title: third instar larval wing disc, control, rep 1

status: Public on Mar 10 2026

city: Chicago

first: Maria

middle: Paula

last: Zappia

state: IL

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

description:
Library name: Wing_Mef2mcherryKD_1
10x Genomics

data_processing:
After demultiplexing sequence reads were processed through IndexHopping (v1.1.0)
The alignment, filtering, barcode counting and UMI counting was done using Cell Ranger (v7.1.0) with the command count and default settings
Assembly: Dmel 6.32 (Ensembl 109)
Supplementary files format and content: Tab-separeted values files and matrix files
Supplementary files format and content: List of cell barcodes used for the analysis of the myoblasts. Includes cell type annotation as in reference atlas (DOI:10.15252/embr.201949555).
Supplementary files format and content: Processed Seurat object generated from the analysis of the myoblasts. Includes cell type annotation as in reference atlas (DOI:10.15252/embr.201949555).

organism: Drosophila melanogaster

source_name: Wing discs (pouch was removed)

growth_protocol: Flies were kept at 25 °C in vials containing standard cornmeal- agar medium.

extract_protocol:
Wing discs from wandering third instar larvae were dissected for 30-60 min. Discs were harvested in chilled HBSS + 0.1 % BSA. Tissue was dissociated for 15 min in 100-200 μl dissociation buffer (2 mg/ml collagenase A (Roche 11088793001), 0.8U/ml Dispase II (Roche 04942078001), 2 mM CaCl2 in HBSS) in an Eppendorf Thermo mixer C set at 30°C, 500 rpm. Cells were washed two times with 0.5 % BSA in PBS 1x  by centrifugating at 800 g for 5 min at 4°C, and filtered with two consecutive cell strainers: a Bel-Art Flowmi 40 μm and a mini-strainer 10 μm (43-10010-40). Cell viability and concentration was assessed by staining cells with Trypan blue and counting cells using a hemocytometer. Only samples showing cell viability over 90% were used for scRNA-seq.
Chromium Single-Cell 3’ Reagent kits v3 for experiment 1 and Chromium Next GEM Single-Cell 3’ Reagent kits v3.1 for experiment 2 were used according to the manufacturer’s protocol (10x Genomics, CG000183RevA and CG000315 Rev C, respectively). Around 10,000 cells were loaded per sample in the Chromium Controller for experiment 1 and around 20,000 cells in the Chromium X for experiment 2. The pooled barcoded cDNA was cleaned up with Dynabeads, amplified by PCR. The fragments were size selected with SPRIselect reagent during library construction. Libraries were single-indexed for experiment 1 while dual indexed for experiment 2. The qualities of both amplified cDNA and libraries were assessed using Agilent TapeStation 4200 instrument. The libraries were pooled and diluted for paired-end equencing onto HiSeq 4000, NovaSeq 6000, NovaSeq X Plus instruments (PE 150, Illumina).

value: Wing discs (pouch was removed)

tag: developmental stage

value: wandering third instar larva (25 deg C)

value: Exp 1


title: third instar larval wing disc, Mef2>Argk-RNAi, rep 2

type: SRA

country: USA

description:
Library name: Wing_Mef2ArgkKD_2
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

source_name: Wing discs

tag: tissue

value: Wing discs

tag: genotype

tag: batch

value: Exp 2


title: third instar larval wing disc, control, rep 2

description:
Library name: Wing_Mef2mcherryKD_3
10x Genomics


title: third instar larval wing disc, Mef2>Argk-RNAi, rep 1

description:
Library name: Wing_Mef2ArgkKD_1
10x Genomics


title: Worm, E73R, day10, rep 2

status: Public on Mar 02 2026

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
Library name: Worm_E73R_D10_rep2
8202_d10-3

library_source: transcriptomic

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the worm genome ce10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: ce10
Supplementary files format and content: Tab-delimited text files with raw counts per gene per sample from DESeq2.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Worms were maintained on nematode growth medium (NGM) agar plates seeded with Escherichia coli strain OP50 at 20 °C.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit (7BK0001) with xGEN Stubby adaptors (IDT, 336338420) and xGEN 10nt UDIs (IDT, 336338436).

treatment_protocol: No treatment was applied prior to RNA extraction.

tag: cell type

value: whole organism

value: H2B E73R


title: Female, Astrocyte, 3 weeks post-Fx, Input Sample 1

status: Public on Mar 19 2026

city: Palo Alto

first: Vivianne

middle: L.

last: Tawfik

address: 3174 Porter Drive

department: Anesthesiology, Perioperative & Pain Medicine

institute: Stanford University

description:
Library name: Female_3wpFx_Input_1
Column E

data_processing:
FASTQ files were passed through the nf-core RNAseq (v3.12.0) pipeline which performed quality control (FastQC), trimming (Trim Galore), alignment to genome reference (STAR; GRCm38), and transcript quantification (RSEM). Genes with ≥ 25 counts in at least 90% of samples were included for analysis.
Assembly: GENCODE GRCm38
Supplementary files format and content: comma-separated values files report raw gene counts for each sample

organism: Mus musculus

source_name: Homogenized lumbar spinal cord

extract_protocol:
RNA was isolated by Azenta Life Sciences (formerly GeneWiz) using a routine protocol.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences (formerly GeneWiz) using a standard poly-A selection protocol for mRNA species (eukaryotic).

value: Homogenized lumbar spinal cord

value: All spinal cord cell types

tag: treatment

value: Fracture


title: Worm, E73R, day10, rep 1

description:
Library name: Worm_E73R_D10_rep1
8202_d10-2


title: Worm, WT, day10, rep 3

description:
Library name: Worm_WT_D10_rep3
8148_d10-3

value: H2B WT


title: Worm, WT, day10, rep 2

description:
Library name: Worm_WT_D10_rep2
8148_d10-2


title: Worm, WT, day10, rep 1

description:
Library name: Worm_WT_D10_rep1
8148_d10-1


title: Worm, E73R, day3, rep 2

description:
Library name: Worm_E73R_D3_rep2
8202_d3-2


title: Worm, E73R, day3, rep 3

description:
Library name: Worm_E73R_D3_rep3
8202_d3-3


title: Worm, E73R, day3, rep 1

description:
Library name: Worm_E73R_D3_rep1
8202_d3-1


title: Worm, WT, day3, rep 3

description:
Library name: Worm_WT_D3_rep3
8148_d3-3


title: Worm, WT, day3, rep 1

description:
Library name: Worm_WT_D3_rep1
8148_d3-1


title: Worm, WT, day3, rep 2

description:
Library name: Worm_WT_D3_rep2
8148_d3-2


title: Worm, WT, day1, rep 1

description:
Library name: Worm_WT_D1_rep1
8148_d1-2


title: Worm, N2, day1, rep 3

description:
Library name: Worm_N2_D1_rep3
N2_d1-3

value: wild-type


title: Worm, WT, day1, rep 2

description:
Library name: Worm_WT_D1_rep2
8148_d1-3


title: IMR-90 SV40-T cells expressing H2B E76R

description: Library name: IMR90_H2B_E76R

data_processing:
Raw sequencing data were processed using Cell Ranger (v8.0.0) for demultiplexing, alignment to GRCh38 and generation of gene-barcode matrices. Further filtering and analysis were performed using Scanpy (v1.9.8).
Assembly: GRCh38
Supplementary files format and content: Scanpy ANN data objects.

organism: Homo sapiens

growth_protocol: IMR-90 SV40-T cells were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin/streptomycin at 37°C in 5% CO₂ and 5% O₂.

extract_protocol:
Single-cell suspensions were prepared and loaded onto the Chromium controller for partitioning and barcoding.
Libraries were prepared using the Chromium Single Cell 3’ v3.1 kit (10x Genomics) following the manufacturer’s protocol.

tag: cell line

value: fibroblast

value: SV40-T, H2B E76R


title: Worm, N2, day1, rep 2

description:
Library name: Worm_N2_D1_rep2
N2_d1-2


title: Worm, N2, day1, rep 1

description:
Library name: Worm_N2_D1_rep1
N2_d1-1


title: IMR-90 SV40-T cells expressing H2B E76K

description: Library name: IMR90_H2B_E76K

value: SV40-T, H2B E76K


title: IMR-90 SV40-T cells, SLAM, E76R, rep 3

description: Library name: IMR90_SV40T_SLAM_E76R_rep3

data_processing:
Reads were trimmed for low-quality bases (Q<20) using Trimmomatic and aligned to the GRCh38 reference genome. T>C conversions were quantified using the SLAM-DUNK pipeline, which includes filtering, mapping, mutation calling and quantification. Differential expression analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing normalized T>C conversion counts per transcript per sample.

source_name: IMR-90 SV40-T

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq V2 FWD Library Generation Module (Lexogen) with Lexogen UDI 12 nt Set A1 and amplified using the Library Amplification Module.

treatment_protocol: 100 µM 4sU for 6 h

value: IMR-90 SV40-T

value: Fibroblast

value: H2B E76R

value: 100 µM 4sU for 6 h


title: IMR-90 SV40-T cells, SLAM, E76R, rep 2

description: Library name: IMR90_SV40T_SLAM_E76R_rep2


title: IMR-90 SV40-T cells, SLAM, E76R, rep 1

description: Library name: IMR90_SV40T_SLAM_E76R_rep1


title: IMR-90 SV40-T cells, SLAM, E76K, rep 3

description: Library name: IMR90_SV40T_SLAM_E76K_rep3

value: H2B E76K


title: IMR-90 SV40-T cells, SLAM, E76K, rep 1

description: Library name: IMR90_SV40T_SLAM_E76K_rep1


title: IMR-90 SV40-T cells, SLAM, E76K, rep 2

description: Library name: IMR90_SV40T_SLAM_E76K_rep2


title: IMR-90 SV40-T cells, SLAM, WT, rep 3

description: Library name: IMR90_SV40T_SLAM_WT_rep3


title: IMR-90 SV40-T cells, SLAM, WT, rep 1

description: Library name: IMR90_SV40T_SLAM_WT_rep1


title: IMR-90 SV40-T cells, SLAM, WT, rep 2

description: Library name: IMR90_SV40T_SLAM_WT_rep2


title: IMR-90 SV40-T cells, SLAM, Empty, rep 3

description: Library name: IMR90_SV40T_SLAM_Empty_rep3

value: Empty


title: IMR-90 SV40-T cells, SLAM, Empty, rep 2

description: Library name: IMR90_SV40T_SLAM_Empty_rep2


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, rep 2

description: Library name: IMR90_SV40-T_ATAC_E76K_rep2

library_source: genomic

data_processing:
Sequencing reads were quality-checked with FastQC and trimmed using Trim Galore!. Clean reads were aligned to GRCh38 using Bowtie2, sorted and indexed with SAMtools and deduplicated using Picard Tools. Peaks were called with MACS2, quantified using featureCounts and analyzed for differential accessibility with DESeq2.
Assembly: hg38
Supplementary files format and content: Peak annotation files obtained from MACS2 are provided in GFF format. Normalized count matrices obtained from DESeq2 are included as tab-delimited text.

