title: Spleen, cDC1s, pIC alone, 2h, HTO-derived cDNA

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO012.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

data_processing:
The Cell Ranger pipeline (10x Genomics, v6.0.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1 and read 2 for the gene expression and cell surface protein libraries. Read 2 of the gene expression libraries was mapped to the reference genome (mouse mm10) using STAR. Subsequent barcode processing, Unique Molecular Identifier (UMI) filtering and gene counting was performed using the Cell Ranger suite. CITE-seq reads were quantified using the feature-barcoding functionality.
Pre-processing of the RNA UMI matrix was done by the scater and scran R packages (v1.18.6) according to the workflow proposed by the Marioni lab. Subsequent processing was done with Seurat v4.0.5 workflow (gene filtering, log normalization, scaling, clustering, dimensionality reduction, differential gene expression analysis).
DoubletFinder (v2.0.3) was performed to predict any remaining doublets in the dataset.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files for individual samples: The .h5 files contain a gene or hashtag by cell barcode matrix.
Supplementary files format and content: ADT feature and HTO overview: feature_reference_VBO_LNP.csv
Supplementary files format and content: Seurat object for the nine samples merged together: seuratObj_VBO_4-12.rds
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Spleen

extract_protocol:
DCs were enriched by magnisort negative selection and 4-8 million cells were stained with FACS antibodies, TruStain FcX Block (BioLegend, 101320) and the mouse cell surface protein antibody panel containing 155 oligo-conjugated antibodies (TotalSeq-A, BioLegend), 9 TotalSeq-A isotype controls and 4 different hashing antibodies. Each biological replicate was stained with a different hashing antibody, 20.000 cells were sorted per biological replicate and pooled together. For the steady state condition, 15.000 CCR7- cDC1s and 5.000 CCR7+ cDC1s were sorted. For the LNP conditions, 20.000 LNP+ cDC1s were sorted based on the Cy5 fluorochrome which was incorporated in the LNPs. For the pIC alone condition, 20.000 total cDC1s were sorted. Sorting was done on a FACS Symphony S6 (BD). cDC1s were gated on LD-, CD3e-, CD19-, CD64-, F4/80dim, CD11c+, MHCII+, XCR1+, CD172- and only the steady state condition was sorted based on CCR7.
Sorted single-cell suspensions were resuspended at an estimated final concentration of 1000 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version NextGEM 3.1 (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primer (3 nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos. Size selection with SPRIselect Reagent Kit (Beckman Coulter) was used to separate amplified cDNA molecules for 3’ gene expression and cell surface protein construction. TotalSeq-A protein library construction including sample index PCR using Illumina’s Truseq Small RNA primer sets and SPRIselect size selection was performed according to the manufacturer’s instructions. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq 6000 flow cell at the VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 70:20:10 ratio for the combined 3’ gene expression, cell surface protein (antibody-derived tags (ADT)) expression and HashTag-Oligo (HTO) data, respectively.

treatment_protocol: LNPs (eLNPs, pIC-LNPs and CpG-LNPs) and pIC alone were intravenously injected with 100 uL in the tail veins of the mice and 2 or 8 hours later the mice were sacrificed.

value: Spleen

tag: strain

value: pIC alone

tag: time

tag: library type

value: HTO

tag: hto

value: See Custom feature_type in feature_reference_VBO_LNP.csv (Anti CD45 + Anti MHC class I :Replicate 1 = TotalSeq-A0301 ; Replicate 2 = TotalSeq-A0302 ; Replicate 3 = TotalSeq-A0303;  ; Replicate 4 = TotalSeq-A0304)


title: DSP-1001660016237-E-D03

status: Public on Jul 01 2025

type: SRA

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Fastq files were converted to DCC files using the GeoMx NGS Pipeline software and the mm10 reference genome.
Digital Count Conversion files, containing expression count data and sequencing quality metadata, and Probe Kit Configuration files, containing probe assay and sample metadata, were imported into R. Gene expression counts with a value of 0 were shifted to 1 to facilitate downstream transformations. ROI segments were filtered and removed if they met the criteria: “<1000 raw reads”, “below 80% Aligned or 80% Trimmed”, “80% Stitched”, and “below 50% sequencing saturation”. Genes were filtered and removed if they were not detected in at least 10% of segments. Next, counts were normalized using quartile 3 normalization and visualized by uniform manifold approximation and projection, a non-linear dimensionality reduction visualization tool. Gene expression in both datasets was relatively well separated according to ROI brain region.
Assembly: mm10
Supplementary files format and content: Late_stage_count_table.csv. A count table containing normalized counts for probes and segments that passed the quality control steps mentioned in the data processing step.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Two slides were for late-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 30 wk, n=2 controls 30 wk)

extract_protocol:
One brain hemisphere was fixed in 4% paraformaldehyde (PFA) for 24 h, cryoprotected in escalating sucrose gradients, embedded, and cryosectioned in coronal plane sections onto histologic slides [10 μm thickness for spatial transcriptomics sections, 14 μm thickness for subsequent fluorescent in situ hybridization (FISH)] and stored at –80 °C.
Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner
Other: Spatial transcriptomics-Nanostring GeoMx DSP

tag: tissue

value: Brain

tag: genotype


title: Erythroid cells, Control rep2, Day7

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

country: China

institute: zzu

description: Library name: CUT_Tag_H3K27me3_Control_rep2

library_source: genomic

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1 with options: “--end-to-end --very-sensitive”. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential binding sites of H3K14la were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The CUT&Tag peak/region <1000bp from the nearest transcriptional start site (TSS) was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The day of CD34+ cell harvest was recorded as day 0. The cell culture procedure consisted of 3 phases. The basic culture medium consisted of Iscove's Modified Dulbecco's Medium (IMDM), 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL human holo-transferrin, 3 IU/mL heparin and 10 μg/mL insulin. From day 0 to day 7, CD34+ cells were cultured at a concentration of 105/mL in the presence of 10 ng/mL stem cell factor (SCF), 1 ng/mL interleukin-3 (IL-3) and 3 IU/mL erythropoietin (EPO).  The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature. 1×105 cells were washed twice in 500μL wash buffer by gentle pipetting. Concanavalin A coated magnetic beads were prepared as the kit manual described, 10 µL of activated beads were added per sample and incubated at RT for 10 min. According to the kit instructions, cells were sequentially incubated with ConA Beads, primary antibody (anti-H3K27me3 antibody, secondary antibody (Goat anti-Rabbit IgG) and Hyperactive PG-TN5/PA-TN5 Transposon and then fragmented. The fragmented DNA was extracted from the samples and amplified by PCR.
CUT&Tag libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

treatment_protocol: The JMJD3/UTX inhibitor GSK-J4 (Catalog #HY-5648B; MedChemExpress) was dissolved in DMSO and administered to cell cultures at a final concentration of 1 and 1.5 μM. After treated with 1μM GSK-J4 for 5 days, we performed a CUT&Tag of DMSO and GSK-J4 treated cells.

value: Cord blood

tag: cell type

value: Erythroid cells

tag: treatment

value: DMSO


title: DSP-1001660016237-E-C09


title: Spleen, cDC1s, pIC alone, 2h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO012.h5
seuratObj_VBO_4-12.rds

molecule: polyA RNA

value: mRNA


title: M8, SPL, Combination, rep 1

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: Mouse-8-SPL-PCR1

data_processing:
Fastq files were processed using the BARtab v1.4 pipeline (https://github.com/DaneVass/BARtab) for bulk population analysis. The bartools v1.0 R package (https://github.com/DaneVass/bartools) was used for further downstream quality control using default settings before analysis and visualisation.
Assembly: SPLINTR GFP barcode reference library
Supplementary files format and content: text

growth_protocol: Molm-13 cells were cultured at 37 C and 5% CO2 in RPMI-1640, 10% heat inactivated fetal bovine serum (FBS), 2 mM L-Glutamine, 100 IU/ml Penicillin and 100 g/ml Streptomycin. Cells were transduced with a lentiviral vector containing a SPLINTR barcode sequence and sorted 72 hours after transduction. Cells were expanded for 2 weeks before injecting 1 million cells into each mouse via tail vein.

extract_protocol:
5E5 cells from bone marrow and spleen were lysed using Viagen DNA lysis buffer following manufacturers instructions.
DNA Barcode-sequencing libraries were constructed using an amplicon approach. Briefly, viagen lysed samples were split in half to generate PCR replicates. Barcode sequences were amplified using primers flanking the constant region of the barcode before adding i5 and i7 indexes compatible with NGS sequencing. Samples were sequenced on an Illumina NextSeq2000 using 100-bp single end chemistry targeting 2 million reads per sample.

treatment_protocol: Mice were randomised into treatment groups (Vehicle, 5mg/kg PF-9363, 10 mg/kg SNDX-5613 and Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613) n=5 per group) based on leukemia burden detected by flow cytometry before beginning treatment 7 days post tumor transplantation. Mice were dosed twice daily via oral gavage. At disease endpoint, mice were humanely euthanised and spleen and bone marrow were collected.

tag: cell line

value: SPLINTR-GFP-Barcode


title: DSP-1001660016237-E-C08


title: Spleen, cDC1s, pIC alone, 2h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO012.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

library_source: other

value: ADT

tag: adt

value: See Antibody Capture feature_type in feature_reference_VBO_LNP.csv


title: DSP-1001660016237-E-C07


title: M8, BM, Combination,  rep 2

description: Library name: Mouse-8-BM-PCR2

value: Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613)


title: DSP-1001660016237-E-C06


title: mouse hippocampus,shControl1

city: Hefei

first: Ziyu

last: Qiu

address: Huangshan Road

institute: USTC

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing sequencing adapter sequences and  low-quality sequences.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

growth_protocol: C57BL/6 J mice were provided with adequate food and water, and housed under suitable temperature and a 12:12 h light-dark cycle.

extract_protocol:
Total RNA was extracted from brain tissues in TRIzol (Invitrogen). 2 μg of total RNA was used for construction of sequencing libraries
RNA libraries  were prepared for sequencing using standard illumina protocols.

treatment_protocol: AAV was injected into CA1 region of bilateral hippocampus to knock down hepaCAM.

