title: STING-polysome-2

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Polysome-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the human genome (hg19) using Tophat v2.1.1 with default parameters. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) using Cufflinks v2.2.1. The RNA abundance of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Briefly, sequencing reads were mapped to ERCC reference to obtain the ratio of ERCC reads to human reads. Then gene abundance was normalized by multiplying the raw FPKM values by a normalization factor (normalization factor = percentage of ERCC in control polysome-free sample/percentage of ERCC in the sample). Samples prepared in different batches were normalized by the control polysome-free sample in each batch. Genes with FPKM < 1 in all samples were excluded, and for the remaining genes, all FPKM values smaller than 1 were set to 1 in subsequent analyses. The ribosome load was defined as the ratio of the proportion of an mRNA in the polysome-bound and the polysome-free pool.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: HEK293 cells

growth_protocol: HEK293 cells were obtained from ATCC, and  were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C in 5% CO2 (v/v).

extract_protocol:
Cells transfected with different plasmids  were pretreated with 100 mg/ml cycloheximide for 30 min at 37°C prior to washing with ice-cold PBS containing 100 mg/ml cycloheximide. Cells were then lysed in polysome lysis buffer (20 mM Tris-HCl (pH 7.4), 100 mM KCl, 5 mM MgCl2, 100 mg/ml cycloheximide and 1% NP40). After 20 min on ice, the lysates were centrifuged (12,000 rpm for 15 min at 4°C), and the supernatants were loaded onto 10-50% sucrose gradients and centrifuged for 15 h at 25,000 rpm and 4°C in a SW41 rotor. Separated samples were fractionated at 0.75 ml/min through an automated fractionation system that continually monitors OD254 values. An aliquot of the ribosomal fraction was used for extraction of total RNA with TRIzol reagent (Yeasen). Purified RNAs and ERCC spike-in (0.4 μl 1:1000 diluted) mixtures were used for cDNA synthesis using the Smart-seq2 method (Picelli et al., 2014). Briefly, the polyadenylated mRNAs were captured usingby the PolyT primers. After 3 min lysis at 72°C, the Smart-seq2 reverse transcription reactions were performed. After the first-strand reaction, the cDNA was amplified using a limited number of cycles (12∼14 cycles).
Sequencing libraries were constructed from 1 ng of amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer's instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform in the 150 bp paired-end mode.

treatment_protocol: A total of 7*106 cells were transfected with 5ug Vector/MAVS or STING plasmid for 24 hours.

value: Ectopic expression of STING

tag: molecule

value: polysome


title: ZnO_NP_0ug_24H_1

status: Public on Jan 18 2024

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: ON

address: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to 8x60K Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (Agilent Technologies, Inc., Santa Clara, USA) slides in a hybridization chamber for 17 h at 65°C rotating at 10 rpm.

scan_protocol: Microarray slides were washed according to manufacturer’s protocol and scanned on an Agilent G4900DA Microarray Scanner (Agilent Technologies, Inc., Santa Clara, USA). Data was retrieved using the Feature Extraction 11.0.1.1 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

molecule: total RNA

organism: Mus musculus

source_name: Immortalized Lung Epithelial cells (FE1)

label_protocol: In brief, 200 ng of total RNA per cell pellet sample or Universal Mouse Reference RNA (UMRR; Agilent Technologies) were used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: FE1 immortalized alveolar lung epithelial cells were cultured as described in Decan et al 2015, in Dulbecco’s Modified Eagle’s Medium Nutrient Mixture F-12HAM (DMEM F12HAM) supplemented with 2 % fetal bovine serum (FBS), 1 ng/mL epidermal growth factor (EGF), 1 U/mL penicillin G, and 1 µg/mL streptomycin and maintained at 37°C, with 5 % CO2.

extract_protocol: RNA extraction, quantification, and integrity analysis were conducted as in Boyadzhiev et al., 2021. Following exposure and collection of cell pellets, TRIzol reagent was used to isolate RNA in conjunction with Direct-zol RNA Miniprep Kit (Zymo Research Corp, Irvine, USA) according to manufacturer’s protocol . Total RNA concentration and purity was determined using a NanoDropOne spectrophotometer (Thermo Fisher Scientific Inc, Waltham, USA). RNA integrity and quality analysis was conducted using an Agilent 2100 Bioanalyzer system and an Agilent 4200 Tapestation System (Agilent Technologies, Inc., Santa Clara, USA). RNA samples with an RNA Integrity Number (RIN) of ≥6 were used for subsequent microarray experiments.

treatment_protocol: Cells were plated at a cell density of 130 000 cells/well in 6-well plates. Following overnight incubation, cells were exposed to 1.8 mL of 0 - 118 ug/mL metal oxide NPs, MPs, or metal chlorides. For all exposures, blank media exposed cells served as negative controls. Following 2, 24, and 48 h of exposure, cell supernatant was harvested, cells were washed with PBS, trypsinized and suspended in fresh cell culture media. An aliquot of cell suspension was used for Trypan Blue dye exclusion staining and the rest of the cells were pelleted by centrifugation (8000 rpm, 10 minutes, 4°C) and frozen at -80°C for microarray analysis. Two to four biological replicates were used for each condition.

tag: strain

value: MutaMouse

tag: treatment

value: ZnO Nanoparticle

tag: time point

value: 24 Hour

tag: dose

value: Media Control

tag: biological replicate

source_name: Universal Mouse Reference RNA

tag: sample type

value: 11 mouse cell lines


title: SF519_5

type: SRA

city: Calgary

first: Marco

last: Gallo

state: AB

address: 2500 University Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

description: single-nucleus ATAC-seq, 10x genomics

library_source: genomic single cell

data_processing:
Samples were processed individually using CellRanger ATAC v1.2.0 and aligned to the hg38 reference genome. Files were generated using CellRanger ATAC count.
Spatially delineated samples from the same patient were processed and merged in Signac v1.6.0, thresholded by features present in 10+ cells, peak_region_fragments > 3000, pct_reads_in_peaks > 15, blacklist_ratio < 0.05 and lowmapq < 30000.  and normalized by the mean signal from a randomly selected subpopulation of 5000 peaks.
Data was processed using TF-IDF and LSI in Signac, followed by UMAP construction on components  2:30 with the following parameters: n.neighbours=71L, min.dist=0.4, spread=1.5, repulsion.strength=1.1 followed by Louvain nearest neighbour clustering.
Copy-scAT was used to call copy number alterations and putative ecDNAs, followed by cluster-based averaging. ChromVAR and GeneActivity matrices were generated using Signac and the JASPAR 2021 and Ensembl v86 references respectively.
Assembly: hg38
Supplementary files format and content: Sample-level raw h5 matrix, singlecell.csv metadata file
Supplementary files format and content: Patient-level processed GeneActivity and ChromVAR Matrix (.rdata format), and filtered patient-level metadata file (.tsv)

molecule: genomic DNA

organism: Homo sapiens

source_name: multiregional profiling, primary glioblastoma tumour

extract_protocol:
Samples were obtained either as previously cryopreserved extracted nuclei (P519, P521) or as individually snap-frozen tissue fragments (P524, P529). Frozen tissue samples were processed using an iodixanol gradient centrifugation method adapted from Corces et al, with dounce homogenization and centrifugation. Extracted nuclei were washed 1x in 10X wash buffer and resuspended in 100 uL of 0.1X 10X lysis buffer for 2 minutes, followed by a second wash and resuspension into 10X nuclear buffer.
Libraries were constructed as per the 10X protocol usin the Chromium NextGEM Single Cell ATAC Kit v2 (10X genomics), targeting the maximum number of nuclei up to a ceiling of 8000 nuclei. Sequencing was performed on an Illumina NovaSeq 6000 at the Center for Health Genomics and Informatics with paired-end reads with a 2x100 configuration to a targeted depth of 50,000 reads per cell.

tag: tissue

value: brain (tumour)

tag: cell type

value: glioblastoma


title: ZnO_NP_0ug_2H_1

value: 2 Hour


title: STING-polysome-1

city: Hangzhou

country: China

library_source: transcriptomic


title: SF521_8

description: single-nucleus ATAC-seq, 10x genomics


title: AMY_MDMA_3

city: New York

first: Jennifer

last: Warner-Schmidt

state: NY

address: 220 5th Ave 17th Floor

country: USA

institute: Transcend Therapeutics

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
Assembly: rnor_6.0
Supplementary files format and content: TXT format; Tab-delimited text files include counts.
Supplementary files format and content: CSV format; Data output from DESeq2 on all genes for each sample in the analysis including: ID, log2foldchange, pvalue, padj, gene name and normalized counts for each sample.

organism: Rattus norvegicus

source_name: brain (amygdala)

extract_protocol:
Total RNA was extracted from fresh frozen brain samples (amygdala or frontal cortex) using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 5 lanes of a flowcell.

value: brain (amygdala)

value: MDMA


title: PGC-ESC BaxKO 3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Raw RNA-Seq reads were aligned against UCSC mm10 and transcript annotations using STAR (2.7.7a; Dobin et al., 2012) with parameter ‘--quantMode GeneCounts’.
Assembly: UCSC mm10
Supplementary files format and content: csv file includes gene count for each Sample

molecule: polyA RNA

source_name: PGC-ESC

growth_protocol: For routine embryonic stem cell (ESC) culture, cells were maintained on gelatin coated plates (0.2%, G1393, Merk) in 2i/LIF medium. 2i/LIF medium contains 10mg/ml of mouse leukaemia inhibitor factor (LIF) (ESG1107, Merk), 3 mM of GSK3 inhibitor CHIR99021 (SM13-10, Cambridge Bioscience) and 1 mM of MEK inhibitor PD0325901 (72182, Stem Cell Technologies) in N2B27 medium (Mulas et al., 2019). Cells were expanded by single cell dissociation with accutase (SF006, Millipore), 5% BSA quenching and replated every 2 days.

extract_protocol:
Genewiz
Genewiz-Illumina by RNA Poly(A) selection

value: PGC-ESC

tag: genotype

value: BaxKO


title: MAVS-polysome-2

value: Ectopic expression of MAVS


title: AMY_MDMA_2


title: SF519_4

description: single-nucleus ATAC-seq, 10x genomics


title: AMY_MDMA_1


title: 51435-lung-CD31

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Alignment of RNAseq reads was performed using STAR v2.7.9a and quantified using RSEM v1.3.3
Murine genome version 39 was used with GENCODE M26 annotation.
FPKM and raw counts of transcripts with the same gene symbol were pooled. Non-protein coding genes, pseudogenes, predicted genes, predicted pseudogenes, and genes with 0 FPKM in all samples were filtered out.
A total of  18,665 genes for mouse were retained and their expression was normalized between samples using the TMM method (edgeR version 3.36.0) and log2 transformed with voom (limma version 3.50.3)
Differential expression was computed using limma. Genes with p.adj value <0.05 and -1>LFC>1 were called significantly differentially expressed in all comparisons.
Assembly: mm10
Supplementary files format and content: tab separated, raw, FPKM and normalized count matrices.

