title: 41_T193

description:
Library name: lib90603
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 28_T182

status: Public on Oct 30 2025

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

description:
Library name: lib90590
combined_counts_ALI.csv

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. Resulting bcl files were deconvoluted and converted to fastq format using Casava from Illumina. Fastq files were aligned to the Ensembl version of the human genome (GRCh38, Ensembl 91) by using STAR (version 2.4.2a). HTSeq-count (version 0.4.1) was used to generate gene counts with mode as “intersection (nonempty)” and minimum alignment quality set to 20 and otherwise set to default parameters. Quality metrics were compiled from PICARD (version 1.134), FASTQC (version 0.11.3), Samtools (version 1.2), and HTSeq-count (version 0.4.1). For quality control, samples that had human aligned counts greater than 1 million mapped reads and a median coefficient of variation coverage less than 0.7 were kept. Genes were filtered to include those that had a trimmed mean of M value normalization count of at least 0.3 in at least 10% of samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights by using voomWithQualityWeights from the limma R package (version 4.2.1).
Assembly: Human GRCh38
Supplementary files format and content: csv file voom normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: Organotypic airway epithelial cell culture

extract_protocol:
Bronchial epithelial cells (BECs) from children with asthma (n=37) and healthy children (n=3)  ages 6-18 years of age were obtained from subjects while under general anesthesia for an elective surgery using 4-mm Harrell unsheathed bronchoscope cytology brushes (CONMED®) inserted through an endotracheal tube as we have previously described (8, 42). Cells were then seeded onto T-25 cell culture flasks (Corning®) precoated with type I collagen and proliferated under submerged culture conditions using PneumaCult™EX-Plus medium (Stemcell™) (8). BECs (passage 2 or 3) were proliferated on transwells under submerged culture conditions using PneumaCult™EX-Plus medium (Stemcell™) for 4-7 days then differentiated to an organotypic pseudostratified ciliated state (Supplemental Figure 1) for 21 days at ALI using PneumaCult™ALI medium (Stemcell™) as previously described (8, 43–45). We have previously demonstrated stability of gene expression in primary BEC ALI cultures between passages 1 and 3 (46).RNA was collected from BEC cultures pre-infection and at 2d, 4d, 7d, and 10d post RV infection. To collect RNA from BEC cultures, media was first removed from the basolateral chamber of transwells. 800 µL of lysis buffer (Invitrogen®, Product No. AM1912) was added to the apical surface of cultures. A pipet tip was then used to gently scratch each apical well in a crosshatch pattern to loosen BECs from the transwell membrane. RNA was extracted using the RNAqueous™ kit for total RNA isolation (Thermo Fisher Scientific). BEC cultures from SE (n=6) and NSE (n=6) donors were treated with IFN-β or CXCL10 starting 2 days prior to RV infection and continued for 2 days following RV infection. Recombinant human recombinant human IFN-β (1 ng/mL; AbcamⓇ) or CXCL10 (2 ng/mL; R&D SystemsⓇ) was added to BEC ALI medium starting 2 days prior to RV infection and refreshed with each medium change (every other day). Two days following initiation of treatment with IFN-β or CXCL10 BEC cultures were infected with human RV-A16 at an MOI of 0.5 as described above. RNA was collected from BEC cultures pre-infection and 2d following RV infection.
Total RNA was used to construct libraries by using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, San Jose, Calif), with reverse transcription followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed by using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina, San Diego, Calif) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Mass). Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 53-base reads with a target depth of 5 million reads per sample

tag: studygroup

value: Asthma

tag: donorid

tag: cell type

value: Severe Exacerbation

tag: treatment

tag: age

tag: Sex

value: female

tag: ethnicity

value: White

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

value: Yes

tag: viral load

tag: total reads

tag: pct aligned

tag: batch


title: 30_T182

description:
Library name: lib90592
combined_counts_ALI.csv

value: Organotypic airway epithelial cell culture

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 33_T182

description:
Library name: lib90595
combined_counts_ALI.csv

tag: studygroup

tag: donorid

tag: cell type

tag: treatment

tag: age


title: 26_T192

description:
Library name: lib90588
combined_counts_ALI.csv

tag: Sex

tag: ethnicity

value: Hispanic

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

value: No


title: 21_T192

description:
Library name: lib90583
combined_counts_ALI.csv

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load

tag: total reads

tag: pct aligned


title: 23_T192

description:
Library name: lib90585
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

value: Control

tag: fef25-75 (%_predicted)

tag: batch


title: 64_T194

description:
Library name: lib90626
combined_counts_ALI.csv

tag: studygroup

tag: donorid

tag: cell type

tag: treatment

value: male

tag: median cv_coverage


title: 19_T192

description:
Library name: lib90581
combined_counts_ALI.csv

tag: age

tag: Sex

tag: ethnicity

tag: allergic sensitization

tag: eos absolute_(mm2)


title: 17_T168

description:
Library name: lib90579
combined_counts_ALI.csv

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load

tag: total reads


title: 14_T168

description:
Library name: lib90576
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 12_T168

description:
Library name: lib90574
combined_counts_ALI.csv

tag: studygroup

tag: donorid

tag: cell type

tag: treatment

tag: batch


title: 8_T188

description:
Library name: lib90570
combined_counts_ALI.csv

tag: age

tag: Sex

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 10_T168

description:
Library name: lib90572
combined_counts_ALI.csv

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 6_T188

description:
Library name: lib90568
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 5_T188

description:
Library name: lib90567
combined_counts_ALI.csv

tag: studygroup

tag: donorid

tag: cell type

tag: treatment

tag: pct aligned


title: 2024-07-22_MJT_stage_23_male_3

status: Public on Oct 29 2025

city: Athens

first: Matthew

last: Treaster

state: GA

address: 120 E Green St

department: Genetics

institute: University of Georgia

description: Library name: m23.8

data_processing:
We trimmed raw reads for quality and sequencing adapters with Trimmomatic (v. 0.39) using leading and trailing quality threshold of 3, a sliding window of 4 with quality threshold of 15, and minimum length cutoff of 36.
We aligned paired and orphan reads to the threespine stickleback reference genome (GAculeatus_UGA_version5, NCBI RefSeq assembly GCF_016920845.1) using HISAT-3N with default parameters except for reversing RNA strandedness (R for Read 1 and F for Read 2).
We generated Indexed BAM files of the alignments with Samtools (v. 1.17)
We generated transcript counts against the NCBI annotation GTF file (release 100) for GCF_016920845.1 with HTseq (v. 2.0.2) using HTSeq-count with default parameters except for reversing RNA strandedness (R for Read 1 and F for Read 2).
We combined the counts from paired and orphaned reads for each sample and used DESeq2 (v. 1.44.0) in R (v. 4.4.1) and RStudio (v. 2024.04.2+764) to generate normalized read counts .
Assembly: GCF_016920845.1
Supplementary files format and content: TSV file with raw read counts for each sample
Supplementary files format and content: TSV file with normalized read counts for each sample

molecule: polyA RNA

organism: Gasterosteus aculeatus

source_name: whole organism

extract_protocol:
We preserved whole embryos in RNAlater Stabilization Solution (Invitrogen AM7021) following manufacturer guidelines and stored at -80 °C until analysis. We extracted RNA using TRIzol Reagent (Invitrogen 15596026) and the Direct-zol RNA Microprep Kit (Zymo R2062).
We created sequencing libraries using the Illumina TruSeq Stranded mRNA Library Prep kit (20020594). We pooled the libraries from all samples and 150 bp paired end reads were sequenced on two lanes using a NovaSeq X Plus by Azenta Life Sciences (South Plainfield, NJ, USA).

tag: tissue

value: whole organism


title: 2024-07-22_MJT_stage_23_male_2

description: Library name: m23.4


title: 1_T188

description:
Library name: lib90563
combined_counts_ALI.csv

tag: age

tag: Sex

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage

tag: batch


title: 3_T188

description:
Library name: lib90565
combined_counts_ALI.csv

tag: exacerbation status

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 2024-07-22_MJT_stage_23_female_2

description: Library name: f23.2


title: 2024-07-22_MJT_stage_23_male_1

description: Library name: m23.10


title: 2024-07-22_MJT_stage_23_female_3

description: Library name: f23.3


title: 2024-07-22_MJT_stage_23_female_1

description: Library name: f23.1


title: 2024-07-22_MJT_stage_20_male_1

description: Library name: m20.2


title: 2024-07-22_MJT_stage_20_female_3

description: Library name: f20.5


title: 2024-07-22_MJT_stage_20_female_1

description: Library name: f20.12


title: 2024-07-22_MJT_stage_20_male_2

description: Library name: m20.6


title: 2024-07-22_MJT_stage_17_male_3

description: Library name: m17.6


title: 2024-07-22_MJT_stage_17_male_1

description: Library name: m17.11


title: 2024-07-22_MJT_stage_17_male_2

description: Library name: m17.4


title: 2024-07-22_MJT_stage_20_female_2

description: Library name: f20.1


title: 2024-07-22_MJT_stage_17_female_2

description: Library name: f17.3


title: 15_T168

description:
Library name: lib90577
combined_counts_ALI.csv

tag: studygroup

tag: donorid

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 2024-07-22_MJT_stage_17_female_1

description: Library name: f17.10

tag: tissue


title: 2024-07-22_MJT_8_dah_male_2

description: Library name: md8.5


title: 2024-07-22_MJT_stage_17_female_3

description: Library name: f17.5


title: 2024-07-22_MJT_8_dah_male_1

description: Library name: md8.3


title: 2024-07-22_MJT_8_dah_male_3

description: Library name: md8.8


title: 2024-07-22_MJT_8_dah_female_3

description: Library name: fd8.6


title: 2024-07-22_MJT_8_dah_female_2

description: Library name: fd8.4


title: 2024-07-22_MJT_8_dah_female_1

description: Library name: fd8.1


title: 2024-07-22_MJT_4_dah_male_2

description: Library name: md4.2


title: 2024-07-22_MJT_stage_20_male_3

description: Library name: m20.7


title: 2024-07-22_MJT_4_dah_female_3

description: Library name: fd4.7


title: 2024-07-22_MJT_4_dah_male_1

description: Library name: md4.1


title: 2024-07-22_MJT_4_dah_female_1

description: Library name: fd4.4


title: 2024-07-22_MJT_4_dah_female_2

description: Library name: fd4.6


title: 2024-07-22_MJT_0_dah_male_3

description: Library name: md0.5


title: 2024-07-22_MJT_0_dah_male_1

description: Library name: md0.11


title: 2024-07-22_MJT_0_dah_male_2

description: Library name: md0.2


title: 2024-07-22_MJT_0_dah_female_2

description: Library name: fd0.1


title: 2024-07-22_MJT_0_dah_female_1

description: Library name: fd0.12


title: 2024-07-22_MJT_0_dah_female_3

description: Library name: fd0.3


title: RMC-Replicate-2

status: Public on Oct 22 2025

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

description: Library name: RMC-2

library_source: transcriptomic single cell

data_processing:
Count matrices were generated by aligning sequencing reads using Cell Ranger (version 8.0.1)(66) with default settings and the mouse reference transcriptome, GRCm39-2024-A. To remove potential ambient RNA contamination, CellBender's `removebackground` function was applied (version 1.0) 45. The resulting ambient-corrected count matrices were analyzed using Seurat (version 5.1.0) 46. Quality control was performed for each sample with custom thresholds, selected based on the distribution of quality control metrics. Key metrics included the percentage of mitochondrial and ribosomal reads, the number of features detected, and the per-cell library size. Since neutrophils exhibited overall lower library sizes compared to other cell types, quality control filters were adjusted accordingly. For downstream analysis, Seurat’s standard procedures for normalization, dimensionality reduction, and clustering were followed. The number of principal components was determined using the Talus plot method 47. Cell counts were normalized using SCTransform, with cell cycle scores regressed out using the gene list from Kowalczyk et al. 48 , along with the percentage of mitochondrial and ribosomal reads. Optimal clustering resolution was selected using the clustree R package (version 0.5.0), and clusters were assigned cell types based on the expression of known marker genes from the literature. Cluster identities were further validated by comparing them with annotations from ImmGen49 using SingleR (version 2.6.0) 50. This clustering approach was applied to each sample independently, allowing for the removal of sample-specific artifacts. For CD45+ cell analysis, to refine the cell population structure, subclustering was performed independently for major cell types. This approach enabled the identification of finer cell population structures and facilitated the removal of doublets and low-quality cells through inspection of population marker gene expression and quality control metrics. Plots were generated using R (v.4.4.1; 14 June 2024) and R visualization packages such as ComplexHeatmap 51 and scCustomize 52.
Assembly: GRCm39-2024-A
Supplementary files format and content: Cellranger output h5 files (cell by gene matrix),  Cellbender output h5 files (cell by gene matrix with ambient RNA removed), R rds file (Seurat object of processed cell by gene matrix with annotations)

organism: Mus musculus

extract_protocol:
At the time points, tumors were harvest under sterile conditions and weighted. Single-cell suspensions were obtained by enzymatic digestion, following the MACS tumor dissociation kit instructions (cat. #130-096-730; Miltenyi Biotec) and the number of viable cells counted
Single-cell RNA sequencing was conducted using the 10X Genomics Chromium System (10X Genomics, Pleasanton, CA) by the Molecular Genomics Core at Moffitt Cancer Center and Research Institute. Following tissue harvest and dissociation, single-cell suspensions were prepared, washed twice with 1X PBS (calcium- and magnesium-free) containing 0.04% BSA (w/v), and resuspended in the same buffer according to the 10X Genomics cell preparation protocol. Cell viability and concentration were assessed using acridine orange/propidium iodide (AO/PI) dual fluorescent staining on the Nexcelom Cellometer K2 (Nexcelom Bioscience LLC, Lawrence, MA). Cells were then loaded onto the 10X Chromium Single Cell Controller at a concentration of 1,000 cells/µL to target recovery of approximately 10,000 cells per sample. Briefly, individual cells, reagents, and gel beads were encapsulated into nanoliter-sized Gel Beads-in-Emulsion (GEMs), and reverse transcription of polyadenylated mRNA occurred within each droplet at 48°C. Gene expression (GEX) libraries, T-cell receptor (TCR) V(D)J enrichment, and VDJ libraries were generated according to the Chromium GEM-X Single Cell 5’ v3 Gene Expression User Guide. Sequencing was performed on the Illumina NovaSeq 6000 platform, generating approximately 50,000 reads per cell. Data processing—including demultiplexing, barcode assignment, alignment, and gene counting—was carried out using Cell Ranger v9.0.0 (10X Genomics). Visualization and downstream analysis were performed with the 10X Genomics Loupe Browser v8.1.2.

