title: Nap1l1-WT-rep4

description: Library name: Tamar_WT_serum_S18_L001_R1_001

value: mESC

value: wild-type


title: WT, AD ReN, differentiation 1, clone F2

status: Public on Aug 06 2026

type: SRA

city: New York

first: Anna

last: Podlesny-Drabiniok

state: NY

address: 1425 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: F2_WT_AD

library_source: transcriptomic single cell

data_processing:
Raw base call files were demultiplexed into FASTQ files using PIPseeker (Fluent Biosciences). Reads were aligned to the human reference genome (GRCh38), followed by barcode assignment and UMI counting to generate feature-barcode matrices. Sensitivity setting 3 was used
Quality control, normalization, clustering, and visualization were performed using Seurat v4.0. Cells were filtered based on the following criteria: <100 detected genes, <500 UMIs, >95% of UMIs from a single gene, or >10% mitochondrial reads. Count data were normalized using SCTransform (v0.4.1) with regression for mitochondrial gene percentage. Principal component analysis (PCA) was used for dimensionality reduction.
Assembly: hg38
Supplementary files format and content: barcode.tsv, features.tsv, matrix.mtx files provided for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: iPSC lines were differentiated to hematopoietic precursor cells (HPCs) using StemDiff kit (StemCell Technologies). 20,833 cells/cm2 HPCs were plated and differentiated for 24 days to microglia (iMGL) in iMGL media (DMEM/F12, 2xB27, 0.5xN2, 2xITSG, 400uM monothioglycerol, 5ug/ml insulin, 1xNEAA, 1xGlutaMax) supplemented with three factors (IL34 (100ng/ml), TGFb (50ng/ml), and MCSF (25ng/ml). iMGLs were fed Monday, Wednesday and Friday with 1ml of iMGL media with three factors. Cells were splitted in 1:2 ratio if too confluent. Day 24 iMGLs were lifted with gentle pipetting and Accutase and plated 62,500 cells/cm2 in 1ml of conditioned media and 1ml of fresh media iMGL media with three factors supplemented additionally with two factors (CX3CL1 and CD200 100ng/ml each) for 3 additional days (day 25, day 26,  day 27). At day 26 of iMGL differentiation, iMGL received 1ml of five factor iMGL media and treatment with myelin or LPS. Cells were collected at day 27.  ReNcell VM human neural progenitor cells (NPCs) were obtained from the laboratories of Drs. Rudolph Tanzi and Doo Kim. Two cell lines were used: (1) control cells expressing GFP and (2) Alzheimer’s disease (AD) cells harboring APP (Swedish and London) and PSEN1 (ΔE9) mutations, expressing both GFP and mCherry.For maintenance, ReN NPCs were cultured on BD Matrigel–coated T75 flasks (Corning, cat. 356231) in expansion medium consisting of DMEM/F12 supplemented with 2% B27 neural supplement, heparin (2 µg/mL), epidermal growth factor (EGF, 20 ng/mL), basic fibroblast growth factor (bFGF, 20 ng/mL), and 1× penicillin/streptomycin. Media were replaced every 72 hours until cultures reached approximately 80% confluency. For 3D neuron/astrocyte differentiation, cells were dissociated with Accutase, counted, and plated at 250,000 cells per well in 96-well plates in expansion medium supplemented with 10% cold Matrigel. Twenty-four hours later, medium was fully replaced with differentiation medium (expansion medium lacking EGF and bFGF). Media were refreshed by 50% every 3–4 days. Cultures were differentiated for four weeks to generate mature neuronal and astrocytic populations. After four weeks of differentiation, mature neuronal/astrocyte cultures were overlaid with mature iPSC-derived microglia (iMGLs). A total of 50,000 iMGLs were added per well. The neuronal/astrocyte medium was supplemented with microglia-supporting three cytokines (IL34, TGFb, MCSF) to maintain iMGL survival. Tricultures were maintained for one additional week prior to scRNAseq

extract_protocol:
Cells were washed with PBS and dissociated using Papain Dissociation System (Worthington Biochemical, cat.LK003153) according to the manufacturer’s instructions for 40 minutes at 37°C according to manufacturer's instructions. Cells were centrifuged at 400 × g for 5 minutes and resuspended in 1.0% PBS/bovine serum albumin (BSA). The cell suspension was filtered through a 40 μm cell strainer to remove aggregates. Cell number and viability were assessed using trypan blue exclusion and an automated cell counter (Countess, Thermo Fisher Scientific). Only samples with high viability (typically >90%) were used for downstream processing.
Single cells were partitioned into PIP droplets using the PIPseq T20 3’ Single Cell RNA Kit v4.0 (Fluent Biosciences, Watertown, MA, USA) according to the manufacturer’s instructions. Briefly, approximately 40,000 live cells were combined with template beads, gently mixed, vortexed for 3 minutes to generate stable PIP emulsions, and processed following the recommended workflow. Captured mRNA was released upon cell lysis within the droplets, followed by reverse transcription, cDNA amplification, cDNA purification, and library preparation. Libraries were sequenced by Azenta (New Jersey, USA) on an Illumina NovaSeq X platform, generating ~50,000 reads per cell (~2 billion reads per sample).

tag: cell line

tag: cell type

value: triculture

tag: genotype

value: WT

tag: treatment

value: AD ReN

tag: batch


title: MEF2C-KO, AD ReN, differentiation 1, clone D9

description: Library name: D9_KO_AD


title: full-KO-2D-3

city: Jerusalem

first: Tamar

last: Segal

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: Library name: C20_3_2D_S43

library_source: transcriptomic

data_processing:
Raw fastq files were checked for quality control using fastqc software.
Reads were aligned to the mouse RefSeq reference genome (mm10) using STAR aligner version 2.7.1a with the default parameters.
Raw counts for each gene were generated using - quantMode GeneCounts.
Assembly: mm10
Supplementary files format and content: Comma-separated values includes raw counts for each sample

organism: Mus musculus

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
mRNA libraries were prepared using KAPA Stranded mRNA-Seq kit.

value: NAP1L1 knock-out


title: MEF2C-KO, AD ReN, differentiation 1, clone G2

description: Library name: G2_KO_AD


title: MEF2C-KO, AD ReN, differentiation 1, clone D8

description: Library name: D8_KO_AD


title: WT, CTRL ReN, differentiation 1, clone H2

description: Library name: H2_WT_CTRL

value: CTRL ReN


title: WT, CTRL ReN, differentiation 1, clone C2

description: Library name: C2_WT_CTRL


title: MEF2C-KO, LPS-treated, differentiation 2, clone D8

description:
Library name: D8_KO_LPS_B2
column name in WTC11_bulkRNAseq_iMGL_raw_counts.tsv: D8_KO_LPS_B2

data_processing:
Raw base call files were converted to FASTQ format and processed using the nf-core/rnaseq pipeline (DOI: 10.5281/zenodo.1400710).
Reads were quality controlled, adapter-trimmed, and aligned to the human reference genome (GRCh38). Gene-level quantification was performed within the nf-core/rnaseq pipeline using standard parameters.
Gene-level count matrices were imported into R (v4.3.3) for downstream analysis. Differential gene expression analysis was performed using the DREAM method implemented in the variancePartition package (v1.23.1), applying linear mixed-effects models.
Assembly: hg38
Supplementary files format and content: tab-separated values (tsv) file containing raw counts for each sample

molecule: polyA RNA

growth_protocol: iPSC lines were differentiated to hematopoietic precursor cells (HPCs) using StemDiff kit (StemCell Technologies). 20,833 cells/cm2 HPCs were plated and differentiated for 24 days to microglia (iMGL) in iMGL media (DMEM/F12, 2xB27, 0.5xN2, 2xITSG, 400uM monothioglycerol, 5ug/ml insulin, 1xNEAA, 1xGlutaMax) supplemented with three factors (IL34 (100ng/ml), TGFb (50ng/ml), and MCSF (25ng/ml). iMGLs were fed Monday, Wednesday and Friday with 1ml of iMGL media with three factors. Cells were splitted in 1:2 ratio if too confluent. Day 24 iMGLs were lifted with gentle pipetting and Accutase and plated 62,500 cells/cm2 in 1ml of conditioned media and 1ml of fresh media iMGL media with three factors supplemented additionally with two factors (CX3CL1 and CD200 100ng/ml each) for 3 additional days (day 25, day 26,  day 27). At day 26 of iMGL differentiation, iMGL received 1ml of five factor iMGL media and treatment with myelin or LPS. Cells were collected at day 27.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74136) according to the manufacturer’s instructions. RNA quantity was assessed using NanoDrop 8000 (Thermo Fisher Scientific). RNA integrity was evaluated by Azenta using Qubit and BioAnalyzer, with all samples demonstrating RNA integrity number (RIN) > 9.0 prior to library preparation.
RNA-seq libraries were prepared by Azenta (New Jersey, USA) using the TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the manufacturer’s protocol. Libraries were paired-end sequenced on an Illumina HiSeq2500 platform with 150 bp read length, generating approximately 20–30 million mapped fragments per sample.

treatment_protocol: Myelin 20ug/ml, 24h, LPS 50ng/ml 24h

value: iPSC-derived microglia

value: LPS


title: MEF2C-KO, non-treated, differentiation 2, clone D8

description:
Library name: D8_KO_NT_B2
column name in WTC11_bulkRNAseq_iMGL_raw_counts.tsv: D8_KO_NT_B2

value: non-treated


title: WT, AD ReN, differentiation 1, clone C2

description: Library name: C2_WT_AD


title: full-KO-0D-1

description: Library name: C20_1_0D_S34


title: MEF2C-KO, CTRL ReN, differentiation 1, clone D9

description: Library name: D9_KO_CTRL


title: full-KO-0D-2

description: Library name: C20_2_0D_S23


title: WT, CTRL ReN, differentiation 1, clone E2

description: Library name: E2_WT_CTRL


title: MEF2C-KO, CTRL ReN, differentiation 1, clone G2

description: Library name: G2_KO_CTRL


title: full-KO-4D-2

description: Library name: C20_2_4D_S47


title: SNCA-GR mouse M9376, olfactory bulb, snRNA-seq 10x 5' v2 (short-read)

city: Seattle

first: Benjamin

last: Logsdon

state: WA

address: 1150 Eastlake Ave E Ste 600/700

institute: Cajal Therapeutics

description:
Library name: LX3-250506-02
10x Chromium Next GEM Single Cell 5' v2, dual-indexed with SI-TT-A2; libraries sequenced across three Illumina NextSeq 2000 P3 flow-cell runs (RX1-0227, RX1-0228, RX1-0229) and merged before Cell Ranger v6.1.1 processing.

data_processing:
[10X] Bcl -> FASTQ demultiplexing with Illumina DRAGEN BCL Convert v3.10.4 on BaseSpace, one FASTQ set per NextSeq 2000 P3 flow cell (RX1-0227 / RX1-0228 / RX1-0229). Per-sample FASTQs from all three runs were merged before Cell Ranger input.
[10X] cellranger count --include-introns --chemistry fiveprime (Cell Ranger v6.1.1; martian v4.0.6) against a mouse reference (confirm exact build). Outputs: filtered_feature_bc_matrix {barcodes,features,matrix} + .h5, metrics_summary.csv, web_summary.html, analysis/ (clustering, PCA, tSNE, UMAP, diffexp).
[ONT] Real-time basecalling with MinKNOW on PromethION P2 Solo, R10.4.1 chemistry, LSK114 kit; POD5 signals recorded; basecalls written to <libID>_live_basecall.fastq.gz.
[ONT] minimap2 alignment of ONT basecalls with splice-aware parameters (-ax splice -uf -k14) against the same mouse reference used for Cell Ranger. Alignments sorted and indexed with samtools. No gene- or isoform-level quantification is included in this Series.
Assembly: GRCh38 (GenBank assembly accession GCA_000001405.15, primary assembly/no-alt analysis set)
Supplementary files format and content: [10X] For each 10x library: three 10x Market Exchange files (<libID>_barcodes.tsv.gz cell barcodes, <libID>_features.tsv.gz gene features, <libID>_matrix.mtx.gz sparse UMI matrix), the same matrix in HDF5 (<libID>_filtered_feature_bc_matrix.h5), and <libID>_metrics_summary.csv Cell Ranger QC metrics.
Supplementary files format and content: [ONT] <libID>_live_basecall_minimap2_sorted.bam: coordinate-sorted BAM of minimap2 splice-aware alignments of ONT basecalls to the same mouse reference; retains 10x cell-barcode + UMI, basecalled read sequences, and per-base Q-scores. Same BAM is listed as the *raw file for each ONT library -- basecalled FASTQ can be regenerated with `samtools fastq`. Full FASTQs are archived in the source bucket and available on reasonable request.

