title: Mk cells-1 (PAO2)

city: Chongqing,China

first: Hongli

last: Zhou

state: --- Select One ---

address: No. 83 Xinqiao Main Street, Shapingba District, Chongqing, China

institute: The Second Affiliated Hospital of the Army Medical University

description: Library name: Sampel 4

data_processing:
The indexed samples were clustered on a cBot cluster generation system.
After clustering, the library was sequenced on the Illumina Novaseq6000 platform, generating 150 bp paired-end reads.
Differentially expressed genes were identified using DESeq2 (v1.34.0).
Genes with FDR ≤ 0.05 and log2(Fold Change) ≥ 1 were defined as differentially expressed and selected for further investigation.
Significantly enriched GO terms were identified using an FDR threshold of ≤ 0.05.
Assembly: GRCm38
Supplementary files format and content: txt file includes raw counts and FPKM values for each group

source_name: Lung

extract_protocol:
Total RNA was extracted following standard procedures, and RNA concentration was measured simultaneously using Qubit 3.0 (Thermo Fisher Scientific, MA, USA) and Nanodrop One (Thermo Fisher Scientific, MA, USA).
mRNA sequencing libraries were constructed using the NEB Next® Ultra™ Directional RNA Library Prep Kit (New England Biolabs, MA, USA), following the manufacturer's protocol.

value: Lung

value: Megakaryocytes

value: PAO1 infection


title: Subject_N, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28

status: Public on May 13 2025

type: SRA

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

country: USA

institute: The Emmes Company

library_source: transcriptomic

data_processing:
Gene expression quantification was conducted on the gene level using the function featureCounts within the Subread v1.4.6 software counting mapped paired-reads to obtain fragment counts per gene. Fragments that overlapped with multiple genes or had multiple mapping locations on the reference genome were excluded.
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample
Assembly: Paired-end reads were mapped against the human reference genome (GRCh38) using TopHat2 (Version 2.1.1). Human gene models and annotations were obtained from ENSEMBL v84, (March 2016).

molecule: total RNA

organism: Homo sapiens

source_name: breast milk lymphocyte (BML)

extract_protocol:
Mononuclear cells from fresh breast milk and whole blood and extract total RNA from fresh mononuclear cells were extracted using Trizol ® (Invitrogen, Life Technologies Corporation) according to the manufacturer’s instructions
The integrity of all RNA samples was checked using an Agilent 2100 Bioanalyzer. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit.

tag: tissue

value: breast milk lymphocyte (BML)

tag: treatment

tag: day


title: Subject_N, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: Mk cells-1 (PAO1)

country: China

description: Library name: Sampel 3

organism: Mus musculus

tag: cell type

tag: genotype

value: WT


title: Subject_N, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day8


title: 31_empty_ctrl_H3K27me3_Rep2

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Library name: Sample 4
empty_ctrl_H3K27me3_Rep2

library_source: genomic

data_processing:
Reads were trimmed with cutadapt (v4.6).
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.4.5).
Multimapping reads and PCR duplicates were removed with Picard (v2.2) and Samtools (v1.10).
Coverage signal tracks (bigWigs) of alignments were generated using DeepTools (v3.5.1).
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Anopheles gambiae

growth_protocol: Ag55 cells were cultured in Leibovitz L15 media with 10% FBS (Gibco, 10270-10,6 Lot: 2260092) and 1x penicillin-streptomycin (Gibco, 15140122) at 27°C at 80% humidity.

extract_protocol:
The experiment was performed following the native protocol dx.doi.org/10.17504/protocols.io.bcuhiwt6. Antibodies are listed with the respective samples. We used pA-Tn5 prepared by the IMB protein production core facilty.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing. The pool was sequenced on a NextSeq 2000 P3 (200 cycles) flowcell for 2x111 cycles plus 2x8 cycles for the index reads.

treatment_protocol: 1.5 Mio. Ag55 cells were seeded in a 60 mm plate. After 48 hours, 300 μl of an empty baculovirus in Sf-900 media was added to the cells. After 6 hours the media was changed to fresh. Cells were collected for further processing 48h from the addition of the baculovirus and sorted for GFP-positive (infected) cells only. 50 000 nuclei per reaction were isolated and cryopreserved for further processing.

tag: cell line

tag: antibody

value: H3K27me3 (Active Motif, 39055)

tag: baculovirus

value: HA-tagged empty control


title: P023, PBMC, After 12 months of treatment, scRNAseq

city: Besançon

first: Olivier

last: Adotévi

state: Franche-Comté

address: 8 rue du Dr JFX Girod

department: Oncology

country: France

institute: Université de Franche-Comté

description:
Library name: P023_PBMC_FT
10x Genomics Chromium Single Cell 3'

library_source: transcriptomic single cell

data_processing:
The raw data files were demultiplexed into FASTQ file by cellranger mkfastq. v.7.1.0. Then reads were aligned against GRCh38 human reference genome 2020-A provided by 10x Genomics based on GENCODE v32/Ensembl98
Using the Read10X function of the Seurat v.4.9.9 package of R v.4.2.2, we loaded expression data from the cellranger count pipeline into R and then created Seurat Object by CreateSeuratObject, with the selection criterion being cells expressing at least 200 genes expressed in more than 3 cells.
Cells with 300-5000 unique genses and < 20% mitochondrial reads were retained for downstream analyses. Doublets were removed by DoubletFinder v.2.0.4. Count matrices were merged to a single Seurat object.
Log normalized counts were used to identify 2000 most variably expressed genes using the FindVariableFeatures function with the variance stabilizing transformation.
Integration was performed using respectively SelectIntegrationFeatures, PrepSCTIntegration and FindIntegrationAnchors of Seurat. Principal component (PC) analysis was performed, and the first 10 PCs were selected for UMAP dimensionality reduction.
To cluster cells, we first used Seurat's FindNeighbors method to determine the biologically closest cells, before grouping them together using Seurat's FindClusters function with a resolution of 0.3.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separate values files and matrix files

molecule: polyA RNA

source_name: PBMC

extract_protocol: PBMC isolated from blood patient were stored in cryostore in liquid nitrogen, then defrozed in water bath at 37C, the cells were resuspended in RMPI 20% human serum, centrifuged at low speed for 7 min. The cells were counted and washed 2 times in PBS 0,04% BSA and resuspended in PBS 0,04% BSA for the experiment at 1200cells/uL

treatment_protocol: PBMC from selected patients were thawed and in vitro stimulated during 6 days with vaccinated-derived peptides

value: PBMC

tag: age


title: P005,CD4+IFN+, scRNAseq

description:
Library name: P005_POS
10x Genomics Chromium Single Cell 5'

extract_protocol:
IFNγ secreting cells were sorted by using IFNγ secretion-detection assay (Mitenyi) before cell sorting on MACSQuant Tyto (Miltenyi Biotec, Germany). IFNγ+CD4+ T cells were then encapsulated using the 10x Genomics Chromium Controller.
Library was performed according to the manufacturer's instruction Chromium Next GEM Single cells 5′ Library Kit v2 ( 10x Genomics).


title: P023, CD4+IFN+ scRNAseq

description:
Library name: P023_POS
10x Genomics Chromium Single Cell 5'


title: 19_empty_ctrl_IgG_Rep2

description:
Library name: Sample 3
empty_ctrl_IgG_Rep2

value: IgG control Rabbit (Abcam ab37415)


title: P023, PBMC, Baseline, scRNAseq

description:
Library name: P023_PBMC_Baseline
10x Genomics Chromium Single Cell 3'


title: 13_empty_ctrl_H3K27me3_Rep1

description:
Library name: Sample 2
empty_ctrl_H3K27me3_Rep1


title: Subject_N, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day2


title: Mk cells-1 (Sham)

description: Library name: Sampel 1

value: Sham


title: Subject_H, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: 01_empty_ctrl_IgG_Rep1

description:
Library name: Sample 1
empty_ctrl_IgG_Rep1


title: ATAC-seq on mitotic C2C12 cells R1

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description: 75bp paired end

data_processing:
Sequence data was mapped to mm10 and processed according to previous publication (Oomen et. al. 2019, Genome Research)
For more information see methods section of associated publication
Assembly: mm10
Supplementary files format and content: BigWig files of 50bp binned and normalized signal

source_name: Myoblast

growth_protocol: For culture conditions see methods of associated publication

extract_protocol:
Cells lwere lysed and processed for ATAC-seq fresh
ATAC-seq libraries were prepared according to published protocol Buenrostro et. al. 2015

treatment_protocol: Mitotic cells for both C2C12 were obtained using 100ng/mL Nocodazole for 12 hrs followed by a gentle shake off

value: Myoblast

value: Myoblasts

value: 12hr Nocodazole


title: Pooled P020-P037, CD4+IFN+, scRNAseq

description:
Library name: P020-P037_POS
10x Genomics Chromium Single Cell 5'


title: CY-ZB-JAK-after

city: Chengdu

first: Qiang

last: Qiu

state: Sichuan

address: No. 17, the Third Part of Renmin South Road

institute: SKLB

description:
Library name: Sample2
Peripheral blood was obtained from patients after CAR-T treatment, and single-cell suspension was prepared after red blood cells were removed for single-cell RNA sequencing.

data_processing:
We used the default parameters of Cell Ranger single-cell software suite (v2.2.0) (10x Genomics). The quality of the sample-specific FASTQ file was evaluated by the counts of Cell Ranger which were aligned to the human reference genome (GRCh38) using a STAR aligner to generate the digital gene expression matrix. The expression level for each transcript was determined using the number of unique molecular identifiers (UMI) assigned to the transcript. The filtered gene expression matrices were then used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: peripheral blood

extract_protocol:
PB samples from patient at initial diagnosis and CR2 were removed erythrocytes by incubating with RBC lysis buffer. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and then centrifuged at 4°C 300g for 5min (repeated twice). The cell activity was detected by trypan blue staining, and it was required to be >85%. The number of cells was counted using a hemocytometer, and the cell concentration was adjusted to 103 cells/μL.
Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10×Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 10,000-15,000 cells. cDNA amplification and library construction were performed according to standard protocols.

value: peripheral blood


title: group5, GSK2879552 treatment, bio rep 2

city: Hershey

first: Lisa

middle: M

last: Schneper

state: PA

address: 700 HMC Crescent Rd

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University College of Medicine

description: Library name: H-49-4

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0) allowing no mismatches in the index read. BBDuk (bbtools version 38.69) was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the mouse reference genome (mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)) was done using HISAT2 (version 2.2.1) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq (version 0.11.2) by supplementing Ensembl gene annotation (release 67: "Mus_musculus.Ensembl.NCBIM37.67.gtf").
Assembly: mouse Ensembl release 67 (GRCm37 / NCBIM37 / mm9)
Supplementary files format and content: csv file containing raw read counts for each sample

source_name: retina

extract_protocol:
RNA were isolated with RNeasy mini kit (Qiagen)
The cDNA libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (IDT® for Illumina® RNA UD Indexes Set A, Ligation, Illumina) were incorporated in the adaptors for multiplexed high-throughput sequencing.

treatment_protocol: Mice were treated daily with intraperitoneal injections of inhibitors or saline as a control from PN9 till PN24

value: retina

value: FACS sorted rod photoreceptors

value: rd10 x  B6.Cg-Tg(Nrl-EGFP)1Asw/J


title: Subject_H, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28


title: group5, control, biol rep2

description: Library name: H-49-2

value: no


title: CY-ZB-JAK-before

description:
Library name: Sample1
Peripheral blood was obtained from patients  at initial diagnosis, and single-cell suspension was prepared after red blood cells were removed for single-cell RNA sequencing.


