title: Sublibrary 8

city: La Jolla

first: Jack

last: Olmstead

institute: UC San Diego

description:
Library name: JO8
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.

data_processing:
Raw nucleus-by-gene count matrices were generated from the FASTQ files using the Parse Biosciences Trailmaker software pipeline (running split-pipe v1.4.1) through the Parse Biosciences web portal. split-pipe used STAR v2.7.11b for alignment and samtools v1.21, with chemistry v3 and the WT kit.
Trailmaker produced a raw Seurat object (110,728 nuclei) with the digital gene-count matrix, associated sample metadata, and DoubletFinder scores. Per-nucleus percent mitochondrial reads were computed and nuclei were filtered to retain UMI count >= 1500, gene count >= 1500, and percent mitochondrial reads <= 5% (108,748 nuclei remaining).
Allen Brain Cell (ABC) atlas taxonomic labels (Class > Subclass > Supertype > Cluster) were assigned to each nucleus using the MapMyCells online tool.
Raw gene counts were normalized with Seurat SCTransform (v0.4.1), regressing out percent mitochondrial reads and SPLiT-seq sublibrary, computed across all samples. Normalized counts were used for principal component analysis, nearest-neighbor graph construction, Leiden clustering, and UMAP embedding.
Leiden clusters were manually curated by cross-referencing UMI count, gene count, percent mitochondrial reads, DoubletFinder scores, and putative ABC cell type; 6 low-quality clusters and nuclei with DoubletFinder score < 0.02 were removed, leaving a final dataset of 93,066 nuclei that underwent final PCA, Leiden clustering, and UMAP embedding.
Assembly: Mouse GRCm39 (Ensembl release 113); Parse Biosciences prebuilt reference genome version 1.4.0 (genome label GRCm39-113).
Supplementary files format and content: Seurat object (.rds) containing the raw nucleus-by-gene count matrix, per-nucleus sample metadata, DoubletFinder scores, and ABC taxonomic assignments.
Supplementary files format and content: Digital gene expression matrix in Matrix Market sparse format: count matrix (.mtx) with all_genes.csv (gene_id, gene_name, genome) and cell_metadata.csv (per-nucleus barcode and sample metadata).

source_name: Brain

growth_protocol: All experiments used wild-type C57BL/6J mice (The Jackson Laboratory, JAX #000664), approximately four weeks old, with balanced proportions of males and females distributed across control and experimental groups. Mice were group-housed in a vivarium on a 12-hour light/dark cycle with food provided ad libitum. Animal experiments were approved by the University of California San Diego Institutional Animal Care and Use Committee and followed the NIH Guide for the Care and Use of Laboratory Animals.

extract_protocol:
For sacrifice, mice were rapidly anesthetized with isoflurane; brains were removed into ice-cold dPBS (Gibco #14040133), hippocampus was extracted from one hemisphere, the approximate CA1 area was microdissected, and tissue was flash-frozen and stored at -70C. For nucleus isolation, all buffers, tubes, and instruments were pre-cooled, and Dounce tubes and pestles (Millipore #D8938-1SET) were cleaned with RNAse-free PBS and RNAse Away. All buffers contained recombinant RNAsin (Promega #N2111) to preserve RNA integrity and actinomycin D (Tocris #1229) to prevent artifactual transcription. Nucleus-isolation medium (NIM) consisted of 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl (pH 7.4), 1 mM DTT, 0.2 U/uL RNAsin, 25 uM actinomycin D, and cOmplete protease inhibitor (Roche #11836170001) in 10 mL; NIM-DP buffer was NIM with 0.1% Triton X-100. Thawed samples were homogenized in 1 mL NIM-DP with 10 strokes of the loose and 17 strokes of the tight pestle, spun at 800 x g for 8 min at 4C, resuspended in 500 uL NIM, filtered through a 70 um filter, spun at 200 x g for 10 min at 4C, resuspended in 187.5 uL Parse Biosciences Resuspension Buffer, and strained through a 20 um filter. Nuclei were then fixed using the Parse Biosciences Evercode Nuclei Fixation protocol (version 1.1, kit chemistry v3).
snRNA-seq library construction was performed using the Parse Biosciences Evercode Whole Transcriptome (WT) v3 kit (chemistry v3) according to the manufacturer's protocol. Nuclei from different samples were multiplexed and barcoded by the SPLiT-seq (split-pool) combinatorial barcoding method, in which individual nuclei undergo four serial rounds of in-well barcoding, pooling, and splitting across a 96-well plate of well-specific oligo barcodes, yielding a unique barcode combination per nucleus. All samples were loaded and barcoded together to avoid batch effects from separate library preparations, generating 8 sublibraries. Libraries were sequenced at the UC San Diego Institute for Genomic Medicine on an Illumina NovaSeq X Plus using paired-end 100-bp reads, targeting ~90,000 reads per nucleus (final mean depth 66,702 reads per nucleus).

treatment_protocol: To avoid non-experimental stimulation artifacts, mice in their home cage were placed in a standard environment (SE; a sound-dampened, light-controlled box mimicking the vivarium 12-hour light/dark cycle) at least 18 hours before experiments. Circadian timepoints were reported on the 24-hour Zeitgeber time (ZT) scale, with ZT0 = lights-on (06:00 PST) and ZT12 = lights-off (18:00 PST). Enriched-environment (EE) animals were transferred to a larger cage in a different room containing toys, tunnels, vertical scaffolds, and a running wheel, with at least one cagemate, and left to explore for 30 minutes or 6 hours. Kainic-acid (KA) seizures were induced by intraperitoneal injection of 15 mg/kg kainic acid (Santa Cruz #SC-200454); seizure onset was scored as rearing with bilateral forelimb clonus (~Racine stage 4), and mice were sacrificed 30 minutes or 6 hours after onset. Home-cage SE animals served as negative controls.

value: Brain

value: wild type


title: f4_0h_rep1

status: Public on Aug 07 2026

type: SRA

city: Geneva

first: Hongrui

last: Wang

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

country: USA

institute: Cornell University

description: Library name: Sample 53

library_source: transcriptomic

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number*10'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
ORA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

molecule: polyA RNA

organism: Vitis vinifera

source_name: bud

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

tag: tissue

value: bud

tag: genotype

value: Cabernet Sauvignon

tag: field collection_date

tag: field chilling_(nc_model)

tag: field collection_id


title: DS_Cas9_R1_fraction_2

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Belanger

country: Canada

institute: Montreal Heart Institute

description: Library name: DS_sample_4

library_source: genomic

data_processing:
Using gRNA list, gRNA counts were establsihed from fastq files. The raw counts were normalized without suppervision to remove sequenciing batch effect to create normalized counts.
Assembly: Homo_sapiens.GRCh38.cdna.all
Supplementary files format and content: Unsuppervised normalized count for each gRNA in the given Percoll gradient fraction. Each file contain the data for 1 fraction. First column: gRNA name, second column: normalized count (relative gRNA abundance in the fraction)
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HUDEP-2 were culture in StemSpan medium supplemented with 1 µg/ml doxycycline, 0.4 µg/ml dexamethasone, 0.1 µg/ml Stem Cell Factor, 3 units/ml erythropoietin, 2 mM L-glutamine, 200 IU penicillin, 200 µg/ml streptomycin and incubated at 37°C and 5% CO2.

extract_protocol:
The gDNA was extracted using the Qiagen DNeasy blood and tissue kit. PCR products from gDNA was purified with either the Qiagen QIAquick PCR Purification Kit or SPRISelect reagen. 2 µg of purified PCR product was purified on agarose gel using Qiagen QIAquick gel extraction kit.
The PCR amplification was adding the Illumina TruSeq LT adapator and sample index.

treatment_protocol: gRNA either librairies or single gRNA were transduced in HUDEP-2 cells using lentivirus. The MOI for gRNA librarie was 0.3, while 200 Kcells were infected with 300 µl of viral suspension for single gRNA. Selection with appropriate antibiotic was performed 6 days for Cas9, 5 days for dCas9-KRAB, and 4 days for dCas9-VP64

tag: cell line

tag: cell type

value: erythropoietic

tag: treatment

value: gRNA transduction

tag: batch


title: f2_24h_rep2

description: Library name: Sample 52


title: DS_Cas9_R1_fraction_1

description: Library name: DS_sample_3


title: D02066_SCC_IS_Cohort 2

city: Houston

first: Veena

last: Kochat

state: TX

address: 1901 East Road

department: Genomic Medicine

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: D02066
AtlasXomics

data_processing:
FASTQ files were aligned to the human reference genome (hg38), using Chromap38/Cell Ranger ATAC v.1.2 and the BED-like fragments files were mapped to Tixel barcodes.
Assembly: GRCh38
Supplementary files format and content: fragments.tsv.gz: Mapped be-like fragment files generated from FASTQ
Supplementary files format and content: metadata.json : Metadata in json format
Supplementary files format and content: scalefactors_jason : Scalefactors in json format
Supplementary files format and content: tissue_hires_image.png : High resolution image stitched from 10X frames
Supplementary files format and content: tissue_lowres_image.png : Low resolution image of the stitched image
Supplementary files format and content: tissue positions list.csv : list of spatial barcodes and co-ordinates specifying spots
Library strategy: spatial ATAC-seq

source_name: Tumor

extract_protocol:
After sample collection, tissues were snap frozen in liquid nitrogen, embedded in OCT and cryosectioned at 10µM thickness
Spatial ATAC libraries were generated using the AtlasXomics Deterministic Barcoding in Tissue (DBiT) platform

value: Tumor

tag: sample type

value: Fresh frozen

tag: histology

value: SCC

tag: study group

value: IS

tag: cohort

value: Cohort 2


title: D02064_SCC_IC_Cohort 2

description:
Library name: D02064
AtlasXomics

value: IC


title: Sublibrary 7

state: CA

description:
Library name: JO7
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.

