title: RNA-Seq ESUS_9

city: Pamplona

first: Josune

last: Orbe

address: Avenida Pio XII 55

country: Spain

institute: CIMA

description: Library name: Evs_TB66_TROMBO_S5

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR-2.7.0d with default parameters.
UMI deduplication was performed using UMI-tools v1.0.0
featureCounts v1.6.0 software and Gencode v38 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Thrombus

growth_protocol: Frozen thrombus obtained after cranial thrombectomy  in patients with ischemic stroke

extract_protocol:
Thrombus extracelular vesicles (EVs). The thrombus was digested with Accutase (StemPro® Accutase® Cell Dissociation Reagent, GIBCO) adding 1µL accutase per 1mg of thrombus – minimum 250µL of accutase, and was incubated during 60 min at 37ºC at 600 rpm for cell detachment. Then, the digested thrombus was centrifuged at 900 xg (Mikro 22R, Hettich Zentrifugen) for 10 min at room temperature (RT). The obtained supernantant was collected and centrifuged a second time at 12500 x g for 5 min at RT (Mikro 22R, Hettich Zentrifugen). Finally, the obtained cell-free supernatant was centrifuged at 20,000 x g for 70 min at 4ºC (Mikro 22R, Hettich Zentrifugen), and the resulting pellet (enriched in thrombus-derived EVs) was homogenized in 100 µL of filtered PBS (1x0.22 µm, followed by 1x0.1 µm filter) and stored at −80ºC
RNA-Seq was performed in EVs isolated from thrombi  as previously described (Jaitin et al., 2014; F. Machado et al., 2024; Saenz-Pipaon et al., 2020). Briefly, thrombus EVs were separated by sequential centrifugation as previously described (Medium/large size EVs separation from IS thrombi) and resuspended in 100 μL of lysis/binding Buffer (Invitrogen). RNA transcripts were captured with dynabeads oligo (dT) (Invitrogen) and reverse transcribed. RNA samples underwent a linear amplification by in vitro transcription followed by a fragmentation into 250–350 bp. Partial Illumina adaptor sequences were used, and a second reverse transcription reaction was performed. Full Illumina adaptor sequences were successfully added and the libraries sequenced (NextSeq 2000, Illumina).

value: Thrombus

tag: group

value: ESUS


title: 20240612_B_mRNA

status: Public on Dec 02 2025

type: SRA

city: Copenhagen N

first: NNF CBMR

last: Single-Cell Omics Platform

address: Blegdamsvej 3B

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description:
Library name: 20240612_B_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: Skeletal muscle

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

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

tag: reaction id

tag: tissue

value: Skeletal muscle

tag: date of_reaction

tag: treatment

value: Mixed sample (day 0 - 14)

tag: batch within_date

value: B

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: Tada2b_g3_2

city: Philadelphia

first: Michael

last: Haney

state: PA

address: 422 Curie Boulevard

country: USA

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

description: Library name: Tada2b_g3_2

library_source: genomic

data_processing:
Reads were mapped to the mouse GRCm38 (mm10) reference genome using STAR (v.2.5.1b). Raw read counts were generated with STAR using the GeneCounts function. Differential expression in RNA-seq was analyzed using the R package DESeq2 (Love et al. 2014).
Assembly: mm10
Supplementary files format and content: ReadsPerGene.out.tab

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
RNA was extracted from indicated cell populations using the Zymo Direct-zol RNA MicroPrep kit.
RNA sequencing was performed by Novogene using polyA enrichment and sequencing on a Novoseq X (20M reads/sample).

value: Bone marrow

tag: cell type

value: HSPC


title: RNA-Seq Cardio_9

description: Library name: Evs_TB57_TROMBO_S13

value: Cardio

tag: batch


title: F1568_002, nonAD, rep1

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

institute: PreCyte, Inc.

description:
Library name: 23_08_02_17
library name V2: 23_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

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

source_name: iCell Neurons

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

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

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

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 016

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: 20240612_A_mRNA

description:
Library name: 20240612_A_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: tissue

tag: date of_reaction

tag: treatment

tag: batch within_date

value: A

tag: sample state

tag: included samples

tag: included htos

tag: library type


title: F1303_002, preAD, rep1

description:
Library name: 17_08_02_17
library name V2: 17_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: RNASeq QC


title: Tada2b_OE_2

description: Library name: Tada2b_OE_2

tag: tissue


title: RNA-Seq Cardio_8

description: Library name: Evs_TB33_TROMBO_S10

value: Thrombus

tag: group

tag: batch


title: 20240610_B_mRNA

description:
Library name: 20240610_B_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

value: Skeletal muscle

tag: date of_reaction

tag: treatment

tag: batch within_date

tag: sample state


title: F1499_002, nonAD, rep1

description:
Library name: 16_08_02_17
library name V2: 16_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Tada2b_OE_1

description: Library name: Tada2b_OE_1

tag: tissue


title: RNA-Seq ESUS_8

description: Library name: Evs_TB30_TROMBO_S2

tag: group

value: ESUS


title: RNA-Seq ESUS_10

description: Library name: Evs_TB95_TROMBO_S8

tag: batch


title: 20240610_A_mRNA

description:
Library name: 20240610_A_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

value: Mixed sample (day 0 - 14)

tag: included samples

tag: included htos

tag: library type


title: reference_001, reference, rep46

description:
Library name: 15_08_02_17
library name V2: 15_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: reference


title: F2050_001, normal, rep1

description:
Library name: 18_08_02_17
library name V2: 18_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: F119_006, nonAD, rep1

description:
Library name: 21_08_02_17
library name V2: 21_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Tada2b_KO_rep4

description: Library name: Tada2b_KO_rep4

tag: tissue


title: Tada2b_KO_rep3

description: Library name: Tada2b_KO_rep3


title: RNA-Seq Cardio_10

description: Library name: Evs_TB6_TROMBO_S1

tag: group

tag: batch


title: RNA-Seq ESUS_7

description: Library name: Evs_TB25_TROMBO_S14


title: C4-2 oeALKBH5-3-ip

city: Tianjin

first: Yutong

last: Chen

address: Pingjiang road, tianjin

country: China

institute: tianjin medical university

description:
Library name: C4-2 oeALKBH5-3-ip
C-396-3.IP

data_processing:
MeRIP-Seq: Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
RNA-seq: Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC HG19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: UCSC HG19
Supplementary files format and content: bed,XLSX
Supplementary files format and content: Supplementary files format and content: txt. File with counts
Library strategy: MeRIP-Seq

molecule: total RNA

extract_protocol:
MeRIP-Seq, RNA-seq: Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
MeRIP-Seq: m6A RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China). Briefly, m6A RNA immunoprecipitation was performed with the GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina NovaSeq 6000 instrument with 150bp paired-end reads.
RNA-seq: RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

tag: cell line

value: prostate cancer cells

tag: genotype

tag: treatment


title: RNA-Seq Atero_10

description: Library name: Evs_TB179_TROMBO_S15

value: Atero


title: Tada2b_KO_rep2

description: Library name: Tada2b_KO_rep2

value: Bone marrow

value: HSPC


title: C4-2 oeALKBH5-2-input

description:
Library name: C4-2 oeALKBH5-2-input
mRNA Expression Profiling.txt
C-396-2.Input

