title: LNCKO-Butyrate

first: Yunhuan

last: Gao

address: No. 94, Weijin Road, Nankai District, Tianjin, China

description:
Library name: Sample 4
HD0015571-R3-2_S8

data_processing:
All the reads were mapped to the mouse reference genome (GRCm38/mm10) using STAR aligner (v2.5.0c).
Alignments were guided by a Gene Transfer File (Ensembl GTF version GRCm38.74) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard/).
The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4).
Read count tables were generated using HTSeq (v0.6.0) normalized based on their geometric library size factors using DESeq2 (v3.0) and Deferential Expression (DE) analyses were performed.
Assembly: mm10
Supplementary files format and content: tab-demilited text files includ FPKM values for each sample

source_name: bone marrow

extract_protocol:
BMDMs were treatment with 500 µM Butyrate for 24h. One days later, all cells with or without Butyrate treatment were collected for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: Bone marrow-derived macrophages

value: LNCKO

value: Butyrate


title: Sample 124

status: Public on Dec 02 2025

type: genomic

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

country: USA

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

organism: Homo sapiens

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: Female


title: AC090_001, preAD, rep1

type: SRA

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

institute: PreCyte, Inc.

description:
Library name: 21_02_01_17
library name V2: 21_02_01_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

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 004

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: LNCKO-Control

city: Tianjin

country: China

institute: Nankai University

description:
Library name: Sample 3
HD0015569-NC-2_S6

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment

value: Control


title: reference_001, reference, rep5

description:
Library name: 20_02_01_17
library name V2: 20_02_01_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: reference


title: LNCaP cells, Vector treated, replicate 2

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_2
Column name in TPM_Data.tsv is Vector_2

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

value: Xenograft into mice


title: LNCaP cells, Vector treated, replicate 1

description:
Library name: Vector_1
Column name in TPM_Data.tsv is Vector_1


title: Sample 119

tag: Sex

value: Male


title: Sample 118


title: 2BQ6147_001, MCI, rep1

description:
Library name: 19_02_01_17
library name V2: 19_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

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: Sample 117


title: AC127_001, preAD, rep1

description:
Library name: 2_02_01_17
library name V2: 02_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: WT-Butyrate

description:
Library name: Sample 2
HD0015567-But-2_S4

tag: tissue

value: bone marrow

tag: cell type

value: Bone marrow-derived macrophages

tag: genotype

value: WT

tag: treatment


title: Control, Rep2, 3m, prefrontal cortex

city: Atlanta

first: Yulin

last: Jin

state: GA

address: 615 Micheal Street

department: Human Genetics

institute: Emory University

description:
Library name: cortex_CTL2
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were obtained with 10x Genomics pipeline CellRanger (v5.0.0) ‘mkfastq’ with default parameters. Reads from each sample were then aligned to the mouse genome (mm10) with reference data ‘refdata-cellranger-mm10-2020-A-2.0.0’, and the gene-by-cell count matrices were generated. R package Seurat (V4.3.0.1) was performed for quality control (QC) analyses and downstream analyses, including data normalization, clustering, highly variable gene selection.
Assembly: Mus musculus 10 (mm10)
Supplementary files format and content: Tap-seperated values files and matrix files

source_name: Prefrontal cortex

extract_protocol:
Frontal cortex of FXTAS mice and littermate controls was rapidly dissected in ice-cold homogenization buffer (HB: 260 mM sucrose, 30 mM KCl, 10 mM NaCl, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.5 mM Spermidine, 0.2 mM Spermine, 0.3% NP40, Complete Protease inhibitor (Roche), and Ribolock RNase inhibitor (ThermoFisher)) and immediately transferred to a Dounce homogenizer filled with 1 mL HB. Tissue was homogenized by 20 strokes with each pestle A and pestle B. The homogenate was then filtered through a 70um strainer followed by centrifugation for 10 min at 300g at 4°C. The pallets were then resuspended in a homogenization buffer and mixed with 1 volume of 50% Iodixanol (Sigma D1556) to make a final concentration of 25% iodixanol. Without disturbing the mixture, 30% Iodixanol was slowly layered underneath the 25% iodixanol mixture, and then 40% Iodixanol was gently added under the 30% mixture to generate a density gradient. A clearly defined interface should be visible between all three layers. The nuclei were centrifuged for 20 min at 1485g and 4°C in a swinging bucket centrifuge with the brake off. After the centrifugation, the nuclei band was transferred from the interface between 30% and 40% iodixanol solutions to a pre-chilled tube. The nuclei were washed with wash buffer at 4°C and counted after adding trypan blue.
Libraries were generated with the 10x Genomics Single Cell Gene Expression reagent kit following the manufacturer’s instructions with minor modifications. Briefly, per sample, 16,100 nuclei were resuspended in 1x diluted nuclei buffer (10x Genomics) with 2% BSA (Sigma), and 10,000 nuclei were captured. For 10,000 nuclei capture targeted, single nuclei expression libraries were sequenced to 20,000 read pairs per nuclei on an Illumina NovaSeq 6000 instrument.

value: Prefrontal cortex

tag: developmental stage

value: 3-4 months

tag: Sex

value: male


title: LNCaP cells, ECD overexpression with pLenti-C-Myc-DDK-P2A-Puro, replicate 2

description:
Library name: ECD_2
Column name in TPM_Data.tsv is ECD_2

tag: cell line

value: WT+ECD overexpressed


title: Sample 116

value: buccal


title: WT-Control

description:
Library name: Sample 1
HD0015565-WT-2_S2


title: LNCaP cells, ECD overexpression with pLenti-C-Myc-DDK-P2A-Puro, replicate 3

description:
Library name: ECD_3
Column name in TPM_Data.tsv is ECD_3


title: AC609_001, preAD, rep1

description:
Library name: 18_02_01_17
library name V2: 18_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 004

tag: plasma thaw_number

value: #N/A


title: LNCaP cells, ECD overexpression with pLenti-C-Myc-DDK-P2A-Puro, replicate 4

description:
Library name: ECD_4
Column name in TPM_Data.tsv is ECD_4

value: LNCaP

value: Prostate Cancer Cells


title: BQ0440_001, MCI, rep1

description:
Library name: 17_02_01_17
library name V2: 17_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

value: pass


title: Sample 115

tag: tissue

value: Female


title: Sample 114

tag: Sex

value: Male


title: ELACBQ363_001, MCI, rep1

description:
Library name: 16_02_01_17
library name V2: 16_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: LNCaP cells, ECD overexpression with pLenti-C-Myc-DDK-P2A-Puro, replicate 1

