title: Long-chain polyphosphate stimulated, snATAC-seq, biological replicate 4

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 E Concord Street

department: Pulmonary Centre, Department of Medicine

institute: Boston University

data_processing:
The mkref module in 10X Genomics cellranger-arc (v2.0.1) was used to generate the GRCm39 mouse genome reference based on the fasta and GTF files from Gencode (vM33) and the JASPAR 2022 core vertebrates non-redundant pfm file, following the 10X Genomics tutorial.
Cellranger-arc was used to quantify the multiome fastq files based on GRCm39 mouse genome reference.
The filtered matrix and fragments file were loaded in Rstudio Server running R (v4.1.2) for further processing using Seurat (v4.1.1) and Signac (v1.7.0).
A GRCm39 annotation file was generated separately in R (v4.3.1) using the AnnotationHub (v3.10.1) package based on Ensembl database (v110), with annotations set to UCSC style.
After annotating the data based on GRCm39, low-quality cells were filtered, and peak calling was perfomed through Signac's wrapper for MACS2 using the default parameters. This was followed by filtering out blacklisted regions for mm39. The mm39 blacklisted regions were downloaded from the exclusion set from the  developers of excluderanges package (https://drive.google.com/drive/folders/1sF9m8Y3eZouTZ3IEEywjs2kfHOWFBSJT).
Further analysis were performed as per the Seurat/Signac tutorial.
Assembly: GRCm39/mm39
Supplementary files format and content: Cellranger-arc output files: HDF5 file of the filtered counts matrix: filtered_feature_bc_matrix.h5, ATAC peak fragment files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: Peritoneum

growth_protocol: Peritoneal cells were isolated by lavage from healthy untreated C57BL/6JRj mice as described before (Roewe, Julian et al.  Nature communications vol. 11,1 4035. 12 Aug. 2020, doi:10.1038/s41467-020-17639-x).

extract_protocol:
7-AAD-CD45+ cells were flow sorted and nuclei were isolated according to the manufacturer's instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 10xGenomics, Pleasanton, CA, USA).
Library preparation was performed following manufacturer's instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 10xGenomics, Pleasanton, CA, USA).
Single-nucleus ATAC (assay for transposase-accessible chromatin) and gene expression sequencing

treatment_protocol: 1.5 x 10^6 cells in 1.5 ml medium on a 6-well plate were stimulated with long chain polyphosphates for 18 hours or left untreated.

value: Peritoneum

value: Immune cells

value: wild type

value: Long-chain polyphosphates


title: mouse rRNA-depleted total-RNA seq Brain Ftsj1_DF 1654

status: Public on Mar 17 2026

type: SRA

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

description:
Library name: 22Jan49-G01-L3_S55_L003_R1_001
rRNA-depleted total-RNA seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

library_source: transcriptomic

data_processing:
Samples sequenced across 2 flowcells are concatenated
Samples are mapped to the mouse genome GRCm39 using NextGenMap (v0.5.5)
For the poly-A data genes are counted using featureCounts (subread-2.0.3) with the full Ensembl annotation (v108). The rRNA-depletion total RNA seq data is counted four times, using the Ensembl annotation filtered to gene_biotype “lncRNA”, “snRNA”, and “snoRNA” and the RNAcentral annotation filtered to “tRNA”.
Four each respective dataset, DESeq2 is used organ-wise to perform differential expression analysis
Assembly: GRCm39, annotation version 108
Supplementary files format and content: DESeq2 output of each experiment as csv-file. As differential expression was done individually for each ncRNA type, 4 output files are created for the rRNA-depleted total RNA seq data.

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: All mice were fed ad libitum and had acces to water until euthanization

extract_protocol:
Tissues were extracted and frozen on dry ice. A bead mill (Retsch, Düsseldorf, Germany) was used to pulverize the tissue. RNA was subsequently extracted from the tissue powder using PeqGold TRIFAST, a phenol-based extraction protocol, (VWR, Germany) according to the manufacturer's protocol. RNA integrity was visualized using a Bioanalyzer (Agilent, Santa Clara, CA, USA)
Each sample was prepared for library construction separately. The 60 libraries were prepared using the (30x) Illumina stranded mRNA Prep and (30x) Illumina stranded total RNA Prep (Illumina, San Diego, CA, USA) according to the manufacturer's recommendations

treatment_protocol: No special treatments were carried out

tag: tissue

value: Brain

tag: cell line

value: male. 4 months old

tag: cell type

value: whole Brain tissue

tag: genotype

tag: batch


title: Long-chain polyphosphate stimulated, snRNA-seq, biological replicate 3

country: USA

library_source: transcriptomic single cell

molecule: nuclear RNA

tag: treatment


title: TCR_ICI27

city: Rochester

first: Hu

last: Zeng

state: MN

address: 209 Third Ave SW

department: Rheumatology

institute: Mayo Clinic

description:
Library name: Sample52
ICI control (ICI)

library_source: other

data_processing:
Cell type annotation was conducted using the Azimuth package with the Human PBMC reference dataset.
To refine cell type classifications, we manually reviewed cluster-specific gene markers identified by Immunopipe and further annotated subpopulations of CD8 T cells. Gene set enrichment analysis was performed using the clusterProfiler package in R.
Additionally, ANOVA test was applied to compare gene expression scores across patient groups for selected genes involved in the CD8 T cell cytotoxicity pathway.
Assembly: GRCh38
Supplementary files format and content: vdj_filtered_contig_annotations.csv

molecule: other

organism: Homo sapiens

source_name: PBMC

growth_protocol: Blood samples were collected into sodium heparin tubes, and plasma was collected after centrifuging at 4 °C, 1300 rpm for 10 mins.

extract_protocol:
Specifically, 13 mL Ficoll-Paque™ PLUS density gradient media (GE Healthcare, Cat# 17-1440-02) were added to the bottom of 30 mL diluted peripheral blood, and centrifuged at 4 °C, 400 g for 25 min with the acceleration and deceleration at lower speed. The PBMC layer was collected and washed with wash buffer (1×PBS + 10 mM HEPES + 0.1% BSA + 2 mM EDTA), and PBMCs were aliquoted and cryopreserved in a liquid nitrogen tank.
FASTQ files generated from the Gene Expression and Feature Barcode libraries were processed using the 10x Genomics Cell Ranger multi pipeline to create expression matrices for downstream analysis.
Integrated single-cell analysis of gene expression and T cell receptor data was performed using the Immunopipe package.

treatment_protocol: Peripheral blood mononuclear cells were isolated from the peripheral blood using Ficoll-Paque gradient centrifugation.

value: PBMC

tag: sample group

value: ICI control (ICI)


title: mouse poly-A seq Spleen WT 1655

description:
Library name: 22Jan49-D01-L1_S13_L001_R1_001
poly-A seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

molecule: polyA RNA

source_name: Spleen

value: Spleen

value: whole Spleen tissue

value: WT


title: Colony 107 Forager Day 26 Replicate 1

city: Edmonton

first: Olav

last: Rueppell

state: Alberta

address: 11355 - Saskatchewan Drive

department: Biological Sciences

country: Canada

institute: University of Alberta

description:
Library name: Sample 9
All samples were prepared together using an in-house TagSeq library preparation.

data_processing:
FastQC
TagTrimmer.pl & RemovePCRDups.pl
HiSat2
Samtools
Deseq2 in R
Assembly: GCF_003254395.2
Supplementary files format and content: csv files containing the cumulative read counts for genes for each sample from Deseq2

organism: Apis mellifera

source_name: Whole bee

growth_protocol: 1-day-old adults were equally dispered to three different nuclear hives with existing queens and honey frames. Bees inside the colony were undisturbed.

extract_protocol:
Honey bees were captured on days 7 and 26 in order. Nurses and foragers were grabbed and frozen on dry ice and left in -80 until further analysis
RNA libraries were created using an in-house TagSeq protocol

treatment_protocol: Untreated

value: Whole bee

value: untreated


title: Colony 107 Nurse Day 7 Replicate 2

description:
Library name: Sample 6
All samples were prepared together using an in-house TagSeq library preparation.


title: TCR_H013

description:
Library name: Sample49
healthy control (HC)

value: healthy control (HC)


title: mouse rRNA-depleted total-RNA seq Brain Ftsj1_DF 1647

description:
Library name: 22Jan49-B02-L3_S36_L003_R1_001
rRNA-depleted total-RNA seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Long-chain polyphosphate stimulated, snRNA-seq, biological replicate 4


title: TCR_ANRF-22

description:
Library name: Sample47
rheumatoid arthritis control (RAC)

value: rheumatoid arthritis control (RAC)


title: Colony 107 Nurse Day 7 Replicate 3

description:
Library name: Sample 7
All samples were prepared together using an in-house TagSeq library preparation.


title: Long-chain polyphosphate stimulated, snATAC-seq, biological replicate 2

library_source: genomic

molecule: genomic DNA


title: TCR_ANRF24

description:
Library name: Sample48
healthy control (HC)


title: TCR_ANRF-08

description:
Library name: Sample45
healthy control (HC)


title: mouse poly-A seq Spleen WT 1653

description:
Library name: 22Jan49-H01-L1_S28_L001_R1_001
poly-A seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 107 Nurse Day 7 Replicate 3 #2

description:
Library name: Sample 8
All samples were prepared together using an in-house TagSeq library preparation.


title: TCR_ANRF-16

description:
Library name: Sample46
rheumatoid arthritis control (RAC)


title: Colony 107 Forager Day 26 Replicate 2

description:
Library name: Sample 10
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 107 Nurse Day 7 Replicate 1

description:
Library name: Sample 5
All samples were prepared together using an in-house TagSeq library preparation.