tag: Sex

value: Female

tag: cell line

tag: strain


title: RMC-Replicate-1

description: Library name: RMC-1


title: RMC-Replicate-3

description: Library name: RMC-3


title: PD1-Replicate-2

description: Library name: PD1-2


title: PD1-Replicate-1

description: Library name: PD1-1


title: Control-Replicate-3

description: Library name: Control-3


title: Control-Replicate-2

description: Library name: Control-2


title: PD1-Replicate-3

description: Library name: PD1-3


title: Control-Replicate-1

description: Library name: Control-1


title: ABE_PCSK9_E1

status: Public on Oct 20 2025

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description:
Library name: CRL4484
CHANGE-seq-BE for ABE targets

library_source: genomic

data_processing:
CHANGE-seq-BE analysis. Adapter trimming was performed using cutadapt (v1.18) with parameters of "--overlap 40 -e 0.15" to remove Tn5 adapter (CTGTCTCTTATACACATCTACGTAGATGTGTATAAGAGACAG). Then paired-end reads were mapped using bwa mem with default parameters. Reads with zero mapping quality were filtered out (e.g., MAPQ=0). CHANGE-seq-BE paired-end reads should be in an outward orientation with some degree of self-overlapping bases. For ABE, assuming an editing window from position 1 to position 10, we used min_overlap=5 and max_overlap=15, because the deamination event occurred at +2 position. Similariy, for CBE, we used min_overlap=6 and max_overlap=16, because the deamination event occurred at +1 position. Reads were filtered based on the above criteria. The start positions of the valid reads were then tabulated, and genomic intervals enriched in nuclease-treated samples were identified. The interval and 30 bp of flanking reference sequence on either side were searched for potential nuclease-induced off-target sites with up to 6 mismatches, 1 insertion, or 1 deletion. CHANGE-seq-BE data analyses were performed using open-source CHANGE-seq analysis software (https://github.com/tsailabSJ/changeseq/dev).
Assembly: hg38
Supplementary files format and content: MS excel, list of called off-targets with annotation

molecule: genomic DNA

source_name: Tcell

extract_protocol:
Genomic DNA extracted from primary human cells using Gentra Puregene Kit (Qiagen) according to manufacturer’s protocol.
Purified genomic DNA was tagmented  and circularized using a custom Tn5-transposome. Genomic DNA circles modified by base editors and selectively sequenced by end-repair and adaptor ligation for sequencing. ABE libraries were pooled and loaded on NextSeq 500 or 2000 with paired-end sequencing 151 8 8 151 cycles according to the manufacturer’s instructions.

treatment_protocol: Primary human cells were cultured in X-VIVO media with cytokines. Cells were harvested accordingly to extract required genomic DNA for CHANGE-seq-BE.

value: Tcell

tag: cell type

value: Human Primary T-Cells


title: Combo-Replicate-2

description: Library name: Combo-2


title: Combo-Replicate-3

description: Library name: Combo-3


title: ABE_PCSK9_E2

description:
Library name: CRL4485
CHANGE-seq-BE for ABE targets


title: 2024-07-22_MJT_4_dah_male_3

description: Library name: md4.3


title: ABE_PCSK9_Control

description:
Library name: CRL4486
CHANGE-seq-BE for ABE targets


title: ABE_CD7_E2

description:
Library name: CRL4447
CHANGE-seq-BE for ABE targets


title: ABE_PDCD1_E2

description:
Library name: CRL4449
CHANGE-seq-BE for ABE targets


title: ABE_PDCD1_E1

description:
Library name: CRL4443
CHANGE-seq-BE for ABE targets


title: ABE_CD7_E1

description:
Library name: CRL4441
CHANGE-seq-BE for ABE targets


title: ABE_CBLB_E1

description:
Library name: CRL4440
CHANGE-seq-BE for ABE targets


title: ABE_CBLB_E2

description:
Library name: CRL4446
CHANGE-seq-BE for ABE targets


title: ABE_B2M_E1

description:
Library name: CRL4439
CHANGE-seq-BE for ABE targets


title: ABE_MKSR_control

description:
Library name: CRL3132
CHANGE-seq-BE for ABE targets

value: CD34+ HSPCs


title: ABE_B2M_E2

description:
Library name: CRL4445
CHANGE-seq-BE for ABE targets


title: ABE_MKSR_E2

description:
Library name: CRL3129
CHANGE-seq-BE for ABE targets


title: ABE_MKSR_E1

description:
Library name: CRL3128
CHANGE-seq-BE for ABE targets


title: Oligo-organoid

city: Stockholm

first: Carl

middle: M

last: Sellgren

address: Solnavagen 1

country: Sweden

institute: Karolinska Institute

description: 10X Genomics

data_processing:
Fastq files were processed using the cellranger (v6.1.2) pipeline with read alignment to the human GRCh38/hg38 reference genome. Barcodes and sorted bam files generated by cellranger were used for genotype demultiplexing of the two individual cell lines by souporcell package, with k=2 and a common variants file (limited to >=2% MAF) of GRCh38.
Each cell was assigned to the respective individual cell line. UMI count matrices were processed in R using the Seurat package
Assembly: GRCh38
Supplementary files format and content: .rds file containng seurat object
Supplementary files format and content: cellranger output files (.mtx, .tsv)

source_name: Brain organoid

extract_protocol:
To isolate single nuclei from fresh organoid tissue samples, organoids were subjected to cold mechanical dissociation with glass pipettes to obtain a single-cell suspension. Dissociated cells were centrifuged at 500 g for 5 minutes at 4°C. The cell pellet was washed and exposed to a freshly prepared lysis buffer (as demonstrated in protocol CG000366 RevD, 10x Genomics) followed by centrifugation at 500g for 5 minutes at 4°C. To remove cellular debris, the nuclei suspension was further subjected to an iodoxinol gradient (Optiprep; 25% and 29%) with centrifugation at 13500 g for 20 minutes at 4°C
Isolated nuclei were equally pooled and loaded onto the Chromium controller (10x Genomics) with a target recovery of 10000 cells. The assay was processed according to the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) user guide (RevD). Upon GEM generation, barcoding, cleanup and cDNA amplification, a single barcoded library was constructed and sequenced on Illumina NovaSeq S1-100 (v1.5, 2 x 100 bp)
3' scRNAseq (1 pooled library)

value: Brain organoid

tag: age

value: DIV 250


title: skin, ACD SalB, RS09

status: Public on Oct 14 2025

city: São Paulo

first: Maria

middle: Notomi

last: Sato

state: São Paulo

address: Av. Dr. Eneas de Carvalho Aguia, 470

department: Dermatology

country: Brazil

institute: University of São Paulo

description: Library name: RS09

data_processing:
These libraries were sequenced on the NextSeq 500 platform (Illumina) using the V2.5 Mid Output kit, 2 x 75 cycles.
The high-quality reads that were obtained from Fastp were then aligned to the reference genome with Subread v2.0.6 using the human genome GRCh38 version 104. The gene expression levels of the aligned reads were quantified using the FeatureCounts v2.0.6 tool.
Differentially expressed genes were identified using the DESeq2 package from R/Bioconductor, with statistical significance determined at an adjusted p-value ≤ 0.05 (Benjamini-Hochberg correction).
sequencing reads QA
adapters removal
Reads base correction and filtering
Reads mapping and counting
Sample outliers removal
Normalization
Differential expression calculation
Assembly: GRCh38 release-104
Supplementary files format and content: A tab-separated values (TSV) file containing normalized gene counts, with genes in rows and samples in columns.

source_name: skin

extract_protocol:
To obtain mRNA, skin samples stored in RNA later were thawed and fragmented using the Tissue Ruptor apparatus (Qiagen, Hilden, Germany) and the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's recommendations.
Libraries for sequencing were constructed with purified RNAs and TruSeq Stranded mRNA Library Prep kits (Illumina, San Diego, CA, USA), following the manufacturer's instructions.

treatment_protocol: Skin fragments measuring approximately 6 mm in diameter were collected from the region where the Alergo Chamber (Neoflex, São Paulo, SP, Brazil) with MI or saline was applied to individuals in the ACD MI+ and ACD MI- groups (controls), respectively. Biopsies were performed 48 hours after reapplication of the patch tests, both in the ACD MI+ and ACD MI- groups. The tissue was collected with a punch after antisepsis with 0.5% chlorhexidine alcohol solution, placement of sterile cloth fields, application of local infiltrative anesthesia with a 27-gauge needle and a sterilized metal syringe, and injection of 0.5 mL of a 2% lidocaine hydrochloride solution with norepinephrine hemitartrate 1:50,000. The collected tissue fragment was cut in half vertically, and one of the halves was stored in a 10% formalin solution at room temperature for later processing. The other half of the skin fragment was placed in RNA later solution (Sigma Chemical Co, St. Louis, MO, USA) and kept at -80°C for further processing.

value: skin

tag: treatment

value: Saline

tag: condition

value: Allergic Contact Dermatitis


title: skin, ACD MI-, UM05

description: Library name: UM05

value: Methilizolinone


title: skin, ACD MI-, UM06

description: Library name: UM06


title: skin, ACD MI-, UM03

description: Library name: UM03


title: skin, ACD SalA, RS08

description: Library name: RS08


title: Combo-Replicate-1

description: Library name: Combo-1


title: skin, ACD MI-, UM02

description: Library name: UM02


title: skin, ACD SalA, RS06

description: Library name: RS06


title: skin, ACD MI-, UM01

description: Library name: UM01


title: ABE_CHANGE_seq_BE_Control_2

description:
Library name: CRL4450
CHANGE-seq-BE for ABE targets


title: ABE_CIITA_E2

description:
Library name: CRL4448
CHANGE-seq-BE for ABE targets


title: skin, ACD SalB, RS05

description: Library name: RS05


title: skin, ACD SalB, RS04

description: Library name: RS04


title: skin, ACD SalA, RS03

description: Library name: RS03


title: ABE_CHANGE_seq_BE_Control_1

description:
Library name: CRL4444
CHANGE-seq-BE for ABE targets


title: ABE_CIITA_E1

description:
Library name: CRL4442
CHANGE-seq-BE for ABE targets


title: skin, ACD SalA, RS07

description: Library name: RS07


title: skin, ACD SalA, RS02

description: Library name: RS02


title: skin, ACD SalB, RS01

description: Library name: RS01


title: skin, ACD MIA, RM09

description: Library name: RM09


title: skin, ACD MIA, RM08

description: Library name: RM08


title: skin, ACD MIB, RM06

description: Library name: RM06


title: skin, ACD MIA, RM05

description: Library name: RM05


title: skin, ACD MIB, RM03

description: Library name: RM03


title: Skin, ACD MIB, RM04

description: Library name: RM04


title: skin, ACD MIA, RM02

description: Library name: RM02


title: skin, ACD MI-, UM04

description: Library name: UM04


title: skin, ACD MIB, RM01

description: Library name: RM01


title: Aged3_PlateSeq

status: Public on Oct 09 2025

city: San Francisco

first: Diana

middle: Matthew

last: Laird

state: CA

address: 35 Medical Center Way RM913D

institute: University of California

description:
Library name: Sample 12
SmartSeq2

data_processing:
Sequencing and Demultiplexing: 10X libraries were pooled and sequenced on NovaSeq S2 flow cells. Smart-seq2 libraries were pooled equimolar in sets of 4 to 16 384-well plates and sequenced on NextSeq 2000 P3 and NovaSeq S4 flow cells using the following cycling parameters:  Read 1: 100 cycles, Index 1: 12 cycles, Index 2: 12 cycles, Read 2: 100 cycles. The target read depth was 1–2 million paired-end reads per sample for Smart-seq2 libraries and 20,000 reads per cell for 10X 3’ GEX libraries. Raw BCL files were converted to FASTQ format and demultiplexed using Illumina’s bcl2fastq software (v2.20.0.422). For 10X Genomics libraries, FASTQ files were further processed and demultiplexed using CellRanger (v7.0.1).
Alignment and Gene Quantification: 10X Genomics data were aligned using CellRanger (v7.0.1) with the mm10 (mouse) reference genome. Smart-seq2 mouse reads were aligned to Gencode M31 (GRCm39) using STAR (v2.7.10a) with the following parameters:    ```   --outFilterMultimapNmax 20    --outSAMstrandField intronMotif    --outSAMtype BAM Unsorted    --outSAMattributes NH;HI;NM;MD    --outReadsUnmapped fastx    --alignIntronMin 20    --alignIntronMax 1000000    --alignMatesGapMax 1000000    --alignSJoverhangMin 8    --alignSJDBoverhangMin 1    ``` Gene counts were generated using HTSeq-count (v2.0.5) with stranded="no" and mode="intersection-nonempty". Gene counts were produced using HTSeq (v2.0.5) with stranded="false" and mode="intersection-nonempty".
Analysis: Samples were integrated usinf harmony and analysed using Seurat's standard workflow.
Non-Project Cell Removal: Within two of our samples (Young2, Aged2), naked mole rat iPSCs were added to the mouse cell suspension before sequencing for a separate experiment. All Oct4-positive naked mole rat cells that were successfully aligned to the mouse genome were removed.
Assembly: Mouse 10X: mm10 Mouse SS2:  GRCm39
Supplementary files format and content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post SoupX ambient RNA removal but pre Seurat filtration.