library_source: transcriptomic single cell

molecule: nuclear RNA

organism: Mus musculus


title: D02045_BCC_IC_Cohort 2

description:
Library name: D02045
AtlasXomics

value: BCC


title: DS_Plasmid_pMS2

description: Library name: DS_sample_2


title: f3_24h_rep3

description: Library name: Sample 51


title: Sublibrary 6

description:
Library name: JO6
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.


title: f1_3d_rep3

description: Library name: Sample 50


title: Sublibrary 5

description:
Library name: JO5
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.


title: DS_Plasmid_pHKO

description: Library name: DS_sample_1


title: D02044_SCC_IC_Cohort 2

description:
Library name: D02044
AtlasXomics


title: iPSC-derived OPCs, control_1, CT30, differtiation 1

city: Palo Alto

first: Erin

middle: M

last: Gibson

state: California

address: 3165 Porter Drive

department: Psychiatry and Behavioral Sciences

institute: Stanford University

description: Library name: TDR72Z_28_CT30_300_1

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

molecule: total RNA

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 1


title: Sublibrary 4

description:
Library name: JO4
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.


title: f4_2h_rep1

description: Library name: Sample 49


title: H1299 cells, siRNA of S-adenosylmethionine synthase isoform type-2 (MAT2A) , rep2

city: Shanghai

first: Yimin

last: Chen

state: Shanghai

address: No. 555, Zuchongzhi Road, Zhangjiang, Pudong, Shanghai

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description: Library name: H1299_siMAT2A_rep2

data_processing:
Sequencing was carried out on the Illumina NovaSeq platform with PE 150 bp module.
Raw fastq was processed using fastp to remove adapter sequences and low-quality reads.
Clean reads were aligned to the human reference genome (hg38) using Bowtie2.
Duplicate reads were marked and removed using Picard MarkDuplicates tool.
ATAC-seq peaks were called with MACS2 using the --nomodel parameter.
For visualization, normalized coverage tracks (bigWig files) were generated using deepTools (bamCoverage) with counts per million (CPM) normalization.
Assembly: hg38
Supplementary files format and content: bigWig files

extract_protocol:
Cells were washed with cold PBS, and 50,000 cells were collected and subjected to chromatin isolation.
ATAC-seq libraries were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711) following the manufacturer’s instructions. After chromatin isolation, the samples were followed by Tn5 transposase-mediated tagmentation at 37 °C for 30 minutes. The tagmented DNA was then PCR-amplified using indexed primers and purified to generate sequencing-ready libraries. Library quality and concentration were assessed using a Qubit Fluorometer and Agilent TapeStation.

value: Human non-small cell lung cancer cells


title: Sublibrary 3

description:
Library name: JO3
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.


title: H1299 cells, siRNA of S-adenosylmethionine synthase isoform type-2 (MAT2A) , rep1

description: Library name: H1299_siMAT2A_rep1


title: f1_2h_rep2

description: Library name: Sample 48


title: D02037_BCC_IS_Cohort 2

description:
Library name: D02037
AtlasXomics


title: Sublibrary 2

description:
Library name: JO2
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.


title: D02036_SCC_IS_Cohort 2

description:
Library name: D02036
AtlasXomics


title: f4_3d_rep1

description: Library name: Sample 47


title: H1299 cells, siRNA of negative control, rep2

description: Library name: H1299_NC_rep2


title: f1_3d_rep2

description: Library name: Sample 46


title: D02035_SCC_IS_Cohort 2

description:
Library name: D02035
AtlasXomics


title: Sublibrary 1

description:
Library name: JO1
Parse Biosciences Evercode WT v3 sublibrary; one paired-end NovaSeq X Plus run. Each sublibrary is a pool of nuclei from all 48 biological samples, combinatorially barcoded by SPLiT-seq; the genomics core demultiplexed the flow cell by sublibrary index into these R1/R2 FASTQ files.


title: H1299 cells, siRNA of negative control, rep1

description: Library name: H1299_NC_rep1


title: D01958_BCC_IS_Cohort 2

description:
Library name: D01958
AtlasXomics


title: f3_2h_rep3

description: Library name: Sample 45


title: D01957_BCC_IS_Cohort 2

description:
Library name: D01957
AtlasXomics


title: ABM_5

city: Columbus

first: Ana

middle: Isabel

last: Salazar Puerta

state: OH

address: 140 W 19th Ave Building 151

institute: The Ohio State University

description: Library name: J_15

data_processing:
Clean reads were mapped to the mouse genome using Hisat2 (v2.0.5) -- this part was done by Novogene
Gene expression was quantified with featureCounts (v1.5.0-p3) and expressed as FPKM -- by Novogene
Assembly: r_4.3.1 -- Mus Musculus(GRCm39/mm39)
Supplementary files format and content: txt files include raw counts for each sample
Supplementary files format and content: txt files include fpkm values for each sample

source_name: Muscle

extract_protocol:
Total RNA from the gastrocnemious muscle tissue, were collected in TRIzol Reagent 5 weeks post-transfection. Tissue was homogenized using poly-T oligo-attached magnetic beads. PureLink RNA Mini Kit (Invitrogen) was used for RNA isolation followed by DNAse treatment and cDNA synthesis as described previously.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. -- this part was done by Novogene

treatment_protocol: For these experiments, 7-10 week-old C57BL/6 mice were used. To evaluate the effects of TNT-mediated delivery of the neurogenic ABM cocktail on the preservation of the muscle tissue in a denervated mouse model by transecting the sciatic nerve, where proximal and distal ends of the nerve were left free-floating. We examine transcriptomic changes in muscle tissue 5 weeks post-denervation and transfection.

value: Muscle

tag: strain

value: WT

value: ABM


title: D01139_BCC_IC_Cohort 1

description:
Library name: D01139
AtlasXomics

value: Cohort 1


title: ABM_4

description: Library name: J_14


title: f6_2h_rep3

description: Library name: Sample 44

value: bud

value: Cabernet Sauvignon


title: ABM_3

description: Library name: J_13


title: D01956_SCC_IS_Cohort 2

description:
Library name: D01956
AtlasXomics


title: f2_4h_rep3

description: Library name: Sample 43


title: D01138_BCC_IC_Cohort 1

description:
Library name: D01138
AtlasXomics


title: ABM_2

description: Library name: J_12


title: D01152_BCC_IC_Cohort 1

description:
Library name: D01152
AtlasXomics


title: f4_24h_rep3

description: Library name: Sample 41


title: f6_3d_rep2

description: Library name: Sample 42


title: D01955_SCC_IS_Cohort 2

description:
Library name: D01955
AtlasXomics


title: ABM_1

description: Library name: J_11


title: D01147_BCC_IC_Cohort 1

description:
Library name: D01147
AtlasXomics


title: f4_4h_rep1

description: Library name: Sample 40


title: Sham_5

description: Library name: J_10

value: Sham


title: Primary DIPG biopsy sample

city: Chicago

first: Xiao-Nan

last: Li

state: Illinois

address: 303 E Superior st

institute: Northwestern University

description:
Library name: Patient9119DIPG_Biopsy
Primary patient biopsy from DIPG patient 9119

data_processing:
Raw FASTQ files were processed using Cell Ranger v7.2.0. Reads were aligned to a combined GRCh38/mm10 reference.
Tab-separated values files and matrix files
Assembly: Human: GRCh38 & Mouse: mm10
Supplementary files format and content: RDS (Seurat object) for downstream integration.

source_name: Brainstem tumor

growth_protocol: DIPG PDOX tumors were grown intracranially in SCID mice until neurological symptoms emerged. Tumors were dissected at survival endpoint.

extract_protocol:
Tissues were dissociated into single-cell suspensions using enzymatic digestion and debris removal, followed by AO/PI-based viability assessment.
Libraries were prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v3.1, following the manufacturer’s instructions.

treatment_protocol: Mice were treated with control, abemaciclib (CDK4/6 inhibitor), radiation, temozolomide + radiation, abemaciclib + radiation, or abemaciclib + temozolomide + radiation.

value: Brainstem tumor

value: Tumor cells

value: H3K27M mutant

value: Patient


title: D01146_BCC_IS_Cohort 1

description:
Library name: D01146
AtlasXomics

value: Tumor

value: Fresh frozen

value: IS


title: Sham_4

description: Library name: J_9


title: D01145_BCC_IC_Cohort 1

description:
Library name: D01145
AtlasXomics

value: BCC

value: IC


title: AML12, p87

city: Bochum

first: Leyla

last: Sirkinti

address: Universitätsstraße 150

department: Translational and Computational Infection Research

country: Germany

institute: Ruhr University

description: Library name: Sample 59

data_processing:
Raw FASTQ sequencing reads were checked for quality using FastQC (version 0.12.1; available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc), followed by quality trimming with Trimmomatic 84. Low-quality and overrepresented sequences were trimmed. The trimmed reads from PMH, MLT, and 56D cells were mapped to the Mus musculus (GRCm39) reference genome (GCF_000001635.27), while the trimmed reads from HepG2 cells were mapped to the Homo sapiens (GRCh38) reference genome (GCF_000001405.40), both obtained from National Center for Biotechnology Information (NCBI). Mapping was performed using HISAT2 version 2.2.1 85. Picard was used to remove optical duplicates (available online at: https://broadinstitute.github.io/picard/). FeatureCounts version 2.0.6. 86 was used to generate gene counts, determining how many reads mapped to each gene in the reference genome. Unmapped reads from HISAT2 were mapped to the viral genome using Burrows-Wheeler Aligner version 0.7.18 87, and were used to algin to the HEV strain Kernow-C1 (GenBank accession Nr. HQ709170.1). Samtools version 1.21 88 was used to sort, index, and calculate coverage. Viral coverage plots were visualized in R using the ggplot2 library.
Assembly: GRCm39, GRCh38 and GenBank accession Nr. HQ709170.1
Supplementary files format and content: .txt file and exon reads

extract_protocol:
RNA extraction was done using the NucleoSpin RNA kit (Macherey-Nagel)
Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs) and the recommended related reagents by following the manufacturer’s instructions.