molecule: genomic DNA

extract_protocol:
A total of 1 × 10⁵ cells were washed with PBS, resuspended in ATAC-seq lysis buffer and incubated with Tagmentation master mix at 37°C for 30 min in a thermomixer at 1,000 rpm.
Libraries were prepared using the Active Motif ATAC-seq Kit (53150), indexed with i5 and i7 primers, and size-selected using AMPure XP beads (Beckman Coulter, A63881) at a 0.5–1.3× ratio.

treatment_protocol: 2 ng/ml TGFβ1 for 24 h


title: IMR-90 SV40-T cells, SLAM, Empty, rep 1

description: Library name: IMR90_SV40T_SLAM_Empty_rep1


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, TGFβ1, rep 2

description: Library name: IMR90_SV40-T_ATAC_E76K_TGFβ1_rep2

value: 2 ng/ml TGFβ1 for 24 h


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, TGFβ1, rep 2

description: Library name: IMR90_SV40-T_ATAC_Empty_TGFβ1_rep2


title: ATAC-Seq, IMR-90 SV40-T cells, WT, TGFβ1, rep 2

description: Library name: IMR90_SV40-T_ATAC_WT_TGFβ1_rep2


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, TGFβ1, rep 1

description: Library name: IMR90_SV40-T_ATAC_E76K_TGFβ1_rep1


title: ATAC-Seq, IMR-90 SV40-T cells, WT, TGFβ1, rep 1

description: Library name: IMR90_SV40-T_ATAC_WT_TGFβ1_rep1


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, rep 2

description: Library name: IMR90_SV40-T_ATAC_Empty_rep2


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, TGFβ1, rep 1

description: Library name: IMR90_SV40-T_ATAC_Empty_TGFβ1_rep1


title: ATAC-Seq, IMR-90 SV40-T cells, WT, rep 2

description: Library name: IMR90_SV40-T_ATAC_WT_rep2


title: T21, R23875

status: Public on Apr 08 2026

city: New York City

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Library name: R23875

data_processing:
Raw sequencing reads were processed using the RAPiD-nf pipeline, with alignment to the GRCh38 reference genome performed using STAR v2.7.3a.
Alignment quality was assessed with RSeQC and Picard. PCR duplicates were marked but not removed prior to quantification.
Gene-level counts were generated using featureCounts (Subread v2.0.1) with GENCODE v32 annotations.
Counts were normalized usingthe VOOM method from the limma package (v3.48.3), and log2-transformed expression matrices were created seperately for DLPFC and hippocampus.
Assembly: GRCh38 (Ensembl release 95)
Supplementary files format and content: tab-delimited text file (T21_raw_counts.txt) includes raw counts for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from frozen dorosolateral prefrontal cortex and hippocampal tissues using the AllPrep DNA/RNA Mini Kit, and only samples with RIN ≥ 9.0 were included.
RNA-seq libraries were generatred from 300 ng of high-quality total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

value: Hippocampus

tag: karyotype

tag: rin

tag: gestational age

tag: Sex

value: Male

tag: race

value: Caucasian


title: IMR-90 SV40-T cells, D68N/E76K, rep 3

description: Library name: IMR90_SV40T_D68N/E76K_rep3

data_processing:
Reads were trimmed using Trimmomatic. Alignment was performed using HISAT2 to human genome hg38. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with raw counts per gene per sample from DESeq2.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
NEBNext Ultra II DNA Library Prep Kit (E7645) with NEBNext Multiplex Oligos (E6609)

value: H2B D68N/E76K


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, rep 1

description: Library name: IMR90_SV40-T_ATAC_Empty_rep1


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, rep 1

description: Library name: IMR90_SV40-T_ATAC_E76K_rep1


title: ATAC-Seq, IMR-90 SV40-T cells, WT, rep 1

description: Library name: IMR90_SV40-T_ATAC_WT_rep1


title: IMR-90 SV40-T cells, D68N/E76K, rep 1

description: Library name: IMR90_SV40T_D68N/E76K_rep1


title: IMR-90 SV40-T cells, D68N/E76K, rep 2

description: Library name: IMR90_SV40T_D68N/E76K_rep2


title: IMR-90 SV40-T cells, E76R, rep 3

description: Library name: IMR90_SV40T_E76R_rep3


title: IMR-90 SV40-T cells, E76R, rep 2

description: Library name: IMR90_SV40T_E76R_rep2


title: IMR-90 SV40-T cells, E76R, rep 1

description: Library name: IMR90_SV40T_E76R_rep1


title: IMR-90 SV40-T cells, E76K, rep 3

description: Library name: IMR90_SV40T_E76K_rep3


title: IMR-90 SV40-T cells, E76K, rep 1

description: Library name: IMR90_SV40T_E76K_rep1


title: IMR-90 SV40-T cells, E76K, rep 2

description: Library name: IMR90_SV40T_E76K_rep2


title: IMR-90 SV40-T cells, D68N, rep 3

description: Library name: IMR90_SV40T_D68N_rep3

value: H2B D68N


title: IMR-90 SV40-T cells, D68N, rep 2

description: Library name: IMR90_SV40T_D68N_rep2


title: IMR-90 SV40-T cells, WT, rep 2

description: Library name: IMR90_SV40T_WT_rep2

value: H2B WT


title: IMR-90 SV40-T cells, WT, rep 3

description: Library name: IMR90_SV40T_WT_rep3


title: IMR-90 SV40-T cells, WT, rep 1

description: Library name: IMR90_SV40T_WT_rep1


title: IMR-90 SV40-T cells, Empty, rep 3

description: Library name: IMR90_SV40T_Empty_rep3


title: IMR-90 SV40-T cells, Empty, rep 1

description: Library name: IMR90_SV40T_Empty_rep1


title: Mouse, Liver, E76R, rep 4

description:
Library name: Mouse_Liver_E76R_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R4

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: No processed data files are included in this submission. Only raw FASTQ files are provided for each sample.

source_name: Liver

growth_protocol: Mice were housed five per cage and maintained under controlled temperature (22.5 °C) and a 12 h light/dark cycle, with food and water provided ad libitum.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit with xGEN Stubby adaptors and xGEN 10nt UDIs.

value: Liver

value: Whole tissue


title: IMR-90 SV40-T cells, Empty, rep 2

description: Library name: IMR90_SV40T_Empty_rep2

value: fibroblast


title: Mouse, Liver, E76R, rep 5

description:
Library name: Mouse_Liver_E76R_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R5


title: Mouse, Liver, E76R, rep 2

description:
Library name: Mouse_Liver_E76R_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R2


title: Mouse, Liver, E76R, rep 1

description:
Library name: Mouse_Liver_E76R_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R1


title: Mouse, Liver, E76K, rep 5

description:
Library name: Mouse_Liver_E76K_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver20_E76K


title: Mouse, Liver, E76K, rep 4

description:
Library name: Mouse_Liver_E76K_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver16_E76K


title: Mouse, Liver, E76K, rep 2

description:
Library name: Mouse_Liver_E76K_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver4_E76K


title: Mouse, Liver, D68N, rep 3

description:
Library name: Mouse_Liver_D68N_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver13_D68N


title: Mouse, Liver, D68N, rep 1

description:
Library name: Mouse_Liver_D68N_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver5_D68N


title: Mouse, Liver, D68N, rep 4

description:
Library name: Mouse_Liver_D68N_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver17_D68N


title: Mouse, Liver, D68N, rep 2

description:
Library name: Mouse_Liver_D68N_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver10_D68N


title: Mouse, Liver, WT, rep 4

description:
Library name: Mouse_Liver_WT_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver14_WT


title: Mouse, Liver, WT, rep 2

description:
Library name: Mouse_Liver_WT_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver6_WT


title: Mouse, Liver, Empty, rep 4

description:
Library name: Mouse_Liver_Empty_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver12_Empty


title: Mouse, Liver, Empty, rep 3

description:
Library name: Mouse_Liver_Empty_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver11_Empty


title: Mouse, Liver, WT, rep 1

description:
Library name: Mouse_Liver_WT_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver1_WT


title: Mouse, Liver, Empty, rep 6

description:
Library name: Mouse_Liver_Empty_rep6
Normalized_counts_file_mRNA-seq_liver.tabular
Liver19_Empty


title: Mouse, Liver, Empty, rep 2

description:
Library name: Mouse_Liver_Empty_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver9_Empty


title: Mouse, Liver, Empty, rep 1

description:
Library name: Mouse_Liver_Empty_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver2_Empty


title: Mouse, heart, E76R, rep 4

description:
Library name: Mouse_heart_E76R_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart18_E76R

source_name: Heart

value: Heart


title: Mouse, heart, E76R, rep 3

description:
Library name: Mouse_heart_E76R_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart15_E76R


title: Mouse, heart, E76R, rep 1

description:
Library name: Mouse_heart_E76R_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart4_E76R


title: Mouse, heart, E76K, rep 5

description:
Library name: Mouse_heart_E76K_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K5


title: Mouse, heart, E76K, rep 4

description:
Library name: Mouse_heart_E76K_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K4


title: HIRA_KO_FOV_33

status: Public on Apr 02 2026

type: RNA

description:
R6289_E3_Liver_exprMat_file.csv
R6289_E3_Liver_metadata_file.csv
R6289_E3_Liver_tx_file.csv
R6289_E3_Liver_fov_positions_file.csv
R6289_E3_Liver-polygons.csv
NanoString CosMx Spatial Molecular Imager

data_processing: AtoMx Spatial Informatics Platform was used to decode transcripts and segment cells from CosMx SMI raw image data.

source_name: liver

extract_protocol: Transcript were detected in situ on FFPE tissue sections using the NanoString CosMx Spatial Molecular Imager. FFPE tissue blocks were sectioned at 5 μm thickness and processed according to the manufacturer's CosMx SMI FFPE slide preparation protocol.

treatment_protocol: Virus suspension was injected at a dose of 3.33 x 1011 viral genomes per mouse in 100 µl sterile PBS retro-orbitally.