source_name: Ovary

extract_protocol:
To minimize batch effects, young and aged murine ovaries were collected on the same day for sequencing. Following removal of murine ovaries and receipt of human ovaries, surrounding tissue was removed by fine dissection. Ovaries were gently chopped using a razor blade and then transferred to a Conical tube with 2 mg/mL collagenase type IV (Gibco, 17104019) in DMEM (Gibco, 11960044). Tubes were incubated at +37oC shaking at 250rpm for 20 min then centrifuged at 250 x g for 5min. The supernatant was aspirated and 0.25 % trypsin-EDTA (Gibco, 25200056) was added. Tubes were incubated at +37oC shaking at 250rpm for 20 min then centrifuged at 250 x g for 5 min. The supernatant was aspirated, and the tissue was quenched with 10% FBS (Gibco, 10438026) in DMEM. Using a P1000, tissue was gently triturated to generate a single cell suspension. The cell suspension was filtered using a reversible 37µm sieve (STEMCELL Technologies, 27215). The sieve was rinsed with quench buffer (<37µm filtered flow through) and then flipped and placed in a new tube for rinsing with quench buffer (>37µm unfiltered mature oocyte pool hand-picked for SmartSeq2).
Smart-seq2 Library Preparation: Single oocytes were handpicked using an EZ-Grip pipette with a 125 μm EZ-Tip, briefly washed in 0.04% BSA-PBS, and transferred into individual wells containing lysis buffer master mix. Lysed oocytes were snap-frozen on dry ice and stored at −80°C for further processing by the Genomics Platform at the Chan Zuckerberg Biohub SF.   Reverse transcription (RT) and complementary DNA (cDNA) synthesis were performed in 96-well plates using the Smart-seq2 protocol. To preserve RNA integrity, 2–4 lysis plates were thawed on ice and processed in a pre-PCR laboratory. RT master mix (6 μL per well in 96-well plates; 0.6 μL per well in 384-well plates) was prepared using the following components: 0.06 μL 1M MgCl₂, 2 μL 5× First-Strand Buffer (Takara Bio, 639538), 2 μL 5M Betaine, 0.5 μL 100 mM DTT, 0.1 μL 100 μM TSO (Exiqon, 5′-AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG-3′), 0.25 μL RRI, 1 μL SmartScribe Reverse Transcriptase (Takara Bio, 639538), and 0.09 μL water. The RT master mix was dispensed into each well using an SPT Labtech Dragonfly Discovery liquid handler. Plates were sealed with a clear microseal, centrifuged at 1,000 rcf for 1 min, and incubated in a thermal cycler (Applied Biosystems ProFlex or Bio-Rad C1000 Touch Thermal Cycler**) under the following conditions: 42°C for 90 min, followed by 70°C for 5 min.  SmartSeq2 library construction: Second-strand synthesis and cDNA amplification were performed by adding 15 μL of cDNA master mix per 96-well plate (1.5 μL per 384-well plate), containing 12.5 μL KAPA HiFi HotStart ReadyMix 2X (Kapa Biosystems, KK2602), 0.25 μL 10 μM IS PCR primer (IDT, 5′-AAGCAGTGGTATCAACGCAGAGT-3′), 0.113 μL Lambda Exonuclease (NEB, M0262L), and 2.14 μL water. The cDNA master mix was dispensed using an SPT Labtech Dragonfly Discovery, and the plates were sealed, centrifuged at 1,000 rcf for 1 min, and subjected to the following cycling conditions: 37°C for 30 min; 95°C for 3 min; 21 cycles of 98°C for 20 s, 67°C for 15 s, 72°C for 4 min; followed by a final extension at 72°C for 5 min.   cDNA quantity was spot-checked using a Quant-iT dsDNA High Sensitivity Kit (Thermo Fisher, Q33120) and fluorescence was measured using a SpectraMax M5 microplate reader (Molecular Devices). cDNA quality was assessed on an Agilent 5300 Fragment Analyzer. High-concentration cDNA samples were diluted 1:10 with nuclease-free water for optimal enzymatic fragmentation.   Library preparation was performed using Illumina’s Nextera XT DNA Library Prep Kit (FC-131-1096), miniaturized for 384-well plates using an SPT Labtech Firefly liquid handler. Briefly, 0.4 μL cDNA (<1 ng) was stamped into each well of a 384-well plate, followed by 1.4 μL of tagmentation master mix (0.2 μL Tagment DNA buffer (TD) and 1.2 μL Amplicon Tagment Mix (ATM)). The plates were sealed, centrifuged at 2,000 rcf for 1 min, and incubated at 55°C for 5 min. Tagmentation was stopped by adding 0.4 μL of Neutralize Tagment Buffer (NT), followed by centrifugation at 2,000 rcf for 5 min.   Index PCR was performed by adding 1.2 μL of Nextera PCR Master Mix (NPM) and 0.8 μL of Nextera index adapters (0.4 μL of 5 μM i5 indexing primer, 0.4 μL of 5 μM i7 indexing primer, IDT). The thermal cycling program consisted of: 72°C for 3 min; 95°C for 30 s; 12 cycles of 95°C for 10 s, 55°C for 30 s, 72°C for 30 s; followed by a final extension at 72°C for 5 min.   Barcoded libraries were pooled using an SPT Labtech Mosquito LV, purified with two consecutive 0.7× AMPure XP bead clean-ups (Beckman Coulter, A63881), and eluted in 30 μL of nuclease-free water. Library fragment size was analyzed on an Agilent 4150 Tapestation System with D5000 ScreenTape (5067-5588) and quantified via qPCR (Bio-Rad CFX96 RT System) using the KAPA Library Quantification Kit (Kapa Biosystems, KK4923).  10X Genomics Library Preparation: Filtered cell suspensions were counted and adjusted to 1,000 cells/μL in 0.04% BSA (Research Products International, A30075) in 1X PBS. Library preparation was performed by the UCSF Genomics CoLabs using the 10X Genomics Chromium Next GEM Single Cell 3’ Kit with dual indexing, following the manufacturer’s protocol.

value: Ovary

value: Oocytes

tag: genotype

value: Wildtype

tag: batch


title: Aged2_PlateSeq

description:
Library name: Sample 10
SmartSeq2


title: Young1_PlateSeq

description:
Library name: Sample 2
SmartSeq2


title: Young2_PlateSeq

description:
Library name: Sample 4
SmartSeq2


title: HeLa, low-input, IP, replicate 4

status: Public on Oct 05 2025

city: Boston

first: Ryan

middle: A.

last: Flynn

state: MA

address: 1 Blackfan Circle

department: Department of Pediatrics

institute: Boston Children’s Hospital

description:
Library name: dVH4p
count_matrix_homo.csv

library_source: other

data_processing:
FASTQ files were demultiplexed by Illumina software. Reads were trimmed with cutadapt (v4.9) to remove UMIs, adapters, poly(A/G) tails, and low-quality bases, discarding reads <15 nt. Trimmed reads were aligned with bowtie2 (v2.5.4) to curated small ncRNA transcriptomes (human, mouse, or dog), retaining multimappers. Multi-mapped reads were resolved by an EM-based probabilistic assignment scheme adapted from salmon/alevin, yielding transcript-level counts. After EM hard-assignment, per-base pileups were generated from BAM files using samtools (v1.21) mpileup and processed with cpup (https://github.com/y9c/cpup) to extract per-position base counts (reference vs. non-reference bases, insertions, deletions, skips, mismatches). Count matrices were annotated with sample metadata (Input, IP, Control) and deposited as processed data. Software: cutadapt v4.9; bowtie2 v2.5.4; samtools v1.21; cpup v0.1; R v4.3.3
Assembly: Curated small ncRNA transcriptomes (see GitHub: www.github.com/FlynnLab/rPAL-seq)
Supplementary files format and content: count_matrix_homo.csv, count_matrix_mus.csv, count_matrix_canis.csv: Species-specific, EM-assigned transcript-level raw read counts (rounded to nearest integer). Each row corresponds to a transcript. Each column corresponds to a library. Values are raw counts used for DESeq2 analysis.
Supplementary files format and content: counts_long.csv: Per-base variant count matrix in long format. Each row represents one genomic position within a transcript. Columns include transcript/position identifiers (chr_pos, chr, pos, ref_base), sample metadata (super_group, group_name, replicates, pair_id, sample_id, sample, condition), sequencing depth (depth_raw), reference counts (REF), variant subcategories (SGID, A_star, C_star, G_star, T_star), and summary totals (mismatches, total_variant, nonvariant). Values are raw base counts used as input for variant enrichment analyses.

molecule: other

source_name: HeLa

growth_protocol: OCI-AML2, OCI-AML3, Molm13, Jurkat, Jeko1, Nalm6, and EMT6 cells were cultured in RPMI-1640 medium (Gibco, cat. no. 61870036); HeLa, A549, 293T, Huh7, LPS853 and LN308 were cultured in DMEM medium (Gibco, cat. no. 10566024). DiFi and MDCK cells were cultured in DMEM medium supplemented with 1% L-glutamine (Gibco, cat. no. 25030081) and 1% non-essential amino acids (Gibco, cat. no. 11140050). All media were supplemented with 10% FBS (R&D Systems, cat. no. S11150) and 1% penicillin-streptomycin (Gibco, cat. no. 15140122). Cells were maintained at 37 °C, 5% CO2. All cell lines tested negative for mycoplasma contamination (Universal mycoplasma detection kit; ATCC, cat. no. 30-1012K).

extract_protocol:
Cells were washed with PBS and lysed directly in RNAzol (Molecular Research Center) without trypsinization (1 mL per 10 cm plate of adherent cells or per 5 × 10^6 suspension cells). Lysates were homogenized, clarified by centrifugation, and crude small RNA was precipitated with isopropanol and water. RNA was purified on Zymo Research spin columns using guanidine/ethanol washes, on-column Proteinase K digestion, and water elution. Purified RNA was further treated with StcE mucinase (Sigma) followed by an additional Zymo column cleanup. Small RNAs were fractionated by mixing RNA with adjusted RNA binding buffer (Zymo RNA binding buffer mixed with one volume of ethanol) and recovered from the flow-through on a second Zymo column._x000B_To obtain secreted fractions, cells were cultured to ~80% confluence, washed with PBS, and incubated in serum-free medium for 48 h. Conditioned medium was cleared by centrifugation and filtration, concentrated with a 100 kDa cutoff filter, and ultracentrifuged to obtain small EVs (sEVs). Exomeres were isolated from the supernatant by additional ultracentrifugation, and supermeres were recovered from the exomere supernatant by higher-speed ultracentrifugation. Crude sEVs were further purified by iodixanol (Sigma) density-gradient centrifugation, and pooled fractions containing sEVs were washed and pelleted in PBS.
Total or small RNA (50 ng–2 µg) was 3' polyadenylated with end blocking and purified. Polyadenylated RNA was subjected to enhanced rPAL labeling, biotin enrichment on neutravidin beads, and sialidase-mediated release of sialoglycoRNA. Released RNA was reverse-transcribed using anchored oligo-dT primers with template switching, followed by PCR amplification with dual-indexed primers. Amplicons (200–500 bp) were purified by gel extraction and bead clean-up. Libraries were assessed by TapeStation, pooled by concentration, and sequenced on an Illumina NovaSeq X (single-end 100 bp, dual 8 bp indexes).

treatment_protocol: For production of extracellular vesicles (EVs) and non-vesicular extracellular nanoparticles (NVEPs), cells were cultured until 80% confluent. The cells were then washed three times with PBS and cultured in serum-free medium for 48 h.