molecule: nuclear RNA

source_name: Olfactory bulb

extract_protocol:
Brains from three SNCA-GR homozygous male mice (JAX #39166; DOB 2025-03-04; sacrificed 2025-04-28 at age 55 days) were flash-frozen and stored at -80 C. On 2025-04-30 (M9376) and 2025-05-01 (M9377, M9378), 50 um coronal sections were cut on a dry-ice-cooled sectioning stage and the substantia nigra / VTA and olfactory bulb were microdissected under a stereo microscope from both hemispheres, then homogenized in 1 mL Homogenization Buffer (NIM pH 8.0 with 0.2 U/uL RNase Inhibitor, 1x protease inhibitor cocktail, 0.1 mM DTT) using a Dounce homogenizer (10 loose + 10 tight strokes). Nuclei were purified by Debris Removal Solution gradient (Miltenyi), washed in 2X BSA/PBS, filtered through a 30 um strainer, and resuspended in 1% BSA blocking buffer. Nuclei counts (Trypan blue, Neubauer hemocytometer) were adjusted to 200-700 nuclei/uL for 10x loading.
[10X] 10x Genomics Chromium Next GEM Single Cell 5' v2: nuclei loaded onto a Chromium Next GEM Chip K at target recovery of 7,500 cells (12,000 loaded). GEM-RT, Dynabead cleanup, and 13-cycle cDNA amplification per manufacturer protocol. Gene expression libraries constructed from 50 ng of amplified cDNA with the 10x Library Construction Kit; 14-cycle indexing PCR with Dual Index Kit TT Set A wells A1-A6 (one index per sample).
[ONT] 10 ng of the same amplified 10x cDNA per sample was re-amplified (7 cycles, LongAmp Hot Start Taq 2X, 66->58 C ramp, 6 min extension) with custom oligos Fwd_3580_partial_read1_defined_for_5'_cDNA (5'-/5phos/ACTTGCCTGTCGCTCTATCTTCCTACACGACGCTCTTCCGATCT-3') and Rev_PR2_partial_TSO_defined_for_5'_cDNA (5'-/5phos/TTTCTGTTGGTGCTGATATTGCAAGCAGTGGTATCAACGCAGAG-3') to add ONT-compatible ends preserving the 10x cell barcode + UMI at the 5' of the read. Products bead-cleaned (1x SPRIselect), end-prepped (NEBNext Ultra II End Repair / dA-tailing), ligated to ONT LSK114 sequencing adapters with Salt-T4 DNA Ligase; cleaned with SPRIselect (0.4x) and eluted in 34 uL Elution Buffer.

tag: tissue

value: Olfactory bulb

value: nuclei

tag: age

value: 55 days

tag: Sex

value: male

value: SNCA-GR homozygous (humanized SNCA gene-replacement knock-in; JAX #39166)

tag: strain

value: SNCA-GR (JAX #39166)


title: SNCA-GR mouse M9376, SNc-VTA (midbrain), snRNA-seq 10x 5' v2 (short-read)

description:
Library name: LX3-250506-01
10x Chromium Next GEM Single Cell 5' v2, dual-indexed with SI-TT-A1; libraries sequenced across three Illumina NextSeq 2000 P3 flow-cell runs (RX1-0227, RX1-0228, RX1-0229) and merged before Cell Ranger v6.1.1 processing.

source_name: Substantia nigra pars compacta / ventral tegmental area (SNc-VTA), midbrain


title: WT, CTRL ReN, differentiation 1, clone F2

description: Library name: F2_WT_CTRL


title: WT.F.DMSO.set1_F4

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description:
Library name: WT.F.DMSO.set1_F4
transcriptome of DMSO treated WT female retina

data_processing:
Illumina bulk RNAseq reads were quality checked and aligned to Ensembl reference transcriptomes of Mus musculus (version 115) for control and treated samples of rd10 retinas. Analysis pipeline has been described previously (Song, et al. 2025). Briefly, transcriptome alignments were performed with Kallisto and processed with the R package tximport, before differential expression analysis with edgeR and limma.
Differentially expressed genes (DEG) were identified by setting a p-value filter of 0.05 and selecting the top 500 over and under expressing genes with at least 1.2-fold change. DEGs were mapped to KEGG pathways using gProfiler and filtered to identify pathways that had minimum 3 DEG mappings and at least 5% of the pathway impacted by differential genes.
Assembly: GRCm39/ENSv115
Supplementary files format and content: Comma-delimited text files containing transcript level counts, gene level counts, normalized gene level counts-per-million results, or diffierential expressed gene results.

source_name: Retina

growth_protocol: B6.CXB1-Pde6brd10/J (Strain #: 004297; RRID: IMSR_JAX:004279), including both female and male, were obtained from the Jackson Laboratory and intercrossed to generate the pups. Mice were maintained under controlled environment conditions (temperature: 22 °C ± 2 °C, humidity: 30-70%) with a 12-hour light/dark cycle and had ad libitum access to food and water. Bedding, food, and water were replaced on a weekly basis.

extract_protocol:
Total RNA was isolated from homogenized mouse retinas using RNeasy Mini Kit (QIAGEN), following the manufacturer’s instructions. RNA quality was evaluated using the TapeStation system (Agilent), and only samples with high quality (RNA RIN ≥9) were used for the downstream applications.
For library preparation, 100 ng of total RNA was used to generate  strand-specific mRNA sequencing libraries using the TruSeq stranded RNA Kit (Illumina).

treatment_protocol: For intravitreal injections in mice at P10 and P24, pups received intraperitoneal anesthesia with ketamine (50 mg/kg body weight) and xylazine (5 mg/kg body weight). Either  DMSO or Halofantrine (1 μL, 20 μM) was delivered into the vitreous using a Hamilton syringe fitted with a 34-gauge needle. Mice showing evidence of ocular or lens injury following injection were excluded from further analysis.

value: Retina

tag: group

value: F

value: DMSO


title: rd10.F.HAL.last_rd10_F2_F

description:
Library name: rd10.F.HAL.last_rd10_F2_F
transcriptome of HAL treated rd10 female retina

value: HAL


title: full-KO-2D-1

description: Library name: C20_1_2D_S41

value: mESC


title: alpha-KO-4D-3

description: Library name: C6_3_4D_S45

value: NAP1L1 alpha knock-out


title: MEF2C-KO, CTRL ReN, differentiation 1, clone H11

description: Library name: H11_KO_CTRL

value: triculture


title: alpha-KO-2D-3

description: Library name: C6_3_2D_S40


title: alpha-KO-2D-2

description: Library name: C6_2_2D_S39


title: WT, non-treated, differentiation 1, clone C2 (ATAC-seq)

description: Library name: C2_WT

library_source: genomic

data_processing:
Raw FASTQ files were processed using the nf-core/atacseq pipeline. Adapter trimming was performed using Trim Galore. Reads were aligned to the reference genome hg38  using BWA-MEM. Aligned BAM files were filtered to remove unmapped reads, mitochondrial reads, low-quality reads (MAPQ < 30), and PCR duplicates. Only properly paired reads were retained for downstream analysis.
Peak calling was performed independently for each sample using MACS2 with parameters optimized for ATAC-seq (--shift -100 --extsize 200, q-value cutoff 0.01). Peaks were reported in narrowPeak format. Signal tracks were normalized to reads per million (RPM) and converted to bigWig format for visualization.
Consensus peak regions were generated by merging peaks across all samples using BEDTools. Read counts per consensus peak were quantified across all samples. Differential chromatin accessibility analysis was performed using DiffBind in R. Peaks with FDR < 0.05 were considered significantly differentially accessible
Assembly: hg38
Supplementary files format and content: narrowPeak file per sample

molecule: genomic DNA

extract_protocol:
Day 27 iMGLs were harvested, and approximately 2 × 10^6 cells (viability >85%) were cryopreserved in Synth-A-Freeze medium and stored at −80°C for 24 hours. The following day, vials were transferred to liquid nitrogen for long-term storage until all samples were collected (no longer than one month). Samples were subsequently shipped to Azenta (New Jersey, USA) for nuclei isolation, library preparation, and sequencing.  Nuclei were isolated from bulk cell pellets using a detergent-based lysis buffer to release intact nuclei. Following nuclei isolation, chromatin accessibility was assayed using the Omni-ATAC protocol. Briefly, 50,000–100,000 nuclei per sample were incubated with Tn5 transposase (Illumina Nextera DNA Library Prep kit) at 37°C for 30 minutes to simultaneously fragment DNA and insert sequencing adapters into accessible chromatin regions. Transposed DNA was purified using a silica column-based purification system
Following transposition, libraries were PCR-amplified using indexed primers to incorporate sample-specific barcodes. Amplification cycles were determined by qPCR to avoid over-amplification. Libraries were purified using AMPure XP beads to remove primer dimers and fragments <100 bp. Library quality and fragment size distribution were assessed using an Agilent TapeStation system. Libraries were quantified using fluorometric methods and pooled equimolarly prior to sequencing. Paired-end sequencing was performed on an Illumina platform to generate 50–75 bp paired-end reads.

value: WT


title: alpha-KO-4D-1

description: Library name: C6_1_4D_S27


title: full-KO-4D-1

description: Library name: C20_1_4D_S46

value: NAP1L1 knock-out


title: alpha-KO-0D-3

description: Library name: C6_3_0D_S33


title: MEF2C-KO, non-treated, differentiation 1, clone D9 (ATAC-seq)

description: Library name: D9_KO

value: iPSC-derived microglia


title: alpha-KO-0D-1

description: Library name: C6_1_0D_S31


title: full-KO-2D-2

description: Library name: C20_2_2D_S42


title: WT, non-treated, differentiation 1, clone E2 (ATAC-seq)

description: Library name: E2_WT

value: non-treated


title: MEF2C-KO, CTRL ReN, differentiation 1, clone D8

description: Library name: D8_KO_CTRL

value: CTRL ReN


title: Nap1l1-full-KO-rep2

description: Library name: Tamar_KO_serum_S12_L001_R1_001

data_processing:
Illumina output was analyzed using an in-house Perl script that produced a reads matrix that was aligned using RSEM with Bowtie.
The resulting matrix was analyzed in R (Seurat v4.1.1)
Assembly: mm10
Supplementary files format and content:
gene abundances matrices for each sample seperated to single cells; Each column represents a cell, and the column header indicates the specific barcode from the fastq file.

extract_protocol:
Cells (~1,000 cells/µl) were loaded into a chilled syringe pump and injected into a custom-designed microfluidics device. Flow settings were adjusted to allow individual cells to become encapsulated with single hydrogel beads presenting cell-specific barcoding oligonucleotide primers inside 3-5 nL encapsulation mixture droplets that contain 20 U µL-1 reverse transcriptase (SuperScript III, Thermo Fisher Scientific), First-Strand Buffer (Thermo Fisher Scientific), 0.6% (v/v) IGEPAL CA-630 (Sigma-Aldrich), 1 mM dNTPs (New England Biolabs), 6.67 mM DTT (Thermo Fisher Scientific), 2,700 units mL-1 RNase inhibitor (New England Biolabs), and 0.1 M Tris-HCl (pH 8.0). 2 Primers consisted of a poly-T sequence to trap mRNA molecules, two 7-to-10 base cell-specific barcodes, 5-base unique molecular identifier (UMI) sequence, and a T7 promoter sequence. Droplets were collected, the primers were photo-cleaved by exposing the emulsion to UV (365 nm 10 mW cm-2, BlackRay Xenon lamp) for 10 minutes at room temperature, and reverse transcription of trapped mRNA was performed at 50 ºC for 2 hours. Droplets were then demulsified by adding 1H,1H,2H,2H-perfluoro-1-octanol (Sigma Aldrich) dissolved in HFE-7500 (Novec) at 20% (v/v).
Single-stranded DNA primers and primer dimers were digested using 1 unitµL-1 ExoI (New England Biolabs) and 1 U µL-1 HinFI (Thermo Fisher Scientific). mRNA:cDNA hybrids were purified using Agencout AMPure XP beads (Beckman Coulter Genomics) according to the manufacturer’s instructions. Second-strand cDNA synthesis was performed using NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (New England Biolabs) and amplified by in vitro transcription (HiScribe, New England Biolabs). RNA products were fragmented using Ambion RNA Fragmentation Reagents (AM8740, Thermo Fischer Scientific), purified using Agencout AMPure XP beads, and reverse-transcribed using random hexamer primers (SuperScript III, Thermo Fisher Scientific). Single-stranded DNA fragments were linearly amplified via 14 PCR cycles (HiFi HotStart ReadyMix, Kapa Biosystems).