value: hepatocytes

value: no treatment

value: passage 87


title: f3_3d_rep1

description: Library name: Sample 39


title: AML12, p91

description: Library name: Sample 58

value: passage 91


title: f1_24h_rep2

description: Library name: Sample 38


title: Maus, 103, mIFNa, 48, hpi

description: Library name: Sample 57

source_name: liver

value: liver

value: interferon treated, 48 h


title: Sham_2

description: Library name: J_7

value: Muscle

value: WT


title: D01143_BCC_IS_Cohort 1

description:
Library name: D01143
AtlasXomics

value: Cohort 1


title: Maus MH211103, untreated, 48 hpi

description: Library name: Sample 56

value: untreated, 48 h


title: f1_24h_rep1

description: Library name: Sample 37

value: bud

value: Cabernet Sauvignon


title: D01134_BCC_IS_Cohort 1

description:
Library name: D01134
AtlasXomics

value: Tumor


title: Maus MH211103, mIFNa, 12 hpi

description: Library name: Sample 55

value: interferon treated, 12 h


title: f2_3d_rep2

description: Library name: Sample 36


title: Sham_1

description: Library name: J_6

value: Sham


title: Control_5

description: Library name: J_5

value: Control


title: D01133_BCC_IS_Cohort 1

description:
Library name: D01133
AtlasXomics

value: Fresh frozen

value: BCC

value: IS


title: Control_4

description: Library name: J_4


title: f1_0h_rep3

description: Library name: Sample 35


title: Maus MH211103, untreated, 12 hpi

description: Library name: Sample 54

value: hepatocytes

value: untreated, 12 h


title: D01132_SCC_IC_Cohort 1

description:
Library name: D01132
AtlasXomics

value: SCC

value: IC


title: Maus MH211103, mIFNa, 6 hpi

description: Library name: Sample 53

value: liver

value: interferon treated, 6 h


title: Control_3

description: Library name: J_3

value: Muscle

value: WT


title: D01131_SCC_IS_Cohort 1

description:
Library name: D01131
AtlasXomics

value: Cohort 1


title: f4_7d_rep1

description: Library name: Sample 33

value: bud

value: Cabernet Sauvignon


title: Maus MH211103, untreated, 6 hpi

description: Library name: Sample 52

value: untreated, 6 h


title: Control_2

description: Library name: J_2


title: f6_24h_rep1

description: Library name: Sample 32


title: Control_1

description: Library name: J_1


title: f1_0h_rep2

description: Library name: Sample 31


title: D01128_BCC_IC_Cohort 1

description:
Library name: D01128
AtlasXomics

value: Tumor


title: Maus MH210923, p6, 72 hpi

description: Library name: Sample 48

value: Kernow-C1/p6 virus inoculated, 72 hpi


title: AML12, p90

description: Library name: Sample 60

value: no treatment

value: passage 90


title: f2_7d_rep2

description: Library name: Sample 30


title: D01127_BCC_IS_Cohort 1

description:
Library name: D01127
AtlasXomics

value: Fresh frozen

value: BCC

value: IS


title: Maus MH210923, CM, 72 hpi

description: Library name: Sample 47

value: hepatocytes

value: conditioned medium inoculated, 72 hpi


title: f4_24h_rep2

description: Library name: Sample 29


title: Sorted gamma-delta T cells, tumor HG618

city: Philadelphia

first: Ronald

last: DeMatteo

state: PA

address: 3400 Spruce St

department: Department of Surgery

institute: University of Pennsylvania

description:
Library name: HG618-T-gdT
10x Genomics

data_processing:
Read count matrices from scRNA-seq data were generated from raw FASTQ files using CellRanger v.7.1.0, with alignment to the GRCh38-2020-A human transcriptome reference
Assembly: GRCh38-2020-A
Supplementary files format and content: Output from CellRanger v.7.1.0 (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) included for each sample

source_name: gastrointestinal stromal tumor

extract_protocol:
RNeasy Mini Kit (Qiagen)
NextGEM3' V3.1

value: gastrointestinal stromal tumor

value: gamma-delta T cells

value: untreated


title: Maus MH190923, untreated

description: Library name: Sample 51

value: liver


title: Maus MH211103, p6, 48 hpi

description: Library name: Sample 46

value: Kernow-C1/p6 virus inoculated, 48 hpi


title: Maus MH240111-2, untreated

description: Library name: Sample 50


title: f6_3d_rep1

description: Library name: Sample 28

value: bud


title: Sorted gamma-delta T cells, PBMC HG618

description:
Library name: HG618-P-gdT
10x Genomics

source_name: blood

value: blood


title: Maus MH211103, CM, 48 hpi

description: Library name: Sample 45

value: conditioned medium inoculated, 48 hpi


title: MIN6 cells shDDX3X (DDX3X), 24h CPA treated n=3

city: Lincoln

first: Terence

middle: Patrick

last: Herbert

address: Green Lane

department: Pharmacy

country: United Kingdom

institute: University of Lincoln

description:
Library name: Sample 12
DDX3X1_CPA3

data_processing:
150 bp paired-end sequencing using Illumina PE150 technology
Original image data file from Illumina was transformed to sequenced reads ( Raw Data) by CASAVA base recognition. Raw data was stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
alignments were performed  with HISAT2 to the reference
Assembly: mm10
Supplementary files format and content: FPMK counts for all samples supplied as a Txt file

growth_protocol: MIN6 cells, passage 40-75, were cultured in DMEM-High Glucose supplemented with 15% FBS, 1% P/S, 1% Glutamine (2mM), 20 mM HEPES and 50 μM beta-mercaptoethanol. Medium was changed every 2-3 days. Cells were grown to 70-80% confluency prior to treatment

extract_protocol:
Total RNA was extracted from cells using Monarch® Total RNA Miniprep kit (New England BioLabs, USA)
Carried out by Novogene: Sample Quality Control (Sample QC) followed by the generation of RNA libraries through polyA capture and reverse transcription into cDNA, followed by quality assessment.

treatment_protocol: Cells were treated with 200 µM of cyclopiazonic acid (CPA) dissolved in DMSO or vehicle alone for 24 h

value: Pancreatic beta cells

value: DDX3X KD

value: CPA

tag: time


title: f3_24h_rep2

description: Library name: Sample 27

value: Cabernet Sauvignon


title: Sorted gamma-delta T cells, PBMC HG589

description:
Library name: HG589-P-gdT
10x Genomics

value: imatinib


title: MIN6 cells shDDX3X (DDX3X), 24h CPA treated n=2

description:
Library name: Sample 11
DDX3X1_CPA2


title: Maus MH211103, p6, 24 hpi

description: Library name: Sample 44

value: Kernow-C1/p6 virus inoculated, 24 hpi


title: f3_2h_rep2

description: Library name: Sample 26


title: Maus MH211103, CM, 24 hpi

description: Library name: Sample 43

value: conditioned medium inoculated, 24 hpi


title: MIN6 cells shDDX3X (DDX3X), 24h CPA treated n=1

description:
Library name: Sample 10
DDX3X1_CPA1


title: f6_7d_rep2

description: Library name: Sample 25


title: Sorted gamma-delta T cells, PBMC HG642

description:
Library name: HG642-P-gdT
10x Genomics


title: Maus MH210923, p6, 24 hpi

description: Library name: Sample 42

value: hepatocytes


title: D01154_SCC_IS_Cohort 1

description:
Library name: D01154
AtlasXomics

value: Tumor

value: Fresh frozen

value: SCC

value: IS

value: Cohort 1


title: MIN6 cells shDDX3X (DDX3X1), 24h DMSO Vehicle control n=3

description:
Library name: Sample 9
DDX3X1_DMSO3

value: DMSO


title: D01954_SCC_IS_Cohort 2

description:
Library name: D01954
AtlasXomics

value: Cohort 2


title: MIN6 cells shDDX3X (DDX3X1), 24h DMSO Vehicle control n=2

description:
Library name: Sample 8
DDX3X1_DMSO2


title: f6_4h_rep2

description: Library name: Sample 24

value: bud


title: Maus MH210923, CM, 24 hpi

description: Library name: Sample 41

value: liver


title: f6_2h_rep2

description: Library name: Sample 23


title: Sorted gamma-delta T cells, tumor HG610

description:
Library name: HG610-T-gdT
10x Genomics

value: gastrointestinal stromal tumor

value: gamma-delta T cells

value: untreated


title: 3D macroVET replicate 3

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

description:
Library name: ML231876
10x Genomics

data_processing:
Data were processed with Cellranger 7.1.0 which performed alignment and gene quantification per-cell
Assembly: GRCh38 2020-A from 10x
Supplementary files format and content: filtered h5 files produced by Cellranger