title: Long-chain polyphosphate stimulated, snATAC-seq, biological replicate 3


title: mouse poly-A seq Spleen WT 1646

description:
Library name: 22Jan49-A04-L1_S4_L001_R1_001
poly-A seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: mouse poly-A seq Spleen Ftsj1_DF 1656

description:
Library name: 22Jan49-E03-L1_S19_L001_R1_001
poly-A seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Long-chain polyphosphate stimulated, snATAC-seq, biological replicate 1


title: mouse poly-A seq Spleen Ftsj1_DF 1647

description:
Library name: 22Jan49-A03-L1_S3_L001_R1_001
poly-A seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 107 Forager Day 7 Replicate 3 #2

description:
Library name: Sample 4
All samples were prepared together using an in-house TagSeq library preparation.


title: TCR_ANRF-06

description:
Library name: Sample44
rheumatoid arthritis control (RAC)


title: mouse poly-A seq Spleen Ftsj1_DF 1654

description:
Library name: 22Jan49-D02-L1_S14_L001_R1_001
poly-A seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Long-chain polyphosphate stimulated, snRNA-seq, biological replicate 2


title: TCR_ANRF05

description:
Library name: Sample43
rheumatoid arthritis control (RAC)


title: Long-chain polyphosphate stimulated, snRNA-seq, biological replicate 1


title: Colony 107 Forager Day 7 Replicate 2

description:
Library name: Sample 2
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 107 Forager Day 7  Replicate 1

description:
Library name: Sample 1
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse poly-A seq Liver WT 1653

description:
Library name: 22Jan49-F04-L1_S24_L001_R1_001
poly-A seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Liver

value: Liver

value: whole Liver tissue


title: mouse poly-A seq Liver WT 1646

description:
Library name: 22Jan49-A01-L1_S1_L001_R1_001
poly-A seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Unstimulated, snATAC-seq, biological replicate 3

value: Peritoneum

value: Immune cells

value: Unstimulated


title: Unstimulated, snATAC-seq, biological replicate 4

value: wild type


title: mouse poly-A seq Liver WT 1655

description:
Library name: 22Jan49-D03-L1_S15_L001_R1_001
poly-A seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old


title: mouse poly-A seq Liver Ftsj1_DF 1656

description:
Library name: 22Jan49-G02-L1_S26_L001_R1_001
poly-A seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: TCR_ANRF03

description:
Library name: Sample41
immune-related adverse event (irAE)

value: immune-related adverse event (irAE)


title: SB 22 696

type: RNA

city: Bethesda

first: Laurie

middle: T

last: Krug

state: MD

address: Building 10, 9000 Rockville Pike

institute: NIH

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S44

hyb_protocol: NanoString nCounter

scan_protocol: NanoString nCounter

data_processing: Applying RUV

label: color-coded fluorescent tags

source_name: cutaneous KS tumor

label_protocol: NanoString nCounter

extract_protocol: total RNA

value: cutaneous KS tumor

tag: diagnosis

value: N

value: Yes

value: Non-Responder

tag: response

value: Low

value: Not detectable

tag: meankshv

value: below


title: Unstimulated, snRNA-seq, biological replicate 4


title: eCLIP-Seq, A549, MYC, IP, rep1

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

description: Library name: eCLIP_A549_MYC_IP_rep1

data_processing:
Briefly, we followed CLIP Tool Kit (CTK) pipeline for most of the data processing steps and used MACS2 to do peak calling, as previously described (PMID: 40378850).
For each cell line, eCLIP-Seq data were first demultiplexed using fastx_barcode_splitter.pl from fastx-toolkit, with default parameters, yielding two IP replicates and one input sample. The adapters were trimmed using Cutadapt with “--match-read-wildcards --times 1 --quality-cutoff 5 -O 1 -m 15 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGGCTA -a ATTGCTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a ACAAGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a AACTTGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a AGGACCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG ” parameters and the low-quality reads were dropped.
Then, the analysis was mainly based on CTK pipeline. Briefly, the exact PCR duplicates were collapsed using fastq2collapse.pl with default parameters. The 10-nt random-mers were removed from read 2 and stored in the read ID for further analysis, using stripBarcode.pl with default parameters. The processed read 2 sequences were mapped to the hg38 genome using bwa (Li and Durbin, 2009), with parameters “-t 4 -n 0.06 -q 20”. Only uniquely mapped reads were kept for further analysis. Tags from rRNA and repetitive RNA were removed using tagoverlap.pl with recommended parameters. Then, based on the random-mers, the PCR duplicates were collapsed using tag2collpase.pl with recommended parameters. For each replicate, we separated the reads into plus and minus strand.
Next, we used MACS2 to do peak calling by the following steps. (1) For each replicate, we first call peaks in IP to identify the potential RNA binding sites with “--keep-dup all --nomodel -s $tagsize --extsize 100 --max-gap 50 -q 1e-2” parameters. Since the length eCLIP-Seq reads various a lot after adapter trimming, the average “tagsize” was calculated by an ad hoc script. These peaks are considered as “IP-only” peaks. (2) To identify MYC-specific binding peaks, we called peak by comparing IP versus input with the same parameters. These peaks are considered as “enriched” peaks. (3) “IP-only” peaks that are overlapped with the “enriched” peaks are considered as MYC-specific binding sites (enriched in IP). (4) Then the overlapped MYC-specific binding sites from the two replicates were considered as the reproducible MYC-specific binding sites. (5) To make downstream analysis simple and get a uniform peak list for each cell line, replicates of IP were merged and then used to call peaks by comparing the merged IP with input using the same parameters. The peaks that overlap with the reproducible MYC-specific binding sites will be considered as the final peak list and used for following analysis. Finally, for each sample, peaks from plus and minus strands were merged as the MYC eCLIP-Seq peaks for each sample.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using CTK “tag2profile.pl” with “-ss -exact --normalize multiply==$factor -of bedgraph” in which factor indicates the counts per million (CPM) normalization factor. Then the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.

growth_protocol: A549 cell lines were obtained from the American Type Culture Collection (ATCC) and maintained as suggested by ATCC’s guidelines.

extract_protocol:
Protein-associated RNAs by eCLIP and input RNAs were extracted using acid phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.6) (Invitrogen) and RNA cleanup was performed with RNA Clean & Concentrator-5 columns (Zymo). After reverse transcription, qPCR was performed to the Ct value of the cDNA with Power SYBR Green Master Mix (Applied Biosystems).
eCLIP-seq libraries were prepared with primers containing Illumina adapter sequences using Q5 High-Fidelity 2× Master Mix (NEB) for 9 to 18 cycles and PCR products were purified with Agencourt AMPureXP beads (Beckman Coulter). After separating on a 3% Nusieve GTG agarose gel (Lonza), DNA ranging from 175 - 300 bp gel fragments was excised and extracted using the MinElute Gel Extraction Kit (Qiagen) and libraries were validated using the 1× High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Cells at the exponential phase were washed twice with ice-cold PBS, UV-crosslinked on ice with 254 nm at 400 mJ/cm2 with a UV crosslinker (XL-1000, Spectrolinker). For each reaction, 20 million cells were lysed in eCLIP lysis buffer for 15 min on ice and incubated at 37°C for 5 min with RNase I (Ambion) and Turbo DNase (Ambion) on a ThermoMixer C (Eppendorf).

tag: eclip antibody


title: Colony 107 Forager Day 7 Replicate 3

description:
Library name: Sample 3
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee

value: WT

value: untreated


title: Unstimulated, snRNA-seq, biological replicate 3


title: mouse poly-A seq Liver Ftsj1_DF 1647

description:
Library name: 22Jan49-F01-L1_S21_L001_R1_001
poly-A seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Liver

value: whole Liver tissue


title: eCLIP-Seq, A549, MYC, IP, rep2

description: Library name: eCLIP_A549_MYC_IP_rep2


title: SB 22 2963

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S43

value: No

value: Responder

value: Y

value: High


title: Unstimulated, snATAC-seq, biological replicate 2

value: Peritoneum

value: Immune cells

value: wild type

value: Unstimulated


title: Unstimulated, snRNA-seq, biological replicate 2


title: eCLIP-Seq, A549, input

description: Library name: eCLIP_A549_input


title: mouse poly-A seq Liver Ftsj1_DF 1654

description:
Library name: 22Jan49-B04-L1_S8_L001_R1_001
poly-A seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old


title: SB 22 2594

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S41

value: cutaneous KS tumor

value: N

value: Yes

value: Non-Responder

value: Low


title: Unstimulated, snATAC-seq, biological replicate 1


title: UMSCC01 oral fibroblast secretome 3

city: Manchester

first: Amaya

last: Viros

address: Wilmslow Road

department: Skin Cancer Ageing

country: United Kingdom

institute: Cancer Research UK

description: Library name: UMSCC01_oral_3

data_processing:
The RNA sequencing reads underwent quality checking using the FASTQC program. Then, Trim Galore v. 0.6.10 was utilized to inspect and remove adapter contamination. Subsequently, the clean reads were aligned to the human reference genome assembly (GRCh38) using the STAR aligner v.2.5.1b in either single-end or paired-end mode based on the sequencing protocol, with default parameters. The mapped data were then converted to gene level integer read counts using featureCounts and the Ensemble gene annotation (Homo_sapiens.GRCh38.85.gtf).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts for all samples

growth_protocol: Cells were seeded at 80% confluence a day prior to the treatment. Prior to treatment, cells were washed twice with PBS.

extract_protocol:
RNA from cells were extracted using Qiagen RNA extraction kit (Qiagen, Cat no. 74104) as per manual instructions
Libraries were prepared by Azenta/GENEWIZ using their Standard Bulk RNA-Seq workflow with poly(A) selection and sequenced on an Illumina NovaSeq platform (paired-end 2×150 bp)

treatment_protocol: SCC cells were treated for 24 hours with serum free DMEM (control) or serum free conditioned media (DMEM) collected from dermal, oral, or lung fibroblasts. Conditioned media was collected by culturing firboblasts in serum free DMEM for 72 hours before collecting secretome. Serum free DMEM contained 1% penicillin streptomycin, 1x L-glutamine.

