title: experiment_H001AS8_B08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

status: Public on Sep 30 2025

type: SRA

city: Torino

first: Elisa

last: Balmas

address: via Nizza 52

country: Italy

institute: University of Torino

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt

library_source: transcriptomic single cell

data_processing:
Illumina base calls for iPS2-sci-seq were converted to fastq and demultiplexed with bcl2fastq v2.20.0.422, using i7 and i5 PCR indexes.
count data were obtained from fastq files with the catcheR_scicount function  implemented in our catcheR package https://github.com/alessandro-bertero/catcheR
Reads 1 and 2 were concatenated, adaptor trimmed with TrimGalore 0.6.10, aligned with STAR 2.5.1b to human GRCh38 (GENECODE v21/Ensembl77) gene annotation, and filtered to have a MAPQ score equal of higher than 30 with samtools 1.7. Uniquely mapping reads were extracted, and reads with identical UMI, RT index, and tagmentation site were collapsed as PCR duplicates. RT_primers_conditions.txt file was used to demultiplex the first level of indexing.  Samtools and bedtools 2.27.1 were used to calculate the percentage of ribosomal RNA and to assign reads to genes. Reads were finally assigned to nuclei by further demultiplexing with the RT indexes. Cells with less than 500 UMI were filtered out as noise/low quality. The remaining sparse count matrix was converted to a complete count matrix with the sparsetodense function of Monocle 2.22.
shRNA and cell barcodes have been identified with catcheR_scicatch function implemented in our catcheR package https://github.com/alessandro-bertero/catcheR (this allow to link the cell ID to a cell perturbation)
Assembly: custom reference combining human reference genome (hg19), mouse reference genome (mm10), built by UW genome research (Seattle,WA) and used for Cao J et al. 2017 PMID: 28818938
Supplementary files format and content: sci_RNA_cds_monocle_cell_info.txt is the annotation file post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_counts_norm.txt normalized read count post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_counts_prenorm.txt unnormalized read count post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_processed.rds full post QC and processing single cell dataset file

molecule: polyA RNA

organism: Homo sapiens

source_name: hPSC derived cardiomyocytes

growth_protocol: hPSC were differentiated into cardiomyocites with RBA media.

extract_protocol:
Nuclear extraction by IGEPAL 0.3% ipotonic buffer. PFA fixation. RNAse inhibitors have been used during all steps to avoid RNA degradation.
2-level indexing sci-RNAseq protocol for the gene expression library and the barcode library. shRNA barcodes have been enriched during RT and PCR indexing by a nested PCR binding the TET repressor.
sci-RNASeq 2 levels of combinatorial indexing

treatment_protocol: hPSC tranfected in pool with iPS-2seq plasmids in AAVS1 locus (multiple perturbations in pool). shRNA expression has been induced throughout differentiation with Tetracycline. hPSC derived cardiomyocytes were cultured for 23 days with tetracycline. Then Harvested at single cell suspension and processed for nuclear extraction.

tag: tissue

value: hPSC derived cardiomyocytes

tag: cell line

tag: cell type

value: hPSC derived cardiomyocytes DD23

tag: treatment

value: Tetracycline


title: experiment_H001AS8_B06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_A01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_counts_prenorm.txt
sci_RNA_cds_monocle_processed.rds


title: Veh-Mor-S16

status: Public on Sep 22 2025

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

country: USA

institute: University of Alabama at Birmingham

description: Library name: Veh-Mor-S16

data_processing:
All raw fastq files were aligned to the Ensembl mRatBn7.2 (Rn7) genome using CellRanger v9.0.1 with the associated Ensembl gene transfer format (gtf) file (version 105) modified to add annotation for the Xist gene. CellRanger filtered outputs were analyzed with Seurat v5.2.1 in R v4.4.0.
To filter out background contamination, cell-free ambient RNA was removed using SoupX v.1.6.2. Next, we continued quality filtering in R with Seurat v.5.2.1 by removing nuclei containing <200 genes and >5% of reads mapping to the mitochondrial genome (50,449 nuclei post-processing). The counts data for each individual were then normalized, scaled by a factor of 10,000, and log-transformed. Heterotypic doublets were identified and removed using scDblFinder with the default expected doublet rate of 1% per 1,000 cells. Cell sex was predicted using a logistic regression model, which was trained and validated using previously published rat VTA snRNA-seq data (CITE Twa et al BioRxiv). A classification threshold for cell sex predicted probabilities from 0.25-0.75 was used to exclude cells with low confidence predictions from analysis.
For each sample, we used Seurat to determine the 2,000 genes with highest cell-to-cell variability. We then integrated the individual datasets in Harmony, using the PCA cell embeddings with 50 principal components (PCs). Downstream analysis was performed on the integrated dataset.
Expression for each gene in the integrated dataset was scaled to a mean of 0 and variance of 1 across cells. We first performed dimensionality reduction via PCA retaining 20 PCs, followed by UMAP with the 20 previously identified PCs as input. Cells were then clustered under a graph-based approach by first identifying K-nearest neighbors in PCA space, and then clustering under a Louvain algorithm with a resolution of 0.4. After removing additional low-quality cells, we repeated the dimensionality reduction and clustering steps. We annotated the resulting clusters as specific cell types based on known marker genes from previous work and the Allen Institute's Whole Mouse Brain taxonomy via the MapMyCells web interface.
Differential expression analyses were conducted within each cell type cluster using pseudobulking expression of each GEM well split by predicted sex using DESeq2 likelihood-ratio test. To test the effect of CFA on the transcriptome, CFA(+) (CFA(+)/Mor(-) and CFA(+)/Mor(+)) pseudobulked sample transcriptomes were compared to CFA negative (CFA(-)/Mor(+) and CFA(-)/Mor(-)). For DESeq2 the formula for the full model was ~ CFA, and the reduced model was ~ 1. When testing with adjustment for sex, the full model was ~ CFA + Sex, and the reduced model was ~ Sex. Tests for the effect of morphine with and without adjustment for sex were carried out likewise. To test the interaction effect of treatment the formula for the full model was ~ CFA + Morphine + CFA:Morphine , and ~ CFA + Morphine for the reduced model. Similarly, when testing with adjustment for sex, the full model was ~Sex + CFA + Morphine + CFA:Morphine, and the reduced model was ~Sex + CFA + Morphine. DESeq2 was run using `fittype = local` but otherwise default parameters. This parameter was chosen as the mean absolute residual of the local model was smaller than the default parametric model in all cell types, indicating a better dispersion model fit. For all cell types the sample size was N = 6 (Mor(+)) or N = 8(Mor(-)) per treatment-sex for both analyses unless noted otherwise below. We excluded from analysis the following cell type groups because they did not have at least two CFA(-)/Mor(-) pseudobulk samples from independent GEM wells: Ependymal and Glut.3. For each cell type, genes with <5 total counts were excluded from testing.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

organism: Rattus norvegicus

source_name: ventral tegmental area

growth_protocol: Male and female 8-12 week old adult Sprague-Dawley rats (~200-300g) were purchased from Charles River Laboratories (Wilmington, MA) and pair-housed in an AAALAC-approved animal care facility during the experiment. Rats were maintained on a 12 h light/dark cycle with ad libitum access to food and water and were briefly handled for 3 days prior to beginning baseline Von Frey measurements (1-2min/day) to acclimate them to the experimenters. All experimental procedures were approved by the University of Alabama at Birmingham Institutional Animal Care and Use Committee and were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
One hour after systemic injections of saline or morphine (10mg/kg) rats were euthanized by live decapitation and whole brains were briefly flash frozen in 2-methyl butane. Chilled brains were then blocked into 1-mm-thick coronal sections on a combination of dry and wet ice. Sections containing the VTA (ranging from -4.92-6.46 anterior-posterior (AP) to Bregma) were transferred to glass microscope slides on dry ice, and the VTA was microdissected away from neighboring brain regions (n = 3-4/sex/treatment group). Dissected VTA tissue was then transferred to ice-cold centrifuge tubes, and stored at -80°C until the day of 10X GEM capture. Frozen microdissected VTA tissue was prepared as previously described (Phillips et al., 2022). Briefly, tissue was thawed on wet ice and chopped with a scalpel prior to being transferred to 5 ml of ice cold lysis buffer (10 mM tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal in nuclease-free water (Sigma-Aldrich, 18896-50ML). After 15 min the lysis was quenched with 5 ml of complete Hibernate A media (Thermo Fisher Scientific, A1247501) supplemented with B27, GlutaMAX (Life Technologies, 35050-061), and NxGen RNase Inhibitor (0.2 U/m; Lucigen, 30281-2). Tissue was then triturated by fire-polished Pasteur pipette (three pipettes of decreasing diameter) and filtered with a 40µm pre-wet cell strainer. Samples were pelleted and then washed in nuclei wash and resuspension buffer (phosphate-buffered saline (PBS), 1% bovine serum albumin (BSA), and NxGen RNase Inhibitor). The resulting pellet was resuspended in 800 ml of wash buffer and 7-aminoactinomycin D (7-AAD; Thermo Fisher Scientific, 00-6993-50) was added prior to fluorescence-activated cell sorting (FACS) on a FACSAria instrument (70 µm nozzle, BD Biosciences). Immediately after FACS, nuclei were washed a final time at 250 rcf in 10 ml of supplemented Hibernate A containing 1% BSA and RNase Inhibitor for 5 min at 4C. Nuclei were brought to a concentration of 1,000 nuclei/µL. A total of 8,000 nuclei pooled from two rats (4,000 male nuclei/4,000 female nuclei from the same treatment group) and were loaded into individual wells of the Chromium NextGem Single Cell Chip (10x Genomics, catalog no. 10000121).
Libraries were constructed according to manufacturer’s instructions for Chromium Next GEM single cell 3’ library and gel bead kit (10x Genomics, v3.1 single index, catalog no. 10000121, version 3 chemistry)

treatment_protocol: To assess neuropathic pain response, Complete Freund’s Adjuvant (CFA; Sigma Aldrich, St. Louis, MO) or saline vehicle (100 µl) was injected into the plantar surface of one hind paw of male and female rats (n = 3-4/sex/treatment group). Mechanical sensitivity was then evaluated 48 hours and 7 days after the injection using the Von Frey assay. Morphine (10mg/kg) or saline was administered I.P. 7 days after CFA treatment, creating a 2x2 experimental design.