title: group5, GSK2879552 treatment, bio rep 1

description: Library name: H-49-3


title: Bacterial metagenome E5

city: Shanghai

first: Li

last: Cheng

state: Shanghai

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

description:
Library name: E5
China：BeiJing (116.20 N 39.56 W)

data_processing:
This 16S analysis pipeline conducts quality control on raw sequencing data by first using fastp to filter and trim low-quality reads, then employing cutadapt in QIIME2 to remove primers, and finally applying DADA2's denoise-paired function in QIIME2 to denoise sequences, remove chimeras, and generate ASV tables and representative sequences.
Assembly: silva-138-99
Supplementary files format and content: tab-delimited text files include all samples' relative quantitative value for each identified taxonomy
Library strategy: 16S rRNA-seq

source_name: Environmental sample

extract_protocol:
DNA was isolated by grinding, shaking, centrifugation, adsorption, elution with Mixed lysis buffer (buffer) containing Proteinase K, Isopropyl alcohol buffer solution, Ethanol buffer solution, ddH2O and so on.
The V3/V4 regions of the bacteria were amplified using a pair of specific primers 341F/ 805R.

value: Environmental sample

tag: time


title: ATAC-seq on mitotic C2C12 cells R2

description: 75bp paired end


title: Subject_H, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day8


title: group5, control, biol rep1

description: Library name: H-49-1


title: Bacterial metagenome E4

description:
Library name: E4
China：BeiJing (116.20 N 39.56 W)


title: Mk cells-2 (Sham)

description: Library name: Sampel 2

value: Lung

value: Megakaryocytes


title: Subject_H, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day2

value: breast milk lymphocyte (BML)


title: Subject_K, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day28


title: Bacterial metagenome E3

description:
Library name: E3
China：BeiJing (116.20 N 39.56 W)


title: ATAC-seq on asynchronous C2C12 cells R1

description: 75bp paired end

value: Untreated


title: group4, UNC1999 treatment, biol rep2

description: Library name: H-50-5


title: B6 MC903 treated, sample 1, 3' scRNA-seq [B6_inflamed]

city: Cambridge

first: Evgenij

last: Fiskin

state: MA

address: 415 Main St

institute: Broad Institute of MIT and Harvard, Massachusetts General Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0
Assembly: GRCh38 (human samples) and mm10 (murine samples)
Supplementary files format and content: h5ad files

source_name: Dorsal skin

extract_protocol:
Whole skin punch biopsies (3-4mm) or mouse dorsal skin was cut into two pieces, such that each piece contains all skin layers and storage medium was removed. Enzymatic dissociation was performed using Whole Skin Dissociation kit (Miltenyi Biotec, #130-101-540) with a modified protocol. Cut biopsies were transferred into a gentleMACS C-tube containing 435µl Buffer L, 12.5µl Enzyme P, 50µl Enzyme D and 2.5µl Enzyme A. Enzymatic dissociation was performed for 3.5h at 37°C. After incubation, 500µl of cold DMEM containing 10% FBS and 2 mM L-glutamine were added. The tissue was mechanically dissociated using a gentleMACS dissociator run on program h_skin_01. The resulting cellular suspension was filtered through a 70µm cell strainer (Falcon, #352350) and 4.5ml cold DMEM containing 10% FBS and 2 mM L-glutamine were added. Cells were spun down at 300g for 10min at 4°C. The supernatant was then aspirated and cells were resuspended in 1.2ml ACK buffer (A10492-01). Suspensions were transferred to 1.5ml tubes and incubated for 2min for red blood cell lysis and spun at 350g for 4min at 4°C. Supernatants were aspirated and cells were resuspended in 50-100µl 0.4% BSA in PBS. Cell viability and cell counts were determined and cells were processed for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, single cell supsension from whole skin biopsies were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Dorsal skin

tag: strain

value: 2nM MC903 in Ethanol


title: Bacterial metagenome E2

description:
Library name: E2
China：BeiJing (116.20 N 39.56 W)


title: Subject_K, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day28


title: group4, UNC1999 treatment, biol rep1

description: Library name: H-50-4


title: Subject_K, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day8


title: Bacterial metagenome E1

description:
Library name: E1
China：BeiJing (116.20 N 39.56 W)


title: SYF1136-HTGTS-day9-iNs-AraC-bait-chromosome1-NHLH1

city: Bethesda

first: Chuanyuan

last: Chen

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

description: Library name: Sample 12

data_processing:
Raw reads were trimmed and mapped to hg19 genome by Bowtie2 through the HTGTS pipeline with --no-dedup parameters (https://github.com/robinmeyers/transloc_pipeline). Translocation junctions were further filtered to remove reads mapping to blacklisted regions (http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability).
Assembly: hg19
Supplementary files format and content: bed and bedgraph files include translocation signal for each sample

source_name: iPSC-derived i3Neurons

growth_protocol: Human iPSC lines (WTC11) were cultured on Matrigel-coated dishes in Essential 8 Medium (E8) supplemented with 10 μM ROCK inhibitor at 37°C and 5% CO2. The medium was replaced every 1–2 days, and cells were passaged using Accutase and replated in E8 with ROCK inhibitor to promote survival, with the inhibitor removed once colonies formed. For iPSC-derived i3Neuron differentiation, NGN2-expressing iPSCs were plated in N2 medium with doxycycline and ROCK inhibitor. After two days, the cells were replated onto poly-L-ornithine-coated plates and cultured in iN Culture Media, including BrainPhys media, BDNF, NT-3, laminin, and doxycycline. The media was changed twice a week from day 6 onwards. For primary cortical neurons, cortices were dissected from E16.5 mouse embryos, digested with Papain and DNase I, and triturated in Neurobasal complete medium. The cells were then filtered, seeded on poly-d-lysine and laminin-coated plates, and aphidicolin was added to eliminate dividing cells.

extract_protocol:
For LAM-HTGTS, genomic DNA was extracted using DNeasy® Blood & Tissue (QIAGEN; cat. No. 69504) following the manufacturer’s instructions.
For LAM-HTGTS, 10 µg genomic DNA from iNs were sonicated and subjected to LAM-PCR with a biotinylated primer. The ssDNA products are enriched with streptavidin magnetic beads enrichment and ligated to a bridge adaptor. Nested PCR and tagged PCR were used to amplify the translocation junctions and barcode for next-generation sequencing.

value: iPSC-derived i3Neurons

value: Neurons

value: WT

value: AraC fo 3 days


title: Subject_M, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day28


title: group4, control, biol rep3

description: Library name: H-50-3


title: group4, control, biol rep2

description: Library name: H-50-2


title: ATAC-seq on asynchronous C2C12 cells R2

description: 75bp paired end

value: Myoblast

value: Myoblasts


title: Bacterial metagenome H10

description:
Library name: H10
China：BeiJing (116.20 N 39.56 W)

source_name: Human serum

value: Human serum


title: Bacterial metagenome H8

description:
Library name: H8
China：BeiJing (116.20 N 39.56 W)


title: group3, DZNep treatment, biol rep2

description: Library name: G-981-17

value: retina

value: DZNep


title: SYF1183-HTGTS-day9-TDGdegron-iNs-AraC-bait-chromosome15-B2M

description: Library name: Sample 10

value: TDG-degron

value: B2M-VLP and AraC fo 3 days


title: Subject_M, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day28


title: Subject_M, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day8


title: Bacterial metagenome H9

description:
Library name: H9
China：BeiJing (116.20 N 39.56 W)


title: group4, UNC1999 treatment, biol rep3

description: Library name: H-50-6


title: Bacterial metagenome H7

description:
Library name: H7
China：BeiJing (116.20 N 39.56 W)


title: Subject_D, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: group3, DZNep treatment, biol rep1

description: Library name: G-981-16


title: group4, control, biol rep1

description: Library name: H-50-1

value: no


title: SYF1182-HTGTS-day9-LIG4KO-c40-iNs-AraC-bait-chromosome15-B2M

description: Library name: Sample 9

value: Lig4 knockout clone 40


title: Subject_D, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28

value: breast milk lymphocyte (BML)


title: SYF1181-HTGTS-day9-LIG4KO-c13-iNs-AraC-bait-chromosome15-B2M

description: Library name: Sample 8

value: Lig4 knockout clone 13


title: Bacterial metagenome H6

description:
Library name: H6
China：BeiJing (116.20 N 39.56 W)


title: group3, control, biol rep4

description: Library name: G-981-15


title: B6 control treated, sample 1, 3' scRNA-seq [B6_control]

description: 10x Genomics

value: Dorsal skin

value: Ethanol control


title: Subject_I, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: Bacterial metagenome H5

description:
Library name: H5
China：BeiJing (116.20 N 39.56 W)


title: SYF1180-HTGTS-day9-WT-iNs-AraC-bait-chromosome15-B2M

description: Library name: Sample 7

value: iPSC-derived i3Neurons


title: group3, control, biol rep3

description: Library name: G-981-14


title: SYF1188-HTGTS-day9-iNs-AraC-bait-chromosome15-B2M-replicate3

description: Library name: Sample 6

value: Neurons


title: Bacterial metagenome H4

description:
Library name: H4
China：BeiJing (116.20 N 39.56 W)


title: Subject_I, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28


title: SYF1184-HTGTS-day9-TDGdegron-dTAG-iNs-AraC-bait-chromosome15-B2M

description: Library name: Sample 11

value: dTAG13, B2M-VLP and AraC fo 3 days


title: Subject_O, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: group3, control, biol rep2

description: Library name: G-981-13


title: group3, control, biol rep1

description: Library name: G-981-12


title: SYF1187-HTGTS-day9-iNs-AraC-bait-chromosome15-B2M-replicate2

description: Library name: Sample 5

value: WT


title: Bacterial metagenome H3

description:
Library name: H3
China：BeiJing (116.20 N 39.56 W)


title: Bacterial metagenome H2

description:
Library name: H2
China：BeiJing (116.20 N 39.56 W)


title: Subject_G, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: group2, UNC0642 treatment, biol rep2

description: Library name: G-981-10


title: Bacterial metagenome H1

description:
Library name: H1
China：BeiJing (116.20 N 39.56 W)


title: SYF1186-HTGTS-day9-iNs-bait-chromosome15-B2M-replicate3

description: Library name: Sample 3

value: B2M-VLP fo 3 days


title: SYF1185-HTGTS-day9-iNs-bait-chromosome15-B2M-replicate2

description: Library name: Sample 2


title: Subject_G, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28


title: Bacterial metagenome A47

description:
Library name: A47
China：BeiJing (116.20 N 39.56 W)


title: group2, control, biol rep2

description: Library name: G-981-8


title: SYF1165-HTGTS-day9-iNs-bait-chromosome15-B2M-replicate1

description: Library name: Sample 1


title: group2, control, biol rep1

description: Library name: G-981-7


title: Bacterial metagenome A46

description:
Library name: A46
China：BeiJing (116.20 N 39.56 W)


title: LNCaP_BMH21_Pol2

city: BALTIMORE

first: Marikki

last: Laiho

state: Maryland

address: 1550 Orleans St

department: Department of Radiation Oncology and Molecular Radiation Sciences

institute: Johns Hopkins University

data_processing:
CASAVA 1.8.2 (Illumina) was used to convert BCL files to FASTQ files using default parameters. Mapping of  reads was conducted using bowtie 2.2.1 to the hg19 human reference genome. Metagene plot of the occupancy of RNA polymerase II (Pol II) within 2,000 bp of transcription start site was generated by Deeptools (v3.5.4).
Assembly: hg19
Supplementary files format and content: bed, narrowPeak

source_name: prostate

growth_protocol: RPMI-1640+10%FBS. Cells were maintained at 37ºC and 5% CO2 in a humidified atmosphere.

