title: Patient VX059

city: Antwerpen

first: Nicolaas

last: Van Renne

address: Universiteitsplein 1

country: Belgium

institute: Laboratory of Experimental Medicine and Pediatrics (LEMP)

data_processing:
Clustering and DNA sequencing using the Illumina cBot and HiSeq 4000 was performed according to manufacturer's protocols. A concentration of 1.0 nM of DNA was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.7.7 and Bcl2fastq v2.17. Raw sequencing reads were trimmed with fastp using default settings. Reads were subsequently aligned to the gencode v38 human reference genome primary assembly with STARv2.7.8a using default settings and --sjdbOverhang 150. STAR was also used to generate per sample count tables in parallel (--quantMode GeneCounts).
Assembly: gencode v38 human reference genome
Supplementary files format and content: training_raw_counts.txt: Tab-delimited text file showing raw read counts.
Supplementary files format and content: training_RPM.txt: Tab-delimited text file showing RPM normalized reads.

extract_protocol:
Total RNA was extracted from 5 to 10 slides of 10 micron each per liver biopsy using the RNeasy FFPE Kit (Qiagen).
The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina".

value: liver

tag: virus

value: HCV

tag: gender

tag: age

tag: metavir

tag: hcc

value: NoHCC


title: Patient VX058

status: Public on Dec 02 2025

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: liver

tag: tissue

value: Male


title: Sample 26

type: genomic

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

country: USA

institute: Oregon Health and Science University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
In brief, we removed probes which had either low detection P values, contained a SNP with MAF of at least 5% within 3bp of the CpG interrogation site, or mapped to the X chromosome. Raw probe values were background corrected using preprocessIllumina and quantile normalization was performed using Enmix (32). The effects of slide, DNA concentration (< or > 12 ng/ml and extraction batch were removed using ComBat (33).
Normalized beta

label: cy3, cy5

molecule: genomic DNA

source_name: buccal

label_protocol: Standard Illumina Protocol

extract_protocol: Buccal DNA was extracted using the Maxwell® 16 Instrument (Promega AS3000) and   Maxwell® 16 Blood DNA Extraction Kit (Promega AS1010). Proteinase K (Promega   20mg/ml) was added to 15ml conicals containing 4 swabs and ~1.6ml SLB. Tubes were   vortexed to collect SLB at bottom. Tubes were incubated in s 56°C water bath for 1 hr  and then vortexed. Lysate (800ul) was added to well #7 of the Maxwell® 16 Blood DNA  cartridge. The remaining lysate was stored for a second DNA extraction. Alcohol Wash  Buffer (2 parts Milli-Q water, 1 part 100% EtOH, 1 part 100% isopropanol) was added to  wells #4, #5 and #6. Cartridges were processed using the Buffy Coat Protocol on the  Maxwell® 16 Instrument and eluted in 400ul elution buffer. Purity was measured by  spectrophotometer and concentration measured with the Quant-iT PicoGreen dsDNA  Assay (Invitrogen® P7589).

treatment_protocol: Patients were instructed not to eat or drink at least 30 minutes before buccal sample   collection. Buccal DNA was collected using 4 Sterile HydraFlock® Large Tip Flocked  Swabs (Puritan 253406H). Each swab was applied to the inside of the child’s cheek and  rolled up and down for 30-60 seconds, making certain to roll the swab over the entire  inner cheek and upper gum. Swabs were placed together in a 15 ml conical tube  containing 1600ul of 1X Saliva Lysis Buffer (SLB) before capping tube and vortexing for  10 seconds. The swabs were frozen upright in SLB at -20°C within 1 week from sampling  and stored until DNA extraction.  2X Saliva Lysis Buffer: 0.3 M TRIS-HCl; 0.67 M urea;   0.67 M NaOAc;  0.6% sodium dodecyl sulfate;  3.3 mM EDTA;  30% ethanol)

value: buccal

tag: Sex

value: Female


title: CD8TILs, Donor49, HighCelltrace, rep2

city: Durham

first: Charles

middle: A

last: Gersbach

state: NC

address: 101 Science Drive

institute: Duke University

description: Library name: CD8-T49-2-H

library_source: genomic

data_processing:
FASTQ files were aligned to custom indexes for each ORF barcode library (generated from the bowtie2-build function) using Bowtie 2.
Assembly: Custom assembly, TF ORF library barcodes from 2023 Zheng Cell paper
Supplementary files format and content: For all processed data files, the format is: column 1 = TF barcode ID, column 2 = number of aligned counts

source_name: NSCLC tumor

extract_protocol:
Genomic DNA was isolated using Zymo’s QuickDNA Miniprep Plus kit.
Genomic DNA was split across 100 μl PCR reactions (22 cycles at 98 °C for 10 s, 60 °C for 10 s, and 72 °C for 25 s) with NEBNext 2× Master Mix and up to 3 μg of genomic DNA per reaction. PCRs were pooled together for each sample and purified using double-sided (SPRI)bead selection at 0.5× and 1.0×. Libraries were run on a 1% agarose gel to confirm amplicon size and quantified using Qubit’s dsDNA High Sensitivity assay. Libraries were diluted to 2 nM, pooled together at equal volumes, run on a High Sensitivity D1000 tape (Agilent) to confirm amplicon size, and sequenced using Illumina’s MiSeq Reagent Kit v2 (50 cycles). Primers used for the gDNA PCR are listed in Supplemental Table 4.

value: NSCLC tumor

tag: cell line

value: tumor-infiltrating lymphocytes

tag: cell type

tag: treatment

value: High CellTrace


title: Patient VX057

value: HCC


title: CP91149 treated 3h (biol rep2, batch S1)

city: St Lucia

first: Benjamin

middle: D

last: Weger

state: QLD

address: 306 Carmody Road

department: IMB

country: Australia

institute: University of Queensland

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_3h_rep2

data_processing:
Raw reads were mapped using STAR on the GRCm38/mm10 genome assembly (Ensembl release 102). The BRB-seqTools suite (http://github.com/DeplanckeLab/BRB-seqTools) was subsequently applied to retrieve raw counts per gene.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited raw read count matrix

organism: Mus musculus

growth_protocol: AML12 (alpha mouse liver 12) hepatocyte cells from a 3-month-old mouse donor (CD1 strain, line MT42) were purchased from ATCC (CRL-2254) and stored in liquid nitrogen before usage. Cells were maintained in an incubator (37°C, 5% CO2) in base medium (DMEM:F12 Medium supplemented with 10% fetal bovine serum, 10 µg/ml insulin, 5.5 µg/ml transferrin, 5 ng/ml selenium, 40 ng/ml dexamethasone).

