title: DSP-1001660038290-A-A01, No Template Control

description: Library name: DSP-1001660038290-A-A01

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

source_name: No Template Control

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

value: No Template Control

tag: mouse

tag: castration

tag: lobe

tag: slide


title: BPH + rmCXCL13 mouse 5

status: Public on Dec 02 2025

type: SRA

city: Beijing

first: Zheng

last: Li

state: Beijing

address: No. 8 Xishiku Street, Xicheng District

country: China

institute: Peking University First hospital

description:
Library name: CXCL13_5
BPH BALB/c mouse treated with rmCXCL13

library_source: transcriptomic

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.

molecule: total RNA

organism: Mus musculus

source_name: prostate

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

value: prostate

tag: strain

value: BALB/c

tag: treatment

value: rmCXCL13 treatment

tag: batch


title: Senescent BPH epithelial cell, replicate 1

description:
Library name: Sen_1
T1-szm

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.

organism: Homo sapiens

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.

tag: cell type

value: epithelial cell

value: CD4+ T cell co-culture


title: KC MRTX1133 3

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

country: USA

institute: UT MD Anderson Cancer Center

description: Treated for 18 weeks

data_processing:
The raw FASTQ files were processed using Space Ranger 2.0.1
Assembly: mm10
Supplementary files format and content: Image and alignment files for Space Ranger

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
Tissues were processed according to the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics) protocol
Libraries were constructed according to the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics) protocol
Spatial transcriptomics

value: Pancreas

tag: genotype

value: LSL-KrasG12D; Pdx1-Cre


title: 66197_001, normal, rep1

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

institute: PreCyte, Inc.

description:
Library name: 24_03_08_17
library name V2: 24_03_08_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)

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.

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 010

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: KC MRTX1133 2

description: Treated for 18 weeks

tag: tissue

tag: genotype

tag: treatment


title: 67010_001, normal, rep1

description:
Library name: 9_03_08_17
library name V2: 09_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: BPH + rmCXCL13 mouse 4

description:
Library name: CXCL13_4
BPH BALB/c mouse treated with rmCXCL13

tag: strain

tag: batch


title: 65072_001, MCI, rep1

description:
Library name: 23_03_08_17
library name V2: 23_03_08_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

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: PRM1_RNA_R1

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: Library name: DE74NGSLABR105996

data_processing:
nf-core/rnaseq pipeline (FastQC for quality control, Cutadapt for adaptor trimming, STAR for alignment and Salmon for quantification)
Mithocondrial genes removal
Calculation of reads per kilobase of transcript per million mapped reads (RPKM)
Further normalization by total number of reads per sample
Assembly: hg38
Supplementary files format and content: normalized count matrix

extract_protocol:
NucleoSpin RNA Plus Kit
QuantSeq 3´ mRNA Library Prep Kit

tag: cell line


title: PRM2_RNA_R3

description: Library name: DE74NGSLABR104153


title: 61638_001, preAD, rep1

description:
Library name: 22_03_08_17
library name V2: 22_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

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: BPH + rmCXCL13 mouse 3

description:
Library name: CXCL13_3
BPH BALB/c mouse treated with rmCXCL13

tag: tissue

tag: treatment


title: KC MRTX1133 1

description: Treated for 18 weeks

tag: genotype


title: KC vehicle 3

description: Treated for 18 weeks

value: Vehicle


title: BPH + rmCXCL13 mouse 2

description:
Library name: CXCL13_2
BPH BALB/c mouse treated with rmCXCL13

tag: strain

tag: batch


title: 63205_001, preAD, rep1

description:
Library name: 3_03_08_17
library name V2: 03_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: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: BPH model mouse 5

description:
Library name: BPH_5
Prostate tissue from BPH-induced BALB/c mouse

value: BPH induction


title: BPH + rmCXCL13 mouse 1

description:
Library name: CXCL13_1
BPH BALB/c mouse treated with rmCXCL13


title: PRM1_RNA_R2

description: Library name: DE47NGSLABR105997

tag: cell line


title: reference_001, reference, rep18

description:
Library name: 2_03_08_17
library name V2: 02_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: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: reference


title: PRM2_RNA_R1

description: Library name: DE31NGSLABR104151

tag: genotype


title: 95T_blood_CD4,acute-infection,rep1

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

description: Library name: 95T_blood_CD4

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for brain and blood samples were made using the Cell Ranger software v7.1.0
The demultiplexing, barcoded processing, gene counting and aggregation for cell cocultivation were made using the Cell Ranger software v9.0.1
Assembly: For brain and blood samples from rhesus macaques, Mmul10, NCBI RefSeq assembly and SIVmac251 were used. For cell cocultivation experiment, GRCh38 GENCODE v44/Ensembl110 annotations were used
Supplementary files format and content: H5 files contain feature and cell barcode matrix

organism: Macaca mulatta

source_name: Blood

growth_protocol: For cocultivation study, the monocytes were isolated from the peripheral blood mononuclear cells (PBMC) of healthy donors. They were cultured in 6-well plates (3 million cells per well) using macrophage-derived macrophage (MDM) culture medium for one week before the experiment. The MDM culture medium consisted of 50 mL macrophage serum-free medium (Catalog# 12065-074, Gibco, Grand Island, NY, USA), 500 μL HEPES (Catalog# 15630-080, Gibco, Grand Island, NY, USA), 50 μL Gentamicin (Catalog# G1397, Sigma-Aldrich, St. Louis, MO, USA), 5 μL Ciprofloxacin (20 mg/mL dissolved in 1% HCL, Catalog# 16626133, Honeywell Fluka, Charlotte, NC, USA), 500 μL Nutridoma (Catalog# 21952600, Roche, Indianapolis, IN), and 5 μL M-CSF (Catalog# 300-25-250UG, Gibco, Grand Island, NY, USA), which was filtered using Millipore Steriflip filter (Catalog# SCGP00525, Sigma-Aldrich, St. Louis, MO, USA) before use. The jurkat cells (a human T-cell cell line) was obtained from ATCC and cultured in RPMI 1640 medium (Catalog# SH30027.02, Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (Catalog# F8067, Sigma-Aldrich, St. Louis, MO, USA) and 1% antibiotic-antimycotic (Catalog# SV30079.01, Hyclone, Logan, UT, USA). The Jurkat cells were seeded in 24-well plates at a density of 300,000 cells per well one day before the experiment.

