title: DSP-1001660038290-A-E11, Castration+, DLP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-E11

tag: castration


title: DSP-1001660038290-A-F05, Castration+, DLP, Treatment-, Mouse 347

status: Public on Dec 02 2025

type: SRA

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

description: Library name: DSP-1001660038290-A-F05

library_source: transcriptomic

data_processing:
FASTQ files were processed using the GeoMx NGS Pipeline 2.0.21 (DRAGEN_GeoMx_3.8.4-96)
Supplementary files format and content: *.dcc, digital count conversion file (one per ROI)
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc, probe annotation file for the Nanostring mouse whole transcriptome atlas.
Supplementary files format and content: S25097_20250604T0723_LabWorksheet_forR.xlsx, worksheet produced by the GeoMx NGS pipeline, needed for downstream analysis.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: Prostate

extract_protocol:
Murine prostate samples were harvested and fixed in 4% PFA, then paraffin wax-embedded. 5 µm sections were cut, and baked for 30 min at 60 °C. The nuclei and the epithelial cells were stained using SYTO™ 83 Orange Fluorescent Nucleic Acid Stain (S11364, Thermo Fischer) and the Alexa Fluor 488 anti-mouse CD236 (Ep-CAM) antibody (#AB237384, dilution 1/100, Abcam), respectively. In-situ hybridisation of RNA-directed DNA oligo probes (Nanostring Mouse Whole Transcriptome Atlas) was performed according to the manufacturer’s protocol. For each mouse, the EPCAM+ cells in 5 regions of interest (ROI) in the DLP and 5 in the AP were selected.
Sequencing libraries were generated following the Nanostring GeoMx NGS protocol

tag: tissue

value: Prostate

tag: mouse

tag: lobe

value: DLP

tag: treatment

tag: slide


title: F1436_003, normal, rep1

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

country: USA

institute: PreCyte, Inc.

description:
Library name: 20_05_03_17
library name V2: 20_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

data_processing:
Step 1: RNA-seq data were processed using R packages using a custom workflow using SnakeMake workflow management system for reproducibility. The workflow included adapter read trimming using Trimmomatic (Bolger, Lohse and Usadel, 2014).
Step 2: Sequences were reference aligned to GRCh using STAR (Dobin et al., 2013)
Step 3: Transcripts were quantified at gene-level resolution using the R software package featureCounts (Liao, Smyth and Shi, 2014). Read duplicates were removed by using –ignoreDups setting in R:featureCounts.
Step 4: RNA-seq QC was performed using MultiQC, dupRadar and GATK estimate of library complexity.
Step 5: Next, data for some samples were excluded based on data quality (technical omissions) as indicated in the methods section of the manuscript. Data were omitted for three reasons:  1) RNA quality score (RQS) < 8; 2) low RNA integrity (RIN) <6 and 3) low RNA-seq quality based on the analysis of metrics in Step 4.
Step 6: RNA-seq data from all 24 AD-iCAP batches were merged into a single file and several preprocessing steps were performed in R to detect and correct technical noise in the data to reduce error as described below in the following steps. First, genes were filtered to remove those below the limit of detection. To do this, ERCC controls were removed and a histogram of expression levels for each gene across all patient samples was generated, showing a bimodal curve indicating some genes were below the limit of detection. A threshold was selected to separate the curves corresponding to 35 counts and genes were filtered to remove those below this threshold for greater than 10% of the samples.
Step 7: Next, data for a subset of samples were excluded based on patient class uncertainty. Samples with class uncertainty included those with conflicting amyloid beta (Aβ) pathology from cerebrospinal fluid (CSF) and positron emission tomography (PET) imaging, CSF Aβ₄₂ values near the diagnostic threshold, or absence of Aβ data at the time of blood draw. Codes include: F1, those with conflicting PET and CSF data for presence of AB pathology;  F2, no AB pathology data at time of blood draw or only CSF AB42 data that is close to threshold; F3, longitudinal AB data show transition from AD  to normal pathology; F4, CSF AB42 value is close to threshold of pathogenic levels.
Step 8: Counts were adjusted to correct for GC bias using either full quantile normalization (FQN) or conditional quantile normalization (CQN) determined by the R-EdgeR package.
Step 9: Data were normalized for heteroskedasticity by variance transformation (VST) using the DESeq2 package and batch corrected using the removeBatchEffect function from the R package Limma (Ritchie et al., 2015).
Step 10: For RNA-seq data generated with mouse plasma, differential expression analysis was performed using R-DESeq2 (Love, Huber and Anders, 2014). GSEA analysis was applied using the R-fgsea package. Raw gene-level counts were normalized using the median-of-ratios method, and a negative binomial generalized linear model was fit with design ~ condition. Wald tests were used to evaluate pairwise contrasts between conditions, and p-values were adjusted using the Benjamini–Hochberg method to control the false discovery rate. Genes with FDR < 0.05 were considered differentially expressed.
Assembly: GRCh
Supplementary files format and content: For RNA-seq data generated with human plasma, processed data included are: 1) feature_counts data containing raw feature counts (ADSBIRII.completeData.20180223.rds) and 2) processed/normalized data (as described) (all.cqn.vst_12032024_2.rds). Both are R data files.
Supplementary files format and content: For RNA-seq data generated with mouse plasma, processed data included are: 1) feature_counts data containing  raw feature counts (feature_counts_GEO2.csv and feature_counts_GEO.csv) and  2) results of differential expression analysis ( log2 fold change and FDR values). Both are .csv files with filenames corresponding to experimental condition (e.g. 2wk,29HEMI_NCAR,cqn.csv)

molecule: polyA RNA

organism: Homo sapiens

source_name: iCell Neurons

growth_protocol: Indicator cells were a commercially available, pan-neuronal population of human neurons (glutamatergic and GABAergic) derived from induced pluripotent stem cells (iPSCs) (iCell Neurons from Fujifilm (formerly Cellular Dynamics International (CDI)). Cells were grown according to manufacturer’s instructions with a modification to the culture duration described below. 12-well Eppendorf moat plates were coated with 0.01% poly-L-ornithine solution (Sigma P4957) for 1 h followed by 3.3 µg/mL laminin (Sigma L2020) for 1 h. Next, iCell neurons were thawed and plated a density of 488,875 cells/well in a total volume of 1 mL/well. Medium was exchanged 24 h after plating. Cells were treated after culturing for a total of 48 h.

extract_protocol:
For experiments with human plasma samples, RNA was isolated manually using an RNeasy Micro kit (Qiagen) and for experiments with mouse plasma samples, automated RNA isolation was performed using a MagMax mirVana kit (Invitrogen, A27828) on either a KingFisher Flex or a Kingfisher Duo Prime liquid handling robot as per the manufacturer’s recommendation (Thermo Fisher Scientific). Total RNA was stored at -80°C.
100 - 250 ng of total RNA from each iCAP sample was used for automated library preparation and RNA sequencing (RNA-seq) performed by Covance/Labcorp. Strand-specific library prep was performed with PolyA selection using TruSeq RNA Library Prep kit (Illumina) with unique dual indices (IDT) and resulting DNA samples were pooled and spread evenly across lanes and sequenced on a HiSeq 4000 (Illumina) with paired-end 150 bp reads yielding 20-30 M total reads per sample.

treatment_protocol: Cells were exposed to 5% plasma containing 0.2 mg/mL heparin sodium salt (Stem Cell Technologies, 07980) in PBS for 6 h.