value: hippocampus

value: WT


title: Whole Lymph Node, Donor HuLN9

city: Oxford

first: Jacqueline

middle: HY

last: Siu

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

description: Library name: HuLN9_wCTRL

library_source: transcriptomic single cell

data_processing:
Cell Ranger v7.0.0 count, with include intron parameter set to TRUE, was used to align reads to the GRCh38-2020-A human transcriptome and generate feature-barcode matrices from the Chromium single-cell RNA-sequencing output.
Panpipes (doi: 10.1186/s13059-024-03322-7) was used to perform quality control, batch correction, and clustering pipelines.
Quality control for high-quality single cells include removing cells expressing fewer than log1p(6) genes, and cells with mitochondria gene count percentage greater than 30.
Assembly: Cell Ranger v7.0.0 count  was used to align reads to the GRCh38-2020-A human transcriptome
Supplementary files format and content: Filtered .h5 files from CellRanger run

source_name: lymph node

growth_protocol: Culture in RPMI + 10% FCS + 1x Glutamine + 50U/ml Pen/Strep + 50mM b-mercaptoethanol + 1mM sodium pyruvate + 1x non-essential amino acids + 20mM HEPES

extract_protocol:
LNs were mechanically disrupted with scissors before being enzymatically digested in RPMI containing 0.8mg/ml Dispase, 0.2mg/ml Collagenase-P and 0.1mg/ml DNase, with mixing. This was performed at 37°C for 3 x 20 mins incubations for whole LN preparations, and 2 x 15 mins for slice preparations. After digestion cells were collected in cold PBS supplemented with 2% FCS and 2mM EDTA and filtered through a 100mM cell strainer. Cells were stained with live/dead near infra-red (nIR), anti-CD3, anti-CD20, anti-CD235a, and 7AAD added directly before sorting with the SONY SH800S cell sorter. Dead cells and red blood cells were removed by sorting (CD235a-7AAD-Live/Dead-), while T (CD3+CD20-) and B (CD3-CD20+) cells were sorted separately and spiked back at ratio of 1:20 of sorted non-T/B (CD3-CD20-) cells. Approximately 20,000 cells per sample were loaded onto the 10X Genomics Chromium Controller (Chip G).
Gene expression sequencing libraries were prepared using the 10X Genomics Single Cell 3' Reagent Kits v3.1 following the manufacturer user’s guide (CG000330).

treatment_protocol: 12.5ml of LMQ adjuvant, a liposome-based adjuvant containing a synthetic toll-like receptor 4 (TLR4) agonist 3D-6-acyl-PHAD and QS-21 saponin.

value: lymph node


title: Spleen, cDC1s, CpG-LNP, 2h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO011.h5
seuratObj_VBO_4-12.rds

value: CpG-LNP


title: Whole Lymph Node, Donor HuLN11

description: Library name: HuLN11_wCTRL


title: Whole Lymph Node, Donor HuLN12

description: Library name: HuLN12_wCTRL


title: M7, SPL, PF-9363, rep 1

description: Library name: Mouse-7-SPL-PCR1


title: Erythroid cells, Control rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27me3_Control_rep1


title: DSP-1001660016237-E-C05


title: M7, BM, PF-9363,  rep 2

description: Library name: Mouse-7-BM-PCR2


title: DSP-1001660016237-E-C04


title: Spleen, cDC1s, CpG-LNP, 2h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO011.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: Spleen


title: Whole Lymph Node, Donor HuLN10

description: Library name: HuLN10_wCTRL


title: Precision cut (slice) Lymph Node, Culture with LMQ adjuvant, Donor HuLN10

description: Library name: HuLN10_sLMQ

value: 20 hour culture, LMQ adjuvant


title: Spleen, cDC1s, pIC-LNP, 2h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO010.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: pIC-LNP

value: HTO


title: Precision cut (slice) Lymph Node, Control culture, Donor HuLN10

description: Library name: HuLN10_sCTRL

value: 20 hour culture, control


title: DSP-1001660016237-E-C03

value: Brain


title: M6, SPL, Vehicle, rep 2

description: Library name: Mouse-6-SPL-PCR2

value: Vehicle


title: DSP-1001660016237-E-C02


title: M8, BM, Combination, rep 1

description: Library name: Mouse-8-BM-PCR1


title: Spleen, cDC1s, pIC-LNP, 2h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO010.h5
seuratObj_VBO_4-12.rds


title: M6, SPL, Vehicle, rep 1

description: Library name: Mouse-6-SPL-PCR1


title: Spleen, cDC1s, CpG-LNP, 2h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO011.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: See Custom feature_type in feature_reference_VBO_LNP.csv (Anti CD45 + Anti MHC class I :Replicate 1 = TotalSeq-A0301 ; Replicate 2 = TotalSeq-A0302 ; Replicate 3 = TotalSeq-A0303;  ; Replicate 4 = TotalSeq-A0304)


title: Whole Lymph Node, Donor HuLN8

description: Library name: HuLN8_wCTRL


title: Spleen, cDC1s, pIC-LNP, 2h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO010.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds


title: DSP-1001660016237-E-C01


title: Spleen, cDC1s, eLNP, 2h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO009.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: eLNP


title: M7, SPL, PF-9363, rep 2

description: Library name: Mouse-7-SPL-PCR2

value: SPLINTR-GFP-Barcode


title: M6, BM, Vehicle, rep 2

description: Library name: Mouse-6-BM-PCR2


title: DSP-1001660016237-E-B12


title: Whole Lymph Node, Donor HuLN7

description: Library name: HuLN7_wCTRL


title: Precision cut (slice) Lymph Node, Culture with LMQ adjuvant, Donor HuLN7

description: Library name: HuLN7_sLMQ


title: M6, BM, Vehicle, rep 1

description: Library name: Mouse-6-BM-PCR1


title: DSP-1001660016237-E-B11


title: M7, BM, PF-9363, rep 1

description: Library name: Mouse-7-BM-PCR1


title: M5, SPL, PF-9363, rep 2

description: Library name: Mouse-5-SPL-PCR2


title: Spleen, cDC1s, eLNP, 2h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO009.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: ADT


title: DSP-1001660016237-E-B10


title: M5, BM, PF-9363,  rep 2

description: Library name: Mouse-5-BM-PCR2


title: Precision cut (slice) Lymph Node, Control culture, Donor HuLN7

description: Library name: HuLN7_sCTRL


title: M5, SPL, PF-9363, rep 1

description: Library name: Mouse-5-SPL-PCR1


title: DSP-1001660016237-E-B08


title: Precision cut (slice) Lymph Node, Culture with LMQ adjuvant, Donor HuLN6

description: Library name: HuLN6_sLMQ


title: Spleen, cDC1s, pIC alone, 8h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO008.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: pIC alone


title: Precision cut (slice) Lymph Node, Control culture, Donor HuLN6

description: Library name: HuLN6_sCTRL


title: DSP-1001660016237-E-B07


title: Spleen, cDC1s, pIC alone, 8h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO008.h5
seuratObj_VBO_4-12.rds

value: mRNA


title: DSP-1001660016237-E-B09


title: Spleen, cDC1s, CpG-LNP, 8h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO007.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds


title: Spleen, cDC1s, pIC alone, 8h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO008.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: See Antibody Capture feature_type in feature_reference_VBO_LNP.csv


title: M5, BM, PF-9363, rep 1

description: Library name: Mouse-5-BM-PCR1


title: Precision cut (slice) Lymph Node, Culture with LMQ adjuvant, Donor HuLN5

description: Library name: HuLN5_sLMQ


title: Spleen, cDC1s, CpG-LNP, 8h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO007.h5
seuratObj_VBO_4-12.rds


title: Precision cut (slice) Lymph Node, Control culture, Donor HuLN5

description: Library name: HuLN5_sCTRL


title: M4, SPL, Vehicle, rep 2

description: Library name: Mouse-4-SPL-PCR2


title: Precision cut (slice) Lymph Node, Culture with LMQ adjuvant, Donor HuLN4

description: Library name: HuLN4_sLMQ


title: DSP-1001660016237-E-B06


title: DSP-1001660016237-E-B05


title: Spleen, cDC1s, eLNP, 2h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO009.h5
seuratObj_VBO_4-12.rds


title: M4, SPL, Vehicle, rep 1

description: Library name: Mouse-4-SPL-PCR1


title: M4, BM, Vehicle, rep 2

description: Library name: Mouse-4-BM-PCR2


title: Spleen, cDC1s, CpG-LNP, 8h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO007.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds


title: DSP-1001660016237-E-B04


title: Precision cut (slice) Lymph Node, Control culture, Donor HuLN4

description: Library name: HuLN4_sCTRL


title: Spleen, cDC1s, pIC-LNP, 8h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO006.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds


title: M4, BM, Vehicle, rep 1

description: Library name: Mouse-4-BM-PCR1


title: Spleen, cDC1s, pIC-LNP, 8h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO006.h5
seuratObj_VBO_4-12.rds


title: Precision cut (slice) Lymph Node, Culture with LMQ adjuvant, Donor HuLN3

description: Library name: HuLN3_sLMQ


title: M3, SPL, Combination, rep 2

description: Library name: Mouse-3-SPL-PCR2

value: Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613)


title: DSP-1001660016237-E-B03


title: Precision cut (slice) Lymph Node, Control culture, Donor HuLN3

description: Library name: HuLN3_sCTRL

value: lymph node


title: Spleen, cDC1s, pIC-LNP, 8h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO006.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds


title: M3, BM, Combination,  rep 2

description: Library name: Mouse-3-BM-PCR2


title: DSP-1001660016237-E-B02


title: Spleen, cDC1s, eLNP, 8h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO005.h5
seuratObj_VBO_4-12.rds


title: DSP-1001660016237-E-A12


title: DSP-1001660016237-E-B01


title: Spleen, cDC1s, eLNP, 8h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO005.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds


title: HAP1 HELLS KO cells, rep3

city: Birmingham

first: Wioletta

last: Czaja

state: AL

address: 1918 University Blvd

department: Department of Genetics

institute: University of Alabama at Birmingham

description: column name in counts.txt and fpkm.txt: HELLSKO_3

data_processing:
RNA-seq was aligned to the human genome (hg38) using STAR 2.7.3a.
Gene counts were generated and annotated with GENECODE Human release 22 (GRCh38.p2) using featureCounts 2.0.6.
FPKM was calculated using DESeq2 1.44.0 package in R.
Assembly: hg38
Supplementary files format and content: txt file containing FPKM values for all samples: fpkm.txt
Supplementary files format and content: txt file containing read counts for all samples: counts.txt

source_name: HAP1 HELLS KO

extract_protocol:
Total RNA was prepared from 1x106 cells of HAP1 and HELLS KO using Direct-zol RNA Microprep kit (Zymo Research).
The libraries were made with the NEB Next Ultra II Directional RNA Seq kit following the manufacturer’s protocols

value: HAP1 HELLS KO

value: chronic myelogenous leukemia

value: HELLS KO

value: Normal Growth

tag: batch


title: Whole Lymph Node, Donor HuLN2

description: Library name: HuLN2_wCTRL


title: HAP1 WT cells, rep3

description: column name in counts.txt and fpkm.txt: HAP1_3

value: WT


title: DSP-1001660016237-E-A11


title: Spleen, cDC1s, eLNP, 8h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO005.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: Spleen


title: M20, SPL, Combination, rep 2

description: Library name: Mouse-20-SPL-PCR2


title: M3, SPL, Combination, rep 1

description: Library name: Mouse-3-SPL-PCR1


title: MC8_N19-32

city: los angeles

first: yizhou

last: wang

address: 8700 beverly blvd

institute: cedars-sinai medical center

description: Library name: Sample 16

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format using bcl2fastq v2.20 (Illumina, San Diego, California). Then reads were aligned to the transcriptome using STAR (version 2.6.1)33/ RSEM (version 1.2.28)34 with default parameters, using a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on mouse GENCODE version 24 annotation. DESeq2 (version 1.46.0)35 was used for normalization and principal component analysis. Batch effect was corrected using limma36. Gene expression was fitted into a negative binomial generalized linear model, and differential expression was assessed using the Wald test. Multiple hypothesis testing was controlled with the Benjamini-Hochberg procedure, with differentially expressed (DE) genes selected based on a false discovery rate (FDR) threshold of <0.05. Visualization of significant DE genes, including heatmaps and volcano plots, was performed using the ggplot2 package (v3.0.3)37 in R. DEGs were further analyzed for KEGG and Gene Ontology (GO) enrichment using cluster Profiler (v3.20)38.
Assembly: GRCh38
Supplementary files format and content: csv file include raw read counts for each sample

source_name: CORNEA

growth_protocol: Human primary LECs were transfected with a hsa-miR-10b-5p mimic or negative controls (Invitrogen, Life Technologies cat #4464066 ASSAY ID: MC11108, cat #4464058) using Lipofectamine RNAiMAX (Thermo Fisher Scientific, MA cat #13778075) at a concentration of 50 nM. Transfection media were prepared by diluting the reagents in OPTI-MEM TM (Thermo Fisher Scientific MA cat #31985062) and their corresponding cell culture medium per manufacturer specification. Cells were transfected for 48 h and allowed to recover for a further 24 h in cell culture media before processing.