source_name: valve engineered tissue

growth_protocol: stem cell-derived valve cells were cultured as 3D constructs in RPMI 1640 supplemented with L-Ascorbic acid, Dexamethasone, L-Proline, 1X ITS and 10% Fetal Bovine Serum for 30 days

extract_protocol:
After 30 days in culture, cells were isolated from macroVETs using Miltenyi Cell Isolation Kit - Umbilical cord kit (130-105-737) as per manufacturers instructions and cells were sorted with flow cytometry
10X  Chromium Next GEM Single Cell 3' protocol

value: valve engineered tissue

value: PSC-derived valve cells


title: Maus MH211103, p6, 6 hpi

description: Library name: Sample 40

value: Kernow-C1/p6 virus inoculated, 6 hpi


title: MIN6 cells shDDX3X (DDX3X1), 24h DMSO Vehicle control n=1

description:
Library name: Sample 7
DDX3X1_DMSO1

value: Pancreatic beta cells

value: DDX3X KD


title: f3_24h_rep1

description: Library name: Sample 22

value: Cabernet Sauvignon


title: 3D macroVET replicate 2

description:
Library name: ML231875
10x Genomics


title: Sham_3

description: Library name: J_8

value: Muscle

value: WT

value: Sham


title: MIN6 cells shCONTROL (PLKO1), 24h CPA treated n=3

description:
Library name: Sample 6
PLKO1_CPA3

value: CPA


title: Maus MH211103, CM, 6 hpi

description: Library name: Sample 39

value: hepatocytes

value: conditioned medium inoculated, 6 hpi


title: f2_24h_rep1

description: Library name: Sample 21

value: bud


title: D01136_BCC_IC_Cohort 1

description:
Library name: D01136
AtlasXomics

value: Tumor

value: Fresh frozen

value: BCC

value: IC

value: Cohort 1


title: Maus MH210923, p6, 6 hpi

description: Library name: Sample 38

value: liver


title: 3D macroVET replicate 1

description:
Library name: ML231874
10x Genomics

value: valve engineered tissue

value: PSC-derived valve cells


title: MIN6 cells shCONTROL (PLKO1), 24h CPA treated n=2

description:
Library name: Sample 5
PLKO1_CPA2

value: Pancreatic beta cells


title: f6_0h_rep1

description: Library name: Sample 20

value: Cabernet Sauvignon


title: HEK293, No antibody

city: Jinan

first: Can

middle: xin

last: Wen

address: 44 West Wenhua Rd

department: Center for Reproductive Medicine

institute: Shandong University

data_processing:
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150bp paired-end reads were generated
The read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software, and all low-quality reads and PCR adapters were removed
High-quality mapped reads (MAPQ > 30) reads were aligned to the UCSC mm10 genome or hg19 genome using Bowtie2.
All peak calling was performed with MACS2 v2.1.2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dupall’.
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10；hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
The genomic DNA was extracted by the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903).
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903). Libraries were amplified using TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China; TD202) at 11 cycles on the thermocycler. Libraries were purified with the VAHTS DNA Clean Beads (Vazyme Biotech, China; N411) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Human embryonic kidney

value: wildtype

value: no primary antibody used


title: Maus MH210923, CM, 6 hpi

description: Library name: Sample 37


title: MIN6 cells shCONTROL (PLKO1), 24h CPA treated n=1

description:
Library name: Sample 4
PLKO1_CPA1

value: WT

value: CPA


title: f6_7d_rep1

description: Library name: Sample 19


title: NF84, 56D, p6, IFN

description: Library name: Sample 36

value: hepatoma

value: Kernow-C1/p6 RNA transfected, interferon treated


title: MIN6 cells shCONTROL (PLKO1), 24h DMSO Vehicle control n=3

description:
Library name: Sample 3
PLKO1_DMSO3

value: DMSO


title: f3_0h_rep2

description: Library name: Sample 18

value: bud


title: NF84, 56D, p6, Mock

description: Library name: Sample 35

value: Kernow-C1/p6 RNA transfected


title: HEK293, S9.6

value: S9.6 antibody used


title: HEK293, FLAG MCM8

value: transfected with FLAG-MCM8 plasmid, anti-FLAG antibody used


title: f2_3d_rep1

description: Library name: Sample 34


title: f3_4h_rep2

description: Library name: Sample 17


title: GSC267- 203504930031_R08C01

type: genomic

city: Amsterdam

first: Bart A.

last: Westerman

address: van der Boechorststraat 6b

department: Human Genetics

country: Netherlands

institute: Amsterdam UMC

description: Methylation array of surgically removed GBM modelsample that was cultured without experimental treatment

hyb_protocol: According to Infinium Methylation HD EPIC manufacturers protocol

data_processing:
CNV analysis and graphing was done using the Bioconductor minfi and conumee R packages 28 or by using Python pylluminator==2.2. Gene locations for annotation were derived with the UCSC genome browser database, using the Table browser tool 29. Assembly hg19 was used as reference genome.
Processed values consist of NOOB background-corrected and nonlinear dye-bias-corrected DNA-methylation beta values for Infinium MethylationEPIC CpG probes, together with corresponding pOOBAH detection P values. Beta values range from 0 to 1 and represent the proportion of methylated signal at each CpG site. Detection P values indicate whether the measured probe signal is distinguishable from background.

label: Cy3, Cy5

source_name: Human GBM brain tumor

growth_protocol: According to Krishna P L Bhat. Mesenchymal differentiation mediated by NF-κB promotes radiation resistance in glioblastoma. Cancer Cell 2013 Sep 9;24(3):331-46.

extract_protocol: Genomic DNA was isolated from untreated cell pellets using the DNeasy Blood & Tissue Kit (Qiagen, 69504), according to manufacturer’s protocol. Additionally, samples were treated with RNase A (DNase and protease-free, 10 mg/mL, Thermo Scientific™, EN0531) to remove RNA from samples.

treatment_protocol: Cells were grown in steady state

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -2.95 to 0.94EGFR min to max

value: None (steady state culture)


title: MIN6 cells shCONTROL (PLKO1), 24 h DMSO Vehicle control n=1

description:
Library name: Sample 1
PLKO1_DMSO1

value: Pancreatic beta cells


title: NF84, 56D, tRNA, IFN

description: Library name: Sample 34

value: tRNA transfected, interferon treated


title: D01130_SCC_IC_Cohort 1

description:
Library name: D01130
AtlasXomics

value: Tumor

value: Fresh frozen

value: SCC

value: IC

value: Cohort 1


title: f6_4h_rep1

description: Library name: Sample 16

value: Cabernet Sauvignon


title: MIN6 cells shCONTROL (PLKO1), 24 h DMSO Vehicle control  n=2

description:
Library name: Sample 2
PLKO1_DMSO2

value: WT

value: DMSO


title: GSC264- 203504930031_R07C01

scan_protocol: According to Infinium Methylation HD EPIC manufacturers protocol

value: -0.56 to 1.13EGFR min to max


title: Maus MH211103, p6, 72 hpi

description: Library name: Sample 49

value: liver

value: hepatocytes

value: Kernow-C1/p6 virus inoculated, 72 hpi


title: NF84, 56D, tRNA, Mock

description: Library name: Sample 33

value: hepatoma

value: tRNA transfected


title: f3_2h_rep1

description: Library name: Sample 15

value: bud


title: GSC262- 203504930031_R06C01

label_protocol: According to Infinium Methylation HD EPIC manufacturers protocol

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: 0.25 to 3.38EGFR min to max

value: None (steady state culture)


title: IBs-9119DIPG PDOX model treated with abemaciclib, temozolomide, and radiation

description:
Library name: 9119DIPG_XRT_Abemaciclib_TMZ
PDOX model treated with abemaciclib, temozolomide, and radiation (XRT)

value: Brainstem tumor

value: Tumor cells

value: H3K27M mutant

value: Abemaciclib + Temozolomide + Radiation (XRT)


title: NF84, MLT, p6, IFN

description: Library name: Sample 32

source_name: MLT

value: MLT

value: Kernow-C1/p6 RNA transfected, interferon treated


title: IBs-9119DIPG PDOX model treated with abemaciclib and radiation

description:
Library name: 9119DIPG_XRT_Abemaciclib
PDOX model treated with abemaciclib and radiation (XRT)

value: Abemaciclib + Radiation (XRT)


title: GSC231- 203504930031_R05C01

value: -2.97 to 1.94EGFR min to max


title: f2_2h_rep2

description: Library name: Sample 14

value: Cabernet Sauvignon


title: NF84, MLT, p6, Mock

description: Library name: Sample 31

value: Kernow-C1/p6 RNA transfected


title: GSC38- 203504930031_R04C01

value: -1.69 to 2.18EGFR min to max


title: IBs-9119DIPG PDOX model treated with temozolomide and radiation

description:
Library name: 9119DIPG_XRT_TMZ
PDOX model treated with temozolomide and radiation (XRT)

value: Temozolomide + Radiation (XRT)


title: f2_2h_rep1

description: Library name: Sample 13

value: bud


title: f1_3d_rep1

description: Library name: Sample 12


title: NF84, MLT, tRNA, IFN

description: Library name: Sample 30

value: hepatoma

value: tRNA transfected, interferon treated


title: GSC34- 203504930031_R03C01

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -1.52 to 2.25EGFR min to max


title: IBs-9119DIPG PDOX model treated with radiation

description:
Library name: 9119DIPG_XRT
PDOX model treated with radiation (XRT)

value: Brainstem tumor

value: Tumor cells

value: Radiation (XRT)


