title: GFPc5_BioRep1_0h_rep4_RNAseq

description: Library name: GFPc5_B1_0_4


title: GFPc5_BioRep1_0h_rep5_RNAseq

status: Public on Apr 01 2026

type: SRA

city: Boulder

first: Mingfeng

last: Liu

state: CO

address: 709 Mohawk Dr

country: USA

institute: University of Colorado

description: Library name: GFPc5_B1_0_5

library_source: transcriptomic

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/rnaseq v3.14.0 (Ewels et al. 2020).
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome and quantified using GENCODE v38 annotations.
Supplementary files format and content: .csv, raw gene counts and tpm

molecule: total RNA

organism: Homo sapiens

source_name: hiPSCs

extract_protocol:
RNA was harvested using Directzol RNA Miniprep kit (ZymoResearch). RNA integrity and quantity were assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Ribosomal RNA was depleted from total RNA using a commercial rRNA depletion kit. Strand-specific sequencing libraries were constructed following standard Illumina-compatible protocols. Library quality was assessed, and paired-end sequencing was performed on an Illumina platform. All library construction and sequencing steps were conducted by Novogene Co., Ltd.

tag: cell line

value: hiPSCs


title: GFPc5_BioRep1_96h_rep3_RNAseq

description: Library name: GFPc5_B1_96_3


title: CD45_010_Week 1_MI-PAtch

city: Tucson

first: Jordan

middle: M

last: Fink

state: AZ

address: 1501 N Campbell Ave

department: Sarver Heart Center

institute: University of Arizona

description: Library name: DSP-1012340076101-H-C10

data_processing:
FASTQs were processed into .dcc files as per Nanostring's pipeline
.dcc files were combined, normalized, and batch adjusted to generate the combined count matrix
Assembly: mm10
Supplementary files format and content: Compiled_Count_Matrix.csv contains  metadata and counts
Supplementary files format and content: pkc file needed for processing the data
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Cardiac

extract_protocol:
Nanostring UV cleaving of molecular probes and collection
DNA probes were processed according to nanostring's protocols

treatment_protocol: MI_alone with no treatment; treated with biologic

tag: tissue

value: Cardiac

tag: treatment

value: Biologic

tag: batch

tag: tissue type

value: Formalin Fixed Tissue


title: GFPc5_BioRep1_96h_rep2_RNAseq

description: Library name: GFPc5_B1_96_2


title: E46_FU1 Alpha

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 249
Illumina

data_processing:
The analysis pipeline described in Li et al., 2019 was used to obtain bulk TCR CDR3 sequences found in blood samples (Li et al., Nat. Protoc. 2019)
Assembly: Human GRCh38
Supplementary files format and content: csv files
Library strategy: TCR-Seq

source_name: PBMCs

extract_protocol:
Matched peripheral blood was collected prior to initiation of treatment and at serial timepoints aligned with tumor samples as described in the protocol.
Concentration, 260/280 and 260/230nm ratios were measured with ND1000 spectrophotometer (Nanodrop Technologies, Thermo-Fisher Scientific) and then DNA/RNA was quantified using a Qubit fluorometer (Life Technologies).

value: PBMCs


title: Desmin_011_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C12


title: E46_FU1 Beta

description:
Library name: Sample 250
Illumina


title: GFPc5_BioRep1_48h_rep2_RNAseq

description: Library name: GFPc5_B1_48_2


title: GFPc5_BioRep1_48h_rep3_RNAseq

description: Library name: GFPc5_B1_48_3


title: Tissue_009_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C09


title: GFPc5_BioRep1_24h_rep3_RNAseq

description: Library name: GFPc5_B1_24_3


title: E46_B Alpha

description:
Library name: Sample 247
Illumina


title: GFPc5_BioRep1_48h_rep1_RNAseq

description: Library name: GFPc5_B1_48_1


title: Desmin_009_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C08


title: GFPc5_BioRep1_24h_rep2_RNAseq

description: Library name: GFPc5_B1_24_2


title: E46_B Beta

description:
Library name: Sample 248
Illumina


title: Tissue_008_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C07


title: GFPc5_BioRep1_24h_rep1_RNAseq

description: Library name: GFPc5_B1_24_1


title: GFPc5_BioRep1_96h_rep1_RNAseq

description: Library name: GFPc5_B1_96_1


title: E45_FU1 Alpha

description:
Library name: Sample 245
Illumina


title: E45_FU1 Beta

description:
Library name: Sample 246
Illumina


title: GFPc5_BioRep1_12h_rep2_RNAseq

description: Library name: GFPc5_B1_12_2


title: GFPc5_BioRep1_12h_rep3_RNAseq

description: Library name: GFPc5_B1_12_3


title: GFPc5_BioRep1_12h_rep1_RNAseq

description: Library name: GFPc5_B1_12_1


title: GFPc5_BioRep1_0h_rep3_RNAseq

description: Library name: GFPc5_B1_0_3


title: CD45_008_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C06


title: GFPc5_BioRep1_0h_rep2_RNAseq

description: Library name: GFPc5_B1_0_2


title: CD45_007_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C04


title: GFPc5_BioRep1_0h_rep1_RNAseq

description: Library name: GFPc5_B1_0_1


title: E45_B Beta

description:
Library name: Sample 244
Illumina


title: E45_B Alpha

description:
Library name: Sample 243
Illumina


title: FENDRR_96h_rep3_RNAseq

description: Library name: FENDRR_96_3


title: Tissue_006_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C03


title: E44_FU2 Beta

description:
Library name: Sample 242
Illumina


title: FENDRR_96h_rep2_RNAseq

description: Library name: FENDRR_96_2


title: Tissue_007_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C05


title: FENDRR_48h_rep2_RNAseq

description: Library name: FENDRR_48_2


title: FENDRR_96h_rep1_RNAseq

description: Library name: FENDRR_96_1


title: E44_FU2 Alpha

description:
Library name: Sample 241
Illumina


title: FENDRR_48h_rep3_RNAseq

description: Library name: FENDRR_48_3


title: Tissue_005_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C01


title: CD45_006_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-C02


title: FENDRR_48h_rep1_RNAseq

description: Library name: FENDRR_48_1


title: FENDRR_24h_rep3_RNAseq

description: Library name: FENDRR_24_3


title: Desmin_005_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B12


title: E44_FU1 Beta

description:
Library name: Sample 240
Illumina


title: FENDRR_16h_rep3_RNAseq

description: Library name: FENDRR_16_3


title: E44_FU1 Alpha

description:
Library name: Sample 239
Illumina


title: FENDRR_16h_rep2_RNAseq

description: Library name: FENDRR_16_2


title: Tissue_004_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B11


title: Tissue_003_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B09


title: CD45_004_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B10


title: FENDRR_24h_rep2_RNAseq

description: Library name: FENDRR_24_2


title: E44_B Beta

description:
Library name: Sample 236
Illumina


title: FENDRR_16h_rep1_RNAseq

description: Library name: FENDRR_16_1


title: E44_EOT Alpha

description:
Library name: Sample 237
Illumina


title: FENDRR_8h_rep3_RNAseq

description: Library name: FENDRR_8_3


title: FENDRR_8h_rep1_RNAseq

description: Library name: FENDRR_8_1


title: FENDRR_24h_rep1_RNAseq

description: Library name: FENDRR_24_1


title: FENDRR_4h_rep2_RNAseq

description: Library name: FENDRR_4_2


title: FENDRR_8h_rep2_RNAseq

description: Library name: FENDRR_8_2


title: Desmin_003_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B08


title: FENDRR_4h_rep3_RNAseq

description: Library name: FENDRR_4_3


title: E44_B Alpha

description:
Library name: Sample 235
Illumina


title: Tissue_002_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B07


title: FENDRR_4h_rep1_RNAseq

description: Library name: FENDRR_4_1


title: FENDRR_2h_rep3_RNAseq

description: Library name: FENDRR_2_3


title: CD45_002_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B06


title: E43_FU2 Beta

description:
Library name: Sample 234
Illumina


title: E43_FU1 Beta

description:
Library name: Sample 232
Illumina


title: FENDRR_2h_rep1_RNAseq

description: Library name: FENDRR_2_1


title: Tissue_001_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B05


title: Desmin_001_Week 1_MI-PAtch

description: Library name: DSP-1012340076101-H-B04


title: FENDRR_2h_rep2_RNAseq

description: Library name: FENDRR_2_2


title: Tissue_007_Week 1_MI

description: Library name: DSP-1012340076101-H-B03


title: DANCR203_96h_rep2_RNAseq

description: Library name: DANCR203_96_2


title: DANCR203_48h_rep3_RNAseq

description: Library name: DANCR203_48_3


title: DANCR203_96h_rep3_RNAseq

description: Library name: DANCR203_96_3


title: DANCR203_96h_rep1_RNAseq

description: Library name: DANCR203_96_1


title: FENDRR_0h_rep2_RNAseq

description: Library name: FENDRR_0_2


title: E43_FU2 Alpha

description:
Library name: Sample 233
Illumina


title: E44_EOT Beta

description:
Library name: Sample 238
Illumina


title: E43_EOT Beta

description:
Library name: Sample 230
Illumina


title: DANCR203_48h_rep2_RNAseq

description: Library name: DANCR203_48_2


title: FENDRR_0h_rep1_RNAseq

description: Library name: FENDRR_0_1


title: Tissue_006_Week 1_MI

description: Library name: DSP-1012340076101-H-B01


title: Desmin_007_Week 1_MI

description: Library name: DSP-1012340076101-H-B02


title: FENDRR_0h_rep3_RNAseq

description: Library name: FENDRR_0_3


title: E43_FU1 Alpha

description:
Library name: Sample 231
Illumina


title: Desmin_006_Week 1_MI

description: Library name: DSP-1012340076101-H-A12


title: DANCR203_24h_rep3_RNAseq

description: Library name: DANCR203_24_3


title: E43_B Beta

description:
Library name: Sample 228
Illumina


title: DANCR203_48h_rep1_RNAseq

description: Library name: DANCR203_48_1


title: E43_B Alpha

description:
Library name: Sample 227
Illumina


title: DANCR203_24h_rep1_RNAseq

description: Library name: DANCR203_24_1


title: E42_FU2 Alpha

description:
Library name: Sample 225
Illumina


title: Tissue_004_Week 1_MI

description: Library name: DSP-1012340076101-H-A09


title: E43_EOT Alpha

description:
Library name: Sample 229
Illumina


title: Tissue_005_Week 1_MI

description: Library name: DSP-1012340076101-H-A11


title: DANCR203_24h_rep2_RNAseq

description: Library name: DANCR203_24_2


title: DANCR203_16h_rep3_RNAseq

description: Library name: DANCR203_16_3


title: DANCR203_16h_rep2_RNAseq

description: Library name: DANCR203_16_2


title: Desmin_005_Week 1_MI

description: Library name: DSP-1012340076101-H-A10


title: DANCR203_8h_rep2_RNAseq

description: Library name: DANCR203_8_2


title: DANCR203_4h_rep2_RNAseq

description: Library name: DANCR203_4_2


title: DANCR203_8h_rep3_RNAseq

description: Library name: DANCR203_8_3


title: DANCR203_16h_rep1_RNAseq

description: Library name: DANCR203_16_1


title: DANCR203_4h_rep1_RNAseq

description: Library name: DANCR203_4_1


title: E42_FU1 Beta

description:
Library name: Sample 224
Illumina


title: DANCR203_4h_rep3_RNAseq

description: Library name: DANCR203_4_3


title: E42_FU2 Beta

description:
Library name: Sample 226
Illumina


title: Desmin_004_Week 1_MI

description: Library name: DSP-1012340076101-H-A08


title: DANCR203_8h_rep1_RNAseq

description: Library name: DANCR203_8_1


title: E42_FU1 Alpha

description:
Library name: Sample 223
Illumina


title: DANCR203_2h_rep1_RNAseq

description: Library name: DANCR203_2_1


title: DANCR203_0h_rep3_RNAseq

description: Library name: DANCR203_0_3


title: Tissue_002_Week 1_MI

description: Library name: DSP-1012340076101-H-A05


title: DANCR203_0h_rep2_RNAseq

description: Library name: DANCR203_0_2


title: E42_EOT Beta

description:
Library name: Sample 222
Illumina


title: DANCR203_2h_rep3_RNAseq

description: Library name: DANCR203_2_3


title: SpnIII E locked replicate E8

city: Leicester

first: Richard

middle: David

last: Haigh

state: Leicestershire

address: Medical Sciences Building, University Road

department: Department of Respiratory Sciences

country: United Kingdom

institute: University of Leicester

description: Library name: TSB-E8

data_processing:
Fastq reads were trimmed with Trimmomatic 0.36, TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed fastq reads were aligned to D39 genome using Rockhopper2.0.3 using default settings
Read count normalisation, gene expression level determination and operon prediction were performed using Rockhopper2.0.3 with default settings
Assembly: Streptococcus pneumoniae D39 chromosome, complete genome, NC_008533.1
Supplementary files format and content: tab-delimited text file contains raw counts and normalised counts for each sample
Supplementary files format and content: tab-delimited text file contains RPKM and expression values plus p and q values for each sample