value: HeLa

value: epithelial

tag: sample group

value: HeLa, low-input, IP


title: HeLa, low-input, IP, replicate 2

description:
Library name: dVH2p
count_matrix_homo.csv


title: HeLa, low-input, Control, replicate 4

description:
Library name: dVH4h
count_matrix_homo.csv

value: HeLa, low-input, Control


title: Aged1_PlateSeq

description:
Library name: Sample 8
SmartSeq2


title: HeLa, low-input, IP, replicate 3

description:
Library name: dVH3p
count_matrix_homo.csv


title: HeLa, low-input, Control, replicate 3

description:
Library name: dVH3h
count_matrix_homo.csv


title: HeLa, low-input, Control, replicate 2

description:
Library name: dVH2h
count_matrix_homo.csv


title: Skin, ACD MIA, RM07

description: Library name: RM07


title: AML3, low-input, IP, replicate 4

description:
Library name: dVA4p
count_matrix_homo.csv

value: hematopoietic

value: AML3, low-input, IP


title: AML3, low-input, Control, replicate 4

description:
Library name: dVA4h
count_matrix_homo.csv

value: AML3, low-input, Control


title: AML3, low-input, Control, replicate 3

description:
Library name: dVA3h
count_matrix_homo.csv


title: AML3, low-input, IP, replicate 2

description:
Library name: dVA2p
count_matrix_homo.csv


title: AML3, low-input, IP, replicate 3

description:
Library name: dVA3p
count_matrix_homo.csv


title: AML3, low-input, IP, replicate 1

description:
Library name: dVA1p
count_matrix_homo.csv


title: AML3, low-input, Control, replicate 2

description:
Library name: dVA2h
count_matrix_homo.csv


title: AML3, low-input, Control, replicate 1

description:
Library name: dVA1h
count_matrix_homo.csv


title: HeLa, Control, replicate 3

description:
Library name: VH3h
count_matrix_homo.csv
counts_long.csv

value: HeLa, Control


title: HeLa, Input, replicate 4

description:
Library name: VH4i
count_matrix_homo.csv
counts_long.csv

value: HeLa, Input


title: HeLa, IP, replicate 3

description:
Library name: VH3p
count_matrix_homo.csv
counts_long.csv

value: HeLa, IP


title: HeLa, Input, replicate 3

description:
Library name: VH3i
count_matrix_homo.csv
counts_long.csv


title: HeLa, IP, replicate 4

description:
Library name: VH4p
count_matrix_homo.csv
counts_long.csv


title: HeLa, Control, replicate 2

description:
Library name: VH2h
count_matrix_homo.csv
counts_long.csv


title: Young3_PlateSeq

description:
Library name: Sample 6
SmartSeq2


title: HeLa, IP, replicate 2

description:
Library name: VH2p
count_matrix_homo.csv
counts_long.csv


title: HeLa, low-input, Control, replicate 1

description:
Library name: dVH1h
count_matrix_homo.csv


title: HeLa, Input, replicate 2

description:
Library name: VH2i
count_matrix_homo.csv
counts_long.csv


title: HeLa, low-input, IP, replicate 1

description:
Library name: dVH1p
count_matrix_homo.csv


title: HeLa, IP, replicate 1

description:
Library name: VH1p
count_matrix_homo.csv
counts_long.csv


title: HeLa, Control, replicate 1

description:
Library name: VH1h
count_matrix_homo.csv
counts_long.csv


title: AML3, IP, replicate 4

description:
Library name: VA4p
count_matrix_homo.csv
counts_long.csv

value: AML3, IP


title: AML3, Input, replicate 4

description:
Library name: VA4i
count_matrix_homo.csv
counts_long.csv

value: AML3, Input


title: HeLa, Input, replicate 1

description:
Library name: VH1i
count_matrix_homo.csv
counts_long.csv


title: AML3, Control, replicate 4

description:
Library name: VA4h
count_matrix_homo.csv
counts_long.csv

value: AML3, Control


title: AML3, IP, replicate 3

description:
Library name: VA3p
count_matrix_homo.csv
counts_long.csv


title: AML3, Control, replicate 2

description:
Library name: VA2h
count_matrix_homo.csv
counts_long.csv


title: AML3, Control, replicate 3

description:
Library name: VA3h
count_matrix_homo.csv
counts_long.csv


title: HeLa, Control, replicate 4

description:
Library name: VH4h
count_matrix_homo.csv
counts_long.csv


title: AML3, Input, replicate 2

description:
Library name: VA2i
count_matrix_homo.csv
counts_long.csv


title: AML3, IP, replicate 1

description:
Library name: VA1p
count_matrix_homo.csv
counts_long.csv


title: AML3, Input, replicate 3

description:
Library name: VA3i
count_matrix_homo.csv
counts_long.csv


title: AML3, Control, replicate 1

description:
Library name: VA1h
count_matrix_homo.csv
counts_long.csv


title: AML3, IP, replicate 2

description:
Library name: VA2p
count_matrix_homo.csv
counts_long.csv


title: AML3, Input, replicate 1

description:
Library name: VA1i
count_matrix_homo.csv
counts_long.csv


title: DiFi, IP, replicate 3

description:
Library name: e24p
count_matrix_homo.csv
counts_long.csv

source_name: DiFi

value: DiFi

value: DiFi, IP


title: DiFi, Input, replicate 3

description:
Library name: e24i
count_matrix_homo.csv
counts_long.csv

value: DiFi, Input


title: DiFi, IP, replicate 2

description:
Library name: e23p
count_matrix_homo.csv
counts_long.csv


title: DiFi, Input, replicate 2

description:
Library name: e23i
count_matrix_homo.csv
counts_long.csv


title: DiFi, Control, replicate 2

description:
Library name: e23h
count_matrix_homo.csv
counts_long.csv

value: DiFi, Control


title: DiFi, Control, replicate 1

description:
Library name: e22h
count_matrix_homo.csv
counts_long.csv


title: DiFi, Input, replicate 1

description:
Library name: e22i
count_matrix_homo.csv
counts_long.csv


title: MDCK, Control, replicate 3

description:
Library name: e21h
count_matrix_canis.csv

source_name: MDCK

value: MDCK

value: MDCK, Control


title: MDCK, IP, replicate 3

description:
Library name: e21p
count_matrix_canis.csv

value: epithelial

value: MDCK, IP


title: MDCK, Input, replicate 3

description:
Library name: e21i
count_matrix_canis.csv

value: MDCK, Input


title: MDCK, Control, replicate 2

description:
Library name: e20h
count_matrix_canis.csv


title: MDCK, IP, replicate 2

description:
Library name: e20p
count_matrix_canis.csv


title: DiFi Supermere, IP, replicate 3

description:
Library name: e18p
count_matrix_homo.csv

value: DiFi Supermere, IP


title: MDCK, Control, replicate 1

description:
Library name: e19h
count_matrix_canis.csv


title: DiFi Supermere, Control, replicate 3

description:
Library name: e18h
count_matrix_homo.csv

value: DiFi Supermere, Control


title: MDCK, IP, replicate 1

description:
Library name: e19p
count_matrix_canis.csv


title: MDCK, Input, replicate 1

description:
Library name: e19i
count_matrix_canis.csv


title: DiFi, Control, replicate 3

description:
Library name: e24h
count_matrix_homo.csv
counts_long.csv


title: DiFi Exomere, Control, replicate 3

description:
Library name: e17h
count_matrix_homo.csv

value: DiFi Exomere, Control


title: DiFi Supermere, Input, replicate 3

description:
Library name: e18i
count_matrix_homo.csv

value: DiFi Supermere, Input


title: DiFi Supermere, IP, replicate 2

description:
Library name: e15p
count_matrix_homo.csv


title: DiFi sEV, IP, replicate 3

description:
Library name: e16p
count_matrix_homo.csv

value: DiFi sEV, IP


title: DiFi sEV, Control, replicate 3

description:
Library name: e16h
count_matrix_homo.csv

value: DiFi sEV, Control


title: DiFi, IP, replicate 1

description:
Library name: e22p
count_matrix_homo.csv
counts_long.csv


title: DiFi Supermere, Input, replicate 2

description:
Library name: e15i
count_matrix_homo.csv


title: DiFi Exomere, IP, replicate 3

description:
Library name: e17p
count_matrix_homo.csv

value: DiFi Exomere, IP


title: DiFi Exomere, Input, replicate 3

description:
Library name: e17i
count_matrix_homo.csv

value: DiFi Exomere, Input


title: DiFi Exomere, Control, replicate 2

description:
Library name: e14h
count_matrix_homo.csv

value: DiFi


title: DiFi Exomere, IP, replicate 2

description:
Library name: e14p
count_matrix_homo.csv


title: DiFi sEV, IP, replicate 2

description:
Library name: e13p
count_matrix_homo.csv


title: DiFi Supermere, Control, replicate 2

description:
Library name: e15h
count_matrix_homo.csv


title: DiFi sEV, Input, replicate 2

description:
Library name: e13i
count_matrix_homo.csv

value: DiFi sEV, Input


title: DiFi sEV, Control, replicate 2

description:
Library name: e13h
count_matrix_homo.csv


title: DiFi sEV, Input, replicate 3

description:
Library name: e16i
count_matrix_homo.csv


title: DiFi Supermere, Control, replicate 1

description:
Library name: e12h
count_matrix_homo.csv


title: DiFi Supermere, IP, replicate 1

description:
Library name: e12p
count_matrix_homo.csv


title: MDCK, Input, replicate 2

description:
Library name: e20i
count_matrix_canis.csv


title: DiFi Supermere, Input, replicate 1

description:
Library name: e12i
count_matrix_homo.csv


title: DiFi Exomere, Input, replicate 2

description:
Library name: e14i
count_matrix_homo.csv


title: DiFi Exomere, IP, replicate 1

description:
Library name: e11p
count_matrix_homo.csv


title: DiFi Exomere, Control, replicate 1

description:
Library name: e11h
count_matrix_homo.csv


title: DiFi Exomere, Input, replicate 1

description:
Library name: e11i
count_matrix_homo.csv


title: DiFi sEV, Control, replicate 1

description:
Library name: e10h
count_matrix_homo.csv


title: DiFi sEV, IP, replicate 1

description:
Library name: e10p
count_matrix_homo.csv


title: Nalm6, Control, replicate 4

description:
Library name: 44h
count_matrix_homo.csv
counts_long.csv

value: hematopoietic

value: Nalm6, Control


title: DiFi sEV, Input, replicate 1

description:
Library name: e10i
count_matrix_homo.csv


title: Nalm6, Input, replicate 4

description:
Library name: 44i
count_matrix_homo.csv
counts_long.csv

value: Nalm6, Input


title: Nalm6, IP, replicate 3

description:
Library name: 43p
count_matrix_homo.csv
counts_long.csv

value: Nalm6, IP


title: Nalm6, Control, replicate 3

description:
Library name: 43h
count_matrix_homo.csv
counts_long.csv


title: Nalm6, Control, replicate 2

description:
Library name: 42h
count_matrix_homo.csv
counts_long.csv


title: Nalm6, IP, replicate 2

description:
Library name: 42p
count_matrix_homo.csv
counts_long.csv


title: Nalm6, Input, replicate 1

description:
Library name: 41i
count_matrix_homo.csv
counts_long.csv


title: Nalm6, Control, replicate 1

description:
Library name: 41h
count_matrix_homo.csv
counts_long.csv


title: Nalm6, Input, replicate 2

description:
Library name: 42i
count_matrix_homo.csv
counts_long.csv


title: Nalm6, Input, replicate 3

description:
Library name: 43i
count_matrix_homo.csv
counts_long.csv


title: Jeko1, Control, replicate 4

description:
Library name: 40h
count_matrix_homo.csv
counts_long.csv

value: Jeko1, Control


title: Nalm6, IP, replicate 1

description:
Library name: 41p
count_matrix_homo.csv
counts_long.csv


title: Jeko1, Control, replicate 3

description:
Library name: 39h
count_matrix_homo.csv
counts_long.csv


title: Jeko1, IP, replicate 3

description:
Library name: 39p
count_matrix_homo.csv
counts_long.csv

value: Jeko1, IP


title: Jeko1, Input, replicate 3

description:
Library name: 39i
count_matrix_homo.csv
counts_long.csv

value: Jeko1, Input


title: Jeko1, Control, replicate 2

description:
Library name: 38h
count_matrix_homo.csv
counts_long.csv


title: Jeko1, Input, replicate 2

description:
Library name: 38i
count_matrix_homo.csv
counts_long.csv


title: Jeko1, Input, replicate 4

description:
Library name: 40i
count_matrix_homo.csv
counts_long.csv


title: Jeko1, Control, replicate 1

description:
Library name: 37h
count_matrix_homo.csv
counts_long.csv


title: Jeko1, IP, replicate 1

description:
Library name: 37p
count_matrix_homo.csv
counts_long.csv


title: AML2, Control, replicate 4

description:
Library name: 32h
count_matrix_homo.csv
counts_long.csv

value: AML2, Control


title: Nalm6, IP, replicate 4

description:
Library name: 44p
count_matrix_homo.csv
counts_long.csv


title: AML2, IP, replicate 4

description:
Library name: 32p
count_matrix_homo.csv
counts_long.csv

value: AML2, IP


title: AML2, Input, replicate 4

description:
Library name: 32i
count_matrix_homo.csv
counts_long.csv

value: AML2, Input


title: Jeko1, Input, replicate 1

description:
Library name: 37i
count_matrix_homo.csv
counts_long.csv


title: AML2, IP, replicate 3

description:
Library name: 31p
count_matrix_homo.csv
counts_long.csv


title: AML2, Control, replicate 3

description:
Library name: 31h
count_matrix_homo.csv
counts_long.csv


title: AML2, Control, replicate 2

description:
Library name: 30h
count_matrix_homo.csv
counts_long.csv


title: AML2, IP, replicate 2

description:
Library name: 30p
count_matrix_homo.csv
counts_long.csv


title: AML2, Input, replicate 3

description:
Library name: 31i
count_matrix_homo.csv
counts_long.csv


title: AML2, Input, replicate 2

description:
Library name: 30i
count_matrix_homo.csv
counts_long.csv


title: AML2, Control, replicate 1

description:
Library name: 29h
count_matrix_homo.csv
counts_long.csv


title: Jeko1, IP, replicate 4

description:
Library name: 40p
count_matrix_homo.csv
counts_long.csv


title: AML2, Input, replicate 1

description:
Library name: 29i
count_matrix_homo.csv
counts_long.csv


title: A549, Control, replicate 3

description:
Library name: 23h
count_matrix_homo.csv
counts_long.csv

value: epithelial

value: A549, Control


title: A549, IP, replicate 4

description:
Library name: 24p
count_matrix_homo.csv
counts_long.csv


title: A549, IP, replicate 3

description:
Library name: 23p
count_matrix_homo.csv
counts_long.csv


title: AML2, IP, replicate 1

description:
Library name: 29p
count_matrix_homo.csv
counts_long.csv


title: Jeko1, IP, replicate 2

description:
Library name: 38p
count_matrix_homo.csv
counts_long.csv


title: A549, Input, replicate 4

