 50 ng of samples were separated for the sgRNA enrichment library preparation.

treatment_protocol: Cells were infected with lenti-dCas9-KRAB-blast (Addgene:89567) to stablly express dCas9-KRAB. After stablly expressed dCAs9-KRAB, the cells were infected by a lentivirus sgRNA library targeting breast cancer associated enhancers and under antibiotics selection for two weeks.

tag: experiment

value: Single-cell Expression


title: iAM07, NRG1

description: Immortalized atrial cardiomyocytes - iAM07


title: Microbiota in mouse stool, sample MN34

description: 16s rRNA v3-v4 sequencing