value: liver

value: AAV8 Tbg-Cre


title: Mouse, heart, E76K, rep 1

description:
Library name: Mouse_heart_E76K_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K1


title: IMR-90 SV40-T cells expressing H2B WT

description: Library name: IMR90_H2B_WT

value: SV40-T, H2B WT


title: Mouse, heart, D68N, rep 4

description:
Library name: Mouse_heart_D68N_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N4


title: HIRA_KO_FOV_34


title: Mouse, heart, E76K, rep 2

description:
Library name: Mouse_heart_E76K_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K2


title: Mouse, heart, D68N, rep 3

description:
Library name: Mouse_heart_D68N_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N3


title: Mouse, heart, D68N, rep 1

description:
Library name: Mouse_heart_D68N_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N1


title: Mouse, heart, WT, rep 5

description:
Library name: Mouse_heart_WT_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT5


title: Mouse, heart, WT, rep 4

description:
Library name: Mouse_heart_WT_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT4


title: Mouse, heart, WT, rep 3

description:
Library name: Mouse_heart_WT_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT3


title: Mouse, heart, WT, rep 2

description:
Library name: Mouse_heart_WT_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT2


title: Mouse, heart, WT, rep 1

description:
Library name: Mouse_heart_WT_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT1


title: Mouse, heart, Empty, rep 4

description:
Library name: Mouse_heart_Empty_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty4


title: Mouse, heart, Empty, rep 5

description:
Library name: Mouse_heart_Empty_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty5


title: Mouse, heart, Empty, rep 3

description:
Library name: Mouse_heart_Empty_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty3


title: Mouse, heart, Empty, rep 2

description:
Library name: Mouse_heart_Empty_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty2


title: Mouse, heart, Empty, rep 1

description:
Library name: Mouse_heart_Empty_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty1


title: Mouse, ske, E76R, rep 5

description:
Library name: Mouse_ske_E76R_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R5

source_name: Quadriceps

value: Quadriceps

value: H2B E76R


title: Mouse, ske, E76R, rep 4

description:
Library name: Mouse_ske_E76R_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R4


title: Mouse, ske, E76R, rep 3

description:
Library name: Mouse_ske_E76R_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R3


title: Mouse, ske, E76K, rep 5

description:
Library name: Mouse_ske_E76K_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske20_E76K

value: H2B E76K


title: Mouse, ske, E76R, rep 1

description:
Library name: Mouse_ske_E76R_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R1


title: Mouse, ske, E76K, rep 2

description:
Library name: Mouse_ske_E76K_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske6_E76K


title: Mouse, ske, E76K, rep 1

description:
Library name: Mouse_ske_E76K_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske3_E76K


title: Mouse, ske, E76K, rep 3

description:
Library name: Mouse_ske_E76K_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske9_E76K


title: Mouse, ske, D68N, rep 4

description:
Library name: Mouse_ske_D68N_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske17_D68N


title: Mouse, ske, D68N, rep 2

description:
Library name: Mouse_ske_D68N_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske11_D68N


title: Mouse, Liver, E76R, rep 3

description:
Library name: Mouse_Liver_E76R_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R3


title: Mouse, ske, WT, rep 5

description:
Library name: Mouse_ske_WT_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske18_WT


title: Mouse, ske, E76K, rep 4

description:
Library name: Mouse_ske_E76K_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske15_E76K


title: Mouse, ske, WT, rep 4

description:
Library name: Mouse_ske_WT_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske13_WT


title: Mouse, ske, WT, rep 2

description:
Library name: Mouse_ske_WT_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske8_WT


title: Mouse, ske, Empty, rep 6

description:
Library name: Mouse_ske_Empty_rep6
Normalized_counts_file_mRNA-seq_ske.tabular
Ske19_Empty

value: Empty


title: Mouse, ske, Empty, rep 5

description:
Library name: Mouse_ske_Empty_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske14_Empty


title: Mouse, ske, Empty, rep 4

description:
Library name: Mouse_ske_Empty_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske12_Empty


title: Mouse, ske, Empty, rep 3

description:
Library name: Mouse_ske_Empty_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske5_Empty


title: Mouse, ske, Empty, rep 2

description:
Library name: Mouse_ske_Empty_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske4_Empty


title: Mouse, ske, Empty, rep 1

description:
Library name: Mouse_ske_Empty_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske2_Empty


title: HSPCs, E76R, rep 2

description: Library name: HSPCs_E76R_rep2

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with raw counts per gene per sample by DESeq2.

source_name: HSPCs

growth_protocol: HSPCs were cultured in DMEM supplemented with 15% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin, 20 ng/ml mouse SCF, 10 ng/ml mouse IL-6 and 6 ng/ml mouse IL-3 at 37°C in 5% CO₂ and 5% O₂.

treatment_protocol: The cells were subjected to differentiation into myeloid and megakaryocyte/erythroid lineages using MethoCult GF M3434 supplemented with 20 ng/ml mouse FLT3L and 50 ng/ml mouse TPO. After 9 days, cells were collected.

value: HSPCs


title: IMR-90 SV40-T cells, D68N, rep 1

description: Library name: IMR90_SV40T_D68N_rep1


title: HSPCs, E76R, rep 1

description: Library name: HSPCs_E76R_rep1

value: MethoCult GF M3434 supplemented with 20 ng/ml mouse FLT3L and 50 ng/ml mouse TPO.


title: HSPCs, E76K, rep 2

description: Library name: HSPCs_E76K_rep2


title: HSPCs, E76K, rep 3

description: Library name: HSPCs_E76K_rep3


title: HSPCs, E76K, rep 1

description: Library name: HSPCs_E76K_rep1


title: HSPCs, D68N, rep 3

description: Library name: HSPCs_D68N_rep3


title: HSPCs, D68N, rep 2

description: Library name: HSPCs_D68N_rep2


title: HSPCs, D68N, rep 1

description: Library name: HSPCs_D68N_rep1


title: HSPCs, WT, rep 3

description: Library name: HSPCs_WT_rep3

value: WT


title: HSPCs, WT, rep 1

description: Library name: HSPCs_WT_rep1


title: HSPCs, WT, rep 2

description: Library name: HSPCs_WT_rep2


title: HSPCs, Empty, rep 3

description: Library name: HSPCs_Empty_rep3


title: HSPCs, Empty, rep 2

description: Library name: HSPCs_Empty_rep2


title: HSPCs, Empty, rep 1

description: Library name: HSPCs_Empty_rep1


title: pCEC.1

status: Public on Feb 28 2026

city: Wenzhou

first: zhengbiao

last: zhu

state: Zhejiang

address: Ouhai District

department: The Affiliated Eye Hospital of Wenzhou Medical University

country: China

institute: Wenzhou Medical University

description: Library name: pCEC.1

data_processing:
RNA-seq data processing was performed in R using the edgeR package. Raw count data were imported to construct a DGEList object and normalized using the trimmed mean of M-values (TMM) method to account for library size differences. Normalized expression values were calculated as counts per million (CPM) and used for downstream analyses.
Assembly: mm10
Supplementary files format and content: csv file

source_name: Primary Corneal Endothelial Cells

growth_protocol: Primary CECs and primary NCCs were resuspended in DMEM supplemented with 10% FBS, 1% NEAA, and 1% L-glutamine, and maintained at 37°C in a 5% CO₂ atmosphere.

extract_protocol:
Total RNA was extracted using the E.Z.N.A Total RNA kit (Omega Bio-tek)
Sequencing libraries were prepared with the NEBNext Ultra RNA Library Prep Kit (NEB), clustered using the HiSeq PE Cluster Kit v4-cBot-HS (Illumina), and sequenced on an Illumina platform to generate 150-bp paired-end reads.

treatment_protocol: NCCs were plated at 1 × 10⁴ cells/well on gelatin-coated 24-well plates. At 80% confluence, medium was switched to differentiation medium: DMEM/F12 supplemented with 5% KSR, 1% NEAA, 0.1 mM 2-mercaptoethanol, and 5 μM SB431542 (Sigma-Aldrich). Medium was refreshed every 2 days. CEC-like clusters emerged by day 4; colonies were characterized on day 12.

value: Primary Corneal Endothelial Cells


title: H520 cells,ZNF200-KD

status: Public on Feb 26 2026

city: hefei

first: xiaozheng

last: wei

address: tanghelu

institute: Anhui Medical University

description: library name: H520_shZNF200

data_processing:
Use FastQC software to perform quality assessment of sequencing data, identify and remove low-quality sequences.
Use Bowtie2 software to accurately align the quality-controlled sequences with the reference genome.Use samtools to remove mitochondrial genes.
Use the Macs3 software to perform Peak Calling on the comparison results, identifying the gene promoter regions associated with specific DNA-binding proteins.
Normalize the peak sets obtained from Peak Calling using DeepTools software.
Use IGV software to generate visual charts that intuitively display the peak position of the combination.
Assembly: hg19
Supplementary files format and content: bigWig,fastq

source_name: lung

growth_protocol: A549,H520 cells were cultured in DMEM medium (Vivocell) with 10% FBS. They were all cultured at 37 °C with 5% CO2.

extract_protocol:
After the cells are digested, add serum-containing culture medium to stop digestion, and perform cell counting. For each sample, take 1-1.5x10^6 cells and centrifuge at 110xg for 5 minutes, discard the culture medium, wash once with 1xPBS, and then resuspend. According to the kit instructions, use lectin-coated magnetic beads to capture the cells, permeabilize the cells, and then add secondary antibodies corresponding to the primary antibodies (without HRP). Use Mg2* to activate Protein A/G-Tn5 transposase to cut the target fragment, terminate the reaction with proteinase K, and add adapters for amplification at both ends before purification and sequencing. Based on the analysis of the sequencing results, decide on the subsequent experiments.
Using the Novogene library amplification kit, first prepare the components required for library amplification in a sterilized PCR tube: the components and their corresponding volumes are: 15 μl of resuspended DNA Extract Beads Pro, 25 μl of 2×CAM, 5 μl of N5XX, 5 μl of N7XX, totaling 50 μl. Then, gently pipette the mixed components to ensure they are well combined, and perform the reaction in the PCR machine according to the following program: 72°C for 3 minutes; 95°C for 3 minutes; then 98°C for 10 seconds, followed by 60°C for 5 seconds for 9 to 20 cycles; then 72°C for 1 minute, and hold at 4°C.

treatment_protocol: In H520 cells, knockdown of ZNF200 was performed and then we did ATAC-seq.

value: lung

value: Non-Small Cell Lung Cancer


title: H520 cells,DDX17-KD

description: library name: H520_shDDX17

treatment_protocol: In H520 cells, knockdown of DDX17 was performed and then we did ATAC-seq.


title: H520 cells,SHC

description: library name: H520_SHC

treatment_protocol: In H520 cells, the control group was infected with the SHC virus, and then we did ATAC-seq.

value: SHC


title: A549 cells,DDX17-KD

description: library name: A549_shDDX17

treatment_protocol: In A549 cells, knockdown of DDX17 was performed and then we did ATAC-seq.


title: A549 cells,ZNF200-KD

description: library name: A549_shZNF200

treatment_protocol: In A549 cells, knockdown of ZNF200 was performed and then we did ATAC-seq.


title: A549 cells,SHC

description: library name: A549_SHC

treatment_protocol: In A549 cells, the control group was infected with the SHC virus, and then we did ATAC-seq.