description:
Library name: 24i
count_matrix_homo.csv
counts_long.csv

value: A549, Input


title: A549, Control, replicate 4

description:
Library name: 24h
count_matrix_homo.csv
counts_long.csv


title: A549, IP, replicate 2

description:
Library name: 22p
count_matrix_homo.csv
counts_long.csv


title: A549, Input, replicate 2

description:
Library name: 22i
count_matrix_homo.csv
counts_long.csv


title: A549, Control, replicate 2

description:
Library name: 22h
count_matrix_homo.csv
counts_long.csv


title: A549, Control, replicate 1

description:
Library name: 21h
count_matrix_homo.csv
counts_long.csv


title: A549, Input, replicate 1

description:
Library name: 21i
count_matrix_homo.csv
counts_long.csv


title: Molm13, Control, replicate 4

description:
Library name: 20h
count_matrix_homo.csv
counts_long.csv

value: Molm13, Control


title: Molm13, IP, replicate 4

description:
Library name: 20p
count_matrix_homo.csv
counts_long.csv

value: Molm13, IP


title: A549, IP, replicate 1

description:
Library name: 21p
count_matrix_homo.csv
counts_long.csv


title: Molm13, Control, replicate 3

description:
Library name: 19h
count_matrix_homo.csv
counts_long.csv


title: Molm13, Input, replicate 4

description:
Library name: 20i
count_matrix_homo.csv
counts_long.csv

value: Molm13, Input


title: Molm13, IP, replicate 3

description:
Library name: 19p
count_matrix_homo.csv
counts_long.csv


title: Molm13, Input, replicate 3

description:
Library name: 19i
count_matrix_homo.csv
counts_long.csv


title: Molm13, Control, replicate 2

description:
Library name: 18h
count_matrix_homo.csv
counts_long.csv


title: Molm13, Input, replicate 2

description:
Library name: 18i
count_matrix_homo.csv
counts_long.csv


title: Molm13, IP, replicate 2

description:
Library name: 18p
count_matrix_homo.csv
counts_long.csv


title: Molm13, Input, replicate 1

description:
Library name: 17i
count_matrix_homo.csv
counts_long.csv


title: Huh7, IP, replicate 4

description:
Library name: 16p
count_matrix_homo.csv
counts_long.csv

value: Huh7, IP


title: Molm13, IP, replicate 1

description:
Library name: 17p
count_matrix_homo.csv
counts_long.csv

value: hematopoietic


title: Huh7, Input, replicate 4

description:
Library name: 16i
count_matrix_homo.csv
counts_long.csv

value: Huh7, Input


title: A549, Input, replicate 3

description:
Library name: 23i
count_matrix_homo.csv
counts_long.csv


title: Huh7, IP, replicate 3

description:
Library name: 15p
count_matrix_homo.csv
counts_long.csv


title: Huh7, Input, replicate 3

description:
Library name: 15i
count_matrix_homo.csv
counts_long.csv


title: MDCK Supermere, Input, replicate 3

description:
Library name: e9i
count_matrix_canis.csv

organism: Canis lupus familiaris

value: MDCK

value: MDCK Supermere, Input


title: Huh7, Control, replicate 2

description:
Library name: 14h
count_matrix_homo.csv
counts_long.csv

value: Huh7, Control


title: MDCK Exomere, Control, replicate 3

description:
Library name: e8h
count_matrix_canis.csv

value: MDCK Exomere, Control


title: Huh7, IP, replicate 2

description:
Library name: 14p
count_matrix_homo.csv
counts_long.csv


title: MDCK sEV, Control, replicate 3

description:
Library name: e7h
count_matrix_canis.csv

value: MDCK sEV, Control


title: Huh7, Control, replicate 1

description:
Library name: 13h
count_matrix_homo.csv
counts_long.csv


title: Huh7, IP, replicate 1

description:
Library name: 13p
count_matrix_homo.csv
counts_long.csv


title: LN308, Control, replicate 4

description:
Library name: 12h
count_matrix_homo.csv
counts_long.csv

value: neural (glial)

value: LN308, Control


title: MDCK sEV, IP, replicate 3

description:
Library name: e7p
count_matrix_canis.csv

value: MDCK sEV, IP


title: MDCK sEV, Input, replicate 3

description:
Library name: e7i
count_matrix_canis.csv

value: epithelial

value: MDCK sEV, Input


title: MDCK Exomere, IP, replicate 3

description:
Library name: e8p
count_matrix_canis.csv

value: MDCK Exomere, IP


title: MDCK Supermere, Control, replicate 2

description:
Library name: e6h
count_matrix_canis.csv

value: MDCK Supermere, Control


title: Huh7, Input, replicate 1

description:
Library name: 13i
count_matrix_homo.csv
counts_long.csv


title: LN308, IP, replicate 4

description:
Library name: 12p
count_matrix_homo.csv
counts_long.csv

value: LN308, IP


title: Molm13, Control, replicate 1

description:
Library name: 17h
count_matrix_homo.csv
counts_long.csv

value: Molm13, Control


title: LN308, Control, replicate 3

description:
Library name: 11h
count_matrix_homo.csv
counts_long.csv


title: Huh7, Control, replicate 4

description:
Library name: 16h
count_matrix_homo.csv
counts_long.csv


title: MDCK Supermere, Input, replicate 2

description:
Library name: e6i
count_matrix_canis.csv


title: MDCK Supermere, IP, replicate 2

description:
Library name: e6p
count_matrix_canis.csv

value: MDCK Supermere, IP


title: LN308, Input, replicate 4

description:
Library name: 12i
count_matrix_homo.csv
counts_long.csv

value: LN308, Input


title: Huh7, Control, replicate 3

description:
Library name: 15h
count_matrix_homo.csv
counts_long.csv


title: LN308, IP, replicate 3

description:
Library name: 11p
count_matrix_homo.csv
counts_long.csv


title: LN308, Input, replicate 3

description:
Library name: 11i
count_matrix_homo.csv
counts_long.csv


title: MDCK Supermere, Control, replicate 3

description:
Library name: e9h
count_matrix_canis.csv


title: MDCK Supermere, IP, replicate 3

description:
Library name: e9p
count_matrix_canis.csv


title: Huh7, Input, replicate 2

description:
Library name: 14i
count_matrix_homo.csv
counts_long.csv

value: Huh7, Input


title: MDCK Exomere, Control, replicate 2

description:
Library name: e5h
count_matrix_canis.csv

value: MDCK


title: MDCK Exomere, IP, replicate 2

description:
Library name: e5p
count_matrix_canis.csv


title: MDCK Exomere, Input, replicate 2

description:
Library name: e5i
count_matrix_canis.csv

value: MDCK Exomere, Input


title: LN308, IP, replicate 2

description:
Library name: 10p
count_matrix_homo.csv
counts_long.csv


title: LN308, Control, replicate 2

description:
Library name: 10h
count_matrix_homo.csv
counts_long.csv


title: MDCK Exomere, Input, replicate 3

description:
Library name: e8i
count_matrix_canis.csv


title: MDCK sEV, Control, replicate 2

description:
Library name: e4h
count_matrix_canis.csv


title: LN308, Input, replicate 2

description:
Library name: 10i
count_matrix_homo.csv
counts_long.csv


title: MDCK sEV, Input, replicate 2

description:
Library name: e4i
count_matrix_canis.csv


title: LN308, Control, replicate 1

description:
Library name: 9h
count_matrix_homo.csv
counts_long.csv


title: LN308, IP, replicate 1

description:
Library name: 9p
count_matrix_homo.csv
counts_long.csv


title: MDCK Supermere, Control, replicate 1

description:
Library name: e3h
count_matrix_canis.csv


title: LN308, Input, replicate 1

description:
Library name: 9i
count_matrix_homo.csv
counts_long.csv


title: MDCK Supermere, IP, replicate 1

description:
Library name: e3p
count_matrix_canis.csv


title: MDCK Exomere, Control, replicate 1

description:
Library name: e2h
count_matrix_canis.csv


title: LPS853, IP, replicate 4

description:
Library name: 8p
count_matrix_homo.csv
counts_long.csv

value: mesenchymal

value: LPS853, IP


title: LPS853, Control, replicate 3

description:
Library name: 7h
count_matrix_homo.csv
counts_long.csv

value: LPS853, Control


title: MDCK Exomere, IP, replicate 1

description:
Library name: e2p
count_matrix_canis.csv


title: LPS853, IP, replicate 3

description:
Library name: 7p
count_matrix_homo.csv
counts_long.csv


title: MDCK Supermere, Input, replicate 1

description:
Library name: e3i
count_matrix_canis.csv

value: MDCK Supermere, Input


title: MDCK sEV, Control, replicate 1

description:
Library name: e1h
count_matrix_canis.csv

value: MDCK sEV, Control


title: MDCK sEV, IP, replicate 1

description:
Library name: e1p
count_matrix_canis.csv

value: MDCK sEV, IP


title: LPS853, Input, replicate 4

description:
Library name: 8i
count_matrix_homo.csv
counts_long.csv

value: LPS853, Input


title: LPS853, Control, replicate 2

description:
Library name: 6h
count_matrix_homo.csv
counts_long.csv


title: LPS853, Input, replicate 3

description:
Library name: 7i
count_matrix_homo.csv
counts_long.csv


title: LPS853, IP, replicate 2

description:
Library name: 6p
count_matrix_homo.csv
counts_long.csv


title: LPS853, Input, replicate 2

description:
Library name: 6i
count_matrix_homo.csv
counts_long.csv


title: MDCK sEV, Input, replicate 1

description:
Library name: e1i
count_matrix_canis.csv

value: epithelial

value: MDCK sEV, Input


title: LPS853, Control, replicate 1

description:
Library name: 5h
count_matrix_homo.csv
counts_long.csv


title: LPS853, IP, replicate 1

description:
Library name: 5p
count_matrix_homo.csv
counts_long.csv


title: LPS853, Input, replicate 1

description:
Library name: 5i
count_matrix_homo.csv
counts_long.csv


title: 293T, IP, replicate 4

description:
Library name: 4p
count_matrix_homo.csv
counts_long.csv


title: 293T, Control, replicate 3

description:
Library name: 3h
count_matrix_homo.csv
counts_long.csv

value: 293T, Control


title: 293T, Input, replicate 4

description:
Library name: 4i
count_matrix_homo.csv
counts_long.csv

value: 293T, Input


title: LPS853, Control, replicate 4

description:
Library name: 8h
count_matrix_homo.csv
counts_long.csv


title: 293T, Input, replicate 3

description:
Library name: 3i
count_matrix_homo.csv
counts_long.csv


title: 293T, IP, replicate 2

description:
Library name: 2p
count_matrix_homo.csv
counts_long.csv


title: MDCK sEV, IP, replicate 2

description:
Library name: e4p
count_matrix_canis.csv


title: 293T, Control, replicate 4

description:
Library name: 4h
count_matrix_homo.csv
counts_long.csv


title: MDCK Exomere, Input, replicate 1

description:
Library name: e2i
count_matrix_canis.csv


title: 293T, Input, replicate 2

description:
Library name: 2i
count_matrix_homo.csv
counts_long.csv


title: 293T, Control, replicate 1

description:
Library name: 1h
count_matrix_homo.csv
counts_long.csv


title: 293T, Input, replicate 1

description:
Library name: 1i
count_matrix_homo.csv
counts_long.csv


title: EMT6, Control, replicate 4

description:
Library name: 28h
count_matrix_mus.csv

value: EMT6, Control


title: 293T, IP, replicate 3

description:
Library name: 3p
count_matrix_homo.csv
counts_long.csv


title: 293T, IP, replicate 1

description:
Library name: 1p
count_matrix_homo.csv
counts_long.csv


title: EMT6, IP, replicate 4

description:
Library name: 28p
count_matrix_mus.csv

value: EMT6, IP


title: EMT6, Input, replicate 4

description:
Library name: 28i
count_matrix_mus.csv

value: EMT6, Input


title: EMT6, Control, replicate 3

description:
Library name: 27h
count_matrix_mus.csv


title: EMT6, Control, replicate 2

description:
Library name: 26h
count_matrix_mus.csv


title: EMT6, IP, replicate 2

description:
Library name: 26p
count_matrix_mus.csv


title: EMT6, IP, replicate 3

description:
Library name: 27p
count_matrix_mus.csv


title: EMT6, IP, replicate 1

description:
Library name: 25p
count_matrix_mus.csv


title: EMT6, Input, replicate 3

description:
Library name: 27i
count_matrix_mus.csv


title: EMT6, Input, replicate 1

description:
Library name: 25i
count_matrix_mus.csv


title: Human lung organoid, period 20

status: Public on Sep 27 2025

city: Xianmen

first: Yuchen

last: Liu

address: Xiangan South Road

country: China

institute: Xianmen University

description:
Library name: Human lung organoid period 20
SeekOne

data_processing:
Cell heterogeneity, clustering, integration, and visualization: Preliminary data preprocessing was performed using SeekSoulTools (v1.2.2, http://seeksoul.seekgene.com/)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hESC-drived alveolar organoids

growth_protocol: Alveolar organoids were culture in Matrigel and maintained in medium containing dexamethasone, 8-Br-cAMP, 3-isobutyl-1-methylxanthine, KGF, CHIR99021, and SB431542

extract_protocol:
Alveolar organoids were differentiated from H9 hESCs in a stepwise protocol.
Single-cell RNA-Seq libraries were prepared using SeekOne® Single Cell Whole Trancriptome Kit according to manufacturer’s instructions (SeekGene Catalog No.K00801). Briefly, an appropriate number of cells were mixed with reverse transcription reagents and added to the sample wells of the SeekOne® DD Chip S3 (Chip S3). Then, Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in Chip S3. Subsequently, Cell-containing reverse transcription reagents and BHBs were encapsulated into emulsion droplets using SeekOne® Digital Droplet System. Immediately following transferring emulsion droplets into PCR tubes, fifteen cycles of annealing (ramping from 8 °C to 42 °C) followed by a 5-min heat inactivation at 85°C were performed to obtain barcoded cDNA. Next, the barcoded cDNA was purified from broken droplet and then twice PCR reactions were performed to remove the majority of ribosomal and mitochondrial cDNA. AMPure beads were used to purify cDNA from the post PCR reaction mixture. Finally, one forth volume of cDNA was fragmented, end repaired, A-tailed and ligated into sequencing adaptor. DNA amplified by index PCR contains any part of polyA or non-PolyA RNA as well as Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were purified using AMPure beads and quantified by quantitative PCR (KAPA Biosystems KK4824). The libraries were then sequenced on Illumina NovaSeq 6000 with PE150 read length or DNBSEQ-T7 platform with PE150 read length.

