title: M20_3 [exome-seq]

description: Library name: Sample 24


title: M1_3

status: Public on Jan 11 2026

type: SRA

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

country: USA

institute: Dana-Farber Cancer Institute

description: Library name: Sample 3

library_source: transcriptomic

data_processing:
VIPER pipeline (https://github.com/hanfeisun/viper-rnaseq/blob/master/cfce/README_CFCE.md) was used for alignment, assembly and gene counting.
Assembly: rn6
Supplementary files format and content: csv files including raw counts for each gene and each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: mammary tumor

extract_protocol:
A piece of tumors were cut and grinded. Then RNA was harvested using RNeasy Micro Kit. 3000 ng RNA of each sample was submitted for the construction of sequencing libraries by GENEWIZ.
Libraries preparation with poly(A) selection and 150-bp paired-end sequencing on an Illumina HiSeq platform were performed by GENEWIZ (USA; www.GENEWIZ.com).

tag: tissue

value: mammary tumor

tag: age


title: M12_3 [exome-seq]

description: Library name: Sample 21

library_source: genomic

data_processing:
Somatic mutation calling was performed using the nf-core/sarek pipeline (v3.4.1) with Singularity. Raw sequencing reads were aligned to rat Rnor_6.0 reference genome. Following GATK Best Practices, GATK4 was used for duplicate marking, and Strelka2 was applied for variant calling using matched normal liver tissue as control. High-confidence variants were annotated with Ensembl VEP v107 and converted to Mutation Annotation Format (MAF) using vcf2maf (https://github.com/mskcc/vcf2maf).
Assembly: Rnor_6.0
Supplementary files format and content: vcf files including the mutations for each sample

molecule: genomic DNA

extract_protocol:
A piece of tumors were cut and grinded. Then genomic DNA was harvested using AllPrep DNA/RNA/Protein Mini Kit.
Whole-exome sequencing libraries were prepared using the Agilent SureSelectXT Target Enrichment System following the manufacturer’s protocol. DNA from the liver of an untreated healthy rat served as a normal control. Briefly, 3 µg of genomic DNA extracted from rat tumors was sheared to the desired fragment size using ultrasonication, followed by end-repair, A-tailing, and adapter ligation. The adapter-ligated DNA was hybridized to biotinylated RNA baits targeting exome regions, and captured DNA fragments were enriched using streptavidin-coated magnetic beads. After PCR amplification, the final libraries were quantified, assessed for quality using a Bioanalyzer, and sequenced on an Illumina platform to generate paired-end reads.


title: M6_1 [exome-seq]

description: Library name: Sample 17


title: M6_2 [exome-seq]

description: Library name: Sample 18


title: M3_6

description: Library name: Sample 13


title: M3_7 [exome-seq]

description: Library name: Sample 15


title: NC-1

city: nantong

first: wen

last: li

address: qixiu road 19

country: China

institute: Nantong University

description:
Library name: SAMPLE 1
NC-1

data_processing:
RNA-Seq
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
Unmapped reads were collected to identify the circRNA utilizing ACFS
Assembly: Rnor 6.0
Supplementary files format and content: xlsx file includes raw counts for each Sample

molecule: total RNA

source_name: hippocampus

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus


title: M1_1

description: Library name: Sample 1


title: M3_8 [exome-seq]

description: Library name: Sample 16


title: M3_6 [exome-seq]

description: Library name: Sample 14


title: M3_1

description: Library name: Sample 8


title: EXP-3

description:
Library name: SAMPLE 6
EXP-3


title: M1_2

description: Library name: Sample 2


title: EXP-2

description:
Library name: SAMPLE 5
EXP-2


title: M12_2 [exome-seq]

description: Library name: Sample 20


title: M3_5 [exome-seq]

description: Library name: Sample 13


title: M20_1 [exome-seq]

description: Library name: Sample 22


title: NC-2

description:
Library name: SAMPLE 2
NC-2


title: M20_4 [exome-seq]

description: Library name: Sample 25


title: Normal_liver [exome-seq]

description: Library name: Sample 26

source_name: Normal liver

value: Normal liver


title: M3_3 [exome-seq]

description: Library name: Sample 11


title: M1_8 [exome-seq]

description: Library name: Sample 8


title: M12_1 [exome-seq]

description: Library name: Sample 19


title: M3_2 [exome-seq]

description: Library name: Sample 10


title: M3_2

description: Library name: Sample 9


title: M1_7 [exome-seq]

description: Library name: Sample 7


title: 20m_1

description:
Library name: Sample 8
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, feature counting and aggregation was done using Cell Ranger (v8.0.0).
Assembly: Rnor_6
Supplementary files format and content: Supplementary files format and content: tsv files and matrix files

extract_protocol:
Rats were euthanized by CO₂ inhalation, and tumors were harvested as previously described. Briefly, tumors were enzymatically digested in DMEM/F12 medium containing 2 mg/mL collagenase IV, 2 mg/mL hyaluronidase, and 2 mg/mL bovine serum albumin (BSA) at 37ºC for 1–2 hours, followed by freezing in cryopreservation medium (90% fetal bovine serum (FBS) and 10% dimethyl sulfoxide) in liquid nitrogen.
For mammary tumor scRNA-seq, viable cells were resuspended in PBS with 0.04% BSA at a cell concentration of 1000 cells/μL. 10,000 cells were loaded onto a 10x Genomics Chromium™ instrument (10x Genomics) according to the manufacturer's instructions. The scRNA-seq libraries were prepared according to the Chromium Next GEM Single Cell 5’ HT v2 protocol (10x Genomics). Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The pooled libraries were sequenced on Illumina NovaSeq X plus platform.


title: 12m_2

description:
Library name: Sample 6
10x Genomics


title: M3_4 [exome-seq]

description: Library name: Sample 12


title: 20m_4

description:
Library name: Sample 9
10x Genomics


title: Liver, Myosin5b Control, neonatal 280

city: Ladson

first: Rachel

last: Edens-Valentine

state: SC

address: 9675 Spencer Woods Rd

institute: Medical University of South Carolina

description: Library name: AE-M5B280-LivC

data_processing:
The featurecounts matrix was generated from aligned bam files using the featurcounts package of Rsubread (2.20.0) in Rstudio (R 4.4.1)
Assembly: GRMm38
Supplementary files format and content: csv file containing raw counts for each sample

organism: Mus musculus

source_name: whole Liver

extract_protocol:
mRNA was isolated using Trizol extraction and QIAGEN RNA easy kit according to the manufacturer’s instructions.
fastq files were aligned to GRMm38 using Rsubread (2.20.0) and BiocManager (v1.30.26) in Rstudio (R 4.4.1)

value: whole Liver

tag: genotype

value: CD1 germline Myosin5b heterozygous/wildtype


title: Vh_32_G

description:
Library name: Vh_32_G
10X Genomics 5'HTv40

data_processing:
Sequenced reads were processed and aligned to the rat reference genome (Rnor_6) using 10x Genomics Cell Ranger (version 6.1.2).
Assembly: Rnor_6
Supplementary files format and content: Filter matrix h5

source_name: Tumor

extract_protocol:
Tissue digestion was performed using 2 mg/mL collagenase type IV (Worthington, LS004189) in DMEM/F12 (Thermo Fisher Scientific, MT10090CV) with constant stirring at 37°C for 1–2 hours.
For single-cell RNA sequencing (scRNAseq) of whole mammary glands, viable cells were resuspended in PBS containing 0.04% BSA at a concentration of 1,000 cells/μL. A total of 10,000 cells were loaded onto a 10x Genomics Chromium instrument (10x Genomics) following the manufacturer's protocol. scRNAseq libraries were constructed using the Chromium Next GEM Single Cell 5’ HT v2 kit (10x Genomics). Quality control of the amplified cDNA and final sequencing libraries was conducted using the Bioanalyzer High Sensitivity DNA Kit (Agilent). The pooled libraries were sequenced on an Illumina NovaSeq S4 platform.

value: Tumor

tag: treatment

value: Vh

tag: batch


title: M1_2 [exome-seq]

description: Library name: Sample 2


title: M1_1 [exome-seq]

description: Library name: Sample 1


title: M1_5 [exome-seq]

description: Library name: Sample 5


title: Vh_35_G

description:
Library name: Vh_35_G
10X Genomics 5'HTv41


title: M3_1 [exome-seq]

description: Library name: Sample 9


title: M1_6 [exome-seq]

description: Library name: Sample 6


title: Vh_8_G

description:
Library name: Vh_8_G
10X Genomics 5'HTv42


title: 12m_3

description:
Library name: Sample 7
10x Genomics


title: Liver, Myosin5b Control, neonatal 281

description: Library name: AE-M5B281-LivC


title: Liver, Myosin5b Control, neonatal 282

description: Library name: AE-M5B282-LivC


title: M1_4 [exome-seq]

description: Library name: Sample 4


title: M1_3 [exome-seq]

description: Library name: Sample 3


title: 6m_2

description:
Library name: Sample 5
10x Genomics


title: 6m_1

description:
Library name: Sample 4
10x Genomics


title: Liver, Myosin5b Control, neonatal 279

description: Library name: AE-M5B279-LivC


title: 1m_9

description:
Library name: Sample 3
10x Genomics


title: NIS_Pd_56_G

description:
Library name: NIS_Pd_56_G
10X Genomics 5'HTv38


title: Vh_2_G

description:
Library name: Vh_2_G
10X Genomics 5'HTv39


title: Liver, Myosin5b Knockout, neonatal 278

description: Library name: AE-M5B278-LivKO

value: CD1 germline Myosin5b KO


title: Liver, Myosin5b Knockout, neonatal 277

description: Library name: AE-M5B277-LivKO


title: Liver, Myosin5b Knockout, neonatal 275

description: Library name: AE-M5B275-LivKO


title: Liver, Myosin5b Knockout, neonatal 276

description: Library name: AE-M5B276-LivKO


title: NIS_Pd_49_S

description:
Library name: NIS_Pd_49_S
10X Genomics 5'HTv37


title: RVVC vaginal epithelial tissue2

city: Kunming

first: xiang

middle: wen

last: lan

address: 300 Bailong Temple, Panlong District, Kunming, Yunnan 650224, China

institute: Southwest Forestry University

description: Library name: C_2

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Excel  file includes FPKM values for each Sample

source_name: vaginal epithelial tissue

extract_protocol:
RNA was extracted using TRIzol Reagent (Ambion).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: vaginal epithelial tissue


title: 1m_7

description:
Library name: Sample 2
10x Genomics


title: 1m_5

description:
Library name: Sample 1
10x Genomics


title: HDF cell with S. micracanthum treatment-1

city: Gwangju

first: Hyeongwoo

last: Choi

address: 77, Yongbong-ro, Buk-gu

country: Afghanistan

institute: Chonnam National University

description: Library name: Smi-Treat-1

data_processing:
Raw sequencing reads were filtered to obtain clean reads using Trim Galore (version 0.6.10).
Adapter sequences and low-quality bases (Q < 30) were removed, and reads shorter than 80 bp were filtered out. The cleaned reads were then aligned to the human reference genome (GRCh38) using STAR (version 2.7.11b).
Assembly: For gene expression quantification, mapped reads were assigned to exon regions using FeatureCounts (version 2.0.8).
Supplementary files format and content: Differentially expressed genes (DEGs) were identified using the DESeq2 package in R, with significance thresholds set at p-value < 0.05 and |log2 Fold Change| ≥ 1.
Supplementary files format and content: tab-delimited text file includes gene counts for each Sample

organism: Homo sapiens

growth_protocol: Human dermal fibroblast (HDF) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cells were maintained in DMEM supplemented with 10% FBS and incubated at 37 °C under a humidified atmosphere of 5% CO2. Subculturing was performed when cells reached 70%–80% confluence. HDFs at passage number under 8 were nsity of 5 × 104 cells/well in 500 μL of culture medium.

