title: Muscle_DMSOforDex_WT_rep1

description:
Library name: Muscle_DMSOforDex_WT_rep1_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC1B

status: Public on Aug 07 2026

type: SRA

city: Stanford

first: Mengrui

last: Zhang

state: CA

address: 291 Campus Drive

department: Division of Immunology and Rheumatology

country: USA

institute: Stanford University

description:
Library name: PC1B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix

library_source: transcriptomic single cell

data_processing:
GEX FASTQ files were processed with 10x Genomics Cell Ranger to generate filtered feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) aligned to the human GRCh38 reference transcriptome.
CITE-seq/ADT libraries were processed to UMI count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for antibody-derived tags; antibody feature definitions are provided in feature_README.txt.
BCR V(D)J FASTQ files were processed with 10x Genomics Cell Ranger VDJ to generate filtered contig FASTA and filtered_contig_annotations.csv files.
Processed files were assigned unique sample-specific filenames for GEO deposition while retaining Cell Ranger file contents.
Assembly: GRCh38
Supplementary files format and content: For each GEX sample: Cell Ranger filtered feature-barcode matrix Market Exchange (MEX) files (*_GEX_barcodes.tsv.gz, *_GEX_features.tsv.gz, *_GEX_matrix.mtx.gz) containing UMI counts for gene expression features. For each CITE-seq sample: ADT UMI count MEX files (*_CITE_barcodes.tsv.gz, *_CITE_features.tsv.gz, *_CITE_matrix.mtx.gz). For each BCR sample: Cell Ranger filtered_contig_annotations.csv and filtered_contig.fasta. Supplementary feature_README.txt maps ADT barcodes to antibody names.
Supplementary files format and content: Matrix Market files store sparse cell-by-feature UMI counts; features are Ensembl gene IDs (GEX) or antibody-derived tags (CITE). BCR annotation CSV includes contig-level V(D)J calls and cell barcodes.

molecule: polyA RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: Not applicable (ex vivo peripheral blood B cells; no cell culture growth protocol).

extract_protocol:
Peripheral blood was collected and B cells were enriched for single-cell multiomics profiling. Gene expression, surface protein (ADT), and BCR V(D)J libraries were prepared using 10x Genomics Chromium workflows according to the manufacturer protocols.
Single-cell gene expression, CITE-seq/ADT, and BCR V(D)J libraries were constructed with the 10x Genomics Chromium platform and sequenced on an Illumina NovaSeq X Plus instrument.

treatment_protocol: No experimental treatment was applied. Samples are paired longitudinal peripheral blood draws (pre and post) from healthy controls, ACPA-positive non-converters, and ACPA-positive individuals who converted to clinical rheumatoid arthritis.

tag: tissue

value: peripheral blood

tag: disease state

value: ACPA-positive converter to clinical RA

tag: cell type

value: B cells

tag: Sex

value: female

tag: timepoint

value: post

tag: subject group

value: converter


title: WT 0nM insulin control, biol rep 1

city: Oxford

first: Fadil

middle: M

last: Hannan

state: Oxfordshire

address: Level 3, Women's Centre, John Radcliffe Hospital

department: Nuffield Department of Women's and Reproductive Health

country: United Kingdom

institute: University of Oxford

description:
Library name: WTCTRL1
WTCTRL1

library_source: transcriptomic

data_processing:
The sequencing libraries were multiplexed and loaded on an Illumina NovaSeq 6000 instrument. Samples were sequenced using a 2x150 paired-end (PE) configuration. Image analysis and base calling were conducted on instrument, and raw sequence data were converted into FASTQ files and demultiplexed using Illumina bcl2fastq program version 2.20.
Assembly: HC11: mm9, NCBI Build 37. MCF-12A and MFG: human (hg19, GRCh37).
Supplementary files format and content: CSV files containing raw counts data for each sample; one counts file per dataset.

extract_protocol:
HC11 and MCF-12A RNA was extracted using the RNeasy mini plus kit (Qiagen). MFG RNA was extracted using the RNeasy plus universal kit (Qiagen).
HC11 and MCF-12A RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). MFG RNA libraries were prepared using rRNA depletion followed by NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s recommendations.

tag: cell line

value: Mammary epithelial cell

tag: genotype

value: WT

value: 0nM insulin control


title: Muscle_Dex_WT_rep3

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

description:
Library name: Muscle_Dex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

organism: Mus musculus

source_name: Muscle

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2–3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: Muscle

tag: strain

value: Male

tag: age

value: 2 months

tag: mouse id


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC1A

description:
Library name: PC1A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix

value: pre


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC1A

description:
Library name: PC1A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

library_source: other

data_processing:
GEX FASTQ files were processed with 10x Genomics Cell Ranger to generate filtered feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) aligned to the human GRCh38 reference transcriptome.
CITE-seq/ADT libraries were processed to UMI count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for antibody-derived tags; antibody feature definitions are provided in feature_README.txt.
BCR V(D)J FASTQ files were processed with 10x Genomics Cell Ranger VDJ to generate filtered contig FASTA and filtered_contig_annotations.csv files.
Processed files were assigned unique sample-specific filenames for GEO deposition while retaining Cell Ranger file contents.
Assembly: GRCh38
Supplementary files format and content: For each GEX sample: Cell Ranger filtered feature-barcode matrix Market Exchange (MEX) files (*_GEX_barcodes.tsv.gz, *_GEX_features.tsv.gz, *_GEX_matrix.mtx.gz) containing UMI counts for gene expression features. For each CITE-seq sample: ADT UMI count MEX files (*_CITE_barcodes.tsv.gz, *_CITE_features.tsv.gz, *_CITE_matrix.mtx.gz). For each BCR sample: Cell Ranger filtered_contig_annotations.csv and filtered_contig.fasta. Supplementary feature_README.txt maps ADT barcodes to antibody names.
Supplementary files format and content: Matrix Market files store sparse cell-by-feature UMI counts; features are Ensembl gene IDs (GEX) or antibody-derived tags (CITE). BCR annotation CSV includes contig-level V(D)J calls and cell barcodes.
Library strategy: CITE-seq

molecule: protein


title: Peripheral B cells, healthy control, post, BCR-seq, NN3B

description:
Library name: NN3B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

data_processing:
GEX FASTQ files were processed with 10x Genomics Cell Ranger to generate filtered feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) aligned to the human GRCh38 reference transcriptome.
CITE-seq/ADT libraries were processed to UMI count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for antibody-derived tags; antibody feature definitions are provided in feature_README.txt.
BCR V(D)J FASTQ files were processed with 10x Genomics Cell Ranger VDJ to generate filtered contig FASTA and filtered_contig_annotations.csv files.
Processed files were assigned unique sample-specific filenames for GEO deposition while retaining Cell Ranger file contents.
Assembly: GRCh38
Supplementary files format and content: For each GEX sample: Cell Ranger filtered feature-barcode matrix Market Exchange (MEX) files (*_GEX_barcodes.tsv.gz, *_GEX_features.tsv.gz, *_GEX_matrix.mtx.gz) containing UMI counts for gene expression features. For each CITE-seq sample: ADT UMI count MEX files (*_CITE_barcodes.tsv.gz, *_CITE_features.tsv.gz, *_CITE_matrix.mtx.gz). For each BCR sample: Cell Ranger filtered_contig_annotations.csv and filtered_contig.fasta. Supplementary feature_README.txt maps ADT barcodes to antibody names.
Supplementary files format and content: Matrix Market files store sparse cell-by-feature UMI counts; features are Ensembl gene IDs (GEX) or antibody-derived tags (CITE). BCR annotation CSV includes contig-level V(D)J calls and cell barcodes.
Library strategy: BCR-Seq

value: healthy control


title: MoDCs, Tg, biol rep 3

city: Geneva

first: María

last: Cruz Cobo

address: Rue Michel-Servet 1, CMU

department: Pathology and Immunology

country: Switzerland

institute: University of Geneva

description: Library name: Tg_609

data_processing:
Illumina bcl2fastq was used for basecalling. Sequenced reads were mapped to Ensembl GRCh38 whole genome using STAR v.2.7.10b with default parameters. Raw counts were produced by htseq-count (HTSeq v.0.11.3). Normalization and differential expression analysis were performed with edgeR v.3.42.4
Assembly: Ensembl genome GRCh38
Supplementary files format and content: NunesHasler_CruzCobo_0124-rawcounts.txt = tab-delimited text files include raw count values for each Sample
Supplementary files format and content: NunesHasler_CruzCobo_0124-normcounts.txt = tab-delimited text files include normalized expression values (cpm = count per millions) for each Sample
Supplementary files format and content: NunesHasler_CruzCobo_0124-log2_normcounts.txt = tab-delimited text files include normalized expression values (log 2 cpm = count per millions) for each Sample

molecule: total RNA

source_name: Matured human monocyte-derived dendritic cells (MoDCs)

extract_protocol:
Total RNA was extracted using the Monarch Total RNA miniprep kit (#T2010G, New England Biolabs) according to manufacturer's instructions
RNA libraries were prepared using Illumina Stranded mRNA Prep kit

tag: treatment

value: Antigen-loaded, Tg treated

tag: donor


title: Peripheral B cells, healthy control, post, CITE-seq, NN3B

description:
Library name: NN3B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: MoDCs, Tg, biol rep 2

description: Library name: Tg_561

value: Matured human monocyte-derived dendritic cells (MoDCs)


title: Peripheral B cells, healthy control, post, scRNA-seq, NN3B

description:
Library name: NN3B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, healthy control, pre, BCR-seq, NN3A

description:
Library name: NN3A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Muscle_Dex_WT_rep2

description:
Library name: Muscle_Dex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Muscle_Dex_WT_rep1

description:
Library name: Muscle_Dex_WT_rep1_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Bone_DMSOforDex_WT_rep4

description:
Library name: Bone_DMSOforDex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

source_name: Bone

value: Bone


title: Peripheral B cells, healthy control, pre, scRNA-seq, NN3A

description:
Library name: NN3A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix

value: peripheral blood


title: MoDCs, Tg, biol rep 1

description: Library name: Tg_457


title: Peripheral B cells, healthy control, pre, CITE-seq, NN3A

description:
Library name: NN3A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Peripheral B cells, healthy control, post, CITE-seq, NN2B

description:
Library name: NN2B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Bone_DMSOforDex_WT_rep3