value: ventral tegmental area

tag: age

value: 2-3 months

tag: Sex

value: pooled male and female

tag: animal no.

value: 1 Male, 1 Female

tag: strain

value: Sprague-Dawley

value: Vehicle, Morphine


title: CFA-Sal-S15

description: Library name: CFA-Sal-S15

value: CFA, Saline


title: Veh-Sal-S14

description: Library name: Veh-Sal-S14

value: Vehicle, Saline


title: CFA-Sal-S12

description: Library name: CFA-Sal-S12


title: CFA-Mor-S13

description: Library name: CFA-Mor-S13

value: CFA, Morphine


title: Veh-Sal-S11

description: Library name: Veh-Sal-S11


title: Veh-Sal-S8

description: Library name: Veh-Sal-S8


title: CFA-Mor-S7

description: Library name: CFA-Mor-S7


title: Veh-Mor-S6

description: Library name: Veh-Mor-S6


title: CFA-Sal-S5

description: Library name: CFA-Sal-S5


title: CFA-Mor-S4

description: Library name: CFA-Mor-S4


title: Veh-Mor-S3

description: Library name: Veh-Mor-S3


title: CFA-Sal-S2

description: Library name: CFA-Sal-S2


title: Veh-Sal-S1

description: Library name: Veh-Sal-S1


title: scRNAseq, DKO, Aorta, ApoE, S1

status: Public on Sep 04 2025

city: Boston

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

description:
Library name: L-DKO_Aorta_S1
10x Genomics
combined_AortaApoE_filteredCountData.csv
combined_AortaApoE_metaData.csv

data_processing:
Cell Ranger (version 7.1.0) to map the raw reads of RNA sequencing data to the mouse genome (version mm10) and to count UMI for each gene.
Assembly: mm10
Supplementary files format and content: csv files, in metaData file some columns starts with ABC, that’s means after batch correction

molecule: total RNA

organism: Mus musculus

source_name: Aorta

extract_protocol:
For liver cell isolation, the WT and Liver-DKO mice (n=3) were anesthetized and restrained and the skin sprayed with 70% ethanol.
single-cell RNA-seq library construction following the protocol provided by 10X Genomics.

value: Aorta


title: scRNAseq, WT, Aorta, ApoE, S1

description:
Library name: L-WT_Aorta_S1
10x Genomics
combined_AortaApoE_filteredCountData.csv
combined_AortaApoE_metaData.csv


title: scRNAseq, WT, Liver, S1

description:
Library name: L-WT_Liver_S1
10x Genomics
combined_LiverControl_filteredCountData.csv
combined_LiverControl_metaData.csv

source_name: Liver

value: Liver


title: PB03515-001 flex scRNA-seq

status: Public on Sep 12 2025

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
SRR30204374, SRR30204373, SRR30204372, SRR30204371, SRR30204370, SRR30204369, SRR30204368, SRR30204367, SRR30204365, SRR30204364, SRR30204291, SRR30204290, SRR30204289, SRR30204288, SRR30204287, SRR30204286, SRR30204285, SRR30204284, SRR30204282, SRR30204281, SRR30204280, SRR30204279, SRR30204278, SRR30204277
10x Flex ligation probe-based sequencing

library_source: other

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the  Fixed RNA Profiling capability (version 7.0.0, released May 17, 2022), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For all initial analyses, we used a Python single-cell data analysis package – Scanpy (v1.9.6). High quality cells were selected based on the following cutoffs: <4.5% mitochondria reads, number of genes detected between 500 and 5000, RNA UMIs/cells less than 12000 and number of reads less than 30000. Doublets were detected and filtered out with the Scrublet package accessed through scanpy.external.pp.scrublet call and the doublet filtration threshold was set at less than 0.2
After QC filtering, all remaining cells were clustered using a workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; natural log transformation using scanpy.pp.log1p; dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'; nearest neighbor distance matrix and neighborhood graph computed using scanpy.pp.neighbors with the parameters n_neighbors=50, use_rep='X_pca', n_pcs=30;
Assembly: GRCh38/hg38
Supplementary files format and content: h5 files

molecule: other

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and immediately thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics flex single cell gene expression assay. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq 6000 or X platform.

value: Blood

value: PBMC

tag: subject id

tag: age at_enrollment

value: Male

tag: race

value: Hispanic or Latino origin

tag: cmv status

value: Negative

tag: batch id

tag: sample bridging_control

value: FALSE

tag: pooled sample_id

tag: probe barcode_id


title: PB03741-004 flex scRNA-seq

value: Female

value: Caucasian

value: Positive


title: lower, female, rep6

status: Public on Sep 03 2025

city: Rochester

first: Ania

last: Majewska

state: NY

address: 601 Elmwood Ave.

department: Neuroscience

institute: University of Rochester

description:
Library name: 374
female

library_source: transcriptomic

data_processing:
Data Formatting bcltofastq-2.19.1
Data Cleaning fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification3 salmon-1.5.2, --seqBias --gcBias --posBias
Assembly: mg39 + Gencode-M27 Annotation
Supplementary files format and content: gene counts

source_name: whole cerebellum

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) per manufacturers recommendations
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size.

value: whole cerebellum

value: lower

value: female


title: higher, female, rep6

description:
Library name: 364
female

value: higher


title: lower, male, rep6

description:
Library name: 371
male

value: male


title: higher, male, rep6

description:
Library name: 361
male


title: higher, female, rep5

description:
Library name: 354
female


title: higher, male, rep5

description:
Library name: 351
male


title: lower, female, rep5

description:
Library name: 344
female


title: lower, male, rep5

description:
Library name: 341
male


title: control, male, rep5

description:
Library name: 331
male

value: control


title: control , female, rep5

description:
Library name: 333
female


title: control, male, rep4

description:
Library name: 311
male


title: control , female, rep4

description:
Library name: 314
female


title: higher, female, rep4

description:
Library name: 305
female


title: higher, male, rep4

description:
Library name: 301
male


title: lower, female, rep4

description:
Library name: 297
female


title: lower, male, rep4

description:
Library name: 291
male


title: control , female, rep3

description:
Library name: 283
female


title: control, male, rep3

description:
Library name: 281
male


title: lower, female, rep3

description:
Library name: 274
female


title: higher, female, rep3

description:
Library name: 266
female


title: higher, male, rep3

description:
Library name: 261
male


title: lower, female, rep2

description:
Library name: 255
female


title: lower, male, rep2

description:
Library name: 251
male


title: higher, female, rep2

description:
Library name: 245
female


title: higher, male, rep2

description:
Library name: 241
male


title: control , female, rep2

description:
Library name: 234
female


title: lower, male, rep3

description:
Library name: 271
male


title: control, male, rep2

description:
Library name: 231
male


title: control, male, rep1

description:
Library name: 221
male


title: lower, female, rep1

description:
Library name: 213
female


title: control , female, rep1

description:
Library name: 224
female


title: lower, male, rep1

description:
Library name: 211
male


title: higher, female, rep1

description:
Library name: 205
female


title: TAC_RFP_cells

status: Public on Aug 27 2025

city: Beijing

first: Xiaoyi

last: Wang

address: No.167, Beilishi Road, Xicheng District, 100037

department: Department of Cardiovascular Surgery, Fuwai Hospital

country: China

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

description: one sample from mice left atrium

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters (Cell Ranger software v6.0.1)
Assembly: GRCh38 for human data; mm10 for mice data
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: left atrium

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy

treatment_protocol: C57BL/6 C57BL/6 J Cdh5-CreERT2/RFP  mice were performed transverse aortic constriction or sham surgery at 10-12 weeks

value: left atrium

value: 20 weeks

value: transverse aortic constriction


title: Sham_RFP_cells

description: one sample from mice left atrium

value: sham surgery with transverse aortic constriction


title: higher, male, rep1

description:
Library name: 201
male


title: LA_AF_02

description: one sample from human left atrial appendage

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters (Cell Ranger software v6.0.1)
Assembly: GRCh38 for human data;
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Left atrial appendage

value: Left atrial appendage


title: LA_AF_03


title: LA_AF


title: LA_SR_03


title: LA_SR_02


title: LA_SR_01


title: TCF1.delta.LEF1.delta.BCR

status: Public on Aug 14 2025

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

description: Library name: VDJ_Sophie_4

data_processing:
CellRanger pipeline v.6.0.1 multi run with chemistry parameter = auto, and expect-cells = 5000.
Single-cell RNA sequencing (scRNA-seq) data were processed and analysed using the Seurat package (v5.0.3) in R. Raw gene expression matrices were filtered to exclude low-quality cells based on thresholds for mitochondrial gene content and the number of detected genes per cell, using the PercentageFeatureSet() and subset() functions. The subset function was applied with the following parameters: subset(sce, subset = nFeature_RNA > 500 & nFeature_RNA < 6000 & percent.mt < 5 & nCount_RNA > 1000 & nCount_RNA < 4e4)
Normalisation and integration were performed using the scTransform() workflow. Dimensionality reduction was performed using principal component analysis (PCA) via the RunPCA() function, and the top 20–30 principal components were selected to construct a shared nearest neighbour (SNN) graph using FindNeighbours(). Clustering was carried out using the FindClusters() function. Clusters were visualised using Uniform Manifold Approximation and Projection (UMAP) via the RunUMAP() function. Differential expressed genes for each cluster were identified using the FindAllMarkers() function with test.use set as either “wilcox” or “MAST”.
Assembly: GRCm38
Supplementary files format and content: CellRanger verison 6.0.1 outputs file for expression and BCR .
Library strategy: BCR-Seq

