title: CLLRT_Pool4_GEX+HTO

status: Public on Sep 03 2025

first: Anna

middle: S.

last: Nam

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

description:
Library name: CLLRT_Pool4_GEX+HTO
10x Genomics Gene Expression and Hashing

data_processing:
The pooled gene expression and HTO libraries were processed with Cell Ranger (v7.0.0) using default parameters. RNA reads were aligned to the human genome GRCh38.
Analysis of the genotyping library was carried out with IronThrone-Multi, a modified version of the previously described IronThrone pipeline. Briefly, genotyping amplicon reads were screened for the presence of the LHS sequence (‘primer sequence’) and the expected RHS sequence without the mutation (‘shared sequence’). Next, IronThrone determines whether the wildtype or mutant sequence is at the expected location. This search was done once for the gene sequence and once for the probe barcode. The results were then merged as follows to determine the initial genotype for each cell. Any cell with both gene sequence and probe barcode sequence corresponding to mutant sequences was labelled as mutant. Similarly, any cell with both gene sequence and probe barcode corresponding to wildtype sequences was labelled as wildtype. These initial genotypes were then refined using a machine-learning (ML) framework to enhance accuracy and minimize false positives.  The final genotyping profiles are determined from the adjusted predictions across multiple ML models, based on the best combined performance.
Assembly: GRCh38
Supplementary files format and content: For gene expression, (1) Cellranger outputs are provided: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (2) Cell line or cell type labels are provided in a two-column table : cell barcode, cell line/type.
Supplementary files format and content: Genotyping data is provided as a table with one column for the cell barcode, and one column for their corresponding genotype for each mutation target.

source_name: primary patient sample

extract_protocol:
Cell line Mixing Experiment Extraction Protocol: Cryopreserved MCF-7 and SK-BR-3 cells were rapidly thawed at 37 °C and washed twice with of PBS (without Ca²⁺/Mg²⁺) containing 0.05% BSA. They were then pooled and fixed following the demonstrated protocol CG000478 for fixation of cells & nuclei for Chromium FRP (10x Genomics, Pleasanton, CA). Cells were then hybridized with 10x Genomics gene expression probes (BC001) together with custom genotyping probe pools at 42 °C for 20-24 hours. 2 µL of the genotyping probe pool at 100 µM was added to each hybridization reaction. After hybridization, cells were washed three times to remove unbound probes, counted and then loaded onto Chromium Next GEM Chip Q. Genotyping of Transcriptomes for Multiple Targets and Sample Types (GoT-Multi) was performed by adapting the 10x Genomics Fixed RNA Profiling (FRP) platform.  Primary Cell Mixing Experiment Extraction Protocol: Peripheral blood cells from one IDH2-mutated AML patient and one CALR type I mutated MPN patient were rapidly thawed at 37 °C and separately incubated with hashing antibodies with sample-identifying barcodes using Hashtag Antibodies 1 or 3 (TotalSeq-B, Biolegend) following manufacturer’s instructions. Dead cells were then removed using microbeads (Miltenyi Biotec, #130-090-101) as per manufacturer’s recommendations from each sample. The live cells from the MPN patient were subsequently enriched for CD34+ cells and CD34- CD15+ cells using anti-hCD34 and anti-hCD15 microbeads (Miltenyi Biotec, #130-046-702 and #130-046-601 respectively) following manufacturer’s instructions. Next, live AML cells were pooled with live CD34+ and CD34- CD15+ cells in a 95:5 ratio and then fixed following the demonstrated protocol CG000478 for fixation of cells & nuclei for Chromium FRP (10x Genomics, Pleasanton, CA). Cells were subsequently hybridized with 10x Genomics gene expression probes (BC001) together with custom genotyping probe pools at 42 °C for 20-24 hours. 2 µL of the genotyping probe pool at 100 µM was added to each hybridization reaction. After hybridization, cells were washed three times to remove unbound probes, counted and then loaded onto Chromium Next GEM Chip Q. GoT-Multi was performed by adapting the 10x Genomics FRP platform.  CLL-RT Cryopreserved Cells Extraction Protocol: Single-cell suspensions from cryopreserved Chronic Lymphocytic Leukemia with Richter Transformation (CLL-RT) patient tumors were rapidly thawed at 37 °C and washed in 50 mL of RPMI-1640/20% fetal bovine serum solution. They were then stained with an antibody cocktail composed of KAPPA/LAMBDA-FITC/PE, CD20 PE-Cy7/BUV737, CD38 APC/APC-Fire750, CD45 APC-H7/V500C, CD19 BV421/PE-Cy7, CD5 BV510/BV421, CD3 BUV395 and CD4-APC-A700. Cells were subsequently sorted using a FACSAria-Fusion sorter (75-μm nozzle at 45 psi), collecting Chronic Lymphocytic Leukemia (CLL) cells, large B-cell lymphoma (LBCL) cells and T-cells from each patient tumor. T-cells were isolated based on CD3 expression. CLL cells were distinguished from LBCL cells, either through their distinct phenotyping profile reported at the clinical level or by size. Next, LBCL cells were incubated with one hashing antibody and all other cell populations with another hashing antibody following manufacturer’s instructions, such that they are distinguishable through sample-identifying barcodes (Hashtag Antibodies 1, 2, 3 or 4; TotalSeq-B, Biolegend). Cells from 1-2 samples hashed with up to four distinct hashing antibodies were then pooled together and fixed following the demonstrated protocol CG000478 for fixation of cells & nuclei for Chromium FRP (10x Genomics, Pleasanton, CA). Cells were subsequently hybridized with 10x Genomics gene expression probes (BC001) together with custom genotyping probe pools at 42 °C for 20-24 hours. 2 µL of the genotyping probe pool at 100 µM was added to each hybridization reaction. After hybridization, cells were washed three times to remove unbound probes, counted and then loaded onto Chromium Next GEM Chip Q. GoT-Multi was performed by adapting the 10x Genomics FRP platform. Three of the patient samples (CLL-RT 1-3) were profiled twice to increase the number of cells profiled.  CLL-RT FFPE Extraction Protocol: Three 30 µm thick FFPE tissue sections from one CLL-RT patient were first washed once with 1 mL of Xylene for 10 min at 55 °C and then twice with 1 mL of Xylene for 10 min at room temperature to remove paraffin. Subsequently, they were rehydrated via a sequence of 1 mL ethanol baths, each lasting 1 min: two rounds in 100% ethanol, then in 70%, 50%, and finally 30% ethanol. The sections were next briefly rinsed with 1 mL of RPMI-1640 (Gibco). Then, 100 μL of a digestion mix composed of 1 mg/mL Liberase TH (Roche, #5401135001), 1 mg/mL Collagenase D (Roche, #11088858001), and 1 U/μL of RNAse inhibitor (RiboLock RNAse Inhibitor, Thermo Fisher Scientific, #EO0382) in RPMI-1640 was added to the tissue sections. The tissues were physically disrupted using a pestle and then another 900 μL of digestion mix was added. Digestion was obtained by incubating tissues at 37 °C for 1 hour at 800 rpm. The tissues were next treated with 1x Nuclei Ez lysis buffer (Sigma-Aldrich, #NUC101) that included 2% BSA. Disintegration was further achieved via pipetting using a P1000 pipette. The separated nuclei were filtered through a 70 μm mesh (pluriStrainer Mini 70 μm, pluriSelect, #43-10070-50), rinsed twice with 1x PBS supplemented with 1% BSA, and once with a 0.5x PBS + 0.02% BSA blend. They were then resuspended in this blend and filtered via a 40 μm mesh (pluriStrainer Mini 40 μm, pluriSelect, #43-10040-50). The nuclei were counted using the AO/PI viability kit (Logos, #F23011) and a hemocytometer. Finally, they were loaded onto Chromium Next GEM Chip Q. GoT-Multi was performed by adapting the 10x Genomics FRP platform.
GoT-Multi Library Construction Protocol: GEM incubation and recovery were performed as per manufacturer’s instructions for 10x Genomics FRP. For the cell mixing experiments (cell lines and primary cells), the pre-amplification step and library construction steps were also performed as per manufacturer’s instructions. The transcriptomic profile was obtained from the gene expression library whereas the cell surface protein library contained both the HTO libraries and the genotyping libraries. For all other experiments, the pre-amplification step and library construction steps were first performed as per manufacturer’s instructions, to generate the gene expression and hashing (HTO) libraries. To amplify the ligated genotyping probes, 20 µL of the cleaned pre-amplified product was then re-amplified with the same protocol as the pre-amplification step but with two modifications: (1) 2 µL of an additive primer (Read2N primer, 10 µM) was added to the reaction, and (2) the PCR was run as follows: 98 °C 3 min; 8 cycles of 98 °C 15 sec, 64 °C 20 sec, 72 °C 1 min; 72 °C 1 min; 4 °C hold. The re-amplified product was then cleaned as for the pre-amplified product using SPRI beads (Beckman Coulter). The genotyping libraries were constructed with the same protocol as the HTO library but using the Dual Index Kit TN Set A plate (#1000250) instead. The genotyping and HTO libraries were spiked into the gene expression libraries to be sequenced together on a NovaSeq 6000 (Illumina, San Diego, CA). The cycle settings were as follows: 28 cycles for Read 1, 90 cycles for Read 2, 10 cycles for i7 sample index and 10 cycles for i5 sample index.

value: primary patient sample

tag: disease type

value: Chronic Lymphocytic Leukemia with Richter's Transformation (CLL-RT)

tag: probe set

value: WTandMUTprobes


title: CLLRT_Pool3_GEX+HTO

type: SRA

city: New York

state: New York

country: USA

description:
Library name: CLLRT_Pool3_GEX+HTO
10x Genomics Gene Expression and Hashing

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: MCF10A, UT

status: Public on Oct 30 2025

city: Boulder

first: Brianna

last: Fernandez

state: CO

address: 3415 Colorado Avenue

department: Biochemistry

institute: University of Colorado Boulder

description:
Library name: Sample 1
10x Genomics

data_processing:
scRNA-seq data were processed and analyzed using the Seurat (v5.1.0) package in R (v4.4.1). Raw sequencing reads were pre-processed using CellRanger (v7.1.0) and aligned to the Human (GRCh38) 2020-A reference genome. Gene-cell count matrices were generated, and low-quality cells were filtered out based on the number of detected genes, unique molecular identifiers (UMIs), and mitochondrial gene percentage. Cells with fewer than 3,500 genes were excluded to remove low-quality cells. Cells with greater than 15% mitochondrial gene expression were also removed. Data were log-normalized using Seurat’s NormalizeData() function with a scale factor of 10,000.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: matrix files for counts, features, and barcodes.
Supplementary files format and content: merged_filtered_etop.h5ad: This file contains a .h5ad format file of the merged and filtered seurat object with all treatments combined and metadata annotated (i.e., sample, dose, cluster ID, UMAP dimensions, etc.)
Supplementary files format and content: merged_filtered_etop.rds: This file contains a .rds format file of the merged and filtered seurat object with all treatments combined and metadata annotated (i.e., sample, dose, cluster ID, UMAP dimensions, etc.)