extract_protocol:
Cells were fixed with 1% formalin. After quenching and lysis, chromatin was sonicated using Covaris E220 sonicator.
ChIP-seq samples were prepared by using iDeal ChIP-seq kit for Transcription Factors (Diagenode, cat # C01010170) according to the manufacturer’s protocol.

treatment_protocol: Cells were treated with DMSO (control) or treated with BMH-21, 1 microM for 6 hours.

value: prostate

value: LNCaP

value: prostate cancer

tag: chip antibody

value: RNA polymerase II (4H8), CTD repeat YSPTSPS phosphor S5, Abcam, cat # ab5408

value: BMH-21 1 uM 6 hours


title: Bacterial metagenome A45

description:
Library name: A45
China：BeiJing (116.20 N 39.56 W)

value: Human serum


title: LNCaP_BMH21_Pol1

value: C-1 antibody Santa Cruz Biotechnology, cat # sc-48385


title: group1, Romidepsin treatment, biol rep 3

description: Library name: G-981-6

value: retina

value: Romidepsin


title: Bacterial metagenome A44

description:
Library name: A44
China：BeiJing (116.20 N 39.56 W)


title: group1, Romidepsin treatment, biol rep 2

description: Library name: G-981-5


title: LNCaP_DMSO_Pol2

value: control


title: Sample control liver TMA2 [039]

first: Anjali

last: Garg

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

description: Library name: Sample control liver TMA2 [039]

data_processing:
TMA was analyzed on the GeoMx DSP using the Canine Cancer Atlas panel (1,962 canine specific genes)
Assembly: Canis lupus familiaris
Supplementary files format and content: DCC and PKC files

organism: Canis lupus familiaris

source_name: Canine appendicular osteosarcoma samples

extract_protocol:
Probe capture on GeoMx
GeoMx™ Canine Cancer Atlas | NanoString

treatment_protocol: National Cancer Institute’s Comparative Oncology Trials Consortium


title: Sample control liver TMA2 [040]

description: Library name: Sample control liver TMA2 [040]

value: Canine appendicular osteosarcoma samples


title: SYF1166-HTGTS-day9-iNs-AraC-bait-chromosome15-B2M-replicate1

description: Library name: Sample 4

value: B2M-VLP and AraC fo 3 days


title: LNCaP_DMSO_Pol1


title: Subject_O, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28

value: breast milk lymphocyte (BML)


title: Sample control spleen TMA2 [038]

description: Library name: Sample control spleen TMA2 [038]


title: Bacterial metagenome A43

description:
Library name: A43
China：BeiJing (116.20 N 39.56 W)


title: group1, Romidepsin treatment, biol rep 1

description: Library name: G-981-4


title: Sample control spleen TMA2 [037]

description: Library name: Sample control spleen TMA2 [037]


title: Bacterial metagenome A42

description:
Library name: A42
China：BeiJing (116.20 N 39.56 W)


title: LNCaP_BMH21_input


title: group2, UNC0642 treatment, biol rep1

description: Library name: G-981-9


title: Bacterial metagenome A41

description:
Library name: A41
China：BeiJing (116.20 N 39.56 W)


title: Sample control kidney TMA2 [036]

description: Library name: Sample control kidney TMA2 [036]


title: group1,control, biol rep2

description: Library name: G-981-2

value: no


title: group1,control, biol rep3

description: Library name: G-981-3


title: Bacterial metagenome A40

description:
Library name: A40
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from POI woman 8

city: Jinan

first: Nianyu

last: Li

state: ShanDong

address: 44 wenhua xi road

institute: Shandong University

description: Library name: POI8

data_processing:
Quality assessment of the sequencing results was conducted using the FastQC software. The sequences were filtered using the fastp software. For sequence alignment, the Hisat2 software was employed.
Assembly: GRCh38.102
Supplementary files format and content: FASTQ file includes raw data

source_name: Ovary

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Ovary


title: Bacterial metagenome A39

description:
Library name: A39
China：BeiJing (116.20 N 39.56 W)


title: Sample control kidney TMA2 [035]

description: Library name: Sample control kidney TMA2 [035]


title: LNCaP_DMSO_input


title: Sample 2201 TMA2 [034]

description: Library name: Sample 2201 TMA2 [034]


title: Human granulosa cells from POI woman 7

description: Library name: POI7


title: Sample 2201 TMA2 [033]

description: Library name: Sample 2201 TMA2 [033]


title: Liver, MASH diet, vehicle, rep4

city: Oklahoma City

first: Matthew

last: Potthoff

state: Oklahoma

address: 1100 N Lindsay Ave

institute: University of Oklahoma health sciences center

description: Library name: VEH6

data_processing:
Adaptor sequences were trimmed using TrimGalore (v. 6.10).
Reads were aligned to the mm10 mus musculus genome assembly and counts were generated using Salmon (v. 1.10.2)
Genes with counts of <4 per sample were removed from analysis.
Assembly: mm10
Supplementary files format and content: .xlsx file containing normalized counts for all samples.

source_name: Liver

extract_protocol:
RNA was extracted using Qiagen RNEasy miniprep kit.
Oligo-dT enrichment was performed.

value: Liver

value: MASH diet, vehicle


title: Bacterial metagenome A38

description:
Library name: A38
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from POI woman 6

description: Library name: POI6


title: Liver, MASH diet, vehicle, rep3

description: Library name: VEH5


title: Bacterial metagenome A37

description:
Library name: A37
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from POI woman 5

description: Library name: POI5


title: Liver, MASH diet, vehicle, rep1

description: Library name: VEH3


title: Liver, MASH diet, vehicle, rep2

description: Library name: VEH4


title: Bacterial metagenome A36

description:
Library name: A36
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from POI woman 4

description: Library name: POI4


title: Sample 1701 TMA2 [031]

description: Library name: Sample 1701 TMA2 [031]


title: Sample 1801 TMA2 [030]

description: Library name: Sample 1801 TMA2 [030]


title: Liver, MASH diet, FGF21, rep4

description: Library name: FGF6

value: MASH diet, FGF21


title: Sample 901 TMA2 [029]

description: Library name: Sample 901 TMA2 [029]


title: Bacterial metagenome A35

description:
Library name: A35
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from POI woman 2

description: Library name: POI2


title: Bacterial metagenome A34

description:
Library name: A34
China：BeiJing (116.20 N 39.56 W)


title: Liver, MASH diet, FGF21, rep3

description: Library name: FGF4


title: Bacterial metagenome A33

description:
Library name: A33
China：BeiJing (116.20 N 39.56 W)


title: Sample 2202 TMA2 [028]

description: Library name: Sample 2202 TMA2 [028]


title: group1,control, biol rep1

description: Library name: G-981-1


title: Liver, MASH diet, FGF21, rep2

description: Library name: FGF2


title: Sample 2203 TMA2 [026]

description: Library name: Sample 2203 TMA2 [026]


title: Sample 2203 TMA2 [027]

description: Library name: Sample 2203 TMA2 [027]


title: Sample 1701 TMA2 [032]

description: Library name: Sample 1701 TMA2 [032]


title: Bacterial metagenome A31

description:
Library name: A31
China：BeiJing (116.20 N 39.56 W)


title: Bacterial metagenome A32

description:
Library name: A32
China：BeiJing (116.20 N 39.56 W)


title: Liver, MASH diet, FGF21, rep1

description: Library name: FGF1


title: Human granulosa cells from POI woman 3

description: Library name: POI3


title: Bacterial metagenome A30

description:
Library name: A30
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from control woman 7

description: Library name: C7


title: Human granulosa cells from control woman 6

description: Library name: C6


title: Liver, chow diet, vehicle, rep3

description: Library name: CON3

value: Chow diet, vehicle


title: Sample 2206 TMA2 [024]

description: Library name: Sample 2206 TMA2 [024]


title: Liver, chow diet, vehicle, rep2

description: Library name: CON2


title: Sample 2206 TMA2 [023]

description: Library name: Sample 2206 TMA2 [023]


title: Human granulosa cells from control woman 8

description: Library name: C8


title: Bacterial metagenome A29

description:
Library name: A29
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from control woman 5

description: Library name: C5


title: Bacterial metagenome A28

description:
Library name: A28
China：BeiJing (116.20 N 39.56 W)


title: Liver, chow diet, vehicle, rep1

description: Library name: CON1


title: Sample 501 TMA2 [022]

description: Library name: Sample 501 TMA2 [022]


title: Human granulosa cells from control woman 9

description: Library name: C9


title: Sample 501 TMA2 [021]

description: Library name: Sample 501 TMA2 [021]


title: E3skin

city: Xi'an

first: Beibei

last: Yu

state: Shannxi

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

institute: Xijing hospital

description:
Library name: E3skin
tissue.txt

data_processing:
CLC Genomics Workbench w 11.0.1
Assembly: mm10
Supplementary files format and content: TPM

source_name: Organ

extract_protocol:
A NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs, USA, Catalog #: E7530L) was used according to the manufacturer's guidelines to construct sequencing libraries and incorporate index codes for sample identification
he prepared libraries were sequenced on an Illumina platform using the paired-end 150 strategy at the Novogene Bioinformatics Technology Co. Ltd., Beijing, China. The sequencing process converted the original fluorescence images into raw data, which were then processed in FASTQ format, capturing both nucleotide sequences and their corresponding quality scores

value: Organ

value: WT

value: Organ of No treated old mice (rep15)


title: Human granulosa cells from POI woman 1

description: Library name: POI1


title: Bacterial metagenome A26

description:
Library name: A26
China：BeiJing (116.20 N 39.56 W)

value: Human serum


title: Human granulosa cells from control woman 4

description: Library name: C4


title: E3liver

description:
Library name: E3liver
tissue.txt

value: Organ of No treated old mice (rep14)


title: Liver, chow diet, vehicle, rep4

description: Library name: CON5


title: Sample 404 TMA2 [020]

description: Library name: Sample 404 TMA2 [020]


title: Bacterial metagenome A25

description:
Library name: A25
China：BeiJing (116.20 N 39.56 W)


title: Human granulosa cells from control woman 2

description: Library name: C2


title: Sample 2204 TMA2 [025]

description: Library name: Sample 2204 TMA2 [025]


title: E3kidney

description:
Library name: E3kidney
tissue.txt

value: Organ of No treated old mice (rep13)


title: Sample 404 TMA2 [019]

description: Library name: Sample 404 TMA2 [019]


title: Human granulosa cells from control woman 1

description: Library name: C1


title: E3gut

description:
Library name: E3gut
tissue.txt

value: Organ of No treated old mice (rep12)


title: Bacterial metagenome A24

description:
Library name: A24
China：BeiJing (116.20 N 39.56 W)


title: E3brain

description:
Library name: E3brain
tissue.txt

value: Organ of No treated old mice (rep11)


title: Bacterial metagenome A23

description:
Library name: A23
China：BeiJing (116.20 N 39.56 W)


title: Sample 204 TMA2 [017]

description: Library name: Sample 204 TMA2 [017]

value: Canine appendicular osteosarcoma samples


title: Sample 601 TMA2 [018]

description: Library name: Sample 601 TMA2 [018]


title: Bacterial metagenome A27

description:
Library name: A27
China：BeiJing (116.20 N 39.56 W)


title: Bacterial metagenome A22

description:
Library name: A22
China：BeiJing (116.20 N 39.56 W)


title: Treated-1

city: Tabriz

first: Esmaeil

last: Babaei

state: East Azerbaijan

address: 29th Bahman Blvd.,

department: Biology

country: Iran

institute: University of Tabriz

description: Library name: Treated-1

data_processing:
Adapter trimming and quality filtering were performed using Trimmomatic v0.39
Quality control of trimmed reads was checked using FastQC
Reads were aligned to the human genome (GRCh38) using HISAT2
Gene expression was quantified using HTSeq-count based on Ensembl lncRNA and mRNA annotation.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain raw counts for lncRNAs and mRNAs in tab-delimited text format (.txt). Each file includes gene identifiers and corresponding expression values for each sample.

