title: MM Cell line6

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

description: Library name: ANBL-6

data_processing:
Partek® Flow® software version 11.0.23.1204, Bowtie2 v2.2.5
Partek® Flow® software version 11.0.23.1204, STAR v2.7.8a
Adaptors were trimmed using CUTADAPT v4.2 to conform to a quality trim with a quality cutoff of 20. Trimming was performed on first and second mate adapters from both the 3’ and 5’ ends and read lengths shorter than 16nt were discarded.
RNAs data was aligned to the GRCh38 (hg38) reference genome.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts of miRNAs for each sample
Supplementary files format and content: tab-delimited text file includes raw counts of RNAs for each sample

source_name: Exosomes were isolated from cell line

growth_protocol: All cell lines were cultured in RPMI media (Cytvia) with 10% exosome-depleted fetal bovine serum (Gibco), 1% penicillin-streptomycin (Cytvia), and 1x GlutaMAX (Gibco). The ANBL-6 cell line was dependent on 1 ng/ml IL-6. H929 cells required 50 µM 2-Mercaptoethanol (Thermo Scientific). MM patient samples were obtained from bone marrow aspirate supernatant following centrifugation. Primary human MM cells were recovered from bone marrow aspirates collected from all Mayo Clinic sites. Informed consent was given in writing for collection and research use under Institutional Review Board approval (IRBs 919-04, 15–009436, 18–003198, 2207-02) in accordance with the Declaration of Helsinki.

extract_protocol:
RNAs were isolated from exosomes using the MagMAX™ mirVana™ Total RNA Isolation Kit (Thermo Scientific), following the manufacturer’s protocol. After isolation, the RNA concentration was determined using a NanoDrop spectrophotometer (Thermo Scientific), and RNA integrity was assessed with an Agilent Bioanalyzer (Agilent Technologies).
For library preparation, the isolated RNA was processed using the NEXTFLEX® Small RNA-Seq Kit v4 with UDIs (Revvity) according to the manufacturer’s instructions. This protocol involved 3’ and 5’ adapter ligation, reverse transcription, PCR amplification, and size selection. Libraries were quantified using Qubit dsDNA HS Assay (Thermo Scientific) and validated for size distribution using a Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina NovaSeq X Plus platform, following the standard procedures for small RNA sequencing.

treatment_protocol: The treatments administered to patients prior to sample collection were documented in their medical records. In contrast, the cell line samples were not exposed to any pharmacological agents.

value: Cell line

value: Exosomes were isolated from cell line

tag: gender

value: not applicable

tag: patient status


title: AC841_001, preAD, rep1

status: Public on Dec 02 2025

type: SRA

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

country: USA

institute: PreCyte, Inc.

description:
Library name: 21_02_24_17
library name V2: 21_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: iCell Neurons

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

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

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

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 007

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: siLacZ_rep1

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 1
DEseq_siLacZ-Rep1_vs_siLMNA-Rep1.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

tag: genotype

value: LacZ(WT)

tag: treatment

value: Knockdown


title: LV 180, WT, ncd

city: Paris

first: Jérémie

last: Gautheron

address: 27 rue Chaligny

country: France

institute: Inserm, Sorbonne Université

description: Library name: LV180

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.

molecule: total RNA

organism: Mus musculus

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

value: WT

value: Normal chow diet


title: BQ258_001, normal, rep1

description:
Library name: 23_02_24_17
library name V2: 23_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number


title: MM Cell line4

description: Library name: U-266

tag: gender

tag: patient status


title: TAHU_485_2

city: Xi’an

first: mao

last: zhao

state: Shaanxi

address: No 127 of West Changle Road

country: China

institute: Xijing Hospital, Air Force Medical University

description: Library name: NALA plus A485_2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release101
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: human huvec

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: human huvec

value: endothelial cells

value: NALA plus A485


title: Meningioma Cells from Patient ITA-72, 8803 Treatment

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: ITA-72 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.

source_name: Meningioma

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).

value: Meningioma

value: Tumor

tag: batch


title: LV 165, WT, ncd

description: Library name: LV165


title: MM Cell line5

description: Library name: KMS-11

value: Cell line

value: Exosomes were isolated from cell line

value: not applicable


title: TAHU_485_3

description: Library name: NALA plus A485_3


title: MM Cell line3

description: Library name: JJN-3


title: BQ6149_001, preAD, rep1

description:
Library name: 20_02_24_17
library name V2: 20_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

value: human

tag: experimental batch_number

value: Aim 2 Batch 007

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A


title: TAHU_485_1

description: Library name: NALA plus A485_1

tag: cell line

tag: cell type

tag: treatment


title: MM Cell line2

description: Library name: NCI-H929

tag: genotype


title: eWAT 157, MlklAdi-KO, hfd

description: Library name: eWAT157

source_name: Epididymal adipose tissue

tag: tissue

value: Epididymal adipose tissue

value: MlklAdi-KO

value: High fat diet


title: TAHU_LA_3

description: Library name: NALA3

value: NALA


title: 2BQ6133_001, preAD, rep1

description:
Library name: 18_02_24_17
library name V2: 18_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: eWAT 156, MlklAdi-KO, hfd

description: Library name: eWAT156


title: MM Cell line1

description: Library name: LP1

tag: gender

tag: patient status


title: TAHU_LA_2

description: Library name: NALA2

value: human huvec

value: endothelial cells


title: ACBQ0466_001, MCI, rep1

description:
Library name: 17_02_24_17
library name V2: 17_02_24_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: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: BQ6150_001, MCI, rep1

description:
Library name: 16_02_24_17
library name V2: 16_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: plasma class


title: AC847_001, MCI, rep1

description:
Library name: 19_02_24_17
library name V2: 19_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)


title: reference_001, reference, rep12

description:
Library name: 15_02_24_17
library name V2: 15_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

value: reference

tag: sequencing plate_name

tag: rna-seq date


title: eWAT 153, MlklAdi-KO, hfd

description: Library name: eWAT153

tag: tissue

tag: genotype

tag: treatment


title: Healthy Control7

description: Library name: NormalHuman

source_name: Exosomes were isolated from bone marrow aspirates

value: Control

tag: gender

value: Female

tag: patient status


title: TAHU_3

description: Library name: Vehicle3

tag: cell line

value: Vehicle


title: siLacZ_rep2

description:
Library name: Sample 2
DEseq_siLacZ-Rep2_vs_siLMNA-Rep2.xlsx

value: Breast

value: Normal mammary epithelial cells

value: LacZ(WT)

value: Knockdown


title: TAHU_LA_1

description: Library name: NALA1


title: eWAT 151, MlklAdi-KO, hfd

description: Library name: eWAT151


title: Healthy Control5

description: Library name: HMN822874

value: Exosomes were isolated from bone marrow aspirates


title: Healthy Control6

description: Library name: HMN822875


title: eWAT 164, WT, hfd

description: Library name: eWAT164

value: WT


title: AC078_001, normal, rep1

description:
Library name: 13_02_24_17
library name V2: 13_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

value: human

tag: experimental batch_number

value: Aim 2 Batch 007

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

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN


title: TAHU_2

description: Library name: Vehicle2

value: human huvec

tag: cell type

value: endothelial cells


title: Healthy Control4

description: Library name: HMN822873

value: Control


title: TAHU_1

description: Library name: Vehicle1


title: eWAT 162, WT, hfd

description: Library name: eWAT162

value: Epididymal adipose tissue

value: High fat diet


title: BQ356_001, normal, rep1

description:
Library name: 12_02_24_17
library name V2: 12_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: sample cohort

tag: plasma class

value: pass


title: AC224_001, normal, rep1

description:
Library name: 14_02_24_17
library name V2: 14_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: sequencing plate_name

tag: rna-seq date


title: Healthy Control3

description: Library name: HMN822872

tag: genotype

tag: gender

value: Male

tag: patient status

tag: treatment


title: Job Syndrome Broncho brush KON26

city: Chapel Hill

first: Ling

last: Sun

state: NC

address: 125 Mason Farm RD 7230K Marsico Hall 7230K Marsico Hall

institute: UNC at Chapel Hill

description: Library name: CG-17

data_processing:
Raw data in fastq files were mapped to reference genome/transcriptome using STAR aligner to generate .BAM files.
Gene expression was estimated based on the BAM file with transcript assembler, StringTie v2, and saved as count and TPM values.
Assembly: GRCh38 and Gencode v37
Supplementary files format and content: Estimated raw count in tab-delimited text.
Supplementary files format and content: Estimated TPM (transcripts per million mapped reads) in tab-delimited text.