title: V13M06-404_C1

status: Public on Feb 16 2026

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

description: Library name: V13M06-404_C1

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38 (10x Genomics 2020 reference version)
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: Spatial Transcriptomics

source_name: pons

extract_protocol:
Hypothalamus was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: pons


title: V13M06-404_D1

description: Library name: V13M06-404_D1


title: V13M06-404_B1

description: Library name: V13M06-404_B1


title: V13M06-404_A1

description: Library name: V13M06-404_A1


title: V13M06-403_C1

description: Library name: V13M06-403_C1


title: V13M06-403_A1

description: Library name: V13M06-403_A1


title: V13M06-403_B1

description: Library name: V13M06-403_B1


title: HSPCs, E76R, rep 3

description: Library name: HSPCs_E76R_rep3


title: V13M06-402_D1

description: Library name: V13M06-402_D1


title: V13M06-402_C1

description: Library name: V13M06-402_C1


title: V13M06-402_B1

description: Library name: V13M06-402_B1


title: V13M06-401_D1

description: Library name: V13M06-401_D1


title: V13M06-402_A1

description: Library name: V13M06-402_A1


title: V13M06-401_C1

description: Library name: V13M06-401_C1


title: V13M06-401_B1

description: Library name: V13M06-401_B1


title: V13M06-401_A1

description: Library name: V13M06-401_A1


title: V13M06-386_D1

description: Library name: V13M06-386_D1


title: V13M06-386_C1

description: Library name: V13M06-386_C1


title: V13M06-386_A1

description: Library name: V13M06-386_A1


title: V13M06-386_B1

description: Library name: V13M06-386_B1


title: V13M06-333_D1

description: Library name: V13M06-333_D1


title: V13M06-333_C1

description: Library name: V13M06-333_C1


title: V13M06-333_B1

description: Library name: V13M06-333_B1


title: V13M06-332_C1

description: Library name: V13M06-332_C1


title: V13M06-332_B1

description: Library name: V13M06-332_B1


title: V13M06-332_D1

description: Library name: V13M06-332_D1


title: V13M06-333_A1

description: Library name: V13M06-333_A1


title: Mouse, Liver, WT, rep 5

description:
Library name: Mouse_Liver_WT_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver18_WT

value: Liver

value: Whole tissue

value: H2B WT


title: Mouse, Liver, E76K, rep 3

description:
Library name: Mouse_Liver_E76K_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver7_E76K


title: Mouse, Liver, E76K, rep 1

description:
Library name: Mouse_Liver_E76K_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver3_E76K


title: V13M06-332_A1

description: Library name: V13M06-332_A1


title: V13M06-331_D1

description: Library name: V13M06-331_D1


title: Mouse, Liver, WT, rep 3

description:
Library name: Mouse_Liver_WT_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver8_WT


title: Mouse, Liver, Empty, rep 5

description:
Library name: Mouse_Liver_Empty_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver15_Empty


title: V13M06-331_C1

description: Library name: V13M06-331_C1


title: V13M06-331_B1

description: Library name: V13M06-331_B1


title: V13M06-331_A1

description: Library name: V13M06-331_A1


title: V13F27-339_D1

description: Library name: V13F27-339_D1


title: V13F27-339_C1

description: Library name: V13F27-339_C1


title: V13F27-339_B1

description: Library name: V13F27-339_B1


title: Mouse, heart, E76R, rep 2

description:
Library name: Mouse_heart_E76R_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart6_E76R

value: Heart


title: V13B23-366_A1

description: Library name: V13B23-366_A1


title: V13M06-403_D1

description: Library name: V13M06-403_D1


title: Mouse, heart, E76R, rep 5

description:
Library name: Mouse_heart_E76R_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart22_E76R


title: V13F27-339_A1

description: Library name: V13F27-339_A1


title: V13B23-286_A1

description: Library name: V13B23-286_A1


title: V13B23-284_C1

description: Library name: V13B23-284_C1


title: V13B23-286_B1

description: Library name: V13B23-286_B1


title: V13B23-284_B1

description: Library name: V13B23-284_B1


title: 77_06_Day7

status: Public on Feb 06 2026

first: Joao

last: Barroso-Batista

address: The University of Chicago, KCBD room 9220E, 900 E 57th Street

institute: The University of Chicago

description: Library name: SPF2.77.06.Day7

data_processing:
reads were trimmed with trimmomatic to remove adapter sequence and trailing bases with a quality score less than 20
trimmed reads were mapped to the rhesus macaque genome (RheMac8) using the STAR v2.7.10ac two-pass method
read counts were generated for each gene using HTCseq v2.0 based on overlap of any part of a read with an annotated gene exon
Assembly: RheMac8
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

organism: Macaca mulatta

source_name: blood

extract_protocol:
RNA was extracted using miRNAeasy kit (Qiagen). 300 ng of RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit (Illumina) according to the manufacturer’s protocol

value: blood

value: PBMCs

value: Influenza vaccination


title: V13B23-284_A1

description: Library name: V13B23-284_A1


title: Mouse, heart, E76K, rep 3

description:
Library name: Mouse_heart_E76K_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K3

value: H2B E76K


title: V13B23-284_D1

description: Library name: V13B23-284_D1


title: 77_06_Day1

description: Library name: SPF2.77.06.Day1


title: Mouse, heart, D68N, rep 2

description:
Library name: Mouse_heart_D68N_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N2

value: H2B D68N


title: 77_06_Day0

description: Library name: SPF2.77.06.Day0


title: BMDMs, Smyd5-KO, IL4 treatment, rep2

status: Public on Jan 26 2026

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

description: Library name: Smyd5-IL4_rep2

data_processing:
ATAC-seq reads trimmed for adaptor sequence/low-quality using trim_galore. Discarding reads left with < 50bp
ATAC-seq reads were aligned to the mm10 genome by bowtie2  using the default settings
Coverage profiles represent Reads Per Kilobase Million (RPKM) values, calculated using deeptools2 bamCoverage
Peaks were called by MACS2
Assembly: mm10
Supplementary files format and content: bigwig

source_name: BMDMs

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

extract_protocol:
BMDMs were spun at 500 g for 5 min and then lysed for 10 min at 4°C with pre-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630)
ATAC-seq was carried out using the TruePrep DNA Library Prep Kit V2 (Vazyme) for Illumina following manufacturer's protocols.

value: BMDMs

value: Bone marrow-derived macrophages

value: Smyd5 knockout


title: BMDMs, Smyd5-KO, rep2

description: Library name: Smyd5_rep2

value: non-treatment


title: genomic_DNAmethylation_204316970040_R02C01

status: Public on Jan 16 2026

type: genomic

city: Boston

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

description: Genomic DNA from 204316970040_R02C01

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to manufacturer's protocol

scan_protocol: iScan system according to manufacturer's protocol

data_processing: Quantile and noob normalization, filtering to remove probes with detection p-values > 0.01 in at least one sample, sites mapping to the X and Y chromosomes, sites with annotated probe SNPs, and cross-reactive probes identified by Chen et al. (2013) and Pidsley et al. (2016).

label: Cy3 and Cy5

source_name: spina bifida

label_protocol: Standard Illumina protocol

extract_protocol: Blood and buccal: Qiagen QIAsymphony DSP DNA Midi Kit. Dural tissue: treated with EtOH to remove OCT gel, DNA extracted with Qiagen DNeasy Blood and Tissue Kit.

value: buccal swab

tag: source

value: Genomic DNA from 01-1173-C

tag: basename

value: F


title: genomic_DNAmethylation_204936250027_R06C01

description: Genomic DNA from 204936250027_R06C01

value: Genomic DNA from 01-1178-C


title: genomic_DNAmethylation_204316970116_R03C01

description: Genomic DNA from 204316970116_R03C01

value: Genomic DNA from 01-1164-C

value: M


title: genomic_DNAmethylation_204930640032_R03C01

description: Genomic DNA from 204930640032_R03C01

value: Genomic DNA from 01-1159-C


title: genomic_DNAmethylation_204316970040_R06C01

description: Genomic DNA from 204316970040_R06C01

value: Genomic DNA from 01-1160-C


title: Mouse, heart, Empty, rep 6

description:
Library name: Mouse_heart_Empty_rep6
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty6

value: Heart

value: Whole tissue

value: Empty


title: genomic_DNAmethylation_204316970165_R06C01

description: Genomic DNA from 204316970165_R06C01

value: Genomic DNA from 01-1157-C


title: genomic_DNAmethylation_204936250060_R02C01

description: Genomic DNA from 204936250060_R02C01

value: Genomic DNA from 01-1152-C


title: genomic_DNAmethylation_204316970116_R01C01

description: Genomic DNA from 204316970116_R01C01

value: Genomic DNA from 01-1155-C


title: genomic_DNAmethylation_204936250027_R01C01

description: Genomic DNA from 204936250027_R01C01

value: Genomic DNA from 01-1165-C


title: genomic_DNAmethylation_204316970030_R03C01

description: Genomic DNA from 204316970030_R03C01

value: Genomic DNA from 01-1149-C


title: genomic_DNAmethylation_204936250102_R01C01

description: Genomic DNA from 204936250102_R01C01

value: Genomic DNA from 01-1136-C


title: genomic_DNAmethylation_204936250101_R03C01

description: Genomic DNA from 204936250101_R03C01

value: buccal swab

value: Genomic DNA from 01-1139-C


title: genomic_DNAmethylation_204936250102_R05C01

description: Genomic DNA from 204936250102_R05C01

value: Genomic DNA from 01-1132-C


title: genomic_DNAmethylation_204930640032_R07C01

description: Genomic DNA from 204930640032_R07C01

value: Genomic DNA from 01-1135-C

value: F


title: genomic_DNAmethylation_204930640093_R08C01

description: Genomic DNA from 204930640093_R08C01

value: Genomic DNA from 01-1129-C

value: M


title: genomic_DNAmethylation_204930640094_R02C01

description: Genomic DNA from 204930640094_R02C01

value: Genomic DNA from 01-1130-C


title: genomic_DNAmethylation_204316970165_R03C01

description: Genomic DNA from 204316970165_R03C01

value: Genomic DNA from 01-1127-C


title: genomic_DNAmethylation_204316970040_R04C01

description: Genomic DNA from 204316970040_R04C01

value: Genomic DNA from 01-1123-C


title: genomic_DNAmethylation_204930640032_R05C01

description: Genomic DNA from 204930640032_R05C01

value: Genomic DNA from 01-1120-C


title: genomic_DNAmethylation_204316970116_R07C01

description: Genomic DNA from 204316970116_R07C01

value: Genomic DNA from 01-1119-C


title: genomic_DNAmethylation_204936250027_R02C01

description: Genomic DNA from 204936250027_R02C01

value: Genomic DNA from 01-1126-C


title: genomic_DNAmethylation_204930640094_R04C01

description: Genomic DNA from 204930640094_R04C01

value: Genomic DNA from 01-1111-C


title: Rapamycin treated high fat diet rep9

description: Library name: Rapa_rep9

data_processing:
Raw fastq files were aligned using STAR.
Aligned reads were filtered, sorted and indexed by SAMtools V1.1.0
Raw read counts were obtained by HTSeq V0.11.2
CuffLinks V2.2.160 was used to compute FPKM values
Assembly: mm10
Supplementary files format and content: FPKM matrix
Supplementary files format and content: raw count matrix

extract_protocol:
2-step perfusion, trizol RNA extraction
Genomics mRNA Library Prep Kit (Watchmaker Genomics) and Elevate Long UDI Adapters (Element Biosciences)

treatment_protocol: Three cohorts were examined: normal diet (ND) + vehicle, high fat diet (HFD, 60% calories from fat) + vehicle and high fat diet + rapamycin (42ppm). Mice were initiated on either ND + vehicle or ND + rapamycin at 4-months of age. Once mice reached 18-months of age, they were either maintained on ND + vehicle, or HFD + vehicle, HFD + rapamycin for 9-weeks. Mice were maintained until euthanized and heptocytes were isolated using 2-step perfusion protocol.