data_processing:
MeRIP-Seq: Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
RNA-seq: Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC HG19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: UCSC HG19
Supplementary files format and content: bed,XLSX
Supplementary files format and content: Supplementary files format and content: txt. File with counts


title: RNA-Seq Atero_9

description: Library name: Evs_TB169_TROMBO_S12


title: F637_006, preAD, rep1

description:
Library name: 13_08_02_17
library name V2: 13_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number


title: Tada2b_OE_3

description: Library name: Tada2b_OE_3

tag: cell type


title: RNA-Seq Cardio_7

description: Library name: Evs_TB159_TROMBO_S7

value: Cardio


title: F1710_001, normal, rep1

description:
Library name: 11_08_02_17
library name V2: 11_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

value: human

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name


title: F1481_002, nonAD, rep1

description:
Library name: 12_08_02_17
library name V2: 12_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: Aim 2 Batch 016

value: #N/A

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Tada1_g3_3

description: Library name: Tada1_g3_3

tag: tissue


title: C4-2 oeALKBH5-1-input

description:
Library name: C4-2 oeALKBH5-1-input
mRNA Expression Profiling.txt
C-396-1.Input

tag: cell line

tag: genotype

tag: treatment


title: F1431_002, MCI, rep1

description:
Library name: 10_08_02_17
library name V2: 10_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: pass


title: Tada1_g3_2

description: Library name: Tada1_g3_2

tag: cell type


title: RNA-Seq Atero_7

description: Library name: Evs_TB140_TROMBO_S6

tag: group

tag: batch


title: C4-2 oeALKBH5-1-ip

description:
Library name: C4-2 oeALKBH5-1-ip
C-396-1.IP


title: 20240613_A_mRNA

description:
Library name: 20240613_A_10x
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

tag: reaction id

tag: date of_reaction

tag: batch within_date

value: A

tag: sample state

value: frozen

tag: included samples

tag: included htos

tag: library type

value: mRNA


title: Tada1_g2_3

description: Library name: Tada1_g2_3

tag: tissue


title: F1515_001, nonAD, rep1

description:
Library name: 09_08_02_17
library name V2: 09_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Rosa26_rep4

description: Library name: Rosa26_rep4

tag: cell type


title: C4-2 NC-3-ip

description:
Library name: C4-2 NC-3-ip
C-NC-3.IP

tag: cell line

tag: genotype

value: NC

tag: treatment


title: RNA-Seq Atero_6

description: Library name: Evs_TB130_TROMBO_S3

value: Thrombus

tag: group

tag: batch


title: F1535_003, preAD, rep1

description:
Library name: 07_08_02_17
library name V2: 07_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number


title: C4-2 NC-2-input

description:
Library name: C4-2 NC-2-input
mRNA Expression Profiling.txt
C-NC-2.Input


title: C4-2 oeALKBH5-3-input

description:
Library name: C4-2 oeALKBH5-3-input
C-396-3.Input


title: Tada2b_KO_rep1

description: Library name: Tada2b_KO_rep1

tag: tissue


title: RNA-Seq ESUS_6

description: Library name: Evs_TB104_TROMBO_S11

value: ESUS


title: INFAR_KO_2_Tada2b_Rosa26

description: Library name: INFAR_KO_2_Tada2b_Rosa26


title: Rosa26_rep3

description: Library name: Rosa26_rep3


title: C4-2 oeALKBH5-2-ip

description:
Library name: C4-2 oeALKBH5-2-ip
C-396-2.IP

value: prostate cancer cells


title: F424_006, normal, rep1

description:
Library name: 08_08_02_17
library name V2: 08_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: RNA-Seq Atero_8

description: Library name: Evs_TB153_TROMBO_S9

value: Atero


title: F1591_002, nonAD, rep1

description:
Library name: 06_08_02_17
library name V2: 06_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F1574_002, normal, rep1

description:
Library name: 05_08_02_17
library name V2: 05_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions


title: RNA-Seq Atero_5

description: Library name: Evs_TB94_TROMBO_S15

tag: group

tag: batch


title: RNA-Seq ESUS_5

description: Library name: Evs_TB9_TROMBO_S6


title: INFAR_KO_1_Tada2b_Cas9

description: Library name: INFAR_KO_1_Tada2b_Cas9

value: Bone marrow


title: C4-2 NC-1-input

description:
Library name: C4-2 NC-1-input
mRNA Expression Profiling.txt
C-NC-1.Input

tag: cell line

tag: genotype

tag: treatment


title: C4-2 NC-3-input

description:
Library name: C4-2 NC-3-input
mRNA Expression Profiling.txt
C-NC-3.Input


title: IFNAR_KO_Tada2b_KO_1_sgRNA1

description: Library name: IFNAR_KO_Tada2b_KO_1_sgRNA1

tag: tissue

value: HSPC


title: RNA-Seq Cardio_6

description: Library name: Evs_TB139_TROMBO_S4


title: C4-2 NC-1-ip

description:
Library name: C4-2 NC-1-ip
C-NC-1.IP


title: F1500_001, normal, rep1

description:
Library name: 04_08_02_17
library name V2: 04_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: F1729_001, normal, rep1

description:
Library name: 03_08_02_17
library name V2: 03_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: GSK699_2days_rep4

description: Library name: GSK699_2days_rep4


title: Paeonol_3

city: shanghai

first: yue

last: wu

address: zhanling RD 58-304

institute: shanghai biogenuinetech co., LTD.

description: Library name: Paeonol_3

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (***-AS) and regulated alternative splicing events (***-RAS) between ***-OE and control samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cervix

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: cervix

tag: cell line

value: Hela cells

value: cervix cells

tag: genotype

value: WT

value: Paeonol treated  in Hela cells


title: reference_001, reference, rep45

description:
Library name: 02_08_02_17
library name V2: 02_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

value: human

value: Aim 2 Batch 016

value: reference

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: RNA-Seq ESUS_3

description: Library name: Evs_TB72_TROMBO_S9

tag: tissue

value: Thrombus

tag: group

tag: batch


title: RNA-Seq Cardio_5

description: Library name: Evs_TB7_TROMBO_S1

value: Cardio


title: Paeonol_1

description: Library name: Paeonol_1

tag: treatment


title: GSK699_2days_rep3

description: Library name: GSK699_2days_rep3


title: Paeonol_2

description: Library name: Paeonol_2


title: RNA-Seq Cardio_4

description: Library name: Evs_TB62_TROMBO_S2


title: CellsOnly_001, CellsOnly, rep4

description:
Library name: 20_07_27_17
library name V2: 20_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 015

