title: AA20853_SG2B

description: Library name: S8_AA20853


title: GPS-peptidomic screen replicate 2 Bin 7

status: Public on Jan 14 2026

type: SRA

city: Taipei

first: Hsueh-Chi

middle: S

last: Yen

address: No. 128, Sec. 2, Academia Rd.

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
Library name: Bin7_rep2
GPS-peptidomic screen replicate 2 Bin 7

library_source: other

data_processing:
Amplicon sequences were first translated into amino acid seqeunce. Amino acid sequences that perfectly matched the designed sequences would be counted.
Supplementary files format and content: Tab-delimited text file includes raw data counts in each sample

molecule: other

organism: Homo sapiens

growth_protocol: HEK293T cells (ATCC® CRL-3216) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (Hyclone), 100 μg/ml streptomycin, and 100 U/ml penicillin (Gibco). Cells were maintained at 37 °C in a humidified incubator with 6% CO₂.

extract_protocol:
Genomic DNA from each bin of cells was extracted by phenocloroform.
Genomic DNA from each bin was extracted and used for PCR amplification of the integrated oligos using TaKaRa Ex Taq® DNA Polymerase Hot-Start Version (Takara Bio). PCR products were purified using the MinElute PCR Purification Kit (QIAGEN) and quantified using Qubit™ fluorometric quantification (Thermo Fisher Scientific). A second PCR was performed to add Illumina indices.

tag: cell line

tag: cell type

value: Human embryonic kidney cells

tag: genotype

value: WT


title: AA34059_CTRL

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

description: Library name: AA34059_CTRL

library_source: transcriptomic

data_processing:
The quality of sequencing data was confirmed with FastQC both before and after trimming.
Paired-end reads were independently trimmed with Trimmomatic and aligned to the human reference genome (hg38) using STAR.
SAMtools and NovoSort were respectively used to filter reads with proper mapping and sort the read pairs by name.
RSEM was used to estimate read counts per transcript and generate transcript per million (TPM) counts.
Assembly: hg38
Supplementary files format and content: FPKM counts extracted from RSEM output

molecule: total RNA

source_name: Breast

extract_protocol:
Total RNA was extracted from T47D cells using the RNeasy Plus mini kit (Qiagen).
Libraries were prepared using the TruSeq stranded mRNA library prep kit (Illumina) as per the manufacturer’s protocol.

tag: tissue

value: Breast

value: Mammary epithelial


title: CRISPR screen -UBA5-RT_high

description:
Library name: UBA5-RT_high
CRISPR screen -UBA5-RT_high


title: AA20227_CTRL

description: Library name: S3_AA20227

tag: treatment

value: knockdown of BRRIAR lncRNA using gapmer RNAs


title: XA0045412-833-1012_GAAGACCA-ACTGCCAT_S9,  ED

city: Chapel Hill

first: Sarah

last: Linnstaedt

state: NC

address: 109 Mason Farm Road

country: USA

description: Library name: XA0045412-833-1012_GAAGACCA-ACTGCCAT_S9

data_processing:
Sequencing reads aligned using the STAR(v2.7.6a) against the hg38 reference genome, with GENCODEV47 annotation file. Salmon (v1.4.0) was used to quantify aligned transcript-level expression from the aligned reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Whole Blood

extract_protocol:
Blood samples were collected at the time of enrollment using PAXgene RNA tubes. Total RNA was isolated using the PAXgene blood miRNA kit (QIAGEN) and RNA was stored at −80˚C until use. RNA concentration and purity were measured using a NanoDrop One (Nanodrop Technologies, Wilmington, DE), and RNA integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Template libraries for total RNA sequencing were produced from 600 ng total RNA using Ovation Human Blood RNA-Seq Library Systems kit (NuGen, San Carlos, CA) according to manufacturer's specifications. Libraries were multiplexed in groups of six and sequenced on a HiSeq 4000 (Illumnia) at the University of North Carolina at Chapel Hill High Throughput Sequencing Facility.

value: whole blood

value: mixed

tag: Sex

value: Female

tag: age

value: Midwest

tag: monocytes

value: White


title: R-CON2

city: Hefei

first: Peng

last: Jiao

address: No. 130, Changjiang West Road, Hefei, Anhui Province, Anhui Agricultural University

country: China

institute: Anhui Agricultural University College of Animal Science and Technology

description:
Library name: Sample 2
Hu sheep

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oar_v4.0 whole genome.
Transcript per Kilobase per Million mapped reads (TPM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Oar_v4.0
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Ovis aries

source_name: rumen

growth_protocol: Ewes at 115 days of gestation.

extract_protocol:
RNA was harvested using  Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Restricted feeding.

value: rumen

value: Not available

value: Normal feeding


title: R-TR2

description:
Library name: Sample 5
Hu sheep

value: Restricted feeding


title: R2-TR5

description:
Library name: Sample 20
Hu sheep

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oar_v4.0 whole genome.
Fragment per kilobase of exon model per million mapped reads (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Oar_v4.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

value: female

tag: breed

value: Hu

value: Compensatory feeding


title: AA20484_SG1C

description: Library name: S6_AA20484


title: XA0046311-830-1058_CTAAGACC-CCTAACAG_S19,  ED

institute: University of North Carolina at Chapel Hill

description: Library name: XA0046311-830-1058_CTAAGACC-CCTAACAG_S19

value: SouthEast

value: Other


title: AA20341_SG1A

description: Library name: S4_AA20341

value: Breast


title: DsiBRIAR6_S9

description: Library name: DsiBRIAR6_S9

value: Mammary epithelial


title: GPS-peptidomic screen replicate 2 Bin 6

description:
Library name: Bin6_rep2
GPS-peptidomic screen replicate 2 Bin 6

value: Human embryonic kidney cells

value: WT


title: GPS-peptidomic screen replicate 2 Bin 5

description:
Library name: Bin5_rep2
GPS-peptidomic screen replicate 2 Bin 5


title: DsiBRIAR4_S7

description: Library name: DsiBRIAR4_S7

value: knockdown of BRRIAR lncRNA using the  synthetic dicer-substrate siRNAs (dsi-RNA) system


title: AA20162_CTRL

description: Library name: S1_AA20162


title: R-TR1

description:
Library name: Sample 4
Hu sheep


title: R-CON1

description:
Library name: Sample 1
Hu sheep


title: XA0046007-831-1023_CGAAGGAT-AGTCGCAA_S21,  ED

description: Library name: XA0046007-831-1023_CGAAGGAT-AGTCGCAA_S21

value: whole blood

value: mixed

value: Female

value: Black


title: XA0046011-831-1006_AACCGGTA-TACTGGAC_S22,  ED

description: Library name: XA0046011-831-1006_AACCGGTA-TACTGGAC_S22

value: Male


title: AA20480_SG1B

description: Library name: S5_AA20480

value: knockdown of BRRIAR lncRNA using gapmer RNAs


title: R-CON3

description:
Library name: Sample 3
Hu sheep

value: rumen

value: Not available

value: Normal feeding


title: DsiBRIAR3_S6

description: Library name: DsiBRIAR3_S6


title: XA0047221-830-1047_CTCGAACA-CCAACGAA_S30,  ED

description: Library name: XA0047221-830-1047_CTCGAACA-CCAACGAA_S30


title: GPS-peptidomic screen replicate 1 Bin 8

description:
Library name: Bin8_rep1
GPS-peptidomic screen replicate 1 Bin 8


title: GPS-peptidomic screen replicate 2 Bin 3

description:
Library name: Bin3_rep2
GPS-peptidomic screen replicate 2 Bin 3


title: R2-TR1

description:
Library name: Sample 16
Hu sheep

value: female

value: Hu

value: Compensatory feeding


title: AA20174_CTRL

description: Library name: S2_AA20174

value: Breast


title: GPS-peptidomic screen replicate 1 Bin 7

description:
Library name: Bin7_rep1
GPS-peptidomic screen replicate 1 Bin 7


title: GPS-peptidomic screen replicate 2 Bin 1

description:
Library name: Bin1_rep2
GPS-peptidomic screen replicate 2 Bin 1


title: DsiBRIAR2_S5

description: Library name: DsiBRIAR2_S5

value: Mammary epithelial


title: XA0044782-831-1016_CTGAACAC-ATGAAGCC_S2,  ED

description: Library name: XA0044782-831-1016_CTGAACAC-ATGAAGCC_S2

value: SouthEast


title: XA0045988-831-1003_CGATGAAG-TCGATTCG_S19,  ED

description: Library name: XA0045988-831-1003_CGATGAAG-TCGATTCG_S19


title: R2-TR4

description:
Library name: Sample 19
Hu sheep

value: WT


title: R2-TR3

description:
Library name: Sample 18
Hu sheep


title: DsiBRIAR5_S8

description: Library name: DsiBRIAR5_S8

value: knockdown of BRRIAR lncRNA using the  synthetic dicer-substrate siRNAs (dsi-RNA) system


title: GPS-peptidomic screen replicate 2 Bin 4

description:
Library name: Bin4_rep2
GPS-peptidomic screen replicate 2 Bin 4

value: Human embryonic kidney cells


title: XA0046306-830-1056_CACCGATA-GAGTAACC_S18,  ED

description: Library name: XA0046306-830-1056_CACCGATA-GAGTAACC_S18

value: whole blood

value: mixed


title: XA0045327-833-1026_TCGCACTA-AATCCGCA_S7,  ED

description: Library name: XA0045327-833-1026_TCGCACTA-AATCCGCA_S7

value: Female

value: Midwest

value: White


title: GPS-peptidomic screen replicate 2 Bin 2

description:
Library name: Bin2_rep2
GPS-peptidomic screen replicate 2 Bin 2


title: R2-CON5

description:
Library name: Sample 15
Hu sheep

value: rumen


title: XA0044774-831-1005_TTCGCACA-TATGGCTG_S1,  ED

description: Library name: XA0044774-831-1005_TTCGCACA-TATGGCTG_S1

value: Black


title: R2-TR2

description:
Library name: Sample 17
Hu sheep


title: GPS-peptidomic screen replicate 1 Bin 5

description:
Library name: Bin5_rep1
GPS-peptidomic screen replicate 1 Bin 5


title: XA0046150-830-1021_GCAGACTT-TCCTCTGA_S11,  ED

description: Library name: XA0046150-830-1021_GCAGACTT-TCCTCTGA_S11


title: GPS-peptidomic screen replicate 1 Bin 4

description:
Library name: Bin4_rep1
GPS-peptidomic screen replicate 1 Bin 4


title: R2-CON1

description:
Library name: Sample 11
Hu sheep

value: Normal feeding


title: DsiCON3_S3

description: Library name: DsiCON3_S3


title: DsiCON1_S1

description: Library name: DsiCON1_S1


title: GPS-peptidomic screen replicate 1 Bin 6

description:
Library name: Bin6_rep1
GPS-peptidomic screen replicate 1 Bin 6


title: XA0049436-829-1057_CGCTACAT-AACCTACG_S56,  ED

description: Library name: XA0049436-829-1057_CGCTACAT-AACCTACG_S56


title: DsiBRIAR1_S4

description: Library name: DsiBRIAR1_S4


title: XA0054015-879-1013_AACTTGCC-CCAACTTC_S116,  ED

description: Library name: XA0054015-879-1013_AACTTGCC-CCAACTTC_S116

value: Male

value: NorthEast


title: R2-CON2

description:
Library name: Sample 12
Hu sheep

value: female

value: Hu


title: R2-CON3

description:
Library name: Sample 13
Hu sheep


title: DsiCON2_S2

description: Library name: DsiCON2_S2

value: Breast

value: Mammary epithelial


title: GPS-peptidomic screen replicate 1 Bin 2

description:
Library name: Bin2_rep1
GPS-peptidomic screen replicate 1 Bin 2

value: WT


title: GPS-peptidomic screen replicate 1 Bin 3

description:
Library name: Bin3_rep1
GPS-peptidomic screen replicate 1 Bin 3


title: R1-TR5

description:
Library name: Sample 10
Hu sheep

value: Restricted feeding


title: MSK93202

city: Charlestown

first: Luis Antonio

last: Corchete

institute: Krantz Family Center for Cancer Research

description: L122R, MSK93202

library_source: genomic single cell

data_processing:
Single-cell ATAC sequencing (scATAC-seq) raw base call (BCL) files retrieved from Illumina Basespace underwent demultiplexing and conversion into FASTQ files using the BCL Convert software (v2.0.0) provided by Illumina
The sequence alignment, barcode processing, and gene count processing were made using 10x Genomics Cell Ranger ATAC 2.1.0
Assembly: GRCh38 and mm10
Supplementary files format and content: Tab-delimited value files and matrix files

molecule: genomic DNA

source_name: Soft tissue tumors in PDXs

growth_protocol: PDX(patient-derived xenograft) tumors were dissociated into single-cell suspension, dead cells removed, and viable tumor cells injected into subcutaneous flank of the immune-deficient NSG mouse models.