extract_protocol:
Total RNA was extracted using TRIzol reagent, followed by phase separation with chloroform and centrifugation at 13,000 rpm for 10 minutes at 4 °C. The aqueous phase was mixed with isopropyl alcohol to precipitate RNA, which was then collected by centrifugation at 13,000 rpm for 10 minutes at 4 °C. The resulting RNA pellet was washed with 75% ethanol, dried, and dissolved in diethyl pyrocarbonate-treated water.
RNA-seq libraries were prepared using the MGIEasy Directional Library Prep Set V2.1, generating six libraries (three from the control and three from the treatment group). Paired-end sequencing was performed using the DNBSEQ-G400RS platform, yielding raw reads with a total length of 220 bp and an insert size of 200 bp

treatment_protocol: After 24 hours, cells were treated with various concentrations (25, 50, and 100 μg/L) of S. micracanthum extract and incubated for an additional three days.

tag: cell line


title: RVVC vaginal epithelial tissue3

description: Library name: C_3


title: NIS_Pd_45_G

description:
Library name: NIS_Pd_45_G
10X Genomics 5'HTv36


title: RVVC vaginal epithelial tissue1

description: Library name: C_1


title: HDF cell with S. micracanthum treatment-3

description: Library name: Smi-Treat-3


title: CTRL NHDF-Ad with MDA-MB-468, 1

city: Nagoya

first: Akihiro

last: Sakai

state: Aichi

country: Japan

institute: Nagoya university

description: Library name: TV0053_07A0053_H1

data_processing:
Raw FASTQ files were processed using the Illumina DRAGEN Bio-IT Platform (v4.3.6). The DRAGEN RNA Pipeline was used for alignment to the human reference genome (GRCh38) and for quantification of gene-level raw read counts.
The raw count data were analyzed in R (v4.3.2) using the edgeR package (v4.2.1). Read counts were normalized using the trimmed mean of M-values (TMM) method. Counts per million (CPM) were calculated and used for downstream visualization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample

source_name: NHDF-Ad and MDA-MB-468

growth_protocol: NHDF-Ad cells were cultured in fibroblast growth medium-2 (Lonza) following the manufacturer’s instructions. MDA-MB-468 cells were cultured in DMEM with 8% fetal bovine serum. Cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (QIAGEN).
RNA-seq libraries were generated using the SMART-Seq LP kit (Takara Bio) and Nextera XT DNA Library Prep Kit (illumina).

treatment_protocol:
NHDF-Ad fibroblasts were transduced with a lentiviral vector carrying human Meflin (ISLR) cDNA (pLV-Puro-CMV>hISLR, VectorBuilder). Control cells were transduced with a lentiviral EGFP vector (pLV-Puro-CMV>EGFP, VectorBuilder).
Three-dimensional co-culture using the cell accumulation technique was performed. NHDF-Ad and MDA-MB-468 cells were treated with Tris-buffered saline containing 150 mM NaCl, 0.04 mg/mL fibronectin, and 0.04 mg/mL gelatin at room temperature for 30 minutes with gentle rocking. After brief centrifugation, the cells were resuspended in culture medium. For co-culture conditions, 1.0 × 10⁶ NHDF-Ad cells and 5.0 × 10³ MDA-MB-468 cells were mixed and seeded into fibronectin-coated culture inserts for 24-well plates. For monoculture conditions, 1.0 × 10⁶ NHDF-Ad cells were seeded alone under the same conditions.All cultures were maintained for 7 days prior to total RNA extraction.

value: NHDF-Ad and MDA-MB-468

tag: cell type

value: fibroblast and breast cancinoma

value: WT


title: VVC vaginal epithelial tissue3

description: Library name: B_3


title: HDF cell with control-2

description: Library name: Control-2


title: Meflin-OE NHDF-Ad with MDA-MB-468, 1

description: Library name: TV0053_05A0051_H1

value: Meflin overexpression


title: VVC vaginal epithelial tissue1

description: Library name: B_1


title: NIS_Pd_37_S

description:
Library name: NIS_Pd_37_S
10X Genomics 5'HTv35


title: CTRL NHDF-Ad, 2

description: Library name: TV0053_04A0050_H1

source_name: NHDF-Ad

value: NHDF-Ad

value: fibroblast


title: A196_Pd_30_S

description:
Library name: A196_Pd_30_S
10X Genomics 5'HTv32


title: A196_Pd_19_G

description:
Library name: A196_Pd_19_G
10X Genomics 5'HTv31


title: Control group vaginal epithelial tissue3

description: Library name: A_3


title: CTRL NHDF-Ad with MDA-MB-468, 2

description: Library name: TV0053_08A0054_H1


title: IhESCs, siPC_3

city: Hangzhou

first: Yongfeng

last: Wu

state: Zhejiang Province

address: No. 261 Huansha Road

institute: Hangzhou First People's Hospital

description: Library name: sample 6

data_processing:
Raw reads in fastq format were first processed using fastp software to remove adapter-containing reads, poly-N-containing reads, and low-quality reads, yielding high-quality clean reads while calculating Q20, Q30, and GC content of the clean reads; reference genome and gene model annotation files were downloaded from public genome databases, with the genome index constructed using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome via the same software, followed by counting the number of reads mapped to each gene using featureCounts v1.5.0-p3 to generate raw gene count data.
Assembly: hg38
Supplementary files format and content: The processed count data file is in CSV format, containing columns for gene_id, gene_name, and raw read count values of each gene corresponding to each sample

source_name: immortalized human endometriotic stromal cells

extract_protocol:
Total RNA was extracted using a standard protocol, and its integrity was assessed via the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA); high-quality RNA samples were selected, with 1 µg of total RNA per sample used as input material, and messenger RNA (mRNA) was specifically purified from total RNA using poly-T oligo-attached magnetic beads for subsequent library construction.
Two types of libraries were constructed: for the NEB library, purified mRNA was fragmented, first-strand cDNA was synthesized with random hexamer primers followed by second-strand cDNA synthesis, and the library was generated after end repair, A-tailing, adapter ligation, size selection, amplification, and purification; for the strand-specific library, the second-strand cDNA was synthesized with dUTP instead of dTTP, and an additional USER enzyme digestion step was included before amplification, with both libraries quantified by Qubit and real-time PCR and their size distribution detected by the Bioanalyzer for quality control.

value: stromal cell

value: siPC


title: Fulv_Pd_63_S

description:
Library name: Fulv_Pd_63_S
10X Genomics 5'HTv30


title: Fulv_Pd_63_G

description:
Library name: Fulv_Pd_63_G
10X Genomics 5'HTv29


title: CTRL NHDF-Ad, 1

description: Library name: TV0053_03A0049_H1


title: IhESCs, siPC_1

description: Library name: sample 4

value: immortalized human endometriotic stromal cells


title: HDF cell with control-3

description: Library name: Control-3


title: IhESCs, NC_3

description: Library name: sample 3

value: NC


title: Meflin-OE NHDF-Ad, 2

description: Library name: TV0053_02A0048_H1


title: Meflin-OE NHDF-Ad with MDA-MB-468, 2

description: Library name: TV0053_06A0052_H1


title: A196_Pd_51_S

description:
Library name: A196_Pd_51_S
10X Genomics 5'HTv34


title: Control group vaginal epithelial tissue1

description: Library name: A_1


title: A196_Pd_5_G

description:
Library name: A196_Pd_5_G
10X Genomics 5'HTv33


title: Fulv_Pd_39_G

description:
Library name: Fulv_Pd_39_G
10X Genomics 5'HTv28


title: Sham Liver 3

city: Bethesda

first: Tim

last: Greten

state: MD

address: Building 10, Room 2B38B

department: Thoracic and GI Malignancies Branch

institute: NIH

data_processing:
Base calling of data and quality scoring utilized RTA 3.4.4 (Illumina). Subsequent data processing was performed with Cell Ranger v7.1.0 (Illumina), including demultiplexing (Bcl2fastq 2.20.0) and alignment (STAR 2.7.2a) onto mouse genomics reference (refdata-gex-mm10-2020-A). Following processing, Mean Reads per Cell = 83, 551, Total Genes Detected = 19,745, and Median UMI Counters per Cell = 6,237 (values averaged across all sample outputs). The sequence saturation ranged from 81%-93% indicating a robust mapping of sequence data to the mouse transcriptome.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Data was placed onto BIowulf (NIH HPC Linux cluster) and downstream analyses was performed using Seurat package (vs 4.3.0.1) under RStudio (vs 2023.09.1+494). The count matrix files were read using Read10X_h5 function, then converted into Seurat objects excluding genes expressed less than 10 cells. Low quality cells were removed by the following criteria: cells with features fewer than 500 or above 4000 genes; nCounts fewer than 500 or above 14000; log10(features/counts) <0.8; mitochondrial RNA content above 20%. Doublets in each sample were removed using DoubletFinder (vs 2.0.3). Normalization was performed using SCTransform function in individual samples, then all samples were merged into a single Seurat object. Harmony (vs 0.1.1) was applied for batch correction and stored as Rdata file.

source_name: Liver

extract_protocol:
Eight samples were prepared for scRNA-seq. Solid RIL175 tumors were excised from SV and HV livers (n = 3 / group) 21 d following tumor initiation.  RIL175 tumor-bearing mice (n = 3 SV, 3 HV mice) from non-tumorous liver and matched (pooled) tumors. Immune cells from tumors and livers were isolated as described in earlier methodology. Following surface staining, Live+CD45+ cells were sorted into PBS + 0.04% BSA (ThermoFisher Scientific, catalogue #B14) at the NIH Flow Cytometry Core using the Aurora CS Cell Sorter (Cytek® Biosciences, RRID:SCR_XXXXX).  Subsequent cell counts and viability were determined with propidium iodide/acridine staining using the Luna FL Automated Fluorescence Cell Counter (Logos Biosystem).
Samples were provided to SCAF (NIH Single Cell Analysis Facility) for library preparation,  sequencing, and data processing. Cell counts were determined via LunaFx7 fluorescent cell counter (Logos Biosystem) and adjusted cell counts targeting 6,000 cells/lane were prepared. Library preparation and sample loading were performed by SCAF and in accordance with the 10X Genomics Single Cell User Guide utilizing Chromium Connect (10X Genomics automation platform).    Sequencing was performed using the NovaSeq 6000 Reagent Kit (Illumina). Two sequencing runs (NovaSeq 6k S1 100-cycle) were performed via 5' Immune Profiling v2 Dual-Index chemistry (10x Genomics).

value: Liver

value: Lymphocytes

value: Sham Vagotomy


title: HDF cell with S. micracanthum treatment-2

description: Library name: Smi-Treat-2


title: HDF cell with control-1

description: Library name: Control-1


title: Meflin-OE NHDF-Ad, 1

description: Library name: TV0053_01A0047_H1


title: Mfn1&2-/- rep3

city: São Carlos

first: Marcos

middle: Roberto

last: Chiaratti

state: SP

address: Rod. Washington Luis km 235

department: Departamento de Genética e Evolução

country: Brazil

institute: Universidade Federal de São Carlos

data_processing:
Sequences were initially converted to fastq format and assessed for quality using the FastQC software v. 0.11.7. The SeqyClean software v. 1.10.07 was then used to remove low-quality bases and adaptor sequences.
Sequences shorter than 75 bp were removed. Reads were aligned to the mm10 reference genome, mapped and transcripts were counted using the STAR software v. 2.7.0a. Reads with ambiguous mapping were discarded.
Differentially expressed genes were calculated using the package edgeR of the R/Bioconducter software. Only genes with count per million (CPM) higher than two in at least three samples were evaluated for statistical significance. Counts from each library were normalized by the trimmed mean of M values (TMM) between each pair of samples.
Data were fitted to a generalized linear model (GLM) using a negative binomial function. Quasi-likelihood ratio tests were used to determine differentially expressed genes between the contrasts of interest, with p-values being corrected for multiple testing using the Benjamini-Hochberg method (FDR). Differences with FDR < 0.05 and log fold change > 1 or < -1 were considered significant.
KEGG analysis was performed using the R software package ClusterProfiler.
Genome_build: mm10
Supplementary_files_format_and_content: count_table_CPM
Supplementary_files_format_and_content: count_table_raw

source_name: Oocytes

extract_protocol:
RNA was extracted with the PicoPure Isolation Kit (Cat.# KIT0204; ThermoFisher Scientific). RNA integrity and quantity were assessed using the RNA 6000 Pico Kit and the 2100 Bioanalyzer (Agilent Technologies).
rRNA depletion, cDNA synthesis, cDNA amplification, and sequencing libraries were performed using the SMARTer Stranded Total RNA Sample Prep Kit - Low Input Mammalian (Cat.# 614861; Takaha Bio Inc). RNAseq libraries were validated using the High Sensitivity DNA Kit (Agilent Technologies) and the 2100 Bioanalyzer, evaluated by electrophoresis on agarose gel and quantified by qPCR. Libraries were sequenced on a HiSeq 2500 (Illumina Inc.) with 100 bp pair-end reads.

