title: 12 week-NCAR-control-14dn-rep3

description:
Library name: 12-NCAR-r3
library name V2: 15
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

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


title: GH4904

status: Public on Dec 02 2025

type: SRA

city: Bethesda

first: Thomas

middle: A

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

country: USA

institute: National Cancer Institute

description:
Library name: GRKO GFP-mGR W718S/Y722S Veh Replicate 1
GRKO GFP-mGR W718S/Y722S Veh Replicate 1

library_source: transcriptomic

data_processing:
RNA reads were aligned using STAR 2.7.0f with default settings.
Cutadapt was used for adapter trimming and quality control.
RNA-Seq data processed with HOMER program version 4.10.4: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -noadj and getDiffExpression.pl -vst
Assembly: mm10
Supplementary files format and content: Excel file of normed counts (RNA-seq)

molecule: total RNA

organism: Mus musculus

source_name: adenocarcinoma cells

growth_protocol: Cell lines use typical growth protocols with DMEM 10% FBS. All cells were grown 24h on media with 10% charcoal stripped serum before dexamethasone treatment.

extract_protocol:
Total RNA was collected using Pure-Link RNA Mini kit (Thermo).
RNA-Seq libraries were made with TruSeq Stranded Total RNA Library Prep.

treatment_protocol: Dexamethasone treatments were 100 nano-molar for 2h.

tag: tissue

value: adenocarcinoma cells

tag: cell line

tag: genotype

value: GRKO GFP-mGR W718S/Y722S

tag: treatment

value: Vehicle


title: GH4901

description:
Library name: GRKO GFP-mGR  P643A 100nM Dex 2h Replicate 1
GRKO GFP-mGR  P643A 100nM Dex 2h Replicate 1

value: GRKO GFP-mGR  P643A

value: Dex 100nM 2h


title: 29 week-NCAR-control-14dn-rep3

city: Potomac

first: Jennifer

last: Smith

address: Windsor View Dr

institute: PreCyte, Inc.

description:
Library name: 29-NCAR-r3
library name V2: 14
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

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

molecule: polyA RNA

organism: Homo sapiens

source_name: iCell Neurons

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

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

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

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: mouse

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

value: MCI

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: SF11_con_1

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

country: Germany

institute: IKMB

description: Library name: SF11_con_1

data_processing:
nf-core pipeline rnaseq
We used Tophat 2 and Bowtie 2 to align reads.
Reads were mapped to mouse genome (MGI assembly version 10) using Tophat program.
Expression counts were normalized by library size.
Normalized gene expression values of the transcripts were computed by HTSeq
Assembly: GRCh38
Supplementary files format and content: comma separated values of the raw reads for each samples
Supplementary files format and content: comma separated values concerning sample information

source_name: colon

growth_protocol: Two guide RNAs (gRNAs) targeting exon 2 of the human IL22RA1 gene were designed and cloned into the gRNA–Cas9 co-expressing plasmid PX458 . To generate the universal donor plasmid for CRISPaint-mediated knockout, pCRISPaint-mNeon-PuroR was digested with BamHI to obtain the backbone, and the CMV-EGFP-T2A-PuroR fragment obtained from the plasmid VB200426 was inserted into the backbone. The mixture of the gRNA plasmid, selector plasmid , and universal donor plasmid was introduced into cells using the NEPA21 electroporation system (NEPAGENE), as previously described.

extract_protocol:
Total RNA was extracted from colonic organoids using the RNeasy Mini Kit (Qiagen). RNA quantity and integrity were assessed using RiboGreen and TapeStation; only samples with RIN >7.0 were used.
Stranded mRNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq Stranded mRNA Sample Prep Kit, following the manufacturer’s protocol.

treatment_protocol: For the rescue and Reg3a treatment experiments, human colonic organoids were treated with rmReg3a and rhREG3A. The stimuli were added 24 hours before the start of the colony-forming assay and continued throughout the experiment.

value: colon

value: organoid

value: intestinal organoid

value: CTRL

tag: batch


title: GH4900

description:
Library name: GRKO GFP-mGR  P643A Veh Replicate 3
GRKO GFP-mGR  P643A Veh Replicate 3


title: 21 week-HEMI-case-14dn-rep4

description:
Library name: 21-HEMI-r4
library name V2: 13
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

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


title: 21 week-HEMI-case-14dn-rep3

description:
Library name: 21-HEMI-r3
library name V2: 19
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)


title: 29 week-HEMI-case-14dn-rep2

description:
Library name: 29-HEMI-r2
library name V2: 12
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma type


title: GH4899

description:
Library name: GRKO GFP-mGR P643A Veh Replicate 2
GRKO GFP-mGR P643A Veh Replicate 2

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: SF13_IL22_2

description: Library name: SF13_IL22_2


title: 29 week-HEMI-case-14dn-rep1

description:
Library name: 29-HEMI-r1
library name V2: 9
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: sequencing plate_name

tag: rna-seq date


title: 12 week-HEMI-case-14dn-rep2

description:
Library name: 12-HEMI-r2
library name V2: 10
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: preAD

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 12 week-HEMI-case-14dn-rep4

description:
Library name: 12-HEMI-r4
library name V2: 17
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: sample cohort

tag: plasma class


title: MIL4-CD14+-derived myeloid angiogenic cells (MACs), rep3

type: RNA

city: Habikino

first: Akifumi

last: Matsuyama

state: Osaka

address: 3-7-1 Habikino

department: Center for reverse Translational Research

country: Japan

institute: Osaka Habikino Medical Center

description:
Gene expression after differentiation derived from cord blood mononuclear cells
SM-3.txt

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: CD14+ cells were isolated from MNCs of cord blood using a magnetic bead‒conjugated anti-CD14 antibody. MACs were obtained from cultured in 5% FBS EGM-2 for 7 days on a fibronectin-coated dish. MIL4-MACs were cultured in 5% FBS EGM-2 in the presence of M-CSF and polarized with IL-4 using a polystyrene-coated dish.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: cord blood

tag: age


title: 12 week-NCAR-control-14dn-rep2

description:
Library name: 12-NCAR-r2
library name V2: 8
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: normal


title: 29 week-NCAR-control-14dn-rep1

description:
Library name: 29-NCAR-r1
library name V2: 11
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

tag: experimental batch_number

tag: plasma thaw_number

tag: sequencing plate_name


title: MIL4-CD14+-derived myeloid angiogenic cells (MACs), rep2

description:
Gene expression after differentiation derived from cord blood mononuclear cells
SM-2.txt


title: GH4898

description:
Library name: GRKO GFP-mGR P643A Veh Replicate 1
GRKO GFP-mGR P643A Veh Replicate 1

value: adenocarcinoma cells

tag: cell line

tag: genotype

tag: treatment


title: SF13_IL22_1

description: Library name: SF13_IL22_1

tag: batch


title: SF11_IL22_3

description: Library name: SF11_IL22_3

tag: cell type


title: 21 week-NCAR-contro-14dnl-rep2

description:
Library name: 21-NCAR-r2
library name V2: 6
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: MIL4-CD14+-derived myeloid angiogenic cells (MACs), rep1

description:
Gene expression after differentiation derived from cord blood mononuclear cells
SM-1.txt

tag: tissue

tag: age


title: SY8_IL22_1

description: Library name: SY8_IL22_1


title: GH4897

description:
Library name: GRKO GFP-mGR  W718E 100nM Dex 2h Replicate 3
GRKO GFP-mGR  W718E 100nM Dex 2h Replicate 3

value: GRKO GFP-mGR  W718E


title: SF13_con_1

description: Library name: SF13_con_1


title: GH4895

description:
Library name: GRKO GFP-mGR  W718E 100nM Dex 2h Replicate 1
GRKO GFP-mGR  W718E 100nM Dex 2h Replicate 1