description:
Library name: Bone_DMSOforDex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, healthy control, post, scRNA-seq, NN2B

description:
Library name: NN2B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, healthy control, post, BCR-seq, NN2B

description:
Library name: NN2B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: MoDCs, pBr, biol rep 3

description: Library name: pBr_609

value: Antigen-loaded, pBr treated


title: Heart_Dex_KO_rep2

description:
Library name: Heart_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Heart

value: Heart

value: Mecp2 KO

value: 1.5 months


title: MoDCs, pBr, biol rep 2

description: Library name: pBr_561


title: Peripheral B cells, healthy control, pre, BCR-seq, NN2A

description:
Library name: NN2A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: B cells

value: female


title: Peripheral B cells, healthy control, pre, CITE-seq, NN2A

description:
Library name: NN2A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: MoDCs, pBr, biol rep 1

description: Library name: pBr_457


title: Bone_DMSOforDex_WT_rep2

description:
Library name: Bone_DMSOforDex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: WT


title: Peripheral B cells, healthy control, pre, scRNA-seq, NN2A

description:
Library name: NN2A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, healthy control, post, CITE-seq, NN1B

description:
Library name: NN1B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

value: post


title: Peripheral B cells, healthy control, post, BCR-seq, NN1B

description:
Library name: NN1B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: MoDCs, CTR, biol rep 3

description: Library name: CTR_609

value: Antigen-loaded, untreated


title: Bone_DMSOforDex_WT_rep1

description:
Library name: Bone_DMSOforDex_WT_rep1_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: Male


title: Bone_Dex_WT_rep4

description:
Library name: Bone_Dex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: 2 months


title: Peripheral B cells, healthy control, post, scRNA-seq, NN1B

description:
Library name: NN1B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, healthy control, pre, BCR-seq, NN1A

description:
Library name: NN1A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: pre


title: Peripheral B cells, healthy control, pre, CITE-seq, NN1A

description:
Library name: NN1A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

value: healthy control


title: Bone_Dex_WT_rep3

description:
Library name: Bone_Dex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: MoDCs, CTR, biol rep 1

description: Library name: CTR_457


title: MoDCs, CTR, biol rep 2

description: Library name: CTR_561


title: Peripheral B cells, healthy control, pre, scRNA-seq, NN1A

description:
Library name: NN1A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC4B

description:
Library name: PC4B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix

value: ACPA-positive converter to clinical RA

value: converter


title: Bone_Dex_WT_rep2

description:
Library name: Bone_Dex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: Bone


title: iPSC-derived OPCs, SPMS_3, CT42, differtiation 3

city: Palo Alto

first: Erin

last: Gibson

state: California

address: 3165 Porter Drive

department: Psychiatry and Behavioral Sciences

description: Library name: TDR72Z_108_CT42_015_3

data_processing:
Data quality control and comparisons were conducted by the Plasmidsaurus online analysis platform in November 2025.  In short, quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR. Optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3. Gene-level expression quantification was performed 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. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values and FDR values were used for further analysis. Samples CT24_300_3, CT24_021_3, CT30_300_3, CT30_021_3, CT36_300_3, CT36_021_3, CT42_300_3, CT42_021_3, CT42_008_3 were excluded from the analysis.
Assembly: GRCh38
Supplementary files format and content: Expression_matrix.tsv includes counts and CPM values for every sample

growth_protocol: Human inducible pluripotent stem cells (hiPSC) from RRMS (relapsing remitting, early-stage MS, n=3) and SPMS (secondary progressive, late-stage MS, n=3) MS patients, and age/sex-matched healthy controls (n=3 control) were acquired from the New York Stem Cell Foundation (see Suppl. Fig. 12A for line details) and differentiated towards OPCs, as previously described132. In short, iPSCs were cultured in 6-well plates coated with matrigel (Corning 354230, 1:100) in iPSC culture media comprising Miltenyi StemMACS iPS-brew XF with supplement (Miltenyi 130-104-368) and 1% Antibiotic Antimycotic Solution (Sigma). ROCK inhibitor Y-27632 (10 µM, Tocris) was added to the iPSC media for the first 24 hours. Once the iPSCs reached 70–80% confluency, cells were detached with pre-warmed EDTA (0.5 mM) for passaging, or pre-warmed accutase (SIGMA A6964) for embryoid bodies (EBs) formation. To form EBs, cells were resuspended in iPSC media supplemented with ROCK inhibitor and seeded (~ 1.5 × 10⁶ cells) in AggreWell™400 microwell culture plates (Stem Cell Technologies 34815) overnight. The EBs were then transferred to 10-cm petri dishes (Falcon 351029), placed on a rotary shaker, and cultured for 7 days in a chemically defined medium (CDM): 1:1 mix of F12 and Iscove’s modified Dulbecco’s medium (Invitrogen) with chemically defined Lipid concentrate 100 (Invitrogen), monothioglycerol (450 µM, Sigma), BSA (5 mg/ml, Sigma), transferrin (15 mg/ml, Roche), insulin (7 mg/ml, Roche), and 1% Antibiotic Antimycotic Solution. N-acetyl cysteine (1 mM, Sigma), Activin inhibitor SB 431542 (10 µM, Sigma), and LDN193189 (0.1 µM, Stratech) were added for neural induction. Next, the neurospheres formed from the EBs were caudalized for 7 days in CDM supplemented with N-acetyl cysteine (1 mM, Sigma), heparin (5 µg/ml, Sigma), retinoic acid (0.1 µM, Sigma), and basic fibroblast growth factor (FGF-2; 10 ng/ml, PeproTech). For morphological assessment of neural conversion, the cells were plated on plates coated with laminin (10 μg/ml, Sigma). Post-neural induction, the spheres were cultured in advanced DMEM medium containing 0.5% GlutaMAX (Invitrogen), 5 µg/ml heparin (Sigma), 1% N2 (Invitrogen), 1% B27 (Invitrogen), and 1% Antibiotic Antimycotic Solution. To initiate ventralization, purmorphamine (1 µM, Calbiochem), retinoic acid (1 µM, Sigma), and FGF-2 (10 ng/ml, PeproTech) were added to the media for 7 days, after which FGF-2 was removed for 14 days. hOPC proliferation was then promoted by supplementing the medium with FGF-2 (10 ng/mL), T3 (60 ng/mL, Sigma), PDGFα (20 ng/mL, PeproTech), SAG (1 µM, Calbiochem), purmorphamine (1 µM, Sigma), and IGF-1 (10 ng/mL, PeproTech). After 14 days, spheres were dissociated using the Worthington papain dissociation system (LK003150 per manufacturer’s instructions) and single cells were seeded in matrigel-coated T-75 Flasks (CELLTREAT 229341). After 24 hours, cells were purified for PDGFRα by MACS using PE-conjugated CD140a antibody (Miltenyi 130-115-238) and Anti-PE MicroBeads (Miltenyi 130-048-801) according to the manufacturer’s instructions.

extract_protocol:
Bulk RNA sequencing was performed by Plasmidsaurus using Illumina Sequencing Technology.
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.

treatment_protocol: PDGFRα+ cells were seeded in matrigel-coated 6-well plates and allowed to recover for 24 hours before synchronization with dexamethasone (100nM, 1h, Sigma-Aldrich D4902). Following complete media change, cells were harvested at 24h (CT24), 30h (CT30), 36h (CT36), or 42h (CT42). Cells lysates were preserved in Zymo DNA/RNA Shield (ZYMO RESEARCH R1100-50) for bulk RNA sequencing performed by Plasmidsaurus.

value: iPSC-derived OPCs

value: differentiation 3


title: iPSC-derived OPCs, SPMS_3, CT42, differtiation 2

description: Library name: TDR72Z_107_CT42_015_2

value: differentiation 2


title: Bone_Dex_WT_rep1

description:
Library name: Bone_Dex_WT_rep1_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Brain tissue from healthy donor

city: Toronto

first: Sagi

last: Abelson

state: ON

address: 661 University Avenue

country: Canada

institute: Ontario Institute for Cancer Research

description: Library name: BRAIN_biomodal

library_source: genomic

data_processing:
Raw sequencing reads were trimmed to remove adapter contamination within either read of a pair. The first base of each trimmed read, representing a residual overhang from library preparation, was removed. Reads were subsequently resolved into canonical sequence representations with associated cytosine modification annotations, enabling discrimination of 5-methylcytosine (5mC) in both CpG and non-CpG contexts, as well as 5-hydroxymethylcytosine (5hmC) at CpG sites. Code is available at https://github.com/abelson-lab/mtDNA-Methylation-Revisited
Assembly: GRCh38
Supplementary files format and content: Tab-separated value (TSV) files containing 5mC and 5hmC levels at every cytosine in the mitochondrial genome.

molecule: genomic DNA

source_name: Brain

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer's instructions.
Genomic DNA libraries were prepared using the Biomodal enzymatic sequencing kit, following the manufacturer's protocol.

value: Brain


title: Lymphocyte cell line NA12878

description: Library name: BLOOD_biomodal

source_name: Blood

value: Blood


title: iPSC-derived OPCs, SPMS_3, CT42, differtiation 1

description: Library name: TDR72Z_106_CT42_015_1

value: differentiation 1


title: iPSC-derived OPCs, SPMS_2, CT42, differtiation 2

description: Library name: TDR72Z_104_CT42_011_2


title: WhiteFat_DMSOforRU486_KO_rep6

description:
Library name: WhiteFat_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: WhiteFat

value: WhiteFat

value: Mecp2 KO


title: iPSC-derived OPCs, SPMS_1, CT42, differtiation 3, excluded from analysis

description: Library name: TDR72Z_102_CT42_008_3


title: iPSC-derived OPCs, SPMS_1, CT42, differtiation 2

description: Library name: TDR72Z_101_CT42_008_2


title: iPSC-derived OPCs, SPMS_2, CT42, differtiation 1

description: Library name: TDR72Z_103_CT42_011_1


title: Cyto RPA2 RIP

city: Hefei City

first: Dun

last: Liu

state: Anhui Province

address: Division of Life Sciences and Medicine, 443 Huangshan Road

institute: University of Science and Technology of China

description: Library name: Sample 4

data_processing:
For data processing, the adapters were trimmed from raw data with Cutadapt (-e 0.1 -O 5) to obtain clean reads, which were subsequently aligned to the human genome (hg19) with BWA-MEM or Bowtie2 allowing one mismatch. For circRNA prediction, two published pipelines CIRI2 and Find_circ were applied to identify high-confidence BSJs. Overlapped circRNAs annotated by both pipelines were used for further analysis and CIRI2-identified BSJ Reads Per Million (BRPM) were used to calculate circRNA levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads for each Sample

molecule: cytoplasmic RNA

source_name: MDA-MB-231 cells

extract_protocol:
Total RNA from frozen specimen or cultured cells was extracted with the TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
For ribosomal RNA-depleted (Ribo-) RNA-seq for two-paired breast cancer specimen and NT tissues, total RNA was depleted rRNA with the Illumina Rio-Zero Gold Kit (Illumina) and subjected to library preparation with the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer’s instructions. For polyadenylated (poly(A)+) RNA-seq for MDA-231 cells with or without circRBM39 OE, total RNA was polyadenylated and subjected to library preparation. For RIP-seq, extracted RNA was subjected to library preparation with NEBNext® Ultra II RNA Library Prep Kit (New England Biolabs, E7770) according to the manufacturer's instructions.