organism: Streptococcus pneumoniae

extract_protocol: Norgen Total RNA Purification Kit

value: SpnIII E locked


title: DANCR203_2h_rep2_RNAseq

description: Library name: DANCR203_2_2


title: Tissue_003_Week 1_MI

description: Library name: DSP-1012340076101-H-A07


title: Desmin_002_Week 1_MI

description: Library name: DSP-1012340076101-H-A04


title: DANCR203_0h_rep1_RNAseq

description: Library name: DANCR203_0_1


title: Desmin_003_Week 1_MI

description: Library name: DSP-1012340076101-H-A06


title: SpnIII E locked replicate E7

description: Library name: TSB-E7


title: SpnIII E locked replicate E6

description: Library name: TSB-E6


title: CRNDE_96h_rep1_RNAseq

description: Library name: CRNDE_96_1


title: CRNDE_96h_rep2_RNAseq

description: Library name: CRNDE_96_2


title: Tissue_001_Week 1_MI

description: Library name: DSP-1012340076101-H-A03


title: CRNDE_48h_rep3_RNAseq

description: Library name: CRNDE_48_3


title: SpnIII E locked replicate E5

description: Library name: TSB-E5


title: CRNDE_48h_rep2_RNAseq

description: Library name: CRNDE_48_2


title: Desmin_001_Week 1_MI

description: Library name: DSP-1012340076101-H-A02


title: SpnIII E locked replicate E1

description: Library name: TSB-E1


title: CRNDE_48h_rep1_RNAseq

description: Library name: CRNDE_48_1


title: No Template Control_Week_1

description: Library name: DSP-1012340076101-H-A01


title: CRNDE_24h_rep2_RNAseq

description: Library name: CRNDE_24_2


title: CRNDE_96h_rep3_RNAseq

description: Library name: CRNDE_96_3


title: MSC_3

city: Chiba

first: Takahisa

last: HISHIYA

state: Chiba

address: 1-8-1,inohana, chuo-ku

country: Japan

institute: Chiba university

description: Library name: MSC_3

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
Peripheral blood was collected from mice 6 hours after cecal ligation and puncture. CD45-positive immune cells were isolated using magnetic bead-based separation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) according to the manufacturer’s protocol. Briefly, isolated CD45-positive immune cells were loaded onto the Chromium Controller to generate single-cell Gel Bead-In-Emulsions (GEMs). Within each GEM, cells were lysed, and mRNA molecules were reverse transcribed to generate barcoded cDNA.

value: blood

tag: cell type

value: Peripheral blood CD45-positive immune cells

tag: genotype

value: Mesenchymal stem cell administration


title: CRNDE_16h_rep2_RNAseq

description: Library name: CRNDE_16_2


title: CRNDE_16h_rep3_RNAseq

description: Library name: CRNDE_16_3


title: SpnIII B locked replicate B8

description: Library name: TSB-B8

value: SpnIII B locked


title: CRNDE_24h_rep3_RNAseq

description: Library name: CRNDE_24_3


title: SpnIII E locked replicate E4

description: Library name: TSB-E4


title: MSC_1

description: Library name: MSC_1


title: CRNDE_24h_rep1_RNAseq

description: Library name: CRNDE_24_1


title: SpnIII B locked replicate B6

description: Library name: TSB-B6


title: SpnIII B locked replicate B4

description: Library name: TSB-B4


title: CRNDE_8h_rep2_RNAseq

description: Library name: CRNDE_8_2


title: SpnIII A locked replicate A6

description: Library name: TSB-A6

value: SpnIII A locked


title: CRNDE_8h_rep3_RNAseq

description: Library name: CRNDE_8_3


title: Control_2

description: Library name: Control_2

value: Vehicle control


title: CRNDE_8h_rep1_RNAseq

description: Library name: CRNDE_8_1


title: CRNDE_16h_rep1_RNAseq

description: Library name: CRNDE_16_1


title: MSC_2

description: Library name: MSC_2


title: CRNDE_4h_rep3_RNAseq

description: Library name: CRNDE_4_3


title: SpnIII A locked replicate A5

description: Library name: TSB-A5


title: CRNDE_4h_rep2_RNAseq

description: Library name: CRNDE_4_2


title: Control_1

description: Library name: Control_1


title: CRNDE_2h_rep3_RNAseq

description: Library name: CRNDE_2_3


title: CRNDE_4h_rep1_RNAseq

description: Library name: CRNDE_4_1


title: engineered neural tissues (ENT), noEF, Day7, rep2

city: ChangChun

first: Xiyao

last: Yu

address: Xinmin Street

country: China

institute: Jilin University

description: Library name: noEF2

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 reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4.
StringTie v2.2.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq2 R package (1.44.0).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: csv file includes raw counts for each Sample

molecule: polyA RNA

source_name: engineered neural tissues (ENT)

growth_protocol: neurosphere suspensions were resuspended in ice-cold Matrigel at a 1:5 ratio (neurospheres: Matrigel) and mixed thoroughly under chilled conditions. This mixture was then polymerised by incubating it at 37°C. The resulting matrix was overlaid with BNb medium, which consists of DMEM/F12 supplemented with N2 and B27 additives, in addition to 20 ng ml−1 recombinant human bFGF.

extract_protocol:
Purity, concentration and integrity of RNA sample were examined by NanoDrop, Qubit 2.0, Agilent 2100, etc. Only RNA with good quality could move on to following procedures.
Qualified RNA was isolated by Oligo(dT)-attached magnetic beads, then randomly fragmented in fragmentation buffer. First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters.  AMPure XP beads were applied here to select fragments within size range of 300-400 bp. cDNA library was obtained by certain rounds of PCR on cDNA fragments.

treatment_protocol: 3D ENT cultures following 3 days of EF stimulation (150 mV/mm, 30 min/day) and then cultured for a further 7 days versus unstimulated controls (n=3 replicates/group)

value: engineered neural tissues (ENT)

value: Neutral Stem Cells

value: noEF


title: CRNDE_2h_rep2_RNAseq

description: Library name: CRNDE_2_2


title: SpnIII A locked replicate A2

description: Library name: TSB-A2


title: CRNDE_0h_rep3_RNAseq

description: Library name: CRNDE_0_3


title: CRNDE_0h_rep2_RNAseq

description: Library name: CRNDE_0_2


title: engineered neural tissues (ENT), EF, Day7, rep2

description: Library name: E3

value: EF


title: engineered neural tissues (ENT), noEF, Day7, rep1

description: Library name: noEF1


title: CRNDE_0h_rep1_RNAseq

description: Library name: CRNDE_0_1


title: CRNDE_2h_rep1_RNAseq

description: Library name: CRNDE_2_1


title: BANCR_96h_rep3_RNAseq

description: Library name: BANCR_96_3


title: BANCR_96h_rep2_RNAseq

description: Library name: BANCR_96_2


title: LBD11_14, rep3

city: Helsinki

first: Leo

middle: Matti Iivari

last: Vainio

state: Uusimaa

address: Viikinkaari 1

department: OEB

country: Finland

institute: University of Helsinki

description:
Library name: LBD11_14_3
Processed file is raw counts from HTSeq

data_processing:
NovoGene-provided FASTQ files were assessed with MultiQC and trimmed with Trimmomatic (Bolger et al., 2014). Adapters were clipped using the preset TruSeq3-PE-2 set with parameters 2:30:10:1:false
We removed 10 bases from the 5′ end, applied sliding-window trimming (4:20), and set a minimum read length of 36 bp; quality control was repeated with MultiQC.
Reads were aligned to the unmasked P. trichocarpa genome (v4.1) using HISAT2 (Kim et al., 2015). The genome index was built with the Phytozome gene annotation Ptrichocarpa_533_v4.1.gene_exons.gff3; the GFF3 file was converted to GTF with the Cufflinks package.
RNA-strandness  unstranded Base quality encoding used  Sanger - Phred+33 How many hits to report per read  5 Minimum intron length  20 Maximum intron length  500000 Disallow soft clipping  Use soft-clipping Require long anchor lengths for subsequent assembly  Don't require Index BAM  no
Gene-level counts were generated with HTSeq and filtered to retain genes with ≥10 reads across samples.
Assembly: Phytozome gene annotation Ptrichocarpa_533_v4.1.gene_exons.gff3
Supplementary files format and content: csv of raw counts from HTSeq

organism: Populus tremula x Populus tremuloides

source_name: stem internode

growth_protocol: 3 week old, green house conditions LD

extract_protocol:
Total RNA was isolated with RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) with an on-column DNase I treatment (QIAGEN, Hilden, Germany).
For RNA-seq analysis, RNA quality control, mRNA library preparation using poly(A) enrichment and subsequent sequencing with Illumina HiSeq PE150 (pair-end sequencing) platform were performed by Novogene (https://www.novogene.com, China)

treatment_protocol: Overexpression of heterologous LBD-gebes (LBD4 or LBD11)

value: stem internode


title: LBD11_14, rep1

description:
Library name: LBD11_14_1
Processed file is raw counts from HTSeq


title: LBD11_14, rep2

description:
Library name: LBD11_14_2
Processed file is raw counts from HTSeq


title: BANCR_96h_rep1_RNAseq

description: Library name: BANCR_96_1

value: hiPSCs


title: BANCR_48h_rep3_RNAseq

description: Library name: BANCR_48_3


title: 3T3-M0

city: Hefei,

first: Xu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

description:
Library name: sample2
RNA-seq

library_source: other

data_processing:
For mecciRNA identification, the clean data were filtered by bowtie2 (v 1.2.1) to remove reads mapped to rDNA. The left reads were mapped to the reference genome by bwa-men (v 0.7.17). The discontinuously mapped reads were extracted and mapped again to mitochondrial genome by bowtie (v 1.2.1). mecciRNA candidates were predicted by pepline mentioned in our article.
Assembly: hg38, mm10,
Supplementary files format and content: comma-separated value files include count values for each Sample

molecule: other

extract_protocol:
The Isolated mitochondria and whole cells were lysed in TRIzol reagent (Life Technologies). RNA from mitochondria and whole cells was extracted using TRIzol reagent according to the manufacturer’s instructions.
For total RNA and mitochondrial RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

value: mouse embryonic fibroblast cell line

value: WT


title: LBD11_2, rep3

description:
Library name: LBD11_2_3
Processed file is raw counts from HTSeq


title: BANCR_48h_rep2_RNAseq

description: Library name: BANCR_48_2


title: engineered neural tissues (ENT), EF, Day7, rep1

description: Library name: E1


title: wks28 scRNA-seq from mandible

city: Chengdu

first: Yi

last: Fan

state: Sichuan

address: No.14, 3Rd Section of Ren Min Nan Rd.

institute: West China Hospital of Stomatology, Sichuan University

description:
Library name: wks28 scRNA-seq from mandible
10x Genomics

data_processing:
The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples. The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low-quality cells from scRNA-seq data, and the filtered data was downscaled and clustered.
Assembly: Mouse
Supplementary files format and content: mtx

source_name: bone

extract_protocol:
Mandibles were dissected from sixteen 8-week-old male C57BL/6 mice (GemPharmatech Co., Ltd.). Soft tissues, molars, incisors, and bone posterior to the condyle were removed. The isolated bone tissue was enzymatically digested in 3 mg/mL collagenase type I (Gibco) and 4 mg/mL dispase II (MilliporeSigma) for 60 minutes at 37°C. Resuspend the single cells in MACS buffer (0.5% BSA, 2 mM EDTA) and add CD45 MicroBeads (Miltenyi). Incubate the mixture for 15 minutes in a 4°C refrigerator. Following incubation, wash the cells with MACS buffer. Then, apply the cell suspension onto the MACS LS column placed within the separator's magnetic field. Collect the flow-through fraction which were CD45⁻ cells. Perform a second magnetic separation step on the collected CD45⁻ cells using anti-Ter119 MicroBeads (Miltenyi).
After generate CD45-/Ter119- single-cell suspensions, single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou,China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: bone

value: primary bone stromal cell

value: Wild type


title: BANCR_24h_rep3_RNAseq

description: Library name: BANCR_24_3


title: LBD11_2, rep2

description:
Library name: LBD11_2_2
Processed file is raw counts from HTSeq


title: BANCR_24h_rep2_RNAseq

description: Library name: BANCR_24_2


title: BANCR_24h_rep1_RNAseq

description: Library name: BANCR_24_1


title: LBD11_1, rep3

description:
Library name: LBD11_1_3
Processed file is raw counts from HTSeq


title: C1

city: Beijing

first: Jichang

last: Li

address: No. 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

description:
Library name: Sample1
10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using Cellranger (Version 7.2.0) (https://support.10xgenomics.com/single-cell-expression/software/pipelines/latest/what-is-cell-ranger). Since the CT-26 cancer cell line was labeled by Luciferase gene, its sequence was added to the refdata-gex-mm10-2020-A genome and its gene information was added to the vM23 (Ensembl98) gene annotation file provided by 10x Genomics.
Assembly: refdata-gex-mm10-2020-A/Ensembl98
Supplementary files format and content: seurat obejct containing gene expression matrix and other information