source_name: brain

growth_protocol: We induced experimental metastasis in PDGFRβ-CreERT2; Rosa-tdTomato mice by intracardially injecting brain-homing cancer cells from breast (PyMT-BrM3) and lung (Sv2T3-BrM1) primary origin. To label PDGFRβ expressing cells in this genetic background, mice were treated with 2mg of tamoxifen daily for 5 consecutive days.

extract_protocol:
Mouse endothelial and mural cell populations were sorted into Trizol LS and submitted to the company “GeneWiz from Azenta Life Sciences” for RNA extraction, quality control analysis, library preparation and sequencing. Total RNA was extracted from cells following the Trizol Reagent User Guide and quantified using Qubit 2.0 Fluorometer. Agilent TapeStation 4200  was used to assess RNA integrity. cDNA synthesis and amplification were performed with the SMART-Seq HT Ultra Low Input Kit for Sequencing.
Illumina Nextera XT library preparation kit  was used for sequencing library preparation

treatment_protocol: BrMs and non-tumor samples were processed immediately after resection and single-cell suspensions were subjected to FACS. To isolate the cell populations of interest, we first excluded immune and cancer cells by gating for CD45-CD11B-EPCAM- cells, followed by positive selection with CD31+ and PDGFRβ-tdTom+ markers to isolate endothelial and mural cells respectively.

value: brain

tag: primary origin

value: lung

tag: condition

value: BrM

tag: mouse


title: 201911H_ZRY_PR

city: Changsha

first: Ting

last: Zhong

state: Hunan

address: 139 people's Central Road, Furong District

department: The Second Xiangya Hospital

institute: Central South University

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were mapped to human reference GRCh38 using 10X Genomics Cell Ranger software suite (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)56. Fastq sequence quality filtering and sequencing alignment were performed sequentially using the Cell Ranger pipeline. The gene barcode matrix from all samples was then combined with the R package Seurat 3.0.57 For data normalization, we employed a global-scaling normalization method "LogNormalize" that normalized the feature expression measurements for each cell by the total expression, multiplied this by a scale factor (10,000), and log-transformed the result.
Next, we applied a linear transformation (scaling) that was a standard pre-processing step prior to dimensional reduction techniques. The gene features that exhibited high cell-to-cell variation in the dataset were calculated by function "FindVariableFeatures". We returned 3,000 - 4,000 features per dataset which would be used in downstream analysis. Then, we constructed Principal Component Analysis (PCA) on the scaled variable features data. As in clustering, we performed a K-Nearest-Neighbor (KNN) graph based on the Euclidean distance in PCA space, and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods. We next used modularity optimization technique "Louvain algorithm" to iteratively cluster cells together. To place similar cells together in low-dimensional space, we performed non-linear t-distributed stochastic neighbor embedding (t-SNE) to visualize.
We applied a multi-dataset integration algorithm "Harmony" (https://github.com/immunogenomics/harmony) to corrected batch effect58. In brief, the batch effects were removed by the R package Harmony version 1.0 based on the top 50 PCA components identified. All the analyses presented in this study were done on the Harmony corrected data.
Cluster marker genes were recognized using the "FindAllMarkers" function, and clusters were annotated manually using classical marker genes (Table S2). Monocytes, cDC, NK/NKT, CD4+ T cells, CD8+ T cells, and B cells were isolated from the whole scRNA-seq profile for a second round of re-clustering.
Differential gene expression analysis was carried out in Seurat using the "FindMarkers" function with the Wilcoxon test. The P-values were adjusted by using Bonferroni correction. DEGs were ranked by log2-transformed fold change (log2FC) after being filtered with a maximum adjusted P-value of 0.05. GSEA59 was performed to enrich the biological function information of DEGs. Pathway-specific gene sets were downloaded from the GSEA database (http://www.gsea-msigdb.org/gsea). AUCell analysis was performed to evaluate the pathway activity based on given gene set60. AUCell was ranking-based and used the “AUC” to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell.
We applied Monocle3 to constructed the pseudo temporal trajectory inference61,62. Monocle3 modeled gene expression level based on pseudo-time values to show variation of gene expression over differentiation trajectory.
SCENIC analysis was performed to constructed simultaneous gene regulatory network60. The SCENIC process had the following 3 parts: (1) Identification of potential TF targets based on co-expression by using GENIE3, (2) Use RcisTarget to determine direct targets (regulons), (3) Performed AUCell to score the activity of regulons on single cells.
CellChat63 was utilized to investigate and visualize signaling pathway networks between different immune cells. CellChat took gene expression data as input and combined ligand-receptor pairs and their cofactor interactions to model cell-cell communication.
Data were presented as the mean ± SD or as median (minimum–maximum). Comparisons between two groups were made using unpaired/paired Student’s t-test. One-way ANOVA was performed to compare groups after adjustment for potentially confounding variables, including age, gender, and BMI (collinearity analysis showed no obvious confounding among the factors). All variables were mathematically (Kolmogorov-Smirnov test) assessed for normal distribution. A few parameters were not normally distributed, and we opted for nonparametric testing for these variables (Wilcoxon test or Mann-Whitney U-test). Associations of the frequencies of T cell subsets with other parameters were determined by Pearson correlation. Statistical analyses were performed using SPSS version 25.0 (IBM Corporation, Chicago, IL) and GraphPad Prism software version 9 (GraphPad Software, San Diego, CA). Differences were considered signiﬁcant at a two-tailed P < 0.05.
Assembly: hg38

source_name: venous blood

growth_protocol: Cohort I consisted of 9 T1D patients and 3 healthy donors for single cell sequencing.

extract_protocol:
Cell density and survivability were checked for fresh PBMCs from cohort I by Count Star (Alit life science, Shanghai, China), with cell viability > 90% for each sample.
Single-cell suspensions were transformed to barcoded scRNA-seq libraries using Chromium Single Cell B Chip Kit (10x Genomics, 1000074) and Single-cell 3′ Library and Gel Bead Kit V3(10x Genomics, 1000075). Then, single-cell cDNA synthesis and amplification were generated in a S1000TM Touch Thermal Cycler (Bio Rad).

treatment_protocol: PR was defined according to the mixed meal tolerance test (MMTT)-stimulated C-peptide levels (≥ 300 pmol/L) or the index of insulin dose adjusted HbA1c (IDAA1c) (IDAA1C = HbA1c (%) + 4* daily insulin dose/kg ≤ 9) in the absence of C-peptide values as previously reported.15 In total, three different subgroups were defined according to the PR status: (i) patients with a duration of diabetes less than 3 months and not meeting the definition of PR were classified as "New-onset", (ii) patients currently in the PR stage were grouped into the "PR", (iii) patients whose PR phase ended were defined as "Post-PR". The course of the "PR" patients was 0.85 ± 0.66 months after the onset of remission. The course for the "Post-PR" patients was 11.54 ± 8.47 months after the end of the remission.  All controls underwent oral glucose tolerance test (OGTT) screening, and we collected their medical history to exclude those with a positive family history of diabetes, infection, autoimmune disease, severe liver and kidney damage, or steroid hormone therapy.

value: venous blood

value: PBMC

value: Remission


title: MAVS-polysome-1

value: polysome


title: AMY_methylone_6

value: methylone


title: ZnO_NP_1ug_2H_1

value: MutaMouse

value: ZnO Nanoparticle

value: 1 ug/mL

value: 11 mouse cell lines


title: PGC-ESC BaxKO 2


title: Control-polysome-2

value: Ectopic expression of Vector


title: PGC-ESC BaxKO 1


title: ESC Host 2

source_name: ESC

value: ESC

value: Wildtype


title: SF519_7

description: single-nucleus ATAC-seq, 10x genomics

value: brain (tumour)

value: glioblastoma


title: AMY_methylone_5

value: brain (amygdala)


title: Control-polysome-1


title: 201911H_WYF_PR


title: ESC Host 1


title: STING-free-2

value: Ectopic expression of STING

value: free


title: 201911G_FZH_NC

value: venous blood

value: Healthy control


title: AMY_methylone_4


title: AMY_methylone_3


title: ESC BaxHet

value: BaxHet


title: 201911F_QZ

value: PBMC


title: ESC BaxKO 1

value: BaxKO


title: 201911F_LZY


title: MAVS-free-2

value: Ectopic expression of MAVS


title: AMY_methylone_2

value: methylone


title: AMY_methylone_1


title: STING-free-1


title: CMO Labels

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

description:
CMO library
sample_302_filtered_feature_bc_matrix.h5
sample_303_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
The 10x CellRanger v7.0.0 mkfastq function was run to generate fastq files for both the CMO and gene expression libraries.
cellranger multi was run on the fastq files to align to the mm10-2020-A genome and demultiplex the samples according to their CMO label.
Assembly: mm10
Supplementary files format and content: Hierarchical Data Format 5 (.h5) files of the demultiplexed samples

molecule: other

source_name: tibialis anterior

growth_protocol: C57BL/6 wild-type male and female mice (3-4 months old) were obtained from Jackson Laboratory or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) and were in accordance with the U.S. National Institute of Health (NIH).

extract_protocol:
Animals were humanely euthanized at 7-dpi in accordance with ethics guidelines. TA muscles were pooled from 3 mice according to treatment, then digested into single cell suspensions as described above. Labeling with cell multiplexing oligos (CMOs) (10x Genomics) was performed according to manufacturer’s instructions (Demonstrated Protocol CG000391 Rev B, Protocol 3). Each treatment condition (vehicle and maresin 1) was labeled with a separate CMO tag. Then equal cell numbers from each sample was pooled, stained with 7-AAD, and FACS sorted to remove dead cells and debris.
Post FACS, 8,000 cells were loaded into the 10x Genomics chromium single cell controller and single cells were captured into nanoliter-scale gel bead-in-emulsions (GEMs). cDNAs were prepared using the single cell 3′ Protocol as per manufacturer’s instructions.