title: NF84, MLT, tRNA, Mock

description: Library name: Sample 29

value: MLT

value: tRNA transfected


title: IBs-9119DIPG PDOX model treated with abemaciclib

description:
Library name: 9119DIPG_Abemaciclib
PDOX model treated with CDK4/6 inhibitor abemaciclib

value: H3K27M mutant

value: Abemaciclib


title: f2_4h_rep2

description: Library name: Sample 11

value: Cabernet Sauvignon


title: GSC28- 203504930031_R02C01

value: -3.06 to 1.61EGFR min to max

value: None (steady state culture)


title: NF81, 56D, p6, IFN

description: Library name: Sample 28

value: Kernow-C1/p6 RNA transfected, interferon treated


title: f1_0h_rep1

description: Library name: Sample 10

value: bud


title: GSC23- 203504930031_R01C01

value: -2.71 to 1.28EGFR min to max


title: IBs-9119DIPG PDOX model under control group

description:
Library name: 9119DIPG_Control
PDOX model treated with vehicle (control)

value: control


title: NF81, 56D, p6, Mock

description: Library name: Sample 27

value: hepatoma

value: Kernow-C1/p6 RNA transfected


title: IBs-A0317DIPG PDOX model treated with abemaciclib, temozolomide, and radiation

description:
Library name: A0317DIPG_XRT_Abemaciclib_TMZ
PDOX model treated with abemaciclib, temozolomide, and radiation (XRT)

value: Abemaciclib + Temozolomide + Radiation (XRT)


title: f2_4h_rep1

description: Library name: Sample 9


title: GBM8- 203497730233_R08C01

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -0.51 to 2.08EGFR min to max


title: Sorted gamma-delta T cells, PBMC HG610

description:
Library name: HG610-P-gdT
10x Genomics

value: blood

value: gamma-delta T cells

value: untreated


title: NF81, 56D, tRNA, IFN

description: Library name: Sample 26

value: tRNA transfected, interferon treated


title: IBs-A0317DIPG PDOX model treated with abemaciclib and radiation

description:
Library name: A0317DIPG_XRT_Abemaciclib
PDOX model treated with abemaciclib and radiation (XRT)

value: Brainstem tumor

value: Tumor cells

value: H3K27M mutant

value: Abemaciclib + Radiation (XRT)


title: f3_0h_rep1

description: Library name: Sample 8

value: bud

value: Cabernet Sauvignon


title: GSC35- 203497730233_R07C01

value: -2.6 to 1.12EGFR min to max

value: None (steady state culture)


title: IBs-A0317DIPG PDOX model treated with temozolomide and radiation_biol rep 2

description:
Library name: A0317DIPG_XRT_TMZ_biol rep 2
PDOX model treated with temozolomide and radiation (XRT)

value: Temozolomide + Radiation (XRT)


title: f1_2h_rep1

description: Library name: Sample 7


title: NF81, 56D, tRNA, Mock

description: Library name: Sample 25

value: hepatoma

value: tRNA transfected


title: IBs-A0317DIPG PDOX model treated with temozolomide and radiation_biol rep 1

description:
Library name: A0317DIPG_XRT_TMZ_biol rep 1
PDOX model treated with temozolomide and radiation (XRT)


title: f3_4h_rep1

description: Library name: Sample 6


title: NF81, MLT, p6, Mock

description: Library name: Sample 23

value: MLT

value: Kernow-C1/p6 RNA transfected


title: IBs-A0317DIPG PDOX model treated with radiation

description:
Library name: A0317DIPG_XRT
PDOX model treated with radiation (XRT)

value: Radiation (XRT)


title: NF81, MLT, tRNA, IFN

description: Library name: Sample 22


title: GSC285- 203497730233_R04C01

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -0.53 to 1.24EGFR min to max


title: f6_2h_rep1

description: Library name: Sample 4


title: IBs-A0317DIPG PDOX model under control group

description:
Library name: A0317DIPG_Control
PDOX model treated with vehicle (control)

value: Brainstem tumor

value: control


title: GSC274- 203497730233_R03C01

value: -2.68 to 1.33EGFR min to max


title: IBs-A0317DIPG PDOX model treated with abemaciclib

description:
Library name: A0317DIPG_Abemaciclib
PDOX model treated with CDK4/6 inhibitor abemaciclib

value: Tumor cells

value: H3K27M mutant

value: Abemaciclib


title: NF74, 56D, p6, IFN

description: Library name: Sample 20

value: Kernow-C1/p6 RNA transfected, interferon treated


title: Parse, contains all samples, sublibrary16

description:
Library name: M16
Parse, contains all samples

data_processing:
FASTQ were processed using the TrailmakerTM pipeline module (https://app.trailmaker.parsebiosciences.com/; pipeline v1.2.1, Parse Biosciences, 2024).
Assembly: GRCm39
Supplementary files format and content: count_matrix.mtx, raw counts per sample
Supplementary files format and content: cell_metadata.csv
Supplementary files format and content: all_genes.csv

source_name: brain

extract_protocol:
PBS-perfused half hemispheres were collected at specific zeitgeber times (ZT0 and 12), ages (5-6 and 20-22 months), and from specific genotypes (OPC-Bmal1-WT and OPC-Bmal1-KO). Brains were flash-frozen and stored at -80°C until use (n=3 per condition). Nuclei were isolated from flash-frozen tissue using nuclei extraction buffer (Miltenyi Biotech, 130-128-024) with 0.2 U/µL RNase inhibitor (New England Biolabs, M0314L) and processed in the Miltenyi gentleMACSTM Octo Dissociator according to the manufacturer’s instructions. Nuclei were passed through a 100 µm SmartStrainer and centrifuged at 350g at 4°C for 5 min. Samples were then incubated in resuspension buffer (1× PBS, 1% BSA, 0.2 U/μL RNase inhibitor) with anti-nucleus microbeads (Miltenyi Biotech, 130-132-997) for 15 min at 4°C. Nuclei were then MACS purified on LS columns (Miltenyi Biotech, 130-042-401) according to manufacturer’s instructions. Post-collection, nuclei suspensions were washed once in resuspension buffer and counted prior to fixation. Using the Nuclei Fixation Kit (Parse Biosciences, SB1003), a total of 1,000,000 nuclei per sample were fixed according to the manufacturer's instructions, with centrifugation of 300g. The nuclei suspensions were preserved as recommended by the manufacturer's instructions and kept at −80 °C until library preparation.
Single-nucleus libraries were generated with the Whole Transcriptome Mega Kit (Parse Biosciences, EC-W01050). cDNA library quantification and quality were assessed with a Qubit dsDNA HS Assay Kit (Invitrogen, Q32851) and D1000 HS Kit (Agilent, 5067-5584 and 5067-5585) for the Agilent TapeStation 4200. Sixteen single-nucleus libraries were sequenced by Novogene using the NovaSeq X Plus platform using 150 bp paired-end sequencing at a sequencing depth of 50,000 read pairs per cell.

value: brain

tag: age

value: young (5-6 months) and aged (20-22 months)

value: OPC-Bmal1-WT or OPC-Bmal1-KO

tag: time point

value: ZT0 or ‘lights-on’ and ZT12 or ‘lights-off’


title: f1_4h_rep2

description: Library name: Sample 2

tag: tissue

value: bud

value: Cabernet Sauvignon


title: NF74, 56D, p6, Mock

description: Library name: Sample 19

value: hepatoma

value: Kernow-C1/p6 RNA transfected


title: Parse, contains all samples, sublibrary15

description:
Library name: M15
Parse, contains all samples

tag: genotype


title: Parse, contains all samples, sublibrary14

description:
Library name: M14
Parse, contains all samples


title: BS153- 203440060073_R05C01

description: Methylation array of surgically removed GBM modelsample that was cultured without experimental treatment

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -0.61 to 3.59EGFR min to max

value: None (steady state culture)


title: NF74, 56D, tRNA, Mock

description: Library name: Sample 17

value: tRNA transfected


title: NOD-Spleen-NK-5

city: Winnipeg

first: Peter

last: Thompson

state: MB

address: 715 McDermot ave

department: Physiology & Pathophysiology

institute: University of Manitoba

description: Library name: NOD-5

data_processing:
Read alignment
Normalize read counts
Assembly: mm10
Supplementary files format and content: Differential_expression_analysis_table.csv

source_name: Spleen

extract_protocol:
Trizol total RNA (ZymoResearch RNA microprep kit)
paired end 150 bp

treatment_protocol: Freshly isolated splenocytes

value: Spleen

value: NOD/ShiLtJ

value: NK cell

value: wild-type


title: NOD-Spleen-NK-4

description: Library name: NOD-4


title: VU609- 203440060073_R04C01

value: -0.3 to 1.31EGFR min to max


title: NF74, MLT, p6, IFN

description: Library name: Sample 16

value: MLT

value: Kernow-C1/p6 RNA transfected, interferon treated


title: Parse, contains all samples, sublibrary12

description:
Library name: M12
Parse, contains all samples

value: brain

value: young (5-6 months) and aged (20-22 months)

value: OPC-Bmal1-WT or OPC-Bmal1-KO

value: ZT0 or ‘lights-on’ and ZT12 or ‘lights-off’


title: VU593- 203440060073_R03C01

value: -0.86 to 2.18EGFR min to max


title: NF74, MLT, p6, Mock

description: Library name: Sample 15

value: hepatoma

value: Kernow-C1/p6 RNA transfected


title: VU598- 203440060073_R02C01

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -0.6 to 0.88EGFR min to max


title: BoneMarrow_DMSOforRU486_KO_rep5

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description:
Library name: BoneMarrow_DMSOforRU486_KO_rep5_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.