source_name: Colon Cancer

extract_protocol:
Mouse colorectal cancer tissues were harvested from tumor-bearing mice. Tissues were collected immediately after euthanasia.Collected tissues were rinsed with PBS to remove blood and debris. They were then cut into small pieces (1-2 mm) using a scalpel.The minced tissues were enzymatically digested using a cocktail of enzymes (e.g., 0.1% collagenase IV and 0.1% DNase I) in a shaking incubator at 37°C for 30-60 minutes, ensuring gentle agitation.The digested tissue was passed through a 70 µm cell strainer to obtain a single-cell suspension. The resulting cells were washed with PBS and Cell viability was assessed using trypan blue exclusion or a flow cytometry-based method to ensure a minimum viability of 90%.Single cells were processed using the 10x Genomics Chromium Single Cell 3' Library Kit, following the manufacturer’s instructions to prepare the libraries for sequencing.
The obtained cDNA was fragmented, repaired, and dA-tailed in one step using a Fragmentation Mix and an End Prep Enzyme Mix. After double-sided size selection, fragments with a length of approximately 300 bp were recovered and both ends were ligated with adaptors. The ligated fragmented cDNA was then amplified by PCR using P5 and P7 primers (P7 allowing for multiplexing) and were purified with beads. The Purified libraries were multiplexed and loaded onto an Illumina NovaSeq 6000 instrument (Illumina) following the manufacturer's instructions. Sequencing was performed using a 2x150 bp paired-end (PE) configuration, with image analysis and base calling done by the NovaSeq Control Software (NCS) and GAPipeline-1.6 on the NovaSeq instrument.

value: Colon Cancer

value: Goblet cells

value: Control


title: BANCR_16h_rep2_RNAseq

description: Library name: BANCR_16_2


title: T2

description:
Library name: Sample2
10x Genomics


title: BANCR_16h_rep3_RNAseq

description: Library name: BANCR_16_3


title: BANCR_48h_rep1_RNAseq

description: Library name: BANCR_48_1


title: LBD11_2, rep1

description:
Library name: LBD11_2_1
Processed file is raw counts from HTSeq


title: BANCR_16h_rep1_RNAseq

description: Library name: BANCR_16_1


title: BANCR_8h_rep3_RNAseq

description: Library name: BANCR_8_3


title: BANCR_8h_rep1_RNAseq

description: Library name: BANCR_8_1


title: LBD11_1, rep1

description:
Library name: LBD11_1_1
Processed file is raw counts from HTSeq


title: BANCR_8h_rep2_RNAseq

description: Library name: BANCR_8_2


title: LBD11_1, rep2

description:
Library name: LBD11_1_2
Processed file is raw counts from HTSeq


title: Microglia treated by vehicle, rep1

city: St. Louis

first: Jinsheng

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: Library name: S25.Veh_MG_1

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined, aligned with STAR v2.5.1a, and quantitated with Subread:featureCount v1.4.6-p5
Assembly: Mouse Ensembl GRCm38.76
Supplementary files format and content: all_27samples.gene_counts.tsv, tab-separated value, contains gene counts of all samples
Supplementary files format and content: all_27samples.gene_TPM.tsv, per sample gene.counts.tsv, tab-separated value, contains gene counts with TPM values

source_name: Microglia

growth_protocol: Primary microglia was cultured as mixed glia in regular astrocyte medium (DMEM supplemented with 10% heat-inactivated FBS, 1× GlutaMAX, 1× sodium pyruvate, and 1× penicillin/streptomycin; all from GIBCO). Microglia cells were collected by shaking at 200rpm for 30mins and cultured overnight in regular astrocyte medium until treatment. BMDM cells were differentiated in BMDM differentiation medium (RPMI-1640, 10% FBS, 25 ng/ml M-CSF, 1× penicillin/streptomycin, 1× GlutaMAX, 1× sodium pyruvate, and 1× non-essential amino acids) for 6 days. Hepatocytes were initially cultured in plating medium (low-glucose DMEM supplemented with FBS and penicillin/streptomycin) on collagen-coated plates. After 6 hours, the medium was replaced with maintenance medium consisting of Williams’ E medium (Gibco 12551-032), 1× GlutaMAX, and penicillin/streptomycin.

extract_protocol:
RNA was isolated using the Quick-RNA Miniprep plus Kit (Zymo Research, Cat. No. R1058).
an oligo-dT based SMARTer Ultra Low RNA kit from the Takara-Clontech was used to prepare the libraries

treatment_protocol: All treatments were done in the same serum-free medium. For GW3965 and Saringosterol treatment, an identical volume of ethanol was added as Vehicle. Mouse primary microglia or BMDMs or hepatocytes were plated at a density of 2 X 105 cells/ml in multiwell plate as needed. Cells were allowed to be attached overnight, media were removed, and the treatments were diluted in serum free media. For BMDM and microglia treatment media include DMEM/F12 supplemented with 1× GlutaMAX, 1× sodium pyruvate, 0.1% fatty-acid-free BSA, 1× penicillin/streptomycin, 1× insulin–transferrin–selenite supplement (R&D Systems AR013), and 25 ng/ml M-CSF (GoldBio 1320-09-10)). For hepatocytes treatment was done in maintenance medium consisting of Williams’ E medium (Gibco 12551-032), 1× GlutaMAX, and penicillin/streptomycin.

value: Microglia

value: vehicle


title: SpnIII A locked replicate A1

description: Library name: TSB-A1

value: SpnIII A locked


title: BANCR_4h_rep3_RNAseq

description: Library name: BANCR_4_3


title: Microglia treated by vehicle, rep3

description: Library name: S27.Veh_MG_3


title: BANCR_4h_rep2_RNAseq

description: Library name: BANCR_4_2


title: LBD4_17, rep3

description:
Library name: LBD4_17_3
Processed file is raw counts from HTSeq


title: Hepatocyte treated by vehicle, rep3

description: Library name: S24.Veh_Hep_3

source_name: Hepatocyte

value: Hepatocyte


title: Microglia treated by vehicle, rep2

description: Library name: S26.Veh_MG_2


title: BANCR_2h_rep3_RNAseq

description: Library name: BANCR_2_3


title: BANCR_2h_rep1_RNAseq

description: Library name: BANCR_2_1


title: LBD4_17, rep1

description:
Library name: LBD4_17_1
Processed file is raw counts from HTSeq


title: Hepatocyte treated by vehicle, rep2

description: Library name: S23.Veh_Hep_2


title: BANCR_2h_rep2_RNAseq

description: Library name: BANCR_2_2


title: BANCR_0h_rep3_RNAseq

description: Library name: BANCR_0_3


title: Hepatocyte treated by vehicle, rep1

description: Library name: S22.Veh_Hep_1


title: LBD4_14, rep2

description:
Library name: LBD4_14_2
Processed file is raw counts from HTSeq


title: BANCR_0h_rep2_RNAseq

description: Library name: BANCR_0_2


title: BANCR_0h_rep1_RNAseq

description: Library name: BANCR_0_1


title: BANCR_4h_rep1_RNAseq

description: Library name: BANCR_4_1


title: LBD4_14, rep1

description:
Library name: LBD4_14_1
Processed file is raw counts from HTSeq


title: TUG1217_2.5h_rep3_ATACseq

description:
Library name: TU7150_3_QKDO250000034-1A_22M737LT4_L1
TUG1217_2.5h_REP3.mLb.clN.sorted.bam

library_source: genomic

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/atacseq v2.1.2.
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome with the GENCODE v38 genome annotation file. Reads located in the ENCODE hg38 blacklist v2 region were removed.
Supplementary files format and content: .csv, consensus peaks raw counts of all samples
Supplementary files format and content: .bigWig, merged replicate ATAC-seq tracks of each sample

molecule: genomic DNA

extract_protocol:
All steps from nuclei isolation through library preparation were performed by Novogene Co., Ltd. using their standardized, optimized ATAC-seq workflow.
The final ATAC-seq libraries were quantified, quality-controlled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end, 150 bp) by Novogene Co., Ltd.


title: Bone marrow-derived macrophage treated by vehicle, rep2

description: Library name: S20.Veh_BMDM_2

source_name: Bone marrow-derived macrophage

value: Bone marrow-derived macrophage


title: LBD4_17, rep2

description:
Library name: LBD4_17_2
Processed file is raw counts from HTSeq


title: TUG1217_2.5h_rep2_ATACseq

description:
Library name: TU7150_2_QKDO250000033-1A_22M737LT4_L1
TUG1217_2.5h_REP2.mLb.clN.sorted.bam


title: TUG1217_2.5h_rep1_ATACseq

description:
Library name: TU7150_1_QKDO250000032-1A_22M737LT4_L1
TUG1217_2.5h_REP1.mLb.clN.sorted.bam


title: TUG1217_2h_rep2_ATACseq

description:
Library name: TU7120_2_QKDO250000030-1A_22M737LT4_L1
TUG1217_2h_REP2.mLb.clN.sorted.bam


title: Microglia treated by saringosterol, rep2

description: Library name: S17.Sari_MG_2

value: saringosterol


title: Microglia treated by saringosterol, rep3

description: Library name: S18.Sari_MG_3


title: LBD4_11, rep2

description:
Library name: LBD4_11_2
Processed file is raw counts from HTSeq


title: TUG1217_2h_rep1_ATACseq

description:
Library name: TU7120_1_QKDO250000029-1A_22M737LT4_L1
TUG1217_2h_REP1.mLb.clN.sorted.bam


title: LBD4_11, rep3

description:
Library name: LBD4_11_3
Processed file is raw counts from HTSeq


title: Bone marrow-derived macrophage treated by vehicle, rep1

description: Library name: S19.Veh_BMDM_1


title: TUG1217_1.5h_rep1_ATACseq

description:
Library name: TU790_1_QKDO250000026-1A_22M737LT4_L1
TUG1217_1.5h_REP1.mLb.clN.sorted.bam


title: WT, rep5

description:
Library name: WT_5
Processed file is raw counts from HTSeq


title: TUG1217_2h_rep3_ATACseq

description:
Library name: TU7120_3_QKDO250000031-1A_22M737LT4_L1
TUG1217_2h_REP3.mLb.clN.sorted.bam


title: TUG1217_1.5h_rep3_ATACseq

description:
Library name: TU790_3_QKDO250000028-1A_22M737LT4_L1
TUG1217_1.5h_REP3.mLb.clN.sorted.bam


title: TUG1217_0.5h_rep2_ATACseq

description:
Library name: TU730_2_QKDO250000021-1A_22M737LT4_L1
TUG1217_0.5h_REP2.mLb.clN.sorted.bam


title: TUG1217_1h_rep2_ATACseq

description:
Library name: TU760_2_QKDO250000024-1A_22M737LT4_L1
TUG1217_1h_REP2.mLb.clN.sorted.bam


title: Bone marrow-derived macrophage treated by vehicle, rep3

description: Library name: S21.Veh_BMDM_3


title: WT, rep3

description:
Library name: WT_3
Processed file is raw counts from HTSeq


title: Microglia treated by saringosterol, rep1

description: Library name: S16.Sari_MG_1


title: TUG1217_1.5h_rep2_ATACseq

description:
Library name: TU790_2_QKDO250000027-1A_22M737LT4_L1
TUG1217_1.5h_REP2.mLb.clN.sorted.bam


title: TUG1217_1h_rep3_ATACseq

description:
Library name: TU760_3_QKDO250000025-1A_22M737LT4_L1
TUG1217_1h_REP3.mLb.clN.sorted.bam


title: WT, rep4

description:
Library name: WT_4
Processed file is raw counts from HTSeq


title: TUG1217_1h_rep1_ATACseq

description:
Library name: TU760_1_QKDO250000023-1A_22M737LT4_L1
TUG1217_1h_REP1.mLb.clN.sorted.bam


title: Hepatocyte treated by saringosterol, rep3

description: Library name: S15.Sari_Hep_3


title: LBD4_11, rep1

description:
Library name: LBD4_11_1
Processed file is raw counts from HTSeq


title: TUG1217_0.5h_rep3_ATACseq

description:
Library name: TU730_3_QKDO250000022-1A_22M737LT4_L1
TUG1217_0.5h_REP3.mLb.clN.sorted.bam