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit after Trizol lysis (Thermo Fisher Scientific) from age-matched non-diabetic (n = 10) human corneas following the manufacturer’s guidelines. The PureLink DNase Set (Thermo Fisher Scientific) was utilized for an on-column DNase digestion. Samples were eluted in RNase-free water. The concentration and quality of the RNA was evaluated using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific), Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Total RNA samples were analyzed for RNA integrity on the 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA) and quantified using the Qubit RNA HS Assay Kit (ThermoFisher Scientific, Waltham, MA). The SMART-Seq V4 Ultra Low RNA Input Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription and generation of double-stranded cDNA for subsequent library preparation using the Nextera XT Library Preparation Kit (Illumina, San Diego, CA). An input of up to 10 ng RNA was used for oligo(dT)-primed reverse transcription, followed by cDNA amplification and cleanup. Quantification of cDNA was performed using Qubit (Thermo Fisher Scientific). cDNA normalized to 80 pg/ml was fragmented, and sequencing primers were added simultaneously. A limiting-cycle PCR added Index 1 (i7) adapters, Index 2 (i5) adapters, and sequences required for cluster formation on the sequencing flow cell. Indexed libraries were then cleaned, library concentration was measured with a Qubit fluorometer (ThermoFisher Scientific), and library size was evaluated on a 4200 TapeStation (Agilent Technologies). Multiplexed libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75 bp single-end sequencing.

value: CORNEA

value: Primary cell

value: LIMBAL EPITHELIAL CELLS

value: miRNA-10b Mimic Control


title: MC6_N19-35

description: Library name: Sample 14

treatment_protocol: Total RNA was isolated using the PureLink RNA Mini Kit after Trizol lysis (Thermo Fisher Scientific) from age-matched non-diabetic (n = 10) human corneas following the manufacturer’s guidelines. The PureLink DNase Set (Thermo Fisher Scientific) was utilized for an on-column DNase digestion. Samples were eluted in RNase-free water. The concentration and quality of the RNA was evaluated using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific), Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).


title: M20, BM, Combination,  rep 2

description: Library name: Mouse-20-BM-PCR2

value: SPLINTR-GFP-Barcode


title: M3, BM, Combination, rep 1

description: Library name: Mouse-3-BM-PCR1


title: Spleen, cDC1s, Steady State, 0h, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO004.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: Steady State

value: HTO

value: See Custom feature_type in feature_reference_VBO_LNP.csv (Anti CD45 + Anti MHC class I :Replicate 1 = TotalSeq-A0301 ; Replicate 2 = TotalSeq-A0302 ; Replicate 3 = TotalSeq-A0303;  ; Replicate 4 = TotalSeq-A0304)


title: Spleen, cDC1s, Steady State, 0h, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
filtered_feature_bc_matrix_VBO004.h5
feature_reference_VBO_LNP.csv
seuratObj_VBO_4-12.rds

value: ADT

value: See Antibody Capture feature_type in feature_reference_VBO_LNP.csv


title: M20, BM, Combination, rep 1

description: Library name: Mouse-20-BM-PCR1

value: Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613)


title: DSP-1001660016237-E-A08

value: Brain


title: DSP-1001660016237-E-A10


title: M20, SPL, Combination, rep 1

description: Library name: Mouse-20-SPL-PCR1


title: MC7_N13-34

description: Library name: Sample 15


title: MC5_n19-13

description: Library name: Sample 13


title: DSP-1001660016237-E-A07


title: DSP-1001660016237-E-A09


title: KO lung tissues, replicate 3

city: Guangzhou

first: Ding

address: Zhong Shan Er Lu, Guangzhou, Guangdong Province, China

institute: Sun yet san university

data_processing:
Phred
HISAT2 (version 2.0.4, parameters--dta -p 6 --max-intronlen 5000000) was used to map the clean reads to Mus_musculus.GRCm38.
StringTie (version 1.3.4d, parameters--merge -F 0.1 -T 0.1) was applied to assemble the mapped reads
Assembly: Mus_musculus.GRCm38_release95.genome.fa
Supplementary files format and content: All_gene_count_fpkm.xlsx

source_name: Lung tissues

growth_protocol: The mice were maintained in a specific pathogen-free environment with a sterilized normal diet, acidified tap water (pH 2.5) using 0.002 N HCl, and autoclaved corn cob bedding.

extract_protocol:
RNA was harvested using TRIzol method. A total 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.

value: Lung tissues

value: Clec7a knockout

value: Intratracheal injection of bleomycin


title: MC4_N19-04

description: Library name: Sample 12

value: WT


title: M2, SPL, Combination, rep 2

description: Library name: Mouse-2-SPL-PCR2


title: DSP-1001660016239-C-A05


title: Spleen, cDC1s, Steady State, 0h, mRNA-derived cDNA

description:
poly A RNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
filtered_feature_bc_matrix_VBO004.h5
seuratObj_VBO_4-12.rds

value: Spleen

value: mRNA


title: WT lung tissues, replicate 3


title: M2, SPL, Combination, rep 1

description: Library name: Mouse-2-SPL-PCR1


title: M2, BM, Combination, rep 1

description: Library name: Mouse-2-BM-PCR1


title: KO lung tissues, replicate 2


title: MC3_N18-23

description: Library name: Sample 11

value: CORNEA

value: Primary cell


title: MC2_N18-19

description: Library name: Sample 10

value: LIMBAL EPITHELIAL CELLS

value: miRNA-10b Mimic Control


title: DSP-1001660016237-E-A05


title: MC1_N17-11

description: Library name: Sample 9


title: KO lung tissues, replicate 1


title: WT lung tissues, replicate 2


title: M19, SPL, SNDX-5613, rep 2

description: Library name: Mouse-19-SPL-PCR2

value: SPLINTR-GFP-Barcode

value: 10 mg/kg SNDX-5613


title: M2, BM, Combination,  rep 2

description: Library name: Mouse-2-BM-PCR2


title: DSP-1001660016237-E-A03


title: M19, SPL, SNDX-5613, rep 1

description: Library name: Mouse-19-SPL-PCR1


title: M8_N19-32

description: Library name: Sample 8

value: miRNA-10b Mimic


title: DSP-1001660016237-E-A01

value: No template control


title: DSP-1001660016237-E-A06


title: WT lung tissues, replicate 1


title: DSP-1001660016237-E-A02


title: M6_N19-35

description: Library name: Sample 6


title: mes-silencer-output5_mes-silencer-output5-16

city: shenzhen

first: Guoli

last: Li

address: penfei street

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

data_processing:
bowtie2 aligns sequencing data to the hg38 genome, samtools filters comparison data, and CRADLE software identifies silencer.
Assembly: hg38
Supplementary files format and content: bed file records silencer location and silencer activity
Library strategy: STARR-seq

source_name: mECSs

extract_protocol:
MEFs were inoculated with 10 % FBS (Gibco; Cat 10437028) and 1% penicillin streptomycin P/S (Sigma; cat P0781) in DMEM (Thermo Fisher; Cat 10566024), MEFs are induced in iCD1 medium(Delicell, Cat 820250). iPSCs and mESCs were cultured in N2B27-2i/LIF medium (Neural Basal, F12,1%Glutamax, 1%NEAA, 1%Sodium pyruvate, 0.1mM β-me, 1%B27, 0.5% N2, 0.5% P/s(optional), mLif(1:8000), 3uM CHIR99021(1:4000), 1 uM PD0325901). The culture conditions of all cells were 37 °C, 5 % carbon dioxide.
The construction of the random input DNA library involves three main steps: creating insert fragments, preparing the linearized vector, and seamless assembly cloning. First, the genome is fragmented into 300-400 base pair segments using an ultrasonic disruptor. The library construction kit (Roche; KK8514) is used to add homologous arms and Illumina adapters to these fragments. Next, the Ss-STARR-seq vector is digested with AgeI-HF and SalI-HF enzymes (NEB). The fragmented DNA is then recombined with the linearized vector using Gibson's homologous recombination enzyme (NEB). The quality of the library clones is verified through Sanger sequencing. Forty recombination reactions are set up, and the products are purified using a DNA purification kit (ZYMO; d4013). The purified DNA is transformed into competent cells (Thermo Fisher Scientific; c6400) and cultured in 15 liters of LB medium. When the bacterial culture reaches an optical density (OD) between 1.0 and 1.2, PCR amplification is performed using 100 ng of plasmid as a template. The PCR conditions include initial denaturation at 98°C for 45 seconds, followed by 20 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 30 seconds, and extension at 72°C for 30 seconds. The amplified products are recovered through 2% agarose gel electrophoresis and prepared for high-throughput sequencing. Cells transfected with the input library were harvested for RNA extraction using TURBOTM DNase (Thermo Fisher Scientific) and Dynabeads Oligo (dT)25 (Thermo Fisher Scientific). The enriched mRNA was reverse transcribed into cDNA using SuperScript TM IV Reverse Transcriptase (Thermo Fisher Scientific) and specific primers. AmbionTM RNase H was then used to degrade any remaining RNA in the cDNA product. The cDNA was purified and amplified via PCR using the HiFi high fidelity enzyme Ready Mix (Roche). The PCR protocol involved initial denaturation at 98°C for 45 seconds, followed by 20 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds. The PCR products were separated by 2% agarose gel electrophoresis to create the output library for high-throughput sequencing.

value: mECSs


title: M7_N13-34

description: Library name: Sample 7


title: DSP-1001660016220-D-G04


title: M19, BM, SNDX-5613, rep 1

description: Library name: Mouse-19-BM-PCR1


title: M19, BM, SNDX-5613,  rep 2

description: Library name: Mouse-19-BM-PCR2


title: mes-silencer-output5_mes-silencer-output5-15

growth_protocol: MEFs were inoculated with 10 % FBS (Gibco; Cat 10437028) and 1% penicillin streptomycin P/S (Sigma; cat P0781) in DMEM (Thermo Fisher; Cat 10566024), MEFs are induced in iCD1 medium(Delicell, Cat 820250). iPSCs and mESCs were cultured in N2B27-2i/LIF medium (Neural Basal, F12,1%Glutamax, 1%NEAA, 1%Sodium pyruvate, 0.1mM β-me, 1%B27, 0.5% N2, 0.5% P/s(optional), mLif(1:8000), 3uM CHIR99021(1:4000), 1 uM PD0325901). The culture conditions of all cells were 37 °C, 5 % carbon dioxide.