source_name: BoneMarrow

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: BoneMarrow

value: Mecp2 KO

tag: Sex

value: Male

value: 2 months

tag: mouse id


title: BoneMarrow_DMSOforRU486_KO_rep2

description:
Library name: BoneMarrow_DMSOforRU486_KO_rep2_RNA-seq
RU486 versus DMSO in KO mice (10 tissues)
RNAseq_KO_RU486_vs_DMSO_count.txt.gz


title: Parse, contains all samples, sublibrary10

description:
Library name: M10
Parse, contains all samples


title: S123 scTCR-seq

first: Moran

last: Amit

address: 1515 Holcombe Blvd

department: Head & Neck Surgery

institute: University of Texas - MD Anderson Cancer Center

description:
Library name: cohort2_11
10x TCR 5' V2 HT (High Throughput)

data_processing:
TCR contigs and V(D)J annotations were generated using the Cell Ranger V(D)J v7.1.0 workflow from 10x Genomics.
Sequencing data was aligned to the Human (GRCh38) 2020-A reference sequence.
Assembly: Human GRCh38
Supplementary files format and content: filtered_contig_annotations.csv: TCR contig annotations with cell barcodes
Library strategy: TCR-Seq

extract_protocol:
After collection, specimens were immediately dissociated by using Human whole skin dissociation kit and Red Blood Cell Lysis Solution (10×) from Military Biotech. Dissociated cells were stained with APC conjugated CD45 (H130) mouse mAb from Cell Signaling. Then CD45 positive cells were sorted by using CytoFLEX SRT Cell Sorter for single cell sequencing.
T-cell receptor (TCR) single cell libraries were generated using the 10X Genomics Chromium Single Cell 5' v2 HT workflow with Feature Barcode technology.

value: Tumor

tag: pathology

value: SCC

value: IS

tag: patient


title: NF74, MLT, tRNA, IFN

description: Library name: Sample 14

tag: cell line

value: MLT

tag: cell type

value: tRNA transfected, interferon treated


title: NF74, MLT, tRNA, Mock

description: Library name: Sample 13

tag: treatment

value: tRNA transfected

tag: batch


title: Parse, contains all samples, sublibrary9

description:
Library name: M9
Parse, contains all samples

value: brain

value: young (5-6 months) and aged (20-22 months)

value: OPC-Bmal1-WT or OPC-Bmal1-KO

value: ZT0 or ‘lights-on’ and ZT12 or ‘lights-off’


title: C57BL6-Spleen-NK-4

description: Library name: C57BL6-4

value: Spleen

value: NK cell

value: wild-type


title: GSC20- 203440060042_R08C01

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -1.03 to 1.36EGFR min to max

value: None (steady state culture)


title: SOD1G93A IAV Infected MM155 F3

city: Hamilton

first: Imran

middle: Syed

last: Ahmed

state: Ontario

address: 1280 Main Street West

institute: McMaster University

description:
Library name: Sample 6
Colum name in MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx: X6.MM155.F3 (SOD1G93A Infected)

data_processing:
The reads were trimmed using TrimGalore and then aligned with GRCm39 reference using STAR83. Next, the reads were counted by using HTSeq count. Genes, showing low levels of expression were removed using EdgeR package in R, resulting in 12,503 genes. Counts for these remaining genes were normalized with TMM normalization method and then transformed using voom transformation. The limma package in R was used to identify genes differentially expressed between the infected and the uninfected groups SOD1G93A mice.
For differential expression analysis, corrected p-values < 0.05 were considered to be significant.
Assembly: GRCm39
Supplementary files format and content: MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx contains log2 transformed expression values

source_name: Lumbar Spinal Cord

growth_protocol: Mice were maintained on a 12 hour light/dark cycle and low-fat dietary chow and water was provided ad libitum. Breeding pairs consisted of male SOD1G93A mice and female WT mice, and mice were bred up to the second generation. Litters were weaned at 21 days of age and housed at a maximum of five mice per cage.

extract_protocol:
The spinal cord was removed at 30 days post-infection (90 days of age) and cut immediately distal to the 13th rib to isolate the lumbar spine. The lumbar spinal cord was hydraulically removed from the vertebrae using 5 mL of PBS and flash frozen in liquid nitrogen. Once frozen, samples within a cryotube were disrupted using a pestle and homogenized by pipetting with 600 µL of RLT buffer (Qiagen). Homogenized samples were then transferred to a Qiashredder spin column (Qiagen), and the flowthrough was subsequently spun in a gDNA eliminator column (Qiagen). Equal volume of 70% ethanol was added and RNA isolation was carried out as per the RNeasy instruction manual (Qiagen)
Sample libraries were prepared using the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina and cDNA libraries were sequenced using an Illumina HiSeq machine (2x50 bp sequence reads).

treatment_protocol: WT and SOD1G93A mice were anesthetized using isoflurane and infected with IAV i.n. in a 40 µL inoculum of PBS. Mice were infected with 300 plaque forming units (PFU) of IAV, equating to a 0.1 median lethal dose (LD50) infection. Mice were monitored for weight loss upto 14 days post-infection.

value: Lumbar Spinal Cord

tag: disease state

value: SOD1G93A mouse model

value: IAV Infected


title: Parse, contains all samples, sublibrary8

description:
Library name: M8
Parse, contains all samples


title: C57BL6-Spleen-NK-3

description: Library name: C57BL6-3


title: Parse, contains all samples, sublibrary6

description:
Library name: M6
Parse, contains all samples


title: SOD1G93A IAV infected MM155 F2

description:
Library name: Sample 5
Colum name in MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx: X5.MM155.F2 (SOD1G93A Infected)


title: GSC11- 203440060042_R06C01

value: -1.51 to 1.97EGFR min to max


title: GSC272- 203497730233_R02C01

value: -1.55 to 1.06EGFR min to max


title: f4_24h_rep1

first: Hongrui

last: Wang

address: 630 W. North Street

institute: Cornell University

description: Library name: Sample 3

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number*10'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
ORA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

value: bud

value: Cabernet Sauvignon

tag: field collection_date

tag: field chilling_(nc_model)

tag: field collection_id


title: SOD1G93A IAV Infected MM154 M4

description:
Library name: Sample 4
Colum name in MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx: X4.MM154.M4 (SOD1G93A Infected)


title: Parse, contains all samples, sublibrary5

description:
Library name: M5
Parse, contains all samples

value: brain

value: young (5-6 months) and aged (20-22 months)


title: ARPE-19 cells, tt-DDE, 24h, rep3

first: Chengpeng

last: Wu

address: Huajiachi, RM C-329, Zhejiang University, Hangzhou, China

institute: Zhejiang University

description: Library name: t3

data_processing:
Raw sequencing data (Raw Data) are first filtered to remove low-quality reads, adapter sequences, and contaminants, yielding high-quality clean reads (Clean Data). These clean reads are then aligned to the species’ reference genome using alignment software (GLC Genomics Workbench v 11.0.1) to map their genomic positions. Based on the alignment results, gene expression levels are quantified to generate read counts per gene, which may be normalized to metrics like FPKM (Fragments Per Kilobase of transcript per Million mapped reads) or TPM (Transcripts Per Million).
Assembly: GCF_000001405.39_GRCh38.p13_genomic.fna
Supplementary files format and content: xlsx file includes raw counts and FPKM values for each sample

growth_protocol: ARPE-19 cells are maintained in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (100 U/mL penicillin, 100 μg/mL streptomycin). Cultures are incubated at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted from tt-2,4-DDE-treated and control ARPE-19 cells using a commercial kit (RNeasy Mini Kit, Qiagen) .RNA concentration and purity were assessed using  NanoDrop measuring absorbance ratios (A260/A280 ≥ 1.8, A260/A230 ≥ 1.5). Integrity was verified via agarose gel electrophoresis or a Bioanalyzer (RIN ≥ 8.0) before library preparation.
Total RNA is processed to enrich for polyadenylated (polyA+) mRNA using Oligo(dT) magnetic beads. The purified mRNA is fragmented to approximately 300 bp via ion-mediated cleavage—this size is selected to balance effective data proportion (avoiding excessive adapter sequence representation in shorter fragments) and sequencing cluster formation efficiency (preventing challenges with longer fragments). First-strand cDNA is synthesized from the fragmented RNA template using 6-base random primers and reverse transcriptase, followed by second-strand cDNA synthesis using the first strand as a template. The constructed library is subjected to PCR amplification for fragment enrichment, then size-selected to retain ~450 bp fragments (including adapters). Library quality is assessed using an Agilent 2100 Bioanalyzer. Total and effective library concentrations are quantified, and individual libraries (each labeled with a unique Index sequence for post-sequencing demultiplexing) are pooled in proportions based on their effective concentrations and target data yields. The pooled library is normalized to 2 nM and denatured with alkali to generate single-stranded libraries, ready for sequencing.

treatment_protocol: When cells reach 70–80% confluency, aspirate the existing medium. Add 40 uM tt-2,4-DDE-containing medium to the treatment group at the target concentration (e.g., determined by prior dose-response assays). Add vehicle control medium (containing the same volume of DMSO as the treatment group, typically ≤0.1% v/v) to the control group. Incubate cells at 37°C with 5% CO₂ for 24 hours.