title: Hepatocyte treated by saringosterol, rep2

description: Library name: S14.Sari_Hep_2


title: WT, rep2

description:
Library name: WT_2
Processed file is raw counts from HTSeq


title: TUG1217_0.5h_rep1_ATACseq

description:
Library name: TU730_1_QKDO250000020-1A_22M737LT4_L1
TUG1217_0.5h_REP1.mLb.clN.sorted.bam


title: TUG1217_0h_rep3_ATACseq

description:
Library name: TU70_3_QKDO250000019-1A_22M737LT4_L1
TUG1217_0h_REP3.mLb.clN.sorted.bam


title: Hepatocyte treated by saringosterol, rep1

description: Library name: S13.Sari_Hep_1


title: WT, rep1

description:
Library name: WT_1
Processed file is raw counts from HTSeq


title: Bone marrow-derived macrophage treated by saringosterol, rep3

description: Library name: S12.Sari_BMDM_3


title: A549_D1B_Y273F cells, 7d doxycyclin-induced DYRK1B overexpression, rep3

city: Aachen

first: Walter

last: Becker

address: Pauwelsstr. 30

department: Institute of Pharmacology and Toxicology

country: Germany

institute: RWTH Aachen University

description: Library name: sample 12

data_processing:
Raw data were demultiplexed and FASTQ files were generated using bcl_convert.
Data were aligned to the GRCh38p14 genome and counted with STAR Aligner (STAR --runThreadN 40 --runMode alignReads --readFilesCommand zcat --outFilterMultimapNmax 10 --outFilterMatchNmin 20 --outSAMtype BAM Unsorted --quantMode GeneCounts --twopassMode Basic --peOverlapNbasesMin 15 --peOverlapMMp 2 --outFileNamePrefix --genomeDir --sjdbGTFtagExonParentTranscript Homo_sapiens.GRCh38.104.gtf --readFilesIn)
ENSG Ids were mapped to HGNC gene names and read counts for all samples was merged
Assembly: GRCh38p14
Supplementary files format and content: tab-delimited text files includes raw read counts from STAR aligner
Supplementary files format and content: tab-delimited text files includes raw read counts annotated with HGNC gene names

source_name: lung

growth_protocol: A total of 7.000 A549-tetON cells were seeded in each 6-well containing 3 ml DMEM/F12 supplemented with 10% FBS and cultured for 7 days in a humidified incubator with 5% CO₂ at 37 °C. The medium was changed once after four days of cultivation.

extract_protocol:
RNA was prepared using Rneasy min kit (Qiagen).
Libraries for RNA-Seq were prepared using the QuantSeq FWD V2 kit (Lexogen)according to the manufacturer's protocol.

treatment_protocol: Overexpression of DYRK1B was induced by adding 2 µg/ml doxycycline to the designated wells.

value: lung

value: lung adenocarcinoma

value: doxycycline (2 µg/ml)


title: TUG1210_2.5h_rep1_ATACseq

description:
Library name: TUG2150_1_QKDO240001135-1A_22MFVNLT4_L3
TUG1210_2.5h_REP1.mLb.clN.sorted.bam

value: hiPSCs


title: A549_D1B_Y273F cells, 7d doxycyclin-induced DYRK1B overexpression, rep2

description: Library name: sample 11


title: TUG1217_0h_rep2_ATACseq

description:
Library name: TU70_2_QKDO250000018-1A_22M737LT4_L1
TUG1217_0h_REP2.mLb.clN.sorted.bam


title: TUG1210_2h_rep3_ATACseq

description:
Library name: TUG2120_3_QKDO240001134-1A_22MFVNLT4_L3
TUG1210_2h_REP3.mLb.clN.sorted.bam


title: Bone marrow-derived macrophage treated by saringosterol, rep2

description: Library name: S11.Sari_BMDM_2


title: TUG1210_2h_rep2_ATACseq

description:
Library name: TUG2120_2_QKDO240001133-1A_22MFVNLT4_L3
TUG1210_2h_REP2.mLb.clN.sorted.bam


title: Microglia treated by GW3596, rep3

description: Library name: S09.GW_MG_3


title: A549_D1B_Y273F cells, 7d doxycyclin-induced DYRK1B overexpression, rep1

description: Library name: sample 10


title: TUG1217_0h_rep1_ATACseq

description:
Library name: TU70_1_QKDO250000017-1A_22M737LT4_L1
TUG1217_0h_REP1.mLb.clN.sorted.bam


title: Bone marrow-derived macrophage treated by saringosterol, rep1

description: Library name: S10.Sari_BMDM_1


title: TUG1210_2h_rep1_ATACseq

description:
Library name: TUG2120_1_QKDO240001132-1A_22MFVNLT4_L3
TUG1210_2h_REP1.mLb.clN.sorted.bam


title: TUG1210_2.5h_rep2_ATACseq

description:
Library name: TUG2150_2_QKDO240001136-1A_22MFVLLT4_L1
TUG1210_2.5h_REP2.mLb.clN.sorted.bam


title: TUG1210_1.5h_rep3_ATACseq

description:
Library name: TUG290_3_QKDO240001131-1A_22MFVNLT4_L3
TUG1210_1.5h_REP3.mLb.clN.sorted.bam


title: Microglia treated by GW3596, rep2

description: Library name: S08.GW_MG_2


title: A549_D1B_Y273F cells, control, rep3

description: Library name: sample 9

value: control


title: TUG1210_1.5h_rep2_ATACseq

description:
Library name: TUG290_2_QKDO240001130-1A_22MFVNLT4_L3
TUG1210_1.5h_REP2.mLb.clN.sorted.bam


title: TUG1210_1.5h_rep1_ATACseq

description:
Library name: TUG290_1_QKDO240001129-1A_22MFVNLT4_L3
TUG1210_1.5h_REP1.mLb.clN.sorted.bam


title: A549_D1B_Y273F cells, control, rep1

description: Library name: sample 7


title: TUG1210_1h_rep3_ATACseq

description:
Library name: TUG260_3_QKDO240001128-1A_22M725LT4_L2
TUG1210_1h_REP3.mLb.clN.sorted.bam


title: Microglia treated by GW3596, rep1

description: Library name: S07.GW_MG_1


title: TUG1210_1h_rep2_ATACseq

description:
Library name: TUG260_2_QKDO240001127-1A_22MFVNLT4_L3
TUG1210_1h_REP2.mLb.clN.sorted.bam


title: TUG1210_0.5h_rep3_ATACseq

description:
Library name: TUG230_1_CKDL250005749-1A_22MKY2LT4_L2
TUG1210_0.5h_REP3.mLb.clN.sorted.bam


title: A549_D1B_WT cells, 7d doxycyclin-induced DYRK1B overexpression, rep3

description: Library name: sample 6


title: Hepatocyte treated by GW3596, rep3

description: Library name: S06.GW_Hep_3


title: Hepatocyte treated by GW3596, rep2

description: Library name: S05.GW_Hep_2


title: TUG1210_0.5h_rep2_ATACseq

description:
Library name: TUG230_2_QKDO240001124-1A_22MFVNLT4_L3
TUG1210_0.5h_REP2.mLb.clN.sorted.bam


title: TUG1210_0.5h_rep1_ATACseq

description:
Library name: TUG230_1_QKDO240001123-1A_22MFVNLT4_L3
TUG1210_0.5h_REP1.mLb.clN.sorted.bam


title: A549_D1B_WT cells, 7d doxycyclin-induced DYRK1B overexpression,, rep2

description: Library name: sample 5


title: TUG1210_0h_rep3_ATACseq

description:
Library name: TUG20_3_QKDO240001122-1A_22M725LT4_L2
TUG1210_0h_REP3.mLb.clN.sorted.bam


title: A549_D1B_WT cells, 7d doxycyclin-induced DYRK1B overexpression, rep1

description: Library name: sample 4


title: TUG1210_0h_rep2_ATACseq

description:
Library name: TUG20_2_QKDO240001121-1A_22MFVNLT4_L3
TUG1210_0h_REP2.mLb.clN.sorted.bam


title: Hepatocyte treated by GW3596, rep1

description: Library name: S04.GW_Hep_1


title: TUG1210_0h_rep1_ATACseq

description:
Library name: TUG20_1_QKDO240001120-1A_22MFVNLT4_L3
TUG1210_0h_REP1.mLb.clN.sorted.bam


title: Bone marrow-derived macrophage treated by GW3596, rep3

description: Library name: S03.GW_BMDM_3


title: A549_D1B_WT cells, control, rep3

description: Library name: sample 3


title: TUG1210_1h_rep1_ATACseq

description:
Library name: TUG260_1_QKDO240001126-1A_22MFVNLT4_L3
TUG1210_1h_REP1.mLb.clN.sorted.bam


title: RP11_2.5h_rep3_ATACseq

description:
Library name: RP150-3
RP11_2.5h_REP3.mLb.clN.sorted.bam


title: RP11_2.5h_rep2_ATACseq

description:
Library name: RP150-2
RP11_2.5h_REP2.mLb.clN.sorted.bam


title: A549_D1B_WT cells, control, rep2

description: Library name: sample 2


title: Bone marrow-derived macrophage treated by GW3596, rep2

description: Library name: S02.GW_BMDM_2


title: RP11_2h_rep3_ATACseq

description:
Library name: RP120-3
RP11_2h_REP3.mLb.clN.sorted.bam


title: Bone marrow-derived macrophage treated by GW3596, rep1

description: Library name: S01.GW_BMDM_1


title: RP11_2.5h_rep1_ATACseq

description:
Library name: RP150-1
RP11_2.5h_REP1.mLb.clN.sorted.bam


title: A549_D1B_WT cells, control, rep1

description: Library name: sample 1


title: RP11_1.5h_rep3_ATACseq

description:
Library name: RP90-3
RP11_1.5h_REP3.mLb.clN.sorted.bam


title: Day 2 IFNb Animal 2 Replicate2

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description: Library name: RetinaDay2_IFNb_AAV_2_Rep2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger 6.0.2 software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger), using Ensembl gene annotations
Assembly: GRCm38
Supplementary files format and content: Original raw (unfiltered) output files from the Cell Ranger software, each sample consists of 3 files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Supplementary files format and content: matrix.mtx.gz: gzipped Cell Ranger Feature Barcode Matrix (MEX Format)
Supplementary files format and content: features.tsv.gz:  gzipped TSV file with features (Ensembl genes)
Supplementary files format and content: barcodes.tsv.gz:  gzipped TSV file with barcodes (cell barcodes)

source_name: Retina

extract_protocol:
Neural Tissue Dissociation Kit-Postnatal Neurons (MACS, Cat. #130-094-802) was used for retinal tissue dissociation.  Retinas (both RPE and neural retina; n=4 for Null-AAV, n=4 for IFN-b-AAV) were dissected out from the anterior segment under normal light in cold D-PBS w/ Ca2+/Mg2+. The retinas were then transferred into pre-warmed buffer containing Buffer Z and Enzyme P, and then incubated for 15 min at 37°C with gentle shaking using a Thermomixer (Eppendorf, Germany). Next, enzyme mix 2 (Buffer Y plus Enzyme A) was added and the retinas were dissociated by gently pipetting up and down using a cropped plastic transfer pipette. The tissue mixture was incubated for 10 min at 37°C on the Thermomixer before adding an additional 7.5 mL Enzyme mix 2. The retinal tissue was further dissociated by trituration and the suspension was filtered through a 70 mm cell strainer and centrifuged for 10 min at 200g (4°C). Dissociated retinal cells were incubated with anti-CD73-PE (MACs, Cat. #130-102-616, 107 cells per tube) followed by anti-PE microBeads (MACs, Cat. #130-048-801, 107 cells per tube) to partially deplete rods. Calcein violet AM (Invitrogen, USA, Cat. #C34858) and eFluor780 (Invitrogen, USA, Cat. #65-0865) were used to enrich live cells. Incubation was done in the dark at 4°C for 20 min. CD73 negative cells were selected via MS Columns (MACs, Cat. #130-042-201) through a Mini MACs Separator (MACs, Milltenyi Biotec, Germany). Viable CD73 negative cells were further enriched by using a FACS sorter (Aria Fusion, BD Biosciences, USA) with gating of Calcein AM positive, eFluor780 negative cell populations. Single, viable cell suspensions were diluted to 1000 cells/mL in PBS with 0.04% BSA for loading into 10x Chromium Single Cell v 3.1 Chips.
Following collection, cDNA libraries were prepared following the manufacturer's protocol and sequenced with a NovaSeq 6000 S1 Reagent kit v1.5.

treatment_protocol: Mice were administered intravitreal AAV2-CAG-m-IFNb-WPRE (treatment) or AAV2-CAG-Null (control) and ocular tissue was collected after 10 weeks.