treatment_protocol: Mice were anesthetized with 5% isoflurane and maintained at 3% isoflurane. Buprenorphine analgesic was administered at 0.1 mg/kg dose via intraperitoneal injection prior to administering a volumetric muscle loss injury. The surgical area was prepared by removing hair and sterilizing through series of 70% ethanol, and betadine scrubbing. An incision of approximately 5 mm was administered to the skin to expose the tibialis anterior muscle. A full thickness volumetric muscle loss injury was administered using a sterile biopsy punch of 2 mm in diameter to the middle of the muscle followed by closure with sutures. At days 1, 3, and 5 post injury, 20uL of Maresin 1 (100ng in 0.1% EtOH in saline) or vehicle (0.1% EtOH in saline) intramuscularly. Animals were monitored daily.

value: tibialis anterior

value: Vehicle (CMO302) and Maresin 1 (CMO303)

tag: timepoint

value: 7 days post injury

value: wild-type

value: mono-nucleated skeletal muscle cell


title: 201911E_YSQ_V1

value: Remission


title: 201911H_ZJL_PR


title: MAVS-free-1


title: SkM, Vehicle & Maresin, GEX

description:
gene expression library
sample_302_filtered_feature_bc_matrix.h5
sample_303_filtered_feature_bc_matrix.h5


title: 201911D_YSQ_0204

value: New-onset


title: Control-free-2

value: Ectopic expression of Vector


title: AMY_vehicle_6

value: brain (amygdala)

value: vehicle


title: AMY_vehicle_5


title: PS19 Grn-/-_3 hippocampal nuclei

city: New Haven

first: Hideyuki

last: Takahashi

state: Connecticut

address: 295 Congress Ave.  BCMM431

department: Neuroscience

institute: Yale University

data_processing:
Sample demultiplexing was performed using Cell Ranger software (10X Genomics, version 3.0.2).
Alignment was performed using Cell Ranger software (10X Genomics, version 3.0.2).
Gene counting was performed using Cell Ranger software (10X Genomics, version 3.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: TSV files were generated using Cell Ranger software (10X Genomics, version 3.0.2)
Supplementary_files_format_and_content: MTX files were generated using Cell Ranger software (10X Genomics, version 3.0.2)

source_name: Hippocampal nuclei

extract_protocol:
Nuclei were isolated with Nuclei EZ Prep Kit (SIGMA #NUC-101). Frozen hippocampus was homogenized using a glass dounce tissue grinder (SIGMA #D8938) 25 times with pastel A and 25 times with pastel B in 2 mL of ice-cold lysis buffer (Nuclei EZ lysis buffer with Complete Mini EDTA-free and Protector RNase Inhibitor (ROCHE)) and transferred to 15 mL tube with additional 2 mL of ice-cold lysis buffer, and then vortexed and incubated on ice for 5 min. Nuclei were centrifuged at 500 x g for 5 min at 4°C, washed with 4 mL of ice-cold lysis buffer, briefly vortexed and incubated on ice for 5 min. After centrifugation at 500 x g for 5 min at 4°C, the nuclei were washed with 4 mL of ice-cold nuclei suspension buffer (0.5 mg/mL BSA (ThermoFisher #AM2616) and 0.1% Protector RNase inhibitor in DPBS (CORNING #21-031-CV)) once, resuspended in 1 mL of nuclei suspension buffer, filtered through a 35 um cell strainer (FALCON #352235) twice, and counted with trypan blue. The samples were diluted to a final concentration of ~1,000 nuclei per uL and used for subsequent analyses. Nuclei of three samples ((WT, Grn+/−, and Grn−/−) or (PS19, PS19 Grn+/−, and PS19 Grn−/−)) were isolated and submitted for the sequencing at a time and the process was repeated six times to obtain three biological replicates for each genotype
Libraries were prepared using Chromium Single Cell 3” Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocol.

value: Hippocampus

tag: age

value: 7 months old

value: PS19 Grn-/-


title: Control-free-1

value: free


title: 201911D_JRT_0204

value: venous blood

value: PBMC


title: AMY_vehicle_4


title: PS19 Grn-/-_2 hippocampal nuclei


title: 201911C_WZN21115


title: HepG2-HBV-Epi  siRNA CTCF rep 3

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

description: siSCRAM-C

data_processing:
Sequencing reads were aligned to the joint human (HG19) and HBV (HBV.NC_003977.2) using the STAR v2.5.2b aligner
Assembly: human (HG19) and HBV (HBV.NC_003977.2)
Supplementary files format and content: tab limited text file containing raw gene counts for all samples

source_name: Liver

growth_protocol: HepG2-HBV-Epi cells were grown in DMEM with Glutamax supplemented with 10% FBS, 1X NEAA, 100 U/mL penicillin , 100ug/mL streptomycin and 500 µg/mL geneticin. The cells were seeded on collagen (Sigma) coated plates and grown at 5% CO2, 37◦C.

extract_protocol:
RNA was extracted from harvested cells using RNeasy mini kit, QIAGEN following manufacturer's instructions
Libraries were prepared using Tru-Seq Stranded mRNA Library Prep kit for NeoPrep (Illumina, San Diego, USA) using 100 ng total RNA. Libraries were pooled and run as 75-cycle-pair end reads on a NextSeq 550 (Illumina) using a high-output flow cell.

treatment_protocol: HepG2-HBV-Epi cells were transfected with either 25 nM CTCF-targeting or non-targeting control (scramble) smart pool siRNA (Dharmacon) using DharmaFECT4 (Dharmacon) as transfection reagent following the manufacturer’s protocol. The transfection mixture was removed after 24 h and cells were harvested 72 h post siRNA delivery.

value: Liver

tag: cell line

value: Human liver epithelial

value: HBV cccDNA stably transfected, CTCF siRNA transfected

value: CTCF siRNA transfected


title: AMY_vehicle_3


title: 201911B_LSJ


title: HepG2-HBV-Epi  siRNA CTCF rep 1

description: siSCRAM-A


title: AMY_vehicle_2


title: HepG2-HBV-Epi  scrambled siRNA rep 3

description: siCTCF-C

value: HBV cccDNA stably transfected, scrambled siRNA transfected

value: scrambled siRNA transfected


title: 201911A_CYH_201221


title: NC3

first: Yan

last: Zhang

address: Ren Min Zhog street

institute: The Second Xiangya Hospital of Central South University

description: 10x Genomics

data_processing:
Raw FASTQ files were mapped to human reference GRCh38 using 10X Genomics Cell Ranger software suite (v.3.1.0) (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger)45. Fastq sequence quality filtering and sequencing alignment were performed sequentially using the Cell Ranger pipeline. The gene barcode matrix from all samples was then combined with the R package Seurat V3. Table S1 showed the sequencing information for each sample. For quality control, only cells with 200-4500 genes and less than 15% of mitochondrial genes were kept for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cord blood

extract_protocol:
Cord blood samples were collected from all subjects immediately after cesarean delivery. All samples were processed within 4 hours after collection. CBMCs were separated from samples by density gradient centrifugation (Histopaque-1077, Sigma-Aldrich) following manufacture instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: cord blood

tag: disease state

value: healthy


title: PS19 Grn+/-_2 hippocampal nuclei

value: PS19 Grn+/-


title: AMY_vehicle_1

value: brain (amygdala)


title: FC_MDMA_6

source_name: brain (frontal cortex)

value: brain (frontal cortex)

value: MDMA


title: HepG2-HBV-Epi  scrambled siRNA rep 2

description: siCTCF-B


title: NC2

description: 10x Genomics


title: NC1

description: 10x Genomics


title: PS19 Grn+/-_1 hippocampal nuclei

value: Hippocampus

value: 7 months old


title: FC_MDMA_5


title: PS19_3 hippocampal nuclei


title: HepG2-HBV-Epi  scrambled siRNA rep 1

description: siCTCF-A


title: PS19_2 hippocampal nuclei


title: HepG2-HBV-Epi  No siRNA rep 3

description: NoSi-C

value: HBV cccDNA stably transfected


title: FC_MDMA_3


title: GDM3

description: 10x Genomics

value: Gestational Diabetes mellitus (GDM)


title: PS19 Grn-/-_1 hippocampal nuclei

value: PS19 Grn-/-


title: Grn-/-_3 hippomcampal nuclei

value: Grn-/-


title: FC_MDMA_2


title: HepG2-HBV-Epi  siRNA CTCF rep 2

description: siSCRAM-B

value: Liver

value: Human liver epithelial


title: GDM2

description: 10x Genomics

value: PBMC


title: PS19 Grn+/-_3 hippocampal nuclei


title: HepG2-HBV-Epi  No siRNA rep 2

description: NoSi-B


title: HepG2-HBV-Epi  No siRNA rep 1

description: NoSi-A


title: Grn-/-_2 hippomcampal nuclei


title: FC_MDMA_1


title: GDM1

description: 10x Genomics


title: FC_methylone_6

value: methylone


title: Grn-/-_1 hippomcampal nuclei


title: Ded_L83

city: Hong Kong

first: Zezhuo

last: Su

address: No. 21 Sasson Rd, Pokfulam

institute: The University of Hong Kong

description: chondrogenic tumor

data_processing:
Raw reads were processed using the standard CellRanger (v3.0.0) pipline.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix from CellRanger output

source_name: primary human tumor

extract_protocol:
Primary human tissues were digested by a cocktail of hyaluronidase, dispase II, and collagenase II to generate single-cell suspensions.
Single-cell cDNA libraries were prepared using 10x Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit.
The library was sequenced by Illumina NovaSeq 6000 using 150 nt paired-end sequencing with 100GB raw reads output per sample.

value: tumor

tag: tumor type

value: dedifferentiated chondrosarcoma

tag: tumor grade

value: high

tag: anatomical site

tag: patient gender

value: M

tag: patient age

value: 72 years old


title: FC_MDMA4

value: brain (frontal cortex)

tag: treatment


title: PLC/PRF5 siCTCF rep 3

library_source: genomic

data_processing:
Reads were trimmed using Trimmomatic v0.39 with the parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50 .
Trimmed reads were aligned to the joint human (HG19) and HBV (HBV.NC_003977.2) using the BWA v0.7.17 aligner.
Peaks were called within the aligned reads using MACS2 v2.2.7.1 with the parameters --keep-dup=auto.
Assembly: the joint human (HG19) and HBV (HBV.NC_003977.2)
Supplementary files format and content: bedGraph files were generated using MACS2 v2.2.7.1; scores represent read coverage
Supplementary files format and content: bed files were generated using MACS2 v2.2.7.1; genomic coordinates represent peak summits

growth_protocol: HepG2-hNTCP and PLC/PRF5 cells were grown in DMEM with Glutamax supplemented with 10% FBS, 1X NEAA and 100 U/mL penicillin and 100ug/mL streptomycin. The cells were seeded on collagen-coated plates and grown at 5% CO2, 37◦C.