title: M5_n19-13

description: Library name: Sample 5


title: DSP-1001660016237-E-A04


title: DSP-1001660016220-D-G03


title: M4_N19-04

description: Library name: Sample 4


title: M18, SPL, SNDX-5613, rep 2

description: Library name: Mouse-18-SPL-PCR2


title: M3_N18-23

description: Library name: Sample 3


title: mes-silencer-output5_mes-silencer-output5-13


title: DSP-1001660016220-D-G02


title: M18, SPL, SNDX-5613, rep 1

description: Library name: Mouse-18-SPL-PCR1


title: DSP-1001660016220-D-G01


title: DSP-1001660016220-D-F12


title: mes-silencer-output5_mes-silencer-output5-11


title: M2_N18-19

description: Library name: Sample 2


title: M18, BM, SNDX-5613, rep 1

description: Library name: Mouse-18-BM-PCR1


title: mes-silencer-output5_mes-silencer-output5-14


title: DSP-1001660016220-D-F11


title: MHCC_97L_Input

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

description: Library name: Sample 4

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: hg38
Supplementary files format and content: wig files were generated using deepTools. Peaks were identified using the MACS2 peak caller

source_name: liver

growth_protocol: MHCC97L was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
ChIP-seq were performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:240-8).
DNA-seq library preparation

treatment_protocol: untreated

value: liver

value: HCC cells

tag: antibody

value: Input


title: M17, SPL, PF-9363, rep 2

description: Library name: Mouse-17-SPL-PCR2


title: mes-silencer-output5_mes-silencer-output5-9


title: DSP-1001660016220-D-F09

value: Brain


title: MHCC_97L_H3K4me3

description: Library name: Sample 3


title: M17, SPL, PF-9363, rep 1

description: Library name: Mouse-17-SPL-PCR1


title: M17, BM, PF-9363,  rep 2

description: Library name: Mouse-17-BM-PCR2


title: mes-silencer-output5_mes-silencer-output5-8


title: mes-silencer-output5_mes-silencer-output5-7


title: M17, BM, PF-9363, rep 1

description: Library name: Mouse-17-BM-PCR1


title: MHCC_97L_H3K27ac

description: Library name: Sample 1


title: mes-silencer-output5_mes-silencer-output5-6


title: M16, SPL, SNDX-5613, rep 2

description: Library name: Mouse-16-SPL-PCR2


title: DSP-1001660016220-D-F06


title: mes-silencer-output5_mes-silencer-output5-12


title: mes-silencer-output5_mes-silencer-output5-5


title: M16, SPL, SNDX-5613, rep 1

description: Library name: Mouse-16-SPL-PCR1


title: mes-silencer-output5_mes-silencer-output5-10


title: mes-silencer-output5_mes-silencer-output5-4


title: SCP28 cells, IGFBP3 KD1

city: Beijing

first: Pan

last: Jingyu

address: Haiding Street

department: School of basic medicine sciences

institute: Tsinghua university

description: Library name: Sample5

data_processing:
Cutadapt--HISAT2--HTSEQ--DESeq2/EdgeR
Assembly: mm39, hg38
Supplementary files format and content: raw counts

source_name: Mammary gland

extract_protocol:
RNA was extracted by RNAiso reagent. 0.1-1ug total RNA was used for constructing RNA-seq library
RNA-seq library was constructed by NEB kit according to the manufacturer's protocol

value: Mammary gland

value: Breast cancer cell

value: IGFBP3 knockdown

value: No


title: DSP-1001660016220-D-F05

value: WT


title: M16, BM, SNDX-5613,  rep 2

description: Library name: Mouse-16-BM-PCR2


title: DSP-1001660016220-D-F04


title: M16, BM, SNDX-5613, rep 1

description: Library name: Mouse-16-BM-PCR1


title: mes-silencer-output5_mes-silencer-output5-3


title: SCP28 cells, Scramble2

description: Library name: Sample4


title: DSP-1001660016220-D-F08


title: MHCC_97L_H3K4me1

description: Library name: Sample 2


title: SCP28 cells, Scramble1

description: Library name: Sample3


title: M15, SPL, PF-9363, rep 2

description: Library name: Mouse-15-SPL-PCR2


title: DSP-1001660016220-D-F03


title: DSP-1001660016220-D-F07


title: M1_N17-11

description: Library name: Sample 1

value: CORNEA

value: Primary cell


title: DSP-1001660016220-D-F02


title: M18, BM, SNDX-5613,  rep 2

description: Library name: Mouse-18-BM-PCR2


title: mes-silencer-output5_mes-silencer-output5-1


title: mes-silencer-output5_mes-silencer-output5-2


title: M15, SPL, PF-9363, rep 1

description: Library name: Mouse-15-SPL-PCR1


title: SCP28 cells, IGFBP3 KD2

description: Library name: Sample6


title: HCT116_sc_DEX_1h

city: Xiamen

first: Siying

last: Wang

state: Fujian

address: 422 Siming Road

institute: Xiamen university

description:
Library name: sample23
with 6sG labeled 12h, 4sU labeled 1h, and DUAL TimeLaplse chemistry treatment

data_processing:
scDUAL-seq pipeline
Assembly: GRCh38
Supplementary files format and content: For bulk assays, a txt file contains the mutation counts of genes. For single-cell experiments, an RDS file contains a gene-by-cell data matrix.

growth_protocol: Human colorectal cancer HCT116 cells (ATCC, CCL-247) and human embryonic kidney HEK293T cells (ATCC, CRL-3216) were cultured in high-glucose Dulbecco’s Modified Eagle Medium (DMEM; BasalMedia, catalog no. L120KJ) supplemented with 10% fetal bovine serum (FBS; Vazyme, catalog no. F101-01) and 1% penicillin-streptomycin (Gibco, catalog no. 15140-122). The cells were maintained at 37℃ in a humidified atmosphere with 5% CO2 and passaged every 3-4 days. For cell harvesting, a trypsin-EDTA solution (0.25% trypsin, 0.02% EDTA, with phenol red; Biosharp, catalog no. BL512B) was applied for 1-2 min to induce detachment.

extract_protocol:
For bulk RNA extraction, 1×10^6 to 5×10^6 cells were fully lysed in 500 μL of RNA-easy buffer (Vazyme, catalog no. R701-01) following the manufacturer’s protocol. For single-cell experiments, cells are loaded into the Well-Paired-Seq chip (Decoder Cartridge; Dynamic Biosystems, 2203106) for library preparation using the DECODER single cell 3’ kits (Dynamic Biosystems, 2203206, 2203306, 2203406) with an additional step of Dual TimeLapse chemistry treatment before reverse transcription.
For bulk assays, the sequencing library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, catalog no. TD502-01) according to the manufacturer’s instructions. For single-cell experiments, the 3’-end enriched sequencing library was prepared by the reagents in DECODER single cell 3’ kits (Dynamic Biosystems, 2203306, 2203406) without further modifications.

treatment_protocol: For metabolic RNA labeling, cells were first cultured with 200 μM 6sG for 12 h, followed by replacement with medium containing 200 μM 4sU for different durations (0 h, 0.5 h, 1 h, and 2 h). For DEX treatment experiments, cells were first cultured in a 6sG-containing medium for 12 h and then cultured in a medium supplemented with 100 nM DEX and 200 μM 4sU for different durations (0 h, 0.5 h, 1 h, and 2 h). After labeling, the cells were detached using trypsin, centrifuged at 1,500 rpm for 3 min at 4 ℃, and washed once with 1× phosphate-buffered saline (PBS).

value: human colorectal cancer cells


title: DSP-1001660016220-D-F10


title: HCT116_sc_DEX_0.5h

description:
Library name: sample22
with 6sG labeled 12h, 4sU labeled 0.5h, and DUAL TimeLaplse chemistry treatment


title: M15, BM, PF-9363,  rep 2

description: Library name: Mouse-15-BM-PCR2

value: SPLINTR-GFP-Barcode


title: MES-silencer-output4_MES-silencer-output4-20


title: DSP-1001660016220-D-F01


title: DSP-1001660016220-D-E12


title: HCT116_sc_DEX_0h

description:
Library name: sample21
with 6sG labeled 12h, 4sU labeled 0h, and DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-E11


title: MES-silencer-output4_MES-silencer-output4-19


title: M15, BM, PF-9363, rep 1

description: Library name: Mouse-15-BM-PCR1


title: MES-silencer-output4_MES-silencer-output4-18


title: M14, SPL, Vehicle, rep 2

description: Library name: Mouse-14-SPL-PCR2

value: Vehicle


title: DSP-1001660016220-D-E10


title: HCT116_sc_DEX_2h

description:
Library name: sample24
with 6sG labeled 12h, 4sU labeled 2h, and DUAL TimeLaplse chemistry treatment


title: HCT116_sc_1h

description:
Library name: sample19
with 6sG labeled 12h, 4sU labeled 1h, and DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-E09


title: M14, SPL, Vehicle, rep 1

description: Library name: Mouse-14-SPL-PCR1


title: HCT116_sc_2h

description:
Library name: sample20
with 6sG labeled 12h, 4sU labeled 2h, and DUAL TimeLaplse chemistry treatment


title: HCT116_sc_0.5h

description:
Library name: sample18
with 6sG labeled 12h, 4sU labeled 0.5h, and DUAL TimeLaplse chemistry treatment


title: M14, BM, Vehicle, rep 2

description: Library name: Mouse-14-BM-PCR2


title: DSP-1001660016220-D-E08


title: M13, SPL, Vehicle, rep 2

description: Library name: Mouse-13-SPL-PCR2


title: M14, BM, Vehicle, rep 1

description: Library name: Mouse-14-BM-PCR1


title: HCT116_sc_0h

description:
Library name: sample17
with 6sG labeled 12h, 4sU labeled 0h, and DUAL TimeLaplse chemistry treatment


title: MES-silencer-output4_MES-silencer-output4-15


title: HCT116_sc_control

description:
Library name: sample16
with 6sG labeled 12h and 4sU labeled 2h while without DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-E06


title: MES-silencer-output4_MES-silencer-output4-13


title: M13, SPL, Vehicle, rep 1

description: Library name: Mouse-13-SPL-PCR1


title: DSP-1001660016220-D-E05


title: MES-silencer-output4_MES-silencer-output4-12


title: HEK293T_bulk_2h

description:
Library name: sample15
with 6sG labeled 12h, 4sU labeled 2h, and DUAL TimeLaplse chemistry treatment

value: human embryonic kidney cells


title: M13, BM, Vehicle, rep 2

description: Library name: Mouse-13-BM-PCR2


title: M13, BM, Vehicle, rep 1

description: Library name: Mouse-13-BM-PCR1


title: MES-silencer-output4_MES-silencer-output4-16


title: DSP-1001660016220-D-E04


title: DSP-1001660016220-D-E03


title: MES-silencer-output4_MES-silencer-output4-10


title: MES-silencer-output4_MES-silencer-output4-11


title: HEK293T_bulk_1h

description:
Library name: sample14
with 6sG labeled 12h, 4sU labeled 1h, and DUAL TimeLaplse chemistry treatment