value: Retina

value: C57BL/6J WT


title: RP11_1.5h_rep2_ATACseq

description:
Library name: RP90-2
RP11_1.5h_REP2.mLb.clN.sorted.bam


title: Combo3

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

description: Library name: Combo3

data_processing:
Novogene Standard RNA-Seq pipeline
Assembly: Homo_sapiens_hg38
Supplementary files format and content: standard BAM files

source_name: Mesothelioma

growth_protocol: MSTO-211H cells were grown in RPMI supplemented with SM1, epidermal growth factor (EGF), fibroblast growth factor 2 (bFGF), heparin, and 1% penicillin-streptomycin media at 37°C in a 5% CO2 incubator. Cells were grown in suspension and seeded at 100,000 cells into T25 flasks.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) columns for RNA isolation by following manufacturer's protocol.
The RNA sequencing library was generated using NEBNext® Ultra RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols. The library concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies), and then diluted to 1 ng/uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: MSTO-211H mesothelioma-initiating cells were seeded in suspension in a flask. Cells were treated with QTP (10 uM) or vehicle control and irradiated with 4 Gy or sham irradiated the next day. 48 hours after the irradiation, RNA was isolated.

value: Mesothelioma

value: Cell Line


title: Day 2 IFNb Animal 2 Replicate1

description: Library name: RetinaDay2_IFNb_AAV_2_Rep1


title: RP11_2h_rep1_ATACseq

description:
Library name: RP120-1
RP11_2h_REP1.mLb.clN.sorted.bam


title: Day 2 IFNb Animal 1 Replicate2

description: Library name: RetinaDay2_IFNb_AAV_1_Rep2


title: RP11_1h_rep3_ATACseq

description:
Library name: RP60-3
RP11_1h_REP3.mLb.clN.sorted.bam


title: Combo1

description: Library name: Combo1


title: RP11_2h_rep2_ATACseq

description:
Library name: RP120-2
RP11_2h_REP2.mLb.clN.sorted.bam


title: RP11_1h_rep2_ATACseq

description:
Library name: RP60-2
RP11_1h_REP2.mLb.clN.sorted.bam


title: Combo2

description: Library name: Combo2


title: Rx3

description: Library name: Rx3


title: Day 2 IFNb Animal 1 Replicate1

description: Library name: RetinaDay2_IFNb_AAV_1_Rep1


title: RP11_1.5h_rep1_ATACseq

description:
Library name: RP90-1
RP11_1.5h_REP1.mLb.clN.sorted.bam


title: TUG1210_2.5h_rep3_ATACseq

description:
Library name: TUG2150_3_QKDO240001137-1A_22MFVNLT4_L3
TUG1210_2.5h_REP3.mLb.clN.sorted.bam


title: RP11_0.5h_rep2_ATACseq

description:
Library name: RP30-2
RP11_0.5h_REP2.mLb.clN.sorted.bam


title: RP11_1h_rep1_ATACseq

description:
Library name: RP60-1
RP11_1h_REP1.mLb.clN.sorted.bam


title: A549_D1B_Y273F cells, control, rep2

description: Library name: sample 8


title: Day 2 Null Animal 2 Replicate 2

description: Library name: RetinaDay2_Null_AAV_2_Rep2


title: RP11_0.5h_rep3_ATACseq

description:
Library name: RP30-3
RP11_0.5h_REP3.mLb.clN.sorted.bam


title: Rx2

description: Library name: Rx2


title: RP11_0.5h_rep1_ATACseq

description:
Library name: RP30-1
RP11_0.5h_REP1.mLb.clN.sorted.bam


title: RP11_0h_rep3_ATACseq

description:
Library name: RP0-3
RP11_0h_REP3.mLb.clN.sorted.bam


title: Control_3

description: Library name: Control_3

value: blood

value: Peripheral blood CD45-positive immune cells

value: Vehicle control


title: Rx1

description: Library name: Rx1


title: IR3

description: Library name: IR3


title: Day 2 Null Animal 1 Replicate2

description: Library name: RetinaDay2_Null_AAV_1_Rep2


title: RP11_0h_rep2_ATACseq

description:
Library name: RP0-2
RP11_0h_REP2.mLb.clN.sorted.bam


title: PNKY_2.5h_rep3_ATACseq

description:
Library name: PNKY150_3
PNKY_2.5h_REP3.mLb.clN.sorted.bam


title: RP11_0h_rep1_ATACseq

description:
Library name: RP0-1
RP11_0h_REP1.mLb.clN.sorted.bam


title: PNKY_2.5h_rep2_ATACseq

description:
Library name: PNKY150_2
PNKY_2.5h_REP2.mLb.clN.sorted.bam


title: PNKY_2h_rep2_ATACseq

description:
Library name: PNKY120_2
PNKY_2h_REP2.mLb.clN.sorted.bam


title: PNKY_2.5h_rep1_ATACseq

description:
Library name: PNKY150_1
PNKY_2.5h_REP1.mLb.clN.sorted.bam


title: Day 2 Null Animal 1 Replicate1

description: Library name: RetinaDay2_Null_AAV_1_Rep1


title: Day 1 IFNb Animal 2 Replicate2

description: Library name: RetinaDay1_IFNb_AAV_2_Rep2


title: IR2

description: Library name: IR2


title: Day 2 Null Animal 2 Replicate1

description: Library name: RetinaDay2_Null_AAV_2_Rep1


title: IR1

description: Library name: IR1


title: PNKY_2h_rep1_ATACseq

description:
Library name: PNKY120_1
PNKY_2h_REP1.mLb.clN.sorted.bam


title: PNKY_2h_rep3_ATACseq

description:
Library name: PNKY120_3
PNKY_2h_REP3.mLb.clN.sorted.bam


title: Day 1 IFNb Animal 2 Replicate1

description: Library name: RetinaDay1_IFNb_AAV_2_Rep1


title: Day 1 IFNb Animal 1 Replicate2

description: Library name: RetinaDay1_IFNb_AAV_1_Rep2


title: PNKY_1.5h_rep3_ATACseq

description:
Library name: PNKY90_3
PNKY_1.5h_REP3.mLb.clN.sorted.bam


title: Con3

description: Library name: Con3


title: PNKY_1.5h_rep2_ATACseq

description:
Library name: PNKY90_2
PNKY_1.5h_REP2.mLb.clN.sorted.bam


title: Con1

description: Library name: Con1


title: Con2

description: Library name: Con2


title: PNKY_1h_rep3_ATACseq

description:
Library name: PNKY60_3
PNKY_1h_REP3.mLb.clN.sorted.bam


title: PNKY_1h_rep1_ATACseq

description:
Library name: PNKY60_1
PNKY_1h_REP1.mLb.clN.sorted.bam


title: Day 1 IFNb Animal 1 Replicate1

description: Library name: RetinaDay1_IFNb_AAV_1_Rep1


title: PNKY_1.5h_rep1_ATACseq

description:
Library name: PNKY90_1
PNKY_1.5h_REP1.mLb.clN.sorted.bam


title: Day 1 Null Animal 2 Replicate 2

description: Library name: RetinaDay1_Null_AAV_2_Rep2


title: PNKY_0.5h_rep3_ATACseq

description:
Library name: PNKY30_3
PNKY_0.5h_REP3.mLb.clN.sorted.bam


title: MTA, Biological Replicate 3

city: Chapel Hill

first: Adam

middle: C

last: Palmer

state: NC

address: 116 Manning Drive

department: Pharmacology

institute: University of North Carolina at Chapel Hill

description:
Library name: Sample 39
Basal bulk mRNA expression fromMTA, Replicate 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughin-house perl scripts. In this step, clean data (clean reads) were obtainedbyremoving reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. At the same time, Q20, Q30 and GC content thecleandata were calculated. All the downstream analyses were based on thecleandata with high quality
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean 1 reads were aligned to the referencegenome using Hisat2 v2.0.5. We selected Hisat2 [2] as the mapping tool for that Hisat2 can generate a database of splice junctions based on the genemodel annotation file and thus a better mapping result than other non-splice mappingtools.
featureCounts [3] v1.5.0-p3 was used to count the reads numbers mappedto each gene. And then FPKM of each gene was calculated based onthelength of the gene and reads count mapped to this gene. FPKM, expectednumber of Fragments Per Kilobase of transcript sequence per Millions basepairs sequenced, considers the effect of sequencing depth and gene lengthfor the reads count at the same time, and is currently the most commonly usedmethod for estimating gene expression levels
Assembly: Alignment performed usin HISAT2, The whole sequence was aligned to a single exon. The sequencing sequence was piecewise aligned to two exons of the genome. The sequencing sequence was segmented and aligned to more than three (including three) exons of the genome.
Supplementary files format and content: Processed Data file containes Log2 FPKM for all samples. The top variably expressed transcripts from the set of raw data are identified, and data from the two batches of RNAseq are combined into one csv.

source_name: MTA

growth_protocol: Cells were grown continuously with passaging down to 100,000 live cells per mL in human plasma like medium +FBS every 48 hours. RNA was extracted after a two-day period of growth for each cell line

extract_protocol:
Rneasy Blood and Tissue Kit from QIAGEN
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

treatment_protocol: no treatment, cultures were profiled by RNA-seq at basal conditions

value: MTA

value: established cell line, hematopoeitic

value: WT

value: basal expression


title: Day 1 Null Animal 2 Replicate1

description: Library name: RetinaDay1_Null_AAV_2_Rep1


title: NK-92

description:
Library name: Sample 37
Basal bulk mRNA expression from NK-92


title: PNKY_1h_rep2_ATACseq

description:
Library name: PNKY60_2
PNKY_1h_REP2.mLb.clN.sorted.bam


title: PNKY_0h_rep1_ATACseq

description:
Library name: PNKY0_1
PNKY_0h_REP1.mLb.clN.sorted.bam


title: PNKY_0h_rep3_ATACseq

description:
Library name: PNKY0_3
PNKY_0h_REP3.mLb.clN.sorted.bam


title: PNKY_0.5h_rep2_ATACseq

description:
Library name: PNKY30_2
PNKY_0.5h_REP2.mLb.clN.sorted.bam


title: Day 1 Null Animal 1 Replicate2

description: Library name: RetinaDay1_Null_AAV_1_Rep2


title: TLBR-3

description:
Library name: Sample 38
Basal bulk mRNA expression from TLBR-3


title: PNKY_0.5h_rep1_ATACseq

description:
Library name: PNKY30_1
PNKY_0.5h_REP1.mLb.clN.sorted.bam


title: HD-MAR-2

description:
Library name: Sample 36
Basal bulk mRNA expression from HD-MAR-2


title: PNKY_0h_rep2_ATACseq

description:
Library name: PNKY0_2
PNKY_0h_REP2.mLb.clN.sorted.bam


title: Day 1 Null Animal 1 Replicate1

description: Library name: RetinaDay1_Null_AAV_1_Rep1


title: LNCPRESS1_2.5h_rep2_ATACseq

description:
Library name: PRE230-2
LNCPRESS1_2.5h_REP2.mLb.clN.sorted.bam


title: SUP-M2

description:
Library name: Sample 35
Basal bulk mRNA expression from SUP-M2


title: LNCPRESS1_2.5h_rep3_ATACseq

description:
Library name: PRE230-3
LNCPRESS1_2.5h_REP3.mLb.clN.sorted.bam


title: LNCPRESS1_2.5h_rep1_ATACseq

description:
Library name: PRE230-1
LNCPRESS1_2.5h_REP1.mLb.clN.sorted.bam


title: LNCPRESS1_2h_rep2_ATACseq

description:
Library name: PRE2-2
LNCPRESS1_2h_REP2.mLb.clN.sorted.bam


title: hippocampal tissue from Meth3

city: Nanjing

first: fang

last: lu

address: 300 Guangzhou Road

department: Department of Nephrology

institute: the First Affiliated Hospital of Nanjing Medical University

description:
Library name: sample6
10x Genomics

data_processing:
Results from Illumina sequencing were converted to FASTQ format using bcl2fastq software (v.5.0.1). The snRNA-seq data were aligned to the reference genome using CellRanger (v.7.0.0), and 3′ end transcripts from individual cells were identified and quantified.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
After the mice had been exsanguinated via transcranial perfusion with physiological saline (PS, Thermo Fisher Scientific), hippocampal tissues for analysis were dissected. Briefly, the tissue was added to 1 ml of pre-chilled lysate, sheared into small pieces of approximately 1 mm3, and 2 ml of pre-chilled lysate was added. The tissue was transferred to a tissue homogenizer (885300-0007, Kimble Dounce Homogenizer) and ground slowly five times. Then the tissue was incubated on ice for 5 min. Subsequently, 4 ml of pre-cooled 2% BSA solution was added, and the process was terminated by pipetting with a barrel pipette. The samples were passed through a 30 μm cell sieve, and the filtrate was collected and centrifuged at 300×g for 5 min at 4 °C. The supernatant was discarded. The cells were resuspended in 5 ml of 2% BSA, centrifuged at 4 °C for 5 min at 300×g, and the supernatant was discarded again. The cells were then resuspended in 500 μL of resuspension solution (1×PBS, 2% BSA, 0.1% RNase inhibitor). The cells were stained with Propidium Iodide (PI) and sorted to remove debris and impurities using a BD FACSAria II flow cytometer. The sorted cells were collected and counted.
Single-nucleus suspension was added to the 10×Chromium chip according to the instructions for the 10×Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8000 nuclei. After the reverse transcription step, single-nucleus Gel Bead-In-Emulsions (GEMs) were broken, and barcoded cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors, and index PCR amplified. Libraries were sequenced by LC-Biotechnology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (paired-end sequencing, 150 bp) at a minimum depth of 20,000 reads per nucleus.