title: 12 week-HEMI-case-14dn-rep1

description:
Library name: 12-HEMI-r1
library name V2: 5
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: sample cohort

tag: plasma class


title: 12 week-NCAR-control-14dn-rep1

description:
Library name: 12-NCAR-r1
library name V2: 3
feature_counts_GEO2.csv
2wk,12HEMI_NCAR,cqn.csv
2wk,12HEMI_NCAR,fqn.csv

tag: cell type

tag: plasma thaw_number

tag: sequencing plate_name


title: CD14+-derived myeloid angiogenic cells (MACs), rep2

description:
Gene expression after differentiation derived from cord blood mononuclear cells
240314 4.35x10^5.txt


title: CD14+-derived myeloid angiogenic cells (MACs), rep3

description:
Gene expression after differentiation derived from cord blood mononuclear cells
240314 5.48x10^5.txt


title: SF11_IL22_1

description: Library name: SF11_IL22_1

tag: cell line

tag: treatment

tag: batch


title: SF13_con_3

description: Library name: SF13_con_3


title: GH4894

description:
Library name: GRKO GFP-mGR  W718E Veh Replicate 3
GRKO GFP-mGR  W718E Veh Replicate 3

tag: genotype

value: Vehicle


title: 21 week-NCAR-control-2dn-rep4

description:
Library name: 47-10-25-21
library name V2: 21-NCAR-r4
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-HEMI-case-2dn-rep4

description:
Library name: 48-10-25-21
library name V2: 21-HEMI-r4
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: CD14+-derived myeloid angiogenic cells (MACs), rep1

description:
Gene expression after differentiation derived from cord blood mononuclear cells
240118 3.91x10^5.txt

tag: tissue

tag: age


title: 21 week-HEMI-case-14dn-rep2

description:
Library name: 21-HEMI-r2
library name V2: 7
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

tag: cell type

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: GH4896

description:
Library name: GRKO GFP-mGR  W718E 100nM Dex 2h Replicate 2
GRKO GFP-mGR  W718E 100nM Dex 2h Replicate 2

tag: cell line

tag: genotype

tag: treatment


title: GH4893

description:
Library name: GRKO GFP-mGR W718E Veh Replicate 2
GRKO GFP-mGR W718E Veh Replicate 2


title: 29 week-HEMI-case-2dn-rep3

description:
Library name: 45-10-25-21
library name V2: 29-HEMI-r3
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: preculture time_(days)

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: GH4892

description:
Library name: GRKO GFP-mGR  W718E Veh Replicate 1
GRKO GFP-mGR  W718E Veh Replicate 1


title: 21 week-NCAR-control-2dn-rep3

description:
Library name: 42-10-25-21
library name V2: 21-NCAR-r3
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: SY8_con_1

description: Library name: SY8_con_1

tag: tissue

tag: cell type

tag: batch


title: GH4890

description:
Library name: GRKO GFP-mGR P631A 100nM Dex 2h Replicate 2
GRKO GFP-mGR P631A 100nM Dex 2h Replicate 2

tag: cell line

tag: genotype

value: GRKO GFP-mGR P631A


title: 29 week-NCAR-control-2dn-rep4

description:
Library name: 46-10-25-21
library name V2: 29-NCAR-r4
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: SF11_con_3

description: Library name: SF11_con_3

tag: treatment


title: 12 week-HEMI-case-2dn-rep4

description:
Library name: 41-10-25-21
library name V2: 12-HEMI-r4
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: incubation conditions

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: 21 week-HEMI-case-14dn-rep1

description:
Library name: 21-HEMI-r1
library name V2: 2
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: SY8_con_3

description: Library name: SY8_con_3

tag: tissue

tag: cell line

tag: cell type

tag: batch


title: 21 week-HEMI-case-2dn-rep3

description:
Library name: 43-10-25-21
library name V2: 21-HEMI-r3
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: GH4891

description:
Library name: GRKO GFP-mGR P631A 100nM Dex 2h Replicate 3
GRKO GFP-mGR P631A 100nM Dex 2h Replicate 3

tag: genotype

tag: treatment

value: Dex 100nM 2h


title: 29 week-NCAR-control-14dn-rep2

description:
Library name: 29-NCAR-r2
library name V2: 4
feature_counts_GEO2.csv
2wk,29HEMI_NCAR,cqn.csv
2wk,29HEMI_NCAR,fqn.csv

value: iCell Neurons

tag: incubation conditions

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: SY8_IL22_3

description: Library name: SY8_IL22_3

tag: tissue


title: GH4889

description:
Library name: GRKO GFP-mGR P631A 100nM Dex 2h Replicate 1
GRKO GFP-mGR P631A 100nM Dex 2h Replicate 1

tag: cell line


title: 29 week-HEMI-case-2dn-rep4

description:
Library name: 40-10-25-21
library name V2: 29-HEMI-r4
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: cell type

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-NCAR-control-14dn-rep1

description:
Library name: 21-NCAR-r1
library name V2: 1
feature_counts_GEO2.csv
2wk,21HEMI_NCAR,cqn.csv
2wk,21HEMI_NCAR,fqn.csv

tag: preculture time_(days)

value: mouse

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: 29 week-NCAR-control-2dn-rep3

description:
Library name: 38-10-25-21
library name V2: 29-NCAR-r3
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: 29 week-HEMI-case-2dn-rep2

description:
Library name: 36-10-25-21
library name V2: 29-HEMI-r2
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: MCI

tag: rna-seq date


title: 12 week-HEMI-case-2dn-rep2

description:
Library name: 34-10-25-21
library name V2: 12-HEMI-r2
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: cell type

value: pass


title: IgA nephropathy, Normal, Normal-4-G3

city: Seuol

first: Hwajin

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

description:
Library name: NC | Normal-4-G3
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:female

data_processing:
Raw sequencing data were processed using the GeoMx NGS Pipeline (v2.3.3.10) to generate FASTQ and DCC files
QC was conducted using the following threshold: raw reads ≥ 1,000, aligned reads ≥ 80%, stitched reads ≥ 80%, trimmed reads ≥ 80%, sequencing saturation ≥ 50%, negative probe count geomean ≤ 10, and no-template control ≤ 1,000
Assembly: GRCh38
Supplementary files format and content: raw_count.csv: merged raw counts from DCC files
Library strategy: Spatial Transcriptomics

source_name: Renal glomerulus

extract_protocol:
Formalin-fixed paraffin-embedded biopsy tissues were used for GeoMx DSP-based spatial transcriptomic profiling.
Spatial transcriptomic libraries were prepared according to the manufacturer’s instructions using the GeoMx DSP NGS Readout User Manual

tag: tissue

value: Renal glomerulus

tag: sample group

value: control

tag: classification

value: Normal

tag: age

tag: Sex

value: female


title: GH4887

description:
Library name: GRKO GFP-mGR P631A Veh Replicate 2
GRKO GFP-mGR P631A Veh Replicate 2

tag: cell line

tag: genotype

tag: treatment


title: 12 week-NCAR-control-2dn-rep4

description:
Library name: 44-10-25-21
library name V2: 12-NCAR-r4
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 12 week-HEMI-case-2dn-rep3

description:
Library name: 37-10-25-21
library name V2: 12-HEMI-r3
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: cell type

tag: incubation conditions

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: preAD

tag: sequencing plate_name

tag: rna-seq date


title: GH4888

description:
Library name: GRKO GFP-mGR P631A Veh Replicate 3
GRKO GFP-mGR P631A Veh Replicate 3