extract_protocol:
For isolating brain lymphocytes, a necropsy was performed on deeply anesthetized (ketamine plus xylazine) animals, following intracardial perfusion with sterile PBS containing 1 U/ml heparin. Brains were harvested, and approximately half of the brain was taken for cell isolation.The brain was minced and homogenized in cold Hank’s Balanced Salt Solution (HBSS, Invitrogen, Carlsbad, CA, USA). After being centrifuged, the brain tissue was digested at 37° C in HBSS containing 28 U/ml DNase I and 8 U/ml papain for 30 minutes. After digestion, the enzymes were inactivated by adding 2.5% FBS, and the cells were centrifuged and resuspended in cold HBSS. The cell suspension was brought to a final concentration of 20% Percoll by the addition of 90% Percoll (GE HealthCare, Pittsburg, PA, USA) and centrifuged at 4° C for 15 minutes at 550 x g. The cell pallet at the bottom was resuspended in HBSS and passed through a 40 μm strainer to remove cell clumps and/or aggregates. Cells were again pelleted by centrifugation. A final wash was performed before the resulting cells were quantified on a hemocytometer and Coulter Counter Z1.The brain cells were cryopreserved before the cell sorting and scRNA-seq. To isolate the brain lymphocytes, samples of cryopreserved brain cell isolates, stored in liquid nitrogen , were rapidly thawed in a 37° C water bath. After the recovery, cells were washed and counted by Coulter Counter Z1. Once cell concentration was known, cells were transferred to ice-cold PBS, staining with Live/Dead and PE-labeled anti-CD45 antibody (Biolegend, San Diego, CA). The live cells that were CD45+ were collected for scRNA-seq capture and library preparation. For isolating blood CD4+ lymphocytes, freshly isolated EDTA-anticoagulated blood was centrifuged, and the cells washed with PBS and then stained with UV-blue live/dead for 30 minutes at 4° C. After being blocked with FACS buffer for 3 minutes, the cells were centrifuged and resuspended in the antibody cocktail mixed in Brilliant Stain buffer (Catalog# 563794, BD Biosciences, San Jose, CA, USA) for 45 minutes. After incubation, red blood cell (RBC) lysing buffer was added to the sample and the cells were pelleted at 300 x g for 8 minutes. After centrifugation, the cells were resuspended in RBC lysing buffer, which was repeated to completely remove RBCs. The cells were then pelleted and resuspended in MACS buffer for FACS sorting. The antibody cocktail included V500-labeled anti-CD3 antibody (Catalog# 561417, BD Biosciences, San Jose, CA, USA), BV786-labeled anti-CD4 antibody (Catalog# 563881, BD Biosciences, San Jose, CA, USA), PE-CF594-labeled anti-CD20 antibody (Catalog# 562295, BD Biosciences, San Jose, CA, USA) The selection of cells was based on the size, singlet, live, and expression of CD20, CD3, and CD4. The CD20-positive cells were excluded, and the CD20-negative cells that were positive for CD3 and CD4 were collected for scRNA-seq library preparations.  For cell cocultivation experiment, MDM or MDM-jurkats cocultivation system was harvested by incubating with trypLE (Catalog# 12605-010, Gibco, Grand Island, NY, USA)  for 10 minutes at 37 ℃, then after one step of washing with 1mL PBS, another 1 mL PBS (Catalog# 14190-136, Gibco, Grand Island, NY, USA) with 0.04% BSA (Catalog# 130-091-376, Miltenyi Biotec, Bergisch Gladbach, Germany) was added for scraping the cells from the plate. For the cocultivation groups,  the harvested cells were directly used for library preparations. For the non-cocultivation group, the MDM was mixed with jurkat cells for library preparations.
Post-sorting, isolates were concentrated to approximately 1000 cells per µL and assessed by trypan blue for viability and concentration. Brain immune cells and blood CD4+ T cells are isolated from the acutely infected macaques that were processed using the 10× Genomics (Pleasanton, CA, USA) Chromium 3’ v3 GEM kit targeting 8000 cells. And cocultivation study used 10× Genomics GEM-X Universal 3' Gene Expression v4 4-plex kit targeting 5000 cells. Based on the targeting cell number, the ideal volume of cells was loaded onto the 10× Genomics Chromium GEM Chip and placed into the Chromium Controller for cell capturing and library preparation. In short, this occurs through microfluidics and combining with Single Cell 3’ Gel Beads containing unique barcoded primers with a unique molecular identifier (UMI), followed by lysis of cells and barcoded reverse transcription of RNA, amplification of barcoded cDNA, fragmentation of cDNA to 200 bp, 5’ adapter attachment, and sample indexing as the manufacturer instructed with version 3 reagent kits. The prepared libraries were sequenced using Illumina (San Diego, CA, USA) Nextseq550 and Novaseq6000 sequencers.

treatment_protocol: For three acute-infected rhesus macaques (93T, 94T, and 95T), they were intravenously inoculated with SIVmac251. For cell cocultivation experiment, we cocultured MDMs and jurkat cells in NoApop, CD95, and Campto groups for 1 hour. The jurkats in CD95 and Campto groups were treated with apoptotic agents (i.e. CD95 and camptothecin) for 3 hours prior to cocultivation . The MDMs and jurkats in NoCoCul group did not receive any cocultivation, and they were mixed before library preparations to assess the the artefactual dual capture.

tag: tissue

value: Blood

value: CD3+CD4+ positive cells

tag: treatment

value: 12-days of SIVmac251 infection


title: KC vehicle 2

description: Treated for 18 weeks


title: Emp_RNA_R3

description: Library name: DE58NGSLABR104150

value: Emp


title: KC vehicle 1

description: Treated for 18 weeks


title: Emp_RNA_R2

description: Library name: DE85NGSLABR104149


title: BPH model mouse 4

description:
Library name: BPH_4
Prostate tissue from BPH-induced BALB/c mouse

value: prostate

tag: strain

value: BALB/c

tag: batch


title: 64446_001, normal, rep1

description:
Library name: 19_03_08_17
library name V2: 19_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: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: PRM1_RNA_R3

description: Library name: DE20NGSLABR105998

tag: cell line


title: 94T_blood_CD4,acute-infection,rep1

description: Library name: 94T_blood_CD4


title: Emp_RNA_R1

description: Library name: DE15NGSLABR104148


title: BPH model mouse 3

description:
Library name: BPH_3
Prostate tissue from BPH-induced BALB/c mouse


title: 93T_blood_CD4,acute-infection,rep1

description: Library name: 93T_blood_CD4


title: 86142_001, preAD, rep1

description:
Library name: 18_03_08_17
library name V2: 18_03_08_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

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: 65001_001, normal, rep1

description:
Library name: 21_03_08_17
library name V2: 21_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: BPH model mouse 1

description:
Library name: BPH_1
Prostate tissue from BPH-induced BALB/c mouse

tag: tissue

tag: strain

tag: treatment

tag: batch


title: PRM2_RNA_R2

description: Library name: DE04NGSLABR104152

tag: genotype


title: 63762_001, preAD, rep1

description:
Library name: 17_03_08_17
library name V2: 17_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: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 92T_blood_CD4,non-infection, rep1

description: Library name: 92T_blood_CD4


title: P159_p20

city: Barcelona

first: Genís

last: Camprecios

state: Catalonia

address: Rosselló 153

department: Hepatic Hemodynamics

country: Spain

institute: IDIBAPS

description: Library name: P15920

data_processing:
Sequence quality was checked with FastQC (version 0.11.9).
Reads were pseudoaligned to the human genome (version GRCh38.p13) with the Kallisto aligner
Read count extraction and normalization were performed with the sleuth R package (version 0.30.1)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include normalized estimated counts for all samples
Supplementary files format and content: tab-delimited text files include normalized tpm for all samples

source_name: Portal vein

growth_protocol: PVECs were maintained in EGMTM-2 Endothelial Cell Growth Medium-2 BulletKitTM (EGM-2) in a humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
ECs were collected in RLT + ß-mercaptoethanol and RNA isolated with the RNeasy Micro kit (Qiagen) with on-column DNAseI treatment.
RNA purity and quality was analyzed with Bioanalyzer and only samples with a RNA Integrity Number above 8 were used for subsequent steps.
Libraries were synthesized with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) starting with 20-50 ug total RNA

treatment_protocol:
PVECs were isolated from explanted livers from patients undergoing liver transplant. Cells plated in a 6-well plate (passage 0). Once celles reached confluence, we FACS sorted the samples to isolate pure endothelial cells (CD31+/VE-Cadherin+). Cells were then explanded. We sequenced passage 1 cells.
Passage 1 hPVECs were seeded in a 24-well plate at a concentration of 1x104cells/ml and transduced with 1 μl/ml of lentiviral particles (MOI of 5) expressing the SV40 large T-antigen and containing the GFPpuromycin fusion dual marker. Transduced cells were selected using EGM-2 medium supplemented with puromycin at 1,5 μg/ml.

value: Portal vein

value: Endothelial cell


title: reference_001, reference, rep17

description:
Library name: 15_03_08_17
library name V2: 15_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

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


title: 65941_001, MCI, rep1

description:
Library name: 20_03_08_17
library name V2: 20_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: 64848_001, normal, rep1

description:
Library name: 14_03_08_17
library name V2: 14_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: human


title: Control mouse 5

description:
Library name: Ctrl_5
Prostate tissue from control BALB/c mouse

tag: tissue

tag: strain

tag: treatment

tag: batch


title: 64948_001, preAD, rep1

description:
Library name: 16_03_08_17
library name V2: 16_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: Aim 2 Batch 010

tag: sequencing plate_name

tag: rna-seq date


title: P156_p20

description: Library name: P15620


title: Control mouse 4

description:
Library name: Ctrl_4
Prostate tissue from control BALB/c mouse


title: Control mouse 3

description:
Library name: Ctrl_3
Prostate tissue from control BALB/c mouse


title: P155_p20

description: Library name: P15520


title: 66078_001, MCI, rep1

description:
Library name: 13_03_08_17
library name V2: 13_03_08_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

tag: plasma thaw_number

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: P152_p20

description: Library name: P15220


title: Control mouse 2

description:
Library name: Ctrl_2
Prostate tissue from control BALB/c mouse


title: 64846_001, MCI, rep1

description:
Library name: 12_03_08_17
library name V2: 12_03_08_17
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

value: pass


title: P137_p20

description: Library name: P13720

tag: tissue

tag: cell type

tag: treatment


title: mouse strain FztDU, biological rep5

type: RNA

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

description: Gene expression data

hyb_protocol: Hybridization was carried out overnight (16 h) at 45°C in the GeneChipR Hybridisation Oven 645 (Affymetrix).