title: MEF2C-KO, AD ReN, differentiation 1, clone H11

description: Library name: H11_KO_AD

value: AD ReN


title: WT-4D-3

description: Library name: WT_3_4D_S26

value: wild-type


title: WT, non-treated, differentiation 1, clone H2 (ATAC-seq)

description: Library name: H2_WT


title: WT, non-treated, differentiation 1, clone F2 (ATAC-seq)

description: Library name: F2_WT


title: alpha-KO-4D-2

description: Library name: C6_2_4D_S44


title: WT-0D-3

description: Library name: WT_3_0D_S30


title: full-KO-4D-3

description: Library name: C20_3_4D_S48


title: alpha-KO-0D-2

description: Library name: C6_2_0D_S32


title: 14_pllp1245_LP4_FigureS7RNAseq

city: Chapel Hill

first: Jieun

last: Park

state: North Carolina

address: 116 Manning Drive, CB 7250, Unive7008B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

description: Library name: pd1245_LP_Rep4_FigureS7

data_processing:
1. Read quality was assessed with FastQC v0.12.1. 2. Reads were quality-filtered with fastp v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, minimum Phred quality 15, minimum length 50 bp. 3. Filtered reads were aligned to the reference genome with STAR v2.7.11 (non-canonical splice-junction removal; unmapped reads output), then coordinate-sorted with samtools v1.22.1. 4. PCR/optical duplicates were removed by UMI-based deduplication with UMIcollapse v1.1.0 (14 bp UMI carried in the read name). 5. Alignment QC, strand specificity, and read distribution were assessed with RSeQC v5.0.4 and Qualimap v2.3, aggregated with MultiQC v1.32. 6. Gene-level counts were generated with featureCounts (subread v2.1.1): strand-specific counting, fractional assignment of multi-mapping reads, features = exon and three-prime UTR, grouped by gene_id. Counts were annotated with gene biotype/metadata from the reference GTF, and per-sample CPM values were computed. → TLHYNJ-expression-matrix.tsv 7. Downstream analysis (R 4.5.0): fractional counts were rounded to integers and low-count genes removed (kept genes with count ≥10 in ≥3 samples; 32,612 → 16,803 genes). DESeq2 v1.48.1 was used with design ~ genotype + diet + genotype:diet; a variance-stabilizing transformation (VST, blind=FALSE) produced the matrix used for heatmaps and PCA. → vst_transformed_counts.csv 8. Differential expression (DESeq2, Wald test) tested pd1245 vs EK within each diet (HP, LP); DEGs defined as padj < 0.05 and |log2FC| > 1.
Assembly: GRCz11/danRer11
Supplementary files format and content: TLHYNJ-expression-matrix.tsv — tab-delimited. Rows = 32,612 genes; columns = gene_id (Ensembl), gene_name, gene_biotype, and per-sample raw counts (*_count) and CPM (*_cpm) for all 14 samples. Counts are fractional owing to fractional multi-mapping assignment. Primary gene-level quantification.
Supplementary files format and content: vst_transformed_counts.csv — comma-delimited. Rows = 16,803 expressed genes (after low-count filtering); columns = gene_id, gene_name, and VST-transformed expression values for all 14 samples. Used for heatmaps and PCA.

organism: Danio rerio

source_name: 20 dpf whole larvae

extract_protocol:
Total RNA was extracted by adding 300 µL of TRIzol reagent and allowing the homogenate to thaw. Following the addition of 60 µL of chloroform and vigorous vortexing, the phases were separated using Phase Lock Gel Heavy tubes (QuantaBio) centrifuged at 12,000 rcf for 15 minutes at 4°C. The aqueous phase was recovered and further purified using the RNeasy MinElute Cleanup protocol (Qiagen). Briefly, the sample was mixed with 70% ethanol and transferred to an RNeasy MinElute spin column. The membrane was washed with Buffer RPE and 80% ethanol, followed by a 5-minute centrifugal drying step with open lids to eliminate residual ethanol. RNA was eluted in 14 µL of RNase-free water.
Stranded RNA-seq libraries with unique molecular identifiers (UMIs) were prepared and sequenced on an Illumina platform to generate single-end 94 bp reads. Library preparation and sequencing were performed by Plasmidsaurus.

value: 20 dpf whole larvae

value: pllp pd1245

value: Low Protein (LP)


title: 13_pllp1245_LP3_FigureS7RNAseq

description: Library name: pd1245_LP_Rep3_FigureS7


title: WT-2D-2

description: Library name: WT_2_2D_S36


title: 12_pllp1245_LP2_FigureS7RNAseq

description: Library name: pd1245_LP_Rep2_FigureS7


title: WT-0D-2

description: Library name: WT_2_0D_S29


title: MEF2C-KO, non-treated, differentiation 1, clone H11 (ATAC-seq)

description: Library name: H11_KO


title: 11_pllp1245_LP1_FigureS7RNAseq

description: Library name: pd1245_LP_Rep1_FigureS7


title: MEF2C-KO, non-treated, differentiation 1, clone G2 (ATAC-seq)

description: Library name: G2_KO


title: 10_EK_LP4_FigureS7RNAseq

description: Library name: EK_LP_Rep4_FigureS7

value: EK


title: WT-4D-1

description: Library name: WT_1_4D_S24


title: WT-4D-2

description: Library name: WT_2_4D_S25


title: 7_EK_LP1_FigureS7RNAseq

description: Library name: EK_LP_Rep1_FigureS7


title: 9_EK_LP3_FigureS7RNAseq

description: Library name: EK_LP_Rep3_FigureS7


title: MEF2C-KO, non-treated, differentiation 1, clone D8 (ATAC-seq)

description: Library name: D8_KO


title: 6_pllp1245_HP3_FigureS7RNAseq

description: Library name: pd1245_HP_Rep3_FigureS7

value: High Protein (HP)


title: AC61_T4

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

description:
Library name: Sample 75
Column name in raw counts file: AC61_T4

data_processing:
The quality of the sequencing was first assessed using the fastQC tool (v0.11.9). Raw reads were quality trimmed and filtered by a length of 20 bases using trimmomatic (v0.39). Trimmed reads were mapped to the human Grch38 reference genome using a splice aware aligner HiSat2 (v2.2.1), resulting BAM files were processed using samtools (v.1.3), and gene expression was quantified with featureCounts (subread v2.0.1, featureCounts v1.5.0-p3) as raw counts
Assembly: Grch38 reference genome
Supplementary files format and content: The excel file named "MONOCYTE RNA SEQ healthy.xlsx" includes counts for each sample

source_name: Blood (monocytes)

extract_protocol:
Total RNA for transcriptome analysis was extracted from isolated monocytes using TRIzol® (Gibco BRL Life Technologies, Rockville, MD). RNA was purified using Qiagen-RNeasy Mini Kit. RNA pellets were resuspended in diethyl pyrocarbonate-treated water. RNA integrity was assessed (prior to beginning target processing) using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). We analyzed samples with RNA Integrity Number (RIN) between 6.7 and 10 (average 9.59).
The libraries were constructed using the Illumina stranded mRNA sample preparation kit. The construction begins mRNA enrichment using oligodT beads and fragmentation of the RNA. First strand synthesis uses random primers and reverse transcriptase. Second strand synthesis is completed with a marking mix that allows retention of the strandedness. The cDNA end repaired and adenylated before ligation of the Illumina barcoded adapters. Adapter ligated libraries are PCR amplified and then quantified by Kapa qPCR and multiplexed.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from EDTA-treated blood using OptiPrep® Density Gradient Medium (SIGMA). Monocytes were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Monocyte Isolation Kit II Human and the autoMACS® Pro Separator). The Monocyte Isolation Kit was developed to isolate monocytes from human PBMCs with minimum perturbation. Non-monocytes, i.e., T cells, NK cells, B cells, dendritic cells and basophils, are indirectly magnetically labeled using a cocktail of biotin-conjugated antibodies against CD3, CD7, CD16, CD19, CD56, CD123 and Glycophorin A, and Anti-Biotin MicroBeads. Our monocyte isolation procedure consistently yielded high-purity monocytes, with an average purity of 90.8% (ranging from 79% to 97%), as shown by flow cytometry (stained with CD14-FITC).

value: Blood (monocytes)

tag: time

value: male


title: AC61_T2

description:
Library name: Sample 73
Column name in raw counts file: AC61_T2


title: WT-2D-3

description: Library name: WT_3_2D_S37

value: mESC


title: 5_pllp1245_HP2_FigureS7RNAseq

description: Library name: pd1245_HP_Rep2_FigureS7


title: WT-2D-1

description: Library name: WT_1_2D_S35


title: 4_pllp1245_HP1_FigureS7RNAseq

description: Library name: pd1245_HP_Rep1_FigureS7


title: Casp3flox_MPTP_ female_rep3

type: RNA

city: Seville

first: Miguel

last: Burguillos

address: Antonio Maura Montaner

country: Spain

institute: IBiS-CSIC

description:
C3WT_MPTP_Female_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with MPTP for 96h

hyb_protocol: Hybridazation (GeneChip Hybridization Oven 654,Thermo Fisher Scientific, Inc.) and, washing and staining (GeneChip Fluidics Station 450, Thermo Fisher Scientific, Inc.), were performed following protocols outlined in the user manual for cartridge arrays

scan_protocol: Scanning with a GeneChip® Scanner 3000 7G system (Thermo Fisher Scientific, Inc.) was performed following protocols outlined in the user manual for cartridge arrays.

data_processing:
CEL files were analyzed using Transcriptome Analysis Console (TAC) version 4.0 (Thermo Fisher Scientific, Inc.) for normalization and differential gene expression analysis. Gene Set Enrichment Analysis (GSEA) was also performed for pathway-level interpretation of the data.
#%array_type=Clariom_S_Mouse
#%annotation=Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv

label: biotin

source_name: Adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with MPTP for 96h

label_protocol: Total RNA was amplified and labeled using the GeneChip® PICOReagent Kit (Thermo Fisher Scientific, Inc.)

growth_protocol: 24 samples were collected from experimental groups. Casp3flox Saline Male (3); Casp3flox Saline Female (3); Casp3floxCx3cr1 Male Saline (3); Casp3floxCx3cr1 Female Saline (3); Casp3flox MPTP Male (3); Casp3flox MPTP Female (3); Casp3floxCx3cr1 Male MPTP (3); Casp3floxCx3cr1 Female MPTP (3).

extract_protocol: Microglia were isolated from the substantia nigra using CD11b MicroBeads (Miltenyi Biotec) following the manufacturer’s protocol, with a slight modification: all steps were performed at 4 °C to preserve RNA integrity. Total RNA was then extracted using TRI Reagent® reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Nineteen days after the final tamoxifen injection, mice were treated with either MPTP (16 mg/kg, intraperitoneally, 4 injections at 2-hour intervals) or saline (same injection schedule) over a 96-hour period. After treatment, animals were euthanized by intracardial perfusion with ice-cold saline. The substantia nigra was dissected, and myelin was removed using a Percoll gradient prior to downstream processing.