value: Head and neck SCC

value: Oral fibroblst secretome


title: Unstimulated, snRNA-seq, biological replicate 1


title: mouse poly-A seq Kidney WT 1653

description:
Library name: 22Jan49-B03-L1_S7_L001_R1_001
poly-A seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Kidney

value: Kidney

value: whole Kidney tissue

value: WT


title: SB 22 1394

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S33

value: KS

value: Y

value: Not detectable

value: below


title: UMSCC01 oral fibroblast secretome 1

description: Library name: UMSCC01_oral_1


title: SB 22 1215

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S40

value: High


title: SB 22 2794

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S42

value: above


title: UMSCC01 oral fibroblast secretome 2

description: Library name: UMSCC01_oral_2


title: SB 21 9542

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S24

value: No

value: Responder

value: Detectable


title: UMSCC01 lung fibroblast secretome 2

description: Library name: UMSCC01_lung_2

value: Lung firboblast secretome


title: Pre-Enriched Cerebellum, Integrated-ACE-Seq

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

description: Library name: PreEnrichedCerebellumIntegratedACE

data_processing:
For ACE/EM-Seq samples, raw reads were trimmed for base quality and adaptor sequences using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and reads below a length of 20 bases were discarded.
For ACE/EM-Seq samples, the trimmed reads were then aligned to the reference genomes using Bismark (v0.22.3) with the following parameters -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2.
For ACE/EM-Seq samples, to account for A3A failure due to double-stranded DNA, reads with three or more consecutive non-converted cytosines in the CpH context were removed using the filter_non_conversion script included in the Bismark package.
For Integrated-Seq samples, the Epimatcher code used for processing Integrated-Seq data is described and available at https://github.com/zhou-lab/epimatcher/tree/main
Assembly: mm10
Supplementary files format and content: Bismark.cov is a tab-delimited file containing the chromosome, start position, end position, methylation percentage, count methylated, count unmethylated
Supplementary files format and content: Mods.bed is a tab-delimited file containing the chromosome, start position, end position, count methylated, count hydroxymethylated, count unmethylated

source_name: Cerebellum

extract_protocol:
Genomic DNA from different tissue types (cerebellum, heart, kidney, blood) were extracted from C57BL/6J mice (Jackson Labs). Extraction was carried out using a phenol/chloroform/isoamyl alcohol protocol. 500 µL of the lysed mouse tissues were transferred to pre-centrifuged (at 20,000g for 1 min) 5PRIME Phase Lock Gel tube (Quanta bio, 10847- 802). In a fume hood, 500 µL of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich, 77617) was added to the phase Lock Gel tube. The aqueous phase was then transferred to a new 1.5 mL tube. 500 µl of 100% isopropanol (MilliporeSigma), 1.7 µl of GlycoBlue (Invitrogen), and 33 µl of 7.5 M ammonium acetate solution (Sigma-Aldrich) were added. The mixture was vortexed and incubated at -20°C for 30 min overnight. The samples were subsequently centrifuged at 16,000g for 30 min at 4°C. Following centrifugation, the samples were washed twice with 1 mL of 70% ethanol (MilliporeSigma). After the final wash and removal of 70% ethanol, the samples were air-dried for 10 min and then resuspended in 46 to 200 µL of Tris buffer pH 8.0 at 55°C for 10 min. If the DNA was not fully dissolved, it was further incubated at 4°C for one to two days. DNA concentration was measured using a Qubit 4.0 Fluorometer (Invitrogen) with the dsDNA HS Assay Kit (Invitrogen).
For shallow-sequenced mouse tissues, 30 ng of purified mouse gDNA was mixed with 5% of unmethylated λ gDNA spike-in and 5% 5mCpG methylated plasmid spike-in, in a total volume of 50 µL in low TE buffer. This input DNA was then sheared to 350 bp using a Covaris instrument. Each sample was then split three ways to serve as technical replicates, with each treated as a sample starting from a 10 ng input. Libraries were prepared using the ACE-Seq, EM-Seq, Integrated ACE-Seq, or Integrated EM-Seq protocols detailed in the corresponding manuscript. Final libraries were quantified with a Qubit HS kit (Invitrogen), assessed for quality using an Agilent TapeStation D1000, and sequenced on an Illumina MiSeq. For deeply sequenced samples, the same protocol was used except with 50 ng of input used, without splitting.

value: Cerebellum


title: mouse poly-A seq Kidney Ftsj1_DF 1654

description:
Library name: 22Jan49-B01-L1_S5_L001_R1_001
poly-A seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old


title: Blood, Integrated-EM-Seq, rep3

description: Library name: BloodIntegratedEMrep3

source_name: Blood

value: Blood


title: mouse poly-A seq Kidney Ftsj1_DF 1656

description:
Library name: 22Jan49-C04-L1_S12_L001_R1_001
poly-A seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: mouse poly-A seq Kidney WT 1646

description:
Library name: 22Jan49-A02-L1_S2_L001_R1_001
poly-A seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Enriched Cerebellum, Integrated-ACE-Seq

description: Library name: EnrichedCerebellumIntegratedACE


title: UMSCC01 lung fibroblast secretome 1

description: Library name: UMSCC01_lung_1

value: Head and neck SCC


title: Blood, Integrated-EM-Seq, rep2

description: Library name: BloodIntegratedEMrep2


title: mouse poly-A seq Kidney Ftsj1_DF 1647

description:
Library name: 22Jan49-F02-L1_S22_L001_R1_001
poly-A seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Kidney


title: UMSCC01 lung fibroblast secretome 3

description: Library name: UMSCC01_lung_3


title: mouse poly-A seq Kidney WT 1655

description:
Library name: 22Jan49-G03-L1_S27_L001_R1_001
poly-A seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: whole Kidney tissue


title: SB 21 6978

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S21

value: cutaneous KS tumor

value: N

value: Yes

value: Non-Responder

value: Low


title: SB 21 8797

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S23

value: Not detectable

value: below


title: mouse poly-A seq Heart WT 1655

description:
Library name: 22Jan49-E04-L1_S20_L001_R1_001
poly-A seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Heart

value: Heart

value: whole Heart tissue

value: WT


title: Blood, Integrated-EM-Seq, rep1

description: Library name: BloodIntegratedEMrep1


title: UMSCC01 dermal fibroblast secretome 2

description: Library name: UMSCC01_dermal_2

value: Dermal fibroblast secretome


title: SB 21 7662

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S22

value: KS

value: Y

value: No

value: Responder


title: UMSCC01 dermal fibroblast secretome 3

description: Library name: UMSCC01_dermal_3

value: Head and neck SCC


title: UMSCC01 dermal fibroblast secretome 1

description: Library name: UMSCC01_dermal_1


title: mouse poly-A seq Heart WT 1653

description:
Library name: 22Jan49-C02-L1_S10_L001_R1_001
poly-A seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old


title: Kidney, Integrated-EM-Seq, rep3

description: Library name: KidneyIntegratedEMrep3

value: Kidney


title: SB 21 4614

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S20

value: cutaneous KS tumor

value: N

value: Detectable


title: SB 21 3933

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S19

value: Yes

value: Non-Responder

value: Low

value: High

value: above


title: Kidney, Integrated-EM-Seq, rep1

description: Library name: KidneyIntegratedEMrep1


title: TCR_ANRF-04

description:
Library name: Sample42
healthy control (HC)

value: PBMC

value: healthy control (HC)


title: mouse poly-A seq Heart Ftsj1_DF 1656

description:
Library name: 22Jan49-E01-L1_S17_L001_R1_001
poly-A seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Heart

value: whole Heart tissue


title: UMSCC01 serum free control 1

description: Library name: UMSCC01_control_1

value: Control


title: UMSCC01 serum free control 3

description: Library name: UMSCC01_control_3


title: SB 21 11361

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S39

value: KS

value: Y

value: Not detectable

value: below


title: UMSCC01 serum free control 2

description: Library name: UMSCC01_control_2

value: Head and neck SCC


title: mouse poly-A seq Heart WT 1646

description:
Library name: 22Jan49-H02-L1_S29_L001_R1_001
poly-A seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old

value: WT


title: Kidney, Integrated-EM-Seq, rep2

description: Library name: KidneyIntegratedEMrep2

value: Kidney


title: SKMES1 oral fibroblast secretome 3

description: Library name: SKMES1_oral_3

value: Lung SCC

value: Oral fibroblst secretome


title: mouse poly-A seq Heart Ftsj1_DF 1647

description:
Library name: 22Jan49-F03-L1_S23_L001_R1_001
poly-A seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: mouse poly-A seq Brain WT 1655

description:
Library name: 22Jan49-E02-L1_S18_L001_R1_001
poly-A seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Brain

value: whole Brain tissue


title: Heart, Integrated-EM-Seq, rep1

description: Library name: HeartIntegratedEMrep1


title: SKMES1 oral fibroblast secretome 1

description: Library name: SKMES1_oral_1


title: Heart, Integrated-EM-Seq, rep3

description: Library name: HeartIntegratedEMrep3


title: mouse poly-A seq Brain WT 1653

description:
Library name: 22Jan49-C01-L1_S9_L001_R1_001
poly-A seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: SKMES1 lung fibroblast secretome 3

description: Library name: SKMES1_lung_3

value: Lung firboblast secretome


title: SB 20 3779

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S14

value: cutaneous KS tumor

value: unknown

value: Low

value: N

value: above


title: Cerebellum, Integrated-EM-Seq, rep2

description: Library name: CerebellumIntegratedEMrep2

value: Cerebellum


title: mouse poly-A seq Brain WT 1646

description:
Library name: 22Jan49-D04-L1_S16_L001_R1_001
poly-A seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Heart, Integrated-EM-Seq, rep2