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: 12 week-NCAR-control-2dn-rep3

description:
Library name: 39-10-25-21
library name V2: 12-NCAR-r3
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: IgA nephropathy, Normal, Normal-4-G1

description:
Library name: NC | Normal-4-G1
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:female

tag: sample group

tag: classification

tag: age

tag: Sex


title: IgA nephropathy, Normal, Normal-3-G3

description:
Library name: NC | Normal-3-G3
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:male

value: male


title: 12 week-NCAR-control-2dn-rep2

description:
Library name: 32-10-25-21
library name V2: 12-NCAR-r2
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: cell type

tag: incubation conditions

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sample cohort

tag: plasma class

value: normal

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-NCAR-control-2dn-rep2

description:
Library name: 30-10-25-21
library name V2: 21-NCAR-r2
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

tag: plasma shipment_batch

tag: sequencing plate_name

tag: rna-seq date


title: IgA nephropathy, Normal, Normal-4-G2

description:
Library name: NC | Normal-4-G2
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:female

tag: tissue

tag: sample group

tag: classification


title: IgA nephropathy, Normal, Normal-3-G2

description:
Library name: NC | Normal-3-G2
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:male

tag: age

tag: Sex


title: SF11_IL22_2

description: Library name: SF11_IL22_2

value: colon

tag: cell line

value: organoid

tag: cell type

value: intestinal organoid

tag: treatment

tag: batch


title: 29 week-NCAR-control-2dn-rep1

description:
Library name: 35-10-25-21
library name V2: 29-NCAR-r1
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sample cohort


title: 12 week-NCAR-control-2dn-rep1

description:
Library name: 27-10-25-21
library name V2: 12-NCAR-r1
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

tag: plasma shipment_batch

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: GH4878

description:
Library name: GRKO GFP-mGRwt 100nM Dex 2h Replicate 2
GRKO GFP-mGRwt 100nM Dex 2h Replicate 2

tag: tissue

value: adenocarcinoma cells

tag: cell line

tag: genotype

value: GRKO-mGRwt

tag: treatment


title: GH4886

description:
Library name: GRKO GFP-mGR P631A Veh Replicate 1
GRKO GFP-mGR P631A Veh Replicate 1

value: GRKO GFP-mGR P631A

value: Vehicle


title: 29 week-HEMI-case-2dn-rep1

description:
Library name: 33-10-25-21
library name V2: 29-HEMI-r1
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: cell type

value: iCell Neurons

tag: incubation conditions

value: 5% plasma, 6 h

value: mouse

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: 29 week-NCAR-control-2dn-rep2

description:
Library name: 28-10-25-21
library name V2: 29-NCAR-r2
feature_counts_GEO.csv
2day,29HEMI_NCAR,cqn.csv
2day,29HEMI_NCAR,fqn.csv

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sample cohort

value: pass


title: 12 week-HEMI-case-2dn-rep1

description:
Library name: 29-10-25-21
library name V2: 12-HEMI-r1
feature_counts_GEO.csv
2day,12HEMI_NCAR,cqn.csv
2day,12HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

tag: plasma shipment_batch

tag: plasma class

tag: sequencing plate_name


title: SY8_con_2

description: Library name: SY8_con_2

tag: tissue

tag: cell line

value: CTRL

tag: batch


title: 21 week-HEMI-case-2dn-rep2

description:
Library name: 31-10-25-21
library name V2: 21-HEMI-r2
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: cell type

tag: incubation conditions

value: MCI

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-HEMI-case-2dn-rep1

description:
Library name: 26-10-25-21
library name V2: 21-HEMI-r1
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: GH4876

description:
Library name: GRKO GFP-mGRwt Veh Replicate 3
GRKO GFP-mGRwt Veh Replicate 3

tag: genotype

tag: treatment


title: 21 week-NCAR-control-2dn-rep1

description:
Library name: 25-10-25-21
library name V2: 21-NCAR-r1
feature_counts_GEO.csv
2day,21HEMI_NCAR,cqn.csv
2day,21HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: sample cohort


title: GH4879

description:
Library name: GRKO GFP-mGRwt 100nM Dex 2h Replicate 3
GRKO GFP-mGRwt 100nM Dex 2h Replicate 3

tag: tissue

tag: cell line

value: Dex 100nM 2h


title: IgA nephropathy, Normal, Normal-2-G3

description:
Library name: NC | Normal-2-G3
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:male

value: Renal glomerulus

tag: sample group

value: control

tag: classification

value: Normal

tag: age

tag: Sex


title: 21 week-NCAR-control-5dn-rep4

description:
Library name: 23-10-25-21
library name V2: 21-NCAR-r4
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: cell type

tag: incubation conditions

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma shipment_batch

tag: plasma class

value: normal

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-HEMI-case-5dn-rep4

description:
Library name: 24-10-25-21
library name V2: 21-HEMI-r4
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

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: GH4875

description:
Library name: GRKO GFP-mGRwt Veh Replicate 2
GRKO GFP-mGRwt Veh Replicate 2

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: IgA nephropathy, Normal, Normal-2-G2

description:
Library name: NC | Normal-2-G2
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:male

tag: sample group

tag: classification

tag: age

tag: Sex

value: male


title: 29 week-HEMI-case-5dn-rep3

description:
Library name: 21-10-25-21
library name V2: 29-HEMI-r3
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: cell type

tag: incubation conditions

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: 12 week-NCAR-control-5dn-rep4

description:
Library name: 20-10-25-21
library name V2: 12-NCAR-r4
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

tag: preculture time_(days)

tag: plasma type

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-HEMI-case-5dn-rep3

description:
Library name: 19-10-25-21
library name V2: 21-HEMI-r3
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: cell type


title: 12 week-HEMI-case-5dn-rep4

description:
Library name: 17-10-25-21
library name V2: 12-HEMI-r4
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

tag: incubation conditions

value: preAD


title: 21 week-NCAR-control-5dn-rep3

description:
Library name: 18-10-25-21
library name V2: 21-NCAR-r3
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: plasma used_in_icap_(plasmakey)


title: 29 week-NCAR-control-5dn-rep4

description:
Library name: 22-10-25-21
library name V2: 29-NCAR-r4
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: plasma sample_replicate_number


title: GH4874

description:
Library name: GRKO GFP-mGRwt Veh Replicate 1
GRKO GFP-mGRwt Veh Replicate 1

tag: tissue

value: adenocarcinoma cells

tag: cell line

tag: genotype

tag: treatment


title: 29 week-HEMI-case-5dn-rep4

description:
Library name: 16-10-25-21
library name V2: 29-HEMI-r4
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: WAT male vehicle (WM12_S25)

city: St Lucia

first: Benjamin

middle: D

last: Weger

state: QLD

address: 306 Carmody Road

department: IMB

country: Australia

institute: University of Queensland

data_processing:
Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i To count uniquely mapped reads per gene we were using the --quantMode GeneCounts option of STAR.
Assembly: mm10
Supplementary files format and content: STAR outputs read counts per gene into ReadsPerGene.out.tab file with 4 columns which correspond to different strandedness options: column 1: gene ID column 2: counts for unstranded RNA-seq column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes) column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

source_name: WAT

extract_protocol:
WAT and liver were disrupted using the tissue homogenizer (Precellys) and RNA extracted using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer's protocol.
.

treatment_protocol: Seven-week-old female and male animals were fed a high-fat diet (HFD; Specialty Feeds; special premix diet SF013) for21weeks to induce obesity. Mice were housed in a temperature-controlled room at 23-25°C and maintained on a reversed 12-hour light/dark cycle during the entire experiment. Starting in week16 of the experiment, C57BL/6 mice were subcutaneously injected with either vehicle (PBS) or 1 mg/kg/day PTP-r via subcutaneous injection for5weeks.