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: CellsOnly


title: NC_2

description: Library name: NC_2

tag: cell type

value: Hela  cell (control plasmid)


title: C4-2 NC-2-ip

description:
Library name: C4-2 NC-2-ip
C-NC-2.IP

tag: cell line

value: prostate cancer cells

value: NC


title: F104_001, nonAD, rep1

description:
Library name: 21_07_27_17
library name V2: 21_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: RNA-Seq ESUS_4

description: Library name: Evs_TB82_TROMBO_S10

tag: tissue

tag: group

value: ESUS

tag: batch


title: RNA-Seq Atero_3

description: Library name: Evs_TB4_TROMBO_S14

value: Atero


title: GSK699_2days_rep2

description: Library name: GSK699_2days_rep2

value: Bone marrow

value: HSPC


title: RNA-Seq Atero_4

description: Library name: Evs_TB87_TROMBO_S11


title: GFP_ctl_1

description: Library name: GFP_ctl_1


title: IFNAR_KO_Tada2b_KO_2_sgRNA2

description: Library name: IFNAR_KO_Tada2b_KO_2_sgRNA2


title: F329_006, normal, rep1

description:
Library name: 14_08_02_17
library name V2: 14_08_02_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

value: Aim 2 Batch 016

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: NC_3

description: Library name: NC_3

value: cervix

value: Hela cells

value: cervix cells

tag: genotype

value: WT

tag: treatment


title: NC_1

description: Library name: NC_1

tag: cell line

tag: cell type


title: CellsOnly_001, CellsOnly, rep3

description:
Library name: 18_07_27_17
library name V2: 18_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: no plasma, 6 h

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 015

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: CellsOnly

value: #N/A


title: RNA-Seq Cardio_3

description: Library name: Evs_TB2_TROMBO_S5

tag: tissue

value: Thrombus

tag: group

value: Cardio

tag: batch


title: U937, SAHA_3

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
Library name: NG-A0804_S3
Column name S3 in U937_RawCounts.csv

data_processing:
RNA-Seq data processing step was performed by Eurofins Genomics. Sequencing data were quality-checked, including adapter trimming and removal of low-quality bases. Reads were aligned to the reference genome using a splice-aware aligner for accurate mapping. Transcript assembly and quantification were performed based on known transcriptome models to estimate gene expression levels. Gene counts were normalized using methods such as TMM or DESeq2 to correct for library size and sequencing depth. Differential expression analysis was conducted using statistical tools. Principal component analysis (PCA) was used to explore sample relationships, and significance testing identified differentially expressed genes. Results were summarized with visualizations such as heatmaps, volcano plots, and QC metrics.
Assembly: hg38
Supplementary files format and content: csv files include raw counts for each Sample

source_name: Lymphoma

extract_protocol:
Eurofins Genomics performed RNA extraction.Total RNA was used as starting material. For eukaryotic samples using polyA selection, 150 ng of total RNA was used (up to 25 µl, with an optimal concentration of 6–50 ng/µl and a maximum of 200 ng/µl). For both eukaryotic and prokaryotic samples using rRNA depletion or mRNA enrichment, 20 ng of RNA was used (up to 15 µl, at a concentration above 1.4 ng/µl).
Eurofins Genomics prepared a library for us. Library preparation included purification of poly-A mRNA (if required), followed by mRNA fragmentation and strand-specific cDNA synthesis using random primers. Adaptors were ligated, and the libraries were amplified by adapter-specific PCR. Sequencing was performed on the Illumina platform using paired-end 150 bp reads, with a guaranteed yield of 30 million read pairs (±3%).

treatment_protocol: MC2726 2µM 10h; SAHA 2µM 10h

value: Lymphoma

value: Pro-monocytic leukemia cell


title: F1889_001, normal, rep1

description:
Library name: 01_08_02_17
library name V2: 01_08_02_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: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

value: pass


title: reference_001, reference, rep43

description:
Library name: 17_07_27_17
library name V2: 17_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: 5% plasma, 6 h

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: reference

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: GFP_ct3_1

description: Library name: GFP_ct3_1

value: Bone marrow

value: HSPC


title: CellsOnly_001, CellsOnly, rep2

description:
Library name: 16_07_27_17
library name V2: 16_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: U937, SAHA_2

description:
Library name: NG-A0804_S2
Column name S2 in U937_RawCounts.csv

tag: tissue

tag: cell line


title: RNA-Seq Cardio_2

description: Library name: Evs_TB137_TROMBO_S4

tag: group

tag: batch


title: GFP_ct2_1

description: Library name: GFP_ct2_1


title: U937, SAHA_1

description:
Library name: NG-A0804_S1
Column name S1 in U937_RawCounts.csv


title: RNA-Seq ESUS_1

description: Library name: Evs_TB14_TROMBO_S7

value: ESUS


title: reference_001, reference, rep44

description:
Library name: 19_07_27_17
library name V2: 19_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: GSK699_2days_rep1

description: Library name: GSK699_2days_rep1

tag: cell type


title: DMSO_2days_rep3

description: Library name: DMSO_2days_rep3


title: DMSO_2days_rep4

description: Library name: DMSO_2days_rep4


title: U937, CAY10603_3

description:
Library name: NG-A0804_M3
Column name M3 in U937_RawCounts.csv


title: reference_001, reference, rep42

description:
Library name: 15_07_27_17
library name V2: 15_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: RNA-Seq Atero_2

description: Library name: Evs_TB103_TROMBO_S12

value: Atero


title: DMSO_2days_rep2

description: Library name: DMSO_2days_rep2


title: F2110_001, normal, rep1

description:
Library name: 14_07_27_17
library name V2: 14_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F1569_003, normal, rep1

description:
Library name: 13_07_27_17
library name V2: 13_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position


title: RNA-Seq Atero_1

description: Library name: Evs_TB1_TROMBO_S13

tag: tissue

tag: group

tag: batch


title: U937, CAY10603_1

description:
Library name: NG-A0804_M1
Column name M1 in U937_RawCounts.csv

tag: cell line


title: DMSO_2days_rep1

description: Library name: DMSO_2days_rep1


title: F2081_001, normal, rep1

description:
Library name: 12_07_27_17
library name V2: 12_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch


title: RNA-Seq ESUS_2

description: Library name: Evs_TB18_TROMBO_S8


title: U937, Control_3

description:
Library name: NG-A0804_C3
Column name C3 in U937_RawCounts.csv

tag: cell type


title: F1278_004, normal, rep1

description:
Library name: 11_07_27_17
library name V2: 11_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma used_in_icap_(plasmakey)

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date


title: E_cd45NEG_Patient E CD45- HLADR+

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

description:
Library name: E_cd45NEG
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

library_source: transcriptomic single cell

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

source_name: Islet

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

value: Islet

tag: age

tag: Sex

value: male

tag: ethnicity

value: Hispanic/Latino

tag: bmi


title: Ctl1_WT_Cas9_L1

description: Library name: Ctl1_WT_Cas9_L1

tag: tissue


title: D_cd45POS_Patient D CD45+ HLADR+

description:
Library name: D_cd45POS
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

value: female

value: White


title: U937, CAY10603_2

description:
Library name: NG-A0804_M2
Column name M2 in U937_RawCounts.csv

tag: cell line


title: F357_007, MCI, rep1

description:
Library name: 10_07_27_17
library name V2: 10_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 015