extract_protocol:
Tumor tissue were freshly collected by homogenization, enzyme digestion, and filtering. Viable tumor cells were purified by debris removal, dead cell and mouse cell removal. Suspended single cells were used for scATACseq on the 10X Genomics platform, Chromium Next GEM Single Cell ATAC v2 kit.
Single-cell ATAC libraries were prepared according to the manual from 10XGenomics Chromium Next GEM Single Cell ATAC v2 kit.

treatment_protocol: No specific treatment was performed.

value: Soft tissue tumors in PDXs

tag: myod1 status


title: XA0048107-830-1060_GAACAAGC-ACGACCAT_S42,  ED

description: Library name: XA0048107-830-1060_GAACAAGC-ACGACCAT_S42

value: whole blood

value: SouthEast


title: R1-TR4

description:
Library name: Sample 9
Hu sheep


title: GPS-peptidomic screen replicate 1 Bin 1

description:
Library name: Bin1_rep1
GPS-peptidomic screen replicate 1 Bin 1

value: Human embryonic kidney cells


title: R2-CON4

description:
Library name: Sample 14
Hu sheep


title: PLCO096

city: Houston

first: Warapen

last: Treekitkarnmongkol

state: TX

address: 2130 W. Holcombe Blvd.,  Unit 2951

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

description: PLCO

data_processing:
Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.
Assembly: The miRNA probe list is based on miRBase version 20.
Supplementary files format and content: Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.

source_name: Plasma

extract_protocol:
15 uL of plasma was profiled for miRNAs by the extraction-free method using the HTG edge miRNA whole transcriptome assay kit (HTG Molecular, Tuscon, AZ, Cat# 916-001-024) according to the recommended vendor’s protocol.
Probes hybrized to target miRNAs were retrieved and added sequencing adapters as well as sample barcodes via PCR for preparing library. The libraries were quantified by quantitative PCR (qPCR) using KAPA Library Quantification kit (Roche, Cat# KK4824) and loaded onto the MiSeq (Illumina) together with the MiSeq Reagent Kit v3 (150 cycles) (Illumina, Cat# MS-102-3001).

value: Plasma

tag: cohort

value: Pre-diagnostic PLCO cohort

tag: disease


title: ST67

description: L122R, ST67


title: PLCO093

description: PLCO


title: XA0047274-829-1035_CGAAGGAT-AGTCGCAA_S31,  ED

description: Library name: XA0047274-829-1035_CGAAGGAT-AGTCGCAA_S31

value: mixed

value: Female

value: Midwest


title: XA0048067-829-1046_CAAGCGTA-TGACGTCA_S39,  ED

description: Library name: XA0048067-829-1046_CAAGCGTA-TGACGTCA_S39

value: Black


title: PLCO094

description: PLCO


title: XA0053109-831-1058_CGATGAAG-TCGATTCG_S79,  ED

description: Library name: XA0053109-831-1058_CGATGAAG-TCGATTCG_S79


title: MSK74711

description: L122R, MSK74711


title: PLCO095

description: PLCO


title: R1-TR3

description:
Library name: Sample 8
Hu sheep

value: rumen


title: XA0048042-829-1041_GAAGACCA-ACTGCCAT_S38,  ED

description: Library name: XA0048042-829-1041_GAAGACCA-ACTGCCAT_S38


title: R1-TR2

description:
Library name: Sample 7
Hu sheep

value: female


title: MSK93202 [scRNA-seq]

description: L122R, MSK93202

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing (scRNA-seq) raw base call (BCL) files retrieved from Illumina Basespace underwent demultiplexing and conversion into FASTQ files using the BCL Convert software (v2.0.0) provided by Illumina.
The sequence alignment, barcode processing, and gene count processing were made using 10x Genomics Cell Ranger 7.1.0
Assembly: GRCh38 and mm10
Supplementary files format and content: Tab-delimited value files and matrix files

molecule: polyA RNA

extract_protocol:
Tumor tissue were freshly collected by homogenization, enzyme digestion, and filtering. Viable tumor cells were purified by debris removal, dead cell and mouse cell removal. Suspended single cells were used for scRNAseq on the 10X Genomics platform, v3 expression kit.
Single-cell RNA libraries were prepared according to the manual from 10XGenomics Expression kit v3


title: SJRHB015720_X1 (MAST161)

description: L122R, MAST161


title: XA0048071-829-1033_CTGAACAC-ATGAAGCC_S40,  ED

description: Library name: XA0048071-829-1033_CTGAACAC-ATGAAGCC_S40


title: ST67 [scRNA-seq]

description: L122R, ST67


title: R1-CON5

description:
Library name: Sample 5
Hu sheep

value: Hu

value: Normal feeding


title: R1-TR1

description:
Library name: Sample 6
Hu sheep


title: PLCO091

description: PLCO


title: R1-CON3

description:
Library name: Sample 3
Hu sheep


title: XA0046393-830-1052_AGCAGCAA-GTAGAAGC_S20,  ED

description: Library name: XA0046393-830-1052_AGCAGCAA-GTAGAAGC_S20

value: Male


title: PLCO092

description: PLCO


title: XA0045552-829-1027_CGAAGCAA-CCACAATC_S4,  ED

description: Library name: XA0045552-829-1027_CGAAGCAA-CCACAATC_S4


title: XA0046282-830-1054_GAAGGATC-AGGCTCTT_S16,  ED

description: Library name: XA0046282-830-1054_GAAGGATC-AGGCTCTT_S16


title: R1-CON1

description:
Library name: Sample 1
Hu sheep

value: WT


title: PLCO087

description: PLCO


title: Ruch2, L122R, H3K4me3, R2

description: Ruch2, L122R, H3K4me3, R2

library_source: genomic

data_processing:
Reads were trimmed for quality and adapters were removed using trimgalore (v.0.4.3)
Alignment against the human genome (version hg38, Ensembl) was carried out using the BWA-MEM algorithm (v. 0.7.15) and the resulting SAM files were transformed to BAM, sorted by coordinates and indexed using the samtools tool (v.1.4.1). Samtools was also used for the removal of the mitochondrial chromosome and unscaffolded regions. The cDNA-detector (v. 0.1.0) program was used to remove possible cDNA contamination in the BAM files. Duplicate marking was carried out as the sambamba tool (v. 1.0.1). Low-quality reads were removed with the FilterBAM tool (v. 2) by setting a Phred score of 30 as the minimum alignment quality.
Determination of the ChIP-seq peaks for each of the histone markers was carried out with the macs2 (v. 2.0.10) program using the “callpeak” option and input samples as a control. Blacklisted regions were obtained from ENCODE (version GRCh38)and removed using the “subtract” command of bedtools (v. 2.30.0)
Bigwig files were generated using the “bamCoverage” option of the deeptools tool (v.3.1.2), with a bin size of 10 bp and applying a counts per million (CPM)-like normalization along with the “–centerReads” and “–ignoreDuplicates” options. The scores for each genomic region were calculated using the “computeMatrix” option also from deeptools, using an upstream to downstream distance of 1,500 bp from the center of the interval.
Assembly: GRCh38
Supplementary files format and content: bigWig, encodePeak (except for input samples)

growth_protocol: RD and Ruch2 cells with or without treatment were cultured in DMEM supplemented with 10% FBS, PenStrep, and collected before confluency for ChIP-seq experiments.

extract_protocol:
Cells were crosslinked with a 1% formaldehyde final concentration, then resuspended and digested with Micrococcal nuclease. Digested DNA fragments between 150-900 base pairs were sonicated using a Branson 250 sonicator, with pulse amplitude of 32%, pulsing for 0.7 seconds with 1.3 seconds in between for a total pulse period of 5 minutes on ice. Chromatin was diluted 10x and incubated with 3-5 ug of antibodies overnight at 4°C with agitation. Histone complexes were precipitated by Protein G Magnetic Beads, then washed 3x with a low salt solution and 1x with a high salt solution. Chromatin was eluted and cross-linking was reversed with 5M NaCl and then treated with Proteinase K. DNA was purified using DNA wash Buffer and then eluted with Elution Buffer.
ChIP libraries were built by starting from ChIP DNA (5ng), followed by end preparation, adaptor ligation and amplification, indexed with Dual Index 7 Primers and 5 Primers from Multiplex Oligos (CST# 47538) compatible with Illumina. AMPure XP and SPRI Select beads were used to clean up amplified DNA.

treatment_protocol: RD and Ruch2 cells with the dox-inducible contruct, were seeded, and then treated with doxycycline, for 72 hours, before collection for chromatine immunoprecipitation.

tag: replicate

tag: chip antibody


title: PLCO090

description: PLCO


title: Ruch2, L122R, L122R, R2

description: Ruch2, L122R, L122R, R2

value: Flag


title: PLCO089

description: PLCO


title: XA0054568-830-1131_AACACCGA-CTAGGAAG_S120,  ED

description: Library name: XA0054568-830-1131_AACACCGA-CTAGGAAG_S120

value: White


title: R1-CON2

description:
Library name: Sample 2
Hu sheep


title: XA0054998-828-1216_CATTCGTC-TTGGTGCA_S123,  ED

description: Library name: XA0054998-828-1216_CATTCGTC-TTGGTGCA_S123

value: whole blood

value: NorthEast


title: Ruch2, L122R, Input, R2

description: Ruch2, L122R, Input, R2


title: SJRHB015720_X1 (MAST161) [scRNA-seq]

description: L122R, MAST161

value: Soft tissue tumors in PDXs


title: XA0046083-830-1023_GAACAGAC-GTCTACCT_S9,  ED

description: Library name: XA0046083-830-1023_GAACAGAC-GTCTACCT_S9

value: SouthEast


title: PLCO086

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: PLCO085

description: PLCO


title: XA0053314-828-1206_TCCAACTG-TGTGTCAG_S74,  ED

description: Library name: XA0053314-828-1206_TCCAACTG-TGTGTCAG_S74

value: mixed


title: Ruch2, MYOD1, H3K4me3, R2

description: Ruch2, MYOD1, H3K4me3, R2

value: Wild type


title: PLCO088

description: PLCO


title: Ruch2, MYOD1, H3K27ac, R2

description: Ruch2, MYOD1, H3K27ac, R2


title: ID 2, 3 month milk EV

type: RNA

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

country: Japan

institute: Morinaga Milk Industry Co., Ltd.

hyb_protocol: Cy3 labelled RNA samples were hybridized to rat miRNA microarrays (Release 21.0, SurePrint G3 Human miRNA 8x60K) (Agilent Technologies) at 55 ºC for 20 hr. After hybridyzation, the microarray slides were washed and dried according to the manufacture's instruction.

scan_protocol: The microarray slides were scanned on an Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: Fluorescent signal intensities were extracted from the images with SureScan Microarray Scanner Extraction Software (v.12.0.3.1) (Agilent Technologies). The raw signal values were normalized to 75th percentile shit when importing the Feature Extraction files into GeneSpring GX 14.9.

source_name: human breast milk derived extracellular vesicles

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the miRNA Complete Labeling Reagent and Hyb kit (Agilent) according to the manufacture's instruction.

extract_protocol: Total RNA was extracted and purified using an miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany). Briefly, milk-derived EVs samples were diluted with five volumes of QIAzol Lysis Reagent, mixed thoroughly by vortexing and incubated for 5 min. Then chloroform (equal volume to sample) was added to homogenate, mixed thoroughly by vortexingand incubated for 3 min. The homogenate were centrifuged (12,000 x g, 4 ºC, 15 min). The resulting aqueous phase was mixed thoroughly with 1.5 volumes of 100 % ethanol and passed through an miRNeasy column. The column was washed according to the manufacture's protocol, and RNA was eluted in nuclease free water. The quanity and integrity of the RNA were assessed using RNA 6000 Pico Kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: A 1:100 volume of acetic acid was added to defatted human breast milk and centrifuged at 4,500 g, 30 min at 4°C to remove residual fat and casein. The whey was passed through a 0.22 μm filter to remove cell debris. A qEV column was used to purify extracellular vesicles (EVs).