title: MES-silencer-output4_MES-silencer-output4-14


title: MES-silencer-output4_MES-silencer-output4-17


title: DSP-1001660016220-D-E07


title: M12, SPL, SNDX-5613, rep 2

description: Library name: Mouse-12-SPL-PCR2

value: 10 mg/kg SNDX-5613


title: M12, SPL, SNDX-5613, rep 1

description: Library name: Mouse-12-SPL-PCR1


title: MES-silencer-output4_MES-silencer-output4-9

value: mECSs


title: HEK293T_bulk_0h

description:
Library name: sample12
with 6sG labeled 12h, 4sU labeled 0h, and DUAL TimeLaplse chemistry treatment


title: HEK293T_bulk_control

description:
Library name: sample11
with 6sG labeled 12h and 4sU labeled 2h while without DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-E01


title: M12, BM, SNDX-5613,  rep 2

description: Library name: Mouse-12-BM-PCR2


title: HCT116_bulk_rep2_2h

description:
Library name: sample10
with 6sG labeled 12h, 4sU labeled 2h, and DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-E02


title: DSP-1001660016220-D-D12


title: MES-silencer-output4_MES-silencer-output4-8


title: HCT116_bulk_rep2_1h

description:
Library name: sample9
with 6sG labeled 12h, 4sU labeled 1h, and DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-D11


title: MES-silencer-output4_MES-silencer-output4-6


title: M11, SPL, PF-9363, rep 2

description: Library name: Mouse-11-SPL-PCR2


title: HEK293T_bulk_0.5h

description:
Library name: sample13
with 6sG labeled 12h, 4sU labeled 0.5h, and DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-D10


title: HCT116_bulk_rep2_0h

description:
Library name: sample7
with 6sG labeled 12h, 4sU labeled 0h, and DUAL TimeLaplse chemistry treatment


title: M11, SPL, PF-9363, rep 1

description: Library name: Mouse-11-SPL-PCR1


title: MES-silencer-output4_MES-silencer-output4-4


title: M11, BM, PF-9363,  rep 2

description: Library name: Mouse-11-BM-PCR2


title: HCT116_bulk_rep2_control

description:
Library name: sample6
with 6sG labeled 12h and 4sU labeled 2h while without DUAL TimeLaplse chemistry treatment


title: M11, BM, PF-9363, rep 1

description: Library name: Mouse-11-BM-PCR1


title: HCT116_bulk_rep1_2h

description:
Library name: sample5
with 6sG labeled 12h, 4sU labeled 2h, and DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-D09


title: DSP-1001660016220-D-D08


title: MES-silencer-output4_MES-silencer-output4-3


title: MES-silencer-output4_MES-silencer-output4-7


title: DSP-1001660016220-D-D06


title: M10, SPL, Combination, rep 2

description: Library name: Mouse-10-SPL-PCR2

value: Combination (5 mg/kg PF-9363 and 10 mg/kg SNDX-5613)


title: M12, BM, SNDX-5613, rep 1

description: Library name: Mouse-12-BM-PCR1


title: DSP-1001660016220-D-D07


title: HCT116_bulk_rep1_1h

description:
Library name: sample4
with 6sG labeled 12h, 4sU labeled 1h, and DUAL TimeLaplse chemistry treatment


title: M10, SPL, Combination, rep 1

description: Library name: Mouse-10-SPL-PCR1


title: HCT116_bulk_rep1_0.5h

description:
Library name: sample3
with 6sG labeled 12h, 4sU labeled 0.5h, and DUAL TimeLaplse chemistry treatment


title: MES-silencer-output4_MES-silencer-output4-1


title: mES-silencer-output2_mES-silencer-output2-20


title: HCT116_bulk_rep2_0.5h

description:
Library name: sample8
with 6sG labeled 12h, 4sU labeled 0.5h, and DUAL TimeLaplse chemistry treatment


title: HCT116_bulk_rep1_0h

description:
Library name: sample2
with 6sG labeled 12h, 4sU labeled 0h, and DUAL TimeLaplse chemistry treatment


title: DSP-1001660016220-D-D04


title: mES-silencer-output2_mES-silencer-output2-19


title: DSP-1001660016220-D-D05


title: M10, BM, Combination,  rep 2

description: Library name: Mouse-10-BM-PCR2


title: MES-silencer-output4_MES-silencer-output4-2


title: M1, SPL, Vehicle, rep 2

description: Library name: Mouse-1-SPL-PCR2


title: DSP-1001660016220-D-D03


title: mES-silencer-output2_mES-silencer-output2-17


title: MCC84

city: Montreal

first: Richie

last: Jeremian

state: Quebec

address: 1001 Decarie Blvd, Research Institute of the McGill University Health Centre (RI-MUHC)

country: Canada

institute: McGill University Division of Dermatology

description: Library name: MCC84

data_processing:
bcl2fastq2 v2.20
Assembly: hg19
Supplementary files format and content: Processed count data

source_name: Merkel cell carcinoma

extract_protocol:
Total RNA from FFPE-preserved MCC
NEBNext Ultra II DNA Library Prep Kit

value: Merkel cell carcinoma

tag: age

tag: Sex

value: Female

tag: immunosuppressed

value: Yes

tag: mcpyv

value: Positive

tag: tumor

value: Metastatic


title: mES-silencer-output2_mES-silencer-output2-18


title: M10, BM, Combination, rep 1

description: Library name: Mouse-10-BM-PCR1


title: MCC91

description: Library name: MCC91

value: missing


title: MCC77

description: Library name: MCC77

value: Male


title: mES-silencer-output2_mES-silencer-output2-15


title: M1, SPL, Vehicle, rep 1

description: Library name: Mouse-1-SPL-PCR1


title: M1, BM, Vehicle, rep 1

description: Library name: Mouse-1-BM-PCR1


title: DSP-1001660016220-D-D01

value: Brain

value: WT


title: Molm-13, mixed treatment groups, single crosslinked, 5% input, Menin

description:
Library name: Mix-Input-SXL_Menin
Menin antibody (Bethyl Laboratories A300-105A)

data_processing:
Read quality was assess by FastQC v0.11.6 before trimming adapters with cutadapt v1.14. Reads were aligned to Hg38 using Bowtie2v.2.3.4.1 with the --no-unal, --no-discordant and --no-mixed flags plus -I 10 and -X 700 in addition to default settings. Duplicates were removed using the Picard toolkit v2.6.0. Sorting and indexing were performed with SAMtools v1.9. Broad peaks were called with MACS2 v2.1.1. Reads per genomic content (RPGC) normalised bigwigs and heatmaps were generated with deeptools v3.5.0.
Assembly: Hg38
Supplementary files format and content: bigwig

growth_protocol: Molm-13 cells were cultured at 37 C and 5% CO2 in RPMI-1640, 10% heat inactivated fetal bovine serum (FBS), 2 mM L-Glutamine, 100 IU/ml Penicillin and 100 g/ml Streptomycin.

extract_protocol:
Crosslinked cells were lysed in shearing buffer (50mM Tris pH 8.0, 1% (v/v) SDS, 10mM EDTA supplemented with protease and phosphatase inhibitors). Chromatin was sonicated to 250-1000 bp fragments using the Covaris ME220 Focused-ultrasonicator. Debris was cleared by retaining the supernatant after centrifugation at 20,000 x g for 15 min at 10 C. MLL1 and Menin immunoprecipitations were performed from 50 ug and 20 ug of sonicated chromatin respectively following quantification by Quibit DNA BR quantification kit. Chromatin was diluted with wash buffer (50mM Tris pH 8.0, 150mM NaCl, 2mM EDTA, 1% v/v Triton X-100, supplemented with protease inhibitors) and immunoprecipitation overnight at 4oC with rotation mixing. Antibody bound complexes were immobilised with 30μL of pre-washed Protein A Dynabeads (Thermofisher) for 4 hours at 4oC with rotation mixing and collected using a magnetic rack. Beads were washed five times with wash buffer, once with high-salt wash buffer (wash buffer with 500mM NaCl and 0.1% SDS)  followed by a final wash with TE buffer (10mM Tris pH 8.0, 1mM EDTA). Crosslinks were reversed by incubating beads in elution buffer (20mM Tris pH 7.5, 200mM NaCl, 5mM EDTA, 1% v/v SDS, 200μg/mL Proteinase K (Roche) and 200ug/mL RNAse A (Qiagen) at 65 C overnight with gentle agitation (1000 rpm). Immunoprecipitated DNA was purified using Qiagen MinElute columns (Qiagen).
ChIP-seq libraries were prepared using the Takara Bio Thruplex DNA-Seq Kit as per manufacturers instructions. Samples were sequened

treatment_protocol: Approximately 65 million Molm-13 cells were treated with 0.1% DMSO, 2.5 uM PF-9363, 100 nM VTP50469 or the combination of 2.5 uM PF-9363 and 100 nM VTP50469 for 6 hours. 30 million cells Molm-13 cells were crosslinked with single (1% methanol-free formaldehyde/PBS for 15 mins) and another 30 million were dual crosslinked (2mM DSG/PBS for 30 mins followed by 1% formaldehyde for 15 mins). Crosslinking was quenched with 250 mM Tris pH 8.0

value: Mix of all treatment samples used in Menin IP


title: mES-silencer-output2_mES-silencer-output2-16


title: M1, BM, Vehicle, rep 2

description: Library name: Mouse-1-BM-PCR2


title: DSP-1001660016220-D-C10


title: HCT116_bulk_rep1_control

description:
Library name: sample1
with 6sG labeled 12h and 4sU labeled 2h while without DUAL TimeLaplse chemistry treatment

value: human colorectal cancer cells


title: DSP-1001660016220-D-C12


title: MES-silencer-output4_MES-silencer-output4-5


title: mES-silencer-output2_mES-silencer-output2-14


title: DSP-1001660016220-D-C11


title: mES-silencer-output2_mES-silencer-output2-13


title: MCC81

description: Library name: MCC81

value: No


title: MCC67

description: Library name: MCC67


title: DSP-1001660016220-D-C09


title: MCC76

description: Library name: MCC76


title: mES-silencer-output2_mES-silencer-output2-12


title: DSP-1001660016220-D-C08


title: DSP-1001660016220-D-D02


title: MCC64

description: Library name: MCC64

value: Primary


title: Molm-13, mixed treatment groups, single crosslinked IgG antibody for Menin IPs

description:
Library name: Mix-IgG-SXL_Menin
anti-rabbit IgG XP Isotype control (CST, 3900S)


title: mES-silencer-output2_mES-silencer-output2-11


title: Molm-13, mixed treatment groups, dual crosslinked IgG antibody for MLL1 IPs

description:
Library name: Mix-IgG-DXL_MLL
anti-rabbit IgG XP Isotype control (CST, 3900S)

