title: T cells, blood, OCM, TCR

city: New Haven

first: Benjamin

last: Lu

state: CT

address: 300 George Street

institute: Yale School of Medicine

description:
Library name: MEL-1_BLD_TCR
10x Genomics

data_processing:
FASTQ files were generated and analyzed with CellRanger (version 7.1.0) using the GRCh38 human reference genome for alignment.
Assembly: GRCh38
Supplementary files format and content: tab-separated value files and matrix files

source_name: Tumor

extract_protocol:
Whole blood was first centrifuged to separate plasma, after which the remaining fraction was diluted 1:1 with PBS and carefully layered over Ficoll (1.077 g/mL). Samples were centrifuged at 400 g for 30 min at room temperature. The PBMC layer was collected, washed twice with PBS, and counted. Cells were then cryopreserved in 90% FBS/10% DMSO using controlled-rate freezing to −80 °C before transfer to liquid nitrogen. Pleural fluid samples were centrifuged at 400 g for 10 min, with the supernatant preserved and cell pellets resuspended in PBS supplemented with 2% FBS. Cells were cryopreserved in 90% FBS/10% DMSO using controlled-rate freezing to −80 °C and stored in liquid nitrogen. Fresh tumor specimens were minced into small fragments and enzymatically digested with collagenase and DNase I. The digested material was filtered through a 70-µm cell strainer, centrifuged at 1,500 rpm for 5 minutes, and washed with PBS containing 2% FBS. Cells were counted and cryopreserved in freezing medium (90% FBS, 10% DMSO) using a controlled-rate freezing protocol before transfer to liquid nitrogen for long-term storage. Cryopreserved samples were thawed in pre-warmed RPMI with 10% FBS, per 10X Genomics protocols CG000233 and CG000447. Cells were stained for flow cytometry by sequentially staining with fixable live/dead dye, a master mix of fluorophore-conjugated surface antibodies (Table S4), and cell washing, as previously described (36). Stained cells were analyzed on a Cytek Aurora using the SpectroFlo software (v3.3.0).
Sorted cells were processed following the recommended protocol with the GEM-X Universal 5’ Gene Expression v3 and V(D)J Enrichment 4-plex On-chip Multiplexing kits (10x Genomics). Libraries were sequenced on an Illumina NovaSeq 6000 instrument. scRNAseq libraries were sequenced at a read length of 28 x 10 x 90bp and a depth of 400 million read pairs. scTCRseq libraries were sequenced at a read length of 150x150bp and a depth of 100 million read pairs.

value: Tumor

value: blood

value: T cell


title: MASLD mouse, liver, rep3

status: Public on Aug 05 2026

type: SRA

city: Qingdao

first: Liangxiu

last: Xing

state: Shandong

address: Laoshan

country: China

institute: Qingdao University

description:
Library name: CTRL_03
bulk_Con&Exo_all_counts.txt

library_source: transcriptomic

data_processing:
Raw reads were filtered using fastp (v1.3.3).
Reads were aligned to the mm10 reference genome using Hisat2 (v2.2.1).
Gene-level counts were generated using featureCounts implemented in the Subread package (v2.0.2) based on the vM25 annotation, producing a gene-by-sample count matrix.
Genes with counts more than 10 in at least 20% of samples were retained. TPM values were calculated based on the vM25 annotation
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Male C57BL/6 mouse were housed under specific pathogen-free conditions with a 12-h light/dark cycle, controlled temperature and humidity, and free access to food and water. Mice were started on a high-fat diet (HFD) at 4 weeks of age and fed the HFD for 18 weeks.

extract_protocol:
Total RNA was extracted from liver tissues using TRIzol reagent (TIANGEN, Cat# DP424) according to the manufacturer's instructions. RNA concentration was measured using a Qubit Fluorometer (Thermo Fisher Scientific), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 5400 system (Agilent Technologies, Cat# DNF-471).
RNA libraries were prepared using the Fast RNA-seq Lib Prep Kit V2 (ABclonal, Cat# RK20306) following the manufacturer's protocol.

treatment_protocol: Bulk RNA-seq was performed on three groups: Control (untreated HFD-fed mice, n=9), Exosome (HFD-fed mice treated with UCMSC-Exos, n=9), and LSCR (HFD-fed mice treated with LSCR, n=9). UCMSC-Exos and LSCR were administered via tail-vein injection every 72 hours for 8 weeks at a dose of 5×108 particles/g body weight.

tag: tissue

value: Liver

tag: sample group

value: MASLD mouse


title: T cells, blood, OCM, GEX

country: USA

description:
Library name: MEL-1_BLD_GEX
10x Genomics

library_source: transcriptomic single cell

organism: Homo sapiens

tag: cell line

tag: cell type


title: Osteoporosis sample 4

city: México city

first: Rogelio Frank

last: Jiménez-Ortega

state: Alcaldía Tlalpan

address: Calzada México-Xochimilco No. 289

department: Subdirección de investigación Biomédica

country: Mexico

institute: Instituto Nacional de Rehabilitación

description:
Library name: ID-11
Condition: Osteoporosis; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_11; processed matrix column: ID-11.

data_processing:
FASTQ files were evaluated with FastQC. Seqtk was used to remove the first three bases from each read, stretches of more than 15 adenines, and Illumina small RNA adapter sequence was removed with reaper.
Small RNA-seq reads were processed with the exceRpt pipeline. Low-quality or contaminant reads were filtered, and surviving reads were aligned to miRBase v21, transcriptome, and genome using STAR against GRCh38.
Processed matrix OP_gene_raw_counts_matrix.tsv.gz contains raw gene-level counts for all 14 libraries.
Processed matrix OP_gene_TPM_normalized_matrix.tsv.gz contains TPM-normalized expression values for all 14 libraries.
Library identifiers in the processed matrices correspond to library names ID-1 through ID-14 in the SAMPLES section.
Differential expression was evaluated using TMM normalization, voomWithQualityWeights, and limma-based linear modeling.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: OP_gene_raw_counts_matrix.tsv.gz: tab-delimited raw count matrix; rows are gene identifiers and columns are library names ID-1 through ID-14.
Supplementary files format and content: OP_gene_TPM_normalized_matrix.tsv.gz: tab-delimited TPM-normalized expression matrix; rows are gene identifiers and columns are library names ID-1 through ID-14.

source_name: peripheral blood

growth_protocol: Not applicable; primary human peripheral blood samples were analyzed.

extract_protocol:
Peripheral blood was collected in CPT tubes. Peripheral blood mononuclear cells were obtained and CD14-positive monocytes were enriched using an EasySep negative-selection kit. Total RNA was purified using the miRNeasy Mini Kit (QIAGEN). RNA quantity and integrity were assessed using a Qubit 3.0 Fluorometer and an Agilent 2100 Bioanalyzer.
Small RNA sequencing libraries were prepared from total RNA using the SMARTer small RNA-Seq Kit for Illumina (Clontech). Libraries were prepared by polyadenylation, cDNA synthesis, adapter incorporation, PCR amplification with Illumina adapters, size selection with Agencourt AMPure XP beads, and sequencing for 50 cycles on an Illumina NextSeq 500.

treatment_protocol: No in vitro treatment was applied. Samples were classified according to clinical/densitometric status as non-osteoporotic control or osteoporosis.

value: peripheral blood

value: CD14-positive monocyte

tag: treatment

value: Osteoporosis

tag: batch


title: MASLD mouse, liver, rep2

description:
Library name: CTRL_02
bulk_Con&Exo_all_counts.txt


title: T cells, pleural effusion, OCM, TCR

description:
Library name: MEL-1_MPE_TCR
10x Genomics

value: malignant pleural effusion


title: Osteoporosis sample 3

description:
Library name: ID-10
Condition: Osteoporosis; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_10; processed matrix column: ID-10.


title: MASLD mouse, liver, rep1

description:
Library name: CTRL_01
bulk_Con&Exo_all_counts.txt


title: MASLD mouse, liver, rep8

description:
Library name: CTRL_08
bulk_Con&Exo_all_counts.txt


title: Osteoporosis sample 6

description:
Library name: ID-13
Condition: Osteoporosis; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_13; processed matrix column: ID-13.


title: T cells, pleural effusion, OCM, GEX

description:
Library name: MEL-1_MPE_GEX
10x Genomics


title: Normal sample 7

description:
Library name: ID-7
Condition: Non-osteoporotic control; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_7; processed matrix column: ID-7.

value: Normal


title: Normal sample 6

description:
Library name: ID-6
Condition: Non-osteoporotic control; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_6; processed matrix column: ID-6.


title: hepAGT+/+, liver, thermoneutral housing, Western diet, biol rep 7

city: Lexington

first: Liyuan

last: Zhu

state: KY

address: 741 South Limestone Street

institute: University of Kentucky

description: Library name: TNWTL7

data_processing:
FASTQ reads were adapter-trimmed and quality-filtered using fastp.
Trimmed reads were aligned to the mouse GRCm38/mm10 reference genome using STAR v2.6.1d, and gene-level read counts were generated using featureCounts v1.5.0-p3.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for all submitted samples. Rows correspond to genes/features and columns correspond to library names listed in the SAMPLES section.

source_name: liver

growth_protocol: Male hepAGT+/+ and hepAGT-/- littermate mice were maintained in a barrier facility on a 14:10-hour light:dark cycle. Mice were housed at room temperature (20-22 degrees C) or thermoneutrality (30 degrees C) and fed a Western diet (TD.88137; 21% milk fat and 0.2% cholesterol) for 12 weeks.

extract_protocol:
Tissue samples were snap-frozen in homogenization solution (#Z305H, Promega) containing 1-thioglycerol (#A208B, Promega). Total RNA was extracted using Maxwell RSC simplyRNA Tissue Kits (#AS1340, Promega) according to the manufacturer's protocol.
Bulk mRNA-seq libraries were prepared by Novogene from total RNA using NEBNext Ultra RNA Library Prep Kits for Illumina (New England Biolabs). Libraries were sequenced in paired-end mode on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were assigned to room-temperature or thermoneutral housing and fed Western diet for 12 weeks. Liver, brown adipose tissue, and epididymal white adipose tissue were collected at study termination for bulk RNA-seq.

value: liver

tag: genotype

value: hepAGT+/+

value: Western diet for 12 weeks; thermoneutral housing (30 degrees C)

tag: Sex

value: male


title: T cells, tumor, OCM, TCR

description:
Library name: MEL-1_TIL_TCR
10x Genomics

value: lung metastasis


title: hepAGT+/+, liver, thermoneutral housing, Western diet, biol rep 6

description: Library name: TNWTL6


title: Normal sample 5

description:
Library name: ID-5
Condition: Non-osteoporotic control; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_5; processed matrix column: ID-5.