value: MDA-MB-231 cells


title: iPSC-derived OPCs, SPMS_2, CT42, differtiation 3

description: Library name: TDR72Z_105_CT42_011_3


title: WhiteFat_DMSOforRU486_KO_rep5

description:
Library name: WhiteFat_DMSOforRU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: WhiteFat_DMSOforRU486_KO_rep4

description:
Library name: WhiteFat_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, SPMS_1, CT42, differtiation 1

description: Library name: TDR72Z_100_CT42_008_1


title: iPSC-derived OPCs, RRMS_3, CT42, differtiation 3

description: Library name: TDR72Z_99_CT42_112_3


title: iPSC-derived OPCs, RRMS_3, CT42, differtiation 2

description: Library name: TDR72Z_98_CT42_112_2


title: Non-tumor tissue 3

description: Library name: Sample 1

source_name: Adjacent non-tumor tissues

value: Adjacent non-tumor tissues


title: WhiteFat_DMSOforRU486_KO_rep3

description:
Library name: WhiteFat_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male


title: iPSC-derived OPCs, RRMS_3, CT42, differtiation 1

description: Library name: TDR72Z_97_CT42_112_1


title: WhiteFat_DMSOforRU486_KO_rep1

description:
Library name: WhiteFat_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: 2 months


title: PBMC CITE-seq, S015-C, antibody-derived tags (ADT)

city: Seattle

first: Kavita

last: Dhodapkar

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Library name: S015-C_ADT
10x Genomics

data_processing:
Cell Ranger version: cellranger-7.1.0 ; Seurat ( R ) Analysis
Assembly: GRCh38
Supplementary files format and content: 10x Cell Ranger matrices: barcodes.tsv.gz), features.tsv.gz, matrix.mtx.gz. One combined GEX+ADT triplet per sample.
Library strategy: CITE-seq

extract_protocol:
PBMC isolation / cell preparation (count, viability) / CITEseq protocol
Chromium Next GEM Single Cell 5' (10x Genomics) with Feature Barcoding for cell-surface protein (TotalSeq ADT)

value: peripheral blood

value: PBMC


title: iPSC-derived OPCs, RRMS_2, CT42, differtiation 3, excluded from analysis

description: Library name: TDR72Z_96_CT42_021_3


title: iPSC-derived OPCs, RRMS_2, CT42, differtiation 2

description: Library name: TDR72Z_95_CT42_021_2


title: iPSC-derived OPCs, RRMS_2, CT42, differtiation 1

description: Library name: TDR72Z_94_CT42_021_1


title: WhiteFat_RU486_KO_rep6

description:
Library name: WhiteFat_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: WhiteFat_RU486_KO_rep5

description:
Library name: WhiteFat_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, RRMS_1, CT42, differtiation 3

description: Library name: TDR72Z_93_CT42_029_3


title: PBMC CITE-seq, S015-C, gene expression (GEX)

description:
Library name: S015-C_GEX
10x Genomics

data_processing:
Cell Ranger version: cellranger-7.1.0 ; Seurat ( R ) Analysis
Assembly: GRCh38
Supplementary files format and content: 10x Cell Ranger matrices: barcodes.tsv.gz), features.tsv.gz, matrix.mtx.gz. One combined GEX+ADT triplet per sample.


title: iPSC-derived OPCs, RRMS_1, CT42, differtiation 2

description: Library name: TDR72Z_92_CT42_029_2


title: iPSC-derived OPCs, RRMS_1, CT42, differtiation 1

description: Library name: TDR72Z_91_CT42_029_1


title: WhiteFat_RU486_KO_rep4

description:
Library name: WhiteFat_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S015-A, gene expression (GEX)

description:
Library name: S015-A_GEX
10x Genomics


title: iPSC-derived OPCs, control_3, CT42, differtiation 3

description: Library name: TDR72Z_90_CT42_425_3


title: iPSC-derived OPCs, control_3, CT42, differtiation 2

description: Library name: TDR72Z_89_CT42_425_2


title: iPSC-derived OPCs, control_3, CT42, differtiation 1

description: Library name: TDR72Z_88_CT42_425_1


title: PBMC CITE-seq, S014-C, antibody-derived tags (ADT)

description:
Library name: S014-C_ADT
10x Genomics


title: iPSC-derived OPCs, control_2, CT42, differtiation 3

description: Library name: TDR72Z_87_CT42_659_3


title: WhiteFat_RU486_KO_rep2

description:
Library name: WhiteFat_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, control_2, CT42, differtiation 2

description: Library name: TDR72Z_86_CT42_659_2


title: Thymus_DMSOforRU486_KO_rep6

description:
Library name: Thymus_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Thymus

value: Thymus


title: iPSC-derived OPCs, control_2, CT42, differtiation 1

description: Library name: TDR72Z_85_CT42_659_1


title: PBMC CITE-seq, S014-C, gene expression (GEX)

description:
Library name: S014-C_GEX
10x Genomics


title: iPSC-derived OPCs, control_1, CT42, differtiation 3, excluded from analysis

description: Library name: TDR72Z_84_CT42_300_3


title: PBMC CITE-seq, S014-A, antibody-derived tags (ADT)

description:
Library name: S014-A_ADT
10x Genomics


title: iPSC-derived OPCs, control_1, CT42, differtiation 2

description: Library name: TDR72Z_83_CT42_300_2


title: Thymus_DMSOforRU486_KO_rep4

description:
Library name: Thymus_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: NiVG-5, rVSV-NiV, 10 DPI

type: RNA

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

hyb_protocol: Overnight hybridization according to standard NanoString protocol

scan_protocol: Scanned and quantified via nCounter SPRINT profiler according to standard protocol

data_processing: Raw RCC files were background-thresholded using the NSolver v4.0 default parameters to generate the sample matrix.

organism: Chlorocebus sabaeus

source_name: African green monkey, whole blood, 10 DPI

extract_protocol: Total RNA extracted from AVL spiked with carrier RNA via the QIAgen Viral RNA Kit

tag: virus

value: HeV-R

value: Vaccinated

tag: vaccine

value: rVSV-NiV

tag: dpi

tag: nhp

value: 10 DPI


title: iPSC-derived OPCs, control_1, CT42, differtiation 1

description: Library name: TDR72Z_82_CT42_300_1

value: iPSC-derived OPCs


title: PBMC CITE-seq, S014-A, gene expression (GEX)

description:
Library name: S014-A_GEX
10x Genomics

tag: tissue


title: Thymus_DMSOforRU486_KO_rep3

description:
Library name: Thymus_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S013-B, antibody-derived tags (ADT)

description:
Library name: S013-B_ADT
10x Genomics


title: iPSC-derived OPCs, SPMS_3, CT36, differtiation 3

description: Library name: TDR72Z_81_CT36_015_3

value: differentiation 3


title: NiVG-5, rVSV-NiV, 7 DPI

source_name: African green monkey, whole blood, 7 DPI

value: 7 DPI


title: PBMC CITE-seq, S013-B, gene expression (GEX)

description:
Library name: S013-B_GEX
10x Genomics


title: NiVG-5, rVSV-NiV, 4 DPI

source_name: African green monkey, whole blood, 4 DPI

value: 4 DPI


title: iPSC-derived OPCs, SPMS_3, CT36, differtiation 2

description: Library name: TDR72Z_80_CT36_015_2

value: differentiation 2


title: Thymus_DMSOforRU486_KO_rep2

description:
Library name: Thymus_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: PBMC CITE-seq, S013-A, antibody-derived tags (ADT)

description:
Library name: S013-A_ADT
10x Genomics


title: Thymus_DMSOforRU486_KO_rep1

description:
Library name: Thymus_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: NiVG-5, rVSV-NiV, baseline

source_name: African green monkey, whole blood, 0 DPI

value: Baseline


title: iPSC-derived OPCs, SPMS_3, CT36, differtiation 1

description: Library name: TDR72Z_79_CT36_015_1

value: differentiation 1


title: Thymus_RU486_KO_rep6

description:
Library name: Thymus_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male


title: PBMC CITE-seq, S013-A, gene expression (GEX)

description:
Library name: S013-A_GEX
10x Genomics


title: NiVG-1, rVSV-NiV, 10 DPI


title: iPSC-derived OPCs, SPMS_2, CT36, differtiation 3

description: Library name: TDR72Z_78_CT36_011_3


title: Thymus_RU486_KO_rep5

description:
Library name: Thymus_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: 2 months


title: NiVG-1, rVSV-NiV, 7 DPI


title: PBMC CITE-seq, S012-C, antibody-derived tags (ADT)

description:
Library name: S012-C_ADT
10x Genomics

value: peripheral blood


title: iPSC-derived OPCs, SPMS_2, CT36, differtiation 2

description: Library name: TDR72Z_77_CT36_011_2


title: Thymus_RU486_KO_rep4

description:
Library name: Thymus_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S012-C, gene expression (GEX)

description:
Library name: S012-C_GEX
10x Genomics

value: PBMC


title: NiVG-1, rVSV-NiV, 4 DPI


title: Thymus_RU486_KO_rep3

description:
Library name: Thymus_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Thymus


title: iPSC-derived OPCs, SPMS_2, CT36, differtiation 1

description: Library name: TDR72Z_76_CT36_011_1


title: NiVG-1, rVSV-NiV, baseline

value: HeV-R


title: PBMC CITE-seq, S012-A, antibody-derived tags (ADT)