tag: gender

value: Female

value: MPTP 96h


title: 8_EK_LP2_FigureS7RNAseq

description: Library name: EK_LP_Rep2_FigureS7


title: WT-0D-1

description: Library name: WT_1_0D_S28


title: Casp3flox_MPTP_ female_rep2

description:
C3WT_MPTP_Female_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with MPTP for 96h


title: 1_EK_HP1_FigureS7RNAseq

description: Library name: EK_HP_Rep1_FigureS7


title: IRF9, 1 hour, rep 3

city: University Park

first: Grace

last: Schmidt

state: PA

address: 323 AVBS Bldg

institute: Penn State University

description: Library name: Sample G3

data_processing:
). Read quality was assessed with FastQC (v0.12.1), and adaptor trimming was performed using Trim Galore (v0.6.10). Reads were aligned to the bGalGal1.mat.broiler.GRCg7b reference genome using STAR (v2.7.11b). Gene-level counts were extracted with HTSeq (v2.0.5) and analyzed in R using edgeR (v3.40.2). Counts were normalized using the TMM method, and low-expression genes were filtered by CPM thresholds.
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab delimited .txt files contains raw counts for each sample

organism: Gallus gallus

growth_protocol: Cells were cultured at 25* C in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic at 5% atmospheric CO2

extract_protocol:
Total RNA was extracted using the Direct-Zol RNA miniprep kit by Zymo
Directional mRNA library preparation (poly A enrichment) was done by Novogene

value: Embryonic fibroblast

value: IRF9 knockdown

value: 1 hour


title: Casp3flox_Saline_male_rep3

description:
C3WT_Saline_Male_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with Saline for 96h

source_name: Adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with Saline for 96h

value: Male

value: Saline 96h


title: Casp3flox_Saline_female_rep1

description:
C3WT_Saline_Female_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with Saline for 96h

source_name: Adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with Saline for 96h


title: Casp3flox_Saline_female_rep2

description:
C3WT_Saline_Female_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with Saline for 96h


title: Casp3flox_Saline_female_rep3

description:
C3WT_Saline_Female_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with Saline for 96h


title: Casp3flox_MPTP_male_rep3

description:
C3WT_MPTP_Male_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with MPTP for 96h

source_name: Adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with MPTP for 96h


title: 3_EK_HP3_FigureS7RNAseq

description: Library name: EK_HP_Rep3_FigureS7


title: IRF9, 0 hours, rep 3

description: Library name: Sample E3

value: 0 hours


title: Mock, 6 hours, rep 3

description: Library name: Sample D3

value: Wildtype

value: 6 hours


title: Casp3flox_Saline_male_rep2

description:
C3WT_Saline_Male_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with Saline for 96h


title: 2_EK_HP2_FigureS7RNAseq

description: Library name: EK_HP_Rep2_FigureS7

value: 20 dpf whole larvae


title: Casp3flox_MPTP_male_rep2

description:
C3WT_MPTP_Male_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with MPTP for 96h


title: Mock, 1 hour, rep 3

description: Library name: Sample C3


title: IRF9, 30 min, rep 3

description: Library name: Sample F3

value: 30 min


title: IRF9, 6 hours, rep 2

description: Library name: Sample H2


title: Casp3flox_MPTP_ female_rep1

description:
C3WT_MPTP_Female_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3flox mice treated with MPTP for 96h


title: Casp3floxCx3cr1_Saline_female_rep2

description:
C3KO_Saline_Female_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with Saline for 96h

source_name: Adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with Saline for 96h


title: Casp3flox_MPTP_male_rep1

description:
C3WT_MPTP_Male_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with MPTP for 96h


title: IRF9, 6 hours, rep 3

description: Library name: Sample H3


title: IRF9, 1 hour, rep 2

description: Library name: Sample G2


title: Casp3floxCx3cr1_MPTP_female_rep3

description:
C3KO_MPTP_Female_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with MPTP for 96h

source_name: Adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with MPTP for 96h


title: Casp3flox_Saline_male_rep1

description:
C3WT_Saline_Male_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3flox mice treated with Saline for 96h


title: Mock, 30 min rep 3

description: Library name: Sample B3


title: Casp3floxCx3cr1_MPTP_female_rep2

description:
C3KO_MPTP_Female_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with MPTP for 96h


title: Casp3floxCx3cr1_Saline_female_rep1

description:
C3KO_Saline_Female_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with Saline for 96h


title: Casp3floxCx3cr1_Saline_female_rep3

description:
C3KO_Saline_Female_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with Saline for 96h


title: Mock, 0 hours, rep 3

description: Library name: Sample A3


title: IRF9, 30 min, rep 2

description: Library name: Sample F2


title: Mock, 1 hour, rep 2

description: Library name: Sample C2


title: Mock, 30 min rep 2

description: Library name: Sample B2


title: Casp3floxCx3cr1_MPTP_female_rep1

description:
C3KO_MPTP_Female_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  female Casp3floxCx3cr1 mice treated with MPTP for 96h


title: Casp3floxCx3cr1_Saline_male_rep2

description:
C3KO_Saline_Male_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with saline for 96h

source_name: Adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with Saline for 96h


title: Casp3floxCx3cr1_MPTP_male_rep3

description:
C3KO_MPTP_Male_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with MPTP for 96h

source_name: Adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with MPTP for 96h


title: Mock, 6 hours, rep 2

description: Library name: Sample D2


title: Casp3floxCx3cr1_Saline_male_rep3

description:
C3KO_Saline_Male_rep3
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with saline for 96h


title: IRF9, 6 hours, rep 1

description: Library name: Sample H1


title: IRF9, 1 hour, rep 1

description: Library name: Sample G1


title: Primary muscle stem cells, TRF2 knockout 3 days post-injury, Rep 3

city: Philadelphia

first: Ji-Hyung

last: Lee

state: Pennsylvania

address: 3450 Hamilton Walk, Stemmler Hall

department: Department of Orthopaedic surgery

institute: University of Pennsylvania

data_processing:
Quality control, read trimming, and alignment were performed using the nf-core/rnaseq pipeline v3.9 (Ewels et al., 2020)
Trim Galore! v.0.6.7 with default parameters were used for adapters and quality trimming.
STAR v.2.6.1d with default parameters was used for read alignment
Salmon v.1.5.2 with default parameters was used for quantification.
Assembly: GRCm38_mm10
Supplementary files format and content: tab-delimited text file include raw counts of each samples
Supplementary files format and content: tab-delimited text file include scaled counts of each samples

source_name: Skeletal muscle

growth_protocol: Animals were housed and bred in a local animal facility at a 12-hour dark/12-hour light cycle.

extract_protocol:
RNA extraction and purification followed the manufacturer protocol from Direct-zol RNA MiniPrep (Zymo Research Corporation).
CORALL Total RNA-Seq Library Prep from Lexogen GmbH was used to generate RNA-seq libraries according to manufacturer's insturcitons.

treatment_protocol: 10 µl of Notexin was injected into TA muscles in samples from 3 days post-injury.

value: Skeletal muscle

value: Primary cells

value: Muscle stem cells

value: TRF2 knockout

value: 3 days-post notexin injury


title: Casp3floxCx3cr1_MPTP_male_rep1

description:
C3KO_MPTP_Male_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with MPTP for 96h


title: Casp3floxCx3cr1_Saline_male_rep1

description:
C3KO_Saline_Male_rep1
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with saline for 96h


title: Primary muscle stem cells, TRF2 knockout 3 days post-injury, Rep 4


title: Primary muscle stem cells, TRF2 knockout 3 days post-injury, Rep 2


title: Casp3floxCx3cr1_MPTP_male_rep2

description:
C3KO_MPTP_Male_rep2
Gene expression data from adult isolated microglia obtained from Sustantia nigra in  male Casp3floxCx3cr1 mice treated with MPTP for 96h


title: Primary muscle stem cells, TRF2 knockout 3 days post-injury, Rep 1


title: IRF9, 30 min, rep 1

description: Library name: Sample F1


title: Mock, 6 hours, rep 1

description: Library name: Sample D1


title: IRF9, 0 hours, rep 1

description: Library name: Sample E1


title: Primary muscle stem cells, Wild type 3 days post-injury, Rep 4


title: Mock, 1 hour, rep 1

description: Library name: Sample C1


title: Primary muscle stem cells, Wild type 3 days post-injury, Rep 3


title: Primary muscle stem cells, Wild type 3 days post-injury, Rep 2


title: Primary muscle stem cells, Wild type 3 days post-injury, Rep 1


title: Primary muscle stem cells, TRF2 knockout uninjured, Rep 4

value: Uninjured


title: Mock, 0 hours, rep 1

description: Library name: Sample A1


title: day5itapre4

city: XIAMEN

first: Peida

last: Yang

state: 福建

address: XIAMEN UNIVERSITY

country: China

institute: XIAMEN UNIVERSITY

description: Library name: Z119

data_processing:
Program:featureCounts v2.0.3; Command:"featureCounts" "-a" "GCF_017639785.1_BCM_Maur_2.0_genomic.gtf" "-o" "output.txt" "-t" "exon" "-g" "gene_id" "-p" "-B" "-C" "--largestOverlap" "--fracOverlap" "0.5"
Assembly: GCF_017639785.1(BCM_Maur_2.0)
Supplementary files format and content: txt files includes counts for each sample

organism: Mesocricetus auratus

source_name: Pre-exposure intranasal ITA prophylaxis group at 5 dpi lung tissue

extract_protocol:
lung tissue was homogenized and RNA extraction was performed using the QIAamp Viral RNA Mini Kit (Qia-gen) following the manufqcturer’s instructions. The RNA samples were then sent to Shanghai OE Biotechnology Co., Ltd. for sequencing.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufqcturer's protocols.

value: Lung


title: Primary muscle stem cells, TRF2 knockout uninjured, Rep 3


title: day5itapre3

description: Library name: Z118

value: Pre-exposure intranasal ITA prophylaxis group at 5 dpi lung tissue


title: day5itapre2

description: Library name: Z117


title: Primary muscle stem cells, Wild type uninjured, Rep 4


title: day3itapre4

description: Library name: Z115

source_name: Pre-exposure intranasal ITA prophylaxis group at 3 dpi lung tissue


title: Primary muscle stem cells, Wild type uninjured, Rep 3


title: day3itapre3

description: Library name: Z114

value: Pre-exposure intranasal ITA prophylaxis group at 3 dpi lung tissue


title: Primary muscle stem cells, Wild type uninjured, Rep 2


title: day3itapre2

description: Library name: Z113


title: alpha-KO-2D-1

description: Library name: C6_1_2D_S38

value: mESC

value: NAP1L1 alpha knock-out


title: day3itapre1

description: Library name: Z112


title: P2_T8_Post_HSCT_30days

city: Bergamo

first: Nicola

last: Bianchi

address: Piazza OMS 1

department: Department of Pathology

country: Italy

institute: ASST Papa Giovanni XXIII Hospital

description:
Library name: P2_T8
hg38

data_processing:
1. Sequencing reads were processed with the SomaMethyl pipeline (v0.3.8) implemented within the SeqOne platform (v2.1.8), yielding per-CpG methylation calls with matched methylated and unmethylated read counts on hg38
2. Per-CpG methylation percentage was computed as count_methylated / (count_methylated + count_unmethylated) × 100.
3. For downstream analysis (REMODEL framework), CpGs with coverage < 5 reads were removed and retained CpGs were aggregated into fixed 5-kb genomic bins. Bin-level beta was computed as summed methylated reads / summed total reads, only for bins with ≥ 20 reads and ≥ 3 informative CpGs. Bins observed in ≥ 60% of the patient's timepoints were retained
Assembly: hg38
Supplementary files format and content: tab-delimited text (gzipped), one file per sample, with columns chr, start, end, methylation_percent, count_methylated, count_unmethylated. Additional supplementary files provide 5-kb bin-level beta, count, coverage and informative-CpG matrices per patient.

source_name: peripheral blood plasma

growth_protocol: Peripheral blood was collected in 10-mL Streck Cell-Free DNA BCT tubes. Plasma was isolated by two-step centrifugation (2,300 rpm, 10 min, 4 °C, followed by a second high-speed 10-min spin to remove residual cellular debris) and stored at −80 °C

extract_protocol:
Cell-free DNA was extracted automatically from plasma
Genome-wide targeted methylation profiling was performed using the Avida Methyl 3400 DMR Cancer Panel and the Avida Duo Methyl Reagent Kit (Agilent Technologies), which targets 3,400 differentially methylated regions. Library preparation and target enrichment followed the manufacturer's protocol. Libraries were normalized to 4 nM, pooled, and sequenced on an Illumina NovaSeq X Plus.