value: hESC-drived alveolar organoids

value: wild type


title: geo_submission_scRNAseq

status: Public on Oct 03 2025

city: Cambridge

first: Samouil

middle: L

last: Farhi

address: 75 Ames St

department: Spatial Technology Platform

institute: Broad Institute of MIT and Harvard

description:
Library name: geo_submission_scRNAseq
10x Chromium Single Cell Gene Expression FLEX
Multitissue TMAs including: Bladder cancer, Breast cancer, Colorectal cancer, Head and Neck Squamous Cell Carcinoma, Melanoma, Non-Small Cell Lung Cancer, Ovarian cancer, Renal cell carcinoma, Pancreatic cancer, Prostate cancer, Hepatocellular carcinoma (liver cancer), Thyroid cancer, Lymphoma, Testicular cancer, Kidney cancer, Squamous Cell Carcinoma, and Liposarcoma.

data_processing:
The sequencing data was demultiplexed using bcl2fastq (Illumina). The resulting FASTQ files were processed with Cell Ranger v7.0.1 (10X Genomics) using the multi pipeline and the GRCh38-2020-A reference genome.
Assembly: GRCh38-2020-A
Supplementary files format and content: tsv.gz and mtx.gz files: barcodes, features, and matrix.
Supplementary files format and content: bri2614_8plex.csv: metadata that maps raw data to two TMA (tTMA1 and tTMA2).

source_name: Multitissue TMAs (detailed in the description field)

extract_protocol:
For each sample, two formalin-fixed paraffin-embedded (FFPE) curls (25 μm each) were dissociated using the Miltenyi Biotech FFPE Tissue Dissociation Kit (CG000632 RevA, 10X Genomics). The resulting cell suspension was divided equally into four centrifuge tubes, each containing approximately 300,000 cells. Cells in each tube were hybridized with a unique Probe Barcode, as per the instructions in the "Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples" user guide (CG000527, 10X Genomics). Post-hybridization, cells from the four tubes were washed, counted, and pooled in equal proportions. Approximately 40,000 cells from the pooled suspension were loaded onto a Chromium Q chip (PN-1000422, 10X Genomics). Sequencing libraries were prepared and sequenced on an Illumina NovaSeq platform using paired-end dual-indexing (49 cycles for Read 1, 10 cycles for i7, 10 cycles for i5, and 90 cycles for Read 2). The sequencing data was demultiplexed using bcl2fastq (Illumina). The resulting FASTQ files were processed with Cell Ranger v7.0.1 (10X Genomics) using the multi pipeline and the GRCh38-2020-A reference genome.
"Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples" user guide (CG000527, 10X Genomics)


title: Tail_Female_8_weeks_bACE [209362530044_R06C02]

status: Public on Sep 26 2025

type: genomic

city: Phialdelphia

first: Wanding

last: Zhou

state: Pennsylvania

address: 3501 Civic Center Blvd, Philadelphia, PA 19104, Colket Translational Research Building, 9300, Colket Translational Research Building

department: Pathology & Lab Medicine

institute: Children's Hospital of Philadelphia

description:
Mouse_ID:ZM22
209362530044_R06C02

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.20
Normalized average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Phenol/Chloroform/Isoamyl alcohol

value: Tail

tag: gender

value: Female

value: 8 weeks

value: bACE

value: Normal


title: Tail_Female_8_weeks_BS [209362530044_R05C02]

description:
Mouse_ID:ZM22
209362530044_R05C02

value: BS


title: Human lung organoid, period 3

description:
Library name: Human lung organoid period 3
SeekOne


title: EMT6, Input, replicate 2

description:
Library name: 26i
count_matrix_mus.csv


title: Ears_Female_8_weeks_bACE [209362530044_R04C02]

description:
Mouse_ID:ZM22
209362530044_R04C02

value: Ears


title: Ears_Female_8_weeks_BS [209362530044_R03C02]

description:
Mouse_ID:ZM22
209362530044_R03C02


title: 293T, Control, replicate 2

description:
Library name: 2h
count_matrix_homo.csv
counts_long.csv


title: Human lung organoid, period 7

description:
Library name: Human lung organoid period 7
SeekOne


title: Spleen_Female_8_weeks_bACE [209362530044_R02C02]

description:
Mouse_ID:ZM22
209362530044_R02C02

value: Spleen


title: EMT6, Control, replicate 1

description:
Library name: 25h
count_matrix_mus.csv

value: epithelial


title: Kidney_Female_8_weeks_BS [209362530044_R05C01]

description:
Mouse_ID:ZM22
209362530044_R05C01

value: Kidney


title: Colon_Female_8_weeks_bACE [209362530044_R04C01]

description:
Mouse_ID:ZM22
209362530044_R04C01

value: Colon


title: Colon_Female_8_weeks_BS [209362530044_R03C01]

description:
Mouse_ID:ZM22
209362530044_R03C01


title: Kidney_Female_8_weeks_bACE [209362530044_R06C01]

description:
Mouse_ID:ZM22
209362530044_R06C01


title: Tail_Female_8_weeks_bACE [209362530044_R02C01]

description:
Mouse_ID:ZM21
209362530044_R02C01


title: Tail_Female_8_weeks_BS [209362530044_R01C01]

description:
Mouse_ID:ZM21
209362530044_R01C01


title: Ears_Female_8_weeks_bACE [209362530039_R06C02]

description:
Mouse_ID:ZM21
209362530039_R06C02


title: Ears_Female_8_weeks_BS [209362530039_R05C02]

description:
Mouse_ID:ZM21
209362530039_R05C02


title: Spleen_Female_8_weeks_bACE [209362530039_R04C02]

description:
Mouse_ID:ZM21
209362530039_R04C02


title: Spleen_Female_8_weeks_BS [209362530039_R03C02]

description:
Mouse_ID:ZM21
209362530039_R03C02


title: Colon_Female_8_weeks_bACE [209362530039_R06C01]

description:
Mouse_ID:ZM21
209362530039_R06C01


title: Kidney_Female_8_weeks_BS [209362530039_R01C02]

description:
Mouse_ID:ZM21
209362530039_R01C02


title: Kidney_Female_8_weeks_bACE [209362530039_R02C02]

description:
Mouse_ID:ZM21
209362530039_R02C02


title: Colon_Female_8_weeks_BS [209362530039_R05C01]

description:
Mouse_ID:ZM21
209362530039_R05C01


title: Tail_Male_8_weeks_bACE [209362530039_R04C01]

description:
Mouse_ID:ZM20
209362530039_R04C01

value: Male


title: Ears_Male_8_weeks_BS [209362530039_R01C01]

description:
Mouse_ID:ZM20
209362530039_R01C01


title: Spleen_Male_8_weeks_BS [209362530043_R05C02]

description:
Mouse_ID:ZM20
209362530043_R05C02


title: Spleen_Male_8_weeks_bACE [209362530043_R06C02]

description:
Mouse_ID:ZM20
209362530043_R06C02


title: Tail_Male_8_weeks_BS [209362530039_R03C01]

description:
Mouse_ID:ZM20
209362530039_R03C01


title: Kidney_Male_8_weeks_bACE [209362530043_R04C02]

description:
Mouse_ID:ZM20
209362530043_R04C02


title: Kidney_Male_8_weeks_BS [209362530043_R03C02]

description:
Mouse_ID:ZM20
209362530043_R03C02


title: Ears_Male_8_weeks_bACE [209362530039_R02C01]

description:
Mouse_ID:ZM20
209362530039_R02C01


title: Colon_Male_8_weeks_BS [209362530043_R01C02]

description:
Mouse_ID:ZM20
209362530043_R01C02


title: Tail_Male_8_weeks_BS [209362530043_R05C01]

description:
Mouse_ID:ZM19
209362530043_R05C01


title: Ears_Male_8_weeks_bACE [209362530043_R04C01]

description:
Mouse_ID:ZM19
209362530043_R04C01


title: Spleen_Female_8_weeks_BS [209362530044_R01C02]

description:
Mouse_ID:ZM22
209362530044_R01C02


title: Tail_Male_8_weeks_bACE [209362530043_R06C01]

description:
Mouse_ID:ZM19
209362530043_R06C01


title: Ears_Male_8_weeks_BS [209362530043_R03C01]

description:
Mouse_ID:ZM19
209362530043_R03C01


title: Spleen_Male_8_weeks_bACE [209362530043_R02C01]

description:
Mouse_ID:ZM19
209362530043_R02C01


title: Colon_Male_8_weeks_bACE [209362530043_R02C02]

description:
Mouse_ID:ZM20
209362530043_R02C02


title: Colon_Male_8_weeks_BS [209267990075_R03C02]

description:
Mouse_ID:ZM19
209267990075_R03C02


title: Spleen_Male_8_weeks_BS [209362530043_R01C01]

description:
Mouse_ID:ZM19
209362530043_R01C01


title: Adrenal_Male_8_weeks_BS [209267990075_R05C01]

description:
Mouse_ID:ZM31
209267990075_R05C01

value: Adrenal


title: Adrenal_Male_8_weeks_bACE [209267990075_R02C02]

description:
Mouse_ID:ZM32
209267990075_R02C02


title: Adrenal_Male_8_weeks_BS [209267990075_R01C02]

description:
Mouse_ID:ZM32
209267990075_R01C02


title: Kidney_Male_8_weeks_BS [209267990075_R05C02]

description:
Mouse_ID:ZM19
209267990075_R05C02


title: Adrenal_Female_8_weeks_BS [209267990075_R03C01]

description:
Mouse_ID:ZM30
209267990075_R03C01


title: Colon_Male_8_weeks_bACE [209267990075_R04C02]

description:
Mouse_ID:ZM19
209267990075_R04C02


title: Kidney_Male_8_weeks_bACE [209267990075_R06C02]

description:
Mouse_ID:ZM19
209267990075_R06C02


title: Adrenal_Female_8_weeks_BS [209267990075_R01C01]

description:
Mouse_ID:ZM29
209267990075_R01C01


title: Adrenal_Female_8_weeks_bACE [209267990075_R04C01]

description:
Mouse_ID:ZM30
209267990075_R04C01


title: Sciatic_Nerve_Male_8_weeks_bACE [209362530035_R06C02]

description:
Mouse_ID:ZM32
209362530035_R06C02


title: Sciatic_Nerve_Female_8_weeks_bACE [209362530035_R02C02]

description:
Mouse_ID:ZM30
209362530035_R02C02


title: Sciatic_Nerve_Female_8_weeks_BS [209362530035_R05C01]

description:
Mouse_ID:ZM29
209362530035_R05C01


title: Sciatic_Nerve_Female_8_weeks_bACE [209362530035_R06C01]

description:
Mouse_ID:ZM29
209362530035_R06C01


title: Spinal_Cord_Male_8_weeks_BS [209362530035_R03C01]

description:
Mouse_ID:ZM32
209362530035_R03C01


title: Spinal_Cord_Male_8_weeks_bACE [209362530035_R02C01]

description:
Mouse_ID:ZM31
209362530035_R02C01


title: Spinal_Cord_Female_8_weeks_bACE [209362530065_R04C02]

description:
Mouse_ID:ZM29
209362530065_R04C02


title: Spinal_Cord_Female_8_weeks_BS [209362530065_R05C02]

description:
Mouse_ID:ZM30
209362530065_R05C02


title: Spinal_Cord_Male_8_weeks_BS [209362530035_R01C01]

description:
Mouse_ID:ZM31
209362530035_R01C01


title: Spinal_Cord_Female_8_weeks_bACE [209362530065_R06C02]

description:
Mouse_ID:ZM30
209362530065_R06C02


title: Spinal_Cord_Male_8_weeks_bACE [209362530035_R04C01]