description:
Library name: S012-A_ADT
10x Genomics


title: iPSC-derived OPCs, SPMS_1, CT36, differtiation 3

description: Library name: TDR72Z_75_CT36_008_3


title: Cyto Input

description: Library name: Sample 3

value: MDA-MB-231 cells


title: Thymus_RU486_KO_rep2

description:
Library name: Thymus_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: NiVG-2, rVSV-NiV, 10 DPI

value: Vaccinated

value: rVSV-NiV


title: PBMC CITE-seq, S012-A, gene expression (GEX)

description:
Library name: S012-A_GEX
10x Genomics


title: iPSC-derived OPCs, SPMS_1, CT36, differtiation 2

description: Library name: TDR72Z_74_CT36_008_2

value: iPSC-derived OPCs


title: Thymus_RU486_KO_rep1

description:
Library name: Thymus_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: NiVG-2, rVSV-NiV, 7 DPI


title: Breast cancer specimen 3

description: Library name: Sample 2

source_name: Breast cancer tumors

value: Breast cancer tumors


title: iPSC-derived OPCs, SPMS_1, CT36, differtiation 1

description: Library name: TDR72Z_73_CT36_008_1


title: PBMC CITE-seq, S010-BC, antibody-derived tags (ADT)

description:
Library name: S010-BC_ADT
10x Genomics


title: Telencephalon_DMSOforRU486_KO_rep6

description:
Library name: Telencephalon_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Telencephalon

value: Telencephalon


title: PBMC CITE-seq, S010-BC, gene expression (GEX)

description:
Library name: S010-BC_GEX
10x Genomics

source_name: peripheral blood


title: NiVG-2, rVSV-NiV, 4 DPI

value: 4 DPI


title: iPSC-derived OPCs, RRMS_3, CT36, differtiation 3

description: Library name: TDR72Z_72_CT36_112_3

value: differentiation 3


title: PBMC CITE-seq, S010-A, antibody-derived tags (ADT)

description:
Library name: S010-A_ADT
10x Genomics


title: iPSC-derived OPCs, RRMS_3, CT36, differtiation 2

description: Library name: TDR72Z_71_CT36_112_2

value: differentiation 2


title: NiVG-2, rVSV-NiV, baseline

value: Baseline


title: Telencephalon_DMSOforRU486_KO_rep5

description:
Library name: Telencephalon_DMSOforRU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Telencephalon_DMSOforRU486_KO_rep4

description:
Library name: Telencephalon_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male


title: PBMC CITE-seq, S010-A, gene expression (GEX)

description:
Library name: S010-A_GEX
10x Genomics


title: iPSC-derived OPCs, RRMS_3, CT36, differtiation 1

description: Library name: TDR72Z_70_CT36_112_1

value: differentiation 1


title: HeV-C3, control, 7 DPI/terminal

value: Control

value: Terminal


title: Telencephalon_DMSOforRU486_KO_rep3

description:
Library name: Telencephalon_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: 2 months


title: PBMC CITE-seq, S015-A, antibody-derived tags (ADT)

description:
Library name: S015-A_ADT
10x Genomics

value: peripheral blood

value: PBMC


title: PBMC CITE-seq, S009-B, antibody-derived tags (ADT)

description:
Library name: S009-B_ADT
10x Genomics


title: HeV-C3, control, 4 DPI

value: HeV-R


title: iPSC-derived OPCs, RRMS_2, CT36, differtiation 3, excluded from analysis

description: Library name: TDR72Z_69_CT36_021_3


title: Telencephalon_DMSOforRU486_KO_rep2

description:
Library name: Telencephalon_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: HeV-C3, control, baseline


title: PBMC CITE-seq, S009-B, gene expression (GEX)

description:
Library name: S009-B_GEX
10x Genomics


title: Telencephalon_DMSOforRU486_KO_rep1

description:
Library name: Telencephalon_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S009-A, antibody-derived tags (ADT)

description:
Library name: S009-A_ADT
10x Genomics


title: iPSC-derived OPCs, RRMS_2, CT36, differtiation 2

description: Library name: TDR72Z_68_CT36_021_2


title: iPSC-derived OPCs, RRMS_2, CT36, differtiation 1

description: Library name: TDR72Z_67_CT36_021_1


title: Telencephalon_RU486_KO_rep6

description:
Library name: Telencephalon_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S009-A, gene expression (GEX)

description:
Library name: S009-A_GEX
10x Genomics


title: NiVG-4, rVSV-NiV, 10 DPI

value: Vaccinated

value: rVSV-NiV

value: 10 DPI


title: iPSC-derived OPCs, RRMS_1, CT36, differtiation 3

description: Library name: TDR72Z_66_CT36_029_3

value: iPSC-derived OPCs


title: WhiteFat_RU486_KO_rep1

description:
Library name: WhiteFat_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: WhiteFat


title: Telencephalon_RU486_KO_rep5

description:
Library name: Telencephalon_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Telencephalon


title: NiVG-4, rVSV-NiV, 7 DPI

value: 7 DPI


title: PBMC CITE-seq, S008-C, antibody-derived tags (ADT)

description:
Library name: S008-C_ADT
10x Genomics


title: iPSC-derived OPCs, RRMS_1, CT36, differtiation 2

description: Library name: TDR72Z_65_CT36_029_2

value: differentiation 2


title: Telencephalon_RU486_KO_rep4

description:
Library name: Telencephalon_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: NiVG-4, rVSV-NiV, 4 DPI

value: 4 DPI


title: NiVG-4, rVSV-NiV, baseline

value: Baseline


title: iPSC-derived OPCs, RRMS_1, CT36, differtiation 1

description: Library name: TDR72Z_64_CT36_029_1

value: differentiation 1


title: PBMC CITE-seq, S008-C, gene expression (GEX)

description:
Library name: S008-C_GEX
10x Genomics


title: Telencephalon_RU486_KO_rep2

description:
Library name: Telencephalon_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male


title: HeV-C1, control, 6 DPI/terminal

source_name: African green monkey, whole blood, 6 DPI

value: Control

value: Terminal


title: iPSC-derived OPCs, control_3, CT36, differtiation 3

description: Library name: TDR72Z_63_CT36_425_3

value: differentiation 3


title: PBMC CITE-seq, S008-A, gene expression (GEX)

description:
Library name: S008-A_GEX
10x Genomics

value: peripheral blood

value: PBMC


title: PBMC CITE-seq, S008-A, antibody-derived tags (ADT)

description:
Library name: S008-A_ADT
10x Genomics


title: Telencephalon_RU486_KO_rep1

description:
Library name: Telencephalon_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: 2 months


title: iPSC-derived OPCs, control_3, CT36, differtiation 2

description: Library name: TDR72Z_62_CT36_425_2


title: HeV-C1, control, 4 DPI

value: HeV-R


title: Telencephalon_RU486_KO_rep3

description:
Library name: Telencephalon_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S006-C, antibody-derived tags (ADT)

description:
Library name: S006-C_ADT
10x Genomics


title: iPSC-derived OPCs, control_3, CT36, differtiation 1

description: Library name: TDR72Z_61_CT36_425_1

value: iPSC-derived OPCs


title: HeV-C1, control, baseline


title: Spleen_DMSOforRU486_KO_rep5

description:
Library name: Spleen_DMSOforRU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Spleen

value: Spleen


title: PBMC CITE-seq, S006-C, gene expression (GEX)

description:
Library name: S006-C_GEX
10x Genomics


title: HeV-C2, control, 6 DPI/terminal


title: iPSC-derived OPCs, control_2, CT36, differtiation 3

description: Library name: TDR72Z_60_CT36_659_3


title: HeV-C2, control, 4 DPI


title: Spleen_DMSOforRU486_KO_rep4

description:
Library name: Spleen_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Spleen_DMSOforRU486_KO_rep2

description:
Library name: Spleen_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S006-A, antibody-derived tags (ADT)

description:
Library name: S006-A_ADT
10x Genomics


title: iPSC-derived OPCs, control_2, CT36, differtiation 2

description: Library name: TDR72Z_59_CT36_659_2


title: PBMC CITE-seq, S006-A, gene expression (GEX)

description:
Library name: S006-A_GEX
10x Genomics


title: iPSC-derived OPCs, control_2, CT36, differtiation 1

description: Library name: TDR72Z_58_CT36_659_1


title: PBMC CITE-seq, S004-B, antibody-derived tags (ADT)

description:
Library name: S004-B_ADT
10x Genomics


title: HeV-C2, control, baseline


title: Spleen_DMSOforRU486_KO_rep1

description:
Library name: Spleen_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: NiVG-3, rVSV-NiV, 10 DPI

value: Vaccinated

value: rVSV-NiV

value: 10 DPI


title: iPSC-derived OPCs, control_1, CT36, differtiation 3, excluded from analysis

description: Library name: TDR72Z_57_CT36_300_3


title: iPSC-derived OPCs, control_1, CT36, differtiation 2

description: Library name: TDR72Z_56_CT36_300_2

value: differentiation 2


title: Spleen_RU486_KO_rep5

description:
Library name: Spleen_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: PBMC CITE-seq, S004-B, gene expression (GEX)

description:
Library name: S004-B_GEX
10x Genomics


title: Spleen_RU486_KO_rep6

description:
Library name: Spleen_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: NiVG-3, rVSV-NiV, 4 DPI

value: 4 DPI


title: NiVG-3, rVSV-NiV, 7 DPI

value: 7 DPI


title: PBMC CITE-seq, S004-A, antibody-derived tags (ADT)

description:
Library name: S004-A_ADT
10x Genomics


title: iPSC-derived OPCs, control_1, CT36, differtiation 1

description: Library name: TDR72Z_55_CT36_300_1

value: differentiation 1


title: Spleen_RU486_KO_rep4

description:
Library name: Spleen_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male


title: Spleen_RU486_KO_rep3

description:
Library name: Spleen_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S004-A, gene expression (GEX)

description:
Library name: S004-A_GEX
10x Genomics


title: iPSC-derived OPCs, SPMS_3, CT30, differtiation 3

description: Library name: TDR72Z_54_CT30_015_3


title: NiVG-3, rVSV-NiV, baseline

value: Baseline


title: PBMC CITE-seq, S003-C, antibody-derived tags (ADT)

description:
Library name: S003-C_ADT
10x Genomics


title: iPSC-derived OPCs, SPMS_3, CT30, differtiation 2

description: Library name: TDR72Z_53_CT30_015_2


title: Spleen_RU486_KO_rep2

description:
Library name: Spleen_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Female_Thymus_WT

description:
Library name: Female_Thymus_WT_scATAC-seq
UUATAC-seq

library_source: genomic single cell

data_processing:
Raw FASTQ files were split by i7 indexes of DNBSEQ-T7 using splitBarcode (v0.1.6) then converted to BAM format. The 30-bp barcodes were tagged and reads with low quality were removed. Barcodes were next corrected and combined with the i7 indexes to label cells. The barcode-corrected BAM files were split by barcode 3 which label samples. Cell barcodes (i7 indexes + 30-bp barcodes) were added to the query name of each read. BAM files were then converted to FASTQ files with 30-bp barcodes and reverse complementary mosaic end (ME) sequences trimmed. Reads were aligned to mm10 using BWA (version 0.7.15) in paired-end mode. The aligned and sorted BAM files were shifted using the alignmentSieve function in deepTools (version 3.5.1) to correct the 9-bp gap. The shifted BAM files were next merged per sample and converted to BEDPE files (BED format). BEDPE files were cleaned to fragment files for subsequent analyses.
Assembly: mm10
Supplementary files format and content: Compressed BED  files containing sorted fragments
Supplementary files format and content: Compressed Tab-delimited text files containing metadata of cells analyzed