treatment_protocol: GV oocytes were collected from unprimed mice aged 21-23 days. Oocytes, retrieved in ⍺-MEM (Cat.# 12000-022; ThermoFisher Scientific) supplemented with 6 mg/ml HEPES, 1mg/ml BSA and antibiotics (Cat.# 15140-122; ThermoFisher), were denuded of surrounding cumulus cells by vigorous pipeting. Oocytes were then washed in PBS (Cat.# D1408; Sigma-Aldrich) and placed (pools of 50 oocyts) in 0.2-ml tubes in 20 µl of PicoPure RNA Extraction Buffer (Cat.# KIT0203; ThermoFisher Scientific). Samples were incubated at 42oC for 30 min, centrifuged at 800 x g for 2 min, and stored at -80oC until use.

tag: strain

tag: developmental stage

value: GV oocytes


title: Sham Liver 2


title: Control group vaginal epithelial tissue2

description: Library name: A_2


title: Mfn2-/- rep3


title: Vagatomized Liver 3

value: Vagotomy


title: Mfn1&2-/- rep2


title: Mfn1&2-/- rep1


title: IhESCs, siPC_2

description: Library name: sample 5


title: Iki_Pd_66_S

description:
Library name: Iki_Pd_66_S
10X Genomics 5'HTv26

value: Tumor


title: IhESCs, NC_2

description: Library name: sample 2


title: Fulv_Pd_22_S

description:
Library name: Fulv_Pd_22_S
10X Genomics 5'HTv27


title: SW620-shECM1_3

city: Chongqing

first: Huihui

last: Xiao

address: shapingba

institute: Chongqing university

description: Library name: SW620-shECM1_3

data_processing:
Raw sequencing data were first filtered to remove low-quality reads, adapter sequences, and ribosomal RNA reads using fastp. Clean reads were aligned to the reference genome using STAR aligner. Gene expression quantification was performed using FeatureCounts to generate a read count matrix. Subsequent analyses included principal component analysis (PCA), differential expression analysis using DESeq2 or Seurat, and functional enrichment analysis (GO and KEGG) of differentially expressed genes. For single-cell data, cell clustering was performed using Seurat, and cell-type annotation was conducted based on marker genes.
Assembly: Homo sapiens genome build GRCh38/hg38 was used for read alignment and subsequent bioinformatics analyses.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Colorectal cancer tissue

extract_protocol:
Total RNA was extracted from SW620-shECM1 and SW620-shNC cells using a commercial RNA extraction kit (Trizol reagent or RNeasy Mini Kit) following the manufacturer's instructions. RNA quality and integrity were assessed using Nanodrop and Agilent 2100 Bioanalyzer, with RIN (RNA Integrity Number) ≥ 7.0 considered acceptable for subsequent experiments.
Single-cell RNA sequencing libraries were constructed using a single-cell RNA library preparation kit (10x Genomics Chromium Single Cell 3' Reagent Kit). Briefly, viable cells were sorted, and single-cell suspensions were prepared; then, cell barcoding and cDNA synthesis were performed via reverse transcription. After cDNA amplification, library fragmentation, adapter ligation, and PCR enrichment were conducted. The final libraries were quantified using Qubit and validated by Agilent 2100 Bioanalyzer for size distribution (typically 200-500 bp).

value: Colorectal cancer tissue

value: Human colorectal cancer cells


title: Sham Liver 1


title: Iki_Pd_66_G

description:
Library name: Iki_Pd_66_G
10X Genomics 5'HTv25


title: IhESCs, NC_1

description: Library name: sample 1


title: Iki_Pd_47_S

description:
Library name: Iki_Pd_47_S
10X Genomics 5'HTv24


title: VVC vaginal epithelial tissue2

description: Library name: B_2

value: vaginal epithelial tissue


title: Vagatomized Liver 2


title: Mfn2-/- rep2


title: Vagatomized Liver 1


title: Mn2-/- rep1


title: SW620-shNC3

description: Library name: SW620-shNC3


title: SW620-shECM1_2

description: Library name: SW620-shECM1_2


title: Mfn1-/- rep2


title: A196_64_G

description:
Library name: A196_64_G
10X Genomics 5'HTv21


title: A196_64_S

description:
Library name: A196_64_S
10X Genomics 5'HTv22


title: Sham Tumor


title: Mfn1-/- rep3


title: SW620-shNC1

description: Library name: SW620-shNC1


title: SW620-shNC2

description: Library name: SW620-shNC2


title: DIPG007_TEPA_rep1

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

data_processing:
QC with Fastqc
alignment of the reads with hisat 2
Counting reads to genomic features with featureCounts using Homo_sapiens.GRCh38.103.gtf as reference. Command: featureCounts -T 7 -p -s 2 -t exon -g gene_name -a Homo_sapiens.GRCh38.103.gtf
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: diffuse intrinsic pontine glioma

growth_protocol: The human diffuse intrinsic pontine glioma cancer cell lines were plated at 5x10^5 cells/T75 flask in DMEM/F12 and Neurobasal media (1:1) supplemented with HEPES, non-essential amino acids, antibiotic/antimycotic, pyruvate, glutamax, heparin, B27, human EGF, human FGF, PDGF-AA and PDGF-BB, 10% FCS.

extract_protocol:
Cells were washed with PBS, and then lysed using the Qiagen RNA Extraction Kit. The RNA purity and concentration was then assessed using the Nanodrop.
Quality control and library preparation were carried out by Ramaciotti Centre for Genomics (UNSW, Australia). Paired-end 100 bp sequencing was performed on the Illumina NovaSeq 6000 using TruSeq stranded mRNA for a total of 1.6B reads.

treatment_protocol: Treatment with copper chelator occurred for 24h (VUMC-DIPG10:TEPA 4mM; HSJD-DIPG007: TEPA 2mM).

value: brain

value: Treated with TEPA (24 hours)


title: Iki_52_S

description:
Library name: Iki_52_S
10X Genomics 5'HTv18

value: Iki


title: A196_53_S

description:
Library name: A196_53_S
10X Genomics 5'HTv20


title: WT rep 3

value: WT


title: Vagatomized Tumor


title: A196_23_G

description:
Library name: A196_23_G
10X Genomics 5'HTv19


title: Mfn1-/- rep1


title: SW620-shECM1_1

description: Library name: SW620-shECM1_1


title: WT rep2


title: Apoe-/- MiR26b-/- , rep3

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

data_processing:
FastQC (v0.11.8) was used to inspect the quality of the raw sequences.
Low quality reads were filtered out using FilterByTile.sh provided in BBMap (v38.90).
Adapters were trimmed by TrimGalore (v0.6.5).
Sequences were aligned by Kallisto (v0.46.2) with the setting of bootstrap = 100. Gene expression were aggregated from the transcript abundances estimated by Kallistro and were further converted into Transcripts Per Million (TPM).
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Normalized TPM and read counts estimated by Kallisto for each sample

source_name: Aortic arch and thoracic aorta

extract_protocol:
RNA extraction was performed using Micro Rneasy kit (Qiagen). Average RIN value was 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were fed a HFD for 4 weeks. After sacrifice, the mice were flushed with PBS and aortic arch and thoracic aorta were extracted.

value: Apoe-/- MiR26b-/-

value: 4 weeks HFD

value: Aortic arch and thoracic aorta


title: DIPG007_TEPA_rep3


title: DIPG007_TEPA_rep2


title: Apoe-/- MiR26b-/- , rep1


title: WT rep1


title: DIPG007_CON_rep3

value: Untreated


title: Apoe-/- MiR26b-/- , rep2


title: Iki_52_G

description:
Library name: Iki_52_G
10X Genomics 5'HTv17


title: DIPG007_CON_rep1


title: Donor C UDP 24h

type: RNA

city: Catanzaro

first: Giuseppe

last: Fiume

address: Viale Europa, Campus "S. Venuta", Ed. Bioscienze,Germaneto

department: Department of Experimental and Clinical Medicine

institute: University of Catanzaro "Magna Graecia"

description: Donor C UDP 24h

hyb_protocol: nCounter Immunological Panel Nanostring, according manufacturer's protocol

label: Nanostring Immunology Panel v2

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: PBMC were cultuerd in RPMI medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 1% Glutamine at 37 °C with 5% CO2

extract_protocol: Total RNA extraction was performed in Trizol reagent

treatment_protocol: PBMC were treated with 100 uM UDP for 2, 6 and 24h

tag: agent

value: Donor C UDP (100uM) 24h


title: MDA-MB-231 cells, 10 weeks treatment at pH=6.4, replicate 2

city: Baltimore

first: Konstantinos

last: Konstantopoulos

address: 3400 N Charles St, Croft Hall G65

department: Chemical and Biomolecular Engineering

institute: Johns Hopkins University

description: Library name: 10w_6-4-2

data_processing:
FASTQ files were trimmed using Trim Galore! (v0.6.10) and cutadapt (v4.4) with -a “CTGTCTCTTATACACATCT” -a “AGATGTGTATAAGAGACAG” -q 30
Trimmed FASTQ files were aligned using STAR (v2.7.11b) with default arguments including all FASTQ files for a given sample against Gencode Genes Human Release 44 GRCh38.p14 Genome sequence (GRCh38.p14) (GRCh38.p14.genome.fa)
Aligned SAM files were converted to BAM format using samtools view (v1.17) with default arguments
BAM files were then sorted using samtools sort (v1.17) with default arguments
Sorted BAM files were counted against Gencode Genes Human Release 44 GRCh38.p14 Comprehensive gene annotation gtf file (gencode.v44.chr_patch_hapl_scaff.annotation.gtf) using Subread featureCounts (v2.0.8) with -g “gene_name”
Assembly: Gencode Genes Release 44 of Human GRCh38.p14 https://www.gencodegenes.org/human/release_44.html
Supplementary files format and content: count

growth_protocol: MDA-MB-231 cells were cultured in high glucose DMEM with 10% Fetal Bovine Serum  and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep Plus kit (Zymo Research). 20 ng of RNA per sample were used for the construction of sequencing libraries.
RNA-libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocol.

treatment_protocol: Cell culture medium was supplemented with 25 mM  HEPES and PIPES (Sigma), and pH was adjusted to 7.4 or 6.4 with addition of NaOH and HCl.