extract_protocol:
Cells were lysed on ice in QIAzol Lysis Reagent, collected using a cell scraper, and homogenized by passing several times through a syringe. RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen, #73404), following the manufacturer’s protocol.
BRB-Seq

treatment_protocol: AML12 cells (300,000 cells/well) were seeded into sterile 6-well plates and incubated overnight at 37°C. The following day, cells were washed twice with 1x PBS, and the medium was replaced with a base medium containing either 67 μM CP-91149 or vehicle control (0.03% DMSO). After 3, 6, 14 and 24 hours of treatment RNA was extracted.

value: hepatocyte

tag: genotype

value: CD1 strain, line MT42

tag: batch


title: Sample 25


title: DPTILs, Donor44, HighCelltrace, rep1

description: Library name: DP-T44-1-H

value: DP


title: Sample 2

city: Manchester

first: Terence

middle: S

last: Garner

address: St Mary's Hospital, Oxford Road

department: Division of Developmental Biology and Medicine

country: United Kingdom

institute: University of Manchester

description: Library name: RP2_S2

data_processing:
Data were demultiplexed (allowing one mismatch) and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.17.1.14
Salmon quantification of RNA-seq reads
Assembly: hg38
Supplementary files format and content: EdgeR processed log2 CPM

molecule: polyA RNA

source_name: blood

extract_protocol:
RNA was extracted from blood samples collected in PAXgene blood RNA tubes from children with varying growth parameters
Libraries were generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol

value: blood

tag: decimal age_(y)

value: male

tag: systolic blood_pressure_(mmhg)


title: CP91149 treated 3h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_C_S1_3h_rep1


title: Sample 24


title: Vehicle treated 3h (biol rep3, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_3h_rep3

value: 3h vehicle


title: Patient VX054

value: HBV


title: Patient VX056

value: liver


title: DPTILs, Donor44, LowCelltrace, rep1

description: Library name: DP-T44-1-L

value: Low CellTrace


title: Patient VX053

value: NoHCC


title: Vehicle treated 6h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_6h_rep1

value: 6h vehicle


title: CD8TILs, Donor49, LowCelltrace, rep1

description: Library name: CD8-T49-1-L


title: Sample 22

value: buccal

value: Male


title: Sample 23


title: Vehicle treated 3h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_3h_rep1


title: DPTILs, Donor44, HighCelltrace, rep2

description: Library name: DP-T44-2-H

value: NSCLC tumor


title: Patient VX052

value: HCV


title: CD8TILs, Donor49, LowCelltrace, rep2

description: Library name: CD8-T49-2-L

value: tumor-infiltrating lymphocytes


title: DPTILs, Donor44, LowCelltrace, rep2

description: Library name: DP-T44-2-L


title: Sample 21

value: Female


title: Patient VX051


title: Sample 20


title: HSPCs, M. avium infected

city: Houston

first: Pamela

last: Luna

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

library_source: genomic single cell

data_processing:
The CellRanger pipeline was used to demultiplex the raw reads using cellranger-atac mkfastq (v1.2.0) and perform initial quantification of single cell accessibility using cellranger-atac count (v2.1.0) aligned to the mm10 reference genome with default parameters.
Data QC and analysis was performed in R (v4.4.1) using the Seurat (v5.1.0) and Signac (v1.14.0) R packages. QC filters: >500 and <30000 peak region fragments, >25% reads in peaks, blacklist ratio <0.1, nucleosome signal <2.5, TSS enrichment >1.5
Assembly: mm10
Supplementary files format and content: filtered_peak_bc_matrix.h5 - Filtered peak barcode matrix in hdf5 format
Supplementary files format and content: fragments.tsv.gz - Barcoded and aligned fragment file
Supplementary files format and content: fragments.tsv.gz.tbi - Fragment file index

source_name: whole bone marrow (WBM)

extract_protocol:
Isolated bone marrow from M. avium infected and naïve mice were collected pooled by sample group, red blood cell lysed (BioLegend 420301), and cKit-enriched via magnetic bead enrichment (Miltenyi 130-097-146). Specific HSPCs, including LT-HSCs (Lin-, cKit+, CD48-, CD150+, Flk2-, CD34-),, CD41+ HSCs (Lin-, cKit+, CD150+, CD41+), MPP3s (Lin-, cKit+, CD48+, CD150-, Flk2-, CD34+), and GMPs (Lin-, cKit+, CD41-, CD16/32+), and lineage cells, including macrophages (B220-, CD3-, CD11c-,Gr1+, Mac-1+, Ly6g-, Ly6c+), neutrophils (B220-,CD3-, CD11c-, Gr1+, Ly6g+, Ly6c+), and B cells (B220+, CD3-, Gr1-, Mac-1+), were stained and sorted for with FACS on BD Aria IIs. Cells were counted and combined in equal ratios per group based on live/dead counts post-sort at roughly 50,000 cells per group.
Nuclei were isolated and loaded onto the Chromium controller system to generate 10X scATAC-seq libraries. Library preparation and generation was handled by the Baylor Single Cell and Genetics core using an Illumina NovaSeq, and quality control of libraries was completed using a Bioanalyzer and Nandrop system.

treatment_protocol: Naïve and previously M. avium infected CD45.2 mice were infected intravenously (IV) via retro-orbital injection with 2 x 106 CFU Mycobacterium avium for four weeks prior to bone marrow isolation.

value: whole bone marrow (WBM)

value: hematopoietic cells

value: Mycobacterium avium (1 month)


title: DPTILs, Donor49, HighCelltrace, rep1

description: Library name: DP-T49-1-H

value: DP

value: High CellTrace


title: HSPCs, WT naïve

value: Control - no treatment


title: Patient VX049

value: HBV


title: Vehicle treated 3h (biol rep2, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_3h_rep2

value: hepatocyte

value: CD1 strain, line MT42

value: 3h vehicle


title: Sample 37


title: Sample 19


title: Sample 18


title: DPTILs, Donor49, HighCelltrace, rep2

description: Library name: DP-T49-2-H


title: bone marrow, samr1

city: Beijing

first: Yutong

last: Guo

address: No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100081, PR China.

country: China

institute: Peking University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https //support. 10xgenomics com/single-cell-gene-expression/software/pipelines/latestwhat-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix files of SAMP6 and SAMR1

source_name: femur bone marrow

extract_protocol:
BM cells of 12-week male SAMP6 and SAMR1 mice were separately flushed from the femur and tibia bones with 3 mL HBSS+2mM EDTA and filtered through a 70 μm cell strainer. Cells were centrifuged for 5 min at 500g. To remove the red blood cells, 2 mL GEXSCOPE® red blood cell lysis buffer (Singleron Biotechnologies, China) was added at 25°C for 10 min. The sample was stained with trypan blue (Sigma) and microscopically evaluated for cell viability and counting, and samples with viabilities >80% were used for sequencing.
BM cells of 12-week male SAMP6 and SAMR1 mice were separately flushed from the femur and tibia bones with 3 mL HBSS+2mM EDTA and filtered through a 70 μm cell strainer. Cells were centrifuged for 5 min at 500g. To remove the red blood cells, 2 mL GEXSCOPE® red blood cell lysis buffer (Singleron Biotechnologies, China) was added at 25°C for 10 min. The sample was stained with trypan blue (Sigma) and microscopically evaluated for cell viability and counting, and samples with viabilities >80% were used for sequencing.