extract_protocol:
Total RNA was extracted from treated and control HT-29 cells using TRIzol reagent (Thermo Fisher Scientific, USA) according to the manufacturer’s protocol. RNA was purified with DNase I treatment and its quality was assessed by NanoDrop and agarose gel electrophoresis.
The library was prepared by random fragmentation of cDNA samples followed by 5' and 3' adaptor ligation.

value: mutant TP53

value: Gemini-Cur (IC50)


title: Treated-2

description: Library name: Treated-2


title: Human granulosa cells from control woman 3

description: Library name: C3


title: Sample 502 TMA2 [016]

description: Library name: Sample 502 TMA2 [016]


title: E2liver

description:
Library name: E2liver
tissue.txt

value: Organ of No treated old mice (rep9)


title: Control-2

description: Library name: Control-2

value: No treatment


title: Sample 809 TMA2 [015]

description: Library name: Sample 809 TMA2 [015]


title: Bacterial metagenome A21

description:
Library name: A21
China：BeiJing (116.20 N 39.56 W)


title: Control-1

description: Library name: Control-1


title: E2skin

description:
Library name: E2skin
tissue.txt

value: Organ of No treated old mice (rep10)


title: E2kidney

description:
Library name: E2kidney
tissue.txt

value: Organ of No treated old mice (rep8)


title: Sample 214 TMA2 [014]

description: Library name: Sample 214 TMA2 [014]


title: Bacterial metagenome A19

description:
Library name: A19
China：BeiJing (116.20 N 39.56 W)


title: PrimaryNK

city: Bangkok

first: Methichit

last: Wattanapanitch

state: Bangkok

address: 2 Prannok rd., Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi

department: Research Department

country: Thailand

institute: Mahidol University

description: 10X genomics

data_processing:
Sequenced libraries were processed using 10X Cell Ranger pipeline (cellranger-7.0.1).
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab separated values files and matrix files. 10X Cell Ranger exported files.

source_name: Blood

growth_protocol: Cells were seeded onto a cell culture plate in a monolayer format and differentiated into hematopoietic cells. Subsequently, cells were treated with NK cell culturing medium, directing them to become iNK cells, followed by marker validation with flow cytometry.

extract_protocol:
Differentiated iNK cells were collected upon completion of the differentiation protocol outlined in this study and submitted for single-cell RNA sequencing. To compare with native NK cells, PBMCs were obtained and enriched for primary NK cells, which were then collected for single-cell RNA sequencing.
Libray contruction was performed according the manufacturer's user guide CG000331 from 10X Genomics. The cells were then barcoded, loaded into a 10X Chromium, and processed for library preparation using the Chromium Next GEM Single Cell 5’ Reagent Kits v2.

value: Blood

value: Primary

value: NK Cells


title: Sample 610 TMA2 [013]

description: Library name: Sample 610 TMA2 [013]


title: iNK

description: 10X genomics

source_name: Stem cells

value: Stem cells

value: Induced Pluripotent Stem cells


title: Bacterial metagenome A17

description:
Library name: A17
China：BeiJing (116.20 N 39.56 W)

value: Human serum


title: E1skin

description:
Library name: E1skin
tissue.txt

value: Organ

value: WT

value: Organ of No treated old mice (rep5)


title: Donor 25, Stimulated ASCs, scRNAseq

city: Providence

first: Eric

last: Darling

state: RI

address: 171 Meeting St

institute: Brown University

description: 10x Genomics

data_processing:
CellRanger v7.0.0
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Adipose

extract_protocol:
SVF cells were obtained from human lipoaspirate following an IRB-approved protocol and previously established methodologies with slight modifications (Estes et al. 2010; Parsons et al. 2018). Briefly, lipoaspirate waste was serially washed with phosphate buffered saline (PBS), followed by dissociation of the tissue by collagenase digestion. A series of phosphate-buffered saline (PBS) washes and centrifugations followed by red blood cell lysis yielded isolated SVF cells, which were then frozen in the vapor phase of liquid nitrogen. Prior to use in experiments involving cytokine stimulation, cells were thawed, equilibrated, and expanded in culture for one passage. Passage 0 (P0) samples were defined as SVF cells that had been frozen but never expanded or cultured in vitro. For Cultured ASCs: SVF cells from five human donors were enriched for ASCs through plastic adherence twice, yielding effectively enriched P2 ASCs, which were then frozen in the vapor phase of liquid nitrogen until use. Subsequent culturing was based on previously established and optimized protocols (Menard et al. 2013; Parsons and Darling 2021). Prior to cytokine stimulation, P2 ASCs were thawed and counted, and 0.5-1.25x106 cells were plated in four T-182 flasks and equilibrated for two days in an expansion medium consisting of DMEM/F-12, 10% FBS (ZenBio), 1% antibiotic/antimycotic (A/A), 5 ng/mL endothelial growth factor, 1 ng/mL fibroblast growth factor, and 0.25 ng/mL transforming growth factor-β1. Following expansion, cells were cultured in either control or inflammatory conditions for 48 hours. Control, stromal maintenance medium consisted of DMEM/F-12 with 10% FBS and 1% A/A. Inflammatory stimulation medium consisted of control medium supplemented with IFN-γ (10 ng/mL) and tumor necrosis factor (TNF)-α (15 ng/mL).
Chromium Single Cell 3’ Reagent Kit v3

value: Adipose

value: Stem/stromal cells

value: IFN-γ (10 ng/mL) and TNF-α (15 ng/mL)


title: Sample 1405 TMA2 [011]

description: Library name: Sample 1405 TMA2 [011]

value: Canine appendicular osteosarcoma samples


title: Bacterial metagenome A16

description:
Library name: A16
China：BeiJing (116.20 N 39.56 W)


title: E1liver

description:
Library name: E1liver
tissue.txt

value: Organ of No treated old mice (rep4)


title: Donor 25, Control ASCs, scRNAseq

description: 10x Genomics


title: Sample 309 TMA2 [010]

description: Library name: Sample 309 TMA2 [010]


title: Bacterial metagenome A15

description:
Library name: A15
China：BeiJing (116.20 N 39.56 W)


title: Bacterial metagenome A20

description:
Library name: A20
China：BeiJing (116.20 N 39.56 W)


title: Donor 49, P0 SVF, scRNAseq

description: 10x Genomics

value: Stromal Vascualr Fraction


title: E1kidney

description:
Library name: E1kidney
tissue.txt

value: Organ of No treated old mice (rep3)


title: Bacterial metagenome A14

description:
Library name: A14
China：BeiJing (116.20 N 39.56 W)


title: E1gut

description:
Library name: E1gut
tissue.txt

value: Organ of No treated old mice (rep2)


title: Donor 25, P0 SVF, scRNAseq

description: 10x Genomics


title: Sample 706 TMA2 [008]

description: Library name: Sample 706 TMA2 [008]


title: Bacterial metagenome A13

description:
Library name: A13
China：BeiJing (116.20 N 39.56 W)


title: E1brain

description:
Library name: E1brain
tissue.txt

value: Organ of No treated old mice (rep1)


title: E2gut

description:
Library name: E2gut
tissue.txt

value: Organ of No treated old mice (rep7)


title: Sample 1403 TMA2 [009]

description: Library name: Sample 1403 TMA2 [009]


title: Bacterial metagenome A18

description:
Library name: A18
China：BeiJing (116.20 N 39.56 W)


title: Sample 701 TMA2 [007]

description: Library name: Sample 701 TMA2 [007]


title: Bacterial metagenome A12

description:
Library name: A12
China：BeiJing (116.20 N 39.56 W)


title: ABMSC2

description:
Library name: ABMSC2
cell.txt

organism: Rattus norvegicus

source_name: EVs

value: EVs

value: ABMSC-EV1 (rep2)


title: ABMSC3

description:
Library name: ABMSC3
cell.txt

value: ABMSC-EV1 (rep3)


title: E2brain

description:
Library name: E2brain
tissue.txt

value: Organ of No treated old mice (rep6)


title: D3skin

description:
Library name: D3skin
tissue.txt

value: Organ

value: Organ of FBMC_EVs treated old mice (rep15)


title: Sample 702 TMA2 [006]

description: Library name: Sample 702 TMA2 [006]


title: Sample 610 TMA2 [012]

description: Library name: Sample 610 TMA2 [012]


title: Bacterial metagenome A11

description:
Library name: A11
China：BeiJing (116.20 N 39.56 W)

value: Human serum


title: ABMSC1

description:
Library name: ABMSC1
cell.txt

value: WT

value: ABMSC-EV1 (rep1)


title: D3liver

description:
Library name: D3liver
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep14)


title: Sample 702 TMA2 [005]

description: Library name: Sample 702 TMA2 [005]

value: Canine appendicular osteosarcoma samples


title: Bacterial metagenome A10

description:
Library name: A10
China：BeiJing (116.20 N 39.56 W)


title: D3kidney

description:
Library name: D3kidney
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep13)


title: FBMSC3

description:
Library name: FBMSC3
cell.txt

value: FBMSC-EV1 (rep3)


title: Sample 1001 TMA2 [004]

description: Library name: Sample 1001 TMA2 [004]


title: Bacterial metagenome A9

description:
Library name: A9
China：BeiJing (116.20 N 39.56 W)


title: D3gut

description:
Library name: D3gut
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep12)


title: Sample 1001 TMA2 [003]

description: Library name: Sample 1001 TMA2 [003]


title: Bacterial metagenome A8

description:
Library name: A8
China：BeiJing (116.20 N 39.56 W)


title: FBMSC1

description:
Library name: FBMSC1
cell.txt

value: FBMSC-EV1 (rep1)


title: Sample 1002 TMA2 [002]

description: Library name: Sample 1002 TMA2 [002]


title: D2liver

description:
Library name: D2liver
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep9)


title: Bacterial metagenome A6

description:
Library name: A6
China：BeiJing (116.20 N 39.56 W)


title: Bacterial metagenome A7

description:
Library name: A7
China：BeiJing (116.20 N 39.56 W)


title: ABPC2

description:
Library name: ABPC2
cell.txt

value: ABPC-EV1 (rep2)


title: Sample 1701 TMA1 [040]

description: Library name: Sample 1701 TMA1 [040]