value: Triple Negative Breast Cancer

value: Extracellular pH=7.4 for 10 weeks


title: Iki_50_S

description:
Library name: Iki_50_S
10X Genomics 5'HTv16


title: Apoe-/- control, rep2

value: Apoe-/- control


title: Fulv_44_G

description:
Library name: Fulv_44_G
10X Genomics 5'HTv15

value: Fulv


title: MDA-MB-231 cells, 10 weeks treatment at pH=6.4, replicate 3

description: Library name: 10w_6-4-3


title: Iki_Pd_16_G

description:
Library name: Iki_Pd_16_G
10X Genomics 5'HTv23

value: Tumor


title: DIPG010_TEPA_rep3


title: Fulv_27_G

description:
Library name: Fulv_27_G
10X Genomics 5'HTv13


title: Apoe-/- control, rep3


title: Fulv_27_S

description:
Library name: Fulv_27_S
10X Genomics 5'HTv14


title: Donor B UDP 24h

description: Donor B UDP 24h

scan_protocol: nCounter Immunological Panel Nanostring, according manufacturer's protocol

value: Donor B UDP (100uM) 24h


title: Donor A UDP 24h

description: Donor A UDP 24h

data_processing: nCounter Immunological Panel Nanostring, according manufacturer's protocol

value: Donor A UDP (100uM) 24h


title: DIPG007_CON_rep2


title: MDA-MB-231 cells, 10 weeks treatment at pH=6.4, replicate 1

description: Library name: 10w_6-4-1

value: Extracellular pH=6.4 for 10 weeks


title: Apoe-/- control, rep1


title: MDA-MB-231 cells, 10 weeks treatment at pH=7.4, replicate 3

description: Library name: 10W_7-4-3


title: Donor B UDP 6h

description: Donor B UDP 6h

label_protocol: nCounter Immunological Panel Nanostring, according manufacturer's protocol

value: Donor B UDP (100uM) 6h


title: NIS_38_S

description:
Library name: NIS_38_S
10X Genomics 5'HTv11

value: NIS


title: Donor C UDP 6h

description: Donor C UDP 6h

value: Donor C UDP (100uM) 6h


title: DIPG010_CTRL_rep3

value: brain


title: NIS_38_G

description:
Library name: NIS_38_G
10X Genomics 5'HTv10


title: MDA-MB-231 cells, 10 weeks treatment at pH=7.4, replicate 1

description: Library name: 10w_7-4-1

value: WT


title: MDA-MB-231 cells, 10 weeks treatment at pH=7.4, replicate 2

description: Library name: 10w_7-4-2


title: MDA-MB-231 cells, 24 h treatment at pH=6.4, replicate 4

description: Library name: 24h_O

value: Extracellular pH=6.4 for 24 h


title: DIPG010_TEPA_rep1

value: Treated with TEPA (24 hours)


title: DIPG010_TEPA_rep2


title: NIS_48_G

description:
Library name: NIS_48_G
10X Genomics 5'HTv9


title: Donor A UDP 6h

description: Donor A UDP 6h

value: Donor A UDP (100uM) 6h


title: DIPG010_CTRL_rep1

value: Untreated


title: MDA-MB-231 cells, 24 h treatment at pH=6.4, replicate 3

description: Library name: 24h_L

value: Triple Negative Breast Cancer


title: DIPG010_CTRL_rep2


title: NIS_32_S

description:
Library name: NIS_32_S
10X Genomics 5'HTv8


title: Fulv_17_S

description:
Library name: Fulv_17_S
10X Genomics 5'HTv12


title: MDA-MB-231 cells, 24 h treatment at pH=6.4, replicate 2

description: Library name: 24h_I


title: PDL1_7_GLI

description:
Library name: PDL1_7_GLI
10X Genomics 5'HTv7


title: Donor A UDP 2h

description: Donor A UDP 2h

value: Donor A UDP (100uM) 2h


title: THP_1_RBP4_3

city: Beijing

first: Huayuan

last: Liu

state: Beijing

address: New Student Apartment Building, No. 17, South Panjiayuan, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences Cancer Hospital

description: Library name: sample 6

data_processing:
Gene Set Enrichment Analysis  Gene Set Enrichment Analysis (GSEA) is a computational approach to  determine if a pre-defined Gene Set can show a significant consistent  difference between two biological states. The genes were ranked  according to the degree of differential expression in the two samples,  and then the predefined Gene Set were tested to see if they were  enriched at the top or bottom of the list. Gene set enrichment analysis  can include subtle expression changes. We use the local version of the  GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO,  KEGG, Reactome, DO, DisGeNET data set were used for GSEA  independently
Assembly: GRh38
Supplementary files format and content: Excels
Supplementary files format and content: This table contains information on RNA modification sites identified in each sample, RNA counts, and standardized values.

extract_protocol:
RNAquantification andqualification  ①RNAdegradation and contamination was monitored on 1% agarose gels.  ② RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA) .  ③RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing  Atotal amount of 1 µg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached  magnetic beads. Fragmentation was carried out using divalent cations under elevated  temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand  cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of  preferentially 250~300 bp in length, the library fragments were purified with AMPure  XP system (Beckman Coulter, Beverly, USA). Then 3 µlUSER Enzyme (NEB, USA)  was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5  min at 95 °Cbefore PCR. Then PCR was performed with Phusion High-Fidelity DNA  polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products  were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system


title: MDA-MB-231 cells, 24 h treatment at pH=6.4, replicate 1

description: Library name: 24h_C


title: THP_1_RBP4_1

description: Library name: sample 4


title: PDL1_7_GEr

description:
Library name: PDL1_7_GEr
10X Genomics 5'HTv6


title: MDA-MB-231 cells, 24 h treatment at pH=7.4, replicate 4

description: Library name: 24h_M

value: Extracellular pH=7.4 for 24 h


title: THP_1_RBP4_2

description: Library name: sample 5


title: Donor C untreated

description: Donor C untreated


title: PDL1_33_S

description:
Library name: PDL1_33_S
10X Genomics 5'HTv5


title: Donor B untreated

description: Donor B untreated


title: MDA-MB-231 cells, 24 h treatment at pH=7.4, replicate 2

description: Library name: 24h_G


title: Donor C UDP 2h

description: Donor C UDP 2h

value: Donor C UDP (100uM) 2h


title: Donor B UDP 2h

description: Donor B UDP 2h

value: Donor B UDP (100uM) 2h


title: THP_1_3

description: Library name: sample 3


title: PDL1_25_S

description:
Library name: PDL1_25_S
10X Genomics 5'HTv4

value: Tumor


title: THP_1_2

description: Library name: sample 2


title: Vh_36_G

description:
Library name: Vh_36_G
10X Genomics 5'HTv3

value: Vh


title: THP_1_1

description: Library name: sample 1


title: Double Cdon/Boc Mutant Sample 8, 30 hpf, Block2

status: Public on Jan 10 2026

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

description:
Library name: Double8
column name: Double8
RawCounts_30hpf.txt

data_processing:
RNA-seq reads were aligned to the zebrafish genome Ensembl GRCz11 annotation version 112 using STAR Aligner v2.7.11b.
Read counts were quantified using FeatureCounts as implemented in the Subread package using the Ensemble GRCz11 annotation version 112
Assembly: Ensembl GRCz11
Supplementary files format and content: tab-delimited raw counts file for all 30 hpf samples
Supplementary files format and content: tab-delimited raw counts file for all 4 dpf samples

organism: Danio rerio

source_name: bulk dissected head tissue from 30 hpf embryos

growth_protocol: Zebrafish reared at 28.5C under standard conditions

extract_protocol:
Samples were placed into TRIZOL reagent and total RNA was extracted using the Direct-Zol RNA miniprep kit (Zymo).
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: Standard growth conditions

value: Double cdon/boc mutant

value: batch 2


title: Vh_34_G

description:
Library name: Vh_34_G
10X Genomics 5'HTv2


title: Double Cdon/Boc Mutant Sample 7, 30 hpf, Block1

description:
Library name: Double7
column name: Double7
RawCounts_30hpf.txt

value: bulk dissected head tissue from 30 hpf embryos

value: batch 1


title: Wildtype Sample 1, 30 hpf, Block1

description:
Library name: Wildtype1
column name: Wildtype1
RawCounts_30hpf.txt

value: Wildtype AB background


title: Wildtype Sample 2, 30 hpf, Block2

description:
Library name: Wildtype2
column name: Wildtype2
RawCounts_30hpf.txt


title: Double Cdon/Boc Mutant Sample 5, 30 hpf, Block2

description:
Library name: Double5
column name: Double5
RawCounts_30hpf.txt


title: Double Cdon/Boc Mutant Sample 6, 30 hpf, Block2

description:
Library name: Double6
column name: Double6
RawCounts_30hpf.txt


title: Wildtype Sample 4, 30 hpf, Block2

description:
Library name: Wildtype4
column name: Wildtype4
RawCounts_30hpf.txt


title: Wildtype Sample 3, 30 hpf, Block2

description:
Library name: Wildtype3
column name: Wildtype3
RawCounts_30hpf.txt


title: extra-embryonic ectoderm, CTR, rep1

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Library name: BAP1_CTR_exe_RNA_rep1

data_processing:
Raw RNA-seq read pairs were trimmed by Trimgalore (v0.6.6)(https://github.com/FelixKrueger/TrimGalore) with the option “--paired --clip_R2 5”, and aligned to mm10 by STAR (v2.7.9) with the options “--outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outSAMattributes NH HI NM MD XS AS --alignIntronMax 1000000 --alignMatesGapMax 1000000 --limitBAMsortRAM 30000000000 --outFilterType BySJout”.
Uniquely aligned read pairs were identified by sambamba (v0.6.8) with the option “-F “mapping_quality >=255”. StringTie (v2.1.7) to generate FPKM values for each gene.
Assembly: mm10
Supplementary files format and content: csv

source_name: E6.5 extraembryonic ectoderm

growth_protocol: Embryos were cultured in KSOM (Millipore) at 37 °C under 5% CO2 with air

extract_protocol:
For RNA-seq, oocytes and embryos were suspended in 7 μl RRI water (199 μl ultrapure H2O with 1 μl RNase inhibitor). Then, 6 μl shearing master mix (1 μl 10X lysis mix, 1 μl Smart scN6, 4 μl scRT Buffer) was added and incubated at 85°C for 6 min and immediately put on ice for 2 min.
The total RNA‐seq libraries were generated using the SMART‐Seq Stranded Kit (Takara) following the manufacturer's protocol.
The polyA RNA-seq libraries were generated using the SMART-Seq mRNA (Takara) in combination with the Nextera XT Sample Preparation Kit (Illumina)

treatment_protocol: Conditional KO in oocytes was achieved using Gdf9-iCre mediated recombination of Bap1 flox/flox allele

value: E6.5 extraembryonic ectoderm

value: Bap1flox/flox x PWK


title: MDA-MB-231 cells, 24 h treatment at pH=7.4, replicate 3

description: Library name: 24h_J

value: WT


title: MDA-MB-231 cells, 24 h treatment at pH=7.4, replicate 1

description: Library name: 24h_A


title: epiblast, CTR, rep2

description: Library name: BAP1_CTR_epi_RNA_rep2

source_name: E6.5 epiblast

value: E6.5 epiblast


title: extra-embryonic ectoderm, matKO, rep2

description: Library name: BAP1_mKO_exe_RNA_rep2

value: Gdf9-iCre, Bap1flox/flox x PWK


title: visceral endoderm, CTR, rep2

description: Library name: BAP1_CTR_ve_RNA_rep2

source_name: E6.5 visceral endoderm

value: E6.5 visceral endoderm


title: visceral endoderm, matKO, rep2

description: Library name: BAP1_mKO_ve_RNA_rep2


title: epiblast, CTR, rep1

description: Library name: BAP1_CTR_epi_RNA_rep1


title: epiblast, matKO, rep2

description: Library name: BAP1_mKO_epi_RNA_rep2


title: visceral endoderm, CTR, rep1

description: Library name: BAP1_CTR_ve_RNA_rep1


title: extra-embryonic_ectoderm, matKO, H3K27me3, rep1

description:
Library name: BAP1_mKO_EXE_H3K27me3_rep1
mKO_EXE_merged.bw
mKO_EXE_mat_merged.bw
mKO_EXE_pat_merged.bw

data_processing:
Raw paired-end reads from CUT&RUN experiments were trimmed using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore) with the --paired option. For FGOs, trimmed reads were aligned to the mm10 mouse reference genome using Bowtie2 (v2.4.2)(Langmead and Salzberg, 2012) with the parameters:
--no-unal --no-mixed --no-discordant -I 0 -X 1000. Uniquely mapped reads were filtered using Sambamba (v0.6.8) (Tarasov et al., 2015) with the criteria: -F "mapping_quality >= 30 and not (unmapped or mate_is_unmapped)". PCR duplicates were removed using Picard (v2.18.22) (http://broadinstitute.github.io/picard/). BigWig coverage files were generated using deepTools (v2.0.0)(Ramirez et al., 2016) with the options:
--binSize 25 --normalizeUsing RPKM --scaleFactor 1.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

extract_protocol:
For CUT&RUN, oocytes and embryos were directly added to the binding buffer containing conA beads.
The CUT&RUN libraries were prepared as previously described (PMID: 40418442)