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 013

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: 20240430_5_HTO

city: Copenhagen N

first: NNF CBMR

last: Single-Cell Omics Platform

address: Blegdamsvej 3B

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description:
Library name: 20240430_5_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

library_source: other

data_processing:
Binary base call (BCL) sequence files were demultiplexed into FASTQ files using BCL Convert v4.0.3.
Reads were pseudoaligned using Salmon Alevin v1.10.3 with the flags --read-geometry 2[1-15] --bc-geometry 1[1-16] --umi-geometry 1[17-26] set.
RNA libraries were pseudoaligned to the GENCODE vM33 reference transcriptome, distinguishing between spliced and unspliced transcripts. Alevin-fry v0.9.0 was used to quantify both the RNA and HTO libraries.
Assembly: mm10/hg39
Supplementary files format and content: mtx file with read counts
Supplementary files format and content: barcodes.txt file with 10x droplet barcodes
Supplementary files format and content: features.txt gene IDs
Supplementary files format and content: feature_README.txt containes sample/HTO information and treatment groups for samples
Supplementary files format and content: barcode_data.csv.gz information on individual barcodes
Library strategy: CITE-seq

molecule: protein

source_name: Skeletal muscle

extract_protocol:
The injured part (medial part) of the gastrocnemius muscle as previously confirmed by immunohistochemistry was dissected, minced and transferred to 1.5 ml nonstick tubes containing 1.5 ml of lysis buffer (Pure lysis buffer [L9286-180 ml; Sigma], 0.1% DTT [43816-10 ml; Sigma] and 1% Triton [T1565-1.7 ml; Sigma]). Samples were resuspended for 5 min in an ice box and centrifuged for 5 minutes at 750g and 4°C using rotor swing arms. The supernatant was removed, and the pellet was resuspended in 1 ml nuclei buffer (PBS, 10% BSA (SRE0036-25 ml; Sigma), 1M MgCl₂ [M1028-100 ml; Sigma] and 0.1 % Protector RNase inhibitor 40 U/μl [3335399001; Sigma]). Samples were then filtered through a 40 μm strainer (43-10040-40; pluriSelect) into a 1.5 ml tube and incubated on ice for 10 minutes. After incubation, samples were centrifuged for 5 minutes at 750g and 4°C. The supernatant was removed, and the pellet was resuspended in 100 µl nuclei buffer. Each sample received 1 µl of individual TotalSeq-A antibodies (BioLegend) from 0.5 μg/μl stocks to enable multiplexing. Samples were incubated on ice for 30 minutes. Following this, 1 ml nuclei buffer was added, and the samples were centrifuged for 10 minutes at 1000g and 4°C. The supernatant was discarded, and the pellet was resuspended in 200 µl nuclei buffer for fluorescence-activated cell sorting (FACS) and library preparation.
snRNA-seq was performed by the Single-Cell Omics platform at the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, using the 10x Genomics Chromium single-cell 3′ reagent kit. Libraries were sequenced on an Illumina NovaSeq 6000.

treatment_protocol: Twelve-week-old male C57BL/6NCrl mice were randomly assigned to an injury protocol consisting of 30 electrically-evoked lengthening contractions or to a control procedure (i.e., no lengthening contractions). Experiments started at day 0 with an initial torque measurement immediately followed by the injury or control protocol. Torque production was measured before and 2, 4, 7, 14, and 28 days after injury. Gastrocnemius muscle was collected for single-nucleus RNA sequencing (snRNA-seq) analysis.

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type

value: HTO


title: CD4TILs, Thy1.1, Donor36

city: Durham

first: Charles

middle: A

last: Gersbach

state: NC

address: 101 Science Drive

institute: Duke University

description: Library name: T36 CD4 Thy1.1

data_processing:
Reads were first trimmed using Trimmomatic v0.32 to remove adapters and then aligned to GRCh38 using STAR v2.4.1a aligner
Gene counts were obtained with featureCounts from the subread package (version 1.4.6-p4) using the comprehensive gene annotation in Gencode v22.
Differential expression analysis was determined with DESeq2 where gene counts are fitted into a negative binomial generalized linear model and a Wald test determines significant DEGs
Assembly: GRCh38, Gencode v43
Supplementary files format and content: Processed count file include GeneID (ENSG), chromosome coordinates, strand orientation, length, and aligned counts.

source_name: NSCLC tumor

extract_protocol:
RNA was isolated using Norgen’s Total RNA Purification Plus Kit.
RNA was submitted to Azenta for standard RNA-seq with polyA selection.

value: NSCLC tumor

tag: cell line

value: tumor-infiltrating lymphocytes

tag: cell type

value: ORF lentivirus


title: DSP-1001660038290-A-E10, Castration-, AP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E10

tag: mouse

tag: castration

tag: lobe

value: AP

tag: slide


title: F1435_001, MCI, rep1

description:
Library name: 14_05_03_17
library name V2: 14_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: 20240430_4_HTO

description:
Library name: 20240430_4_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: F1298_001, MCI, rep1

description:
Library name: 12_05_03_17
library name V2: 12_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN


title: NORlungSC490 [scRNA-seq]

city: Pittsburgh

first: Eleanor

last: Valenzi

state: PA

address: 3459 Fifth Avenue

institute: University of Pittsburgh

description: Library name: Sample 31

library_source: transcriptomic single cell

data_processing:
Chromium snRNA-seq and snATAC-seq data produced by the 10X Chromium Platform were processed to generate sample-specific and assay specific fastq files.
Processed reads were then examined by quality metrics, mapped to the hg38 human genome and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger ARC pipeline (10X Genomics).
CellRanger ATAC pipeline (v2.0.0) and CellRanger Arc pipeline (v2.0.2) with h38 human genome reference were used for initial read processing, library quality control, peak calling and cell calling. Samples were filtered for: minimum features>200 and <150,000, peak region fragments>200 and < 150,000, nucleosome signal<10.
Assembly: GrCh38A genome
Supplementary files format and content: feature_bc_matrix.h5
Supplementary files format and content: fragments.tsv.gz
Supplementary files format and content: peak_bc_matrix.h5

molecule: nuclear RNA

source_name: Lung

extract_protocol:
Explanted subpleural peripheral lung tissue was digested to single-cell suspensions using Liberase DL (Roche) and bovine pancreas DNAse I (Sigma-Aldrich) as previously described in PMID: 33859634.
Experimental procedures followed established techniques using the Chromium Single Cell 3’ Library V2 kit, the Chromium Single Cell ATAC kit, or the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit.

tag: tissue

value: Lung

tag: health status

value: Healthy Control


title: F1455_003, normal, rep1

description:
Library name: 13_05_03_17
library name V2: 13_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: CD4TILs, RELB, Donor36

description: Library name: T36 CD4 RELB

tag: cell line

tag: cell type

tag: treatment


title: NORlungSC486 [scRNA-seq]

description: Library name: Sample 30


title: 20240430_3_HTO

description:
Library name: 20240430_3_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: date of_reaction

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: DSP-1001660038290-A-E09, Castration-, AP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E09

tag: tissue

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: slide


title: DSP-1001660038290-A-E07, Castration-, AP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E07


title: DSP-1001660038290-A-E08, Castration-, AP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E08


title: DSP-1001660038290-A-F02, Castration+, DLP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F02

value: DLP


title: 20240430_2_HTO

description:
Library name: 20240430_2_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads


title: F1428_001, preAD, rep1

description:
Library name: 16_05_03_17
library name V2: 16_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 013

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240429_5_mRNA

description:
Library name: 20240429_5_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: F1186_002, normal, rep1

description:
Library name: 1_05_03_17
library name V2: 01_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: #N/A

value: #REF!