source_name: Peritoneal Cavity

extract_protocol:
Total B cells (CD19+CD3-) from peritoneal cavity of  three 8 weeks old mice were sorted by the FACS Aria II cell sorting system (BD Immunocytometry Systems, San Jose, CA, USA)
According to the manufacturer’s instructions for the Chromium Next GEM Single Cell 5’Kit v2

value: Peritoneal Cavity

value: B cells

tag: genotype

value: 8 weeks


title: TCF1.WT.LEF1.WT.BCR

description: Library name: VDJ_Sophie_3

tag: tissue


title: TCF1.delta.LEF1.delta.EXP

description: Library name: GEX_Sophie_4

data_processing:
CellRanger pipeline v.6.0.1 multi run with chemistry parameter = auto, and expect-cells = 5000.
Single-cell RNA sequencing (scRNA-seq) data were processed and analysed using the Seurat package (v5.0.3) in R. Raw gene expression matrices were filtered to exclude low-quality cells based on thresholds for mitochondrial gene content and the number of detected genes per cell, using the PercentageFeatureSet() and subset() functions. The subset function was applied with the following parameters: subset(sce, subset = nFeature_RNA > 500 & nFeature_RNA < 6000 & percent.mt < 5 & nCount_RNA > 1000 & nCount_RNA < 4e4)
Normalisation and integration were performed using the scTransform() workflow. Dimensionality reduction was performed using principal component analysis (PCA) via the RunPCA() function, and the top 20–30 principal components were selected to construct a shared nearest neighbour (SNN) graph using FindNeighbours(). Clustering was carried out using the FindClusters() function. Clusters were visualised using Uniform Manifold Approximation and Projection (UMAP) via the RunUMAP() function. Differential expressed genes for each cluster were identified using the FindAllMarkers() function with test.use set as either “wilcox” or “MAST”.
Assembly: GRCm38
Supplementary files format and content: CellRanger verison 6.0.1 outputs file for expression and BCR .


title: TCF1.WT.LEF1.WT.EXP

description: Library name: GEX_Sophie_3


title: Subject 14

city: Denver

first: Elizabeth

last: Wynn

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description:
Library name: Subject 14
Bronchoalveolar lavage cells from healthy adult after LPS exposure

data_processing:
Initial pre-processing of the 10 subjects’ 10X scRNA-seq data, including demultiplexing, alignment to the hg38 human genome, and UMI-based gene expression quantification, was performed using Cell Ranger (version 3.0, 10X Genomics)
Assembly: hg38
Supplementary files format and content: comma separated (.csv) matrix of raw counts. Rows are features and columns are cells.
Supplementary files format and content: integrated_all_samples_v5.RDS: Integrated Seurat object containing single-cell RNA-seq data from paired baseline samples (GSE151928) and LPS-treated samples (GSE300946). The object includes all cell types, with processed, normalized, and integrated expression data, as well as annotated metadata including cluster identities and cell type classifications.
Supplementary files format and content: macrophage_recluster_v5.RDS: Subset Seurat object containing macrophage cells extracted from the integrated dataset of paired baseline (GSE151928) and LPS-treated (GSE300946) samples. Macrophages were reclustered to resolve subpopulations, and the object includes integrated expression data, and subcluster identities.

source_name: Bronchoalveolar lavage cells

extract_protocol:
Enrolled subjects underwent flexible fiberoptic bronchoscopy and bronchoalveolar lavage with serial installation and aspiration of normal saline. Lavage fluid was centrifuged to pellet cells. Cell pellet was resuspended at 1x10^6 cells per ml in PBS containing 0.04% bovine serum albumin.
Single cells were captured using The Chromium Box (10x Genomics, Pleasanton, CA). The Chromium Single Cell 3’ GEM, library, and gel bead kit PN-1000075 were used along with Bead Chip B PN-1000092 for cell capture and library construction. Libraries were sequenced with the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA) using an S4 flow cell.

value: Bronchoalveolar lavage cells

tag: diagnosis

value: healthy

tag: timepoint

value: day 1 post-LPS


title: Subject 15

description:
Library name: Subject 15
Bronchoalveolar lavage cells from healthy adult after LPS exposure

tag: cell type

value: day 3 post-LPS


title: Subject 11

description:
Library name: Subject 11
Bronchoalveolar lavage cells from healthy adult after LPS exposure

tag: age


title: Subject 13

description:
Library name: Subject 13
Bronchoalveolar lavage cells from healthy adult after LPS exposure

tag: Sex

value: day 5 post-LPS


title: Subject 10

description:
Library name: Subject 10
Bronchoalveolar lavage cells from healthy adult after LPS exposure


title: Subject 9

description:
Library name: Subject 9
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 2 post-LPS


title: Subject 7

description:
Library name: Subject 7
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: female


title: Subject 8

description:
Library name: Subject 8
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: day 4 post-LPS


title: Subject 6

description:
Library name: Subject 6
Bronchoalveolar lavage cells from healthy adult after LPS exposure

value: male


title: Subject 5

description:
Library name: Subject 5
Bronchoalveolar lavage cells from healthy adult after LPS exposure


title: Subject 4

description:
Library name: Subject 4
Bronchoalveolar lavage cells from healthy adult after LPS exposure


title: Subject 3

description:
Library name: Subject 3
Bronchoalveolar lavage cells from healthy adult after LPS exposure


title: Subject 2

description:
Library name: Subject 2
Bronchoalveolar lavage cells from healthy adult after LPS exposure


title: WT - AB

description:
Library name: SHE6920A9
single cell RNA sequencing, 10X genomics

data_processing:
CellRanger multi run with chemistry = SC5P-R2
Single cell BCR sequencing analysis. B-cell receptor (BCR) repertoire analysis was conducted with the Immcantation framework, implemented in a Python environment (v.3.11.10)
Assembly: mm10-2020
Supplementary files format and content: CellRanger verison 7.0.1 outputs file for expression, HTO and BCR .
Supplementary files format and content: Only B-1 cells from peritoneal cavity labelled with hashtag antibodies (C0303, C0304, C0306, Biolegend) are used for the further VDJ and diversity analysis
Library strategy: CITE-seq

molecule: protein

source_name: foetal liver, bone marrow, spleen and peritoneal cavity

extract_protocol: B-1 progenitor cells (Lin-CD93+IgM-CD19+B220neg-lo) from E18.5 foetal livers (three foetal livers were pooled together as one replicate) or bone marrow from three 8 weeks mice, B-1 cells (CD19+B220neg-lo ) from peritoneal cavity and spleen from three 8 weeks old mice were sorted by the FACS Aria II cell sorting system (BD Immunocytometry Systems, San Jose, CA, USA)

value: B-1 progenitor cells and B-1 cells

value: WT

value: E18.5 and 8 weeks old


title: Subject 1

description:
Library name: Subject 1
Bronchoalveolar lavage cells from healthy adult after LPS exposure


title: WT - BCR

description:
Library name: SHE6920A8
single cell RNA sequencing, 10X genomics

data_processing:
CellRanger multi run with chemistry = SC5P-R2
Single cell BCR sequencing analysis. B-cell receptor (BCR) repertoire analysis was conducted with the Immcantation framework, implemented in a Python environment (v.3.11.10)
Assembly: mm10-2020
Supplementary files format and content: CellRanger verison 7.0.1 outputs file for expression, HTO and BCR .
Supplementary files format and content: Only B-1 cells from peritoneal cavity labelled with hashtag antibodies (C0303, C0304, C0306, Biolegend) are used for the further VDJ and diversity analysis
Library strategy: scBCR-Seq

value: foetal liver, bone marrow, spleen and peritoneal cavity


title: dKO - BCR

description:
Library name: SHE6920A4
single cell RNA sequencing, 10X genomics

value: dKO


title: WT - GEX

description:
Library name: SHE6920A7
single cell RNA sequencing, 10X genomics

data_processing:
CellRanger multi run with chemistry = SC5P-R2
Single cell BCR sequencing analysis. B-cell receptor (BCR) repertoire analysis was conducted with the Immcantation framework, implemented in a Python environment (v.3.11.10)
Assembly: mm10-2020
Supplementary files format and content: CellRanger verison 7.0.1 outputs file for expression, HTO and BCR .
Supplementary files format and content: Only B-1 cells from peritoneal cavity labelled with hashtag antibodies (C0303, C0304, C0306, Biolegend) are used for the further VDJ and diversity analysis


title: ALSP2_WM

status: Public on Aug 13 2025

city: Saint Louis

first: Siling

last: Du

address: 4515 Mckinley Ave

institute: Washington University in St. Louis

description:
Library name: ALSP2_WM
10x Genomics

data_processing:
Sample demultiplexing, barcode processing and single-cell counting was performed using the Cell Ranger Single-Cell Software Suite (5.0.0, 10x Genomics). Cellranger count was used to align samples to the reference genome provided by 10X Genomics (GRCh38-2020-A for human) with “include introns = TRUE”.
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated values files and count matrix of processed Seurat object

source_name: white matter

extract_protocol:
Post-mortem frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
Chromium Single Cell 5′ Reagent Kits (v2)

value: white matter

tag: disease state

value: ALSP

value: M

tag: sample identifier


title: ALSP2_OC

description:
Library name: ALSP2_OC
10x Genomics

source_name: occipital cortex

value: occipital cortex


title: ALSP2_FC

description:
Library name: ALSP2_FC
10x Genomics

source_name: frontal cortex

value: frontal cortex


title: ALSP2_CB

description:
Library name: ALSP2_CB
10x Genomics

source_name: cerebellum

value: cerebellum


title: ALSP1_WM

description:
Library name: ALSP1_WM
10x Genomics


title: ALSP1_FC

description:
Library name: ALSP1_FC
10x Genomics


title: ALSP1_OC

description:
Library name: ALSP1_OC
10x Genomics


title: Control3_WM

description:
Library name: Control3_WM
10x Genomics

value: Control


title: ALSP1_CB

description:
Library name: ALSP1_CB
10x Genomics


title: Control3_FC

description:
Library name: Control3_FC
10x Genomics


title: Control2_WM

description:
Library name: Control2_WM
10x Genomics


title: Control3_CB

description:
Library name: Control3_CB
10x Genomics


title: Control2_FC

description:
Library name: Control2_FC
10x Genomics


title: Control2_CB

description:
Library name: Control2_CB
10x Genomics


title: Control1_OC

description:
Library name: Control1_OC
10x Genomics

value: F


title: Patient 10, run 1

status: Public on Aug 06 2025

type: RNA

city: Houston

first: Kelli

last: McCord

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

description: 10X Xenium V1 in situ sequencing

hyb_protocol: Probes from the predesigned Xenium Human Multi-Tissue and Cancer Gene Expression and hMulti_v1 design (chemistry v1: 10x Genomics), consisting of 377 genes as well as an additional 100 custom gene panel containing key T cell, tumor cell, and TCR-targeting probes were used for gene detection.