title: oe_NC_3

city: wuhan

first: sen

last: ren

state: hubei

address: donghu road

department: Department of Neurosurgery

institute: Zhongnan Hospital of Wuhan University

description:
Library name: sample6
RPKM.oe_NC_3

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

source_name: adipose tissue

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

value: adipose tissue

value: adipose stem cells

value: stem cells


title: visceral endoderm, CTR, H3K27me3, rep1

description:
Library name: BAP1_CTR_VE_H3K27me3_rep1
CTR_VE_merged.bw
CTR_VE_mat_merged.bw
CTR_VE_pat_merged.bw


title: visceral endoderm, CTR, H3K27me3, rep2

description:
Library name: BAP1_CTR_VE_H3K27me3_rep2
CTR_VE_merged.bw
CTR_VE_mat_merged.bw
CTR_VE_pat_merged.bw


title: visceral endoderm, matKO, rep1

description: Library name: BAP1_mKO_ve_RNA_rep1


title: oe_NC_1

description:
Library name: sample4
RPKM.oe_NC_1


title: Donor A untreated

description: Donor A untreated

value: Untreated


title: extra-embryonic ectoderm, matKO, rep1

description: Library name: BAP1_mKO_exe_RNA_rep1


title: extra-embryonic_ectoderm, CTR, H3K27me3, rep1

description:
Library name: BAP1_CTR_EXE_H3K27me3_rep1
CTR195_E65_EXE1_mm10.sorted.multi.Q30.dedup.bw
CTR195_E65_EXE1_mm10.sorted.multi.Q30.dedup.genome1.sorted.multi.bw
CTR195_E65_EXE1_mm10.sorted.multi.Q30.dedup.genome2.sorted.multi.bw


title: oe_FADS2_2

description:
Library name: sample2
RPKM.oe_FADS2_2

value: FADS2 overexpression


title: epiblast, CTR, H3K27me3, rep1

description:
Library name: BAP1_CTR_EPI_H3K27me3_rep1
CTR_EPI_merged.bw
CTR_EPI_mat_merged.bw
CTR_EPI_pat_merged.bw


title: epiblast, matKO, rep1

description: Library name: BAP1_mKO_epi_RNA_rep1


title: CD3 T cells, in vitro cell culture Day2, Sitagliptin group replicate 3

city: Hefei

first: Liang

last: Wang

state: Anhui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

description: Library name: Sample 9

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release111
Supplementary files format and content: tab-delimited text files include tpm values for each Sample

source_name: CD3+ T cells

growth_protocol: CD3+ T cells were removed from fresh PBMCs by immunomagnetic depletion using CD3 microbeads (Miltenyi Biotech, #130-050-101) and cultured in AIMV (Gibco) medium at 2 × 105 cells/ml supplemented with 100 IU/ml human IL-2 and 10% FBS and cultured in a 37°C humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.After total RNA was extracted, eukaryotic mRNA was enriched with oligo (dT) beads.
The enriched mRNA was subsequently fragmented into short fragments via fragmentation buffer and reverse transcribed into cDNA via the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, poly(A) was added, and the fragments were ligated to Illumina sequencing adapters. The ligation reaction mixture was purified with AMPure XP beads (1.0X), and polymerase chain reaction (PCR) amplification was performed.

treatment_protocol: PHA-L (1.25 μg/mL) or PHA-L (1.25 μg/mL) + recombinant human CD26/DPPIV protein (1000 ng/mL) or  PHA-L (1.25 μg/mL) + Sitagliptin (200 μg/mL) was added to CD3+ cells (4 × 105 cells/well) and cultured in vitro for  2 days

value: CD3+ T cells

value: cultured with PHA-L (1.25 μg/mL) + Sitagliptin (200 μg/mL)


title: CD3 T cells, in vitro cell culture Day2, Sitagliptin group replicate 2

description: Library name: Sample 8


title: extra-embryonic_ectoderm, matKO, H3K27me3, rep2

description:
Library name: BAP1_mKO_EXE_H3K27me3_rep2
mKO_EXE_merged.bw
mKO_EXE_mat_merged.bw
mKO_EXE_pat_merged.bw


title: morula, CTR, H3K27me3,rep2

description:
Library name: BAP1_CTR_morula_H3K27me3_rep2
CTR_mor_merged.bw
CTR_mat_mor_merged.bw
CTR_pat_mor_merged.bw

source_name: morula

value: morula


title: oe_FADS2_3

description:
Library name: sample3
RPKM.oe_FADS2_3


title: oe_FADS2_1

description:
Library name: sample1
RPKM.oe_FADS2_1


title: morula, CTR, H3K27me3,rep1

description:
Library name: BAP1_CTR_morula_H3K27me3_rep1
CTR_mor_merged.bw
CTR_mat_mor_merged.bw
CTR_pat_mor_merged.bw


title: CD3 T cells, in vitro cell culture Day2, control replicate 3

description: Library name: Sample 3

value: cultured with PHA-L (1.25 μg/mL)


title: visceral endoderm, matKO, H3K27me3, rep2

description:
Library name: BAP1_mKO_VE_H3K27me3_rep2
mKO_VE_merged.bw
mKO_VE_mat_merged.bw
mKO_VE_pat_merged.bw


title: CD3 T cells, in vitro cell culture Day2, control replicate 2

description: Library name: Sample 2


title: FGO, CTR, H3K27ac, rep3

description:
Library name: BAP1_CTR_GV_H3K27ac_rep3
CTR_K27ac_rep3_4_merged.bw

source_name: Fully grown oocyte

value: Fully grown oocyte


title: FGO, CTR, H3K27ac, rep4

description:
Library name: BAP1_CTR_GV_H3K27ac_rep4
CTR_K27ac_rep3_4_merged.bw


title: FGO, CKO, H3K27ac, rep4

description:
Library name: BAP1_CKO_GV_H3K27ac_rep4
CKO_K27ac_rep3_4_scaled.bw

value: Gdf9-iCre, Bap1flox/flox


title: visceral endoderm, matKO, H3K27me3, rep1

description:
Library name: BAP1_mKO_VE_H3K27me3_rep1
mKO_VE_merged.bw
mKO_VE_mat_merged.bw
mKO_VE_pat_merged.bw


title: Hep3B SOX4 KO #1

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Library name: Hep3B-3-8

data_processing:
Genomic DNA was extracted using the Gentra Puregene Cell Kit (Qiagen) and quantified using a NanoDrop ND-2000 Spectrophotometer (ThermoFisher Scientific). Construction of DNA libraries and subsequent DNA sequencing were performed by the Genomic Medicine Core Laboratory, Linkou, Chang Gung Memorial Hospital. Briefly, bisulfite sequencing libraries were prepared using the Truseq methyl capture EPIC library kit (Illumina). Unmethylated λ-phage DNA was spiked in at input DNA quantity to determine conversion efficiency, which was 99% for all libraries. Libraries were sequenced in 125-bp paired-end on Illumina HiSEq. 4000 (Illumina). Sequencing reads were processed to remove the first six bases, adapter sequences, and poor-quality reads; the remaining sequences were mapped to human genome build GRCh37/hg19 using CLC Genomics Workbench v11.0.0 (Qiagen). The CpG methylation calls were extracted and analyzed using MATLAB software. Global comparison, correlation and PCA analysis of CpG methylation between samples was calculated by MATLAB software.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include site-level methylation data for each sample. Columns include chromosome (Chromosome), region or position (Region), name (Name), total coverage (Total coverage), strand coverage (Strand coverage), context coverage (Context coverage), methylated coverage (Methylated coverage), and methylation level (Methylation level).

extract_protocol:
QIAwave DNA Blood & Tissue Kit (qiagen)
Genomic DNA (gDNA) was fragmented into 150–200 bp pieces using a Covaris S2 ultrasonicator (Covaris Inc., Woburn, MA, USA). Library preparation utilized the TruSeq® Methyl Capture EPIC Library Prep Kit (Illumina, San Diego, CA, USA) with 500 ng of gDNA. After end-repair, A-tailing, and ligation with methylated adapters, pre-capture libraries were pooled and enriched using Illumina EPIC probe sets targeting over 3.3 million CpG sites through two hybridization and capture rounds. Bisulfite conversion was performed with kit reagents, followed by PCR amplification with Kapa HiFi HotStart Uracil+ polymerase (Kapa Biosystems, London, UK). Library quality and quantity were evaluated using a Qubit DNA Assay Kit and Agilent 2100 Bioanalyzer. Sequencing was conducted on the Illumina NovaSeq 6000 platform.

value: Liver cancer

value: Bisulfied modified

value: Knockout SOX4


title: Hep3B SOX4 KO #2

description: Library name: Hep3B-7-2


title: Hep3B-gDNA

description: Library name: Hep3B-gDNA

value: Parental cell


title: CD3 T cells, in vitro cell culture Day2, control replicate 1

description: Library name: Sample 1


title: CD3 T cells, in vitro cell culture Day2, sCD26 group replicate 3

description: Library name: Sample 6

value: cultured with PHA-L (1.25 μg/mL) + recombinant human CD26/DPPIV protein (1000 ng/mL)


title: K562/ADR,EX,H3K9AC,5W,BS,spike,rep1

city: guagnzhou

first: tang

last: guorun

address: xingang

institute: Sun Yat-sen University

description: Library name: K562/ADR_EX_H3K9AC_5W_BS_spike_rep1

data_processing:
Adapter sequences were removed using trim-galore
fastp was used to trim 10 bp from both the 5' and 3' ends
For the bisulfite-treated DNA fragments, alignment, deduplicate and  Single-base resolution methylation information extraction was performed using bismark . bismark_methylation_extractor function.
For control samples that were not subjected to BS treatment, the same workflow was preformed to obtain clean data. These data were then aligned to the reference genome using Bowtie2,dupliate reads were removed using Picard
We use MACS2 to call peak
Assembly: hg38,mm39
Supplementary files format and content: bed,cov.gz, bw

extract_protocol:
After the cells were treated according to the Cut-tag protocol, the DNA was extracted using DNA clean beads.
For 5mC-CUT&Tag, pA/G-Tn5 assembled with Tn5-P5-mC was utilized to profile various histone modifications in K562, HEK-293T, and L1210 cells. This protocol was executed using the Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903), following the manufacturer’s instructions. For 5mC-Multi-CUT&Tag, we employed anti-rabbit and anti-mouse nb-Tn5 assembled with Multi-P5-mC-1/2 to simultaneously profile multiple histone modifications in K562, HEK-293T, and L1210 cells. This process was performed using the Multi-CUT&Tag Library Prep Kit for Illumina (YEASEN, 12592ES), adhering to the provided guidelines. The 5mC-ATAC protocol was conducted in HEK-293T cells using Tn5 assembled with Tn5-P5-mC, facilitated by the ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).  In each of the methods described above, the procedures were halted prior to library PCR amplification. At this stage, 10% of the library templates were reserved for direct 3’ adaptor ligation (Vazyme, NE103) as the IN group (without bisulfite treatment). The remaining 90% of the library templates underwent bisulfite conversion (Zymo, D5030), followed by 3’ adaptor ligation, constituting the BS group (with bisulfite treatment). Additionally, 1 ng of fragmented λDNA with methylated adaptors, prepared using the NEBNext Ultra II DNA Library Prep Kit (E7645S), was spiked in with the library templates before bisulfite conversion to monitor C-to-U conversion rates.
Library PCR amplification was carried out using KAPA HiFi HotStart Uracil+ ReadyMix (KAPA, KK2801) with N5/D7 primers for 5mC-CUT&Tag and 5mC-ATAC, or Multi-P5/D7 primers for 5mC-Multi-CUT&Tag. DNA clean beads (Vazyme, N411) were employed for purification and size selection of the final library products.