tag: rna-seq date

value: pass


title: DSP-1001660038290-A-E05, Castration-, AP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E05

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: slide


title: 16419_001, preAD, rep1

description:
Library name: 9_03_29_17
library name V2: 09_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: Aim 2 Batch 012

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240430_1_HTO

description:
Library name: 20240430_1_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type

value: HTO


title: 20240429_3_mRNA

description:
Library name: 20240429_3_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: tissue


title: CD8TILs, RELB, Donor36

description: Library name: T36 CD8 RELB

value: NSCLC tumor

tag: cell line

value: tumor-infiltrating lymphocytes

tag: cell type

value: ORF lentivirus


title: DSP-1001660038290-A-E06, Castration-, AP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E06

value: Prostate

tag: mouse

tag: castration

tag: lobe

value: AP

tag: slide


title: F1321_001, MCI, rep1

description:
Library name: 10_05_03_17
library name V2: 10_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: low RIN


title: NORlungSC421 [scRNA-seq]

description: Library name: Sample 26

tag: tissue

value: Lung

tag: health status

value: Healthy Control


title: 62911_001, normal, rep1

description:
Library name: 8_03_29_17
library name V2: 08_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

value: human

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: NORlungSC422 [scRNA-seq]

description: Library name: Sample 27


title: 20240429_2_mRNA

description:
Library name: 20240429_2_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

value: Skeletal muscle

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: DSP-1001660038290-A-E04, Castration-, AP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E04

tag: mouse

tag: castration

tag: lobe

tag: slide


title: NORlungSC466 [scRNA-seq]

description: Library name: Sample 29

tag: tissue


title: DSP-1001660038290-A-E03, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E03

value: DLP


title: NORlungSC398 [scRNA-seq]

description: Library name: Sample 25

tag: health status


title: SSClungSC449 [scRNA-seq]

description: Library name: Sample 24

value: Systemic sclerosis


title: 20240429_1_mRNA

description:
Library name: 20240429_1_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Mixed sample (day 0 - 14)

value: frozen


title: 20240425_C_HTO

description:
Library name: 20240425_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: C

value: HTO


title: F132_005, normal, rep1

description:
Library name: 11_05_03_17
library name V2: 11_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 013

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: 65270_001, preAD, rep1

description:
Library name: 7_03_29_17
library name V2: 07_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

value: Aim 2 Batch 012

value: #REF!

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-E01, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E01

tag: tissue

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: DSP-1001660038290-A-E02, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-E02


title: SSClungSC430 [scRNA-seq]

description: Library name: Sample 23

value: Lung

tag: health status


title: NORlungSC453 [scRNA-seq]

description: Library name: Sample 28

value: Healthy Control


title: 64387_001, preAD, rep1

description:
Library name: 5_03_29_17
library name V2: 05_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: #N/A


title: 20240429_4_mRNA

description:
Library name: 20240429_4_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

value: Skeletal muscle

tag: date of_reaction

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: 20240425_B_HTO

description:
Library name: 20240425_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: tissue

tag: treatment

value: Mixed sample (day 0 - 14)

value: B


title: SSClungSC381  [scRNA-seq]

description: Library name: Sample 20

tag: health status

value: Systemic sclerosis


title: DSP-1001660038290-A-D11, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-D11

tag: mouse

tag: castration

tag: lobe

value: DLP

tag: slide


title: DSP-1001660038290-A-D12, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-D12


title: SSClungSC395  [scRNA-seq]

description: Library name: Sample 21


title: 65158_001, MCI, rep1

description:
Library name: 4_03_29_17
library name V2: 04_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: SSClungSC402 [scRNA-seq]

description: Library name: Sample 22

tag: tissue

tag: health status


title: 24915_001, MCI, rep1

description:
Library name: 3_03_29_17
library name V2: 03_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma thaw_number

tag: icap cell_culture_plate_number


title: DSP-1001660038290-A-D10, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-D10

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: reference_001, reference, rep35

description:
Library name: 23_03_29_17
library name V2: 23_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: reference


title: reference_001, reference, rep36

description:
Library name: 24_03_29_17
library name V2: 24_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: SSClungSC369 [scRNA-seq]

description: Library name: Sample 19

tag: tissue

tag: health status


title: 20240425_B_mRNA

description:
Library name: 20240425_B_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type


title: 64017_001, normal, rep1

description:
Library name: 6_03_29_17
library name V2: 06_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: pass


title: 20240425_A_HTO

description:
Library name: 20240425_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

value: A

value: HTO


title: DSP-1001660038290-A-D08, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-D08

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: slide


title: reference_001, reference, rep34

description:
Library name: 22_03_29_17
library name V2: 22_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

value: Aim 2 Batch 012

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: reference_001, reference, rep33

description:
Library name: 21_03_29_17
library name V2: 21_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: DSP-1001660038290-A-D07, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-D07

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: 20240424_B_HTO

description:
Library name: 20240424_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: date of_reaction

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: DSP-1001660038290-A-D06, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-D06


title: SC336

description: Library name: Sample 17

library_source: genomic single cell

molecule: genomic DNA

value: Lung

tag: health status


title: SC346

description: Library name: Sample 18


title: 20240425_C_mRNA

description:
Library name: 20240425_C_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: C


title: SC316

description: Library name: Sample 16

value: Healthy Control


title: DSP-1001660038290-A-D09, Castration-, DLP, Treatment-, Mouse 416

description: Library name: DSP-1001660038290-A-D09


title: reference_001, reference, rep32

description:
Library name: 20_03_29_17
library name V2: 20_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

value: #N/A

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240424_A_HTO

description:
Library name: 20240424_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: SC324

description: Library name: Sample 15

tag: health status


title: DSP-1001660038290-A-D05, Castration-, AP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-D05

tag: mouse

tag: castration

tag: lobe

value: AP

tag: slide


title: reference_001, reference, rep31

description:
Library name: 2_03_29_17
library name V2: 02_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: reference

tag: sequencing plate_name

value: #REF!


title: DSP-1001660038290-A-D04, Castration-, AP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-D04

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment


title: 20240425_A_mRNA

description:
Library name: 20240425_A_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: batch within_date

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: reference_001, reference, rep30

description:
Library name: 19_03_29_17
library name V2: 19_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240424_C_mRNA

description:
Library name: 20240424_C_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state


title: 20240424_B_mRNA

description:
Library name: 20240424_B_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: B

tag: included samples

tag: included htos

tag: library type


title: NORlungSC490 [scATAC-seq]

description: Library name: Sample 13

tag: health status


title: reference_001, reference, rep29

description:
Library name: 18_03_29_17B
library name V2: 18_03_29_17B
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: DSP-1001660038290-A-D02, Castration-, AP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-D02

tag: tissue

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: 20240424_A_mRNA

description:
Library name: 20240424_A_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: batch within_date

value: A

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: 20240424_C_HTO

description:
Library name: 20240424_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: HTO


title: DSP-1001660038290-A-D03, Castration-, AP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-D03


title: reference_001, reference, rep28

description:
Library name: 18_03_29_17
library name V2: 18_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 012

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-D01, Castration-, AP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-D01