title: Bacterial metagenome A5

description:
Library name: A5
China：BeiJing (116.20 N 39.56 W)


title: Bacterial metagenome A4

description:
Library name: A4
China：BeiJing (116.20 N 39.56 W)


title: Sample 1002 TMA2 [001]

description: Library name: Sample 1002 TMA2 [001]


title: D2kidney

description:
Library name: D2kidney
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep8)


title: Sample 1801 TMA1 [039]

description: Library name: Sample 1801 TMA1 [039]


title: FBMSC-EV3

description:
Library name: FBMSC-EV3
cell.txt

source_name: Cell

value: Cell

value: Cells of FBMSC-EV treated ABMSC (rep3)


title: D2gut

description:
Library name: D2gut
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep7)


title: D2skin

description:
Library name: D2skin
tissue.txt

value: Organ

value: Organ of FBMC_EVs treated old mice (rep10)


title: ABPC1

description:
Library name: ABPC1
cell.txt

value: EVs

value: ABPC-EV1 (rep1)


title: FBMSC2

description:
Library name: FBMSC2
cell.txt

value: WT

value: FBMSC-EV1 (rep2)


title: Sample control liver TMA1 [037]

description: Library name: Sample control liver TMA1 [037]

value: Canine appendicular osteosarcoma samples


title: Bacterial metagenome A2

description:
Library name: A2
China：BeiJing (116.20 N 39.56 W)

value: Human serum


title: D2brain

description:
Library name: D2brain
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep6)


title: FBMSC-EV1

description:
Library name: FBMSC-EV1
cell.txt

value: Cells of FBMSC-EV treated ABMSC (rep1)


title: Sample control spleen TMA1 [036]

description: Library name: Sample control spleen TMA1 [036]


title: ABPC3

description:
Library name: ABPC3
cell.txt

value: ABPC-EV1 (rep3)


title: Vehicle3

description:
Library name: Vehicle3
cell.txt

value: Cells of PBS treated ABMSC cells (rep3)


title: Bacterial metagenome A3

description:
Library name: A3
China：BeiJing (116.20 N 39.56 W)


title: FBMSC-EV2

description:
Library name: FBMSC-EV2
cell.txt

value: Cells of FBMSC-EV treated ABMSC (rep2)


title: Bacterial metagenome A1

description:
Library name: A1
China：BeiJing (116.20 N 39.56 W)


title: Sample control spleen TMA1 [035]

description: Library name: Sample control spleen TMA1 [035]


title: D3brain

description:
Library name: D3brain
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep11)


title: D1kidney

description:
Library name: D1kidney
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep3)


title: D1skin

description:
Library name: D1skin
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep5)


title: Vehicle2

description:
Library name: Vehicle2
cell.txt

value: Cell

value: Cells of PBS treated ABMSC cells (rep2)


title: Sample control kidney TMA1 [034]

description: Library name: Sample control kidney TMA1 [034]


title: D1gut

description:
Library name: D1gut
tissue.txt

value: Organ

value: Organ of FBMC_EVs treated old mice (rep2)


title: Sample control kidney TMA1 [033]

description: Library name: Sample control kidney TMA1 [033]


title: D1brain

description:
Library name: D1brain
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep1)


title: ABPC-EV3

description:
Library name: ABPC-EV3
cell.txt

value: WT

value: Cells of ABPC-EV treated ABMSC cells (rep3)


title: Sample 2201 TMA1 [032]

description: Library name: Sample 2201 TMA1 [032]

value: Canine appendicular osteosarcoma samples


title: Sample control liver TMA1 [038]

description: Library name: Sample control liver TMA1 [038]


title: ABPC-EV2

description:
Library name: ABPC-EV2
cell.txt

value: Cells of ABPC-EV treated ABMSC cells (rep2)


title: PC3 cells, LUC 2

city: Minneapolis

first: Aiden

middle: James

last: Deacon

state: Minnesota

address: 425 East River Parkway

institute: University of Minnesota

description:
Library name: PL2
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv

data_processing:
RNA Seq: Reads were trimmed for low quality and adaptors using Trimmomatic. Sequences were mapped to the human reference genome (GRCh38.110) using HISAT2 and sorted using SAMTools. Raw gene counts were generated with featureCounts and converted to normalized oounts and variance stabilizing transformed (VST) normalized counts using DESeq2. Genes with zero expression across all samples were filtered out and duplicate gene names were made unique.
Assembly: GRCh38.110
Supplementary files format and content: DESeq2 normalized count values for each LNCaP or PC3 or all sample
Supplementary files format and content: DESeq2 VST normalized count values for each LNCaP or PC3 or all sample
Supplementary files format and content: raw count values for each sample

source_name: Prostate tissue

growth_protocol: The human prostate cancer lines PC3 and LNCaP were cultured in RPMI medium 1640, supplemented with 10% FBS, 0.2% GlutaMax, and 1% Penicillin Streptomycin, grown at 37 degrees C and 5% CO2

extract_protocol:
RNA was harvested using the Rneasy mini plus kit from Qiagen
RNA library prep was done by novogene

value: Prostate tissue

value: AR- Prostate cancer

value: Luciferase overexpression


title: PC3 cells, CTNNB1 3

description:
Library name: PC3
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv

value: CTNNB1 overexpression


title: PC3 cells, LUC 1

description:
Library name: PL1
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv


title: PC3 cells, LUC 3

description:
Library name: PL3
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv


title: Sample 2201 TMA1 [031]

description: Library name: Sample 2201 TMA1 [031]


title: ABPC-EV1

description:
Library name: ABPC-EV1
cell.txt

value: Cells of ABPC-EV treated ABMSC cells (rep1)


title: PC3 cells, CTNNB1 2

description:
Library name: PC2
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv


title: C3skin

description:
Library name: C3skin
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep15)


title: D1liver

description:
Library name: D1liver
tissue.txt

value: Organ of FBMC_EVs treated old mice (rep4)


title: Sample 2206 TMA1 [030]

description: Library name: Sample 2206 TMA1 [030]


title: PC3 cells, RSPO2 3

description:
Library name: PR3
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv

value: RSPO2 overexpression


title: C3kidney

description:
Library name: C3kidney
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep13)


title: Sample 2206 TMA1 [029]

description: Library name: Sample 2206 TMA1 [029]


title: PC3 cells, CTNNB1 1

description:
Library name: PC1
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv


title: ABMSC-EV2

description:
Library name: ABMSC-EV2
cell.txt

value: Cell

value: Cells of ABMSC-EV treated ABMSC (rep2)


title: Vehicle1

description:
Library name: Vehicle1
cell.txt

value: Cells of PBS treated ABMSC cells (rep1)


title: C3gut

description:
Library name: C3gut
tissue.txt

value: Organ

value: Organ of ABMC_EVs treated old mice (rep12)


title: Sample 2204 TMA1 [028]

description: Library name: Sample 2204 TMA1 [028]


title: PC3 cells, RSPO2 2

description:
Library name: PR2
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv


title: C3brain

description:
Library name: C3brain
tissue.txt

value: WT

value: Organ of ABMC_EVs treated old mice (rep11)


title: Sample 2203 TMA1 [027]

description: Library name: Sample 2203 TMA1 [027]

value: Canine appendicular osteosarcoma samples


title: ABMSC-EV1

description:
Library name: ABMSC-EV1
cell.txt

value: Cells of ABMSC-EV treated ABMSC (rep1)


title: PC3 cells, RSPO2 1

description:
Library name: PR1
rspo2_PC3_deseq2_normalized_counts.csv
rspo2_PC3_deseq2_vst_normalized_counts.csv

value: Prostate tissue

value: AR- Prostate cancer


title: C2skin

description:
Library name: C2skin
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep10)


title: MII_Med12KO_3

city: Fort Collins

first: Michelle

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Raw reads were trimmed with Trim_Galore (v0.6.7) and aligned to the GRCm39 assembly with STAR (v2.7.10b). Low quality alignments (q < 5) were removed with SAMtools (v1.16) and raw counts for genes in the Ensembl (v108) annotation were calculated with HTSeq (v2.0.2) in mode “intersection-nonempty”.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample

source_name: Metaphase II oocytes

growth_protocol: Ovaries from 12 day old females were incubated in digestion media (1x DPBS, 2 mg/mL collagenase type 1, 2 mg/mL BSA) at 37°C for 1 hr, then supplemented with 40 mM EDTA (pH 8.0) and incubated at 37°C for 10 min. Digested ovaries were centrifuged at 1000 rpm for 5 min, and cell pellets resuspended in pick-up media (1x MEM-Alpha, 25 mM NaHCO3, 2 mg/mL BSA). Oocytes were transferred to wash buffer (1x MEM-Alpha, 25 mM NaHCO3, 1 mg/mL BSA), then to 1x DPBS, and stored in media at -80°C. For GV and MII oocyte collection, female mice older than 6 weeks were synchronized by 5 IU PMSG. For GV oocytes, ovaries were collected 48 h after PMSG administration and transferred to collection media (1X Hepes-MEM, 6 mM NaHCO3, 0.23 mM sodium pyruvate, 3 mg/mL BSA) with 1/1000 cilostamide. Follicles were mechanically disrupted using two needles and oocytes were selected based on size and morphology. Oocytes were washed in maturation media (1X MEM-Alpha, 6 mM NaHCO3, 3 mg/mL BSA) with 1/1000 cilostamide, then in 1X DPBS, and stored in Trizol solution at -80°C. For MII oocytes, female mice were injected with 5 IU hCG 48 h after PMSG, and oocytes were collected 12-15 h after hCG. Ovaries were transferred to collection media. After follicle disruption, cumulus complexes were transferred to maturation media and denuded with 0.3 mg/mL hyaluronidase for 1 min. Denuded oocytes were washed in maturation media, then 1X DBPS, and stored in Trizol at -80°C. For E7,5 embryo collection, female mice older than 6 weeks were synchronized by 5 IU PMSG for 48 h, then injected with 5 IU hCG and mated with wild-type stud males of proven fertility. Uteri were collected from euthanized females 8 days post conception and transferred to HEPES-buffered DMEM supplemented with 10% FBS. Each embryo was carefully separated from the maternal decidua and dissected into the ectoplacental cone, extraembryonic ectoderm, and epiblast. Tissues were stored in Trizol solution at -80°C prior to RNA extraction.

extract_protocol:
For samples stored in Trizol solution at -80°C (GV and MII oocytes, E7.5 embryonic tissues), total RNA was extracted by phenol-chloroform extraction. The aqueous phase was subjected to column purification using the PicoPure RNA Isolation kit (ThermoFisher, KIT0204) and treated with DNase I (Qiagen, 79254) to remove genomic DNA. For samples stored in collection media at -80°C, total RNA was extracted using the Extraction Buffer provided in the PicoPure RNA Isolation kit.
For RNA extracted from oocytes, libraries were constructed with the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio). For RNA extracted from E7.5 embryonic tissues, libraries were constructed with the Tecan Universal Plus Total RNA library preparation kit (Tecan Life Sciences).