description:
Library name: ECD_1
Column name in TPM_Data.tsv is ECD_1

tag: cell line

tag: genotype

tag: treatment

value: Xenograft into mice


title: Wild-type U87 cells, replicate 3

city: 广州市

first: Cuiying

last: Xie

state: 广东省

address: 广州大道北1838号南方医院菜鸟驿站

institute: Southern Medical University

description: Library name: U87WT-3

data_processing:
Quality Control: Raw sequencing reads were assessed for quality using FastQC (version 0.11.9). Low-quality reads and adapter sequences were trimmed using Trimmomatic (version 0.39) to ensure high-quality data for downstream analysis.
Alignment: The cleaned reads were aligned to the human genome (GRCh38) using HISAT2 (version 2.2.1) with default parameters. BAM files containing mapped reads were generated as output.
Quantification: Gene-level expression quantification was performed using featureCounts (version 2.0.5) based on GENCODE annotation (version 38). Raw read counts were obtained for each gene.
Normalization: To calculate transcript abundance, the raw counts were converted to Transcripts Per Million (TPM) using R (version 4.2.0). This step involved normalizing the data by dividing each gene's read count by its length in kilobases and then scaling by the total mapped reads in millions.
Log Transformation: To facilitate downstream analysis and visualization, the TPM values were log-transformed using the formula log(TPM + 1).
Assembly: GRCh38
Supplementary files format and content: CSV file including log(TPM+1) values for each sample, where rows represent genes and columns represent individual samples.

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol. The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, rRNAs were removed from Total RNA usingQIAseqFastSelct-rRNA HRM KIT(QIAGEN,Germany)and fragmented to approximately 200bp.
Subsequently, the purified RNAfragments were subjected to first strand and second strand cDNA synthesisfollowing by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina(NEB, USA). The purified library products were evaluatedusing the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequencedby Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: Glioblastoma cell


title: Sample 113


title: FXTAS, Rep2, 3m, prefrontal cortex

description:
Library name: cortex_FXTAS2
10x Genomics

value: Prefrontal cortex

tag: developmental stage

value: FMRpolyG+RNA (+/-);Nestin-Cre (+)


title: BQ0436_001, normal, rep1

description:
Library name: 15_02_01_17
library name V2: 15_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: FXTAS, Rep1, 3m, prefrontal cortex

description:
Library name: cortex_FXTAS1
10x Genomics

value: 3-4 months

value: male


title: Sample 112

value: buccal


title: Wild-type U87 cells, replicate 2

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87WT-2


title: AC082_001, preAD, rep1

description:
Library name: 14_02_01_17
library name V2: 14_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: untreated-M

city: Columbus

first: Rodney

last: Britt

state: Oh

address: 575 Childrens Crossroad

department: Center for Perinatal Research

institute: Nationwide Children's Hospital

description:
Library name: untreated-M
10x Genomics

data_processing:
Demultiplexing and feature counting was performed using 10x Genomics Cell Ranger 7.0.0 against the standard 10x Genomics reference genome refdata-gex-mm10-2020-A genome
Count matrices were loaded useing Seurat, doublets we annotated with scDoubletfinder, merged, normalized with SCTransform, and combined with Harmony.
Individual experiments were uploaded to LungMap, and the Azimuth tool used to annotate each cell type.
Pseudo-bulk differential analysis was performed using EdgeR following the standard workflow in the EdgeR handbook.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: 10X Genomics cellranger-7.0.0 count tab-delimeted matrix and metadata files
Supplementary files format and content: .RDS

source_name: Lung

extract_protocol:
Freshly harvested lung tissue from C57BL/6J mice was minced to a slurry and suspended in complete media (Dulbecco’s modified Eagle’s medium [DMEM], 10% FBS, 1% Gibco™ Antibiotic-Antimycotic) containing collagenase (1 mg/ml) and DNase I (0.25 ml or 250 KU units). The suspension was incubated on a rocker for 30 min at 37°C followed by centrifugation at 500 x g for 10 min. The supernatant was decanted, and each pellet was briefly resuspended in sterile water for RBC lysis, neutralized by adding 10 ml of complete media. Cells were centrifuged and pellets resuspended in 5 ml complete media and passed through a 100 μm nylon screen to obtain a single-cell suspension. Cells were centrifuged and resuspended in PBS. FACS was used to isolate live cells (absence of DAPI staining).
Library was generated  according to the manufacturer’s protocol CG000315 Rev C for the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, Pleasanton, CA, USA).

treatment_protocol: To generate allergic airway inflammation in mice 20 µl of dust mite, ragweed, and aspergillus (DRA) allergen mixture was administered intranasally on experimental days 0, 5, 12, 14, and 17. Whole body ozone exposure (2 ppm for 3 hours) was performed on experimental day 18. Mice were euthanized and samples collected on experimental day 19.

tag: tissue

value: Lung

tag: cell type

value: Homogenate

tag: genotype

value: Veh


title: Wild-type U87 cells, replicate 1

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87WT-1

tag: cell line


title: ACBQ265_001, normal, rep1

description:
Library name: 13_02_01_17
library name V2: 13_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

value: human

value: Aim 2 Batch 004

value: #N/A

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Sample 110

tag: Sex

value: Female


title: Radioresistant glioblastoma stem cells, replicate 3

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87GSC-3

value: Glioblastoma stem cell


title: untreated-F

description:
Library name: untreated-F
10x Genomics

tag: treatment


title: ACBQ0264_001, normal, rep1

description:
Library name: 12_02_01_17
library name V2: 12_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: pass


title: 2BQ0342_001, normal, rep1

description:
Library name: 11_02_01_17
library name V2: 11_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: Sample 108

tag: tissue

value: Male


title: Sample 109


title: O3-F

description:
Library name: O3-F
10x Genomics

tag: cell type

tag: genotype


title: Radioresistant glioblastoma stem cells, replicate 1

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87GSC-1

tag: cell line


title: AXBQ351_001, MCI, rep1

description:
Library name: 10_02_01_17
library name V2: 10_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: RQS


title: Radioresistant glioblastoma stem cells, replicate 2

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87GSC-2


title: Control, Rep1, 3m, prefrontal cortex

description:
Library name: cortex_CTL1
10x Genomics

value: Prefrontal cortex

tag: developmental stage

tag: Sex

value: WT


title: Sample 106


title: Sample 107


title: Radioresistant glioblastoma cells differentiated from radioresistant glioblastoma stem cells, replicate 3

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87DIFF-3

value: Glioblastoma cell


title: O3-M

description:
Library name: O3-M
10x Genomics

tag: treatment


title: DRAO3-M

description:
Library name: DRAO3-M
10x Genomics

value: DRA O3


title: Sample 105

value: buccal


title: DRAO3-F

description:
Library name: DRAO3-F
10x Genomics

value: Lung


title: Sample 111


title: 2BQ9110_001, MCI, rep1

description:
Library name: 9_01_26_17
library name V2: 09_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 003

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: DRA-M

description:
Library name: DRA-M
10x Genomics

tag: tissue

tag: cell type

value: Homogenate

value: DRA


title: Radioresistant glioblastoma cells differentiated from radioresistant glioblastoma stem cells, replicate 2