description: Library name: HeartIntegratedEMrep2

value: Heart


title: SB 20 1637

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S11

value: Yes

value: Non-Responder

value: Detectable

value: Y


title: SB 21 2796

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S18

value: KS


title: mouse poly-A seq Brain Ftsj1_DF 1656

description:
Library name: 22Jan49-H03-L1_S30_L001_R1_001
poly-A seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old


title: SB 21 11056

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S17

value: Not detectable

value: below


title: SKMES1 oral fibroblast secretome 2

description: Library name: SKMES1_oral_2

value: Lung SCC

value: Oral fibroblst secretome


title: SKMES1 dermal fibroblast secretome 3

description: Library name: SKMES1_dermal_3

value: Dermal fibroblast secretome


title: SB 19 7884

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S9

value: cutaneous KS tumor

value: unknown

value: High


title: Cerebellum, Integrated-EM-Seq, rep3

description: Library name: CerebellumIntegratedEMrep3


title: mouse poly-A seq Brain Ftsj1_DF 1647

description:
Library name: 22Jan49-B02-L1_S6_L001_R1_001
poly-A seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Brain

value: whole Brain tissue


title: mouse poly-A seq Heart Ftsj1_DF 1654

description:
Library name: 22Jan49-C03-L1_S11_L001_R1_001
poly-A seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Heart

value: whole Heart tissue


title: SKMES1 lung fibroblast secretome 2

description: Library name: SKMES1_lung_2

value: Lung firboblast secretome


title: SB 21 10183

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S16

value: Yes

value: Responder

value: Low

value: Detectable


title: SB 19 7967

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S10

value: KS

value: Y

value: Non-Responder

value: N

value: Not detectable


title: SKMES1 lung fibroblast secretome 1

description: Library name: SKMES1_lung_1

value: Lung SCC


title: SB 20 6585

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S15

value: cutaneous KS tumor

value: below


title: Blood, EM-Seq, rep2

description: Library name: BloodEMrep2

value: Blood


title: Cerebellum, Integrated-EM-Seq, rep1

description: Library name: CerebellumIntegratedEMrep1

value: Cerebellum


title: mouse poly-A seq Brain Ftsj1_DF 1654

description:
Library name: 22Jan49-G01-L1_S25_L001_R1_001
poly-A seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Brain

value: male. 4 months old

value: whole Brain tissue


title: SB 19 7845

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S7

value: Yes


title: SB 19 5920

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S30

value: No

value: Responder


title: mouse circRNA Spleen WT 1655 batch 2

description:
Library name: 221000001049-DS17_22Oct1049-DL017_S17_L001_R1_001_b2
circRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

data_processing:
Samples sequenced across 2 flowcells are concatenated
Samples are mapped to the mouse genome GRCm39 using BWA (v0.7.17-r1188)
SAM files are used as input for CIRI2 (v2.0.6) to find circRNAs
circRNAs with hits in less than 3 samples across both batches are dropped
counts are merged by summing over the two batches
DESeq2 is used organ-wise to perform diff. expr. analysis
Assembly: GRCm39, annotation version 108
Supplementary files format and content: DESeq2 output of each experiment as csv-file

extract_protocol:
Tissues were extracted and frozen on dry ice. A bead mill (Retsch, Düsseldorf, Germany) was used to pulverize the tissue. RNA was subsequently extracted from the tissue powder using a phenol-based extraction protocol (PeqGold TRIFAST, VWR) according to the manufacturer's protocol. RNA integrity was visualized using a Bioanalyzer (Agilent, Santa Clara, CA, USA)
5 µg total RNA was rRNA depleted using hybridization based protocol (siTOOLS Biotech, Martinsried, Germany). The RNA was subsequently polyadenylated and digested with Rnase R for digestion of linear fragments. After purification the remaining RNA was fragmented and used for library construction using the NEBNext Ultra II RNA Library Kit. Libraries were sequenced using the Novaseq 6000 platform (Illumina, San Diego, CA, USA)

value: Spleen

tag: age

value: 4 months old

value: whole Spleen tissue

value: WT

tag: Sex

value: male


title: mouse circRNA Spleen WT 1646 batch 2

description:
Library name: 221000001049-DS6_22Oct1049-DL006_S6_L001_R1_001_b2
circRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Kidney, EM-Seq, rep2

description: Library name: KidneyEMrep2

value: Kidney


title: Blood, EM-Seq, rep3

description: Library name: BloodEMrep3


title: mouse circRNA Spleen WT 1653 batch 2

description:
Library name: 221000001049-DS11_22Oct1049-DL011_S11_L001_R1_001_b2
circRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: SB 19 5736

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S6

value: N

value: Non-Responder

value: Low

value: Not detectable

value: above


title: SB 20 1639

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S12

value: cutaneous KS tumor


title: Blood, EM-Seq, rep1

description: Library name: BloodEMrep1

value: Blood


title: SKMES1 serum free control 2

description: Library name: SKMES1_control_2

value: Lung SCC

value: Control


title: mouse circRNA Spleen Ftsj1_DF 1656 batch 2

description:
Library name: 221000001049-DS3_22Oct1049-DL003_S3_L001_R1_001_b2
circRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Kidney, EM-Seq, rep3

description: Library name: KidneyEMrep3


title: SB 19 7860

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S8

value: KS

value: Y

value: No


title: SKMES1 serum free control 1

description: Library name: SKMES1_control_1


title: SKMES1 dermal fibroblast secretome 1

description: Library name: SKMES1_dermal_1

value: Dermal fibroblast secretome


title: Kidney, EM-Seq, rep1

description: Library name: KidneyEMrep1


title: SB 19 5476

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S5

value: Yes

value: High

value: Detectable


title: mouse circRNA Spleen Ftsj1_DF 1654 batch 2

description:
Library name: 221000001049-DS28_22Oct1049-DL028_S28_L001_R1_001_b2
circRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Spleen

value: 4 months old

value: whole Spleen tissue

value: male


title: SKMES1 serum free control 3

description: Library name: SKMES1_control_3


title: Heart, EM-Seq, rep3

description: Library name: HeartEMrep3

value: Heart


title: SB 19 5090

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S4

value: Non-Responder

value: N

value: Not detectable

value: above


title: IC19 oral fibroblast secretome 2

description: Library name: IC19_oral_2

value: Cutaneous SCC

value: Oral fibroblst secretome


title: Heart, EM-Seq, rep2

description: Library name: HeartEMrep2


title: mouse circRNA Spleen Ftsj1_DF 1647 batch 2

description:
Library name: 221000001049-DS7_22Oct1049-DL007_S7_L001_R1_001_b2
circRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: mouse circRNA Liver WT 1655 batch 2

description:
Library name: 221000001049-DS23_22Oct1049-DL023_S23_L001_R1_001_b2
circRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Liver

value: whole Liver tissue

value: WT


title: IC19 oral fibroblast secretome 1

description: Library name: IC19_oral_1


title: Heart, EM-Seq, rep1

description: Library name: HeartEMrep1


title: Cerebellum, EM-Seq, rep3

description: Library name: CerebellumEMrep3

value: Cerebellum


title: mouse circRNA Liver WT 1653 batch 2

description:
Library name: 221000001049-DS13_22Oct1049-DL013_S13_L001_R1_001_b2
circRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: SB 19 473

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S2

value: cutaneous KS tumor

value: KS

value: Y

value: Yes

value: Responder

value: High


title: mouse circRNA Liver WT 1646 batch 2

description:
Library name: 221000001049-DS10_22Oct1049-DL010_S10_L001_R1_001_b2
circRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old

value: male


title: Cerebellum, EM-Seq, rep2

description: Library name: CerebellumEMErep2


title: IC19 lung fibroblast secretome 2

description: Library name: IC19_lung_2

value: Lung firboblast secretome


title: mouse circRNA Liver Ftsj1_DF 1656 batch 2

description:
Library name: 221000001049-DS12_22Oct1049-DL012_S12_L001_R1_001_b2
circRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: IC19 lung fibroblast secretome 1

description: Library name: IC19_lung_1


title: SB 19 2016

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S1

value: N

value: No

value: Low

value: Not detectable


title: SKMES1 dermal fibroblast secretome 2

description: Library name: SKMES1_dermal_2

value: Lung SCC

value: Dermal fibroblast secretome


title: Cerebellum,EM-Seq, rep1

description: Library name: CerebellumEMrep1


title: Blood, Integrated-ACE-Seq, rep3

description: Library name: BloodIntegratedACErep3

value: Blood


title: mouse circRNA Liver Ftsj1_DF 1654 batch 2

description:
Library name: 221000001049-DS9_22Oct1049-DL009_S9_L001_R1_001_b2
circRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Liver

value: whole Liver tissue


title: IC19 oral fibroblast secretome 3

description: Library name: IC19_oral_3

value: Cutaneous SCC

value: Oral fibroblst secretome


title: SB 18 6283

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S32

value: cutaneous KS tumor

value: KS

value: Y

value: below


title: IC19 dermal fibroblast secretome 3

description: Library name: IC19_dermal_3


title: SB 18 5577

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S38

value: Yes

value: Non-Responder

value: above


title: Blood, Integrated-ACE-Seq, rep2

description: Library name: BloodIntegratedACErep2


title: mouse circRNA Kidney WT 1655 batch 2

description:
Library name: 221000001049-DS25_22Oct1049-DL025_S25_L001_R1_001_b2
circRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Kidney