extract_protocol:
100,000 cells were lysed, and total DNA tagmented and purified using the ATAC-seq kit (Active Motif) in accordance with the manufacturer’s protocol.
Libraries were generated using ATAC-seq kit (Active Motif) and sequenced using Illumina NextSeq 550 paired end sequencing.

treatment_protocol:
HBV wild type and CTCF BS1/2m viruses were generated by transfecting HepG2-hNTCP cells with either pUC57-HBV1.3 D3 WT or CTCF BS1/2m plasmid and cells maintained in media supplemented with 2.5% DMSO and 2.5% FBS. The supernatants were collected every four days for three weeks. The viral particles were precipitated with 10% PEG8000 overnight and separated by centrifugation at 4600 rpm for 1 h, at 4°C. The supernatant was discarded, and the pellet resuspended in DMEM to reach a 200X concentration.
HepG2-hNTCP cells were seeded on collagen-coated plates and infected with PEG precipitated WT or CTCF BS1/2m virus in the presence of 4% PEG8000. The viral inoculum was removed after 16 h, the cells extensively washed with PBS and maintained in the presence or absence of 2.5% DMSO. The supernatants were collected, and cells harvested at 3- and 6- days post infection.
PLC/PRF5 cells were transfected with either 25 nM CTCF-targeting or non-targeting control (scramble) smart pool siRNA (Dharmacon) using DharmaFECT4 (Dharmacon) as transfection reagent following the manufacturer’s protocol. The transfection mixture was removed after 24 h and cells were harvested 72 h post siRNA delivery.

value: Alexander cell

value: Wildtype

value: CTCF knockdown


title: PLC/PRF5 siCTCF rep 2


title: GDM4

description: 10x Genomics

value: cord blood


title: FC_methylone_5


title: PLC/PRF5 siCTCF rep 1


title: Grn+/-_3 hippomcampal nuclei

value: Hippocampus

tag: strain

value: 7 months old

value: Grn+/-


title: Low_L81

description: chondrogenic tumor

tag: tissue

value: conventional central chondrosarcoma

value: low

value: chest

value: 51 years old


title: FC_methylone_4

value: methylone


title: Grn+/-_2 hippomcampal nuclei


title: Med_L80

description: chondrogenic tumor

value: tumor

value: conventional peripheral chondrosarcoma

value: medium

value: pelvis

value: F

value: 35 years old


title: PS19_1 hippocampal nuclei


title: PLC/PRF5 siSCR rep 3

value: Liver

tag: cell type

value: Alexander cell

value: Wildtype

value: scrambled siRNA transfected


title: Grn+/-_1 hippomcampal nuclei

value: Hippocampus

value: 7 months old

tag: genotype


title: PLC/PRF5 siSCR rep 2


title: FF_L75

description: fetal femur

source_name: human fetal femur

value: femur

value: 18 weeks old


title: FC_methylone_3

value: brain (frontal cortex)


title: Med_L63

description: chondrogenic tumor

value: conventional central chondrosarcoma

value: M

value: 50 years old


title: WT_3 hippomcampal nuclei

value: WT


title: PLC/PRF5 siSCR rep 1


title: WT_2 hippomcampal nuclei


title: FC_methylone_1

value: methylone


title: FC_methylone_2


title: Ben_L49

description: chondrogenic tumor

value: tumor

value: enchondroma

value: benign

value: finger

value: 38 years old


title: WT_1 hippomcampal nuclei


title: High_L44

description: chondrogenic tumor

value: high

value: 68 years old


title: HepG2-hNTCP CTCF BS1/2m rep3

value: Liver

value: Human liver epithelial

value: HBV 1.3 D3 plasmid with CTCF binding sites 1 and 2 mutated transfected


title: FC_vehicle_6

value: vehicle


title: HepG2-hNTCP CTCF BS1/2m rep2


title: FC_vehicle_5

value: brain (frontal cortex)


title: HepG2-hNTCP CTCF BS1/2m rep1


title: PBMC, biological replicate 4, scRNAseq

city: Uppsala

first: Robert

last: Söderlund

address: Ulls väg 2B

country: Sweden

institute: National veterinary institute (SVA)

description: 10x Genomics

data_processing:
Read counting of raw data using Cell Ranger (1.2.0) standard workflow (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Removal of doublets using Doublet Detection (https://github.com/JonathanShor/DoubletDetection)
Filtering of data to remove  RBCs and broken cells, removal of cells with >5% HB genes, removal of cells with >20 % MT genes, removal of cells with unique feature count < 300, removal of features present in < 3 cells
Normalization (scttrandform) and integration of data using Seurat (https://satijalab.org/seurat/articles/integration_introduction.html)
Guided clustering in Seurat and DE-analysis (https://satijalab.org/seurat/articles/pbmc3k_tutorial.html)
GO-term enrichment on DE-markers using gprofiler2 (https://biit.cs.ut.ee/gprofiler/page/r)
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Excel files (.xlsx) with differentially expressed genes and GO-term enrichment of said genes per cluster

organism: Gallus gallus

source_name: Blood

extract_protocol:
Blood samples were taken from four healthy adult female birds (24-week-old laying hen hybrids, Bovans Robust) kept in a clean but not sterile environment as blood donors at SVA. The blood was collected using regular blood sampling from the jugular vein into sample tubes with heparin as an anticoagulant.   In order to remove RBCs and enrich the leukocytes in the samples, leukocytes were separated from RBCs using gradient centrifugation on Ficoll (GE Healthcare) according to established protocols. Chicken platelets (thrombocytes) are nucleated and, therefore, contain mRNA. They may consequently constitute a considerable amount of the cells obtained after gradient centrifugation on Ficoll (20-70%). Thus, the proportion of platelets in the samples was reduced to obtain better sequencing of rarer populations of white blood cells. For this immunomagnetic cell separation with EasySep PE Selection Kit (StemCell Technologies, protocol no. 28898), methodology was used according to protocols previously used with chicken white blood cells at SVA (Wattrang et al. 2019). This was done using an antibody to integrin CD41/61 (OriGene) that is expressed exclusively on platelets in chicken blood cells (Lacoste-Eleaume et al. 1994). In addition to sequencing, the purified cell preparations were also analysed by immunofluorescence and flow cytometry to determine the proportion of various known types of leukocytes. (Wattrang et al. 2020).
Sequencing libraries were prepared from 5000 cells using  the Chromium Next GEM Single Cell 3’ Reagent kit v3.1  with dual-index (cat# 1000268/269/120/127/1000215, 10x  Genomics), according to the manufacturer’ protocol  (CG000315 (Dual Index) Chromium Next GEM Single Cell  3’ Reagent Kit User Guide, v3.1 chemistry, 10x Genomics).

value: Blood

value: PBMC

value: Bovans Robust

value: 24 week


title: FC_vehicle_4


title: High_L31

description: chondrogenic tumor

value: conventional central chondrosarcoma

value: thigh

value: M

value: 52 years old


title: FC_vehicle_3


title: Low_L28

description: chondrogenic tumor

value: tumor

value: low

value: os calcis

value: 16 years old


title: HepG2-hNTCP  WT rep 2

value: Liver

value: HBV 1.3 D3 plasmid transfected


title: PBMC, biological replicate 2, scRNAseq

description: 10x Genomics


title: PBMC, biological replicate 3, scRNAseq

description: 10x Genomics


title: Low_L07

description: chondrogenic tumor

value: femur

value: F

value: 76 years old


title: Biotin-MOTS-c

type: protein

city: Xi'an

first: Yue

last: Zhai

address: #169, Changle West Road

institute: Fourth Military Medical University

hyb_protocol: Briefly, proteome microarrays were blocked with blocking buffer (5% BSA in 0.1% Tween 20, PBST) for 1 h at room temperature with gentle agitation. Biotin-MOTS-c were diluted to in PBST and incubated on proteome microarray at room temperature for 1 h. After washing with PBST three times, microarray was incubated with 0.1% Cy5-Streptavidn solution for 20 min at room temperature in the dark, followed by three 5-min washes in PBST.

scan_protocol: The microarray was spun dry at 1000 rpm for 2 min and scanned with GenePixTM 4000B (Axon Instruments, CA).

data_processing: GenePixTM Pro v6.0 was used for data analysis. The median fluorescence signal at each site (F635_Median) was divided by the background (B635_Median) for data analysis, that is, original signal strength (I) = F635_Median/B635_Median. The median and SD of I were calculated to obtain the corrected data Z-Score (corrected signal strength) for each site.

label: biotin

molecule: protein

source_name: purified protein

label_protocol: labeled with biotin,

extract_protocol: Biotin-MOTS-c was incubated with human proteome microarray to screen the positive signals

tag: molecular weight


title: FC_vehicle_1

value: brain (frontal cortex)

value: vehicle


title: HepG2-hNTCP  WT rep 3

value: Human liver epithelial


title: PBMC, biological replicate 1, scRNAseq

description: 10x Genomics

value: Blood

value: PBMC

value: Bovans Robust

value: 24 week


title: FC_vehicle_2


title: HepG2-hNTCP  WT rep 1


title: ENL-AID ctrl RPB1

status: Public on Jan 17 2024

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

institute: Shenzhen University

data_processing:
Raw reads were aligned to hg19 using bwa. The sam files were converted to bam with samtools.
MACS2 was used to call peaks on the bam files with signals from input DNA as reference.
Assembly: hg19
Supplementary files format and content: Bigwig files were generated using bamCoverage from Deeptools.

source_name: ENL-AID ctrl RPB1

growth_protocol: HCT116 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum. For selection of AID clones, HCT116 cells transfected with indicated plasmids were cultured with 2 ug/ml puromycin and 3 ug/ml blasticidin.