title: T cells, tumor, OCM, GEX

description:
Library name: MEL-1_TIL_GEX
10x Genomics


title: Human U2OS cells, untreated control (WT), Biol. Rep. 3

city: Hangzhou

first: Nuo

last: Chen

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

institute: Zhejiang University

description:
Library name: WT3
Column name in Processed data.xls: WT3

data_processing:
Raw FASTQ reads were processed using fastp software to remove adapter sequences, poly-N reads, and low-quality reads, yielding clean reads. Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 v2.0.5. Gene expression levels were quantified using featureCounts v1.5.0-p3, and FPKM values were calculated for each gene. Differential expression analysis was performed using DESeq2 R package (1.20.0), with genes showing adjusted p-value ≤ 0.05 considered differentially expressed.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data.xls: Excel file containing count and FPKM values for all 12 samples (4 conditions × 3 biological replicates), with genes as rows and samples as columns.

source_name: Human U2OS cells

growth_protocol: U2OS cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies).
Messenger RNA 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 second-strand cDNA synthesis. The library was prepared after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed using Qubit, real-time PCR, and Bioanalyzer.

treatment_protocol: Cells were treated with 50 μM CCCP (carbonyl cyanide 3-chlorophenylhydrazone) for 30 minutes, followed by washout with fresh DMEM medium for 0, 1, or 6 hours. Control cells were treated with an equivalent volume of DMSO.

value: Human U2OS cells

value: Osteosarcoma cells

value: WT

value: untreated control (WT)


title: Normal sample 3

description:
Library name: ID-3
Condition: Non-osteoporotic control; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_3; processed matrix column: ID-3.


title: hepAGT+/+, liver, thermoneutral housing, Western diet, biol rep 24

description: Library name: TNWTL24


title: Normal sample 2

description:
Library name: ID-2
Condition: Non-osteoporotic control; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_2; processed matrix column: ID-2.


title: Normal sample 1

description:
Library name: ID-1
Condition: Non-osteoporotic control; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_1; processed matrix column: ID-1.


title: hepAGT+/+, liver, thermoneutral housing, Western diet, biol rep 1

description: Library name: TNWTL1


title: LN-18 sgATM VSVΔ51 rep3

city: Guangzhou

first: xiaohui

last: chen

address: No.106 Zhongshan 2nd Road,Yuexiu District

institute: Guangdong Provincial People's Hospital

description: Library name: LN18sgATM_V_SV_3

data_processing:
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCm38
Supplementary files format and content: genes_fpkm_expression.xlsx

source_name: Brain

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)

value: Brain

value: Glioblastoma cells

value: sgATM (ATM KO)

value: VSVΔ51 MOI=5, 10h


title: 4238-041-60

city: Boston

first: Minyi

last: Lee

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: 4238-041-60

data_processing:
Demultiplexing and creation of FASTQ files were automatically performed using the Illumina BaseSpace platform with default parameters.
Reads were aligned to the Genome Reference Consortium human build 37 (GRCh37) using STAR v2.6.0c.
Both gene and transcript level counts were calculated using RSEM v1.3.1 with annotation from Ensembl build 107.
Assembly: hg37
Supplementary files format and content: counts.tsv: tab-separated values (TSV) file containing 57736 x 183 matrix of "expected_count" values computed by RSEM

source_name: Bronchial brushing

extract_protocol:
Total RNA was isolated from bronchial brushings using the miRNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries were generated using the Illumina TruSeq RNA Access kit (Illumina, San Diego, CA)

value: Bronchial brushing

tag: subject id

tag: cancer status

value: Malignant

tag: smoking status

value: Former

value: female

tag: age

tag: nodule size_(cm)

tag: tfa (total_fat_area)

tag: fev1 percent_predicted

tag: fev1/fvc ratio

tag: copd status

value: FALSE


title: hepAGT+/+, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 8

description: Library name: TNWTE8

source_name: epididymal white adipose tissue

tag: tissue

value: epididymal white adipose tissue

value: hepAGT+/+


title: 4790-070-60

description: Library name: 4790-070-60

value: Current

value: male

value: TRUE


title: LN-18 sgATM VSVΔ51 rep2

description: Library name: LN18sgATM_V_SV_2


title: 4798-014-60

description: Library name: 4798-014-60

value: Benign


title: LN-18 sgATM VSVΔ51 rep1

description: Library name: LN18sgATM_V_SV_1


title: 4798-021-60

description: Library name: 4798-021-60


title: 4202-009-60

description: Library name: 4202-009-60

value: not collected


title: hepAGT+/+, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 7

description: Library name: TNWTE7

value: Western diet for 12 weeks; thermoneutral housing (30 degrees C)


title: LN-18 wild-type VSVΔ51 rep3

description: Library name: LN18_V_SV_3

value: Brain

value: sgNC (wild-type)


title: 4202-006-60

description: Library name: 4202-006-60


title: 4795-035-60

description: Library name: 4795-035-60


title: LN-18 wild-type VSVΔ51 rep2

description: Library name: LN18_V_SV_2

value: Glioblastoma cells


title: 4790-077-60

description: Library name: 4790-077-60


title: hepAGT+/+, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 23

description: Library name: TNWTE23


title: 4790-017-60

description: Library name: 4790-017-60


title: 4438-042-60

description: Library name: 4438-042-60


title: hepAGT+/+, brown adipose tissue, thermoneutral housing, Western diet, biol rep 1

description: Library name: TNWT_B1

source_name: brown adipose tissue

value: brown adipose tissue


title: hepAGT+/+, brown adipose tissue, thermoneutral housing, Western diet, biol rep 7

description: Library name: TNWTB7


title: 4793-020-60

description: Library name: 4793-020-60

value: Bronchial brushing


title: LN-18 sgATM mock rep2

description: Library name: LN18sgATM_2

value: sgATM (ATM KO)

value: Mock


title: 4795-096-60

description: Library name: 4795-096-60

value: Malignant


title: hepAGT+/+, brown adipose tissue, thermoneutral housing, Western diet, biol rep 6

description: Library name: TNWTB6


title: LN-18 sgATM mock rep1

description: Library name: LN18sgATM_1


title: 4791-011-60

description: Library name: 4791-011-60

value: Former


title: 4790-053-60

description: Library name: 4790-053-60


title: hepAGT+/+, brown adipose tissue, thermoneutral housing, Western diet, biol rep 24

description: Library name: TNWTB24


title: 4790-006-60

description: Library name: 4790-006-60


title: 4790-016-60

description: Library name: 4790-016-60


title: hepAGT-/-, liver, thermoneutral housing, Western diet, biol rep 5

description: Library name: TNKOL5

value: liver

value: hepAGT-/-


title: LN-18 wild-type mock rep2

description: Library name: LN18_2


title: 4798-017-60

description: Library name: 4798-017-60

value: Current


title: 4790-008-60

description: Library name: 4790-008-60

value: male


title: hepAGT-/-, liver, thermoneutral housing, Western diet, biol rep 4

description: Library name: TNKOL4


title: 4790-019-60

description: Library name: 4790-019-60

value: TRUE


title: LN-18 wild-type mock rep1

description: Library name: LN18_1


title: 4790-028-60

description: Library name: 4790-028-60

value: Benign


title: Osteoporosis sample 5

description:
Library name: ID-12
Condition: Osteoporosis; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_12; processed matrix column: ID-12.

value: peripheral blood

value: CD14-positive monocyte

value: Osteoporosis


title: 4795-139-60

description: Library name: 4795-139-60


title: Osteoporosis sample 2

description:
Library name: ID-9
Condition: Osteoporosis; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_9; processed matrix column: ID-9.


title: 4791-005-60

description: Library name: 4791-005-60


title: 786-O,control,rep2

city: Shanghai

first: Wenjie

last: Xu

address: Dongan road

institute: Fudan University

description:
Library name: sample6
shControl-2

data_processing:
QC reports were generated from FastQC (version: 0.11.9)
Following quality assessment, Low-quality reads were trimmed and adapters were removed with Trim Galore (version: 0.6.7)
Cleaned data were then aligned to the reference genome (hg38) using HISAT2 (version: 2.2.1)
Reads for genes were counted from the sorted BAM file using StringTie (version: 2.2.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: kidney

growth_protocol: Human clear cell renal cell carcinoma (ccRCC) tumor tissues and matched adjacent normal kidney tissues were collected from patients undergoing surgical resection at Fudan University Shanghai Cancer Center (FUSCC). Fresh tissues were immediately snap-frozen and stored at −80°C until RNA extraction. For cell line experiments, 786-O cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum under standard culture conditions.

extract_protocol:
Total RNA was extracted from snap-frozen ccRCC tumor tissues, matched adjacent normal kidney tissues, and cultured 786-O cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA quality and concentration were assessed using a NanoDrop spectrophotometer and agarose gel electrophoresis. High-quality RNA samples were used for subsequent library preparation.
RNA sequencing libraries were prepared using the Abclonal RNA-seq Library Preparation Kit (RK20348) according to the manufacturer's instructions. Briefly, total RNA was processed for library construction, followed by RNA fragmentation, reverse transcription, adapter ligation, PCR amplification, and library quality assessment. Qualified libraries were sequenced on an Illumina sequencing platform in paired-end mode.

treatment_protocol: No specific treatment was applied before RNA extraction.

value: kidney

value: human renal cell carcinoma

value: WT


title: 4796-050-60

description: Library name: 4796-050-60

value: Bronchial brushing

value: female

value: FALSE


title: Osteoporosis sample 1

description:
Library name: ID-8
Condition: Osteoporosis; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_8; processed matrix column: ID-8.


title: hepAGT-/-, liver, thermoneutral housing, Western diet, biol rep 2

description: Library name: TNKOL2

value: Western diet for 12 weeks; thermoneutral housing (30 degrees C)


title: 786-O,control,rep1

description:
Library name: sample5
shControl-1


title: 4714-010-60

description: Library name: 4714-010-60

value: Malignant

value: Former

value: not collected


title: hepAGT-/-, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 5

description: Library name: TNKOE5

value: epididymal white adipose tissue

value: hepAGT-/-


title: 4794-006-60

description: Library name: 4794-006-60

value: male


title: Normal sample 4

description:
Library name: ID-4
Condition: Non-osteoporotic control; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_4; processed matrix column: ID-4.