data_processing:
Samples were run on Xenium Analyzer. April 13th 2024 run used intrument software version 2.0.0.0, analysis version xenium-2.0.0.10. May 6th 2024 run used instrument software version 2.0.1.0 and analysis version xenium-2.0.0.10. September 11th 2024 run used instrument software version 3.0.2.0 and analysis version xenium-2.0.1.1. November 21st 2024 run used instrument software version 3.1.0.0 and analysis version xenium-2.0.2.0.
Post-Xenium H&E imaging

source_name: Ameloblastoma

label_protocol: Patient numbers (in title) were assigned to sample name for simplicity.

growth_protocol: Immediate following tumor resection, tumor samples were embedded in optimal cutting temperature (OCT) compound and flash frozen in a dry ice/isopentane bath before being stored in the vapor phase of liquid nitrogen.

extract_protocol: Xenium slides were prepared following the Xenium In Situ for Fresh Frozen Tissues User Guides CG000579, CG000581, CG000760, and CG000613 from 10x Genomics.

treatment_protocol: For each tumor sample, 10 µm sections were mounted onto Xenium V1 slides and stored at -80ºC for under one week prior to initiating the Xenium experiment.

tag: p16 status

tag: recurrence

value: Primary

tag: pack years

tag: site of tumor resection

value: Oral Cavity


title: Patient 28, run 2

description: 10X Xenium V1 in situ sequencing

scan_protocol: Samples were run on Xenium Analyzer. April 13th 2024 run used intrument software version 2.0.0.0, analysis version xenium-2.0.0.10. May 6th 2024 run used instrument software version 2.0.1.0 and analysis version xenium-2.0.0.10. September 11th 2024 run used instrument software version 3.0.2.0 and analysis version xenium-2.0.1.1. November 21st 2024 run used instrument software version 3.1.0.0 and analysis version xenium-2.0.2.0

source_name: HNSCC tumor

value: Positive

value: Recurrent

value: Oropharynx


title: Patient 28, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 23, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 20, run 2

description: 10X Xenium V1 in situ sequencing

value: Negative

value: Hypopharynx


title: Patient 20, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 19, run 1

description: 10X Xenium V1 in situ sequencing

value: Larynx


title: Patient 17, run 2

description: 10X Xenium V1 in situ sequencing


title: Patient 19, run 2

description: 10X Xenium V1 in situ sequencing


title: Patient 17, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 15, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 13, run 2

description: 10X Xenium V1 in situ sequencing


title: Patient 13, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 12, run 2

description: 10X Xenium V1 in situ sequencing


title: Patient 12, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 9, run 2

description: 10X Xenium V1 in situ sequencing


title: Patient 9, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 1, run 1

description: 10X Xenium V1 in situ sequencing


title: Lung-InVitro-Smad4OFF_r2

status: Public on Jun 12 2025

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: Library name: Lung-InVitro-Smad4OFF_r2

library_source: genomic

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
FASTQ files were trimmed with trimGalore and cutadapt (PMID: 28715235), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2 (PMID: 22388286).
Peaks were called over input using MACS2 (PMID: 18798982), and only peaks with a p-value of ≤ 0.001 and outside the ENCODE blacklist region were kept. All peaks from all samples were merged by combining peaks within 500 bp of each.
featureCounts (PMID: 24227677) was used to count the mapped reads for each sample. The resulting peak atlas was normalized using DESeq2 (PMID: 25516281). For comparison to DepthNorm, samples were normalized to 10 million mapped reads. Normalized bigWig files were created using the normalization factors from DESeq2 as previously described (PMID: 30429377) and BEDTools genomeCoverageBed (PMID: 20110278). Dynamic ATAC peaks were called if they had an absolute log2-transformed fold change ≥ 0.58 and FDR ≤ 0.1.
Assembly: Reads were aligned to the mouse genome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

molecule: genomic DNA

source_name: Lung

growth_protocol: Cell lines were generated from tumor-bearing pancreata, livers, or lungs. Tumors were dissected, chopped with razor blades, and digested with 1 mg/ml collagenase V (Sigma-Aldrich) diluted in HBSS for 30-60 min, followed by 0.25% trypsin for 5-10 min. Digested tissues were washed with complete DMEM (DMEM, 10% FBS (Gibco), 1X penicillin–streptomycin), passed through a 100-μm filter, and cultured in complete DMEM on collagen-coated plates (0.1 mg/ml PurCol, Advanced Biomatrix) supplemented with 1 μg/ml doxycycline at 37°C. Cells were passaged at least five times to eliminate any non-tumor cells before using them in experiments.

extract_protocol:
Cells were harvested by trypsinization. Then, 60,000 mKate2+ cells per sample were isolated by FACS, washed once with 50 μl cold PBS and resuspended in 50 μl cold lysis buffer. Cells were then centrifuged immediately for 10 min at 500g at 4°C, and the pellet of nuclei was subjected to transposition with Nextera Tn5 transposase (Illumina #FC-121–1030) for 30 min at 37°C, according to the manufacturer’s instructions. DNA was eluted using a DNA Clean & Concentrator Kit in 21 μl elution buffer (Zymo Research #D4013).
ATAC-seq libraries were prepared using the NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) as previously described (PMID: 25559105). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).
Approximately 50 million paired-end 150-bp reads (25 million each side) were sequenced per replicate on a HiSeq instrument (Illumina).

treatment_protocol: Cells were cultured under continunous treatment with 1 μg/ml doxycycline at 37°C.

value: Lung

value: PDAC Lung Metastasis Cells


title: Lung-InVitro-Smad4OFF_r1

description: Library name: Lung-InVitro-Smad4OFF_r1


title: Liv-InVitro-Smad4OFF_r2

description: Library name: Liv-InVitro-Smad4OFF_r2

value: Liver

value: PDAC Liver Metastasis Cells


title: Liv-InVitro-Smad4OFF_r1

description: Library name: Liv-InVitro-Smad4OFF_r1


title: Panc-InVitro-Smad4OFF_r2

description: Library name: Panc-InVitro-Smad4OFF_r2

source_name: Pancreas

value: Pancreas

value: PDAC Primary Tumor Cells


title: Panc-InVitro-Smad4OFF_r1

description: Library name: Panc-InVitro-Smad4OFF_r1


title: KCS-B87_TGFb_DoxOn_24h

description: Library name: KCS-B87_TGFb_DoxOn_24h

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: PDAC Primary Tumor

growth_protocol: Cell lines were generated from tumor-bearing pancreata. Tumors were dissected, chopped with razor blades, and digested with 1 mg/ml collagenase V (Sigma-Aldrich) diluted in HBSS for 30-60 min, followed by 0.25% trypsin for 5-10 min. Digested tissues were washed with complete DMEM (DMEM, 10% FBS (Gibco), 1X penicillin–streptomycin), passed through a 100-μm filter, and cultured in complete DMEM on collagen-coated plates (0.1 mg/ml PurCol, Advanced Biomatrix) supplemented with 1 μg/ml doxycycline at 37°C. Cells were passaged at least five times to eliminate any non-tumor cells before using them in experiments.

extract_protocol:
Total RNA was isolated using TRIzol LS (Thermo Fisher Scientific # 10296028) followed by column clean-up using an RNeasy kit (Qiagen #74106).
100-500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA HT Kit, Illumina #20020595), with 15 cycles of PCR.
Samples were barcoded and run on a HiSeq (Illumina) in a 75-bp SE run, with an average of 50 million reads per sample.

treatment_protocol: For ‘DoxOn’ conditions, cells were cultured under continuous Dox treatment (1 mg/ml). For ‘DoxOff’ conditions, cells were cultured in the absence of Dox for five days prior to the start of the experiment. Then, cells were treated for 24 h with either recombinant mouse TGFb-1 (100 pM; R&D Systems #7666-MB-005) or TGFb inhibitor SB505124 (2.5 µM; Sigma #S4696).

value: PDAC Primary Tumor

value: PDAC primary tumor cells

tag: time


title: KCS-B87_TGFb_DoxOff_24h

description: Library name: KCS-B87_TGFb_DoxOff_24h


title: KCS-B87_SB_DoxOff_24h

description: Library name: KCS-B87_SB_DoxOff_24h


title: KCS-B87_SB_DoxOn_24h

description: Library name: KCS-B87_SB_DoxOn_24h


title: KCS-B73_TGFb_DoxOff_24h

description: Library name: KCS-B73_TGFb_DoxOff_24h


title: KCS-B73_TGFb_DoxOn_24h

description: Library name: KCS-B73_TGFb_DoxOn_24h


title: KCS-B73_SB_DoxOff_24h

description: Library name: KCS-B73_SB_DoxOff_24h


title: KCS-B73_SB_DoxOn_24h

description: Library name: KCS-B73_SB_DoxOn_24h


title: A549, IP, replicate 3

status: Public on Oct 05 2025

first: Ryan

middle: A.

last: Flynn

state: MA

address: 1 Blackfan Circle

department: Department of Pediatrics

institute: Boston Children's Hospital

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

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.