value: femur bone marrow

value: male


title: DPTILs, Donor49, LowCelltrace, rep1

description: Library name: DP-T49-1-L

value: Low CellTrace


title: Sample 17

value: buccal


title: DPTILs, Donor49, LowCelltrace, rep2

description: Library name: DP-T49-2-L

value: NSCLC tumor


title: Patient VX046

value: liver

value: HCV

value: Male

value: HCC


title: Patient VX047

value: NoHCC


title: Vehicle treated 14h (biol rep1, batch S1)

description: Column name in L1204BW01_01.read.counts.sampleIDs.txt:  CE_V_S1_14h_rep1

value: 14h vehicle


title: Sample 16


title: bone marrow, samp6


title: Patient VX045

value: Female


title: 3 AL PBMCs without CD8 18.7.17

city: Solna

first: Lucas

last: Arruda

address: Nanna Svartz väg  4

country: Sweden

institute: CuraCell AB

description: Library name: TRB_99944

data_processing:
iRepertoire webserver
Assembly: hg38
Supplementary files format and content: csv files contain the assembled CDR3 sequences
Library strategy: TCR-Seq

source_name: Blood

extract_protocol:
RNAeasy mini plus kit (Qiagen). 50 ng was used for library construction.
iRepertoire proprietary TRB multiplex kit

value: Blood

value: PBMC


title: Sample 15


title: Mouse brain, Adar1-2KO, circRNA, Illumina, rep2

first: Erika

last: Larrea de Orte

state: Beijing

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

department: DNA & RNA Modifications

institute: Chinese Institute for Brain Research (CIBR)

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar1-2vsWT.csv
Adar1-2KO-2-circRNA-Illumina

data_processing:
*library strategy: circRNA-seq
For Illumina sequencing:
Basecalling: Bcl2Fastq
Quality filtering: Fastp (version 0.19.7). (1) Discard paired reads if either one  contains adapter contamination; (2) Discard paired reads if more than 10% of bases are uncertain in either one read; (3) Discard paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one
FASTQ files were mapped to the mouse reference genome (GRCm39) using BWA v0.7.17
CIRI-2 v2.0.6 pipeline was used to call circRNAs and CIRI-quant v1.1.2 for circRNA quantification. For the differential expression analysis Deseq2  2.11.40.8 tool was employed. As input, BSJ reads were used as counts.
FASTQ files were obtained using Guppy v6.1.2. Adapters were trimmed using PoreChop v0.2.4 and reads shorter than 500bp were discarded. For circular RNA identification, CIRIlong v1.0.3 was run using GRCm39 as the reference mouse genome. Circular RNAs occurring in genomic repetitive regionsor encoding ribosomal RNA or shorter than 30nt wereexcluded from subsequent analysis.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files named as "_ciri2.txt" correspond to the CIRI2 output for each sample
Supplementary files format and content: Tab-delimited text files named as "_ciriquant.txt" correspond to the CIRIquant output for each sample
Supplementary files format and content: DEAcircRNAsAdar2vsWT.csv coresponds to the differential expression analysis betweeen Adar2KO samples and WT samples
Supplementary files format and content: DEAcircRNAsAdar1-2vsWT.csv coresponds to the differential expression analysis betweeen Adar1-2KO samples and WT samples
Supplementary files format and content: Bed files correspond to the CIRIlong output after QC filtering

source_name: whole brain

growth_protocol: Whole brains from adult 3–4-month-old male mice were used for circRNA-seq.

extract_protocol:
Adult mice were euthanized and brains were immediately isolated, quickly washed with ice-cold DPBS and fully homogenized in 3mL TRIzol Reagent using a dounce tissue homogenizer. Total RNA was extracted, treated with DNAseI (0.2U/μg total RNA) and cleaned up with phenol chloroform followed by isopropanol precipitation. 5μg total RNA were used to deplete ribosomal RNA and enrich for circRNAs using RnaseR. Enriched RNA was  reverse transcribed using random hexamers primer with an adaptor sequence allowing a rolling amplification of circRNAs. TdT enzyme was used to add a deoxycytidine tail in the single stranded cDNA molecules. An oligo(dG)12 primer coupled with an adaptor sequence was used for second strand synthesis. Double-stranded cDNA samples were size selected with AMPure XP beads  using a sample-bead ratio of 0.5X. The purified cDNA was PCR amplified for 14 cycles and PCR products size selected again (sample-bead ratio of 0.5X) prior to sequencing library preparations
For Illumina sequencing, 5ng cDNA were used for TruePrep DNA Library Prep Kit V2 for Illumina. After cDNA tagmentation and adaptor ligation, 9 PCR cycles were used followed by size selection using AMPure XP beads to enrich for insert length around 350bp.  PE-150 reads were generated.
For Oxford Nanopore Sequencing, 100ng cDNA were used for Ligation Sequencing Kit V12 (SQK-LS112) and sequenced in FLO-MIN112 flow cells.

value: whole brain

tag: strain

value: 3-4 months


title: 1 AL PBMC without CD8 22.5.17

description: Library name: TRB_99926


title: Patient VX044


title: Mouse brain, Adar1-2KO, circRNA, Illumina, rep3

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar1-2vsWT.csv
Adar1-2KO-3-circRNA-Illumina


title: Sample 14


title: Mouse brain, Adar2KO, circRNA, Illumina, rep3

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar2vsWT.csv
Adar2KO-3-circRNA-Illumina


title: Patient VX043


title: Mouse brain, Adar1-2KO, circRNA, Illumina, rep1

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar1-2vsWT.csv
Adar1-2KO-1-circRNA-Illumina


title: Sample 13


title: 7 AL PBMC without CD8 6.8.18

description: Library name: TRB_99834


title: Patient VX048


title: Sample 12


title: Patient VX042


title: AL tumor 1 (RNA)

description: Library name: TRB_95678

source_name: Tumor

value: Tumor

value: Glioblastoma


title: Mouse brain, Adar2KO, circRNA, Illumina, rep2

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar2vsWT.csv
Adar2KO-2-circRNA-Illumina


title: Patient VX041


title: Sample 11


title: Mouse brain, Adar2KO, circRNA, Illumina, rep1

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar2vsWT.csv
Adar2KO-1-circRNA-Illumina