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87DIFF-2

tag: cell line


title: Sample 104


title: Radioresistant glioblastoma cells differentiated from radioresistant glioblastoma stem cells, replicate 1

address: 广州大道北1838号南方医院菜鸟驿站

description: Library name: U87DIFF-1


title: BQ0457_001, preAD, rep1

description:
Library name: 7_01_26_17
library name V2: 07_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

value: human

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

value: RNASeq QC


title: DRA-F

description:
Library name: DRA-F
10x Genomics

tag: genotype

tag: treatment


title: Sample 103

tag: Sex


title: Post-TIL-1

city: Solna

first: Lucas

last: Arruda

address: Nanna Svartz väg  4

country: Sweden

institute: CuraCell AB

description:
Library name: S07604514_S659Nr34
WES

library_source: genomic

data_processing:
Illumina DRAGEN platform
Assembly: hg38
Supplementary files format and content: tsv files contain the annotated mutations

source_name: Tumor

extract_protocol:
DNAeasy mini plus kit (Qiagen). 200 ng was used for library construction.
SureSelectXT Human All Exon V6

value: Tumor

value: Glioblastoma


title: Post-TIL-2

description:
Library name: S07604514_S659Nr37
WES


title: ACBQ278_001, normal, rep1

description:
Library name: 6_01_26_17
library name V2: 06_01_26_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

value: #N/A

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: 4T1 cells,Limch1_OE, rep2

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

description:
Library name: Sample5
FPKM.Limch1_OE_2

data_processing:
Raw reads were filtered and cleaned by fastp software (v0.23.2).
Gene expression levels were quantified with featureCounts v2.0.1, referencing the GENCODE M23 annotations.
Sequences were then aligned to the mm10 reference genome using STAR v2.7.10.
Transcript assembly and abundance estimation were performed using StringTie v2.2.1.
R was used for visualization.
Assembly: mm10
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text file includes TPM values for each sample

growth_protocol: 4T1 cells were maintained  in RPMI 1640, all with 10% FBS, penicillin (100 IU/ml), and streptomycin (100 μg/ml) in a 5% CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: The mouse LIMCH1 gene sequence was cloned into the PLVX-ires-neo vector. The target plasmid and packaging plasmids (psPAX2,pMD2.G) were co-transfected into HEK293T cells, and viral supernatants were collected and filtered after 48 hours. The virus was used to infect 4T1 cells, and 48 hours post-infection,appropriate antibiotics were used to select stable LIMCH1 overexpression or control cell lines

tag: cell type

value: mouse breast cancer cell


title: Sample 101

tag: tissue

value: Female


title: Pre-TIL.

description:
Library name: S07604514_S659Nr31
WES


title: reference_001, reference, rep4

description:
Library name: 5_01_26_17
library name V2: 05_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: reference


title: 4T1 cells,Limch1_OE, rep1

institute: Tianjin Union Medical Center of Nankai Univercity

description:
Library name: Sample4
FPKM.Limch1_OE_1

tag: cell line


title: 4T1 cells,Limch1_OE, rep3

description:
Library name: Sample6
FPKM.Limch1_OE_3

tag: genotype


title: Sample 102

value: Male


title: ELBQ299_001, MCI, rep1

description:
Library name: 1_02_01_17
library name V2: 01_02_01_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: Aim 2 Batch 004

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: Sample 100

value: buccal

tag: Sex


title: BQ339_001, normal, rep1

description:
Library name: 3_01_26_17
library name V2: 03_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: rna-seq date

value: RQS


title: Post-TIL

description: Library name: RNA_S864Nr51

data_processing:
STAR (version 2.7.3) (Dobin et al. 2013).
Assembly: hg38
Supplementary files format and content: tsv files contain the raw read counts

source_name: tumor

extract_protocol:
RNAeasy mini plus kit (Qiagen). 10 ng was used for library construction.
SMARTer Stranded Total RNA Seq Kit v2- Pico Input (Takara)

tag: tissue

value: tumor

value: autologous tumor

tag: cell type

value: glioblastoma


title: Sample 99


title: 4T1 cells,Vector, rep2

description:
Library name: Sample2
FPKM.Vector_2

value: Vector


title: Pre-TIL

description: Library name: RNA_S864Nr48


title: BQ6138_001, normal, rep1

description:
Library name: 23_01_26_17
library name V2: 23_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

value: human

tag: experimental batch_number

value: Aim 2 Batch 003

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN


title: 4T1 cells,Vector, rep3

description:
Library name: Sample3
FPKM.Vector_3

tag: cell line

tag: genotype


title: 4T1 cells,Vector, rep1

description:
Library name: Sample1
FPKM.Vector_1


title: W5 3

city: Chongqing

first: Li

middle: Min

last: Yang

state: Chongqing

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
equence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38 genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw fragment counts values for each sample.

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Liver

value: hepatocellular carcinoma cells


title: BQ9119_001, MCI, rep1

description:
Library name: 8_01_26_17
library name V2: 08_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A

value: pass


title: Sample 98

tag: Sex

value: Female


title: W5 2


title: ISRIB3

city: guangzhou

first: Weiyong Wang

last: Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

description: Library name: ISRIB3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About xxxxx raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2 2 . FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2 5 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar . Based on the hypergeometric distribution, GO 6 , KEGG 7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: ovary

extract_protocol:
Total RNA was isolated using the RNA Tissue Miniprep System (Promega, Madison, WI, USA).
VAHTS Universal V5 RNA-seq Library Prep Kit

value: ovary

tag: treatment

value: ISRIB in DMSOculture ovary


title: ELACBQHC303_001, MCI, rep1

description:
Library name: 22_01_26_17
library name V2: 22_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

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


title: W5 1

tag: tissue

tag: cell type


title: 2BQ0404_001, preAD, rep1

description:
Library name: 21_01_26_17
library name V2: 21_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Sample 97

value: buccal


title: ISRIB2

description: Library name: ISRIB2

value: ISRIB in DMSO culture ovary


title: 2BQ8107_001, preAD, rep1

description:
Library name: 20_01_26_17
library name V2: 20_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: W4 2

tag: cell line


title: AC602_001, preAD, rep1

description:
Library name: 4_01_26_17
library name V2: 04_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma class

value: RQS


title: AC828_001, preAD, rep1

description:
Library name: 2_01_26_17
library name V2: 02_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: sequencing plate_name


title: Sample 94

tag: tissue

tag: Sex

value: Male


title: Sample 95


title: W4 3

tag: cell type


title: ISRIB1

description: Library name: ISRIB1

tag: treatment


title: W4 1


title: AC626_001, MCI, rep1

description:
Library name: 19_01_26_17
library name V2: 19_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rna-seq date


title: Sample 93


title: Control2

description: Library name: Control2

value: DMSO culture ovary


title: Control3

description: Library name: Control3


title: Sample 92


title: W3 3


title: W3 2


title: 2BQ0340_001, MCI, rep1

description:
Library name: 17_01_26_17
library name V2: 17_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: CP91149 treated 24h (biol rep4)

city: St Lucia

first: Benjamin

middle: D

last: Weger

state: QLD

address: 306 Carmody Road

department: IMB

country: Australia

institute: University of Queensland

description:
Library name: ATP_C_24h_rep4
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S2_24h_rep2