molecule: polyA RNA

extract_protocol:
Single-cell suspensions were prepared following the 10x Genomics “Cell Preparation for Single Cell Protocols” guide with a viability of >95%. Single-cell encapsulation, barcoding, cDNA amplification, library preparation, and sequencing were performed by the University of Colorado Anschutz Genomics Shared Resource facility. Cells were encapsulated into droplets using the Chromium Controller, where reverse transcription occurred within individual gel beads-in-emulsion (GEMs).
Single-cell RNA sequencing (scRNA-seq) libraries were generated using the 10x Genomics Chromium platform with the 3' mRNA capture kit. Single-cell suspensions were prepared following the 10x Genomics “Cell Preparation for Single Cell Protocols” guide with a viability of >95%. Single-cell encapsulation, barcoding, cDNA amplification, library preparation, and sequencing were performed by the University of Colorado Anschutz Genomics Shared Resource facility. Cells were encapsulated into droplets using the Chromium Controller, where reverse transcription occurred within individual gel beads-in-emulsion (GEMs). Following barcoding and cDNA amplification, sequencing libraries were constructed according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeqX to a depth of 81,810 reads per cell for untreated, 74,214 reads per cell for 2.5µM, 81,254 reads per cell for 10µM, and 76,973 reads per cell for 25µM.

treatment_protocol: MCF10A cells were split 1:10 (from a confluent plate) into a plastic 10cm culture plate before being treated with 2.5, 10, or 25μM etoposide the following day for 24 h. Cells were then washed twice with PBS before being returned to full-growth media. Full-growth media was refreshed every 3d during the drug recovery period.

tag: cell line

tag: cell type

value: normal human breast epithelial cell

tag: treatment

value: Untreated


title: FM79 Cells, siScr 72h, Trametinib 5nM 48h, biol rep 3

status: Public on Sep 01 2025

city: Wuerzburg

first: Rupesh

last: Paudel

state: Bavaria

address: Josef-Schneider Straße 2

department: Department of Dermatology, Venerology und Allergology

country: Germany

institute: University Hospital Wuerzburg

description: Library name: Sample 6

library_source: transcriptomic

data_processing:
quality/adapter trimming of FASTQ files with Cutadapt
Reads alignment to Human reference genome (GCF_000001405.39_GRCh38.p13) primary assembly and mitochondrion, read quantification on gene level based on annotated exons via featureCounts using both, uniquely and multimapping reads.
Differentially expressed genes between different groups were compared in two arms: siScr vs Tram/SiScr =(Tram-regulated genes) or Tram/siScr vs Tram/siMEK5 (=siMEK5-regulated genes) using DeSeq2 (Bioconductor)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab delimited CSV file includes original and normalized FPKM values

growth_protocol: Cells were grown at 37°C with 5% CO2 in RPMI1640 GlutaMAX medium (ThermoFisher Scientific), supplemented with 10% fetal calf serum (Capricorn) and 30 µg/ml Gentamycin (Sigma Aldrich)

extract_protocol:
Toral RNA was extracted using RNAeasy Kit (Qiagen).
cDNA library preparation was done using TruSeq Kit, (Illumina) according to manufacturers protocol.

treatment_protocol: Day 0 : Cells seeded, Day 1:  cells were either transfected with siScr or siMEK5 Day 2:  Cells were either treated with vehicle or Trametinib 5nM Day 4: Cells were lysed

value: melanoma cell lines

tag: genotype

value: WT

value: Trametinib 5nM 48h


title: RNA seq - lane A

status: Public on Oct 06 2025

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

description: GEX-A

data_processing:
Single cell reads for RNA and CITE-seq antibodies are mapped to the human transcriptome and counted using cellranger (version 6.1.2)
TCR-seq reads are mapped and assembled using cellranger
Assembly: hg38
Supplementary files format and content: h5 files forGEX/CITE assays
Supplementary files format and content: csv of mapped and assembled VDJ reads for TCR assay
Supplementary files format and content: csv formatted metadata for filtered and annotated single cells

source_name: breast/blood

growth_protocol: ex vivo

extract_protocol:
CD3 positive cells were sorted from fresh breast tissue sections
Sample preparation followed by 10x Genomics scRNA-seq v3 chemistry protocol. Samples were processed as described on the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).

value: breast/blood

value: CD3 pos cells


title: FM79 Cells, siScr 72h, Trametinib 5nM 48h, biol rep 2

description: Library name: Sample 5


title: IA1037

status: Public on Aug 20 2025

city: Chicago

first: Issam

middle: A

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

institute: University of Chicago

description:
Library name: IA1037
miRNA_raw_count.csv

library_source: other

data_processing:
Adaptor trimming performed with sRNAbench from SRNAtoolbox version 0.0.4, with adapter minimum length of 10, adapter sequence "TGGAATTCTCGGGTGCCAAGG", no recursive trimming, and 1 allowed mismatch in the adapter.
Read Mapping to known libraries of mouse miRNA was performed  using sRNAbench from SRNAtoolbox version 0.0.4. Wth mmu library as reference, species set for GRCm39, minimum read count of 2, number of mitmatches set to 1, seed = 19, hierarchical alignment type, isoMIR set to false.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include matrix with reads  mapped to mature miRNA from sense strand summarized by sRNAbench.

molecule: other

organism: Mus musculus

source_name: Blood plasma

extract_protocol:
RNAs was extracted using an RNA isolation kit (miRNeasy Serum/Plasma Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared for sequencing using commercially available Illumina small RNA-Seq kits (San Diego, California, USA),

value: Blood plasma

tag: Sex

value: Female

tag: phenotype


title: IA1033

description:
Library name: IA1033
miRNA_raw_count.csv

value: Male


title: IA1035

description:
Library name: IA1035
miRNA_raw_count.csv


title: IA1031

description:
Library name: IA1031
miRNA_raw_count.csv

value: E4FAD (5xFAD+/-; human APOE4+/+, C57BL/6 background)

value: CMB


title: IA1030

description:
Library name: IA1030
miRNA_raw_count.csv


title: CLLRT_Pool2_GEX+HTO

description:
Library name: CLLRT_Pool2_GEX+HTO
10x Genomics Gene Expression and Hashing


title: CLLRT_Pool1_GEX+HTO

description:
Library name: CLLRT_Pool1_GEX+HTO
10x Genomics Gene Expression and Hashing


title: IA1032

description:
Library name: IA1032
miRNA_raw_count.csv


title: FM79 Cells, siScr 72h, Trametinib 5nM 48h, biol rep 1

description: Library name: Sample 4


title: IA1036

description:
Library name: IA1036
miRNA_raw_count.csv


title: IA1034

description:
Library name: IA1034
miRNA_raw_count.csv


title: hma437

description: Library name: IA1113

data_processing:
Adaptor trimming performed with sRNAbench from SRNAtoolbox version 0.0.4, with adapter minimum length of 10, adapter sequence "TGGAATTCTCGGGTGCCAAGG", no recursive trimming, and 1 allowed mismatch in the adapter.
Read Mapping to known libraries of Human miRNA was performed  using sRNAbench from SRNAtoolbox version 0.0.4. Wth hsa library as reference, species set for GRCh38_p13_mp, minimum read count of 2, number of mitmatches set to 1, seed = 19, hierarchical alignment type, isoMIR set to false.
Assembly: GRCh38_p13
Supplementary files format and content: tab-delimited text file include matrix with reads  mapped to mature miRNA from sense strand summarized by sRNAbench.

tag: disease state

value: Healthy Old


title: IA1029

description:
Library name: IA1029
miRNA_raw_count.csv


title: IA1028

description:
Library name: IA1028
miRNA_raw_count.csv


title: aim3-16

description: Library name: IA1112


title: aim3-50

description: Library name: IA1119


title: IA1027

description:
Library name: IA1027
miRNA_raw_count.csv


title: aim3-2

description: Library name: IA1108

value: HMA


title: aim3-29

description: Library name: IA1107


title: hma435

description: Library name: IA1118


title: hma442

description: Library name: IA1117


title: aim3-15

description: Library name: IA1111


title: aim3-14

description: Library name: IA1115


title: hma445

description: Library name: IA1116


title: Aim3-27

description: Library name: IA1102


title: mb429

description: Library name: IA1114


title: aim3-31

description: Library name: IA1110


title: aim3-13

description: Library name: IA1100


title: SK7334

description: Library name: IA1101


title: Y-83K-7d-Virus

status: Public on Jul 18 2025

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

description: Library name: Y-83K-7d-Virus

data_processing:
Illumina bcl2fastq v2.19 used for basecalling.
Sequence reads in FASTQ files were mapped to GRCh38 reference genome appended with SARS-CoV-2 RefSeq genome (NC045512) with GENCODE 37 gene annotation and SARS-CoV-2 gene annotation from ENSEMBL COVID-19 by STAR, and gene expression estimates were derived from StringTie using default parameters.
Viral TPM values were estimated with StringTie with combined human and viral gene annotations
Human gene expression (hG) estimates were extracted with StringTie using GENCODE 37 gene annotation only, which exclude viral specific transcripts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include estimated count values as integers for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Primary bronchial airway epithelial cells

growth_protocol: Human bronchial epithelial (HBE) cells were obtained from freshly isolated large airway epithelium of non-smoker lung transplant donors with lungs unsuitable for transplant. Isolated HBE cells were expanded using a modified conditional reprogramming cell culture. The cells were seeded onto 12mm Transwell inserts at 0.25 millon cells per insert.The cells were cultured under submerged condition until confluence. Then they were cultured under air-liquid interface (ALI) culture until full-differention confirmed by ciliation under light microscopic examination.

extract_protocol:
Cell culture membranes were kept in TRI Reagent and the RNA extracted according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop-8000 spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The HBE cells were inoculated with SARS-CoV-2 (D614G strain) at MOI=0.5 for two hours. The cells were maintained under ALI culture until 1-, 3- 7- and 14-day post inoculation.RNAs were extracted from the cell lysates.