title: morula, matKO, H3K27me3, rep2

description:
Library name: BAP1_mKO_morula_H3K27me3_rep2
CKO_mor_merged.bw
CKO_mat_mor_merged.bw
CKO_pat_mor_merged.bw

value: Gdf9-iCre, Bap1flox/flox x PWK


title: epiblast, matKO, H3K27me3, rep1

description:
Library name: BAP1_mKO_EPI_H3K27me3_rep1
mKO_EPI_merged.bw
mKO_EPI_mat_merged.bw
mKO_EPI_pat_merged.bw

value: E6.5 epiblast


title: CD3 T cells, in vitro cell culture Day2, sCD26 group replicate 2

description: Library name: Sample 5


title: K562/ADR,EX,H3K9AC,5W,IN,rep1

description: Library name: K562/ADR_EX_H3K9AC_5W_IN_rep1


title: epiblast, matKO, H3K27me3, rep2

description:
Library name: BAP1_mKO_EPI_H3K27me3_rep2
mKO_EPI_merged.bw
mKO_EPI_mat_merged.bw
mKO_EPI_pat_merged.bw


title: morula, matKO, H3K27me3, rep1

description:
Library name: BAP1_mKO_morula_H3K27me3_rep1
CKO_mor_merged.bw
CKO_mat_mor_merged.bw
CKO_pat_mor_merged.bw


title: epiblast, CTR, H3K27me3, rep2

description:
Library name: BAP1_CTR_EPI_H3K27me3_rep2
CTR_EPI_merged.bw
CTR_EPI_mat_merged.bw
CTR_EPI_pat_merged.bw

value: Bap1flox/flox x PWK


title: CD3 T cells, in vitro cell culture Day2, Sitagliptin group replicate 1

description: Library name: Sample 7


title: oe_NC_2

description:
Library name: sample5
RPKM.oe_NC_2

value: adipose tissue

value: adipose stem cells

value: stem cells

value: WT


title: M8_3, Primary adipocytes

city: Chengdu

first: Ganran

last: Xu

address: No. 14, Section 3, Renmin South Road, Wuhou District

department: West China School of Stomatology

institute: Sichuan University

description:
Library name: sample 3
8 weeks group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes different expression gene for each samples

source_name: inguinal white adipose tissue

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissues were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: inguinal white adipose tissue

value: Primary adipocytes

tag: Sex

value: male


title: M4_4, Primary adipocytes

description:
Library name: sample 6
4 weeks group, replicate biosample 3


title: M8_2, Primary adipocytes

description:
Library name: sample 2
8 weeks group, replicate biosample 2


title: K562/ADR,EX,H3K9AC,5W,BS,spike,rep2

description: Library name: K562/ADR_EX_H3K9AC_5W_BS_spike_rep2


title: K562/ADR,EX,H3K9AC,5W,BS,rep2

description: Library name: K562/ADR_EX_H3K9AC_5W_BS_rep2


title: CD3 T cells, in vitro cell culture Day2, sCD26 group replicate 1

description: Library name: Sample 4

value: CD3+ T cells


title: K562/ADR,EX,H3K9AC,5W,IN,rep2

description: Library name: K562/ADR_EX_H3K9AC_5W_IN_rep2


title: M4_2, Primary adipocytes

description:
Library name: sample 5
4 weeks group, replicate biosample 2


title: FGO, CKO, H3K27ac, rep3

description:
Library name: BAP1_CKO_GV_H3K27ac_rep3
CKO_K27ac_rep3_4_scaled.bw

value: Fully grown oocyte

value: Gdf9-iCre, Bap1flox/flox


title: M4_1, Primary adipocytes

description:
Library name: sample 4
4 weeks group, replicate biosample 1


title: M8_1, Primary adipocytes

description:
Library name: sample 1
8 weeks group, replicate biosample 1


title: K562/ADR,EX,H3K4ME1,5W,BS,spike,rep1

description: Library name: K562/ADR_EX_H3K4ME1_5W_BS_spike_rep1


title: M8_4

description:
Library name: sample 6
8 weeks group, replicate biosample 3


title: M8_3

description:
Library name: sample 5
8 weeks group, replicate biosample 2


title: K562/ADR,EX,H3K9AC,5W,BS,rep1

description: Library name: K562/ADR_EX_H3K9AC_5W_BS_rep1


title: K562/ADR,EX,H3K4ME1,5W,IN,rep1

description: Library name: K562/ADR_EX_H3K4ME1_5W_IN_rep1


title: K562/ADR,EX,H3K4ME1,5W,IN,rep2

description: Library name: K562/ADR_EX_H3K4ME1_5W_IN_rep2


title: K562/ADR,EX,H3K4ME1,5W,BS,spike,rep2

description: Library name: K562/ADR_EX_H3K4ME1_5W_BS_spike_rep2


title: M8_2

description:
Library name: sample 4
8 weeks group, replicate biosample 1


title: iw962

description:
Library name: sample 6
control group, AdipoqCre;Ctnnb1flox/+, replicate biosample 3


title: iw844

description:
Library name: sample 4
control group, AdipoqCre;Ctnnb1flox/+, replicate biosample 1


title: K562/ADR,EX,H3K4ME3,5W,BS,spike,rep2

description: Library name: K562/ADR_EX_H3K4ME3_5W_BS_spike_rep2


title: iw967

description:
Library name: sample 2
mutant group, AdipoqCre;Ctnnb1flox/flox, replicate biosample 2


title: iw958

description:
Library name: sample 5
control group, AdipoqCre;Ctnnb1flox/+, replicate biosample 2


title: M4_1

description:
Library name: sample 2
4 weeks group, replicate biosample 2


title: K562/ADR,EX,H3K4ME3,5W,IN,rep1

description: Library name: K562/ADR_EX_H3K4ME3_5W_IN_rep1


title: K562/ADR,EX,H3K4ME1,5W,BS,rep2

description: Library name: K562/ADR_EX_H3K4ME1_5W_BS_rep2


title: K562/ADR,EX,H3K4ME3,5W,IN,rep2

description: Library name: K562/ADR_EX_H3K4ME3_5W_IN_rep2


title: M4_3

description:
Library name: sample 3
4 weeks group, replicate biosample 3


title: K562/ADR,EX,H3K4ME3,5W,BS,spike,rep1

description: Library name: K562/ADR_EX_H3K4ME3_5W_BS_spike_rep1


title: K562/ADR,EX,H3K4ME1,5W,BS,rep1

description: Library name: K562/ADR_EX_H3K4ME1_5W_BS_rep1


title: M3_1

description:
Library name: sample 1
4 weeks group, replicate biosample 1


title: HEK293T,CON,H3K4ME3,5W,BS,spike,rep2

data_processing:
Adapter sequences were removed using trim-galore
fastp was used to trim 10 bp from both the 5' and 3' ends
For the bisulfite-treated DNA fragments, alignment, deduplicate and  Single-base resolution methylation information extraction was performed using bismark . bismark_methylation_extractor function.
For control samples that were not subjected to BS treatment, the same workflow was preformed to obtain clean data. These data were then aligned to the reference genome using Bowtie2,dupliate reads were removed using Picard
We use MACS2 to call peak
Assembly: hg38,mm39
Supplementary files format and content: bed,cov.gz


title: Parascaris univalens, 2-4-cell embryos, Hi-C

city: Knoxville

first: Jianbin

state: TN

address: 1311 Cumberland Avenue, Ken and Blaire Mossman Building Rm 309

institute: The University of Tennessee

description: Library name: Pu_2-4-cell_Hi-C_rep1

data_processing:
Paired-end Hi-C reads are mapped and analyzed with HiC-Pro.  A shell script was used to convert the allValidPairs file to a .hic file.
Assembly: Pu_v3
Supplementary files format and content: .hic

organism: Parascaris univalens

source_name: 2-4-cell embryo

extract_protocol:
Parascaris embryos and larvae were fixed in formaldehyde then run through a metal dounce.
Hi-C was performed using the Arima-HiC 2.0 kit according to the manufacturer’s protocol (Arima, #A410110).

value: 2-4-cell embryo


title: iw995

description:
Library name: sample 3
mutant group, AdipoqCre;Ctnnb1flox/flox, replicate biosample 3


title: Parascaris univalens, 4-8-cell embryos, Hi-C

description: Library name: Pu_4-8-cell_Hi-C_rep1

source_name: 4-8-cell embryo

value: 4-8-cell embryo


title: iw826

description:
Library name: sample 1
mutant group, AdipoqCre;Ctnnb1flox/flox, replicate biosample 1


title: HEK293T,CON,H3K4ME3,5W,IN,rep2


title: HEK293T,CON,H3K4ME3,5W,IN,rep1


title: HEK293T,CON,H3K4ME3,5W,BS,spike,rep1


title: Parascaris univalens, L1 larvae, Hi-C

description: Library name: Pu_L1_Hi-C_rep1

source_name: L1 larvae

value: L1 larvae


title: K562/ADR,EX,H3K4ME3,5W,BS,rep1

description: Library name: K562/ADR_EX_H3K4ME3_5W_BS_rep1


title: K562/ADR,EX,H3K4ME3,5W,BS,rep2

description: Library name: K562/ADR_EX_H3K4ME3_5W_BS_rep2


title: Parascaris univalens, 1-cell embryos, Hi-C

description: Library name: Pu_1-cell_Hi-C_rep1

source_name: 1-cell embryo

value: 1-cell embryo


title: Parascaris univalens, 1-2-cell embryos, Hi-C

description: Library name: Pu_1-2-cell_Hi-C_rep1

source_name: 1-2-cell embryo

value: 1-2-cell embryo


title: HEK293T,CON,H3K4ME3,5W,BS,rep2


title: HEK293T,CON,H3K4ME3,2W,BS,spike,rep2


title: Double Sample 13, 4dpf, Block2

description:
Library name: Double13
column name: Double13
RawCounts_4dpf.txt

source_name: bulk dissected head tissue from 4 dpf embryos, eyes removed

value: Double cdon/boc mutant

value: batch 2


title: Double Sample 12, 4dpf, Block2

description:
Library name: Double12
column name: Double12
RawCounts_4dpf.txt

value: bulk dissected head tissue from 4 dpf embryos, eyes removed


title: HEK293T,CON,H3K4ME3,5W,BS,rep1


title: Double Sample 11, 4dpf, Block1

description:
Library name: Double11
column name: Double11
RawCounts_4dpf.txt

value: batch 1


title: HEK293T,CON,H3K4ME3,2W,BS,spike,rep1


title: HEK293T,CON,H3K4ME3,2W,IN,rep2


title: HEK293T,ATAC,BS,rep1


title: HEK293T,ATAC,IN,rep2


title: HEK293T,ATAC,BS,rep2


title: HEK293T,CON,H3K4ME3,2W,IN,rep1


title: Sting-deficient GM-BMCs treated with cGAMP for 6h (replicate 2)

city: Tokyo

first: Hideo

last: Negishi

address: 4-6-1 Shirokanedai, Minato-ku

department: Vaccine Science

institute: The Institute of Medical Science, The University of Tokyo

description: Library name: StingKO_cGAMP_6h_rep2

data_processing:
Sequencing was performed by using Illumina Novaseq 6000 (Illumina, USA). Single-end Fastq files were processed as follows. Adapter trimming and quality filtering of sequencing data were performed by using cutadapt 4.1. Trimmed reads were mapped to the reference genome (build GRCm39 release-107) by using STAR (2.7.10b) with the following parameters:–outSAMmultNmax 1 –outFilterScoreMinOverLread 0 –outFilterMatchNminOverLread 0 –outFilterMultimapScoreRange 0 –seedSearchStartLmax 30. Then, read counts of each gene symbol were calculated by using featureCounts v2.0.2 by following parameters: -T 2 -Q 0 -s 1 -t gene -g gene_name –primary -M -O –largestOverlap –fraction -R BAM. Resulted gene-expression count data from each fastq file were merged into a single gene-expression count matrix.
For STAR index build and FeatureCounts analysis, small RNA annotations were filtered out from gencode.vM30 gtf file.
Assembly: GRCm39 released-107
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