data_processing:
Raw reads were mapped using STAR on the GRCm38/mm10 genome assembly (Ensembl release 102). The BRB-seqTools suite (http://github.com/DeplanckeLab/BRB-seqTools) was subsequently applied to retrieve raw counts per gene.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited raw read count matrix

source_name: liver

extract_protocol:
Snap-frozen liver tissue was homogenized in 2 mL tubes with QIAzol Lysis Reagent and 1.4 mm ceramic beads (Cappella Science, #19-627) using a Precellys tissue homogenizer. RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen, #73404), following the manufacturer’s protocol.
BRB-Seq

treatment_protocol: Mice were exposed to 12-hour night restricted feeding for four days before receiving a subcutaneous injection of CP-91149 (40 mg/kg; volume of 10 µl per g body weight) or vehicle (5% PEG400/5% Tween80/5% DMSO) at Zeitgeber Time 0

value: liver

value: male

tag: strain

tag: genotype

value: wild-type

tag: time


title: reference_001, reference, rep3

description:
Library name: 18_01_26_17
library name V2: 18_01_26_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: plasma sample_replicate_number

value: Aim 2 Batch 003

tag: plasma class

value: reference

tag: sequencing plate_name


title: Sample 91

tag: tissue

tag: Sex


title: Sample 96


title: Sample 90


title: W2 3

value: Liver

tag: cell line

tag: cell type

value: hepatocellular carcinoma cells


title: CP91149 treated 24h (biol rep3)

description:
Library name: ATP_C_24h_rep3
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S2_24h_rep1

tag: treatment


title: Sample 89

value: Female


title: AC834_001, normal, rep1

description:
Library name: 15_01_26_17
library name V2: 15_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

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

value: #N/A

tag: rna-seq date

value: low RIN

value: pass


title: Vehicle treated 24h (biol rep4)

description:
Library name: ATP_V_24h_rep4
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S2_24h_rep2

tag: strain

tag: genotype

value: vehicle

tag: time


title: W2 2


title: AC072_001, preAD, rep1

description:
Library name: 14_01_26_17
library name V2: 14_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Sample 88

tag: tissue

value: buccal

tag: Sex

value: Male


title: W2 1

tag: cell line

tag: cell type


title: Vehicle treated 24h (biol rep3)

description:
Library name: ATP_V_24h_rep3
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S2_24h_rep1

tag: treatment


title: Sample 87


title: CP91149 treated 6h (biol rep4)

description:
Library name: ATP_C_6h_rep4
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S2_6h_rep2


title: BQ6129_001, normal, rep1

description:
Library name: 13_01_26_17
library name V2: 13_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

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: rna-seq date


title: Sample 86


title: CP91149 treated 6h (biol rep3)

description:
Library name: ATP_C_6h_rep3
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S2_6h_rep1

value: liver

tag: strain

tag: genotype

tag: time


title: Control1

description: Library name: Control1

value: ovary

value: DMSO culture ovary


title: BQ8123_001, normal, rep1

description:
Library name: 12_01_26_17
library name V2: 12_01_26_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: plasma sample_replicate_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: shRPL6-2 1

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: GRCh38.100
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

tag: tissue

tag: cell line

tag: cell type

value: RPL6  knockdown


title: Sample 85

tag: Sex


title: ACBQ328_001, MCI, rep1

description:
Library name: 16_01_26_17
library name V2: 16_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: experimental batch_number

value: Aim 2 Batch 003

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: RQS


title: W3 1

value: Liver

value: hepatocellular carcinoma cells


title: Sample 84


title: shRPL6-1 3

tag: genotype


title: ACBQ293_001, preAD, rep1

description:
Library name: 10_01_26_17
library name V2: 10_01_26_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

value: #N/A

tag: rna-seq date


title: Vehicle treated 6h (biol rep3)

description:
Library name: ATP_V_6h_rep3
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S2_6h_rep1

tag: tissue

value: male

tag: strain

value: wild-type

tag: treatment

tag: time


title: CP91149 treated 24h (biol rep2)

description:
Library name: ATP_C_24h_rep2
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S1_24h_rep2

tag: Sex


title: Sample 83


title: shRPL6-1 2

tag: cell line

tag: cell type


title: Sample 82

value: Female


title: CP91149 treated 24h (biol rep1)

description:
Library name: ATP_C_24h_rep1
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S1_24h_rep1


title: BQ0476_001, MCI, rep1

description:
Library name: 1_01_26_17
library name V2: 01_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: shRPL6-1 1

tag: genotype


title: BQHC297_001, MCI, rep1

description:
Library name: 9_01_25_17
library name V2: 09_01_25_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

value: Aim 2 Batch 002

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date


title: shRPL6-2 3

tag: tissue

tag: cell line

tag: cell type


title: Sample 81

value: buccal

tag: Sex


title: shRPL6-2 2


title: ACBQ0279_001, normal, rep1

description:
Library name: 11_01_26_17
library name V2: 11_01_26_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: sample cohort

value: RNASeq QC


title: Vehicle treated 24h (biol rep1)

description:
Library name: ATP_V_24h_rep1
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S1_24h_rep1

value: liver

tag: strain

tag: genotype

tag: treatment

value: vehicle

tag: time


title: Vehicle treated 24h (biol rep2)

description:
Library name: ATP_V_24h_rep2
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S1_24h_rep2


title: Sample 80


title: AC906_001, MCI, rep1

description:
Library name: 7_01_25_17
library name V2: 07_01_25_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: plasma sample_replicate_number

tag: icap cell_culture_well_position

tag: plasma class

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN


title: Vehicle treated 6h (biol rep4)

description:
Library name: ATP_V_6h_rep4
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S2_6h_rep2

tag: tissue

tag: Sex


title: ACBQ353_001, normal, rep1

description:
Library name: 6_01_25_17
library name V2: 06_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date


title: CP91149 treated 6h (biol rep2)

description:
Library name: ATP_C_6h_rep2
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S1_6h_rep2

tag: strain

tag: genotype

tag: treatment

tag: time


title: shCont 1

tag: cell line

value: WT


title: shCont 3

value: Liver


title: Sample 79


title: BQ0474_001, normal, rep1

description:
Library name: 5_01_25_17
library name V2: 05_01_25_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: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class


title: CP91149 treated 6h (biol rep1)

description:
Library name: ATP_C_6h_rep1
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_C_S1_6h_rep1

tag: tissue

tag: Sex


title: Sample 78

value: Male


title: Sample 77


title: Patient Derived Organoid (PDO5) IKKa KO CLDN2 inh

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 from 10xGenomics (executed with default parameters).
Used reference: refdata-gex-GRCh38-2020-A from 10x Genomics documentation
See methods section in published paper for detailed methods for downstream analysis (QC, dim reduction, clustering and automated cell type annotation) applied for obtaining the final Seurat object (RDS file).
Assembly: hg38
Supplementary files format and content: Tab-separated values files (barcodes and features) and matrix files - (Filtered output from CellRanger)
Supplementary files format and content: RDS file including Seurat object (v5.0.0) with processed data (QC, dimensionality reduction and clustering process)

source_name: Colorectal Tumoroid

growth_protocol: PDOs cultured in matrigel at 37 °C, 5% CO2 and medium changed every week.