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Library preparations were performed with the UUATAC-seq protocol

value: Thymus

value: WT

value: Female

value: 3.5 months


title: Female_WhiteFat_WT

description:
Library name: Female_WhiteFat_WT_scATAC-seq
UUATAC-seq

value: WhiteFat


title: iPSC-derived OPCs, SPMS_3, CT30, differtiation 1

description: Library name: TDR72Z_52_CT30_015_1

value: iPSC-derived OPCs


title: Spleen_RU486_KO_rep1

description:
Library name: Spleen_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Spleen

value: 2 months


title: Female_Telencephalon_WT

description:
Library name: Female_Telencephalon_WT_scATAC-seq
UUATAC-seq

value: Telencephalon


title: PBMC CITE-seq, S003-C, gene expression (GEX)

description:
Library name: S003-C_GEX
10x Genomics

value: peripheral blood

value: PBMC


title: PBMC CITE-seq, S003-A, antibody-derived tags (ADT)

description:
Library name: S003-A_ADT
10x Genomics


title: iPSC-derived OPCs, SPMS_2, CT30, differtiation 3

description: Library name: TDR72Z_51_CT30_011_3

value: differentiation 3


title: Muscle_DMSOforRU486_KO_rep6

description:
Library name: Muscle_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Muscle

value: Muscle

value: Mecp2 KO


title: Female_Pituitary_WT

description:
Library name: Female_Pituitary_WT_scATAC-seq
UUATAC-seq

source_name: Pituitary

value: Pituitary


title: PBMC CITE-seq, S003-A, gene expression (GEX)

description:
Library name: S003-A_GEX
10x Genomics


title: Muscle_DMSOforRU486_KO_rep5

description:
Library name: Muscle_DMSOforRU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male


title: iPSC-derived OPCs, SPMS_2, CT30, differtiation 2

description: Library name: TDR72Z_50_CT30_011_2

value: differentiation 2


title: PBMC CITE-seq, S002-B, antibody-derived tags (ADT)

description:
Library name: S002-B_ADT
10x Genomics


title: Female_Muscle_WT

description:
Library name: Female_Muscle_WT_scATAC-seq
UUATAC-seq


title: Muscle_DMSOforRU486_KO_rep4

description:
Library name: Muscle_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, SPMS_2, CT30, differtiation 1

description: Library name: TDR72Z_49_CT30_011_1

value: differentiation 1


title: Female_BoneMarrow_WT

description:
Library name: Female_BoneMarrow_WT_scATAC-seq
UUATAC-seq

source_name: BoneMarrow

value: BoneMarrow

value: WT


title: iPSC-derived OPCs, SPMS_1, CT30, differtiation 3

description: Library name: TDR72Z_48_CT30_008_3


title: PBMC CITE-seq, S002-B, gene expression (GEX)

description:
Library name: S002-B_GEX
10x Genomics


title: Muscle_DMSOforRU486_KO_rep3

description:
Library name: Muscle_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S002-A, antibody-derived tags (ADT)

description:
Library name: S002-A_ADT
10x Genomics


title: Female_WhiteFat_KO

description:
Library name: Female_WhiteFat_KO_scATAC-seq
UUATAC-seq

value: Female

value: 3.5 months


title: iPSC-derived OPCs, SPMS_1, CT30, differtiation 2

description: Library name: TDR72Z_47_CT30_008_2

value: iPSC-derived OPCs


title: Muscle_DMSOforRU486_KO_rep2

description:
Library name: Muscle_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: PBMC CITE-seq, S002-A, gene expression (GEX)

description:
Library name: S002-A_GEX
10x Genomics


title: Female_Thymus_KO

description:
Library name: Female_Thymus_KO_scATAC-seq
UUATAC-seq

value: Thymus


title: iPSC-derived OPCs, SPMS_1, CT30, differtiation 1

description: Library name: TDR72Z_46_CT30_008_1


title: Muscle_DMSOforRU486_KO_rep1

description:
Library name: Muscle_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: 2 months


title: Female_Telencephalon_KO

description:
Library name: Female_Telencephalon_KO_scATAC-seq
UUATAC-seq

value: Telencephalon


title: Muscle_RU486_KO_rep6

description:
Library name: Muscle_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, RRMS_3, CT30, differtiation 3

description: Library name: TDR72Z_45_CT30_112_3


title: Female_Pituitary_KO

description:
Library name: Female_Pituitary_KO_scATAC-seq
UUATAC-seq


title: TotalseqB_NEA7_ADT4

city: San Francisco

first: Gian Carlo

middle: L.

last: Baldonado

address: 2340 Sutter Street

department: Dermatology

institute: University of California San Francisco

description:
Library name: TotalseqB_NEA7_ADT4
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

data_processing:
Raw FASTQ files were processed using Cell Ranger v8.0 (10x Genomics).
Cell Ranger count was run with the GRCh38 reference genome (refdata-gex-GRCh38-2020-A) and a custom TotalSeq-B antibody feature reference for ADT.
Donor demultiplexing was performed using Demuxlet with matched genotyping data.
Quality filtering, normalization, dimensionality reduction, and clustering performed using Seurat v5 with Weighted Nearest Neighbor (WNN) analysis for joint RNA and protein modalities.
Cell type annotation performed manually based on canonical marker gene and protein expression.
Assembly: GRCh38 (hg38)
Supplementary files format and content: MEX format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene and ADT features), matrix.mtx.gz (count matrix) output by Cell Ranger v8.0. Each file prefixed with sample name for unique identification.
Supplementary files format and content: feature_reference.csv: TotalSeq-B antibody panel feature reference used by Cell Ranger.

molecule: other

extract_protocol:
Gene expression and ADT libraries were prepared using the 10x Genomics Chromium Single Cell 5' Library & Gel Bead Kit with Feature Barcode Technology. Libraries were sequenced on an Illumina NovaSeq 6000.
PBMCs from multiple donors were multiplexed per sequencing batch using hashtag oligonucleotides (HTOs) and loaded onto the 10x Genomics Chromium Controller.

treatment_protocol: PBMCs were isolated from whole blood using Ficoll density gradient centrifugation and cryopreserved. Cells were thawed, washed, and stained with a TotalSeq-B antibody panel (BioLegend) per manufacturer protocol, then loaded onto the 10x Genomics Chromium Controller. Donors were multiplexed per batch using hashtag oligonucleotides (HTOs).

value: peripheral blood

tag: batch


title: TotalseqB_NEA7_ADT3

description:
Library name: TotalseqB_NEA7_ADT3
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

tag: cell type

value: PBMC


title: iPSC-derived OPCs, RRMS_3, CT30, differtiation 2

description: Library name: TDR72Z_44_CT30_112_2


title: Muscle_RU486_KO_rep5

description:
Library name: Muscle_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

tag: Sex


title: Female_Muscle_KO

description:
Library name: Female_Muscle_KO_scATAC-seq
UUATAC-seq


title: TotalseqB_NEA7_ADT2

description:
Library name: TotalseqB_NEA7_ADT2
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Muscle_RU486_KO_rep4

description:
Library name: Muscle_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Female_BoneMarrow_KO

description:
Library name: Female_BoneMarrow_KO_scATAC-seq
UUATAC-seq


title: iPSC-derived OPCs, RRMS_2, CT30, differtiation 3, excluded from analysis

description: Library name: TDR72Z_42_CT30_021_3

value: differentiation 3


title: Muscle_RU486_KO_rep3

description:
Library name: Muscle_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Muscle


title: TMA2_003406_IS_Cohort1

city: Houston

first: Veena

last: Kochat

address: 1901 East Road

department: Genomic Medicine

institute: The University of Texas MD Anderson Cancer Center

description: XENIUM

data_processing:
Raw images were processed using Xenium software to generate spatially resolved transcript maps for downstream analysis.
Raw Xenium images were processed with 10x Genomics Xenium software to detect transcripts and generate spatially resolved gene expression matrices. Low-confidence spots were filtered, and background correction was applied. Spatial transcriptomic analyses, including transcript density mapping, cell type annotation, and niche composition analysis, were performed in R using standard packages and custom scripts. Data visualization was performed using ggplot2 and Xenium overlays.
cell_boundaries.csv.gz : Polygon coordinates defining the boundaries of each segmented cell. Used for assigning transcripts to cells and generating cell-level features.
cell_feature_matrix.h5 : Cell-by-feature matrix (containing counts of transcripts per cell and other computed features.
cells.csv.gz : Metadata for each cell, including cell IDs, centroids to link transcripts to cell boundaries.
gene_panel.json : List of genes targeted in the Xenium panel, including probe sequences and gene IDs for mapping transcript counts to gene names.
morphology.ome.tif : High-resolution tissue morphology image (OME-TIFF format). Used for overlaying transcript and cell data on tissue morphology.
transcripts.parquet : Coordinates and gene assignments for individual transcripts for spatial plotting and cell-level assignment.
transcripts.csv.gz : Coordinates and gene assignments for individual transcripts  in compressed CSV format

source_name: Tumor

extract_protocol:
TMA samples were embedded into FFPE blocks and 5um sections were prepared. Frozen tissues were OCT embedded and 10um cryosections were prepared.
Tissue specimens were sectioned at 5–10 µm thickness and mounted onto Xenium-compatible slides (10x Genomics). Sections were fixed in 4% paraformaldehyde, permeabilized using a tissue-optimized buffer, and hybridized with target-specific probes according to the manufacturer’s instructions (10x Genomics Xenium User Guide). Signal amplification and labeling were performed in situ, followed by high-resolution imaging on the Xenium instrument.