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature (RT) with gentle swirling, and crosslinking was stopped by adding glycine to a final concentration of 0.125 M and incubating at RT for 5 min. Cells were harvested and an aliquot of 1 × 107 cells were used per ChIP reaction. Each cell aliquot was resuspended in 0.5 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS, pH 7.4), and chromatin was fragmented on ice to 200 to 500 bp in size with 5 pulses of 30 sec at 50% power with a Sonics VibraCell sonicator. 5-10 μg primary antibodies or control IgG were pre-conjugated with Protein G magnetic beads (Pierce) at 4°C overnight. 1% of sheared chromatin was saved as input, and the rest was incubated with pre-conjugated antibody on a rotator at 4°C overnight. The beads were washed 5 times with LiCl wash buffer (0.1 M Tris, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate, pH 7.5) followed by a single wash with TE buffer (10 mM Tris-HCl, 0.1 mM Na2EDTA, pH 7.5). The beads were then resuspended in 200 μL IP elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65°C for 1 hour in a heat block with vortexing. The supernant was collected and together with input was incubated at 65°C for 16 hours to reverse cross-links. DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 50 μL EB.
ChIP’s DNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. Fragments were amplified by PCR and PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit.

treatment_protocol: The HCT116 ENL-AID cells was treated with or without 500 um auxin (IAA) for 3 hours and an additional group of IAA treated cells were subjected to PBS washout and subsequent culture in normal medieum for another 48 hours . The resulting cells were harvested for analysis as described below.

tag: cell origin

value: HCT116 colon cancer cells

tag: antibody


title: ENL-AID ctrl BRD4

source_name: ENL-AID ctrl BRD4


title: ENL-AID IAA BRD4

source_name: ENL-AID IAA BRD4


title: ENL-AID dBET1 rep2

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on DNBseq G400 platform. Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the pair-end 150bp sequence tags from DNBseq G400 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
The bowtie2 was used to generate the bam file of each sample from fastq with following parameters: -3 5 --local -x hg19 -U SE_clean.fq
htseq-count was used to get the count of each gene from bam using -r name -f bam bamfile gencode.v19.annotation.gtf
edgeR was used to identify the differentially expressed genes between groups.
Assembly: hg19
Supplementary files format and content: Abaundance count file for each sample.

source_name: HCT116 colon cancer cells

extract_protocol:
Total RNA was extracted from  cells using Trizol reagent from Thermofisher according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: The ENL-AID HCT116 cells were treated with or without 5μm dBET1 for 6 hours . The resulting cells were harvested for analysis as described below.

value: colon cancer


title: ENL-AID dBET1 rep1


title: ENL-AID DMSO rep2


title: Cos_L43

description: chondroblastic osteosarcoma

value: tumor

value: chondroblastic osteosarcoma

value: high

value: M

value: 39 years old


title: ENL-AID IAA rep1

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on DNBseq G400 platform. Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the pair-end 150bp sequence tags from DNBseq G400 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
The bowtie2 was used to generate the bam file of each sample from fastq with following parameters: -3 5 --local -x hg19 -U SE_clean.fq
htseq-count was used to get the count of each gene from bam using -r name -f bam bamfile gencode.v19.annotation.gtf
edgeR was used to identify the differentially expressed genes between groups.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM for each sample.

value: colon cancer cells

tag: tag

value: IAA treated


title: ENL-AID ctrl rep1

value: control


title: ENL-AID IAA rep2


title: ENL-AID ctrl SSRP1


title: ENL-AID ctrl rep2


title: ENL-AID IAA SSRP1


title: ENL-AID IAA washout rep1

value: IAA treated + PBS washout


title: ENL-AID IAA SPT16


title: ENL-AID ctrl SPT16


title: ENL-AID IAA H3K27ac


title: ENL-AID ctrl H3K27ac


title: ENL-AID IAA washout H3K27ac


title: ENL-AID IAA washout input


title: ENL-AID IAA input


title: ENL-AID ctrl input


title: ENL-AID IAA RPB1

source_name: ENL-AID IAA RPB1


title: Hep3B cells

city: Nanning

first: liao

last: zhouxiang

address: Shuangyong road #22

institute: Guangxi Medical University

data_processing:
Base calling and data QC were performed by DNBSEQ-G400 built-in control software.
After base calling, tags were processed to remove those Q<30, be contaminanted with 5' primer, without 3' primer or insertion, with poly A tail, or shorter than 18nt, to keep only clean tags remaining.
By using Bowtie2 (parameters: -D 15 -R 2 -N 0 -L 16 -i S,1,1.15), clean tags were aligned to mirbase 22.1 and Rfam12.2, with remaining tags aligned to human genome GRCh38.p12 to predict novel miRNA with miRDeep2.
UMI_tools was employed to reduce the quantitative bias introduced by PCR and calculate the accurate quantitative of sRNAs.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include tag count for each Sample

growth_protocol: HL7702, Huh7, and HepG2 were cultured in T25 culture flask with DMEM high glucose medium (Gibco, USA) supplied with 10% FBS (Gibco, New Zealand). Hep3B was cultured in T25 culture flask with MEM (Gibco, USA) supplied with 10% FBS (Gibco, New Zealand). All cell cultures grow at 37℃ with 5% CO2.

extract_protocol:
After cell confluence reaches 60%, discard the medium and add 1 mL of TRIzol reagent (Invitrogen, USA) to each sample. Total RNAs were extracted following the manufacturer's protocols.
RNA libraries for RNA-seq were prepared using MGIEasy Small RNA Library Prep Kit following manufacturer's protocols.

value: Liver

value: hepatocellular carcinoma


title: Huh7 cells


title: HepG2 cells


title: HL7702 cells

value: hepatocyte


title: ENL-AID DMSO rep1


title: npe08

city: Dresden

first: Mark

last: Boltengagen

state: Saxony

address: Fiedlerstraße 42

department: Physiological Chemistry

country: Germany

institute: Dresden Technical University

description: S288C_pFMP233_(25mer 601 WT); methylated by M.SssI

data_processing:
Basecalling and demultiplexing were done using ONT guppy software by Oxford Nanopore Technologies (version 5.0.16).
Resulting fastq files were split per barcode by guppy_barcoder_out using the following parameters: –barcode_kits "EXP-NBD104 EXP-NBD114" --device auto.
FASTQ files were merged into a single file for each barcode.
Demultiplexed FASTQ files for each barcode were mapped to the SacCer3 (R64-1-1) reference genome by minimap2 (version 2.24), using minimap2 -ax map-ont.
Resulting alignments were further filtered, sorted and indexed by Samtools (version 1.9) using the following parameters: samtools view –F 2052 –q 30 –b –S; samtools sort –o; samtools index –b.
CpG methylation for each barcode were called by Nanopolish (version 0.13.2), using default parameters for ‘cpg’ motif with DNA sequences in FASTQ files, mapping results in BAM files and the same genome reference as was used for the sequence alignment as inputs.
Methylation states for each CpG, derived by Nanopolish, were defined by log likelihood using the following thresholds: methylated (≥ 2.5), unmethylated (≤ -2.5) and ambiguous (between -2.5 and 2.5).
Methylation rate was defined as a ratio of number of methylated sites per read to the total number of either methylated or unmethylated sites in the read. Reads longer than 1000 bp and containing methylation rates between 0.1 and 0.9 were selected for the further analysis in R.
Assembly: SacCer3
Library strategy: Fiber-Seq

organism: Saccharomyces cerevisiae

source_name: haploid cells

growth_protocol: WT yeast strains were grown at 30°C in YPAD.

extract_protocol:
Genomic DNA was purified by Phenol:Chloroform:Isoamylalcohol approach.
Library preparation of isolated DNA was performed with the SQK-LSK109 ligation sequencing kit (Oxford Nanopore Technologies) according the manufacturer’s protocol. For multiplexing up to 24 samples, native barcode expansion kits (EXP-NBD104/114) were used. Libraries were loaded onto MinION R9.4.1 flow cells (Oxford Nanopore Technologies) and run for 72 hrs using MinKNOW software (version 20.06.4) with disabled basecalling, barcoding and alignment. Output was saved in FAST5 format.

treatment_protocol: 25 µg of DNA, 20 µl RNase A of a 10 mg/ml stock, 10 µl M.SssI methyltransferase (20.000 U/ml), 601-nucleosome arrays (75-100 ng DNA) as an internal spike-in and cold 1x M.SssI buffer to a final volume of 397.5 µl was mixed and samples were incubated for 30-180 minutes.

value: haploid cells

tag: treatment time


title: npd09

tag: cell line


title: npd08


title: npd10


title: ENL-AID IAA washout rep2


title: PBMCs from animal 74 at timepoint 8 wpi

city: Stanford

first: Aaron

middle: James

last: Wilk

state: California

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

data_processing:
mRNA reads in read 2 FASTQ files tagged with cell barcode and UMI from read 1 file with dropTag (dropEst)
Tagged reads aligned with STAR using M nemestrina genome build 1.0 and gft 1.0.98 with added viral genome sequences of SIVMneCL8 and SIVMne170
Count matrices built from BAM files using dropEst
Assembly: M nemestrina genome build 1.0 and gft 1.0.98 with added viral genome sequences of SIVMneCL8 and SIVMne170
Supplementary files format and content: .rds files containing exonic, intronic, and spanning count matrices

organism: Macaca nemestrina

source_name: Peripheral blood mononuclear cells

extract_protocol:
Immediately after Ficoll separation, 50,000 PBMCs were resuspended in RPMI + 10% FCS at a concentration of 75,000 cells/mL. 200 μL of this cell suspension (15,000 cells) was then loaded onto Seq-Well arrays pre-loaded with mRNA capture beads (ChemGenes). Following four washes with DPBS to remove serum, the arrays were sealed with a polycarbonate membrane (pore size of 0.01 µm) for 30 minutes at 37°C and then frozen at -80°C for no less than 24 hours and no more than 14 days to allow batching of samples processed at irregular hours. Next, arrays were thawed, cells lysed, transcripts hybridized to the mRNA capture beads, and beads recovered from the arrays and pooled for downstream processing.
Library preparation was performed with a Nextera XT DNA library preparation kit (Illumina FC-131-1096) with 1 ng of pooled library using dual-index primers. Tagmented and amplified libraries were again purified by Agencourt AMPure XP beads with a 0.6x volume wash followed by a 1.0x volume wash, and quality and concentration determined by Fragment Analysis. Libraries between 400-1000bp with no primer peaks were considered successful and pooled for sequencing. Sequencing was performed on a NovaSeq S2 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with read 1 beginning from a custom read 1 primer11 containing a 12bp cell barcode and an 8 bp unique molecular identifier (UMI), and with read 2 containing 50bp of mRNA sequence.