value: peripheral blood plasma

tag: patient

tag: patient's sex

value: Male

tag: patient's age

tag: lymphoma subtype

value: PTCL, NOS

tag: timepoint

tag: timepoint order

tag: clinical status

tag: molecule subtype

value: cell-free DNA (cfDNA)


title: day5ctrl5

description: Library name: Z100

source_name: PBS intranasal control group at 5 dpi lung tissue

tag: treatment


title: P2_T7_Post_ASCT_Complete_Response

description:
Library name: P2_T7
hg38

tag: therapy at sampling

value: ICE


title: day5ctrl3

description: Library name: Z98

tag: tissue

value: PBS intranasal control group at 5 dpi lung tissue


title: P2_T6_Post_ASCT_Relapse

description:
Library name: P2_T6
hg38


title: day5ctrl2

description: Library name: Z97


title: P2_T5_Post_ASCT_90days

description:
Library name: P2_T5
hg38


title: day5ctrl1

description: Library name: Z96


title: P2_T4_Post_ASCT_30days

description:
Library name: P2_T4
hg38


title: day3ctrl4

description: Library name: Z95

source_name: PBS intranasal control group at 3 dpi lung tissue


title: P2_T3_Cycle_6

description:
Library name: P2_T3
hg38


title: day3ctrl3

description: Library name: Z94

value: PBS intranasal control group at 3 dpi lung tissue


title: day3ctrl2

description: Library name: Z93


title: P2_T1_Cycle_2

description:
Library name: P2_T1
hg38


title: day3ctrl1

description: Library name: Z92


title: P2_T0_Diagnosis

description:
Library name: P2_T0
hg38

value: Diagnosis


title: day5itatreat5

description: Library name: Z90

source_name: Post-infection intranasal ITA treatment group at 5 dpi lung tissue


title: P1_T7_Post_ASCT_365days

description:
Library name: P1_T7
hg38

value: ALCL ALK-


title: day5itatreat4

description: Library name: Z89

value: Post-infection intranasal ITA treatment group at 5 dpi lung tissue


title: Primary muscle stem cells, Wild type uninjured, Rep 1

value: Skeletal muscle

tag: cell line

value: Primary cells

tag: cell type

value: Muscle stem cells

tag: genotype

value: Wildtype


title: P2_T2_Cycle_5

description:
Library name: P2_T2
hg38


title: P1_T6_Post_ASCT_180days

description:
Library name: P1_T6
hg38


title: P1_T5_Post_ASCT_90days

description:
Library name: P1_T5
hg38


title: day5itatreat2

description: Library name: Z87

value: Lung


title: P1_T4_Post_ASCT_30days

description:
Library name: P1_T4
hg38


title: P1_T3_Cycle_6

description:
Library name: P1_T3
hg38

value: bv-CHP


title: P1_T2_Cycle_4

description:
Library name: P1_T2
hg38


title: day3itatreat4

description: Library name: Z85

source_name: Post-infection intranasal ITA treatment group at 3 dpi lung tissue


title: P1_T1_Cycle_2

description:
Library name: P1_T1
hg38


title: day3itatreat3

description: Library name: Z84

value: Post-infection intranasal ITA treatment group at 3 dpi lung tissue


title: P1_T0_Diagnosis

description:
Library name: P1_T0
hg38

value: peripheral blood plasma


title: SJEWS063826_C1_DYE4094

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description: Library name: SJEWS063826_C1

data_processing:
Single-cell (scRNA-seq) and single-nucleus (snRNA-seq) RNA sequencing data were generated from patient tumors, patient-derived xenografts (PDXs), and in vitro culture models (2D, 3D, and Cancer Cell Line Factory [CCLF]) representing multiple pediatric solid tumor types. Analyses were conducted using consistent methodological principles within an evolving computational framework. Although individual datasets were processed with slightly different versions of analytical tools, all followed a unified workflow for alignment, quality control, normalization, integration, and downstream analysis as described below.
Raw sequencing reads in FASTQ format were first assessed for quality using FASTQC (v0.11.5). Alignment and gene quantification were performed using Cell Ranger (v7.0.0 or v8.0.1, 10x Genomics) against the appropriate genome references. Patient samples were aligned to the human GRCh38 reference genome, whereas xenograft and mixed-origin datasets (PDX, 3D) were aligned to a dual human–mouse reference (GRCh38 + mm10 or GRCh38 + GRCm39). In all cases, intronic reads were included during counting to enhance transcript detection sensitivity. For rhabdomyosarcoma samples, the cell count parameter in Cell Ranger was fixed at 10,000 to mitigate barcode overestimation.
Comprehensive quality control (QC) filtering was applied to remove debris, damaged cells, multiplets, and nonhuman contaminants. Cells were excluded based on a combination of criteria, including the number of detected genes, total UMI counts, and the proportion of mitochondrial reads. Typical thresholds included the retention of cells with at least 100–1,000 detected genes and ≥500 UMIs, and exclusion of cells with >5–25% mitochondrial transcripts, depending on dataset type (≤10% for most scRNA-seq, ≤1% for snRNA-seq). For select samples, Outlier cells exceeding three median absolute deviations (MADs) from the median number of detected genes or UMIs were also removed.For select samples, doublets were detected and filtered using demuxafy (PMID 38622708) and Seurat-based outlier identification. In xenograft and culture samples, potential mouse contamination was addressed by removing barcodes showing predominant alignment to the mouse genome. For select tumor datasets, background ambient RNA contamination was further reduced using CellBender (v0.2.0) (PMID 37550580).
Quality-controlled gene expression matrices were processed using Seurat (v4.4.0 or v5.0; Hao et al., 2021). Data were normalized using the NormalizeData() function (log-normalization with a scale factor of 10,000) and scaled via linear regression to account for differences in sequencing depth and mitochondrial content. Highly variable genes (typically 2,000–3,000 per dataset) were identified for downstream analysis. Dimensionality reduction was performed using principal component analysis (PCA), with the top 30 principal components retained for nonlinear projection via Uniform Manifold Approximation and Projection (UMAP). Graph-based clustering was implemented using the Leiden algorithm (Traag et al., 2019) through Seurat’s FindClusters() function at resolutions between 0.1 and 0.4.
To integrate datasets across experimental models, replicates, and biological conditions, multiple batch-correction frameworks were employed, including Harmony (Korsunsky et al., 2019), Reciprocal PCA (RPCA) (Stuart et al., 2019), fastMNN (Haghverdi et al., 2018), and scVI (Lopez et al., 2018). The choice of integration method was dataset-dependent and guided by visual inspection of inter-sample mixing and Local Inverse Simpson’s Index (LISI) metrics (Korsunsky et al., 2019). All integrated datasets were subsequently clustered and analyzed uniformly.
Automated annotation was performed using SingleR (Aran et al., 2019) by comparison with the Human Cell Atlas and the Database of Immune Cell Expression (DICE). Clusters identified as immune populations or doublets were excluded prior to reintegration. For select datasets, copy-number variation (CNV) inference was carried out using inferCNV (https://github.com/broadinstitute/inferCNV/wiki), supplemented by Numbat for single-nucleus variant calling (PMID 36163550). In some analyses, cell cycle scores were computed using Seurat’s CellCycleScoring() function to quantify the proportion of S- and G2/M-phase genes. Differential gene expression analysis was performed using Seurat’s FindMarkers() function (Wilcoxon rank-sum test) with thresholds of log₂ fold change ≥ 0.25, a minimum expression frequency of 0.1, and adjusted p < 0.01.Additionally, cells were annotated using known gene expression profiles from a reference dataset (Patel et al., 2022) using scRNA-seq reference label transfer method, FindTransferAnchors(), from Seurat, enabling the classification of cells in query datasets at specified clustering resolution.
For multi-tumor cohorts (Ewing sarcoma, neuroblastoma, osteosarcoma, and rhabdomyosarcoma), analyses were executed using the Snap workflow (https://github.com/stjude-dnb-binfcore/sc-rna-seq-snap), a containerized and reproducible pipeline maintained by the St. Jude Bioinformatics Core. All dependencies were configured for R v4.4.0 and Seurat v4.4.0, ensuring full computational reproducibility (see GitHub repository for versioning reports). Each cohort was subdivided into three analytical groups: 1. Dual-genome cohort (PDX and 3D samples): aligned to GRCh38 + GRCm39 and filtered for low-quality and mouse-derived cells. 2. Human-genome cohort (patient, 2D, CCLF samples): aligned to GRCh38 and processed using identical QC parameters. 3. Integrated cohort: merged from the two above and analyzed jointly after Harmony-based integration. Cells with fewer than 500 UMIs, fewer than 300–1,000 genes (depending on tumor type), or >10% mitochondrial reads were removed prior to normalization and scaling. Highly variable features (n = 3,000) were used for PCA, followed by clustering with Leiden at resolution 0.1. Marker genes were identified per cluster, and top-ranked genes were examined for biological interpretability.
Interactive visualization and exploratory analysis were facilitated using ShinyCell (v2.1.0) (Ouyang et al., 2021). Processed datasets and interactive R Shiny applications are available through institutional repositories and project-specific GitHub resources (URLs to be provided upon publication).
Assembly: hg38
Supplementary files format and content: barcodes, matrix, features

source_name: cells

growth_protocol: Cells dissociated from O-PDX tumors were seeded onto PrimeSurface 96-well low-adhesion U-bottom plates at 25,000-50,000 cells/well (S-Bio, MS-9096UZ). Plates were centrifuged at 300xg for 3 minutes to aggregate the cells in each well. After 5-7 days, organoids had formed and were transferred to 0.5% geltrex- (Thermo, A14133-02) coated 10cm standard tissue culture plates. Cells that migrate from the organoid were considered a 2D culture and referred to as passage 0. Additional organoids were collected for downstream applications and cryopreserved in 90% FBS and 10% DMSO. After 7-10 days, 2D cells were passaged to fresh geltrex-coated 10cm dishes for 5-7 days and harvested for downstream molecular assays and cryopreserved stocks.

extract_protocol:
Extract protocol: To dissociate organoids into single-cell suspension 40U papain was added to 400uL of papain buffer(1mM L-cystein, 0.5mM EDTA in PBS -/-) and incubated at 37°C for ~5 min. The organoids were added and incubating at 37°C for ~5 min with occasional flicking until the organoid dissociated to the point of floating. 40uL of DNase was added and the dissociated cells were incubated at 37 °C for an additional 5 min. The cell suspension was filtered with a 40-μm mesh cell strainer and washed with 2mL PBS−/−. The filtered cells were slowly added to a 5 ml BSA cushion medium (4% BSA in Retinal Explant media) and spun at 500g for 10 min at 4 °C to separate the cells from the debris. The supernatant was removed and resuspend the cell pellet in 400 μl of explant culture medium. To generate single-nucleus suspensions from flash-frozen tissue frozen fragments were manually dissociated using Noyes spring scissors in 1 mL TST buffer (73 mM sodium chloride, 5 mM Tris [pH 8.0], 0.5 mM calcium chloride, 10.5 mM magnesium chloride, 0.01% bovine serum albumin, 0.03% Tween-20). Nuclear suspensions were filtered through a 40 μm strainer and diluted with an additional 1 mL TST buffer and 3 mL ST buffer (73 mM sodium chloride, 5 mM Tris [pH 8.0], 0.5 mM calcium chloride, 10.5 mM magnesium chloride) and centrifuged at 500xg at 4°C for 5 min. The nuclear pellet was resuspended in ST buffer and filtered through a 40 μm strainer to generate single-nuclear suspensions for snRNA-seq. To generate single-cell suspensions from fresh tissue, samples were rinsed with PBS -/-, minced with a scalpel, and processed using the Papain Dissociation System (Worthington). The tumors were incubated in 5 mL papain-DNase I solution at 37°C for 15-30 min, filtered through a 40 μm strainer, and centrifuged at 500 x g for 5 min. The cell pellets were then resuspended in 3.1 mL resuspension buffer (2.7 mL Earle’s buffered saline solution, 300 μL albumin-ovomucoid inhibitor, 150 μL DNase I) and layered over 5 mL albumin-ovomucoid inhibitor cushion and centrifuged at 100xg for 6 min. The pellet was resuspended in PBS and filtered through a 40 μm strainer.
Single cell RNA sequencing and library preparation was preformed using the 10X genomics 3’ gene expression kits.