value: Primary cells

value: Epithelial cells

tag: donor code

tag: age group

value: Y

value: M

value: Virus

tag: time

tag: titer

tag: titer duplicate

tag: batch


title: Y-83K-3d-Virus

description: Library name: Y-83K-3d-Virus

value: Primary bronchial airway epithelial cells


title: Y-83K-3d-Mock

description: Library name: Y-83K-3d-Mock

value: Mock


title: Y-46M-7d-Virus

description: Library name: Y-46M-7d-Virus

value: F


title: aim3-45

description: Library name: IA1106


title: Y-46M-1d-Virus

description: Library name: Y-46M-1d-Virus


title: Y-46M-7d-Mock

description: Library name: Y-46M-7d-Mock


title: Y-46M-14d-Virus

description: Library name: Y-46M-14d-Virus


title: aim3-1

description: Library name: IA1105


title: Y-18I-3d-Virus

description: Library name: Y-18I-3d-Virus


title: aim3-21

description: Library name: IA1103


title: Y-46M-14d-Mock

description: Library name: Y-46M-14d-Mock


title: aim3-44

description: Library name: IA1109


title: Y-18I-14d-Mock

description: Library name: Y-18I-14d-Mock


title: Y-18I-14d-Virus

description: Library name: Y-18I-14d-Virus


title: Y-83K-7d-Mock

description: Library name: Y-83K-7d-Mock


title: IA1026

description:
Library name: IA1026
miRNA_raw_count.csv


title: Y-83K-1d-Virus

description: Library name: Y-83K-1d-Virus


title: Y-83K-1d-Mock

description: Library name: Y-83K-1d-Mock


title: Y-83K-14d-Virus

description: Library name: Y-83K-14d-Virus


title: Y-46M-3d-Virus

description: Library name: Y-46M-3d-Virus


title: M-51K-3d-Mock

description: Library name: M-51K-3d-Mock


title: M-51K-1d-Virus

description: Library name: M-51K-1d-Virus


title: Y-46M-3d-Mock

description: Library name: Y-46M-3d-Mock


title: Y-46M-1d-Mock

description: Library name: Y-46M-1d-Mock


title: M-35P-7d-Virus

description: Library name: M-35P-7d-Virus


title: Y-18I-7d-Virus

description: Library name: Y-18I-7d-Virus


title: Y-83K-14d-Mock

description: Library name: Y-83K-14d-Mock


title: M-51K-14d-Virus

description: Library name: M-51K-14d-Virus


title: Y-18I-1d-Virus

description: Library name: Y-18I-1d-Virus


title: M-35P-3d-Virus

description: Library name: M-35P-3d-Virus


title: Y-18I-7d-Mock

description: Library name: Y-18I-7d-Mock


title: Y-18I-1d-Mock

description: Library name: Y-18I-1d-Mock


title: M-35P-3d-Mock

description: Library name: M-35P-3d-Mock


title: Y-18I-3d-Mock

description: Library name: Y-18I-3d-Mock


title: M-51K-7d-Virus

description: Library name: M-51K-7d-Virus


title: M-51K-7d-Mock

description: Library name: M-51K-7d-Mock


title: M-35P-14d-Mock

description: Library name: M-35P-14d-Mock


title: M-51K-3d-Virus

description: Library name: M-51K-3d-Virus


title: M-51K-1d-Mock

description: Library name: M-51K-1d-Mock


title: M-51K-14d-Mock

description: Library name: M-51K-14d-Mock


title: M-21M-3d-Virus

description: Library name: M-21M-3d-Virus


title: M-21M-7d-Virus

description: Library name: M-21M-7d-Virus


title: M-21M-3d-Mock

description: Library name: M-21M-3d-Mock


title: E-41T-1d-Virus

description: Library name: E-41T-1d-Virus

value: E


title: E-41T-1d-Mock

description: Library name: E-41T-1d-Mock


title: M-35P-7d-Mock

description: Library name: M-35P-7d-Mock


title: M-35P-1d-Virus

description: Library name: M-35P-1d-Virus


title: E-41T-14d-Virus

description: Library name: E-41T-14d-Virus


title: E-30T-1d-Virus

description: Library name: E-30T-1d-Virus


title: M-35P-1d-Mock

description: Library name: M-35P-1d-Mock


title: E-30T-3d-Virus

description: Library name: E-30T-3d-Virus


title: M-35P-14d-Virus

description: Library name: M-35P-14d-Virus


title: E-11G-3d-Mock

description: Library name: E-11G-3d-Mock


title: E-11G-1d-Mock

description: Library name: E-11G-1d-Mock


title: E-11G-14d-Mock

description: Library name: E-11G-14d-Mock


title: M-21M-1d-Virus

description: Library name: M-21M-1d-Virus


title: M-21M-1d-Mock

description: Library name: M-21M-1d-Mock


title: M-21M-7d-Mock

description: Library name: M-21M-7d-Mock


title: M-21M-14d-Virus

description: Library name: M-21M-14d-Virus


title: CowO8

status: Public on Jun 20 2025

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

description: Bulk RNA-seq

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Rat reference was used for gene annotation and counting (mRatBN7.2). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: mRatBN7.2
Supplementary files format and content: Input tables are included as tab separated files.

organism: Rattus norvegicus

source_name: Sprague Dawley

extract_protocol:
Tissue was processed for RNA extraction using a modified manufacturer’s procedure (miRNA Easy Kit, Qiagen)
Tissue was processed for RNA extraction using a modified manufacturer’s procedure (miRNA Easy Kit, Qiagen). Frozen samples were sent to BGI Americas Cooperation (Cambridge, MA) and sequencing was performed using polyA mRNA directional RNA-seq library preparation using a DNBSEQTM platform.

tag: strain

value: Sprague Dawley

value: Cocaine

value: eGFP

value: 13-15 weeks


title: M-21M-14d-Mock

description: Library name: M-21M-14d-Mock


title: CowO6

description: Bulk RNA-seq


title: E-41T-7d-Mock

description: Library name: E-41T-7d-Mock


title: CowO21

description: Bulk RNA-seq


title: E-41T-3d-Virus

description: Library name: E-41T-3d-Virus


title: E-41T-7d-Virus

description: Library name: E-41T-7d-Virus


title: CowO14

description: Bulk RNA-seq

value: Saline


title: CowO13

description: Bulk RNA-seq


title: E-41T-3d-Mock

description: Library name: E-41T-3d-Mock


title: E-30T-7d-Virus

description: Library name: E-30T-7d-Virus


title: E-30T-7d-Mock

description: Library name: E-30T-7d-Mock


title: E-41T-14d-Mock

description: Library name: E-41T-14d-Mock


title: E-30T-3d-Mock

description: Library name: E-30T-3d-Mock


title: E-30T-1d-Mock

description: Library name: E-30T-1d-Mock


title: CowO11

description: Bulk RNA-seq


title: E-30T-14d-Virus

description: Library name: E-30T-14d-Virus


title: CowO10

description: Bulk RNA-seq


title: E-30T-14d-Mock

description: Library name: E-30T-14d-Mock


title: Ferret 9028 Bleomycin Replicate 2

status: Public on Jun 16 2025

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

data_processing:
Illuina BCL files where proccessed to fastq format using bcl2fastq v2.2.0.
To generate a count matrix, the sequenced files from each independent sample were processed through 10X Genomics Cell Ranger software v7.1.0, using defualt include intron mode.
Assembly: Mustela putorius furo (domestic ferret) reference built from NCBI genome ASM1176430v1.1
Supplementary files format and content: Tab separated value files and matrix files containing raw UMI counts for all genes and all barcodes above Cellranger automated cutoff
Supplementary files format and content: h5ad files

molecule: nuclear RNA

organism: Mustela putorius furo

source_name: lung

extract_protocol:
Lung nuclei from saline and bleomycin injured ferrets were isolated using a CST buffer as described previously. Snap frozen lung tissues (50 mg) were immediately placed into a nuclei isolation using CST buffer (20 mM Tris-HCl pH 7.5, 292 mM NaCl, 2 mM CaCl2, 42 mM MgCl2, 1% CHAPS, and 2% BSA) and homogenized using a dounce homogenizer to mechanically dissociate nuclei from cells. The resulting homogenate was filtered through a 40 µm strainer, and nuclei were pelleted by centrifugation at 300 × g for 2 minutes at 4°C. Nuclei were resuspended in 0.04% BSA buffer to a final concentration of 1,000 nuclei/µl.
Single-nuclei RNA sequencing (snRNA-seq) libraries were prepared using the 10x Genomics 5' Kit v2, following the manufacturer's protocol (10X Genomics). Libraries were sequenced on an Illumina Nextseq 550 platform using 75-cycle paired-end sequencing, using 8bp for index read 28bp for R1 and 56bp for R2.

treatment_protocol: Ferrets were injured with 3 doses of bleomycin or saline control at 1 week interval, the lung tissues were harvested at 6-8 weeks post the injury. The collectedlLung tissues were immediately snap frozen and grounded in liquid nitrogen prior to being  placed into a nuclei isolation using CST buffer for nuclei isolation.

value: Bleomycin

value: lung


title: E-11G-7d-Virus

description: Library name: E-11G-7d-Virus


title: E-11G-7d-Mock

description: Library name: E-11G-7d-Mock


title: Ferret 6872 Bleomycin Replicate 1


title: Ferret 6294 Bleomycin Replicate 2


title: E-11G-3d-Virus

description: Library name: E-11G-3d-Virus


title: E-11G-1d-Virus

description: Library name: E-11G-1d-Virus


title: E-11G-14d-Virus

description: Library name: E-11G-14d-Virus


title: Ferret 4665 Bleomycin Replicate 2


title: Ferret 6872 Bleomycin Replicate 2


title: Ferret 9078 Saline Replicate 1


title: Ferret 0869 Bleomycin Replicate 1


title: Ferret 8849 Saline Replicate 2


title: CowO7

description: Bulk RNA-seq


title: CowO2

description: Bulk RNA-seq


title: Ferret 4626 Saline Replicate 2


title: Ferret 4626 Saline Replicate 1


title: CowO15

description: Bulk RNA-seq


title: CowO3

description: Bulk RNA-seq


title: MCF10CA1a, Bio Rep 2, Library 2

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

description: Micro-C library

library_source: genomic

data_processing:
Reads are aligned to the human genome with bwa mem
Pairtools is used to parse, sort, and remove duplicates
Pairtools and samtools are used to generate .pairs and .bam files
Samtools is used to sort and index the .bam files
Juicer_tools pre is used to generate a .hic file
Assembly: hg38 (NCBI GRCh38, iGenomes)
Supplementary files format and content: .hic files for individual samples
Supplementary files format and content: *.hic: Micro-C matrix files produced by Juicer tools. Includes contact frequencies at 2.5Mb, 1Mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, 5kb, and 1kb resolutions, and SCALE, VC, VC_SQRT, KR, and NONE normalizations.
Supplementary files format and content: *CALDER-sub-compartments.bed: BED-formatted file of subcompartments at 10kb resolution, generated by CALDER
Supplementary files format and content: *10kb-IS_100kb.bed: BED-formatted file of insulation scores at 10kb resolution, generated by FAN-C based on a sliding window size of 100kb
Supplementary files format and content: *10kb-ISboundaries.bed: BED-formatted file of insulation score boundaries at 10kb resolution, generated by FAN-C based on a sliding window size of 100kb
Supplementary files format and content: *loopCalled.bedpe: BEDPE-formatted file of chromatin loop calls at 5kb and 10kb resolutions, generated by SIP
Library strategy: Micro-C

molecule: genomic DNA

growth_protocol: Cells were grown in DMEM/F12 supplemented with 1.05 mM CaCl2, 5% horse serum, and 10mM HEPES. Media for MCF10A and MCF10AT1 cells was additionally supplemented with 10 ug/ml insulin, 20ng/ml EGF, 0.5 ug/ml hydrocortisone, and 0.1 ug/ml cholera enterotoxin. Cells were grown to ~70% confluence in 15cm plates.