tag: subject id

value: ID 2

tag: age at delivery

value: 33 yr

tag: period

value: 3 month


title: XA0054541-830-1127_GACAGCTT-GATACGTG_S119,  ED

description: Library name: XA0054541-830-1127_GACAGCTT-GATACGTG_S119

value: Female

value: Black


title: Ruch2, MYOD1, MYOD1, R2

description: Ruch2, MYOD1, MYOD1, R2

tag: cell line


title: ID 4, 3 month milk EV

value: ID 4

value: 32 yr


title: XA0053386-828-1202_CTAGCTCA-AACTGAGG_S78,  ED

description: Library name: XA0053386-828-1202_CTAGCTCA-AACTGAGG_S78

tag: cell type


title: ID 14, 3 month milk EV

value: ID 14

value: 29 yr


title: ID 14, 4-5 month milk EV

value: 4-5 month


title: PLCO084

description: PLCO


title: PLCO083

description: PLCO


title: XA0053358-828-1190_TCTAGTCC-CGGTAATC_S77,  ED

description: Library name: XA0053358-828-1190_TCTAGTCC-CGGTAATC_S77

value: whole blood

value: Male

value: NorthEast


title: PLCO082

description: PLCO

value: Plasma


title: ID 14, 2 month milk EV

value: 2 month


title: ID 14, 1 month milk EV

value: 1 month


title: PLCO081

description: PLCO

value: Pre-diagnostic PLCO cohort


title: Porphyridium_residual_nitrate_0.5gL_rep3

city: AUBIERE

first: Maurean

middle: Tehani

last: Guerreiro

state: Auvergne-Rhône-Alpes

address: 4, Avenue Blaise Pascal

department: Axe GePEB : Génie des Procédés, Énergétique et Biosystèmes

country: France

institute: Institut Pascal, UMR 6602 – Université Clermont Auvergne (UCA)

description:
Library name: PP_N_0_5_techRep3
Column name in PP_gene_count_matrix.txt: PP_N_0_5_techRep3

data_processing:
QC - Raw FASTQ files were inspected using FastQC and trimmed if necessary.
Reads were aligned to the Porphyridium purpureum reference genome using STAR (v2.7.8a) with default parameters on the Galaxy platform.
Gene-level counts were obtained using featureCounts (v2.0.1) with the genome annotation file (GFF, version 2), selecting “gene” as feature type.
Count data were processed with DESeq2 (v1.34.0). Variance stabilizing transformation (VST) was applied for PCA. Differential expression was performed using the likelihood ratio test (LRT) with FDR correction (Benjamini–Hochberg). Genes with adjusted p-value < 0.01 were considered significantly differentially expressed.
Assembly: Porphyridium purpureum genome assembly and annotation v2 (Porphyridium_purpureum_v2_genemodels.gff), downloaded from the Rutgers Porphyridium genome portal.
Supplementary files format and content: Processed data consist of a raw gene-level count matrix (PP_raw_gene_count_matrix.txt). The file reports read counts per gene for each sample, with genes in rows and samples in columns. Counts were generated from aligned reads using standard RNA-seq quantification tools. No normalization or transformation was applied to the counts.

organism: Porphyridium purpureum

source_name: unicellular red microalga

growth_protocol: Porphyridium purpureum strain 1380/1A was cultured in modified Provasoli medium (N/P ≈ 4) containing NaCl, NaNO₃, K₂HPO₄, MgSO₄·7H₂O, CaCl₂·2H₂O, trace metals, and vitamins. Cultures (4 L) were grown in 5 L cylindrical photobioreactors at pH 8, 22.5 °C, under continuous illumination (158 µmol m⁻² s⁻¹) and agitation (150 rpm). Aeration was supplied with air supplemented with ~1000 ppm CO₂ at 100 mL min⁻¹. Samples were collected at defined kinetic points corresponding to nitrogen-replete (NR), nitrogen-limitation (NL1, NL2), and nitrogen-deprivation (ND) phases.

extract_protocol:
Biomass was flash-frozen and ground manually in liquid nitrogen. Total RNA was extracted using the TRIzol reagent protocol. Approximately 100 mg cells were homogenized in 1 mL TRIzol and incubated for 5 min at room temperature. Phase separation was performed by adding 0.2 mL chloroform per 1 mL TRIzol, followed by centrifugation (12,000 × g, 15 min, 4 °C). The aqueous phase was recovered and RNA precipitated with 0.5 mL isopropanol per 1 mL TRIzol. The pellet was washed with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA integrity was verified on agarose gels.
Stranded mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit following the manufacturer’s instructions. Poly-A RNA was enriched, fragmented, reverse-transcribed, and converted to indexed cDNA libraries. Libraries were pooled and sequenced on an Illumina NovaSeq SP flow cell, generating paired-end 2 × 150 bp reads. Replicates correspond to independent technical sequencing libraries prepared from the same biological sample at each nitrate concentration.

treatment_protocol: Cells were taken at three nitrogen availability phases defined by culture kinetics:  nitrogen-replete (NR), nitrogen-limitation (NL1, NL2), and nitrogen-deprivation (ND) phases

tag: residual nitrate_concentration

tag: technical replicate

tag: strain

value: unicellular red microalga

tag: nitrate depletion_phase


title: Porphyridium_residual_nitrate_0.3gL_rep2

description:
Library name: PP_N_0_3_techRep2
Column name in PP_gene_count_matrix.txt: PP_N_0_3_techRep2

value: ND


title: PLCO080

description: PLCO

tag: tissue


title: Porphyridium_residual_nitrate_0.3gL_rep3

description:
Library name: PP_N_0_3_techRep3
Column name in PP_gene_count_matrix.txt: PP_N_0_3_techRep3


title: ID 14, transition milk EV

value: transition


title: Ruch2, MYOD1, Input, R2

description: Ruch2, MYOD1, Input, R2

value: Wild type


title: PLCO079

description: PLCO


title: XA0053671-830-1101_CAATTGGC-TCTGTCCA_S113,  ED

description: Library name: XA0053671-830-1101_CAATTGGC-TCTGTCCA_S113

value: mixed

tag: Sex

tag: age

value: SouthEast

tag: monocytes

value: Black


title: XA0053602-830-1104_CCTTGTAC-CTCCTACA_S97,  ED

description: Library name: XA0053602-830-1104_CCTTGTAC-CTCCTACA_S97

value: Female


title: XA0050316-828-1171_AGCAGACA-AGAGGATG_S48,  ED

description: Library name: XA0050316-828-1171_AGCAGACA-AGAGGATG_S48

value: White


title: PLCO078

description: PLCO

tag: cohort


title: Porphyridium_residual_nitrate_0.3gL_rep1

description:
Library name: PP_N_0_3_techRep1
Column name in PP_gene_count_matrix.txt: PP_N_0_3_techRep1


title: Porphyridium_residual_nitrate_0.5gL_rep1

description:
Library name: PP_N_0_5_techRep1
Column name in PP_gene_count_matrix.txt: PP_N_0_5_techRep1


title: ID 14, colostrum milk EV

value: ID 14

value: 29 yr

value: colostrum


title: XA0050472-830-1099_CAACCTAG-ATGACCGA_S93,  ED

description: Library name: XA0050472-830-1099_CAACCTAG-ATGACCGA_S93

value: whole blood


title: XA0053682-830-1105_CTAATGCC-AACCAAGG_S115,  ED

description: Library name: XA0053682-830-1105_CTAATGCC-AACCAAGG_S115


title: ID 1, 3 month milk EV

value: ID 1

value: 32 yr

value: 3 month


title: Porphyridium_residual_nitrate_0.5gL_rep2

description:
Library name: PP_N_0_5_techRep2
Column name in PP_gene_count_matrix.txt: PP_N_0_5_techRep2


title: PLCO076

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort

tag: disease


title: Porphyridium_residual_nitrate_0.6gL_rep2

description:
Library name: PP_N_0_6_techRep2
Column name in PP_gene_count_matrix.txt: PP_N_0_6_techRep2

value: unicellular red microalga


title: XA0053287-828-1145_CTTCCTTC-TTCCAGGT_S72,  ED

description: Library name: XA0053287-828-1145_CTTCCTTC-TTCCAGGT_S72

value: NorthEast


title: ID 13, 2 month milk EV

value: ID 13

value: unknown

value: 2 month


title: Porphyridium_residual_nitrate_0.6gL_rep3

description:
Library name: PP_N_0_6_techRep3
Column name in PP_gene_count_matrix.txt: PP_N_0_6_techRep3


title: XA0050492-830-1120_CACAACGT-GATCGTAC_S94,  ED

description: Library name: XA0050492-830-1120_CACAACGT-GATCGTAC_S94

value: mixed

value: SouthEast

value: Black


title: ID 13, 4-5 month milk EV

value: 4-5 month


title: ID 13, 3 month milk EV


title: Porphyridium_residual_nitrate_0.6gL_rep1

description:
Library name: PP_N_0_6_techRep1
Column name in PP_gene_count_matrix.txt: PP_N_0_6_techRep1


title: XA0048139-830-1066_GTTACACC-AGAAGTGC_S48,  ED

description: Library name: XA0048139-830-1066_GTTACACC-AGAAGTGC_S48

value: Male


title: XA0050099-830-1093_GCAGCATA-GTCATCGA_S64,  ED

description: Library name: XA0050099-830-1093_GCAGCATA-GTCATCGA_S64

value: Female


title: PLCO075

description: PLCO


title: PLCO074

description: PLCO


title: Porphyridium_residual_nitrate_1.5gL_rep2

description:
Library name: PP_N_1_5_techRep2
Column name in PP_gene_count_matrix.txt: PP_N_1_5_techRep2

value: NR


title: PLCO077

description: PLCO


title: ID 13, 1 month milk EV

value: 1 month


title: XA0048474-828-1086_CTCCTAGT-CCTCATCT_S40,  ED

description: Library name: XA0048474-828-1086_CTCCTAGT-CCTCATCT_S40

value: whole blood


title: ID 12, 2 month milk EV

value: ID 12

value: 28 yr


title: ID 12, 4-5 month milk EV


title: XA0047742-828-1091_CGCAACTA-CATTGACG_S28,  ED

description: Library name: XA0047742-828-1091_CGCAACTA-CATTGACG_S28


title: ID 12, 3 month milk EV

value: 3 month


title: PLCO073

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: PLCO070

description: PLCO


title: GA0518 cells, YAP knockout, biol rep 1

city: Camden

first: Yanting

last: Zhang

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

description: Library name: GA0518_YAP_KO_D_1

data_processing:
RNA-seq data was initially preprocessed by trimming and clipping with fastqp (v1.0.1) to remove adapter sequences and low-quality bases
Transcript quantification was performed with salmon (v1.10.0) against the human reference genome GRCh38 primary assembly, annotated with GENCODE release 38.
For differential gene expression analysis, the standard edgeR pipeline (v4.6.2) was used. Non-protein-coding genes and lowly expressed genes were filtered out using the edgeR’s filterByExpr function. Differential expression testing was conducted using the glmTreat function with a log-fold change cutoff of log2(1.5) and an FDR cutoff of 0.05.
Assembly: GRCh38 primary assembly
Supplementary files format and content: tab-delimeted text file includes raw counts for each sample
Supplementary files format and content: comma-delimeted file includes differential gene expression results for all comparisons

growth_protocol: Cells were cultured in RPMI1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 100 U/ml penicillin, and 100 mg/ml streptomycin (Invitrogen), and maintained at 37°C in a humidified incubator of 5% CO2.

extract_protocol:
Total RNAs were isolated and purified using the RNeasy Mini Kit (Qiagen, 74106) and converted to cDNA using Luna® Universal One-Step RT-qPCR Kit (New England Biolabs, E3005).
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 the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand specific library

treatment_protocol: GA0518 cells (100K cells) seeded into 6 well culture plate. After the cells attached on the plate(24h later),  the old culture medium was replaced by 2 ml fresh cell culture medium with 200 nM VT00278 and incubute for 24 hr.

value: gastric adenocarcinoma

tag: genotype

value: YAP knockout

tag: treatment


title: Porphyridium_residual_nitrate_1.5gL_rep3

description:
Library name: PP_N_1_5_techRep3
Column name in PP_gene_count_matrix.txt: PP_N_1_5_techRep3

value: unicellular red microalga


title: ID 13, transition milk EV

tag: subject id

value: ID 13

value: unknown

value: transition


title: PLCO071

description: PLCO


title: PLCO068

description: PLCO


title: XA0046927-846-1002_ATCGTGGT-CTCTATCG_S39,  ED

description: Library name: XA0046927-846-1002_ATCGTGGT-CTCTATCG_S39

value: mixed

value: NorthEast

value: Black


title: GA0518 cells, YAP knockout, biol rep 2

description: Library name: GA0518_YAP_KO_D_2


title: XA0046930-846-1019_AATGACGC-TGGACCAT_S40,  ED

description: Library name: XA0046930-846-1019_AATGACGC-TGGACCAT_S40

value: Female


title: ID 11, 4-5 month milk EV

value: ID 11

tag: age at delivery

value: 36 yr

value: 4-5 month


title: Porphyridium_residual_nitrate_1.5gL_rep1

description:
Library name: PP_N_1_5_techRep1
Column name in PP_gene_count_matrix.txt: PP_N_1_5_techRep1

value: NR


title: GA0518 cells, VT00278-treated, biol rep 1

description: Library name: GA0518_VT_200_1

value: WT


title: GA0518 cells, untreated, biol rep 2

description: Library name: GA0518_untreated_2

value: untreated


title: XA0046902-846-1012_ACTCTCCA-TGATCACG_S34,  ED

description: Library name: XA0046902-846-1012_ACTCTCCA-TGATCACG_S34

value: whole blood


title: ID 12, transition milk EV

value: ID 12

value: 28 yr

tag: period


title: PLCO072

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: PLCO067

description: PLCO


title: PLCO066

description: PLCO


title: XA0046270-828-1076_AACTCGGA-TGCAAGAC_S13,  ED

description: Library name: XA0046270-828-1076_AACTCGGA-TGCAAGAC_S13

value: White


title: ID 12, colostrum EV

value: colostrum


title: XA0046892-846-1017_GTCTCATC-CGGATCAA_S33,  ED

description: Library name: XA0046892-846-1017_GTCTCATC-CGGATCAA_S33

value: mixed


title: PLCO065

description: PLCO


title: Case4 metastasis

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Library name: GA81279
Thyroid cancer metastasis site

data_processing:
Sequencing was performed on NovaSeq 6000 or NovaSeq X Plus platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 or RTA4 software was used for base calling.
Generated reads were mapped to the human (GRCh38.p13) reference genome using HISAT2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Thyroid

extract_protocol:
Total RNA was isolated from the human thyroid FFPE using a QIAGEN RNeasy FFPE Kit.
The cDNA library was prepared using a SMART-Seq stranded Kit (Takara Bio).