value: cells

tag: disease

value: EWS

tag: batch


title: day3itatreat1

description: Library name: Z82


title: day5itatreat1

description: Library name: Z86


title: day3itatreat2

description: Library name: Z83


title: day5itatreat3

description: Library name: Z88


title: day5itaip5

description: Library name: Z80

source_name: Therapeutic ITA group with intraperitoneal injection at 5 dpi lung tissue


title: SJOS030605_C1_DYE4093

description: Library name: SJOS030605_C1

value: OST


title: day3itaip4

description: Library name: Z79

source_name: Therapeutic ITA group with intraperitoneal injection at 3 dpi lung tissue


title: SJRHB000026_C1_DYE4091

description: Library name: SJRHB000026_C1

value: RMS


title: day5itaip3

description: Library name: Z77

value: Therapeutic ITA group with intraperitoneal injection at 5 dpi lung tissue


title: day5itaip2

description: Library name: Z76


title: SJNBL030721_C5_DYE4090

description: Library name: SJNBL030721_C5

value: NBL


title: day5itaip1

description: Library name: Z75


title: SJRHB010928_C2_DYE4088

description: Library name: SJRHB010928_C2


title: day3itaip3

description: Library name: Z74

value: Therapeutic ITA group with intraperitoneal injection at 3 dpi lung tissue


title: SJEWS063826_C2_DYE4087

description: Library name: SJEWS063826_C2


title: day3itaip2

description: Library name: Z73


title: SJNBL030721_C10_DYE4086

description: Library name: SJNBL030721_C10


title: SJNBL031239_C3_DYE4085

description: Library name: SJNBL031239_C3


title: day3itaip1

description: Library name: Z72


title: High endothelial cells from mouse Peyer's patch, ATAC-seq

city: Palo Alto

first: Yuhan

last: Bi

state: CA

address: 3801 Miranda Ave

department: Pathology

institute: Stanford University

description: Library name: PP-HEV

data_processing:
Adapters were trimmed using cutadapt (ENCODE ATAC-seq pipeline).
Reads were aligned to the mm10 genome using Bowtie2 (ENCODE ATAC-seq pipeline).
PCR duplicates were removed and reads were Tn5-shift corrected.
Peaks were called using MACS2, and fold-change signal tracks were generated and converted to bigWig format.
Assembly: mm10
Supplementary files format and content: bigWig files containing ATAC-seq fold-change signal tracks, generated from deduplicated, Tn5-shift-corrected, properly-paired-filtered reads (ENCODE ATAC-seq pipeline convention: trim -> nodup -> tn5 shift -> pf -> fold change signal -> bigWig)

source_name: Peyer's patch

growth_protocol: C57BL/6, 8-12 weeks old, male

extract_protocol:
High endothelial cells (HECs) were isolated from mouse peripheral lymph nodes (PLNs) and Peyer's patches (PPs) by flow cytometric sorting using tissue-specific vascular addressin markers, essentially as described by Lee et al. PLN HECs were identified by PNAd expression using the MECA-79 antibody; PP HECs were identified by MAdCAM-1 expression using the MECA-367 antibody. Sorted cells were lysed in cold hypotonic lysis buffer to isolate nuclei for downstream tagmentation.
ATAC-seq libraries were generated according to the method of Buenrostro et al. (2013, Nat Methods 10:1213-1218). Briefly, nuclei from sorted HECs were incubated with Tn5 transposase loaded with sequencing adapters, which simultaneously fragments and tags accessible genomic DNA (tagmentation). Tagmented DNA was purified and PCR-amplified with indexed Nextera primers to generate sequencing-ready libraries, which were paired-end sequenced on an Illumina NextSeq 500 instrument.

value: Peyer's patch

value: High endothelial cells (HEC), MAdCAM-1+ (MECA-367+)

value: wild type


title: SJNBL012407_C2_DYE4084

description: Library name: SJNBL012407_C2


title: High endothelial cells from mouse peripheral lymph node, ATAC-seq

description: Library name: PLN-HEV

source_name: peripheral lymph node

value: peripheral lymph node

value: High endothelial cells (HEC), PNAd+ (MECA-79+)


title: SJRHB000026_C3_DYE4083

description: Library name: SJRHB000026_C3


title: SJOS030605_C2_DYE4082

description: Library name: SJOS030605_C2


title: Subject HC080 (HC080)

type: protein

city: Stanford

first: Paul

middle: Joseph

last: Utz

address: 269 Campus Dr

institute: Stanford University School of Medicine

description:
reason for sample removal: NA
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™

hyb_protocol: A fluorescent secondary antibody was added to a PBS solution containing conjugated beads bound to antibodies.

scan_protocol: A Luminex FlexMAP 3D instrument was used to quantify autoantibody levels in each sample by measuring fluorescence (in MFI) from each barcoded bead.

data_processing: See methods section for detailed description. MFI values for unconjugated beads were subtracted from MFI values for antigen conjugated bead IDs, with MFI averages calculated after background subtraction.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Serum/Plasma

label_protocol: Secondary antibody with a conjugated fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

extract_protocol: Blood was collected from patients and healthy controls. Blood was then processed into serum or plasma.

value: Serum/Plasma

tag: condition

value: Healthy control


title: SJRHB013758_C7_DYE2558

description: Library name: SJRHB013758_C7


title: Subject HC018 (HC018)


title: SJEWS063826_C4_DYE2557

description: Library name: SJEWS063826_C4


title: Subject HC077 (HC077)


title: SJOS030605_C4_DYE2556

description: Library name: SJOS030605_C4


title: Subject HC081 (HC081)


title: SJRHB000026_C6_DYE2555

description: Library name: SJRHB000026_C6


title: Subject HC072 (HC072)


title: SJEWS056156_C4_DYE2554

description: Library name: SJEWS056156_C4


title: SJNBL013762_C3_DYE2552

description: Library name: SJNBL013762_C3


title: Mock, 0 hours, rep 2

description: Library name: Sample A2

value: Embryonic fibroblast

value: Wildtype

tag: time

value: 0 hours


title: Subject HC074 (HC074)


title: SJNBL030721_C14_DYE2551

description: Library name: SJNBL030721_C14

value: cells


title: Subject HC070 (HC070)


title: Subject HC075 (HC075)


title: IRF9, 0 hours, rep 2

description: Library name: Sample E2

value: IRF9 knockdown


title: SJNBL031239_C5_DYE2550

description: Library name: SJNBL031239_C5


title: Subject HC073 (HC073)


title: Subject HC067 (HC067)


title: SJRHB013758_C6_DYE2549

description: Library name: SJRHB013758_C6

value: EWS


title: SJEWS030393_C3_DYE2547

description: Library name: SJEWS030393_C3

value: RMS


title: SJEWS063826_C3_DYE2548

description: Library name: SJEWS063826_C3


title: Subject HC060 (HC060)


title: Subject HC071 (HC071)


title: Subject HC056 (HC056)


title: SJNBL046148_C3_DYE2546

description: Library name: SJNBL046148_C3


title: day5itapre5

description: Library name: Z120

value: Lung

value: Pre-exposure intranasal ITA prophylaxis group at 5 dpi lung tissue


title: SJNBL012407_C3_DYE2545

description: Library name: SJNBL012407_C3

value: NBL


title: Subject HC068 (HC068)


title: SJEWS056156_C3_DYE2111

description: Library name: SJEWS056156_C3


title: Subject HC049 (HC049)


title: SJOS030605_C3_DYE2109

description: Library name: SJOS030605_C3

value: OST


title: SJRHB010928_C3_DYE1682

description: Library name: SJRHB010928_C3


title: Subject HC064 (HC064)


title: Subject HC046 (HC046)


title: hBMMSC, Mock 500uM, 0h chase

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Library name: hBMMSC, Mock 500uM 0h chase

data_processing:
For BrdU-labeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114 or FLO-PRO114M) and unlabeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M), basecalling and alignment to the hg19 human reference genome were performed using Dorado v0.6.2. Chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v4.1.1 was used to detect the nucleoside analog within individual reads. CpG methylation and hydroxymethylation were called using Dorado v0.6.2. Nanoplot v1.41.6 was used to assess and visualize read-level statistics such as the number of reads, read length N50, mean and median read length, and mean and median read quality.
Please note that the raw BAM files are basecalled but unaligned. We chose to submit unaligned BAM files to allow users to align the reads to the reference genome or assembly of their choice. Therefore, they are not aligned to a reference genome, and no genome assembly is associated with these BAM files. The "GRCh37 (hg19)" refers to the reference genome used for our downstream alignment and analysis of the processed data, but it doesn't apply to the uploaded raw BAM files.
Assembly: GRCh37 (hg19)
Supplementary files format and content: Processed data are available in bedMethyl files (.bed) and read-level calls (.tsv).
Supplementary files format and content: The uploaded BED files in the folder are the output of modkit pileup (Oxford Nanopore Technologies), and they are in the UCSC bedMethyl format, which is an extended BED format for base modification data. They retain the standard BED coordinate fields and can be visualized in genome browsers that support bedMethyl tracks, including the UCSC Genome Browser.

source_name: bone marrow

growth_protocol: HUES64 and HUES8 TKO hESCs were cultured on Geltrex (Thermo Fisher Scientific, A1413302) coated tissue culture plates with mTeSR (STEMCELL Technologies) media. Cells were incubated at 37°C with 5% CO2. Media was changed daily and cells were passaged upon reaching 80% confluency using ReleSR (STEMCELL Technologies). H9 hESCs (WiCell) were cultured on tissue culture plates coated with Cultrex Reduced Growth Factor Basement Membrane Extract (R&D Systems, 343301001) in StemFlex medium (Thermo Fisher Scientific, A3349401). Cells were maintained at 37°C with 5% CO2. Medium was changed daily or every other day, and cells were passaged at ~80% confluency using Accutase (Innovative Cell Technologies, AT104). Following passaging, 2µM Thiazovivin (Selleck Chemicals LLC, S1049) was added for 24 h only. MDA-MB-231 breast cancer cells were maintained in DMEM (Gibco) media supplemented with 10% Fetal Bovine Serum (FBS, Seradigm). Cells were incubated at 37°C with 5% CO2. Media was changed every other day and cells were passaged upon reaching 80% confluency using  TrypLE (Gibco). BJ human fibroblasts were expanded in Fibroblast Growth Medium (FGM-2, Lonza Bioscience). Cells were maintained at 37°C with 5% CO₂. Medium was changed every other day, and cells were passaged upon reaching approximately 80% confluency using TrypLE (Gibco). THP-1 cells were maintained in suspension in RPMI 1640 medium (Gibco, A10491-01) supplemented with 10% FBS and 0.1% β-mercaptoethanol. Cells were incubated at 37°C with 5% CO₂ and subcultured by dilution as needed to maintain an appropriate cell density. Human bone marrow-derived mesenchymal stem cells (hBMMSCs, PCS-500-012) were obtained from ATCC and cultured in ATCC Mesenchymal Stem Cell Basal Medium (ATCC, PCS-500-030) plus Mesenchymal Stem Cell Growth Kit (ATCC, PCS-500-041). Cells were maintained at 37°C with 5% CO₂. Medium was changed every other day, and cells were passaged upon reaching approximately 80% confluency using 0.05% Trypsin-EDTA (Gibco). Dicer1-positive mouse bone marrow-derived mesenchymal stem cells (mBMMSC mBMMSCs, CRL-3220) were obtained from ATCC and cultured in α-Minimum Essential Medium supplemented with 10% FBS. Cells were maintained at 37°C with 5% CO₂. Medium was changed every other day, and cells were passaged upon reaching approximately 80% confluency using 0.05% Trypsin-EDTA (Gibco).