value: PBMCs

tag: timepoint

value: 8 wpi

tag: infection


title: PBMCs from animal 74 at timepoint pre-infection

value: pre-infection


title: npd07


title: PBMCs from animal 74 at timepoint 2 wpi

value: 2 wpi


title: PBMCs from animal 74 at timepoint 3 wpi

value: 3 wpi


title: PBMCs from animal 74 at timepoint 20 wpi

value: 20 wpi


title: PBMCs from animal 61 at timepoint pre-infection


title: PBMCs from animal 74 at timepoint 1 wpi

value: 1 wpi


title: PBMCs from animal 61 at timepoint 8 wpi


title: PBMCs from animal 61 at timepoint 3 wpi


title: PBMCs from animal 61 at timepoint 4 wpi

value: 4 wpi


title: PBMCs from animal 61 at timepoint 20 wpi


title: PBMCs from animal 61 at timepoint 1 wpi


title: PBMCs from animal 55 at timepoint 6 wpi

value: 6 wpi


title: PBMCs from animal 61 at timepoint 12 wpi

value: 12 wpi


title: PBMCs from animal 55 at timepoint 8 wpi


title: PBMCs from animal 55 at timepoint pre-infection


title: PBMCs from animal 61 at timepoint 2 wpi


title: PBMCs from animal 61 at timepoint 6 wpi


title: PBMCs from animal 55 at timepoint 3 wpi


title: PBMCs from animal 55 at timepoint 20 wpi


title: PBMCs from animal 55 at timepoint 2 wpi


title: PBMCs from animal 55 at timepoint 1 wpi


title: PBMCs from animal 55 at timepoint 12 wpi


title: PBMCs from animal 33 at timepoint pre-infection


title: PBMCs from animal 33 at timepoint 6 wpi


title: PBMCs from animal 33 at timepoint 8 wpi


title: PBMCs from animal 74 at timepoint 12 wpi


title: PBMCs from animal 74 at timepoint 4 wpi


title: PBMCs from animal 33 at timepoint 4 wpi


title: PBMCs from animal 33 at timepoint 20 wpi


title: PBMCs from animal 33 at timepoint 3 wpi


title: PBMCs from animal 33 at timepoint 2 wpi


title: PBMCs from animal 33 at timepoint 12 wpi


title: PBMCs from animal 33 at timepoint 1 wpi -2

description: This sample is a repeated analysis of sample 33_1 from a different aliquot of the same blood draw. Both are included in the final count matrices


title: PBMCs from animal 33 at timepoint 1 wpi


title: PBMCs from animal 55 at timepoint 4 wpi


title: AAU_B_II

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

institute: Marine Biological Association of the UK

data_processing:
The De-multiplexing fastQ  files were filtering high-quality sequencing reads, and the adapter contamination was removed using fastp an ultra-fast all-in-one FASTQ preprocessor
The quality of the reads was verified using FastQC
Processed reads from each sample were mapped to the respective genome and gene models (indexed bowtie2) by using STAR
The number of reads mapping to the respective gene model were extracted from STAR output using the featureCounts tool
Assembly: Nematostella vectensis (ASM20922v1); Aurelia aurita (GCA_004194395.1);  Acropora tenuis  ( GCA_014633955.1); Acropora millepora (GCF_013753865.1)
Supplementary files format and content: Tab-delimited text files include read counts

organism: Aurelia aurita

source_name: larval body tissue

growth_protocol: Nematostella: Polyps were grown in 16 ‰ artificial seawater at 18°C in the dark and fed with freshly hatched Artemia nauplii. Aurelia aurita: Ephyras were collected using a plankton net in the vicinity of Plymouth Sound, UK and cultured in seawater at 18°C in a 12:12 light and dark cycle. The jellyfish were fed twice a day with freshly hatched Artemia nauplii. Acropora millepora and Acropora tenuis: The corals were cultured in ex-situ. During the annual spawning, the embryos were collected after fertilisation. The larvae are maintained in artificial seawater and collected for experimentation at the planula stage.

extract_protocol:
For RNA isolation, due to the sheer size, samples collected from multiple batches were combined to acquire an adequate amount of RNA for sequencing. Total RNA was isolated using the TRI Reagent® according to the manufacturer’s protocol. RNA quality was assessed using Agilent RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer (Agilent, USA), and samples with RNA integrity number ≥ 8.0 were used for sequencing.
The CORALL RNA-Seq Library Prep Kit (Lexogen GmbH) was used for library preparation. Before sequencing, the libraries were pre-assessed by Agilent High Sensitivity DNA Kit (Agilent, USA) and quantified using Qubit™ 1X dsDNA HS Assay Kit (Invitrogen™).
The sequencing was outsourced (GENEWIZ Illumina NovaSeq™ 2x150 bp sequencing), generating 15 million paired-end reads per replicate.

treatment_protocol: To separate the apical region from the rest of the larval body, we performed microdissection on Nematostella, Aurelia aurita, Acropora millepora and Acropora tenuis larvae as described in our previous study in Nematostella. Apical tissue containing the apical organ was isolated using 34 gauge needles under a stereomicroscope with 10X magnification. Motile larvae were placed into a fresh plastic Petri dish filled with Nematostella medium or filtered seawater. The larvae tend to adhere briefly to the bottom of a new plastic Petri dish, allowing enough time to separate the apical tissue by cutting. Each sample was pooled from a minimum of 100 individual larvae. For each planula prior to dissection, the frontal region is identified by means of the direction of larvae swimming. The samples were carefully collected using glass Pasteur pipettes, the excess medium was removed, and the samples were snap-frozen in liquid nitrogen and stored at -80°C until further processing.

value: larval body tissue

tag: developmental stage

value: planula

value: wild type (WT)


title: AAU_B_III


title: AAU_AO_III

source_name: larval aboral tissue

value: larval aboral tissue


title: AAU_AO_II


title: AAU_AO_I


title: AAU_B_I


title: AMI_B_II

organism: Acropora millepora


title: AMI_AO_I


title: AMI_B_I


title: HeLa_sgKDM5C, input, ChIP-Rx

city: Wuhan

first: Yulong

last: Qiang

address: 185 Donghu Road

institute: Wuhan University

data_processing:
Basecalls were performed using fastq Novaseq output.
ChIP-seq reads were trimmed with fastp.
ChIP-seq reads were aligned to the hg38 and mm10 genome using Bowtie2 (v2.4.2).
Peaks were called uing MACS v2.2.7.1 (q-value takes default setting).
BigWig files were obtained by deepTools (v3.5.1).
Assembly: Heatmap and metaplot files were made by plotHeatmap and plotProfile of deepTools (v3.5.1).
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: HeLa

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed in 1% formaldehyde for 10min and then quenched with 0.125M glycine for 10min at room temperature with rotation. Cell pellet was lysed with cell lysis buffer (10mM Tris, pH8.0; 10mM NaCl; 0.2% NP-40; protease inhibitor) on ice for 10min and chromatin DNA was sonicated to 200-500bp average in size. Chromatin fragments lysates were immune-precipitated with primary antibodies at 4°C overnight and then conjugated with protein A/G Beads 4FF (Smart-lifesciences, SA032500). Bound fractions were washed and eluted from agarose beads. ChIP and input samples were de-crosslinked at 55°C overnight.
ChIP-seq libraries were prepared using the NEBNext ultra II DNA library prep kit for Illumina.

value: HeLa

value: Cervical cancer cells

tag: chip antibody

value: none (input)


title: HeLa_Parental, input, ChIP-Rx

value: Parental


title: HeLa_sgKDM5C, BRD4, ChIP-Rx


title: HeLa_Parental, BRD4, ChIP-Rx


title: WT rep3

city: Suzhou

first: Fan

address: 100 Chongwen Road

institute: Suzhou Institute of Systems Medicine

data_processing:
The sequencing data were analyzed by CLC Genomic Workbench 23 (Qiagen).
Specifically, the adapter sequences on reads were trimmed using the 'Trim Reads' program with default parameters.
Then, the trimmed reads were mapped to the hg38 reference genome using 'RNA-Seq Analysis' program.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

extract_protocol:
The cell samples were lysed in TRlzol and extract total RNA for RNA-seq
rRNAs were removed by Vazyme Ribo-off Globin & rRNA Depletion Kit (Human/Mouse/Rat) (Cat. No: Vazyme N408), and the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Cat. No: Vazyme NR604) was used for library construction following the manufacturer's instructions with the following modifications: 1. The secondary structure of RNA was opened at 80°C for 2 minutes, but the RNAs were not fragmented. 2. The library was conducted with a broader range (200~1000bp) selection using Agencourt AMPure XP Reagent (Cat. No: Beckman A63881). 3. Gel electrophoresis was performed to obtain a library within the range of 300~400bp.

value: adenocarcinomic human alveolar basal epithelial cells

value: wild type


title: WT rep2


title: WT rep1


title: RNVU1-18-/- rep3

value: RNVU1-18 knock out


title: RNVU1-18-/- rep2


title: HepG2 cells-Ctrl-3

city: nanjing

first: ying

last: zheng

address: 639 Longmian Avenue, Jiangning District

institute: China pharmaceutical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: hg38
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

growth_protocol: HepG2 cells were treated with DMSO or 20μM lefamulin for 48 hours

extract_protocol:
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.

treatment_protocol: HepG2 cells, rapidly frozen in liquid nitrogen, were stored at -80°C for subsequent RNA extraction.

value: DMSO


title: HepG2 cells-Lef-3

value: Lefamulin


title: AMI_AO_II


title: HepG2 cells-Ctrl-2


title: HepG2 cells-Ctrl-1


title: HepG2 cells-Lef-2


title: T24, H3K27Me3, ChIP, Combination

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
Nextflow (version 22.10.5) nfcore/chipseq pipeline was used for ChIP-seq analysis
ChIP-seq reads were aligned to the human genome (hg38) using nf-core/chip-seq pipeline
The parameters used to run nfcore/chip seq were as follows: genome=GRCh38, macs_gsize = 2913022398, and p-value cutoff = 0.00001
Peaks were called using MACS v2.1.0 with the significance p<10−5
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak(.txt), featureCounts(.txt)

growth_protocol: T24 cells were maintained in DMEM (Gibco) medium with non-essential amino acids, L-glutamine, and 4.5g/L D-glucose supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Thermo Fisher), in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Covaris sonicator.
ChIP-seq libraries were prepared using the TruSeq DNA Sample prep Kit. TruSeq ChIP Sample Preparation Guide 15023092 Rev. B protocol was followed. 50 ng of DNA was used as starting material for samples. Libraries were validated using the Agilent High Sensitivity DNA Kit.
TruSeq ChIP-seq library

treatment_protocol: T24 were treated with DMSO (Vehicle Control); or GSK-126 (Selleck Chemicals) (5 μM for 72 h); or fenretinide (5 μM for 72 h) (Merck) or drug combination (5 μM fenretinide and GSK-126 for 72 h)

value: Human Urinary Bladder Cancer

value: Combination


title: T24, H3K27Me3, ChIP, Fenretinide

value: Fenretinide


title: T24, Input, Fenretinide


title: T24, Input, Combination


title: T24, H3K27Me3, ChIP, GSK-126


title: WJ-MSC, 3R4F 5%,rep1

city: Seoul

first: Kyung-rok

last: Yu

address: 1, Gwanak-ro, Gwanak-gu, Seoul

country: South Korea

institute: Seoul National University

data_processing:
removing the adapter sequence and filtering the low-quality reads using an in-house script
HISAT2
featureCounts
edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text file with normal count for each sample

source_name: wharton's jelly

growth_protocol: Wharton's jelly derived mesenchymal stem cells are cultured in DMEM+10% FBS+1x Antibiotic-Antimycotic + 25ng/mL EGF + 50ng/mL BFGF

extract_protocol:
Trizol
Libraries were generated using the Illumina TruSeq strand mRNA sample preparation kit (Illumina, San Diego, CA, USA) and sequenced on a NovaSeq 6000 (2 x 150 paired end sequencing, Illumina) according to the manufacturer's protocol.