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: Ctl2_WT_Rosa26

description: Library name: Ctl2_WT_Rosa26

tag: cell type


title: AAVS1_3

description: Library name: AAVS1_3


title: C_cd45POS_Patient C CD45+ HLADR+

description:
Library name: C_cd45POS
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

value: Asian


title: U937, Control_2

description:
Library name: NG-A0804_C2
Column name C2 in U937_RawCounts.csv

value: Lymphoma

value: Pro-monocytic leukemia cell


title: F357_005, MCI, rep1

description:
Library name: 08_07_27_17
library name V2: 08_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: pass


title: D_cd45NEG_Patient D CD45- HLADR+

description:
Library name: D_cd45NEG
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

tag: tissue

tag: age

tag: Sex

tag: ethnicity

tag: bmi


title: HL60, SAHA_3

description:
Library name: NG-26593_C3
Column name C3 in HL60_RawCounts.csv

value: Bone marrow

tag: cell line

value: Promyelocytic leukemia cell


title: C_cd45NEG_Patient C CD45- HLADR+

description:
Library name: C_cd45NEG
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv


title: RNA-Seq Cardio_1

description: Library name: Evs_TB123_TROMBO_S3

value: Thrombus

tag: group

value: Cardio

tag: batch


title: HL60, SAHA_2

description:
Library name: NG-26593_C2
Column name C2 in HL60_RawCounts.csv


title: AAVS1_2

description: Library name: AAVS1_2

value: HSPC


title: AAVS1_1

description: Library name: AAVS1_1


title: F5_001, nonAD, rep1

description:
Library name: 07_07_27_17
library name V2: 07_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

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: icap cell_culture_well_position

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: HL60, SAHA_1

description:
Library name: NG-26593_C1
Column name C1 in HL60_RawCounts.csv

tag: tissue

tag: cell type


title: B_cd45POS_Patient B CD45+ HLADR+

description:
Library name: B_cd45POS
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

value: Islet

tag: age

tag: Sex


title: F2078_001, normal, rep1

description:
Library name: 06_07_27_17
library name V2: 06_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class


title: B_cd45NEG_Patient B CD45- HLADR+

description:
Library name: B_cd45NEG
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

value: female

tag: ethnicity

tag: bmi


title: HL60, CAY10603_3

description:
Library name: NG-26593_B3
Column name B3 in HL60_RawCounts.csv

tag: cell line


title: Lung tissue of C57BL/J mice，Silica and DMSO6

city: Anhui

first: Yukang

last: Zhu

address: No. 203,Huai Bin Road, Huainan City,Anhui Province

institute: The First Hospital of AUST

description:
Library name: Sample15
gene.TPM.matrix.annot.txt:SD6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM were calculated using a protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include TPM values for each Sample …

source_name: Lung

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: treatment

value: Silica and DMSO solution


title: F1484_001_2, MCI, rep1

description:
Library name: 05_07_27_17
library name V2: 05_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 015

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

value: #N/A

tag: sequencing plate_name

tag: rna-seq date


title: Lung tissue of C57BL/J mice，Silica and DMSO5

description:
Library name: Sample14
gene.TPM.matrix.annot.txt:SD5

tag: tissue


title: A_cd45POS_Patient A CD45+ HLADR+

description:
Library name: A_cd45POS
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

tag: age

tag: Sex


title: AAVS_4

description: Library name: AAVS_4

tag: cell type


title: HL60, CAY10603_2

description:
Library name: NG-26593_B2
Column name B2 in HL60_RawCounts.csv


title: U937, Control_1

description:
Library name: NG-A0804_C1
Column name C1 in U937_RawCounts.csv

value: Lymphoma


title: F1392_001_2, normal, rep1

description:
Library name: 04_07_27_17
library name V2: 04_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: A_cd45NEG_Patient A CD45- HLADR+

description:
Library name: A_cd45NEG
SMARTseq
teyton_don_2025_processed_human_normalized_matrix.csv

tag: ethnicity

tag: bmi


title: Lung tissue of C57BL/J mice，Silica and DMSO4

description:
Library name: Sample13
gene.TPM.matrix.annot.txt:SD4

tag: treatment


title: HL60, CAY10603_1

description:
Library name: NG-26593_B1
Column name B1 in HL60_RawCounts.csv

tag: cell line


title: F1321_001_2, MCI, rep1

description:
Library name: 03_07_27_17
library name V2: 03_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: sequencing plate_name

tag: rna-seq date


title: F357_006, MCI, rep1

description:
Library name: 09_07_27_17
library name V2: 09_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id


title: Lung tissue of C57BL/J mice，Silica and DMSO2

description:
Library name: Sample12
gene.TPM.matrix.annot.txt:SD2

tag: tissue


title: HL60, Control_3

description:
Library name: NG-26593_A3
Column name A3 in HL60_RawCounts.csv


title: Lung tissue of C57BL/J mice，Silica7

description:
Library name: Sample11
gene.TPM.matrix.annot.txt:S7

value: Silica


title: reference_001, reference, rep41

description:
Library name: 02_07_27_17
library name V2: 02_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: reference

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: M3_LEI_S60

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

description:
Library name: Sample6
Illumina NextSeq 2000

data_processing:
The overall quality of sequencing reads was evaluated using FastQC. STAR (v.2.7.10a) 61 was used to sequence alignments to the reference mouse genome (GRCm39). Gene Transfer File (GTF) vM27 by Gencode was used to quantify gene expression at gene level.
Further analysis were performed in R Statistical environment (v.4.1.0). Genes without counts were removed for the analysis, and differential expression analysis was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw counts for each samples

source_name: BM-derived MDSC

growth_protocol: Mouse BM-MDSCs were differentiated in vitro as previously described . In brief, bone marrow cells were flushed from the legs of C57BL/6 with RPMI 1640 medium. The cell pellets were lysed with ACK buffer (Gibco, A1049201) to prepare the progenitors. For BM-MDSCs, cells are resuspended in complete RPMI containing 40 ng/ml GM-CSF, 40 ng/ml IL-6 for 4 days and PMN-MDSCs were isolated with the MDSCs isolation Kit (Miltenyi Biotec, 130-094-538) according to the reference.

extract_protocol:
RNA sequencing was performed at the Institute of Oncology Research using the NEBNext Ultra Directional II RNA library preparation kit for Illumina and sequenced on the Illumina NextSeq2000 with single-end, 75 base pair long reads
RNA sequencing was performed at the Institute of Oncology Research using the NEBNext Ultra Directional II RNA library preparation kit for Illumina and sequenced on the Illumina NextSeq2000 with single-end, 75 base pair long reads

treatment_protocol: BM-MDSCs were washed and re-seeded in 24-well plate at 1_106/ml density with fresh culture media after differentiation and either treated with heat inactivated N.Glabtratus at MOI =5 for 24h.