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) at 0.7-micron resolution.

data_processing: The generated data were analyzed using the Transcriptome Analysis Console (TAC) version 4.0.2.15 (Thermo Fisher Scientific). Differentially expressed genes (DEG) were identified based on absolute fold change of >1.75 and FDR q value < 0.05.

source_name: Reference mouse line

label_protocol: The DNA labeling reagent biotin-11-dXTP was added by a desoxynucleotidyl transferase.

growth_protocol: Mice were kept under SPF conditions in the institute's mouse facility. They were killed at an age of 21-22 weeks, and hippocampi were isolated.

extract_protocol: RNA was extracted using the RNeasy Plus Kit (Qiagen, Hilden, Germany). First, entire hippocampi were separately homogenized in liquid nitrogen under addition of 1ml RLT Plus buffer (RNeasy Plus Kit, Qiagen). Subsequently, 150-µl aliquots of the 600 µl tissue-powder homogenates were diluted in 550 ml RNeasy Plus buffer (Qiagen) in a 1.5-ml reaction tube. Finally, an extraction using phenol/chloroform/isoamyl alcohol (25:24:1, pH 6.6; Thermo Fisher Scientific, Waltham, MA, USA) was performed, followed by a DNA-removal step according to the manufacturer’s protocol.

treatment_protocol: Hippocampi were snap frozen in liquid nitrogen.

tag: group

value: Physiological metabolism

value: Hippocampus


title: P132_p20

description: Library name: P13220

tag: batch


title: mouse strain FztDU, biological rep4

description: Gene expression data


title: 65130_001, MCI, rep1

description:
Library name: 10_03_08_17
library name V2: 10_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 class

tag: sequencing plate_name


title: BPH model mouse 2

description:
Library name: BPH_2
Prostate tissue from BPH-induced BALB/c mouse

tag: strain

value: BPH induction


title: SH99_CH

description: Library name: SH99_CH

source_name: Inferior Cava Vein

value: Inferior Cava Vein


title: p2 utricle, gentamicin control, bio rep3

city: SHANGHAI

first: yunzhong

last: zhang

state: SHANGHAI

address: 83 fenyang road, xuhui district

department: Department of ENT Institute and Otorhinolaryngology

institute: Eye & ENT Hospital of Fudan University

description: Library name: Fos_C_3

data_processing:
Preliminary processing of raw reads was performed using TrimGalore (v0.6.10) for removing adapters and low-quality bases. Trimmed reads for each sample were aligned to the Mus musculus Ensembl mm10 genome (release-110) using HISAT2 (v2.2.1), and aligned reads were summarized with featureCounts (v2.0.6). Differential expression analysis between conditions was performed using the DESeq2 R package (1.34.0), and genes with an adjusted p-value (padj) < 0.05 and log2 fold change > 0.25 were regarded as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: mouse utricle explants

growth_protocol: P2 mouse utricles were quickly removed from the temporal bone, and the tectorial membrane was peeled off under sterile conditions. The otoconia were removed and the utricles were attached to coverslips pre-coated with CellTak (BD Biosciences) and placed in 4-well Petri dishes. Whole organs were cultured in serum-free media consisting of DMEM/F12 (1:1; Invitrogen), N2 (1:100 dilution, Invitrogen), B27 (1:50 dilution, Invitrogen), and ampicillin (50 ng/ml; Sigma) at 37°C with 5% CO2.

extract_protocol:
Each group of 12 utricles was separately used for extracting total RNA with the AllPrep DNA/RNA/Protein Mini kit (QIAGEN).
Sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

value: mouse utricle explants

tag: genotype

value: WT

value: gentamicin


title: p2 utricle, gentamicin control, bio rep2

description: Library name: Fos_C_2


title: mouse strain FztDU, biological rep2

description: Gene expression data


title: mouse strain FztDU, biological rep3

description: Gene expression data


title: SH87_CH

description: Library name: SH87_CH


title: 62701_001, normal, rep1

description:
Library name: 9_03_01_17
library name V2: 09_03_01_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 009

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: mouse strain DU6, biological rep5

description: Gene expression data

source_name: Obesity mouse line

value: Polygenic obesity

tag: tissue


title: p2 utricle, gentamicin control, bio rep1

description: Library name: Fos_C_1

tag: treatment


title: SH75_CH

description: Library name: SH75_CH

tag: cell type

tag: batch


title: 62703_001, normal, rep1

description:
Library name: 11_03_08_17
library name V2: 11_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: 63403_001, normal, rep1

description:
Library name: 8_03_01_17
library name V2: 08_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma class

tag: sequencing plate_name


title: MOLM13_AAVS1_SR-0813_rep3

city: La Jolla

first: Michael

last: Erb

state: CA

address: 10550 N. Torrey Pines

institute: The Scripps Research Institue

description:
Library name: Sample18
AAVS1-SR0813_03_PB004

data_processing:
Data was assessed for read quality using FastQC and then aligned to the genome hg19 using SlamDunk software for alignment and quantification of reads.
Filtered for row CPM greater than 3 in at least one row.
Assembly: hg19
Supplementary files format and content: Processed data (PAB_PAF1_RNAseq_cpm_greaterthan_3_allsamples_processed_data.xlsx) the input to the Rscript which goes through comparisons over the DMSO condition and all plotting shown in the manuscript.
Supplementary files format and content: PAB_PAF1_RNAseq_cpm_greaterthan_3_allsamples_processed_data.xlsx the columns are the triplicates of the samples and the rows are the CPM values for each gene

growth_protocol: MOLM-13 Cells expressing Cas9 selected in Blast for Cas9 expression and then transduced with PAF1 guides 1 and 4 or AAVS1 control. sgPAF1 expressing cells were treated with SR-0813 for a month to select for resistance alleles. All cells grown in RPMI 1640 media supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
RNA was etracted using the Qiagen Rneasy kit 500ng input was used for each sample for the creation of the library
Library was constructed using the Lexogen QuantSeq 3'-mRNA-Seq Prep Kit FWD with UDI.

treatment_protocol: Selected PAF1 cell lines and AAVS1 control were removed from selection and then treated with 10µM SR-0813 or DMSO for 8hours.

tag: cell line

tag: genotype

value: sgAAVS1 control


title: p2 utricle, gentamicin+AAV-PHP.eB Fos , bio rep4

description: Library name: Fos_OE_4

value: gentamycin+AAV-PHP.eB Fos


title: Control mouse 1

description:
Library name: Ctrl_1
Prostate tissue from control BALB/c mouse

value: prostate

tag: strain

value: BALB/c


title: 23875_001, MCI, rep1

description:
Library name: 7_03_01_17
library name V2: 07_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

value: human

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: p2 utricle, gentamicin+AAV-PHP.eB Fos , bio rep3

description: Library name: Fos_OE_3

tag: tissue

tag: treatment


title: mouse strain FztDU, biological rep1

description: Gene expression data

tag: group


title: mouse strain DU6, biological rep2

description: Gene expression data


title: mouse strain DU6, biological rep3

description: Gene expression data


title: MOLM13_AAVS1_SR-0813_rep2

description:
Library name: Sample17
AAVS1-SR0813_02_PB004


title: 64263_001, preAD, rep1

description:
Library name: 5_03_01_17
library name V2: 05_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

value: #N/A

value: pass


title: SH124_CH

description: Library name: S124_1

value: Endothelial cell

tag: batch


title: 67019_001, normal, rep1

description:
Library name: 6_03_01_17
library name V2: 06_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma class

tag: sequencing plate_name

value: low RIN


title: SH111_CH

description: Library name: S111_1

value: Inferior Cava Vein


title: 65322_001, preAD, rep1

description:
Library name: 1_03_08_17
library name V2: 01_03_08_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

value: Aim 2 Batch 010

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: mouse strain DU6, biological rep1

description: Gene expression data

tag: group

tag: tissue

value: Hippocampus


title: SH121_CH

description: Library name: S121_1

tag: cell type

tag: treatment


title: MOLM13_AAVS1_DMSO_rep3

description:
Library name: Sample15
AAVS1-DMSO_03_PB004

tag: cell line

tag: genotype

value: DMSO


title: CastratedMouseProstate_C57BL6_rep2

city: Ann Arbor

first: Evan

middle: T

last: Keller

state: Michigan

address: 1109 Geddes Avenue

department: Urology

institute: University of Michigan

description:
Library name: Si_5197-4
10x chromium 3′ gene expression V3.1

data_processing:
After sequencing, read demultiplexing, alignment and gene quantification were conducted with the 10X Genomics Cell Ranger pipeline (v5.0) and the pre-built reference genome, mm10 for mouse
Assembly: mm10
Supplementary files format and content: filtered_ feature_matrix.h5: Per-sample non-zero count matrix files in H5 format.
Supplementary files format and content: raw_ feature_matrix.h5: Per-sample non-zero count matrix files in H5 format.
Supplementary files format and content: SingleMetadata.csv : Per-sample metadata table containing cell annotation for each sequenced cell.