value: Tumor

value: SCC/BCC

value: IS

value: Cohort 1


title: iPSC-derived OPCs, RRMS_2, CT30, differtiation 2

description: Library name: TDR72Z_41_CT30_021_2

value: differentiation 2


title: TMA1_003393_IC_IS_Cohort1

description: XENIUM

value: IC/IS


title: Muscle_RU486_KO_rep1

description:
Library name: Muscle_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO

value: Male


title: iPSC-derived OPCs, RRMS_2, CT30, differtiation 1

description: Library name: TDR72Z_40_CT30_021_1

value: differentiation 1


title: 813_SCC_IS_Cohort2

description: XENIUM

value: SCC

value: Cohort 2


title: TotalseqB_NEA7_cDNA2

description:
Library name: TotalseqB_NEA7_cDNA2
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, RRMS_1, CT30, differtiation 3

description: Library name: TDR72Z_39_CT30_029_3

value: iPSC-derived OPCs


title: LymphNode_DMSOforRU486_KO_rep6

description:
Library name: LymphNode_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: LymphNode

value: LymphNode

value: 2 months


title: 738_SCC_IS_Cohort2

description: XENIUM


title: 723_SCC_IS_Cohort2

description: XENIUM


title: iPSC-derived OPCs, RRMS_1, CT30, differtiation 1

description: Library name: TDR72Z_37_CT30_029_1


title: TotalseqB_NEA6_ADT4

description:
Library name: TotalseqB_NEA6_ADT4
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood

value: PBMC


title: 654_BCC_IS_Cohort2

description: XENIUM

value: BCC


title: TotalseqB_NEA6_ADT3

description:
Library name: TotalseqB_NEA6_ADT3
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: LymphNode_DMSOforRU486_KO_rep3

description:
Library name: LymphNode_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, control_3, CT30, differtiation 3

description: Library name: TDR72Z_36_CT30_425_3

value: differentiation 3


title: TotalseqB_NEA7_ADT1

description:
Library name: TotalseqB_NEA7_ADT1
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: 564_BCC_IS_Cohort2

description: XENIUM

value: Tumor


title: LymphNode_DMSOforRU486_KO_rep4

description:
Library name: LymphNode_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, control_3, CT30, differtiation 2

description: Library name: TDR72Z_35_CT30_425_2


title: 336_SCC_IS_Cohort2

description: XENIUM

value: IS


title: 218_SCC_IS_Cohort2

description: XENIUM


title: LymphNode_DMSOforRU486_KO_rep1

description:
Library name: LymphNode_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: LymphNode_DMSOforRU486_KO_rep2

description:
Library name: LymphNode_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, control_2, CT30, differtiation 3

description: Library name: TDR72Z_33_CT30_659_3


title: TotalseqB_NEA6_cDNA_4

description:
Library name: TotalseqB_NEA6_cDNA_4
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: LymphNode_RU486_KO_rep6

description:
Library name: LymphNode_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: TotalseqB_NEA6_cDNA_3

description:
Library name: TotalseqB_NEA6_cDNA_3
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, control_2, CT30, differtiation 2

description: Library name: TDR72Z_32_CT30_659_2


title: iPSC-derived OPCs, control_2, CT30, differtiation 1

description: Library name: TDR72Z_31_CT30_659_1


title: TotalseqB_NEA6_cDNA_2

description:
Library name: TotalseqB_NEA6_cDNA_2
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: LymphNode_RU486_KO_rep4

description:
Library name: LymphNode_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: 11_SCC_IC_Cohort2

description: XENIUM

value: IC


title: LymphNode_RU486_KO_rep3

description:
Library name: LymphNode_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: 6_BCC_IC_Cohort2

description: XENIUM


title: TotalseqB_NEA5_ADT4

description:
Library name: TotalseqB_NEA5_ADT4
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, control_1, CT30, differtiation 2

description: Library name: TDR72Z_29_CT30_300_2

value: differentiation 2


title: LymphNode_RU486_KO_rep2

description:
Library name: LymphNode_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: 4_SCC_IC_Cohort2

description: XENIUM


title: TotalseqB_NEA5_ADT3

description:
Library name: TotalseqB_NEA5_ADT3
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Leaves

city: China

first: Yue

last: Jin

address: 100 Guilin Road,Xuhui DistrictC

institute: Shanghai Normal University

description: Library name: sample3-Leaves

data_processing:
Raw reads in fastq format were processed using fastp software (version 0.20.1) to remove reads with adapters, reads with poly-Ns,and low-quality reads. The resulting clean reads were mapped to the genome (IRGSP1.0_genome) using bowtie2 (version 2.4.2). Peaks were called using MACS2 (version2.2.7.1), visualized with IGV software, and annotated using the ChIPseeker R package.
Assembly: IRGSP1.0
Supplementary files format and content: bigWigs

organism: Oryza sativa

source_name: Leaves

extract_protocol:
Take the leaves at the 5-12 stage and inflorescences at the reproductive stage from GAR1-eGFP transgenic rice plants, and extract chromatin after formaldehyde cross-linking.
Approximately 5 μg of eGFP agarose beads (MBL, Japan) (or an IgG antibody as a negative control) were used to immunoprecipitate chromatin samples extracted from 2g of plant tissue.For ChIP-seq, sequencing libraries of immunoprecipitated chromatin DNA were generated and indexed using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, USA, cat.E7645L). Qubit was used for library quantification, and a high-sensitivity DNA chip was used to test the library insert size. The libraries were sequenced on the Illumina NovaSeq 6000 platform to obtain 150-bp paired-end reads.

value: Leaves


title: TotalseqB_NEA5_ADT2

description:
Library name: TotalseqB_NEA5_ADT2
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, SPMS_3, CT24, differtiation 3

description: Library name: TDR72Z_27_CT24_015_3


title: Milk fat globule_day 4_low insulin resistance_biol rep 5

description:
Library name: MFG079
MFG079

source_name: Breastmilk-derived milk fat globules

value: Breastmilk-derived milk fat globules

value: WT

value: Low


title: ChIPseq_RelA*_purF-_Rep1

city: Madison

first: Michael

last: Wolfe

state: WI

address: 1300 University Ave

institute: University of Wisconsin-Madison

description: Library name: RL3939_ChIP_Rep1

data_processing:
ChIP-seq data was processed as described previously Hustmyer et al. mBio (2022) and reproduced and modified here. Read quality control was performed using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (10.1093/bioinformatics/btw354). All ChIP-seq analysis were performed using an open-source-software-based ChIP-seq pipeline (https://github.com/mikewolfe/ChIPseq_pipeline). The pipeline manages computational jobs using Snakemake (https://doi.org/10.12688/f1000research.29032.2) and maintains the relationship between samples and their metadata using peppy (https://doi.org/10.1093/gigascience/giab077). Paired- and single-end reads were trimmed of adapter sequences using CutAdapt (10.14806/ej.17.1.200) with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT’. Quality trimming was performed using trimmomatic (10.1093/bioinformatics/btu170) with parameters "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15". The reads were aligned to the E. coli (Genbank accession: U00096.3) and B. sub (Genbank accession: AL009126.3) chromosomes using bowtie2 (10.1038/nmeth.1923) with parameters "-- end-to-end --very-sensitive --phred33". Raw read coverage was calculated using deepTools (10.1093/nar/gkw257) with the parameters "--binSize 5 --samFlagInclude 67 --extendReads". The raw coverage counts were first scaled by multiplying the raw coverage by a spike-in based scaling factor determined as described in Bonhoure et al. Genome Research 2014 (10.1101/gr.168260.113). Briefly, a background subtracted fragment count is determined in the spike-in fragments by taking the raw fragment counts across the B. sub chromosome AL009126.3 for paired extracted and input samples, dividing the read fragments by the total number of B. sub read fragments per million for each sample and then determining a background subtracted fragment count as follows: w_i = max(0,z_i-βx_i) Where, w_i is the background subtracted fragment count per position i, z_i is the fragment counts in the extracted sample, x_i is the fragment counts in the paired input sample, and β is a regression-based scale factor determined by linear regression with regions outside the full coding region of all genes plus an additional 300 bp upstream of each gene. The average enrichment for a given sample, k, is then calculated using the background subtracted fragment count per position j in each coding region plus an additional 300 bp upstream for each gene as follows: η_k=mean(w_j)  Finally, the spike-in based scaling factor for each sample k is determined as follows: S_k=η_k-(∑_(i=1)^n η_i )/n Where n is the total number of samples to be scaled together. This spike-in factor is then applied to the non-spike in fragments mapping to the E. coli genome by taking the raw fragment counts and first scaling by the total number of fragments per million that mapped to the E. coli genome per sample and then scaling by the spike-in scale factor S_k described above.  After initial scaling, all ChIP traces were copy-number corrected to account for changes in DNA content between the two genotypes as described in the input correction section below.
NET-seq scaling factors: To determine the scaling factor for each sample, we first identified specific regions in the B. subtilis genome (Accession: NC_000964.3) to which E. coli reads did not map (Bsu-unique regions) using an E. coli-only NET-seq dataset (10.1093/nar/gkae209). We mapped reads from the E. coli-only NET-seq library to a combined E. coli MG1655 and B. subtilis strain 168 genome file using Bowtie with options to suppress reads that map to multiple loci and allowing no mismatches (options –best -a -m 1 -v 0). After conversion to BAM and BED files, total locus coverage (read coverage not 3′-end coverage) was determined for the B. subtilis str 168 genome. We then generated a BED table of regions with zero coverage (i.e., regions of the B. subtilis genome to which E. coli-only reads did not map) to detect B. subtilis-unique reads present in E. coli NET-seq samples containing a B. subtilis spike-in. To determine the number of B. subtilis-unique reads in each sample with B. subtilis spike-ins, we followed the same NET-seq processing pipeline used to generate the table of B. subtilis unique loci above but used Bedtools to count 3′-end coverage for both B. subtilis unique reads and reads mapping to both B. subtilis and E. coli (i.e., not mapping to the B. subtilis unique loci). To determine the B. subtilis-unique scaling factor for each sample, the fraction of B. subtilis-unique reads was calculated as the B. subtilis-unique counts divided by the total number of reads mapping to E. coli and B. subtilis loci (Table Sa). The smallest B. subtilis-unique fraction was identified among the set of samples to be compared, and this number was divided by the B. subtilis-unique fraction for each sample to obtain the B. subtilis-unique scaling fraction. The scaling fraction was converted to a scaling factor by multiplying it by 107 divided by the total reads mapped to E. coli. The scaling factor was then used to generate scaled reads per 107 reads for each sample. For most analyses, the average of the two scaled reads per genome position was used.
Assembly: U00096.3 and AL009126.3
Supplementary files format and content: Spike-in scaled NETseq and ChIP-seq coverage wig files