value: Normal


title: 786-O,LINC02068-kd2,rep2

description:
Library name: sample4
shRNA2-2

value: LINC02068 knockdown


title: 4714-002-60

description: Library name: 4714-002-60


title: 4796-152-60

description: Library name: 4796-152-60

value: Benign

value: TRUE


title: patient with sepsis-associated ARDS 2

status: Public on Aug 06 2026

city: Nanning City

first: Qicheng

last: Long

state: Guangxi Zhuang Autonomous Region

address: No.6 Shuangyong Road

department: Department of Intensive Care Unit

institute: The First Affiliated Hospital of Guangxi Medical University

description: Library name: SA2

data_processing:
For mRNA and lncRNA analysis, raw sequencing reads were filtered using SOAPnuke to remove adapter contamination, low-quality reads, and reads containing excessive ambiguous bases. Clean reads were aligned to the human reference genome using HISAT2. Novel transcripts were assembled using StringTie and compared with the reference annotation using Cuffcompare to identify putative novel lncRNA transcripts. Gene-level read counts were generated using featureCounts based on the final gene annotation. Gene expression levels were normalized and reported as fragments per kilobase of transcript per million mapped reads (FPKM). Differential expression analysis was performed using DESeq2 based on the raw read counts.Novel transcripts were assembled using StringTie and compared with the reference annotation using Cuffcompare. The processed expression matrices include both annotated genes and putative novel transcripts. Novel transcripts are represented by StringTie-generated XLOC identifiers.
For circRNA analysis, raw sequencing reads were filtered using SOAPnuke. Clean reads were aligned to the reference genome using both Bowtie2 and BWA. Candidate circular RNAs were identified independently using find_circ and CIRI, and the integrated results were used for downstream analysis. CircRNA expression levels were normalized as reads per million mapped reads (RPM). Differentially expressed circRNAs were identified using NOISeq.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM or RPM table for all Samples

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from peripheral whole blood samples using a commercially available RNA extraction kit according to the manufacturer’s instructions. The concentration and purity of the extracted RNA were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer or equivalent platform. Only RNA samples that met the quality control requirements were used for subsequent library construction.
ribosomal RNA was removed from total RNA, and strand-specific transcriptome libraries were constructed following the standard protocol. The purified RNA was fragmented and reverse-transcribed into cDNA, followed by end repair, adaptor ligation, PCR amplification, and library purification

value: Peripheral blood

tag: disease state

value: patient with sepsis-associated ARDS


title: FOXL2-WT, dox, rep1

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

description: Library name: Sample 4

data_processing:
primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5)
Fastq files were then aligned using STAR algorithm (version 2.7.11b)
Reads were then counted using RSEM (v1.3.3)
the statistical analyses on the read counts were performed with R (version 4.4.2) and the DESeq2 package (DESeq2_1.42.1)
Assembly: Ensembl release 113, GRCh38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: KGN FOXL2WT/WT

growth_protocol: KGN cells were maintained in DMEM-F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA extractions were performed with the TRI-reagent supplier’s instructions (Life technologies, 15596-018).
350 ng of high-quality total RNA sample (RIN =10) was processed using Stranded mRNA Prep kit (Illumina) according to manufacturer instructions, Illumina Nextseq 2000 instrument using 59 base-length reads in a paired-end mode

treatment_protocol: treated with 500 ng/ml doxycycline for 24 h before RNA extraction

tag: cell line

value: KGN FOXL2WT/WT

value: Granulosa cell line

value: FOXL2WT/WT, pLVX-TetOne-Puro-FOXL2WT

value: 500 ng/ml doxycycline, 24h


title: hepAGT-/-, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 4

description: Library name: TNKOE4

value: Western diet for 12 weeks; thermoneutral housing (30 degrees C)


title: 786-O,LINC02068-kd2,rep1

description:
Library name: sample3
shRNA2-1

value: kidney

tag: cell type

value: human renal cell carcinoma


title: hepAGT-/-, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 3

description: Library name: TNKOE3

tag: treatment


title: 4202-011-60

description: Library name: 4202-011-60

value: Bronchial brushing

value: Malignant

value: Current

value: not collected


title: 786-O,LINC02068-kd1,rep2

description:
Library name: sample2
shRNA1-2


title: 4796-150-60

description: Library name: 4796-150-60

value: Former

value: female


title: 4790-041-60

description: Library name: 4790-041-60

value: male

value: FALSE


title: hepAGT+/+, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 6

description: Library name: TNWTE6

value: epididymal white adipose tissue

value: hepAGT+/+


title: hepAGT-/-, brown adipose tissue, thermoneutral housing, Western diet, biol rep 5

description: Library name: TNKOB5

value: brown adipose tissue

value: hepAGT-/-


title: 4798-006-60

description: Library name: 4798-006-60

value: TRUE


title: 4796-133-60

description: Library name: 4796-133-60

value: Benign


title: Healthy bone reference sample 7

description:
Library name: ID-14
Condition: Healthy bone; source folder: 20171010_14; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.

data_processing:
FASTQ files were quality-controlled and processed through a standardized RNA-seq workflow.
Reads were aligned or quantified against the human GRCh38/hg38 reference genome/transcriptome.
Gene-level raw count and TPM-normalized expression matrices were generated for downstream differential expression and pathway analyses.
Assembly: GRCh38/hg38
Supplementary files format and content: counts_matrix.tsv.gz: tab-delimited gene-level raw count matrix; rows are genes/features and columns are GEO library identifiers ID-1 through ID-14.
Supplementary files format and content: TPM_normalized_matrix.tsv.gz: tab-delimited gene-level TPM-normalized matrix; rows are genes/features and columns are GEO library identifiers ID-1 through ID-14.

source_name: bone tissue

growth_protocol: Not applicable; human biospecimens were analyzed.

extract_protocol:
Total RNA was extracted from human tissue-derived biospecimens according to the laboratory protocol used for this RNA-seq experiment. RNA quality-control criteria and extraction reagent/kit details should be confirmed by the submitter if requested by GEO.
RNA-seq libraries were prepared for paired-end sequencing using an Illumina-compatible library preparation workflow. Library preparation kit, RNA selection/depletion strategy, read length, and sequencing chemistry should be confirmed by the submitter if requested by GEO.

treatment_protocol: Samples were classified by biological condition as osteosarcoma tumor or healthy bone reference samples.

value: bone tissue

value: Healthy bone

tag: batch


title: 4714-020-60

description: Library name: 4714-020-60


title: hepAGT-/-, brown adipose tissue, thermoneutral housing, Western diet, biol rep 4

description: Library name: TNKOB4

tag: genotype

value: Western diet for 12 weeks; thermoneutral housing (30 degrees C)


title: 4796-130-60

description: Library name: 4796-130-60

value: Bronchial brushing

tag: Sex


title: 4796-073-60

description: Library name: 4796-073-60

tag: subject id

value: Malignant


title: Healthy bone reference sample 6

description:
Library name: ID-13
Condition: Healthy bone; source folder: 20171010_13; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: hepAGT-/-, brown adipose tissue, thermoneutral housing, Western diet, biol rep 3

description: Library name: TNKOB3


title: 4790-047-60

description: Library name: 4790-047-60

tag: cancer status

value: Current


title: LSCR-treated MASLD mouse, liver, rep6

description:
Library name: LNP_06
bulk_LNP_all_counts.xlsx

value: Liver

tag: sample group

value: LSCR-treated MASLD mouse


title: 4797-014-63

description: Library name: 4797-014-63

tag: smoking status

tag: age


title: Healthy bone reference sample 5

description:
Library name: ID-12
Condition: Healthy bone; source folder: 20171010_12; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: 4797-011-60

description: Library name: 4797-011-60

value: Former

value: female

tag: nodule size_(cm)

tag: tfa (total_fat_area)


title: 4796-080-60

description: Library name: 4796-080-60

value: male

tag: fev1 percent_predicted

tag: fev1/fvc ratio


title: hepAGT-/-, brown adipose tissue, thermoneutral housing, Western diet, biol rep 2

description: Library name: TNKO_B2

tag: tissue


title: hepAGT+/+, liver, room temperature, Western diet, biol rep 18

description: Library name: RTWTL18

value: liver

value: Western diet for 12 weeks; room temperature housing (20-22 degrees C)


title: Healthy bone reference sample 3

description:
Library name: ID-10
Condition: Healthy bone; source folder: 20171010_10; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.

tag: disease state


title: 4795-081-60

description: Library name: 4795-081-60

tag: copd status


title: hepAGT+/+, liver, room temperature, Western diet, biol rep 15

description: Library name: RTWTL15

value: hepAGT+/+


title: 4790-049-60

description: Library name: 4790-049-60


title: Healthy bone reference sample 2

description:
Library name: ID-9
Condition: Healthy bone; source folder: 20171010_9; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: 4202-014-60

description: Library name: 4202-014-60

value: not collected


title: Healthy bone reference sample 1

description:
Library name: ID-8
Condition: Healthy bone; source folder: 20171010_8; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: 4790-014-60

description: Library name: 4790-014-60

value: TRUE


title: 4790-105-60

description: Library name: 4790-105-60

value: Benign


title: hepAGT+/+, liver, room temperature, Western diet, biol rep 11

description: Library name: RTWTL11


title: 4790-065-60

description: Library name: 4790-065-60


title: Osteosarcoma tumor sample 7

description:
Library name: ID-7
Condition: Osteosarcoma; source folder: 20171010_7; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.

source_name: osteosarcoma tumor tissue

value: osteosarcoma tumor tissue

value: Osteosarcoma


title: hepAGT+/+, epididymal white adipose tissue, room temperature, Western diet, biol rep 18

description: Library name: RTWTE18

value: epididymal white adipose tissue


title: 4438-086-60

description: Library name: 4438-086-60

value: Bronchial brushing

value: FALSE


title: Osteosarcoma tumor sample 6

description:
Library name: ID-6
Condition: Osteosarcoma; source folder: 20171010_6; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: hepAGT+/+, epididymal white adipose tissue, room temperature, Western diet, biol rep 15

description: Library name: RTWTE15


title: 4714-022-60

description: Library name: 4714-022-60


title: 4790-012-60

description: Library name: 4790-012-60

value: Malignant

value: Current


title: 4202-007-60

description: Library name: 4202-007-60


title: hepAGT+/+, epididymal white adipose tissue, room temperature, Western diet, biol rep 13

description: Library name: RTWTE13


title: 4797-018-63

description: Library name: 4797-018-63


title: Osteosarcoma tumor sample 4

description:
Library name: ID-4
Condition: Osteosarcoma; source folder: 20171010_4; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: 4794-007-60

description: Library name: 4794-007-60


title: 4793-034-60

description: Library name: 4793-034-60


title: Osteosarcoma tumor sample 3

description:
Library name: ID-3
Condition: Osteosarcoma; source folder: 20171010_3; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: 4790-011-60

description: Library name: 4790-011-60


title: hepAGT+/+, brown adipose tissue, room temperature, Western diet, biol rep 18

description: Library name: RTWTB18

value: brown adipose tissue


title: 4796-078-60

description: Library name: 4796-078-60

value: Former


title: Osteosarcoma tumor sample 2

description:
Library name: ID-2
Condition: Osteosarcoma; source folder: 20171010_2; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: hepAGT+/+, brown adipose tissue, room temperature, Western diet, biol rep 17

description: Library name: RTWTB17


title: Osteosarcoma tumor sample 1

description:
Library name: ID-1
Condition: Osteosarcoma; source folder: 20171010_1; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.