value: Thyroid

tag: disease state

value: Metastasis site

tag: tumor stage


title: PLCO069

description: PLCO


title: GA0518 cells, VT00278-treated, biol rep 2

description: Library name: GA0518_VT_200_2

tag: cell line

tag: cell type

value: gastric adenocarcinoma


title: XA0047401-846-1025_GTACCACA-GCGCATAT_S41,  ED

description: Library name: XA0047401-846-1025_GTACCACA-GCGCATAT_S41

value: Male

value: NorthEast


title: ID 11, 1 month milk EV

value: ID 11

value: 36 yr

value: 1 month


title: ID 11, 2 month milk EV

value: 2 month


title: PLCO063

description: PLCO


title: ID 11, 3 month milk EV

value: 3 month


title: ID 11, colostrum EV


title: XA0046915-846-1010_TCTACGCA-CGCCTTAT_S38,  ED

description: Library name: XA0046915-846-1010_TCTACGCA-CGCCTTAT_S38

value: whole blood

value: Black


title: GA0518 cells, untreated, biol rep 1

description: Library name: GA0518_untreated_1

value: WT

value: untreated


title: Case4 primary

description:
Library name: GA81277
Thyroid cancer primary site

value: Primary site


title: Case5 metastasis

description:
Library name: GA81275
Thyroid cancer metastasis site


title: XA0046903-846-1011_CTCCAATC-ATAGGTCC_S35,  ED

description: Library name: XA0046903-846-1011_CTCCAATC-ATAGGTCC_S35

value: Female

value: White


title: XA0046909-846-1018_GCCAGAAT-TACTAGCG_S37,  ED

description: Library name: XA0046909-846-1018_GCCAGAAT-TACTAGCG_S37

value: mixed


title: R1-CON4

description:
Library name: Sample 4
Hu sheep

value: rumen

value: female

tag: breed

value: Hu

value: Normal feeding


title: Case5 primary

description:
Library name: GA81274
Thyroid cancer primary site

value: Thyroid


title: ID 10, 4-5 month milk EV

value: ID 10

value: 29 yr

value: 4-5 month


title: PLCO061

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: XA0046907-846-1008_GCTACAAC-ACTGCTTG_S36,  ED

description: Library name: XA0046907-846-1008_GCTACAAC-ACTGCTTG_S36

value: whole blood

value: NorthEast


title: XA0047391-828-1065_CGCTACAT-AACCTACG_S22,  ED

description: Library name: XA0047391-828-1065_CGCTACAT-AACCTACG_S22

value: Other


title: XA0047369-828-1073_CGTCTAAC-CAACGAGT_S21,  ED

description: Library name: XA0047369-828-1073_CGTCTAAC-CAACGAGT_S21


title: PLCO058

description: PLCO


title: ID 10, 1 month milk EV

value: 1 month


title: PLCO059

description: PLCO


title: Case5 Normal

description:
Library name: GA81273
Normal thyroid tissue

value: Normal


title: Ruch2, L122R, H3K27ac, R2

description: Ruch2, L122R, H3K27ac, R2

tag: myod1 status

tag: replicate

tag: chip antibody


title: XA0045547-828-1032_GCTCAGTT-GTATCGAG_S7,  ED

description: Library name: XA0045547-828-1032_GCTCAGTT-GTATCGAG_S7

tag: tissue

tag: Sex

value: Male

tag: age

value: White


title: PLCO064

description: PLCO

tag: cohort

tag: disease


title: PLCO062

description: PLCO


title: PLCO056

description: PLCO


title: ID 9, 3 month milk EV

value: ID 9

value: 36 yr

value: 3 month


title: PLCO055

description: PLCO


title: PLCO057

description: PLCO


title: XA0045894-828-1059_TAACGTCG-TCAGCCTT_S9,  ED

description: Library name: XA0045894-828-1059_TAACGTCG-TCAGCCTT_S9

value: mixed

value: Female

tag: monocytes


title: Case4 Normal

description:
Library name: GA81276
Normal thyroid tissue

value: Thyroid


title: MV3 cells, M1 EV 2

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: Library name: MV3_RNAseq_M1EV_rep2

data_processing:
Paired-end reads were aligned to human genome hg38 using STAR aligner (v.2.6.1b).
Transcript-level count matrix (rawCounts.MV3_RNAseq.txt) was produced from exon regions using analyzeRepeats function (analyzeRepeats.pl rna hg38 -raw -count exons -strand +) in homer (v4.10).
Assembly: hg38
Supplementary files format and content: tab-delimited file with refSeq transcript ID and counts for each sample.

source_name: cell line

growth_protocol: MV3 cells were cultured in DMEM supplemented with 10% FBS, 1% P/S and 1% L-glutamine at 37 °C under 5% CO2 .

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
RNA samples were sent to Novogene (Germany) for quality control, directional mRNA library preparation with poly A enrichment and strand specific mRNA-sequencing with NovaSeq X Plus Series

treatment_protocol: MV3 cells were plated on 12-well plate. On the next day,  culture media was exhanged to RPMI 1640 supplemented with 1% EV-depleted FBS, 1% P/S and 1% L-glutamine for 3 h. Then, cells were treated for 24 h M0, M1 and M2 EVs (1E10 particles/well). As a control, equal amount of PBS was added to the control wells.

value: cell line

value: melanoma cells

tag: treatment

value: M1 EV treatment


title: MV3 cells, M2 EV 2

description: Library name: MV3_RNAseq_M2EV_rep2

value: M2 EV treatment


title: XA0045068-828-1031_ACTCTGAG-AGTTGTGC_S5,  ED

description: Library name: XA0045068-828-1031_ACTCTGAG-AGTTGTGC_S5

value: whole blood

value: Black


title: ID 9, 2 month milk EV

tag: subject id

tag: age at delivery

value: 2 month


title: XA0045919-828-1044_ATCTGACC-GTACGATC_S11,  ED

description: Library name: XA0045919-828-1044_ATCTGACC-GTACGATC_S11

value: NorthEast


title: ID 10, transition milk EV

value: ID 10

value: 29 yr

tag: period

value: transition


title: ID 10, 3 month milk EV


title: ID 9, transition milk EV

value: ID 9


title: ID 10, 2 month milk EV


title: ID 11, transition milk EV

value: ID 11

value: 36 yr


title: XA0047544-867-1010_ACTGCACT-AGATCGTC_S46,  ED

description: Library name: XA0047544-867-1010_ACTGCACT-AGATCGTC_S46

value: mixed


title: XA0048483-846-1030_CCTGTCAA-AGGTCTGT_S55,  ED

description: Library name: XA0048483-846-1030_CCTGTCAA-AGGTCTGT_S55

value: Female

value: White


title: MV3 cells, M2 EV 1

description: Library name: MV3_RNAseq_M2EV_rep1

value: cell line


title: MV3 cells, M1 EV 3

description: Library name: MV3_RNAseq_M1EV_rep3

value: melanoma cells


title: MV3 cells, M2 EV 3

description: Library name: MV3_RNAseq_M2EV_rep3


title: PLCO060

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: PLCO051

description: PLCO


title: PLCO052

description: PLCO


title: MV3 cells, M0 EV 1

description: Library name: MV3_RNAseq_M0EV_rep1

value: M0 EV treatment


title: PLCO050

description: PLCO


title: XA0049665-867-1005_GACATCTC-TGTCACAC_S75,  ED

description: Library name: XA0049665-867-1005_GACATCTC-TGTCACAC_S75

value: whole blood

value: Black


title: ID 8, 2 month milk EV

value: ID 8

value: 32 yr

value: 2 month


title: MV3 cells, Ctrl 3

description: Library name: MV3_RNAseq_ctrl_rep3

value: Control


title: PLCO049

description: PLCO


title: XA0049478-867-1017_GTTCCATG-CAATGCGA_S71,  ED

description: Library name: XA0049478-867-1017_GTTCCATG-CAATGCGA_S71

value: Male

value: NorthEast


title: PLCO048

description: PLCO


title: ID 10, colostrum EV

value: ID 10

value: 29 yr

value: colostrum


title: MV3 cells, M1 EV 1

description: Library name: MV3_RNAseq_M1EV_rep1

value: M1 EV treatment


title: PLCO054

description: PLCO


title: XA0049468-867-1002_TCCAACTG-TGTGTCAG_S70,  ED

description: Library name: XA0049468-867-1002_TCCAACTG-TGTGTCAG_S70

value: mixed

value: Female


title: MV3 cells, M0 EV 3

description: Library name: MV3_RNAseq_M0EV_rep3

value: cell line

value: melanoma cells


title: ID 9, colostrum EV

value: ID 9

value: 36 yr


title: PLCO053

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: MV3 cells, M0 EV 2

description: Library name: MV3_RNAseq_M0EV_rep2

value: M0 EV treatment


title: XA0045028-828-1021_ACCAAGCA-TGCTTGCT_S1,  ED

description: Library name: XA0045028-828-1021_ACCAAGCA-TGCTTGCT_S1

value: whole blood

value: White


title: PLCO047

description: PLCO


title: XA0047986-846-1054_ACGATCAG-ATCGCAAC_S48,  ED

description: Library name: XA0047986-846-1054_ACGATCAG-ATCGCAAC_S48

value: Black


title: XA0049676-867-1000_CTAGCTCA-AACTGAGG_S76,  ED

description: Library name: XA0049676-867-1000_CTAGCTCA-AACTGAGG_S76

value: NorthEast


title: PLCO046

description: PLCO


title: XA0045582-828-1005_GACATCTC-TGTCACAC_S8,  ED

description: Library name: XA0045582-828-1005_GACATCTC-TGTCACAC_S8


title: XA0054483-846-1033_TCCTGGTA-CAGATCCT_S118,  ED

description: Library name: XA0054483-846-1033_TCCTGGTA-CAGATCCT_S118


title: PLCO045

description: PLCO


title: ID 8, 3 month milk EV

value: ID 8

value: 32 yr

value: 3 month


title: MV3 cells, Ctrl 2

description: Library name: MV3_RNAseq_ctrl_rep2

value: Control


title: ID 5, 1 month milk EV

value: ID 5

value: 30 yr

value: 1 month


title: J-Lat 10.6, DMSO, 24 h

city: Guangzhou

first: Xianyuan

last: Yang

state: Guangdong

address: No.132 East Ring Road

institute: Sun Yat-Sen University

description:
Library name: Sample 1
Column name in A4_vs_NC.degseq.annotation.txt and A16_vs_NC.degseq.annotation.txt is: NC_count
A4_vs_NC.degseq.annotation.txt
A16_vs_NC.degseq.annotation.txt

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts permillion reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DEGseq. DEGs with |log2FC|>=1 and FDR<0.001 were considered to be significantly different expressed genes.
Assembly: The clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Supplementary files format and content: txt file containing counts for each sample

growth_protocol: J-Lat 10.6 cells were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Newzerum) and 1% Penicillin-Streptomycin (Gibco) at 37 °C under 5% CO2.

extract_protocol:
Total RNA were extracted by TRIeasyTM Total RNA Extraction Reagent (Yeasen)
RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (SanDiego, CA) using 1 μg of total RNA.

treatment_protocol: J-Lat 10.6 cells were treated with either DMSO, 10μM compound 4, or 10μM compound 16 for 24 h.