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: NORlungSC486 [scATAC-seq]

description: Library name: Sample 12

value: Lung

tag: health status

value: Healthy Control


title: NORlungSC466 [scATAC-seq]

description: Library name: Sample 11


title: reference_001, reference, rep27

description:
Library name: 17_03_29_17
library name V2: 17_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

value: #N/A


title: 20240416_C_HTO

description:
Library name: 20240416_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

value: Skeletal muscle

tag: date of_reaction

value: Mixed sample (day 0 - 14)

tag: batch within_date

value: C

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: DSP-1001660038290-A-C12, Castration-, DLP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-C12

tag: tissue

tag: mouse

tag: castration

tag: lobe

value: DLP

tag: treatment

tag: slide


title: 20240416_A_HTO

description:
Library name: 20240416_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: frozen


title: DSP-1001660038290-A-C11, Castration-, DLP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-C11


title: NORlungSC422 [scATAC-seq]

description: Library name: Sample 9

tag: health status


title: reference_001, reference, rep25

description:
Library name: 16_03_29_17
library name V2: 16_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

value: reference

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240416_C_mRNA

description:
Library name: 20240416_C_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: DSP-1001660038290-A-C10, Castration-, DLP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-C10

tag: mouse

tag: castration

tag: lobe

tag: slide


title: NORlungSC421 [scATAC-seq]

description: Library name: Sample 8

tag: health status


title: 20240416_B_mRNA

description:
Library name: 20240416_B_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: B


title: DSP-1001660038290-A-C09, Castration-, DLP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-C09

value: Prostate


title: SC294

description: Library name: Sample 14

value: Systemic sclerosis


title: NORlungSC398 [scATAC-seq]

description: Library name: Sample 7


title: DSP-1001660038290-A-C08, Castration-, DLP, Treatment-, Mouse 455

description: Library name: DSP-1001660038290-A-C08


title: SSClungSC449 [scATAC-seq]

description: Library name: Sample 6


title: 20240416_B_HTO

description:
Library name: 20240416_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: HTO


title: SSClungSC402 [scATAC-seq]

description: Library name: Sample 4


title: DSP-1001660038290-A-C07, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-C07

value: AP


title: reference_001, reference, rep21

description:
Library name: 13_03_29_17
library name V2: 13_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 012

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: reference_001, reference, rep26

description:
Library name: 16_03_29_17B
library name V2: 16_03_29_17B
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

value: #REF!

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-C06, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-C06

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: NORlungSC453 [scATAC-seq]

description: Library name: Sample 10

value: Lung

tag: health status

value: Healthy Control


title: SSClungSC430 [scATAC-seq]

description: Library name: Sample 5


title: reference_001, reference, rep23

description:
Library name: 14_03_29_17
library name V2: 14_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

value: #N/A


title: reference_001, reference, rep22

description:
Library name: 13_03_29_17B
library name V2: 13_03_29_17B
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: 20240415_B_HTO

description:
Library name: 20240415_B_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: DSP-1001660038290-A-C05, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-C05

tag: mouse

tag: castration

tag: lobe

tag: slide


title: 20240415_A_HTO

description:
Library name: 20240415_A_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: A

value: frozen


title: 65777_001, MCI, rep1

description:
Library name: 12_03_29_17
library name V2: 12_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: SSClungSC395  [scATAC-seq]

description: Library name: Sample 3

tag: tissue

tag: health status


title: 64555_001, preAD, rep1

description:
Library name: 11_03_29_17
library name V2: 11_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: 20240415_C_mRNA

description:
Library name: 20240415_C_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: treatment

tag: batch within_date

value: C

tag: sample state

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: reference_001, reference, rep24

description:
Library name: 15_03_29_17
library name V2: 15_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: reference


title: DSP-1001660038290-A-C04, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-C04

tag: tissue

value: Prostate

tag: mouse

tag: castration

tag: lobe

value: AP

tag: treatment

tag: slide


title: SSClungSC381  [scATAC-seq]

description: Library name: Sample 2

tag: health status

value: Systemic sclerosis


title: 20240415_B_mRNA

description:
Library name: 20240415_B_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: batch within_date

value: B

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: SSClungSC369 [scATAC-seq]

description: Library name: Sample 1


title: DSP-1001660038290-A-C03, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-C03


title: 65195_001, normal, rep1

description:
Library name: 1_03_29_17
library name V2: 01_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 012

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 20240416_A_mRNA

description:
Library name: 20240416_A_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state

tag: included samples

tag: included htos


title: 20240415_C_HTO

description:
Library name: 20240415_C_HTO
Hashtag derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

tag: library type

value: HTO


title: 20240415_A_mRNA

description:
Library name: 20240415_A_10X
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Skeletal muscle


title: DSP-1001660038290-A-C02, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-C02

tag: mouse

tag: castration

tag: lobe

tag: slide


title: DSP-1001660038290-A-C01, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-C01


title: ACBQ248_001, normal, rep1

description:
Library name: 22_03_22_17
library name V2: 22_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 011

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A


title: ACBQ0286_001, MCI, rep1

description:
Library name: 21_03_22_17
library name V2: 21_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: TGF-b-TET3

city: Nanjing

first: yujia

last: xue

address: Longmian Avenue 639

country: China

institute: China Pharmaceutical University

description: Library name: sample 1

library_source: genomic

data_processing:
Removing reads containing adapters;
Removing reads containing more than 10% of unknown nucleotides (N); Removing reads containing adapters;Removing reads containing more than 10% of unknown nucleotides (N); Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
BWA (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak B WA[1] (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak  scanning.
Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics. It is based on the fact that a high quality IP-seq experiment produces significant clustering of enriched DNA sequence tags at locations bound by the protein of interest, and that the sequence tag density accumulates on forward and reverse strands centered around the binding site. SPP R package was used to calculate the correlation between forward and reverse strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.
MACS (version: macs14)( -p 1e-3 -m 10,30) is a computational method that was designed to identify read-enriched regions from ChIP-seq data. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value<1e-5. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number were displayed.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Heart

extract_protocol:
ConA Beads Pro intended for nucleus binding and DNA Extract Beads Pro intended for DNA extraction by using Vazyme Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro TD904
VAHTS DNA Clean Beads (Vazyme #N411) is used for library purification.10 ng of DNA was used as startnig material for input amout. Libraries were amplified using 10 cycles on thr thermocycle.

tag: tissue

value: Heart

tag: cell line

value: Fibroblast

tag: treatment

value: TGF-b


title: OE2

city: Shanghai

first: Jun

last: Li

state: None Selected

institute: Shanghai Jiao Tong University School of Medicine affiliated Ruijin Hospital

description: Library name: Sample 11

data_processing:
we analyzed the changes in mRNA expression levels in UBE2S-treated cells through RNA sequencing. This approach allowed us to determine the activation of relevant signaling pathways within the cells.
Assembly: hg19
Supplementary files format and content: Tab-separated values files

source_name: Colon

extract_protocol:
we analyzed the changes in mRNA expression levels in UBE2S-treated cells through RNA sequencing. This approach allowed us to determine the activation of relevant signaling pathways within the cells.
RKO is a poorly differentiated colon carcinoma cell line developed by Michael Brattain.