extract_protocol:
Tumor spheres were collected and digested with an adequate amount of trypsin to single cells. Then were sorted (DAPI (-)) to purify >95% viable cells without debris (Concentration of 1000 cells/ul). Final target cell recovery of 10000 cells.
Library was performed according to the manufacturer's instructions (Chromium Next GEM Single cell 3' Reagent Kits v3.1 Dual Index, 10x Genomics).

treatment_protocol: YM201636 (CLDN2) inhibitor was used at 0,5 µM O/N

value: Colorectal Tumoroid

value: IKKa-/-

value: knock-out treated with CLDN2 inhibitor


title: AC919_001, preAD, rep1

description:
Library name: 4_01_25_17
library name V2: 04_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: #N/A

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: AC613_001, preAD, rep1

description:
Library name: 8_01_25_17
library name V2: 08_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

tag: plasma type

tag: rna-seq date


title: Sample 76


title: Patient Derived Organoid (PDO5) IKKa KO

tag: genotype

tag: treatment

value: knock-out untreated


title: Vehicle treated 6h (biol rep1)

description:
Library name: ATP_V_6h_rep1
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S1_6h_rep1

value: male

tag: strain

value: wild-type

tag: time


title: reference_001, reference, rep2

description:
Library name: 3_01_25_17
library name V2: 03_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 002

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class

value: reference


title: Patient Derived Organoid (PDO5) WT

tag: tissue

value: IKKa+/+

value: wildtype untreated


title: shCont 2

tag: cell line

tag: cell type

value: hepatocellular carcinoma cells


title: Vehicle treated 6h (biol rep2)

description:
Library name: ATP_V_6h_rep2
L1204BW02_01.read.counts.sampleIDs.txt column:  ATP_V_S1_6h_rep2

value: liver

tag: Sex

value: vehicle


title: P122_CT

first: Genís

last: Camprecios

state: Catalonia

address: Rosselló 153

department: Hepatic Hemodynamics

institute: IDIBAPS

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

source_name: Portal vein

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

extract_protocol:
Passage 1 PVECs were collected in RLT + ß-mercaptoethanol and RNA isolated with the RNeasy Micro kit (Qiagen) with on-column DNAseI treatment.
RNA purity and quality was analyzed with Bioanalyzer and only samples with a RNA Integrity Number above 8 were used for subsequent steps.
Libraries were synthesized with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) starting with 50 ug total RNA

treatment_protocol: PVECs were isolated from explanted livers from patients undergoing liver transplant. Cells plated in a 6-well plate (passage 0). Once celles reached confluence, we FACS sorted the samples to isolate pure endothelial cells (CD31+/VE-Cadherin+). Cells were then explanded. We sequenced passage 1 cells.

value: Portal vein

value: portal vein endothelial cells (PVEC)

value: endothelial cells (CD31+/VE-Cadherin+)


title: Sample 75

value: buccal

value: Female


title: 2AX0316_001, MCI, rep1

description:
Library name: 23_01_25_17
library name V2: 23_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: human

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: #N/A

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: RNASeq QC

value: pass


title: Sample 74

value: Male


title: Wwox_KO2_PBT

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_KO2_PBT

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: Plasmablastic plasmacytoma tissue

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: Plasmablastic plasmacytoma tissue

tag: genotype

value: Wwox Knock out


title: WT_M1_FA_N

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

description:
Library name: WT
RNA-seq

data_processing:
Data quality control (adapter trimming, remove reads when bases with quality score less than 5 constitutes more than 50% of the reads) was performed at Novogene.
eads were aligned to mouse (mm10) reference genome using HISAT2  aligner.
The reads mapped to each gene were calculated at Novogene.
The EdgeR Bioconductor package   was used to perform the differential expression analysis. Genes with cutoff (pvalue < 0.05 and |log2FoldChange| > 1) were denoted as Differentially Expressed Genes (DEGs).
Assembly: mm10
Supplementary files format and content: Raw gene counts provided as tab-delimited excel file

source_name: Bone marrow

growth_protocol: Murine bone marrow cells were isolated from tibias and femurs of WT or FRβ KO male C57BL/6 mice and the cells were differentiated to M0-macrophages by culturing for 7 days in complete growth medium (regular RPMI 1640 medium supplemented with 10% FBS and 1% Penicillin/streptomycin) containing 20 ng/mL recombinant mouse M-CSF.

extract_protocol:
Quick-RNA Micro-Perp Kit (Zymo Research) was used to isolate total RNA from the M1-like macrophages.
Library preparation was performed at Novogene.

treatment_protocol: The resulting M0-macrophages were then polarized into M1-like macrophages by treatment for 24 hours in complete growth medium containing 20 ng/mL recombinant mouse IFNγ and 1 ng/mL LPS.

value: Bone marrow

value: Macrophages

value: Wild type

tag: strain


title: LP151_002, MCI, rep1

description:
Library name: 24_01_25_17
library name V2: 24_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 002

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq date

value: RQS


title: AC837_001, MCI, rep1

description:
Library name: 22_01_25_17
library name V2: 22_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: sample cohort

tag: plasma class


title: P106_CT

tag: tissue

value: Portal vein

value: portal vein endothelial cells (PVEC)

value: endothelial cells (CD31+/VE-Cadherin+)

tag: treatment


title: Sample 73

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

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).

value: buccal

tag: Sex

value: Female


title: P105_CT


title: AC126_001, preAD, rep1

description:
Library name: 21_01_25_17
library name V2: 21_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

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

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

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: human

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: #N/A


title: KO_HFD3

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

country: South Korea

institute: Chonnam Univ. Med. Sch.

description: Library name: KO_HFD3

data_processing:
Sequencing was performed on a NovaSeq 6000 platform (Illumina) with paired-end 100 sequencing. FastQC was used for the initial quality check of the sequencing results. The reads with low quality were removed with Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic). The expression counts were calculated using the STAR aligner with DCC algorithm followed by normalization by the total counts of mRNAs in each sample. We selected mRNAs with a mean read count of at least 1 across all samples. was performed on a NovaSeq 6000 platform (Illumina) with paired-end 100 sequencing. FastQC was used for the initial quality check of the sequencing results. The reads with low quality were removed with Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic). The expression counts were calculated using the STAR aligner with DCC algorithm followed by normalization by the total counts of circRNAs in each sample. We selected circRNAs with a mean read count of at least 1 across all samples.
Assembly: mm10
Supplementary files format and content: Microsoft Excel Worksheet file that includes normalized counts of sequencing reads.