value: liver

value: hepatocyte

value: Rapamycin treated high fat diet


title: genomic_DNAmethylation_204936250101_R02C01

description: Genomic DNA from 204936250101_R02C01

value: buccal swab

value: Genomic DNA from 01-1114-C


title: genomic_DNAmethylation_204936250060_R01C01

description: Genomic DNA from 204936250060_R01C01

value: Genomic DNA from 01-1110-C


title: genomic_DNAmethylation_204936250101_R08C01

description: Genomic DNA from 204936250101_R08C01

value: Genomic DNA from 01-1101-C


title: genomic_DNAmethylation_204930640032_R06C01

description: Genomic DNA from 204930640032_R06C01

value: dural tissue

value: Genomic DNA from 01-1178-C

value: F


title: Rapamycin treated high fat diet rep8

description: Library name: Rapa_rep8


title: UNCseq1804 ROI2 ARID1A Negitive_Mutated

status: Public on Apr 22 2026

city: Chapel Hill

first: Andrew

middle: B

last: Gladden

state: NC

address: 160 N. Medical Drive

department: Department of Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

description: Library name: UNCseq1804 ROI2 ARID1A Neg

data_processing:
The .dcc files generated by the NanoString GeoMx Digital Spatial Profiler represent ROI digital counts derived from spatially resolved transcriptomic profiling.
The Hs_R_NGS_WTA_v1.0.pkc file is the probe annotation (PKC) file for the GeoMx Human RNA Whole Transcriptome Atlas (NGS-based) panel, used to map probe-level counts in .dcc files to gene targets and associated control probes during downstream processing.
Assembly: FASTQ files process into DCC files by geomxngspipline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC file format
Library strategy: Spatial Transcriptomics

source_name: Endometrium

growth_protocol: No growth protocol

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

treatment_protocol: No treatment protocol

value: Endometrium

value: ARID1A Mutated

value: total RNA


title: genomic_DNAmethylation_204316970165_R02C01

description: Genomic DNA from 204316970165_R02C01

value: Genomic DNA from 01-1165-C


title: Rapamycin treated high fat diet rep5

description: Library name: Rapa_rep5


title: UNCseq0585 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI3 ARID1A Neg


title: genomic_DNAmethylation_204930640094_R03C01

description: Genomic DNA from 204930640094_R03C01

value: Genomic DNA from 01-1164-C

value: M


title: high fat diet rep7

description: Library name: HFD_rep7

value: high fat diet


title: genomic_DNAmethylation_204316970116_R08C01

description: Genomic DNA from 204316970116_R08C01

value: Genomic DNA from 01-1160-C


title: Rapamycin treated high fat diet rep4

description: Library name: Rapa_rep4

value: liver

value: hepatocyte


title: genomic_DNAmethylation_204936250060_R08C01

description: Genomic DNA from 204936250060_R08C01

value: Genomic DNA from 01-1159-C


title: normal diet rep8

description: Library name: ND_rep8

value: normal diet


title: genomic_DNAmethylation_204930640093_R06C01

description: Genomic DNA from 204930640093_R06C01

value: Genomic DNA from 01-1157-C


title: Rapamycin treated high fat diet rep3

description: Library name: Rapa_rep3

value: Rapamycin treated high fat diet


title: high fat diet rep6

description: Library name: HFD_rep6


title: genomic_DNAmethylation_204316970116_R02C01

description: Genomic DNA from 204316970116_R02C01

value: dural tissue

value: Genomic DNA from 01-1155-C


title: normal diet rep7

description: Library name: ND_rep7


title: genomic_DNAmethylation_204316970116_R06C01

description: Genomic DNA from 204316970116_R06C01

value: Genomic DNA from 01-1152-C

value: F


title: genomic_DNAmethylation_204930640032_R02C01

description: Genomic DNA from 204930640032_R02C01

value: Genomic DNA from 01-1149-C


title: Rapamycin treated high fat diet rep2

description: Library name: Rapa_rep2


title: normal diet rep6

description: Library name: ND_rep6


title: genomic_DNAmethylation_204316970030_R01C01

description: Genomic DNA from 204316970030_R01C01

value: Genomic DNA from 01-1139-C


title: high fat diet rep5

description: Library name: HFD_rep5


title: genomic_DNAmethylation_204316970040_R08C01

description: Genomic DNA from 204316970040_R08C01

value: Genomic DNA from 01-1136-C


title: Rapamycin treated high fat diet rep1

description: Library name: Rapa_rep1


title: genomic_DNAmethylation_204316970165_R08C01

description: Genomic DNA from 204316970165_R08C01

value: Genomic DNA from 01-1135-C


title: normal diet rep5

description: Library name: ND_rep5


title: genomic_DNAmethylation_204936250101_R01C01

description: Genomic DNA from 204936250101_R01C01

value: Genomic DNA from 01-1132-C

value: M


title: high fat diet rep4

description: Library name: HFD_rep4

value: high fat diet


title: genomic_DNAmethylation_204936250102_R02C01

description: Genomic DNA from 204936250102_R02C01

value: Genomic DNA from 01-1129-C


title: genomic_DNAmethylation_204936250027_R04C01

description: Genomic DNA from 204936250027_R04C01

value: Genomic DNA from 01-1130-C


title: genomic_DNAmethylation_204930640109_R01C01

description: Genomic DNA from 204930640109_R01C01

value: Genomic DNA from 01-1128-C


title: high fat diet rep3

description: Library name: HFD_rep3

value: liver

value: hepatocyte


title: normal diet rep4

description: Library name: ND_rep4

value: normal diet


title: high fat diet rep2

description: Library name: HFD_rep2


title: genomic_DNAmethylation_204930640109_R02C01

description: Genomic DNA from 204930640109_R02C01

value: dural tissue

value: Genomic DNA from 01-1126-C


title: normal diet rep3

description: Library name: ND_rep3


title: genomic_DNAmethylation_204936250102_R06C01

description: Genomic DNA from 204936250102_R06C01

value: Genomic DNA from 01-1127-C


title: high fat diet rep1

description: Library name: HFD_rep1


title: genomic_DNAmethylation_204930640109_R03C01

description: Genomic DNA from 204930640109_R03C01

value: Genomic DNA from 01-1123-C

value: F


title: normal diet rep2

description: Library name: ND_rep2


title: genomic_DNAmethylation_204930640094_R08C01

description: Genomic DNA from 204930640094_R08C01

value: Genomic DNA from 01-1120-C


title: genomic_DNAmethylation_204930640093_R02C01

description: Genomic DNA from 204930640093_R02C01

value: Genomic DNA from 01-1119-C


title: genomic_DNAmethylation_204936250060_R07C01

description: Genomic DNA from 204936250060_R07C01

value: Genomic DNA from 01-1115-C


title: normal diet rep1

description: Library name: ND_rep1


title: genomic_DNAmethylation_204930640094_R06C01

description: Genomic DNA from 204930640094_R06C01

value: Genomic DNA from 01-1114-C


title: genomic_DNAmethylation_204316970030_R06C01

description: Genomic DNA from 204316970030_R06C01

value: Genomic DNA from 01-1111-C

value: M


title: genomic_DNAmethylation_204930640109_R04C01

description: Genomic DNA from 204930640109_R04C01

value: Genomic DNA from 01-1110-C


title: genomic_DNAmethylation_204930640093_R01C01

description: Genomic DNA from 204930640093_R01C01

value: whole blood

value: Genomic DNA from 01-1178-C


title: genomic_DNAmethylation_204316970030_R04C01

description: Genomic DNA from 204316970030_R04C01

value: Genomic DNA from 01-1173-C


title: genomic_DNAmethylation_204316970030_R05C01

description: Genomic DNA from 204316970030_R05C01

value: Genomic DNA from 01-1101-C


title: genomic_DNAmethylation_204316970030_R02C01

description: Genomic DNA from 204316970030_R02C01

value: Genomic DNA from 01-1164-C


title: genomic_DNAmethylation_204930640094_R01C01

description: Genomic DNA from 204930640094_R01C01

value: Genomic DNA from 01-1160-C


title: genomic_DNAmethylation_204930640093_R07C01

description: Genomic DNA from 204930640093_R07C01

value: Genomic DNA from 01-1159-C


title: genomic_DNAmethylation_204930640094_R07C01

description: Genomic DNA from 204930640094_R07C01

value: Genomic DNA from 01-1152-C


title: genomic_DNAmethylation_204936250101_R06C01

description: Genomic DNA from 204936250101_R06C01

value: Genomic DNA from 01-1155-C


title: genomic_DNAmethylation_204316970165_R05C01

description: Genomic DNA from 204316970165_R05C01

value: Genomic DNA from 01-1139-C

value: F


title: genomic_DNAmethylation_204936250027_R05C01

description: Genomic DNA from 204936250027_R05C01

value: Genomic DNA from 01-1149-C


title: genomic_DNAmethylation_204316970040_R07C01

description: Genomic DNA from 204316970040_R07C01

value: Genomic DNA from 01-1157-C


title: genomic_DNAmethylation_204930640032_R01C01

description: Genomic DNA from 204930640032_R01C01

value: buccal swab

value: Genomic DNA from 01-1115-C


title: genomic_DNAmethylation_204936250102_R07C01

description: Genomic DNA from 204936250102_R07C01

value: Genomic DNA from 01-1135-C


title: genomic_DNAmethylation_204936250027_R07C01

description: Genomic DNA from 204936250027_R07C01

value: Genomic DNA from 01-1132-C

value: M


title: Rapamycin treated high fat diet rep6

description: Library name: Rapa_rep6

value: liver

value: hepatocyte

value: Rapamycin treated high fat diet


title: Rapamycin treated high fat diet rep7

description: Library name: Rapa_rep7


title: genomic_DNAmethylation_204930640094_R05C01

description: Genomic DNA from 204930640094_R05C01

value: whole blood

value: Genomic DNA from 01-1130-C


title: genomic_DNAmethylation_204930640093_R05C01

description: Genomic DNA from 204930640093_R05C01

value: Genomic DNA from 01-1129-C


title: genomic_DNAmethylation_204316970040_R05C01

description: Genomic DNA from 204316970040_R05C01

value: Genomic DNA from 01-1128-C


title: genomic_DNAmethylation_204936250060_R03C01

description: Genomic DNA from 204936250060_R03C01

value: dural tissue

value: Genomic DNA from 01-1173-C


title: genomic_DNAmethylation_204316970165_R04C01

description: Genomic DNA from 204316970165_R04C01

value: Genomic DNA from 01-1127-C


title: genomic_DNAmethylation_204930640109_R07C01

description: Genomic DNA from 204930640109_R07C01

value: Genomic DNA from 01-1123-C

value: F


title: genomic_DNAmethylation_204316970116_R04C01

description: Genomic DNA from 204316970116_R04C01


title: genomic_DNAmethylation_204936250102_R04C01

description: Genomic DNA from 204936250102_R04C01

value: Genomic DNA from 01-1120-C


title: genomic_DNAmethylation_204936250027_R03C01

description: Genomic DNA from 204936250027_R03C01

value: Genomic DNA from 01-1119-C


title: genomic_DNAmethylation_204936250060_R06C01

description: Genomic DNA from 204936250060_R06C01

value: Genomic DNA from 01-1111-C


title: genomic_DNAmethylation_204936250101_R07C01

description: Genomic DNA from 204936250101_R07C01

value: Genomic DNA from 01-1126-C


title: genomic_DNAmethylation_204936250101_R05C01

description: Genomic DNA from 204936250101_R05C01

value: Genomic DNA from 01-1114-C

value: M


title: genomic_DNAmethylation_204930640109_R08C01

description: Genomic DNA from 204930640109_R08C01

value: Genomic DNA from 01-1110-C


title: genomic_DNAmethylation_204930640032_R04C01

description: Genomic DNA from 204930640032_R04C01

value: Genomic DNA from 01-1101-C


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + miR-200 (+DOX) rep 3

status: Public on Jan 12 2026

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description: Library name: Clone2_DOX_200c_1

data_processing:
The FASTQ files were analyzed and quality-checked using FastQC v0.11.9 18.
Reads were mapped against the human reference genome (build hg38) using the STAR (v2.6.1d) spliced alignment algorithm 19 with parameters --twopassMode basic and --quantMode GeneCounts and otherwise default parameters.
STAR output files containing the number of reads mapping to each gene were combined and rows for summary statistics have been removed. Additional processed data files are available as supplementary files for the associated journal article.
Assembly: hg38
Supplementary files format and content: counts of reads aligning to each gene in each sample

growth_protocol: The MDA-MB-231 (ATCC: HTB-26) immortalised human breast cancer cell line was obtained from American Type Culture Collection (ATCC, Rockville, MD) and used to generate ZEB-expressing stable cell lines. All MDA-MB-231 derived cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% fetal bovine serum (Invitrogen). Cells were sub-cultured every 2–3 days, using 0.2% Trypsin/1× PBS to dissociate cells during passaging. All cell lines tested negative for mycoplasma.