value: Metaphase II oocytes

value: Med12 knockout

tag: developmental stage

value: Adult


title: LNCaP cells, LUC 2

description:
Library name: LL2
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv

value: LNCaP

value: AR+ Prostate cancer

value: Luciferase overexpression


title: Sample 2203 TMA1 [026]

description: Library name: Sample 2203 TMA1 [026]


title: C2liver

description:
Library name: C2liver
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep9)


title: MII_Med12KO_2


title: Sample 2202 TMA1 [025]

description: Library name: Sample 2202 TMA1 [025]


title: C3liver

description:
Library name: C3liver
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep14)


title: MII_Med12KO_1


title: LNCaP cells, LUC 3

description:
Library name: LL3
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv


title: C2kidney

description:
Library name: C2kidney
tissue.txt

value: Organ

value: Organ of ABMC_EVs treated old mice (rep8)


title: LNCaP cells, LUC 1

description:
Library name: LL1
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv


title: GV_WT_3

source_name: Germinal vesicle oocytes

value: Germinal vesicle oocytes

value: WT


title: Sample 1701 TMA1 [023]

description: Library name: Sample 1701 TMA1 [023]

value: Canine appendicular osteosarcoma samples


title: C2gut

description:
Library name: C2gut
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep7)


title: LNCaP cells, CTNNB1 3

description:
Library name: LC3
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv

value: Prostate tissue

value: CTNNB1 overexpression


title: Sample 404 TMA1 [022]

description: Library name: Sample 404 TMA1 [022]


title: GV_WT_2


title: LNCaP cells, CTNNB1 2

description:
Library name: LC2
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv


title: GV_WT_1


title: C1skin

description:
Library name: C1skin
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep5)


title: Sample 404 TMA1 [021]

description: Library name: Sample 404 TMA1 [021]


title: GV_Med12KO_3


title: C1liver

description:
Library name: C1liver
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep4)


title: Sample 809 TMA1 [020]

description: Library name: Sample 809 TMA1 [020]


title: ABMSC-EV3

description:
Library name: ABMSC-EV3
cell.txt

value: Cell

value: Cells of ABMSC-EV treated ABMSC (rep3)


title: LNCaP cells, RSPO2 3

description:
Library name: LR3
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv

value: LNCaP

value: RSPO2 overexpression


title: LNCaP cells, CTNNB1 1

description:
Library name: LC1
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv

value: AR+ Prostate cancer


title: C1kidney

description:
Library name: C1kidney
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep3)


title: C2brain

description:
Library name: C2brain
tissue.txt

value: Organ of ABMC_EVs treated old mice (rep6)


title: LNCaP cells, RSPO2 2

description:
Library name: LR2
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv


title: GV_Med12KO_2

value: Med12 knockout

value: Adult


title: Sample 1403 TMA1 [019]

description: Library name: Sample 1403 TMA1 [019]


title: C1gut

description:
Library name: C1gut
tissue.txt

value: Organ

value: Organ of ABMC_EVs treated old mice (rep2)


title: Sample 601 TMA1 [018]

description: Library name: Sample 601 TMA1 [018]

value: Canine appendicular osteosarcoma samples


title: LNCaP cells, RSPO2 1

description:
Library name: LR1
rspo2_LNCaP_deseq2_normalized_counts.csv
rspo2_LNCaP_deseq2_vst_normalized_counts.csv


title: Sample 901 TMA1 [024]

description: Library name: Sample 901 TMA1 [024]


title: C1brain

description:
Library name: C1brain
tissue.txt

value: WT

value: Organ of ABMC_EVs treated old mice (rep1)


title: Sample 501 TMA1 [017]

description: Library name: Sample 501 TMA1 [017]


title: D12_WT_2

source_name: Growing oocytes

value: Growing oocytes

value: 12 days old


title: D12_WT_3


title: B3skin

description:
Library name: B3skin
tissue.txt

value: Organ of No treated young mice (rep15)


title: 293T, HA-CIC::DUX4, replicate 2 (April 2023 Dataset)

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

description: Library name: D2

data_processing:
FASTQ files were aligned to GRCh38 using STAR (version 2.7.10b).
Gene counts were extracted during alignment using STAR parameter --quantMode GeneCounts
Differental expression analysis was performed in R (version 4.2.2) with edgeR (version 3.40.2).
Log2(cpm) data were obtained from TMM-normalized data using edgeR with the cpm function (log = T) which with this version of edgeR adds an average prior count of 2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file, STAR gene counts for all samples, data taken from column 4 of STAR output due to the strandedness of the library prep kit used. File name = counts_April2023.txt
Supplementary files format and content: Tab-delimited text file, log2(counts per million) measurements for all samples after edgeR processing. File name = logcpm_April2023.txt

growth_protocol: 293T cells were maintained in DMEM (high glucose, +L-Glutamine, +Sodium Pyruvate) with 10% fetal bovine serum (FBS) and 1% Pen-Strep (100 U/mL Penicillin, 100 ug/mL Streptomycin) at 37C in a 5% CO2 humidified incubator.

extract_protocol:
RNA was harvested with the Qiagen RNeasy Mini kit including on-column DNAse digestion and an extra, short Buffer RPE wash.
Libraries were constructed by Novogene by polyA-enriching RNA and then using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: 293T cells were reverse transfected with plasmids encoding no (empty vector), HA-CIC(ex20)::NUTM1(ex6), or HA-CIC::DUX4 inserts using Fugene 6 and Opti-MEM. 300,000 cells per condition were transfected on separate days for separate replicates, and RNA was harvested approximately 48 hours later.

value: human embryonic kidney

tag: genetic modification

value: HA-CIC::DUX4 overexpression


title: Sample 501 TMA1 [016]

description: Library name: Sample 501 TMA1 [016]


title: D12_WT_1


title: B3liver

description:
Library name: B3liver
tissue.txt

value: Organ of No treated young mice (rep14)


title: 293T, HA-CIC::DUX4, replicate 1 (April 2023 Dataset)

description: Library name: D1


title: Sample 204 TMA1 [015]

description: Library name: Sample 204 TMA1 [015]


title: Sample 502 TMA1 [014]

description: Library name: Sample 502 TMA1 [014]


title: D12_Med12KO_3


title: 293T, HA-CIC(ex20)::NUTM1(ex6), replicate 3 (April 2023 Dataset)

description: Library name: B3

value: HA-CIC(ex20)::NUTM1(ex6) overexpression


title: B3gut

description:
Library name: B3gut
tissue.txt

value: Organ of No treated young mice (rep12)


title: D12_Med12KO_2


title: Sample 214 TMA1 [013]

description: Library name: Sample 214 TMA1 [013]


title: GV_Med12KO_1

value: Germinal vesicle oocytes


title: D12_Med12KO_1


title: 293T, HA-CIC(ex20)::NUTM1(ex6), replicate 2 (April 2023 Dataset)

description: Library name: B2


title: B3brain

description:
Library name: B3brain
tissue.txt

value: Organ of No treated young mice (rep11)


title: 293T, HA-CIC(ex20)::NUTM1(ex6), replicate 1 (April 2023 Dataset)

description: Library name: B1


title: B2skin

description:
Library name: B2skin
tissue.txt

value: Organ of No treated young mice (rep10)


title: DpnII Hi-C on asynchronous mESCs R1

first: Marlies

last: Oomen

address: Feodor-Lynen-Strasse 21

institute: Helmholtz Zentrum München

description: 50bp paired-end sequenced

data_processing:
Sequence data was mapped to mm10 and processed using the publicly available distiller-nf pipeline and cooltools
For more information see methods section of associated publication
Assembly: mm10
Supplementary files format and content: multitire cooler files '.mcool' of all interactions

extract_protocol:
Cells were fixed with 1% formaldehyde and stored at -80C until further processing according to Hi-C protocol
DpnII Hi-C2.0 protocol as published by Belaghzal et al 2017 Methods

treatment_protocol: Mitotic cells for both C2C12 and mESCs were obtained using 50ng/mL Nocodazole (8hr and 6hr respectively) followed by a gentle shake off

value: Stem cells

value: Untreated


title: DpnII Hi-C on mitotic mESCs R1

description: 50bp paired-end sequenced

value: 6hr Nocodazole


title: Sample 610 TMA1 [012]

description: Library name: Sample 610 TMA1 [012]

value: Canine appendicular osteosarcoma samples


title: 293T, HA-CIC::DUX4, replicate 3 (April 2023 Dataset)

description: Library name: D3


title: Sample 610 TMA1 [011]

description: Library name: Sample 610 TMA1 [011]


title: 293T, empty vector, replicate 3 (April 2023 Dataset)

description: Library name: A3

value: empty vector transfected


title: 293T, empty vector, replicate 2 (April 2023 Dataset)

description: Library name: A2


title: B2liver

description:
Library name: B2liver
tissue.txt

value: Organ

value: WT

value: Organ of No treated young mice (rep9)


title: DpnII Hi-C on asynchronous mESCs R2

description: 50bp paired-end sequenced


title: B2kidney

description:
Library name: B2kidney
tissue.txt

value: Organ of No treated young mice (rep8)


title: Sample 309 TMA1 [009]

description: Library name: Sample 309 TMA1 [009]


title: DpnII Hi-C on mitotic mESCs R2

description: 50bp paired-end sequenced


title: Parse sequencing, sublibrary15 (contains all samples)

city: Baltimore

first: Sarah

middle: R

last: Amend

address: 600 N Wolfe St

department: Brady Urological Institute

description: Library name: sublibrary15

data_processing:
RNA barcodes were filtered on Total UMI Count ( > 500 UMIs), feature count ( > 350 features), and percentage of mitochondrial genes ( < 25%). Seurat v4.3.057 was used for handling of normalization, identification of variable genes, scaling, principal component analysis, UMAP dimensional reduction, and SNN generation followed by Leiden clustering.
Assembly: Human GRCh38/hg38
Supplementary files format and content: matrix file

growth_protocol: DMEM medium supplemented with 10%FBS and 1% penicilin/streptomycin

extract_protocol:
Cells were collected on timepoint day using tubes pre-coated with bovine serum albumin (BSA). Cell fixation was performed on timepoint day using Parse Biosciences Fixation kit (Parse Biosciences) according to manufacturer protocol, except for no cell filtering steps were performed. No cell filtering steps were performed during barcoding and library prep to prevent loss of the large cells surviving chemotherapy.
Barcoding and library prep for MDA-MB-231 cells untreated and surviving cisplatin or docetaxel was done using the Evercode Whole Transcriptome Mega kit according to manufacturer protocol (V2, Parse Biosciences). Sequencing was performed on an Illumina NovaSeq 6000 and alignment done using v0.7.2p alignment pipeline (Parse Biosciences).