value: 0.1% DMSO


title: ID 8, 1 month milk EV


title: PLCO044

description: PLCO


title: J-Lat 10.6, compound 16, 24 h

description:
Library name: Sample 3
Column name in A16_vs_NC.degseq.annotation.txt is: A16_count
A16_vs_NC.degseq.annotation.txt

value: 10μM compound 16


title: J-Lat 10.6, compound 4, 24 h

description:
Library name: Sample 2
Column name in A4_vs_NC.degseq.annotation.txt is: A4_count
A4_vs_NC.degseq.annotation.txt

value: 10μM compound 4


title: ID 5, colostrum EV

value: colostrum


title: XA0045510-828-1013_GTTCCATG-CAATGCGA_S6,  ED

description: Library name: XA0045510-828-1013_GTTCCATG-CAATGCGA_S6

value: mixed

value: Female


title: MV3 cells, Ctrl 1

description: Library name: MV3_RNAseq_ctrl_rep1

value: cell line

value: melanoma cells


title: ID 5, transition milk EV

value: transition


title: PLCO043

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: XA0048117-830-1062_CGTCATAC-TCCAACGA_S44,  ED

description: Library name: XA0048117-830-1062_CGTCATAC-TCCAACGA_S44

value: whole blood

value: SouthEast

value: Black


title: ID 5, 3 month milk EV

value: ID 5

value: 3 month


title: ID 4, 2 month milk EV

value: ID 4

value: 32 yr

value: 2 month


title: 3DP-HHO-2, 3D Bio-Printed, day7

city: Hangzhou

first: Zhichao

last: Ye

address: Huajiachi Campus

institute: Zhejiang University

description: Library name: 3DP-HHO-2

data_processing:
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the EBSeq R package. The resulting FDR (false discovery rate) were adjusted using the PPDE(posterior probability of being DE).The FDR < 0.05 & |log2（foldchange）| ≥1 was set as the threshold for significantly differential expression.
Assembly: https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Liver

growth_protocol: hiHeps or 3DP-HHO were subsequently cultured in hepatocyte maintenance medium (HMM) supplemented with insulin-transferrin-selenium (ITS, TBD41100-045, TBD, China), NeuroCultTM SM1 Neuronal Supplement (STEMCELL, Canada), 40 ng/mL TGF-α (100-16a, Perprotech, USA), 40 ng/mL EGF (af-100-15, Perprotech, USA) and 10 μM dexamethasone (D4902, Sigma, Germany).

extract_protocol:
RNA was isolated with TRIzol.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: 3DP-HHO was bio-printed with hiHeps and cultured in HMM.

value: Liver

value: hiHeps

value: human induced hepatocytes

value: 3D Bio-Printed


title: 3DP-HHO-1, 3D Bio-Printed, day7

description: Library name: 3DP-HHO-1


title: ID 4, 4-5 month milk EV

value: 4-5 month


title: PLCO041

description: PLCO


title: hiHeps-3, 2D Cultured, day7

description: Library name: hiHeps-3

value: 2D Cultured


title: 3DP-HHO-3, 3D Bio-Printed, day7

description: Library name: 3DP-HHO-3


title: XA0048386-830-1076_GCGTAGAT-AATCGCAC_S51,  ED

description: Library name: XA0048386-830-1076_GCGTAGAT-AATCGCAC_S51

value: mixed

value: Female


title: ID 6, 4-5 month milk EV

value: ID 6

value: 30 yr


title: ID 7, 1 month milk EV

value: ID 7

value: 34 yr

value: 1 month


title: hiHeps-2, 2D Cultured, day7

description: Library name: hiHeps-2


title: PLCO039

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: PLCO042

description: PLCO


title: XA0049679-826-1320_TCACTCTG-CTGTTACG_S61,  ED

description: Library name: XA0049679-826-1320_TCACTCTG-CTGTTACG_S61

value: whole blood

value: Midwest

value: Black


title: XA0048399-830-1086_CCTGTATG-GCTCTATG_S52,  ED

description: Library name: XA0048399-830-1086_CCTGTATG-GCTCTATG_S52

value: SouthEast


title: Tcells, 7_TH17

city: Edmonton

first: Shima

last: Shahbaz

state: Alberta

address: 7-096 Katz Group Center for Pharmacy and Health Research

country: Canada

institute: University of Alberta

data_processing:
Kallisto pseudoalignment and bias correction was used for fragment alignment to the human cDNA database (GRCh38)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited counts files

source_name: T cells

extract_protocol:
Total RNA was extracted using a Direct-zol RNA MicroPrep kit
100 ng RNA was used to make libraries using TruSeq RNA Library Prep Kit v2.
Bulk RNA-seq

value: T cells

tag: agent

value: Yes


title: PLCO038

description: PLCO


title: XA0048126-830-1061_ACAGATCC-AGCGTACA_S47,  ED

description: Library name: XA0048126-830-1061_ACAGATCC-AGCGTACA_S47


title: XA0045867-827-1001_GTGATCCA-ACTCAACG_S13,  ED

description: Library name: XA0045867-827-1001_GTGATCCA-ACTCAACG_S13

value: Male

value: NorthEast

value: White


title: PLCO035

description: PLCO


title: PLCO036

description: PLCO


title: ID 3, 1 month milk EV

value: ID 3

value: 33 yr


title: hiHeps-1, 2D Cultured, day7

description: Library name: hiHeps-1

value: Liver

tag: cell line

value: hiHeps

value: human induced hepatocytes

value: 2D Cultured


title: ID 3, 2 month milk EV

value: 2 month


title: ID 4, transition milk EV

value: ID 4

value: 32 yr

value: transition


title: ID 4, colostrum EV

value: colostrum


title: XA0053370-827-1027_CAATGTGG-TGTCAACG_S83,  ED

description: Library name: XA0053370-827-1027_CAATGTGG-TGTCAACG_S83

value: whole blood

tag: cell type

value: mixed

value: Female


title: PLCO037

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: ID 2, 4-5 month milk EV

value: ID 2

value: 4-5 month


title: Tcells, 6_TH17

value: T cells

value: Yes


title: PLCO033

description: PLCO


title: XA0053300-826-1318_GAGCCTAT-CTCTGTAC_S82,  ED

description: Library name: XA0053300-826-1318_GAGCCTAT-CTCTGTAC_S82

value: Midwest

value: Black


title: PLCO034

description: PLCO


title: Tcells, 7_Stim+SUP

value: Stim+SUP


title: ID 3, 4-5 month milk EV

value: ID 3

value: 33 yr


title: XA0050763-846-1039_AGCAGACA-AGAGGATG_S96,  ED

description: Library name: XA0050763-846-1039_AGCAGACA-AGAGGATG_S96

value: NorthEast

value: White


title: PLCO032

description: PLCO


title: Tcells, 6_Stim+GABA

value: Stim+GABA


title: Tcells, 6_Stim

value: control

value: No


title: XA0050834-826-1120_ATTCCGCT-TGTCGACT_S101,  ED

description: Library name: XA0050834-826-1120_ATTCCGCT-TGTCGACT_S101

value: whole blood

value: mixed

value: Male


title: Tcells, 7_Stim+GABA


title: PLCO040

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: Tcells, 7_Stim

value: T cells


title: XA0045856-827-1008_ACAGCAAG-GTCTGCAA_S12,  ED

description: Library name: XA0045856-827-1008_ACAGCAAG-GTCTGCAA_S12


title: ID 2, transition milk EV

value: ID 2

value: transition


title: ID 4, 1 month milk EV

value: ID 4

value: 32 yr

value: 1 month


title: ID 3, transition milk EV

value: ID 3

value: 33 yr


title: ID 3, colostrum EV

value: colostrum


title: XA0049654-826-1117_GCCTTAAC-CCGTTATG_S74,  ED

description: Library name: XA0049654-826-1117_GCCTTAAC-CCGTTATG_S74

value: Female

value: Midwest

value: Black


title: PLCO029

description: PLCO


title: XA0050854-826-1125_TCTAGTCC-CGGTAATC_S102,  ED

description: Library name: XA0050854-826-1125_TCTAGTCC-CGGTAATC_S102

value: whole blood

value: White


title: Tcells, 6_Stim+SUP

value: Stim+SUP

value: Yes


title: XA0050882-826-1111_AGCCAACT-AGTGCATC_S103,  ED

description: Library name: XA0050882-826-1111_AGCCAACT-AGTGCATC_S103

value: mixed


title: PLCO031

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: Tcells, 5_TH17

value: T cells


title: ID 2, colostrum EV

value: ID 2


title: Tcells, 5_Stim+SUP


title: XA0049699-826-1126_CTCGACTT-GAGTGTGT_S77,  ED

description: Library name: XA0049699-826-1126_CTCGACTT-GAGTGTGT_S77


title: ID 2, 2 month milk EV

value: 2 month


title: ID 2, 1 month milk EV

value: 1 month


title: Tcells, 5_Stim+GABA

value: Stim+GABA


title: ID 1, 2 month milk EV

value: ID 1

value: 32 yr


title: PLCO030

description: PLCO


title: ID 1, 4-5 month milk EV

value: 4-5 month


title: PLCO027

description: PLCO


title: Tcells, 4_Stim+GABA


title: Tcells, 5_Stim

value: control

value: No


title: XA0054650-826-1092_ACCGGATT-TGGCATGA_S116,  ED

description: Library name: XA0054650-826-1092_ACCGGATT-TGGCATGA_S116

value: whole blood

value: Female

value: Midwest


title: PLCO026

description: PLCO


title: PLCO028

description: PLCO


title: XA0053608-826-1081_GTCAGGAA-TCTTCGGA_S91,  ED

description: Library name: XA0053608-826-1081_GTCAGGAA-TCTTCGGA_S91

value: Black


title: ID 1, 1 month milk EV


title: MDBK cells, BHV1 infection, 9hpi,  tech rep 1 & 2

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: Institute of Virology, University Medical Center Freiburg

description:
Library name: MDBK_9hpi1
Column Name counts_MDBK.tsv: MDBKBHV19h1_01_good and  MDBKBHV19h2_01_good ; Techn. replicates at library-prep level

data_processing:
mRNASeq pipeline from snakePipes 3.1.0 was used; TrimGalore was used for adapter and base quality trimming, STAR was used for the alignment.
Assembly: Hybrid genomes of host and virus: HFF: hg38 (GRCh38.p14, Release 47) & GCA_027937515.1; Ederm: TB-T2T genome (GCF_041296265.1) & GCA_000844025.1; MDBK: ARS-UCD2.0 (GCF_002263795.3) & GCA_008777455.1
Supplementary files format and content: counts files generated by featurecounts

organism: Bos taurus

extract_protocol:
Prior to RNA isolation and purification samples were thawed (frozen at -80°C) and incubated at room temperature for at least 5 min. RNA was isolated and purified following manufacturers’ instructions  (RNA clean and concentrator kit Zymo Research).
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) with 9 cycles PCR amplification

value: cell line

value: MDBK (NBL-1)

value: Bovine kidney epithelial

tag: genotype

value: WT

tag: batch


title: XA0054577-826-1093_ATACGAGC-GCCAATCA_S109,  ED

description: Library name: XA0054577-826-1093_ATACGAGC-GCCAATCA_S109

value: mixed


title: XA0048288-842-1054_AAGTCCTC-AGCTACCA_S21,  ED

description: Library name: XA0048288-842-1054_AAGTCCTC-AGCTACCA_S21

value: Male


title: Tcells, 4_Stim+SUP

value: T cells

value: Stim+SUP

value: Yes


title: ID 1, colostrum EV

value: ID 1

value: 32 yr

value: colostrum


title: PLCO025

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: XA0053666-826-1079_ACCGCAAT-GCTTCGAA_S96,  ED

description: Library name: XA0053666-826-1079_ACCGCAAT-GCTTCGAA_S96

value: whole blood

value: Female

value: White


title: ID 1, transition milk EV

value: transition


title: PLCO024

description: PLCO


title: MDBK cells, BHV1 infection, 2hpi, tech rep 1 & 2

description:
Library name: MDBK_2hpi1
Column Name counts_MDBK.tsv: MDBK2h1_01_good and MDBK2h2_01_good ; Techn. replicates at library-prep level

value: cell line

value: MDBK (NBL-1)


title: Tcells, 4_TH17


title: PLCO022

description: PLCO


title: Tcells, 3_Stim+GABA

value: Stim+GABA


title: XA0053663-826-1078_AACACCGA-CTAGGAAG_S95,  ED

description: Library name: XA0053663-826-1078_AACACCGA-CTAGGAAG_S95

value: mixed

value: Midwest


title: XA0050981-842-1200_TCGTGCAT-CTGTACCA_S77,  ED

description: Library name: XA0050981-842-1200_TCGTGCAT-CTGTACCA_S77

value: Black


title: MDBK cells, Mock,  tech rep 1 & 2

description:
Library name: MDBK_Mock1
Column Name counts_MDBK.tsv: MDBKMock1_01_good and MDBKMock2_01_good ; Techn. replicates at library-prep level

value: Bovine kidney epithelial

value: WT

value: Mock


title: XA0049653-826-1313_TGTATGGC-CTACCACT_S60,  ED

description: Library name: XA0049653-826-1313_TGTATGGC-CTACCACT_S60


title: MDBK cells, BHV1 infection, 6hpi,  tech rep 1 & 2

description:
Library name: MDBK_6hpi1
Column Name counts_MDBK.tsv: MDBKBHV16h1_01_good and MDBKBHV16h2_01_good ; Techn. replicates at library-prep level