growth_protocol: All animal work was performed in accordance with the University of Michigan Institutional Animal Care and Use Committee (IACUC),  Male C57BL/6 mice 10 to 18 weeks old were either purchased from The Jackson Laboratory, or bred in-house from purchased mice.

extract_protocol: The 10x barcoding and complementary DNA (cDNA) synthesis were performed using 10x chromium 3′ scRNA-seq  V3.1 chemistry according to the manufacturer’s instructions. Briefly, an appropriate volume of single-cell suspension/enzyme mix, barcoded beads, and partitioning oil were loaded in distinct lanes on the chip and processed in a 10x chromium controller instrument. The 10x GemCode Technology uses a droplet-based method to partition thousands of cells to generate nanoliter-scale Gel Bead-In-Emulsions (GEMs). Inside each GEM, cDNA generated from an individual cell shares a common 10x barcode. The prepared GEMs were incubated in a thermomixer to produce cDNA. Recovered cDNA was cleaned up and amplified by polymerase chain reaction to generate enough quantity for library construction. The size and yield were evaluated using a high-sensitivity bioanalyzer assay chip (Agilent). A set of recommended primers (P5, P7, and R2) in the manufacturer’s standard protocol were added to prepare the Illumina-ready sequencing library. The final library was evaluated for size and yield using a high-sensitivity bioanalyzer assay chip (Agilent). The final libraries were sequenced with the NovaSeq 6000 according to recommended specifications.

treatment_protocol: The mice were either sham-operated or castrated. Prostate tissues were harvested from these animals10 or 20 days after surgical procedure and upon removal of adhering fats, minced. minced tissues were digested with 5mg/mL collagenase Type II (Gibco, 17101015) for 1 hour at 37°C followed by TryLE (Gibco, 17101015) digestion for 10 min. After TryLE digestion, samples were inactivated with an excess of DMEM containing 10% fetal bovine serum (FBS), and samples were sequentially passed through 100 mm and 40 mm cell strainers to remove debris, followed by a 0.5% BSA in 1xPBS wash. Cell suspensions were then processed for scRNAseq.

value: mixed

value: Castration


title: SH73_CH

description: Library name: SH73_1

tag: batch


title: 64737_001, preAD, rep1

description:
Library name: 3_03_01_17
library name V2: 03_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: Aim 2 Batch 009

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: 63845_001, MCI, rep1

description:
Library name: 4_03_01_17
library name V2: 04_03_01_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

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma class

tag: sequencing plate_name


title: MOLM13_AAVS1_DMSO_rep2

description:
Library name: Sample14
AAVS1-DMSO_02_PB004

tag: cell line

value: sgAAVS1 control

tag: treatment


title: p2 utricle, gentamicin+AAV-PHP.eB Fos , bio rep1

description: Library name: Fos_OE_1

tag: tissue

value: mouse utricle explants

tag: genotype

value: WT

value: gentamycin+AAV-PHP.eB Fos


title: mouse strain DU6, biological rep4

description: Gene expression data

tag: group

value: Polygenic obesity


title: SH100_CH

description: Library name: S100_1

tag: cell type

tag: batch


title: CastratedMouseProstate_C57BL6_rep1

description:
Library name: Si_5197-3
10x chromium 3′ gene expression V3.1

value: prostate


title: 64956_001, MCI, rep1

description:
Library name: 22_03_01_17
library name V2: 22_03_01_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

value: human

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: #N/A

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: NormalMouseProstate_C57BL6_rep2

description:
Library name: Si_5197-2
10x chromium 3′ gene expression V3.1


title: p2 utricle, gentamicin+AAV-PHP.eB Fos , bio rep2

description: Library name: Fos_OE_2


title: 65945_001, preAD, rep1

description:
Library name: 21_03_01_17
library name V2: 21_03_01_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

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma shipment_batch

tag: sample cohort

value: pass


title: CB172_CD7+

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA59022

data_processing:
Sequencing was performed on the NovaSeq 6000 platform in 151-base single-end mode.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver.2.3.5.1 and SAMtools ver.1.2.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: cord blood

extract_protocol:
Total RNA was extracted from cells using the miRNeasy Micro kit (QIAGEN N.V.) according to the enclosed instructions.
The cDNA libraries were constructed according to the manufacturer's instructions using the SMARTer Stranded RNA-Seq Kit HT (Clontech Laboratories, Inc., San Jose, CA) and the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA).

tag: tissue

value: cord blood

value: CD7+CD56-CD34-HLA-DR-Lin- NK progenitor cells

tag: genotype


title: NormalMouseProstate_C57BL6_rep1

description:
Library name: Si_5197-1
10x chromium 3′ gene expression V3.1

tag: cell type

tag: treatment


title: MOLM13_PAF1-4_SR-0813_rep3

description:
Library name: Sample12
PAF1-4-SR0813_03_PB004

tag: cell line

value: selected sgPAF1-4


title: 66087_001, normal, rep1

description:
Library name: 20_03_01_17
library name V2: 20_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma class

tag: sequencing plate_name


title: Slide4D_CastratedMouseProstate_C57BL6_rep4

description: Library name: Slide4D

data_processing:
Visium sequencing depth was 100m reads/sample. All sequencing was performed at the University of Michigan Advanced Sequencing core on the NovaSeq6000 with 300 cycles and paired end 150.
Raw Sequencing data were processed using the 10x genomics space ranger pipeline to generate FastQs
Reads were aligned to the mm10 mouse transcriptomewith tr the Spatial Space Ranger 1.3 default settings
Gene expression levels of Refseq coding genes were quantifed using Space Ranger default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: scalefactors_json.json : scalefactors in json format
Supplementary files format and content: tissue_hires_image.png : hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png : low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv : list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

growth_protocol: All animal work was performed in accordance with the University of Michigan Institutional Animal Care and Use Committee (IACUC),  Male C57BL/6 mice 10 to 18 weeks old were either purchased from The Jackson Laboratory, or bred in-house from purchased mice

extract_protocol:
Dissected whole prostates were placed in histocassettes sandwiched between sponges and fixed in 10% Formaldehyde for 4 hours and paraffin embedded within 24 hrs
Spatial transcriptome sequencing libraries were prepared with 10x visium spatial gene expressionslides and reagent kit according to the manufacturs instructions.

treatment_protocol: The mice were either sham-operated or castrated at 8 weeks of age. Mice were orchiectomized  and prostates harvested 10 or 20 days later.  Adhering fats were removed

value: mixed

value: Castracted D20


title: MOLM13_AAVS1_SR-0813_rep1

description:
Library name: Sample16
AAVS1-SR0813_01_PB004


title: MOLM13_PAF1-4_SR-0813_rep2

description:
Library name: Sample11
PAF1-4-SR0813_02_PB004


title: SH109_CH

description: Library name: S109_1

value: Inferior Cava Vein

value: Endothelial cell

tag: batch


title: reference_001, reference, rep16

description:
Library name: 2_03_01_17
library name V2: 02_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 009