value: BM-derived MDSC

value: MDSC

tag: treatment

value: Mock


title: M2_LEI_S59

description:
Library name: Sample5
Illumina NextSeq 2000


title: F1428_001_2, preAD, rep1

description:
Library name: 01_07_27_17
library name V2: 01_07_27_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

tag: plasma sample_replicate_number

tag: experimental batch_number

value: pass


title: M1_LEI_S58

description:
Library name: Sample4
Illumina NextSeq 2000


title: C9_6_LEI_S63

description:
Library name: Sample3
Illumina NextSeq 2000

value: Nakaseomyces glabratus


title: Lung tissue of C57BL/J mice，Silica2

description:
Library name: Sample10
gene.TPM.matrix.annot.txt:S2


title: Lung tissue of C57BL/J mice，Silica1

description:
Library name: Sample9
gene.TPM.matrix.annot.txt:S1


title: HL60, Control_1

description:
Library name: NG-26593_A1
Column name A1 in HL60_RawCounts.csv

value: Bone marrow

tag: cell line

value: Promyelocytic leukemia cell


title: HL60, Control_2

description:
Library name: NG-26593_A2
Column name A2 in HL60_RawCounts.csv


title: Lung tissue of C57BL/J mice，DMSO7

description:
Library name: Sample8
gene.TPM.matrix.annot.txt:ND7

value: DMSO solution


title: sgKMT5A2

city: Shanghai

first: Xiaoling

last: Tian

address: Dongchuan road,500

institute: East China Normal University

description:
Library name: SAMPLE 4
column name in Processed date files:sgPrdm12-1

data_processing:
RNA-seq reads were trimmed with Trimmomatic, aligned to GRCh38 using STAR, and analyzed with DESeq2 for differential expression. GO and KEGG enrichment analyses were performed using clusterProfiler
Assembly: GRCh38
Supplementary files format and content: excel files include FPKM values for each Sample

source_name: peripheral blood

growth_protocol: Human CD8+ cells were cultured at a concentration of 1e6 cells/ml in X-Vivo medium (Lonza, 04-418Q) supplemented with 10% foetal bovine serum (Gibco, #A5256701), 1% penicillin‒streptomycin (P/S) (Gibco, 15140122) and IL-2 (100 U/ml) (R&D systems, #202-IL-050) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The quality and concentration of RNA were assessed using a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer to ensure RNA integrity (RIN > 8.0) before library preparation.
mRNA was isolated with Dynabeads Oligo(dT) (Thermo Fisher Scientific), fragmented using the Magnesium RNA Fragmentation Module (NEB). First-strand cDNA synthesis was performed using SuperScript™ II Reverse Transcriptase (Invitrogen). Second-strand cDNA synthesis was carried out using E. coli DNA Polymerase I (NEB), RNase H (NEB), and dUTP solution (Thermo Fisher Scientific). The double-stranded cDNA was end-repaired, A-tailed, and ligated with Illumina-compatible adapters using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, USA). Adapter-ligated cDNA fragments were size-selected (300-500 bp) using AMPure XP beads (Beckman Coulter, USA) and subsequently amplified by PCR. The average insert size for the final cDNA libraries was 300 ± 50 bp.

treatment_protocol: Human CD8+T cells were electroporated using P3 Primary Cell Nucleofection Solution (Catalog No. V4XP-3032, Lonza) according to the manufacturer's instructions. Ribonucleoprotein (RNP) complexes were generated by mixing 300 pmol of sgRNA (sgCTRL or sgKMT5A) synthesized by Synthego with 300 pmol of Cas9 protein and incubated for 10 minutes at room temperature prior to electroporation.

value: peripheral blood

tag: genotype

value: RNP

tag: batch


title: F1501_002, normal, rep1

description:
Library name: 9_05_11_17
library name V2: 09_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: human

value: Aim 2 Batch 014

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: sequencing plate_name

value: #REF!

tag: rna-seq date


title: sgKMT5A3

description:
Library name: SAMPLE 5
column name in Processed date files:sgPrdm12-2

tag: tissue


title: F1549_001, MCI, rep1

description:
Library name: 7_05_11_17
library name V2: 07_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

value: #N/A


title: C9_5_LEI_S62

description:
Library name: Sample2
Illumina NextSeq 2000

tag: treatment


title: Lung tissue of C57BL/J mice，DMSO6

description:
Library name: Sample7
gene.TPM.matrix.annot.txt:ND6

value: Lung


title: F1498_002, normal, rep1

description:
Library name: 8_05_11_17
library name V2: 08_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma class

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: C9_4_LEI_S61

description:
Library name: Sample1
Illumina NextSeq 2000

value: BM-derived MDSC

tag: cell type


title: F1548_001, normal, rep1

description:
Library name: 6_05_11_17
library name V2: 06_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: Lung tissue of C57BL/J mice，DMSO4

description:
Library name: Sample6
gene.TPM.matrix.annot.txt:ND4

tag: tissue


title: F1504_001, MCI, rep1

description:
Library name: 5_05_11_17
library name V2: 05_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: sequencing plate_name

tag: rna-seq date


title: sgKMT5A1

description:
Library name: SAMPLE 3
column name in Processed date files:sgNTC-3

tag: cell line

tag: genotype

tag: batch


title: Lung tissue of C57BL/J mice，DMSO1

description:
Library name: Sample5
gene.TPM.matrix.annot.txt:ND1

tag: treatment


title: sgCTRL2

description:
Library name: SAMPLE 2
column name in Processed date files:sgNTC-2


title: DSP-1001660038290-A-H09, Castration+, AP, Treatment+, Mouse 306

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

description: Library name: DSP-1001660038290-A-H09

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

source_name: Prostate

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

value: Prostate

tag: mouse

tag: castration

tag: lobe

value: AP

tag: slide


title: DSP-1001660038290-A-H08, Castration+, AP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H08


title: sgCTRL1

description:
Library name: SAMPLE 1
column name in Processed date files:sgNTC-1


title: Lung tissue of C57BL/J mice，Control7

description:
Library name: Sample4
gene.TPM.matrix.annot.txt:N7

value: Physiological saline


title: DSP-1001660038290-A-H07, Castration+, AP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H07


title: F1183_002, MCI, rep1

description:
Library name: 4_05_11_17
library name V2: 04_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: F1287_003, nonAD, rep1

description:
Library name: 3_05_11_17
library name V2: 03_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: incubation conditions

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: sequencing plate_name

tag: rna-seq date


title: Lung tissue of C57BL/J mice，Control4

description:
Library name: Sample3
gene.TPM.matrix.annot.txt:N4

tag: tissue

tag: treatment


title: DPTILs, Untransduced, Donor50

city: Durham

first: Charles

middle: A

last: Gersbach

state: NC

address: 101 Science Drive

institute: Duke University

description: Library name: T50 DP Untransduced

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

source_name: NSCLC tumor

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

value: NSCLC tumor

tag: cell line

value: tumor-infiltrating lymphocytes

value: DP

value: ORF lentivirus


title: DSP-1001660038290-A-H06, Castration+, AP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H06

tag: mouse

tag: castration

tag: lobe

tag: slide


title: DPTILs, RELB, Donor50

description: Library name: T50 DP RELB


title: Lung tissue of C57BL/J mice，Control2

description:
Library name: Sample2
gene.TPM.matrix.annot.txt:N2


title: F423_002, MCI, rep1

description:
Library name: 20_05_11_17
library name V2: 20_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: CD8TILs, Untransduced, Donor50

description: Library name: T50 CD8 Untransduced

tag: cell type

value: Untransduced


title: Lung tissue of C57BL/J mice，Control1

description:
Library name: Sample1
gene.TPM.matrix.anno.txt:N1


title: reference_001, reference, rep40

description:
Library name: 2_05_11_17
library name V2: 02_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

value: human

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma class

value: reference

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-H04, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H04

tag: tissue

tag: mouse

tag: castration

tag: lobe

value: DLP

tag: treatment

tag: slide


title: CD8TILs, RELB, Donor50

description: Library name: T50 CD8 RELB

tag: cell line


title: F835_004, preAD, rep1

description:
Library name: 19_05_11_17
library name V2: 19_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 014