source_name: Broncho brushing tissue

extract_protocol:
Total RNA was isolated from broncho brushing tissues using the Trizol and Diret-zol RNA Miniprep kit(Zymo Research)
PolyA selection for mRNA species, 30M read per sample

tag: tissue

value: Broncho brushing tissue


title: AC643_001, preAD, rep1

description:
Library name: 11_02_24_17
library name V2: 11_02_24_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: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: eWAT 161, WT, hfd

description: Library name: eWAT161


title: Job Syndrome Broncho brush KON23

description: Library name: CG-16


title: eWAT 155, WT, hfd

description: Library name: eWAT155


title: eWAT 154, WT, hfd

description: Library name: eWAT154


title: 2BQ0292_001, normal, rep1

description:
Library name: 10_02_24_17
library name V2: 10_02_24_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: rnaseq qc_(basis_for_omission)_(step_5)


title: Healthy Control1

description: Library name: HMN822870

tag: genotype


title: Job Syndrome Broncho brush KON17

description: Library name: CG-14


title: eWAT 152, MlklAdi-KO, hfd

description: Library name: eWAT152

value: MlklAdi-KO


title: Job Syndrome Broncho brush KON16

description: Library name: CG-13


title: MM patient24

description: Library name: BM071870PL001

value: Hyperdiploid

value: Exosomes were isolated from bone marrow aspirates

tag: gender

value: Alive


title: Job Syndrome Broncho brush KON13

description: Library name: CG-11


title: MM patient23

description: Library name: BM071591PL001

value: t(11;14), 1q gain and monosomy 13

tag: patient status

value: Deceased

value: VRd//KRd//DRd//ASCT//DR//VEN +DRd//Pd


title: 2ELBQ0287_001, MCI, rep1

description:
Library name: 08_02_24_17
library name V2: 08_02_24_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

value: Aim 2 Batch 007

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date


title: BQ6164_001, normal, rep1

description:
Library name: 07_02_24_17
library name V2: 07_02_24_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: icap cell_culture_well_position


title: eWAT 199, MlklAdi-KO, ncd

description: Library name: eWAT199

tag: tissue

value: Epididymal adipose tissue

tag: treatment

value: Normal chow diet


title: eWAT 179, MlklAdi-KO, ncd

description: Library name: eWAT179


title: MM patient22

description: Library name: BM070356PL001

value: 1q gain, t(14;16) and monosomy 13

tag: cell type

value: Whitout treatment Newly diagnosed


title: AC097_001, preAD, rep1

description:
Library name: 05_02_24_17
library name V2: 05_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: pass


title: Healthy Control2

description: Library name: HMN822871

tag: genotype

value: Control

tag: gender

value: Male

tag: patient status


title: Job Syndrome Broncho brush KON10

description: Library name: CG-10

value: Broncho brushing tissue


title: MM patient21

description: Library name: BM070087PL001

value: trisomy 7, trisomy 11, monosomy 13

value: Exosomes were isolated from bone marrow aspirates

value: Alive


title: MM patient19

description: Library name: BM069122PL001

value: Rd//IPd//Ven


title: AXBQ0402_001, MCI, rep1

description:
Library name: 09_02_24_17
library name V2: 09_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma sample_replicate_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: RQS


title: AC807_001, preAD, rep1

description:
Library name: 04_02_24_17
library name V2: 04_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

value: human

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: eWAT 166, MlklAdi-KO, ncd

description: Library name: eWAT166

tag: tissue

value: MlklAdi-KO

tag: treatment


title: MM patient20

description: Library name: BM069513PL001

value: monosomy 17, monosomies 13, 14, 1, and 8.

tag: cell type

value: Deceased

value: VRd/KRd//ASCT//DKd//KPd


title: Job Syndrome Broncho brush KON9

description: Library name: CG-9


title: Healthy Donor Broncho brush KON27

description: Library name: CG-8


title: Healthy Donor Broncho brush KON24

description: Library name: CG-6


title: MM patient18

description: Library name: BM068035PL001

value: 1q gain, monosomy 13, and trisomies 3, 8, 9 and 11.

value: Whitout treatment Newly diagnosed


title: reference_001, reference, rep11

description:
Library name: 02_02_24_17
library name V2: 02_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: Aim 2 Batch 007

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: reference

value: #N/A


title: eWAT 180, WT, ncd

description: Library name: eWAT180

value: Epididymal adipose tissue

tag: genotype

value: WT

value: Normal chow diet


title: Healthy Donor Broncho brush KON20

description: Library name: CG-4

value: Broncho brushing tissue


title: AC108_001, normal, rep1

description:
Library name: 01_02_24_17
library name V2: 01_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma sample_replicate_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

value: pass


title: Healthy Donor Broncho brush KON25

description: Library name: CG-7


title: BQO142_001, preAD, rep1

description:
Library name: 03_02_24_17
library name V2: 03_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: MM patient16

description: Library name: BM067722PL001

value: Exosomes were isolated from bone marrow aspirates

tag: gender

value: Male

tag: patient status

value: Alive

tag: treatment

value: VRd


title: eWAT 182, WT, ncd

description: Library name: eWAT182

tag: tissue


title: resistant_3

city: Kobe

first: Weijia

last: Zang

address: Hyogo, Kobe, Chuo Ward, Minatojima Minamimachi, 6 Chome−３−7

department: Department of Hematology-Oncology

country: Japan

institute: Foundation for Biomedical Research and Innovation at Kobe

description: Library name: Smaple 8

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 at a depth of ~30M 2x151 bp reads per sample.
The FASTQ-sequenced reads were mapped to the mm10 genome using Hisat2.
Gene counts calculated by FeatureCounts were normalized and differentially expressed genes were identified with Adjusted p value < 0.05 by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Bone marrow

extract_protocol:
MACS sorted cells were proceeded to RNA extraction using RNeasy columns (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Preparation Kit.

value: Bone marrow

tag: strain

tag: cell type

value: c-Kit+ CD45.2+ bone marrow cells


title: MM patient17

description: Library name: BM067850PL001

value: 1q amplification (5 copies), t(4;14), trisomy 8 and monosomy 13

value: Deceased

value: VRD//Kd//Rd//IxaPd


title: eWAT 165, WT, ncd

description: Library name: eWAT165


title: 2BQ0334_001, MCI, rep1

description:
Library name: 06_02_24_17
library name V2: 06_02_24_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

value: Aim 2 Batch 007

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: #N/A


title: eWAT 183, WT, ncd

description: Library name: eWAT183

value: Epididymal adipose tissue

tag: genotype

value: WT

value: Normal chow diet


title: Healthy Donor Broncho brush KON14

description: Library name: CG-3

value: Broncho brushing tissue


title: 2AC2BQ0222_001, preAD, rep1

description:
Library name: 9_02_10_17
library name V2: 09_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 006

tag: plasma thaw_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

value: pass


title: eWAT 197, MlklAdi-KO, ncd

description: Library name: eWAT197

tag: tissue

value: MlklAdi-KO

tag: treatment


title: 2ACBQ071_001, preAD, rep1

description:
Library name: 8_02_10_17
library name V2: 08_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: EL301_001, MCI, rep1

description:
Library name: 7_02_10_17
library name V2: 07_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_plate_number


title: MM patient15

description: Library name: BM067593PL001

tag: genotype

value: Exosomes were isolated from bone marrow aspirates

tag: gender

value: Male

tag: patient status

value: Alive

value: Whitout treatment Newly diagnosed


title: treatment_2

description: Library name: Smaple 5

value: Bone marrow

tag: strain

value: c-Kit+ CD45.2+ bone marrow cells


title: Healthy Donor Broncho brush KON12

description: Library name: CG-2


title: resistant_2

description: Library name: Smaple 7


title: Healthy Donor Broncho brush KON11

description: Library name: CG-1


title: MM patient14

description: Library name: BM065549PL001

value: 1q gain, monosomy 13, deletion MYC, trisomies 3, 7, 9 and 15.