extract_protocol:
Cells were trypsinized and counted. 5M cells at a time were pelleted down and resuspended in PBS. Aliquots of 1M cells were generated, spun down, supernatant was removed, and the 1M cell pellets were flash frozen in liquid nitrogen and sent to Cantata Bio for extraction and library prep.
The Micro-C library was prepared using the Dovetail® Micro-C Kit according to the manufacturer’s protocol. Briefly, the chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde in the nucleus. The cross-linked chromatin was then digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed with SDS to extract the chromatin fragments and the chromatin fragments were bound to Chromatin Capture Beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends. After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified then converted into a sequencing library using Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification.

value: epithelial (metastatic)


title: CowO12

description: Bulk RNA-seq


title: Ferret 9028 Bleomycin Replicate 1


title: MCF10AT1, Bio Rep 1, Library 3

description: Micro-C library

value: epithelial (pre-malignant)


title: Ferret 4665 Bleomycin Replicate 1


title: MCF10A, Bio Rep 2, Library 4

description: Micro-C library

value: epithelial (normal-like)


title: MCF10A, Bio Rep 2, Library 3

description: Micro-C library


title: MCF10A, Bio Rep 2, Library 2

description: Micro-C library


title: Ferret 8849 Saline Replicate 1


title: Ferret 9078 Saline Replicate 2


title: MCF10CA1a, Bio Rep 2, Library 3

description: Micro-C library


title: Ferret 0359 Saline Replicate 2


title: MCF10A, Bio Rep 1, Library 3

description: Micro-C library

data_processing:
Reads are aligned to the human genome with bwa mem
Pairtools is used to parse, sort, and remove duplicates
Pairtools and samtools are used to generate .pairs and .bam files
Samtools is used to sort and index the .bam files
Juicer_tools pre is used to generate a .hic file
Assembly: hg38 (NCBI GRCh38, iGenomes)
Supplementary files format and content: .hic files
Supplementary files format and content: .hic files for individual samples
Supplementary files format and content: *.hic: Micro-C matrix files produced by Juicer tools. Includes contact frequencies at 2.5Mb, 1Mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, 5kb, and 1kb resolutions, and SCALE, VC, VC_SQRT, KR, and NONE normalizations.
Supplementary files format and content: *CALDER-sub-compartments.bed: BED-formatted file of subcompartments at 10kb resolution, generated by CALDER
Supplementary files format and content: *10kb-IS_100kb.bed: BED-formatted file of insulation scores at 10kb resolution, generated by FAN-C based on a sliding window size of 100kb
Supplementary files format and content: *10kb-ISboundaries.bed: BED-formatted file of insulation score boundaries at 10kb resolution, generated by FAN-C based on a sliding window size of 100kb
Supplementary files format and content: *loopCalled.bedpe: BEDPE-formatted file of chromatin loop calls at 5kb and 10kb resolutions, generated by SIP
Library strategy: Micro-C


title: Ferret 0359 Saline Replicate 1


title: MCF10CA1a, Bio Rep 2, Library 4

description: Micro-C library


title: MCF10CA1a, Bio Rep 2, Library 1

description: Micro-C library


title: scRNAseq CCl4, liver cells

status: Public on May 30 2025

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: out_CCl4
10X Genomics (cDNA)

data_processing:
scRNAseq fastq files were processed via CellRanger 4.0.0 and mapped to mm10 genome.
Assembly: mm10
Supplementary files format and content: .h5 filtered feature matrix

source_name: Liver

growth_protocol: Starting at 8 weeks of age, C57B6 mice were administered 1 mL/g body weight carbon tetrachloride (CCl4) or olive oil  twice weekly  for 6 weeks to induce fibrosis before sacrifice.

extract_protocol:
Mice non-parenchymal cells were isolated using previously published protocols. Primary mice hepatocytes were isolated using a modification of the two-step collagenase perfusion method. Cell viability was >95% as measured by Trypan Blue staining.
For scRNAseq:Samples were then prepared as outlined by the 10x Genomics Single Cell 3v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Following counting, the appropriate volume for each sample was calculated for a target capture of 12000 cells. Samples were loaded onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen): cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles.

value: Liver

value: Mixed liver single cell suspension


title: Ferret 0869 Bleomycin Replicate 2


title: MCF10CA1a, Bio Rep 1, Library 4

description: Micro-C library


title: MCF10CA1a, Bio Rep 1, Library 3

description: Micro-C library


title: MCF10CA1a, Bio Rep 1, Library 2

description: Micro-C library


title: wt_NI_4

status: Public on May 29 2025

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

data_processing:
fastp v0.23.4, STAR v2.7.0, RSEM v1.3.3
Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 (qualified_quality_phred=20, nqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30)
passing filter reads were mapped to the genome reference (Danio rerio GRCz11v110, Ensembl v110 ) using STAR v2.7.10 with standard parameters, except for the sjdbOverhang option set on read length
Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix applying a dedicated RSEM command (rsem-generate-data-matrix).
Assembly: Danio rerio GRCz11v110, Ensembl v110
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

organism: Danio rerio

source_name: skeletal muscle

growth_protocol: Wild-type (wt) fish AB (Oregon) and ankrd1abns502 (mut) were maintained under standard conditions, in circulating water system, under 14 h light/10 h dark cycle and at 28.5 ◦C.

extract_protocol:
Skeletal muscle tissue dissected out from the region around the injury and complementary region of non-injured wt and ankrd1a-/- fish was homogenized in TRIzol Reagen (Invitorgen, Thermo Fisher Scientific, USA) and total RNA was extracted using RNA Clean and concentrator kit (ZYMO Research, USA), according to the manufacturer instructions. Total RNA was eluted in 25 µl of RNase-free water and its quantity and purity were measured promptly after isolation, using BioSpec-nano (Shimadzu, Japan) and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM (Thermo Scientific Fisher, USA).
cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina, California, USA)

treatment_protocol: Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail, in line with the anal opening. Immediately, after the injury, fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle, just behind the anal opening and containing the injury area anterior and posterior to the needle lesion, was dissected by a razor blade and used for RNA isolation.

value: skeletal muscle

value: wt

value: non-injured


title: wt_NI_2


title: wt_NI_1


title: MCF10CA1a, Bio Rep 1, Library 1

description: Micro-C library


title: MCF10AT1, Bio Rep 2, Library 4

description: Micro-C library


title: MCF10AT1, Bio Rep 2, Library 3

description: Micro-C library


title: PBMC, vitamin D bolus, day 1, Individual 45

status: Public on May 22 2025

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description:
After 1 day of vitamin D bolus intake
d1_Ind45

data_processing:
Trimming of files using Trimmomatic v0.39
Read alignment using STAR v2.7.10b using default parameters
Quantification using FastQC v0.12.1 and featureCounts v2.0.3 using default parameters for reverse strand
Filtering for protein coding genes and read counts normalization via EdgeR v4.0.14 (TMM-normalized CPM)
Assembly: GRCh38.p14, Aligned to Ensembl annotation version 112, final annotation (via Biomart) to Ensembl version 112.38
Supplementary files format and content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)

source_name: PBMC

growth_protocol: no in vitro culture

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: Before and after intake of 1000 IU/kg of vitamin D3

tag: individual

value: Individual 45

value: Healthy Individuals

value: PBMC

value: 80000 IU vitamin D3

value: day 1


title: MCF10AT1, Bio Rep 2, Library 2

description: Micro-C library


title: PBMC, vitamin D bolus, day 1, Individual 44

description:
After 1 day of vitamin D bolus intake
d1_Ind44

value: Individual 44


title: MCF10AT1, Bio Rep 2, Library 1

description: Micro-C library


title: PBMC, vitamin D bolus, day 1, Individual 43

description:
After 1 day of vitamin D bolus intake
d1_Ind43

value: Individual 43


title: MCF10AT1, Bio Rep 1, Library 4

description: Micro-C library


title: Ferret 6294 Bleomycin Replicate 1

value: Bleomycin


title: PBMC, vitamin D bolus, day 1, Individual 38

description:
After 1 day of vitamin D bolus intake
d1_Ind38

value: Individual 38


title: MCF10AT1, Bio Rep 1, Library 1

description: Micro-C library


title: PBMC, vitamin D bolus, day 1, Individual 42

description:
After 1 day of vitamin D bolus intake
d1_Ind42

value: Individual 42


title: PBMC, vitamin D bolus, day 1, Individual 35

description:
After 1 day of vitamin D bolus intake
d1_Ind35

value: Individual 35


title: MCF10AT1, Bio Rep 1, Library 2

description: Micro-C library

value: epithelial (pre-malignant)


title: PBMC, vitamin D bolus, day 1, Individual 32

description:
After 1 day of vitamin D bolus intake
d1_Ind32

value: Individual 32


title: MCF10A, Bio Rep 2, Library 1

description: Micro-C library

value: epithelial (normal-like)


title: MCF10A, Bio Rep 1, Library 4

description: Micro-C library


title: PBMC, vitamin D bolus, day 1, Individual 28

description:
After 1 day of vitamin D bolus intake
d1_Ind28

value: Individual 28


title: MCF10A, Bio Rep 1, Library 2

description: Micro-C library


title: PBMC, vitamin D bolus, day 1, Individual 24

description:
After 1 day of vitamin D bolus intake
d1_Ind24

value: Individual 24


title: PBMC, vitamin D bolus, day 1, Individual 34

description:
After 1 day of vitamin D bolus intake
d1_Ind34

value: Individual 34


title: PBMC, vitamin D bolus, day 1, Individual 27

description:
After 1 day of vitamin D bolus intake
d1_Ind27

value: Individual 27


title: scRNAseq Healthy, liver cells

description:
Library name: out_Healthy
10X Genomics (cDNA)