title: PLCO021

description: PLCO


title: PLCO023

description: PLCO


title: Tcells, 4_Stim

value: T cells

value: control

value: No


title: XA0053630-826-1076_CTAATGCC-AACCAAGG_S92,  ED

description: Library name: XA0053630-826-1076_CTAATGCC-AACCAAGG_S92


title: RNA-Seq of mus musculus: adult male spleen; LNP-GS Group rep2

first: Shaolong

address: Wenyixi Road 1369

institute: liangzhu Laboratory

description:
Library name: LNP-GS2-RNA
LNP-GS2

data_processing:
After library preparation, rigorous quality control (QC) was performed, evaluating total library yield (>30 ng), fragment size distribution (main peak: 300-600 bp), large fragment contamination (900-5,000 bp fragments <20%), and residual small fragments (<300 bp fragments <20%). Libraries meeting these criteria were subjected to paired-end sequencing on the Illumina NovaSeq 6000 platform.
TCR sequences were extracted with the CeleScope AccuraCode pipeline (v1.2.0; Singleron) aligned to the mouse reference genome. To suppress CDR3 diversity introduced by sequencing error, CDR3 amino-acid sequences were collapsed if hamming_distance(low_umi_cdr3, high_umi_cdr3) == 1 and，low_count / high_count < percent, merge low to high. Reads mapping to the constant regions of TRA and TRB (≥95 % coverage, IgBLAST-n v2.20) were retained; 150 bp of 5’ soft-clipped sequence was used for clonotype calling.
Assembly: mm10
Supplementary files format and content: RNA_UMI_counts_matrix.tsv: A tab-separated values file representing the raw UMI count matrix for gene expression. Rows correspond to genes, columns correspond to samples.
Supplementary files format and content: TCR_rearrangement.csv: A comma-separated values file containing annotated T-cell receptor (TCR) rearrangement data for clonality and diversity analysis. Key columns include barcode (sample identifier), chain (TRA or TRB), v_gene, j_gene, c_gene, cdr3 (amino acid sequence), reads, and umis.

organism: Mus musculus

source_name: spleen

extract_protocol:
The cDNA library was constructed from urine-derived cellular RNA (stored at −80 °C) using the Singleron AccuraCode HTP OneStep RNA-seq Kit (Singleron, Nanjing, China), following the manufacturer’s instructions.
Raw sequencing reads were processed using Celescope (v2.0.7) with default settings to generate gene expression profiles. Briefly, barcodes and unique molecular identifiers (UMIs) were extracted from R1 reads and subjected to error correction. Adapter sequences and poly-A tails were trimmed from R2 reads using Cutadapt (v3.7). The cleaned R2 reads were then aligned to the Mus musculus GRCm38 (mm10) reference genome using STAR (v2.7.11a). Uniquely mapped reads were assigned to genes using featureCounts (v2.0.1). Finally, reads with identical barcodes, UMIs, and gene annotations were aggregated to construct the gene expression matrix for downstream analysis.

value: spleen


title: Tcells, 3_Stim+SUP

value: Stim+SUP

value: Yes


title: RNA-Seq of mus musculus: adult male spleen; LNP-GS Group rep3

description:
Library name: LNP-GS3-RNA
LNP-GS3


title: XA0050288-826-1065_ACCGAGAT-CACCACAA_S46,  ED

description: Library name: XA0050288-826-1065_ACCGAGAT-CACCACAA_S46

data_processing:
Sequencing reads aligned using the STAR(v2.7.6a) against the hg38 reference genome, with GENCODEV47 annotation file. Salmon (v1.4.0) was used to quantify aligned transcript-level expression from the aligned reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count for each sample

value: whole blood

value: Male

value: White


title: Tcells, 3_TH17


title: PLCO020

description: PLCO

value: Plasma

value: Pre-diagnostic PLCO cohort


title: PLCO018

description: PLCO


title: XA0050513-826-1064_GTCAAGTC-AAGAGGAG_S57,  ED

description: Library name: XA0050513-826-1064_GTCAAGTC-AAGAGGAG_S57

value: mixed

value: Female


title: Tcells, 2_Stim+GABA

value: Stim+GABA


title: Tcells, 3_Stim


title: RNA-Seq of mus musculus: adult male spleen; LNP-GS Group rep1

description:
Library name: LNP-GS1-RNA
LNP-GS1


title: XA0047552-826-1061_GCACTACA-GAAGCACA_S13,  ED

description: Library name: XA0047552-826-1061_GCACTACA-GAAGCACA_S13

value: Midwest


title: PLCO017

description: PLCO


title: Tcells, 2_TH17


title: PLCO019

description: PLCO


title: RNA-Seq of mus musculus: adult male spleen; LNP-G Group rep3

description:
Library name: LNP-G3-RNA
LNP-G3


title: XA0054511-873-1054_GCTACAAC-ACTGCTTG_S108,  ED

description: Library name: XA0054511-873-1054_GCTACAAC-ACTGCTTG_S108

value: NorthEast


title: PLCO016

description: PLCO


title: RNA-Seq of mus musculus: adult male spleen; LNP-G Group rep2

description:
Library name: LNP-G2-RNA
LNP-G2


title: XA0050375-826-1052_TGTTAGCG-AGACGGTT_S51,  ED

description: Library name: XA0050375-826-1052_TGTTAGCG-AGACGGTT_S51


title: PLCO014

description: PLCO


title: Tcells, 1_Stim+GABA


title: Tcells, 2_Stim


title: XA0050102-842-1159_CTCGACTT-GAGTGTGT_S42,  ED

description: Library name: XA0050102-842-1159_CTCGACTT-GAGTGTGT_S42


title: Tcells, 1_Stim+SUP


title: PLCO013

description: PLCO


title: Tcells, 2_Stim+SUP


title: PLCO015

description: PLCO


title: RNA-Seq of mus musculus: adult male spleen; PBS Group rep1

description:
Library name: PBS1-RNA
PBS1


title: RNA-Seq of mus musculus: adult male spleen; PBS Group rep3

description:
Library name: PBS3-RNA
PBS3


title: XA0048655-826-1034_AACCGAAC-CATACTCG_S63,  ED

description: Library name: XA0048655-826-1034_AACCGAAC-CATACTCG_S63

value: Black


title: XA0048599-826-1033_CTAAGACC-CCTAACAG_S57,  ED

description: Library name: XA0048599-826-1033_CTAAGACC-CCTAACAG_S57


title: PLCO010

description: PLCO


title: PLCO011

description: PLCO


title: XA0050238-873-1002_CACAGTCA-TCAACGCT_S43,  ED

description: Library name: XA0050238-873-1002_CACAGTCA-TCAACGCT_S43


title: Tcells, 1_TH17

value: T cells


title: PLCO012

description: PLCO


title: CD8+ cells, C57BL/6J mice, Hmgb2fl/fl;Cd4-Cre-3, Day5

city: SHANGHAI

first: WEIFENG

last: QU

address: No.180 Fenglin Road

institute: Zhongshan Hospital, Fudan university

description: Library name: CKO-3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq6000 platform and 150 bp paired-end reads were generated
Assembly: STAR is used to align clean reads to reference genome
Supplementary files format and content: CSV file including reads count for each sample

source_name: splenic CD8+ T cells

extract_protocol:
Total RNA was extracted by the trizol protocol
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: splenic CD8+ T cells


title: CD8+ cells, C57BL/6J mice, Hmgb2fl/fl;Cd4-Cre-2, Day5

description: Library name: CKO-2


title: XA0047578-826-1056_CAATGTGG-TGTCAACG_S14,  ED

description: Library name: XA0047578-826-1056_CAATGTGG-TGTCAACG_S14

extract_protocol:
Blood samples were collected at the time of enrollment using PAXgene RNA tubes. Total RNA was isolated using the PAXgene blood miRNA kit (QIAGEN) and RNA was stored at −80˚C until use. RNA concentration and purity were measured using a NanoDrop One (Nanodrop Technologies, Wilmington, DE), and RNA integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Template libraries for total RNA sequencing were produced from 600 ng total RNA using Ovation Human Blood RNA-Seq Library Systems kit (NuGen, San Carlos, CA) according to manufacturer's specifications. Libraries were multiplexed in groups of six and sequenced on a HiSeq 4000 (Illumnia) at the University of North Carolina at Chapel Hill High Throughput Sequencing Facility.


title: PLCO009

description: PLCO


title: 6_Stim

data_processing:
Kallisto pseudoalignment and bias correction was used for fragment alignment to the human cDNA database (GRCh38)
Assembly: GRCh38
Supplementary files format and content: CD14_rawcount.txt

value: No


title: 6_Stim+Sup


title: XA0050258-873-1005_GAAGGATC-AGGCTCTT_S45,  ED

description: Library name: XA0050258-873-1005_GAAGGATC-AGGCTCTT_S45


title: XA0046126-826-1025_TCTAGGAG-TTGCAACG_S31,  ED

description: Library name: XA0046126-826-1025_TCTAGGAG-TTGCAACG_S31


title: Tcells, 1_Stim

value: control


title: PLCO008

description: PLCO


title: 5_Stim


title: CD8+ cells, C57BL/6J mice, Control-2, Day5

description: Library name: NC-2


title: XA0046117-826-1021_ATCGTCTC-AGAAGGAC_S30,  ED

description: Library name: XA0046117-826-1021_ATCGTCTC-AGAAGGAC_S30


title: CD8+ cells, C57BL/6J mice, Control-3, Day5

description: Library name: NC-3


title: CD8+ cells, C57BL/6J mice, Control-1, Day5

description: Library name: NC-1


title: RNA-Seq of mus musculus: adult male spleen; LNP-G Group rep1

description:
Library name: LNP-G1-RNA
LNP-G1

value: spleen


title: PLCO007

description: PLCO


title: 5_Stim+Sup

value: Yes


title: CD8+ cells, C57BL/6J mice, Hmgb2fl/fl;Cd4-Cre-1, Day5

description: Library name: CKO-1


title: PLCO005

description: PLCO


title: XA0049714-842-1162_GTACCACA-GCGCATAT_S34,  ED

description: Library name: XA0049714-842-1162_GTACCACA-GCGCATAT_S34

value: whole blood


title: PLCO006

description: PLCO


title: CL_HGS2_1

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

description:
Library name: sample37
CL_HGS2_1

data_processing:
RNA-Seq reads were quality trimmed using trimgalore  v0.6.5 and were mapped to the mouse genome ( mm10, Genome Reference Consortium GRCm38)  using using STAR 2.7.0f
Number of reads aligned to the exonic region of each gene were counted using rsem based on the Ensembl annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain rsem counts for each sample

growth_protocol: HGS2 and 60577 described previously 13 were cultured in complete DMEM:F12 1:1 with GlutaMax medium (Gibco) with the addition of 4% heat inactivated FBS (Hyclone, Gibco), 1x Pen/Strep (Invitrogen), 1x insulin/transferrin/selenium (Invitrogen, 51300), 100 ng/ml hydrocortisone (Sigma, H0135), 20 ng/ml murine Epidermal Growth Factor (EGF, Sigma, E4127), 1x antibiotic-antimycotic (Gibco)

extract_protocol:
Total RNA was extracted from frozen murine tumors or cell lines. The tumor samples were transferred into RNAlater and homogenized with Miltenyi GentleMACS in RLT buffer. Tumour samples and cell lines were further processed using Qiagen RNeasy Mini kit with on-column DNAse digestion.
RNA-Seq. Library preparation and RNASeq were performed by the Wellcome Trust Oxford Genomics Centre (Oxford, UK) using RiboZero to deplete rRNA species.

value: cell line


title: XA0049750-842-1196_TCCTGGTA-CAGATCCT_S35,  ED

description: Library name: XA0049750-842-1196_TCCTGGTA-CAGATCCT_S35

value: Male


title: RNA-Seq of mus musculus: adult male spleen; PBS Group rep2

description:
Library name: PBS2-RNA
PBS2


title: 4_Stim+Sup

description: Raw file is loaded up to the point of corruption.


title: PLCO003

description: PLCO

data_processing:
Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.
Assembly: The miRNA probe list is based on miRBase version 20.
Supplementary files format and content: Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.

value: Plasma


title: 3_Stim


title: XA0046092-826-1024_CCAACACT-GACGAACT_S25,  ED

description: Library name: XA0046092-826-1024_CCAACACT-GACGAACT_S25

value: White


title: 4_Stim


title: PLCO004

description: PLCO

value: Pre-diagnostic PLCO cohort


title: 3_Stim+Sup


title: XA0046093-826-1013_CGACCTAA-CTAACCTG_S26,  ED

description: Library name: XA0046093-826-1013_CGACCTAA-CTAACCTG_S26

value: mixed


title: PLCO002

description: PLCO


title: spleen CD8+ T cells, DHEA

city: haidian district

first: yao

last: feng

state: Beijing

address: No.38 xueyuan road

institute: Peking University

description:
Library name: DHEA
10x Genomics

data_processing:
The Cell ranger software pipeline (version 8.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen CD8+ T cells