organism: Escherichia coli

growth_protocol: A single colony was inoculated into MOPS EZ rich defined medium with 0.2% (w/v) glucose (RDM, Teknova) for overnight growth at 37 °C. A 2.5-mL portion of the overnight culture was inoculated into 0.85 L RDM supplemented with ampicillin (100 µg/mL) to maintain plasmids pALS13 or pALS14. The cultures were grown in Fernbach flasks on an orbital shaker at 200 rpm and 37 °C until cell density reached early log-phase (apparent OD600 ~0.39 +/– 0.02). RelA expression was then induced by addition of IPTG to 1 mM with continued shaking at 37 °C. After 5 minutes of induction, cells for GTP quantitation were removed and rapidly filtered (described in detail below). FLAG-tagged RNAP B. subtilis cells (strain RL3116) were then added as spike-in, 50 mL samples were removed for ChIP, and the remaining culture for NET-Seq analysis was rapidly filtered through a 0.45 µ cellulose filter, quickly scraped from the filter with a spatula, and plunged into liquid nitrogen before storage at –80 °C as described previously (Churchman et al. 2012). Cells for ChIP were immediately mixed with sodium phosphate (pH 7.6, 10 mM final) and formaldehyde (1% final) and incubated at 37 °C for crosslinking as described previously, (Hustmyer et al. 2022) followed by quenching with glycine (100 mM final) for 30 min at 4 °C. The crosslinked cells were then centrifuged, washed multiple times with phosphate-buffered saline (PBS; 137 mM NaCl, 2.7 KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4), and stored at –80 °C. Biological triplicate samples were collected for each strain or experimental condition. B. subtilis cells were added from pre-measured and stored aliquots to E. coli cultures immediately before harvest at a ratio of 3.3% B. subtilis-to-E. coli cells as calculated from a pre-determined relationship between apparent OD600 and colony-forming units for each E. coli strain grown in RDM. Aliquots of B. subtilis RL3116 cells at measured cell densities were prepared from late log–phase cultures that were cooled on ice, mixed with cold glycerol to a final concentration of 15% glycerol, flash-frozen in liquid nitrogen, and stored at –80°C. Prior to adding B. subtilis cells to the E. coli cultures, aliquots were thawed in ice water and stored on ice.

extract_protocol:
ChIP-seq was performed as previously described (Hustmyer et al. 2022; Mooney et al. 2009). A cell pellet corresponding to 50 mL of crosslinked E. coli culture was mixed with separately formaldehyde-crosslinked B. subtilis RL3116 cells (using a volume of B. subtilis cells equivalent to 1% of the E. coli cells) and used for each IP reaction. Immunoprecipitation was performed as described (Hustmyer et al. 2022) using an antibody against the beta subunit of RNAP or the FLAG tag on the C-terminal end of the beta prime subunit.
Paired-end libraries were prepared using NEBNext Ultra II DNA library reagents according to the manufacturer’s protocols and sequenced on Illumina NovaSeq 6000.

value: RL3000 rpoC::3XFLAG yja::cat pALS13 purF[R45A]


title: Milk fat globule_day 5_high insulin resistance_biol rep 7

description:
Library name: MFG092
MFG092

value: High


title: dgD-aPDL1, replicate 1, scRNAseq

city: Xiamen

first: Chaolong

last: Lin

address: 4221-117 Xiang Annan Road, Xiang 'an District, Xiamen City, Fujian Province

institute: Xiamen University

description: 10x Genomics

data_processing:
The demultiplexing，barcoded processing,gene counting and aggregation were made using the Cell Ranger software v5.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor-infiltrating lymphocytes

extract_protocol:
The tumors were excised and homogenized using a gentleMACS tissue dissociator with a Tumor Dissociation Kit for mice. The resulting cell mixture was filtered through a 70-µm cell strainer to obtain a single-cell suspension. Following centrifugation, the supernatant was discarded, and the pellet was resuspended in 1 ml of cold PBS supplemented with 2% FBS. The cell suspensions were stained with 7AAD and APC/Cyanine7-labeled anti-mouse CD45 antibodies. Subsequently, fluorescence-activated cell sorting (FACS) was employed to isolate CD45+ cells, ensuring a cell viability exceeded 90%. These sorted cells were then prepared for single-cell RNA sequencing (scRNA-seq) using the Chromium Next GEM Single Cell 3ʹ Kit v3.1, following the manufacturer’s protocols.
Library was performed according to the manufacter's (single cell3' v2 protocol,10x Genomics)

value: Tumor-infiltrating lymphocytes

value: immune cells


title: ChIPseq_InactiveRelA_purF-_Rep2

description: Library name: RL3940_ChIP_Rep2

value: RL3000 rpoC::3XFLAG yja::cat pALS14 purF[R45A]


title: ChIPseq_RelA*_purF-_site1_Rep2

description: Library name: RL3941_ChIP_Rep2

value: RL3000 delrpoZ[del2-5] rpoC[R362A, R417A, K615A]::3XFLAG yja::cat pALS13 purF[R45A]


title: LymphNode_RU486_KO_rep1

description:
Library name: LymphNode_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: LymphNode

value: Mecp2 KO

value: Male

value: 2 months


title: TotalseqB_NEA5_ADT1

description:
Library name: TotalseqB_NEA5_ADT1
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood

value: PBMC


title: Flowers

description: Library name: sample2-Flowers

source_name: Inflorescences

value: Inflorescences


title: iPSC-derived OPCs, SPMS_3, CT24, differtiation 2

description: Library name: TDR72Z_26_CT24_015_2

value: iPSC-derived OPCs

value: differentiation 2


title: Lung_DMSOforRU486_KO_rep5

description:
Library name: Lung_DMSOforRU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Lung

value: Lung


title: Input(leaves:flowers=1:1)

description: Library name: sample1-Input


title: TotalseqB_NEA5_cDNA_4

description:
Library name: TotalseqB_NEA5_cDNA_4
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, SPMS_3, CT24, differtiation 1

description: Library name: TDR72Z_25_CT24_015_1

value: differentiation 1


title: TotalseqB_NEA5_cDNA_3

description:
Library name: TotalseqB_NEA5_cDNA_3
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Lung_DMSOforRU486_KO_rep3

description:
Library name: Lung_DMSOforRU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, SPMS_2, CT24, differtiation 3

description: Library name: TDR72Z_24_CT24_011_3

value: differentiation 3


title: Lung, wildtype FF, male, rep6

city: Kansas City

first: Emily

last: Schueddig

state: KS

address: 2901 Rainbow Boulevard

department: Department of Biostatistics & Data Science

institute: University of Kansas Medical Center

description: Library name: Sample-70

data_processing:
Read quality was assessed using FastQC (v0.12.1, RRID:SCR_014583). UMI-tools (v1.1.6, RRID:SCR_017048) was used for UMI and read extraction, then cutadapt (v5.0, RRID:SCR_011841) was used to retain reads with a minimum read length of 14 base pairs and maximum of 100 base pairs. BWA (v0.7.18, RRID:SCR_010910) with the aln algorithm was used for mapping with parameters set for no gaps (-o 0) and no mismatches (-n 0). Reads were aligned to the genomic sequence of aminoacetylated, mature mitochondrial mt-TR. Since there are known SNP in the mt-tRNA-Arg sequence for different mouse strains, each sample was mapped to its respective reference sequence. Aligned reads were deduplicated using UMI-tools. The resulting set of aligned reads were then mapped to the full mouse genome with the UCSC mm10 assembly as the reference using the bowtie (v1.3.1, RRID:SCR_005476) aligner. If the sequence mapped to another location, it was marked as a false positive and removed from downstream analysis. The number of reads for each unique sequence was extracted for each sample.
Assembly: NC_005089.1, CM004255.1, CM004184.1
Supplementary files format and content: counts.txt is a matrix of tRFs x samples that contains the extracted counts of sequences to the mt-tRNA-Arg gene

source_name: lung

extract_protocol:
Tissues were preserved in RNAlater (Invitrogen, AM7024) and frozen prior to RNA extraction. Small RNA was isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, AM1560) according to the manufacturer’s instructions with one exception: rather than being discarded, the corresponding large RNA fractions of small RNA isolations were retained, washed, and eluted to assess RNA integrity by visualization of 28S and 18S rRNA bands following agarose gel electrophoresis. Intact RNA samples were pooled by sodium acetate-propanol precipitation, followed by resuspension in nuclease-free water. RNA concentration was quantified using the Qubit microRNA Assay Kit (ThermoFisher Scientific, Q32881).
RNA isolated from mouse lungs using the mirVana miRNA Isolation Kit was sent to RealSeq (Santa Cruz, CA) for exploratory tRNA fragment sequencing using a single-adapter circularization-based library preparation approach.

value: lung

value: FF


title: Lung_DMSOforRU486_KO_rep4

description:
Library name: Lung_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.