value: WAT

tag: Sex

tag: strain

value: wild-type

value: vehicle


title: WAT male PTP-r (WM11_S26)

value: PTP-r


title: GH4877

description:
Library name: GRKO GFP-mGRwt 100nM Dex 2h Replicate 1
GRKO GFP-mGRwt 100nM Dex 2h Replicate 1

value: GRKO-mGRwt


title: IgA nephropathy, Normal, Normal-2-G1

description:
Library name: NC | Normal-2-G1
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:male

tag: sample group

tag: classification

tag: age


title: 12 week-NCAR-control-5dn-rep3

description:
Library name: 15-10-25-21
library name V2: 12-NCAR-r3
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: mouse

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: WAT male vehicle (WM10_S27)

tag: tissue

tag: genotype

tag: treatment


title: IgA nephropathy, Normal, Normal-1-G2

description:
Library name: NC | Normal-1-G2
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:female

tag: Sex

value: female


title: WAT male vehicle (WM09_S28)

tag: strain


title: 12 week-HEMI-case-5dn-rep3

description:
Library name: 13-10-25-21
library name V2: 12-HEMI-r3
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: WAT male PTP-r (WM07_S30)


title: 29 week-NCAR-control-5dn-rep3

description:
Library name: 14-10-25-21
library name V2: 29-NCAR-r3
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: experimental batch_number

tag: plasma thaw_number


title: IgA nephropathy, E0 classification, E0-3-3

description:
Library name: E0 | E0-3-3
IgA nephropathy (E0 classification), biopsy sample, age:40s, sex:female

tag: tissue

value: Renal glomerulus

tag: sample group

value: IgA nephropathy

tag: classification

value: E0 classification

tag: age


title: 29 week-HEMI-case-5dn-rep2

description:
Library name: 12-10-25-21
library name V2: 29-HEMI-r2
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: MCI

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 29 week-NCAR-control-5dn-rep1

description:
Library name: 11-10-25-21
library name V2: 29-NCAR-r1
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: plasma sample_replicate_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: normal

tag: sequencing plate_name


title: IgA nephropathy, Normal, Normal-3-G1

description:
Library name: NC | Normal-3-G1
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:male

value: control

value: Normal

tag: Sex

value: male


title: 12 week-NCAR-control-5dn-rep2

description:
Library name: 8-10-25-21
library name V2: 12-NCAR-r2
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: experimental batch_number

tag: rna-seq date


title: IgA nephropathy, Normal, Normal-1-G1

description:
Library name: NC | Normal-1-G1
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:female

tag: tissue

tag: sample group

tag: classification

tag: age


title: 12 week-HEMI-case-5dn-rep2

description:
Library name: 10-10-25-21
library name V2: 12-HEMI-r2
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

tag: plasma used_in_icap_(plasmakey)

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: preAD

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 21 week-HEMI-case-5dn-rep2

description:
Library name: 7-10-25-21
library name V2: 21-HEMI-r2
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: plasma sample_replicate_number

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: WAT male PTP-r (WM06_S31)

value: WAT

tag: Sex

tag: strain

tag: genotype

value: wild-type

tag: treatment


title: WAT male PTP-r (WM05_S32)

tag: tissue

value: PTP-r


title: 21 week-NCAR-control-5dn-rep2

description:
Library name: 6-10-25-21
library name V2: 21-NCAR-r2
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: experimental batch_number

tag: rna-seq date


title: IgA nephropathy, Normal, Normal-1-G3

description:
Library name: NC | Normal-1-G3
Control (non-tumorous kidney tissue of renal malignancy), biopsy sample, age:50s, sex:female

tag: sample group

tag: classification

tag: age


title: 12 week-HEMI-case-5dn-rep1

description:
Library name: 5-10-25-21
library name V2: 12-HEMI-r1
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

value: 5% plasma, 6 h

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: 29 week-NCAR-control-5dn-rep2

description:
Library name: 4-10-25-21
library name V2: 29-NCAR-r2
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)

value: mouse

tag: plasma class

tag: sequencing plate_name


title: WAT male vehicle (WM04_S33)

tag: tissue

tag: Sex

tag: strain

tag: genotype

tag: treatment

value: vehicle


title: IgA nephropathy, E0 classification, E0-2-2

description:
Library name: E0 | E0-2-2
IgA nephropathy (E0 classification), biopsy sample, age:50s, sex:female

tag: sample group

tag: classification

tag: age

value: female


title: WAT male vehicle (WM03_S34)


title: 12 week-NCAR-control-5dn-rep1

description:
Library name: 3-10-25-21
library name V2: 12-NCAR-r1
feature_counts_GEO.csv
5day,12HEMI_NCAR,cqn.csv
5day,12HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq date

value: pass


title: IgA nephropathy, E0 classification, E0-3-1

description:
Library name: E0 | E0-3-1
IgA nephropathy (E0 classification), biopsy sample, age:40s, sex:female

tag: tissue

value: Renal glomerulus

value: IgA nephropathy


title: 21 week-HEMI-case-5dn-rep1

description:
Library name: 2-10-25-21
library name V2: 21-HEMI-r1
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: MCI

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: IgA nephropathy, E0 classification, E0-3-4

description:
Library name: E0 | E0-3-4
IgA nephropathy (E0 classification), biopsy sample, age:40s, sex:female

tag: sample group

tag: classification

value: E0 classification

tag: age

tag: Sex


title: 21 week-NCAR-control-5dn-rep1

description:
Library name: 1-10-25-21
library name V2: 21-NCAR-r1
feature_counts_GEO.csv
5day,21HEMI_NCAR,cqn.csv
5day,21HEMI_NCAR,fqn.csv

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

value: normal


title: WAT male PTP-r (WM02_S35)

tag: tissue

tag: strain

tag: genotype

tag: treatment


title: IgA nephropathy, E0 classification, E0-2-1

description:
Library name: E0 | E0-2-1
IgA nephropathy (E0 classification), biopsy sample, age:50s, sex:female


title: 29 week-HEMI-case-5dn-rep1

description:
Library name: 9-10-25-21
library name V2: 29-HEMI-r1
feature_counts_GEO.csv
5day,29HEMI_NCAR,cqn.csv
5day,29HEMI_NCAR,fqn.csv

tag: cell type

tag: preculture time_(days)

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: rna-seq date


title: IgA nephropathy, E0 classification, E0-1-4

description:
Library name: E0 | E0-1-4
IgA nephropathy (E0 classification), biopsy sample, age:30s, sex:male

tag: sample group

tag: classification

tag: age

tag: Sex


title: AgilentRNA_001, Ref_RNA, rep5

description:
Library name: 5_Ref_RNA
library name V2: 5_Ref_RNA
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: experimental batch_number

tag: plasma thaw_number

value: AgilentRNA

tag: sequencing plate_name

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: AgilentRNA_001, Ref_RNA, rep4

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

tag: cell type

tag: preculture time_(days)

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: AgilentRNA_001, Ref_RNA, rep3

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

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: rna-seq date


title: IgA nephropathy, E0 classification, E0-1-3

description:
Library name: E0 | E0-1-3
IgA nephropathy (E0 classification), biopsy sample, age:30s, sex:male

tag: tissue

tag: sample group

tag: classification

tag: age

tag: Sex

value: male


title: AgilentRNA_001, Ref_RNA, rep1

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

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: IgA nephropathy, E0 classification, E0-3-2

description:
Library name: E0 | E0-3-2
IgA nephropathy (E0 classification), biopsy sample, age:40s, sex:female


title: WAT male PTP-r (WM01_S36)

value: WAT

tag: strain

tag: genotype

value: wild-type

tag: treatment


title: IgA nephropathy, E0 classification, E0-1-2

description:
Library name: E0 | E0-1-2
IgA nephropathy (E0 classification), biopsy sample, age:30s, sex:male


title: WAT female vehicle (WF12_S37)


title: F1549_001_2, MCI, rep1

description:
Library name: 11_10_10_17
library name V2: 11_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

tag: preculture time_(days)

value: Aim 2 Batch 025

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: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: IgA nephropathy, E0 classification, E0-1-1

description:
Library name: E0 | E0-1-1
IgA nephropathy (E0 classification), biopsy sample, age:30s, sex:male

tag: tissue

tag: sample group

tag: classification

tag: age

tag: Sex


title: F1548_001_2, normal, rep1

description:
Library name: 10_10_10_17
library name V2: 10_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: plasma class

tag: rna-seq date


title: WAT female vehicle (WF10_S39)

tag: strain

tag: genotype

tag: treatment

value: vehicle


title: F835_004_2, preAD, rep1

description:
Library name: 07_10_10_17
library name V2: 07_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