value: retinal pigment epithelial cell line

value: WT

value: trans, trans-2,4-decadienal


title: GSC811- 203440060042_R05C01

value: -2.54 to 0.63EGFR min to max


title: Parse, contains all samples, sublibrary4

description:
Library name: M4
Parse, contains all samples

value: OPC-Bmal1-WT or OPC-Bmal1-KO

value: ZT0 or ‘lights-on’ and ZT12 or ‘lights-off’


title: GSC710- 203440060042_R04C01

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -0.66 to 1.18EGFR min to max


title: SOD1G93A Uninfected MM155 F5

description:
Library name: Sample 2
Colum name in MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx: X2.MM155.F5 (SOD1G93A Uninfected)

value: Lumbar Spinal Cord

value: SOD1G93A mouse model

value: Uninfected


title: Parse, contains all samples, sublibrary3

description:
Library name: M3
Parse, contains all samples


title: ARPE-19 cells, tt-DDE, 24h, rep1

description: Library name: t1


title: SOD1G93A Uninfected MM155 F4

description:
Library name: Sample 1
Colum name in MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx: X1.MM155.F4. (SOD1G93A Uninfected)


title: Parse, contains all samples, sublibrary2

description:
Library name: M2
Parse, contains all samples


title: ARPE-19 cells, DMSO 24h, rep3

description: Library name: c3

value: DMSO


title: GSC627- 203440060042_R02C01

description: Methylation array of surgically removed GBM modelsample that was cultured without experimental treatment

value: -1.67 to 2.27EGFR min to max

value: None (steady state culture)


title: Ovariectomized Progesterone

city: Dallas

first: Mala

last: Mahendroo

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Library name: OvxP4
10x Genomics

data_processing:
scRNA-seq libraries were demultiplexed and mapped to the mouse reference genome (mm10) by using the Cellranger software (ver 3.0.2, 10X Genomics)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values file and matrix file

source_name: Cervix

extract_protocol:
Cervices were collected by dissection below the transition zone and all vaginal tissue was removed. Tissues were minced with a sterile razor. Minced cervices were dissociated with 10mg/ml cold protease (Sigma-Aldrich; Cat No: P5380) with 1mg/ml DNase I (Roche; Cat No: 11284932001) and 0.5M EDTA (Fisher Scientific; Cat No: SKU-20-158). After a 60 min incubation at 4ºC, cells were filters through a 40 µm cell strainer (BD Biosciences; Cat No: 08-771-1 ) and washed twice with fresh ice cold 1x PBS and then resuspended in 1x PBS +0.005% BSA.
10x Genomics Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index) on the 10x Genomics Chromium Controller

treatment_protocol: C57BL6/129 female mice (7 to 8 weeks old) were OVX and allowed a 2-weeks recovery period before treatment. Females were then separated and assigned to one of the two groups: Control, and progesterone (P4). Control group: OVX-control mice received no treatment during the 15-day experimental period.  Progesterone (P4) group: OVX mice received a subcutaneous injection of E2 (100 µg/d in 100 µL of corn oil) for 2 consecutive days to induce progesterone receptor expression, followed by implantation of a 25 mg, 21-day release pellet, (Innovative Research of America; Cat No:  E-121 and P-131) providing an estimate daily release of 1mg.

value: Cervix

tag: strain

value: Progesterone


title: Parse, contains all samples, sublibrary1

first: Erin

last: Gibson

address: 3165 Porter Drive

institute: Stanford University

description:
Library name: M1
Parse, contains all samples

value: brain

tag: age

value: young (5-6 months) and aged (20-22 months)


title: ARPE-19 cells, DMSO, 24h, rep2

description: Library name: c2

value: retinal pigment epithelial cell line

value: WT


title: GSC2- 203440060042_R01C01

value: -1.8 to 2.01EGFR min to max


title: Ovariectomized Control

description:
Library name: OvxC
10x Genomics

value: No treatment


title: GM12878_Direct_CAD-C_L

city: New York

first: Viviana

middle: I

last: Risca

address: 1230 York Ave

institute: The Rockefeller University

description: Library name: GM12878_Direct_CAD-C_L

data_processing:
Paired-end reads were aligned to the human reference genome (hg38) using bwa-mem2, converted to BAM format, and processed with a pairtools-based pipeline to parse contacts, correct orientation, sort, remove duplicates, and generate final high-confidence contact pairs for downstream analysis.
Assembly: hg38
Supplementary files format and content: cool, bw

growth_protocol: GM12878 cells were cultured in the media and conditions recommended by Coriell Institute for Medical Research.

extract_protocol:
For CADwalk, crosslinked cells were processed by CAD digestion and in situ proximity ligation without end repair or biotin labeling; proximity-ligation concatemer DNA was isolated after crosslink reversal and protein digestion, size-selected by agarose gel electrophoresis, and recovered by gel extraction.
Purified DNA was either sonicated and subjected to streptavidin-based enrichment followed by Illumina library preparation, processed directly with the NEBNext UltraExpress FS kit, or converted into long-read PacBio libraries via ligation-based adapter construction, followed by PCR amplification and sequencing.

value: B lymphoblastoid cell line


title: ARPE-19 cells, DMSO, 24h, rep1

description: Library name: c1


title: Normal control, vessel, ROI048

status: Public on Aug 06 2026

city: Goyang-si

first: Sung-Eun

last: Choi

state: --- Select One ---

address: 100 Ilsan-ro, Ilsan-donggu

country: South Korea

institute: NHIS Ilsan hospital

description:
Library name: ROI048
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-H01; AOI surface area 33550.6 um2; nuclei count 116; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI048

data_processing:
GeoMx NGS Pipeline v3.1.1.6
Paired-end FASTQ reads were quality-trimmed, adapter-trimmed, and stitched, then aligned to Readout Tag Sequence (RTS) barcodes; PCR duplicates were removed using unique molecular identifiers (UMIs), yielding deduplicated probe counts in DCC files (one per ROI).
DCC files were uploaded to the GeoMx DSP Data Analysis Suite and interpreted using the Hs_R_NGS_WTA_v1.0.pkc probe configuration file to collapse probe-level counts to gene-level (target-level) counts for 18,677 WTA targets.
Gene-level counts were normalized using the third-quartile (Q3) method across the 48 ROIs.
Assembly: GRCh38.p13
Supplementary files format and content: GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: tab-delimited text file. Rows are the 18,677 WTA gene targets; columns are the 48 ROIs (ROI001-ROI048); values are Q3-normalized counts. Column names correspond to the 'library name' field of each sample.
Supplementary files format and content: DCC files (one per ROI): raw deduplicated read counts per RTS_ID (probe barcode). RTS_IDs are interpreted using Hs_R_NGS_WTA_v1.0.pkc, provided as a study-level supplementary file.
Library strategy: Spatial Transcriptomics

source_name: kidney, normal

extract_protocol:
Formalin-fixed paraffin-embedded kidney biopsy sections (5 um) were mounted on slides, deparaffinized, subjected to target retrieval and proteinase K digestion, and hybridized overnight with the GeoMx Human NGS Whole Transcriptome Atlas RNA probe set (v1.0), in which each target-specific probe carries a UV-photocleavable oligonucleotide barcode. Slides were stained with morphology markers and imaged on the GeoMx DSP. Regions of interest corresponding to glomeruli, peritubular capillaries, and vessels were selected, and barcodes were released by UV illumination and collected into a microplate.
Collected oligonucleotide barcodes were uniquely indexed by PCR using GeoMx Seq Code primers, pooled, and purified with AMPure XP beads. Libraries were sequenced paired-end on an Illumina NovaSeq 6000.

value: kidney, normal

tag: patient id

value: patient 5

tag: diagnosis

value: normal kidney (non-transplant control)

tag: dsa status

value: not applicable

tag: anatomical compartment

value: vessel

tag: roi id


title: ARPE-19 cells, tt-DDE, 24h, rep2

description: Library name: t2

tag: genotype

value: trans, trans-2,4-decadienal


title: Normal control, vessel, ROI047

description:
Library name: ROI047
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G12; AOI surface area 61877.9 um2; nuclei count 113; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI047

tag: tissue


title: Normal control, peritubular capillary, ROI044

description:
Library name: ROI044
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G09; AOI surface area 21909.5 um2; nuclei count 106; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI044

value: peritubular capillary


title: Normal control, peritubular capillary, ROI045

description:
Library name: ROI045
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G10; AOI surface area 26480.1 um2; nuclei count 135; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI045


title: GSC72- 203440060042_R03C01

value: Human GBM brain tumor

tag: cell line

value: GBM tumor cell culture model

value: -0.37 to 1.63EGFR min to max

value: None (steady state culture)


title: Normal control, peritubular capillary, ROI043

description:
Library name: ROI043
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G08; AOI surface area 18909.2 um2; nuclei count 102; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI043


title: Normal control, glomerulus, ROI041

description:
Library name: ROI041
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G06; AOI surface area 20774.7 um2; nuclei count 120; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI041

value: glomerulus


title: Normal control, glomerulus, ROI042

description:
Library name: ROI042
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G07; AOI surface area 20649.4 um2; nuclei count 130; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI042


title: GSC300- 203497730233_R06C01

tag: cell type

value: -0.95 to 2.9EGFR min to max


title: DSA-NER, vessel, ROI039

description:
Library name: ROI039
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G04; AOI surface area 18221.6 um2; nuclei count 110; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI039

source_name: kidney allograft biopsy

value: kidney allograft biopsy

value: patient 4

value: no evidence of rejection

value: negative


title: DSA-NER, vessel, ROI038

description:
Library name: ROI038
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G03; AOI surface area 39248.4 um2; nuclei count 100; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI038