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: reference

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: CB162_CD7-

description: Library name: GA59019

tag: tissue

value: CD7-CD56-CD34-HLA-DR-Lin- cells

value: WT


title: CB162_CD7+

description: Library name: GA59020

tag: genotype


title: MOLM13_PAF1-4_SR-0813_rep1

description:
Library name: Sample10
PAF1-4-SR0813_01_PB004


title: MOLM13_PAF1-4_DMSO_rep3

description:
Library name: Sample9
PAF1-4-DMSO_03_PB004

value: DMSO


title: Slide4C_CastratedMouseProstate_C57BL6_rep3

description: Library name: Slide4C

value: prostate

tag: cell type


title: 84130_001, preAD, rep1

description:
Library name: 18_03_01_17
library name V2: 18_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma shipment_batch

tag: sample cohort


title: Slide4B_CastratedMouseProstate_C57BL6_rep2

description: Library name: Slide4B

tag: treatment


title: MOLM13_PAF1-4_DMSO_rep2

description:
Library name: Sample8
PAF1-4-DMSO_02_PB004

tag: cell line


title: CB153_CD7+

description: Library name: GA58450


title: Slide4A_CastratedMouseProstate_C57BL6_rep1

description: Library name: Slide4A


title: 65446_001, nonAD, rep1

description:
Library name: 19_03_01_17
library name V2: 19_03_01_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 class

value: #N/A

tag: sequencing plate_name


title: MOLM13_PAF1-4_DMSO_rep1

description:
Library name: Sample7
PAF1-4-DMSO_01_PB004


title: Slide2D_CastratedMouseProstate_C57BL6_rep4

description: Library name: Slide2D

value: Castracted D10


title: 63843_001, MCI, rep1

description:
Library name: 17_03_01_17
library name V2: 17_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rna-seq date

value: pass


title: MOLM13_PAF1-1_SR-0813_rep3

description:
Library name: Sample6
PAF1-1-SR0813_03_PB004

tag: genotype

value: selected sgPAF1-1


title: Slide2C_CastratedMouseProstate_C57BL6_rep3

description: Library name: Slide2C

tag: tissue

tag: cell type

value: mixed


title: MDM_Jurkats, non-apoptosis, CD95-treated

description:
Library name: Cocul_library1
Two repeated samples for NoApop and CD95-treated groups in cocultivation study

source_name: Monocyte-derived macrophages (MDM), jurkats

value: MDM and jurkats cocultivation; MDM  and CD95-treated jurkats cocultivation


title: Slide2B_CastratedMouseProstate_C57BL6_rep2

description: Library name: Slide2B


title: 65425_001, preAD, rep1

description:
Library name: 15_03_01_17
library name V2: 15_03_01_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

tag: plasma shipment_batch

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: MOLM13_PAF1-1_SR-0813_rep2

description:
Library name: Sample5
PAF1-1-SR0813_02_PB004

tag: cell line

tag: treatment


title: TPH1-Venus negative, sample 4

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Library name: D508rna.neg

data_processing:
Sequenced reads were trimmed for adapter sequences using cutadapt, mapped to the primary human genome (GRCh38) using STAR, and raw counts generated with featureCounts.
Differential gene expression modelling and normalised counts per million were generated using DESeq2.
Assembly: hs38
Supplementary files format and content: Count matrix, exported by featureCounts, are in tab-separated delimited (tsv) text format.

source_name: duodenum organoid

growth_protocol: Cultures were passaged every 7 days and seeded in BME. To promote differentiation, EGF was removed from the culture medium 2-3 days after seeding (IF medium). Subsequently, organoids were grown in IF medium for 5-7 days, at which point fluorescent TPH1-Venus cells could be observed.

extract_protocol:
Differentiated organoids were dissociated to single cell, and sorted into two populations (Venus-positive and -negative) using an Influx Cell Sorter (BD Biosciences) at the Cambridge Institute of Medical Research (CIMR) Flow Cytometry Core Facility. DAPI and DRAQ5 staining, side scatter, forward scatter and pulse width gates were used to remove debris and cell clusters. RNA extraction and isolation were performed using RNAeasy Micro Plus kit (Qiagen). RNA concentration and quality (RIN 7-9) were assessed using RNA6000 Pico Kit and Bioanalyser 2000 (Agilent).
The library was constructed with using the SMARTer Stranded Total RNA-Seq v2 Pico Input Mammalian kit (Takara Bio).

value: duodenum organoid

value: EC cells

value: TPH1-Venus negative


title: MOLM13_AAVS1_DMSO_rep1

description:
Library name: Sample13
AAVS1-DMSO_01_PB004

value: sgAAVS1 control


title: reference_001, reference, rep15

description:
Library name: 14_03_01_17
library name V2: 14_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: Aim 2 Batch 009

tag: sample cohort

tag: plasma class

value: reference


title: Slide2A_CastratedMouseProstate_C57BL6_rep1

description: Library name: Slide2A


title: MOLM13_PAF1-1_SR-0813_rep1

description:
Library name: Sample4
PAF1-1-SR0813_01_PB004


title: TPH1-Venus negative, sample 3

description: Library name: D506rna.neg


title: CB172_CD7-

description: Library name: GA59021

value: cord blood

value: CD7-CD56-CD34-HLA-DR-Lin- cells

value: WT


title: 63455_001, normal, rep1

description:
Library name: 13_03_01_17
library name V2: 13_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sequencing plate_name


title: CB153_CD7-

description: Library name: GA58449

tag: tissue

tag: cell type

tag: genotype


title: MOLM13_PAF1-1_DMSO_rep2

description:
Library name: Sample2
PAF1-1-DMSO_02_PB004

value: DMSO


title: 65908_001, normal, rep1

description:
Library name: 16_03_01_17
library name V2: 16_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma shipment_batch

value: #N/A

tag: rna-seq date


title: TPH1-Venus negative, sample 2

description: Library name: D504rna.neg


title: 65816_001, MCI, rep1

description:
Library name: 12_03_01_17
library name V2: 12_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: DIO4

city: Chapel Hill

last: Coleman

state: NC

address: 135 Dauer Dr

institute: University of North Carolina

description: Library name: SBM218

data_processing:
The reads were mapped to mouse genome using cell ranger
Mapped reads were counted using cell ranger
Seurat was used for darta processing and subclustering
Assembly: mm10
Supplementary files format and content: processed data: h5 files

source_name: tumor

growth_protocol: C57BL/6J mice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain on their respective diets or the same diet supplemented with 140ppm of sulindac.

extract_protocol:
cells were dissociated by cold protease, and flow sorted for viability and to remove dublets.
10x genomics 5' scRNAseq kit

treatment_protocol: 5 weeks after initial randomization mice were orthotopically injected with E0771 cells into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint tumor was removed and used for 10x genomics 5’ scRNAseq analysis.

value: tumor

tag: cell line

tag: strain

value: mouse mammary cancer

value: wt


title: MOLM13_PAF1-1_DMSO_rep3

description:
Library name: Sample3
PAF1-1-DMSO_03_PB004

value: selected sgPAF1-1

tag: treatment


title: TPH1-Venus negative, sample 1

description: Library name: D502rna.neg

value: duodenum organoid

value: EC cells

value: TPH1-Venus negative


title: MDM_Jurkats, Campto-treated, non-cocultivation

description:
Library name: Cocul_library2
Two repeated samples for Campto-treated and NoCoCul groups in cocultivation study

value: Monocyte-derived macrophages (MDM), jurkats

value: MDM and camptothecin-treated jurkats cocultivation; MDM mixed with jurkats


title: 64680_001, normal, rep1

description:
Library name: 11_03_01_17
library name V2: 11_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 009

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class


title: DIO3

description: Library name: SBM213

tag: tissue

tag: cell type

tag: genotype


title: MOLM13_PAF1-1_DMSO_rep1

description:
Library name: Sample1
PAF1-1-DMSO_01_PB004


title: Con3

description: Library name: SBM200


title: TPH1-Venus positive, sample 4

description: Library name: D507rna.pos

value: TPH1-Venus positive


title: 65608_001, MCI, rep1

description:
Library name: 10_03_01_17
library name V2: 10_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sequencing plate_name

value: RNASeq QC


title: AC16 cell, HMGN3 knockdown, ChIP-seq, replicate 3

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description:
Library name: AC16-siHMGN3_ChIP-3
ChIP-seq of AC16 cell, HMGN3 knockdown

library_source: genomic

data_processing:
For Bulk RNAseq, reads in fastq files were trimmed via trim-galore software; then, via the STAR v.2.5 toolkit, the trimmed reads were mapped into the Human GRCh38 Reference Genome to identify the gene corresponding to each read. F
or ChIP-seq, the DNA fragments (from fastq file) were aligned to human GRCh38 reference genome. Then, the alignment result files were formatted by SamTools, HMGN3 binding intensity throughout the genome was quantified via the bamCoverage function of deepTools version 3.5.6 toolkit, and binding peak was called by MACS2 program.
Assembly: GRCh38
Supplementary files format and content: Bulk RNAseq: the count of each transcript in each sample
Supplementary files format and content: ChIP-seq: bedGraph file for HMGN3 binding in each sample

molecule: genomic DNA

source_name: Human cardiomyocyte AC16 cell

growth_protocol: Human cardiomyocyte-like AC16 cells were acquired from ATCC (CRL-3568) and cultured in DMEM/F-12 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin (Sigma-Aldrich) at 37°C with 95% air and 5% CO₂ in a humidified incubator. The cells were typically cultured in 12-well plates at a density of 1 × 105 cells.