value: untreated, 1, 5, and 10 DPT


title: Sample 701 TMA1 [008]

description: Library name: Sample 701 TMA1 [008]


title: B2gut

description:
Library name: B2gut
tissue.txt

value: Organ of No treated young mice (rep7)


title: B3kidney

description:
Library name: B3kidney
tissue.txt

value: Organ of No treated young mice (rep13)


title: 293T, empty vector, replicate 1 (April 2023 Dataset)

description: Library name: A1

value: human embryonic kidney


title: Parse sequencing, sublibrary14 (contains all samples)

description: Library name: sublibrary14


title: DpnII Hi-C on asynchronous C2C12 cells R1

city: München

description: 50bp paired-end sequenced

source_name: Myoblast

value: Myoblast

value: Myoblasts


title: B2brain

description:
Library name: B2brain
tissue.txt

value: Organ of No treated young mice (rep6)


title: Sample 702 TMA1 [006]

description: Library name: Sample 702 TMA1 [006]


title: sTO03, bulk, rep 3

city: Durham

first: Cole

last: McCutcheon

state: North Carolina

address: 3 Genome Court

department: Department of Integrative Immunobiology

institute: Duke University

description: Library name: sTO03_bulk_r3

data_processing:
QIAGEN CLC Genomics (v20)
genome build/assembly: Sus scrofa genome v11.1
processed data files format and content: mapped reads in .csv format

organism: Sus scrofa

source_name: swine tropoblast organoids

extract_protocol:
Total RNA was isolated with the Sigma GenElute total mammalian RNA miniprep kit (Cat # RTN350-1KT) or Qiagen RNAeasy Mini Kit (Cat #74104)
Illumina

value: swine tropoblast organoids


title: B1skin

description:
Library name: B1skin
tissue.txt

value: Organ of No treated young mice (rep5)


title: Parse sequencing, sublibrary13 (contains all samples)

description: Library name: sublibrary13


title: Sample 702 TMA1 [007]

description: Library name: Sample 702 TMA1 [007]


title: sTO03, bulk, rep 2

description: Library name: sTO03_bulk_r2


title: Sample 706 TMA1 [005]

description: Library name: Sample 706 TMA1 [005]


title: Sample 1405 TMA1 [010]

description: Library name: Sample 1405 TMA1 [010]


title: B1kidney

description:
Library name: B1kidney
tissue.txt

value: Organ of No treated young mice (rep3)


title: sTO03, bulk, rep 1

description: Library name: sTO03_bulk_r1


title: Parse sequencing, sublibrary12 (contains all samples)

description: Library name: sublibrary12


title: Parse sequencing, sublibrary11 (contains all samples)

description: Library name: sublibrary11


title: Sample 1001 TMA1 [004]

description: Library name: Sample 1001 TMA1 [004]


title: B1gut

description:
Library name: B1gut
tissue.txt

value: Organ of No treated young mice (rep2)


title: sTO02, bulk, rep 3

description: Library name: sTO02_bulk_r3


title: Parse sequencing, sublibrary10 (contains all samples)

description: Library name: sublibrary10


title: sTO02, bulk, rep 2

description: Library name: sTO02_bulk_r2


title: B1brain

description:
Library name: B1brain
tissue.txt

value: Organ of No treated young mice (rep1)


title: Sample 1001 TMA1 [003]

description: Library name: Sample 1001 TMA1 [003]

value: Canine appendicular osteosarcoma samples


title: Parse sequencing, sublibrary9 (contains all samples)

description: Library name: sublibrary9


title: sTO02, bulk, rep 1

description: Library name: sTO02_bulk_r1


title: Sample 1002 TMA1 [001]

description: Library name: Sample 1002 TMA1 [001]


title: A3skin

description:
Library name: A3skin
tissue.txt

value: Organ

value: Organ of ABPC_EVs treated old mice (rep15)


title: Parse sequencing, sublibrary8 (contains all samples)

description: Library name: sublibrary8


title: sTO01, bulk, rep 2

description: Library name: sTO01_bulk_r2


title: Parse sequencing, sublibrary7 (contains all samples)

description: Library name: sublibrary7


title: A3liver

description:
Library name: A3liver
tissue.txt

value: WT

value: Organ of ABPC_EVs treated old mice (rep14)


title: No Template Control

description: Library name: No Template Control


title: sTO01, bulk, rep 1

description: Library name: sTO01_bulk_r1


title: A3kidney

description:
Library name: A3kidney
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep13)


title: B1liver

description:
Library name: B1liver
tissue.txt

value: Organ of No treated young mice (rep4)


title: Parse sequencing, sublibrary6 (contains all samples)

description: Library name: sublibrary6

value: untreated, 1, 5, and 10 DPT


title: A3gut

description:
Library name: A3gut
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep12)


title: maternal-fetal interface, sample 94, visium

description: Library name: MFI094

data_processing:
Spaceranger v2.1.1
genome build/assembly: Sus scrofa genome v11.1
processed data files format and content: aligned_fiducials.jpg from Spaceranger v2.1.1
processed data files format and content: detected_tissue_image.jpg from Spaceranger v2.1.1
processed data files format and content: filtered_feature_bc_matrix.h5 from Spaceranger v2.1.1
processed data files format and content: scalefactors_json.json from Spaceranger v2.1.1
processed data files format and content: spatial_enrichment.csv from Spaceranger v2.1.1
processed data files format and content: tissue_hires_image.png from Spaceranger v2.1.1
processed data files format and content: tissue_lowres_image.png from Spaceranger v2.1.1
processed data files format and content: tissue_positions.csv from Spaceranger v2.1.1
Library strategy: Spatial Transcriptomics

source_name: swine placenta

extract_protocol:
Visium Spatial Transcriptomics
Illumina

value: swine placenta


title: Parse sequencing, sublibrary5 (contains all samples)

description: Library name: sublibrary5


title: A3brain

description:
Library name: A3brain
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep11)


title: maternal-fetal interface, sample 31, visium

description: Library name: MFI031


title: MLL-AF9_HMX3_X006_S09

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description:
Library name: MLL-AF9_HMX3_X006_S09
CAGE

data_processing:
rRNA reads were filtered. Reads were mapped using BWA (MAPQ >= 20). Reads with MAPQ < 20 were mapped again using HISAT2. Read bam files were processed to CTSS by HeliScopeCAGE read alignment. Bigwig files were generated using convertBED2BigWig from CAGEfightR R package.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: AML

extract_protocol:
RNA was isolated using Mini RNA Isolation II Kit (Zymo Research). 2 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for CAGE-seq were prepared by DNAFOM CAGE library preparation.

value: AML

value: high HMX3 MLL-AF9


title: A2skin

description:
Library name: A2skin
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep10)


title: MLL-AF9_HMX3_TH12_S08

description:
Library name: MLL-AF9_HMX3_TH12_S08
CAGE


title: Parse sequencing, sublibrary4 (contains all samples)

state: MD

description: Library name: sublibrary4


title: maternal-fetal interface, sample 25, visium

description: Library name: MFI025


title: MLL-AF9_HMX3_TH11_S07

description:
Library name: MLL-AF9_HMX3_TH11_S07
CAGE


title: Parse sequencing, sublibrary3 (contains all samples)

description: Library name: sublibrary3


title: Sample 1002 TMA1 [002]

description: Library name: Sample 1002 TMA1 [002]

source_name: Canine appendicular osteosarcoma samples


title: A2liver

description:
Library name: A2liver
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep9)


title: ARIH2-edited control NK cells from donor B80

city: Moonee Ponds

first: Nicholas

middle: D

last: Huntington

state: VIC

address: 27 Norwood Cres

country: Australia

institute: oNKo-innate Pty Ltd

description: Library name: B80_ARIH2

data_processing:
FASTQ files containing RNA sequencing data underwent processing with the Nextflow nf-core RNAseq pipeline (v3.5). Briefly, data underwent adapter trimming using cutadapt (v3.4), alignment with STAR (v2.6.1d) and quantification with Salmon (v1.5.2).
Assembly: GRCh38 (release 75; via iGenomes)
Supplementary files format and content: salmon.merged.gene_counts.tsv: gene-level count data obtained from salmon quantification against STAR aligment results
Supplementary files format and content: salmon.merged.gene_tpm_length_scaled.tsv: gene-level length-scaled TPM data obtained from salmon quantification against STAR aligment results

growth_protocol: For human NK cell isolation and cell culture, peripheral blood mononuclear cells (PBMC) were isolated from fresh buffy coats using density gradient centrifugation (Ficoll-Paque PLUS, Cytiva). Fresh buffy coats from healthy donors were obtained from the Australian Red Cross with ethical approval from the Monash University Human Research Ethics Committee (Project ID: 25946). Primary human NK cells were isolated from either fresh or cryopreserved PBMCs using the human NK cell isolation kit (Miltenyi Biotec, cat# 130-092-657). Feeder cells, modified K562 cells (ATCC) expressing 4-1BBL, membrane-bound IL-21 and mScarlet (termed iKE2-F9), were previously irradiated at 100 Gy, aliquoted and cryopreserved in 10% DMSO (Sigma) + 90% heat-inactivated FCS. iKE2-F9 cells were thawed and seeded at 1:2 (PB-derived NK) NK to feeder ratio, with a total of 0.5x106 cells seeded in a 48-well G-Rex well (Wilson Wolf Manufacturing) in NK growth media (NK MACS + Supplements (Miltenyi Biotec, cat# 130-114-429) + 10% human serum (Sigma)) + 5 ng/mL-1 IL-15 (premium grade, Miltenyi Biotec, cat# 130-095-764). Half of the media was refreshed as needed. Cells were reseeded at initial seeding density on day 7 with fresh iKE2-F9 feeders.

extract_protocol:
RNA isolation from sorted NK cells were extracted using a RNeasy Plus Mini Kit (QIAGEN), according to the manufacturer’s protocol. RNA samples were quantified using the Agilent 2200 TapeStation System (Agilent).
Next-generation sequencing libraries were prepared with quality-controlled RNA samples (RIN > 7.0) from at least three biological replicates per genotype using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). cDNA libraries were pooled and subjected to 75 bp paired-end sequencing on a NextSeq 500 next-generation sequencer (Illumina) to obtain approximately 20 million reads per sample.

treatment_protocol: For electroporation reactions, 1.5 μL Cas9 (61uM, purified in-house) was mixed with 1 μL sgRNA (100 μM, Synthego) and incubated for 10 min at RT before adding 1 μL Cas9 electroporation enhancer (100 μM, IDT, cat# 1075916) and K buffer up to 5 μL total volume. 1×106 day 7 K562-CSTX002 feeder-expanded NK cells were then added as 15 μL cell suspension, the resulting mixture transferred into 20 μL electroporation strips and pulsed using CM137 program (4D-Nucleofector X Unit, Lonza). Immediately after, 80 μL of warm complete media was added and the strips were transferred to the incubator at 37C for 30 min. Electroporated NK cells were then seeded in 48-well G-Rex in co-culture with the feeder cells at 1:2 E:T ratio for further expansion.