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.

tag: cell line

value: epithelial

tag: sample group


title: NP460 ATAC_rep2

status: Public on Jun 06 2025

city: HK

first: Lai Shun Dittman

last: CHUNG

state: HK

address: 21 Sassoon Road, Pokfulam

department: Department of Clinical Oncology

country: Hong Kong

institute: the University of Hong Kong

description: Normal NPE

data_processing:
Trimmomatic was used to remove the adapter sequences and poor-quality bases and reads.
The ENCODE ATAC-Seq pipeline (v1.0) was applied for alignment, peak calling, and quality evaluation.
The peaks for differential analysis were obtained by merging the narrowPeaks files of the same condition.
The bioinformatics tool featureCounts was used for creating the count matrices. DESeq2 was used for identifying the differentially accessible regions. Only the regions with absolute log2 fold change ≥ 2 and q-value <0.01 were considered as significant. The function rlog was used for normalization.
Assembly: hg19 & EBV genome (NC_007605)
Supplementary files format and content: .bw file can be visualised in IGV browser
Supplementary files format and content: .narrowPeak files were generated by ENCODE ATAC-Seq pipeline

source_name: cell line

growth_protocol: Fresh cells cultured in 37oC, 5% CO2

extract_protocol:
Briefly, 50,000 cells were lysed in a cold lysis buffer. The cell lysates were incubated with Tn5 transposase (Illumina Cat# E7645S) at 37°C for 30 min. Libraries were sequenced on the NovaSeq 6000 platform. Data analysis was performed following the ENCODE ATAC-Seq pipeline (v1.0).
Tn5 transposase (Illumina Cat# E7645S)

treatment_protocol: No treatment

value: cell line

value: nasopharyngeal epithelial cells

value: Wild-type


title: A549, Input, replicate 2

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

value: A549, Input


title: A549, Input, replicate 3

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


title: A549, Control, replicate 3

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

value: A549, Control


title: Jurkat, Input, replicate 2

description:
Library name: 34i
count_matrix_homo.csv
counts_long.csv

source_name: Jurkat

value: Jurkat

value: hematopoietic

value: Jurkat, Input


title: NP460 ATAC_rep1

description: Normal NPE


title: AML2, Control, replicate 3

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

value: AML2, Control


title: NP69 ATAC_rep2

description: Normal NPE


title: Panc-shSmad4_Cerulein_d2

status: Public on May 14 2025

description:
Library name: T4.shSmad4.587-1
10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v4.0.12 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the mouse reference genome version gex-mm10-2020-A, available from the 10X Genomics website.
Assembly: mm10
Supplementary files format and content: Filtered single cell cell/gene matrices in .h5 format generated by cellbender v0.3.0

source_name: Pancreas (pre-malignant)

growth_protocol: Mice were generated by 8-cell or blastocyst injection of KC-shSmad4 or KC-shRen ESCs.

extract_protocol:
Cells were freshly isolated from non-tumor-bearing KC-shRen and KC-shSmad4 pancreata by FACS for mKate2+GFP+DAPI- cells. Sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed by 0.2% (w/v) Trypan Blue staining (Countess II).
Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction (Chromium instrument (10X Genomics) user guide manual for 3’ v2).
Around 5,000 cells were targeted for each sample. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). Single-cell RNA-seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X Genomics) following the user guide manual for 3’ v2.

treatment_protocol: shRNAs were induced by treatment of the resulting mice with doxycycline (625 mg/kg; Envigo) in the chow starting at 5-6 weeks of age. To examine the effects of tissue injury and Smad4 depletion on the premalignant pancreas, 8-week-old KC-shRen and KC-shSmad4 mice were treated with eight-hourly i.p. injections of cerulein (80 μg/kg; Bachem) or PBS for two consecutive days.

value: Pancreas (pre-malignant)

tag: treatment

value: Dox+Cerulein

value: M


title: NP69 ATAC_rep1

description: Normal NPE

tag: genotype


title: Panc-shRen_Cerulein_d2

description:
Library name: T4.shRen.584-3
10x Genomics

tag: tissue

value: shRen


title: Panc-shSmad4_PBS_d2

description:
Library name: T3.shSmad4.588-2
10x Genomics

value: Dox+PBS


title: Lung-d14-Smad4ON_m4

description: single-end sequencing

source_name: PDAC Lung Metastasis

growth_protocol: For pancreatic tumors, mouse hosts were placed on doxycycline chow 5-7 days before transplantation. Mice were anesthetized and a survival surgery was performed to expose the pancreas. 1 x 10^5 tumor-derived cells were resuspended in 25 uL 1:1 DMEM (Gibco) : Matrigel (Corning) mix and injected in the tail of the pancreas of each mouse. For liver metastasis assays, mice were anesthetized and a survival surgery was performed to expose the spleen. 4 x 10^5 tumor-derived cells resuspended in 20 uL PBS were injected in the splenic parenchyma of each mouse, followed by removal of the spleen and cauterization (splenectomy). For lung metastasis assays, mice were restrained, and 2.5 x 10^5 tumor-derived cells resuspended in 250 uL PBS were injected in the tail vein of each mouse.

extract_protocol:
Total RNA was extracted using Trizol Total RNA was isolated using TRIzol LS (Thermo Fisher Scientific # 10296028) followed by column clean-up using an RNeasy kit (Qiagen #74106). the RNeasy Mini Kit (Qiagen)
100-500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA HT Kit, Illumina #20020595), with 15 cycles of PCR.
Samples were barcoded and run on a HiSeq (Illumina) in a 75-bp SE run, with an average of 50 million reads per sample.

treatment_protocol: Mouse hosts were fed Doxycycline chow. Where applicable, doxycycline withdrawal was done at 4 (pancreas), 5 (liver) or 6 weeks (lungs) post-injection by switching the food source to regular chow.

value: PDAC lung metastasis cells

value: day 14


title: Lung-d14-Smad4ON_m3

description: single-end sequencing


title: Panc-shRen_PBS_d2

description:
Library name: T3.shRen.584-0
10x Genomics


title: Lung-d14-Smad4ON_m2

description: single-end sequencing


title: Lung-d14-Smad4ON_m1

description: single-end sequencing


title: Lung-d14-Smad4OFF_m3

description: single-end sequencing


title: Lung-d14-Smad4OFF_m1

description: single-end sequencing


title: Lung-d14-Smad4OFF_m4

description: single-end sequencing


title: Lung-d14-Smad4OFF_m2

description: single-end sequencing


title: Liv-d14-Smad4ON_m3

description: single-end sequencing

source_name: PDAC Liver Metastasis

value: PDAC liver metastasis cells


title: Liv-d14-Smad4ON_m2

description: single-end sequencing


title: Liv-d14-Smad4ON_m1

description: single-end sequencing


title: Liv-d14-Smad4OFF_m3

description: single-end sequencing


title: Liv-d14-Smad4OFF_m1

description: single-end sequencing


title: Panc-d14-Smad4ON_m2

description: single-end sequencing

value: PDAC primary tumor cells


title: Panc-d14-Smad4ON_m3

description: single-end sequencing


title: Liv-d14-Smad4OFF_m2

description: single-end sequencing


title: Panc-d14-Smad4ON_m1

description: single-end sequencing


title: Panc-d14-Smad4OFF_m2

description: single-end sequencing


title: Panc-d14-Smad4OFF_m1

description: single-end sequencing


title: Lung-d7-Smad4ON_m2

description: single-end sequencing

value: day 7


title: Lung-d7-Smad4OFF_m4

description: single-end sequencing


title: Lung-d7-Smad4ON_m1

description: single-end sequencing


title: Lung-d7-Smad4OFF_m3

description: single-end sequencing


title: Lung-d7-Smad4OFF_m2

description: single-end sequencing


title: Liv-d7-Smad4ON_m3

description: single-end sequencing


title: Panc-Smad4OFF_m3_multiome_ATAC

description: 10x Genomics

library_source: genomic single cell

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the mouse reference genome version gex-mm10-2020-A, available from the 10X Genomics website.
Assembly: mm10
Supplementary files format and content: Filtered single cell 3' cell/gene matrices in .h5 format generated by Cell Ranger
Supplementary files format and content: single cell atac fragments generated by Cell Ranger

growth_protocol: Mouse hosts were placed on doxycycline chow 5-7 days before transplantation. Mice were anesthetized and a survival surgery was performed to expose the pancreas. 1 x 10^5 tumor-derived cells were resuspended in 25 uL 1:1 DMEM (Gibco) : Matrigel (Corning) mix and injected in the tail of the pancreas of each mouse.

extract_protocol:
Single Cell Multiome ATAC + Gene Expression was performed with 10X Genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog #1000282) and ATAC Kit A (catalog #1000280) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and demonstrated protocol, Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing.
Briefly, cells (viability 95%) were lysed for 4 min and resuspended in Diluted Nuclei Buffer (10X Genomics #PN-2000207). Lysis efficiency and nuclei concentration was evaluated on Countess II automatic cell counter by trypan blue and DAPI staining. 11,000 nuclei were loaded per transposition reaction, targeting recovery of 7,000 nuclei after sequencing. After transposition reaction, nuclei were encapsulated and barcoded.
Next-generation sequencing libraries were constructed following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and sequenced on an Illumina NovaSeq 6000 system.