title: GSC295- 203497730233_R05C01

value: -2.75 to 1.08EGFR min to max

tag: treatment


title: NF81, MLT, p6, IFN

description: Library name: Sample 24

value: MLT

value: hepatoma

value: Kernow-C1/p6 RNA transfected, interferon treated

tag: batch


title: DSA-NER, vessel, ROI037

description:
Library name: ROI037
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G02; AOI surface area 37958.6 um2; nuclei count 112; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI037

value: vessel


title: f2_7d_rep1

city: Geneva

description: Library name: Sample 5

source_name: bud

value: bud

value: Cabernet Sauvignon


title: Normal control, glomerulus, ROI040

description:
Library name: ROI040
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G05; AOI surface area 19987.6 um2; nuclei count 119; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI040

value: kidney, normal

value: patient 5

value: normal kidney (non-transplant control)

value: not applicable


title: NF81, MLT, tRNA, Mock

description: Library name: Sample 21

value: tRNA transfected


title: DSA-NER, peritubular capillary, ROI036

description:
Library name: ROI036
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G01; AOI surface area 14992.8 um2; nuclei count 141; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI036

value: peritubular capillary


title: DSA-NER, peritubular capillary, ROI035

description:
Library name: ROI035
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F12; AOI surface area 21603.3 um2; nuclei count 101; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI035

value: kidney allograft biopsy


title: GSC268- 203497730233_R01C01

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -0.55 to 1.29EGFR min to max

value: None (steady state culture)


title: DSA-NER, peritubular capillary, ROI034

description:
Library name: ROI034
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F11; AOI surface area 14376.5 um2; nuclei count 119; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI034

value: patient 4

value: no evidence of rejection

value: negative


title: DSA-NER, glomerulus, ROI033

description:
Library name: ROI033
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F10; AOI surface area 24811.7 um2; nuclei count 102; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI033

value: glomerulus


title: DSA-NER, glomerulus, ROI031

description:
Library name: ROI031
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F08; AOI surface area 35363.5 um2; nuclei count 137; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI031


title: DSA-NER, glomerulus, ROI032

description:
Library name: ROI032
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F09; AOI surface area 25574.9 um2; nuclei count 112; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI032


title: DSA+NER, vessel, ROI030

description:
Library name: ROI030
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F07; AOI surface area 13539.9 um2; nuclei count 108; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI030

value: patient 3

value: positive

value: vessel


title: HEK293T- 203440060073_R06C01

description: Methylation array of surgically removed GBM modelsample that was cultured without experimental treatment

source_name: Human Embryonic Kidney

value: Human Embryonic Kidney

value: Human Embryonic Kidney culture


title: DSA+NER, vessel, ROI029

description:
Library name: ROI029
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F06; AOI surface area 8776.9 um2; nuclei count 103; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI029


title: NF74, 56D, tRNA, IFN

description: Library name: Sample 18

value: hepatoma

value: tRNA transfected, interferon treated


title: DSA+NER, peritubular capillary, ROI027

description:
Library name: ROI027
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F04; AOI surface area 22028.9 um2; nuclei count 125; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI027

value: peritubular capillary


title: DSA+NER, vessel, ROI028

description:
Library name: ROI028
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F05; AOI surface area 15302.7 um2; nuclei count 107; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI028

value: kidney allograft biopsy


title: Parse, contains all samples, sublibrary13

city: Palo Alto

description:
Library name: M13
Parse, contains all samples

value: brain

value: young (5-6 months) and aged (20-22 months)

value: OPC-Bmal1-WT or OPC-Bmal1-KO

tag: time point

value: ZT0 or ‘lights-on’ and ZT12 or ‘lights-off’


title: DSA+NER, peritubular capillary, ROI026

description:
Library name: ROI026
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F03; AOI surface area 15952.4 um2; nuclei count 111; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI026


title: DSA+NER, glomerulus, ROI024

description:
Library name: ROI024
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F01; AOI surface area 32283.2 um2; nuclei count 112; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI024


title: DSA+NER, peritubular capillary, ROI025

description:
Library name: ROI025
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-F02; AOI surface area 22443.1 um2; nuclei count 115; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI025


title: DSA+NER, glomerulus, ROI023

description:
Library name: ROI023
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E12; AOI surface area 34706.4 um2; nuclei count 154; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI023


title: DSA+NER, glomerulus, ROI021

description:
Library name: ROI021
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E10; AOI surface area 25370.1 um2; nuclei count 108; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI021


title: DSA+NER, glomerulus, ROI022

description:
Library name: ROI022
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E11; AOI surface area 34937.6 um2; nuclei count 139; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI022


title: DSA-CAMR, vessel, ROI020

description:
Library name: ROI020
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E09; AOI surface area 39574.0 um2; nuclei count 212; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI020

value: patient 2

value: chronic antibody-mediated rejection


title: DSA-CAMR, vessel, ROI019

description:
Library name: ROI019
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E08; AOI surface area 14678.8 um2; nuclei count 115; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI019

value: negative


title: DSA-CAMR, vessel, ROI018

description:
Library name: ROI018
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E07; AOI surface area 11693.4 um2; nuclei count 114; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI018


title: DSA-CAMR, peritubular capillary, ROI016

description:
Library name: ROI016
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E05; AOI surface area 17181.7 um2; nuclei count 173; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI016


title: DSA-CAMR, peritubular capillary, ROI017

description:
Library name: ROI017
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E06; AOI surface area 16019.2 um2; nuclei count 145; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI017


title: Parse, contains all samples, sublibrary11

description:
Library name: M11
Parse, contains all samples


title: DSA-CAMR, glomerulus, ROI014

description:
Library name: ROI014
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E03; AOI surface area 64876.0 um2; nuclei count 642; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI014

value: glomerulus


title: DSA-CAMR, glomerulus, ROI013

description:
Library name: ROI013
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E02; AOI surface area 25767.7 um2; nuclei count 253; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI013


title: NOD-Spleen-NK-3

description: Library name: NOD-3

value: Spleen

value: NOD/ShiLtJ

value: NK cell

value: wild-type


title: Normal control, vessel, ROI046

description:
Library name: ROI046
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-G11; AOI surface area 80085.1 um2; nuclei count 135; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI046

value: kidney, normal

value: patient 5

value: normal kidney (non-transplant control)

value: not applicable

value: vessel


title: DSA-CAMR, glomerulus, ROI011

description:
Library name: ROI011
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D12; AOI surface area 22067.7 um2; nuclei count 200; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI011

value: kidney allograft biopsy


title: DSA+CAMR, vessel, ROI010

description:
Library name: ROI010
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D11; AOI surface area 81374.4 um2; nuclei count 405; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI010

value: patient 1

value: positive


title: DSA-CAMR, glomerulus, ROI012

description:
Library name: ROI012
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-E01; AOI surface area 61830.4 um2; nuclei count 559; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI012


title: Lung, MNX CF, female, rep2

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: RSB527-10

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: CF


title: DSA+CAMR, vessel, ROI009

description:
Library name: ROI009
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D10; AOI surface area 30292.9 um2; nuclei count 165; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI009

value: chronic antibody-mediated rejection


title: DSA+CAMR, vessel, ROI008

description:
Library name: ROI008
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D09; AOI surface area 67638.3 um2; nuclei count 209; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI008


title: DSA+CAMR, peritubular capillary, ROI007

description:
Library name: ROI007
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D08; AOI surface area 15565.5 um2; nuclei count 124; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI007

value: peritubular capillary


title: DSA+CAMR, peritubular capillary, ROI006

description:
Library name: ROI006
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D07; AOI surface area 14308.7 um2; nuclei count 109; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI006


title: NOD-Spleen-NK-2

description: Library name: NOD-2


title: DSA+CAMR, peritubular capillary, ROI005

description:
Library name: ROI005
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D06; AOI surface area 46612.3 um2; nuclei count 162; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI005


title: DSA+CAMR, glomerulus, ROI002

description:
Library name: ROI002
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D03; AOI surface area 22015.7 um2; nuclei count 127; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI002

value: glomerulus


title: DSA+CAMR, glomerulus, ROI001

description:
Library name: ROI001
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D02; AOI surface area 19285.6 um2; nuclei count 110; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI001


title: Monocytes_CNS_LPS_rep1

city: Austin

first: Anna

last: Warden

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: human_MNCbrainMGLPS1

data_processing:
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR (v2.7.11b).
Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0).
Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’
Batch correction was performed using CombatSeq and the sva package (v3.52.0)
Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Quantified read counts were normalized and analyzed using DESeq2 (v1.44.0) to determine differential expression between groups, within the R statistical computing environment (v4.4.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample
Supplementary files format and content: tab-delimited text file inclues raw TPM for each Sample

source_name: umbilical cord blood

extract_protocol:
To perform the mRNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries
RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

value: umbilical cord blood

value: Monocytes

value: LPS


title: Monocytes_CNS_LPS_rep2

description: Library name: human_MNCbrainMGLPS2


title: DSA+CAMR, glomerulus, ROI004

description:
Library name: ROI004
GeoMx DSP area of illumination (AOI), Full ROI segment; DSP well DSP-1001660023291-D-D05; AOI surface area 16818.1 um2; nuclei count 118; column name in GeoMx_WTA_Q3norm_counts_gene_x_ROI.tsv: ROI004


title: CD34_CNS_LPS_rep1

description: Library name: human_CD34brainMGLPS1


title: iHPC_CNS_LPS_rep2

description: Library name: human_ec11brainMGLPS2

source_name: iPSC-derived cells

value: iPSC-derived cells

value: iHPC