value: Female


title: resistant_1

description: Library name: Smaple 6


title: treatment_1

description: Library name: Smaple 4


title: D45Q Mu-STAT3 IL1b

description: Library name: 54

data_processing:
Raw data in fastq files were mapped to reference genome/transcriptome using STAR aligner to generate .BAM files.
Gene expression was estimated based on the BAM file with transcript assembler, StringTie v2, and saved as count and TPM values.
Assembly: GRCh38 and Gencode v40
Supplementary files format and content: Estimated raw count in tab-delimited text.
Supplementary files format and content: Estimated TPM (transcripts per million mapped reads) in tab-delimited text.

source_name: human broncho epithelial cell

value: human broncho epithelial cell

tag: batch

value: 2nd batch


title: AC122_001, preAD, rep1

description:
Library name: 6_02_10_17
library name V2: 06_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A


title: MM patient13

description: Library name: BM061446PL001

value: Hyperdiploid, 1q amplification (4 copies)

tag: cell type

tag: treatment


title: D45Q WT-STAT3 IL1b

description: Library name: 53


title: vehicle_3

description: Library name: Smaple 3

tag: tissue


title: MM patient12

description: Library name: BM061265PL001

value: Vd + Doxil//ASCT//R//Venetoclax


title: MM patient10

description: Library name: BM060682PL001

value: Hyperdiploid

value: Rd//ASCT//R//Vd


title: MM patient11

description: Library name: BM060685PL001

value: Hyperdiploid, 1q gain


title: BQ206_001, MCI, rep1

description:
Library name: 5_02_10_17
library name V2: 05_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: Aim 2 Batch 006

tag: icap cell_culture_plate_number

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: BQ9121_001, normal, rep1

description:
Library name: 4_02_10_17
library name V2: 04_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: 2BQ0484_001, MCI, rep1

description:
Library name: 3_02_10_17
library name V2: 03_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: vehicle_1

description: Library name: Smaple 1

value: Bone marrow

tag: strain

tag: cell type

tag: genotype


title: D45Q NC IL1b

description: Library name: 52

value: NC

tag: treatment

tag: batch


title: MM patient9

description: Library name: BM060512PL001

value: Hyperdiploid, monosomy 13, 1q gain

value: Exosomes were isolated from bone marrow aspirates

tag: gender

tag: patient status

value: Deceased

value: CyBORd//ASCT//IxaRd//DKCd//DPKd


title: D45Q Mu-STAT3

description: Library name: 51

value: human broncho epithelial cell

value: Vehicle

value: 2nd batch


title: vehicle_2

description: Library name: Smaple 2

tag: tissue

value: c-Kit+ CD45.2+ bone marrow cells


title: D45Q NC

description: Library name: 49


title: P23H/Gnat2-kO double-mutant mice

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

description:
Library name: Sc-RNAseq-Sample 2
10× Genomics Chromium Single Cell system using v3 chemistry

library_source: transcriptomic single cell

data_processing:
The preprocessing steps such as generation and demultiplexing of FASTQ files from raw sequencing reads (bclfastq, v2.20), aligning to UCSC mm10 transcriptome, and generating raw count matrices were conducted using Cell Ranger (v6.0.1) with default parameters. Cumulus software v1.5.0 was used to combine expression matrices  and to remove cell doublets by Scrublet v0.2.1 . The pipelines were run in Terra Cloud Platform (https://app.terra.bio/).  Seurat v3.2.2 was used to perform downstream analysis following the standard pipeline using cells with >=200 genes, resulting in of 5805 Gnat2-/- and 7266 P23H/Gnat2-/- cells. Principal Component (PC) analysis was performed on a submatrix of the top 2,000 most variable genes computed using the function FindVariableGenes in Seurat. Batch effect between experimental conditions was minimzed using the Harmony package v0.1.0 to remove non-cell-type-specific factors that may impact clustering. The number of top PCs was assessed by the elbow method, keeping 25 PCs for clustering and data visualization. Cells were clustered using a shared nearest neighbor modularity optimization-based algorithm (FindClusters in Seurat). Cluster-specific genes were computed by FindAllMarkers in Seurat, using the MAST test with number of UMIs detected as a latent variable. The same test was used to identify differentially expressed genes between experimental groups within cell clusters, which were annotated according to retinal cell-type-specific markers.
Assembly: mm10
Supplementary files format and content: bam, mtx,txt
Supplementary files format and content: bam, mtx,txt

source_name: retina

growth_protocol: All mice were housed under vivarium conditions throughout their life with ad libitum access to food and water.

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, the retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions.
In each experimental group, one retina each from n=4 mice (2 females and 2 males) were pooled and used for single cell RNA-seq (scRNA-seq). For each group, freshly dissociated cells (~16,500) were loaded into a 10× Genomics Chromium Single Cell system using v3 chemistry following the manufacturer’s instructions. Libraries were pooled and sequenced on Illumina NovaSeq6000 platform.

value: retina


title: BQ6127_001, normal, rep1

description:
Library name: 23_02_10_17
library name V2: 23_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_plate_number

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name


title: D45Q WT-STAT3

description: Library name: 50


title: MM patient8

description: Library name: BM060412PL001

value: Hyperdiploid, 1q duplication (4 copies)

value: Female

value: Whitout treatment Newly diagnosed


title: MM patient7

description: Library name: BM060175PL001

value: 1q gain, t(11;14), monosomy 13

value: Male

value: Alive


title: D75P Mu-STAT3 IL1b

description: Library name: 48


title: LP0495_001, MCI, rep1

description:
Library name: 22_02_10_17
library name V2: 22_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 006

tag: plasma thaw_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: Gnat2-knockout mice

description:
Library name: Sc-RNAseq-Sample 1
10× Genomics Chromium Single Cell system using v3 chemistry

treatment_protocol: All mice were housed under vivarium conditions throughout their life with ad libitum access to food and water.

tag: tissue

tag: genotype

tag: batch


title: D75P WT-STAT3 IL1b

description: Library name: 47

tag: cell type

value: human broncho epithelial cell

tag: treatment


title: ACBQ0392_001, normal, rep1

description:
Library name: 24_02_10_17
library name V2: 24_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_plate_number

value: RQS


title: Liver tissues, MSA_ConA 3#

city: Tianjin

first: Zhang

last: Qian

address: No. 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

description: Library name: MSA_ConA 3#

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: Eight-week-old male C57BL/6J mice (20–25 g) were sourced from Beijing Vital River Laboratory Animal Technology Co., Ltd. (Beijing, China). The selection of male mice was to preclude any potential effects of the estrous cycle or hormonal fluctuations on the experimental outcomes.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were randomized into three groups: (1) Normal control, (2) ConA, (3) MSA + ConA. The normal control group received an equivalent volume of sterile phosphate-buffered saline (PBS) via tail vein injection. ConA and MSA were dissolved in sterile PBS to achieve the specified concentrations. The ConA group received a single dose of ConA (20 mg/kg body weight, 4 mg/ml in PBS, Sigma-Aldrich, China) via tail vein injection. The MSA + ConA group received an intraperitoneal injection of MSA (250 mg/kg body weight, 50 mg/ml in PBS, Sigma-Aldrich, China) 6 hours before ConA injection. Twelve hours post-ConA administration, mice were euthanized, and  liver tissues (n=3) for RNA-Seq.