value: Colon

value: RKO

tag: cell type

value: epithelial cell


title: DSP-1001660038290-A-B12, Castration+, AP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-B12

value: Prostate

tag: mouse

tag: castration

tag: lobe

value: AP

tag: slide


title: Vec3

address: Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 9


title: AC119_001, preAD, rep1

description:
Library name: 20_03_22_17
library name V2: 20_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: pass


title: Campylobacter jejuni puls defined consortium of 13 bacterial isolates mouse colon

city: Gainesville

first: Christian

last: Jobin

state: Florida

department: Medicine

institute: University of Florida

description:
Library name: C13CJ
Formalin-fixed paraffin-embedded (FFPE) Spatial Transcriptomics D1_4_1

data_processing:
Data were processed using 10x Genomics Space Ranger with mm10 reference genome
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz: gene expression count data stored in Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: colon

extract_protocol:
FFPE blocks were faced at 10 μm to expose the tissue, then sectioned at 5 um thickness using a microtome.
Spatial Transcriptomics  libraries were prepared according to the 10x Genomics Visium protocols

value: colon

tag: genotype


title: DSP-1001660038290-A-B10, Castration+, DLP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-B10

tag: tissue

value: DLP


title: Germ free mouse colon

description:
Library name: GF
Formalin-fixed paraffin-embedded (FFPE) Spatial Transcriptomics A1_3_1

value: Germ free


title: Defined consortium of 13 bacterial isolates mouse colon

description:
Library name: C13
Formalin-fixed paraffin-embedded (FFPE) Spatial Transcriptomics A1_1_1

value: defined consortium of 13 bacterial isolates


title: Vec2

description: Library name: Sample 8

tag: cell line


title: DSP-1001660038290-A-B11, Castration+, DLP, Treatment-, Mouse 328

description: Library name: DSP-1001660038290-A-B11

tag: treatment


title: 25711_001, MCI, rep1

description:
Library name: 10_03_29_17
library name V2: 10_03_29_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

value: 5% plasma, 6 h

value: human

value: Aim 2 Batch 012

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: ACBCHC 298_001, MCI, rep1

description:
Library name: 18_03_22_17
library name V2: 18_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 011

value: #N/A


title: AC243_001, preAD, rep1

description:
Library name: 19_03_22_17
library name V2: 19_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number


title: Vec1

description: Library name: Sample 7

tag: tissue

tag: cell line

tag: cell type


title: Hippocampus WT female mouse D51 low extinction level

city: New Haven

first: In-Jung

last: Kim

state: CT

address: 300 George Street

department: Ophthalmology

institute: Yale University

description:
Library name: Sample 12
D_5-1_009_184_S11
processed_file_CD-all-genes_DEseq2.txt
processed_file_CD_tpm_values_all_samples.txt

data_processing:
The samples were sequenced on an Illumina NovaSeq S2.
Low-quality base calls, sequences with low-complexity tails, and adaptor sequences were removed using fqTrim2.py (Yale Center for Genome Analysis). Trimmed paired-end (PE) reads were aligned to the mouse genome (GRCm38.p5) using Tophat2/Bowtie2 (Langmead and Salzberg, 2012). Raw read counts per gene were calculated using HTSeq (version v.0.6.1p1) and expression levels in transcripts per million (TPM) were estimated by StringTie (version 1.3.3b) on GENCODE vM15 annotation (Anders et al., 2015; Pertea et al., 2015). Differential expression analysis was performed using DESeq2, which produced fold change and statistical significance of changes between samples (Love et al., 2014).
Assembly: GRCm38.p5 (mm10)
Supplementary files format and content: DEseq2
Supplementary files format and content: tab-delimited text files includeTPM values for each Sample

source_name: Hippocampus

extract_protocol:
Hippocampi were dissected, snap-frozen on dry ice and stored at -80C. Total RNA was prepared using the RNeasy PowerLyzer Tissue & Cell kit (Qiagen). RNA quality was assessed by estimating the A260/A280 and A260/A230 ratios bynanodrop. RNA integrity was determined by running Agilent Bioanalyzer 2100 gel
1 µg of total RNA per sample was enriched for polyA RNA and converted into libraries using the Kapa mRNA Hyper Prep Kit for Illumina Platforms (KAPA Biosystems)

value: Hippocampus

tag: strain

tag: genotype

value: Wild-type

tag: age

value: 18 weeks

tag: Sex

value: female

tag: sample group

value: low extinction level


title: AC746_001, preAD, rep1

description:
Library name: 17_03_22_17
library name V2: 17_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Hippocampus WT female mouse D22 low extinction level

description:
Library name: Sample 11
D_2-2_305_272_S12
processed_file_CD-all-genes_DEseq2.txt
processed_file_CD_tpm_values_all_samples.txt


title: DSP-1001660038290-A-B08, Castration-, AP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B08

value: Prostate

tag: mouse

tag: castration

tag: lobe

value: AP

tag: treatment

tag: slide


title: SH3

description: Library name: Sample 6

tag: tissue

value: Colon

tag: cell line

value: RKO

tag: cell type

value: epithelial cell


title: AC163_001, MCI, rep1

description:
Library name: 16_03_22_17
library name V2: 16_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: pass


title: OE3

description: Library name: Sample 12


title: Hippocampus WT female mouse D73 low extinction level

description:
Library name: Sample 10
D_7-3_021_172_S10
processed_file_CD-all-genes_DEseq2.txt
processed_file_CD_tpm_values_all_samples.txt

tag: strain

tag: genotype

tag: age

tag: Sex

tag: sample group


title: DSP-1001660038290-A-B07, Castration-, AP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B07

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: OE1

description: Library name: Sample 10

tag: tissue

tag: cell line

tag: cell type


title: SH2

description: Library name: Sample 5


title: AC075_001, normal, rep1

description:
Library name: 15_03_22_17
library name V2: 15_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: reference_001, reference, rep20

description:
Library name: 14_03_22_17
library name V2: 14_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: reference


title: DSP-1001660038290-A-B06, Castration-, AP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B06

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: Hippocampus WT female mouse C33 high extinction level

description:
Library name: Sample 8
C_3-3_033_160_S9
processed_file_CD-all-genes_DEseq2.txt
processed_file_CD_tpm_values_all_samples.txt

tag: strain

tag: genotype

tag: age

tag: Sex

tag: sample group

value: high extinction level


title: SH1

description: Library name: Sample 4

tag: cell line

tag: cell type


title: Hippocampus WT female mouse C44 high extinction level

description:
Library name: Sample 9
C_4-4_045_148_S8
processed_file_CD-all-genes_DEseq2.txt
processed_file_CD_tpm_values_all_samples.txt


title: NC3

description: Library name: Sample 3


title: AC112_001, normal, rep1

description:
Library name: 13_03_22_17
library name V2: 13_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 011

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-B09, Castration-, AP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B09

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: AC005_001, preAD, rep1

description:
Library name: 12_03_22_17
library name V2: 12_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: #N/A


title: DSP-1001660038290-A-B05, Castration-, AP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B05


title: Hippocampus WT female mouse C34 high extinction level

description:
Library name: Sample 7
C_3-4_057_136_S7
processed_file_CD-all-genes_DEseq2.txt
processed_file_CD_tpm_values_all_samples.txt

value: Hippocampus

tag: strain

tag: genotype

value: Wild-type

tag: age

tag: Sex

tag: sample group


title: NC2

description: Library name: Sample 2

tag: tissue

tag: cell line


title: DSP-1001660038290-A-B02, Castration-, DLP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B02

tag: mouse

tag: castration

tag: lobe

value: DLP


title: DSP-1001660038290-A-B03, Castration-, DLP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B03

tag: treatment

tag: slide


title: NC1

description: Library name: Sample 1

tag: cell type


title: Hippocampus WT male mouse B73 low extinction level

description:
Library name: Sample 6
B_7-3_081_112_S5
processed_file_AB-all-genes_DEseq2.txt
processed_file_AB_tpm_values_all_samples.txt

value: 18 weeks

value: male

value: low extinction level


title: AC815_001, preAD, rep1

description:
Library name: 10_03_22_17
library name V2: 10_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BQ6146_001, normal, rep1

description:
Library name: 11_03_22_17
library name V2: 11_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number


title: shRAB30-DT rep3

city: Shenzhen City

first: lantian

last: zhang

state: Guangdong Province

address: Haiyuan Road, Futian District

institute: The University of Hong Kong-Shenzhen Hospital

description: Library name: Sample 6

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data of fastq format were firstly processed through fastp software. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: hg38
Supplementary files format and content: A CSV file contains the TPM values for all the samples.