value: Mix of all treatment samples used in MLL1 IP


title: DSP-1001660016220-D-C07


title: mES-silencer-output2_mES-silencer-output2-9


title: Molm-13, PF-9363 and VTP50469, MLL IP

description:
Library name: Combo-MLL
MLL1 antibody (Bethyl Laboratories A300-086A)


title: Molm-13, PF-9363 and VTP50469, Menin IP

description:
Library name: Combo-Menin
Menin antibody (Bethyl Laboratories A300-105A)


title: DSP-1001660016220-D-C06


title: MCC63

description: Library name: MCC63


title: MCC57

description: Library name: MCC57


title: Molm-13, mixed treatment groups, dual crosslinked, 5% input, MLL1

description:
Library name: Mix-Input-DXL_MLL
MLL1 antibody (Bethyl Laboratories A300-086A)


title: MCC50

description: Library name: MCC50


title: MCC34

description: Library name: MCC34


title: Molm-13, VTP50469, MLL IP

description:
Library name: VTP-MLL
MLL1 antibody (Bethyl Laboratories A300-086A)


title: DSP-1001660016220-D-C02


title: MCC32

description: Library name: MCC32


title: MCC43

description: Library name: MCC43


title: Molm-13, VTP50469, Menin IP

description:
Library name: VTP-Menin
Menin antibody (Bethyl Laboratories A300-105A)


title: mES-silencer-output2_mES-silencer-output2-7


title: DSP-1001660016220-D-C05


title: mES-silencer-output2_mES-silencer-output2-8


title: DSP-1001660016220-D-C04


title: DSP-1001660016220-D-C01


title: mES-silencer-output2_mES-silencer-output2-4


title: Molm-13, PF-9363, MLL IP

description:
Library name: CTX-MLL
MLL1 antibody (Bethyl Laboratories A300-086A)


title: MCC24

description: Library name: MCC24

value: Negative


title: mES-silencer-output2_mES-silencer-output2-10

value: mECSs


title: DSP-1001660016220-D-B12


title: mES-silencer-output2_mES-silencer-output2-3


title: MCC14

description: Library name: MCC14


title: Molm-13, DMSO, Menin IP

description:
Library name: VEH-Menin
Menin antibody (Bethyl Laboratories A300-105A)

value: 0.1% DMSO


title: MCC7

description: Library name: MCC7

value: Merkel cell carcinoma


title: Molm-13, DMSO, MLL IP

description:
Library name: VEH-MLL
MLL1 antibody (Bethyl Laboratories A300-086A)


title: DSP-1001660016220-D-B10


title: DSP-1001660016220-D-B11


title: mES-silencer-output2_mES-silencer-output2-2


title: MCC3

description: Library name: MCC3

value: Female


title: HumanLymphNode_H3K27ac CUT&Tag

city: New Haven

first: Timothy

middle: S

last: McConnell

state: CT

address: 290 Congress Ave

institute: AtlasXomics

description:
Library name: D01630_h3k27ac_1
DBiT-Seq

data_processing:
Processing of fastq files and downstream analysis is described in ATX_epigenomics repo on github.com. Briefly, reads that do not contain barcode linker sequences are filtered out using BBduk.  The remaining reads were aligned to human genome reference using chromap aligner, producing a fragement file.
Downstream analysis, also described in the ATX_epigenomics repository, employed ArchR and Seurat packages along with software package found in AtlasXbrowser repo on github.com to generate spatial clustering and analyses using the fragment file, postB_BSA.tiff and bc96FG_11DEC.txt as input.
Assembly: human GRCh38
Supplementary files format and content: Block zipped fragment file *.tsv.gz

extract_protocol:
The experimental protocol followed the detailed instructions for CUT&Tag tissue preparation (AXO-0456), FlowGel stamping and lysing (AXO-0457), and CUT&Tag library preparation (AXO-0460).  Protocols are available at https://www.atlasxomics.com/resources?category=Protocol#hello. On the glass slide, tissue is fixed, quenched, washed, permeabilized, and tagmented (AXO-0456). Using an AtlasXomics clamp, the FlowGel Chip, two barcode chips are applied perpendicular to each other to create a grid of paired barcodes spanning the region of interest (ROI), and each is ligated to the available DNA fragments at each spot (AXO-0457). The tissue is then lysed, and the DNA is purified.
The DNA library is then prepared by PCR amplification, purification, and qualified prior to sequencing (AXO-0460).

value: lymph node

value: H3K27ac CUT&Tag FlowGel DBiT


title: mES-silencer-output2_mES-silencer-output2-5


title: Molm-13, PF-9363, Menin IP

description:
Library name: CTX-Menin
Menin antibody (Bethyl Laboratories A300-105A)


title: HAP1 HELLS KO cells, rep2

description: column name in counts.txt and fpkm.txt: HELLSKO_2

growth_protocol: Normal Growth

value: HAP1 HELLS KO

value: chronic myelogenous leukemia

value: HELLS KO

value: Normal Growth


title: DSP-1001660016220-D-C03

value: Brain

value: WT


title: mES-silencer-output2_mES-silencer-output2-6


title: mES-silencer-output2_mES-silencer-output2-1


title: MCF10A_YAP5SA_prexasertib_rep2

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

country: Germany

institute: University of Wuerzburg

description:
Library name: Sample 10
MapR assay to detect R-loops

data_processing:
Galaxy was used to analyze NGS data (https://usegalaxy.eu)
Adaptors were rtrimmed with Trimmomatic (0.38.1)
Reads were mapped to the human genome (hg38) using Bowtie2 (2.4.2)
Bigwig files were generated using bamCoverage (3.5.4)
Broad peaks were called using MACS2 (2.2.9.1) with the significance value q<0.05
Differential peak analysis was performed with Diffbind (3.12)
Assembly: hg38
Supplementary files format and content: bigWig files for each sample

source_name: cell line

growth_protocol: MCF10A stably expressing doxycycline inducible YAP5SA or ER-YAP2SA and MY-COMP were grown in were cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.

extract_protocol:
Cells were immobilized on concanavalin A-coated beads and permeabilized. GST-RHΔ-MNase to target RNA–DNA hybrids (R-loops) was added. Following enzymatic cleavage at R-loops sites, released genomic DNA was extracted using phenol-chloroform purification and ethanol precipitation.
Library was prepared using NEBNext Ultra II DNA Library Prep Kit (NEB) according to the manufacturer’s protocol.

treatment_protocol: YAP5SA was induced with 0.5µg/ml doxycycline for 48 hours. CHK1 was inhibited with 100 nM prexasertib for 8 hours. BRD4 was inhibited with 500 nM JQ1 for 16 hours.

value: breast epitehlial

value: YAP5SA 48  hours/ 100 nM prexasertib 8 hours


title: MCF10A_YAP5SA_prexasertib_rep1

description:
Library name: Sample 9
MapR assay to detect R-loops


title: MEF-silencer-output4_MEF-silencer-output4-16

source_name: MEFs

value: MEFs


title: DSP-1001660016220-D-B09


title: DSP-1001660016220-D-B08


title: HAP1 HELLS KO cells, rep1

description: column name in counts.txt and fpkm.txt: HELLSKO_1


title: MEF-silencer-output4_MEF-silencer-output4-15


title: MEF-silencer-output4_MEF-silencer-output4-14


title: DSP-1001660016220-D-B07


title: MEF-silencer-output4_MEF-silencer-output4-13


title: MCF10A_prexasertib_rep1

description:
Library name: Sample 7
MapR assay to detect R-loops

value: 100 nM prexasertib 8 hours


title: HUH7_NR2C2_ChIP

description: ChIPseq_HUH7_NR2C2_vs_Input-NR2C2_peaks.loc.anno.gene.xlsx

data_processing:
For ChIP-seq assays, raw FASTQ ﬁles were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters. For RNA-seq assays, the paired-end reads were aligned to hg38 using STAR. After calculating raw gene expression levels (raw read counts) with FeatureCounts, normalized profiling data were obtained with DESeq2 for differential expression analysis.
For CRISPR screening, the raw FASTQ ﬁles were demultiplexed using Geneious 7.0 (Biomatters Inc.) and processed such that they contained only the unique sgRNA sequence. The designed barcode sequences from the library were assembled into a mapping reference sequence to align the processed reads to the library. The reads were then aligned to the reference sequence using the "Map to Reference" function in Geneious 7.0. After alignment, the number of uniquely aligned reads for each library sequence was calculated. The number of reads of each unique sgRNA for a certain sample was normalized as follows: normalized read counts per unique barcode = reads per barcode/total reads for all barcodes in the sample × 10^6 + 1. The sgRNA score was generated and ranked according to the depletion or enrichment of the normalized sgRNA counts (Sequence_results_T_vs_C.xlsx).
For ChIP-seq assays, bam files were converted to BigWig files using deepTools.
For ChIP-seq assays, peaks were identified using the MACS2 peak caller with the following parameters: -t treatment -c input –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: For RNA-seq and ChIP-seq assays, hg38. For CRISPR screening, the reads were aligned to the reference sequence of the library.
Supplementary files format and content: peak files were generated using MACS2.

growth_protocol: HUH7 was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.  ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.  Methods.2009;48:240-8)；
Total RNA extracted using TRIzol was used for library preparation with an Illumina mRNA sequencing (mRNAseq) sample preparation kit.  Quality control of the RNA sequencing libraries was performed using a Bioanalyzer 2100 (Agilent, CA, USA) prior to paired-end sequencing on the HiSeq 6000 platform (Illumina, CA, USA);  ChIP-seq was performed according to the manufacturer’s protocol (NEB, Shanghai, China). For CRISPR screening, Genomic DNA of day 0 cell samples and xenograft tumor samples were extracted with the Qiagen Blood & Cell Culture Midi Kit (Qiagen, Hilden, Germany). SgRNA cassettes were amplified from genomic DNA samples as the ﬁrst PCR, the amplicons resulting from the second PCR were extracted with beads (Beckman Coulter, USA), quantiﬁed, mixed, and sequenced using a NextSeq 500 instrument (Illumina, USA).

treatment_protocol: siRNAs targeting DDX41 and negative control siRNAs (NC) were procured from RiboBio (Guangzhou, China).  Cells were transfected with the specified targeted or control siRNA  using Lipofectamine RNAiMAX reagent (Invitrogen, CA, USA).  After 48 hours of transfection, the cells were collected for further experiments.HUH7 cells with stable overexpression of Flag-DDX41, Flag-RNASEH1-Mu (for R-ChIP assay), Flag-NR2C1, Flag-NR2C2 were collected for further experiments. For CRISPR screening, customized library containing 4992 sgRNAs specifically targeting 832 transcription factor (TF) and chromatin regulator (CR) genes (6 sgRNAs per gene), with 500 negative control sgRNAs and 12 positive control sgRNAs for 2 validated oncogenes. HUH7 cells were transduced with the pooled sgRNA lentiviral library at a low MOI value of 0.3. After 7 days of puromycin (Invitrogen, USA) selection (5 μg/ml), the surviving cells were considered to be the day 0 sample, and 3×10^7 of these cells were stored for further processing. The remaining cells were counted, and 1×10^7 cells per mouse were subcutaneously injected into NOD/Scidil2Rγ-/- (NSG) mice for xenograft tumor formation. Genomic DNA of day 0 cell samples (C1-C5) and xenograft tumor samples (T1-T5) were extracted and amplified for sequencing.