value: Liver

tag: strain

tag: Sex

value: male

value: WT


title: D75P NC IL1b

description: Library name: 46

value: NC

value: 2nd batch


title: Liver tissues, MSA_ConA 2#

description: Library name: MSA_ConA 2#

value: The MSA + ConA group received an intraperitoneal injection of MSA (250 mg/kg body weight, 50 mg/ml in PBS, Sigma-Aldrich, China) 6 hours before ConA injection.


title: reference_001, reference, rep10

description:
Library name: 2_02_10_17
library name V2: 02_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class

value: reference

tag: sequencing plate_name

value: #N/A


title: MM patient6

description: Library name: BM059766PL001

tag: genotype

value: Hyperdiploid, 1q gain, monosomy 13

value: Exosomes were isolated from bone marrow aspirates

tag: gender

value: Female

tag: patient status

value: Deceased

value: CyBORd//ASCT//KCd//Ixa+Cyclo+Pred//Dara


title: BQ2AC0048_001, preAD, rep1

description:
Library name: 20_02_10_17
library name V2: 20_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

value: 5% plasma, 6 h

value: Aim 2 Batch 006

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: D75P WT-STAT3

description: Library name: 44

value: human broncho epithelial cell

tag: treatment

value: Vehicle

tag: batch


title: D75P Mu-STAT3

description: Library name: 45


title: BQ9101_001, MCI, rep1

description:
Library name: 21_02_10_17
library name V2: 21_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: icap cell_culture_plate_number


title: MM patient4

description: Library name: BM058749PL001

tag: genotype

value: Hyperdiploid

value: Male

value: unknown


title: MM patient2

description: Library name: BM058699PL001

tag: gender

value: Alive

value: Whitout treatment Newly diagnosed


title: 2BQ0400_001, normal, rep1

description:
Library name: 18_02_10_17
library name V2: 18_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

tag: plasma thaw_number

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name


title: 2BQ8118_001, preAD, rep1

description:
Library name: 19_02_10_17
library name V2: 19_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date


title: D4R Mu-STAT3 IL1b

description: Library name: 42

tag: treatment

tag: batch

value: 2nd batch


title: Liver tissues, ConA 2#

description: Library name: ConA 2#

tag: tissue

value: Liver

tag: strain

tag: Sex

value: male

value: WT

value: The ConA group received a single dose of ConA (20 mg/kg body weight, 4 mg/ml in PBS, Sigma-Aldrich, China) via tail vein injection.

value: ConA


title: D75P NC

description: Library name: 43

tag: genotype

value: NC


title: BQ6168_001, preAD, rep1

description:
Library name: 17_02_10_17
library name V2: 17_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 006

tag: icap cell_culture_plate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: MM patient1

description: Library name: BM058695PL001

tag: cell type

value: Exosomes were isolated from bone marrow aspirates

tag: gender

value: Female

tag: patient status

value: Deceased

value: VRd//CyBORd//KCd//Doxo + Pd//KPd + Bendamustine//Kd//DPd//Venetoclax


title: MM patient5

description: Library name: BM059338PL001

value: Hyperdiploid

value: Vd + Doxil//ASCT//Rd


title: Liver tissues, ConA 1#

description: Library name: ConA 1#


title: Liver tissues, Control 3#

description: Library name: Control 3#

value: The normal control group received an equivalent volume of sterile phosphate-buffered saline (PBS) via tail vein injection

value: Control


title: AC070_001, preAD, rep1

description:
Library name: 16_02_10_17
library name V2: 16_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: human

tag: plasma thaw_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


title: MM patient3

description: Library name: BM058727PL001

tag: genotype

tag: treatment

value: CyBORd//Rd


title: PDX005 TAK228+CB839 biol rep 4

city: Los Angeles

first: Milica

last: Momcilovic

state: CA

address: 10833 LeConte Ave

institute: University of California Los Angeles

description:
Library name: PDX005_TAK228CB839_4
PDX005_TAK228CB839_4

data_processing:
Galaxy platform
fastp was used for pre-processing FASTQ files
HISAT2 was used for alignment using hg38 reference genome
featureCounts was used to count reads
Assembly: hg38
Supplementary files format and content: tab-delimited txt files containing log2CPM counts

source_name: xenograft

extract_protocol:
RNeasy Mini Kit (Quiagen)
KAPA mRNA HyperPrep Kit (KAPA Biosystems)

tag: tissue

value: xenograft

tag: cell line

value: patient derived xenograft

value: 1 mg/kg TAK228 + 200 mg/kg CB839


title: D4R NC IL1b

description: Library name: 40

value: human broncho epithelial cell

value: NC

tag: batch

value: 2nd batch


title: Liver tissues, MSA_ConA 1#

description: Library name: MSA_ConA 1#

value: Liver

tag: strain

tag: Sex

value: male

value: WT

value: The MSA + ConA group received an intraperitoneal injection of MSA (250 mg/kg body weight, 50 mg/ml in PBS, Sigma-Aldrich, China) 6 hours before ConA injection.


title: Liver tissues, ConA 3#

description: Library name: ConA 3#

value: The ConA group received a single dose of ConA (20 mg/kg body weight, 4 mg/ml in PBS, Sigma-Aldrich, China) via tail vein injection.

value: ConA


title: Liver tissues, Control 2#

description: Library name: Control 2#

value: The normal control group received an equivalent volume of sterile phosphate-buffered saline (PBS) via tail vein injection


title: D4R Mu-STAT3

description: Library name: 39

tag: cell type

value: Vehicle


title: AC066_001, normal, rep1

description:
Library name: 14_02_10_17
library name V2: 14_02_10_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: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 006

tag: icap cell_culture_plate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: PDX005 TAK228+CB839 biol rep 2

description:
Library name: PDX005_TAK228CB839_2
PDX005_TAK228CB839_2

value: xenograft

value: patient derived xenograft

value: 1 mg/kg TAK228 + 200 mg/kg CB839


title: reference_001, reference, rep9

description:
Library name: 15_02_10_17
library name V2: 15_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: reference

tag: sequencing plate_name

value: #N/A

tag: rna-seq date


title: BQ318_001, MCI, rep1

description:
Library name: 13_02_10_17
library name V2: 13_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type


title: PDX005 TAK228+CB839 biol rep 1

description:
Library name: PDX005_TAK228CB839_1
PDX005_TAK228CB839_1

tag: tissue

tag: cell line

tag: treatment


title: D4R WT-STAT3

description: Library name: 38

value: human broncho epithelial cell

tag: genotype

tag: batch

value: 2nd batch


title: Liver tissues, Control 1#

description: Library name: Control 1#

value: Liver

tag: strain

tag: Sex

value: male

value: WT

value: Control


title: D4R NC

description: Library name: 37

value: NC

value: Vehicle


title: MOT scRNAseq

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description:
Library name: Male Old Tibia
10x Genomics

data_processing:
Sequencing libraries were processed using Cell Ranger v.7.2.0. FASTQ files were aligned to the mouse reference genome (mm10) to generate UMI count tables for gene expression. The single-cell data were loaded into count matrices, and all samples were integrated using Seurat v5. Filtering thresholds for excluding cells included a high proportion of mitochondrial transcripts (>25%); low-quality or empty droplets (fewer than 200 or more than 9,000 detected genes). This filtering retained a total of 27,494 cells for further analyses with Seurat v.5.
Assembly: GRCm39
Supplementary files format and content: tab separated values file and matrix file

extract_protocol:
Tibiae and femora were harvested and cleaned of muscle and tissue. The bone marrow was isolated at 2500 g for 40 seconds, then resuspended into 100 μl of PBS, and kept on ice. Red blood cells were lysed using RBC lysing buffer for 5 minutes at room temperature, followed by a PBS wash. To enrich MkP cells, BM cells were stained with CD41+ and CD42d+ antibodies and sorted using MACS, followed by a BD FACSAria III 4L.
Cells from 12 young mice were pooled in two tube (6 male, 6 females), and the cells from 11 old mice were pooled into another (5 males, 6 females). The pooled cells were then counted and resuspended at a concentration of 1000 cells/μL. Each cell was individually captured and uniquely barcoded using the 10X Chromium, following the manufacturer’s protocol (10XGenomics, CA, USA). After generating Gel Beads-in-emulsion (GEMs), cell lysis and Gel bead dissolution within each reaction vesicle allowed for reverse transcription of polyadenylated mRNA, resulting in cDNA tagged with both a universal cell barcode and a unique molecular index (UMI). The cDNA library was then amplified and sequenced using the Illumina NovaSeq 6000 platform (Novogene, Singapore).