title: Patient VX040


title: Sample 10


title: Mouse brain, wild type, circRNA, Illumina, rep3

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar2vsWT.csv
DEAcircRNAsAdar1-2vsWT.csv
WT3-circRNA-Illumina

value: wild type


title: Sample 9


title: Mouse brain, wild type, circRNA, Illumina, rep2

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar2vsWT.csv
DEAcircRNAsAdar1-2vsWT.csv
WT2-circRNA-Illumina


title: 13 AL TIL 7.7.17 CD8+

description: Library name: TRB_95612

source_name: TIL

value: TIL

value: T-cells


title: Patient VX039


title: Mouse brain, wild type, circRNA, Illumina, rep1

description:
Total RNA was enriched for circRNAs
DEAcircRNAsAdar2vsWT.csv
DEAcircRNAsAdar1-2vsWT.csv
WT1-circRNA-Illumina


title: 14 AL TIL 14.8.17 CD4+

description: Library name: TRB_95604


title: 2 AL CD8 (pbmcs) 22.5.17

description: Library name: TRB_99872


title: Patient VX037


title: Mouse brain, Adar1-2KO, mRNA, rep3

description:
Adar1-2KO-3-mRNA
Adar1-2KOvsWT.MATS.JC.tar

data_processing:
Basecalling: Bcl2Fastq
Quality filtering: Fastp (version 0.19.7). (1) Discard paired reads if either one  contains adapter contamination; (2) Discard paired reads if more than 10% of bases are uncertain in either one read; (3) Discard paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one
FASTQ files were mapped to the mouse reference genome (GRCm39) using STAR v2.7.10b
For  alternative splicing analysis, rMATS v4.1.2 was employed using default parameters and allowing read clipping
Assembly: mm39
Supplementary files format and content: Adar2KOvsWT.MATS.JC.tar: Alternative splicing events identified in Adar2KO samples compared to wild type samples. Tar format (.tar).  Junction count output files from rMATs. The document contains 5 files corresponding to 5 different alternative splicing events.
Supplementary files format and content: Adar1-2KOvsWT.MATS.JC.tar: Alternative splicing events identified in Adar1-2KO samples compared to wild type samples. Tar format (.tar).  Junction count output files from rMATs. The document contains 5 files corresponding to 5 different alternative splicing events.

growth_protocol: Whole brains from adult 3–4-month-old male mice were used for RNA-seq.

extract_protocol:
Adult mice were euthanized and brains were immediately isolated, quickly washed with ice-cold DPBS and fully homogenized in 3mL TRIzol™ Reagent using a dounce tissue homogenizer. Total RNA was extracted, treated with DNAseI (0.2U/μg total RNA) and cleaned up with phenol chloroform followed by isopropanol precipitation. RNA yield and purity were measured with Nanodrop One Spectrophotometer and  RNA integrity was assessed using Fragment Analyzer Automated CE System.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used for library preparation, following polyA workflow and using 1μg total RNA as starting material. cDNA fragments of preferentially 370~420 bp in length were purified for PE150 sequencing.


title: AL tumor 3 (RNA)

description: Library name: TRB_95630


title: Patient VX038

value: HBV


title: Sample 8

value: buccal


title: Sample 7


title: 13 AL TIL 7.7.17 CD4+

description: Library name: TRB_95491


title: Patient VX036

value: liver

value: HCV


title: Sample 6


title: Patient VX034

value: Male

value: HCC


title: AL tumor 2 (RNA)

description: Library name: TRB_95643


title: Mouse brain, Adar1-2KO, mRNA, rep1

description:
Adar1-2KO-1-mRNA
Adar1-2KOvsWT.MATS.JC.tar


title: 4 AL CD8  (pbmcs) 18.7.18

description: Library name: TRB_95476


title: Patient VX035

value: NoHCC


title: Sample 4

value: Female


title: 8 AL CD8 (pbmcs) 6.8.17

description: Library name: TRB_95442

value: Blood


title: Patient VX033


title: Mouse brain, Adar2KO, mRNA, rep3

description:
Adar2KO-3-mRNA
Adar2KOvsWT.MATS.JC.tar


title: Mouse brain, Adar2KO, mRNA, rep2

description:
Adar2KO-2-mRNA
Adar2KOvsWT.MATS.JC.tar


title: Sample 3


title: Sample 1


title: Mouse brain, wild type, mRNA, rep3

description:
WT3-mRNA
Adar2KOvsWT.MATS.JC.tar
Adar1-2KOvsWT.MATS.JC.tar


title: KAT6A-K815Q3

city: Newark

first: Michinari

last: Nakamura

state: NJ

address: 185 South Orange Ave, Medical Science Building G609

department: Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

description: Library name: Sample 12

data_processing:
Raw reads were quality trimmed using Trimmomatic-0.39 with leading and trailing Q score 20, minimum length 35 bp.
The cleaned reads were mapped to Rattus norvegicus genome Rnor_6.0 using HISAT2 (Version 2.2.1).
The aligned read counts were obtained using htseq-count as part of the package HTSeq-0.6.1. The Bioconductor package edgeR was used to perform the differential gene expression analysis under R environment
Assembly: Rattus norvegicus genome Rnor_6.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Primary rat neonatal ventricular cardiomyocytes

extract_protocol:
Total RNA was isolated using TRIzol. Isolated RNA was checked for integrity on an Agilent Bioanalyzer 2100; samples with RNA integrity number (RIN) >7.0 were used for subsequent processing. Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T)25 magnetic beads (New England Biolabs). A paired-end (strand specific) cDNA library was prepared using the NEB Next Ultra-directional RNA-seq protocol. Briefly, poly(A)+ RNA was fragmented by heating at 94C for 10 min followed by reverse transcription and second strand cDNA synthesis using the reagents provided in the NEB Next kit. End-repaired cDNA was then ligated with double stranded DNA adapters, followed by purification of ligated DNA with AmpureXP beads. cDNA was then amplified by PCR for 15 cycles with a universal forward primer and a reverse primer with bar code.
The sequencing of the cDNA libraries was performed on the Illumina NextSeq 500 platform (Illumina, San Diego, CA) using the single-read 1x75 cycles configuration.