title: 4796-008-60

description: Library name: 4796-008-60


title: hepAGT+/+, brown adipose tissue, room temperature, Western diet, biol rep 15

description: Library name: RTWTB15


title: 4798-011-60

description: Library name: 4798-011-60


title: HCT118 StemCells, PSCA siRNA_3

city: Changchun

first: Jinyue

last: Duan

state: Jilin

address: 1266 Fujin Street

department: Department of Regenerative Medicine

institute: Jilin University

description:
Library name: P3
P3

data_processing:
Cluster amplification was performed on a cBot Cluster Generation System with the TruSeq PE Cluster Kit v3-cBot-HS (Illumina), followed by paired-end RNA sequencing on the Illumina platform.
Assembly: GRCh38
Supplementary files format and content: An xls file containing FPKM values for each sample.

source_name: HCT116 Stemcells

growth_protocol: HCT116 Stemcells (Colorectal cancer stem cells derived from HCT116) were cultured in serum-free DMEM/F12 medium (Gibco, Thermo Fisher Scientific, NY, USA). The culture medium was supplemented with 20 ng/mL epidermal growth factor (EGF, Invitrogen, Thermo Fisher Scientific, VNO, Lithuania), 20 ng/mL basic fibroblast growth factor (bFGF, Invitrogen) and 1× B27 serum-free supplement (Gibco, Thermo Fisher Scientific, NY, USA). Cells were maintained in a humidified atmosphere at 37 °C and 5% CO2 to form tumor spheres. The medium was refreshed with growth factors per 3 days to sustain stem cell proper-ties.

extract_protocol:
Cells transfected with negative control siRNA and PSCA siRNA were collected separately, and TRIzol reagent (Invitrogen) was adopted to extract total RNA follow-ing official product instructions.
RNA integrity and purity were detected before constructing sequencing libraries. Sequencing libraries were built using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB; Ipswich, MA, USA), and unique index barcodes were added to each sample for read classification.

treatment_protocol: PSCA and negative control (NC) siRNAs were obtained from Ribo Bio (Guang-zhou, China). The PSCA siRNA sequences were as follows: siPSCA#1 (5′-TCRCTGACRCGTCATCAGCAA-3′), PSCA siRNA#2 (5′-GCTTGAACTGCGTGGATGA-3′), and PSCA siRNA#3 (5′-GTGGGCAAGAAGAACATCA-3′). Three-day cultured CR-CSC tumor spheres were digested into single-cell suspensions. Cells were counted and seeded in six-well plates at a density of (1.0×106) cells/well with antibiotic-free CR-CSC medium. Transfection was conducted using Hieff Trans Liposomal Transfection Reagent (Yeasen, Shanghai, China) in accord-ance with the manufacturer’s protocol. To elaborate, siRNA fragments or plasmid DNA, together with liposome transfection reagent, were diluted separately with Opti-MEM medium. After uniform mixing and 5-min standing at room temperature to form transfection complexes, the mixture was slowly added to cell layers.Cells were incubated at 37 °C under 5% CO2, and harvested 48 h later for subsequent experiments.

tag: cell line

value: HCT116 Stemcells

tag: cell type

value: Colorectal Cancer Stemcells

value: PSCA knockdown

value: PSCA siRNA transfection rep3


title: 4796-143-60

description: Library name: 4796-143-60

value: female


title: 4202-018-60

description: Library name: 4202-018-60


title: hepAGT+/+, brown adipose tissue, room temperature, Western diet, biol rep 12

description: Library name: RTWTB12

value: hepAGT+/+

tag: treatment

value: Western diet for 12 weeks; room temperature housing (20-22 degrees C)

value: male


title: 4795-084-60

description: Library name: 4795-084-60

value: Benign


title: HCT117 StemCells, PSCA siRNA_2

description:
Library name: P2
P2

tag: genotype

value: PSCA siRNA transfection rep2


title: 4714-024-60

description: Library name: 4714-024-60

tag: Sex

value: TRUE


title: hepAGT-/-, liver, room temperature, Western diet, biol rep 9

description: Library name: RTKOL9

value: liver

value: hepAGT-/-


title: 4238-027-60

description: Library name: 4238-027-60

value: Bronchial brushing

tag: subject id


title: hepAGT-/-, liver, room temperature, Western diet, biol rep 19

description: Library name: RTKOL19


title: 4796-033-60

description: Library name: 4796-033-60

tag: cancer status

value: FALSE


title: HCT116 StemCells, Negative Control siRNA_3

description:
Library name: N3
N3

value: WT

value: NC siRNA transfection rep3


title: hepAGT-/-, liver, room temperature, Western diet, biol rep 16

description: Library name: RTKOL16


title: 4792-014-60

description: Library name: 4792-014-60

value: Former


title: HCT116 StemCells, Negative Control siRNA_2

description:
Library name: N2
N2

value: HCT116 Stemcells

value: Colorectal Cancer Stemcells

value: NC siRNA transfection rep2


title: LN-18 wild-type VSVΔ51 rep1

description: Library name: LN18_V_SV_1

value: Brain

value: Glioblastoma cells

value: sgNC (wild-type)

value: VSVΔ51 MOI=5, 10h


title: 4238-026-60

description: Library name: 4238-026-60

value: Benign

value: male


title: hepAGT-/-, liver, room temperature, Western diet, biol rep 10

description: Library name: RTKOL10

value: Western diet for 12 weeks; room temperature housing (20-22 degrees C)


title: 4202-016-60

description: Library name: 4202-016-60

value: Current


title: HCT116 StemCells, Negative Control siRNA_1

description:
Library name: N1
N1

value: NC siRNA transfection rep1


title: 4790-034-60

description: Library name: 4790-034-60

value: Bronchial brushing

value: TRUE


title: hepAGT-/-, epididymal white adipose tissue, room temperature, Western diet, biol rep 9

description: Library name: RTKOE9

value: epididymal white adipose tissue

value: hepAGT-/-


title: LPC18_2_10uM_3

city: La Jolla

first: Sonia

last: Sharma

state: CA

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

institute: La Jolla Institute of Immunology

description:
Library name: LPC18_2_10uM_3
LPC18_2_10uM

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ-lite v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5)  and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: count matrix with rows as genes and columns as samples

source_name: Blood

extract_protocol:
Total RNA was extracted from 2 million cells using Direct-zol RNA Miniprep Kit (Zymo Research). Libraries were prepared using the NEB Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module (supplier info). 20 ng total RNA was used for each sample and libraries underwent 16 cycles of PCR amplification. Agilent Universal Human Reference RNA was prepared as a process control. Libraries were sequenced on the Novaseq 6000 using a 50x50 run configuration at a targeted depth of 25M (50M paired-end) reads.
RNA-seq 50 x 50 Paired-end sequencing reads

treatment_protocol: Cells were seeded in deep-well 96-well plates at a density of 2 × 10⁶ cell in 1ml  of FBS-free RPMI media, with or without LPC 18:2 at 10uM, and incubated at 37°C for 2 hours.

value: Blood

value: Human primary neutrophils


title: 4792-010-60

description: Library name: 4792-010-60


title: hepAGT-/-, epididymal white adipose tissue, room temperature, Western diet, biol rep 19

description: Library name: RTKOE19


title: 4798-009-60

description: Library name: 4798-009-60

value: Former


title: LPC18_2_10uM_2

description:
Library name: LPC18_2_10uM_2
LPC18_2_10uM


title: 4790-063-60

description: Library name: 4790-063-60

value: Malignant


title: LPC18_2_10uM_1

description:
Library name: LPC18_2_10uM_1
LPC18_2_10uM


title: 4794-004-60

description: Library name: 4794-004-60

value: FALSE


title: hepAGT-/-, epididymal white adipose tissue, room temperature, Western diet, biol rep 10

description: Library name: RTKOE10


title: 4790-073-60

description: Library name: 4790-073-60


title: Unstim_3

description:
Library name: Unstim_3
Unstim

value: Unstimulated


title: hepAGT-/-, epididymal white adipose tissue, room temperature, Western diet, biol rep 16

description: Library name: RTKOE16


title: 4795-087-60

description: Library name: 4795-087-60


title: hepAGT+/+, epididymal white adipose tissue, room temperature, Western diet, biol rep 12

description: Library name: RTWTE12

value: hepAGT+/+


title: 4202-001-60

description: Library name: 4202-001-60

value: female


title: hepAGT-/-, brown adipose tissue, room temperature, Western diet, biol rep 9

description: Library name: RTKOB9

value: brown adipose tissue


title: 4794-011-60

description: Library name: 4794-011-60

value: male


title: 4795-128-60

description: Library name: 4795-128-60


title: Unstim_2

description:
Library name: Unstim_2
Unstim


title: 4796-120-60

description: Library name: 4796-120-60


title: 4795-032-60

description: Library name: 4795-032-60

value: Benign


title: 4714-003-60

description: Library name: 4714-003-60

value: Current


title: hepAGT-/-, brown adipose tissue, room temperature, Western diet, biol rep 19

description: Library name: RTKOB19

value: Western diet for 12 weeks; room temperature housing (20-22 degrees C)


title: Unstim_1

description:
Library name: Unstim_1
Unstim


title: hepAGT-/-, brown adipose tissue, room temperature, Western diet, biol rep 14

description: Library name: RTKOB14


title: 4796-045-60

description: Library name: 4796-045-60

value: Bronchial brushing


title: 4714-014-60

description: Library name: 4714-014-60

value: not collected


title: 4796-132-60

description: Library name: 4796-132-60


title: Macrophages 27_3_7

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
Library name: 27_3_7
D27_MCSF IFN_LPS  48H

data_processing:
Skewer v0.2.2 was used to remove the low-quality reads and trimming the Illumina adapter. STAR program against genome (GRCh38) was used for mapping the reads followed by the quantification of genes with the RSEM (RNA-Seq by Expectation-Maximization) software package  for estimating gene and isoform expression levels from RNA-Seq data, using GENCODE v26 reference annotation .
Assembly: GRCh38
Supplementary files format and content: RSEM gene results

source_name: Macrophage

extract_protocol:
Macrophages were washed with PBS and disrupted with QIAzol Lysis Reagent (217084, Qiagen), and RNA was extracted using the miRNeasy Mini Kit (217084, Qiagen). mRNA-seq with three biological replicates was performed by the Genomics Platform at the Centre for Genomic Regulation (CRG, Barcelona). RNA integrity was assessed using a Fragment Analyzer with the Standard Sensitivity RNA kit (DNF-471, Agilent).
Libraries were prepared from total RNA using the TruSeq Stranded mRNA Library Prep Kit (20020595, Illumina) and following the manufacturer’s instructions, generating strand-specific cDNA libraries suitable for cluster generation and sequencing on the NovaSeq 6000 platform using a 2×50 bp paired-end strategy with 30 million reads per sample and a 100-cycle S2 flow cell.

value: Macrophage

value: IFNLPS

tag: time


title: hepAGT-/-, brown adipose tissue, room temperature, Western diet, biol rep 10

description: Library name: RTKOB10

value: hepAGT-/-


title: HCT116 StemCells, PSCA siRNA_1

description:
Library name: P1
P1

value: HCT116 Stemcells

value: Colorectal Cancer Stemcells

value: PSCA knockdown

value: PSCA siRNA transfection rep1


title: 4796-004-63

description: Library name: 4796-004-63

tag: smoking status

value: TRUE


title: Macrophages 27_3_4

description:
Library name: 27_3_4
D27_MCSF_HEPG2 48H


title: 4796-072-60

description: Library name: 4796-072-60

tag: age


title: R-LYC-PD-3

city: Jiamusi

first: Jun

last: Xia

address: No. 258 Xuefu Street, Xiangyang District

department: School of Basic Medical Sciences

institute: Jiamusi University

description:
Library name: R-LYC-PD-3
Mice were simultaneously administered lycopene (5 mg/kg) by oral gavage and MPTP (30 mg/kg) by intraperitoneal injection.