source_name: Epididymal white adipose tissue

extract_protocol:
Tota RNA was extracted using Trizol. Ribosomal RNAs were removed from total RNA with Ribo-Zero Gold rRNA Removal Kit (Illumina).
Libraries were prepared using the CORALL RNA-Seq V2 Library Prep Kit (LEXOGEN), with mRNA isolated using the Poly(A) RNA Selection Kit (LEXOGEN). Indexed libraries were enriched by PCR, and quality was confirmed using TapeStation HS D1000 Screen Tape.

value: Epididymal white adipose tissue

tag: cell line

value: Primary

value: adipocyte

tag: genotype

value: RFP KO

value: High-fat diet


title: Sample 72

institute: Oregon Health and Science University

value: Male


title: KO_HFD2

description: Library name: KO_HFD2


title: P89_PVT


title: KO_HFD1

description: Library name: KO_HFD1


title: P127_PVT


title: Sample 71


title: WT_HFD3

description: Library name: WT_HFD3

value: WT


title: 2BQ006_001, preAD, rep1

institute: PreCyte, Inc.

description:
Library name: 20_01_25_17
library name V2: 20_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 002

tag: icap cell_culture_plate_number

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: Sample 70

tag: tissue


title: ACBQ289_001, preAD, rep1

description:
Library name: 2_01_25_17
library name V2: 02_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class

tag: rna-seq date

value: RNASeq QC


title: P125_PVT

value: Portal vein

value: portal vein endothelial cells (PVEC)

value: endothelial cells (CD31+/VE-Cadherin+)

tag: treatment


title: KO_M1_FA_N

description:
Library name: KO
RNA-seq

value: Bone marrow

value: Macrophages

value: FRB Knock out

tag: strain


title: Sample 69

value: buccal

tag: Sex

value: Female


title: BQ6167_001, normal, rep1

description:
Library name: 19_01_25_17
library name V2: 19_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: human

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: #N/A


title: Sample 68

value: Male


title: 2BQ0168_001, preAD, rep1

description:
Library name: 18_01_25_17
library name V2: 18_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: icap cell_culture_plate_number

tag: sequencing plate_name


title: P112_PVT

tag: tissue

tag: cell type


title: WT_HFD1

description: Library name: WT_HFD1

value: Epididymal white adipose tissue

tag: cell line

value: Primary

value: adipocyte

tag: genotype

value: WT

value: High-fat diet


title: WT_HFD2

description: Library name: WT_HFD2

tag: treatment


title: CP91149 treated 24h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_24h_rep3

growth_protocol: AML12 (alpha mouse liver 12) hepatocyte cells from a 3-month-old mouse donor (CD1 strain, line MT42) were purchased from ATCC (CRL-2254) and stored in liquid nitrogen before usage. Cells were maintained in an incubator (37°C, 5% CO2) in base medium (DMEM:F12 Medium supplemented with 10% fetal bovine serum, 10 µg/ml insulin, 5.5 µg/ml transferrin, 5 ng/ml selenium, 40 ng/ml dexamethasone).

extract_protocol:
Cells were lysed on ice in QIAzol Lysis Reagent, collected using a cell scraper, and homogenized by passing several times through a syringe. RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen, #73404), following the manufacturer’s protocol.
BRB-Seq

treatment_protocol: AML12 cells (300,000 cells/well) were seeded into sterile 6-well plates and incubated overnight at 37°C. The following day, cells were washed twice with 1x PBS, and the medium was replaced with a base medium containing either 67 μM CP-91149 or vehicle control (0.03% DMSO). After 3, 6, 14 and 24 hours of treatment RNA was extracted.

value: hepatocyte

value: CD1 strain, line MT42

tag: batch


title: CP91149 treated 24h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_24h_rep2


title: P99_CH

value: Portal vein

value: portal vein endothelial cells (PVEC)

value: endothelial cells (CD31+/VE-Cadherin+)


title: P87_CH


title: CP91149 treated 24h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_24h_rep1


title: BQ0422_001, normal, rep1

description:
Library name: 15_01_25_17
library name V2: 15_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

value: Aim 2 Batch 002

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: Sample 67

value: buccal

tag: Sex


title: LP151_001, MCI, rep1

description:
Library name: 14_01_25_17
library name V2: 14_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: reference_001, reference, rep1

description:
Library name: 16_01_25_17
library name V2: 16_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma sample_replicate_number

tag: icap cell_culture_plate_number

value: reference

tag: sequencing plate_name

value: #N/A


title: Sample 65

tag: tissue

value: Male


title: P80_CH

tag: treatment


title: AC840_001, normal, rep1

description:
Library name: 13_01_25_17
library name V2: 13_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class


title: Vehicle treated 24h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_24h_rep2

tag: cell line

tag: genotype

value: 24h vehicle

tag: batch


title: Sample 63

tag: Sex


title: Sample 62

value: Female


title: BQ6117_001, MCI, rep1

description:
Library name: 12_01_25_17
library name V2: 12_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Vehicle treated 24h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_24h_rep1

tag: cell type


title: Sample 66

tag: tissue


title: AC639_001, normal, rep1

description:
Library name: 11_01_25_17
library name V2: 11_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma sample_replicate_number

tag: icap cell_culture_plate_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sequencing plate_name


title: Sample 61


title: P73_CH

tag: treatment


title: P83_CH


title: AC106_001, preAD, rep1

description:
Library name: 10_01_25_17
library name V2: 10_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: sample cohort

tag: plasma class


title: AXACBQ370_001, MCI, rep1

description:
Library name: 17_01_25_17
library name V2: 17_01_25_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: RNASeq QC


title: P124_CH


title: CP91149 treated 14h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_14h_rep2

tag: cell line

value: hepatocyte

tag: genotype

tag: batch


title: P119_PVT

tag: tissue

tag: cell type


title: Sample 60

tag: Sex


title: P121_CH


title: AC046_001, normal, rep1

description:
Library name: 1_01_25_17
library name V2: 01_01_25_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: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Sample 59


title: Vehicle treated 24h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_24h_rep3

value: CD1 strain, line MT42

tag: treatment


title: Vehicle treated 14h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_14h_rep3

value: 14h vehicle


title: Sample 64


title: P72_CH

value: Portal vein

value: portal vein endothelial cells (PVEC)


title: P75_CH

value: endothelial cells (CD31+/VE-Cadherin+)


title: Vehicle treated 14h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_14h_rep2


title: Sample 58


title: CP91149 treated 14h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_14h_rep3


title: Sample 30

city: Manchester

first: Terence

middle: S

last: Garner

address: St Mary's Hospital, Oxford Road

department: Division of Developmental Biology and Medicine

country: United Kingdom

institute: University of Manchester

description: Library name: RP31_S30

data_processing:
Data were demultiplexed (allowing one mismatch) and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.17.1.14
Salmon quantification of RNA-seq reads
Assembly: hg38
Supplementary files format and content: EdgeR processed log2 CPM

source_name: blood

extract_protocol:
RNA was extracted from blood samples collected in PAXgene blood RNA tubes from children with varying growth parameters
Libraries were generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol

value: blood

tag: decimal age_(y)

value: male

tag: systolic blood_pressure_(mmhg)


title: CP91149 treated 14h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_14h_rep1


title: Vehicle treated 14h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_14h_rep1


title: P109_CH


title: P100_CH


title: Sample 56

first: Lyndsey

last: Shorey-Kendrick

value: buccal


title: Sample 55


title: P111_CH


title: Sample 54


title: Sample 28

description: Library name: RP29_S28

value: female


title: Sample 31

description: Library name: RP32_S31


title: Sample 26

description: Library name: RP27_S26


title: LNCaP PACT knockout 2

city: Nedlands

first: Andrew

middle: Jonghan

last: Woo

state: WA

address: 6 Verdun Street

department: UWA Centre for Medical Research

institute: University of Western Australia

data_processing:
Primary sequence data generation using the Illumina bcl2fastq 2.20.0.422 pipeline
The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences
The transcripts were assembled with the Stringtie tool v1.3.3
The featureCounts v1.5.3 summarised the counts of reads mapping to each known gene.
Assembly: Homo sapiens (HG38)
Supplementary files format and content: Tab delimited text matrix file that consists of a first column of gene IDs and a column of read counts for each sample.

source_name: Prostate

growth_protocol: 1x106 LNCaP parental and LNCaP PACT CRISPR KO cells were plated in triplicate into 10 cm dishes and total RNA extracted from these using Trizol 48 hours post plating (~80% confluency).

extract_protocol:
Using Trizol (Thermo Fisher Scientific) and according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS)

value: Prostate

value: LNCaP

value: PACT knockout


title: LNCaP PACT knockout 1


title: CP91149 treated 6h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_6h_rep1


title: Sample 53

city: Beaverton

address: 505 NW 185th Ave

source_name: buccal

value: Male


title: Vehicle treated 6h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_6h_rep3

value: 6h vehicle


title: Sample 24

description: Library name: RP25_S24


title: LNCaP wild type parents 3

value: wild type


title: Sample 29

description: Library name: RP30_S29


title: LNCaP wild type parents 2


title: Vehicle treated 6h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_6h_rep2


title: Sample 23

description: Library name: RP24_S23


title: Sample 52


title: CP91149 treated 6h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_6h_rep3


title: Vehicle treated 6h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_6h_rep1


title: Sample 25

description: Library name: RP26_S25


title: Sample 50

value: Female


title: Sample 49


title: CP91149 treated 6h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_6h_rep2

value: hepatocyte


title: LNCaP wild type parents 1


title: Sample 57


title: CP91149 treated 3h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_3h_rep3

value: CD1 strain, line MT42


title: Sample 48


title: CP91149 treated 3h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_3h_rep2


title: Sample 51


title: Sample 20

description: Library name: RP21_S20


title: Sample 21

description: Library name: RP22_S21


title: OTUD1_si01_2

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: tab-delimited text files include fpkm_expression  values for each Sample

source_name: kidney

growth_protocol: ACHN cells were cultured in minimum essential medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (#15596026, Invitrogen, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: kidney

value: ACHN cells

value: renal cancer cells

tag: sirna

value: the treat group of knockdown of OTUD1 by siRNA

value: transfection infection


title: Sample 47


title: CP91149 treated 3h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S2_3h_rep1

tag: cell line


title: OTUD1_si01_1


title: Sample 27

description: Library name: RP28_S27

value: blood

value: male


title: LNCaP PACT knockout 3

tag: genotype


title: Sample 46

value: buccal


title: Vehicle treated 3h (biol rep3, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_3h_rep3

value: 3h vehicle

tag: batch


title: Sample 45

tag: tissue


title: Vehicle treated 3h (biol rep2, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_3h_rep2

tag: cell type


title: OTUD1_NC_3

value: the control group of knockdown of OTUD1 by siRNA


title: Sample 18

description: Library name: RP19_S18

tag: Sex

value: female


title: Sample 17

description: Library name: RP18_S17


title: OTUD1_NC_2


title: Sample 22

description: Library name: RP23_S22


title: Sample 44


title: Vehicle treated 3h (biol rep1, batch S2)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S2_3h_rep1


title: OTUD1_si01_3


title: Sample 16

description: Library name: RP17_S16


title: Sample 43

value: Male


title: OTUD1_NC_1


title: CP91149 treated 24h (biol rep3, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_24h_rep3


title: MDA-MB-231_Ponatinib_rep3

city: Chengdu

first: Yumei

address: 1166 LiuTai

institute: Chengdu University of TCM

data_processing:
Basecalls performed using CASAVA1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38/GRCm39 whole genome using hisat2 with parameters -t -q -x -p 8
Count were calculated using htseq with parameters -f -r -s no -a 10 -i
Assembly: hg38/GRCm39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Breast

growth_protocol: The MDA-MB-231 and 4T1 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol following manufacturer's protocol.
The libraries were constructed by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and following manufacturer's protocol.

treatment_protocol: Cells were treated with 1 µmol/L ponatinib or DMSO for 24 h.

value: Breast

value: epithelial cell

value: WT

value: Ponatinib


title: Sample 15

description: Library name: RP16_S15


title: Sample 19

description: Library name: RP20_S19


title: Sample 42

value: Female


title: MDA-MB-231_Ponatinib_rep2


title: CP91149 treated 24h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_24h_rep1

value: hepatocyte

value: CD1 strain, line MT42


title: Vehicle treated 24h (biol rep3, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_24h_rep3

value: 24h vehicle


title: Sample 14

description: Library name: RP15_S14


title: Sample 40


title: Sample 41


title: Sample 13

description: Library name: RP14_S13


title: MDA-MB-231_Ponatinib_rep1


title: MDA-MB-231_DMSO_rep3

value: DMSO


title: Vehicle treated 24h (biol rep2, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_24h_rep2


title: Sample 12

description: Library name: RP13_S12


title: Sample 11

description: Library name: RP12_S11


title: Sample 38


title: MDA-MB-231_DMSO_rep2


title: Vehicle treated 24h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_24h_rep1


title: MDA-MB-231_DMSO_rep1


title: CP91149 treated 14h (biol rep3, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_14h_rep3


title: Sample 10

description: Library name: RP11_S10


title: Sample 9

description: Library name: RP10_S9


title: Sample 39


title: CP91149 treated 14h (biol rep2, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_14h_rep2