extract_protocol:
Total RNA was harvested 72 hrs post transfection using TRIzol (Invitrogen), following standard manufacturers protocol.
High quality RNA samples (in biological duplicate from parental, endogZEB and oexZEB cells + 5nM negative control or miR-200c-3p miRNA mimic (genepharma)) were DNAse treated according to manufacturers protocol (#AM1907, TURBO DNA-freeTM Kit) prior to library preparation. Total RNA was treated with RNAseH and strand-specific libraries were prepared and sequenced using a single-end 75 cycle high output kit on an Illumina NextSeq500 at the ACRF Cancer Genomics Facility.

treatment_protocol:
To generate cell lines with inducible ZEB1 and ZEB2 expression, pENTR2B-ZEB2 (HsCD00829572, Centre for Personalized Diagnostics, DNASU) was recombined with pInducer21 using LR Clonase to produce pInducer21-ZEB2-GFP 15,16. GFP is independently encoded within the same vector as ZEB2 and is driven by the same promoter though is not a fusion protein. pInducer20-ZEB1 was previously generated by PCR and restriction enzyme cloning 17. Plasmids were transformed into competent E. coli cells, purified by QIAfilter Plasmid Midi Kit (#12243, Qiagen) and sanger sequenced for insert verification. For lentivirus production, HEK293T cells were plated at 2 × 106 cells in T25 flasks. The following day, cells were transfected with pLP1, pLP2, pLP-VSVG, pTAT (1µg of each) and 4µg of either pInducer20-ZEB1 or pInducer21-ZEB2-GFP. DNA was mixed in 500µl opti-MEM (Invitrogen) and transfected in combination with 12µl Lipofectamine-2000 (Invitrogen). Transfection reagent was removed 6hrs post transfection and viral supernatant of either pInducer20-ZEB1 and pInducer21-ZEB2-GFP was collected after 72hrs. MDA-MB-231 cells were seeded at 2 × 10^5 cells in T25 flasks. The following day, cells were co-transduced with viral supernatant of pInducer20-ZEB1 and pInducer21-ZEB2-GFP (1:8 each) in the presence of polybrene (4mg/ml). Polyclonal or single cell selection was done using 1.0mg/ml of G418, followed by cell sorting for GFP expression (encoded on pInducer21-ZEB2 vector).
For cell sorting, MDA-MB-231_ZEB1/2 cells were washed twice with warm washing buffer (1× PBS + 10 mM EDTA) followed by short incubation with 3 mM EDTA in 1× PBS. Semi-detached cells were treated with TrypLE followed by dilution in 1× PBS + 10 mM EDTA. Cells were centrifuged at 350×g for 5 min, washed with 1× PBS + 10 mM EDTA and resuspended in sorting buffer (ice cold 1× PBS, 5 mM EDTA, 1% FCS and 25 mM HEPES; pH 7.0). Cells were then filtered using a 30µm Filcon sterile filter (BD Biosciences) and sorted by GFP fluorescence intensity compared to control cells (parental MDA-MB-231, no colour). Single cells separated in 96-well plates were grown in conditioned media before transferring into larger 6-well plates. Flow Cytometry sorting was performed on the MoFlo Astrios EQ High Speed Cell Sorter using Summit Software version: 6.3.1 (Beckman Coulter, Miami, FL, USA) utilising the 488 nm (150 mW) laser line and 100 micron nozzle at 30 PSI. Laser and light filter usage are displayed on plot axes. No forward scatter masks were used. Flow cytometry data was analysed using the Apple Macintosh-version of FCS express 6 (De Novo Software, Los Angeles, CA, USA). Single clones and pools were selected for strength of ZEB1 and ZEB2 induction by qPCR and western blotting, ensuring endogenous-like and supraphysiological levels of expression following miR-200c transfection.
Transfection Cells were seeded at 2 × 105 cells per well in 6-well plates and treated with or without 0.5µg/mL Doxycycline (DOX) to induce expression of ZEB1 and ZEB2. The following day, cells were transfected with 5nM miR-200c mimic (GenePharma) or 5nM negative control RNA, using optiMEM (Invitrogen) and Lipofectamine RNAiMAX (Invitrogen) as per manufacturers protocol. Media was replaced 6hrs post transfection. DOX was replenished in fresh media every 48hrs.

value: breast

value: WT with dox-inducible ZEB1 and ZEB2

value: DOX treatment

value: miR-200c transfection

tag: replicate

value: replicate 3


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + miR-200 (+DOX) rep 1

description: Library name: Clone2_DOX_200c_3

value: replicate 1


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + control miRNA (+DOX) rep 3

description: Library name: Clone2_DOX_Scr_1

value: control (scrambled; scr) miRNA transfection


title: MDA-MB-231 cells + miR-200 (+DOX) rep 3

description: Library name: Parental_DOX_200c_1

value: WT


title: MDA-MB-231 cells + miR-200 (+DOX) rep 1

description: Library name: Parental_DOX_200c_3


title: MDA-MB 231 cells + ZEB1/2 expression constructs (to over-express ZEBs) + control miRNA (+DOX) rep 1

description: Library name: Clone2_DOX_Scr_3


title: MDA-MB-231 cells + control miRNA (+DOX) rep 1

description: Library name: Parental_DOX_Scr_3


title: MDA-MB-231 cells + control miRNA rep 3

description: Library name: Parental_NO-DOX_Scr_1


title: MDA-MB-231 cells + control miRNA rep 1

description: Library name: Parental_NO-DOX_Scr_3


title: MDA-MB-231 cells + control miRNA (+DOX) rep 3

description: Library name: Parental_DOX_Scr_1


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + miR-200 (+DOX) rep 3

description: Library name: Pool_DOX_200c_1


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + control miRNA (+DOX) rep 3

description: Library name: Pool_DOX_Scr_1


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + miR-200 (+DOX) rep 1

description: Library name: Pool_DOX_200c_3


title: MDA-MB 231 cells + ZEB1/2 expression constructs (at near-endogenous levels) + control miRNA (+DOX) rep 1

description: Library name: Pool_DOX_Scr_3


title: genomic_DNAmethylation_CLG-5

status: Public on Dec 30 2025

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

description: Genomic DNA from CLG-5

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to the standard Illumina protocol

scan_protocol: HiScan2000 according to the standard Illumina settings

data_processing: minfi preprocessRaw function, betas extracted

source_name: placenta (chorionic villi)

extract_protocol: Qiagen Dneasy blood & tissue kit

value: placenta (chorionic villi)

value: Genomic DNA from CLG-5

tag: status

value: CIUE low grade

value: Female

value: NO

value: Y


title: genomic_DNAmethylation_NP-8

description: Genomic DNA from NP-8

value: Genomic DNA from NP-8

value: Non-CIUE

value: Male

value: N


title: genomic_DNAmethylation_SPLA-12_v

description: Genomic DNA from SPLA-12_v

value: Genomic DNA from SPLA-12_v


title: genomic_DNAmethylation_NP-9_v

description: Genomic DNA from NP-9_v

value: Genomic DNA from NP-9_v


title: genomic_DNAmethylation_SPLA-11_v

description: Genomic DNA from SPLA-11_v

value: Genomic DNA from SPLA-11_v


title: genomic_DNAmethylation_CLG-7_v

description: Genomic DNA from CLG-7_v

value: Genomic DNA from CLG-7_v

value: YES


title: genomic_DNAmethylation_CHG-13_v

description: Genomic DNA from CHG-13_v

value: Genomic DNA from CHG-13_v

value: CIUE high grade


title: genomic_DNAmethylation_SPLN-18_v

description: Genomic DNA from SPLN-18_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-18_v


title: genomic_DNAmethylation_CHG-18_v

description: Genomic DNA from CHG-18_v

value: Genomic DNA from CHG-18_v


title: genomic_DNAmethylation_SPLA-13_v

description: Genomic DNA from SPLA-13_v

value: Genomic DNA from SPLA-13_v

value: partial T1 due to t(1;10)


title: genomic_DNAmethylation_CHG-14_v

description: Genomic DNA from CHG-14_v

value: Genomic DNA from CHG-14_v

value: NO

value: Y


title: genomic_DNAmethylation_CLG-9_v

description: Genomic DNA from CLG-9_v

value: Genomic DNA from CLG-9_v

value: CIUE low grade

value: Male


title: genomic_DNAmethylation_SPLN-9_v

description: Genomic DNA from SPLN-9_v

value: Genomic DNA from SPLN-9_v

value: Non-CIUE

value: Female

value: N


title: genomic_DNAmethylation_CHG-4_v

description: Genomic DNA from CHG-4_v

value: Genomic DNA from CHG-4_v

value: YES


title: genomic_DNAmethylation_CHG-9_v

description: Genomic DNA from CHG-9_v

value: placenta (chorionic villi)

value: Genomic DNA from CHG-9_v

value: CIUE high grade


title: genomic_DNAmethylation_NP-2_v

description: Genomic DNA from NP-2_v

value: Genomic DNA from NP-2_v


title: genomic_DNAmethylation_CHG-1_v

description: Genomic DNA from CHG-1_v

value: Genomic DNA from CHG-1_v


title: genomic_DNAmethylation_SPLN-12_v

description: Genomic DNA from SPLN-12_v

value: Genomic DNA from SPLN-12_v


title: genomic_DNAmethylation_SPLN-7_v

description: Genomic DNA from SPLN-7_v

value: Genomic DNA from SPLN-7_v

value: NO


title: genomic_DNAmethylation_CHG-10_v

description: Genomic DNA from CHG-10_v

value: Genomic DNA from CHG-10_v


title: genomic_DNAmethylation_CLG-8_v

description: Genomic DNA from CLG-8_v

value: Genomic DNA from CLG-8_v

value: CIUE low grade

value: Y


title: genomic_DNAmethylation_CHG-19_v

description: Genomic DNA from CHG-19_v

value: Genomic DNA from CHG-19_v


title: genomic_DNAmethylation_SPLN-14_v

description: Genomic DNA from SPLN-14_v

value: Genomic DNA from SPLN-14_v

value: Non-CIUE

value: Female


title: genomic_DNAmethylation_SPLN-11_v

description: Genomic DNA from SPLN-11_v

value: Genomic DNA from SPLN-11_v

value: Male

value: N


title: genomic_DNAmethylation_CHG-6_v

description: Genomic DNA from CHG-6_v

value: placenta (chorionic villi)