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

value: #N/A


title: CD8TILs, Thy1.1, Donor50

description: Library name: T50 CD8 Thy1.1

tag: cell type


title: pfc old morphine 3

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

description: Library name: AF7

data_processing:
Raw sequencing reads were aligned to the murine Ensembl transcriptome (v95) with salmon v1.4.0 using options “--seqBias --useVBOpt --gcBias --posBias --numBootstraps 30 --validateMappings”. Length-scaled transcripts per million were acquired using the tximport v1.18.0 function, and log2 fold changes and false discovery rates (FDR) were determined by DESeq2 v1.30.1 in R. t-stochastic neighboring embedding analysis was performed using Rtsne v0.15, with counts transformed by the varianceStabilizingTransformation (VST) function from DESeq2. Comparisons were conducted between old saline and young saline groups, old morphine and old saline groups, and young morphine and young saline groups.
Assembly: GRCm38
Supplementary files format and content: ".sf files from salmon v1.4.0. The columns represent the following: Name: the name of the target transcript provided in the input transcript database (FASTA file). Length: the length of the target transcript in nucleotides. EffectiveLength: the computed effective length of the target transcript. TPM: the estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). NumReads: the estimate of the number of reads mapping to each transcript that was quantified."

source_name: Prefrontal cortex of brain

extract_protocol:
Brain tissues were homogenized using Trizol (Thermo Fisher) reagent and RNA extracted by phase separation.
500ng of total RNA was used for library preparation via the KAPA RNA HyperPrep kit with RiboErase (HMR; Roche) according to the manufacturer's recommendations (Mavrikaki, Lee et al. 2022). Briefly, hybridization with hybridization oligos (HMR) was performed at 95 oC for 2 min. rRNA depletion using RNAse H was performed at 45 oC for 30 min. Following rRNA cleanup via KAPA pure beads, DNase digestion was performed at 37 oC for 30 min followed by cleanup, RNA elution, fragmentation (6 min at 94oC), and priming. First and second strand synthesis and A-tailing were performed according to manufacturer's recommendations. 1.5 uM KAPA Unique Dual-Indexed (UDI; Roche) adapters were ligated to the second strand synthesis product in the presence of a ligation master mix in a reaction that was performed at 20 oC for 15 min. Following cleanup, all libraries underwent 10 cycles of amplification. Successful library production, quality control, and quantification was assessed using Tapestation (High sensitivity D1000 Screen Tape; Agilent Technologies, Inc). Libraries were pooled together and subjected to NovaSeq 6000.

value: Prefrontal cortex of brain

tag: strain

tag: Sex

value: Female

tag: age

value: morphine

tag: matching group

value: D


title: F1468_003, normal, rep1

description:
Library name: 18_05_11_17
library name V2: 18_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: pfc old morphine 2

description: Library name: AF5

tag: tissue

tag: treatment


title: CD4TILs, Untransduced, Donor50

description: Library name: T50 CD4 Untransduced

tag: cell line


title: DSP-1001660038290-A-H03, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H03

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: slide


title: pfc old morphine 1

description: Library name: AF4

tag: strain

tag: Sex

tag: age


title: CD4TILs, Thy1.1, Donor50

description: Library name: T50 CD4 Thy1.1

tag: cell type


title: pfc old saline 3

description: Library name: AF10

value: saline

tag: matching group

value: C


title: F710_004, preAD, rep1

description:
Library name: 17_05_11_17
library name V2: 17_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

value: pass


title: DSP-1001660038290-A-H02, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H02

tag: tissue

tag: mouse

tag: castration

tag: lobe

tag: treatment

tag: slide


title: F79_004, preAD, rep1

description:
Library name: 16_05_11_17
library name V2: 16_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-G12, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-G12


title: DSP-1001660038290-A-H01, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H01


title: reference_001, reference, rep39

description:
Library name: 15_05_11_17
library name V2: 15_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: CD4TILs, RELB, Donor50

description: Library name: T50 CD4 RELB

tag: tissue

value: NSCLC tumor

tag: cell line

value: tumor-infiltrating lymphocytes

value: ORF lentivirus


title: pfc old saline 2

description: Library name: AF9

tag: strain

tag: Sex

tag: age

tag: treatment

tag: matching group


title: DSP-1001660038290-A-G11, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-G11

tag: mouse

tag: castration

tag: lobe

tag: slide


title: DPTILs, Untransduced, Donor49

description: Library name: T49 DP Untransduced

tag: cell type

value: DP

value: Untransduced


title: DSP-1001660038290-A-H05, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-H05

value: DLP


title: pfc old saline 1

description: Library name: AF6


title: DSP-1001660038290-A-G10, Castration+, DLP, Treatment+, Mouse 306

description: Library name: DSP-1001660038290-A-G10


title: DPTILs, RELB, Donor49

description: Library name: T49 DP RELB


title: F1238_002, normal, rep1

description:
Library name: 13_05_11_17
library name V2: 13_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

value: Aim 2 Batch 014

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-G09, Castration+, AP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G09

tag: tissue

tag: mouse

value: AP

tag: treatment


title: CD8TILs, Untransduced, Donor49

description: Library name: T49 CD8 Untransduced

tag: cell line


title: CD8TILs, Thy1.1, Donor49

description: Library name: T49 CD8 Thy1.1

tag: cell type


title: pfc young morphine 3

description: Library name: F8

value: Prefrontal cortex of brain

tag: strain

tag: Sex

value: Female

tag: age

value: morphine

tag: matching group

value: B


title: F1509_002, normal, rep1

description:
Library name: 11_05_11_17
library name V2: 11_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: pfc young morphine 1

description: Library name: F2

tag: tissue


title: pfc young morphine 2

description: Library name: F3

tag: treatment


title: DSP-1001660038290-A-G07, Castration+, AP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G07

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: slide


title: F1542_002, MCI, rep1

description:
Library name: 10_05_11_17
library name V2: 10_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

value: 5% plasma, 6 h

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: pass


title: pfc young saline 2

description: Library name: F5

tag: strain

tag: Sex

tag: age

value: saline

tag: matching group

value: A


title: CD4TILs, Untransduced, Donor49

description: Library name: T49 CD4 Untransduced

tag: tissue

value: NSCLC tumor

tag: cell line

value: tumor-infiltrating lymphocytes

tag: treatment


title: DSP-1001660038290-A-G08, Castration+, AP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G08

tag: mouse

tag: castration

tag: lobe


title: F1187_002, normal, rep1

description:
Library name: 1_05_11_17
library name V2: 01_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

value: #REF!