value: wharton's jelly

value: WJ-MSC

value: Mesenchymal Stem cell

value: 3R4F 5percent


title: WJ-MSC,control,rep1


title: T24, Input, GSK-126


title: RNVU1-18-/- rep1


title: T24, H3K27Me3, ChIP, Vehicle Control


title: WJ-MSC,control,rep2


title: T24, Input, Vehicle Control


title: I-Res Female [TRA00195186]

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
RNA-seq raw reads are 100-bp reversely stranded paired-end reads. The reads are trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp. The count table is generated by aligning reads to the human transcriptome (Ensembl version 98) using kallisto and converting transcript counts to gene counts using tximport.
Assembly: Human transcriptome (Ensembl version 98)
Supplementary files format and content: CSV of counts

source_name: I-Res Female

extract_protocol:
Total RNA from all the cell types was isolated using TRIzol (ThermoFisher) following the chloroform/isopropanol/ethanol extraction method.
RNA libraries for RNA-seq were prepared using The KAPA mRNA HyperPrep kit for Illumina sequencing following manufacturer's protocols.

value: iPSCs-derived myoblasts (iMyos)

value: 928 I-Res Female

tag: gender

value: female

value: insulin resistant (I-Res)


title: I-Sen Female [TRA00195182]

source_name: I-Sen Female

value: 516 I-Sen Female

value: insulin sensitive (I-Sen)


title: I-Sen Female [TRA00195183]

value: 345 I-Sen Female


title: HepG2 cells-Lef-1


title: I-Res Female [TRA00195189]

value: 60 I-Res Female


title: I-Res Female [TRA00195187]

value: 358 I-Res Female


title: I-Sen Female [TRA00195184]

value: 845 I-Sen Female


title: I-Sen Female [TRA00195185]

value: 107 I-Sen Female


title: WJ-MSC, 3R4F 5%,rep2


title: I-Res Male [TRA00195181]

source_name: I-Res Male

value: 961 I-Res Male

value: male


title: I-Res Male [TRA00195179]

value: 496 I-Res Male


title: I-Sen Male [TRA00195176]

source_name: I-Sen Male

value: 864 I-Sen Male


title: I-Res Male [TRA00195180]

value: 551 I-Res Male


title: I-Res Male [TRA00195178]

value: 998 I-Res Male


title: I-Sen Male [TRA00195175]

value: iPSCs-derived myoblasts (iMyos)

value: 411 I-Sen Male


title: I-Sen Male [TRA00195174]

value: 410 I-Sen Male


title: HUVECs treatment with intersectant hypoxia [IH3]

city: Jinan

first: guanghao

last: zhang

address: NO.247 Beiyuan street

institute: The second hospital of Shandong University

description: Nitrogen was introduced to reduce the O2 concentration to 1%, which was maintained for 35 minutes. Thereafter, sterile air was introduced to counterbalance and increase the O2 concentration to 21%, which was maintained for 25 minutes. Each cycle lasted for an hour, and the model was sustained for 72 cycles.

data_processing:
clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2-v2.0.5 and paired-end clean reads were mapped to the reference genome.
Use find_circ (Memczak et al., 2013) and CIRI2 (Gao et al., 2017) for detection and authentication Determined circRNA.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered as significantly enriched GO functions of gene set. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecularlevel information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: Homo_sapiens.GRCh38.109
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...

source_name: umbilical veins

extract_protocol:
RNA was harvested using Trizol reagent.
A total of 2 µg total RNA per sample was used as input material for the cirRNA library preparation.
ribosomal RNA is removed and rRNA residues are removed by ethanol precipitation. Subsequently, linear RNA was digested with 3 U of RNase R (Epicentre, USA) per µg of RNA.Sequencing library by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) is produced as recommended by the manufacturer Agreed.recommendations and index codes were added to attribute sequences to each sample

value: umbilical veins

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: intermittent hypoxia


title: HUVECs treatment with intersectant hypoxia [IH2]


title: HUVECs treatment with intersectant hypoxia [IH1]


title: HUVECs treatment with control [CK3]

description: control

value: control


title: HUVECs treatment with control [CK2]

description: control


title: Occluded vein graft, O, patient3

city: Tianjin

first: Xiankun

last: Liu

address: South  Taierzhuang road num 261

institute: Tianjin Chest Hospital

data_processing:
The data generated from Illumina/BGI platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology.
Raw data of fastq format were firstly processed throuht in-house perl scripts. In this step, remove the adapter sequence and filter out low quality(low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N(N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software to obtain mapped reads.
The mapped reads were spiced with Stringtie software, and then use the Gffcompare software to compare with the reference genme GTP/GPP file to find the orignal unannotated transcription region and discover new transcripts and new gene of the species.
FeatureCounts was used to count the reads number mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38

source_name: Occluded vein graft

extract_protocol:
RNA was harvested  using TRIzol® Reagent according the manufacturer's instructions(Magen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ABclonal mRNA-seq Lib Prep Kit(Abclnal, China) following the manufacturer's instructions.

value: Occluded vein graft


title: Occluded vein graft, O, patient2


title: I-Res Female [TRA00195188]

value: 178 I-Res Female

value: female

value: insulin resistant (I-Res)


title: Intraoperative spare great saphenous vein,C,patient3


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML9_34p]

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

data_processing:
obtained sequence reads were processed using CellRanger (10X Genomics) pipeline
The data was processed using Scarf.
Assembly: hg38
Supplementary files format and content: Each tar file gives the counts in mtx format, the ADT counts, and the metadata for each cell including UMAP co-ordinates.

source_name: bone marrow

extract_protocol:
FACS sorted Lin-CD34+ and Lin-CD34+CD38- cells are directly proceeded to single-cell droplet generation with 10X Genomics platform and further undergone library preparation.
library preparation was done according to the Chromium Single Cell 3’ Reagent Kit v3.1 protocol

value: bone marrow

value: hematopoietic stem and progenitor cells


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML8_38n]


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML9_38n]


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML6_38n]


title: Intraoperative spare great saphenous vein,C,patient2


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML7_38n]


title: I-Sen Male [TRA00195177]

value: 356 I-Sen Male

value: male

value: insulin sensitive (I-Sen)


title: Intraoperative spare great saphenous vein,C,patient1


title: Occluded vein graft, O, patient1


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML5_38n]


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML4_38n]


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML6_34p]


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML3_34p]


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML3_38n]


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML5_34p]


title: HUVECs treatment with control [CK1]

description: control


title: tandem601-OLTN

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: Sequenced reads were mapped to the tandemly connected three Widom 601 sequences

data_processing:
Adapter DNAs were trimmed using Trim Galore (version 0.6.7) with the options: --paired.
The paired-end reads were mapped to the GRCh38 for the Hela samples and the tandemly connected three Widom 601 sequences for the in vtiro sample using bowtie (version 2.3.5.1) with the default options.
Data of Hela samples were filtered using the following specifications; OLTN: 337 (+/- 5) bp, OLDN: 248 (+/- 5) bp and mono-nucleosome: 147 (+/- 5) bp, respectively.
For Hela data, the bigWig files were created by 50 bp intervals on the genome, and then the counts were normalized as CPM (Reads Per Million reads) using deepTools (version 3.5.1) with the option: -bs 1 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates --normalizeUsing CPM.
For in vitro data, a count file was created by counting fragments by lengths.
Assembly: GRCh38
Supplementary files format and content: bigwig files were genelated using deepTools (version 3.5.1, bamCoverage function)  with the option

organism: synthetic construct

source_name: Synthetic DNA

growth_protocol: The HeLa cells were commercially obtained and stored at -80ºC until use.

extract_protocol:
The HeLa cells were suspended in the washing solution containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, and a proteinase inhibitor (Roche). The detergent buffer containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, proteinase inhibitor (Roche), and 1% NP-40 was then added to the cell suspension, and the mixture was rotated at 4 ºC for 10 minutes. The HeLa nuclei were collected by centrifugation and were resuspended in the washing solution. A large amount of MNase (3 units/µL) and CaCl2 (2 mM) were added to the HeLa nuclei suspension. The MNase treatment was performed under 37 ºC for 30 minutes, and was terminated by EDTA (pH 8.0) addition. The MNase fragments were precipitated by ethanol, and were electrophoresed by 4% agarose gel.
Libraries were prepared using ThruPLEX DNA-Seq Kit (Clontech, #R400674).

value: Synthetic DNA


title: HeLa_Parental, C3b,48h, KDM5C

data_processing:
Basecalls were performed using fastq Novaseq output.
ChIP-seq reads were trimmed with fastp.
ChIP-seq reads were aligned to the hg38 genome using Bowtie2 (v2.4.2).
Peaks were called uing MACS v2.2.7.1 (q-value takes default setting).
BigWig files were obtained by deepTools (v3.5.1).
Heatmap and metaplot files were made by plotHeatmap and plotProfile of deepTools (v3.5.1).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

treatment_protocol: Cells were treated with DMSO for 48h, or 1.5μM JQ1 for 12h, or 30μM compound 3b for 48h, or in combination.

value: HeLa

value: Cervical cancer cells

value: KDM5C(Bethyl, #A301-035A)


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML1_34p]


title: HeLa_Parental, C3b,24h, KDM5C


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML8_34p]