extract_protocol:
Cells were harvested 72 hours after transfection. Total RNA were extracted for Bulk-RNA seq. DNA immunoprecipitation were applied to extract DNA fragment binding to HMGN3
The polyadenylated total RNAs were converted into complementary (c)DNA (reads), then processed according to Illumina NextSeq500 guideline

treatment_protocol: AC16 were transfected with siRNA: ON-TARGETplus SMARTpool Human HMGN3 (5 nmol, Horizon Discovery, L-011932-00-0005) or ON-TARGETplus Non-targeting Pool (5 nmol, Horizon Discovery, D-001810-10-05) at a concentration of 200 nM using Lipofectamine 2000 reagent (Thermo Scientific, 11668019) according to the manufacturer’s instructions. Transfection efficiency was assessed after 48 or 72 hours.

tag: cell line

value: Human cardiomyocyte AC16 cell

value: HMGN3 knockdown


title: 63054_001, preAD, rep1

description:
Library name: 1_03_01_17
library name V2: 01_03_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

value: human

value: #N/A

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: TPH1-Venus positive, sample 3

description: Library name: D505rna.pos


title: AC16 cell, HMGN3 knockdown, ChIP-seq, replicate 2

description:
Library name: AC16-siHMGN3_ChIP-2
ChIP-seq of AC16 cell, HMGN3 knockdown


title: 63059_001, normal, rep1

description:
Library name: 9_02_28_17
library name V2: 09_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 008

tag: icap cell_culture_well_position

value: pass


title: TPH1-Venus positive, sample 1

description: Library name: D501rna.pos

tag: tissue

tag: cell type


title: AC16 cell, HMGN3 knockdown, ChIP-seq, replicate 1

description:
Library name: AC16-siHMGN3_ChIP-1
ChIP-seq of AC16 cell, HMGN3 knockdown

tag: genotype


title: 63872_001, normal, rep1

description:
Library name: 8_02_28_17
library name V2: 08_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: sample cohort

tag: plasma class


title: Con4

description: Library name: SBM205

value: tumor

tag: strain

value: mouse mammary cancer

value: wt


title: DIOSul4

description: Library name: SBM194

tag: cell line


title: PCS-480-011, 40 hours post-infection with C. trachomatis 2

city: Kuala Lumpur

first: Heng Choon

last: Cheong

address: Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya

country: Malaysia

institute: Universiti Malaya

description:
Library name: Sample 8
Column name in all.fpkm_anno.txt: 40hr-Post-Infection-2

data_processing:
Paired-end raw reads were demultiplexed using bcl2fastq.gz (Illumina) and quality filtered with fastq.gzC and Cutadapt
Clean reads were aligned to the referernce genome (GRCh38.p13) using Hisat2
Differential expression analysis was performed with DESeq2
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited file includes raw counts for each Sample
Supplementary files format and content: tab-delimited file includes FPKM values for each Sample

growth_protocol: Primary endocervical epithelial cells (PCS-480-011) were cultured in cervical epithelial cell basal medium (PCS-480-032) (ATCC) supplemented with cervical epithelial cell growth kit (PCS-480-042) (ATCC). To improve adherence, Primary endocervical epithelial cells were cultured in flasks precoated with 10 mg/mL poly-L-lysine solution (Merck Millipore) and maintained at 37°C with 5% CO2

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared with the VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme).

treatment_protocol: Primary endocervical epithelial cells (PCS-480-011) were infected with C. trachomatis (MOI = 1,000) by centrifugation at 500 × g for 30 min and incubated for 8, 24, or 40 hours

value: primary endocervical epithelial cells

tag: treatment


title: 65303_001, MCI, rep1

description:
Library name: 7_02_28_17
library name V2: 07_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sequencing plate_name


title: 65329_001, preAD, rep1

description:
Library name: 6_02_28_17
library name V2: 06_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: PCS-480-011, 40 hours post-infection with C. trachomatis

description:
Library name: Sample 7
Column name in all.fpkm_anno.txt: 40hr-Post-Infection

tag: cell type


title: ConSul3

description: Library name: SBM192

tag: tissue

tag: genotype


title: AC16 cell, wildtype, ChIP-seq, replicate 2

description:
Library name: AC16-ChIP-2
ChIP-seq of AC16 cell, wildtype

tag: cell line

value: wildtype


title: 65371_001, preAD, rep1

description:
Library name: 5_02_28_17
library name V2: 05_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: sample cohort

tag: plasma class


title: Con2

description: Library name: SBM159

tag: strain


title: DIO2

description: Library name: SBM198


title: PCS-480-011, 24 hours post-infection with C. trachomatis

description:
Library name: Sample 5
Column name in all.fpkm_anno.txt: 24hr-Post-Infection

tag: treatment


title: PCS-480-011, 8 hours post-infection with C. trachomatis 2

description:
Library name: Sample 4
Column name in all.fpkm_anno.txt: 8hr-Post-Infection-2


title: TPH1-Venus positive, sample 2

description: Library name: D503rna.pos

value: duodenum organoid

value: EC cells


title: AC16 cell, HMGN3 knockdown, BulkRNA-seq, replicate 2

description:
Library name: AC16siHMGN3-BulkRNA-2
Bulk-RNA seq of AC16 cell, HMGN3 knockdown


title: ConSul4

description: Library name: SBM195


title: Con1

description: Library name: SBM141


title: AC16 cell, HMGN3 knockdown, BulkRNA-seq, replicate 1

description:
Library name: AC16siHMGN3-BulkRNA-1
Bulk-RNA seq of AC16 cell, HMGN3 knockdown


title: AC16 cell, wildtype, ChIP-seq, replicate 1

description:
Library name: AC16-ChIP-1
ChIP-seq of AC16 cell, wildtype


title: 64881_001, MCI, rep1

description:
Library name: 4_02_28_17
library name V2: 04_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sequencing plate_name


title: DIO1

description: Library name: SBM134


title: DIOSul2

description: Library name: SBM131


title: AC16 cell, wildtype, BulkRNA-seq, replicate 3

description:
Library name: AC16-BulkRNA-3
Bulk-RNA seq of AC16 cell, wildtype


title: AC16 cell, wildtype, ChIP-seq, replicate 3

description:
Library name: AC16-ChIP-3
ChIP-seq of AC16 cell, wildtype


title: 84888_001, preAD, rep1

description:
Library name: 3_02_28_17
library name V2: 03_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DIOSul3

description: Library name: SBM168

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: ConSul2

description: Library name: SBM120

tag: strain


title: PCS-480-011, uninfected control 2

description:
Library name: Sample 2
Column name in all.fpkm_anno.txt: Uninfected-Control-2

tag: treatment

value: Uninfected control


title: PCS-480-011, 24 hours post-infection with C. trachomatis 2

description:
Library name: Sample 6
Column name in all.fpkm_anno.txt: 24hr-Post-Infection-2


title: AC16 cell, HMGN3 knockdown, BulkRNA-seq, replicate 3

description:
Library name: AC16siHMGN3-BulkRNA-3
Bulk-RNA seq of AC16 cell, HMGN3 knockdown


title: ConSul1

description: Library name: SBM102


title: 63389_001, preAD, rep1

description:
Library name: 22_02_28_17
library name V2: 22_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: experimental batch_number

tag: plasma thaw_number

tag: sample cohort

tag: plasma class


title: AC16 cell, wildtype, BulkRNA-seq, replicate 1

description:
Library name: AC16-BulkRNA-1
Bulk-RNA seq of AC16 cell, wildtype


title: PCS-480-011, uninfected control

description:
Library name: Sample 1
Column name in all.fpkm_anno.txt: Uninfected-Control


title: DIOSul1

description: Library name: SBM101


title: T4, Tumor, hepatocellular carcinoma, scTCR-seq

city: Xi'an, Shaanxi Province

first: Yungang

last: Xu

state: Shaanxi

address: Xi'an, Shaanxi Province

institute: Xi'an Jiaotong University

description:
Library name: T4-TCR
10x Genomics

data_processing:
The demuitiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.comsingle-cell.gene-expression/software/pipelines/atestwhat-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
The cells are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM. For single-cell isolation, Gel Beads in Emulsion (GEMs) were constructed based on the target cell count. Post oil treatment, the amplified cDNA was purified using magnetic beads, followed by cDNA amplification and quality assessment.
The single-cell suspension was loaded onto a microfluidic device to construct a single-cell 3' gene expression library. The final library was sequenced on the Illumina Nova6000 platform using 150 bp paired-end reads.