value: PDAC Primary Tumor

value: DoxON


title: Panc-Smad4OFF_m3_multiome_RNA

description: 10x Genomics


title: Lung-d7-Smad4OFF_m1

description: single-end sequencing


title: Liv-d7-Smad4ON_m2

description: single-end sequencing


title: Liv-d7-Smad4OFF_m2

description: paired-end sequencing


title: Liv-d7-Smad4OFF_m1

description: single-end sequencing


title: Panc-Smad4OFF_m2_multiome_RNA

description: 10x Genomics


title: Panc-Smad4OFF_m2_multiome_ATAC

description: 10x Genomics


title: Panc-Smad4OFF_m1_multiome_ATAC

description: 10x Genomics


title: Panc-d7-Smad4ON_m2

description: single-end sequencing


title: Panc-Smad4OFF_m1_multiome_RNA

description: 10x Genomics


title: Panc-d7-Smad4ON_m1

description: single-end sequencing


title: Panc-d7-Smad4OFF_m3

description: single-end sequencing


title: Panc-d7-Smad4OFF_m1

description: single-end sequencing


title: Lung-Smad4ON_m3

description: paired-end sequencing

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
FASTQ files were trimmed with trimGalore and cutadapt (PMID: 28715235), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2 (PMID: 22388286).
Peaks were called over input using MACS2 (PMID: 18798982), and only peaks with ap-value of ≤ 0.001 and outside the ENCODE blacklist region were kept. All peaks from all samples were merged by combining peaks within 500 bp of each.
featureCounts (PMID: 24227677)was used to count the mapped reads for each sample. The resulting peak atlas was normalized using DESeq2 (PMID: 25516281). For comparison to DepthNorm, samples were normalized to 10 million mapped reads. Normalized bigWig files were created using the normalization factors from DESeq2 as previously described (PMID: 30429377)and BEDTools genomeCoverageBed (PMID: 20110278). Dynamic ATAC peaks were called if they had an absolute log2-transformed fold change≥0.58 and FDR≤0.1.
Assembly: Reads were aligned to the mouse genome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

extract_protocol:
A total of 60,000 mKate2+cells were isolated by FACS, washed once with 50 μl cold PBS and resuspended in 50 μl cold lysis buffer. Cells were then centrifuged immediately for 10 min at 500gat 4°C, and the pellet of nuclei was subjected to transposition with Nextera Tn5 transposase (Illumina #FC-121–1030) for 30 min at 37°C, according to the manufacturer’s instructions. DNA was eluted using a DNA Clean & Concentrator Kit in 21 μl elution buffer (Zymo Research #D4013).
ATAC-seq libraries were prepared using the NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) as previously described (PMID: 25559105). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).
Approximately 50 million paired-end 150-bp reads (25 million each side) were sequenced per replicate on a HiSeq instrument (Illumina).


title: Lung-Smad4ON_m2

description: paired-end sequencing


title: Lung-Smad4ON_m1

description: paired-end sequencing


title: Lung-Smad4OFF_m1

description: paired-end sequencing


title: Lung-Smad4OFF_m3

description: paired-end sequencing


title: Liv-Smad4ON_m2

description: paired-end sequencing


title: Liv-Smad4OFF_m2

description: paired-end sequencing


title: Liv-Smad4OFF_m1

description: paired-end sequencing


title: Liv-Smad4ON_m1

description: paired-end sequencing


title: Panc-Smad4ON_m3

description: paired-end sequencing


title: Panc-Smad4ON_m2

description: paired-end sequencing


title: Panc-Smad4ON_m1

description: paired-end sequencing


title: Panc-Smad4OFF_m3

description: paired-end sequencing


title: Panc-Smad4OFF_m2

description: paired-end sequencing


title: CRISPR library from Cal27 cells, week 0, replicate 2

status: Public on Apr 28 2025

city: Stanford

first: Luca

last: Ducoli

state: California

address: 269 Campus Drive CCSR 2150

institute: Stanford University

description: Library name: LD_Cal27_W0_2

data_processing:
In each screen, UMI was compressed using umi_tools extract, and adaptor sequences were removed using cutadapt. Subsequently, the remaining reads were aligned on the guide sequences using bowtie (maximum error: 1, minimum length: 16). The count for each guide was collected using umi_tools count, then transformed into scc format. For in vitro screen analysis, MaGeCK MLE was performed based on the guide counts with the design matrix of comparing the timepoint of the initial collection and the post-screen collection as described in (W. Li et al. 2015). In vivo and in vitro CRISPR screens were integrated by first determining the ß scores of each sample against plasmid DNA determined by miSeq (Illumina) using the MaGeCK MLE algorithm (W. Li et al. 2015). ß scores were normalized and visualized using the MaGeCKFlute R package (B. Wang et al. 2019) following the authors’ guidelines.
Assembly: hg38
Supplementary files format and content: tab separated txt file containing unnormalized feature (guide) counts
Library strategy: CRISPR Screen

growth_protocol: The human A431 and Cal27 cell lines were cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

extract_protocol:
Three mice (a total of six tumors) were performed on each cell line. Based on the visual observation of subcutaneous tumor growths, the mice injected with the same cell lines were sacrificed on the same days after 3-4 weeks. (A431: 3.5 weeks, Cal27: 4.5 weeks) The tumors were surgically harvested, minced, and homogenized in an MP Biomedical lysing matrix A tube. Genomic DNA was isolated using QIAGEN DNeasy Blood and Tissue Kit
Sequencing library was made as described in (Mathiowetz et al. 2023, PMID: 37000620) with an adjustment of using <10g of gDNA in PCR1 reaction and a pair of primers matching with our sequences and manually determining PCR2 cycles based on a trial run to prevent overamplification.

treatment_protocol: The pooled oligo Lenti virus was made and transfected on dCas9-KRAB expressing A431 and Cal27 with MOI of 0.3.. After the 3 days of selection in puromycin, the transfection rates were chekced with Cell Titer Blue. Four million cells in 100ul were gently mixed with 50ul Matrigel (Corning) until it turned into a homogenous mixture and injected with 28G insulin syringe into both sides of rear flanks of SCID Hairless Outbred (SHO®) mice (Charles River). Triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80C for each replicate as the initial screen time point.

value: Lentivirus-mediated CRISPR library infection


title: CRISPR library from Cal27 cells, week 0, replicate 3

description: Library name: LD_Cal27_W0_3


title: Single cell sequencing of transformed human KC with CDK4(R24C)-Ras(G12V)

description: Library name: scSeq_transformed_KC

data_processing:
Single-cell RNA-seq data from Cal27 xenograft (Ji et al. 2020) and CDK4(R24C)-Ras(G12V) transformed spheroids were mapped as described above. Seurat objects were generated, and expression values were normalized using the SCTransform() function from the Seurat R package (Satija et al. 2015).
Assembly: hg38
Supplementary files format and content: cellranger outputs including barcode, feature, matrix, and h5 files

source_name: Human Kertatinocyte

growth_protocol: The cultures were incubated at 37°C in a 5% CO2 incubator for a week.

extract_protocol:
Spheroids were then collected in a 15mL falcon tube and reduced to single-cell suspension using 0.25% trypsin with DNase I (0.2 mg/mL, Worthington) and Collagenase I (5 mg/mL, Gibco) for 30 minutes at 37°C. Cells were washed 3 times in DMEM containing 10% FBS. Cells were collected by centrifugation at 450g for 5min and finally resuspended in PBS (Gibco) containing 0.04% BSA. Cell count was determined using a Countess machine (Thermo Fisher). After passing through a cell strainer (Corning), 25’000 cells were loaded into a 10x Chromium machine (10x genomics).
Library preparation was performed using the Chromium GEM-X Single Cell 3’ Kit (10x Genomics), followed by sequencing at Novogene.

treatment_protocol: A 10mg/mL solution of Poly(2-hydroxyethyl methacrylate) (pHEMA, sigma) was prepared in 95% ethanol and warmed at 37°C until fully dissolved. Two layers of PHEMA were applied to 10cm dishes by spreading 5mL of the solution and allowing it to dry under a tissue culture hood for 24 hours per layer. The coated dishes were sterilized under UV light for at least 15 minutes prior to use. For spheroid formation, CDK4(R24C)-Ras(G12V) cells were seeded into pHEMA-coated 10cm dishes at a final concentration of 2.5x105 cells/mL in KGM medium for spheroid formation.

value: Human Kertatinocyte

value: Lentiviral transfection of CDK4(R24C)-Ras(G12V)


title: CRISPR library from Cal27 cells, week 0, replicate 1

description: Library name: LD_Cal27_W0_1


title: CRISPR library from Cal27 derived tumor 2 from mouse replicate 3

description: Library name: LD_Cal27_T_3_2

value: Lentivirus-mediated CRISPR library infection and a tumor grown in mouse


title: CRISPR library from Cal27 derived tumor 1 from mouse replicate 2

description: Library name: LD_Cal27_T_2_1


title: CRISPR library from Cal27 derived tumor 1 from mouse replicate 1

description: Library name: LD_Cal27_T_1_1


title: CRISPR library from Cal27 derived tumor 1 from mouse replicate 3

description: Library name: LD_Cal27_T_3_1


title: CRISPR library from A431 cells, week 0, replicate 3

description: Library name: LD_A431_W0_3


title: CRISPR library from A431 cells, week 0, replicate 2

description: Library name: LD_A431_W0_2


title: CRISPR library from A431 cells, week 0, replicate 1

description: Library name: LD_A431_W0_1


title: FFPE breast cancer patient (B11) sample profiled with the Xenium human breast gene panel

status: Public on Mar 27 2026

city: Lausanne

first: Raphael

last: Gottardo

state: Vaud

address: Rue du Bugnon 21

department: Biomedical Data Science Center

country: Switzerland

institute: Lausanne University Hospital

description: Breast cancer tissues analyzed with Xenium human breast gene panel

scan_protocol: https://cdn.10xgenomics.com/image/upload/v1670350987/user-guides-pdfs/CG000601_XeniumInSituGeneExpression_ProtocolPlanner_RevB.pdf Post-Xenium multiplex immunofluorescence-stained slides were imaged using fluorescence microscopy or whole-slide fluorescence scanning. Fluorescence channels corresponding to DAPI, CD8, and pan-cytokeratin were acquired.