treatment_protocol: Meth or saline intraperitoneal injection

value: hippocampus

value: Meth


title: MT-4

description:
Library name: Sample 33
Basal bulk mRNA expression from MT-4


title: hippocampal tissue from Meth2

description:
Library name: sample5
10x Genomics


title: LNCPRESS1_2h_rep3_ATACseq

description:
Library name: PRE2-3
LNCPRESS1_2h_REP3.mLb.clN.sorted.bam


title: LNCPRESS1_1.5h_rep2_ATACseq

description:
Library name: PRE130-2
LNCPRESS1_1.5h_REP2.mLb.clN.sorted.bam


title: LNCPRESS1_1.5h_rep3_ATACseq

description:
Library name: PRE130-3
LNCPRESS1_1.5h_REP3.mLb.clN.sorted.bam


title: hippocampal tissue from Meth1

description:
Library name: sample4
10x Genomics


title: SU-DHL-1, Biological Replicate 6

description:
Library name: Sample 32
Basal bulk mRNA expression from SU-DHL-1, Replicate 6


title: SUP-T1

description:
Library name: Sample 34
Basal bulk mRNA expression from SUP-T1


title: LNCPRESS1_1h_rep3_ATACseq

description:
Library name: PRE1-3
LNCPRESS1_1h_REP3.mLb.clN.sorted.bam


title: SU-DHL-1, Biological Replicate 5

description:
Library name: Sample 31
Basal bulk mRNA expression from SU-DHL-1, Replicate 5


title: LNCPRESS1_1.5h_rep1_ATACseq

description:
Library name: PRE130-1
LNCPRESS1_1.5h_REP1.mLb.clN.sorted.bam


title: LNCPRESS1_1h_rep2_ATACseq

description:
Library name: PRE1-2
LNCPRESS1_1h_REP2.mLb.clN.sorted.bam


title: SU-DHL-1, Biological Replicate 4

description:
Library name: Sample 30
Basal bulk mRNA expression from SU-DHL-1, Replicate 4


title: LNCPRESS1_1h_rep1_ATACseq

description:
Library name: PRE1-1
LNCPRESS1_1h_REP1.mLb.clN.sorted.bam


title: hippocampal tissue from control2

description:
Library name: sample2
10x Genomics

value: Saline


title: Week 10- AAV2-CAG-Null n=4

description: Library name: Null-2425

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: GRCm38
Supplementary files format and content: csv file with raw read counts per ENSEMBL gene ID and gene name

source_name: RPE/choroid

extract_protocol:
Total RNA was extracted from 8 mouse RPE/choroid tissues using a RNeasy Mini Kit (Qiagen, USA, Cat. #74104) following the manufacturer's protocol.  Samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, USA).
Library preparation and NovaSeq Sequencing were performed at Azenta, USA. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer's instructions (NEB, USA).

value: RPE/choroid


title: LNCPRESS1_2h_rep1_ATACseq

description:
Library name: PRE2-1
LNCPRESS1_2h_REP1.mLb.clN.sorted.bam

source_name: hiPSCs

value: hiPSCs


title: LNCPRESS1_0.5h_rep2_ATACseq

description:
Library name: PRE30-2
LNCPRESS1_0.5h_REP2.mLb.clN.sorted.bam


title: hippocampal tissue from control3

description:
Library name: sample3
10x Genomics


title: hippocampal tissue from control1

description:
Library name: sample1
10x Genomics


title: SR-786

description:
Library name: Sample 29
Basal bulk mRNA expression from SR-786


title: LNCPRESS1_0.5h_rep3_ATACseq

description:
Library name: PRE30-3
LNCPRESS1_0.5h_REP3.mLb.clN.sorted.bam


title: LNCPRESS1_0.5h_rep1_ATACseq

description:
Library name: PRE30-1
LNCPRESS1_0.5h_REP1.mLb.clN.sorted.bam


title: SU-DHL-1, Biological  Replicate 3

description:
Library name: Sample 28
Basal bulk mRNA expression from SU-DHL-1, Replicate 3


title: LNCPRESS1_0h_rep3_ATACseq

description:
Library name: PRE0-3
LNCPRESS1_0h_REP3.mLb.clN.sorted.bam


title: Week 10- AAV2-CAG-Null n=1

description: Library name: Null-2416


title: LINCROR-2.5h_rep2_ATACseq

description:
Library name: ROR230_2
LINCROR.2.5h_REP2.mLb.clN.sorted.bam


title: LNCPRESS1_0h_rep2_ATACseq

description:
Library name: PRE0-2
LNCPRESS1_0h_REP2.mLb.clN.sorted.bam


title: Week 10- AAV2-CAG-Null n=2

description: Library name: Null-2419


title: SU-DHL-1, Biological  Replicate 2

description:
Library name: Sample 27
Basal bulk mRNA expression from SU-DHL-1, Replicate 2


title: LINCROR-2.5h_rep3_ATACseq

description:
Library name: ROR230_3
LINCROR.2.5h_REP3.mLb.clN.sorted.bam


title: Week 10- AAV2-CAG-Null n=3

description: Library name: Null-2424


title: Week 10- AAV2-CAG-m-IFNb-WPRE n=3

description: Library name: IFNb-2438


title: Week 10- AAV2-CAG-m-IFNb-WPRE n=2

description: Library name: IFNb-2432


title: LINCROR-1.5h_rep3_ATACseq

description:
Library name: ROR130_3
LINCROR.1.5h_REP3.mLb.clN.sorted.bam


title: LINCROR-1h_rep3_ATACseq

description:
Library name: ROR1_3
LINCROR.1h_REP3.mLb.clN.sorted.bam


title: LINCROR-1h_rep2_ATACseq

description:
Library name: ROR1_2
LINCROR.1h_REP2.mLb.clN.sorted.bam


title: Mouse heart Immtfl/fl-Myh6-MCM 3

city: Cincinnati

first: Yasuhide

last: Kuwabara

state: Ohio

address: 240 Albert Sabin Way, Building S

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Library name: MitoCKO3

data_processing:
1. FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.
2. Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
3. Alignment to the appropriate reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads.
4. Coordinate sorting of BAM files using samtools v1.22.1.
5. UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0.
6. Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RSeQC v5.0.4 and Qualimap v2.3.
7. Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
8. Differential expression using edgeR v4.0.16 with filtering for low-expressed genes with edgeR::filterByExpr with default values.
Assembly: GRCm38 (mm10)
Supplementary files format and content: A xlsx file contains expression data, count, and fpkm of all genes in each sample. The xlsx file also contains fold-change data and adjusted p-value.

source_name: Heart

extract_protocol:
Total RNA was extracted from hearts using Trizol according to the manufacture's protocol.
1. Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences).2. Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. 3. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.

value: Heart

value: Tamoxifen injection

tag: time

value: 20 weeks after tamoxifien injection


title: LINCROR-1h_rep1_ATACseq

city: Boulder

first: Mingfeng

address: 709 Mohawk Dr

description:
Library name: ROR1_1
LINCROR.1h_REP1.mLb.clN.sorted.bam


title: MY-LA

description:
Library name: Sample 26
Basal bulk mRNA expression from MY-LA

source_name: MY-LA

value: MY-LA


title: LNCPRESS1_0h_rep1_ATACseq

description:
Library name: PRE0-1
LNCPRESS1_0h_REP1.mLb.clN.sorted.bam


title: LINCROR-2.5h_rep1_ATACseq

description:
Library name: ROR230_1
LINCROR.2.5h_REP1.mLb.clN.sorted.bam


title: Week 10- AAV2-CAG-m-IFNb-WPRE n=4

description: Library name: IFNb-2443

value: C57BL/6J WT


title: LINCROR-2h_rep3_ATACseq

description:
Library name: ROR2_3
LINCROR.2h_REP3.mLb.clN.sorted.bam


title: MTA,Biological  Replicate 2

description:
Library name: Sample 25
Basal bulk mRNA expression from MTA, Replicate 2


title: Mouse heart Immtfl/fl-Myh6-MCM 1

description: Library name: MitoCKO1


title: LINCROR-0.5h_rep3_ATACseq

description:
Library name: ROR30_3
LINCROR.0.5h_REP3.mLb.clN.sorted.bam


title: LINCROR-0h_rep3_ATACseq

description:
Library name: ROR0_3
LINCROR.0h_REP3.mLb.clN.sorted.bam


title: TLBR-2

description:
Library name: Sample 24
Basal bulk mRNA expression from TLBR-2


title: LINCROR-1.5h_rep2_ATACseq

description:
Library name: ROR130_2
LINCROR.1.5h_REP2.mLb.clN.sorted.bam


title: NKL

description:
Library name: Sample 19
Basal bulk mRNA expression from NKL

source_name: NKL

value: NKL


title: LINCROR-1.5h_rep1_ATACseq

description:
Library name: ROR130_1
LINCROR.1.5h_REP1.mLb.clN.sorted.bam


title: LINCROR-2h_rep1_ATACseq

description:
Library name: ROR2_1
LINCROR.2h_REP1.mLb.clN.sorted.bam


title: Week 10- AAV2-CAG-m-IFNb-WPRE n=1

description: Library name: IFNb-2429


title: LINCROR-0h_rep1_ATACseq

description:
Library name: ROR0_1
LINCROR.0h_REP1.mLb.clN.sorted.bam


title: SU9-T01

description:
Library name: Sample 22
Basal bulk mRNA expression from SU9-T01


title: Mouse heart Immt+/+-Myh6-MCM 2

description: Library name: MitoCTRL2


title: Mouse heart Immt+/+-Myh6-MCM 3

description: Library name: MitoCTRL3


title: Mac2a

description:
Library name: Sample 17
Basal bulk mRNA expression from Mac2a


title: LINCPINT_2.5h_rep2_ATACseq

description:
Library name: Pi230_2_QKDO240000984-1A_22J7J5LT4_L4
LINCPINT_2.5h_REP2.mLb.clN.sorted.bam


title: TLBR-1

description:
Library name: Sample 23
Basal bulk mRNA expression from TLBR-1


title: LINCPINT_2.5h_rep3_ATACseq

description:
Library name: Pi230_3_QKDO240000985-1A_22J7J5LT4_L4
LINCPINT_2.5h_REP3.mLb.clN.sorted.bam


title: LINCROR-2h_rep2_ATACseq

description:
Library name: ROR2_2
LINCROR.2h_REP2.mLb.clN.sorted.bam


title: OCI-LY-17

description:
Library name: Sample 21
Basal bulk mRNA expression from OCI-LY-17


title: Mouse heart Immtfl/fl-Myh6-MCM 2

description: Library name: MitoCKO2


title: Mouse heart Immt+/+-Myh6-MCM 1

description: Library name: MitoCTRL1


title: OCI-LY-13.2

description:
Library name: Sample 20
Basal bulk mRNA expression from OCI-LY-13.2


title: LINCROR-0.5h_rep2_ATACseq

description:
Library name: ROR30_2
LINCROR.0.5h_REP2.mLb.clN.sorted.bam


title: LINCROR-0.5h_rep1_ATACseq

description:
Library name: ROR30_1
LINCROR.0.5h_REP1.mLb.clN.sorted.bam


title: MJ

description:
Library name: Sample 18
Basal bulk mRNA expression from MJ

source_name: MJ

value: MJ


title: LINCPINT_2h_rep2_ATACseq

description:
Library name: Pi2_2_QKDO240000981-1A_22J7J5LT4_L4
LINCPINT_2h_REP2.mLb.clN.sorted.bam


title: LINCPINT_2.5h_rep1_ATACseq

description:
Library name: Pi230_1_QKDO240000983-1A_22J7J5LT4_L4
LINCPINT_2.5h_REP1.mLb.clN.sorted.bam


title: LINCPINT_2h_rep3_ATACseq

description:
Library name: Pi2_3_QKDO240000982-1A_22J7J5LT4_L4
LINCPINT_2h_REP3.mLb.clN.sorted.bam


title: DP thymocytes，Kansl1fl/fl CD4-Cre mice-3

first: xiaoyu

last: yi

state: Beijing

address: Taiping Road

institute: NCBA

description: Library name: B3

data_processing:
Raw reads were quality-filtered to remove adapters and low-quality sequences. Clean reads were aligned to the mouse reference genome (GRCm39) using standard aligners (e.g., STAR). Gene-level read counts were quantified using featureCounts or an equivalent tool. Differential expression analysis was performed using DESeq2. Only genes with adjusted P-value < 0.05 and |log2FC| > 1.5 were considered significantly differentially expressed.
Assembly: Mus_musculus.GRCm39.V1
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

source_name: Thymus

growth_protocol: Mice were maintained under specific pathogen–free (SPF) conditions in the institutional animal facility with controlled temperature, humidity, and a 12-hour light/dark cycle. Kansl1fl/fl CD4-Cre mice and littermate controls Kansl1fl/fl mice were used at 8 weeks of age. Animals had ad libitum access to autoclaved food and water.