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: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F80_004_2, normal, rep1

description:
Library name: 06_10_10_17
library name V2: 06_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number


title: F1391_001_2, normal, rep1

description:
Library name: 08_10_10_17
library name V2: 08_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: plasma class

tag: rna-seq date


title: F1394_001_2, MCI, rep1

description:
Library name: 09_10_10_17
library name V2: 09_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type


title: F382_004, normal, rep1

description:
Library name: 12_10_10_17
library name V2: 12_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)


title: F1520_002, preAD, rep1

description:
Library name: 05_10_10_17
library name V2: 05_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_plate_number


title: WAT female PTP-r (WF09_S40)

tag: tissue

tag: Sex

value: female

tag: strain

tag: genotype

tag: treatment

value: PTP-r


title: IgA nephropathy, E1 classification, E1-4-2

description:
Library name: E1 | E1-4-2
IgA nephropathy (E1 classification), biopsy sample, age:50s, sex:female

value: Renal glomerulus

tag: sample group

tag: classification

value: E1 classification

tag: age


title: IgA nephropathy, E1 classification, E1-4-1

description:
Library name: E1 | E1-4-1
IgA nephropathy (E1 classification), biopsy sample, age:50s, sex:female

value: IgA nephropathy


title: ACBQHC324_001, preAD, rep1

description:
Library name: 03_10_10_17
library name V2: 03_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN

value: pass


title: WAT female PTP-r (WF08_S41)

tag: tissue


title: WAT female vehicle (WF07_S42)

tag: Sex


title: BQ0434_001, MCI, rep1

description:
Library name: 04_10_10_17
library name V2: 04_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

value: human

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma class

tag: rna-seq date


title: reference_001, reference, rep62

description:
Library name: 02_10_10_17
library name V2: 02_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: reference


title: AC918_001, normal, rep1

description:
Library name: 01_10_10_17
library name V2: 01_10_10_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: #N/A


title: IgA nephropathy, E1 classification, E1-3-2

description:
Library name: E1 | E1-3-2
IgA nephropathy (E1 classification), biopsy sample, age:20s, sex:female

tag: sample group

tag: classification

tag: age


title: F533_006, normal, rep1

description:
Library name: 24_10_04_17
library name V2: 24_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: Aim 2 Batch 024

tag: sample cohort

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: WAT female vehicle (WF06_S43)

tag: tissue

value: WAT

tag: Sex

tag: strain

tag: genotype

tag: treatment


title: F1632_001, MCI, rep1

description:
Library name: 22_10_04_17
library name V2: 22_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma class

tag: rna-seq date


title: IgA nephropathy, E1 classification, E1-3-3

description:
Library name: E1 | E1-3-3
IgA nephropathy (E1 classification), biopsy sample, age:20s, sex:female

tag: sample group

tag: classification

tag: age


title: F1019_005, nonAD, rep1

description:
Library name: 23_10_04_17
library name V2: 23_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: WAT female PTP-r (WF05_S44)

tag: tissue

tag: Sex

tag: strain

tag: genotype

value: wild-type

tag: treatment


title: WAT female PTP-r (WF11_S38)


title: IgA nephropathy, E1 classification, E1-3-1

description:
Library name: E1 | E1-3-1
IgA nephropathy (E1 classification), biopsy sample, age:20s, sex:female


title: WAT female PTP-r (WF04_S45)


title: F1623_001, MCI, rep1

description:
Library name: 20_10_04_17
library name V2: 20_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: plasma class

tag: rna-seq date


title: WAT female vehicle (WF03_S46)


title: F390_004, normal, rep1

description:
Library name: 21_10_04_17
library name V2: 21_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: F1611_001, MCI, rep1

description:
Library name: 18_10_04_17
library name V2: 18_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: IgA nephropathy, E1 classification, E1-4-3

description:
Library name: E1 | E1-4-3
IgA nephropathy (E1 classification), biopsy sample, age:50s, sex:female

tag: tissue

tag: sample group

tag: classification

tag: age

tag: Sex


title: IgA nephropathy, E1 classification, E1-2-3

description:
Library name: E1 | E1-2-3
IgA nephropathy (E1 classification), biopsy sample, age:50s, sex:female


title: F1613_001, MCI, rep1

description:
Library name: 16_10_04_17
library name V2: 16_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: WAT female vehicle (WF02_S47)

tag: strain

tag: genotype

tag: treatment


title: F291_005, nonAD, rep1

description:
Library name: 19_10_04_17
library name V2: 19_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma used_in_icap_(plasmakey)

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: rna-seq date

value: RNASeq QC


title: F1288_002, nonAD, rep1

description:
Library name: 14_10_04_17
library name V2: 14_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: sequencing plate_name

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F897_005, normal, rep1

description:
Library name: 17_10_04_17
library name V2: 17_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number


title: IgA nephropathy, E1 classification, E1-2-1

description:
Library name: E1 | E1-2-1
IgA nephropathy (E1 classification), biopsy sample, age:50s, sex:female

tag: tissue

tag: sample group

tag: classification

tag: age

tag: Sex


title: IgA nephropathy, E1 classification, E1-2-2

description:
Library name: E1 | E1-2-2
IgA nephropathy (E1 classification), biopsy sample, age:50s, sex:female


title: reference_001, reference, rep61

description:
Library name: 15_10_04_17
library name V2: 15_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma used_in_icap_(plasmakey)

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: WAT female PTP-r (WF01_S48)

tag: strain

tag: genotype

tag: treatment


title: CellsOnly_001, CellsOnly, rep16

description:
Library name: 12_10_04_17
library name V2: 12_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: no plasma, 6 h

tag: plasma type

tag: plasma sample_replicate_number

tag: sample cohort

tag: plasma class

value: CellsOnly

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: IgA nephropathy, E1 classification, E1-1-2

description:
Library name: E1 | E1-1-2
IgA nephropathy (E1 classification), biopsy sample, age:30s, sex:male

tag: tissue

tag: sample group

tag: classification

tag: age

tag: Sex

value: male


title: LIVER male PTP-r (LM11_S2)

source_name: LIVER

value: LIVER

tag: strain

value: PTP-r


title: LIVER male vehicle (LM12_S1)

tag: genotype

value: vehicle


title: IgA nephropathy, E1 classification, E1-1-1

description:
Library name: E1 | E1-1-1
IgA nephropathy (E1 classification), biopsy sample, age:30s, sex:male

value: Renal glomerulus

value: IgA nephropathy

value: E1 classification


title: F771_005, preAD, rep1

description:
Library name: 13_10_04_17
library name V2: 13_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: human

tag: plasma used_in_icap_(plasmakey)