label: Xenium probe set

source_name: primary breast cancer

label_protocol: Xenium probe set

growth_protocol: Not applicable

treatment_protocol: Not applicable

value: primary breast cancer

tag: tissue preservation method

value: FFPE

value: Adenocarcinoma, NOS


title: CRISPR library from A431 derived tumor 2 from mouse replicate 3

description: Library name: LD_A431_T_3_2


title: CRISPR library from A431 derived tumor 2 from mouse replicate 2

description: Library name: LD_A431_T_2_2


title: CRISPR library from A431 derived tumor 1 from mouse replicate 3

description: Library name: LD_A431_T_3_1


title: CRISPR library from A431 derived tumor 1 from mouse replicate 2

description: Library name: LD_A431_T_2_1


title: CRISPR library from A431 derived tumor 1 from mouse replicate 1

description: Library name: LD_A431_T_1_1


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 1.5, replicate 3

description: Library name: LD_Kerat_W1_TSK3

source_name: Human Keratinocyte

growth_protocol: The human A431 and Cal27 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C. Primary human keratinocytes were obtained from fresh, surgically discarded neonatal foreskin, cultured in Keratinocyte-SFM and Medium 154 with Keratinocyte supplement, and subcultured regularly before reaching high confluency for a few cycles.

extract_protocol:
DNA was isolated from the cell pellet using QIAGEN DNeasy Blood and Tissue Kit
The sequencing library was made as described in (Ji et al. 2020) [PMID: 32579974]

treatment_protocol: Lentivirus has been produced in Lenti-X cells seeded higher than 70% in 10cm (or 15cm) dish. Cells in each 10cm dish were transfected with 7.5ug CMV, 3.5ug MDG, 7.5ug Plasmid in 625ul OptiMEM mixed with another tube containing 25ul Lipofectamine in 625ul OptiMEM. (The volume or amount were doubled for cells in 15cm dish). The media was replaced after the overnight incubation, collected after every 24h with media replacement for two times, filtered through a 0.45um PES membrane, and concentrated with Lenti-X concentrator (Takara). Cas9 transfection was performed on A431, Cal27, and Primary Keratinocytes and selected with blasticidin. Pooled guide lentivirus was titrated in each of dCas9-KRAB expressing cell lines to achieve an MOI of 0.3. Following selection with puromycin for two to three days, the transfection rates were checked with Cell Titer Blue, and triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80°C for each replicate as the initial screen time point. Cells were cultured by maintaining at least 1000x coverage with regular basis of subculturing for three weeks (Primary Keratinocyte for 1.5 week due to inherently limited proliferation capacity).

value: Human Keratinocyte


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 1.5, replicate 2

description: Library name: LD_Kerat_W1_TSK2


title: JHH348CAF

status: Public on Apr 01 2026

city: Baltimore

first: Jacquelyn

middle: W

last: Zimmerman

state: Maryland

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

description:
Library name: JHH348CAF
CAF Patient 348, Monoculture

data_processing:
Salmon v.1.9.0
Alignment was performed utilizing Salmon v1.9.0 on the Joint High-Performance Computing Exchange (JHPCE). “salmon_partial_sa_index__default.tgz” was used as the index for alignment for the HG38 genome, which was premade and available on refgenie (http://refgenomes.databio.org/v3/genomes/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4). Salmon quantification, [salmon quant], was completed in mapping-based mode (--validateMappings) with automatic library detection. Salmon quantifications were the imported into R using tximport v1.20.0, with the use of the “tgMap.tsv” file also provided in the HG38 refgenie repository for accurate gene-level summarization.
We evaluated sample quality from the distribution of reads as visualized in a boxplot of log counts. We observed no samples with zero median expression, reflective of a low read count, so samples were not of low quality. We used principal component analysis (PCA) of the variance stabilization transform (vst) RNA-seq data to evaluate sample clustering. Projection of the discovered CoGAPS Pattern 7 onto the VST data was completed using ProjectR (V1.8.0). The bulk-seq normalized data and CoGAPs feature loadings were run through the projectR function of the package(14). The projection results were combined with the bulk-seq metadata and plotted using ggplot2 (V3.3.5) and paired t-test results added using ggpubr (V0.4.0)(14).
Analysis completed using DESeq2
Assembly: HG38
Supplementary files format and content: tab-separated values

source_name: pancreas

extract_protocol:
Cells that were coculture were sorted by FACS and immediately underwent RNA extraction (Qiagen RNeasy kit 74004) per manufacturers protocol. RNA was quantified at 260nm using NanoDrop1000 (Thermo Fisher Scientific) and 200ug of RNA was sent to Novogene Corporation Inc. RNA integrity (RIN) was measured at Novogene with Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). All samples were required to demonstrate RIN > 6.8 and ranged from 7.2 to 10.0.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: pancreas

value: Patient-derived organoid

value: CAF

value: monoculture


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 1.5, replicate 1

description: Library name: LD_Kerat_W1_TSK1


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 0, replicate 3

description: Library name: LD_Kerat_W0_TSK3


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 0, replicate 1

description: Library name: LD_Kerat_W0_TSK1


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 1.5, replicate 3

description: Library name: LD_Kerat_W1_KC3


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 1.5, replicate 2

description: Library name: LD_Kerat_W1_KC2


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 0, replicate 3

description: Library name: LD_Kerat_W0_KC3


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 0, replicate 2

description: Library name: LD_Kerat_W0_KC2


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 0, replicate 1

description: Library name: LD_Kerat_W0_KC1


title: CRISPR library from_Cal27 cells, TSK library, Week 3, replicate 3

description: Library name: LD_Cal27_W3_TSK3


title: CRISPR library from_Cal27 cells, TSK library, Week 3, replicate 2

description: Library name: LD_Cal27_W3_TSK2


title: CRISPR library from_Cal27 cells, TSK library, Week 3, replicate 1

description: Library name: LD_Cal27_W3_TSK1


title: CRISPR library from_Cal27 cells, TSK library, Week 0, replicate 3

description: Library name: LD_Cal27_W0_TSK3


title: CRISPR library from_Cal27 cells, TSK library, Week 0, replicate 2

description: Library name: LD_Cal27_W0_TSK2


title: FFPE NSCLC patient (L6) sample profiled with the Xenium human lung gene panel

description: Lung cancer tissues analyzed with Xenium human lung gene panel

source_name: primary NSCLC

value: primary NSCLC

value: Sq. cell carcinoma, keratinizing, NOS


title: CRISPR library from_Cal27 cells, KC library, Week 3, replicate 2

description: Library name: LD_Cal27_W3_KC2


title: CRISPR library from_Cal27 cells, KC library, Week 3, replicate 3

description: Library name: LD_Cal27_W3_KC3


title: CRISPR library from_Cal27 cells, KC library, Week 0, replicate 3

description: Library name: LD_Cal27_W0_KC3


title: CRISPR library from_Cal27 cells, KC library, Week 3, replicate 1

description: Library name: LD_Cal27_W3_KC1


title: CRISPR library from_Cal27 cells, KC library, Week 0, replicate 2

description: Library name: LD_Cal27_W0_KC2


title: FFPE breast cancer patient (B15) sample profiled with the Xenium human breast gene panel

value: Lobular carcinoma, NOS


title: CRISPR library from_Cal27 cells, KC library, Week 0, replicate 1

description: Library name: LD_Cal27_W0_KC1


title: FFPE breast cancer patient (B13) sample profiled with the Xenium human breast gene panel

value: Infiltrating duct carcinoma, NOS


title: FFPE NSCLC patient (L1) sample (2) profiled with the custom immunooncology gene panel

description: Lung cancer tissues analyzed with a custom Xenium immunooncology 340 gene panel

value: Adenocarcinoma with mixed subtypes


title: CRISPR library from_A431 cells, TSK library, Week 3, replicate 3

description: Library name: LD_A431_W3_TSK3

value: Lentivirus-mediated CRISPR library infection


title: CRISPR library from_A431 cells, TSK library, Week 3, replicate 2

description: Library name: LD_A431_W3_TSK2


title: CRISPR library from_A431 cells, TSK library, Week 3, replicate 1

description: Library name: LD_A431_W3_TSK1


title: CRISPR library from_A431 cells, TSK library, Week 0, replicate 2

description: Library name: LD_A431_W0_TSK2


title: CRISPR library from_A431 cells, TSK library, Week 0, replicate 1

description: Library name: LD_A431_W0_TSK1


title: CRISPR library from_A431 cells, KC library, Week 3, replicate 3

description: Library name: LD_A431_W3_KC1


title: CRISPR library from_A431 cells, KC library, Week 3, replicate 2

description: Library name: LD_A431_W3_KC3


title: CRISPR library from_A431 cells, KC library, Week 0, replicate 3

description: Library name: LD_A431_W0_KC3


title: FFPE breast cancer patient (B7) sample profiled with the Xenium human breast gene panel

value: Carcinoma, NOS


title: CRISPR library from_A431 cells, KC library, Week 0, replicate 1

description: Library name: LD_A431_W0_KC1


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #2). Replicate 3

description: Library name: S18_1116_2_3

data_processing:
For analyzing differentially expressed genes compared to the control, raw reads were first quantified with Salmon (ver. 0.12.0) (Patro et al. 2017) using the gencode release v39 basic annotation with the following settings: -l A -p 8 --gcBias --numGibbsSamples 20 --validateMappings.
Assembly: hg38
Supplementary files format and content: Salmon count output files

growth_protocol: The human A431 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

extract_protocol:
After 48h of ASO transfection, cells were lysed in LRT plus lysis buffer (Qiagen), and RNA isolation was performed using an RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
From each sample, 500ng of RNA was used for the library preparation using the kit (QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI, Lexogen), pooled together with an equal concentration, and then sequenced on a NovaSeq X+, paired-end, 150 bp length, with ~30 M reads for each sample.