extract_protocol:
RNA of Control and RAB-30DT knockdown SK-Hep-1 cells group was extracted by Eastep® Super Total RNA Extraction Kit(Promega).3ug of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell line

tag: genotype

value: RAB30-DT knockdown


title: shRAB30-DT rep2

description: Library name: Sample 5


title: DSP-1001660038290-A-B01, Castration-, DLP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B01

tag: tissue

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: Hippocampus WT male mouse B21 low extinction level

description:
Library name: Sample 4
B_2-1_093_100_S4
processed_file_AB-all-genes_DEseq2.txt
processed_file_AB_tpm_values_all_samples.txt

tag: strain

tag: age

tag: Sex

tag: sample group


title: Hippocampus WT male mouse A84 high extinction level

description:
Library name: Sample 3
A_8-4_010_183_S3
processed_file_AB-all-genes_DEseq2.txt
processed_file_AB_tpm_values_all_samples.txt


title: Hippocampus WT male mouse B33 low extinction level

description:
Library name: Sample 5
B_3-3_069_124_S6
processed_file_AB-all-genes_DEseq2.txt
processed_file_AB_tpm_values_all_samples.txt


title: AXACBQ0383_001, MCI, rep1

description:
Library name: 09_03_22_17
library name V2: 09_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: shRAB30-DT rep1

description: Library name: Sample 4

tag: cell line

tag: genotype


title: DSP-1001660038290-A-A12, Castration-, DLP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-A12

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: AC508_001, preAD, rep1

description:
Library name: 08_03_22_17
library name V2: 08_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Hippocampus WT male mouse A15 high extinction level

description:
Library name: Sample 2
A_1-5_034_159_S1
processed_file_AB-all-genes_DEseq2.txt
processed_file_AB_tpm_values_all_samples.txt

tag: strain

tag: age

tag: Sex

tag: sample group


title: AC074_001, normal, rep1

description:
Library name: 07_03_22_17
library name V2: 07_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: Hippocampus WT male mouse A35 high extinction level

description:
Library name: Sample 1
A_3-5_022_171_S2
processed_file_AB-all-genes_DEseq2.txt
processed_file_AB_tpm_values_all_samples.txt

tag: tissue

tag: genotype


title: DSP-1001660038290-A-A10, Castration-, AP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A10

tag: mouse

tag: castration

tag: lobe

value: AP

tag: treatment

tag: slide


title: DSP-1001660038290-A-A11, Castration-, AP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A11


title: shControl rep2

description: Library name: Sample 2

tag: cell line

value: WT


title: shControl rep3

description: Library name: Sample 3


title: DSP-1001660038290-A-A09, Castration-, AP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A09


title: SARS-CoV-2 infection-8

city: Xi’an

first: Ping

last: Zhu

address: Changle Xi Road

institute: Fourth Military Medical University

description:
Library name: hCD147 mice_8
10x genomics

data_processing:
For rhesus macaques data, spaceranegr (v1.2.1) was used to process spatial sequencing data for mapping to reference genome. SCTransform function in Seurat (v4.1.0) was used to process the gene expression matrix. The pathologists preliminarily divided the pathological areas of the sections in virus-infected group, integrated the matrix and gene expression matrix after stlearn sorted out the H&E sections, and then performed dimensionality reduction clustering, which was defined according to the data of pathological spots in each cluster.
For mouse data, spaceranegr (v1.3.1) was used to process mouse spatial sequencing data for mapping to reference genome. SCTransform function in Seurat (v4.1.0) was used to process the gene expression matrix. Spots with SARS-CoV-2 genes was defined as infected spots; otherwise, defined as uninfected spots. On this basis, the two uninfected positions closest to the infected positions are defined as border positions. runRCTD function in spacexr (v2.2.1) was used for assigning single cell types to spatial transcriptomics spots and defining a spot where the proportion of a certain cell type exceeds 50% as that cell type.
Assembly: macaque reference Ensembl_release105 and mouse reference Ensembl_release111
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: tissue images.gz
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
The spatial transcriptome sequencing was performed by Genedenovo Biotechnology Co., Ltd. The lung tissues of rhesus macaques (Healthy, n=4; Ctrl, n=4; MPZ, n=4; 3E8, n=4; MPZ+3E8, n=4; at 7dpi) and virus-infected hCD147 mice (n=4; at 3dpi) were used to perform spatial transcriptome sequencing. The tissues were embedded in the OCT-filled mold and cut into slices by cryo-sectional technology. Subsequently, the samples were barcoded through 10× Genomics Platform using Visium Spatial Tissue Optimization Reagent Kit and Slide Kit (PN-1000192, PN-1000191, 10× Genomics), Visium Spatial Gene Expression Reagent Kit and Slide Kit (PN-1000189, PN-1000188, 10× Genomics), Library Construction Kit (PN-1000196, 10× Genomics), and Dual Index Kit (PN-1000215, 10× Genomics). Each sequencing library was sequenced using Illumina sequencing platform.
10× Genomics Visium Spatial

value: lung

tag: age

value: 3 months

tag: Sex

value: female

tag: virus

value: SARS-CoV-2 (Beta strain)


title: AC120_001, MCI, rep1

description:
Library name: 05_03_22_17
library name V2: 05_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: SARS-CoV-2 infection-7

description:
Library name: hCD147 mice_7
10x genomics

tag: tissue


title: DSP-1001660038290-A-A08, Castration-, AP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A08

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: AC085_001, normal, rep1

description:
Library name: 06_03_22_17
library name V2: 06_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

value: Aim 2 Batch 011

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date


title: shControl rep1

description: Library name: Sample 1

tag: cell line

tag: genotype


title: Non-senescent BPH epithelial rep 3

city: Beijing

first: Zheng

state: Beijing

address: No. 8 Xishiku Street, Xicheng District

institute: Peking University First hospital

description:
Library name: C3
Non-senescent control sample 3 RNA-seq

data_processing:
Raw reads were filtered for quality and trimmed for adapters using fastp.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner.
Gene-level quantification was performed using featureCounts.
Expression normalization and differential analysis were carried out using DESeq2.
Normalized expression values were converted into FPKM format for each sample.
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited text file including gene-level raw counts (featureCounts output) for each sample.
Supplementary files format and content: CSV file containing FPKM values for each sample.

source_name: prostate

growth_protocol: Primary epithelial cells were microdissected from frozen human BPH tissue sections; no in vitro culture was performed.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA quality was assessed using NanoDrop and Bioanalyzer.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Poly(A)+ RNA was purified, fragmented, and reverse-transcribed. Libraries were adapter-ligated, PCR-amplified, and quality-checked.

treatment_protocol: SA-β-gal staining was performed on adjacent sections to classify regions as senescent or non-senescent prior to microdissection.

value: prostate

value: epithelial cell

tag: batch


title: Non-senescent BPH epithelial rep 2

description:
Library name: C2
Non-senescent control sample 2 RNA-seq


title: DSP-1001660038290-A-B04, Castration-, DLP, Treatment-, Mouse 481

description: Library name: DSP-1001660038290-A-B04

value: DLP


title: SARS-CoV-2 infection-6

description:
Library name: hCD147 mice_6
10x genomics

tag: age

tag: Sex

tag: virus


title: AC113_001, MCI, rep1

description:
Library name: 04_03_22_17
library name V2: 04_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-A06, Castration-, DLP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A06