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

source_name: midbrain

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue samples were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: midbrain


title: 4714-001-60

description: Library name: 4714-001-60

value: Malignant

tag: nodule size_(cm)


title: Macrophages 27_3_1

description:
Library name: 27_3_1
D27_MCSF_IL10 48H


title: 4795-130-60

description: Library name: 4795-130-60

value: Former

tag: tfa (total_fat_area)


title: 4794-005-60

description: Library name: 4794-005-60

value: male

tag: fev1 percent_predicted


title: R-LYC-PD-1

description:
Library name: R-LYC-PD-1
Mice were simultaneously administered lycopene (5 mg/kg) by oral gavage and MPTP (30 mg/kg) by intraperitoneal injection.


title: 4790-062-60

description: Library name: 4790-062-60

value: Benign

tag: fev1/fvc ratio


title: 4791-003-60

description: Library name: 4791-003-60

tag: tissue


title: Macrophages 27_2_7

description:
Library name: 27_2_7
D27_MCSF_IFN_LPS 24H


title: 4798-003-60

description: Library name: 4798-003-60

value: Current


title: R-LYC-PD-5

description:
Library name: R-LYC-PD-5
Mice were simultaneously administered lycopene (5 mg/kg) by oral gavage and MPTP (30 mg/kg) by intraperitoneal injection.


title: Macrophages 27_2_4

description:
Library name: 27_2_4
D27_MCSF_HEPG2 24H


title: 4238-034-60

description: Library name: 4238-034-60


title: R-PD-3

description:
Library name: R-PD-3
Mice received intraperitoneal injection of 1‑methyl‑4‑phenyl‑1,2,3,6‑tetrahydropyridine (MPTP, 30 mg/kg) to establish a subacute Parkinson's disease model.


title: 4791-002-60

description: Library name: 4791-002-60


title: Macrophages 27_2_1

description:
Library name: 27_2_1
D27_MCSF_IL10 24H


title: 4795-031-60

description: Library name: 4795-031-60


title: R-PD-1

description:
Library name: R-PD-1
Mice received intraperitoneal injection of 1‑methyl‑4‑phenyl‑1,2,3,6‑tetrahydropyridine (MPTP, 30 mg/kg) to establish a subacute Parkinson's disease model.


title: 4238-020-60

description: Library name: 4238-020-60


title: Macrophages 27_7

description:
Library name: 27_7
D27_MCSF_IFN_LPS 6H


title: 4238-030-60

description: Library name: 4238-030-60

value: female

value: FALSE


title: R-PD-5

description:
Library name: R-PD-5
Mice received intraperitoneal injection of 1‑methyl‑4‑phenyl‑1,2,3,6‑tetrahydropyridine (MPTP, 30 mg/kg) to establish a subacute Parkinson's disease model.


title: 4793-041-60

description: Library name: 4793-041-60

value: Bronchial brushing

value: not collected


title: Macrophages 27_4

description:
Library name: 27_4
D27_MCSF_HEPG2 6H

value: Macrophage


title: 4796-156-60

description: Library name: 4796-156-60


title: 4795-038-60

description: Library name: 4795-038-60


title: D6_S23_DHT

first: Leigh-Ana

last: Rossitto

address: 9500 Gilman Drive

department: Neurosciences

institute: UC San Diego

description:
Library name: Sample10
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: D6_S23_DHT

data_processing:
RNA samples were first assessed for sequencing quality, analysis, trimming, and filtering using HTStream (v1.3).
Reads were mapped to the mm39 mouse reference genome using STAR (v2.7.10b), and transcripts’ raw counts were generated.
Raw counts were imported to R, and differential expression was performed using DESeq2 (v1.42.0).
Assembly: GRCm39.
Supplementary files format and content: csv file includes raw count for each Sample

source_name: Hippocampus

extract_protocol:
Total RNA was isolated from hippocampi of 9-9.5-month-old female P301S mice using the RNeasy kit (Qiagen). RNA amount was quantified by Qubit, and integrity was assessed by TapeStation (Agilent). 500 ng of RNA was used for library preparation.
cDNA libraries were prepared using the mRNA HyperPrep Kit (KAPA) according to the manufacturer’s protocol.

treatment_protocol: hTau+ PS19 mice with either void or DHT implants

value: Hippocampus

value: hTau

value: DHT Implant


title: 4790-095-60

description: Library name: 4790-095-60


title: Macrophages 27_1

description:
Library name: 27_1
D27_MCSF_IL10 6H


title: 4714-009-60

description: Library name: 4714-009-60


title: 4793-054-60

description: Library name: 4793-054-60


title: Macrophages 27B

description:
Library name: 27B
D27_MCSF

value: MCSF


title: D5_S22_DHT

description:
Library name: Sample9
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: D5_S22_DHT


title: D3_S20_DHT

description:
Library name: Sample8
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: D3_S20_DHT


title: 4790-002-60

description: Library name: 4790-002-60


title: 4714-013-60

description: Library name: 4714-013-60


title: Macrophages 25_3_7

description:
Library name: 25_3_7
D25 MCSF IFN/LPS   48H

value: IFNLPS


title: 4793-050-60

description: Library name: 4793-050-60


title: D2_S19_DHT

description:
Library name: Sample7
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: D2_S19_DHT


title: 4795-102-60

description: Library name: 4795-102-60


title: Macrophages 25_3_4

description:
Library name: 25_3_4
D25 MCSF HEPG2   48H


title: D1_S18_DHT

description:
Library name: Sample6
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: D1_S18_DHT


title: 4790-001-60

description: Library name: 4790-001-60


title: Macrophages 25_3_1

description:
Library name: 25_3_1
D25 MCSF IL10   48H


title: 4714-012-60

description: Library name: 4714-012-60

value: TRUE


title: V9_S9_VOID

description:
Library name: Sample5
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: V9_S9_VOID

value: Void Implant


title: 4795-132-60

description: Library name: 4795-132-60

value: Malignant


title: 4796-006-60

description: Library name: 4796-006-60


title: Macrophages 25_2_7

description:
Library name: 25_2_7
D25 MCSF IFN/LPS   24H


title: V5_S5_VOID

description:
Library name: Sample4
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: V5_S5_VOID


title: Macrophages 25_2_4

description:
Library name: 25_2_4
D25 MCSF HEPG2   24H


title: 4790-026-60

description: Library name: 4790-026-60


title: 4202-034-60

description: Library name: 4202-034-60


title: V4_S4_VOID

description:
Library name: Sample3
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: V4_S4_VOID


title: 4794-002-60

description: Library name: 4794-002-60


title: 4438-007-60

description: Library name: 4438-007-60


title: Macrophages 25_2_1

description:
Library name: 25_2_1
D25 MCSF IL10   24H


title: V11_S11_VOID

description:
Library name: Sample2
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: V11_S11_VOID


title: 4795-116-60

description: Library name: 4795-116-60

value: Former


title: 4798-018-60

description: Library name: 4798-018-60


title: Macrophages 25_7

description:
Library name: 25_7
D25 MCSF INF/LPS   6H

value: INFLPS


title: 4714-015-60

description: Library name: 4714-015-60

value: male


title: 4795-014-60

description: Library name: 4795-014-60

value: Benign

value: Current


title: V10_S10_VOID

description:
Library name: Sample1
Column name in rnaseq_P301S_V_DHT_rawcounts.csv: V10_S10_VOID

value: female


title: Macrophages 25_4

description:
Library name: 25_4
D25 MCSF HEPG2   6H


title: 4791-016-60

description: Library name: 4791-016-60

value: Bronchial brushing


title: Treatment4_FPKM

first: Jiangwei

last: Yang

address: No.234,Gucui Road, Xihu District

department: Mental health centerof Zhejiang Province

institute: Tongde Hospital of Zhejiang Province

description:
Library name: 1885
Treatment4_FPKM

data_processing:
Quality control and adapter trimming: Raw reads were processed with TrimGalore (v0.6.7), which incorporates Cutadapt (v3.4) and FastQC (v0.12.1), to remove adapter sequences and trim low-quality bases.
Alignment: Cleaned reads were aligned to the mouse reference genome using STAR (v2.7.10a) in 2-pass mode for improved splice junction detection.
Quantification: Gene and transcript expression levels were quantified using Salmon (v1.10.1) with GC bias correction and sequence-specific bias correction.
Assembly: GRCm39 (mm39)
Supplementary files format and content: The file contains gene-level raw counts and FPKM values for 12 samples. The first column contains Ensembl gene IDs (gene_id). Subsequent columns contain raw counts (count) and FPKM values (FPKM) for each sample. The file is formatted as a tab-separated text file.

molecule: polyA RNA

source_name: hippocampus

growth_protocol: Male C57BL/6 mice (6-8 weeks old) were purchased from Jiangsu Jicui Yaokang Biotechnology Co., Ltd. (license: SCXK (Su) 2023-0009). Mice were housed under controlled conditions (20-26°C, 40-70% humidity, 12-hour light/dark cycle) with free access to food and water. After 7 days of acclimation, mice with sucrose preference >50% were selected for experiments. All animal procedures were approved by the Animal Ethics Committee of Jiangxi Zhonghong Boyuan Biotechnology Co., Ltd. (approval number: LL202511030001).