value: Genomic DNA from CHG-6_v

value: CIUE high grade

value: YES


title: genomic_DNAmethylation_SPLA-10_v

description: Genomic DNA from SPLA-10_v

value: Genomic DNA from SPLA-10_v


title: genomic_DNAmethylation_SPLN-15_v

description: Genomic DNA from SPLN-15_v

value: Genomic DNA from SPLN-15_v

value: NO


title: genomic_DNAmethylation_NP-12_v

description: Genomic DNA from NP-12_v

value: Genomic DNA from NP-12_v


title: genomic_DNAmethylation_CLG-3_v

description: Genomic DNA from CLG-3_v

value: Genomic DNA from CLG-3_v

value: CIUE low grade


title: genomic_DNAmethylation_CLG-4_v

description: Genomic DNA from CLG-4_v

value: Genomic DNA from CLG-4_v


title: genomic_DNAmethylation_NP-4_v

description: Genomic DNA from NP-4_v

value: Genomic DNA from NP-4_v


title: genomic_DNAmethylation_204936250102_R03C01

description: Genomic DNA from 204936250102_R03C01

value: whole blood

value: Genomic DNA from 01-1165-C

value: F


title: genomic_DNAmethylation_SPLN-10_v

description: Genomic DNA from SPLN-10_v

value: Genomic DNA from SPLN-10_v

value: Non-CIUE

value: Male


title: genomic_DNAmethylation_SPLN-4_v

description: Genomic DNA from SPLN-4_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-4_v

value: Female

value: N


title: genomic_DNAmethylation_CHG-8_v

description: Genomic DNA from CHG-8_v

value: Genomic DNA from CHG-8_v

value: CIUE high grade


title: genomic_DNAmethylation_SPLA-2_v

description: Genomic DNA from SPLA-2_v

value: Genomic DNA from SPLA-2_v

value: NO

value: Y


title: genomic_DNAmethylation_CLG-10_v

description: Genomic DNA from CLG-10_v

value: Genomic DNA from CLG-10_v

value: CIUE low grade


title: genomic_DNAmethylation_CHG-15_v

description: Genomic DNA from CHG-15_v

value: Genomic DNA from CHG-15_v

value: YES


title: genomic_DNAmethylation_NP-7_v

description: Genomic DNA from NP-7_v

value: Genomic DNA from NP-7_v


title: genomic_DNAmethylation_SPLN-2_v

description: Genomic DNA from SPLN-2_v

value: Genomic DNA from SPLN-2_v


title: genomic_DNAmethylation_CHG-3_v

description: Genomic DNA from CHG-3_v

value: Genomic DNA from CHG-3_v


title: genomic_DNAmethylation_204930640093_R04C01

description: Genomic DNA from 204930640093_R04C01

value: whole blood

value: Genomic DNA from 01-1136-C

value: M


title: genomic_DNAmethylation_SPLA-14_v

description: Genomic DNA from SPLA-14_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLA-14_v

value: Non-CIUE

value: Female


title: genomic_DNAmethylation_CLG-12_v

description: Genomic DNA from CLG-12_v

value: Genomic DNA from CLG-12_v

value: Male

value: N


title: genomic_DNAmethylation_CLG-2_v

description: Genomic DNA from CLG-2_v

value: Genomic DNA from CLG-2_v

value: NO


title: genomic_DNAmethylation_CHG-7_v

description: Genomic DNA from CHG-7_v

value: Genomic DNA from CHG-7_v

value: CIUE high grade


title: genomic_DNAmethylation_CHG-2_v

description: Genomic DNA from CHG-2_v

value: Genomic DNA from CHG-2_v

value: YES

value: Y


title: genomic_DNAmethylation_SPLA-5_v

description: Genomic DNA from SPLA-5_v

value: Genomic DNA from SPLA-5_v


title: genomic_DNAmethylation_SPLA-6_v

description: Genomic DNA from SPLA-6_v

value: Genomic DNA from SPLA-6_v


title: genomic_DNAmethylation_CLG-1_v

description: Genomic DNA from CLG-1_v

value: Genomic DNA from CLG-1_v

value: CIUE low grade


title: genomic_DNAmethylation_SPLN-6_v

description: Genomic DNA from SPLN-6_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-6_v


title: genomic_DNAmethylation_SPLA-7_v

description: Genomic DNA from SPLA-7_v

value: Genomic DNA from SPLA-7_v

value: Non-CIUE


title: 77_06_Day3

description: Library name: SPF2.77.06.Day3

value: blood

value: PBMCs

value: Influenza vaccination


title: genomic_DNAmethylation_SPLN-8_v

description: Genomic DNA from SPLN-8_v

value: Genomic DNA from SPLN-8_v

value: Male

value: NO


status: Public on Dec 17 2025

first: Hangnoh

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description:
Library name: W6_WT_Sham_Sp_1
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 1

data_processing:
Base calling was performed using CASAVA version 1.8.2 (Illumina, San Diego, CA).
The GENCODE mouse gene annotation (version M33) was used for alignment and quantification.
Gene-level quantification was performed using RSEM version 1.3.3 (PMID: 21816040).
Assembly: Mouse reference genome GRCm39
Supplementary files format and content: Tab-delimited text files containing Ensembl gene identifiers and gene/isoform expression values in TPM (transcripts per million).

source_name: Spleen

extract_protocol:
Following euthanasia 7 days and 6 weeks after SCI, mice were perfused with 50 mL of ice-cold normal saline. Total RNA was extracted from the spinal cord, lung, and spleen tissue with the miRNeasy Mini Kit (Qiagen, Cat# 74104).  In brief, approximately 600ul of QIAzol were added to each sample and disrupted in a Precellys 24 Touch homogenizer. The aqueous phase containing RNA was collected, mixed with ethanol, and applied to a silica membrane spin column. After a series of washes to remove contaminants, RNA was eluted in RNase-free water. A minimum of 100ng was sent to Novogene Bioinformatics Technology Co., Ltd. (Sacramento, CA) for downstream sequencing assays.
Library preparations were carried out by Novogene (Sacramento, CA) for sequencing on the Illumina platform (paired-end, 150 bp reads). mRNA was enriched through poly-A pulldown.

value: Spleen

tag: strain

value: male

tag: age

value: 19 to 22 months old

value: wild-type

value: Sham

tag: collection time

value: 6 weeks after SCI


description:
Library name: W6_WT_Sham_Sp_2
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 2

tag: tissue

tag: genotype


description:
Library name: W6_WT_Sham_Sp_5
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 5


description:
Library name: W6_WT_Sham_Sp_4
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 4


description:
Library name: W6_WT_Sham_Sp_3
Mouse Spleen, wild-type, Sham, 6 weeks after SCI, Replicate 3


description:
Library name: W6_WT_Sham_SC_5
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 5

source_name: Spinal Cord

value: Spinal Cord


description:
Library name: W6_WT_Sham_SC_4
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 4


description:
Library name: W6_WT_Sham_SC_3
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 3


description:
Library name: W6_WT_Sham_SC_2
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 2


description:
Library name: W6_WT_Sham_Lg_5
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 5

source_name: Lung

value: Lung


description:
Library name: W6_WT_Sham_Lg_4
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 4


description:
Library name: W6_WT_Sham_SC_1
Mouse Spinal Cord, wild-type, Sham, 6 weeks after SCI, Replicate 1


description:
Library name: W6_WT_SCI_Sp_4
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4

value: Spinal Cord Injury (SCI)


description:
Library name: W6_WT_Sham_Lg_3
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 3


description:
Library name: W6_WT_Sham_Lg_1
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 1


description:
Library name: W6_WT_SCI_Sp_5
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5


description:
Library name: W6_WT_Sham_Lg_2
Mouse Lung, wild-type, Sham, 6 weeks after SCI, Replicate 2


description:
Library name: W6_WT_SCI_Sp_3
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3


description:
Library name: W6_WT_SCI_Lg_5
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5


description:
Library name: W6_WT_SCI_Lg_4
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4


description:
Library name: W6_WT_SCI_SC_3
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3


description:
Library name: W6_WT_SCI_Sp_2
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


description:
Library name: W6_WT_SCI_SC_5
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5


description:
Library name: W6_WT_SCI_SC_4
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4


description:
Library name: W6_WT_SCI_SC_2
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


description:
Library name: W6_WT_SCI_Sp_1
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


description:
Library name: W6_WT_SCI_SC_1
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


description:
Library name: W6_WT_SCI_Lg_2
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


description:
Library name: W6_WT_SCI_Lg_3
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3


description:
Library name: W6_Hv1KO_Sham_Sp_5
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 5

value: Hv1 knockout


description:
Library name: W6_Hv1KO_Sham_Sp_2
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 2


description:
Library name: W6_Hv1KO_Sham_Sp_4
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 4


description:
Library name: W6_WT_SCI_Lg_1
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


description:
Library name: W6_Hv1KO_Sham_Sp_3
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 3


description:
Library name: W6_Hv1KO_Sham_Sp_1
Mouse Spleen, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 1


description:
Library name: W6_Hv1KO_Sham_Lg_1
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 1


description:
Library name: W6_Hv1KO_Sham_SC_3
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 3


description:
Library name: W6_Hv1KO_Sham_SC_2
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 2


description:
Library name: W6_Hv1KO_Sham_Lg_2
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 2


description:
Library name: W6_Hv1KO_Sham_Lg_5
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 5


description:
Library name: W6_Hv1KO_Sham_SC_1
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 1


description:
Library name: W6_Hv1KO_Sham_SC_5
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 5


description:
Library name: W6_Hv1KO_Sham_Lg_3
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 3


description:
Library name: W6_Hv1KO_Sham_SC_4
Mouse Spinal Cord, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 4


title: genomic_DNAmethylation_204936250027_R08C01

description: Genomic DNA from 204936250027_R08C01

value: buccal swab

value: Genomic DNA from 01-1128-C

value: M


description:
Library name: W6_Hv1KO_Sham_Lg_4
Mouse Lung, Hv1 knockout, Sham, 6 weeks after SCI, Replicate 4


description:
Library name: W6_Hv1KO_SCI_Sp_5
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5


description:
Library name: W6_Hv1KO_SCI_Sp_4
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4


description:
Library name: W6_Hv1KO_SCI_Sp_3
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3


description:
Library name: W6_Hv1KO_SCI_Sp_2
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


description:
Library name: W6_Hv1KO_SCI_Sp_1
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


description:
Library name: W6_Hv1KO_SCI_SC_4
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4


description:
Library name: W6_Hv1KO_SCI_SC_5
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5


description:
Library name: W6_Hv1KO_SCI_Lg_3
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3


description:
Library name: W6_Hv1KO_SCI_Lg_2
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


description:
Library name: W6_Hv1KO_SCI_SC_1
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


description:
Library name: W6_Hv1KO_SCI_SC_3
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 3


description:
Library name: W6_Hv1KO_SCI_Lg_5
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 5


description:
Library name: D7_WT_Sham_Sp_4
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 4