extract_protocol:
Double-positive thymocytes were isolated by flow cytometry sorting. Total RNA was extracted using TRIzol reagent following the manufacturer’s protocol. RNA integrity was assessed with Bioanalyzer or equivalent, and high-quality RNA was used for library preparation.
A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Then we added fragmentation buffer to break the mRNA into short fragments. First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. And then, the double stranded cDNA was purified by AMPure P beads or QiaQuick PCR kit. The purified double stranded cDNA was repaired at the end, added a tail and connected to the sequencing connector, then the fragment size was selected, and finally the final cDNA library was obtained by PCR enrichment.

treatment_protocol: No in vitro stimulation was performed prior to RNA extraction. Thymocytes were isolated directly after animal euthanasia without additional ex vivo treatment.

value: Thymus

value: DP thymocytes

value: KANSL1 deficiency


title: LINCROR-0h_rep2_ATACseq

institute: University of Colorado

description:
Library name: ROR0_2
LINCROR.0h_REP2.mLb.clN.sorted.bam


title: LINCPINT_1.5h_rep3_ATACseq

description:
Library name: Pi130_3_QKDO240000979-1A_22J7J5LT4_L4
LINCPINT_1.5h_REP3.mLb.clN.sorted.bam


title: LINCPINT_1.5h_rep2_ATACseq

description:
Library name: Pi130_2_QKDO240000978-1A_22J7J5LT4_L4
LINCPINT_1.5h_REP2.mLb.clN.sorted.bam


title: SUDHL-1, Biological Replicate 1

description:
Library name: Sample 14
Basal bulk mRNA expression from SUDHL-1, Replicate 1

value: established cell line, hematopoeitic

value: WT


title: DERL-2

description:
Library name: Sample 15
Basal bulk mRNA expression from DERL-2

value: basal expression


title: DP thymocytes，Kansl1fl/fl CD4-Cre mice-2

description: Library name: B2


title: LINCPINT_2h_rep1_ATACseq

description:
Library name: Pi2_1_QKDO240000980-1A_22J7J5LT4_L4
LINCPINT_2h_REP1.mLb.clN.sorted.bam


title: LINCPINT_1h_rep3_ATACseq

description:
Library name: Pi1_3_QKDO240000976-1A_22HVHJLT4_L1
LINCPINT_1h_REP3.mLb.clN.sorted.bam


title: DP thymocytes，Kansl1fl/fl CD4-Cre mice-1

description: Library name: B1


title: LINCPINT_1.5h_rep1_ATACseq

description:
Library name: Pi130_1_QKDO240000977-1A_22HVHJLT4_L1
LINCPINT_1.5h_REP1.mLb.clN.sorted.bam


title: HH

description:
Library name: Sample 16
Basal bulk mRNA expression from HH

source_name: HH

value: HH


title: LINCPINT_0.5h_rep3_ATACseq

description:
Library name: Pi30_3_QKDO240000973-1A_22HVHJLT4_L1
LINCPINT_0.5h_REP3.mLb.clN.sorted.bam


title: DP thymocytes，Kansl1fl/fl  mice-3

description: Library name: A3


title: LINCPINT_1h_rep1_ATACseq

description:
Library name: Pi1_1_QKDO240000974-1A_22HVHJLT4_L1
LINCPINT_1h_REP1.mLb.clN.sorted.bam


title: MTA, Biological Replicate 1

description:
Library name: Sample 12
Basal bulk mRNA expression from MTA, Replicate 1

value: MTA


title: LINCPINT_1h_rep2_ATACseq

description:
Library name: Pi1_2_QKDO240000975-1A_22HVHJLT4_L1
LINCPINT_1h_REP2.mLb.clN.sorted.bam


title: DP thymocytes，Kansl1fl/fl  mice-2

description: Library name: A2


title: LINCPINT_0.5h_rep2_ATACseq

description:
Library name: Pi30_2_QKDO240000972-1A_22HVHJLT4_L1
LINCPINT_0.5h_REP2.mLb.clN.sorted.bam


title: SMZ1

description:
Library name: Sample 13
Basal bulk mRNA expression from SMZ1


title: MOTN-1

description:
Library name: Sample 11
Basal bulk mRNA expression from MOTN-1


title: LINCPINT_0h_rep2_ATACseq

description:
Library name: Pi0_2_QKDO240000969-1A_22HVHJLT4_L1
LINCPINT_0h_REP2.mLb.clN.sorted.bam


title: KOB

description:
Library name: Sample 10
Basal bulk mRNA expression from KOB

source_name: KOB

value: KOB


title: LINCPINT_0.5h_rep1_ATACseq

description:
Library name: Pi30_1_QKDO240000971-1A_22HVHJLT4_L1
LINCPINT_0.5h_REP1.mLb.clN.sorted.bam

value: hiPSCs


title: LINCPINT_0h_rep3_ATACseq

description:
Library name: Pi0_3_QKDO240000970-1A_22HVHJLT4_L1
LINCPINT_0h_REP3.mLb.clN.sorted.bam


title: heart, rep 5/6 nephrectomy and injected with JV101, rep 3

city: Shanghai

first: Danshu

last: Xie

address: No. 639, Zhizaoju Road

institute: Shanghai Jiaotong University, School of medicine

description:
Library name: NX+JV101_3
Column name in processed data files: NJ3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: Heart

tag: strain

value: cardiomyocytes

value: 5/6 nephrectomy and injected with JV101


title: Karpas384

description:
Library name: Sample 9
Basal bulk mRNA expression from Karpas384


title: heart, rep 5/6 nephrectomy and injected with JV101, rep 2

description:
Library name: NX+JV101_2
Column name in processed data files: NJ2


title: heart, rep 5/6 nephrectomy and injected with JV101, rep 1

description:
Library name: NX+JV101_1
Column name in processed data files: NJ1


title: OCI-LY-12

description:
Library name: Sample 7
Basal bulk mRNA expression from OCI-LY-12


title: DL40

description:
Library name: Sample 8
Basal bulk mRNA expression from DL40


title: LINCPINT_0h_rep1_ATACseq

last: Liu

description:
Library name: Pi0_1_QKDO240000968-1A_22HVHJLT4_L1
LINCPINT_0h_REP1.mLb.clN.sorted.bam


title: LINC01547_2.5h_rep2_ATACseq

description:
Library name: L47230-2
LINC01547_2.5h_REP2.mLb.clN.sorted.bam


title: LINC01547_2.5h_rep1_ATACseq

description:
Library name: L47230-1
LINC01547_2.5h_REP1.mLb.clN.sorted.bam


title: LINC01547_2h_rep2_ATACseq

description:
Library name: L472-2
LINC01547_2h_REP2.mLb.clN.sorted.bam


title: L82

description:
Library name: Sample 6
Basal bulk mRNA expression from L82


title: LINC01547_1.5h_rep1_ATACseq

description:
Library name: L47130-1
LINC01547_1.5h_REP1.mLb.clN.sorted.bam


title: KiJK

description:
Library name: Sample 5
Basal bulk mRNA expression from KiJK

source_name: KiJK

value: KiJK


title: DP thymocytes，Kansl1fl/fl  mice-1

description: Library name: A1


title: LINC01547_1.5h_rep3_ATACseq

description:
Library name: L47130-3
LINC01547_1.5h_REP3.mLb.clN.sorted.bam


title: heart, rep 5/6 nephrectomy and injected with saline, rep 3

description:
Library name: NX_3
Column name in processed data files: NX3


title: LINC01547_1h_rep3_ATACseq

description:
Library name: L471-3
LINC01547_1h_REP3.mLb.clN.sorted.bam


title: KHYG1

description:
Library name: Sample 4
Basal bulk mRNA expression from KHYG1


title: LINC01547_2.5h_rep3_ATACseq

description:
Library name: L47230-3
LINC01547_2.5h_REP3.mLb.clN.sorted.bam


title: LINC01547_2h_rep3_ATACseq

description:
Library name: L472-3
LINC01547_2h_REP3.mLb.clN.sorted.bam


title: heart, rep 5/6 nephrectomy and injected with saline, rep 1

description:
Library name: NX_1
Column name in processed data files: NX1


title: LINC01547_1h_rep2_ATACseq

description:
Library name: L471-2
LINC01547_1h_REP2.mLb.clN.sorted.bam


title: LINC01547_2h_rep1_ATACseq

description:
Library name: L472-1
LINC01547_2h_REP1.mLb.clN.sorted.bam


title: heart, rep 5/6 nephrectomy and injected with saline, rep 2

description:
Library name: NX_2
Column name in processed data files: NX2


title: LINC01547_1.5h_rep2_ATACseq

description:
Library name: L47130-2
LINC01547_1.5h_REP2.mLb.clN.sorted.bam


title: heart, rep sham and injected with JV101, rep 3

description:
Library name: sham+JV101_3
Column name in processed data files: SJ3

value: sham and injected with JV101


title: LINC01547_1h_rep1_ATACseq

description:
Library name: L471-1
LINC01547_1h_REP1.mLb.clN.sorted.bam


title: Karpas299

description:
Library name: Sample 3
Basal bulk mRNA expression from Karpas299


title: LINC01547_0.5h_rep3_ATACseq

description:
Library name: L4730-3
LINC01547_0.5h_REP3.mLb.clN.sorted.bam


title: heart, rep sham and injected with JV101, rep 1

description:
Library name: sham+JV101_1
Column name in processed data files: SJ1


title: LINC01547_0h_rep3_ATACseq

description:
Library name: L470-3
LINC01547_0h_REP3.mLb.clN.sorted.bam


title: heart, rep sham and injected with JV101, rep 2

description:
Library name: sham+JV101_2
Column name in processed data files: SJ2


title: LINC01547_0.5h_rep1_ATACseq

description:
Library name: L4730-1
LINC01547_0.5h_REP1.mLb.clN.sorted.bam


title: Hut78

description:
Library name: Sample 2
Basal bulk mRNA expression from Hut78


title: LINC01547_0h_rep2_ATACseq

description:
Library name: L470-2
LINC01547_0h_REP2.mLb.clN.sorted.bam


title: FE-PD

description:
Library name: Sample 1
Basal bulk mRNA expression from FE-PD

source_name: FE-PD

value: FE-PD


title: heart, rep sham and injected with saline, rep 2

description:
Library name: sham_2
Column name in processed data files: sham2

value: sham and injected with saline


title: LINC01547_0h_rep1_ATACseq

description:
Library name: L470-1
LINC01547_0h_REP1.mLb.clN.sorted.bam


title: heart, rep sham and injected with saline, rep 3

description:
Library name: sham_3
Column name in processed data files: sham3


title: LINC00847_2h_rep2_ATACseq

description:
Library name: L847120_2
LINC00847_2h_REP2.mLb.clN.sorted.bam


title: LINC00847_2h_rep1_ATACseq

description:
Library name: L847120_1
LINC00847_2h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 10-DD

city: Houston

first: Zhao

last: Zheng

state: TX

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

description:
Library name: scATAC_10-DD
scATAC_10-DD

library_source: genomic single cell

data_processing:
1. Alignment and quantification using Cell Ranger ARC count to generate gene expression feature-barcode matrices and ATAC fragments.
2. Reference genome: GRCh38/hg38 (report exact reference package used by Cell Ranger ARC).
3. QC filtering based on RNA (genes/UMIs/mitochondrial fraction) and ATAC (TSS enrichment/fragments in peaks/nucleosome signal) metrics; doublets removed if applicable.
4. Downstream analysis performed in Seurat/Signac/ArchR: normalization, PCA/LSI, clustering, UMAP visualization, and optional peak calling/motif analysis.
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: primary de-differentiated liposarcoma

extract_protocol:
Nuclei were isolated from tissue/cell suspension using a detergent-based lysis buffer on ice following the Chromium Single Cell Multiome ATAC + Gene Expression nuclei isolation guidelines. Nuclei were filtered, washed, counted, and adjusted to the recommended input concentration. Nuclei integrity was confirmed by microscopy.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit following the manufacturer protocol. Nuclei were partitioned into GEMs for barcoding; RNA was reverse transcribed and ATAC DNA was tagmented and barcoded. Gene Expression and ATAC libraries were amplified, indexed, QC’d, and sequenced on an Illumina platform with recommended read structure.