extract_protocol:
Total RNA was extracted from mouse hippocampus tissues using TRIzol Reagent (15596018, CWBIO) according to the manufacturer's instructions. RNA concentration and purity were assessed using a Bioanalyzer 2100 with an RNA 6000 Nano LabChip Kit (Agilent, 5067-1511). Samples with RNA Integrity Number (RIN) > 7.0 were used for library construction.
1 µg of total RNA was used for library preparation. Poly(A) mRNA was isolated using Oligo(dT) magnetic beads. mRNA was fragmented using divalent cations and high temperature. First-strand cDNA was synthesized using random primers, followed by second-strand cDNA synthesis. Purified double-stranded cDNA was end-repaired, A-tailed, and ligated to adapters via T-A ligation. Adapter-ligated DNA was size-selected using DNA Clean Beads. Libraries were amplified by PCR using P5 and P7 primers and validated. Sequencing was performed on an Illumina NovaSeq 6000 with 2x150 bp paired-end configuration.

treatment_protocol: Mice were randomly divided into three groups (n=4 per group for RNA-seq): Control group, Model group, and Model + high-dose Poria cocos acid A (H-PAA) group. The Model and H-PAA groups were subjected to chronic unpredictable mild stress (CUMS) for 28 days, with one stressor applied daily without consecutive repetition. Stressors included: flash illumination (7 h), wet bedding (17 h), tail clamping (1 cm from tail tip, 1 min), overnight illumination, cage tilting (45°, 7 h or 22 h), grouped housing (17 h), novel odor (17 h), novel object (7 h), food deprivation (10 h), food restriction (2 h after 10 h fasting), and water deprivation (10 h). Starting on day 15, the H-PAA group received Poria cocos acid A (CAS: 12220228) at a dose of 20 mg/kg via oral gavage once daily for 14 consecutive days. The Control and Model groups received an equivalent volume of saline.

value: hippocampus

value: CUMS + PAA (20 mg/kg)

tag: batch


title: 4796-001-60

description: Library name: 4796-001-60

tag: copd status


title: Macrophages 25_1

description:
Library name: 25_1
D25 MCSF IL10   6H

value: Macrophage


title: Treatment3_FPKM

description:
Library name: 1636
Treatment3_FPKM


title: 4791-004-60

description: Library name: 4791-004-60


title: Macrophages 25B

description:
Library name: 25B
D25 MCSF


title: 4790-058-60

description: Library name: 4790-058-60


title: 4798-008-60

description: Library name: 4798-008-60

value: not collected


title: Treatment2_FPKM

description:
Library name: 1631
Treatment2_FPKM


title: 4796-104-60

description: Library name: 4796-104-60


title: Treatment1_FPKM

description:
Library name: 1883
Treatment1_FPKM


title: Macrophages 24_3_7

description:
Library name: 24_3_7
D24 MCSF INF/LPS   48H


title: 4438-068-60

description: Library name: 4438-068-60

value: FALSE


title: 4795-138-60

description: Library name: 4795-138-60


title: Macrophages 24_3_4

description:
Library name: 24_3_4
D24 MCSF HEPG2   48H


title: 4202-010-60

description: Library name: 4202-010-60


title: Model4_FPKM

description:
Library name: 1881
Model4_FPKM

value: CUMS + saline


title: 4796-023-60

description: Library name: 4796-023-60


title: Macrophages 24_3_1

description:
Library name: 24_3_1
D24 MCSF IL10  48H


title: 4790-013-60

description: Library name: 4790-013-60


title: Model3_FPKM

description:
Library name: 1871
Model3_FPKM


title: Macrophages 24_2_7

description:
Library name: 24_2_7
D24 MCSF IFN/LPS  24H

value: IFNLPS


title: 4796-081-60

description: Library name: 4796-081-60

value: TRUE


title: 4714-019-60

description: Library name: 4714-019-60


title: Model2_FPKM

description:
Library name: 1878
Model2_FPKM


title: 4798-005-60

description: Library name: 4798-005-60


title: 4714-007-60

description: Library name: 4714-007-60


title: Macrophages 24_2_4

description:
Library name: 24_2_4
D24 MCSF HEPG2  24H


title: Model1_FPKM

description:
Library name: 1872
Model1_FPKM


title: 4714-004-60

description: Library name: 4714-004-60


title: 4202-002-60

description: Library name: 4202-002-60


title: Control4_FPKM

description:
Library name: 1895
Control4_FPKM

value: Control (saline)


title: 4202-035-60

description: Library name: 4202-035-60

value: Malignant


title: Macrophages 24_2_1

description:
Library name: 24_2_1
D24 MCSF IL10  24H


title: Macrophages 24_7

description:
Library name: 24_7
D24 MSCF INF/LPS  6H


title: Control3_FPKM

description:
Library name: 1893
Control3_FPKM


title: 4795-127-60

description: Library name: 4795-127-60


title: 4795-065-60

description: Library name: 4795-065-60

value: Former


title: 4790-010-60

description: Library name: 4790-010-60


title: Macrophages 24_4

description:
Library name: 24_4
D24 MSCF HEPG2  6H


title: 4795-017-60

description: Library name: 4795-017-60


title: Macrophages 24_1

description:
Library name: 24_1
D24 MSCF IL 10  6H


title: Control2_FPKM

description:
Library name: 1868
Control2_FPKM


title: 4202-022-60

description: Library name: 4202-022-60


title: 4202-003-60

description: Library name: 4202-003-60


title: Control1_FPKM

description:
Library name: 1898
Control1_FPKM


title: 4790-003-60

description: Library name: 4790-003-60


title: Tumor, innate agonist treated (12h), HTO

city: Cambridge

first: Tyler

middle: T

last: Dao

address: 45 Carleton St

institute: Massachusetts Institute of Technology

description:
Library name: Masopust_054_E_HTO
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

library_source: other

data_processing:
Raw Illumina output files were processed to fastq files using the Cumulus V2.4.0 CellRanger pipeline on the Terra platform.
Assembly: mm10
Supplementary files format and content: Sample specific filtered_feature_bc_matrix.h5, adt.csv and hto.csv files were uploaded.
Library strategy: CITE-seq

molecule: protein

source_name: B16 tumors

extract_protocol:
Tumors were isolated, dissociated in gentleMACSTM C tubes and dissociator, and filtered. Single cells were processed via the 10x Genomics Next GEM single-cell 3' RNA-seq protocol.
Gene expression, ADT and HTO libraries were generated following the 10x Genomics 3' protocol.

value: B16 tumors

tag: cell line

value: B16.F10 melanoma

value: Melanoma and infiltrated immune cells

value: Innate agonist


title: 4790-024-60

description: Library name: 4790-024-60

value: male


title: Prostate cancer, group C, case 4

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description:
Library name: PC4
Prostate cancer, bad prognosis, seminal vesicles, case 4

data_processing:
Small RNA-seq sequencing data analysis was performed analysed with the XICRA pipeline and XICRA.stats, the R companion package[12]. See additional details in https://xicra.readthedocs.io/en/latest/ or https://github.com/HCGB-IGTP/XICRA.
We checked raw data quality using FASTQC
We performed trimming the reads to discard sequencing adapters with cutadapt.
For the mapping and the biotype feature assignment of all reads we used Bowtie mapping software with parameters specifically intended for small RNAs (-v 1–best–strata). Reads were mapped to the latest available human genome version (GRCh38.p13 2022) and featureCounts was used to assigned counts based on the Human Genome annotation and the RNA central annotations. For miRNA identification, we used miraligner (within the SeqBuster software, which can resolves canonical and other isomiR variants and miRBase (v22) as the reference database. Results were standardized with miRTop, which also generated expression count matrices. MiRNA expression at the gene level was obtained by aggregating isomiR counts for each miRNA. We formatted results into standardized files and generated expression count matrices. After the identification of the miRNAs for each sample at the isomiR level, we obtained total miRNA expression by aggregating counts for each miRNA. For tRNA biotype, we used two different approaches: (i) analysis using all reads, and (ii) a sequential approach in which only reads unaligned in previous steps were processed. using all reads or a sequential processing strategy where only the remaining unaligned reads from a previous analysis step were processed. In that second scenariothe sequential strategy, reads were mapped with the following scheme: miRNA > tsRNAs > piRNA > other biotypes (human). For the tRNA/tsRNA analysis, we used both the MINTmap and miRge softwares (mapped to MINTbase v1). Both isomiRs and tRFs were assigned a license plate ID based on the automated short RNA nomenclature system.
For the analysis of differentially expressed (DE) small RNAs, we employed XICRA.stats, running DESeq2, and other related packages under in the R software environment. For each case, we used the optimalbest dispersion fit obtained, either (local or parametric) was selected. Due to the numbers of expression counts in miRNA and tsRNA analysis, to normalize and determine differential expression between groups of interest, we employedwas estimated using the algorithm named Approximate Posterior Estimation for the Generalized Linear Model (apeglm (Approximate Posterior Estimation for the Generalized Linear Model)[24] designed as a strategy for reducingwhich reduces the number of false-positive DE genes filtering by log2 fold change (LFC) while preserving maintaining the fraction of true positive DE genes. Qualitative analysis was done based on raw counts. A given small RNA was accepted as present when the raw count was of at least 10 copies. For comparison purposes, we generated a complex DE analysis model, where we included age as a putative confounding variable.
Assembly: hg38 (GRCh38.p13 2022), with additional biotype specific reference annotations based on miRBase (v22), and MINTbase (v1).
Supplementary files format and content: Normalized count matrix from DESeq2 for miRNAs, isomiRs and tRFs

source_name: Semen (testis and prostate derived biofluid)

growth_protocol: Semen samples were obtained from 16 healthy individuals consulting for vasectomy at the Andrology Service of Fundació Puigvert (control group 1: HCt); among themincluding, five provided samples prior to vasectomy procedurepre-vasectomy (HCt-noV; age (years): 40 ± 3.08) while and 11 HCt individuals donated samples after post-vasectomy (HCt-V; age (years): 39.82 ± 9.46) donors. In addition, 37 individuals who consulted for diagnosis of PCa at the Urology Service of the Bellvitge Hospital were included. These individuals underwent standard prostate screening including PSA testing and DRE. Patients with moderate PSA levels (4-18 ng/mL) were selected with consent to undergo prostate biopsy. This cohort consisted of 29 men with biopsy-confirmed PCa, including previously vasectomised [PCa-V, n=7; age (years): 58 ±  9.69] and non-vasectomised individuals [PCa-noV, n=22; age (years): 59.04 ± 6.31]; as well as 8 non-vasectomised individuals diagnosed with benign prostatic hyperplasia (BPH) or prostate enlargement [control group 2; age (years): 58.62 ± 4.50] who exhibited elevated PSA levels (>4 ng/mL) but no detectable cancer on biopsy (Table 1; Supplementary Table S1). We also stratified samples by tumour class based on the 8th edition ofaccording to AJCC 8th edition prognostic risk groups [8] (which consider TNM data, pre-treatment PSA levels, and tumour Gleason grade, the latter deserving special concern) into I (low risk, including organ confined GS6 samples and PSA<10ng/mL), IIA (low-intermediate risk, which includes organ confined GS6 samples and PSA>10ng/mL), IIB (intermediate risk, including organ confined GS7(3+4) samples), IIC (intermediate-high risk, which includes organ confined GS7(4+3) samples), IIIB (high risk-advanced due to extra-prostatic extension of the tumour, includes cT3 samples belonging to any GS grade group and PSA levels). All these samples had been used [9] in a previous molecular investigation. The study was approved by the Ethical Review Board of both institutions. The participants signed an informed consent form. All methods were performed in accordance with the relevant guidelines and regulations.