value: Adenovirus-mediated expression of human KAT6A-K815Q mutant


title: Sample 2


title: Patient VX032


title: KAT6A-K815Q1

description: Library name: Sample 10

value: Primary rat neonatal ventricular cardiomyocytes


title: Patient VX028


title: Patient VX029


title: KAT6A-K815R3

description: Library name: Sample 9

value: Adenovirus-mediated expression of human KAT6A-K815R mutant


title: KAT6A-K815Q2

description: Library name: Sample 11


title: Mouse brain, Adar1-2KO, mRNA, rep2

description:
Adar1-2KO-2-mRNA
Adar1-2KOvsWT.MATS.JC.tar

value: whole brain

value: 3-4 months


title: Mouse brain, wild type, mRNA, rep2

description:
WT2-mRNA
Adar2KOvsWT.MATS.JC.tar
Adar1-2KOvsWT.MATS.JC.tar

value: wild type


title: Sample 5


title: 14 AL TIL 14.8.17 CD8+

description: Library name: TRB_95489

value: TIL


title: Mouse brain, wild type, mRNA, rep1

description:
WT1-mRNA
Adar2KOvsWT.MATS.JC.tar
Adar1-2KOvsWT.MATS.JC.tar


title: Patient VX026


title: KAT6A-K815R2

description: Library name: Sample 8


title: KAT6A-K815R1

description: Library name: Sample 7


title: Mouse brain, Adar2KO, mRNA, rep1

description:
Adar2KO-1-mRNA
Adar2KOvsWT.MATS.JC.tar


title: Patient VX025


title: Tumor treatment 3-2

type: RNA

city: Phoenix

first: Jessica

last: Lancaster

state: Arizona

address: 5951 E Mayo Blvd

department: Immunology

institute: Mayo Clinic

description: Total RNA isolated from tumor bearing mice at day 16

hyb_protocol: Followed nCounter Gene Expression CodeSet RNA Hybridization Protocol User manual (available online)

scan_protocol: Samples sequenced using Nanostring nCounter Digital Analyzer

data_processing: Analysis was conducted using Rosalind software (Nanostring)

label_protocol: Samples labeled using Nanostring Tumor Signaling 360 Panel

growth_protocol: 250,000 B16-F10 tumor cells were grown in WT mice for 16 days

extract_protocol: RNA was harvested with RNAeasy Plus Mini  kit (Qiagen)

treatment_protocol: Mice were treated with 200 ug IgG2a isotype control antibodies or a combination of 200ug anti-PD-1 and 200 ug anti-PD-L1 antibodies

value: Whole tumor


title: Patient VX024

value: HBV


title: WT3

description: Library name: Sample 6

value: Adenovirus-mediated expression of human KAT6A-wild type


title: C57 HY19636 MRTX1133 sensitive 2

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

description: Treated for 1 week

data_processing:
The raw FASTQ files were processed using Space Ranger 2.0.1
Assembly: mm10
Supplementary files format and content: Image and alignment files for Space Ranger

source_name: Pancreas

extract_protocol:
Tissues were processed according to the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics) protocol
Libraries were constructed according to the Visium CytAssist Spatial Gene Expression for FFPE (10x Genomics) protocol
Spatial transcriptomics

value: Pancreas

value: MRTX1133 sensitive


title: C57 HY19636 MRTX1133 sensitive 1

description: Treated for 1 week


title: Tumor treatment 3-1


title: Tumor treatment 2-2


title: C57 HY19636 MRTX1133 sensitive 3

description: Treated for 1 week


title: C57 HY19636 isotype/vehicle 3

description: Treated for 1 week

value: Vehicle


title: Patient VX022

value: liver

value: Male


title: WT2

description: Library name: Sample 5


title: Patient VX023

value: NoHCC


title: Patient VX027

value: HCV

value: HCC


title: Tumor treatment 2-1


title: WT1

description: Library name: Sample 4

value: Primary rat neonatal ventricular cardiomyocytes


title: Patient VX021


title: C57 HY19636 isotype/vehicle 2

description: Treated for 1 week


title: LacZ3

description: Library name: Sample 3

value: Adenovirus-mediated expression of LacZ


title: LacZ2

description: Library name: Sample 2


title: Tumor treatment 1-2


title: C57 HY19636 isotype/vehicle 1

description: Treated for 1 week


title: LacZ1

description: Library name: Sample 1


title: Tumor treatment 1-1


title: PKC-HY19636 MRTX1133 CDK8i aCTLA4

description: Collected following 3 weeks of MRTX1133 treatment and 1 week of CDK8i+aCTLA4 treatment

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Pancreas/tumors were digested in 4 mg/mL collagenase IV and 4 mg/mL dispase. Samples were stained with eFluor780 Fixable Viablity dye and live cells sorted. 5,000 to 10,000 cells were loaded 10x Chromium Controller or Chromium X to generate Single Cell 3' Gene Expression dual indexed libraries (10x Genomics).
The creation of Gel Bead-In-Emulsions (GEM) and subsequent cell barcoding, GEM-RT cleanup, cDNA amplification, and library assembly were performed with the Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 (10x Genomics) according to manufacturer’s instructions.

value: MRTX1133 CDK8i aCTLA4


title: Patient VX019

value: Female


title: PKC-HY19636 MRTX1133 CDK8i

description: Collected following 3 weeks of MRTX1133 treatment and 1 week of CDK8i treatment

value: MRTX1133 CDK8i


title: Tumor control 2-2


title: Patient VX018


title: Tumor control 3-1


title: Whole heart tissue, cSirt5KO TAC, rep 6

city: Birmingham

first: Sayan

last: Bakshi

state: Alabama

department: Department of Pathology

institute: University of Alabama at Birmingham

data_processing:
Prior to alignment to the reference mouse genome, each sequence in the raw FASTQ files was trimmed on base call quality and sequencing adapter contamination using the Trim Galore! wrapper tool. Reads shorter than 20 base pairs were removed from the FASTQ files.
Trimmed reads were aligned to the reference genome using the open source short read aligner STAR with settings according to log file.
Pre-filtering was performed to keep only rows that have at least 10 reads total.
Gene annotation was performed using the R package “bioMaRt”.
Assembly: mm39
Supplementary files format and content: excel file include normalized count values for all samples

source_name: Whole heart tissue

extract_protocol:
RNA was isolated using Rneasy Fibrous Tissue Mini Kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB NEXT Ultra II Directional Library Prep Kit following manufacturer's protocols.

treatment_protocol: Whole hearts were excised and were snap frozen in liquid nitrogen and stored at - 80 °C until subjected to further analysis.