value: Bone marrow

value: Pool of megakaryocytes and megakaryocyte progenitor cells

tag: age

value: > 24 months

value: Male

tag: tissue source

value: Tibia


title: BQ206_002, MCI, rep1

description:
Library name: 12_02_10_17
library name V2: 12_02_10_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: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 006

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: RQS

value: pass


title: PDX005 TAK228+CB839 biol rep 5

description:
Library name: PDX005_TAK228CB839_5
PDX005_TAK228CB839_5

tag: tissue

value: xenograft

tag: cell line

tag: cell type

value: patient derived xenograft

tag: treatment

value: 1 mg/kg TAK228 + 200 mg/kg CB839


title: D4R WT-STAT3 IL1b

description: Library name: 41

value: human broncho epithelial cell

tag: genotype

tag: batch

value: 2nd batch


title: PDX005 Veh biol rep 5

description:
Library name: PDX005_Veh_5
PDX005_Veh_5

value: Vehicle


title: MOF scRNAseq

description:
Library name: Male Old Femur
10x Genomics

value: Bone marrow

tag: strain

tag: age

tag: Sex

tag: tissue source

value: Femur


title: PDX005 Veh biol rep 4

description:
Library name: PDX005_Veh_4
PDX005_Veh_4


title: MYT scRNAseq

description:
Library name: Male Young Tibia
10x Genomics

value: Pool of megakaryocytes and megakaryocyte progenitor cells

value: 3 months


title: D78P WT-STAT3 IL1b

description: Library name: 35

value: 1st batch


title: AC532_001, normal, rep1

description:
Library name: 11_02_10_17
library name V2: 11_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: 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


title: MYF scRNAseq

description:
Library name: Male Young Femur
10x Genomics

tag: tissue

tag: cell type

value: Male


title: PDX005 TAK228+CB839 biol rep 3

description:
Library name: PDX005_TAK228CB839_3
PDX005_TAK228CB839_3

tag: cell line

tag: treatment


title: D78P Mu-STAT3 IL1b

description: Library name: 36

tag: genotype

tag: batch


title: D78P NC IL1b

description: Library name: 34

value: NC


title: AC846_001, MCI, rep1

description:
Library name: 10_02_10_17
library name V2: 10_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

value: human

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 006

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: PDX005 Veh biol rep 2

description:
Library name: PDX005_Veh_2
PDX005_Veh_2

value: xenograft

value: patient derived xenograft


title: FOT scRNAseq

description:
Library name: Female Old Tibia
10x Genomics

tag: strain

tag: age

value: > 24 months

tag: Sex

value: Female

tag: tissue source

value: Tibia


title: PDX005 Veh biol rep 3

description:
Library name: PDX005_Veh_3
PDX005_Veh_3

value: Vehicle


title: D78P Mu-STAT3

description: Library name: 33

value: human broncho epithelial cell


title: BQ11019_001, normal, rep1

description:
Library name: 1_02_10_17
library name V2: 01_02_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: PDX005 Veh biol rep 1

description:
Library name: PDX005_Veh_1
PDX005_Veh_1

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: reference_001, reference, rep8

description:
Library name: 9_02_02_17
library name V2: 09_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 005

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: reference

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: D78P NC

description: Library name: 31

tag: genotype

tag: batch

value: 1st batch


title: H2170 TAK228 biol rep 3

description:
Library name: H2170_TAK228_3
H2170_TAK228_3

value: Human lung cancer

value: 1 mg/kg TAK228


title: FOF scRNAseq

description:
Library name: Female Old Femur
10x Genomics

value: Bone marrow

value: Pool of megakaryocytes and megakaryocyte progenitor cells

tag: strain

tag: age

tag: Sex

tag: tissue source

value: Femur


title: D39Q Mu-STAT3 IL1b

description: Library name: 30


title: H2170 TAK228 biol rep 2

description:
Library name: H2170_TAK228_2
H2170_TAK228_2


title: BQ0362_001, MCI, rep1

description:
Library name: 8_02_02_17
library name V2: 08_02_02_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: plasma used_in_icap_(plasmakey)

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


title: BQAC0442_001, normal, rep1

description:
Library name: 6_02_02_17
library name V2: 06_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

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: rnaseq qc_(basis_for_omission)_(step_5)


title: D78P WT-STAT3

description: Library name: 32

tag: genotype

tag: treatment

tag: batch


title: FYF scRNAseq

description:
Library name: Female Young Femur
10x Genomics

tag: tissue

tag: strain

tag: age

value: 3 months

tag: Sex

value: Female

tag: tissue source


title: FYT scRNAseq

description:
Library name: Female Young Tibia
10x Genomics

value: Tibia


title: BBC2_D14

city: Augusta

first: John

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

institute: Augusta University

description: Library name: Leukemic sample at day 14

data_processing:
The raw reads in fastq format was generated using cellranger mkfastq and count matrix was generated by cellranger count acording to cellranger v7.1.0
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

source_name: Pheripheral blood

extract_protocol:
Peripheral blood samples were depleted of red blood cells by lysis, and dead cells were removed using the Miltenyi dead cell removed kit.
scRNA-seq libraries were generataed using 10X 3’ single cell mRNAseq V3 reagents according to manufacturer's protocol.

value: Pheripheral blood

tag: cell line

value: primary cells

value: Immune cells

value: WT


title: H2170 TAK228 biol rep 1

description:
Library name: H2170_TAK228_1
H2170_TAK228_1

value: xenograft


title: ELBQ0424_001, MCI, rep1

description:
Library name: 5_02_02_17
library name V2: 05_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: Aim 2 Batch 005

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: BBC2_D11

description: Library name: Leukemic sample at day 11

tag: cell type

tag: genotype


title: D39Q NC IL1b

description: Library name: 28

value: human broncho epithelial cell

value: NC

tag: treatment

tag: batch

value: 1st batch


title: H2170 Veh biol rep 3

description:
Library name: H2170_Veh_3
H2170_Veh_3

tag: tissue

value: Human lung cancer

value: Vehicle


title: H2170 Veh biol rep 2

description:
Library name: H2170_Veh_2
H2170_Veh_2


title: BalbC_WT

description: Library name: Naïve mouse sample


title: AC624_001, preAD, rep1

description:
Library name: 4_02_02_17
library name V2: 04_02_02_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: icap cell_culture_well_position