extract_protocol:
Total RNA was isolated from sEVs using the miRNeasy Micro Kit (Qiagen) as previously described [9,11]. RNA yield was quantified using the QUBIT fluorometer and the Quant-iT RNA Assay kit (Invitrogen; California, USA). All RNA samples exhibited OD 260/280 nm ratios of 1.7 or higher when using a Nanodrop UV-Vis spectrophotometer (Thermo Fisher Scientific; Massachusetts, USA).
onSmall RNA libraries were generated with the NextFlex Small RNA-Seq Kit v4 with Unique Dual Indices -UDIs- (Revvity) adapted to lower input (10ng total RNA from sEVs to amplify 18 cycles according to specifications) and with an extended range of size selection. An equimolar pool of all samples determined by Bioanalyzer was automatically size selected. QIAquick (Qiagen) column purification was performed prior and after separation with the Pippin Prep system (SAGE Science) on 3% dye free cassettes with DF marker F, using two different settings in range mode [start 135 bp, End 185 bp, Target 160 bp for the first fraction (automated size selection) and then 8 fractions more collected every 4 minutes (manually size selection)]. The first three fractions recovered, which contained most of the small RNA, were pooled together. Pooled libraries were sequenced on a NovaSeq 6000 system (Illumina) on a 200 cycle SP flow cell, to generate paired end reads (2 x 100nt).

treatment_protocol: Semen samples were obtained by masturbation after 3-5 days of sexual abstinence. They were and incubated at 37ºC for 30 min to allow liquefaction. Isolation of sEVs was performedwere isolated by differential centrifugation steps (1600 xg for 10 min, following 16000 xg for 10 min at 4ºC) including a microfiltration step (0.22 μm pore size) and ultracentrifugation (100000 xg for 2h at 4ºC) to sediment sEVs as described elsewhere[6,10]. Collected vVesicles were resuspended in PBS and immediately stored at -80ºC until further analysis. They were characterized by Nnanoparticle tracking analysis was conducted using NanoSight NS300 (Malvern Instruments Ltd.; Malvern, UK) as previously stated.

tag: disease state

value: Prostate Cancer

value: Male

tag: tumor stage

value: Gleason score 4+3 or 4+4

tag: biofluid extracellular_fraction

value: seminal exosomal vesicles (sEVs)


title: 4796-017-63

description: Library name: 4796-017-63

value: Bronchial brushing

tag: Sex


title: Tumor, irrelevant peptide treated (48h), HTO

description:
Library name: Masopust_054_D_HTO
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

tag: cell type

tag: treatment

value: Irrelevant peptide


title: Prostate cancer, group C, case 3

description:
Library name: PC3
Prostate cancer, bad prognosis, seminal vesicles, case 3

value: Semen (testis and prostate derived biofluid)


title: 4202-005-60

description: Library name: 4202-005-60

tag: subject id

tag: cancer status

value: Current

value: not collected


title: 4791-007-60

description: Library name: 4791-007-60

value: Benign

tag: smoking status

tag: age

value: FALSE


title: 4796-041-60

description: Library name: 4796-041-60

value: Malignant

tag: nodule size_(cm)

tag: tfa (total_fat_area)


title: Tumor, irrelevant peptide treated (12h), HTO

description:
Library name: Masopust_054_C_HTO
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16 tumors


title: Prostate cancer, group C, case 2

description:
Library name: PC2
Prostate cancer, bad prognosis, seminal vesicles, case 2


title: 4795-070-60

description: Library name: 4795-070-60

value: Former

tag: fev1 percent_predicted

tag: fev1/fvc ratio

value: TRUE


title: Tumor, relevant peptide treated (48h), HTO

description:
Library name: Masopust_054_B_HTO
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

tag: tissue

value: B16.F10 melanoma

value: Melanoma and infiltrated immune cells

value: Relevant peptide


title: 4795-008-60

description: Library name: 4795-008-60

value: male

tag: copd status


title: 4790-074-60

description: Library name: 4790-074-60


title: Prostate cancer, group C, case 1

description:
Library name: PC1
Prostate cancer, bad prognosis, seminal vesicles, case 1

value: Prostate Cancer

value: Male

value: Gleason score 4+3 or 4+4


title: 4798-010-60

description: Library name: 4798-010-60

value: Bronchial brushing

value: female


title: 4793-001-60

description: Library name: 4793-001-60

value: Current


title: 4795-073-60

description: Library name: 4795-073-60


title: Tumor, relevant peptide treated (12h), HTO

description:
Library name: Masopust_054_A_HTO
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

tag: cell line


title: Prostate cancer, group B, case 4

description:
Library name: PB4
Prostate cancer, good prognosis, seminal vesicles, case 4

value: Semen (testis and prostate derived biofluid)

tag: disease state

value: Gleason score 3+4

value: seminal exosomal vesicles (sEVs)


title: Macrophages 24B

description:
Library name: 24B
D24 MCSF

value: Macrophage

value: MCSF

tag: time


title: Tumor, innate agonist treated (12h), ADT

description:
Library name: Masopust_054_E_ADT
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16 tumors

value: Innate agonist


title: 4202-020-60

description: Library name: 4202-020-60

value: Benign

value: Former

value: FALSE


title: Prostate cancer, group B, case 3

description:
Library name: PB3
Prostate cancer, good prognosis, seminal vesicles, case 3

tag: tumor stage

tag: biofluid extracellular_fraction


title: Tumor, irrelevant peptide treated (48h), ADT

description:
Library name: Masopust_054_D_ADT
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16.F10 melanoma

tag: cell type

value: Melanoma and infiltrated immune cells

value: Irrelevant peptide


title: 4794-003-60

description: Library name: 4794-003-60

value: Malignant

tag: Sex

value: male

value: TRUE


title: 4795-059-60

description: Library name: 4795-059-60

value: Bronchial brushing

tag: subject id


title: Tumor, irrelevant peptide treated (12h), ADT

description:
Library name: Masopust_054_C_ADT
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

tag: treatment


title: 4790-007-60

description: Library name: 4790-007-60

tag: cancer status

tag: smoking status

value: not collected


title: Prostate cancer, group B, case 2

description:
Library name: PB2
Prostate cancer, good prognosis, seminal vesicles, case 2

value: Semen (testis and prostate derived biofluid)

value: Prostate Cancer

value: Male

value: Gleason score 3+4


title: Prostate cancer, group B, case 1

description:
Library name: PB1
Prostate cancer, good prognosis, seminal vesicles, case 1

value: seminal exosomal vesicles (sEVs)


title: 4798-016-60

description: Library name: 4798-016-60

value: Current

tag: age

tag: nodule size_(cm)


title: 4714-011-60

description: Library name: 4714-011-60

tag: tfa (total_fat_area)

tag: fev1 percent_predicted


title: 4238-042-60

description: Library name: 4238-042-60

tag: tissue

value: Benign

tag: fev1/fvc ratio


title: Tumor, relevant peptide treated (48h), ADT

description:
Library name: Masopust_054_B_ADT
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16 tumors

tag: cell line

value: Relevant peptide


title: Prostate cancer, group A, case 4

description:
Library name: PA4
Prostate cancer, benign, seminal vesicles, case 4

tag: disease state

value: Gleason score 6


title: 4795-104-60

description: Library name: 4795-104-60

tag: copd status


title: 4202-024-60

description: Library name: 4202-024-60

value: Former

value: female


title: Prostate cancer, group A, case 3

description:
Library name: PA3
Prostate cancer, benign, seminal vesicles, case 3

tag: tumor stage


title: Tumor, relevant peptide treated (12h), ADT

description:
Library name: Masopust_054_A_ADT
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16.F10 melanoma

value: Melanoma and infiltrated immune cells


title: 4714-008-60

description: Library name: 4714-008-60

value: Malignant

value: male

value: TRUE


title: Tumor, innate agonist treated (12h), RNA

description:
Library name: Masopust_054_E_GEX
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Innate agonist


title: 4795-026-60

description: Library name: 4795-026-60

value: Bronchial brushing


title: Tumor, irrelevant peptide treated (48h), RNA

description:
Library name: Masopust_054_D_GEX
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Irrelevant peptide


title: Prostate cancer, group A, case 2

description:
Library name: PA2
Prostate cancer, benign, seminal vesicles, case 2

value: Semen (testis and prostate derived biofluid)

value: Prostate Cancer

value: Male

tag: biofluid extracellular_fraction


title: 4202-008-60

description: Library name: 4202-008-60

value: Current

value: not collected


title: 4238-004-60

description: Library name: 4238-004-60

value: Benign


title: Prostate cancer, group A, case 1

description:
Library name: PA1
Prostate cancer, low risk, better prognosis, case 1

value: Gleason score 6

value: seminal exosomal vesicles (sEVs)


title: 4794-012-60

description: Library name: 4794-012-60


title: Tumor, irrelevant peptide treated (12h), RNA

description:
Library name: Masopust_054_C_GEX
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16 tumors

tag: cell type


title: 4798-015-60

description: Library name: 4798-015-60

tag: Sex

value: female


title: Benign prostate hyperplasia 4

description:
Library name: BPH4
Benign prostate hyperplasia, seminal vessicles, case 4

value: Control, Benign Prostate Hyperplasia (BPH)

value: Not applicable


title: 4798-007-60

description: Library name: 4798-007-60

tag: subject id

value: Malignant

value: Former

value: male

value: FALSE


title: Tumor, relevant peptide treated (48h), RNA

description:
Library name: Masopust_054_B_GEX
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16.F10 melanoma

value: Melanoma and infiltrated immune cells

tag: treatment

value: Relevant peptide


title: 4714-023-60

description: Library name: 4714-023-60

value: Bronchial brushing

tag: cancer status

value: TRUE


title: Benign prostate hyperplasia 3

description:
Library name: BPH3
Benign prostate hyperplasia, seminal vessicles, case 3

value: Semen (testis and prostate derived biofluid)

value: Male


title: Tumor, relevant peptide treated (12h), RNA

description:
Library name: Masopust_054_A_GEX
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: Benign prostate hyperplasia 2

description:
Library name: BPH2
Benign prostate hyperplasia, seminal vessicles, case 2


title: 4714-021-60

description: Library name: 4714-021-60

tag: smoking status


title: 4238-014-60

description: Library name: 4238-014-60

value: Benign

tag: age


title: 4790-005-60

description: Library name: 4790-005-60

value: Current

tag: nodule size_(cm)


title: Tumor, innate agonist treated, channel 2, HTO

description:
Library name: Masopust_053_6b_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16 tumors

value: Innate agonist


title: 4438-111-60

description: Library name: 4438-111-60

tag: tfa (total_fat_area)

value: not collected


title: 4795-126-60

description: Library name: 4795-126-60

value: female

tag: fev1 percent_predicted


title: Tumor, innate agonist treated, channel 1, HTO

description:
Library name: Masopust_053_6a_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

tag: tissue


title: Benign prostate hyperplasia 1

description:
Library name: BPH1
Benign prostate hyperplasia, seminal vessicles, case 1

value: Control, Benign Prostate Hyperplasia (BPH)

value: Not applicable

value: seminal exosomal vesicles (sEVs)


title: 4238-017-60

description: Library name: 4238-017-60

tag: fev1/fvc ratio

value: FALSE


title: YQ2418 LTL331R ESK+TVB 375L PD5

city: Ann Arbor

first: Arul

middle: M

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description:
Library name: SI_43143
RiboErase

data_processing:
FASTQs were trimmed using BBDuk. Transcripts were quantified by kallisto with human reference genome (GRCh38/hg38) and then summarized to obtain gene level counts and TPM.
Assembly: GRCh38
Supplementary files format and content: LTL331R_Counts_matrix.tsv: Gene-level counts obtained from kallisto.
Supplementary files format and content: LTL331R_TPM_matrix.tsv: Gene-level TPM values obtained from kallisto.