title: Sample 36


title: Multiplexed Day7 Reprogramming scRNASeq

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

data_processing:
Samples were demultiplexed using the hashedDrops function in the DropletUtils package (v1.18.1). Demultiplexed cells were identified with an FDR threshold of 1e-5 and a minimum log fold change confidence level in CMO assignment of 2. Confidently assigned cells were processed using the SCANPY package (v1.9.1)
Cells with more than 250 genes, 500 UMIs, and less than 8% mitochondrial reads were retained for downstream analyses. Genes expressed in fewer than 3 cells were also removed. Counts were normalized across cells and scaled to 1e4 per cell and highly variable genes were identified. Effects due to total UMIs and mitochondrial reads per cell were regressed out and the resulting counts were scaled to unit variance with maximum variance clipped at 10. Cell cycle scoring showed minimal relationship between cell cycle phase and count data. A neighborhood graph was constructed in PCA space followed by Leiden clustering with a resolution of 0.4.
Next, partition-based graph abstraction (PAGA) analysis was performed in the SCANPY package and used to initialize all UMAP embeddings. Gene expression overlays on UMAP embeddings were clipped at the top 99th percentile. Marker genes were identified between clusters using the Wilcoxon test (padj<0.01) and annotated with GO and Reactome terms (padj<0.01) using EnrichR through the GSEApy package (v1.0.3). Finally, diffusion pseudotime trajectory analysis was performed using the Force Atlas 2 graph layout algorithm with PAGA initialization. Genes that varied over diffusion pseudotime were visualized using the paga_path command in SCANPY with the expression values per gene normalized and scaled to 1.
Assembly: GRCh38-2020-A
Supplementary files format and content: Raw feature-barcode matrix in h5 format containing both UMIs and cell-multiplexing oligos (CMOs).

source_name: multiplexed sample: embryonic stem cell, normal & Lmna knockdown dermal fibroblasts

extract_protocol:
Normal, Lamin A/C knockdown, and HGPS fibroblasts were lifted 7 days after reprogramming and prepared for multiplexed single-cell RNA sequencing.
Normal, Lamin A/C knockdown, and HGPS fibroblasts were each labeled with 3’ CellPlex cell multiplexing oligos (CMO; 10X Genomics) and pooled together before loading onto the 10X Genomics chromium single cell controller for single-cell RNA sequencing. The CMOs used for each sample were: Normal-CMO309, HGPS-CMO310, and Lmna KD-CMO311. 30,000 total cells were targeted with 50,000 reads per cell. Libraries were sequenced on a NovaSeq 6000 (Illumina) and aligned to the refdata-gex-GRCh38-2020-A reference transcriptome using CellRanger v7.1.0 (10X Genomics).

value: multiplexed sample:embryonic stem cell, normal & Lmna knockdown dermal fibroblasts


title: HEK293T, CRISPR PE GDF11 Tyr336* - HET cells, Replicate 3

city: West Hartford

first: Sean

last: Congdon

state: CT

address: 200 Bloomfield Rd

institute: University of Hartford

description: Library name: HET-3

data_processing:
Reads were quality-checked (FastQC)
Reads were trimmed (Trimmomatic)
Reads were mapped to hg38 with BWA-MEM
Reads were analyzed using VolcaNoseR, ShinyGO, and ClustVis
Assembly: Hg38
Supplementary files format and content: Data was stored as CSV files and processed using Galaxy

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco #11965118) supplemented with 10% fetal bovine serum (FBS; Fisherbrand #A5256801). All cells were maintained as monolayers at 37°C in a humidified incubator with 5% CO₂ and 95% air. Medium was replaced twice weekly, and cells were passaged at 60–80% confluency.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen #74104) with β-mercaptoethanol
RNA-seq (Illumina MiSeq) was performed at Azenta Life Sciences in triplicate per condition

treatment_protocol: HET cells were edited using Prime Editing to create Heterozyogus GDF11 Y336* cell line

value: GDF11 Tyr336* HET

value: Prime Editing GDF11 Tyr336*


title: CP91149 treated 24h (biol rep2, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_24h_rep2


title: CP91149 treated 14h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_14h_rep1


title: Sample 8

description: Library name: RP9_S8

value: blood

value: male


title: HEK293T, CRISPR PE GDF11 Tyr336* - HET cells, Replicate 2

description: Library name: HET-2


title: Vehicle treated 14h (biol rep2, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_14h_rep2

value: 14h vehicle


title: Sample 7

description: Library name: RP8_S7

value: female


title: Sample 35

state: Oregon

value: buccal


title: Sample 34

value: Male


title: HEK293T, CRISPR PE GDF11 Tyr336* - HET cells, Replicate 1

description: Library name: HET-1


title: Sample 33


title: Sample 6

description: Library name: RP7_S6


title: Sample 32


title: HEK293T, WT, Replicate 3

description: Library name: WT-3


title: CP91149 treated 6h (biol rep3, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_6h_rep3


title: Sample 5

description: Library name: RP5_S5


title: HEK293T, WT, Replicate 2

description: Library name: WT-2


title: Sample 31


title: Sample 4

description: Library name: RP4_S4


title: HEK293T, WT, Replicate 1

description: Library name: WT-1


title: CP91149 treated 6h (biol rep2, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_6h_rep2


title: CP91149 treated 6h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_6h_rep1


title: Sample 3

description: Library name: RP3_S3


title: CD8TILs, Donor44, HighCelltrace, rep1

city: Durham

first: Charles

middle: A

last: Gersbach

state: NC

address: 101 Science Drive

institute: Duke University

description: Library name: CD8-T44-1-H

data_processing:
FASTQ files were aligned to custom indexes for each ORF barcode library (generated from the bowtie2-build function) using Bowtie 2.
Assembly: Custom assembly, TF ORF library barcodes from 2023 Zheng Cell paper
Supplementary files format and content: For all processed data files, the format is: column 1 = TF barcode ID, column 2 = number of aligned counts

source_name: NSCLC tumor

extract_protocol:
Genomic DNA was isolated using Zymo’s QuickDNA Miniprep Plus kit.
Genomic DNA was split across 100 μl PCR reactions (22 cycles at 98 °C for 10 s, 60 °C for 10 s, and 72 °C for 25 s) with NEBNext 2× Master Mix and up to 3 μg of genomic DNA per reaction. PCRs were pooled together for each sample and purified using double-sided (SPRI)bead selection at 0.5× and 1.0×. Libraries were run on a 1% agarose gel to confirm amplicon size and quantified using Qubit’s dsDNA High Sensitivity assay. Libraries were diluted to 2 nM, pooled together at equal volumes, run on a High Sensitivity D1000 tape (Agilent) to confirm amplicon size, and sequenced using Illumina’s MiSeq Reagent Kit v2 (50 cycles). Primers used for the gDNA PCR are listed in Supplemental Table 4.

value: NSCLC tumor

value: tumor-infiltrating lymphocytes

value: High CellTrace


title: Sample 30

value: Female


title: Sample 29


title: CD8TILs, Donor44, LowCelltrace, rep1

description: Library name: CD8-T44-1-L

value: Low CellTrace


title: Sample 28


title: Sample 1

description: Library name: RP1_S1


title: Vehicle treated 6h (biol rep2, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_6h_rep2

value: hepatocyte

value: CD1 strain, line MT42

value: 6h vehicle


title: Vehicle treated 6h (biol rep3, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_6h_rep3


title: Sample 27


title: CD8TILs, Donor49, HighCelltrace, rep1

description: Library name: CD8-T49-1-H


title: CP91149 treated 3h (biol rep3, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_3h_rep3