value: 4 months old

value: whole Kidney tissue

value: WT

value: male


title: SB 19 4896

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S3

value: N

value: Low

value: High

value: Not detectable


title: mouse circRNA Liver Ftsj1_DF 1647 batch 2

description:
Library name: 221000001049-DS16_22Oct1049-DL016_S16_L001_R1_001_b2
circRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Liver

value: whole Liver tissue


title: Blood, Integrated-ACE-Seq, rep1

description: Library name: BloodIntegratedACErep1

value: Blood


title: Kidney, Integrated-ACE-Seq, rep3

description: Library name: KidneyIntegratedACErep3


title: SB 18 5511

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S29

value: cutaneous KS tumor

value: KS

value: Y


title: IC19 dermal fibroblast secretome 2

description: Library name: IC19_dermal_2

value: Cutaneous SCC

value: Dermal fibroblast secretome


title: IC19 dermal fibroblast secretome 1

description: Library name: IC19_dermal_1


title: SB 18 4726

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S13

value: Yes

value: Non-Responder

value: Detectable

value: above


title: Kidney, Integrated-ACE-Seq, rep2

description: Library name: KidneyIntegratedACErep2

value: Kidney


title: IC19 serum free control 3

description: Library name: IC19_control_3

value: Control


title: SB 17 5284

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S37

value: N

value: Low

value: below


title: IC19 serum free control 2

description: Library name: IC19_control_2


title: Kidney, Integrated-ACE-Seq, rep1

description: Library name: KidneyIntegratedACErep1


title: IC19 serum free control 1

description: Library name: IC19_control_1


title: mouse circRNA Kidney WT 1646 batch 2

description:
Library name: 221000001049-DS21_22Oct1049-DL021_S21_L001_R1_001_b2
circRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old

value: whole Kidney tissue

value: WT

value: male


title: mouse circRNA Kidney WT 1653 batch 2

description:
Library name: 221000001049-DS4_22Oct1049-DL004_S4_L001_R1_001_b2
circRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: SB 17 5114

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S36

value: cutaneous KS tumor

value: No

value: Responder


title: Heart, Integrated-ACE-Seq, rep2

description: Library name: HeartIntegratedACErep2

value: Heart


title: SB 18 4918

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S28

value: Y

value: High

value: Not detectable


title: SB 17 2867

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S27

value: Yes

value: Non-Responder


title: Heart, Integrated-ACE-Seq, rep1

description: Library name: HeartIntegratedACErep1


title: SB 16 638

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S25

value: KS

value: above


title: lung1

description:
Library name: lung1
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline (version 2.0.1) using default settings and aligning to GRCh38-2020-A
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: H5 file containing the feature barcode matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fudicials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the co-ordinates specifiying spots
Library strategy: Spatial Transcriptomics

source_name: Lung SCC

extract_protocol:
Sections cut from FFPE blocks
Indexed sequencing libraries were prepared from H&E-stained Visium Spatial Gene Expression Slides using the Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome, (10x Genomics, 1000338) according to the manufacturer’s protocol.

value: Lung SCC


title: mouse circRNA Kidney Ftsj1_DF 1656 batch 2

description:
Library name: 221000001049-DS29_22Oct1049-DL029_S29_L001_R1_001_b2
circRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Kidney


title: cut1

description:
Library name: cutaneaous1
FFPE Spatial transcriptome sequencing

source_name: Cutaneous SCC

value: Cutaneous SCC


title: mouse circRNA Heart WT 1655 batch 2

description:
Library name: 221000001049-DS26_22Oct1049-DL026_S26_L001_R1_001_b2
circRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old

value: whole Heart tissue


title: mouse circRNA Kidney Ftsj1_DF 1654 batch 2

description:
Library name: 221000001049-DS14_22Oct1049-DL014_S14_L001_R1_001_b2
circRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: whole Kidney tissue

value: male


title: SB 12 5422

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S31

value: cutaneous KS tumor

value: No

value: N


title: mouse circRNA Heart WT 1653 batch 2

description:
Library name: 221000001049-DS18_22Oct1049-DL018_S18_L001_R1_001_b2
circRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Heart

value: WT


title: PGK-Lockwood23

city: Vancouver

first: Jana

last: Jajarmi

state: BC

institute: University of British Columbia

description: Library name: Sample 3

data_processing:
Reads were aligned to sgRNA library sequences and counted
Supplementary files format and content: Excel table showing sgRNA name and read count

organism: unidentified plasmid

source_name: Bacterial

extract_protocol:
Plasmid DNA was extracted from bacterial colonies via Qiagen Maxiprep
Sequencing library preparations (Fig4C, Fig6D,E) were performed by setting up 8 20uL PCR reactions (PCR1) using the NEB Next Ultra II Q5 Mastermix (NEB, catalogue number M0544X). 20 ng of plasmid library was used per reaction. Samples were run as a qPCR for approximately 10 cycles. Forward primer mix for PCR1 was an equimolar mix of 8 primers with carrying numbers of degenerate bases (S1-8), sequences are outlined in Supplementary Table 1. PCR1 products were pooled and purified using homemade SPRI beads at at 1X bead ratio, then run on a 2% E-Gel™ EX Agarose Gel (Invitrogen, catalogue number G401002) before being gel extracted. The entire gel extracted product was used as a template for 8 20uL PCR reactions for barcoding and Illumina adapter addition (PCR2). Samples were run as a qPCR for approximately 6 cycles before being pooled and cleaned up using homemade SPRI beads at a 1X ratio. Equal amounts of Old Library and New Library PCR2 products were pooled to make the final sequencing library (Fig6). The sequencing library was diluted to 4nM and denatured with 0.2N NaOH and diluted to 20pM. Sample was loaded at 17pM with ~10% PhiX spike in. Illumina MiSeq was run using the Micro kit in a 1x150bp format. gRNA counts were generated using a custom python pipeline (see Data Availability).

value: Bacterial

value: PGK promoter


title: cut2

description:
Library name: cutaneaous2
FFPE Spatial transcriptome sequencing


title: mouse circRNA Kidney Ftsj1_DF 1647 batch 2

description:
Library name: 221000001049-DS2_22Oct1049-DL002_S2_L001_R1_001_b2
circRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Cerebellum, Integrated-ACE-Seq, rep3

description: Library name: CerebellumIntegratedACErep3

value: Cerebellum


title: oral2

description:
Library name: oral2
FFPE Spatial transcriptome sequencing

source_name: Head and neck SCC

value: Head and neck SCC


title: Cerebellum, Integrated-ACE-Seq, rep2

description: Library name: CerebellumIntegratedACErep2


title: mouse circRNA Heart WT 1646 batch 2

description:
Library name: 221000001049-DS8_22Oct1049-DL008_S8_L001_R1_001_b2
circRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: LcV2-Lockwood23-resequence

description: Library name: Sample 2

value: LcV2 redo


title: Cerebellum, Integrated-ACE-Seq, rep1

description: Library name: CerebellumIntegratedACErep1


title: SB 14 5182

description:
NanoString nCounter PanCancer IO 360 probe panel supplemented with custom KSHV probe
S26

value: KS

value: Y

value: Responder

value: Low

value: Not detectable

value: above


title: dCas9-LcV2-Lockwood23

description: Library name: Sample 1


title: mouse circRNA Heart Ftsj1_DF 1656 batch 2

description:
Library name: 221000001049-DS30_22Oct1049-DL030_S30_L001_R1_001_b2
circRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old

value: whole Heart tissue

value: male


title: mouse circRNA Heart Ftsj1_DF 1654 batch 2

description:
Library name: 221000001049-DS22_22Oct1049-DL022_S22_L001_R1_001_b2
circRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Blood, ACE-Seq, rep3

description: Library name: BloodACErep3

value: Blood


title: patial transcriptomics (Stereo-seq) of heart tissue sections

city: Los Angeles

first: Jun

last: Chen

state: CA

address: 420 Westwood Plaza 5121 Engineering V

department: Bioengineering

institute: University of California, Los Angeles

description: Library name: StereoSeq_Spatial_Transcriptomics

data_processing:
Stereo-seq data were processed with SAW (v8.1.3) to generate GEF outputs and associated spatial/QC files.
Assay-specific processing details and file formats are provided in the corresponding RNA-seq and Spatial Transcriptomics metadata templates.
Assembly: Bulk RNA-seq: Rattus norvegicus reference genome. Spatial transcriptomics: Mus musculus GRCm38 (mm10) with custom MSCLG22S sequence included.
Supplementary files format and content: This Series includes raw FASTQ files and processed expression matrices for bulk RNA-seq, and GEF files, spatial images, and associated QC outputs for Stereo-seq spatial transcriptomics. Detailed file lists are provided in the assay-specific templates.
Library strategy: Spatial Transcriptomics

growth_protocol: Rodents were housed under standard conditions with ad libitum access to food and water and maintained on a regular light/dark cycle, following institutional guidelines.

extract_protocol:
For bulk RNA-seq, total RNA was extracted from heart tissue using standard RNA isolation methods. For spatial transcriptomics, fresh-frozen heart sections were processed on Stereo-seq capture chips according to the manufacturer’s protocol.
Bulk RNA-seq libraries were prepared from total RNA following standard library preparation protocols. Spatial transcriptomics libraries were prepared using the Stereo-seq library preparation workflow compatible with SAW processing.

treatment_protocol: Animals were assigned to WT control or sonogenetic groups (AAV2/9-cTnT-MscL-G22S-mCherry). Samples were collected at defined time points for bulk RNA-seq and/or spatial transcriptomics.