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: For the DHEA induced PCOS model, mice received daily subcutaneous injections of dehydroepiandrosterone (DHEA; 40mg/kg) dissolved in sesame oil (20µL) for 21 consecutive days. Control mice received an equal volume of sesame oil via subcutaneous injection on the same schedule. At the end of the treatment, spleens were collected into pre-cold staining buffer (PBS supplemented with [1–2%] FBS or [0.04%] BSA) and passed through a 70-µm cell strainer. Following red blood cell lysis (ACK buffer, 10 min at room temperature), CD8+ T cells were isolated by magnetic beads.

value: spleen CD8+ T cells

value: WT


title: CL_60577_2

description:
Library name: sample36
CL_60577_2

value: FVB


title: CL_HGS2_2

description:
Library name: sample38
CL_HGS2_2


title: XA0054055-842-1285_CGCAACTA-CATTGACG_S98,  ED

first: Sarah

description: Library name: XA0054055-842-1285_CGCAACTA-CATTGACG_S98

value: Female

value: Midwest


title: XA0054176-825-1088_CGAACAAC-TCGATGAC_S117,  ED

description: Library name: XA0054176-825-1088_CGAACAAC-TCGATGAC_S117

value: Black


title: PDAC121

description: PDAC

extract_protocol:
15 uL of plasma was profiled for miRNAs by the extraction-free method using the HTG edge miRNA whole transcriptome assay kit (HTG Molecular, Tuscon, AZ, Cat# 916-001-024) according to the recommended vendor’s protocol.
Probes hybrized to target miRNAs were retrieved and added sequencing adapters as well as sample barcodes via PCR for preparing library. The libraries were quantified by quantitative PCR (qPCR) using KAPA Library Quantification kit (Roche, Cat# KK4824) and loaded onto the MiSeq (Illumina) together with the MiSeq Reagent Kit v3 (150 cycles) (Illumina, Cat# MS-102-3001).

value: Diagnostic cohort

value: PDAC


title: spleen CD8+ T cells, CTRL

description:
Library name: CTRL
10x Genomics


title: 2_Stim+Sup

value: T cells


title: XA0047856-842-1131_CATTCGTC-TTGGTGCA_S18,  ED

description: Library name: XA0047856-842-1131_CATTCGTC-TTGGTGCA_S18


title: PLCO001

description: PLCO


title: CL_60577_1

description:
Library name: sample35
CL_60577_1


title: XA0047835-842-1081_AGGTTCCT-TCGAACCT_S17,  ED

description: Library name: XA0047835-842-1081_AGGTTCCT-TCGAACCT_S17


title: XA0053411-825-1084_TAGGAGCT-CTAGCAGT_S108,  ED

description: Library name: XA0053411-825-1084_TAGGAGCT-CTAGCAGT_S108


title: 1_Stim

value: No


title: 2_Stim


title: PDAC120

description: PDAC


title: 1_Stim+Sup

value: Yes


title: PDAC118

description: PDAC


title: Melittin2

city: Shanghai

first: Rucheng

last: Yan

address: 1800,yuntai road

institute: Shanghai East Hospital

description: Library name: Melittin2

data_processing:
Samples are sequenced on the platform to getimage files, which are transformed by thesoftware of the sequencing platform, and theoriginal data in FASTQ format(Raw Data) isgenerated. Sequencing data contains a numberof connectors, low-quality Reads, so we usefastp(0.22.0) software to filter the sequencingdata to get high quality sequence (Clean Data)for further analysis.
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: CSV file including Reads count for each sample.
Supplementary files format and content: CSV file including FPKM for each sample.

extract_protocol:
Total RNA was extracted by the chloroformmethod.
RNA-seq library was cunstructed by usingNEBNext Ultra ll RNA Library Prep Kit forIllumina.

value: Human-derived acute monocytic leukemia cell line


title: 338-DRUG_S17_L001_R1_001, Experiment_9_β-cateninagonist_administration

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

description: Library name: 338-DRUG_Sample16

data_processing:
Data processing and analysis were performed using R (version 4.5.1) with the RStudio interface (version 2025.05.1+513) and Bioconductor packages. Transcript abundance was quantified by pseudoalignment with Kallisto (version v0.51.1) Transcript-per-million (TPM) values were normalized for each sample simultaneously and fitted to a linear model using the sleuth R package. Differentially expressed genes (DEGs) were defined as those exhibiting a log2fold change ≥ |.5| with a false discovery rate (FDR) ≤ 5%, after multiple testing correction using the Benjamini–Hochberg method. This data was used for hierarchical clustering and heatmap generation in R. For pathway analysis, Gene Ontology (GO) enrichment was assessed with the gprofiler2 R package using the gost function. Gene Set Enrichment Analysis (GSEA) was performed with the clusterProfiler R package, and the Molecular Signatures Database (MSigDB) , focusing on the Hallmark pathways collection.
Assembly: GRCm39
Supplementary files format and content: Tab-seperated values (.tsv) files containing transcript id, transcript length, effective length, estimated counts, and tpm values.

source_name: lung

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy Mini kit. RNA quality and quantity were assessed with the Agilent 2100 Bioanalyzer.
cDNA was prepared with the Bio-Rad SEQuoia library prep kit, using 1ng total RNA.

value: lung


title: XA0049961-825-1070_AGAACCAG-GCAACCAT_S78,  ED

city: Chapel Hill

last: Linnstaedt

address: 109 Mason Farm Road

institute: University of North Carolina at Chapel Hill

description: Library name: XA0049961-825-1070_AGAACCAG-GCAACCAT_S78

value: whole blood

value: Male


title: 336-DRUG_S15_L001_R1_001, Experiment_7_β-cateninagonist_administration

description: Library name: 336-DRUG_Sample14


title: PDAC117

first: Warapen

address: 2130 W. Holcombe Blvd.,  Unit 2951

institute: UT MD Anderson Cancer Center

description: PDAC

value: Plasma


title: XA0050993-842-1199_ACTGCACT-AGATCGTC_S80,  ED

description: Library name: XA0050993-842-1199_ACTGCACT-AGATCGTC_S80

value: mixed


title: PDAC119

description: PDAC


title: Melittin1

description: Library name: Melittin1


title: 337-DRUG_S16_L001_R1_001, Experiment_8_β-cateninagonist_administration

description: Library name: 337-DRUG_Sample15


title: NC2

description: Library name: NC2


title: XA0047522-825-1069_CAGGTTCA-AACGTAGC_S45,  ED

description: Library name: XA0047522-825-1069_CAGGTTCA-AACGTAGC_S45


title: Melittin3

description: Library name: Melittin3


title: PDAC116

description: PDAC


title: XA0047296-842-1004_CCGGAATA-TCAGTAGG_S10,  ED

description: Library name: XA0047296-842-1004_CCGGAATA-TCAGTAGG_S10


title: XA0045890-842-1015_GACTACGA-TTACCGAC_S1,  ED

description: Library name: XA0045890-842-1015_GACTACGA-TTACCGAC_S1

value: White


title: PDAC115

description: PDAC


title: 328-VEHICLE_S19_L001_R1_001, Control_7

description: Library name: 328-VEHICLE_sample11

value: WT

value: Pristane Challenge, DMSOadministration


title: 330-VEHICLE_S21_L001_R1_001, Control_8

description: Library name: 330-VEHICLE_Sample12


title: XA0045905-842-1028_CAAGCCAA-GAACGAAG_S3,  ED

description: Library name: XA0045905-842-1028_CAAGCCAA-GAACGAAG_S3


title: PDAC114

description: PDAC


title: XA0048003-825-1055_CATACGGA-AACACCAC_S49,  ED

description: Library name: XA0048003-825-1055_CATACGGA-AACACCAC_S49

value: Female


title: mESC_Mettl3cKO_4OHT_m6A

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St., GCIS E319

institute: The University of Chicago

description: Library name: mESC_Mettl3cKO_4OHT_m6A

data_processing:
The FASTQ file was trimmed using Cutadapt (v4.6) and aligned to ribosomal RNA (rRNA) sequences with Bowtie2 (v2.4.2) to filter out rRNA reads. The remaining non-rRNA reads were aligned to the reference genome using STAR (v2.7.3a), and PCR duplicates were removed with UMI-tools (v1.1.1).
Assembly: GRCh38.p13, GENCODE Release 39; GRCm38.p6, GENCODE Release M25
Supplementary files format and content: bigWig files

source_name: Embryonic stem cell

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and  100 U/mL penicillin-streptomycin (Gibco). Mouse embryonic stem cells were cultured in DMEM (Invitrogen) supplemented with 20% FBS (GeminiBio), 1 mmol/L L-glutamine (Gibco), 1% nonessential amino acid (Gibco), 100 U/mL penicillin-streptomycin (Gibco), 1,000 U/mL leukemia inhibitory factor (LIF, Millipore), 0.1 mmol/L 2-mercaptoethanol (Sigma), 3 μmol/L CHIR99021 (Stemcell), 1 μmol/L PD0325901 (Stemcell), and 1% EmbryoMax nucleosides (100×, Millipore). All cell lines were cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1.5% paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 minutes, and permeabilized with 0.5% Triton X-100 on ice for 10 minutes. Samples were then blocked with 1 mg/ml BSA, followed by sequential staining with a primary antibody, a secondary antibody, and protein A/G-reverse transcriptase. In situ reverse transcription was performed at 37°C for 1 h. Subsequently, cells were digested with proteinase K at 37°C for 2 h. Total nucleic acids were extracted using phenol-chloroform and concentrated by ethanol precipitation.
Biotinylated cDNA was enriched using streptavidin beads. A 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated using T4 RNA ligase 1 by incubating at 25°C for 16 h. The cDNA was then recovered from the beads. The library was prepared through PCR amplification using NGS sequencing primers, followed by gel purification to isolate fragments between 180 bp and 400 bp.

value: Embryonic stem cell

value: Mettl3 CKO

value: 4-Hydroxytamoxifen treatment

tag: antibody

value: m6A antibody (CST,Cat #56593)


title: 335-DRUG_S14_L001_R1_001, Experiment_6_β-cateninagonist_administration

description: Library name: 335-DRUG_Sample13


title: XA0046363-842-1009_ATGACAGG-ACATGCCA_S5,  ED

description: Library name: XA0046363-842-1009_ATGACAGG-ACATGCCA_S5

value: Midwest

value: Black


title: 307-CATTG_S4_L001_R1_001, Experiment_4_β-catenin_Stabilization

description: Library name: 307-CATTG_Sample8

value: Pristane Challenge


title: NC3

description: Library name: NC3

value: Human-derived acute monocytic leukemia cell line


title: PDAC111

city: Houston

last: Treekitkarnmongkol

description: PDAC

value: Diagnostic cohort

value: PDAC


title: PDAC112

description: PDAC


title: NC1

description: Library name: NC1


title: PDAC113

description: PDAC


title: XA0045896-842-1005_AACTTGCC-CCAACTTC_S2,  ED

description: Library name: XA0045896-842-1005_AACTTGCC-CCAACTTC_S2

value: whole blood


title: 326-VEHICLE_S18_L001_R1_001, Control_6

description: Library name: 326-VEHICLE_Sample10

value: lung


title: mESC_Mettl3cKO_Ctrl_noAb

description: Library name: mESC_Mettl3cKO_Ctrl_noAb


title: 309-CATTG_S5_L001_R1_001, Experiment_5_β-catenin_Stabilization

description: Library name: 309-CATTG_sample9


title: 306-CATTG_S3_L001_R1_001, Experiment_3_β-catenin_Stabilization

description: Library name: 306-CATTG_Sample7


title: mESC_Mettl3cKO_4OHT_noAb

description: Library name: mESC_Mettl3cKO_4OHT_noAb


title: MouseEmbryo_E11_50um_pixel_adjacent_mRNA

description: Library name: MouseEmbryo_E11_50um_pixel_mRNA

data_processing:
The FASTQ file was initially filtered to remove reads lacking proper adapter ligation, followed by the extraction of unique molecular identifiers (UMIs) and spatial barcodes. Read 1, containing cDNA sequences, was trimmed using Cutadapt (v4.6) and aligned to the ribosome RNA (rRNA) with Bowtie2 (v2.4.2) to isolate non-rRNA reads. These non-rRNA reads were then aligned to the reference genome using STAR (v2.7.3a). PCR duplicates were removed using UMI-tools (v1.1.1), and the data was demultiplexed based on spatial barcodes to generate the gene-by-pixel expression matrix for downstream analysis. Pixel positions lacking tissue coverage were excluded.
Assembly: GRCm38.p6, GENCODE Release M25
Supplementary files format and content: Seurat RDS object
Supplementary files format and content: bigWig files
Library strategy: Spatial Transcriptomics

source_name: Embryo E11

extract_protocol:
The barcoded tissue ROI was enclosed with a clean PDMS reservoir and clamped using acrylic chips. A 2X lysis buffer (20 mM Tris-HCl pH 8.0, 400 mM NaCl, 100 mM EDTA, 4.4% SDS) was prepared. For tissue digestion, 70 μL of lysis mix (30 μL 1X DPBS, 30 μL 2X lysis buffer, 10 μL Proteinase K at 20 μg/μL) was added to the PDMS reservoir, sealed with parafilm, and incubated at 55°C for 2 h. After incubation, the liquid containing cDNA was collected, and 40 μL of fresh lysis mix was added to recover any remaining cDNA. The tissue lysate was incubated overnight at 55°C to reverse crosslinks. Nucleic acids were then extracted by phenol-chloroform (pH 8.0), ethanol-precipitated, and dissolved in 20 μL of water.
Biotinylated cDNA was enriched with streptavidin beads. A 3' cDNA adapter was ligated using T4 RNA ligase 1, with incubation at 25°C for 16 h. The cDNA was subsequently recovered from the beads. Libraries were prepared via PCR amplification using NGS sequencing primers. The amplified libraries were size-selected to a range of 280–500 bp using a 6% Novex TBE gel.