treatment_protocol: For each ASO, we performed a reverse transfection using Lipofectamine RNAiMAX (Thermo Fisher Scientific). In 10cm dishes, 2mL Opti-MEM, 20nM of scrambled control ASO or two ASOs targeting LINC00704 and LINC01116, and 25µL Lipofectamine RNAiMAX (Thermo) were mixed and incubated for 20min. Then, 1x106 A431 cells per dish were seeded into each 10cm dish and cultured for 48h in a 5% CO2 incubator.

value: LINC01116-ASO transfection with Lipofectamine reagents


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #2). Replicate 2

description: Library name: S17_1116_2_2


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #1). Replicate 2

description: Library name: S14_1116_1_2


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #1). Replicate 3

description: Library name: S15_1116_1_3


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #2). Replicate 1

description: Library name: S16_1116_2_1


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #2). Replicate 3

description: Library name: S12_704_2_3

value: LINC00704-ASO transfection with Lipofectamine reagents


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #2). Replicate 2

description: Library name: S11_704_2_2


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #2). Replicate 1

description: Library name: S10_704_2_1


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #1). Replicate 3

description: Library name: S09_704_1_3


title: Bulk RNA-seq in A431 control condition (Non-targeting ASO). Replicate 3

description: Library name: S03_Ctrl_3

value: Non-targeting ASO transfection with Lipofectamine reagents


title: Bulk RNA-seq in A431 control condition (Non-targeting ASO). Replicate 2

description: Library name: S02_Ctrl_2


title: S1B

status: Public on Apr 26 2025

description: pre-cDCs DNGR-1 KO CD45.2 from spleen

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using RSEM v1.3.0  and STAR v2.5.2 with the “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default.
Raw counts were processed using the bioconductor package DESeq2 v1.18.1 in R v3.4.3. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Assembly: GRCm38
Supplementary files format and content: tab delimited vst normalised expression data, where columns are samples and row are ensembl mouse IDs
Supplementary files format and content: tab delimited raw_counts output of STAR alignment and RSEM quantifications. Columns are samples and rows are ensembl mouse IDs

source_name: pre-cDCs DNGR-1 KO CD45.2 from spleen

extract_protocol:
RNeasy Micro kit [Qiagen]
Total RNA (KAPA Hyper prep with Riboerase)

treatment_protocol: No Treatment

value: pre-cDCs DNGR-1 KO CD45.2 from spleen

value: KO


title: S2B

description: pre-cDCs DNGR-1 KO CD45.2 from spleen


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #1). Replicate 1

description: Library name: S07_704_1_1


title: S2A

description: pre-cDCs DNGR-1 WT CD45.2 from spleen

source_name: pre-cDCs DNGR-1 WT CD45.1 from spleen

value: pre-cDCs DNGR-1 WT CD45.1 from spleen

value: WT


title: B2D

description: pre-cDCs DNGR-1 KO CD45.2 from bone marrow


title: B1D

source_name: pre-cDCs DNGR-1 KO CD45.2 from bone marrow


title: B3C

description: pre-cDCs DNGR-1 WT CD45.2 from bone marrow

source_name: pre-cDCs DNGR-1 WT CD45.1 from bone marrow


title: B2C

value: pre-cDCs DNGR-1 WT CD45.1 from bone marrow


title: B1C


title: IntestCrypts_2DG_1month_R1_Mouse_2

status: Public on Apr 10 2025

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_2

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: Murine crypts

growth_protocol: All animal experiments in this study were performed in accordance with protocols approved by the Memorial Sloan Kettering Institutional Animal Care and Use Committee (approval number: 11-06-012). The mice were housed with a 12 h light/dark cycle between 8:00 and 20:00 in a temperature-controlled room (22 ± 1°C) with free access to water and food. Both male and female mice were used in equal proportions for all experiments. .

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: For glycolisis inhibition, mice were injected (intraperitoneally) with 2-deoxyglucose once daily with 500 mg/kg dissolved in PBS. For the vehicle control, mice were injected with PBS. Mice were injected 5 times per week, 4 weeks.

tag: mouse strain

value: Murine crypts

value: 500 mg/Kg 2DG


title: IntestCrypts_2DG_1month_R1_Mouse_1

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_1

tag: cell type


title: IntestCrypts_2GD_Control_R1_Mouse_3

description: Library name: IntestCrypts_2GD_Control_R1_Mouse_3

value: PBS


title: IntestCrypts_2GD_Control_R1_Mouse_2

description: Library name: IntestCrypts_2GD_Control_R1_Mouse_2


title: IntestCrypts_2DG_Control_R1_Mouse_1

description: Library name: IntestCrypts_2DG_Control_R1_Mouse_1


title: shOgdh_Mouse_6

status: Public on Apr 02 2025

description: Library name: shOgdh_Mouse_6

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (2.0.6).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

treatment_protocol: Cag-rtTA3 mediating shRenilla and shOgdh expression was activated by feeding mice with a doxycycline hyclate diet (200 mg/kg) at adult stage. After 3 days on Dox, crypts were isolated as described in the materials and method section.

tag: strain

value: Mix

value: TetO. shOgdh; Cag-rtTA

value: doxycycline


title: shOgdh_Mouse_5

description: Library name: shOgdh_Mouse_5


title: shOgdh_Mouse_4

description: Library name: shOgdh_Mouse_4


title: shOgdh_Mouse_3

description: Library name: shOgdh_Mouse_3


title: shOgdh_Mouse_2

description: Library name: shOgdh_Mouse_2


title: shOgdh_Mouse_1

description: Library name: shOgdh_Mouse_1


title: shRen_Mouse_6

description: Library name: shRen_Mouse_6

value: TetO. shRen; Cag-rtTA


title: shRen_Mouse_5

description: Library name: shRen_Mouse_5


title: shRen_Mouse_4

description: Library name: shRen_Mouse_4


title: shRen_Mouse_3

description: Library name: shRen_Mouse_3


title: shRen_Mouse_2

description: Library name: shRen_Mouse_2


title: shRen_Mouse_1

description: Library name: shRen_Mouse_1


title: Organoids_ISC_Ren_3d_3

description: Library name: ISC_Ren_3d_3

source_name: Organoids

treatment_protocol: Crypts were isolated from mice with the described phenotype and cultured in ENR-CV media for six days before adding DM-αKG or doxycycline. Organoids were then maintained under the indicated treatment for three days.

value: Organoids


title: Organoids_ISC_Ren_3d_2

description: Library name: ISC_Ren_3d_2


title: Organoids_ISC_Ren_3d_1

description: Library name: ISC_Ren_3d_1


title: Bulk RNA-seq in A431 control condition (Non-targeting ASO). Replicate 1

description: Library name: S01_Ctrl_1


title: Organoids_ISC_3d_aKG_2

description: Library name: ISC_3d_aKG_2

value: 600 mg/ Kg DM-aKG


title: Organoids_ISC_3d_aKG_3

description: Library name: ISC_3d_aKG_3


title: Organoids_ISC_3d_2081_3

description: Library name: ISC_3d_2081_3


title: Organoids_ISC_3d_2081_2

description: Library name: ISC_3d_2081_2


title: Organoids_ISC_3d_2081_1

description: Library name: ISC_3d_2081_1


title: Organoids_ISC_3d_346_3

description: Library name: ISC_3d_346_3


title: Organoids_ISC_3d_346_2

description: Library name: ISC_3d_346_2


title: IntestCrypts_2DG_1month_R1_Mouse_4

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_4


title: IntestCrypts_aKG_Day10_R1_Mouse_3

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_3

treatment_protocol: DM-aKG supplementation, mice were injected (intraperitoneally) once daily with 600 mg/kg of DM-aKG (349631-5G, Sigma-Aldrich) dissolved in PBS. For the vehicle control, mice were injected with PBS.


title: IntestCrypts_aKG_Day10_R1_Mouse_2

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_2


title: IntestCrypts_aKG_Day10_R1_Mouse_1

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_1


title: IntestCrypts_Control_R1_Mouse_4

description: Library name: IntestCrypts_Control_R1_Mouse_4


title: IntestCrypts_Control_R1_Mouse_3

description: Library name: IntestCrypts_Control_R1_Mouse_3


title: IntestCrypts_Control_R1_Mouse_1

description: Library name: IntestCrypts_Control_R1_Mouse_1


title: T2065-10-02; 47 mg

status: Public on Mar 19 2025

city: Nashville

first: Qi

last: Liu

state: Tennessee

address: 2525 WEST END AVE

institute: Vanderbilt University Medical Center

data_processing:
Quality control and adapter trimming were performed using FastQC.
Reads were aligned to hg38 using STAR
Gene counts were quantified using featureCounts.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing read counts for each sample.

source_name: Thymus

extract_protocol:
Human thymusd was obtained from anonymous patients undergoing corrective cardiac surgery where a portion of the thymus was removed in order to expose the operative field. Portions of thymi were immediately placed in RNALater, incubated at 4C overnight, and stored in liquid nitrogen until processed.
Frozen tissues were homogenized in a Precelly's soft tissue lysing tube and RNA was extracted using Rneasy Kit according to manufacturer's protocol. RNA was cleaned and concentrated using Turbo DNA-free and Rneasy MiniElute.
Libraries were prepared using a KAPA Stranded mRNA-seq kit.

value: Thymus

tag: age (years)

tag: Sex

value: Female


title: T2065-10-04; 34 mg


title: T2064-08-02; 45 mg

value: Male