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: pass


title: F113_005, nonAD, rep1

description:
Library name: 09_10_04_17
library name V2: 09_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma sample_replicate_number

value: Aim 2 Batch 024

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date


title: F796_005, normal, rep1

description:
Library name: 11_10_04_17
library name V2: 11_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F540_006, MCI, rep1

description:
Library name: 10_10_04_17
library name V2: 10_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type


title: F1417_003, preAD, rep1

description:
Library name: 08_10_04_17
library name V2: 08_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)


title: F1417_001, preAD, rep1

description:
Library name: 07_10_04_17
library name V2: 07_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number


title: LIVER male vehicle (LM10_S3)

tag: tissue

tag: Sex

tag: strain

tag: genotype

value: wild-type

tag: treatment


title: Media Control 3

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

description: Library name: Sample 6

data_processing:
Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Homo sapiens genome build hg19 using STAR3. Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library5. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC6. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library7. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library8, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro9, NCBI10, MSigDB11,12, REACTOME13, WikiPathways14. Enrichment was calculated relative to a set of background genes relevant for the experiment.
Assembly: hg19
Supplementary files format and content: Cell-Cell Interaction in Paracrine Ways_normalizedCounts.xlsx

growth_protocol: Cal27 cells were cultured in DMEM high glucose media supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (i.e., Cal27-GM). SCC25 cells were cultured in 1:1 DMEM and F12 with HEPES supplemented with 10% FBS, 1% penicillin/streptomycin, and 400 ng/ml of hydrocortisone (Sigma; SCC25-GM).

extract_protocol:
After 3 days, RNA was collected by RNeasy Mini Kit (QIAGEN, 74104). Institute for Genomic Medicine at University of California San Diego processed the extracted RNA. RNA integrity and concentration was analyed by Agilent Tape Station system and Qubit 2.0 Fluorometer, respectively. All submitted samples had RIN numbers above 9.0.
RNA library was prepared with Illumina TruSeq Stranded RNA, High Throughput Library Prep Kit, and then sequenced on a NovaSeq 6000.

treatment_protocol: To prepare SCC25 conditioned media, 2x105 SCC25 cells per well were seeded on either 6-well plastic tissue culture plate or 0.48 kPa PA gel on 25 mm coverslip with 2 ml of SCC25 culture media per well. After 24-hour incubation at 37oC and 5% CO2, cell cultured media was replaced and further incubated for 24 hours. Conditioned media was collected and sterile filtered with 0.22 um pore size steriflip (Sigma-Aldrich). Conditioned media was used to culture naïve Cal27 on 0.48 kPa PA gel right after collection without being stored. Cal27 from tissue culture plastic flask were trypsizinized and seeded on collagen-coated 0.48 kPa PA gel (every control and experimental groups but positive control) or 20 kPa PA gel (for positive control). After 2 hours of incubation at 37oC and 5% CO2, cell culture media was replaced with fresh or conditioned media. The effect of indirect co-culturing was observed for 4 days.

tag: cell line

value: Epithelial

value: Control - D3


title: F1095_005, nonAD, rep1

description:
Library name: 05_10_04_17
library name V2: 05_10_04_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 thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: LIVER male vehicle (LM09_S4)


title: LIVER male PTP-r (LM07_S6)


title: F1585_001, preAD, rep1

description:
Library name: 04_10_04_17
library name V2: 04_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Media Control 1

description: Library name: Sample 4

tag: cell type


title: Media Control 2

description: Library name: Sample 5

tag: treatment


title: F1417_002, MCI, rep1

description:
Library name: 06_10_04_17
library name V2: 06_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number


title: F931_005, normal, rep1

description:
Library name: 03_10_04_17
library name V2: 03_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions


title: IgA nephropathy, E1 classification, E1-1-3

description:
Library name: E1 | E1-1-3
IgA nephropathy (E1 classification), biopsy sample, age:30s, sex:male

tag: tissue

tag: sample group

tag: classification

tag: age

tag: Sex


title: F1272_002, MCI, rep1

description:
Library name: 01_10_04_17
library name V2: 01_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: LIVER male PTP-r (LM05_S8)

tag: strain

tag: genotype

tag: treatment


title: reference_001, reference, rep60

description:
Library name: 02_10_04_17
library name V2: 02_10_04_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: sample cohort

tag: plasma class

value: reference

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F757_004, MCI, rep1

description:
Library name: 24_09_27_17
library name V2: 24_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma sample_replicate_number

value: Aim 2 Batch 023

tag: plasma thaw_number

value: low RIN


title: Conditioned Media Day 3, 2

description: Library name: Sample 2

tag: cell line

value: Conditioned Media - D3


title: LIVER male PTP-r (LM06_S7)

tag: tissue

value: LIVER

tag: Sex

value: male

tag: strain

value: PTP-r


title: LIVER male vehicle (LM04_S9)

tag: genotype

tag: treatment

value: vehicle


title: Conditioned Media Day 3, 3

description: Library name: Sample 3

tag: cell type


title: F1463_001, nonAD, rep1

description:
Library name: 21_09_27_17
library name V2: 21_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: human

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: F288_004, MCI, rep1

description:
Library name: 20_09_27_17
library name V2: 20_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: F1424_001, preAD, rep1

description:
Library name: 22_09_27_17
library name V2: 22_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: plasma thaw_number

value: RNASeq QC


title: F1491_001, nonAD, rep1

description:
Library name: 23_09_27_17
library name V2: 23_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: #N/A


title: LIVER male vehicle (LM03_S10)

tag: tissue

tag: Sex

tag: strain

tag: genotype

value: wild-type

tag: treatment


title: F757_005, preAD, rep1

description:
Library name: 18_09_27_17
library name V2: 18_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: F316_005, normal, rep1

description:
Library name: 19_09_27_17
library name V2: 19_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: cfDNA_CONTROL_32

city: Cambridge

first: Fabio

last: Puddu

address: The Trinity Building

country: United Kingdom

institute: biomodal

description: Library name: CEG1984-AM01-D2512-014

library_source: genomic

data_processing:
Library strategy: duet evoC
Trimming and read resolution: internal proprietary software v0.2.0
Alignment: BWA-MEM2 v2.2.1
Duplicate Marking: samtools  v1.19.2
Methylation quantification: internal proprietary softwares 0.5.3 and 0.2.5
Assembly: GRCh38
Supplementary files format and content: bedmethyl file for modC
Supplementary files format and content: bedmethyl file for hmC
Supplementary files format and content: bedmethyl file for mC

molecule: genomic DNA

source_name: cfDNA

extract_protocol:
Where possible, blood was sampled before colonoscopy. 10 mL blood was drawn into a K2 EDTA blood tube, placed on ice, and processed within 4 hours. Samples were centrifuged (2,000g for 10 min at room temperature). The plasma layer was transferred to a clean tube and was again centrifuged (2,000g for 10 min at room temperature) to remove any remaining cellular material. Double-spun plasma was aliquoted into tubes in volumes of at least 1 mL and then immediately frozen and stored at −80°C. cfDNA was extracted using the chemagic™ cfDNA 5k Kit (Revvity) using between 1 and 7 mL of plasma. Resulting cfDNA was quantified using a Qubit Fluorometer (Life Technologies) and quality was assessed using Agilent TapeStation, with samples included if they had >70% for the %cfDNA quality metric on the Cell-free DNA ScreenTape assay.
The duet evoC assay was run according to manufacturer’s instructions. In brief, 10ng of each cfDNA sample was end-repaired, A-tailed, and ligated to hairpin adapters. Adaptors were digested and the 3’ hydroxyl group was extended by a DNA polymerase to generate molecules with the original sample DNA strand connected to its (copied) complementary strand. Y-shaped sequencing adapters were then ligated to molecules. Methylation at 5mC was enzymatically copied across the CpG unit to the C on the copy strand using a DNA methyltransferase, whereas 5hmC was enzymatically glycosylated to prevent such a copy. 5mC on both the original and copy strands was then protected from subsequent deamination. Unmodified Cs were then deaminated to uracil, subsequently read as thymine.