value: Liver

value: Control

value: Mixed liver single cell suspension


title: MCF10A, Bio Rep 1, Library 1

description: Micro-C library


title: PBMC, vitamin D bolus, day 1, Individual 19

description:
After 1 day of vitamin D bolus intake
d1_Ind19

value: Individual 19

value: Healthy Individuals

value: PBMC

value: 80000 IU vitamin D3

value: day 1


title: PBMC, vitamin D bolus, day 1, Individual 23

description:
After 1 day of vitamin D bolus intake
d1_Ind23

value: Individual 23


title: wt_NI_3

value: skeletal muscle

value: wt

value: non-injured


title: PBMC, vitamin D bolus, day 1, Individual 17

description:
After 1 day of vitamin D bolus intake
d1_Ind17

value: Individual 17


title: PBMC, vitamin D bolus, day 1, Individual 13

description:
After 1 day of vitamin D bolus intake
d1_Ind13

value: Individual 13


title: PBMC, vitamin D bolus, day 1, Individual 09

description:
After 1 day of vitamin D bolus intake
d1_Ind09

value: Individual 09


title: PBMC, vitamin D bolus, day 1, Individual 41

description:
After 1 day of vitamin D bolus intake
d1_Ind41

value: Individual 41


title: PBMC, vitamin D bolus, day 1, Individual 08

description:
After 1 day of vitamin D bolus intake
d1_Ind08

value: Individual 08


title: PBMC, vitamin D bolus, day 1, Individual 37

description:
After 1 day of vitamin D bolus intake
d1_Ind37

value: Individual 37


title: PBMC, vitamin D bolus, day 1, Individual 12

description:
After 1 day of vitamin D bolus intake
d1_Ind12

value: Individual 12


title: PBMC, vitamin D bolus, day 1, Individual 39

description:
After 1 day of vitamin D bolus intake
d1_Ind39

value: Individual 39


title: PBMC, vitamin D bolus, day 1, Individual 03

description:
After 1 day of vitamin D bolus intake
d1_Ind03

value: Individual 03


title: PBMC, vitamin D bolus, day 1, Individual 36

description:
After 1 day of vitamin D bolus intake
d1_Ind36

value: Individual 36

value: Healthy Individuals


title: PBMC, vitamin D bolus, day 1, Individual 40

description:
After 1 day of vitamin D bolus intake
d1_Ind40

value: Individual 40

value: PBMC

value: 80000 IU vitamin D3


title: PBMC, vitamin D bolus, day 1, Individual 31

description:
After 1 day of vitamin D bolus intake
d1_Ind31

value: Individual 31

value: day 1


title: PBMC, vitamin D bolus, day 1, Individual 26

description:
After 1 day of vitamin D bolus intake
d1_Ind26

value: Individual 26


title: PBMC, vitamin D bolus, day 1, Individual 01

description:
After 1 day of vitamin D bolus intake
d1_Ind01

value: Individual 01


title: PBMC, vitamin D bolus, day 1, Individual 25

description:
After 1 day of vitamin D bolus intake
d1_Ind25

value: Individual 25


title: PBMC, vitamin D bolus, day 1, Individual 29

description:
After 1 day of vitamin D bolus intake
d1_Ind29

value: Individual 29


title: PBMC, Control, day 0, Individual 43

description:
Before vitamin D bolus intake
d0_Ind43

value: Individual 43

value: control

value: day 0


title: PBMC, Control, day 0, Individual 42

description:
Before vitamin D bolus intake
d0_Ind42

value: Individual 42


title: uninfected_6, run 1

status: Public on Dec 01 2025

city: Ann Arbor

first: Marc

middle: B

last: Hershenson

state: MI

address: 1150 W. Medical Center Drive

department: Department of Pediatric Pulmonology

institute: Michigan Medicine

description: Library name: 9400-JK-21

data_processing:
The reads were trimmed using Cutadapt v4.8 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCh38 (ENSEMBL 109), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.20 (Ewels et al., 2016).
Assembly: GRCh38 (ENSEMBL 109)
Supplementary files format and content: Tab-deliminated text file includes a complete matrix of gene expected count totals for all samples.

source_name: nasal swab

extract_protocol:
Total RNA from nasal swab samples was prepared using Trizol extraction. RNA was purified using RNEasy spin columns and enriched for mRNA using a Poly(A) mRNA Magnetic Isolation Module.
A TruSeq-based Takara kit was used during library preparation. This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan.

value: nasal swab

tag: host viral_infection

value: uninfected

tag: library batch


title: PBMC, vitamin D bolus, day 1, Individual 30

description:
After 1 day of vitamin D bolus intake
d1_Ind30

value: Individual 30


title: PBMC, Control, day 0, Individual 41

description:
Before vitamin D bolus intake
d0_Ind41

value: Individual 41

value: Healthy Individuals


title: RVA_4, run 1

description: Library name: 9400-JK-4

tag: tissue

value: RV-A


title: PBMC, vitamin D bolus, day 1, Individual 20

description:
After 1 day of vitamin D bolus intake
d1_Ind20

value: Individual 20

tag: cell type

value: PBMC

value: 80000 IU vitamin D3


title: PBMC, vitamin D bolus, day 1, Individual 21

description:
After 1 day of vitamin D bolus intake
d1_Ind21

value: Individual 21

tag: treatment

value: day 1


title: PBMC, vitamin D bolus, day 1, Individual 14

description:
After 1 day of vitamin D bolus intake
d1_Ind14

value: Individual 14


title: PBMC, vitamin D bolus, day 1, Individual 18

description:
After 1 day of vitamin D bolus intake
d1_Ind18

value: Individual 18


title: PBMC, vitamin D bolus, day 1, Individual 11

description:
After 1 day of vitamin D bolus intake
d1_Ind11

value: Individual 11


title: PBMC, Control, day 0, Individual 38

description:
Before vitamin D bolus intake
d0_Ind38

value: Individual 38

value: control


title: PBMC, vitamin D bolus, day 1, Individual 16

description:
After 1 day of vitamin D bolus intake
d1_Ind16

value: Individual 16


title: PBMC, vitamin D bolus, day 1, Individual 05

description:
After 1 day of vitamin D bolus intake
d1_Ind05

value: Individual 05


title: PBMC, vitamin D bolus, day 1, Individual 10

description:
After 1 day of vitamin D bolus intake
d1_Ind10

value: Individual 10


title: PBMC, vitamin D bolus, day 1, Individual 07

description:
After 1 day of vitamin D bolus intake
d1_Ind07

value: Individual 07


title: PBMC, vitamin D bolus, day 1, Individual 04

description:
After 1 day of vitamin D bolus intake
d1_Ind04

value: Individual 04


title: PBMC, Control, day 0, Individual 27

description:
Before vitamin D bolus intake
d0_Ind27

value: Individual 27

value: Healthy Individuals

value: day 0


title: PBMC, vitamin D bolus, day 1, Individual 02

description:
After 1 day of vitamin D bolus intake
d1_Ind02

value: Individual 02

value: PBMC


title: PBMC, Control, day 0, Individual 25

description:
Before vitamin D bolus intake
d0_Ind25

value: Individual 25


title: PBMC, Control, day 0, Individual 45

description:
Before vitamin D bolus intake
d0_Ind45

value: Individual 45


title: PBMC, Control, day 0, Individual 44

description:
Before vitamin D bolus intake
d0_Ind44

value: Individual 44


title: PBMC, Control, day 0, Individual 23

description:
Before vitamin D bolus intake
d0_Ind23

value: Individual 23


title: PBMC, Control, day 0, Individual 21

description:
Before vitamin D bolus intake
d0_Ind21

value: Individual 21


title: PBMC, Control, day 0, Individual 20

description:
Before vitamin D bolus intake
d0_Ind20

value: Individual 20


title: PBMC, Control, day 0, Individual 40

description:
Before vitamin D bolus intake
d0_Ind40

value: Individual 40

value: control


title: PBMC, Control, day 0, Individual 39

description:
Before vitamin D bolus intake
d0_Ind39

value: Individual 39


title: PBMC, Control, day 0, Individual 18

description:
Before vitamin D bolus intake
d0_Ind18

value: Individual 18


title: PBMC, Control, day 0, Individual 37

description:
Before vitamin D bolus intake
d0_Ind37

value: Individual 37


title: PBMC, Control, day 0, Individual 36

description:
Before vitamin D bolus intake
d0_Ind36

value: Individual 36


title: PBMC, Control, day 0, Individual 14

description:
Before vitamin D bolus intake
d0_Ind14

value: Individual 14


title: PBMC, Control, day 0, Individual 31

description:
Before vitamin D bolus intake
d0_Ind31

value: Individual 31

value: Healthy Individuals


title: PBMC, Control, day 0, Individual 11

description:
Before vitamin D bolus intake
d0_Ind11

value: Individual 11

value: day 0


title: PBMC, Control, day 0, Individual 09

description:
Before vitamin D bolus intake
d0_Ind09

value: Individual 09

value: PBMC


title: PBMC, Control, day 0, Individual 12

description:
Before vitamin D bolus intake
d0_Ind12

value: Individual 12


title: PBMC, Control, day 0, Individual 29

description:
Before vitamin D bolus intake
d0_Ind29

value: Individual 29


title: PBMC, Control, day 0, Individual 30

description:
Before vitamin D bolus intake
d0_Ind30

value: Individual 30


title: PBMC, Control, day 0, Individual 35

description:
Before vitamin D bolus intake
d0_Ind35

value: Individual 35


title: PBMC, Control, day 0, Individual 34

description:
Before vitamin D bolus intake
d0_Ind34

value: Individual 34


title: PBMC, Control, day 0, Individual 26

description:
Before vitamin D bolus intake
d0_Ind26

value: Individual 26

value: control


title: PBMC, Control, day 0, Individual 04

description:
Before vitamin D bolus intake
d0_Ind04

value: Individual 04


title: PBMC, Control, day 0, Individual 03

description:
Before vitamin D bolus intake
d0_Ind03

value: Individual 03


title: PBMC, Control, day 0, Individual 02

description:
Before vitamin D bolus intake
d0_Ind02

value: Individual 02


title: H358 Drug, scATACseq

status: Public on May 14 2025

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
10x genomics
H358AMGD8_fragments.tsv.gz

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using default Cell Ranger settings for scATAC-seq
Assembly: hg38
Supplementary files format and content: tsv, fragment files

extract_protocol:
DTP cells or untreated control cells were washed twice with PBS to remove dead floating cells. All cells were trypsinized and collocted. Cell pallete were resuspend at a concentration of 1 million cells/ml in PBS +0.04% BSA
Libruary was performed according to manufactor's instruction. Briefly,  Single Nuclei were isolated from the cell sample using standard procedures of microfluidics-based techniques. Transposition reaction were perform for the tagmentation of DNA and barcode incorporation using the Tn5 transposase enzyme according to the manufacturer's. Amplify the tagmented DNA fragments by PCR to generate scATAC-seq libraries.

tag: cell line

value: tumor cell line

value: 500nM Sotorasib for 8days


title: PBMC, Control, day 0, Individual 24

description:
Before vitamin D bolus intake
d0_Ind24

value: Individual 24

value: Healthy Individuals


title: PBMC, Control, day 0, Individual 19

description:
Before vitamin D bolus intake
d0_Ind19

value: Individual 19

value: day 0


title: PBMC, Control, day 0, Individual 01

description:
Before vitamin D bolus intake
d0_Ind01

value: Individual 01

value: PBMC


title: PBMC, Control, day 0, Individual 17

description:
Before vitamin D bolus intake
d0_Ind17

value: Individual 17


title: PBMC, Control, day 0, Individual 16

description:
Before vitamin D bolus intake
d0_Ind16

value: Individual 16


title: PC9 Ctrl, library4, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz

value: without treatment


title: PC9 and H358, scRNAseq (GEX)

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using default Cell Ranger settings
Assembly: hg38
Supplementary files format and content: tsv, matrix files

source_name: PC9 and NCI-H358

extract_protocol:
DTP cells or untreated control cells were washed twice with PBS to remove dead floating cells. All cells were trypsinized and collocted. Cell pallete were resuspend at a concentration of 1 million cells/ml in PBS +0.04% BSA
Libruary was performed according to manufactor's instruction. Briefly,  different samples were labeled with barcoded antibodies and conbined to one scRNAseq sample(cell hashing). Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion. the poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, unique molecular identifier, and the 10X Barcode. The pooled barcoded cDNA was then cleaned up with silane dynabeads, amplified by PCR and the appropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequence and a sample index were added.