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BQ0435_001, normal, rep1

description:
Library name: 3_02_02_17
library name V2: 03_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

value: #N/A


title: D39Q WT-STAT3

description: Library name: 26


title: D39Q Mu-STAT3

description: Library name: 27


title: Sed Low Fat

city: New York

first: Miklos

last: Toth

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
Library name: Sample 4
10X Genomics

data_processing:
Preparation of libraries and sequencing were done by the Epigenomics Core at Weill Cornell Medicine using the Chromium Single Cell 3’ Reagent V3 Kit and sequencing via NovaSeq6000. Raw sequencing data were processed using the CellRanger v6.0.0 pipeline and aligned to the mm10 transcriptome with introns included in the reference. Gene-expression matrices for all samples were loaded into R and preprocessed using Seurat where nuclei with fewer than 500 genes and genes expressed in fewer than 10 nuclei were filtered out. The gene-expression matrices were merged and nuclei with more than 6,000 genes and greater than 0.8% mitochondrial reads were filtered out. The matrix was then separated by sample and normalized using NormalizeData and variable features were found using FindVariableFeatures using the vst selection method and nfeatures = 2000. Features and anchors for integration were found using SelectIntegrationFeatures and FindIntegrationAnchors. Using this anchor set, the data was integrated using IntegrateData. Data was scaled and RunPCA was used with 30 PCs. Nuclei were clustered using a resolution of 0.6. Following clustering, cluster markers were found using FindAllMarkers. For differential gene expression, clusters were combined by cell type and the groups were compared using FindMarkers with a minimum log2FC of 1.3 and adjusted p-value < 0.05 (Bonferonni).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Qiagen RNeasy kit
Punches were taken from frozen livers and nuclei were prepared using the Nuclei Isolation Kit: Nuclei EZ Prep (Sigma, NUC-101) following manufacturers’ guidelines. Tissue from three non-related males were processed together per group.
Libraries were constructed according to manufacterer protocols by the Weill Cornell Epigenomics Core using the Chromium Single Cell 3' Reagent V3 kit.

value: liver

tag: Sex

value: Male

value: Sed Low Fat


title: AC921_001, normal, rep1

description:
Library name: 24_02_02_17
library name V2: 24_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: H1703 TAK228+EIPA biol rep 3

description:
Library name: H1703_TAK228EIPA_3
H1703_TAK228EIPA_3

tag: tissue

tag: cell line

tag: treatment

value: 1 mg/kg TAK228 + 0.75mg/kg EIPA


title: H2170 Veh biol rep 1

description:
Library name: H2170_Veh_1
H2170_Veh_1


title: AC211_001, preAD, rep1

description:
Library name: 7_02_02_17
library name V2: 07_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

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: D39Q NC

description: Library name: 25

tag: genotype

tag: batch


title: Run Low Fat

description:
Library name: Sample 2
10X Genomics

tag: Sex

value: Run Low Fat


title: reference_001, reference, rep7

description:
Library name: 22_02_02_17
library name V2: 22_02_02_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: rna-seq covance/genewiz_id

value: reference

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: H1703 TAK228+EIPA biol rep 1

description:
Library name: H1703_TAK228EIPA_1
H1703_TAK228EIPA_1

tag: tissue

value: xenograft

tag: cell line


title: D29R WT-STAT3 IL1b

description: Library name: 23

tag: treatment


title: D39Q WT-STAT3 IL1b

description: Library name: 29


title: D29R Mu-STAT3 IL1b

description: Library name: 24


title: H1703 TAK228 biol rep 3

description:
Library name: H1703_TAK228_3
H1703_TAK228_3

value: 1 mg/kg TAK228


title: Run Medium Fat

description:
Library name: Sample 1
10X Genomics

value: Run Medium Fat


title: D29R NC IL1b

description: Library name: 22

value: human broncho epithelial cell

value: NC


title: AC207_001, MCI, rep1

description:
Library name: 20_02_02_17
library name V2: 20_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 005

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: H1703 TAK228 biol rep 2

description:
Library name: H1703_TAK228_2
H1703_TAK228_2

tag: cell type

value: Human lung cancer


title: ST125_001, preAD, rep1

description:
Library name: 2_02_02_17
library name V2: 02_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

value: 5% plasma, 6 h

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: RQS


title: D29R Mu-STAT3

description: Library name: 21

tag: genotype

value: Vehicle

tag: batch

value: 1st batch


title: Wwox_WT2_BM

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Library name: Wwox_WT2_BM

data_processing:
Short reads were mapped to the mouse reference genome (mm10) using TopHat v2.0.10. We employed several R/Bioconductor packages to calculate gene expression abundance at the whole-genome level using the aligned records (BAM files).
Differentially expressed genes between Vk*MYC:Wwox WT-BM vs Vk*MYC:Wwox KO-BM and Vk*MYC:Wwox KO-BM vs Vk*MYC:Wwox KO-PBT were identified using DESeq2.
Data integration and visualization of differentially expressed transcripts (FDR < 0.05) were done with Multiexperiment Viewer Software.
Assembly: mm10
Supplementary files format and content: normalized count tables with the following columns: GeneID (Ensembl gene ID); GeneSymbol (gene symbol); other columns (normalized counts for each sample)

source_name: Cd138+ bone marrow plasma cells

extract_protocol:
Total RNA was extracted from Vk*MYC:Wwox WT-BM (n=3), Vk*MYC:Wwox KO-BM (n=3), and Vk*MYC:Wwox KO-PBT (n=4) samples using TRIzol reagent (Invitrogen) following the manufacturer’s protocol. RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies), and samples with RNA integrity number over 8.0 were used for sequencing.
Directional mRNA-seq libraries were constructed using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre). We performed 76 nt paired-end sequencing on an Illumina HiSeq3000 platform, obtaining ∼40 million tags per sample.

value: Cd138+ bone marrow plasma cells

value: Wwox Wildtype


title: Wwox_WT1_BM

description: Library name: Wwox_WT1_BM


title: Sed Medium Fat

description:
Library name: Sample 3
10X Genomics

tag: tissue

value: liver

tag: Sex

value: Male

value: Sed Medium Fat


title: Wwox_KO4_PBT

description: Library name: Wwox_KO4_PBT

source_name: Plasmablastic plasmacytoma tissue

value: Plasmablastic plasmacytoma tissue

value: Wwox Knock out


title: 2AC1BQ199_001, preAD, rep1

description:
Library name: 19_02_02_17
library name V2: 19_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: D29R WT-STAT3

description: Library name: 20

value: human broncho epithelial cell

tag: treatment


title: D29R NC

description: Library name: 19

value: NC


title: D23R Mu-STAT3 IL1b

description: Library name: 18


title: H1703 TAK228+EIPA biol rep 2

description:
Library name: H1703_TAK228EIPA_2
H1703_TAK228EIPA_2

value: xenograft

tag: cell line

value: Human lung cancer

value: 1 mg/kg TAK228 + 0.75mg/kg EIPA


title: Wwox_KO3_PBT

description: Library name: Wwox_KO3_PBT


title: H1703 Veh biol rep 2

description:
Library name: H1703_Veh_2
H1703_Veh_2


title: H1703 Veh biol rep 3

description:
Library name: H1703_Veh_3
H1703_Veh_3


title: BQ6135_001, preAD, rep1

description:
Library name: 21_02_02_17
library name V2: 21_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: 5% plasma, 6 h