description:
Mouse_ID:ZM32
209362530035_R04C01


title: Bile_Duct_Male_8_weeks_bACE [209362530065_R02C02]

description:
Mouse_ID:ZM31
209362530065_R02C02


title: Spinal_Cord_Female_8_weeks_BS [209362530065_R03C02]

description:
Mouse_ID:ZM29
209362530065_R03C02


title: Adrenal_Male_8_weeks_bACE [209267990075_R06C01]

description:
Mouse_ID:ZM31
209267990075_R06C01


title: Bile_Duct_Female_8_weeks_BS [209362530065_R03C01]

description:
Mouse_ID:ZM29
209362530065_R03C01


title: Retina_Male_8_weeks_bACE [209362530065_R02C01]

description:
Mouse_ID:ZM32
209362530065_R02C01

value: Retina


title: Bile_Duct_Female_8_weeks_bACE [209362530065_R04C01]

description:
Mouse_ID:ZM29
209362530065_R04C01


title: Bile_Duct_Female_8_weeks_bACE [209362530065_R06C01]

description:
Mouse_ID:ZM30
209362530065_R06C01


title: Retina_Male_8_weeks_BS [209362530065_R01C01]

description:
Mouse_ID:ZM32
209362530065_R01C01


title: Adrenal_Female_8_weeks_bACE [209267990075_R02C01]

description:
Mouse_ID:ZM29
209267990075_R02C01


title: Retina_Male_8_weeks_bACE [209362530036_R06C02]

description:
Mouse_ID:ZM32
209362530036_R06C02


title: Mammary_Glands_Male_8_weeks_bACE [209362530036_R04C02]

description:
Mouse_ID:ZM32
209362530036_R04C02


title: Urinary_Bladder_Male_8_weeks_bACE [209362530036_R02C02]

description:
Mouse_ID:ZM32
209362530036_R02C02


title: Sciatic_Nerve_Male_8_weeks_BS [209362530035_R05C02]

description:
Mouse_ID:ZM32
209362530035_R05C02


title: Sciatic_Nerve_Female_8_weeks_BS [209362530035_R01C02]

description:
Mouse_ID:ZM30
209362530035_R01C02


title: Mammary_Glands_Male_8_weeks_BS [209362530036_R03C02]

description:
Mouse_ID:ZM32
209362530036_R03C02


title: Urinary_Bladder_Male_8_weeks_BS [209362530036_R01C02]

description:
Mouse_ID:ZM32
209362530036_R01C02


title: Pancreas_Male_8_weeks_bACE [209362530036_R06C01]

description:
Mouse_ID:ZM32
209362530036_R06C01

value: Pancreas


title: Diaphragm_Male_8_weeks_bACE [209362530036_R04C01]

description:
Mouse_ID:ZM32
209362530036_R04C01

value: Diaphragm


title: Bile_Duct_Male_8_weeks_bACE [209362530028_R06C02]

description:
Mouse_ID:ZM32
209362530028_R06C02


title: Diaphragm_Male_8_weeks_BS [209362530036_R03C01]

description:
Mouse_ID:ZM32
209362530036_R03C01


title: Stomach_Male_8_weeks_bACE [209362530036_R02C01]

description:
Mouse_ID:ZM32
209362530036_R02C01

value: Stomach


title: Stomach_Male_8_weeks_BS [209362530036_R01C01]

description:
Mouse_ID:ZM32
209362530036_R01C01


title: Retina_Male_8_weeks_BS [209362530028_R03C02]

description:
Mouse_ID:ZM31
209362530028_R03C02


title: Retina_Male_8_weeks_bACE [209362530028_R04C02]

description:
Mouse_ID:ZM31
209362530028_R04C02


title: Pancreas_Male_8_weeks_BS [209362530036_R05C01]

description:
Mouse_ID:ZM32
209362530036_R05C01


title: Bile_Duct_Female_8_weeks_BS [209362530065_R05C01]

description:
Mouse_ID:ZM30
209362530065_R05C01


title: Retina_Male_8_weeks_BS [209362530036_R05C02]

description:
Mouse_ID:ZM32
209362530036_R05C02


title: Mammary_Glands_Male_8_weeks_bACE [209362530028_R06C01]

description:
Mouse_ID:ZM31
209362530028_R06C01


title: Bile_Duct_Male_8_weeks_BS [209362530065_R01C02]

description:
Mouse_ID:ZM31
209362530065_R01C02


title: Pancreas_Male_8_weeks_bACE [209362530028_R02C01]

description:
Mouse_ID:ZM31
209362530028_R02C01


title: Mammary_Glands_Male_8_weeks_BS [209362530028_R05C01]

description:
Mouse_ID:ZM31
209362530028_R05C01


title: Urinary_Bladder_Male_8_weeks_bACE [209362530028_R04C01]

description:
Mouse_ID:ZM31
209362530028_R04C01


title: Pancreas_Male_8_weeks_BS [209362530028_R01C01]

description:
Mouse_ID:ZM31
209362530028_R01C01


title: Retina_Female_8_weeks_BS [208706080098_R01C02]

description:
Mouse_ID:ZM30
208706080098_R01C02


title: Diaphragm_Male_8_weeks_BS [208706080098_R05C02]

description:
Mouse_ID:ZM31
208706080098_R05C02


title: Bile_Duct_Male_8_weeks_BS [209362530028_R05C02]

description:
Mouse_ID:ZM32
209362530028_R05C02


title: Mammary_Glands_Female_8_weeks_bACE [208706080098_R06C01]

description:
Mouse_ID:ZM30
208706080098_R06C01


title: Mammary_Glands_Female_8_weeks_BS [208706080098_R05C01]

description:
Mouse_ID:ZM30
208706080098_R05C01


title: Urinary_Bladder_Female_8_weeks_bACE [208706080098_R04C01]

description:
Mouse_ID:ZM30
208706080098_R04C01


title: Retina_Male_8_weeks_BS [209362530028_R01C02]

description:
Mouse_ID:ZM31
209362530028_R01C02


title: Urinary_Bladder_Female_8_weeks_BS [208706080098_R03C01]

description:
Mouse_ID:ZM30
208706080098_R03C01


title: Uterus_Female_8_weeks_BS [208706080098_R01C01]

description:
Mouse_ID:ZM30
208706080098_R01C01

value: Uterus


title: Diaphragm_Male_8_weeks_bACE [208706080098_R06C02]

description:
Mouse_ID:ZM31
208706080098_R06C02


title: Uterus_Female_8_weeks_bACE [208706080098_R02C01]

description:
Mouse_ID:ZM30
208706080098_R02C01

value: Female


title: Retina_Male_8_weeks_bACE [209362530028_R02C02]

description:
Mouse_ID:ZM31
209362530028_R02C02

value: 8 weeks


title: Pancreas_Female_8_weeks_bACE [208706080055_R06C02]

description:
Mouse_ID:ZM30
208706080055_R06C02

value: bACE


title: Pancreas_Female_8_weeks_BS [208706080055_R05C02]

description:
Mouse_ID:ZM30
208706080055_R05C02

value: Normal


title: Diaphragm_Female_8_weeks_BS [208706080055_R03C02]

description:
Mouse_ID:ZM30
208706080055_R03C02

value: BS


title: Diaphragm_Female_8_weeks_bACE [208706080055_R04C02]

description:
Mouse_ID:ZM30
208706080055_R04C02


title: Stomach_Female_8_weeks_bACE [208706080055_R02C02]

description:
Mouse_ID:ZM30
208706080055_R02C02


title: Stomach_Female_8_weeks_BS [208706080055_R01C02]

description:
Mouse_ID:ZM30
208706080055_R01C02


title: Urinary_Bladder_Male_8_weeks_BS [209362530028_R03C01]

description:
Mouse_ID:ZM31
209362530028_R03C01


title: Urinary_Bladder_Female_8_weeks_bACE [208706080055_R02C01]

description:
Mouse_ID:ZM29
208706080055_R02C01


title: Retina_Female_8_weeks_BS [208706080055_R05C01]

description:
Mouse_ID:ZM29
208706080055_R05C01


title: Mammary_Glands_Female_8_weeks_bACE [208706080055_R04C01]

description:
Mouse_ID:ZM29
208706080055_R04C01


title: Mammary_Glands_Female_8_weeks_BS [208706080055_R03C01]

description:
Mouse_ID:ZM29
208706080055_R03C01


title: Retina_Female_8_weeks_bACE [208706080098_R02C02]

description:
Mouse_ID:ZM30
208706080098_R02C02


title: Uterus_Female_8_weeks_bACE [209362530045_R06C02]

description:
Mouse_ID:ZM29
209362530045_R06C02


title: Urinary_Bladder_Female_8_weeks_BS [208706080055_R01C01]

description:
Mouse_ID:ZM29
208706080055_R01C01


title: Uterus_Female_8_weeks_BS [209362530045_R05C02]

description:
Mouse_ID:ZM29
209362530045_R05C02


title: Diaphragm_Female_8_weeks_bACE [209362530045_R02C02]

description:
Mouse_ID:ZM29
209362530045_R02C02


title: Pancreas_Female_8_weeks_BS [209362530045_R03C02]

description:
Mouse_ID:ZM29
209362530045_R03C02


title: Diaphragm_Female_8_weeks_BS [209362530045_R01C02]

description:
Mouse_ID:ZM29
209362530045_R01C02


title: Pancreas_Female_8_weeks_bACE [209362530045_R04C02]

description:
Mouse_ID:ZM29
209362530045_R04C02


title: Stomach_Female_8_weeks_bACE [209362530045_R06C01]

description:
Mouse_ID:ZM29
209362530045_R06C01


title: Stomach_Female_8_weeks_BS [209362530045_R05C01]

description:
Mouse_ID:ZM29
209362530045_R05C01


title: Subcortical_Brain_Female_8_weeks_BS [209362530045_R03C01]

description:
Mouse_ID:ZM28
209362530045_R03C01


title: Subcortical_Brain_Female_8_weeks_bACE [209362530045_R04C01]

description:
Mouse_ID:ZM28
209362530045_R04C01


title: Cerebellum_Female_8_weeks_bACE [209362530045_R02C01]

description:
Mouse_ID:ZM28
209362530045_R02C01

value: Cerebellum


title: Cerebellum_Female_8_weeks_BS [209362530045_R01C01]

description:
Mouse_ID:ZM28
209362530045_R01C01


title: Uterus_Female_8 weeks_bACE [207363410021_R06C02]

description:
Mouse_ID:ZM8
207363410021_R06C02

data_processing:
SeSAMe software v1.20
20250221_GEO_processed_matrix_GPL30650.csv = Normalized average Beta
20250221_GEO_signal_intensity_matrix_GPL30650.csv = Unmethylated and methylated signal intensities


title: Uterus_Female_8 weeks_BS [207363410021_R05C02]

description:
Mouse_ID:ZM8
207363410021_R05C02


title: Stomach_Female_8 weeks_bACE [207363410021_R04C02]

description:
Mouse_ID:ZM28
207363410021_R04C02


title: Retina_Female_8_weeks_bACE [208706080055_R06C01]

description:
Mouse_ID:ZM29
208706080055_R06C01


title: Stomach_Female_8 weeks_BS [207363410021_R03C02]

description:
Mouse_ID:ZM28
207363410021_R03C02


title: Pancreas_Female_8 weeks_BS [207363410021_R01C02]

description:
Mouse_ID:ZM28
207363410021_R01C02


title: Uterus_Female_8 weeks_bACE [207363410021_R06C01]

description:
Mouse_ID:ZM28
207363410021_R06C01


title: Pancreas_Female_8 weeks_bACE [207363410021_R02C02]

description:
Mouse_ID:ZM28
207363410021_R02C02


title: Femur_Female_8 weeks_BS [207363410021_R01C01]

description:
Mouse_ID:ZM22
207363410021_R01C01

value: Femur


title: Stomach_Male_8 weeks_BS [207363410021_R03C01]

description:
Mouse_ID:ZM27
207363410021_R03C01


title: Subcortical_Brain_Female_76 weeks_BS [207810940111_R05C02]

description:
Mouse_ID:ZM26
207810940111_R05C02

value: 76 weeks


title: Femur_Female_8 weeks_bACE [207363410021_R02C01]

description:
Mouse_ID:ZM22
207363410021_R02C01


title: Cerebellum_Female_76 weeks_bACE [207810940111_R04C02]

description:
Mouse_ID:ZM26
207810940111_R04C02


title: Subcortical_Brain_Female_76 weeks_bACE [207810940111_R06C02]

description:
Mouse_ID:ZM26
207810940111_R06C02


title: Cerebellum_Female_76 weeks_BS [207810940111_R03C02]

description:
Mouse_ID:ZM26
207810940111_R03C02


title: Stomach_Male_8 weeks_bACE [207363410021_R04C01]

description:
Mouse_ID:ZM27
207363410021_R04C01


title: Liver_Female_76 weeks_BS [207810940111_R05C01]

description:
Mouse_ID:ZM26
207810940111_R05C01

value: Liver


title: Femur_Female_76 weeks_bACE [207810940111_R02C01]

description:
Mouse_ID:ZM26
207810940111_R02C01


title: Liver_Female_76 weeks_bACE [207810940111_R06C01]

description:
Mouse_ID:ZM26
207810940111_R06C01


title: Ears_Female_76 weeks_bACE [207810940111_R04C01]

description:
Mouse_ID:ZM26
207810940111_R04C01

value: Ears


title: Spinal_Cord_Male_8 weeks_BS [207810940111_R01C02]