value: PC9 and NCI-H358

value: untreated, 150nM Osimertinib treated for 4 or 11 days, or 500nM Sotorasib treated for 8 days


title: PC9 and H358, cell hashing (HTO)

description: 10x genomics


title: PBMC, Control, day 0, Individual 28

description:
Before vitamin D bolus intake
d0_Ind28

value: Individual 28

value: control


title: PBMC, Control, day 0, Individual 13

description:
Before vitamin D bolus intake
d0_Ind13

value: Individual 13


title: PBMC, Control, day 0, Individual 10

description:
Before vitamin D bolus intake
d0_Ind10

value: Individual 10


title: PBMC, Control, day 0, Individual 08

description:
Before vitamin D bolus intake
d0_Ind08

value: Individual 08


title: PBMC, Control, day 0, Individual 07

description:
Before vitamin D bolus intake
d0_Ind07

value: Individual 07


title: I2_spo_D18

status: Public on May 07 2025

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

data_processing:
We used two rounds of krakenuniq (i.e. against a database built using EuPathDB and then malariae reads against a database build using genomes from Anopheles gambiae complex and the P. malariae genome) to decontaminate reads and extract potential P.malariae reads (2x150bp)
We used sortmerna to remove rRNA reads
We used hisat2 –very-sensitive to perform alignment
samtools view and Picard’s MarkDuplicates to remove duplication, samtools view and the perl expression “perl -nle 'if (/^@/){ print } else {@ar=split(/\t/); ($n)= $ar[5] =~ /(\d{3,}M)/; if (defined($1)) { print }}'” to filter out reads that did not aligned at least 100 bp
The software coco to perform read counting and quantification.
Assembly: PmUG01
Supplementary files format and content: DESEQ2 to obtain TPM counts and Differentially Expressed Genes subset of genes that are significant (FDR < 0.05) for the comparison between tissues

organism: Anopheles gambiae

source_name: Salivary glands

extract_protocol:
Mosquitoes were maintained under standard insectary conditions (27 ± 2 °C, 80 ± 5% relative humidity, 12:12 LD). Females were fed through membrane feeders on blood containing gametocytes of P. malariae, prepared according to standard protocols. Thereafter the mosquitoes were given access to a solution of 5% glucose/ 0.05% 4-aminobenzoic acid ad libitum
Immediately after dissection, tissues were stored in TRIzol (Invitrogen) and frozen at -80ºC until subsequent processing. Total RNA was extracted from a pool of midguts and salivary glands from ~10 mosquitoes using the TRIzol manufacturer protocol. RNA concentration was quantified using a Qubit® 2.0 Fluorometer, and RNA integrity was determined with an Agilent 2100 Bioanalyzer. We used the Ovation® Universal RNA-seq System (Nugen Technologies) for RNA-seq library construction following the manufacturer’s instructions

value: Salivary glands

value: P. malariae-infection 18 days

tag: replicate


title: I2_ooc-spo_D16

source_name: Midguts

value: Midguts

value: P. malariae-infection 16 days


title: I2_spo_D16


title: H358 Ctrl, scATACseq

description:
10x genomics
H358DMSO_fragments.tsv.gz

value: tumor cell line


title: PC9 Drug, library4, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz

value: 150nM Osimertinib for 11days


title: PBMC, Control, day 0, Individual 05

description:
Before vitamin D bolus intake
d0_Ind05

value: Individual 05

value: Healthy Individuals

value: PBMC

value: day 0


title: PC9 Drug, library3, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz


title: I1_ooc-spo_D16


title: PC9 Drug, library1, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz


title: PC9 non-target sgRNA2, H3K27me3, ChIP

data_processing:
macs2 callpeak --broad --broad-cutoff 0.1 --nolambda
Assembly: hg38
Supplementary files format and content: Bed, BroadPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 minutes. After quenching and cell lysis, chromatin was sonicated for 6 minute using QSONICA
Protein G magnetic beads and indicated antibodies were used to immunoprecipitated the DNA fragment. 10 ng DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit complemented with DNA barcode primers. Libraries were amplified using PCR, and purified  by AMPure beads. Libraries were validated using the Agilent High sensitivity kit

value: 150nM Osimertinib for 4 days

tag: chip antibodies


title: I1_spo_D16


title: PC9 Ctrl, library3, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz

value: without treatment


title: Patient 10 PBMC  Low MOCA scRNAseq

status: Public on Apr 23 2025

city: Boston

first: Kris

last: Kahle

address: 55 Fruit Street

institute: MGH

description:
Library name: Sample 20
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)"
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Animals were anesthetized with Ketamine/Xylazine and transcardially perfused with ice cold TBS before brain removal. Choroid plexi from bilateral lateral ventricles were microdissected in ice cold HBSS with 30uM Actinomycin D (ActD, Sigma, cat#A1410 ) and digested at 37oC for 20 min with Collagenases-I and -IV (10 U/mL, 400 U/mL final, Worthington, Cat# LS004194, and LS004184) and DNase I (30 U/mL, Roche, cat# 04716728001) and ActD (3uM). For Flow sorting, the cell suspension was blocked with CD16-CD32 antibodies (1:100, biolegend, cat#101302) and stained 30 min at 4oC with anti-rat CD45-PE/cy7 (1:100, biolegend, cat#202207) to and DAPI (50ug/mL). Cells were subsequently washed in FACS staining buffer (0.5% BSA, 2mM EDTA in PBS without Calcium/Magnesium) and centrifuged at 350 rcf for 5 minutes. Cells were resuspended in 300ul of FACS buffer and sorted by CD45 positivity on a BD ARIA instrument. CD45 positive and CD45 negative cells were collected in 0.4% BSA/PBS and 3uM ActD and sent for 10X 3prime library preparation and sequencing at Yale Center for Genome Analysis
Sequencing libraries were loaded on an Illumina HiSeq4000 flow cell with sequencing settings following the recommendations of 10x Genomics (read 1: 26 cycles; read 2: 98 cycles; index i7: eight cycles; index i5: no cycles; 2.1 pM loading concentration). The Cell Ranger pipeline was designed to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index. Read 2, containing the cDNA, was mapped to the reference genome (mouse mm10) using STAR

value: Low MOCA


title: Patient 10 CSF Low MOCA scRNAseq

description:
Library name: Sample 19
10x Genomics

source_name: CSF

value: CSF


title: PBMC, Control, day 0, Individual 32

description:
Before vitamin D bolus intake
d0_Ind32

value: Individual 32

tag: disease state

value: control


title: PC9 Ctrl, library2, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz


title: Patient 9 CSF Low MOCA scRNAseq

description:
Library name: Sample 17
10x Genomics


title: PC9 Ctrl, library1, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz


title: Patient 8 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 16
10x Genomics


title: Patient 7 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 14
10x Genomics


title: PC9 Drug, library2, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz


title: PC9 non-target sgRNA1, H3K27me3, ChIP


title: Patient 7 CSF Low MOCA scRNAseq

description:
Library name: Sample 13
10x Genomics


title: Patient 5 CSF High MOCA scRNAseq

description:
Library name: Sample 9
10x Genomics

value: High MOCA


title: Patient 4 CSF High MOCA scRNAseq

description:
Library name: Sample 7
10x Genomics


title: PC9 non-target sgRNA2, H3K9me3, ChIP

value: H3K9me3 (Abcam, #ab8898)


title: Patient 2 CSF High MOCA scRNAseq

description:
Library name: Sample 3
10x Genomics


title: RO50579

status: Public on Apr 21 2025

description: 10x Genomics

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v7.0.0) (PMID: 28091601). The “mkfastq” command was used to generate FASTQ files and the “count” command was used to generate raw gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters. Human Genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates (PMID: 33270111). Samples from 22 patients were combined in R using the Read10X() function from Seurat package(v4.3.0) (PMID: 34062119) and an integrated Seurat object was generated. Filtering was conducted by retaining cells that had unique molecular identifiers (UMIs) less than 20000 and had mitochondrial content less than 20 percent. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers (PMID: 26430063). Doublets were removed using scDblFinder (v1.12.0) (PMID: 35814628). The SCTransform workflow was used for count normalization, initial integration, and to identify highly variable genes (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Batch correction was performed using Harmony (v0.1.1) (PMID: 31740819). Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Celltype annotation was performed using two different approaches: 1) Seurat Reference Mapping and Label Transfer approach, Bone Marrow Atlas was downloaded from DISCO (PMID: 34791375) and was used a reference to transfer labels this data 2) Manual curation was done by gene markers to reflect the prediction results. Hematopoietic Stem Cells (HSC) were identifed by PROM1 and CD34,MultiPotent Progenitors (MPP) by TESPA1, PLEK, Granulocyte/Macrophage Progenitors (GMP) by SPINK2 and SERPINB1, Granulocytes by AZU1 and PRTN3, CD14-Mono by CD14 and S100A8, Macrophages by C1QA and C1QB, Megakaryocytes(MK) by PPBP and PF4, Classical Dendritic Cells (cDC) by CD1C and FCER1A, Plasmacytoid dendritic cells (pDCs) by IRF7 and IRF8, TCells by CD3E and CD8A, NaturalKiller Cells(NK) by NKG7 and IL2RB, Fibroblasts by COL1A1 and CXCL12, MAST cells by CPA3 and KIT, Keratin Expressing Stromal Cells(KESC) by KRT7 and KRT14 and Plasma Cells by JCHAIN
Assembly: hg38
Supplementary files format and content: Matrix fle

source_name: Bone Marrow

extract_protocol:
After evaluating for cell number, cell viability, and cell size, the appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) with a targeted cell recovery of 10,000. Single-cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2. Next GEM Single Cell 3′ reagent kit (10X Genomics, Pleasanton, CA, USA). Following cell capture and cell lysis, cDNA was synthesized and amplified.
An Illumina sequencing library was then prepared with the amplified cDNA with the Chromium™ Next GEM Single-Cell 3′ GEM, Library & Gel Bead Kit v2 (10X Genomics, Pleasanton, CA, USA). The resulting library was sequenced, including cell barcode and UMI sequences, and the read lengths were 26 bp read 1 (cell barcode and UMI) and 91 bp read 2 (RNA read) were generated with Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA) at the Center for Medical Genomics of the Indiana University School of Medicine.