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: AC167_001, normal, rep1

description:
Library name: 03_03_22_17
library name V2: 03_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: DSP-1001660038290-A-A07, Castration-, AP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A07


title: SARS-CoV-2 infection-8 [scRNA-seq]

description:
Library name: hCD147 mice_8
SeekGene

data_processing:
Cellranger (v7.1.0) was used to process scRNA-seq data with macaque reference Ensembl_release105. Seurat (v4.1.0) was used for processing expression matrices. The cells with less than 200 and more than 5000 genes were filtered. Cells with less than 25000 nUMI detected and less than 10 percent of detected reads coming from mitochondrial genes were finally retained. DoubletFinder (v2.0.3) and harmony (v0.1.0) was set to default parameter.
ScRNA-seq data was aligned and quantified using Seeksoultools (v1.2.0) and STAR (v2.7.1a) against the Ensembl_release111 added with SARS-CoV-2 Beta reference genome. The mouse CD147 sequence in the reference genome was replaced with human CD147 sequence. Raw counts were then used for downstream analysis. Seurat (v4.1.0) was used to process the gene expression matrix. Cells with SARS-CoV-2 genes detected were labeled as infected cells. Cells with less than 200 and more than 5600 genes were filtered. Cells with less than 12000 nUMI detected and less than 33 percent of detected reads coming from mitochondrial genes were finally kept. To remove the deviation of double cells, DoubletFinder (v2.0.3) was used with pN parameter of 0.25 and nExp parameter of 4×10-6. The remaining cells were then used for gene expression matrix logarithmic normalization and scaling. To integrate cells into a shared space from different datasets for unsupervised clustering, harmony (v0.1.0) was used to correct the batch effect by default parameters.
Assembly: macaque reference Ensembl_release105 and mouse reference Ensembl_release111
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The scRNA-seq was performed by Genedenovo Biotechnology Co., Ltd. The lung tissues of rhesus macaques (Healthy, n=4; Ctrl, n=4; MPZ, n=4; 3E8, n=4; MPZ+3E8, n=4; at 7dpi) and virus-infected hCD147 mice (n=4; at 3dpi) were cut into 1–2 mm3 pieces in DPBS buffer and digested with collagenase I and DNase I at 37°C for 30–60 min with persistent shaking every 10 min. The digested tissues were then passed through a 70 μm mesh filter, and the cell suspension was centrifuged at 4 °C for 5 min (350 g). The cell pellet was suspended in red blood cell removal solution at 4 °C for 10 min and then resuspended in DPBS buffer (0.04% BSA and 0.01 mM EDTA) after being washed by DPBS buffer. Following the depletion of the dead cells, the cell suspensions were directly performed for scRNA-seq according to the manufacturer's instructions.
For the samples from rhesus macaques, the cells in single-cell suspension were counted by trypan blue dye at a proper concentration of 1000–2000 cells/μL. Single-cell suspensions were loaded onto 10× Genomics Chromium v3.1 system to generate single-cell Gel Beads-In-Emulsions (GEMs), where all generated full-length cDNA share a common 10× barcode. Then, GEMs were disrupted and cDNA was amplified via PCR. The quality control of the sequencing libraries was performed by High Sensitivity DNA assay Kit (5067-4626, Agilent Technologies), and the concentration quantification was conducted using ABI StepOnePlus Real-Time PCR System. Finally, the sequencing was performed on Illumina sequencing platform in PE150 mode. For the samples from hCD147 mice, cell suspensions were barcoded through the SeekOne single cell platform.

tag: age

tag: Sex

tag: virus


title: reference_001, reference, rep19

description:
Library name: 02_03_22_17
library name V2: 02_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: reference

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-A05, Castration-, DLP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A05

tag: tissue

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: SARS-CoV-2 infection-5

description:
Library name: hCD147 mice_5
10x genomics

tag: age

tag: Sex

tag: virus


title: Non-senescent BPH epithelial rep 1

description:
Library name: C1
Non-senescent control sample 1 RNA-seq

tag: cell type

tag: batch


title: Senescent BPH epithelial cells rep 3

description:
Library name: T3
Senescent sample 3 RNA-seq


title: SARS-CoV-2 infection-7 [scRNA-seq]

description:
Library name: hCD147 mice_7
SeekGene


title: DSP-1001660038290-A-A04, Castration-, DLP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A04


title: DSP-1001660038290-A-A03, Castration-, DLP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A03


title: Senescent BPH epithelial cells rep 2

description:
Library name: T2
Senescent sample 2 RNA-seq


title: SARS-CoV-2 infection-6 [scRNA-seq]

description:
Library name: hCD147 mice_6
SeekGene


title: Senescent BPH epithelial cells rep 1

description:
Library name: T1
Senescent sample 1 RNA-seq


title: 64138_001, normal, rep1

description:
Library name: 8_03_08_17
library name V2: 08_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 010

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: BPH + rmCXCL13 + anti-CD4 mouse 5

description:
Library name: CXCL13_CD4_5
BPH mouse treated with rmCXCL13 + anti-CD4 antibody

data_processing:
Raw reads were quality-checked using FastQC.
Adapter sequences and low-quality bases were removed using fastp.
Clean reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2.
Gene-level read counts were quantified using featureCounts.
Gene expression normalization was performed using TPM or FPKM depending on downstream analysis.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file containing normalized expression values (FPKM) per gene per sample.
Supplementary files format and content: Matrix file includes gene identifiers (Ensembl ID or gene symbol) and expression values for all biological replicates.

growth_protocol: Mice were maintained under standard specific pathogen-free (SPF) laboratory conditions with free access to food and water.

extract_protocol:
Total RNA was extracted from prostate tissue using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity was confirmed using an Agilent Bioanalyzer.
RNA libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit. mRNA was enriched with poly(A) selection, fragmented, reverse-transcribed, ligated to adapters, and PCR-amplified. Library quality was assessed using Bioanalyzer.

treatment_protocol: Mice were treated according to group assignments: control, BPH model induction, rmCXCL13 treatment, and rmCXCL13 combined with anti-CD4 antibody treatment.

tag: tissue

tag: strain

value: BALB/c

tag: treatment

value: rmCXCL13 + anti-CD4 Ab


title: 67003_001, normal, rep1

description:
Library name: 6_03_08_17
library name V2: 06_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: RNASeq QC


title: 66010_001, MCI, rep1

description:
Library name: 7_03_08_17
library name V2: 07_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type


title: Non-senescent BPH epithelial cell, replicate 3

description:
Library name: NonSen_3
PTE-TBHP3

data_processing:
Raw reads were quality-filtered and adapter-trimmed using fastp.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner.
Gene-level quantification was performed using featureCounts.
Expression normalization and differential analysis were carried out using DESeq2.
Normalized expression values were converted into FPKM format for each sample.
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited text file including gene-level raw counts (featureCounts output) for each sample.
Supplementary files format and content: CSV file containing FPKM values for each sample.

growth_protocol: Primary BPH epithelial cells were isolated from patient tissues and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) at 37°C with 5% CO₂. CD4⁺ T cells were cultured separately under similar conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA quality was assessed using Nanodrop spectrophotometry and Agilent Bioanalyzer.
RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. mRNA was enriched using oligo(dT) beads, fragmented, reverse-transcribed, adapter-ligated, and PCR-amplified. Library quality was checked using qPCR and Bioanalyzer.