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML7_34p]


title: HeLa_Parental, C3b,24h, input


title: HeLa_Parental, JQ1+C3b, input


title: HeLa_Parental, C3b,48h, input


title: HeLa_Parental, JQ1, BRD4


title: HeLa_OEKDM5C, input


title: HeLa_OEKDM5C_H514K, input


title: HeLa_shRACK7, BRD4


title: HeLa_Parental, C3b,48h, BRD4


title: HeLa_sgKDM5C, inpiut


title: HeLa_shBRD4, H3K4me3


title: HeLa_sgKDM5C, H3K4me1

value: H3K4me1 (ABclonal, #2355)


title: HeLa_Parental, JQ1+C3b, BRD4


title: HeLa_Parental, H3K4me1


title: HeLa_shBRD4, input


title: HeLa_Parental, input


title: HeLa_sgKDM5C, KDM5C


title: HeLa_sgKDM5C, H3K27ac


title: HeLa_shRACK7, input


title: HeLa_OEKDM5C_H514K,BRD4


title: HeLa_Parental, H3K27ac


title: HeLa_OEKDM5C, H3K4me3


title: HeLa_sgKDM5C, H3K4me3


title: HeLa_Parental, H3K4me3


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML2_34p2]


title: HeLa_Parental, C3b,24h, BRD4


title: HeLa_Parental, JQ1, input


title: CML Chronic Phase, Diagnosis, Lin-CD34+CD38-, CITEseq [CML2_38n2]


title: HeLa_OEKDM5C, BRD4


title: Caski_Parental, input


title: CML Chronic Phase, Diagnosis,  Lin-CD34+, CITEseq [CML4_34p]


title: HeLa cells, Parental, C3b, Rep1

data_processing:
Reads were first trimmed with fastp.
Trimmed sequence reads were mapped to hg38 using HISAT2.
Reads falling under repetitive genes were counted using featureCounts
DESeq2 was used to calculate differential pile-up.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Geneid and row counts for each Sample

extract_protocol:
Total RNA was isolated using an RNAiso Plus (TaKaRa, 9108) in accordance with the manufacturer’s instructions.
Library construction was performed with NEBNext Ultra II Directional RNA Library Prep Kit.

value: WT

value: 30uM compound 3b

tag: time


title: HeLa cells, Parental, JQ1+C3b, Rep1

tag: treatment

value: 1.5uM JQ1 and 30uM compound 3b

value: JQ1 12h; compound 3b 48h


title: HeLa cells, Parental, JQ1+C3b, Rep2


title: HeLa cells, Parental, C3b, Rep3


title: HeLa_OEKDM5C_H514K, H3K4me3


title: Caski_Parental, BRD4

source_name: Caski

value: Caski


title: HeLa cells, Parental, JQ1+C3b, Rep3


title: HeLa cells, Parental, JQ1, Rep1

value: 1.5uM JQ1


title: HeLa cells, Parental, JQ1, Rep2


title: HeLa cells, Parental, JQ1, Rep3


title: HeLa_sgKDM5C, BRD4


title: HeLa_Parental, KDM5C


title: HeLa cells, sg-KDM5C, DMSO, Rep1

value: KDM5C knockoff

value: DMSO


title: HeLa cells, Parental, DMSO, Rep1


title: HeLa cells, Parental, DMSO, Rep2


title: HeLa cells, Parental, DMSO, Rep3


title: Disease45_ST

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

description: processed data files include count matrix, metadata and umap files

data_processing:
RNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
RNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
RNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
RNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
RNA-Seq: The output files for 29 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
RNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 50%.
Assembly: RNA-Seq: GRCh38
Supplementary files format and content: RNA-Seq: EXPORT_scRNAseq_counts.rds: combined count matrix of all 11 samples; EXPORT_snRNAseq_metadata.txt: combined metadata; EXPORT_snRNAseq_umap.txt: UMAP embedding values for identified cell types.
scRNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
scRNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
scRNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
scRNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
scRNA-Seq: The output files for 18 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Assembly: scRNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 15%.
Supplementary files format and content: scRNA-Seq: GRCh38
scRNA-Seq: Cell Ranger ATAC v. 2.0.0 (http://10xgenomics.com) was used to process Chromium single cell ATAC-seq output.
ATAC-Seq: The poor quality cells were removed from the matrix using the following criteria: peak_region_fragments < 3000 & peak_region_fragments > 20000 & pct_reads_in_peaks < 15 & nucleosome_signal > 4 & TSS.enrichment > 2
ATAC-Seq: The output files for 18 samples were aggregated into one matrix using Signac v. 1.3.0.
Assembly: ATAC-Seq: GRCh38
Spatial transcriptomics: Space Ranger v1.0.0 (http://10xgenomics.com) was used to process Human FFPE Visium output
Spatial transcriptomics: “spaceranger count” aligned thedata to the human reference genome (GRCh38) by using the human probe dataset (Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38) and data mapped to the H & E stained image.
Spatial transcriptomics: Aligned data was loaded to Seurat object (Seurat . 4.0.1) and normalized by using SCT.
Spatial transcriptomics: The objects of 14 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Spatial transcriptomics: The samples were merged together, using “merge” function of Seurat.  Next, the data was subjected to principle component analysis (PCA) for linear dimension reduction and Harmony was used to integrate the datasets.
Assembly: Spatial transcriptomics: GRCh38
Supplementary files format and content: Spatial transcriptomics: EXPORT_ST_counts.rds: combined count matrix of all 7 samples; EXPORT_ST_metadata.txt: combined metadata; EXPORT_ST_umap.txt: UMAP embedding values for identified cell types.
Library strategy: Spatial transcriptomics

source_name: FFPE kidney tissue

extract_protocol:
scRNA-Seq: 10X Genomics Chromium Prep (10X Genomics, PN-1000120). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
scRNA-Seq: The cDNA libraries were constructed using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer’s original protocol.
ATAC-Seq: Chromium Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000110). Transposing and barcoding were performed according to the manufacturer's instructions.
ATAC-Seq: The libraries were constructed using the Chromium Single Cell ATAC Library & Gel Bead Kit and Chromium i7 Multiplex Kit N (10X Genomics, PN-1000084) according to the manufacturer’s original protocol.
Spatial Transcriptomics: 5 µm tissue samples was cut and onto the Visium Spatial gene Expression Slide. After deparaffinization, H & E staining was performed. Keyence 1266 BZ-X810 microscope was used for whole slide imaging.
Spatial Transcriptomics: After scanning, de-crosslinking, probe hybridization, probe release and extension, library preparation was performed by single Index Kit TS Set A (10X Genomics, PN-3000511) according to the manufacturer’s protocol.

tag: disease

value: DKD

value: adult kidney

tag: age

value: Male


title: Disease44_ST

value: CKD

tag: tissue


title: HeLa_Parental, BRD4

tag: cell type


title: Disease41_ST

value: Female


title: HeLa cells, Parental, C3b, Rep2

value: HeLa

tag: genotype


title: Disease40_ST


title: Disease43_ST


title: Disease42_ST


title: PBMCs from animal 74 at timepoint 6 wpi

value: PBMCs

value: 6 wpi


title: Control37_ST

value: Control


title: Disease38_snRNAseq

data_processing:
RNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
RNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
RNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
RNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
RNA-Seq: The output files for 29 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
RNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 50%.
Assembly: RNA-Seq: GRCh38
Supplementary files format and content: RNA-Seq: EXPORT_scRNAseq_counts.rds: combined count matrix of all 11 samples; EXPORT_snRNAseq_metadata.txt: combined metadata; EXPORT_snRNAseq_umap.txt: UMAP embedding values for identified cell types.
scRNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
scRNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
scRNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
scRNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
scRNA-Seq: The output files for 18 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Assembly: scRNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 15%.
Supplementary files format and content: scRNA-Seq: GRCh38
scRNA-Seq: Cell Ranger ATAC v. 2.0.0 (http://10xgenomics.com) was used to process Chromium single cell ATAC-seq output.
ATAC-Seq: The poor quality cells were removed from the matrix using the following criteria: peak_region_fragments < 3000 & peak_region_fragments > 20000 & pct_reads_in_peaks < 15 & nucleosome_signal > 4 & TSS.enrichment > 2
ATAC-Seq: The output files for 18 samples were aggregated into one matrix using Signac v. 1.3.0.
Assembly: ATAC-Seq: GRCh38
Spatial transcriptomics: Space Ranger v1.0.0 (http://10xgenomics.com) was used to process Human FFPE Visium output
Spatial transcriptomics: “spaceranger count” aligned thedata to the human reference genome (GRCh38) by using the human probe dataset (Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38) and data mapped to the H & E stained image.
Spatial transcriptomics: Aligned data was loaded to Seurat object (Seurat . 4.0.1) and normalized by using SCT.
Spatial transcriptomics: The objects of 14 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Spatial transcriptomics: The samples were merged together, using “merge” function of Seurat.  Next, the data was subjected to principle component analysis (PCA) for linear dimension reduction and Harmony was used to integrate the datasets.
Assembly: Spatial transcriptomics: GRCh38
Supplementary files format and content: Spatial transcriptomics: EXPORT_ST_counts.rds: combined count matrix of all 7 samples; EXPORT_ST_metadata.txt: combined metadata; EXPORT_ST_umap.txt: UMAP embedding values for identified cell types.

source_name: whole kidney tissue

value: HKD


title: Disease39_snRNAseq


title: HeLa cells, sg-KDM5C, DMSO, Rep3

value: Cervical cancer cells


title: HeLa cells, sg-KDM5C, DMSO, Rep2


title: 7042_L5rs_BEB19025, CTRL

city: New York

first: Christina

last: Pressl

address: 1230 York Avenue

institute: The Rockefeller University

description: 1087 nuclei

data_processing:
Sequence and transcript coordinates for human hg38 UCSC genome and gene models were retrieved from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) and TxDb.Haspiens.UCSC.hg38.knownGene (version 3.4.0) Bioconductor libraries respectively. FANSseq reads were aligned to the genome using Rsubread's subjunc method (version 1.30.6).
Aligned reads were exported as bigWigs normalized to reads per million using the rtracklayer package (version 1.40.6).
Aligned reads in genes were counted using the featurecounts function within the Rsubread package against gene exons.
Cell-type specific differential gene expression analyses were performed using DESeq2. Results were filtered for genes with accessible promoters for each cell-type and GO analyses were performed for cell-type specific comparisons between HD and NC as well as between L5a and L6 cells in HD.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files, DESeq2 and GO analyses results in .csv and .xlsx file format

molecule: nuclear RNA

source_name: Cortex BA22

extract_protocol:
RNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234).
RNA-seq libraries were prepared with Trio RNA-Seq™ library preparation kit (Tecan, #0506-A01) and pooled for sequencing on NovaSeq6000 (SP 2 x 150bp).

treatment_protocol: Nuclei were isolated from fresh-frozen post-mortem human cortex, labeled with cell type-specific probes and separated by FACS as described by Pressl et al 2023.

value: Cortex BA22

tag: donor

tag: Sex

value: M

tag: pmi (hrs)

tag: donor category

value: CTRL


title: 7011_L6b-pyramidal-neuron_BEB18135, CTRL

description: 1441 nuclei

value: L6b pyramidal neuron


title: 7229_L5rs_HSB2341, HD

description: 959 nuclei

value: F

value: HD