value: 7 days after SCI


description:
Library name: W6_Hv1KO_SCI_Lg_1
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 1


description:
Library name: W6_Hv1KO_SCI_Lg_4
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 4


description:
Library name: D7_WT_Sham_Sp_2
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 2


description:
Library name: D7_WT_Sham_Sp_1
Mouse Spleen, wild-type, Sham, 7 days after SCI, Replicate 1


description:
Library name: D7_WT_Sham_SC_4
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 4


description:
Library name: W6_Hv1KO_SCI_SC_2
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 6 weeks after SCI, Replicate 2


description:
Library name: D7_WT_Sham_SC_3
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 3


description:
Library name: D7_WT_Sham_SC_2
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 2


description:
Library name: D7_WT_Sham_SC_1
Mouse Spinal Cord, wild-type, Sham, 7 days after SCI, Replicate 1


description:
Library name: D7_WT_Sham_Lg_3
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 3


description:
Library name: D7_WT_Sham_Lg_4
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 4


description:
Library name: D7_WT_Sham_Lg_1
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 1


description:
Library name: D7_WT_SCI_Sp_5
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


description:
Library name: D7_WT_Sham_Lg_2
Mouse Lung, wild-type, Sham, 7 days after SCI, Replicate 2


description:
Library name: D7_WT_SCI_Sp_3
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3


description:
Library name: D7_WT_SCI_SC_5
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


description:
Library name: D7_WT_SCI_Sp_4
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


description:
Library name: D7_WT_SCI_Sp_2
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


description:
Library name: D7_WT_SCI_SC_3
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3


description:
Library name: D7_WT_SCI_Sp_1
Mouse Spleen, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


description:
Library name: D7_WT_SCI_SC_4
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


description:
Library name: D7_WT_SCI_SC_2
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


description:
Library name: D7_WT_SCI_SC_1
Mouse Spinal Cord, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


description:
Library name: D7_WT_SCI_Lg_4
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


description:
Library name: D7_WT_SCI_Lg_5
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


description:
Library name: D7_WT_SCI_Lg_3
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3


description:
Library name: D7_WT_SCI_Lg_2
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


description:
Library name: D7_WT_SCI_Lg_1
Mouse Lung, wild-type, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


description:
Library name: D7_Hv1KO_Sham_Sp_4
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 4


description:
Library name: D7_Hv1KO_Sham_Sp_5
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 5


description:
Library name: D7_Hv1KO_Sham_Sp_1
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 1


description:
Library name: D7_Hv1KO_Sham_Sp_2
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 2


description:
Library name: D7_Hv1KO_Sham_Sp_3
Mouse Spleen, Hv1 knockout, Sham, 7 days after SCI, Replicate 3


description:
Library name: D7_Hv1KO_Sham_SC_2
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 2


description:
Library name: D7_Hv1KO_Sham_SC_5
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 5


description:
Library name: D7_Hv1KO_Sham_SC_1
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 1


description:
Library name: D7_Hv1KO_Sham_SC_4
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 4


description:
Library name: D7_Hv1KO_Sham_SC_3
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 3


description:
Library name: D7_Hv1KO_Sham_Lg_5
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 5


description:
Library name: D7_Hv1KO_Sham_Lg_4
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 4


description:
Library name: D7_Hv1KO_Sham_Lg_3
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 3


description:
Library name: D7_Hv1KO_Sham_Lg_2
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 2


description:
Library name: D7_Hv1KO_Sham_Lg_1
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 1


description:
Library name: D7_Hv1KO_SCI_Sp_7
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 7


description:
Library name: D7_Hv1KO_SCI_Sp_6
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 6


description:
Library name: D7_Hv1KO_SCI_Sp_5
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


description:
Library name: D7_Hv1KO_SCI_Sp_4
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


description:
Library name: D7_Hv1KO_SCI_Sp_3
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3


description:
Library name: D7_Hv1KO_SCI_Sp_1
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


description:
Library name: D7_Hv1KO_SCI_Sp_2
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


description:
Library name: D7_Hv1KO_SCI_SC_6
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 6


description:
Library name: D7_Hv1KO_SCI_SC_7
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 7


description:
Library name: D7_Hv1KO_SCI_SC_2
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


description:
Library name: D7_Hv1KO_SCI_SC_1
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


description:
Library name: D7_Hv1KO_SCI_Lg_5
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


description:
Library name: D7_Hv1KO_SCI_Lg_7
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 7


description:
Library name: D7_Hv1KO_SCI_SC_4
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


description:
Library name: D7_Hv1KO_SCI_SC_3
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3


description:
Library name: D7_Hv1KO_SCI_Lg_4
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


description:
Library name: D7_Hv1KO_SCI_Lg_6
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 6


description:
Library name: D7_Hv1KO_SCI_SC_5
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


description:
Library name: D7_Hv1KO_SCI_Lg_3
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3


description:
Library name: D7_Hv1KO_SCI_Lg_2
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


description:
Library name: D7_Hv1KO_SCI_Lg_1
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


title: Xenium, SSc10, whole skin

status: Public on Dec 12 2025

city: Lebanon

first: Helen

middle: C

last: Jarnagin

state: NH

address: WTRB 6-84, 1 Medical Center Drive

institute: Dartmouth College

hyb_protocol: Xenium protocol

scan_protocol: Xenium protocol

data_processing: Slides were imaged, cells were segmented, and initial QC was completed on the Xenium Analyzer (v3.0.2.0). QC-ed and segmented images were then transferred and converted to anndata objects for downstream Python-based analysis methods.

source_name: Affected skin biopsy

extract_protocol: FFPE histology sections underwent 10X Xenium’s in situ gene expression assay. Proprietary iterative in situ hybridization was conducted using the Xenium Prime 5K Human Pan Tissue and Pathways panel. Tissues were sectioned onto Xenium slides and processed according to the manufacturer’s protocol, including the workflow for cell segmentation staining (CG000760).

value: skin


title: Mouse, ske, D68N, rep 3

description:
Library name: Mouse_ske_D68N_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske16_D68N

value: Quadriceps

tag: cell type

value: Whole tissue

value: H2B D68N


title: Xenium, SSc9, whole skin


title: Xenium, SSc8, whole skin


title: VisiumHD_2, before treatment

status: Public on Dec 03 2025

city: Fukuoka

first: Satoshi

last: Nakamura

state: Fukuoka

address: 3-1-1, Maidashi, higashi-ku

department: Respiratory Medicine

country: Japan

institute: Kyushu University

description: Library name: C

data_processing:
Sequencing data (FASTQ files) were processed and analyzed using Space Ranger (version 3.0.0) software to assess data quality and generate spatial gene expression profiles.
Assembly: GRCh38
Supplementary files format and content: A.tar: Tar archive containing the 2μm resolution binning outputs of pre-treatment sample obtained from space ranger and coordinate data after stardist processing
Supplementary files format and content: C.tar: Tar archive containing the 2μm resolution binning outputs of post-treatment sample obtained from space ranger and coordinate data after stardist processing
Library strategy: Spatial Transcriptomics

extract_protocol:
In this study, a total of two samples consisting of paired pre- and post-treatment samples from a patient were analyzed. The FFPE tissue sections were then subjected to deparaffinization and H&E staining following the Visium HD FFPE Tissue Preparation protocol provided by 10x Genomics (Visium HD FFPE Tissue Preparation Handbook, CG000684 Rev A).
Gene expression libraries were prepared from the H&E-stained sections following the 10X Genomics protocol (Visium HD Spatial Gene Expression Reagent Kits User Guide CG000685 Rev A). The quality of the prepared libraries was evaluated using the 4200 Tape Station, and all libraries were confirmed to have sufficient concentrations. The Visium libraries were sequenced using the NovaSeq X Plus platform with a paired-end configuration (read1: 150 bp, read2: 150 bp).


title: Xenium, SSc7, whole skin


title: Xenium, SSc3, whole skin


title: Xenium, SSc1, whole skin


title: Lung of tumor-bearing (KP) mice replicate 3 (scATAC-seq)

status: Public on Dec 06 2025

city: New York

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
Library name: mm_scATACseq_Lung_KP_Rep3
10x Genomics

library_source: genomic single cell

data_processing:
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: mm10
Supplementary files format and content: scATAC-seq: cellranger processed outputs (barcode, peak/feature matrix).

extract_protocol:
Mouse: myeloid cells were sorted from respective tissues (Lung/BM/blood) based on markers described in Methods section. For scATAC-seq, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei or cells were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Mouse: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. scRNA-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell pooled on the Illumina NovaSeq 6000 S2 100 cycle kit. scATAC-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol: Mouse: myeloid cells excluding mature neutrophils were sorted from processed tissues (Lung/BM/blood) of naïve or KP Tumor-bearing mice in PBS+0.04% BSA, based on surface markers described in Methods section.

value: immune

tag: treatment

value: Tumor-bearing


title: Xenium, SSc6, whole skin


title: Xenium, SSc4, whole skin


title: Lung of tumor-bearing (KP) mice replicate 2 (scATAC-seq)

description:
Library name: mm_scATACseq_Lung_KP_Rep2
10x Genomics

tag: cell line


title: T21, R23867

description: Library name: R23867

data_processing:
Raw sequencing reads were processed using the RAPiD-nf pipeline, with alignment to the GRCh38 reference genome performed using STAR v2.7.3a.
Alignment quality was assessed with RSeQC and Picard. PCR duplicates were marked but not removed prior to quantification.
Gene-level counts were generated using featureCounts (Subread v2.0.1) with GENCODE v32 annotations.
Counts were normalized usingthe VOOM method from the limma package (v3.48.3), and log2-transformed expression matrices were created seperately for DLPFC and hippocampus.
Assembly: GRCh38 (Ensembl release 95)
Supplementary files format and content: tab-delimited text file (T21_raw_counts.txt) includes raw counts for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from frozen dorosolateral prefrontal cortex and hippocampal tissues using the AllPrep DNA/RNA Mini Kit, and only samples with RIN ≥ 9.0 were included.
RNA-seq libraries were generatred from 300 ng of high-quality total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

value: Hippocampus

tag: karyotype

value: Male

value: Caucasian


title: T21, R23864

description: Library name: R23864

tag: rin

value: Female


title: Xenium, SSc2, whole skin


title: Xenium, SSc5, whole skin


title: Bone marrow of tumor-bearing (KP) mice replicate 3 (scATAC-seq)

description:
Library name: mm_scATACseq_BM_KP_Rep3
10x Genomics

source_name: Bone marrow

value: Bone marrow


title: T21, R23854

description: Library name: R23854

tag: gestational age


title: Mouse, ske, D68N, rep 1

status: Public on Mar 02 2026

description:
Library name: Mouse_ske_D68N_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske7_D68N

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: No processed data files are included in this submission. Only raw FASTQ files are provided for each sample.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit with xGEN Stubby adaptors and xGEN 10nt UDIs.


title: Bone marrow of naive mice replicate 2 (scATAC-seq)

description:
Library name: mm_scATACseq_BM_naive_Rep2
10x Genomics

value: Naive


title: Mouse, ske, WT, rep 3

description:
Library name: Mouse_ske_WT_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske10_WT

value: H2B WT


title: VisiumHD_1, before treatment

description: Library name: A

value: Lung