treatment_protocol: CD4⁺ T cells were co-cultured with either senescent or non-senescent primary BPH epithelial cells for 6 hours. Following co-incubation, epithelial cells were harvested for RNA extraction.

value: CD4+ T cell co-culture

tag: batch


title: SARS-CoV-2 infection-5 [scRNA-seq]

description:
Library name: hCD147 mice_5
SeekGene

value: lung

tag: age

value: 3 months

tag: Sex

value: female

tag: virus

value: SARS-CoV-2 (Beta strain)


title: DSP-1001660038290-A-A02, Castration-, DLP, Treatment-, Mouse 2256

description: Library name: DSP-1001660038290-A-A02

tag: mouse

tag: castration

tag: lobe

tag: slide


title: Non-senescent BPH epithelial cell, replicate 2

description:
Library name: NonSen_2
PTE-TBHP2

tag: tissue

tag: treatment


title: Non-senescent BPH epithelial cell, replicate 1

description:
Library name: NonSen_1
PTE-TBHP1


title: BPH + rmCXCL13 + anti-CD4 mouse 3

description:
Library name: CXCL13_CD4_3
BPH mouse treated with rmCXCL13 + anti-CD4 antibody

tag: strain


title: TwoPooledMice_cd45POSspMMasRS_CD45+I-Ag7+

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

description:
Library name: TwoPooledMice_cd45POSspMMasRS
SMARTseq
teyton_don_2025_processed_mouse_raw_counts_matrix.csv

data_processing:
Data processing steps were performed using the nf-core RNA-seq version 3.3 pipeline. Built using Nextflow, the pipeline processes data using the following steps: preprocessing, alignment and quantification, alignment post-processing, transcript assembly and quantification, coverage visualization, quality control, pseudo-alignment and quantification
Statistical analysis and data visualization were done in R using Seurat. Cells with less than 1000 counts and genes with no signal were removed. Only cells with MHC class II transcript (colsums for all HLA-DR and H2-Aa or H2-Ab1>0) were included in analysis. Normalized values were log normalized using the NormalizeData function.
Assembly: GRCh38
Supplementary files format and content: comma separated values, samples as columns and genes as rows

source_name: Islet

extract_protocol:
Human islet single cell flow cytometry and sorting: Fresh human islets (IIDP, Prodo laboratories) were washed once with PBS prior to digestion with trypsin EDTA (Corning) for 20 minutes on ice with light shaking every 5 minutes68. Islets were gently dissociated with a P1000 pipette prior to stopping the enzymatic reaction with DMEM-10% serum. Cell suspensions were filtered through 0.7μm nylon screens. Dissociated islets were stained with antibodies against HLA-DR-Bv421 (L243, BioLegend) and CD45-FITC (HI30, BioLegend) in FACS buffer with 2% serum. PI-/CD45-/HLA-DR+ or PI-/CD45+/HLA-DR+ cells were sorted into semi-skirted 96 well PCR plates in 5μl of reverse transcription solution. Mouse islet isolation and single cell flow cytometry and sorting: Islets were isolated using a modified protocol derived from Li68. Briefly, pancreata were perfused with 0.5mg/mL of collagenase P (Sigma-Aldrich) through the common bile duct and digested at 37ºC for 17min. After several washes, pancreatic slurry was passed through a 0.419mm wire mesh strainer. A density gradient was established by layering histopaque1077 (Sigma-Aldrich) and serum-free RPMI, and sample loaded on top. After centrifugation at 600 g for 20 min, islets were collected at the histopaque/media interface, washed and hand-picked under a dissecting microscope. An average of 300-400 islets were recovered per mouse. For making single cell suspension, islets were digested with trypsin-EDTA and washed extensively before being counted.
Sequencing libraries were prepared from microtiter plates containing 1 cell per well sorted in reverse transcription buffer. The entire volume from each well, 5 μl, was used with the Takara SMARTer HT library prep kit following the manufacturer's recommendations. Briefly, first-strand cDNA synthesis was performed with template switching followed by 19 cycles of PCR. PCR products were quantitated using the Thermo Fisher Qubit system. For each sample, 150 pgs of cDNA were then used for tagmentation, followed by an additional 12 cycles of PCR with 96 unique indexed PCR primers. Samples were then pooled in groups of 48 and purified using Ampure XP beads (0.6X). Before loading library pools onto an Illumina NextSeq2000 sequencer, they were quantitated (Qubit) and bioanalyzed (Agilent Bioanalyzer 2100). This made 101 base single reads with 8 base i5 and 8 base i7 index reads. Each batch of 96 samples underwent sequencing using a single P2 flow cell.

value: Islet

value: 9 weeks


title: TwoPooledMice_cd45NEGspMMasRS_CD45-I-Ag7+

description:
Library name: TwoPooledMice_cd45NEGspMMasRS
SMARTseq
teyton_don_2025_processed_mouse_raw_counts_matrix.csv


title: BPH + rmCXCL13 + anti-CD4 mouse 4

description:
Library name: CXCL13_CD4_4
BPH mouse treated with rmCXCL13 + anti-CD4 antibody


title: BPH + rmCXCL13 + anti-CD4 mouse 2

description:
Library name: CXCL13_CD4_2
BPH mouse treated with rmCXCL13 + anti-CD4 antibody


title: 65903_001, preAD, rep1

description:
Library name: 5_03_08_17
library name V2: 05_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: 65059_001, MCI, rep1

description:
Library name: 4_03_08_17
library name V2: 04_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Senescent BPH epithelial cell, replicate 3

description:
Library name: Sen_3
T3-szm

tag: tissue

value: prostate

value: epithelial cell

tag: treatment

tag: batch


title: Senescent BPH epithelial cell, replicate 2

description:
Library name: Sen_2
T2-szm


title: 2BQ2AC0210_001, preAD, rep1

description:
Library name: 01_03_22_17
library name V2: 01_03_22_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 011

tag: plasma thaw_number


title: BPH + rmCXCL13 + anti-CD4 mouse 1

description:
Library name: CXCL13_CD4_1
BPH mouse treated with rmCXCL13 + anti-CD4 antibody

tag: strain

value: BALB/c

value: rmCXCL13 + anti-CD4 Ab


title: Kdr-FACS nuclei pooled from from E18.5 mouse kidneys

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

description:
Library name: mouse_e18.5d_kdr_facs
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were performed  using the Cell Ranger software v5.0.1  (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-delimited value files and matrix files.

source_name: Kidney

extract_protocol:
Kidneys were dissected in cold PBS without calcium or magnesium, snap-frozen for genotyping, and then thawed on ice for pooling. We minced the kidneys using razorblades and homogenized them with a Dounce homogenizer in Nuclei EZ Lysis buffer (Sigma) supplemented with protease inhibitor (Roche), RNase inhibitor (Promega and Life Technologies). The homogenate was filtered through a 40μm cell strainer (pluriSelect) and centrifuged at 500 x g for 5 min at 4°C. The pellet was resuspended, washed, and filtered again through a 5μm cell strainer (pluriSelect).
The resulting nuclei suspensions were submitted to UTSW Next Gen Sequencing Core for library preparation and sequencing using the Chromium Single Cell 3' Prime Gene Expression kit (10x Genomics) on an Illumina NextSeq 2000.

value: Kidney

tag: age

value: Kidney endothelium

tag: genotype

tag: Sex

value: pooled male and female

tag: background