value: liver

value: HCC cells

value: Flag-NR2C2 overexpression

value: HUH7 cells infected with pCDH-Flag-NR2C2 lentivirus


title: Sublibrary_2

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

description: Library name: CPZ_Sublibrary_2

data_processing:
The Ensembl GRCh38 genome was subsetted to retain only protein coding genes prior to alignment.
FASTQ files were aligned to the GRCh38 transcriptome using the Parse split-pipe v1.2.0 alignment tool
Assembly: Ensembl GRCh38 release 111
Supplementary files format and content: Sublibrary*_all_genes.csv - Taken from the “DGE_Filtered” output directory of SplitPipe. Comma-delimited file that contains all genes names for the analysis.
Supplementary files format and content: Sublibrary*_cell_metadata.csv - Taken from the “DGE_Filtered” output directory of SplitPipe. Comma-delimited file that contains metadata for every cell in the sublibrary.
Supplementary files format and content: Sublibrary*_count_matrix.mtx - Taken from the “DGE_Filtered” output directory of SplitPipe. Matrix file that contains count data for every gene/cell combination.

source_name: Mouse brain

growth_protocol: transplantation protocol: Immunodeficient mice humanized for the CSF1 gene (hCSF1 mice) were xenotransplanted with iPSC-derived hematopoinetic progenitor cells at postnatal day 2. iPSCs contained the G795A mutation to the CSF1R gene, rendering the resulting microglia resistant to PLX3397-induced cell death. Therefore, at three weeks of age, mice were treated with 290mg/kg PLX3397 for two weeks to kill endogenous mouse microglia while allowing for the expansion of xenotransplanted human microglia.

extract_protocol:
Human microglia were isoloated by dounce homogenization of the mouse brain, followed by removal of myelin via Percoll gradient and removal of mouse cells using the Miltenyi Mouse Cell Depletion kit. Immediately after isolation, microglia were fixed using the Parse Evercode Cell Fixation v2 kit.
Cell barcoding and library construction was performed in accordance with the Parse Evercode WT Mini v2 protocol.

treatment_protocol: At 12 weeks of age, mice received either normal chow (n=3) or chow containing 0.2% cuprizone (CPZ; n=3) for four weeks.

value: Mouse brain

value: Microglia

tag: cell sex

value: Male

tag: mouse genotype

tag: mouse sex

tag: mouse age_(weeks)


title: MCF10A_prexasertib_rep2

description:
Library name: Sample 8
MapR assay to detect R-loops


title: HAP1 WT cells, rep2

description: column name in counts.txt and fpkm.txt: HAP1_2


title: DSP-1001660016220-D-B06

data_processing:
Fastq files were converted to DCC files using the GeoMx NGS Pipeline software and the mm10 reference genome.
Digital Count Conversion files, containing expression count data and sequencing quality metadata, and Probe Kit Configuration files, containing probe assay and sample metadata, were imported into R. Gene expression counts with a value of 0 were shifted to 1 to facilitate downstream transformations. ROI segments were filtered and removed if they met the criteria: “<1000 raw reads”, “below 80% Aligned or 80% Trimmed”, “80% Stitched”, and “below 50% sequencing saturation”. Genes were filtered and removed if they were not detected in at least 10% of segments. Next, counts were normalized using quartile 3 normalization and visualized by uniform manifold approximation and projection, a non-linear dimensionality reduction visualization tool. Gene expression in both datasets was relatively well separated according to ROI brain region.
Assembly: mm10
Supplementary files format and content: Late_stage_count_table.csv. A count table containing normalized counts for probes and segments that passed the quality control steps mentioned in the data processing step.
Library strategy: Spatial Transcriptomics

extract_protocol:
One brain hemisphere was fixed in 4% paraformaldehyde (PFA) for 24 h, cryoprotected in escalating sucrose gradients, embedded, and cryosectioned in coronal plane sections onto histologic slides [10 μm thickness for spatial transcriptomics sections, 14 μm thickness for subsequent fluorescent in situ hybridization (FISH)] and stored at –80 °C.
Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner
Other: Spatial transcriptomics-Nanostring GeoMx DSP

tag: tissue


title: MCF10A_YAP5SA_rep2

description:
Library name: Sample 6
MapR assay to detect R-loops

tag: genotype

value: YAP5SA 48  hours


title: MEF-silencer-output4_MEF-silencer-output4-12


title: HAP1 WT cells, rep1

description: column name in counts.txt and fpkm.txt: HAP1_1

tag: cell type

value: chronic myelogenous leukemia


title: MCF10A_JQ1_rep1

description:
Library name: Sample 3
MapR assay to detect R-loops

tag: treatment

value: 500 nM JQ1, 16 hours


title: DSP-1001660016220-D-B04


title: Sublibrary_1

description: Library name: CPZ_Sublibrary_1

tag: cell line


title: DSP-1001660016220-D-B05


title: DSP-1001660016220-D-B01


title: DSP-1001660016220-D-B03


title: MEF-silencer-output4_MEF-silencer-output4-11


title: MCF10A_JQ1_rep2

description:
Library name: Sample 4
MapR assay to detect R-loops


title: HUH7_Input_NR2C2_ChIP


title: MEF-silencer-output4_MEF-silencer-output4-10


title: DSP-1001660016220-D-B02


title: MEF-silencer-output4_MEF-silencer-output4-9


title: DSP-1001660016220-D-A12


title: MEF-silencer-output4_MEF-silencer-output4-8


title: MCF10A_control_rep2

description:
Library name: Sample 2
MapR assay to detect R-loops

value: control


title: HUH7_NR2C1_ChIP

description: ChIPseq_HUH7_NR2C1_vs_Input-NR2C1_peaks.loc.anno.gene.xlsx

value: Flag-NR2C1 overexpression

value: HUH7 cells infected with pCDH-Flag-NR2C1 lentivirus


title: MCF10A_control_rep1

description:
Library name: Sample 1
MapR assay to detect R-loops

value: breast epitehlial

value: WT


title: HUH7_Input_KAT8_ChIP

description: ChIPseq_HUH7_KAT8_vs_input-KAT8_peaks.loc.anno.gene.xlsx


title: HUH7_Input_NR2C1_ChIP


title: HUH7_H3K9ac_ChIP

description: ChIPseq_HUH7_H3K9ac_vs_input-H3K9ac_peaks.loc.anno.gene.xlsx


title: siSCD1 hypoxia 4

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

department: Medicine

institute: Goethe-University

description:
Library name: hyp_siSCD1_4
hyp_siSCD1_4

data_processing:
data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
umi2index
Trimming: bbduk v35.92
Alignment: STAR Aligner with modifi_x001E_ed ENCODE settings
Gene Read Counting: HTSeq-count with kit-specic options (FWD)
differential analysis: log2 fold change and p-adjusted FDR
Assembly: human genome GRCh38
Supplementary files format and content: text files containing the normalized read counts for hypoxic, normoxic, siRNA control and siSCD1 treated macrophages.

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Pancoll gradientsand seeded onto high-adherence culture dishes in RPMI 1640 medium supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin. Non-adherent cells were washed away after 1 h and the remaining cells were maintained in  RPMI 1640 medium supplemented with 100 U/mL penicillin, 100 µg/mL streptomycin and 5% human serum for 7 days to allow for differentiation to MΦ.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit.
cDNA libraries were generated with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI for Illumina (Lexogen).

treatment_protocol: Macrophages were transfected with SCD1 (ON-TARGETplus SMART pool, human #6319) and siRNA control (ON-TARGETplus Non-targeting Pool Cat#D-001810-10-50) using Hiperfect transfection reagent (Qiagen) and harvested 5 days after transfection. A group of samples was cultured under normoxia and another under hypoxia during the 5 days treatment.

value: blood

value: human primary macrophages

value: immune cells

value: SCD1 transfection hypoxia


title: MCF10A_YAP5SA_rep1

description:
Library name: Sample 5
MapR assay to detect R-loops


title: siSCD1 hypoxia 6

description:
Library name: hyp_siSCD1_6
hyp_siSCD1_6


title: MEF-silencer-output4_MEF-silencer-output4-4

value: MEFs


title: siSCD1 hypoxia 3

description:
Library name: hyp_siSCD1_3
hyp_siSCD1_3


title: MEF-silencer-output4_MEF-silencer-output4-7


title: HUH7_KAT8_ChIP

value: liver

value: HCC cells


title: DSP-1001660016220-D-A11

city: Ann Arbor

first: Mohamed

institute: University of Michigan

value: Brain


title: MEF-silencer-output4_MEF-silencer-output4-6


title: DSP-1001660016220-D-A10


title: DSP-1001660016220-D-A07


title: MEF-silencer-output4_MEF-silencer-output4-2


title: siSCD1 hypoxia 5

description:
Library name: hyp_siSCD1_5
hyp_siSCD1_5


title: MEF-silencer-output4_MEF-silencer-output4-5


title: siCtrl hypoxia 6

description:
Library name: hyp_ctrl_6
hyp_ctrl_6

value: control transfection hypoxia


title: MEF-silencer-output4_MEF-silencer-output4-1


title: DSP-1001660016220-D-A06


title: HUH7_Input_H3K9ac_ChIP


title: DSP-1001660016220-D-A09


title: DSP-1001660016220-D-A08


title: HUH7_Input_R-ChIP

description: annoTable_R-ChIP_HUH7_vs_input-R-ChIP_peaks.xlsx

value: Flag-RNASEH1-Mu overexpression

value: HUH7 cells infected with pCDH-Flag-RNASEH1-Mu lentivirus


title: siSCD1 hypoxia 2

description:
Library name: hyp_siSCD1_2
hyp_siSCD1_2


title: MEF-silencer-output4_MEF-silencer-output4-3


title: HUH7_R-ChIP


title: HUH7_DDX41_ChIP

description: annoTable_ChIPseq_HUH7_DDX41__vs_input-DDX41_peaks.xlsx

value: Flag-DDX41 overexpression

value: HUH7 cells infected with pCDH-Flag-DDX41 lentivirus


title: DSP-1001660016220-D-A05


title: siCtrl hypoxia 5

description:
Library name: hyp_ctrl_5
hyp_ctrl_5


title: DSP-1001660016220-D-A04


title: HUH7_Input_DDX41_ChIP


title: MEF-silencer-output3_MEF-silencer-output3-16


title: HUH7_siDDX41-2

value: DDX41 knockdown

value: HUH7 cells transfected with DDX41 siRNA-2


title: siSCD1 hypoxia 1

description:
Library name: hyp_siSCD1_1
hyp_siSCD1_1


title: DSP-1001660016220-D-A03


title: siCtrl hypoxia 4

description:
Library name: hyp_ctrl_4
hyp_ctrl_4


title: MEF-silencer-output3_MEF-silencer-output3-13


title: DSP-1001660016220-D-A02


title: siCtrl hypoxia 3

description:
Library name: hyp_ctrl_3
hyp_ctrl_3


title: MEF-silencer-output3_MEF-silencer-output3-14


title: HUH7_siDDX41-1

value: HUH7 cells transfected with DDX41 siRNA-1


title: siCtrl hypoxia 2

description:
Library name: hyp_ctrl_2
hyp_ctrl_2


title: HUH7_NC

value: WT

value: HUH7 cells transfected with NC siRNA


title: MEF-silencer-output3_MEF-silencer-output3-15


title: DSP-1001660016220-D-A01

value: No template control


title: MCF-7, ZMYND8-KO, E2, TTseq, rep2

city: ShangHai

first: HongJie

last: Shen

address: Dongan road 131

description: treated with E2 for 1h

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to human rRNA and mouse rRNA using Bowtie2 v2.5.1 with parameters "--very-sensitive-local --no-unal -I 1 -X 1000 ".
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameters “-outFilterMultimapNmax 1 -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.02 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000 -outBAMsortingBinsN 100 -outSAMtype BAM SortedByCoordinate” (Dobin et al., 2013).
The counts of spike-in mm10 reads were used to generate normalization factors for coverage profiles.
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: Genome coverage bigwig files
Library strategy: TT-Seq

growth_protocol: MCF-7 cells were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS, Gibco #10099141C), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010) at 37℃ with 5% CO2.  For E2 stimulaiton, cells were shifted to Phenol Red-free RPMI-1640 Medium (Hyclone #SH30605) containing 10% Charcoal Stripped Fetal Bovine Serum (Viva Cell #3830-0050), 1% MEM Non-essential Amino Acid (Gibco #11140),  100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1% Glutamine (Hyclone #SH30034) .