source_name: GM-CSF cultured bone marrow cells

extract_protocol:
Bone marrow cells were isolated from the legs of mice and cultured in RPMI 1640 (Nacalai Tesque, Kyoto, Japan) containing 10% foetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA) and 10 ng/ml of GM-CSF (PeproTech, Cranbury, NJ, USA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) before culture. After 4 days, additional GM-CSF (10 ng/ml) was added and used for the experiment on days 6–7. Cells were treated with HCQ or cGAMP for the indicated time periods.
Transcriptome libraries were prepared from cell lysate resolved in lysis buffer. PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711). To perform reverse transcription, beads were then suspended in 10 μL of RT mix [5× Superscript IV buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma), 6 mM MgCl2, 1 U/μL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/μL Superscript IV (Thermo Fisher Scientific)], and incubated for 5 min at 35ºC, 30 min at 42ºC, and immediately cooled on ice. Beads were washed once with B&W-T buffer [5 mM Tris-HCl (pH 8.0) (Nippon Gene), 1 M NaCl (Merck), 1 mM EDTA (Nippon Gene), and 0.05% Tween-20 (Merck)], and once with Tris-HCl (pH 8.0). To digest the free primer, beads were suspended in 10 μL of Exo I mix [10× Exo I buffer (New England Biolabs), 2 U/μL Exonuclease I (New England Biolabs)], incubated for 30 min at 37ºC, and immediately cooled on ice. Beads were washed twice with B&W-T buffer and once with Tris-HCl (pH 8.0). To add polyC tail, beads were then suspended in 10 μL of polyC tailing mix [10× Thermopol buffer (New England Biolabs), 2 mM dCTP (Roche), 0.1 mM ddCTP (GE Healthcare), 1 mM CoCl2 (Roche), RNaseH (Invitrogen), 15 U/ul TdT enzyme (Roche)], and incubated for 30 min at 37ºC and immediately cooled on ice. Beads were washed once with B&W-T buffer and once with Tris-HCl (pH 8.0). To synthesize the 2nd strand, beads were then suspended in 10 μL of 2nd strand mix [1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), 0.4 μM of primer (illumina-i7-9G)], and the thermal cycling was performed as follows: for 3 min at 95°C, 20 sec at 98°C, 16 cycles of 1 min at 47°C and 2 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. To amplify the total cDNA, 10 μL of beads containing cDNA was added with 15 μL of first PCR mix [0.32 μM of primer (illumina-i7), 0.48 μM of primer (NH2-3’ WTA), and 1x KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as the following condition: for 3 min at 95°C, 12 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The first PCR products were purified using AmPure XP beads (Beckman-Coulter) at a 0.6:1 reagent-to-sample ratio and eluted with 25 μL of nuclease-free water. 6.3uL of purified first PCR product was mixed with the 8.7 μL of second PCR mix [0.4 μM of primers (illumina-i7, NH2-3’ WTA), and 1× KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 5 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The second PCR products were purified using AmPure XP beads at a 0.6:1 reagent-to-sample ratio and eluted with 15 μL of 10 mM Tris-HCl (pH 8.0). 100 ng of the whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) with some modifications. The thermal cycling was performed under the following conditions: for 7 min at 32ºC, 30 min at 65ºC, and hold at 4ºC. Then, 1.25 μL of 1.5 μM Illumina adapter was used for adapter ligation. Ligated products were purified by double size selection with 0.4× → 0.7× (final 1.1×) AmPure XP beads and eluted with 10 μL of nuclease-free water. The barcoding PCR was performed with 22.5 uL of barcoding mix [7.5 μL of the resulted eluates, 1 μM primers (ILMN_[UDI]_i5 and ILMN_[UDI]_i7), and 1× NEBNext Ultra II Q5 (New England Biolabs)], and the thermal cycling was performed as following condition: for 30 sec at 98°C, 9 cycles of 10 sec at 98°C and 75 sec at 65°C, followed by 5 min at 65°C, and hold at 4°C. The resulting products were purified twice by double size selection with 0.5× → 0.8× (final 1.3×) AmPure XP beads and eluted with 12 μL of 10 mM Tris-HCl, pH 8.0. The size distribution of amplified products was analyzed by the MultiNA system (Shimazu) with appropriate dilutions. Final transcriptome libraries, approximately 300 base pairs in length, were quantified using the KAPA Library Quantification Kit (KAPA Biosystems). Pooled libraries were sequenced by the Illumina Novaseq 6000 sequencer (Illumina).

value: GM-CSF cultured bone marrow cells

value: Sting-/-

value: cGAMP

tag: time

tag: replicate

value: replicate 2


title: Sting-deficient GM-BMCs treated with cGAMP for 6h (replicate 1)

description: Library name: StingKO_cGAMP_6h_rep1

value: replicate 1


title: Sting-deficient GM-BMCs treated with medium (control) for 6h (replicate 3)

description: Library name: StingKO_control_6h_rep3

value: culture medium

value: replicate 3


title: Sting-deficient GM-BMCs treated with HCQ for 6h (replicate 1)

description: Library name: StingKO_HCQ_6h_rep1

value: HCQ


title: K562,MULTI,BC,spike,rep1


title: Sting-deficient GM-BMCs treated without treatment (replicate 1)

description: Library name: StingKO_0h_rep1


title: HEK293T,CON,H3K4ME3,2W,BS,rep2


title: HEK293T,ATAC,BS,rep3


title: Sting-deficient GM-BMCs treated with medium (control) for 6h (replicate 2)

description: Library name: StingKO_control_6h_rep2


title: HEK293T,ATAC,IN,rep1


title: Sting-deficient GM-BMCs treated with medium (control) for 6h (replicate 1)

description: Library name: StingKO_control_6h_rep1


title: Wildtype Sample 10, 4dpf, Block2

description:
Library name: Wildtype10
column name: Wildtype10
RawCounts_4dpf.txt

value: Wildtype AB background


title: HEK293T,ATAC,BS,spike,rep2


title: HEK293T,ATAC,IN,rep3


title: Sting-deficient GM-BMCs treated with HCQ for 6h (replicate 2)

description: Library name: StingKO_HCQ_6h_rep2


title: HEK293T,ATAC,BS,spike,rep1


title: Sting-deficient GM-BMCs treated without treatment (replicate 3)

description: Library name: StingKO_0h_rep3


title: HEK293T,CON,H3K4ME3,2W,BS,rep1


title: WT GM-BMCs treated with cGAMP for 12h (replicate 3)

description: Library name: WT_cGAMP_12h_rep3

value: WT


title: WT GM-BMCs treated with cGAMP for 12h (replicate 1)

description: Library name: WT_cGAMP_12h_rep1


title: HEK293T,ATAC,BS,spike,rep3


title: K562,MULTI,BC,H3K9AC,BS,rep1


title: WT GM-BMCs treated with cGAMP for 6h (replicate 2)

description: Library name: WT_cGAMP_6h_rep2


title: K562,MULTI,BC,H3K9AC,IN,rep1


title: WT GM-BMCs treated with cGAMP for 6h (replicate 1)

description: Library name: WT_cGAMP_6h_rep1


title: Wildtype Sample 9, 4dpf, Block1

description:
Library name: Wildtype9
column name: Wildtype9
RawCounts_4dpf.txt


title: K562,MULTI,BC,H3K4ME3,IN,rep1


title: Sting-deficient GM-BMCs treated with HCQ for 6h (replicate 3)

description: Library name: StingKO_HCQ_6h_rep3


title: K562,MULTI,BC,H3K4ME3,IN,rep2


title: WT GM-BMCs treated with cGAMP for 3h (replicate 3)

description: Library name: WT_cGAMP_3h_rep3


title: K562,MULTI,BC,H3K9AC,IN,rep2


title: K562,MULTI,BC,H3K4ME3,BS,rep1


title: WT GM-BMCs treated with cGAMP for 3h (replicate 2)

description: Library name: WT_cGAMP_3h_rep2


title: K562,MULTI,BC,spike,rep2


title: K562,MULTI,AC,BS,spike,rep1


title: Sting-deficient GM-BMCs treated with cGAMP for 6h (replicate 3)

description: Library name: StingKO_cGAMP_6h_rep3


title: WT GM-BMCs treated with HCQ for 12h (replicate 3)

description: Library name: WT_HCQ_12h_rep3


title: K562,MULTI,AC,H3K9AC,IN,rep1


title: WT GM-BMCs treated with HCQ for 12h (replicate 2)

description: Library name: WT_HCQ_12h_rep2


title: WT GM-BMCs treated with HCQ for 12h (replicate 1)

description: Library name: WT_HCQ_12h_rep1


title: Sting-deficient GM-BMCs treated without treatment (replicate 2)

description: Library name: StingKO_0h_rep2


title: K562,MULTI,AC,H3K9AC,BS,rep1


title: WT GM-BMCs treated with medium (control) for 12h (replicate 3)

description: Library name: WT_control_12h_rep3


title: WT GM-BMCs treated with medium (control) for 12h (replicate 2)

description: Library name: WT_control_12h_rep2


title: K562,MULTI,AC,H3K9AC,BS,rep2


title: K562,MULTI,AC,H3K4ME1,IN,rep2


title: K562,MULTI,AC,H3K4ME1,IN,rep1


title: K562,MULTI,BC,H3K4ME3,BS,rep2


title: WT GM-BMCs treated with HCQ for 6h (replicate 2)

description: Library name: WT_HCQ_6h_rep2


title: K562,MULTI,AC,H3K9AC,IN,rep2


title: WT GM-BMCs treated with cGAMP for 12h (replicate 2)

description: Library name: WT_cGAMP_12h_rep2


title: WT GM-BMCs treated with HCQ for 6h (replicate 1)

description: Library name: WT_HCQ_6h_rep1


title: HEK293T,MULTI,AB,H3K4ME3,IN,rep1


title: HEK293T,MULTI,AB,BS,spike,rep1


title: K562,MULTI,BC,H3K9AC,BS,rep2


title: WT GM-BMCs treated with HCQ for 6h (replicate 3)

description: Library name: WT_HCQ_6h_rep3


title: K562,MULTI,AC,H3K4ME1,BS,rep1


title: WT GM-BMCs treated with cGAMP for 3h (replicate 1)

description: Library name: WT_cGAMP_3h_rep1


title: WT GM-BMCs treated with medium (control) for 6h (replicate 3)

description: Library name: WT_control_6h_rep3


title: WT GM-BMCs treated with HCQ for 3h (replicate 1)

description: Library name: WT_HCQ_3h_rep1


title: WT GM-BMCs treated with medium (control) for 12h (replicate 1)

description: Library name: WT_control_12h_rep1


title: WT GM-BMCs treated with HCQ for 3h (replicate 3)

description: Library name: WT_HCQ_3h_rep3


title: WT GM-BMCs treated with cGAMP for 6h (replicate 3)

description: Library name: WT_cGAMP_6h_rep3


title: K562,MULTI,AC,BS,spike,rep2


title: HEK293T,MULTI,BC,BS,spike,rep3


title: WT GM-BMCs treated with HCQ for 3h (replicate 2)

description: Library name: WT_HCQ_3h_rep2


title: HEK293T,MULTI,AB,H3K27ME3,IN,rep1


title: K562,MULTI,AC,H3K4ME1,BS,rep2


title: HEK293T,MULTI,AB,H3K27ME3,BS,rep1


title: WT GM-BMCs treated with medium (control) for 6h (replicate 1)

description: Library name: WT_control_6h_rep1


title: HEK293T,MULTI,BC,BS,spike,rep2


title: HEK293T,MULTI,AB,H3K4ME3,BS,rep1


title: HEK293T,MULTI,BC,BS,spike,rep1


title: WT GM-BMCs treated with medium (control) for 3h (replicate 1)

description: Library name: WT_control_3h_rep1


title: HEK293T,MULTI,BC,H3K9AC,IN,rep3


title: WT GM-BMCs treated with medium (control) for 6h (replicate 2)

description: Library name: WT_control_6h_rep2


title: WT GM-BMCs treated with medium (control) for 3h (replicate 3)

description: Library name: WT_control_3h_rep3


title: WT GM-BMCs treated without treatment (replicate 3)

description: Library name: WT_0h_rep3


title: HEK293T,MULTI,BC,H3K9AC,BS,rep1


title: WT GM-BMCs treated without treatment (replicate 1)

description: Library name: WT_0h_rep1


title: WT GM-BMCs treated without treatment (replicate 2)

description: Library name: WT_0h_rep2


title: Isogenic control-neurons-R2

city: Seattle

first: Colby

last: Samstag

state: WA

address: 300 Ninth Ave

institute: University of Washington

description: Library name: Sample 53

data_processing:
Raw data was processed by Azenta’s standard bioinformatics analysis workflow.
Reads were checked for quality control and adapter sequences were trimmed using Trimmomatic v.0.36.
The resulting BAMs were used to generate hit counts using Subread v.1.5.2, with only exonic regions included for downstream RNA-seq analyses.
Assembly: Sequence data was aligned to the GRCh38 Homo Sapiens reference genome using STAR aligner v.2.5.2b.
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: iPSC-neurons

growth_protocol: iPSC-neurons and -astrocytes were cultured 10-14 days before being pelleted and frozen prior to RNA extraction

extract_protocol:
cDNA libraries were preparation using polyA capture, and sequencing was performed on an Illumina NovaSeq X Plus using 2x150bp paired-end reads at a final read depth of ~20 million reads per sample.
RNA libraries for RNAseq were prepared by Azenta

treatment_protocol: 3 replicates (R1-3) of cell pellets of 1x10^6 of the following clones differentiated into astrocytes and neurons were submitted to Azenta RNA extraction and sequencing: GBA1IVS/+ clones #1,2,6, control GBA1+/+ clones #1,2,4, GBA1+/+ Rev isogenic control clone generated by CRISPR Cas9 editing of GBA1IVS/+ clone #1, and a matched control GBA1IVS/+ A4 clone unedited by the CRISPR Cas9 process.