value: Whole heart tissue

value: TAC


title: Tumor control 3-2

value: Whole tumor


title: PKC-HY19636 MRTX1133 aCTLA4

description: Collected following 3 weeks of MRTX1133 treatment and 1 week of aCTLA-4 treatment

value: MRTX1133 aCTLA4


title: Whole heart tissue, cSirt5KO TAC, rep 5


title: PKC-HY19636 MRTX1133 isotype

description: Collected following 3 weeks of MRTX1133 treatment and 1 week of isotype treatment

value: Pancreas

value: MRTX1133 isotype


title: Patient VX016


title: Patient VX015


title: Whole heart tissue, cSirt5KO TAC, rep 4


title: KPC689 resistant Vehicle

description: Treated for 3 weeks

value: Vehicle


title: Patient VX014

value: liver


title: Whole heart tissue, cSirt5KO TAC, rep 3


title: KPC689 resistant MRTX1133

description: Treated for 3 weeks


title: Whole heart tissue, cSirt5KO TAC, rep 2


title: Patient VX013

value: HBV

value: Male


title: Patient VX020


title: Tumor control 1-1


title: Test R. arrhizus (45 µM Zinc)

city: Chandigarh

first: Rachna

last: Singh

state: Chandigarh

address: Department of Microbial Biotechnology, Technology Block, Panjab University (South Campus), Sector 25

department: Microbial Biotechnology

country: India

institute: Panjab University

description: Library name: Sample 2

data_processing:
The raw fastq reads were preprocessed using Fastp v.0.23.4, and the trimmed fastp reads were aligned against the SILVA database to filter the rRNA reads using RiboDetector v0.3.1. The rRNA filtered reads were aligned to the STAR indexed Rhizopus delemar RA 99-880 genome using STAR aligner v2.7.9a. The sorted BAM files generated from alignment were subjected to RSeQC (rseqc V4.0.0) for read distribution over genome structure and visualization using MultiQC. The rRNA and tRNA features were removed from the GTF file of the Rhizopus delemar, and the genome was indexed using RSEM v2.14.0. The BAM files obtained from STAR alignment were used for quantification of transcripts. edgeR annotated file was filtered based on adjusted p-value (false discovery rate, FDR) ≤ 0.05 and LogFoldChange ≥ 2 for differential expression. The protein sequences were extracted and subjected to eggNOG-mapper for functional annotation, BlastKOALA for KEGG annotation, and PANNZER2 for gene ontology (GO) annotation.
Assembly: Rhizopus delemar RA 99-880
Supplementary files format and content: tab-delimited text file including normalized counts

organism: Rhizopus arrhizus

source_name: Fungal cells (NCCPF 710004)

growth_protocol: R. arrhizus (1 × 106 spores/ml) was cultured in RPMI-1640 broth (pH 7.0) at 37°C, 150 rpm for 6 h without or with 45 µM Zinc sulphate.

extract_protocol:
The resulting growth was collected, washed and resuspended in RNAlater stabilization solution for RNA extraction. Extraction was carried out by RNeasy Mini Kit method (Qiagen #74104).
The library preparation was carried out by using NEBNext Ultra II Directional RNA library Prep Kit (NEB#E7770)

value: Fungal cells (NCCPF 710004)

value: Wild type

value: 45 µM Zinc


title: Whole heart tissue, cSirt5KO TAC, rep 1


title: Patient VX011

value: HCV

value: HCC


title: PKC-HY19636 MRTX1133

description: Treated for 1 week

value: MRTX1133 sensitive


title: Bdp1AA Rna15AA, rapamycin, 2 hours, rep 3

city: Los Angeles

first: Guillaume

last: Chanfreau

state: California

address: 607 Charles E Young Dr E

institute: University of California, Los Angeles

description:
Library name: Sample 9
bdp1rna15_3ends_genes_counts.csv

data_processing:
Basecalling was performed using the built in Dorado basecaller in Minknow (Dorado version: 7.11.2).
Reads were then mapped to S288C reference genome using Minimap 2 (Version 2.17-r941).
Assembly: R64-1-1
Supplementary files format and content: CSV files of 3’ ends for all genes normalized by RPM

organism: Saccharomyces cerevisiae

source_name: HHY168 fpr1delta::hphMX4 BDP1-FRB::kanMX6 RNA15-FRB::His

extract_protocol:
Total RNAs were extracted from frozen cell pellets using hot phenol-chloroform extraction followed by ethanol precipitation.
RNA libraries were prepared from 1 ug of total RNAs using the Direct-RNA sequencing kit from Oxford Nanopore (ONT, catalog #: SQK-RNA004) as per the manufacturer's instructions.


title: Bdp1AA Rna15AA, rapamycin, 2 hours, rep 1

description:
Library name: Sample 7
bdp1rna15_3ends_genes_counts.csv

value: HHY168 fpr1delta::hphMX4 BDP1-FRB::kanMX6 RNA15-FRB::His


title: Whole heart tissue, Control TAC, rep 5

value: Whole heart tissue

value: Control


title: Bdp1AA Rna15AA, rapamycin, 2 hours, rep 2

description:
Library name: Sample 8
bdp1rna15_3ends_genes_counts.csv


title: Patient VX007

data_processing:
Clustering and DNA sequencing using the Illumina cBot and HiSeq 4000 was performed according to manufacturer's protocols. A concentration of 1.0 nM of DNA was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.7.7 and Bcl2fastq v2.17. Raw sequencing reads were trimmed with fastp using default settings. Reads were subsequently aligned to the gencode v38 human reference genome primary assembly with STARv2.7.8a using default settings and --sjdbOverhang 150. STAR was also used to generate per sample count tables in parallel (--quantMode GeneCounts).
Assembly: gencode v38 human reference genome
Supplementary files format and content: training_raw_counts.txt: Tab-delimited text file showing raw read counts.
Supplementary files format and content: training_RPM.txt: Tab-delimited text file showing RPM normalized reads.

extract_protocol:
Total RNA was extracted from 5 to 10 slides of 10 micron each per liver biopsy using the RNeasy FFPE Kit (Qiagen).
The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina".


title: C2C12_5FU-3

city: Shanghai

first: Chenfei

last: Zhou

address: Ruijin No.2 Road

institute: Ruijin Hospital

data_processing:
The mapped reads of each sample were assembled by using StringTie v1.3.1
Assembly: Mus musculus Ensembl_release110
Supplementary files format and content: genes.expression.xls, 21899 genes

source_name: cel line

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: cel line

value: myocytes

value: 5-FU (5ug/L), 24 hours


title: Tumor control 1-2

value: Whole tumor


title: Patient VX008

value: NoHCC


title: Whole heart tissue, Control TAC, rep 6

value: TAC


title: Tumor control 2-1


title: PKC-HY19636 MRTX1133 5w

description: Treated for 5 weeks

value: Pancreas

value: MRTX1133 resistant


title: Bdp1AA, rapamycin, 2 hours, rep 3

description:
Library name: Sample 6
bdp1_3ends_genes_counts.csv


title: Control R. arrhizus (0 µM Zinc)

description: Library name: Sample 1

value: Fungal cells (NCCPF 710004)