value: Heart


title: CARCD4Tregs

city: New York

first: David

last: Scheinberg

state: NY

address: 417 E 68th St

department: Pharmacology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Sample 2
Column name in Proj_14947_B_counts_scaled_DESeq_2.xlsx: s_CARCD4Tregs__CARCD4Tregs

data_processing:
RNA sequencing data analysis was performed by the Bioinformatics Core at MSKCC. FASTQ files were aligned to the reference genome using the STAR aligner [Dobin2012] with a two-pass mapping strategy: known Ensembl splice junctions were used in the first pass, novel junctions were incorporated, and a second pass was performed with noncanonical junctions removed. SAM files were processed with Picard (AddOrReplaceReadGroups) to add read groups, sort, and convert to compressed BAM format. Gene-level counts were generated using HTSeq and normalized/analyzed for differential expression with DESeq. Normalized log2 expression values were used for hierarchical clustering (Pearson correlation), multidimensional scaling, and principal component analysis. Heatmaps (gplots heatmap.2) were generated from the top 100 differentially expressed genes using mean-centered normalized log2 expression. Gene set enrichment analysis (GSEA, MSigDB) was performed for human and mouse datasets, or GSEAPreranked was used when sample size was fewer than three per group.
Assembly: Human; Genome: UCSC HG19; GTF: gencode.v18.annotation
Supplementary files format and content: Proj_14947_B_counts_scaled_DESeq_2.xlsx contain raw counts for all samples
Supplementary files format and content: ALLResDESeq_CARCD4Tcell_vs_CARCD4Tregs.xlsx contain normalized counts for all genes
Supplementary files format and content: ResDESeq_CARCD4Tcell_vs_CARCD4Tregs.xlsx contain normalized counts for select differentially expressed genes

source_name: cell type

growth_protocol: Sorted cells were restimulated with 1μg/ml anti-CD3 antibody (Miltenyi Biotec # 130-093-387) and cultured in complete RPMI media supplemented with 10ng/ml TGFβ (Peprotech), 10nM all-trans retinoic acid (Sigma-Aldrich), and 500 IU IL-2 (Peprotech) for 3 days before sequencing.

extract_protocol:
RNA extraction and library preparation was done by the Integrated Genomics Operation Core at the Memorial Sloan Kettering Cancer Center (MSKCC). Phase separation in cells lysed in TRIzol was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher catalog # A27828) on the KingFisher Flex Magnetic Particle Processor (Thermo Scientific catalog # 5400630) according to the manufacturer’s protocol. Samples were eluted in 15 µL elution buffer.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 6.5-9.1 underwent polyA selection and library preparation using the TruSeq Stranded mRNA LT Kit (Illumina catalog # RS-122-2102) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina).  An average of 175 million paired reads was generated per sample. Ribosomal reads represented 2-6% of the total reads generated and the percent of mRNA bases averaged 87%.

treatment_protocol: CD4 T-cells were genetically modified to either express GD2 CAR alone or GD2 CAR + FoxP3.

value: cell type

value: Primary human CD4 T cells

value: GD2 CAR & FOXP3  transduced

value: Same as above

tag: time

value: Day 13 post PBMC isolation


title: Blood, ACE-Seq, rep1

description: Library name: BloodACErep1


title: Het_BLM

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

country: China

institute: wuhan university

description: Library name: Sample3

library_source: genomic single cell

data_processing:
Raw sequencing reads were mapped to the Mus musculus reference genome (GRCm39 assembly) using dnbc4tools. Individual Seurat objects were created for each sample from mapped reads by Seurat, followed by doublet removal and ambient RNA filtering by DoubletFinder and decontX, respectively. High-quality cells meeting stringent QC thresholds were retained, including: (1) nUMI >= 500; (2) nGene >= 200; (3) log10GenesPerUMI > 0.80; (4) mitoRatio < 0.50. Then, batch correced by Seurat CCA-based method, while RunPCA and RunUMAP to perform PCA and reduction. Finaly clusters were implemented by FindNeighbors and FindClusters under resolution 0.2.
Assembly: GRCm39
Supplementary files format and content: rds, seurat object, barcode.tsv, features.tsv, matrix.mtx

source_name: Lung

extract_protocol:
The fresh lung tissues were cut into approximately 1mm3 pieces and washed with 4mL cold PBS solution 3 times. Then the samples were minced into small pieces, and enzymatically digested using the MACS Tumor Dissociation Kit (Miltenyi Biotec) for 30 min with agitation, according to the manufacturer’s instructions. The dissociated cells were subsequently passed through a 70-μm and 40-μm cell-strainer (Miltenyi Biotec) and centrifuged at 300g for 10 min. After removing the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Tiangen Biotech#RT122-1) and incubated at 4°C for 10 min to lyse red blood cells. The cell pellets were re-suspended in washing buffer (0.04% bovine serum albumin [BSA] in Dulbecco’s phosphate-buffered saline [DPBS]) after washing two times with washing buffer. The final cell concentration was adjusted to 1,000 cells/μL (viability≥80%) in all samples by using Countess™ 3 Automated Cell Counter (Life).
DNBelab C Series High-throughput Single-Cell RNA Library (940-001818-00) was utilized for scRNA-seq library preparation. In brief, Briefly, the cells were diluted to a concentration of 1,000 cells/mL and loaded into the cell reservoir of the microfluidic chip. Barcoded beads and droplet-generation oil were successively added to the beads and oil reservoirs. Encapsulated droplets were generated and collected using a DNBelab C4 /DNBelabTaiM4 system. Beads that captured the mRNA were recovered for reverse transcription (RT). Following polymerase chain reaction (PCR) amplification by polymerase chain reaction, complementary DNA (cDNA) was purified and quan-tified using a Qubit dsDNA kit (Thermo Fisher Scientific). Libraries of 3’-end transcripts were subsequently constructed through cDNA fragmentation, size selection, end repair and A-tailing, adapter ligation, PCR for indexing libraries, and cyclisation of sequencing libraries, according to the manufacturer’s instructions. Sequencing libraries were purified and quantified using the Qubit ssDNA kit (Thermo Fisher Scientific) and Qsep100 (Bioptic).

value: Lung

value: heterozygous BCAT2

value: BLM


title: CARCD4Tcell

description:
Library name: Sample 1
Column name in Proj_14947_B_counts_scaled_DESeq_2.xlsx: s_CARCD4Tcell__CARCD4Tcell

value: Primary human CD4 cells

value: GD2 CAR transduced

value: Cultured in cRPMI supplemented with 10ng/ml TGFβ (Peprotech), 10nM all-trans retinoic acid (Sigma-Aldrich), and 500 IU IL-2 (Peprotech). Post-sorting cells were restimulated with 1μg/ml anti-CD3 antibody (Miltenyi Biotec # 130-093-387) in culture for 3 days before sequencing.


title: mouse circRNA Brain WT 1655 batch 2

description:
Library name: 221000001049-DS1_22Oct1049-DL001_S1_L001_R1_001_b2
circRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Brain

value: whole Brain tissue

value: WT


title: Heart, Integrated-ACE-Seq, rep3

description: Library name: HeartIntegratedACErep3


title: Kidney, ACE-Seq, rep2

description: Library name: KidneyACErep2

value: Kidney


title: Lung fibroblasts 2 replicate 2

description: Library name: Lung_FB2_replicate_2

source_name: Lung fibroblasts 2

treatment_protocol: Fibroblasts were cultured in serum free DMEM for 72 hours then collected

value: Lung fibroblasts 2

value: Fibroblast


title: Lung fibroblasts 2 replicate 1

description: Library name: Lung_FB2_replicate_1


title: mouse circRNA Heart Ftsj1_DF 1647 batch 2

description:
Library name: 221000001049-DS20_22Oct1049-DL020_S20_L001_R1_001_b2
circRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Heart

value: 4 months old

value: whole Heart tissue

value: male


title: nac53-1 78-1 Pst rep 3

city: Wien

first: Gautier

last: Langin

address: Muthgasse 18

country: Austria

institute: BOKU

description:
Library name: Nac_P_03
I19R026a15_01_S15

data_processing:
FastQC
kallisto
Assembly: TAIR10
Supplementary files format and content: EstCnts_Pst_Col_Nac.csv

organism: Arabidopsis thaliana

source_name: plant leaves

extract_protocol:
RNeasy Mini Kit - Qiagen
LunaScript® RT SuperMix - NEB

value: plant leaves

value: Pst


title: Lung fibroblasts 1 replicate 2

description: Library name: Lung_FB1_replicate_2

source_name: Lung fibroblasts 1

value: Lung fibroblasts 1


title: Blood, ACE-Seq, rep2

description: Library name: BloodACErep2

value: Blood


title: Lung fibroblasts 3 replicate 1

description: Library name: Lung_FB3_replicate_1

source_name: Lung fibroblasts 3

value: Lung fibroblasts 3


title: Heart, ACE-Seq, rep3

description: Library name: HeartACErep3


title: nac53-1 78-1 Pst rep 2

description:
Library name: Nac_P_02
I19R026a14_01_S14


title: mouse circRNA Brain WT 1653 batch 2

description:
Library name: 221000001049-DS27_22Oct1049-DL027_S27_L001_R1_001_b2
circRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Brain


title: Lung fibroblasts 3 replicate 2

description: Library name: Lung_FB3_replicate_2


title: oral1

description:
Library name: oral1
FFPE Spatial transcriptome sequencing

value: Head and neck SCC


title: Kidney, ACE-Seq, rep3

description: Library name: KidneyACErep3


title: nac53-1 78-1 Pst rep 1

description:
Library name: Nac_P_01
I19R026a13_01_S13


title: mouse circRNA Brain Ftsj1_DF 1656 batch 2

description:
Library name: 221000001049-DS15_22Oct1049-DL015_S15_L001_R1_001_b2
circRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: nac53-1 78-1 Pst rep 4

description:
Library name: Nac_P_04
I19R026a16_01_S16


title: WT_BLM

description: Library name: Sample2

value: Lung

value: BLM


title: mouse circRNA Spleen WT 1655 batch 1

description:
Library name: 221000001049-DS17_22Oct1049-DL017_S17_L001_R1_001
circRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Spleen