value: Embryo E11

tag: strain

value: C57BL/6 mice

value: DBiT-seq protocol


title: PDAC109

description: PDAC

tag: tissue

value: Plasma


title: 305-CATTG_S2_L001_R1_001, Experiment_2_β-catenin_Stabilization

description: Library name: 305-CATTG_Sample6


title: PDAC108

description: PDAC


title: mESC_Mettl3cKO_Ctrl_m6A

description: Library name: mESC_Mettl3cKO_Ctrl_m6A


title: XA0048956-842-1034_CGACCTAA-CTAACCTG_S28,  ED

description: Library name: XA0048956-842-1034_CGACCTAA-CTAACCTG_S28

value: mixed

tag: Sex

value: Female


title: 289-CATTG_S1_L001_R1_001, Experiment_1_β-catenin_Stabilization

description: Library name: 289-CATTG_Sample5


title: PDAC110

description: PDAC


title: CUT&Tag-seq(JUN), GFP+ AT2 cells,CKO mice-2

city: Tianjin

first: yujun

last: shen

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

description: Library name: CKO-JUN-2

data_processing:
We assessed the quality of the targeted DNA libraries using an Agilent Bioanalyzer high-sensitivity DNA assay. The final CUT & Tag libraries were sequenced using an Illumina NovaSeq 6000 platform. Clean reads were aligned to the mouse reference genome assembly GRCm38 (mm10), and only uniquely mapped reads were retained for analysis. JUN binding peaks were identified using MACS2, excluding the ENCODE blacklist regions during peak filtering. Genomic annotations of the called peaks were generated using Homer with default parameters . Signal profiles of CUT&Tag were used to generate metaplots using the computeMatrix and plotProfile functions in deepTools.
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Lung

extract_protocol:
GFP+ AT2 cells were sorted by flow cytometry from bleomycin-treated(8 days post-injury)  SftpcCreERT2; Rosa26mTmG(Control) or SftpcCreERT2; Rosa26mTmG; IPF/F(CKO) mice. the cells were mixed with 10 μL of ConA beads and incubated at room temperature for 10 min. The samples were then incubated with JUN primary antibody (#9165T;  Cell Signaling Technology) at 4 °C for 1 h, followed by incubation with goat anti-rabbit IgGat room temperature for 1 h. After incubation with the antibody, the samples were mixed with pAG-Tn5 transposomes and subjected to tagmentation for DNA extraction.
CUT&Tag -seq libraries were prepared using the  using the CUT&Tag Assay Kit (#RK20265, Abclonal) .

value: Lung

value: Alveolar type 2 (AT2) epithelial cells

value: SftpcCreERT2; Rosa26mTmG; IPF/F(CKO)

value: Bleomycin lung injury

value: JUN primary antibody (#9165T, Cell Signaling Technology)


title: PDAC106

description: PDAC


title: 415-WT_S13_L001_R1_001, Control_4

description: Library name: 415-WT_Sample4

value: WT

value: Pristane Challenge


title: CUT&Tag-seq(JUN), GFP+ AT2 cells,CKO mice-1

description: Library name: CKO-JUN-1


title: 408-WT_S12_L001_R1_001, Control_3

description: Library name: 408-WT_Sample3


title: XA0048775-825-1024_TCTTCGAC-TACTGCTC_S66,  ED

description: Library name: XA0048775-825-1024_TCTTCGAC-TACTGCTC_S66

source_name: Whole Blood

value: Male

tag: age

value: Midwest

value: Black


title: XA0044969-825-1011_ATGACAGG-ACATGCCA_S4,  ED

description: Library name: XA0044969-825-1011_ATGACAGG-ACATGCCA_S4

value: whole blood


title: PDAC107

description: PDAC

tag: cohort

value: Diagnostic cohort

value: PDAC


title: CUT&Tag-seq(input), GFP+ AT2 cells,CKO mice

description: Library name: CKO-input

value: IgG (#2729S, Cell Signaling Technology)


title: XA0045924-842-1026_AACCGAAC-CATACTCG_S4,  ED

description: Library name: XA0045924-842-1026_AACCGAAC-CATACTCG_S4


title: XA0047490-842-1043_GCACACAA-GAGCAATC_S12,  ED

description: Library name: XA0047490-842-1043_GCACACAA-GAGCAATC_S12


title: CUT&Tag-seq(input), GFP+ AT2 cells,Control mice

description: Library name: Control-input

value: SftpcCreERT2; Rosa26mTmG(Control)


title: PDAC104

description: PDAC

value: Plasma

tag: disease


title: PDAC105

description: PDAC


title: 325-WT_S11_L001_R1_001, Control_2

description: Library name: 325-WT_Sample2

value: lung


title: CUT&Tag-seq(JUN), GFP+ AT2 cells,Control mice-2

description: Library name: Control-JUN-2

value: Lung


title: 324-WT_S10_L001_R1_001, Control_1

description: Library name: 324-WT_Sample1


title: XA0050750-842-1330_TCCAACTG-TGTGTCAG_S69,  ED

description: Library name: XA0050750-842-1330_TCCAACTG-TGTGTCAG_S69

value: mixed

value: Female

tag: monocytes


title: XA0055021-824-1066_TCCATTGC-AGGTAGGA_S131,  ED

description: Library name: XA0055021-824-1066_TCCATTGC-AGGTAGGA_S131

value: NorthEast


title: CUT&Tag-seq(JUN), GFP+ AT2 cells,Control mice-1

description: Library name: Control-JUN-1

value: Alveolar type 2 (AT2) epithelial cells

tag: treatment

value: Bleomycin lung injury

value: JUN primary antibody (#9165T, Cell Signaling Technology)


title: Multiome-seq, GFP+ AT2 cells,CKO mice, bleomycin lung injury, ATAC

description:
Library name: Multiome-seq-snATAC-2
10x Genomics

data_processing:
Raw data were convert raw BCL files to FASTQ files, alignment, aligned to the GRCm39 mouse reference genome, cell calling and counts quantification using Cell Ranger ARC software (v2.0.1). The cell by gene matrices and cell by peak matrices for each sample were individually imported to Seurat(v4.1.0) and Signac (v1.6.0) for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: Control-BLM_barcodes.tsv.gz, Control-BLM_features.tsv.gz, Control-BLM_matrix.mtx.gz, CKO-BLM_barcodes.tsv.gz, CKO-BLM_features.tsv.gz, CKO-BLM_matrix.mtx.gz

extract_protocol:
GFP+ AT2 cells were sorted by flow cytometry from bleomycin-treated(8 days post-injury)  SftpcCreERT2; Rosa26mTmG(Control) or SftpcCreERT2; Rosa26mTmG; IPF/F(CKO) mice.After sorting, nuclei were isolated from the sorted cells as follows: Cells were centrifuged at 500 × g for 5 min at 4 °C, and the supernatant was carefully removed. The cell pellets were resuspended in 1 ml chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl₂, 0.1% Nonidet P40 Substitute, 1% BSA, 0.2 U/µl RNase inhibitor) and incubated on ice for 5 min to induce cell lysis. Subsequently, the lysed cell suspension was washed three times with 1 ml chilled Wash Buffer each time to remove cytoplasmic contaminants.Nuclei permeabilization was carried out following the demonstrated protocol for single-cell multiome ATAC + Gene Expression sequencing from 10× Genomics, after which the estimated nuclei from each sample were used for the transposition step and subsequently loaded on the Chromium Next GEM Single Cell Chip J.
ATAC library and gene expression library construction was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit according to the manufacturer’s instructions(CG000338 Rev A).

value: SftpcCreERT2; Rosa26mTmG; IPF/F(CKO)

value: male


title: MouseEmbryo_E11_bulk_m6A

description: Library name: MouseEmbryo_E11_bulk_m6A

data_processing:
The FASTQ file was initially filtered to remove reads lacking proper adapter ligation, followed by the extraction of unique molecular identifiers (UMIs) and spatial barcodes. Read 1, containing cDNA sequences, was trimmed using Cutadapt (v4.6) and aligned to the ribosome RNA (rRNA) with Bowtie2 (v2.4.2) to isolate non-rRNA reads. These non-rRNA reads were then aligned to the reference genome using STAR (v2.7.3a). PCR duplicates were removed using UMI-tools (v1.1.1), and the data was demultiplexed based on spatial barcodes to generate the gene-by-pixel expression matrix for downstream analysis. Pixel positions lacking tissue coverage were excluded.
Assembly: GRCm38.p6, GENCODE Release M25
Supplementary files format and content: Seurat RDS object
Supplementary files format and content: bigWig files

value: Embryo E11

value: WT

value: C57BL/6 mice

value: m6A-ARTR-DBiT protocol

value: m6A antibody (CST,Cat #56593)


title: PDAC102

description: PDAC

value: Diagnostic cohort

value: PDAC


title: PDAC103

description: PDAC

value: Plasma


title: XA0055427-842-1326_CCTGTCAA-AGGTCTGT_S133,  ED

description: Library name: XA0055427-842-1326_CCTGTCAA-AGGTCTGT_S133

value: whole blood

value: Midwest

value: White


title: XA0049637-824-1053_CTTCCTTC-TTCCAGGT_S31,  ED

description: Library name: XA0049637-824-1053_CTTCCTTC-TTCCAGGT_S31

value: mixed

value: Male

value: NorthEast

value: Black


title: Multiome-seq, GFP+ AT2 cells,Control mice,bleomycin lung injury, ATAC

description:
Library name: Multiome-seq-snATAC-1
10x Genomics

value: Lung

value: Alveolar type 2 (AT2) epithelial cells

value: SftpcCreERT2; Rosa26mTmG(Control)

value: Bleomycin lung injury


title: MouseEmbryo_E11_bulk_noAb

description: Library name: MouseEmbryo_E11_bulk_noAb

value: Embryo E11

value: WT

value: C57BL/6 mice


title: MouseBrain_20um_pixel

description: Library name: MouseBrain_20um_pixel

source_name: Brain

value: Brain

value: m6A-ARTR-DBiT protocol

value: m6A antibody (CST,Cat #56593)


title: XA0049659-824-1048_AACTCGGA-TGCAAGAC_S32,  ED

description: Library name: XA0049659-824-1048_AACTCGGA-TGCAAGAC_S32

value: whole blood

value: Female


title: Multiome-seq, GFP+ AT2 cells,Control mice,bleomycin lung injury, GEX

description:
Library name: Multiome-seq-snRNA-1
10x Genomics

molecule: nuclear RNA

value: male


title: Multiome-seq, GFP+ AT2 cells,CKO mice, bleomycin lung injury, GEX

description:
Library name: Multiome-seq-snRNA-2
10x Genomics

value: SftpcCreERT2; Rosa26mTmG; IPF/F(CKO)


title: PDAC101

description: PDAC

value: Plasma

value: Diagnostic cohort

value: PDAC


title: XA0053566-842-1304_GTCTCATC-CGGATCAA_S84,  ED

description: Library name: XA0053566-842-1304_GTCTCATC-CGGATCAA_S84

value: mixed

value: Male

value: Midwest

value: White


title: XA0050708-842-1325_TGCGTAAC-CGTCTTCA_S66,  ED

description: Library name: XA0050708-842-1325_TGCGTAAC-CGTCTTCA_S66

value: Black


title: MouseBrain_50um_pixel_rep1

description: Library name: MouseBrain_50um_pixel_rep1

value: WT


title: PDAC100

description: PDAC


title: XA0047194-824-1044_ACGCTTCT-CCTAAGTC_S7,  ED

description: Library name: XA0047194-824-1044_ACGCTTCT-CCTAAGTC_S7

value: NorthEast


title: PDAC097

description: PDAC


title: MouseEmbryo_E11_50um_pixel_rep2

description: Library name: MouseEmbryo_E11_50um_pixel_rep2

value: Embryo E11

value: C57BL/6 mice