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 005

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: 2ACBQ134_001, normal, rep1

description:
Library name: 23_02_02_17
library name V2: 23_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: Wwox_KO3_BM

description: Library name: Wwox_KO3_BM

value: Cd138+ bone marrow plasma cells

tag: genotype


title: Wwox_WT3_BM

description: Library name: Wwox_WT3_BM

value: Wwox Wildtype


title: AC907_001, MCI, rep1

description:
Library name: 18_02_02_17
library name V2: 18_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

value: low RIN


title: AC911_001, MCI, rep1

description:
Library name: 17_02_02_17
library name V2: 17_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 2BQ8106_001, MCI, rep1

description:
Library name: 16_02_02_17
library name V2: 16_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma shipment_batch


title: Sample 137

type: genomic

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
In brief, we removed probes which had either low detection P values, contained a SNP with MAF of at least 5% within 3bp of the CpG interrogation site, or mapped to the X chromosome. Raw probe values were background corrected using preprocessIllumina and quantile normalization was performed using Enmix (32). The effects of slide, DNA concentration (< or > 12 ng/ml and extraction batch were removed using ComBat (33).
Normalized beta

label: cy3, cy5

molecule: genomic DNA

source_name: buccal

label_protocol: Standard Illumina Protocol

extract_protocol: Buccal DNA was extracted using the Maxwell® 16 Instrument (Promega AS3000) and   Maxwell® 16 Blood DNA Extraction Kit (Promega AS1010). Proteinase K (Promega   20mg/ml) was added to 15ml conicals containing 4 swabs and ~1.6ml SLB. Tubes were   vortexed to collect SLB at bottom. Tubes were incubated in s 56°C water bath for 1 hr  and then vortexed. Lysate (800ul) was added to well #7 of the Maxwell® 16 Blood DNA  cartridge. The remaining lysate was stored for a second DNA extraction. Alcohol Wash  Buffer (2 parts Milli-Q water, 1 part 100% EtOH, 1 part 100% isopropanol) was added to  wells #4, #5 and #6. Cartridges were processed using the Buffy Coat Protocol on the  Maxwell® 16 Instrument and eluted in 400ul elution buffer. Purity was measured by  spectrophotometer and concentration measured with the Quant-iT PicoGreen dsDNA  Assay (Invitrogen® P7589).

treatment_protocol: Patients were instructed not to eat or drink at least 30 minutes before buccal sample   collection. Buccal DNA was collected using 4 Sterile HydraFlock® Large Tip Flocked  Swabs (Puritan 253406H). Each swab was applied to the inside of the child’s cheek and  rolled up and down for 30-60 seconds, making certain to roll the swab over the entire  inner cheek and upper gum. Swabs were placed together in a 15 ml conical tube  containing 1600ul of 1X Saliva Lysis Buffer (SLB) before capping tube and vortexing for  10 seconds. The swabs were frozen upright in SLB at -20°C within 1 week from sampling  and stored until DNA extraction.  2X Saliva Lysis Buffer: 0.3 M TRIS-HCl; 0.67 M urea;   0.67 M NaOAc;  0.6% sodium dodecyl sulfate;  3.3 mM EDTA;  30% ethanol)

tag: tissue

value: buccal

tag: Sex

value: Male


title: Wwox_KO2_BM

description: Library name: Wwox_KO2_BM

value: Wwox Knock out


title: D23R NC IL1b

description: Library name: 16

tag: treatment

tag: batch

value: 1st batch


title: BQ11004_001, normal, rep1

description:
Library name: 15_02_02_17
library name V2: 15_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

source_name: iCell Neurons

tag: cell type

tag: preculture time_(days)

value: human

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date


title: Sample 135

value: Female


title: H1703 TAK228 biol rep 1

description:
Library name: H1703_TAK228_1
H1703_TAK228_1

value: xenograft

tag: cell line

value: 1 mg/kg TAK228


title: 2ACBQ201_001, preAD, rep1

description:
Library name: 14_02_02_17
library name V2: 14_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: Wwox_KO1_PBT

description: Library name: Wwox_KO1_PBT

source_name: Plasmablastic lymphoma tissue

tag: tissue

value: Plasmablastic lymphoma tissue

tag: genotype


title: Sample 134

tag: Sex


title: Sample 136


title: D23R WT-STAT3

description: Library name: 14

value: human broncho epithelial cell

tag: treatment

value: Vehicle

tag: batch


title: D23R NC

description: Library name: 13

tag: cell type

value: NC


title: BQAC0472_001, normal, rep1

description:
Library name: 13_02_02_17
library name V2: 13_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

value: 5% plasma, 6 h

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 005

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: Fibroblasts co-culture with Th17 cells-2

first: Yena

last: Zhou

address: 94 Weijin Road

institute: Nankai University

description:
Library name: Sample5
Column name in raw_counts_All_Samples.txt: M5

data_processing:
Raw sequencing reads were filtered for quality using Seqtk and aligned to the reference genome with Hisat2 (version 2.0.4)
Gene fragment counts were quantified using StringTie (v1.3.3b), and normalization was performed using the trimmed mean of M values (TMM) method
Differentially expressed genes (DEGs) were identified using edgeR software, applying a False Discovery Rate (FDR) threshold of Q < 0.05 and a fold-change >2
Functional enrichment analysis of DEGs was performed using the "clusterProfiler" package in R4.3.2, focusing on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The top 30 enriched pathways were visualized with the "ggplot2" package, with statistical significance set at P < 0.05. DEG expression patterns were further analyzed using heatmaps generated with the "pheatmap" package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: primary mouse renal fibroblasts

growth_protocol: Renal fibroblast isolation: Mouse kidney tissues were digested in a solution containing PBS, 0.25% trypsin, and 0.2% collagenase IV at 37°C with gentle shaking for 30 minutes. The digested mixture was neutralized with Fibroblast Medium Complete (ScienCell, 2301), filtered through a 70 μm sieve, and red blood cells were lysed using red cell lysis buffer. The cells were washed three times with PBS and cultured in Fibroblast Medium Complete.

extract_protocol:
Total RNA (50 μg) was extracted from renal fibroblasts co-culture with/without Th17 cells using standard protocols.
Library preparation was performed with the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®, and cDNA library quality was assessed using an Agilent 4200 bioanalyzer. Sequencing was conducted on an Illumina NovaSeq 6000 platform following the manufacturer’s instructions.

treatment_protocol: In vitro co-culture of renal fibroblasts and Th17 cells: Primary renal fibroblasts were seeded in 6-well plates and allowed to adhere for 6 hours. A 0.4 μm transwell insert was then placed above the fibroblasts, and induced Th17 cells were seeded in the upper chamber. The co-culture system was maintained at 37°C in a humidified atmosphere with 5% CO₂ for 24 hours. After co-culture, fibroblasts in the lower chamber were collected for further analysis.

value: primary mouse renal fibroblasts

value: WT

value: co-culture with Th17 cells


title: D27R WT-STAT3 IL1b

description: Library name: 11

value: 1st batch


title: AC024_001, preAD, rep1

description:
Library name: 10_02_02_17
library name V2: 10_02_02_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)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: 2BQ0443_002, MCI, rep1

description:
Library name: 12_02_02_17
library name V2: 12_02_02_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

value: #N/A

value: RQS


title: Fibroblasts co-culture with Th17 cells-3

description:
Library name: Sample6
Column name in raw_counts_All_Samples.txt: M6

tag: cell type

tag: genotype

tag: treatment


title: Sample 133

tag: tissue

value: buccal

tag: Sex

value: Male


title: D23R Mu-STAT3

description: Library name: 15

tag: batch


title: BQ0277_001, normal, rep1

description:
Library name: 11_02_02_17
library name V2: 11_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: Sample 130

value: Female


title: 2BQ0443_001, MCI, rep1

description:
Library name: 1_02_02_17
library name V2: 01_02_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma class

tag: sequencing plate_name

value: #REF!