growth_protocol: LTL331R tumors were maintained in SCID male mice.

extract_protocol:
Total RNA was extracted from cultured cells or tumor tissues using the RNeasy mini kit, following the manufacturer’s instructions. 1 μg of total RNA was used to construct the sequencing libraries.
RNA integrity was assessed using an Agilent Bioanalyzer with an RNA Nano chip. For tumor samples, ribosomal RNA was depleted using the RiboErase selection kit (Kapa Biosystems, KK8561). RNA-seq libraries were prepared from 800 ng total RNA using the KAPA RNA HyperPrep Kit (Roche Sequencing, KK8541). Following rRNA depletion or poly(A) enrichment, RNA was fragmented to approximately 200-300 bp, converted to double-stranded cDNA, ligated to NEB adapters, and PCR-amplified using KAPA HiFi HotStart ReadyMix with NEB dual-index barcodes. Library quality and size distribution were assessed using an Agilent 2100 Bioanalyzer with a DNA 1000 chip.

treatment_protocol: NEPC tumor-bearing mice were treated with Vehicle, ESK981, TVB-2640, or ESK981 in combination with TVB-2640 for 5 days.

value: NEPC tumors


title: YQ2418 LTL331R ESK+TVB 375R PD5

description:
Library name: SI_43142
RiboErase


title: Tumor, irrelevant (48h) or relevant peptide treated (12h), channel 2, HTO

description:
Library name: Masopust_053_3b_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

tag: cell line

value: B16.F10 melanoma

value: Melanoma and infiltrated immune cells

value: Relevant and irrelevant peptide


title: 4795-011-60

description: Library name: 4795-011-60

value: Bronchial brushing

value: Former

value: male

value: TRUE


title: 4795-107-60

description: Library name: 4795-107-60

value: Malignant


title: 4714-005-60

description: Library name: 4714-005-60

value: Current


title: Tumor, irrelevant (48h) or relevant peptide treated (12h), channel 1, HTO

description:
Library name: Masopust_053_3a_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16 tumors


title: 4790-027-60

description: Library name: 4790-027-60


title: YQ2418 LTL331R ESK+TVB 368L PD5

description:
Library name: SI_43141
RiboErase


title: D010-B-5_R1

city: Kaghosima City

first: Takuya

last: Tokunaga

address: 8-35-1 Sakuragaoka

country: Japan

institute: Kagoshima University

description:
Library name: sample10
Primary lung adenocarcinoma tissue obtained at initial surgery from a patient who later developed postoperative recurrence

data_processing:
Quality control of raw FASTQ files was performed using FastQC version 0.11.9.
MultiQC version 1.14 was used to summarize sequencing quality metrics and evaluate adapter trimming results.
FASTQ files were processed using CLC Genomics Workbench version 23.0.2. Reads were aligned to the human reference genome hg38 and annotated using miRBase Release 22.
miRNA expression levels were quantified and normalized using the trimmed mean of M values (TMM) method.
Hierarchical clustering, principal component analysis, and differential expression analysis were performed using StrandNGS version 4.0.
Assembly: Human hg38
Supplementary files format and content: Processed data files include UMI read count tables, TMM-normalized miRNA expression data, and differential expression analysis results for Group A versus Group B.

source_name: lung

growth_protocol: Not applicable.

extract_protocol:
Total RNA was extracted from surgically resected lung tissues using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. DNase treatment was performed to remove genomic DNA contamination.
Small RNA libraries were prepared using the QIAseq miRNA Library Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: lung

tag: genotype

value: EGFR mutant


title: Tumor, relevant (48h) or irrelevant peptide treated (12h), channel 2, HTO

description:
Library name: Masopust_053_2b_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: D009-B-4_R1

description:
Library name: sample9
Primary lung adenocarcinoma tissue obtained at initial surgery from a patient who later developed postoperative recurrence


title: YQ2418 LTL331R ESK+TVB 368R PD5

description:
Library name: SI_43140
RiboErase


title: D008-B-3_R1

description:
Library name: sample8
Primary lung adenocarcinoma tissue obtained at initial surgery from a patient who later developed postoperative recurrence


title: Tumor, relevant (48h) or irrelevant peptide treated (12h), channel 1, HTO

description:
Library name: Masopust_053_2a_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: D007-B-2_R1

description:
Library name: sample7
Primary lung adenocarcinoma tissue obtained at initial surgery from a patient who later developed postoperative recurrence


title: YQ2418 LTL331R ESK981 359L PD5

description:
Library name: SI_43139
RiboErase


title: D006-B-1_R1

description:
Library name: sample6
Primary lung adenocarcinoma tissue obtained at initial surgery from a patient who later developed postoperative recurrence


title: Tumor, baseline or relevant peptide treated (12h), channel 2, HTO

description:
Library name: Masopust_053_1b_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Baseline and relevant peptide


title: D005-A-5_R1

description:
Library name: sample5
Normal lung tissue

value: normal


title: YQ2418 LTL331R ESK981 357L PD5

description:
Library name: SI_43138
RiboErase


title: D004-A-4_R1

description:
Library name: sample4
Normal lung tissue


title: Tumor, baseline or relevant peptide treated (12h), channel 1, HTO

description:
Library name: Masopust_053_1a_HTO_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: D003-A-3_R1

description:
Library name: sample3
Normal lung tissue


title: YQ2418 LTL331R ESK981 357R PD5

description:
Library name: SI_43137
RiboErase


title: D002-A-2_R1

description:
Library name: sample2
Normal lung tissue


title: D001-A-1_R1

description:
Library name: sample1
Normal lung tissue


title: Tumor, innate agonist treated, channel 2, ADT

description:
Library name: Masopust_053_6b_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Innate agonist


title: YQ2418 LTL331R TVB-2640 367L PD5

description:
Library name: SI_43136
RiboErase


title: Tumor, innate agonist treated, channel 1, ADT

description:
Library name: Masopust_053_6a_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: BC398

city: Chicago

first: Zhou

last: Zhang

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

description: Library name: BC398

data_processing:
Library strategy: 5hmC-Seal
Raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Assembly: hg19
Supplementary files format and content: csv, genebody count of 5hmC

molecule: other

source_name: Plasma

extract_protocol:
Briefly, circulating cfDNA was extracted from ~2-3 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany) according to manufacturer’s protocols. DNA concentration was quantified using a Qubit fluorometer (Thermo Fisher Scientific Inc.).
The cfDNA samples were randomized for constructing 5hmC-Seal libraries and subsequent sequencing. First, the Illumina-compatible adaptors were ligated onto the cfDNA samples per our published protocols. Next, T4 bacteriophage β-glucosyltransferase was used to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5hmC-modified fragments. The azide group was then reacted with a biotin-conjugated strained alkyne DBCO-PEG4-biotin (Sigma) via click chemistry to biotinylated the DNA fragments. Streptavidin beads (Thermo) were used for affinity enrichment of 5hmC-containing DNA fragments. The 5hmC-Seal libraries were subsequently constructed through PCR amplification using KAPA HyperPlus library construction kit (Roche) and paired-end sequenced (PE60) using the Illumina NextSeq500 platform (Illumina Inc., California, USA) at The University of Chicago Genomics Facility.

value: Plasma


title: BC394

description: Library name: BC394


title: YQ2418 LTL331R TVB-2640 367R PD5

description:
Library name: SI_43135
RiboErase

value: NEPC tumors


title: Tumor, irrelevant (48h) or relevant peptide treated (12h), channel 2, ADT

description:
Library name: Masopust_053_3b_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: B16.F10 melanoma


title: BC27

description: Library name: BC27


title: BC32

description: Library name: BC32


title: YQ2418 LTL331R TVB-2640 343L PD5

description:
Library name: SI_43134
RiboErase


title: BC23

description: Library name: BC23


title: YQ2418 LTL331R TVB-2640 343R PD5

description:
Library name: SI_43133
RiboErase


title: Tumor, irrelevant (48h) or relevant peptide treated (12h), channel 1, ADT

description:
Library name: Masopust_053_3a_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Melanoma and infiltrated immune cells


title: BC13

description: Library name: BC13


title: BC325

description: Library name: BC325


title: Tumor, relevant (48h) or irrelevant peptide treated (12h), channel 2, ADT

description:
Library name: Masopust_053_2b_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Relevant and irrelevant peptide


title: BC324

description: Library name: BC324


title: YQ2418 LTL331R Veh 373R PD5

description:
Library name: SI_43132
RiboErase

value: Vehicle


title: BC322

description: Library name: BC322


title: Tumor, relevant (48h) or irrelevant peptide treated (12h), channel 1, ADT

description:
Library name: Masopust_053_2a_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: BC319

description: Library name: BC319


title: YQ2418 LTL331R Veh 369L PD5

description:
Library name: SI_43131
RiboErase


title: Tumor, baseline or relevant peptide treated (12h), channel 2, ADT

description:
Library name: Masopust_053_1b_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: BC311

description: Library name: BC311


title: BC298

description: Library name: BC298


title: YQ2418 LTL331R Veh 369R PD5

description:
Library name: SI_43117
RiboErase


title: BC295

description: Library name: BC295


title: Tumor, baseline or relevant peptide treated (12h), channel 1, ADT

description:
Library name: Masopust_053_1a_ADT_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: BC294

description: Library name: BC294