value: Spleen

value: whole Spleen tissue


title: Kidney, ACE-Seq, rep1

description: Library name: KidneyACErep1

value: Kidney


title: WT_PBS

description: Library name: Sample1

value: WT

value: PBS


title: mouse circRNA Brain WT 1646 batch 2

description:
Library name: 221000001049-DS24_22Oct1049-DL024_S24_L001_R1_001_b2
circRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Brain

value: whole Brain tissue


title: mouse circRNA Brain Ftsj1_DF 1654 batch 2

description:
Library name: 221000001049-DS19_22Oct1049-DL019_S19_L002_R1_001_b2
circRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old


title: nac53-1 78-1 mock rep 4

description:
Library name: Nac_M_04
I19R026a12_01_S12

value: mock


title: mouse circRNA Spleen WT 1653 batch 1

description:
Library name: 221000001049-DS11_22Oct1049-DL011_S11_L001_R1_001
circRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male


title: Lung fibroblasts 1 replicate 1

description: Library name: Lung_FB1_replicate_1

value: Fibroblast


title: mouse circRNA Brain Ftsj1_DF 1647 batch 2

description:
Library name: 221000001049-DS5_22Oct1049-DL005_S5_L001_R1_001_b2
circRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Heart, ACE-Seq, rep2

description: Library name: HeartACErep2

value: Heart


title: nac53-1 78-1 mock rep 2

description:
Library name: Nac_M_02
I19R026a10_01_S10

value: plant leaves


title: Heart, ACE-Seq, rep1

description: Library name: HeartACErep1


title: Cerebellum, ACE-Seq, rep1

description: Library name: CerebellumACErep1

value: Cerebellum


title: mouse circRNA Spleen Ftsj1_DF 1656 batch 1

description:
Library name: 221000001049-DS3_22Oct1049-DL003_S3_L001_R1_001
circRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Oral fibroblasts 3 replicate 2

description: Library name: Oral_FB3_replicate_2

source_name: Oral fibroblasts 3

value: Oral fibroblasts 3


title: Oral fibroblasts 3 replicate 1

description: Library name: Oral_FB3_replicate_1


title: Oral fibroblasts 2 replicate 2

description: Library name: Oral_FB2_replicate_2

source_name: Oral fibroblasts 2

value: Oral fibroblasts 2


title: mouse circRNA Spleen Ftsj1_DF 1647 batch 1

description:
Library name: 221000001049-DS7_22Oct1049-DL007_S7_L001_R1_001
circRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Cerebellum, ACE-Seq, rep3

description: Library name: CerebellumACErep3

source_name: Cerebellum


title: mouse circRNA Liver WT 1655 batch 1

description:
Library name: 221000001049-DS23_22Oct1049-DL023_S23_L001_R1_001
circRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Liver

value: Liver

value: whole Liver tissue


title: mouse circRNA Spleen WT 1646 batch 1

description:
Library name: 221000001049-DS6_22Oct1049-DL006_S6_L001_R1_001
circRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Spleen

value: whole Spleen tissue


title: Cerebellum, ACE-Seq, rep2

description: Library name: CerebellumACErep2


title: Dermal fibroblasts 3 replicate 1

description: Library name: Dermal_FB3_replicate_1

source_name: Dermal fibroblasts 3

value: Dermal fibroblasts 3


title: Oral fibroblasts 2 replicate 1

description: Library name: Oral_FB2_replicate_1


title: mouse circRNA Spleen Ftsj1_DF 1654 batch 1

description:
Library name: 221000001049-DS28_22Oct1049-DL028_S28_L001_R1_001
circRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Dermal fibroblasts 3 replicate 2

description: Library name: Dermal_FB3_replicate_2


title: Col-0 Pst rep 4

description:
Library name: Col_P_04
I19R026a08_01_S8

value: Pst


title: nac53-1 78-1 mock rep 1

description:
Library name: Nac_M_01
I19R026a09_01_S9


title: Col-0 mock rep 4

description:
Library name: Col_M_04
I19R026a04_01_S4


title: 1.5d, biological rep1

city: Fujisawa

first: Yoshinao

last: Oki

state: Kanagawa

address: 1866 Kameino

department: Department of Applied Biological Science

country: Japan

institute: Nihon University College of Bioresource Sciences

description: Gene expression data from DFAT grew to semiconfluence

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The data were analyzed with RMA using R/Bioconductor.

label: biotin

source_name: Liver after 1.5-day 70% partial hepatectomy in mice.

label_protocol: 5 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: liver


title: Oral fibroblasts 1 replicate 1

description: Library name: Oral_FB1_replicate_1

source_name: Oral fibroblasts 1

value: Oral fibroblasts 1


title: nac53-1 78-1 mock rep 3

description:
Library name: Nac_M_03
I19R026a11_01_S11


title: Col-0 Pst rep 3

description:
Library name: Col_P_03
I19R026a07_01_S7


title: 0.75d, biological rep3

description: Gene expression data from AC derived from fat tissue

source_name: Liver after 0.75-day 70% partial hepatectomy in mice.


title: Oral fibroblasts 1 replicate 2

description: Library name: Oral_FB1_replicate_2


title: 0.75d, biological rep2


title: Col-0 mock rep 2

description:
Library name: Col_M_02
I19R026a02_01_S2


title: Dermal fibroblasts 2 replicate 2

description: Library name: Dermal_FB2_replicate_2

source_name: Dermal fibroblasts 2

value: Dermal fibroblasts 2


title: mouse circRNA Liver Ftsj1_DF 1647 batch 1

description:
Library name: 221000001049-DS16_22Oct1049-DL016_S16_L001_R1_001
circRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old


title: 1.5d, biological rep2


title: Dermal fibroblasts 1 replicate 1

description: Library name: Dermal_FB1_replicate_1

source_name: Dermal fibroblasts 1

value: Dermal fibroblasts 1


title: Col-0 Pst rep 2

description:
Library name: Col_P_02
I19R026a06_01_S6


title: 1.5d, biological rep3


title: 0.75d, biological rep1


title: Col-0 Pst rep 1

description:
Library name: Col_P_01
I19R026a05_01_S5


title: MAN0855_D_Rep3

first: Madison

middle: Rose

last: Glass

address: 3 Blackfan St

department: Neurobiology

institute: Boston Children's Hospital

description: Library name: DW107.MAND.RNA

data_processing:
The raw data were analyzed by Next Generation Diagnostic srl proprietary NEGEDIA Digital mRNA-seq pipeline (v2.0) which involves a cleaning step by quality filtering and trimming, alignment to the reference genome and counting by gene.
Illumina NovaSeq 6000 base call (BCL) files were converted to fastq files using bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files including raw counts and samples names.

source_name: iPSC-derived organoid

growth_protocol: See experimental details in https://doi.org/10.1016/j.nbd.2025.107093

extract_protocol:
RNA was extracted from lysed live cells or frozen cell pellets using TakaraBio's Nucleospin kit (Takara Bio catalog #740971). 125 ng of total RNA was used for library preparation.
NEGEDIA Digital mRNA-seq research grade sequencing service v2.0 (doi: https://doi.org/10.1038/s41598-017-14892-x)

treatment_protocol: no treatment

value: iPSC-derived organoid

value: neuron

value: control


title: mouse circRNA Liver WT 1653 batch 1

description:
Library name: 221000001049-DS13_22Oct1049-DL013_S13_L001_R1_001
circRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: WT

value: male


title: mouse circRNA Liver Ftsj1_DF 1656 batch 1

description:
Library name: 221000001049-DS12_22Oct1049-DL012_S12_L001_R1_001
circRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Dermal fibroblasts 2 replicate 1

description: Library name: Dermal_FB2_replicate_1

value: Fibroblast


title: 0.5d, biological rep2

source_name: Liver after 0.5-day 70% partial hepatectomy in mice.


title: MAN0855_A_Rep3

description: Library name: DW107.MANA.RNA

value: c.1412delA, p.Asp471fs (heterozygous)


title: Dermal fibroblasts 1 replicate 2

description: Library name: Dermal_FB1_replicate_2


title: Col-0 mock rep 3

description:
Library name: Col_M_03
I19R026a03_01_S3

source_name: plant leaves

value: plant leaves

value: mock


title: mouse circRNA Kidney WT 1646 batch 1

description:
Library name: 221000001049-DS21_22Oct1049-DL021_S21_L001_R1_001
circRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Kidney

value: Kidney

value: whole Kidney tissue


title: mouse circRNA Liver WT 1646 batch 1

description:
Library name: 221000001049-DS10_22Oct1049-DL010_S10_L001_R1_001
circRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Liver

value: whole Liver tissue


title: mouse circRNA Liver Ftsj1_DF 1654 batch 1

description:
Library name: 221000001049-DS9_22Oct1049-DL009_S9_L001_R1_001
circRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: 0.5d, biological rep1

value: liver


title: Col-0 mock rep 1

description:
Library name: Col_M_01
I19R026a01_01_S1


title: 0.25d, biological rep1

source_name: Liver after 0.25-day 70% partial hepatectomy in mice.