title: DSP-1001660038290-A-G05, Castration+, AP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G05

tag: tissue

tag: slide


title: CD8TILs, RELB, Donor49

description: Library name: T49 CD8 RELB

tag: cell line

tag: treatment

value: ORF lentivirus


title: F80_004, normal, rep1

description:
Library name: 14_05_11_17
library name V2: 14_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: human

value: Aim 2 Batch 014

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-G04, Castration+, DLP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G04

tag: mouse

tag: castration

tag: lobe

value: DLP


title: CD4TILs, Thy1.1, Donor49

description: Library name: T49 CD4 Thy1.1

tag: cell type


title: CD4TILs, RELB, Donor49

description: Library name: T49 CD4 RELB


title: F1198_002, normal, rep1

description:
Library name: 9_05_03_17
library name V2: 09_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

value: Aim 2 Batch 013

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: #N/A

value: low RIN


title: F1391_001, normal, rep1

description:
Library name: 8_05_03_17
library name V2: 08_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: DPTILs, Untransduced, Donor43

description: Library name: T43 DP Untransduced

tag: tissue

tag: cell line

value: DP

tag: treatment

value: Untransduced


title: F1397_002, MCI, rep1

description:
Library name: 12_05_11_17
library name V2: 12_05_11_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-G03, Castration+, DLP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G03

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: slide


title: pfc young saline 3

description: Library name: F7

value: Prefrontal cortex of brain

tag: strain

tag: Sex

value: Female

tag: age

tag: matching group


title: DSP-1001660038290-A-G02, Castration+, DLP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G02


title: Gata2cKO-2 Mesonephros E16.5

city: Madison

first: Fei

last: Zhao

state: Wisconsin

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin-Madison

description: Library name: W6

data_processing:
Raw data was sent to the University of Wisconsin-Madisons Waisman Center Data Science Core to be analyzed by data scientists.
Protein coding gene counts of W2,W3 and W4 control (CT) and W5, W6, W8 knocked out (KO) samples were analyzed using DEseq2 DEG method (Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014). https://doi.org/10.1186/s13059-014-0550-8).
DESeqDataSetFromMatrix" function in DEseq2 was used to create a DESeqDataSet object from the matrix of read counts using CT/KO as the design to model the samples. Then "DESeq" and "results" functions were used to calculate the Differential Expressed genes with alpha=0.05 for the False Discovery Rate cutoff. DEseq2 uses Benjamini-Hochberg (BH) procedure to adjust the p-values.
Mapping to the reference genome was done using STAR version : STAR 2.7.11a (Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905.)
Assembly: Reads were mapped to GRCm38_M10 Primary Assembly reference genome and GRCm38_M10 Primary Annotations available at Gencode (https://www.gencodegenes.org/mouse/release_M10.html) were used for the gene annotations.
Supplementary files format and content: Processed DEG's are in an Excel sheet titled, "Consolidated_DEGs_GRCm38_M10(1)".
Supplementary files format and content: W2, W3, W4 are controls and W5, W6, and W8 are all knockouts.

source_name: E16.5  Mesonephros

extract_protocol:
RNA was harvested using PicoPure RNA Isolation Kit from ThermoFisher Scientific cat#KIT0204
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: E16.5  Mesonephros

value: Male

tag: genotype


title: Gata2cKO-3 Mesonephros E16.5

description: Library name: W8


title: DPTILs, Thy1.1, Donor43

description: Library name: T43 DP Thy1.1

value: NSCLC tumor

value: tumor-infiltrating lymphocytes

tag: cell type


title: DSP-1001660038290-A-G06, Castration+, AP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G06

tag: tissue

value: AP


title: Gata2cKO-1 Mesonephros E16.5

description: Library name: W5


title: F1392_001, normal, rep1

description:
Library name: 6_05_03_17
library name V2: 06_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

value: #REF!

value: pass


title: DSP-1001660038290-A-G01, Castration+, DLP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-G01

tag: mouse

tag: castration

tag: lobe

value: DLP

tag: treatment

tag: slide


title: F1789_001, MCI, rep1

description:
Library name: 5_05_03_17
library name V2: 05_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

value: Aim 2 Batch 013

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN


title: Control (CT3) Mesonephros E16.5

description: Library name: W4

tag: tissue

tag: Sex

tag: genotype


title: DPTILs, RELB, Donor43

description: Library name: T43 DP RELB

tag: cell line

value: DP

value: ORF lentivirus


title: DSP-1001660038290-A-F12, Castration+, DLP, Treatment+, Mouse 1633

description: Library name: DSP-1001660038290-A-F12

value: Prostate


title: pfc young saline 1

description: Library name: F1

value: Prefrontal cortex of brain

tag: strain

value: Female

tag: age

value: saline

tag: matching group

value: A


title: Control (CT1) Mesonephros E16.5

description: Library name: W2

value: E16.5  Mesonephros

value: Male


title: DSP-1001660038290-A-F11, Castration+, AP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F11

tag: mouse

tag: castration

value: AP


title: Control (CT2) Mesonephros E16.5

description: Library name: W3


title: CD8TILs, RELB, Donor43

description: Library name: T43 CD8 RELB

value: NSCLC tumor

value: tumor-infiltrating lymphocytes

tag: treatment


title: CD8TILs, Thy1.1, Donor43

description: Library name: T43 CD8 Thy1.1


title: CD8TILs, Untransduced, Donor43

description: Library name: T43 CD8 Untransduced

value: Untransduced


title: F373_004, MCI, rep1

description:
Library name: 4_05_03_17
library name V2: 04_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

value: #REF!

value: pass


title: F1345_001, MCI, rep1

description:
Library name: 7_05_03_17
library name V2: 07_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: cell type

tag: preculture time_(days)

value: Aim 2 Batch 013

tag: plasma class

value: #N/A

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)

value: low RIN


title: Control mouse 5

city: Munich

first: Maximilian

last: Fischer

address: Marchioninistr. 15

country: Germany

institute: LMU University

description: Library name: Sample 10

data_processing:
The RNA sequencing libraries were generated with NEBNext® Ultra II Directional RNA Library Prep technology (New England Biolabs, Ipswich, USA) according to the manufacturer’s instructions and internal laboratory quality control. The library generation uses fragmentation, a poly-T oligo, and sequencing adapter ligation. One RNA sequencing library pool was prepared from the 10 generated RNA-Seq libraries. The template amplification and clustering were performed using the Illumina NovaSeq® 6000 next-generation sequencing system applying the exclusion amplification chemistry (Illumina, San Diego, USA), and its high output mode was made with 1 x 100 bp single-read chemistry. The cluster generation and RNA sequencing were operated under the control of the NovaSeq Control Software (NVCS) v1.6.0 (Illumina, San Diego, USA). The processing of primary images was performed on the NovaSeq instrument using Real-Time Analysis (RTA) 3.4.4 software (Illumina, San Diego, USA). The evaluation of the imaging and sequencing running performance utilized the Illumina Sequence Analysis Viewer (SAV) v2.4.7 (Illumina, San Diego, USA). Sequencing reads were aligned to the mouse reference genome (version GRCm39.107) with STAR (version 2.7.10a). Expression values (TPM) were calculated with RSEM (version 1.3.3).
Assembly: mouse reference genome (version GRCm39.107)
Supplementary files format and content: ReadsPerGene.out.tab
Supplementary files format and content: rsem.genes.results