description:
Mouse_ID:ZM7
207810940111_R01C02

value: Male


title: Ears_Female_76 weeks_BS [207810940111_R03C01]

description:
Mouse_ID:ZM26
207810940111_R03C01


title: Femur_Female_76 weeks_BS [207810940111_R01C01]

description:
Mouse_ID:ZM26
207810940111_R01C01


title: Liver_Female_76 weeks_bACE [207810940053_R06C02]

description:
Mouse_ID:ZM25
207810940053_R06C02


title: Ears_Female_76 weeks_bACE [207810940053_R02C02]

description:
Mouse_ID:ZM25
207810940053_R02C02


title: Ears_Female_76 weeks_BS [207810940053_R01C02]

description:
Mouse_ID:ZM25
207810940053_R01C02


title: Liver_Female_76 weeks_BS [207810940053_R05C02]

description:
Mouse_ID:ZM25
207810940053_R05C02


title: Femur_Female_76 weeks_bACE [207810940053_R04C01]

description:
Mouse_ID:ZM25
207810940053_R04C01


title: Eye_Female_76 weeks_bACE [207810940053_R06C01]

description:
Mouse_ID:ZM25
207810940053_R06C01

value: Eye


title: Femur_Female_76 weeks_BS [207810940053_R03C01]

description:
Mouse_ID:ZM25
207810940053_R03C01


title: Liver_Male_76 weeks_bACE [207810940053_R02C01]

description:
Mouse_ID:ZM24
207810940053_R02C01


title: Liver_Male_76 weeks_BS [207810940053_R01C01]

description:
Mouse_ID:ZM24
207810940053_R01C01


title: Uterus_Female_8 weeks_BS [207363410021_R05C01]

description:
Mouse_ID:ZM28
207363410021_R05C01


title: Eye_Female_76 weeks_BS [207810940053_R05C01]

description:
Mouse_ID:ZM25
207810940053_R05C01


title: Thymus_Male_76 weeks_BS [207810940112_R05C02]

description:
Mouse_ID:ZM24
207810940112_R05C02

value: Thymus


title: Eye_Male_76 weeks_BS [207810940112_R03C02]

description:
Mouse_ID:ZM24
207810940112_R03C02


title: Brain_Cortex_Male_76 weeks_bACE [207810940112_R06C01]

description:
Mouse_ID:ZM23
207810940112_R06C01


title: Femur_Male_76 weeks_BS [207810940112_R01C02]

description:
Mouse_ID:ZM24
207810940112_R01C02


title: Femur_Male_76 weeks_bACE [207810940112_R02C02]

description:
Mouse_ID:ZM24
207810940112_R02C02


title: Spinal_Cord_Male_8 weeks_bACE [207810940111_R02C02]

description:
Mouse_ID:ZM7
207810940111_R02C02


title: Brain_Cortex_Male_76 weeks_BS [207810940112_R05C01]

description:
Mouse_ID:ZM23
207810940112_R05C01


title: Liver_Male_76 weeks_bACE [207810940112_R04C01]

description:
Mouse_ID:ZM23
207810940112_R04C01


title: Eye_Male_76 weeks_bACE [207810940112_R04C02]

description:
Mouse_ID:ZM24
207810940112_R04C02


title: Liver_Male_76 weeks_BS [207810940112_R03C01]

description:
Mouse_ID:ZM23
207810940112_R03C01


title: Eye_Male_76 weeks_bACE [207810940112_R02C01]

description:
Mouse_ID:ZM23
207810940112_R02C01


title: Eye_Male_76 weeks_BS [207810940112_R01C01]

description:
Mouse_ID:ZM23
207810940112_R01C01


title: Heart_Male_76 weeks_bACE [207810940109_R04C02]

description:
Mouse_ID:ZM23
207810940109_R04C02

value: Heart


title: Liver_Female_8 weeks_bACE [207810940109_R02C02]

description:
Mouse_ID:ZM22
207810940109_R02C02


title: Testis_Male_76 weeks_BS [207810940109_R05C02]

description:
Mouse_ID:ZM23
207810940109_R05C02

value: Testis


title: Liver_Female_8 weeks_BS [207810940109_R01C02]

description:
Mouse_ID:ZM22
207810940109_R01C02


title: Testis_Male_76 weeks_bACE [207810940109_R06C02]

description:
Mouse_ID:ZM23
207810940109_R06C02


title: Thymus_Female_8 weeks_bACE [207810940109_R06C01]

description:
Mouse_ID:ZM22
207810940109_R06C01


title: non-diseased, patient ND182

status: Public on Sep 29 2025

city: Evanston

first: Timothy

last: Pan

state: IL

address: 633 Clark St

institute: Northwestern University

description:
Library name: ND182
snNanoRNA-seq

data_processing:
Demultiplexing, barcode processing, and gene counting were performed by scNanoGPS (v1.0) with default parameters to generate the gene expression matrix.
Sequence alignment files output by scNanoGPS were merged and used to run IsoQuant (v3.4.2) with the nanopore datatype setting to generate the isoform expression matrix.
Assembly: GRCh38 (GENCODE v44/Ensembl110 annotations)
Supplementary files format and content: "matrix_gene_*.tsv" contains the single cell gene expression for individual samples and was output by the scNanoGPS pipelines
Supplementary files format and content: "matrix_isoform_all_Samples.tsv" contains the single cell isoform expression for all samples and was output by IsoQuant v3.4.2.
Supplementary files format and content: "gtf_isoform_all_Samples.gtf" is the GTF file that was output by IsoQuant v3.4.2 and holds the necessary structural information for both annotated and novel transcripts.

source_name: Heart, left ventricle

extract_protocol:
Single nuclei suspensions were prepared from approximately 50-100 mg frozen heart left ventricle tissues. Tissues were first cut into tiny pieces using scissors in ice-cold nuclei extraction buffer (Miltenyi Biotec) and dissociated in a gentleMACS Octo Dissociator. The resulting suspensions were centrifuged at 300 x g, strained in 70 µm MACS SmartStrainers, and washed in additional nuclei extraction buffer. Nuclei were then pelleted at 300 x g and gently resuspended in 1 mL ice-cold resuspension buffer (PBS, 0.1% BSA, 0.2 U/µL RNAse inhibitor).
Initial cDNA libraries were prepared according to the 10X Genomics Chromium Single Cell 3' v3.1 protocol with a target of 3,000 nuclei per sample. The cDNA PCR amplification elongation step was extended to 3 minutes and fragmentation and subsequent steps were not performed. Full-length Nanopore cDNA libraries were prepared according to the Oxford Nanopore Technologies SQK-LSK114 kit.

value: Heart, left ventricle


title: Heart_Male_76 weeks_BS [207810940109_R03C02]

description:
Mouse_ID:ZM23
207810940109_R03C02


title: Thymus_Female_8 weeks_BS [207810940109_R05C01]

description:
Mouse_ID:ZM22
207810940109_R05C01


title: Thymus_Male_76 weeks_bACE [207810940112_R06C02]

description:
Mouse_ID:ZM24
207810940112_R06C02


title: Eye_Female_8 weeks_BS [207810940109_R03C01]

description:
Mouse_ID:ZM22
207810940109_R03C01


title: Liver_Female_8 weeks_BS [207810940109_R01C01]

description:
Mouse_ID:ZM21
207810940109_R01C01


title: Liver_Male_8 weeks_bACE [207810940113_R06C02]

description:
Mouse_ID:ZM20
207810940113_R06C02


title: Liver_Male_8 weeks_BS [207810940113_R05C02]

description:
Mouse_ID:ZM20
207810940113_R05C02


title: Liver_Female_8 weeks_bACE [207810940109_R02C01]

description:
Mouse_ID:ZM21
207810940109_R02C01


title: Testis_Male_8 weeks_BS [207810940113_R03C02]

description:
Mouse_ID:ZM20
207810940113_R03C02


title: Testis_Male_8 weeks_bACE [207810940113_R04C02]

description:
Mouse_ID:ZM20
207810940113_R04C02


title: Liver_Male_8 weeks_BS [207810940113_R01C02]

description:
Mouse_ID:ZM19
207810940113_R01C02


title: Testis_Male_8 weeks_BS [207810940113_R05C01]

description:
Mouse_ID:ZM19
207810940113_R05C01


title: Testis_Male_8 weeks_bACE [207810940113_R06C01]

description:
Mouse_ID:ZM19
207810940113_R06C01


title: Lung_Female_76 weeks_BS [207810940113_R03C01]

description:
Mouse_ID:ZM26
207810940113_R03C01

value: Lung


title: Lung_Male_76 weeks_bACE [207810940113_R02C01]

description:
Mouse_ID:ZM24
207810940113_R02C01


title: Lung_Male_76 weeks_BS [207810940113_R01C01]

description:
Mouse_ID:ZM24
207810940113_R01C01


title: Lung_Female_76 weeks_bACE [207810940113_R04C01]

description:
Mouse_ID:ZM26
207810940113_R04C01

value: Female


title: Testis_Male_76 weeks_bACE [207363410036_R02C02]

description:
Mouse_ID:ZM24
207363410036_R02C02


title: Femur_Male_76 weeks_bACE [207363410036_R06C01]

description:
Mouse_ID:ZM23
207363410036_R06C01


title: Testis_Male_76 weeks_BS [207363410036_R01C02]

description:
Mouse_ID:ZM24
207363410036_R01C02


title: Thymus_Female_8 weeks_bACE [207363410036_R04C01]

description:
Mouse_ID:ZM21
207363410036_R04C01

value: 8 weeks


title: Thymus_Male_8 weeks_bACE [207363410011_R06C02]

description:
Mouse_ID:ZM20
207363410011_R06C02

value: bACE


title: Femur_Female_8 weeks_bACE [207363410036_R02C01]

description:
Mouse_ID:ZM21
207363410036_R02C01

value: Normal


title: Femur_Female_8 weeks_BS [207363410036_R01C01]

description:
Mouse_ID:ZM21
207363410036_R01C01

value: BS


title: Femur_Male_76 weeks_BS [207363410036_R05C01]

description:
Mouse_ID:ZM23
207363410036_R05C01


title: Thymus_Female_8 weeks_BS [207363410036_R03C01]

description:
Mouse_ID:ZM21
207363410036_R03C01


title: Eye_Female_8 weeks_bACE [207810940109_R04C01]

description:
Mouse_ID:ZM22
207810940109_R04C01


title: Eye_Male_8 weeks_bACE [207363410011_R04C02]

description:
Mouse_ID:ZM20
207363410011_R04C02


title: Lung_Male_76 weeks_bACE [207363410011_R02C02]

description:
Mouse_ID:ZM23
207363410011_R02C02


title: Lung_Male_76 weeks_BS [207363410011_R01C02]

description:
Mouse_ID:ZM23
207363410011_R01C02


title: Eye_Male_8 weeks_BS [207363410011_R03C02]

description:
Mouse_ID:ZM20
207363410011_R03C02


title: Lung_Female_8 weeks_bACE [207363410011_R06C01]

description:
Mouse_ID:ZM22
207363410011_R06C01


title: Lung_Female_8 weeks_BS [207363410011_R05C01]

description:
Mouse_ID:ZM22
207363410011_R05C01


title: Heart_Female_76 weeks_bACE [207363410131_R06C02]

description:
Mouse_ID:ZM26
207363410131_R06C02


title: Femur_Male_8 weeks_bACE [207363410131_R04C02]

description:
Mouse_ID:ZM20
207363410131_R04C02


title: Liver_Male_8 weeks_bACE [207810940113_R02C02]

description:
Mouse_ID:ZM19
207810940113_R02C02


title: Heart_Female_76 weeks_BS [207363410131_R05C02]

description:
Mouse_ID:ZM26
207363410131_R05C02


title: Thymus_Male_8 weeks_bACE [207363410131_R02C02]

description:
Mouse_ID:ZM19
207363410131_R02C02


title: Femur_Male_8 weeks_BS [207363410131_R03C02]

description:
Mouse_ID:ZM20
207363410131_R03C02


title: Thymus_Male_8 weeks_BS [207363410131_R01C02]

description:
Mouse_ID:ZM19
207363410131_R01C02


title: Femur_Male_8 weeks_bACE [207363410131_R06C01]

description:
Mouse_ID:ZM19
207363410131_R06C01


title: Femur_Male_8 weeks_BS [207363410131_R05C01]

description:
Mouse_ID:ZM19
207363410131_R05C01


title: Lung_Female_8 weeks_bACE [207363410131_R04C01]

description:
Mouse_ID:ZM21
207363410131_R04C01


title: Lung_Female_8 weeks_BS [207363410131_R03C01]

description:
Mouse_ID:ZM21
207363410131_R03C01


title: Lung_Male_8 weeks_BS [207363410131_R01C01]

description:
Mouse_ID:ZM20
207363410131_R01C01


title: Heart_Female_76 weeks_bACE [207097260043_R06C02]

description:
Mouse_ID:ZM25
207097260043_R06C02


title: Thymus_Male_8 weeks_BS [207363410011_R05C02]

description:
Mouse_ID:ZM20
207363410011_R05C02


title: Heart_Male_76 weeks_bACE [207097260043_R04C02]

description:
Mouse_ID:ZM24
207097260043_R04C02


title: Heart_Female_8 weeks_BS [207097260027_R05C02]

description:
Mouse_ID:ZM22
207097260027_R05C02


title: Heart_Female_8 weeks_bACE [207097260027_R04C02]

description:
Mouse_ID:ZM21
207097260027_R04C02