extract_protocol:
RNA were extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
Libraries were prepared according to VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazymes, #NR604-01).

treatment_protocol: For E2 stimulation, when the density of MCF-7 cells was up to 40%, DMEM was changed to Phenol Red-free RPMI-1640 with 10% Charcoal Stripped Fetal Bovine Serum for 72 h. Final concentration of 100 nM 17β-estradiol (E2) were added into the cell culture medium, cells were incubated in 37 °C for 1 h.


title: MEF-silencer-output3_MEF-silencer-output3-11


title: de-diff SC-EV lncRNA biol rep 3

city: Cincinnati

first: Leyla

last: Esfandiari

state: OH

address: 2600 Clifton Ave

institute: University of Cincinnati

description:
Library name: Sample 27
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE12
lncRNA_raw_readcounts.tsv

data_processing:
For mRNA seq, RNA-seq reads in FASTQ format were subsampled and standedness of the FASTQ files were auto-inferred using fq. This was followed by quality control analysis using FastQC, adapter and quality trimming using Trim Galore and cutadapt. Reads were aligned using STAR to the reference genome and options were provided for using HISAT2 aligner. SAMtools was used to sort and index alignments followed by marking of PCR duplicates using Picard MarkDuplicates. Transcript assembly and quantification were done using StingTie. BEDTools and bedGrapgToBigWig were used to generate bigWig files. We performed extensive quality control analysis of the RNA-Seq data using RSeQC, Qualimap, dupRadar, and DESeq2. Salmon and tximport were used as the default quantification tools for transcript quantification and conversion of transcript counts to gene counts respectively. Differential gene expressions between groups of samples were assessed with the R package DESeq2 v1.26.0.  Summary report of the analysis was performed using MultiQC.
For miRNA seq, the QC and quantification of miRNA-Seq data was performed using nf-core/smrnaseq (version 2.3.1) pipeline. The pipeline generated raw and normalized (CPM) gene count files. Differential gene expression analysis between groups of samples were assessed with the R package DESeq2 v1.26.0. Summary report of the analysis was performed using MultiQC.
For lncRNA seq, RNA sequencing reads were assessed for quality using FastQC  and subsequently trimmed to remove adapter sequences using Trim Galore and Cutadapt. The cleaned reads were aligned to the rat reference genome using the STAR aligner. Raw counts and lncRNA expression (Transcripts Per Million, TPM) were generated.
Assembly: Rn6
Supplementary files format and content: salmon.merged.gene_counts.tsv
Supplementary files format and content: miRNA_rawCounts.csv
Supplementary files format and content: lncRNA_raw_readcounts.tsv

organism: Rattus norvegicus

growth_protocol: Primary Rat Schwann cells (RSC) (Catalog R842-05a) were purchased from CELL Applications (San Diego, CA, USA) and maintained according to the manufacturer’s protocol. Briefly, Schwann cells were cultured in RSC growth medium (Catalog R825-500) (CELL Applications, San Diego, CA, USA) at 37°C in 5% CO2. The culture medium was replaced every 48 h. Sub-culturing was performed when the cells reached 80% confluency and cells were maintained for no longer than 5 passages. Passages 3 to 5 were used for experiments.

extract_protocol:
1. Whole-transcriptome RNA sequencing was performed by the Genomics, Epigenomics, and Sequencing Core (GESC) at the University of Cincinnati following updated protocols. Total RNA was isolated from Schwann cells for mRNA-seq and SC-EVs for lncRNA-seq, and quality control was assessed using the Agilent Bioanalyzer with the RNA 6000 Pico Kit. 2. For MicroRNA-Sequencing, total RNA was extracted from SC-EVs using the miRNeasy Micro kit as per the manufacturer’s suggested protocol and was quality control-assessed using the RNA 6000 Pico Kit on the Agilent Bioanalyzer
1. For whole RNA sequencing for mRNA and lncRNA, 10 ng of total RNA was used as input for library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).  2. For microRNA-Sequencing, ~5 ng of total RNA was used for library construction with the NEBNext Multiplex Small RNA Library Prep Kit (New England BioLabs, Ipswich, MA), incorporating a protocol modification to increase sensitivity and specificity for small RNA detection.

treatment_protocol: Six-well plates and 11 mm glass coverslips were incubated with Schwann Cells Coating solution (Cat036-20) CELL Applications (San Diego, CA, USA) at 37°C overnight. The remaining solution was aspirated, rinsed twice with PBS, and dried. RSC samples were prepared according to a modified protocol (Zou, 2023).  Cells were seeded into a coated 6-well plate at a density of 2´105 cells/well for western blot and RNA sequencing and seeded into a 24-well plate (covered with coated glass coverslips) at a density of 1´104 cells/well for immunofluorescence staining. Cells were cultured in RSC complete growth medium (R825-500) for 24 h and the medium was changed into the complete medium-RSC basal media containing 10% Exosome-Depleted FBS (Fisher), 2mM of Foskolin (Sigma-Aldrich, catalog number: F6886), 10 ng/mL of human neuregulin 1-β1/heregulin (R&D Systems, Catalog Number: 396-HB/CF), and 100 mg/mL penicillin-streptomycin (Gibco) for 24 h. Then the medium was removed and replaced by a medium containing DMEM, 1% Exosome-depleted FBS, and 100 mg/mL penicillin-streptomycin (starvation medium) overnight to limit mitogenic stimulation.  Cells were then differentiated into myelinating SC by removing the starvation medium and replacing it with medium containing DMEM, 1% Exosome-depleted FBS, 100 mg/mL penicillin-streptomycin, and 1 mM db-cAMP (Sigma, USA).  After 72 h, the medium was replaced with the Exosome-depleted complete medium for an additional 72 h to induce dedifferentiation. Cells maintained in the absence of db-cAMP-inducing agents served as a control for undifferentiated cells.  Cells were monitored daily to observe changes in morphology. At the end of the assay, cells were harvested for SC stage-specific markers for characterization of Schwann cell differentiation stages, and the supernatant was collected for EV isolation.

value: Schwann cell de-differentiation


title: siSCD1 normoxia 6

description:
Library name: norm_siSCD1_6
norm_siSCD1_6

value: blood

value: human primary macrophages

value: immune cells

value: SCD1 transfection normoxia


title: siCtrl hypoxia 1

description:
Library name: hyp_ctrl_1
hyp_ctrl_1


title: diff SC-EV lncRNA biol rep 3

description:
Library name: Sample 26
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE11
lncRNA_raw_readcounts.tsv

source_name: Primary Rat Schwann cells (RSC) (Catalog R842-05a)

value: Schwann cell differentiation


title: MEF-silencer-output3_MEF-silencer-output3-10

value: MEFs


title: siSCD1 normoxia 5

description:
Library name: norm_siSCD1_5
norm_siSCD1_5


title: MEF-silencer-output3_MEF-silencer-output3-9


title: undiff SC-EV lncRNA biol rep 3

description:
Library name: Sample 25
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE10
lncRNA_raw_readcounts.tsv

value: Primary Rat Schwann cells (RSC) (Catalog R842-05a)

value: Schwann cell undifferentiation


title: MCF-7, WT, EtOH, TTseq, rep2

description: treated with EtOH for 1h

value: EtOH


title: MCF-7, WT, E2, TTseq, rep2

description: treated with E2 for 1h


title: siSCD1 normoxia 4

description:
Library name: norm_siSCD1_4
norm_siSCD1_4


title: de-diff SC-EV lncRNA biol rep 2

description:
Library name: Sample 24
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE9
lncRNA_raw_readcounts.tsv


title: MEF-silencer-output3_MEF-silencer-output3-8


title: MCF-7, ZMYND8-KO, E2, TTseq, rep1

description: treated with E2 for 1h


title: MEF-silencer-output3_MEF-silencer-output3-6


title: MEF-silencer-output3_MEF-silencer-output3-7


title: MCF-7, ZMYND8-KO, EtOH, TTseq, rep1

description: treated with EtOH for 1h


title: siSCD1 normoxia 3

description:
Library name: norm_siSCD1_3
norm_siSCD1_3


title: MCF-7, WT, E2, TTseq, rep1

description: treated with E2 for 1h


title: siSCD1 normoxia 2

description:
Library name: norm_siSCD1_2
norm_siSCD1_2


title: diff SC-EV lncRNA biol rep 2

description:
Library name: Sample 23
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE8
lncRNA_raw_readcounts.tsv


title: undiff SC-EV lncRNA biol rep 2

description:
Library name: Sample 22
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE7
lncRNA_raw_readcounts.tsv


title: MEF-silencer-output3_MEF-silencer-output3-5


title: MEF-silencer-output3_MEF-silencer-output3-12


title: de-diff SC-EV lncRNA biol rep 1

description:
Library name: Sample 21
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE6
lncRNA_raw_readcounts.tsv


title: siSCD1 normoxia 1

description:
Library name: norm_siSCD1_1
norm_siSCD1_1


title: MCF-7, WT, EtOH, TTseq, rep1

description: treated with EtOH for 1h


title: MCF-7, ZMYND8-KO, EtOH, TTseq, rep2

description: treated with EtOH for 1h


title: diff SC-EV lncRNA biol rep 1

description:
Library name: Sample 20
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE5
lncRNA_raw_readcounts.tsv


title: siCtrl normoxia 5

description:
Library name: norm_ctrl_5
norm_ctrl_5

value: Control transfection normoxia


title: siCtrl normoxia 6

description:
Library name: norm_ctrl_6
norm_ctrl_6


title: undiff SC-EV lncRNA biol rep 1

description:
Library name: Sample 19
Leyla Esfandiari_PE503_PE504_Project 10239 whole RNA-seq LE4
lncRNA_raw_readcounts.tsv