source_name: whole heart

extract_protocol:
The specimens used for RNA isolation were taken from the mice’s whole heart consisting of both atriums (including the left and right atrial appendages) and ventricles. The animal’s hearts were soaked directly after extraction into Trizol® (Life Technologies, Carlsbad, USA) (1 ml Trizol® reagent was used pro 100 mg heart tissue) and homogenized using IKA T10 Ultra-Turrax basic Homogenizer (Janke & Kunkel KG, Staufen i. Breisgau). The chloroform solution (Sigma-Aldrich, Steinheim, Germany) was added to the homogenized tissues with 0.2 ml pro milliliter Trizol. The mixture was agitated for 15 seconds and incubated at room temperature for 2-3 minutes. The samples were centrifuged 13000 rpm at 4oC for 15 minutes to separate the upper aqueous-, lower emulsion- and middle interphase. The upper aqueous phase containing the desired RNA was transferred into new clean tubes. The isolated RNA was washed by agitation for 15 seconds with 500 µl Isopropanol 99.7% (Sigma-Aldrich, Steinheim, Germany), each 1 ml sample followed by 10 minutes incubation at room temperature. Subsequently, the samples were recentrifuged with the same settings as previously described. The pellets containing the precipitated RNA were afterward cleansed with 1 ml 75% Ethanol followed by centrifugation at 10000 rpm at 4oC for 8 minutes. The supernatant was discharged, and the isolated pellet containing the desired RNA was dried at room temperature before adding 30 µl RNA-free water for dilution.
NEBNext® Ultra II Directional RNA Library Prep technology

treatment_protocol: The animals rested for at least two weeks before the training protocol to avoid unnecessary stress and an additional week of acclimatization. The acclimatization started with a speed of 10 m/min for 10 minutes on the first day. The speed and duration of training were incrementally increased each day until the fifth day, namely 11 m/min, 12 m/min, 13 m/min, and 14 m/min for 20, 30, 40, and 50 minutes respectively. After one week of acclimatization, the training protocol started with the speed of 15 m/min for 120 minutes every day at the same time, five days a week.  10 animals ran for  8 weeks each.  An equivocal number of mice were allocated as sedentary control.  environment for 15 minutes. They are allowed to rest every 15 minutes for 2 minutes during each training session.

tag: tissue

value: whole heart

tag: genotype

value: WT

tag: treatment

value: Sedentary


title: F1427_003, MCI, rep1

description:
Library name: 24_05_03_17
library name V2: 24_05_03_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: F1394_001, MCI, rep1

description:
Library name: 3_05_03_17
library name V2: 03_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: DSP-1001660038290-A-F09, Castration+, AP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F09

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: slide


title: DSP-1001660038290-A-F10, Castration+, AP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F10


title: CD4TILs, Untransduced, Donor43

description: Library name: T43 CD4 Untransduced

tag: cell line

tag: cell type


title: F1191_002, normal, rep1

description:
Library name: 23_05_03_17
library name V2: 23_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-F08, Castration+, AP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F08

tag: tissue

tag: treatment


title: Control mouse 4

description: Library name: Sample 9

tag: genotype


title: CD4TILs, Thy1.1, Donor43

description: Library name: T43 CD4 Thy1.1

value: ORF lentivirus


title: F1471_001, MCI, rep1

description:
Library name: 22_05_03_17
library name V2: 22_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: Control mouse 3

description: Library name: Sample 8


title: DSP-1001660038290-A-F07, Castration+, AP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F07

tag: mouse

tag: castration

tag: lobe

value: AP

tag: slide


title: CD4TILs, RELB, Donor43

description: Library name: T43 CD4 RELB

value: NSCLC tumor

tag: cell line

tag: cell type


title: Control mouse 2

description: Library name: Sample 7

tag: tissue


title: F1483_003, normal, rep1

description:
Library name: 21_05_03_17
library name V2: 21_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: DSP-1001660038290-A-F06, Castration+, DLP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F06

value: DLP

tag: treatment


title: DPTILs, Untransduced, Donor36

description: Library name: T36 DP Untransduced

value: tumor-infiltrating lymphocytes

value: DP

value: Untransduced


title: Control mouse 1

description: Library name: Sample 6

tag: genotype


title: DPTILs, Thy1.1, Donor36

description: Library name: T36 DP Thy1.1


title: DSP-1001660038290-A-F04, Castration+, DLP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F04

tag: mouse


title: Exercise mouse 5

description: Library name: Sample 5

value: Exercise


title: F1484_001, MCI, rep1

description:
Library name: 19_05_03_17
library name V2: 19_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

value: iCell Neurons

tag: incubation conditions

value: 5% plasma, 6 h

tag: plasma type

value: human

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

tag: icap cell_culture_well_position


title: CD8TILs, Untransduced, Donor36

description: Library name: T36 CD8 Untransduced

tag: tissue

tag: cell line

tag: cell type


title: DSP-1001660038290-A-F03, Castration+, DLP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F03

tag: castration

tag: lobe

tag: slide


title: Exercise mouse 4

description: Library name: Sample 4

tag: treatment


title: reference_001, reference, rep38

description:
Library name: 2_05_03_17
library name V2: 02_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

value: Aim 2 Batch 013

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort

tag: plasma class

value: reference

tag: sequencing plate_name

value: #REF!

tag: rna-seq date

value: #N/A

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: F483_005, MCI, rep1

description:
Library name: 17_05_03_17
library name V2: 17_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma thaw_number

tag: icap cell_culture_plate_number

value: pass


title: DPTILs, RELB, Donor36

description: Library name: T36 DP RELB

tag: tissue

tag: cell line

tag: cell type


title: CD8TILs, Thy1.1, Donor36

description: Library name: T36 CD8 Thy1.1

tag: treatment


title: Exercise mouse 2

description: Library name: Sample 2

value: whole heart

tag: genotype

value: WT


title: F1444_003, nonAD, rep1

description:
Library name: 18_05_03_17
library name V2: 18_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: preculture time_(days)

tag: icap cell_culture_well_position

tag: rna-seq covance/genewiz_id

tag: plasma shipment_batch

tag: sample cohort


title: Exercise mouse 3

description: Library name: Sample 3


title: DSP-1001660038290-A-F01, Castration+, DLP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-F01

value: Prostate

tag: mouse

tag: castration

tag: lobe

tag: slide


title: Exercise mouse 1

description: Library name: Sample 1


title: reference_001, reference, rep37

description:
Library name: 15_05_03_17
library name V2: 15_05_03_17
ADSBIRII.completeData.20180223.rds
all.cqn.vst_12032024_2.rds

tag: incubation conditions

tag: plasma type

tag: plasma used_in_icap_(plasmakey)

tag: plasma sample_replicate_number

tag: experimental batch_number

tag: plasma class

tag: sequencing plate_name

tag: rna-seq date

tag: rnaseq qc_(basis_for_omission)_(step_5)


title: CD4TILs, Untransduced, Donor36

description: Library name: T36 CD4 Untransduced

tag: tissue

value: NSCLC tumor

tag: cell line

tag: cell type

tag: treatment


title: DSP-1001660038290-A-E12, Castration+, DLP, Treatment-, Mouse 347

description: Library name: DSP-1001660038290-A-E12

tag: mouse

value: DLP