value: 0 µM Zinc


title: Whole heart tissue, Control TAC, rep 4


title: C2C12_5FU-1

value: Wild type


title: Whole heart tissue, Control TAC, rep 3


title: Patient VX004

value: liver

value: HBV

value: Male


title: Bdp1AA, rapamycin, 2 hours, rep 1

description:
Library name: Sample 4
bdp1_3ends_genes_counts.csv


title: Whole heart tissue, Control TAC, rep 2


title: Patient VX003

value: Female


title: C2C12_NC-2

value: PBS


title: WT, rapamycin, 2 hours, rep 3

description:
Library name: Sample 3
wt_3ends_genes_counts.csv

source_name: HHY168 fpr1delta::hphMX4

value: HHY168 fpr1delta::hphMX4


title: Whole heart tissue, Control TAC, rep 1

value: Whole heart tissue

value: Control


title: Patient VX002

source_name: liver

value: HCC


title: C2C12_NC-1

value: cel line

value: myocytes


title: WT, rapamycin, 2 hours, rep 2

description:
Library name: Sample 2
wt_3ends_genes_counts.csv


title: Patient VX001

value: NoHCC


title: Whole heart tissue, cSirt5KO Sham, rep 5

value: Sham


title: T_cells_plus_3x_checkpoint

city: Charlottesville

first: Gary

middle: K

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

description: Library name: T_cells_plus_3x_checkpoint

data_processing:
RNAseq and CITEseq assay files were processed using Cell Ranger software (v7.1) by 10x Genomics (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Mm10
Supplementary files format and content: Cellranger output files" barcodes.tsv.gz, features.tsv.gz,matrix.mtx.gz

source_name: ovarian cancer

extract_protocol:
The day of library preparation, samples were thawed and like samples were combined. All cells were stained with viability dye, CD4, CD8 and Thy1.1 antibodies for sorting. Samples were acquired with an Aria2-2 or a Symphony sorter (BD). Live engineered T cells (live/dead- CD8+ Thy1.1+), endogenous CD8 T cells (live/dead- CD8+ Thy1.1-), endogenous CD4 T cells (live/dead- CD4+ Thy1.1-), and the remaining live cells (live/dead-) were sorted and each cell population was stained with a unique cell hashing antibody (Hash#1-4). Samples were pooled after hashing and stained with the TotalSeq-C Custom Mouse Panel (Biolegend, Cat:900002538).
A gene expression library was generated (10x Genomics Next GEM Chromium Single Cell 5’ Gene Expression v2 and Mouse TCR amplification Kits) according to Manufacturer's protocol

value: ovarian cancer

value: engineered T cells

value: T cells

value: T cells + 3x Abs


title: Patient VX005

first: Nicolaas

last: Van Renne

institute: Laboratory of Experimental Medicine and Pediatrics (LEMP)

value: liver


title: Patient X078

value: HBV

value: no

tag: censored time


title: WT, rapamycin, 2 hours, rep 1

description:
Library name: Sample 1
wt_3ends_genes_counts.csv


title: Whole heart tissue, cSirt5KO Sham, rep 4


title: testis IgG replicate 1

city: Turku

first: Lin

last: Ma

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

data_processing:
The adapter and low-quality nucleotides were cut off using Trimmomatic (v0.39).
The clean data next were mapped to the reference mouse genome (GRCm38) by using STAR (v2.7.10a).
The reads then were assigned and counted using featureCounts (v2.0.3).
Assembly: GRCm38
Supplementary files format and content: comma-separated text file includes raw counts for all samples

source_name: testis

extract_protocol:
The Dynabeads-protein-RNA complexes were diluted in 30 µl of the lysis buffer and reverse cross-linked at +70°C for 45 min. Reverse cross-linked samples were mixed with 800 µl of TRIsure (Bioline, cat code BIO-38033), incubated for 5 min at RT, followed by RNA phase separation from the DNA and proteins with chloroform and precipitation with isopropanol. Purified RNA pellets were washed twice with ice-cold 75 % ethanol and dissolved in nuclease-free water. RNA was analysed using Bioanalyser RNA 6000 pico assay kit and 2100 Bioanalyser Instrument (Agilent) and samples with >40 ng of total RNA were qualified for library preparation.
Directional libraries without rRNA removal was prepared.

value: testis

value: mouse IgG


title: Whole heart tissue, cSirt5KO Sham, rep 6


title: C2C12_5FU-2

value: Wild type

value: 5-FU (5ug/L), 24 hours


title: Bdp1AA, rapamycin, 2 hours, rep 2

description:
Library name: Sample 5
bdp1_3ends_genes_counts.csv


title: testis IgG replicate 2


title: Patient X077

address: Universiteitsplein 1

value: Male


title: testis TSSK2 IP replicate 1

value: anti-TSSK2 IP


title: testis TSSK2 IP replicate 2


title: Whole heart tissue, cSirt5KO Sham, rep 3

value: Whole heart tissue


title: Tcells_plus_Lag3

description: Library name: Tcells_plus_Lag3

value: T cells + Lag3


title: C2C12_NC-3

value: cel line

value: myocytes

value: PBS


title: Whole heart tissue, cSirt5KO Sham, rep 2

value: Sham


title: Patient X076


title: Whole heart tissue, cSirt5KO Sham, rep 1


title: T_cells_plus_PD1

description: Library name: T_cells_plus_PD1

value: ovarian cancer

value: engineered T cells

value: T cells

value: T cells + PD1


title: mouse NK rep2

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Reads were trimmed using Cutadapt
mapped to mm10  use STAR
Gene count were generated using featureCounts
Gene TPM were generated using kallisto
Assembly: mm10
Supplementary files format and content: tab-delimited text file include TPM for each Sample

source_name: spleen

growth_protocol: Murine HSPCs and monocytes were isolated from C57BL/6 mouse bone marrow cells. Bone marrow cells were collected by flushing the femur with PBS, followed by filtration through a 30 µm nylon mesh (Miltenyi Biotec Pre-Separation Filters, 130-041-407) to eliminate cell clumps. Primary cell isolation used the mouse lineage cell depletion Kit (Miltenyi Biotec, 130-110-470) for HSPCs and the mouse monocyte isolation Kit (Miltenyi Biotec, 130-100-629) for monocytes. Murine B cells, T cells, and NK cells were isolated from C57BL/6 mouse spleen cells. The spleen was isolated, and a single-cell suspension was obtained by passing it through a 100-µm cell strainer. Primary cell isolation utilized specific kits: the B cell isolation Kit (Miltenyi Biotec, 130-90-862) for B cells, the CD8 T cell isolation Kit (Miltenyi Biotec, 130-104-075) for CD8 T cells, and the NK cell isolation Kit (Miltenyi Biotec, 130-115-818) for NK cells. Red blood cell lysis buffer was applied to eliminate red blood cells in all samples.