tag: tissue

value: cfDNA


title: F1449_001, nonAD, rep1

description:
Library name: 17_09_27_17
library name V2: 17_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: cfDNA_CONTROL_31

description: Library name: CEG1984-AM01-D2512-013


title: LIVER male PTP-r (LM01_S12)

tag: Sex

tag: strain

tag: genotype

tag: treatment


title: LIVER male PTP-r (LM02_S48)


title: F540_005, MCI, rep1

description:
Library name: 16_09_27_17
library name V2: 16_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: reference_001, reference, rep59

description:
Library name: 15_09_27_17
library name V2: 15_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: cfDNA_CONTROL_30

description: Library name: CEG1984-AM01-D2512-012

tag: tissue


title: cfDNA_CONTROL_29

description: Library name: CEG1984-AM01-D2512-011


title: F784_004, normal, rep1

description:
Library name: 14_09_27_17
library name V2: 14_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: LIVER female vehicle (LF12_S13)

tag: Sex

value: female

tag: strain

tag: genotype

tag: treatment


title: LIVER female PTP-r (LF11_S14)


title: F1148_004, MCI, rep1

description:
Library name: 13_09_27_17
library name V2: 13_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: F1921_001, nonAD, rep1

description:
Library name: 11_09_27_17
library name V2: 11_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: cfDNA_CONTROL_28

description: Library name: CEG1984-AM01-D2512-010

tag: tissue


title: Conditioned Media Day 3, 1

description: Library name: Sample 1

tag: cell line

tag: cell type

value: Epithelial


title: cfDNA_CONTROL_27

description: Library name: CEG1984-AM01-D2512-006


title: CellsOnly_001, CellsOnly, rep15

description:
Library name: 12_09_27_17
library name V2: 12_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: plasma sample_replicate_number

value: Aim 2 Batch 023

tag: plasma thaw_number

value: CellsOnly

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: LIVER female vehicle (LF10_S15)

value: LIVER

tag: Sex

tag: strain

tag: genotype

tag: treatment


title: F993_004, MCI, rep1

description:
Library name: 10_09_27_17
library name V2: 10_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: F868_004, normal, rep1

description:
Library name: 09_09_27_17
library name V2: 09_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: LIVER female PTP-r (LF09_S16)

tag: tissue


title: F1432_001, MCI, rep1

description:
Library name: 08_09_27_17
library name V2: 08_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: cfDNA_CONTROL_26

description: Library name: CEG1984-AM01-D2512-003


title: F494_004, MCI, rep1

description:
Library name: 06_09_27_17
library name V2: 06_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions


title: LIVER female PTP-r (LF08_S17)

tag: Sex

tag: strain

tag: genotype

tag: treatment


title: cfDNA_I_26

description: Library name: CEG1966-AM01-D2512-016


title: F1460_001, nonAD, rep1

description:
Library name: 07_09_27_17
library name V2: 07_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: F317_005, normal, rep1

description:
Library name: 05_09_27_17
library name V2: 05_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: LIVER female vehicle (LF07_S18)

tag: tissue


title: CellsOnly_001, CellsOnly, rep14

description:
Library name: 03_09_27_17
library name V2: 03_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: cfDNA_I_25

description: Library name: CEG1966-AM01-D2512-015


title: reference_001, reference, rep58

description:
Library name: 02_09_27_17
library name V2: 02_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

value: reference


title: LIVER female vehicle (LF06_S19)

tag: Sex

tag: strain

tag: genotype

tag: treatment


title: LIVER female PTP-r (LF05_S20)

value: PTP-r


title: cfDNA_CONTROL_25

description: Library name: CEG1966-AM01-D2512-008


title: LIVER female PTP-r (LF04_S21)


title: cfDNA_CONTROL_24

description: Library name: CEG1966-AM01-D2512-007


title: F362_005, normal, rep1

description:
Library name: 23_09_20_17
library name V2: 23_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: experimental batch_number

value: Aim 2 Batch 022

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: F364_004, preAD, rep1

description:
Library name: 24_09_20_17
library name V2: 24_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: human

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: F666_004, nonAD, rep1

description:
Library name: 21_09_20_17
library name V2: 21_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: LIVER female vehicle (LF03_S22)

tag: tissue

tag: Sex

tag: strain

tag: genotype

tag: treatment

value: vehicle


title: F403_004, nonAD, rep1

description:
Library name: 19_09_20_17
library name V2: 19_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: #N/A

value: RNASeq QC


title: F1404_001, MCI, rep1

description:
Library name: 18_09_20_17
library name V2: 18_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: cfDNA_CONTROL_22

description: Library name: CEG1966-AM01-D2512-004

tag: tissue

value: cfDNA


title: F660_005, nonAD, rep1

description:
Library name: 17_09_20_17
library name V2: 17_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: cfDNA_CONTROL_21

description: Library name: CEG1966-AM01-D2512-002


title: LIVER female PTP-r (LF01_S24)

tag: Sex

value: female

tag: strain

tag: genotype

value: wild-type

tag: treatment


title: F1566_001, preAD, rep1

description:
Library name: 04_09_27_17
library name V2: 04_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: iCell Neurons

value: 5% plasma, 6 h

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: F1387_001, MCI, rep1

description:
Library name: 16_09_20_17
library name V2: 16_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: Ventricular cardiomyocytes, control, rep7

city: Moscow

first: Vadim

last: Mitrokhin

address: Ostrovityanova

country: Russia

institute: RNRMU

description: Library name: Sample 13

data_processing:
Raw sequencing reads were subjected to quality control using FastQC. Adapter trimming and quality filtering were performed with Trimmomatic. Processed reads were aligned to the rat reference genome using HISAT2 with default parameters. Gene expression quantification was performed using HTSeq-count to generate raw counts. Normalization of gene expression was conducted using the Transcripts Per Kilobase Million (TPM) method, enabling comparability across samples.
Assembly: Rat reference genome mRatBN7.2 (Ensembl Release 104)
Supplementary files format and content: tsv file represents counts

organism: Rattus

source_name: Ventricular cardiomyocytes

extract_protocol:
Total RNA was extracted from isolated ventricular cardiomyocytes using the TRIzol reagent, followed by chloroform phase separation and purification with the RNeasy Mini Kit. RNA integrity and concentration were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer to ensure high-quality RNA for downstream processing. Poly(A)+ RNA was subsequently enriched using the NEBNext Poly(A) Magnetic Isolation Module. All steps were performed according to the manufacturer’s protocols to ensure reproducibility and sample integrity.
Library preparation was performed according to the TruSeq Stranded mRNA library preparation assay

tag: tissue

value: Ventricular cardiomyocytes

value: Wistar

value: male

value: control (no hypergravity)

tag: developmental stage

value: adult (8 weeks old)


title: cfDNA_CONTROL_20

description: Library name: CEG1966-AM01-D2512-001


title: F523_005, normal, rep1

description:
Library name: 14_09_20_17
library name V2: 14_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F1329_001, MCI, rep1

description:
Library name: 13_09_20_17
library name V2: 13_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number


title: Ventricular cardiomyocytes, control, rep6

description: Library name: Sample 12

tag: strain

tag: genotype

tag: Sex

tag: treatment


title: F834_004, preAD, rep1

description:
Library name: 22_09_20_17
library name V2: 22_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: Ventricular cardiomyocytes, control, rep5

description: Library name: Sample 11

tag: tissue

tag: developmental stage


title: LIVER female vehicle (LF02_S23)

value: LIVER


title: F1308_001, MCI, rep1

description:
Library name: 10_09_20_17
library name V2: 10_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

value: Aim 2 Batch 022

tag: plasma thaw_number

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F1641_001, MCI, rep1

description:
Library name: 01_09_27_17
library name V2: 01_09_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

value: Aim 2 Batch 023


title: F541_005, preAD, rep1

description:
Library name: 09_09_20_17
library name V2: 09_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: icap cell_culture_plate_number