value: Male

value: iPSC-neurons

value: H4997 WTRev

value: midbrain dopaminergic neurons


title: HEK293T,MULTI,BC,H3K9AC,IN,rep1


title: HEK293T,MULTI,BC,H3K9AC,BS,rep2


title: Trax[E126A] mutant Tx-737, male, 114 days old

city: Iowa City

first: Junko

last: Kasuya

state: IA

address: 169 Newton Rd

department: Neuroscience and Pharmacology

institute: University of Iowa

description:
Library name: mi Tx mutant-3
mi Tx mutant-3_737

data_processing:
Data analysis was performed using Partek Flow interface (Partek, Illumina, CA)
Assembly: mm
Supplementary files format and content: csv files include raw count for each sample

source_name: hippocampus

growth_protocol: Mice were maintained on a 12h light/12h dark cycle at 22-25 C. Food and water were available ad libitum.

extract_protocol:
Total RNA was prepared using Invitrogen miRVana miRNA Isolation Kit with phenol (Thermo Fisher Scientific, #AM1560) according to manufacturer’s instructions.
Illumina Stranded mRNA Prep, Ligation.

value: hippocampus

value: homozygotes for Trax[E126A]


title: Isogenic control-neurons-R1

description: Library name: Sample 52


title: Trax[E126A] mutant Tx-733, male, 109 days old

description:
Library name: mi Tx mutant-2
mi Tx mutant-2_733


title: HEK293T,MULTI,BC,H3K4ME3,IN,rep3


title: Isogenic control-astrocytes-R3

description: Library name: Sample 51

source_name: iPSC-astrocytes

value: iPSC-astrocytes

value: astrocytes


title: Trax[E126A] mutant Tx-754, male, 102 days old

description:
Library name: mi Tx mutant-4
mi Tx mutant-4_754


title: HEK293T,MULTI,BC,H3K9AC,IN,rep2


title: Isogenic control-astrocytes-R1

description: Library name: Sample 49


title: Isogenic control-astrocytes-R2

description: Library name: Sample 50


title: HEK293T,MULTI,BC,H3K9AC,BS,rep3


title: littermate control Tx-755, male, 102 days old

description:
Library name: mi Control-5
mi Ctrl-5_755


title: WT GM-BMCs treated with medium (control) for 3h (replicate 2)

description: Library name: WT_control_3h_rep2

value: GM-CSF cultured bone marrow cells


title: RESUB Control-clone2-NEURONSR1

description: Library name: Sample 46

value: H1112 clone 2


title: GBA IVS/IVS-B3-neurons-R2

description: Library name: Sample 44

value: GBA1 IVS/IVS


title: Isogenic control-neurons-R3

description: Library name: Sample 54


title: littermate control Tx-736, male, 114 days old

description:
Library name: mi Control-4
mi Ctrl-4_736


title: HEK293T,MULTI,BC,H3K4ME3,BS,rep3


title: RESUB Control-clone2-NEURONSR3

description: Library name: Sample 48


title: littermate control Tx-728, male, 118 days old

description:
Library name: mi Control-3
mi Ctrl-3_728


title: HEK293T,MULTI,BC,H3K4ME3,IN,rep2


title: RESUB Control-clone2-NEURONSR2

description: Library name: Sample 47


title: GBA IVS/IVS-B3-neurons-R3

description: Library name: Sample 45


title: Trax[E126A] mutant Tx-726, male, 119 days old

description:
Library name: mi Tx mutant-1
mi Tx mutant-1_726


title: HEK293T,MULTI,BC,H3K4ME3,BS,rep2


title: littermate control Tx-727, male, 118 days old

description:
Library name: mi Control-2
mi Ctrl-2_727


title: GBA IVS/IVS-B3-astrocytes-R2

description: Library name: Sample 41


title: GBA IVS/IVS-B3-astrocytes-R3

description: Library name: Sample 42


title: GBA IVS/IVS-B3-neurons-R1

description: Library name: Sample 43


title: GBA IVS/+-A4-neurons-R2

description: Library name: Sample 38

value: GBA1 IVS/+


title: HEK293T,MULTI,BC,H3K4ME3,IN,rep1


title: littermate control Tx-719, male, 119 days old

description:
Library name: mi Control-1
mi Ctrl-1_719


title: GBA IVS/+-A4-neurons-R3

description: Library name: Sample 39


title: GBA IVS/+-A4-neurons-R1

description: Library name: Sample 37


title: GBA IVS/IVS-B3-astrocytes-R1

description: Library name: Sample 40


title: HEK293T,MULTI,AC,H3K9AC,IN,rep2


title: HEK293T,MULTI,BC,H3K4ME3,BS,rep1


description:
Library name: Tx mutant-4
Tx-4_754

data_processing:
Data analysis was performed using Partek Flow interface (Partek, Illumina, CA)
Assembly: mm39
Supplementary files format and content: csv files include raw count for each sample


title: GBA IVS/+-A4-astrocytes-R3

description: Library name: Sample 36


title: GBA IVS/+-clone6-neurons-R3

description: Library name: Sample 33

value: H4997 clone 6


title: GBA IVS/+-A4-astrocytes-R2

description: Library name: Sample 35


title: HEK293T,MULTI,AC,H3K9AC,IN,rep3


description:
Library name: Tx mutant-2
Tx-2_733


title: HEK293T,MULTI,AC,H3K9AC,IN,rep1


description:
Library name: Tx mutant-3
Tx-3_737


title: GBA IVS/+-clone6-neurons-R2

description: Library name: Sample 32


title: GBA IVS/+-A4-astrocytes-R1

description: Library name: Sample 34


title: HEK293T,MULTI,AC,H3K9AC,BS,rep3


title: GBA IVS/+-clone6-neurons-R1

description: Library name: Sample 31


title: GBA IVS/+-clone6-astrocytes-R1

description: Library name: Sample 28


title: HEK293T,MULTI,AC,H3K9AC,BS,rep1


title: GBA IVS/+-clone2-neurons-R3

description: Library name: Sample 27

value: H4997 clone 2


description:
Library name: Tx mutant-1
Tx-1_726


title: HEK293T,MULTI,AC,BS,spike,rep2


title: GBA IVS/+-clone2-neurons-R1

description: Library name: Sample 25


description:
Library name: Control-4
Ctrl-4_736


title: HEK293T,MULTI,AC,BS,spike,rep3


title: GBA IVS/+-clone2-neurons-R2

description: Library name: Sample 26


title: HEK293T,MULTI,AC,BS,spike,rep1


title: GBA IVS/+-clone6-astrocytes-R2

description: Library name: Sample 29


description:
Library name: Control-2
Ctrl-2_727


description:
Library name: Control-1
Ctrl-1_719


title: GBA IVS/+-clone2-astrocytes-R1

description: Library name: Sample 22


title: GBA IVS/+-clone2-astrocytes-R3

description: Library name: Sample 24


title: HEK293T,MULTI,AC,H3K9AC,BS,rep2


title: HEK293T,MULTI,AC,H3K4ME1,IN,rep3


title: GBA IVS/+-clone2-astrocytes-R2

description: Library name: Sample 23


title: GBA IVS/+-clone6-astrocytes-R3

description: Library name: Sample 30


title: GBA IVS/+-clone1-astrocytes-R1

description: Library name: Sample 16

value: H4997 clone 1


title: GBA IVS/+-clone1-neurons-R1

description: Library name: Sample 19


title: Parse combined conditions sublibrary 8

city: Ann Arbor

first: Kurt

last: Hankenson

state: MI

address: 109 Zina Pitcher Pl.

department: Department of Orthopaedic Surgery

institute: University of Michigan

description:
Library name: Sample 8
Split-pool combinatorial barcoding of all conditions

data_processing:
Demultiplexing and fastq generation was done via BclConvert, this generated a fastq file for each sub-library (8 sub-libraries generated).
Due to the Parse Biosciences Split Barcode Pipeline, 8 fastq files make up the entire dataset.
The Parse pipeline was run for sample/cell demultiplexing, cell assignment, gene counting.
All sample analysis was performed using the all conditions unfiltered matrix (all_unfiltered_DGE.mtx).
Assembly: Mouse mm10
Supplementary files format and content: comma separated values files (.csv)
Supplementary files format and content: matrix files (.mtx)

source_name: Fracture Callus, Periosteum

extract_protocol:
For single cell RNA sequencing, tibiae were harvested at 4 and 7 days post fracture. Fracture calluses were manually harvested via stereomicroscope dissection from mice at 4 and 7 days post fracture and digested using a shaking waterbath at 37 degrees Celsius for 30 minutes in 10 mL PBS (+Ca/+Mg) supplemented with 2 mg/mL Collagenase P, 2 mg/mL Hyaluronidase, and 200 µg/mL DNase. Periosteum was scraped prior to a 1 hour digestion. scRNAseq (Parse Biosciences pipeline) was used to characterize the transcriptomic differences in early response of Intact and Ischemic WT fracture calluses and CD47-null calluses at 4 and 7 days post fracture and baseline periosteum. For each fracture condition, we sequenced a single biological replicate made up of 8 pooled calluses (equal male/female). Periosteum consisted of 8 pooled limbs (equal male/female). Following enzymatic callus digestion, single cell suspensions were fixed using the Parse fixation kit, frozen down to -80 °C in media containing 1.6% DMSO, and subsequently submitted to the University of Michigan Advanced Genomics Core for sequencing using the Parse Biosciences pipeline.
Samples were counted using AO/PI and the LunaFx7 (Logos Bio).Samples were prepped according to manufacturer's instructions (Parse Biosciences Evercode V1). In short, individual transcriptomes are uniquely labeled by passing fixed cells or nuclei through four rounds of barcoding. In each round, pooled cells are randomly distributed into different wells, and transcripts are labeled with well-specific barcodes. Round 1 does reverse transcription of the RNA and adds the first barcode. Rounds 2 and 3 ligate additional barcodes. Round 4 adds the library index, as well as the complete Illumina adapter sequences. cDNA was quantified by Qubit and assessed on TapeStation 2200 (Agilent). Final libraries were quantified by Qubit and assessed on LabChip GX Touch (Revvity).

value: Fracture Callus, Periosteum

value: WT, CD47-KO

tag: sample names

value: WT_Day_4_Bi-lateral_tibia_fracture, WT_Day_4_Ischemic_tibia_fracture, CD47_KO_Day_4_Bi-lateral_tibia_fracture, WT_Day_7_Bi-lateral_tibia_fracture, WT_Day_7_Ischemic_tibia_fracture, CD47_KO_Day_7_Bi-lateral_tibia_fracture, WT_Periosteum, CD47_KO_Periosteum


title: Control-clone3-neurons-R3

description: Library name: Sample 15

value: Male

value: iPSC-neurons

value: H1112 clone 3


title: GBA IVS/+-clone1-neurons-R2

description: Library name: Sample 20

value: midbrain dopaminergic neurons