extract_protocol:
Genomic DNA was isolated using the Puregene Cell Kit (Qiagen, 158043) according to the manufacturer’s instructions.
For samples labeled with 500 µM BrdU and samples not labeled with BrdU, libraries were prepared using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK114) according to the manufacturer’s instructions. Libraries generated from labeled samples were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114 or FLO-PRO114M) and sequenced using a MinION Mk1b device or a PromethION P2 solo device (Oxford Nanopore Technologies). Libraries for samples labeled with BrdU and samples not labeled with BrdU were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M) and sequenced on a PromethION P2 solo device for 72 hours. Minimum read length was set to 1000 bp. All sequencing data was collected using MinKNOW v23.07.5.

treatment_protocol: For the nocodazole experiment, hESCs were arrested with 1 µg/ml nocodazole for 16h, stained with the Live/Dead Fixable Violet Dead Cell Stain Kit (Invitrogen, L34964), fixed in  75% ethanol, counterstained with Propidium Iodide (Invitrogen, P3566), and live G2/M cells were isolated by FACS before genomic DNA extraction. For the BrdU pulse-chase experiments, BrdU pulses are conducted by adding BrdU to the culture medium at the desired final concentration and incubating for the specified durations (10 minutes, 30 minutes, or 1 hour). Cells are then either collected immediately (0h chase) or washed three times with DPBS and incubated in fresh mTeSR medium for 16 hours (16h chase). For mock treatments, BrdU is replaced with an equivalent volume of Ultrapure H2O. Cells subjected to mock treatments undergo the same incubation times as their BrdU-treated counterparts, with samples collected at 0h or following an 8h or 16h incubation.

value: bone marrow

value: mesenchymal stem cell

value: WT

value: Mock 500 µM, 10m pulse, 0h chase


title: SJRHB000026_C5_DYE1680

description: Library name: SJRHB000026_C5


title: Subject HC062 (HC062)

value: Serum/Plasma


title: Subject HC044 (HC044)

value: Healthy control


title: hBMMSC, BrdU 500uM, 16h chase

description: Library name: hBMMSC, BrdU 500 uM 16h chase

value: 500 µM BrdU, 10m pulse, 16h chase


title: SJRHB013758_C2 Rep 1_DYE1676

description: Library name: SJRHB013758_C2 Rep 1


title: Subject HC061 (HC061)


title: hBMMSC, BrdU 500uM, 0h chase

description: Library name: hBMMSC, BrdU 500 uM 0h chase

value: 500 µM BrdU, 10m pulse, 0h chase


title: Subject HC037 (HC037)


title: day5itaip4

description: Library name: Z78

value: Therapeutic ITA group with intraperitoneal injection at 5 dpi lung tissue


title: Cell line COLO858, JUND shRNA, biological rep 1, ATAC

city: Charlottesville

first: Mohammad

last: Fallahi-Sichani

state: Virginia

address: Box 800759, Health System

department: Biomedical Engineering

institute: University of Virginia

description: Library name: COLO858_JUNDKD_rep1_ATAC

library_source: genomic single cell

data_processing:
Raw BCL files were demultiplexed using cellranger-arc mkfastq, and per-library FASTQ files were aligned and quantified against the GRCh38 reference (refdata-cellranger-arc-GRCh38-2020-A-2.0.0) using cellranger-arc count (Cell Ranger ARC v2.0.0, default parameters). For the chromatin accessibility modality, peaks identified independently in each library by cellranger-arc were merged to generate a unified peak set across samples. ATAC fragments were then re-quantified against this common peak set using Signac. Gene expression count matrices and re-quantified ATAC peak matrices were imported into R for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: H5/HDF5 file containing Cell Ranger ARC filtered feature-barcode matrix with cell-level gene expression and chromatin accessibility counts.
Supplementary files format and content: ATAC fragment files(atac_fragments.tsv.gz + .tbi) from Cell Ranger Arc, containing per barcode genomic fragment intervals

source_name: Skin

growth_protocol: COLO858 cells were grown in RPMI 1640 supplemented with 1% sodium pyruvate and 5% FBS. 100 U/mL Penicillin-Streptomycin (10,000 U/mL) and 0.5 µg/mL Plasmocin Prophylactic were also present in cell culture. COLO858 cells engineered by lentiviral transduction with vectors encoding JUND or JUNB shRNA constructs or non-targeting control were selected and thereafter maintained under 0.5 µg/mL puromycin. Cells were grown at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
Nuclei for single-nucleus multiome analysis were isolated using the 10x Genomics protocol for nuclei isolation from cell suspensions with minor modifications. COLO858 cells expressing non-targeting shRNA control (NTC; n = 2 biological replicates), JUND knockdown (JUNDKD), or JUNB knockdown (JUNBKD) were seeded in T-75 flasks. Two days post-seeding, cells were washed with 10 mL of 1× DPBS and dissociated by incubation with 1 mL of 0.25% trypsin at 37°C for 30 seconds. Cell detachment was confirmed by microscopy, and cells were neutralized with 10 mL of growth medium. Cell suspensions were transferred to 15 mL tubes and centrifuged at 200 × g for 3 minutes at 4°C. The supernatant was removed, and cells were washed once with 5 mL of cold DPBS supplemented with 0.04% BSA, followed by centrifugation at 200 × g for 3 minutes at 4°C. The pellet was resuspended in 2 mL of cold DPBS with 0.04% BSA, and cells were counted. A total of 1 million cells were transferred to 2 mL LoBind tubes and centrifuged at 200 × g for 5 minutes at 4°C. The supernatant was carefully removed without disturbing the pellet. Cells were lysed by gentle resuspension in 100 µL of cold lysis buffer (0.1% NP-40, 0.1% Tween-20, 0.01% digitonin, 1% BSA, 1 mM DTT, 1 U/mL RNase inhibitor, 10 mM NaCl, 3 mM MgCl₂, 10 mM Tris-HCl, pH 7.5) and incubated on ice for 3 minutes. Nuclei were then washed three times with 1 mL of cold wash buffer (0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/mL RNase inhibitor, 10 mM NaCl, 3 mM MgCl₂, 10 mM Tris-HCl, pH 7.5). Following washes, nuclei were resuspended in 100 µL of 1× nuclei buffer supplemented with DTT and RNase inhibitor. Nuclei quality was assessed by acridine orange/propidium iodide (AO/PI) staining and imaging using a Leica Thunder Imaging Systems with a 40× air objective.
Library preparation was performed by the University of Virginia Genome Analysis and Technology Core (RRID: SCR_018883) using the 10x Chromium Next GEM platform and Single Cell Multiome ATAC + Gene Expression reagents. Libraries were sequenced on a NextSeq 2000 platform.

treatment_protocol: To stably knock down JUND or JUNB in parental COLO858 cells, they were seeded in a 6-well plate at a density of 100,000 cells/well in antibiotic-free growth medium. Two days post-seeding, growth medium was aspirated, and cells were treated with 1 mL transduction medium consisting of serum- and antibiotic-free medium supplemented with 10 µg/mL polybrene and SMARTvector lentiviral human JUND or JUNB hCMV-TurboRFP shRNA (Horizon Discovery) at MOI of 0.3. As control, parental COLO858 cells were also similarly transduced in parallel with SMARTvector non-targeting hCMV-TurboRFP control particles 2 (Horizon Discovery). After addition of transduction medium, the plate was centrifuged at 2500 rpm for 30 minutes at 37°C and subsequently incubated in a humidified incubator at 5% CO2 and 37 °C. 48 hours post-transduction, growth medium was replaced with fresh medium supplemented with 0.5 µg/mL puromycin, to enrich for the shRNA-expressing cells. To prevent shRNA-expressing cells from being outcompeted by cells that lost shRNA expression, they were continuously maintained in growth medium supplemented with puromycin at 0.5 µg/mL.

value: Skin

value: Cutaneous melanoma

tag: library type

value: ATAC

value: JUND Knockdown

value: JUND knockdown shRNA


title: THP1, Mock 500uM, 0h chase

description: Library name: THP1, Mock 500uM 0h chase

value: monocyte-like leukemia cell


title: Subject HC057 (HC057)


title: Subject HC036 (HC036)


title: Cell line COLO858, JUND shRNA, biological rep 1, GEX

description: Library name: COLO858_JUNDKD_rep1_GEX

value: mRNA


title: Subject HC055 (HC055)


title: Subject HC031 (HC031)


title: RNA-seq CNOT11-KD replicate 2

city: Onna

first: Saori

last: Nishijima

state: Okinawa

address: 1919-1 Tahncha

department: cell signal unit

country: Japan

institute: OIST

description:
Library name: index4
HeLa cells transfected with siRNA targeting CNOT11 (rep 2)

data_processing:
Adapter sequences were removed using Cutadapt.
Reads were aligned to the human reference genome (GRCh38) using STAR.
Gene-level read counts were generated using featureCounts.
Assembly: GRCh38
Supplementary files format and content: txt file, raw counts

source_name: HeLa

growth_protocol: DMEM high glucose with 10% FBS, streptomycin, and penicillin

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) with polyA selection.

treatment_protocol: Cells were transfected with either scramble siRNA or siRNA targeting CNOT11 using standard transfection reagents.

value: HeLa

value: tumor cell


title: THP1, BrdU 500uM, 16h chase

description: Library name: THP1, BrdU 500 uM 16h chase


title: Cell line COLO858, JUNB shRNA, biological rep 1, ATAC

description: Library name: COLO858_JUNBKD_rep1_ATAC

value: JUNB Knockdown

value: JUNB knockdown shRNA


title: Subject HC053 (HC053)


title: THP1, BrdU 500uM, 0h chase

description: Library name: THP1, BrdU 500 uM 0h chase

value: WT


title: Subject HC030 (HC030)

value: Serum/Plasma


title: Subject HC052 (HC052)

value: Healthy control


title: Cell line COLO858, JUNB shRNA, biological rep 1, GEX

description: Library name: COLO858_JUNBKD_rep1_GEX


title: Subject HC029 (HC029)


title: BJ, Mock 500uM, 0h chase

description: Library name: BJ, Mock 500uM 0h chase

source_name: BJ

value: BJ

value: fibroblast

value: Mock 500 µM, 10m pulse, 0h chase


title: Cell line COLO858, nontargeting control shRNA, biological rep 2, ATAC

description: Library name: COLO858_NTC_rep2_ATAC

value: Skin

value: non-targeting control shRNA


title: Subject HC051 (HC051)


title: BJ, BrdU 500uM, 16h chase

description: Library name: BJ, BrdU 500uM 16h chase

value: 500 µM BrdU, 10m pulse, 16h chase


title: Subject HC012 (HC012)


title: Cell line COLO858, nontargeting control shRNA, biological rep 2, GEX

description: Library name: COLO858_NTC_rep2_GEX

value: Cutaneous melanoma


title: Subject HC043 (HC043)


title: BJ, BrdU 500uM, 0h chase

description: Library name: BJ, BrdU 500uM 0h chase

value: 500 µM BrdU, 10m pulse, 0h chase


title: Subject HC011 (HC011)


title: Cell line COLO858, nontargeting control shRNA, biological rep 1, ATAC

description: Library name: COLO858_NTC_rep1_ATAC

value: ATAC


title: Subject HC008 (HC008)


title: Subject HC016 (HC016)


title: Cell line COLO858, nontargeting control shRNA, biological rep 1, GEX

description: Library name: COLO858_NTC_rep1_GEX

value: mRNA


title: HMC3, Radiotherapy, Replicate 3, 24h

city: Catania

first: Giuseppe

middle: Nicolò

last: Conti

state: CT

address: Via San Sofia, 97

department: Department of Biomedical and Biotechnological Sciences

institute: University of Catania

description: Library name: Treated_HMC3_R3

data_processing:
Data generated during the sequencing were basecalled with MinKNOW.  Then, long reads were processed using the Epi2me Labs, “wf-transcriptome pipeline”. The alignment to the reference genome was performed using Minimap2, followed by transcript assembly (StringTie2), annotation (GffCompare),  and quantification (Salmon).
Differential gene expression and transcript usage were analyzed with DESeq2,  and DEXSeq, with stageR applied for multi-stage false discovery rate control.
Assembly: GRCh38
Supplementary files format and content: unfiltered_transcript_counts_with_genes.tsv

growth_protocol: HMC3 cells were cultured according to the recommendations by ATCC, where EMEM (ATCC® 30–2003TM) was used as the base medium and completed by adding 56 mL FBS (ATCC® 30–2020TM) to a 500 mL of base EMEM