value: pass


title: cfDNA_CONTROL_18

description: Library name: CEG1578-AM01-D1302-015


title: F604_004, preAD, rep1

description:
Library name: 20_09_20_17
library name V2: 20_09_20_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

value: #N/A


title: F475_005, nonAD, rep1

description:
Library name: 11_09_20_17
library name V2: 11_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: sample cohort

value: RNASeq QC


title: CellsOnly_001, CellsOnly, rep13

description:
Library name: 12_09_20_17
library name V2: 12_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: plasma type

value: CellsOnly


title: cfDNA_CONTROL_17

description: Library name: CEG1578-AM01-D1302-011

tag: tissue

value: cfDNA


title: cfDNA_I_24

description: Library name: CEG1578-AM01-D1302-014


title: F1276_001, MCI, rep1

description:
Library name: 06_09_20_17
library name V2: 06_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma sample_replicate_number

tag: plasma thaw_number


title: F294_005, nonAD, rep1

description:
Library name: 05_09_20_17
library name V2: 05_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: 5% plasma, 6 h

tag: plasma class

tag: sequencing plate_name


title: F1279_001, MCI, rep1

description:
Library name: 08_09_20_17
library name V2: 08_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: reference_001, reference, rep57

description:
Library name: 15_09_20_17
library name V2: 15_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: plasma used_in_icap_(plasmakey)

value: reference


title: Ventricular cardiomyocytes, hypergravity, rep6

description: Library name: Sample 6

value: Ventricular cardiomyocytes

tag: strain

value: Wistar

tag: genotype

value: wild-type

tag: Sex

tag: treatment

value: hypergravity (4g for 14 days)

tag: developmental stage


title: F1275_001, MCI, rep1

description:
Library name: 04_09_20_17
library name V2: 04_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: experimental batch_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: Ventricular cardiomyocytes, control, rep4

description: Library name: Sample 10

tag: tissue

value: male

value: control (no hypergravity)

value: adult (8 weeks old)


title: cfDNA_CONTROL_16

description: Library name: CEG1578-AM01-D1302-010


title: cfDNA_CONTROL_19

description: Library name: CEG1578-AM01-D1302-016


title: F530_005, normal, rep1

description:
Library name: 07_09_20_17
library name V2: 07_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

value: human

tag: plasma sample_replicate_number

value: Aim 2 Batch 022

tag: plasma thaw_number

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: Ventricular cardiomyocytes, hypergravity, rep5

description: Library name: Sample 5

tag: strain

tag: genotype

tag: Sex

tag: treatment


title: cfDNA_CONTROL_15

description: Library name: CEG1578-AM01-D1302-009


title: Ventricular cardiomyocytes, hypergravity, rep4

description: Library name: Sample 4

tag: developmental stage


title: cfDNA_I_23

description: Library name: CEG1566-AM01-D1302-008


title: F737_005, nonAD, rep1

description:
Library name: 03_09_20_17
library name V2: 03_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: F1272_001, preAD, rep1

description:
Library name: 01_09_20_17
library name V2: 01_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

value: RNASeq QC


title: Whole mammary gland involution day 7 replicate 3

city: Paris

first: Jérémy

last: Chantrel

state: Ile-de-France

address: 25-28 rue du Dr. Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

description:
Library name: Sample 12
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F12

data_processing:
Quality Control and Preprocessing Raw sequencing reads were subjected to quality control using FastQC (v0.11.9). Low-quality bases and adapter sequences were trimmed using TrimGalore (v0.6.7) with the following parameters: --stringency 4. Reads passing the quality filters were retained for further analysis.
Quantification of Gene Expression Gene expression levels were quantified using RSEM (v1.3.3) against the Mus musculus reference genome GRCm39.
Assembly: GRCm39
Supplementary files format and content: rsem_results_FPKM_counts_original.txt contains the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each sample, generated using RSEM. rsem_results_raw_counts_original.txt contains the raw read counts for each sample, generated using RSEM.

source_name: Mammary gland

growth_protocol: Mammary glands were collected and snap freezed in liquid nitrogen then kept at -80°C.

extract_protocol:
Total RNA from mammary tissues were extracted with Trizol Reagent following manufacturer's instructions Reagent [Invitrogen #15596026] or RNeasy Micro Kit (Qiagen) following manufacturer’s instructions
250-300 bp insert cDNA library, library type BGISEQ-500 RNA-Seq

tag: tissue

value: Mammary gland

tag: genotype

value: WT


title: F1262_001, MCI, rep1

description:
Library name: 24_09_13_17
library name V2: 24_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

value: Aim 2 Batch 021

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: Whole mammary gland involution day 7 replicate 2

description:
Library name: Sample 11
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F11


title: F350_004, normal, rep1

description:
Library name: 22_09_13_17
library name V2: 22_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h


title: F1264_001, MCI, rep1

description:
Library name: 21_09_13_17
library name V2: 21_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: experimental batch_number

tag: icap cell_culture_plate_number


title: cfDNA_I_22

description: Library name: CEG1566-AM01-D1302-007

value: cfDNA


title: Whole mammary gland involution day 7 replicate 1

description:
Library name: Sample 10
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F10


title: cfDNA_I_21

description: Library name: CEG1566-AM01-D1302-006


title: cfDNA_CONTROL_23

description: Library name: CEG1966-AM01-D2512-005


title: F1067_004, nonAD, rep1

description:
Library name: 20_09_13_17
library name V2: 20_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma sample_replicate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F229_004, normal, rep1

description:
Library name: 19_09_13_17
library name V2: 19_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: Whole mammary gland involution day 3 replicate 3

description:
Library name: Sample 9
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F09

tag: tissue

tag: genotype


title: F89_004, nonAD, rep1

description:
Library name: 17_09_13_17
library name V2: 17_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: F1261_001, MCI, rep1

description:
Library name: 18_09_13_17
library name V2: 18_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: sequencing plate_name

tag: rna-seq date


title: reference_001, reference, rep56

description:
Library name: 02_09_20_17
library name V2: 02_09_20_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma used_in_icap_(plasmakey)

value: reference


title: cfDNA_I_18

description: Library name: CEG1566-AM01-D1302-003


title: cfDNA_I_20

description: Library name: CEG1566-AM01-D1302-005


title: Whole mammary gland involution day 3 replicate 1

description:
Library name: Sample 7
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F07


title: F1598_001, normal, rep1

description:
Library name: 16_09_13_17
library name V2: 16_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: experimental batch_number

tag: icap cell_culture_plate_number


title: cfDNA_I_19

description: Library name: CEG1566-AM01-D1302-004


title: F1260_001, MCI, rep1

description:
Library name: 14_09_13_17
library name V2: 14_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: plasma thaw_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F857_004, nonAD, rep1

description:
Library name: 13_09_13_17
library name V2: 13_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id


title: Whole mammary gland involution day 1 replicate 3

description:
Library name: Sample 6
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F06

tag: tissue

tag: genotype


title: CellsOnly_001, CellsOnly, rep12

description:
Library name: 12_09_13_17
library name V2: 12_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: CellsOnly


title: cfDNA_CONTROL_14

description: Library name: CEG1566-AM01-D1302-002


title: Whole mammary gland involution day 1 replicate 2

description:
Library name: Sample 5
Column name in rsem_results_raw_counts_original.txt and rsem_results_FPKM_counts_original.txt: F05


title: F1630_001, preAD, rep1

description:
Library name: 23_09_13_17
library name V2: 23_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: sequencing plate_name

tag: rna-seq date


title: F1587_001, preAD, rep1

description:
Library name: 11_09_13_17
library name V2: 11_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma used_in_icap_(plasmakey)


title: F1587_003, MCI, rep1

description:
Library name: 10_09_13_17
library name V2: 10_09_13_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: experimental batch_number

tag: icap cell_culture_plate_number