value: liver

value: tumor tissue


title: Frozen Meningioma Sample from Patient NU1617, ATAC

city: Chicago

first: Mark

last: Youngblood

state: IL

address: 676 N. St. Clair Street; Suite 2210

department: Department of Neurological Surgery

institute: Northwestern University

description:
Library name: NU1617 ATAC
ATAC: read1 file contains barcodes and UMI; read2 contains ATAC sequences
NU1617_barcodes.tsv.gz
NU1617_features.tsv.gz
NU1617_matrix.mtx.gz

library_source: genomic single cell

data_processing:
Sequencing was performed on the Illumina platform Novaseq X Plus at the Northwestern University NUSeq sequencing facility core, with a targeted sequencing depth of 20,000 and 25,000 reads per sample acquired for RNA and ATAC profiling, respectively. A total of 10,000 nuclei were targeted for each sample, with 25,000 scATAC-seq and 20,000 scRNA-seq reads in each nucleus.
Assembly: GRCh38
Supplementary files format and content: Files are standard output from Cellranger, including barcodes.tsv.gz, features.tsv.gz, and matrix.tsv.gz, which contains combined ATAC and RNA-seq data for each barcode. Additionally each sample has a generated fragments file for the ATAC assay: atac_fragments.tsv.gz

source_name: Meningioma

extract_protocol:
Nuclei were isolated from previously frozen meningioma specimens using the 10x Chromium Nuclei Isolation Kit with a RNase Inhibitor (PN-1000494) according to the manufacturer’s protocol.
RNA and ATAC-seq libraries were constructed using Chromium Next GEM Single Cell Multiome ATAC + Gene expression kit (10X Genomics, PN-1000281).

value: Meningioma

value: Tumor

tag: batch


title: T4, Tumor, hepatocellular carcinoma

description:
Library name: T4
10x Genomics


title: 65024_001, normal, rep1

description:
Library name: 21_02_28_17
library name V2: 21_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sequencing plate_name

value: low RIN


title: 65978_001, MCI, rep1

description:
Library name: 20_02_28_17
library name V2: 20_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: Aim 2 Batch 008

tag: icap cell_culture_well_position

value: #N/A

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: The strain S. oralis CRC211

city: Shanghai

first: yunjie

last: shi

address: No 800，Xiangyin Road

institute: Naval Medical University

description: Library name: strain

data_processing:
The raw data (raw reads) obtained from Illumina NovaSeq 6000 sequencing
The connectors at both ends of the reads, and the reads with fragment length less than 17nt and low-quality read were removed to complete the preliminary filtering of data and obtain high-quality data (clean reads).
C++and R languages were used to control the quality of raw data to obtain clean and high-quality data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Count values
Library strategy: 16S rRNA-seq

source_name: CRC tumor

extract_protocol:
NucleoBond® HMW DNA kit (MN NucleoBond, Germany, 740160.20) was used for high-quality genome extraction of samples. DNA concentration and purity were determined via Qubit4.0 (Thermo, Q33226) and Nanodrop (SMA4000, taiwan, China). DNA integrity was assessed by 0.75% agarosegel electrophoresis.
The libraries were subjected to single-molecule real-time sequencing on PacBio Sequel II using Sequel II Binding Kit 2.0 for template preparation.

tag: tissue

value: CRC tumor

value: paired-end


title: Frozen Meningioma Sample from Patient NU1617, GEX

description:
Library name: NU1617 GEX
3' mRNA library: read1 file contains barcodes and UMI; read 2 file contains transcript
NU1617_barcodes.tsv.gz
NU1617_features.tsv.gz
NU1617_matrix.mtx.gz

molecule: nuclear RNA


title: PCS-480-011, 8 hours post-infection with C. trachomatis

description:
Library name: Sample 3
Column name in all.fpkm_anno.txt: 8hr-Post-Infection

tag: cell line

value: primary endocervical epithelial cells

tag: treatment


title: T3, Tumor, hepatocellular carcinoma

description:
Library name: T3
10x Genomics


title: 65947_001, preAD, rep1

description:
Library name: 24_02_28_17
library name V2: 24_02_28_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)

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.

tag: preculture time_(days)

tag: incubation conditions

tag: experimental batch_number

tag: plasma thaw_number

tag: sample cohort


title: 64782_001, MCI, rep1

description:
Library name: 23_02_28_17
library name V2: 23_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma class


title: 65159_001, preAD, rep1

description:
Library name: 19_02_28_17
library name V2: 19_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sequencing plate_name


title: T2, Tumor, hepatocellular carcinoma

description:
Library name: T2
10x Genomics


title: Frozen Meningioma Sample from Patient NU1142, ATAC

description:
Library name: NU1142 ATAC
ATAC: read1 file contains barcodes and UMI; read2 contains ATAC sequences
NU1142_barcodes.tsv.gz
NU1142_features.tsv.gz
NU1142_matrix.mtx.gz

tag: cell type

tag: batch


title: Frozen Meningioma Sample from Patient NU1142, GEX

description:
Library name: NU1142 GEX
3' mRNA library: read1 file contains barcodes and UMI; read 2 file contains transcript
NU1142_barcodes.tsv.gz
NU1142_features.tsv.gz
NU1142_matrix.mtx.gz

tag: tissue


title: LV 156, MlklAdi-KO, hfd

city: Paris

first: Jérémie

last: Gautheron

address: 27 rue Chaligny

country: France

institute: Inserm, Sorbonne Université

description: Library name: LV156

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene. And then FPKM of each gene was calculated based onthelength of the gene and reads count mapped to this gene.
Assembly: mm39
Supplementary files format and content: Excel file (.xlsx) contains fpkm counts for each sample in separate columns and each gene in separate rows.

source_name: Liver

extract_protocol:
RNA was extracted using TRIzol reagent for adipose tissue and the Nucleospin RNA Mini Kit for liver tissue
The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection. Quantified libraries will bepooled and sequenced on Illumina platforms, according to effective libraryconcentration and data amount.

value: Liver

tag: genotype

value: MlklAdi-KO

tag: treatment

value: High fat diet


title: T1, Tumor, hepatocellular carcinoma

description:
Library name: T1
10x Genomics


title: LV 157, MlklAdi-KO, hfd

description: Library name: LV157


title: AC16 cell, wildtype, BulkRNA-seq, replicate 2

description:
Library name: AC16-BulkRNA-2
Bulk-RNA seq of AC16 cell, wildtype

tag: cell line

value: Human cardiomyocyte AC16 cell

value: wildtype


title: LV 153, MlklAdi-KO, hfd

description: Library name: LV153


title: N4, Normal, hepatocellular carcinoma, scTCR-seq

description:
Library name: N4-TCR
10x Genomics

value: liver

value: adjacent tissue


title: Frozen Meningioma Sample from Patient NU0821, ATAC

description:
Library name: NU0821 ATAC
ATAC: read1 file contains barcodes and UMI; read2 contains ATAC sequences
NU0821_barcodes.tsv.gz
NU0821_features.tsv.gz
NU0821_matrix.mtx.gz

value: Meningioma

value: Tumor


title: 67008_001, normal, rep1

city: Potomac

last: Smith

address: Windsor View Dr

institute: PreCyte, Inc.

description:
Library name: 18_02_28_17
library name V2: 18_02_28_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

value: human

tag: experimental batch_number

tag: icap cell_culture_well_position

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 23508_001, MCI, rep1

description:
Library name: 17_02_28_17
library name V2: 17_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 008

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

value: #N/A

value: RNASeq QC


title: N4, Normal, hepatocellular carcinoma

description:
Library name: N4
10x Genomics


title: LV 152, MlklAdi-KO, hfd

description: Library name: LV152


title: LV 151, MlklAdi-KO, hfd

description: Library name: LV151


title: Frozen Meningioma Sample from Patient NU1795M, ATAC

description:
Library name: NU1795 ATAC
ATAC: read1 file contains barcodes and UMI; read2 contains ATAC sequences
NU1795_barcodes.tsv.gz
NU1795_features.tsv.gz
NU1795_matrix.mtx.gz

tag: cell type

tag: batch


title: N3, Normal, hepatocellular carcinoma

description:
Library name: N3
10x Genomics

tag: tissue


title: LV 164, WT, hfd

description: Library name: LV164

tag: genotype

value: WT

tag: treatment


title: reference_001, reference, rep13

description:
Library name: 15_02_28_17
library name V2: 15_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: reference

tag: sequencing plate_name


title: 66055_001, normal, rep1

description:
Library name: 14_02_28_17
library name V2: 14_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: experimental batch_number

tag: icap cell_culture_well_position

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN

value: pass


title: Frozen Meningioma Sample from Patient NU1795M, GEX

description:
Library name: NU1795 GEX
3' mRNA library: read1 file contains barcodes and UMI; read 2 file contains transcript
NU1795_barcodes.tsv.gz
NU1795_features.tsv.gz
NU1795_matrix.mtx.gz


title: reference_001, reference, rep14

description:
Library name: 2_02_28_17
library name V2: 02_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: sample cohort


title: Meningioma Cells from Patient NU3981, 8803 Treatment

description:
Library name: NU3981 8803
RSEM output file

data_processing:
Following RNA purification, all samples were sequenced on the Illumina platform Novaseq X Plus. Raw FASTQ files were processed using the standard ENCODE pipeline with initial adapted trimming using Trim Galore! (v.0.6.1) with the paired parameter. Subsequently, trimmed reads were mapped to genome (GRCh38) using STAR and quantified using RSEM.
Assembly: GRCh38
Supplementary files format and content: Files are standard output from RSEM which provides a tab delimited file with the expected counts, TPM, and FPKM values.