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

tag: age

tag: Sex

value: Male

tag: race

value: Caucasian

tag: response

value: Refractory

tag: genotype

value: Tosedostat + ARAC


title: Kidney organoids pooled library

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: McCracken-KidOrganoid-Sept2024-20241021-FLEXv1-hg

data_processing:
Aligned using Cellranger v8.0.1
Assembly: GRCh38
Supplementary files format and content: Raw counts and metadata, tab-delimitted

source_name: kidney organoids derived from human pluripotent stem cells

growth_protocol: Ureteric bud (UB) and nephrogenic mesenchyme (NM) were generated as previously described. Kidney organoids were made by assembling 500,000 NM progenitors with 30-60 UB spheroids into dense aggregates plated on transwell filters.

extract_protocol:
Kidney organoids at different timepoints were dissociated using TrypLE Express for 15-30 minutes at 37deg, with intermittent trituration with a P1000 pipette until they were largely dissociated into a single cell suspension. The cells were washed with PBS + 0.04% bovine serum albumin and filtered through a cell strainer snap cap tube. The single cell suspension was fixed and stored using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics), according to manufacturer’s instructions.
Single cell libraries were generated from the multiplexed cell suspensions using the Chromium Flex Fixed RNA Kit, Human Transcriptome (v1, 16 reactions, 10X Genomics).

treatment_protocol: Organoids were profiled under standard conditions, as well as organoids with NOTCH inhibition (DAPT) from days 4-6 and organoids grown in collecting duct (CD) medium +/- A83, U0126, and XAV939 from days 10-14.

value: H9 + iPSC72-3 (GFP)

value: kidney organoid

value: WT

value: Control, DAPT (days 4-6), CD Medium (days 10-14), CD Medium + AUX (days 10-14)


title: Patient 4 PBMC  High MOCA scRNAseq

description:
Library name: Sample 8
10x Genomics

value: PBMC


title: cHET_F

status: Public on Apr 30 2025

description:
10x Genomics
7166-MR-75

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.1.2). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.232) with standard parameters. Mouse genome mm10 was used for the alignment and genecode vM25 was used for gene annotation and coordinates. We used the R package Seurat (v4.1.0) and customized R scripts for data analyses Data from different samples (control vs. cHet) were merged into a unique single cell object. Nuclei with > 250 genes, < 10000 UMIs, and < 5% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) for a resultant expression matrix with 21,516 genes and 52,743 cells. The SCTransform workflow was used for count normalization and data integration using 30 principal components and resolution of 0.5 for Louvain clustering and UMAP. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. After removing 4 clusters showing high expression of glutamatergic neuronal markers and subsequent re-clustering, we identified 20 final distinct clusters. Cell annotation was performed using two different approaches: 1) markers enrichment using a Nucleus Accumbens independent data by Fisher’s exact test and 2) a predictive machine learning model based on a Nucleus Accumbens atlas reference data using the R package scPred. Cell annotation then was manually curated to reflect both analyses. To identify differentially expressed genes between conditions (control vs. cHet) in each defined cell types, the R package LIBRA with option MAST was used to perform zero-inflated regression analysis. Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2. We further confirmed these results using a Wilcoxon’s rank sum test.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: PFC

extract_protocol:
8-week old Mef2c cHetVgat and littermate control mice (Vgat-cre positive) were live-decapitated, and brains were rapidly extracted into ice-cold 4˚C Hibernate A medium, with GlutaMAX (Fisher), B27 (Fisher), and NxGen RNase inhibitor (0.2U/µL, Lucigen), and incubated for approximately 30 seconds. The brain was sectioned into 1 mm sections using a brain matrix and cold razor blades. The PFC was isolated with fine forceps and collected, flash frozen on dry ice, and stored at -80oC until the day of nuclear isolation. Bilateral prefrontal cortices were collected separately from three mice per group. We modified the nuclear isolation protocol described in Savell et al., 2020. On the day of nuclear isolation, the frozen tissue was thawed on ice and chopped with a scalpel blade 200 times in two orthogonal directions on a glass petri dish atop ice. The chopped tissue were then pooled per group and transferred into a lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL (Sigma) in Nuclease-Free Water). Supplemented Hibernate A medium was added to the lysis buffer to quench the reaction, and the tissue was triturated ~30 times/sample using three glass pipettes of decreasing diameter. This trituration cycle was repeated two more times. The mixture was filtered using a 40 micron filter (Fisher). The nuclei were isolated using 500xg centrifugation and washed with 1x PBS+1.0% BSA and 0.2U/µL RNase inhibitor. Nuclei were incubated with 7-aminoactinomycin D (7-AAD) (Invitrogen) for five minutes and sorted for 7-AAD-positive single nuclei using fluorescence-activated nuclear sorting on the BD FACS Aria II. Samples were counted and diluted to 1500 nuclei/µL before processing on the 10x Genomics Single-Cell Protocol by the MUSC Translation Science Lab. Libraries were constructed using the Chromium Single Cell 3’ Library Construction Kit (10x Genomics, v3.1) and sequenced at Vanderbilt’s Next Gen Sequencing Core (Illumina NovaSeq 6000).
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 according to the manufacturer’s protocol. Libraries and sequencing were performed at the Translational Science Lab at MUSC.

value: PFC

tag: library type

value: 10X single-nuclei RNA-seq

value: 8 weeks old

tag: protocol

value: Protocol 1


title: RO50549

description: 10x Genomics

value: Pacific Islander

value: CR


title: Patient 9 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 18
10x Genomics

value: Low MOCA


title: 648T1B_IDH2-Mutant_SRSF2-WT BS

status: Public on Nov 26 2025

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18) with parameter -m25 -U10
Reads were mapped on the GRCh37 human genome with bismark and bismark_methylation_extractor (v. 0.22.1)
Assembly: GRCh37
Supplementary files format and content: Genome-wide cytosine report file (chromosome, position, strand, count methylated, count unmethylated, C context, trinucleotide context)

source_name: Blood

extract_protocol:
AllPrep DNA/RNA kit from Qiagen (Valencia, CA)
Methyl-Seq Kit (Swift Biosciences)

value: Blood

value: M

tag: idh2 genotype

value: Mutant

tag: srsf2 genotype


title: Patient 8 CSF Low MOCA scRNAseq

description:
Library name: Sample 15
10x Genomics

value: CSF


title: Patient 6 PBMC  Unknown MOCA scRNAseq

description:
Library name: Sample 12
10x Genomics

value: Unknown MOCA


title: RO50417

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: Male

value: Caucasian

value: GCLAC


title: Patient 3 CSF High MOCA scRNAseq

description:
Library name: Sample 5
10x Genomics

value: High MOCA


title: Patient 2 PBMC  High MOCA scRNAseq

description:
Library name: Sample 4
10x Genomics

value: PBMC


title: Patient 5 PBMC  High MOCA scRNAseq

description:
Library name: Sample 10
10x Genomics


title: 85T1M_IDH2-WT_SRSF2-WT BS

source_name: Marrow

value: Marrow

value: WT


title: RO50393

description: 10x Genomics

value: Female

value: Refractory

value: Benda + IDA


title: Patient 3 PBMC  High MOCA scRNAseq

description:
Library name: Sample 6
10x Genomics


title: Patient 1 CSF High MOCA scRNAseq

description:
Library name: Sample 1
10x Genomics


title: Patient 6 CSF Unknown MOCA scRNAseq

description:
Library name: Sample 11
10x Genomics


title: RO50377

description: 10x Genomics

value: Benda+Idarubicin


title: RO50634

description: 10x Genomics

value: CR

value: IAP


title: RO50497

description: 10x Genomics


title: PC9 non-target sgRNA1, H3K9me3, ChIP

city: New York

value: 150nM Osimertinib for 4 days

value: H3K9me3 (Abcam, #ab8898)


title: RO50562

description: 10x Genomics

value: Bone Marrow

value: Tosedostat + DAC


title: RO50575

description: 10x Genomics

value: Acute Myeloid leukemia (AML)

value: American Indian or Alaska Native


title: RO50236

description: 10x Genomics

value: Hispanic


title: RO50528

description: 10x Genomics

value: Male

value: Caucasian

value: 46,XY, t(5;12) with rearrangekemts involving 12q13


title: RO50392

description: 10x Genomics

value: Pacific Islander

value: GCLAC


title: RO50378

description: 10x Genomics

value: Unknown


title: RO50183

description: 10x Genomics


title: RO50268

description: 10x Genomics

value: Female

value: Refractory

value: 4 + 3 + Sorafenib


title: RO50324

description: 10x Genomics

value: CR


title: RO50076

description: 10x Genomics


title: RO50256

description: 10x Genomics

value: unknown


title: PBMCs from Healthy4 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

status: Public on Apr 08 2025

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

institute: EF-CLIF

description: single-cell RNA-seq

data_processing:
Cell Ranger v3.1.0 [alignment, filtering, barcode counting, and UMI counting]
Genome_build: human: GRCh38-3.0.0
Supplementary_files_format_and_content: barcodes.tsv: cell barcodes
Supplementary_files_format_and_content: features.tsv: gene names
Supplementary_files_format_and_content: matrix.mtx: count matrix

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
As described in the v3.0 single-cell 3’ mRNA kit (10x Genomics) protocol (CGO00183 Rev C), after GEMs generation and reverse transcription, the cDNA was extracted by Dynabeads MyOne SILANE clean up following manufacturer’s instructions. The obtained cDNA was then used for amplification.
The amplified cDNA was subjected to enzymatic fragmentation, end repair and A-tailing. Size selected fragments subsequently underwent R2 adaptor ligation and Index PCR for the insertion of sample index for library demultiplexing, P5 and P7 Illumina adapters. Libraries were purified by SPRI selected beads clean up. Fragments size distribution and concentration were verified on an Agilent Bioanalyzer High Sensitivity Chip (Agilent Technologies). Libraries were sequenced on a NovaSeq6000 (Illumina) to obtain approximately 25000 reads per cell.

tag: group

value: Healthy

tag: hashing

value: Hashed (Vehicle:HD4-control / Albumin:HD4-HSA)

value: 10X Chromium 3' RNA-seq


title: PBMCs from Healthy2_Vehicle non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)

value: Non-hashed


title: RO50176

description: 10x Genomics

tag: tissue

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: ND

tag: treatment

value: FLAM


title: RO50166

description: 10x Genomics


title: PBMCs from Healthy2_Albumin non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: PBMCs from Patient9_Vehicle non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq

value: Acutely Decompensated Cirrhosis Patient


title: RO50112

description: 10x Genomics

value: American Indian or Alaska Native

value: IAP


title: RO50130

description: 10x Genomics

value: Male

value: Caucasian


title: PBMCs from Healthy1_Vehicle non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: PBMCs from Healthy1_Albumin non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: PBMCs from Healthy3 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:3b-3Veh-HD-3HD / Albumin:3b-3Veh-HD-3HD-HSA)


title: PBMCs from Patient9_Albumin non-hashed - Post discovery cohort (scRNA-seq)

description: single-cell RNA-seq


title: PBMCs from Patient4 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:2b-2Veh-CFL5-2ACFL5 / Albumin:2b-2Veh-CFL5-2ACFL5-HSA)


title: PBMCs from Patient6 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:AD3-control / Albumin:AD3-HSA)


title: PBMCs from Patient5 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:1c-1Veh-AD2-2AD2 / Albumin:1c-1Veh-AD2-2AD2-HSA)


title: PBMCs from Patient2 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:2-2ACFL-2H-ACFL / Albumin:2-2ACFL-2H-ACFL-HSA)


title: PBMCs from Patient3 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:1b-1VehACFL4-1ACFL4 / Albumin:1b-1VehACFL4-1ACFL4-HSA)

value: 10X Chromium 3' RNA-seq


title: PBMCs from Patient1 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Peripheral blood mononuclear cells (PBMCs)

value: Hashed (Vehicle:1-1AD-1H-AD / Albumin:1-1AD-1H-AD-HSA)


title: Whole-blood RNA-seq from preACLF (S65)

description:
S65
Whole-blood RNA-seq from preACLF (S65).
mRNAseq

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability.
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: *.tsv: RSEM expected counts.