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Fibroblasts3

description:
Library name: Sample3
Column name in raw_counts_All_Samples.txt: C6

tag: cell type

tag: genotype


title: Sample 132

tag: tissue


title: D27R Mu-STAT3

description: Library name: 9

value: human broncho epithelial cell

tag: treatment

value: Vehicle


title: Fibroblasts co-culture with Th17 cells-1

description:
Library name: Sample4
Column name in raw_counts_All_Samples.txt: M4


title: D23R WT-STAT3 IL1b

description: Library name: 17

tag: batch


title: Wwox_KO1_BM

description: Library name: Wwox_KO1_BM

value: Cd138+ bone marrow plasma cells

value: Wwox Knock out


title: H1703 Veh biol rep 1

description:
Library name: H1703_Veh_1
H1703_Veh_1

value: xenograft

tag: cell line

value: Human lung cancer


title: D27R NC IL1b

description: Library name: 10

value: NC


title: Sample 128

tag: Sex


title: D27R NC

description: Library name: 7


title: ACBQ323_001, preAD, rep1

description:
Library name: 9_02_01_17
library name V2: 09_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

value: 5% plasma, 6 h

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 004

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq date

value: pass


title: Fibroblasts2

description:
Library name: Sample2
Column name in raw_counts_All_Samples.txt: C5

value: primary mouse renal fibroblasts

value: WT


title: Sample 129

value: buccal


title: Sample 131


title: D27R WT-STAT3

description: Library name: 8

value: 1st batch


title: IgAN Mouse Model4

description:
Library name: Sample8
Column name in raw_counts_All_Samples.txt: Model4

data_processing:
Raw sequencing reads were filtered for quality using Seqtk and aligned to the reference genome with Hisat2 (version 2.0.4)
Gene fragment counts were quantified using StringTie (v1.3.3b), and normalization was performed using the trimmed mean of M values (TMM) method
Differentially expressed genes (DEGs) were identified using edgeR software, applying a False Discovery Rate (FDR) threshold of Q < 0.05 and a fold-change >2
Functional enrichment analysis of DEGs was performed using the "clusterProfiler" package in R4.3.2, focusing on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The top 30 enriched pathways were visualized with the "ggplot2" package, with statistical significance set at P < 0.05. DEG expression patterns were further analyzed using heatmaps generated with the "pheatmap" package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and FPKMs for each Sample

source_name: Kidney

growth_protocol: Balb/c mice were purchased from Cyagen Biosciences (Suzhou, China). Throughout the experimental period, the mice were housed under specific pathogen-free (SPF) conditions with ad libitum access to food and water. The environment was maintained under controlled conditions, including a 12-hour light/dark cycle and a constant temperature of 25°C. The method for IgAN model construction is as previously described

extract_protocol:
Total RNA (50 μg) was extracted from kidney tissues of IgAN and control mice using standard protocols.
Library preparation was performed with the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®, and cDNA library quality was assessed using an Agilent 4200 bioanalyzer. Sequencing was conducted on an Illumina NovaSeq 6000 platform following the manufacturer’s instructions.

treatment_protocol: For the treatment groups, starting at week 12, mice were administered 2-BP (4 mg/kg) via intraperitoneal injection once weekly until week 24. Vehicle-treated mice received equivalent volumes of solvent under identical conditions. Mice in the treatment groups were sacrificed at week 24 for further analysis.

value: Kidney

value: LPS


title: D27R Mu-STAT3 IL1b

description: Library name: 12

value: human broncho epithelial cell


title: AC104_001, normal, rep1

description:
Library name: 6_02_01_17
library name V2: 06_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

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: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A


title: reference_001, reference, rep6

description:
Library name: 7_02_01_17
library name V2: 07_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: reference

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: ACBQHC322_001, MCI, rep1

description:
Library name: 8_02_01_17
library name V2: 08_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)


title: D10R Mu-STAT3 IL1b

description: Library name: 6

tag: genotype

tag: treatment

tag: batch


title: 2BQ6102_001, preAD, rep1

description:
Library name: 5_02_01_17
library name V2: 05_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number


title: Sample 125

tag: tissue

tag: Sex

value: Male


title: IgAN Mouse Model3

description:
Library name: Sample7
Column name in raw_counts_All_Samples.txt: Model3


title: D10R WT-STAT3 IL1b

description: Library name: 5


title: D10R NC IL1b

description: Library name: 4


title: BQ8116_001, preAD, rep1

description:
Library name: 4_02_01_17
library name V2: 04_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rna-seq date


title: D10R Mu-STAT3

description: Library name: 3

tag: cell type

value: Vehicle


title: IgAN Mouse Model1

description:
Library name: Sample5
Column name in raw_counts_All_Samples.txt: Model1


title: D10R WT-STAT3

description: Library name: 2


title: AC634_001, normal, rep1

description:
Library name: 3_02_01_17
library name V2: 03_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: BQ0440_002, MCI, rep1

description:
Library name: 24_02_01_17
library name V2: 24_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

value: RQS


title: Mouse Control3

description:
Library name: Sample3
Column name in raw_counts_All_Samples.txt: Control3

tag: tissue

tag: genotype

tag: treatment

value: physiological saline


title: Sample 122

tag: Sex

value: Female


title: IgAN Mouse Model2

description:
Library name: Sample6
Column name in raw_counts_All_Samples.txt: Model2


title: Fibroblasts1

description:
Library name: Sample1
Column name in raw_counts_All_Samples.txt: C4


title: Sample 123


title: Sample 127


title: Sample 121


title: D10R NC

description: Library name: 1

value: NC

tag: batch


title: Mouse Control4

description:
Library name: Sample4
Column name in raw_counts_All_Samples.txt: Control4


title: AC706_001, normal, rep1

description:
Library name: 23_02_01_17
library name V2: 23_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: Aim 2 Batch 004

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: low RIN

value: pass


title: ACBQ311_001, MCI, rep1

description:
Library name: 22_02_01_17
library name V2: 22_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: rna-seq date


title: Mouse Control1

description:
Library name: Sample1
Column name in raw_counts_All_Samples.txt: Control1

tag: tissue

value: Kidney

value: WT


title: Mouse Control2

description:
Library name: Sample2
Column name in raw_counts_All_Samples.txt: Control2

tag: genotype


title: Sample 126

value: buccal


title: LNCaP cells, Vector treated, replicate 3

city: Omaha

first: Timothy

middle: Edward

last: Reznicek

state: Nebraska

address: S 45th St

department: Genetics Cell Biology & Anatomy

institute: University Of Nebraska Medical Center

description:
Library name: Vector_3
Column name in TPM_Data.tsv is Vector_3

data_processing:
Processing of RNA-seq results was done using the nf-core RNA-seq pipeline version 3.9, accessed via Nextflow version 22.10.3 and executed with Singularity.
STAR version 2.7.11a was used to align transcripts to the hg38 reference genome, with incorporation of Ensembl gene annotations.
StringTie2 1.3.6 quantified transcript abundance.
DESeq2 quantified differential expression between Vector and ECD overexpression groups.
Assembly: hg38
Supplementary files format and content: tab delimited file contains TPM counts of transcripts across samples.

source_name: LNCaP

growth_protocol: LNCaP cells were obtained from the American Type Culture Collection (ATCC). These cells were maintained in complete RPMI medium, with 10% fetal bovine serum, 10mM HEPES, 1mM of sodium pyruvate, 1mM nonessential amino acids, 1mM L-glutamine, and 50ug/mL of gentamicin.

extract_protocol:
Total RNA was isolated from the indicated PC cell lines using the TRIzol reagent (Invitrogen; cat# 15596018.)
Paired-end RNA-seq libraries were prepared and subjected to 100 bp paired-end sequencing on an Illumina NovaSeq 6000 system (UNMC Genomics Core)

treatment_protocol: For ECD overexpression, mammalian expression vector pLenti-C-Myc-DDK-P2A-Puro and empty Vector control plasmid were used. Lentiviral supernatants were generated by transient co-transfection of Lenti-X 293T cells with ECD expression vector and packaging plasmids psPAX2 and pMD2.G using X-treme GENE HP DNA transfection reagent. Collected lentiviral supernatant was added to prostate cancer cells in the presence of polybrene. Post-infection, transduced cells were selected in 1 μg/ml puromycin for 5 days.

tag: cell line

value: LNCaP

value: Prostate Cancer Cells

value: WT+Vector

tag: treatment

value: Xenograft into mice


title: Sample 120

tag: Sex

value: Male


title: LNCaP cells, Vector treated, replicate 4

description:
Library name: Vector_4
Column name in TPM_Data.tsv is Vector_4