value: Blood

value: Natural killer cell

value: ARIH2-edited control

tag: batch


title: maternal-fetal interface, sample 17, visium

description: Library name: MFI017


title: A2kidney

description:
Library name: A2kidney
tissue.txt

value: Organ

value: Organ of ABPC_EVs treated old mice (rep8)


title: Parse sequencing, sublibrary2 (contains all samples)

description: Library name: sublibrary2


title: Parse sequencing, sublibrary1 (contains all samples)

description: Library name: sublibrary1


title: AAVS1-edited control NK cells from donor B80

description: Library name: B80_AAVS1

value: AAVS1-edited control


title: Pooled sample 23, backfat tissue, standard protein diet, indoor conditions

city: Ljubljana

first: Klavdija

last: Poklukar Žnidaršič

state: Ljubljana

address: Hacquetova ulica 17

department: Animal Science department

country: Slovenia

institute: Agricultural Institute of Slovenia

description: Library name: FAT23

data_processing:
Raw sequence data were converted into fastq files and de-multiplexed using Illumina bcl2fastq program (version 2.20).
The sequence reads were trimmed using Trimmomatic v.0.36
The trimmed reads were mapped to Sus scrofa 11.1 reference genome (release 108) using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated using featureCounts (Subread package v.1.5.2.) and summarized using the gene_id feature in the annotation file. Unique reads that fell within the exon region were counted.
Assembly: Sus scrofa 11.1
Supplementary files format and content: text files includes raw counts for each sample

source_name: Backfat tissue at the level of the last rib

extract_protocol:
RNeasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany)
NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA)

tag: breed

value: Krskopolje pig

value: standard protein diet

value: indoor system


title: A2gut

description:
Library name: A2gut
tissue.txt

value: WT

value: Organ of ABPC_EVs treated old mice (rep7)


title: Pooled sample 24, backfat tissue, standard protein diet, indoor conditions

description: Library name: FAT24

value: Backfat tissue at the level of the last rib


title: HCT116 cells, RPL22L1HaloTag expression

first: Marikki

last: Laiho

address: 1550 Orleans St

description: Illumina NovaSeq X Plus

data_processing:
Read 1 for paired-end reads from GoldCLIP libraries containing indexes were first demultiplexed by Ultraplex (v1.2.10) and the adapter sequences were trimmed by Cutadapt (v4.8). The reads were mapped to customized hg38 genomes with a curated rDNA locus (George et al., J Biol Chem. 2023;299(6):104766. doi: 10.1016/j.jbc.2023.104766) using STAR (2.7.10a)
Mapped reads were deduplicated to remove PCR duplicates using UMI-tools (1.1.5)
Mapped reads were split into two bam files with positive or negative strands for peak calling. MACS3 (v3.0.0a6) was used to call peaks
Assembly: hg38
Supplementary files format and content: bed, narrowPeak
Supplementary files format and content: bedGraph, narrowPeak

source_name: colon

growth_protocol: McCoy's5a Medium +10%FBS

extract_protocol:
GoldCLIP protocol (ref. Gu J, Wang M, Yang Y, Qiu D, Zhang Y, Ma J, Zhou Y, Hannon GJ, Yu Y. GoldCLIP: Gel-omitted Ligation-dependent CLIP. Genomics Proteomics Bioinformatics 2018;16(2):136-143)
GoldCLIP protocol (ref. Gu J, Wang M, Yang Y, Qiu D, Zhang Y, Ma J, Zhou Y, Hannon GJ, Yu Y. GoldCLIP: Gel-omitted Ligation-dependent CLIP. Genomics Proteomics Bioinformatics 2018;16(2):136-143)

value: colon

value: Human colorectal carcinoma cell line


title: Pooled sample 22, backfat tissue, standard protein diet, indoor conditions

description: Library name: FAT22


title: A2brain

description:
Library name: A2brain
tissue.txt

source_name: Organ

value: Organ of ABPC_EVs treated old mice (rep6)


title: ARIH2-edited NK cells from donor B78

description: Library name: B78_ARIH2

source_name: Blood


title: Pooled sample 21, backfat tissue, standard protein diet, indoor conditions

description: Library name: FAT21


title: HCT116 cells, RPL22 -HaloTag expression

description: Illumina NovaSeq X Plus

value: RPL22 -HaloTag


title: UBE2F-edited  NK cells from donor B80

description: Library name: B80_UBE2F


title: HCT116 cells, HaloTag expression

description: Illumina NovaSeq X Plus

value: HaloTag


title: Pooled sample 20, backfat tissue, standard protein diet, indoor conditions

description: Library name: FAT20


title: A1liver

description:
Library name: A1liver
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep4)


title: HCT116 cells, RPL22L1 knockout, rep3

data_processing:
Paired-end reads were mapped using HISAT2 software and StringTie was used to estimate transcript abundances and differential expression.
Assembly: hg38
Supplementary files format and content: RPL22_transcripts_FPKM.txt
Supplementary files format and content: txt, transcript expression (FPKM) table

extract_protocol:
Trizol extraction protocol
rRNA was removed using the Ribo-Zero kit. mRNA was fragmented randomly using fragmentation buffer, and cDNA was synthesized using random hexamer primers, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second strand synthesis. Double-stranded cDNA library construction was completed by size selection and PCR enrichment.

value: RPL22L1 knockout


title: AAVS1-edited control NK cells from donor B78

description: Library name: B78_AAVS1

value: Blood

value: Natural killer cell


title: Pooled sample 19, backfat tissue, standard protein diet, indoor conditions

description: Library name: FAT19


title: HCT116 cells, RPL22L1 knockout, rep2


title: UBE2F-edited NK cells from donor B77

description: Library name: B77_UBE2F


title: ARIH2-edited NK cells from donor B77

description: Library name: B77_ARIH2


title: AAVS1-edited control NK cells from donor B77

description: Library name: B77_AAVS1


title: A1kidney

description:
Library name: A1kidney
tissue.txt

value: Organ

value: Organ of ABPC_EVs treated old mice (rep3)


title: A1gut

description:
Library name: A1gut
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep2)


title: A1brain

description:
Library name: A1brain
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep1)


title: HCT116 cells, RPL22 reconstitution, rep3

value: RPL22 reconstitution


title: Pooled sample 18, backfat tissue, low protein diet, indoor conditions

description: Library name: FAT18

value: Krskopolje pig

value: low protein diet

value: indoor system


title: Old3

description:
Library name: Old3
blood.txt

value: WT

value: Blood of No treated old mice (rep3)


title: Pooled sample 16, backfat tissue, low protein diet, indoor conditions

description: Library name: FAT16

value: Backfat tissue at the level of the last rib


title: UBE2F-edited  NK cells from donor B78

description: Library name: B78_UBE2F


title: HCT116 cells, RPL22 reconstitution, rep2

value: colon

value: Human colorectal carcinoma cell line


title: Pooled sample 15, backfat tissue, low protein diet, indoor conditions

description: Library name: FAT15


title: Old2

description:
Library name: Old2
blood.txt

value: Blood of No treated old mice (rep2)


title: A1skin

description:
Library name: A1skin
tissue.txt

value: Organ of ABPC_EVs treated old mice (rep5)


title: HCT116 cells, RPL22 reconstitution, rep1


title: exo_1b

city: Bursa

first: Ceyda

last: Colakoglu Bergel

address: Görükle Kampüsü, Nilüfer

country: Turkey

institute: Bursa Uludag University

description: Library name: Sample 9

data_processing:
RPKM (reads per kilobase of exon per million reads mapped)-normalized count data from total RNA sequencing were used for analysis to identify differentially expressed genes and mature miRNAs via the R Bioconductor package “NOISeq”
Assembly: hg19
Supplementary files format and content: text files

source_name: exosome

growth_protocol: Serum derived exosome, After clinical examinations, peripheral blood (10-12 mL) was collected in PAXgene® Blood RNA Tubes for exosome isolation,

extract_protocol:
Firstly, plasma isolation was performed from blood samples before and 1 week after treatment. For this purpose, samples taken in PAXgene® Blood RNA Tube were centrifuged at 4000 rpm for 15 minutes and plasma was stored at -80 o . Then, exo-RNA isolation was performed using QIAGEN exoRNeasy Midi kit (Qiagen, Hilden, Germany). For exo isolation, exo bound with XBP were collected by passing PBS through the column, and characterization experiments were carried out. 1 ml plasma samples were transferred to 15 ml conical tubes and RNA isolation was performed. The plasma sample was mixed with 2X binding buffer (XBP) at a ratio of 1:1 and added to the exoEasy membrane affinity column. Then, the washed samples were lysed by adding QIAzol. The lysate was collected after centrifugation at 500 g and after adding chloroform, the aqueous phase was recovered and mixed with ethanol. The samples were added to the RNeasy MinElute spin column, centrifuged and, eluted with 30 µl of RNase- free water after washing
To perform RNA sequencing, mRNA and small RNA libraries were generated using the NGS sequencing Illumina NextSeq 500 platform with the SMARTer smRNA-Seq Kit (Illumina, Takara Bio, Shiga, Japan) according to the manufacturer’s instructions. The libraries were gel-purified and assessed using the D1000 ScreenTape System (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: This cohort study enrolled 41 patients diagnosed with NAMD at Bursa Uludağ University Department of Ophthalmology. In current study, bevacizumab was administered as the anti- VEGF treatment in patients with NAMD. Before and after the anti-VEGF treatment, the patients were examined at the Bursa Uludağ University Department of Ophthalmology and the data were recorded. Clinical examinations of the patients were recorded at 1 week, 1 month and 3 months.

value: exosome

value: serum-derived

value: serum-derived exosome

value: After treatment

tag: diagnosis

value: Neovascular Age-Related Macular Degeneration


title: P00296_2_2

description: Library name: Sample 7

tag: tissue


title: Pooled sample 14, backfat tissue, low protein diet, indoor conditions

description: Library name: FAT14

tag: treatment


title: Old1

description:
Library name: Old1
blood.txt

data_processing:
CLC Genomics Workbench w 11.0.1
Assembly: mm10
Supplementary files format and content: TPM

extract_protocol:
A NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs, USA, Catalog #: E7530L) was used according to the manufacturer's guidelines to construct sequencing libraries and incorporate index codes for sample identification
he prepared libraries were sequenced on an Illumina platform using the paired-end 150 strategy at the Novogene Bioinformatics Technology Co. Ltd., Beijing, China. The sequencing process converted the original fluorescence images into raw data, which were then processed in FASTQ format, capturing both nucleotide sequences and their corresponding quality scores

value: Blood

value: Blood of No treated old mice (rep1)


title: Pooled sample 13, backfat tissue, low protein diet, indoor conditions

description: Library name: FAT13

value: Krskopolje pig


title: HCT116 cells, parental cell, rep3

city: BALTIMORE

institute: Johns Hopkins University

value: parental cell


title: HCT116 cells, parental cell, rep2


title: exo_3b

description: Library name: Sample 5

value: Before treatment


title: Pooled sample 17, backfat tissue, low protein diet, indoor conditions

description: Library name: FAT17

value: low protein diet

value: indoor system


title: Pooled sample 12, backfat tissue, low protein diet, outdoor conditions

description: Library name: FAT12

value: Backfat tissue at the level of the last rib

value: outdoor system


title: P00296_1_2

description: Library name: Sample 6


title: HCT116 cells, parental cell, rep1

value: colon

value: Human colorectal carcinoma cell line


title: ABMC_EVs1

description:
Library name: ABMC_EVs1
blood.txt

value: WT

value: Blood of ABMC_EVs treated old mice (rep1)


title: ABMC_EVs2

description:
Library name: ABMC_EVs2
blood.txt

value: Blood of ABMC_EVs treated old mice (rep2)


title: FBMC_EVs3

description:
Library name: FBMC_EVs3
blood.txt

value: Blood of FBMC_EVs treated old mice (rep3)


title: P00296_3

description: Library name: Sample 3

value: exosome

value: serum-derived

value: serum-derived exosome


title: P00296_2

description: Library name: Sample 2

value: Neovascular Age-Related Macular Degeneration


title: HCT116 cells, RPL22L1 knockout, rep1

value: RPL22L1 knockout


title: Pooled sample 10, backfat tissue, low protein diet, outdoor conditions

description: Library name: FAT10

value: Krskopolje pig


title: Pooled sample 9, backfat tissue, low protein diet, outdoor conditions

description: Library name: FAT9


title: P00296_1

description: Library name: Sample 1

value: Before treatment


title: FBMC_EVs2

description:
Library name: FBMC_EVs2
blood.txt

value: Blood

value: Blood of FBMC_EVs treated old mice (rep2)


title: Pooled sample 8, backfat tissue, low protein diet, outdoor conditions

description: Library name: FAT8

value: Backfat tissue at the level of the last rib

value: low protein diet