source_name: Whole blood

extract_protocol:
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 4380204, Applied Biosystems). RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855).
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 40 million paired-end 100nt reads.

value: preACLF

value: Whole blood


title: Whole-blood RNA-seq from preACLF (S66)

description:
S66
Whole-blood RNA-seq from preACLF (S66).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S72)

description:
S72
Whole-blood RNA-seq from preACLF (S72).
mRNAseq


title: Whole-blood RNA-seq from preACLF (pS07)

description:
pS07
Whole-blood RNA-seq from preACLF (pS07).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S88)

description:
S88
Whole-blood RNA-seq from preACLF (S88).
mRNAseq


title: PBMCs from Patient8 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Hashed (Vehicle:AD4-control /  Albumin:AD4-HSA)


title: Whole-blood RNA-seq from preACLF (S68)

description:
S68
Whole-blood RNA-seq from preACLF (S68).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S55)

description:
S55
Whole-blood RNA-seq from preACLF (S55).
mRNAseq


title: PBMCs from Patient7 hashed (Vehicle/Albumin) - Post discovery cohort (HTO scRNA-seq)

description: single-cell RNA-seq

value: Acutely Decompensated Cirrhosis Patient

value: Hashed (Vehicle:ACLF8-control / Albumin:ACLF8-HSA)


title: Whole-blood RNA-seq from preACLF (S59)

description:
S59
Whole-blood RNA-seq from preACLF (S59).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S28)

description:
S28
Whole-blood RNA-seq from preACLF (S28).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S07)

description:
S07
Whole-blood RNA-seq from preACLF (S07).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S42)

description:
S42
Whole-blood RNA-seq from preACLF (S42).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S22)

description:
S22
Whole-blood RNA-seq from preACLF (S22).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S38)

description:
S38
Whole-blood RNA-seq from preACLF (S38).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S37)

description:
S37
Whole-blood RNA-seq from preACLF (S37).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S86)

description:
S86
Whole-blood RNA-seq from preACLF (S86).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S102)

description:
S102
Whole-blood RNA-seq from preACLF (S102).
mRNAseq


title: Whole-blood RNA-seq from preACLF (S99)

description:
S99
Whole-blood RNA-seq from preACLF (S99).
mRNAseq


description:
pS04
Whole-blood RNA-seq from ACLF not treated (pS04).
mRNAseq

value: ACLF not treated


title: Whole-blood RNA-seq from preACLF (S94)

description:
S94
Whole-blood RNA-seq from preACLF (S94).
mRNAseq


description:
S12
Whole-blood RNA-seq from ACLF not treated (S12).
mRNAseq


title: CONTROL_F

description:
10x Genomics
7166-MR-74

value: PFC

value: 10X single-nuclei RNA-seq

tag: strain

value: 8 weeks old

value: Protocol 1


description:
S105
Whole-blood RNA-seq from ACLF not treated (S105).
mRNAseq


description:
pS71
Whole-blood RNA-seq from ACLF not treated (pS71).
mRNAseq


description:
pS19
Whole-blood RNA-seq from ACLF not treated (pS19).
mRNAseq


description:
pS37
Whole-blood RNA-seq from ACLF not treated (pS37).
mRNAseq


description:
S32
Whole-blood RNA-seq from ACLF not treated (S32).
mRNAseq


description:
S10
Whole-blood RNA-seq from ACLF not treated (S10).
mRNAseq


description:
S62
Whole-blood RNA-seq from ACLF not treated (S62).
mRNAseq


description:
S08
Whole-blood RNA-seq from ACLF not treated (S08).
mRNAseq


description:
pS58
Whole-blood RNA-seq from ACLF not treated (pS58).
mRNAseq


title: Patient 1 PBMC  High MOCA scRNAseq

description:
Library name: Sample 2
10x Genomics

value: PBMC

value: High MOCA


description:
pS68
Whole-blood RNA-seq from ACLF not treated (pS68).
mRNAseq


description:
S47
Whole-blood RNA-seq from ACLF not treated (S47).
mRNAseq


description:
pS55
Whole-blood RNA-seq from ACLF not treated (pS55).
mRNAseq


description:
S84
Whole-blood RNA-seq from ACLF not treated (S84).
mRNAseq


description:
pS70
Whole-blood RNA-seq from ACLF not treated (pS70).
mRNAseq


description:
pS41
Whole-blood RNA-seq from ACLF not treated (pS41).
mRNAseq


description:
S41
Whole-blood RNA-seq from ACLF not treated (S41).
mRNAseq


description:
S71
Whole-blood RNA-seq from ACLF treated (S71).
mRNAseq

value: ACLF treated


description:
S67
Whole-blood RNA-seq from ACLF treated (S67).
mRNAseq


description:
pS30
Whole-blood RNA-seq from ACLF not treated (pS30).
mRNAseq


description:
S64
Whole-blood RNA-seq from ACLF treated (S64).
mRNAseq


description:
S89
Whole-blood RNA-seq from ACLF treated (S89).
mRNAseq


description:
S87
Whole-blood RNA-seq from ACLF treated (S87).
mRNAseq


description:
pS10
Whole-blood RNA-seq from ACLF treated (pS10).
mRNAseq


description:
S27
Whole-blood RNA-seq from ACLF treated (S27).
mRNAseq


description:
S09
Whole-blood RNA-seq from ACLF treated (S09).
mRNAseq


description:
S57
Whole-blood RNA-seq from ACLF treated (S57).
mRNAseq


description:
S83
Whole-blood RNA-seq from ACLF treated (S83).
mRNAseq


title: BPRNF SI Tum, replicate 4

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

description:
Library name: BPRNF SI Tum 4
10x Genomics

data_processing:
Demultiplexing, barcode processing and gene counting were performed using Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small Intestine

extract_protocol:
Samples were homogenised and digested using a McIlwain Tissue CHopper and the GentleMACS Octo Dissociator in combination with the Mouse tumor dissociation kit (Miltenyi Biotec). Debris was removed, and then cells were sorted using a FACSAria sorter (BD Biosciences) and DAPI to remove dead cells.
Cells were loaded into a Chromium Chip G using a 10x Chromium Single-Cell 3’ v3 Gel Bead kit and Library (10x Genomics), then libraries were analysed using the Bioanalyzer High Sensitivity DNA kit (Agilent technologies). Sequencing was performed on an Illumina NovaSeq 6000 with paired-end 150-base reads.

treatment_protocol: Recombination of floxed genes was induced with 2mg tamoxifen, administered via intraperitoneal injection. Mice were culled at clinical endpoint, and tumors harvested.

value: Small Intestine

value: whole tumor

value: VilCreER BrafV600E/+ P53fl/fl Rnf43fl/fl

value: Male


title: BPRNF SI Tum, replicate 5

description:
Library name: BPRNF SI Tum 5
10x Genomics


description:
S45
Whole-blood RNA-seq from ACLF treated (S45).
mRNAseq


description:
S34
Whole-blood RNA-seq from ACLF treated (S34).
mRNAseq


title: BPRNF SI Tum, replicate 3

description:
Library name: BPRNF SI Tum 3
10x Genomics


title: BPRNF SI Tum, replicate 1

description:
Library name: BPRNF SI Tum 1
10x Genomics

value: Female


description:
S60
Whole-blood RNA-seq from ACLF treated (S60).
mRNAseq

value: Whole blood


description:
17K042
Whole-blood RNA-seq from Healthy Subjects (17K042).
mRNAseq

value: Healthy Subjects


description:
S103
Whole-blood RNA-seq from ACLF treated (S103).
mRNAseq


description:
S95
Whole-blood RNA-seq from ACLF treated (S95).
mRNAseq


description:
S101
Whole-blood RNA-seq from ACLF treated (S101).
mRNAseq


title: BP SI Tum, replicate 3

description:
Library name: BP SI Tum 3
10x Genomics

value: VilCreER BrafV600E/+ P53fl/fl


description:
S23
Whole-blood RNA-seq from ACLF treated (S23).
mRNAseq


description:
17K032
Whole-blood RNA-seq from Healthy Subjects (17K032).
mRNAseq


title: BP SI Tum, replicate 1

description:
Library name: BP SI Tum 1
10x Genomics


title: BPRNF SI Tum, replicate 2

description:
Library name: BPRNF SI Tum 2
10x Genomics


description:
17K004
Whole-blood RNA-seq from Healthy Subjects (17K004).
mRNAseq


title: BP SI Tum, replicate 2

description:
Library name: BP SI Tum 2
10x Genomics


description:
17K029
Whole-blood RNA-seq from Healthy Subjects (17K029).
mRNAseq


description:
17K007
Whole-blood RNA-seq from Healthy Subjects (17K007).
mRNAseq


description:
17K010
Whole-blood RNA-seq from Healthy Subjects (17K010).
mRNAseq


description:
17K013
Whole-blood RNA-seq from Healthy Subjects (17K013).
mRNAseq


description:
17K008
Whole-blood RNA-seq from Healthy Subjects (17K008).
mRNAseq


description:
pS52
Whole-blood RNA-seq from ACLF with septic shock treated (pS52).
mRNAseq

value: ACLF with septic shock treated


description:
03K003
Whole-blood RNA-seq from Healthy Subjects (03K003).
mRNAseq


description:
17K003
Whole-blood RNA-seq from Healthy Subjects (17K003).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (S77)

description:
S77
Whole-blood RNA-seq from preACLF with septic shock (S77).
mRNAseq

value: preACLF with septic shock


description:
S76
Whole-blood RNA-seq from ACLF with septic shock treated (S76).
mRNAseq


description:
S19
Whole-blood RNA-seq from ACLF with septic shock treated (S19).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (pS63)

description:
pS63
Whole-blood RNA-seq from preACLF with septic shock (pS63).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (S16)

description:
S16
Whole-blood RNA-seq from preACLF with septic shock (S16).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (S18)

description:
S18
Whole-blood RNA-seq from preACLF with septic shock (S18).
mRNAseq


description:
pS22
Whole-blood RNA-seq from ACLF with septic shock treated (pS22).
mRNAseq


description:
S15
Whole-blood RNA-seq from ACLF with septic shock treated (S15).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (pS21)

description:
pS21
Whole-blood RNA-seq from preACLF with septic shock (pS21).
mRNAseq


description:
S13
Whole-blood RNA-seq from ACLF with septic shock treated (S13).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (S14)

description:
S14
Whole-blood RNA-seq from preACLF with septic shock (S14).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (S04)

description:
S04
Whole-blood RNA-seq from preACLF with septic shock (S04).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (pS49)

description:
pS49
Whole-blood RNA-seq from preACLF with septic shock (pS49).
mRNAseq


description:
S05
Whole-blood RNA-seq from ACLF with septic shock treated (S05).
mRNAseq


description:
pS60
Whole-blood RNA-seq from ACLF with septic shock treated (pS60).
mRNAseq


description:
S29
Whole-blood RNA-seq from ACLF with septic shock treated (S29).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (S26)

description:
S26
Whole-blood RNA-seq from preACLF with septic shock (S26).
mRNAseq


description:
S06
Whole-blood RNA-seq from ACLF with septic shock treated (S06).
mRNAseq