title: 0.5d, biological rep3


title: mouse circRNA Kidney WT 1655 batch 1

description:
Library name: 221000001049-DS25_22Oct1049-DL025_S25_L001_R1_001
circRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: MAN0855_D_Rep1

description: Library name: DW74.MAN.D.RNA


title: MAN0855_D_Rep2

description: Library name: DW106.MAND.RNA


title: rpt2a-2, Pma, systemic infection, sample 2

description: Library name: rpt2_syst_P2

data_processing:
FastQC
STAR
htseq-count
Assembly: TAIR10
Supplementary files format and content: txt files with raw counts

source_name: Adult leaves

extract_protocol:
NucleoZOL
RevertAid Reverse Transcriptase

value: Adult leaves

value: Pma

value: SAR


title: mouse circRNA Kidney Ftsj1_DF 1656 batch 1

description:
Library name: 221000001049-DS29_22Oct1049-DL029_S29_L001_R1_001
circRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old


title: rpt2a-2, Pma, systemic infection, sample 3

description: Library name: rpt2_syst_P3


title: rpt2a-2, control, systemic infection, sample 2

description: Library name: rpt2_syst_M2

value: Mock


title: sEVs, HFD-fed Sirt3 AKI replicate 3

city: Anshun

first: Longkun

last: Hu

state: Guizhou

address: Machang Town, Yunmanhu Campus of Guizhou Medical University

institute: Guizhou Medical University

description:
Library name: L1MKG2100442-SIRT3CKIcr3
serum-derived small extracellular vesicles (sEVs) vesicles of HFD-fed Sirt3 AKI mice

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: TPMs, counts

extract_protocol:
The serum from mice were incubated with 0.5 volumes of Total Exosome Isolation Reagent (Invitrogen) overnight at 4 °C. After centrifugation at 10,000 g at 4 °C for 1 h, the sEVs-containing pellet was collected and resuspended in PBS for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adipose-specific Sirt3 overexpression

value: High fat diet-fed


title: sEVs, HFD-fed Sirt3 AKI replicate 2

description:
Library name: L1MKG2100441-SIRT3CKIcr2
serum-derived small extracellular vesicles (sEVs) vesicles of HFD-fed Sir3 AKI mice


title: rpt2a-2, control, systemic infection, sample 3

description: Library name: rpt2_syst_M3


title: rpt2a-2, control, systemic infection, sample 1

description: Library name: rpt2_syst_M1


title: mouse circRNA Kidney WT 1653 batch 1

description:
Library name: 221000001049-DS4_22Oct1049-DL004_S4_L001_R1_001
circRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: WT

value: male


title: sEVs, HFD-fed Sirt3 AKI replicate 1

description:
Library name: L1MKG2100440-SIRT3CKIcr1
serum-derived small extracellular vesicles (sEVs) vesicles of HFD-fed Sirt3 AKI mice


title: MAN0855_A_Rep1

description: Library name: DW74.MAN.A.RNA

value: iPSC-derived organoid

value: neuron

value: c.1412delA, p.Asp471fs (heterozygous)


title: mouse circRNA Kidney Ftsj1_DF 1647 batch 1

description:
Library name: 221000001049-DS2_22Oct1049-DL002_S2_L001_R1_001
circRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Kidney


title: rpt2a-2, Pma, systemic infection, sample 1

description: Library name: rpt2_syst_P1


title: HNDS0083_B_Rep3

description: Library name: DW109.83B.RNA

value: c.1648C > T, p.Arg550* (heterozygous)


title: 0.25d, biological rep3


title: mouse circRNA Heart WT 1655 batch 1

description:
Library name: 221000001049-DS26_22Oct1049-DL026_S26_L001_R1_001
circRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Heart

value: Heart

value: whole Heart tissue


title: mouse circRNA Kidney Ftsj1_DF 1654 batch 1

description:
Library name: 221000001049-DS14_22Oct1049-DL014_S14_L001_R1_001
circRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: whole Kidney tissue


title: 0.25d, biological rep2

value: liver


title: rpt2a-2, Pma, local infection, sample 3

description: Library name: rpt2_lok_P3

value: Adult leaves

value: Pma

value: local


title: HNDS0083_D_Rep3

description: Library name: DW109.83D.RNA

value: control


title: MAN0855_A_Rep2

description: Library name: DW106.MANA.RNA


title: mouse circRNA Heart WT 1653 batch 1

description:
Library name: 221000001049-DS18_22Oct1049-DL018_S18_L001_R1_001
circRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old


title: mouse circRNA Heart Ftsj1_DF 1656 batch 1

description:
Library name: 221000001049-DS30_22Oct1049-DL030_S30_L001_R1_001
circRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: sEVs, HFD-fed WT replicate 2

description:
Library name: L1MKG2100438-SIRT3CKI2
serum-derived small extracellular vesicles (sEVs) vesicles of HFD-fed WT mice

value: Wild type

value: High fat diet-fed


title: HNDS0083_B_Rep2

description: Library name: RNA.DOW53.D35.ACTX.83B


title: mouse circRNA Heart WT 1646 batch 1

description:
Library name: 221000001049-DS8_22Oct1049-DL008_S8_L001_R1_001
circRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: WT

value: male


title: rpt2a-2, control, local infection, sample 3

description: Library name: rpt2_lok_M3

value: Mock


title: sEVs, HFD-fed WT replicate 1

description:
Library name: L1MKG2100437-SIRT3CKI1
serum-derived small extracellular vesicles (sEVs) vesicles of HFD-fed WT mice


title: rpt2a-2, control, local infection, sample 2

description: Library name: rpt2_lok_M2


title: HNDS0083_D_Rep2

description: Library name: RNA.DOW53.D35.ACTX.83D

value: iPSC-derived organoid

value: neuron


title: rpt2a-2, Pma, local infection, sample 1

description: Library name: rpt2_lok_P1


title: mouse circRNA Heart Ftsj1_DF 1647 batch 1

description:
Library name: 221000001049-DS20_22Oct1049-DL020_S20_L001_R1_001
circRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: HNDS0083_B_Rep1

description: Library name: DOW61.83B.RNA

value: c.1648C > T, p.Arg550* (heterozygous)


title: mouse circRNA Heart Ftsj1_DF 1654 batch 1

description:
Library name: 221000001049-DS22_22Oct1049-DL022_S22_L001_R1_001
circRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Heart


title: HNDS0022_A_Rep3

description: Library name: RNA.DOW53.D35.ACTX.22A


title: sEVs, HFD-fed WT replicate 3

description:
Library name: L1MKG2100439-SIRT3CKI3
serum-derived small extracellular vesicles (sEVs) vesicles of HFD-fed WT mice


title: rpt2a-2, control, local infection, sample 1

description: Library name: rpt2_lok_M1


title: HNDS0022_D_Rep3

description: Library name: RNA.DOW53.D35.ACTX.22D


title: rpt2a-2, Pma, local infection, sample 2

description: Library name: rpt2_lok_P2


title: sEVs, Chow-fed WT replicate 2

description:
Library name: L1MKG2100435-WT2
serum-derived small extracellular vesicles (sEVs) vesicles of chow-fed WT mice

value: Chow-fed


title: Col-0, Pma, systemic infection, sample 3

description: Library name: Col0_syst_P3

value: SAR


title: sEVs, Chow-fed WT replicate 1

description:
Library name: L1MKG2100434-WT1
serum-derived small extracellular vesicles (sEVs) vesicles of chow-fed WT mice


title: mouse circRNA Brain WT 1653 batch 1

description:
Library name: 221000001049-DS27_22Oct1049-DL027_S27_L001_R1_001
circRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

source_name: Brain

value: Brain

value: whole Brain tissue


title: Whole lung, ARID1A CKO, E18.5, ATAC

city: CINCINNATI

first: William

last: Zacharias

state: OH

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: ARID1A CKO scATAC
10x Genomics

data_processing:
Raw data was processed by Cellranger 4.0 with default parameters
Assembly: mm10
Supplementary files format and content: tab seperated files

source_name: Lung

extract_protocol:
Cells were digested from whole lung using dispase and collagenase
Libraries were generated using the manufacturer's protocol for RNA version 3v2 and ATAC version 2

value: Lung

value: ARID1A CKO


title: Col-0, Pma, systemic infection, sample 2

description: Library name: Col0_syst_P2

value: Adult leaves

value: Pma


title: sEVs, Chow-fed WT replicate 3

description:
Library name: L1MKG2100436-WT3
serum-derived small extracellular vesicles (sEVs) vesicles of chow-fed WT mice

value: Wild type


title: HNDS0083_D_Rep1

description: Library name: DOW61.83D.RNA

value: control


title: mouse circRNA Brain WT 1655 batch 1

description:
Library name: 221000001049-DS1_22Oct1049-DL001_S1_L001_R1_001
circRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: 4 months old

value: WT


title: HNDS0022_A_Rep2

description: Library name: DW74.22A.RNA


title: Col-0, Pma, systemic infection, sample 1

description: Library name: Col0_syst_P1


title: mouse circRNA Brain WT 1646 batch 1

description:
Library name: 221000001049-DS24_22Oct1049-DL024_S24_L001_R1_001
circRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male


title: Whole lung, ARID1A CKO, E18.5, RNA

description:
Library name: ARID1A CKO scRNA
10x Genomics


title: HNDS0022_D_Rep2

description: Library name: DW74.22D.RNA.1

value: iPSC-derived organoid


title: mouse circRNA Brain Ftsj1_DF 1656 batch 1

description:
Library name: 221000001049-DS15_22Oct1049-DL015_S15_L001_R1_001
circRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Col-0, control, systemic infection, sample 3

description: Library name: Col0_syst_M3

value: Mock


title: mouse circRNA Brain Ftsj1_DF 1654 batch 1

description:
Library name: 221000001049-DS19_22Oct1049-DL019_S19_L001_R1_001
circRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L004 = lane 1-4. Two batches because of low read count in batch 1. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Whole lung, Wild type mouse, E18.5, ATAC

description:
Library name: WT scATAC
10x Genomics


title: HNDS0022_D_Rep1

description: Library name: DOW61.22D.RNA

value: neuron


title: Whole lung, Wild type mouse, E18.5, RNA

description:
Library name: WT scRNA
10x Genomics


title: HNDS0022_A_Rep1

description: Library name: DOW61.22A.RNA


title: Col-0, Pma, local infection, sample 3

description: Library name: Col0_lok_P3

value: local