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germantown, MD, USA, 74104). RNA integrity was assessed using the Agilent 2100 Bioanalyzer with the Eukaryote Total RNA Nano 6000 Assay (Agilent, Santa Clara, USA, 5067-1511), and quantification was performed using the Qubit RNA Broad Range Assay Kit (Invitrogen™, ThermoFisher, Carlsbad, CA, USA Q32851), with 500 ng of total RNA used as input for library preparation.
Full-length cDNA libraries were prepared using the Oxford Nanopore Technologies (ONT) cDNA-PCR Barcoding Kit V14 (SQK‑PCB114.24, Oxford Nanopore Technologies, Oxford, UK). The protocol included a reverse transcription step with strand-switching primers, enabling capture of full-length polyadenylated transcripts and incorporation of unique molecular identifiers (UMIs) to enhance isoform-level resolution.

treatment_protocol: Experiments were performed in triplicate biological replicates (n=3 independent cell cultures per condition). Irradiation was delivered using a 6 MV X-ray beam from an Elekta Synergy linear accelerator (Radiotherapy Department, Cannizzaro Hospital, Catania, Italy) at a dose rate of 3 Gy/min. HMC3 cells were exposed to 0 Gy (control) or 15 Gy (treated). After irradiation, cells were incubated at 37°C in a humidified atmosphere of 5% CO2 for 24 h

value: Microglia

value: acute exposure to canonical radiotherapy


title: HMC3, Radiotherapy, Replicate 2, 24h

description: Library name: Treated_HMC3_R2


title: Subject HC025 (HC025)


title: SW1463, 50nM Soto, 10 Days_2

city: Göttingen

first: Jonas

last: Buchloh

address: Robert-Koch-Straße 40

country: Germany

institute: University Medicine Göttingen

description: Library name: Soto_10d_2

data_processing:
Reads were aligned with the STAR aligner (version v2.7.11) based on the GRCh38 genome
Counts were quantified using Salmon (version v1.10.0)
Assembly: GRCh38
Supplementary files format and content: FASTQ format

source_name: Cell line

extract_protocol:
RNA isolation was conducted with Rneasy Mini Kit (Qiagen, #74106).
RNA sequencing library was prepared with PE150.

value: Sotorasib


title: Experiment 1_LV_T_14

city: Leiden

first: Sen

last: Zhang

address: Albinusdreef 2, Einthoven Laboratory, D4-29

country: Netherlands

institute: Leiden Univesity Medical Center

description:
Library name: LV_T_14
column L

data_processing:
The raw data end reads were trimmed and quality controlled by FASTQ with default parameters (https://github.com/OpenGene/fastp), and the clean reads were separately aligned to the reference genome (GRCm38) with orientation mode (5′ to 3′ orientation) using the HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml). The overall consistency of Q20% and GC% across all samples indicates a stable, consistent sequencing run. Q20 values ranged from 96.21–98.40% and GC content ranged from 46.18–48.39% across all samples, indicating consistent sequencing quality. The mapped reads of each sample were assembled by StringTie in a reference-based approach (https://ccb.jhu.edu/software/stringtie/). To identify differentially expressed genes (DEGs) between the vehicle and SXB groups, the expression levels of each gene were calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundance. Analysis of DEGs was performed using DESeq2, and the resulting P-values were adjusted for multiple comparisons using the Benjamini–Hochberg FDR method. DEGs are defined as fold changes > 2 and adjusted P-values (padj) P < 0.05. Volcano plots were generated using the EnhancedVolcano feature (https://github.com/kevinblighe/EnhancedVolcano). KEGG pathway enrichment analysis was carried out by KOBAS (http://kobas.cbi.pku.edu.cn/home.do). GSEA was conducted to identify gene sets that share common biological function and significantly enriched gene sets were annotated based on the Molecular Signatures Database.
Assembly: clean reads were separately aligned to the reference genome (GRCm38) with orientation mode (5′ to 3′ orientation) using the HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml)
Supplementary files format and content: Liver RNA-seq_processed data_P.xlsx
Supplementary files format and content: Liver RNA-seq_processed data_T.xlsx

source_name: Liver

extract_protocol:
TRIzol RNA isolation reagent
The Illumina HiSeq 2500 platform was used to construct RNA libraries and generate reads of 2 × 150 bp long paired ends (Illumina, San Diego, CA, USA).

value: Liver


title: Subject HC007 (HC007)


title: Subject HC006 (HC006)


title: LCA1.DMSO.PD.3f

first: Matthew

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

institute: NIH

description:
Library name: LCA1.DMSO.PD.3f
transcriptome of DMSO treated LCA retinal organoid

data_processing:
Illumina bulk RNAseq reads were quality checked and aligned to Ensembl reference transcriptomes of Homo sapiens (version 115) for control and treated samples of patient derived retinal organoids (CEP290-LCA). Analysis pipeline has been described previously (Song, et al. 2025). Briefly, transcriptome alignments were performed with Kallisto and processed with the R package tximport, before differential expression analysis with edgeR and limma.
Differentially expressed genes (DEG) were identified by setting a p-value filter of 0.05 and selecting the top 500 over and under expressing genes with at least 1.2-fold change. DEGs were mapped to KEGG pathways using gProfiler and filtered to identify pathways that had minimum 3 DEG mappings and at least 5% of the pathway impacted by differential genes.
Assembly: GRCh38.p14/ENSv115
Supplementary files format and content: Comma-delimited text files containing transcript level counts, gene level counts, normalized gene level counts-per-million results, or diffierential expressed gene results.

source_name: Retinal organoid

growth_protocol: Human induced pluripotent stem cell (iPSC) lines were generated from fibroblasts obtained from a familial control individual and an LCA10 patient (designated LCA-1), derived from skin biopsy samples. Reprogramming was performed using a non-integrating Sendai virus system at the iPSC Core Facility of the National Heart, Lung, and Blood Institute, following established protocol. Retinal organoids were generated from human iPSC using a modified differentiation protocol as previously described (Kelley, et al. 2020). Briefly, small cell aggregates obtained from one well of a six-well plate were resuspended in mTeSRTM1 basal medium supplemented with 10 μM Y-27632 (Tocris) and transferred onto a 10cm hESC-qualified Matrigel-coated dish to initiate differentiation. From day 0 to day 3 (D0-D3), cultures were maintained in neural induction medium (NIM) (DMEM/F-12 (1:1)) (ThermoFisher Scientific), supplemented with 1x N2, 1x NEAA, and 5mM Nicotinamide. At D4, the medium was fully replaced with NIM (Regent, et al. 2022). Beginning at D10, cultures were transitioned to retinal induction medium (RIM) consisting of DMEM/F-12 supplemented with 1x B27 without Vitamin A (ThermoFisher Scientific), 1% antibiotic-antimycotic solution (ThermoFisher Scientific), 1% GlutaMAX and 1x NEAA with daily media changes until D17. At D17, adherent cells were mechanically lifted and transferred as small clusters (<5 mm2) into 90mm suspension culture dishes (SUMITOMO BAKELITE CO, Ltd). Floating aggregates were subsequently cultured in RIM supplemented with IGF1 (ThermoFisher Scientific) until D41. From D42 to D62, the medium was further supplemented with 10% fetal bovine serum, 20ng/ml IGF-1, and 1 mM taurine (Sigma). Between D63 and D91, 1 μM 9-cis retinal was added at each media change. After D91, the concentration of 9-cis retinal was adjusted to 0.5 μM and maintained until the completion of differentiation. Following the transition to suspension culture, a partial media change was carried out every 2–3 days. At each step, media were freshly supplemented with IGF-1, taurine, and 9-cis retinal under dim light.

extract_protocol:
Total RNA was isolated from homogenized retinal organoids using RNeasy Mini Kit (QIAGEN), following the manufacturer’s instructions. RNA quality was evaluated using the TapeStation system (Agilent), and only samples with high quality (RNA RIN ≥9) were used for the downstream applications.
For library preparation, 100 ng of total RNA was used to generate  strand-specific mRNA sequencing libraries using the TruSeq stranded RNA Kit (Illumina).

treatment_protocol: Details of treatment can be found in the accompanying manuscript.

value: Retinal organoid

tag: group

tag: donor

value: PEN1B (Patient)

value: DMSO


title: Subject HC065 (HC065)

value: Serum/Plasma

value: Healthy control


title: Primary muscle stem cells, TRF2 knockout uninjured, Rep 1

source_name: Skeletal muscle

value: Skeletal muscle

value: Primary cells

value: Muscle stem cells

value: TRF2 knockout

value: Uninjured


title: Subject HC005 (HC005)


title: HMC3, Radiotherapy, Replicate 1, 24h

description: Library name: Treated_HMC3_R1


title: Subject HC001 (HC001)


title: LCA1.HAL.PB.8e

description:
Library name: LCA1.HAL.PB.8e
transcriptome of HAL treated LCA retinal organoid

value: HAL


title: LCA1.HAL.PB.9e

description:
Library name: LCA1.HAL.PB.9e
transcriptome of HAL treated LCA retinal organoid


title: Subject P118 (P118-T1F)

value: Patient


title: HMC3, Control, Replicate 3, 24h

description: Library name: Control_HMC3_R3

value: control


title: HMC3, Control, Replicate 2, 24h

description: Library name: Control_HMC3_R2

value: Microglia


title: LCA1.DMSO.PD.1f

description:
Library name: LCA1.DMSO.PD.1f
transcriptome of DMSO treated LCA retinal organoid


title: Subject P161 (P161-T1F)


title: Subject P147 (P147-T1F)


title: Subject P151 (P151-T1F)


title: HMC3, Control, Replicate 1, 24h

description: Library name: Control_HMC3_R1


title: LCA1.HAL.PA.9f

description:
Library name: LCA1.HAL.PA.9f
transcriptome of HAL treated LCA retinal organoid


title: Subject HC048 (HC048)


title: Primary muscle stem cells, TRF2 knockout uninjured, Rep 2


title: Subject P160 (P160-T1F)


title: PN3head, exercised, 5 dpf, rep3

city: wuhan

first: guihua

last: wang

address: hubei

institute: Huazhong University of Science and Technology

description: Library name: PN3

data_processing:
Pathway analyses, specifically Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and Gene Ontology (GO) enrichment analyses were performed using DAVID
Assembly: GRCz11
Supplementary files format and content: To measure gene expression, HT-seq-count (intersection-strict mode) was used for mapping reads. Differentially expressed mRNAs were identified using DESeq2, applying a cut-off value of FC≥2 and adjusted P-value of ≤0.05

source_name: head

extract_protocol:
We conducted RNA-seq analysis using three biological replicates for both WT and pnkp-/- zebrafish. For each replicate, 30 fishes each replicate (5 dpf larvae) was dissected. The tail tissue was used for genotyping, and the heads of homozygote mutant were selected for RNA extraction. Total RNA of WT and pnkp-/- zebrafish heads was isolated and subsequently used for cDNA synthesis. Illumina sequencing, with library construction from Novogene (China), was used for the RNA-seq process.
The RNA-seq data were mapped to the zebrafish GRCz11 genome using the Hisat2 v2.0.4 software. To measure gene expression, HT-seq-count (intersection-strict mode) was used for mapping reads. Differentially expressed mRNAs were identified using DESeq2, applying a cut-off value of FC≥2 and adjusted P-value of ≤0.05.

value: head


title: Subject P143 (P143-T1F)


title: LCA1.DMSO.PC.2g

city: Bethesda

description:
Library name: LCA1.DMSO.PC.2g
transcriptome of DMSO treated LCA retinal organoid


title: Subject P158 (P158-T1F)


title: SJRHB010928_C1_DYE4092

description: Library name: SJRHB010928_C1_Rep2

value: cells

value: RMS


title: Subject P141 (P141-T1F)


title: LCA1.HAL.PA.9e

description:
Library name: LCA1.HAL.PA.9e
transcriptome of HAL treated LCA retinal organoid

value: Retinal organoid


title: PN2head, exercised, 5 dpf, rep3

description: Library name: PN2


title: PN1head, exercised, 5 dpf, rep3

description: Library name: PN1