title: Lung, wildtype FF, male, rep5

description: Library name: Sample-69


title: TotalseqB_NEA5_cDNA_2

description:
Library name: TotalseqB_NEA5_cDNA_2
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: F3 Fertile,3

city: Genève

first: François-Xavier

last: Stubbe

state: Genève

address: 30, quai Ernest-Ansermet

department: MOCEL

description: Library name: Fertile_3

data_processing:
Basecalls were performed using bcl2fastq for NovaSeq output
Single-end sequencing reads were quasi-mapped to the C. elegans transcriptome (WBcel235) using Salmon v1.10.3 with GC bias correction and mapping validation
Transcript-level quantifications were imported into R and summarized to gene level using tximport v1.34.0
DGE analysis was performed usig DESEQ2
Assembly: WBCel235
Supplementary files format and content: Gene level count matrix

organism: Caenorhabditis elegans

source_name: FAS158 F3 Fertile worms

growth_protocol: Worms were on NGM petri dishes, seeded with OP50, at 25C

extract_protocol:
RNA was harvested using TriZol reagent. DNA was removed Ambion Turbo DNAse and cleaned by phenol/cloroform extraction
RNA-seq libraries were made following the Illumina TRUESeq protocol

treatment_protocol: P-1 animals were selected based on presence or absence of H3.3K27Mtet array. Animals carrying the array were placed on tetracylcin, these are P0. We then selected subfertile that we grew in absence of tretracyclin.

value: YA Dissected Germline


title: P0 wt,1

description: Library name: N2_1

source_name: FAS158 that has lost the array


title: iPSC-derived OPCs, RRMS_3, CT30, differtiation 1

description: Library name: TDR72Z_43_CT30_112_1


title: Lung, wildtype HH, male, rep6

description: Library name: Sample-68

value: HH


title: iPSC-derived OPCs, SPMS_2, CT24, differtiation 2

description: Library name: TDR72Z_23_CT24_011_2


title: iPSC-derived OPCs, SPMS_2, CT24, differtiation 1

description: Library name: TDR72Z_22_CT24_011_1


title: Muscle_RU486_KO_rep2

description:
Library name: Muscle_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Muscle


title: TotalseqB_NEA7_cDNA4

description:
Library name: TotalseqB_NEA7_cDNA4
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: TotalseqB_NEA5_cDNA_1

description:
Library name: TotalseqB_NEA5_cDNA_1
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Lung_DMSOforRU486_KO_rep2

description:
Library name: Lung_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung_DMSOforRU486_KO_rep1

description:
Library name: Lung_DMSOforRU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: TotalseqB_NEA7_cDNA3

description:
Library name: TotalseqB_NEA7_cDNA3
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Lung, wildtype HH, male, rep5

description: Library name: Sample-65


title: iPSC-derived OPCs, RRMS_1, CT30, differtiation 2

description: Library name: TDR72Z_38_CT30_029_2


title: TotalseqB_NEA7_cDNA1

description:
Library name: TotalseqB_NEA7_cDNA1
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Lung_DMSOforRU486_KO_rep6

description:
Library name: Lung_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung_RU486_KO_rep6

description:
Library name: Lung_RU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: TotalseqB_NEA4_ADT4

description:
Library name: TotalseqB_NEA4_ADT4
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, SPMS_1, CT24, differtiation 3

description: Library name: TDR72Z_21_CT24_008_3


title: LymphNode_DMSOforRU486_KO_rep5

description:
Library name: LymphNode_DMSOforRU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: LymphNode


title: TotalseqB_NEA4_ADT3

description:
Library name: TotalseqB_NEA4_ADT3
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, SPMS_1, CT24, differtiation 2

description: Library name: TDR72Z_20_CT24_008_2


title: TotalseqB_NEA4_ADT2

description:
Library name: TotalseqB_NEA4_ADT2
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, SPMS_1, CT24, differtiation 1

description: Library name: TDR72Z_19_CT24_008_1


title: Lung_RU486_KO_rep4

description:
Library name: Lung_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Lung, MNX CF, male, rep5

description: Library name: Sample-51

value: CF


title: Lung, wildytpe CC, male, rep6

description: Library name: Sample-62

value: CC


title: Lung, MNX CF, male, rep6

description: Library name: Sample-54


title: Lung_RU486_KO_rep5

description:
Library name: Lung_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male

value: 2 months


title: TotalseqB_NEA4_ADT1

description:
Library name: TotalseqB_NEA4_ADT1
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood

value: PBMC


title: Lung, MNX CH, male, rep6

description: Library name: Sample-49

value: CH


title: iPSC-derived OPCs, RRMS_3, CT24, differtiation 3

description: Library name: TDR72Z_18_CT24_112_3

value: iPSC-derived OPCs


title: Lung_RU486_KO_rep3

description:
Library name: Lung_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Lung


title: iPSC-derived OPCs, RRMS_3, CT24, differtiation 2

description: Library name: TDR72Z_17_CT24_112_2

value: differentiation 2


title: Lung_RU486_KO_rep2

description:
Library name: Lung_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: TotalseqB_NEA6_ADT2

description:
Library name: TotalseqB_NEA6_ADT2
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Lung, MNX CH, male, rep5

description: Library name: Sample-45

value: lung


title: TotalseqB_NEA4_cDNA_3

description:
Library name: TotalseqB_NEA4_cDNA_3
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, RRMS_3, CT24, differtiation 1

description: Library name: TDR72Z_16_CT24_112_1

value: differentiation 1


title: Lung_RU486_KO_rep1

description:
Library name: Lung_RU486_KO_rep1_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, MNX HC, male, rep6

description: Library name: Sample-44

value: HC


title: TotalseqB_NEA4_cDNA_2

description:
Library name: TotalseqB_NEA4_cDNA_2
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Heart_DMSOforRU486_KO_rep6

description:
Library name: Heart_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

source_name: Heart

value: Heart


title: Lung, MNX HC, male, rep5

description: Library name: Sample-42


title: TotalseqB_NEA6_ADT1

description:
Library name: TotalseqB_NEA6_ADT1
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

source_name: peripheral blood


title: TotalseqB_NEA4_cDNA_1

description:
Library name: TotalseqB_NEA4_cDNA_1
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, RRMS_2, CT24, differtiation 3, excluded from analysis

description: Library name: TDR72Z_15_CT24_021_3

value: differentiation 3


title: iPSC-derived OPCs, control_3, CT30, differtiation 1

description: Library name: TDR72Z_34_CT30_425_1


title: iPSC-derived OPCs, RRMS_2, CT24, differtiation 2

description: Library name: TDR72Z_14_CT24_021_2


title: Heart_DMSOforRU486_KO_rep4

description:
Library name: Heart_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: TotalseqB_NEA3_ADT4

description:
Library name: TotalseqB_NEA3_ADT4
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Lung, wildtype FF, female, rep6

description: Library name: Sample-33

value: FF


title: Lung, wildtype HH, female, rep6

description: Library name: Sample-32

value: HH


title: Heart_DMSOforRU486_KO_rep2

description:
Library name: Heart_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Lung, MNX CF, female, rep6

description: Library name: Sample-17

value: CF


title: TotalseqB_NEA3_ADT2

description:
Library name: TotalseqB_NEA3_ADT2
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, RRMS_1, CT24, differtiation 2

description: Library name: TDR72Z_11_CT24_029_2


title: Lung, MNX CH, female, rep7

description: Library name: Sample-14


title: iPSC-derived OPCs, RRMS_1, CT24, differtiation 1

description: Library name: TDR72Z_10_CT24_029_1


title: TotalseqB_NEA3_ADT1

description:
Library name: TotalseqB_NEA3_ADT1
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet


title: TotalseqB_NEA3_cDNA_4

description:
Library name: TotalseqB_NEA3_cDNA_4
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: TotalseqB_NEA4_cDNA_4

description:
Library name: TotalseqB_NEA4_cDNA_4
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: Heart_RU486_KO_rep5

description:
Library name: Heart_RU486_KO_rep5_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: Male


title: Lung, MNX CH, female, rep5

description: Library name: Sample-12


title: iPSC-derived OPCs, control_3, CT24, differtiation 3

description: Library name: TDR72Z_9_CT24_425_3


title: TotalseqB_NEA3_cDNA_3

description:
Library name: TotalseqB_NEA3_cDNA_3
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, control_3, CT24, differtiation 2

description: Library name: TDR72Z_8_CT24_425_2


title: Heart_RU486_KO_rep4

description:
Library name: Heart_RU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: 2 months


title: Lung, MNX CH, female, rep4

description: Library name: Sample-11


title: Heart_RU486_KO_rep3

description:
Library name: Heart_RU486_KO_rep3_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: iPSC-derived OPCs, control_3, CT24, differtiation 1

description: Library name: TDR72Z_7_CT24_425_1


title: Lung, wildtype FF, male, rep4

description: Library name: RSB526-22


title: TotalseqB_NEA3_cDNA_1

description:
Library name: TotalseqB_NEA3_cDNA_1
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet

value: peripheral blood


title: iPSC-derived OPCs, control_2, CT24, differtiation 3

description: Library name: TDR72Z_6_CT24_659_3


title: Heart_RU486_KO_rep2

description:
Library name: Heart_RU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: TotalseqB_NEA2_ADT3

description:
Library name: TotalseqB_NEA2_ADT3
TotalSeq-B CITE-seq ADT antibody capture library; pooled PBMCs; donors demultiplexed using Demuxlet

value: PBMC


title: Lung, wildtype FF, male, rep3

description: Library name: RSB526-21


title: iPSC-derived OPCs, control_2, CT24, differtiation 2

description: Library name: TDR72Z_5_CT24_659_2


title: BoneMarrow_DMSOforRU486_KO_rep6

description:
Library name: BoneMarrow_DMSOforRU486_KO_rep6_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz

value: BoneMarrow


title: Lung, wildtype FF, male, rep1

description: Library name: RSB526-19


title: iPSC-derived OPCs, control_1, CT24, differtiation 3, excluded from analysis

description: Library name: TDR72Z_3_CT24_300_3

value: iPSC-derived OPCs


title: Lung, wildtype HH, male, rep4

description: Library name: RSB526-15


title: iPSC-derived OPCs, control_1, CT24, differtiation 2

description: Library name: TDR72Z_2_CT24_300_2


title: BoneMarrow_DMSOforRU486_KO_rep4

description:
Library name: BoneMarrow_DMSOforRU486_KO_rep4_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Lung, wildtype HH, male, rep3

description: Library name: RSB526-14


title: TotalseqB_NEA2_cDNA_2

description:
Library name: TotalseqB_NEA2_cDNA_2
TotalSeq-B CITE-seq cDNA gene expression library; pooled PBMCs; donors demultiplexed using Demuxlet


title: iPSC-derived OPCs, control_1, CT24, differtiation 1

description: Library name: TDR72Z_1_CT24_300_1