value: primary de-differentiated liposarcoma

value: DD


title: heart, rep sham and injected with saline, rep 1

description:
Library name: sham_1
Column name in processed data files: sham1


title: LINC00847_2h_rep3_ATACseq

description:
Library name: L847120_3
LINC00847_2h_REP3.mLb.clN.sorted.bam


title: LINC00847_2.5h_rep2_ATACseq

description:
Library name: L847150_2
LINC00847_2.5h_REP2.mLb.clN.sorted.bam


title: LINC01547_0.5h_rep2_ATACseq

description:
Library name: L4730-2
LINC01547_0.5h_REP2.mLb.clN.sorted.bam


title: LINC00847_1.5h_rep3_ATACseq

description:
Library name: L84790_3
LINC00847_1.5h_REP3.mLb.clN.sorted.bam


title: LINC00847_2.5h_rep3_ATACseq

description:
Library name: L847150_3
LINC00847_2.5h_REP3.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 12-WD

description:
Library name: scATAC_12-WD
scATAC_12-WD

source_name: primary well-differentiated liposarcoma

value: primary well-differentiated liposarcoma

value: WD


title: LINC00847_2.5h_rep1_ATACseq

description:
Library name: L847150_1
LINC00847_2.5h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 9-WD-B

description:
Library name: scATAC_9-WD-B
scATAC_9-WD-B


title: B222

city: Bern

first: Bryce

last: Evans

address: Murtenstrasse, 28, 365

department: DBMR

institute: Inselspital, Universitätsspital Bern

description:
Library name: B222
Bulk RNA-seq of aortas from BMT control mice with ChemR23 intact

data_processing:
Base call files were demultiplexed and converted to FASTQ using Illumina bcl2fastq v2.20.
Reads were aligned to the Mus musculus GRCm38 (Ensembl release 102) reference genome using HiSat2 v2.2.1.
Read counts per gene were generated using FeatureCounts v2.0.1.
Differential gene expression analysis was performed with DESeq2 v1.36.0 in R v4.2.0.
Pathway enrichment and gene set enrichment analyses were conducted with ClusterProfiler v4.4.4 using KEGG and MSigDB gene sets.
Assembly: Mus musculus GRCm38 (Ensembl release 102).
Supplementary files format and content: Differential expression results:  log2 fold changes, adjusted p-values, and gene annotations; pathway enrichment output

source_name: Aorta (adventitia stripped; media + intima)

growth_protocol: Mice (Apoe⁻/⁻►ChemR23e/eApoe⁻/⁻ and Apoe⁻/⁻►Apoe⁻/⁻) were bred under SPF conditions and maintained on standard chow until initiation of experiments.

extract_protocol:
After 6 weeks of Western diet, aortas were dissected under a microscope, and adventitia was removed to preserve the media and intima. Tissue was homogenized, and total RNA was isolated using the RNeasy Fibrous Tissue Mini Kit (Qiagen). RNA integrity and concentration were assessed with Qubit RNA HS Assay Kit and Agilent Fragment Analyzer.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit with TruSeq RNA UD Indexes according to the manufacturer’s protocol. Libraries were quality controlled with Qubit dsDNA HS Assay Kit and Agilent Fragment Analyzer, pooled, and sequenced on an Illumina NovaSeq 6000 platform (paired-end, 50 bp).

treatment_protocol: At 8–10 weeks of age, mice underwent bone marrow transplantation and were allowed a 4-week recovery period. Following recovery, animals were placed on a Western diet (21% fat, 0.15–0.2% cholesterol) for 6 weeks.

value: Vascular tissue (media and intima, enriched for VSMCs + ECs)

value: Apoe-/-BMT/Apoe-/-

value: 6 weeks Western Diet


title: scMultiomic ATAC-Seq of LPS, 11-WD

description:
Library name: scATAC_11-WD
scATAC_11-WD


title: B220

description:
Library name: B220
Bulk RNA-seq of aortas from BMT control mice with ChemR23 intact

value: Aorta (adventitia stripped; media + intima)


title: B224

description:
Library name: B224
Bulk RNA-seq of aortas from BMT control mice with ChemR23 intact


title: LINC00847_1h_rep3_ATACseq

description:
Library name: L84760_3
LINC00847_1h_REP3.mLb.clN.sorted.bam


title: LINC00847_1h_rep2_ATACseq

description:
Library name: L84760_2
LINC00847_1h_REP2.mLb.clN.sorted.bam


title: B050

description:
Library name: B050
Bulk RNA-seq of aortas from BMT mice lacking ChemR23 in non-hematopoietic cells


title: LINC00847_0.5h_rep3_ATACseq

description:
Library name: L84730_3
LINC00847_0.5h_REP3.mLb.clN.sorted.bam


title: LINC00847_1.5h_rep2_ATACseq

description:
Library name: L84790_2
LINC00847_1.5h_REP2.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 7-WD-B

description:
Library name: scATAC_7-WD-B
scATAC_7-WD-B


title: scMultiomic ATAC-Seq of LPS, 9-WD-A

description:
Library name: scATAC_9-WD-A
scATAC_9-WD-A


title: LINC00847_1h_rep1_ATACseq

description:
Library name: L84760_1
LINC00847_1h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 8-DD-8

description:
Library name: scATAC_8-DD-B
scATAC_8-DD-B


title: scMultiomic ATAC-Seq of LPS, 7-WD-A

description:
Library name: scATAC_7-WD-A
scATAC_7-WD-A


title: B049

description:
Library name: B049
Bulk RNA-seq of aortas from BMT mice lacking ChemR23 in non-hematopoietic cells


title: LINC00847_0h_rep3_ATACseq

description:
Library name: L8470_3
LINC00847_0h_REP3.mLb.clN.sorted.bam


title: LINC00847_1.5h_rep1_ATACseq

description:
Library name: L84790_1
LINC00847_1.5h_REP1.mLb.clN.sorted.bam


title: LINC00847_0.5h_rep1_ATACseq

description:
Library name: L84730_1
LINC00847_0.5h_REP1.mLb.clN.sorted.bam


title: B048

description:
Library name: B048
Bulk RNA-seq of aortas from BMT mice lacking ChemR23 in non-hematopoietic cells


title: scMultiomic ATAC-Seq of LPS, 6-WD-B

description:
Library name: scATAC_6-WD-B
scATAC_6-WD-B


title: LINC00847_0h_rep2_ATACseq

description:
Library name: L8470_2
LINC00847_0h_REP2.mLb.clN.sorted.bam


title: D- 28

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

country: Canada

institute: McGill University

description:
Library name: DM-28
CpG location, BETA, methylated count, unmethylated count

data_processing:
Genpipes V4.4.5 methylation sequencing pipeline was used for alignment  and methylation calls https://genpipes.readthedocs.io/en/genpipes-v4.6.1/
Assembly: mm10
Supplementary files format and content: tab-deliminated file containing beta, methylation counts and unmethylated counts for each Sample

source_name: liver

extract_protocol:
DNA was extracted using standard proteinase K/phenol/chloroform protocol
Library preparation for Illumina, WGBS bisulfite, low throughput (< 48 samples), Lucigen

value: liver

tag: developmental stage

value: 10-11 weeks old

value: ICR

value: hemizygous Kdm5d mutant

tag: Sex

value: M


title: LINC00847_0.5h_rep2_ATACseq

description:
Library name: L84730_2
LINC00847_0.5h_REP2.mLb.clN.sorted.bam

value: hiPSCs


title: scMultiomic ATAC-Seq of LPS, 6-WD-A

description:
Library name: scATAC_6-WD-A
scATAC_6-WD-A


title: LINC00847_0h_rep1_ATACseq

description:
Library name: L8470_1
LINC00847_0h_REP1.mLb.clN.sorted.bam


title: LINC00667-2.5h_rep3_ATACseq

description:
Library name: C42h30_3
LINC00667.2.5h_REP3.mLb.clN.sorted.bam


title: D- 27

description:
Library name: DM-27
CpG location, BETA, methylated count, unmethylated count


title: LINC00667-2.5h_rep2_ATACseq

description:
Library name: C42h30_2
LINC00667.2.5h_REP2.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 5-WD-B

description:
Library name: scATAC_5-WD-B
scATAC_5-WD-B


title: scMultiomic ATAC-Seq of LPS, 5-WD-A

description:
Library name: scATAC_5-WD-A
scATAC_5-WD-A


title: LINC00667-2.5h_rep1_ATACseq

description:
Library name: C42h30_1
LINC00667.2.5h_REP1.mLb.clN.sorted.bam


title: D- 26

description:
Library name: DM-26
CpG location, BETA, methylated count, unmethylated count


title: LINC00667-2h_rep3_ATACseq

description:
Library name: C42h_3
LINC00667.2h_REP3.mLb.clN.sorted.bam


title: D+ 23

description:
Library name: DK-23
CpG location, BETA, methylated count, unmethylated count

value: wild type


title: LINC00667-2h_rep1_ATACseq

description:
Library name: C42h_1
LINC00667.2h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 4-DD-B

description:
Library name: scATAC_4-DD-B
scATAC_4-DD-B


title: scMultiomic ATAC-Seq of LPS, 4-WD

description:
Library name: scATAC_4-WD
scATAC_4-WD


title: LINC00667-1.5h_rep1_ATACseq

description:
Library name: C41h30_1
LINC00667.1.5h_REP1.mLb.clN.sorted.bam


title: LINC00667-2h_rep2_ATACseq

description:
Library name: C42h_2
LINC00667.2h_REP2.mLb.clN.sorted.bam


title: LINC00667-1.5h_rep3_ATACseq

description:
Library name: C41h30_3
LINC00667.1.5h_REP3.mLb.clN.sorted.bam


title: LINC00667-1.5h_rep2_ATACseq

description:
Library name: C41h30_2
LINC00667.1.5h_REP2.mLb.clN.sorted.bam


title: D+ 24

description:
Library name: DK-24
CpG location, BETA, methylated count, unmethylated count


title: LINC00667-1h_rep3_ATACseq

description:
Library name: C41h_3
LINC00667.1h_REP3.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 4-DD-A

description:
Library name: scATAC_4-DD-A
scATAC_4-DD-A


title: D- 25

description:
Library name: DM-25
CpG location, BETA, methylated count, unmethylated count


title: LINC00667-1h_rep1_ATACseq

description:
Library name: C41h_1
LINC00667.1h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS,3-DD-B

description:
Library name: scATAC_3-DD-B
scATAC_3-DD-B


title: LINC00667-0.5h_rep3_ATACseq

description:
Library name: C430_3
LINC00667.0.5h_REP3.mLb.clN.sorted.bam


title: D+ 21

description:
Library name: DK-21
CpG location, BETA, methylated count, unmethylated count


title: LINC00667-1h_rep2_ATACseq

description:
Library name: C41h_2
LINC00667.1h_REP2.mLb.clN.sorted.bam


title: LINC00667-0h_rep2_ATACseq

description:
Library name: C40h_2
LINC00667.0h_REP2.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS,2-WD-B

description:
Library name: scATAC_2-WD-B
scATAC_2-WD-B


title: D+ 22

description:
Library name: DK-22
CpG location, BETA, methylated count, unmethylated count


title: LINC00667-0.5h_rep2_ATACseq

description:
Library name: C430_2
LINC00667.0.5h_REP2.mLb.clN.sorted.bam


title: LINC00667-0.5h_rep1_ATACseq

description:
Library name: C430_1
LINC00667.0.5h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS, 3-DD-A

description:
Library name: scATAC_3-DD-A
scATAC_3-DD-A


title: C+ 5

description:
Library name: CWTM-5
CpG location, BETA, methylated count, unmethylated count


title: LINC00667-0h_rep3_ATACseq

description:
Library name: C40h_3
LINC00667.0h_REP3.mLb.clN.sorted.bam


title: HULC_2.5h_rep3_ATACseq

description:
Library name: HU150-3
HULC_2.5h_REP3.mLb.clN.sorted.bam


title: LINC00667-0h_rep1_ATACseq

description:
Library name: C40h_1
LINC00667.0h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LPS,2-WD-A

description:
Library name: scATAC_2-WD-A
scATAC_2-WD-A


title: scMultiomic ATAC-Seq of LPS,1-WD

description:
Library name: scATAC_1-WD
scATAC_1-WD


title: HULC_2.5h_rep2_ATACseq

description:
Library name: HU150-2
HULC_2.5h_REP2.mLb.clN.sorted.bam


title: C+ 4

description:
Library name: CWTM-4
CpG location, BETA, methylated count, unmethylated count


title: HULC_2h_rep3_ATACseq

description:
Library name: HU120-3
HULC_2h_REP3.mLb.clN.sorted.bam


title: HULC_2h_rep1_ATACseq

description:
Library name: HU120-1
HULC_2h_REP1.mLb.clN.sorted.bam


title: HULC_2.5h_rep1_ATACseq

description:
Library name: HU150-1
HULC_2.5h_REP1.mLb.clN.sorted.bam