growth_protocol: Meningioma cells were washed and then plated as 5 x 105 viable cells/well in triplicates. The cells were incubated for 24-72h at 37°C in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with GlutaMAX™ (Gibco) and 10% FBS.

extract_protocol:
RNA was isolated using the All Prep RNA/DNA Mini kit (Qiagen; cat #80204), after tissue lysis and homogenization steps.
TruSeq Stranded Total RNA Library Preparation Kit (Illumina) was used to prepare sequencing libraries from total RNA. This included Ribo-Zero rRNA Removal, cDNA synthesis, 3′ end adenylation, adapter ligation, library PCR amplification, and validation steps.

treatment_protocol: Cells frpm each patient received both control treatment and treatment with 8803 STING agonist (10μm).

tag: tissue

tag: cell type

tag: batch


title: N2, Normal, hepatocellular carcinoma

description:
Library name: N2
10x Genomics

tag: treatment


title: LV 162, WT, hfd

description: Library name: LV162

value: Liver

tag: genotype

value: High fat diet


title: N1, Normal, hepatocellular carcinoma

description:
Library name: N1
10x Genomics


title: LV 161, WT, hfd

description: Library name: LV161


title: 64708_001, preAD, rep1

description:
Library name: 12_02_28_17
library name V2: 12_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: plasma class


title: shFAM49B_2

city: Dalian

first: ning

last: shen

address: 9 Western Section,Lvshun South Street,Lvshunkou District

institute: Dalian Medical University

description:
Library name: Sample 4
C4

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction: o.8 similarity fraction:0.8 )
Read count extraction and normalization were perommed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Knowdown FAM49B gene

growth_protocol: Human ovarian cancer cell lines OVCAR8 were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with RPMI-1640 (Gibco) medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin and 100 mg/mL streptomycin

extract_protocol:
After the total RNA extraction,RNA degradation and contamination was detected by 1% agarose gels; RNA purity and concentration was checked by Nanodrop2000（Thermo Fisher Scientific，MA，USA）；RNA concentration was checked using the Qubit® 3.0 Flurometer（Thermo Fisher Scientific，MA，USA）；RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The lentiviral vectors encoding short hairpin RNAs (GIPZ shRNAs) targeting FAM49B and scrambled shRNA were purchased from Dharmacon (America). The plasmids were transiently transfected into cells with Lipofectamine 3000 (Invitrogen, CA) according to the manufacturer’s protocol. Cells were harvested and analyzed 36 h after transfection.

tag: cell line

value: ovarian cancer

value: Knockdown FAM49B gene


title: Meningioma Cells from Patient NU3971, 8803 Treatment

description:
Library name: NU3971 8803
RSEM output file


title: Meningioma Cells from Patient NU3981, Control Treatment

description:
Library name: NU3981 Control
RSEM output file

value: Control


title: LV 154, WT, hfd

description: Library name: LV154


title: LV 155, WT, hfd

description: Library name: LV155


title: Meningioma Cells from Patient NU3971, Control Treatment

description:
Library name: NU3971 Control
RSEM output file

value: Meningioma


title: 64206_001, normal, rep1

first: Jennifer

description:
Library name: 11_02_28_17
library name V2: 11_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

source_name: iCell Neurons

tag: incubation conditions

tag: experimental batch_number

tag: icap cell_culture_well_position

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: shFAM49B_1

description:
Library name: Sample 3
C3


title: shCON_2

description:
Library name: Sample 2
C2

source_name: Negative Control


title: shCON_1

description:
Library name: Sample 1
C1


title: LV 199, MlklAdi-KO, ncd

description: Library name: LV199

tag: tissue

value: MlklAdi-KO

value: Normal chow diet


title: 65140_001, preAD, rep1

description:
Library name: 16_02_28_17
library name V2: 16_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: sample cohort


title: 23496_001, MCI, rep1

description:
Library name: 10_02_28_17
library name V2: 10_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: human

value: Aim 2 Batch 008

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id


title: Frozen Meningioma Sample from Patient NU0821, GEX

description:
Library name: NU0821 GEX
3' mRNA library: read1 file contains barcodes and UMI; read 2 file contains transcript
NU0821_barcodes.tsv.gz
NU0821_features.tsv.gz
NU0821_matrix.mtx.gz

value: Tumor

tag: batch


title: 65343_001, normal, rep1

description:
Library name: 1_02_28_17
library name V2: 01_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma shipment_batch

tag: plasma class

value: #N/A


title: LV 197, MlklAdi-KO, ncd

description: Library name: LV197

tag: genotype

tag: treatment


title: Meningioma Cells from Patient ITA-72, Control Treatment

description:
Library name: ITA-72 Control
RSEM output file


title: CellsOnly_001, CellsOnly, rep1

description:
Library name: 24_02_24_17
library name V2: 24_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: experimental batch_number

value: Aim 2 Batch 007

tag: icap cell_culture_well_position

value: CellsOnly

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: siLMNA_rep2

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Biology

country: India

institute: Indian Institute of Science Education and Research PUNE

description:
Library name: Sample 4
DEseq_siLacZ-Rep2_vs_siLMNA-Rep2.xlsx

data_processing:
Reference-based RNA-Seq data analysis
Assembly: hg38
Supplementary files format and content: Excel file containing raw read, normalised read counts, log2(fold change) and adjusted p-values

source_name: Breast

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium/F12 (1:1) medium (Invitrogen #11330-032) supplemented with 5% horse serum (Invitrogen#16050-122), human epidermal growth factor (Peprotech #AF-100-15; 20 ng/ml), hydrocortisone (Sigma #H-0888; 0.5 mg/ml), cholera toxin (0.1 mg/ml) from Vibrio cholerae (Sigma #C-8052), insulin (Sigma #I-1882; 10 mg/ml) from bovine pancreas (Sigma), and 1× antibiotic mixture (Gibco #10378016).

extract_protocol:
Samples in trizol was sent to Medgenome, Bengaluru for futher RNA exraction, qaulity control checks and further sequencing and analysis.
Poly(A) capture, ligation-based addition of adapters and indexes

treatment_protocol: 0.35 million cells are seeded in a well of 6-well plate or 35mm dish a day prior to transfection. On the day of transfection, cells are cultured in Opti-MEM, and 50nM of siRNA is added to the cells along with 4uL of RNAiMAX. Six hours post-transfection, opti-MEM is replaced by maintenance media. At the end of 48 hours, cells were collected in TRIzol.

tag: tissue

value: Breast

tag: cell line

tag: cell type

value: Normal mammary epithelial cells

value: Lamin A/C knockdown

value: Knockdown


title: LV 179, MlklAdi-KO, ncd

description: Library name: LV179

value: Liver


title: siLMNA_rep1

description:
Library name: Sample 3
DEseq_siLacZ-Rep1_vs_siLMNA-Rep1.xlsx


title: Meningioma Cells from Patient ITA-56, 8803 Treatment

description:
Library name: ITA-56 8803
RSEM output file

value: Meningioma


title: LV 166, MlklAdi-KO, ncd

description: Library name: LV166

value: MlklAdi-KO


title: Meningioma Cells from Patient ITA-56, Control Treatment

description:
Library name: ITA-56 Control
RSEM output file

value: Control


title: 24593_001, MCI, rep1

description:
Library name: 13_02_28_17
library name V2: 13_02_28_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: sample cohort

value: pass


title: LV 183, WT, ncd

description: Library name: LV183

value: WT

value: Normal chow diet


title: AC077_001, MCI, rep1

description:
Library name: 22_02_24_17
library name V2: 22_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

value: 5% plasma, 6 h

value: human

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: plasma class


title: LV 182, WT, ncd

description: Library name: LV182

tag: genotype

tag: treatment