extract_protocol:
RNAs are amplified in situ, not extracted from the cells.
Cells (> 97% viability) were fixed with 4% PFA and immobilized with Concanavalin A beads. The bead-bound cells underwent three washes with AMOUR-wash buffer (PBS, 1 mM ATP, 0.2 U μL-1 RNase inhibitor). Subsequently, the beads were resuspended in PBS with RNase Inhibitor (40 U μL-1) and annealed with T7N9 oligo (0.25 μM). The reaction mixture was incubated at 42 °C for 2 min, followed by ramping to 25 °C and a 5-min hold. After washing, linear amplification with T7 RNA Polymerase occurred at 37 °C for 2 h with shaking at 1,200 rpm. The resulting RNA was purified using Dynabeads MyOne Silane beads. The purified RNA was ligated to 3'adapter and reverse transcribed. The cDNA was ligated with cDNA adapter and subjected to limited cycle PCR, ready for sequencing.

treatment_protocol: Murine hematopoietic cells were isolated from C57BL/6 mouse bone marrow cells.

value: spleen

value: NK

value: WT

value: in situ amplification of surface RNA


title: Whole heart tissue, Control Sham, rep 6

value: Control


title: Patient X075

city: Antwerpen

value: liver

value: HBV

value: Male

value: no


title: T_cells_plus_isotype

description: Library name: T_cells_plus_isotype

value: T cells + Isotype


title: Patient X073

value: HCV

value: Female

value: yes


title: mouse NK rep1


title: Patient X2055


title: mouse HSPC rep3

source_name: bone marrow

value: bone marrow

value: HSPC


title: Patient X072


title: BF_22q_M_2

city: Philadelphia

first: Jorge

middle: I.

last: Alvarez

state: PA

address: 310 S University Ave Room H434

department: Pathobiology

institute: University of Pennsylvania

description:
Library name: Sample_6
Column name in gene_fpkm ALL SAMPLES: BZ_22q_M_2

data_processing:
Transcripts were filtered by discarding any with TPMs <1.
Transcripts were then converted to genes, with the transcript with the highest average TPM being used.
Differentially expressed genes were defined as those with both a >1.5 average fold change and a t-test P
Assembly: GRCm38
Supplementary files format and content: Processed data includes: Gene ID, sample name, Gene name, gene chromosomal location, gene start and end loci, strand, gene length, biotype, description, and tf family in separate columns of a .txt file.

source_name: Brain

growth_protocol: All animals were cared for in accordance with the guidelines of the National Institutes of Health and procedures were approved by the University of Pennsylvania Institutional Animal Care and Use Committees. 12–16-weekold male and female Df(h22q11)/+ and wild type (WT) littermates (Taconic) were maintained on a reverse 12 hr light/dark cycle with ad libitum chow and water.

extract_protocol:
Mice were anesthetized by CO2 and transcardially perfused with 1X PBS. Brains were either frozen for whole brain sectioning/western blotting/qPCR or kept in RPMI (1X) + GlutaMAX (Gibco) + 1X MEM NAA for isolation of BBB-ECs. Data was initially analyzed separately and upon confirmation that there was no effect of sex, data from males and females were combined. Brains ECs were isolated using a protocol adapted from Munji et al., 2019 for sequencing experiments. For RNA sequencing, 3 brains of the same sex, genotype and treatment conditions were pooled into each sample (n = 3 samples per treatment condition). Brains were minced in PBS and subsequently digested in papain (Worthington) at 35o C for 90 minutes. Brains were triturated in trypsin inhibitor (ovomucoid; Worthington) and the cell suspension was digested in collagenase (Worthington) and neutral protease (Worthington) for 30 minutes at 35o C . Myelin was removed through density centrifugation with 22% Percoll. Cells were stained with FITC antimouse CD45 (Biolegend, 1:50), Zombie Violet (Biolegend 1:500), PE anti-mouse PDGFRb (Biolegend, 1:100), and APC-Cy7 anti-mouse CD31 (Biolegend, 1:50) for 30 minutes at 4o C in PBS. Live endothelial cells (CD31+ , CD45- , PDGFRb- ) were isolated by sorting on an Influx Cell Sorter (BD Biosciences). Cells were sorted into RNA lysis buffer (RLT buffer, Qiagen) and total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) and sample quality was assessed on 4200 TapeStation (Agilent) as previously performed. mRNA library was prepared using the SMART-Seq HT kit (Clontech).
Illumina indexes were added to cDNA using the Nextera XT DNA library preparation kit (Illumina). RNA-seq libraries were subjected to single end 75 bp read sequencing on an Illumina NextSeq 500 sequencer by Novogene (Beijing, China). Analysis was performed as previously described. In brief, processed reads were de-duplicated and mapped to the mouse transcriptome using Salmon with default settings and using the Ensemble mouse GRCm38 cDNA annotation as a reference transcriptome.

treatment_protocol: In bezafibrate treatment experiments, mice were given 0.5% bezafibrate enriched chow (TestDiet) or irradiated base chow (Animal Specialties and Procurement) for 4 weeks ad libitum. Treatment time point was based on other experiments reporting CNS outcomes of orally administered bezafibrate.

value: Brain

value: Primary isolate

value: Endothelial cell

value: 0.5% Bezafibrate chow ad libitum


title: Whole heart tissue, Control Sham, rep 3

value: Whole heart tissue

value: Sham


title: Patient X071


title: mouse NK rep3

value: spleen

value: NK

value: WT

value: in situ amplification of surface RNA


title: BF_22q_F_1

description:
Library name: Sample_4
Column name in gene_fpkm ALL SAMPLES: BZ_22q_F_1


title: Patient X069

value: liver

value: Male

value: no


title: Tcells_plus_Tim3

description: Library name: Tcells_plus_Tim3

value: ovarian cancer

value: engineered T cells

value: T cells

value: T cells + Tim3


title: Whole heart tissue, Control Sham, rep 4

value: Control


title: pre_transfer_MSLN_T_cells

description: Library name: pre_transfer_MSLN_T_cells

source_name: nome

value: nome


title: BF_22q_M_1

description:
Library name: Sample_5
Column name in gene_fpkm ALL SAMPLES: BZ_22q_M_1

value: Brain

value: Primary isolate

value: Endothelial cell


title: Whole heart tissue, Control Sham, rep 1

value: Whole heart tissue

value: Sham


title: UT_22q_M_1

description:
Library name: Sample_3
Column name in  gene_fpkm ALL SAMPLES: UT_22q_M_2

value: Irradiated base chow ad libitum


title: Patient X065

value: HBV


title: mouse T cell rep2

value: spleen

value: T cell

value: WT

value: in situ amplification of surface RNA


title: mouse HSPC rep1

value: bone marrow

value: HSPC


title: UT_22q_F_2

description:
Library name: Sample_2
Column name in  gene_fpkm ALL SAMPLES: UT_22q_F_2


title: Patient X063

value: liver

value: Male

value: no


title: WT_P7_4

first: Brendan

middle: H

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

data_processing:
quality assessment: FastQC 0.11.9
adapter removal: Cutadapt 3.5
read quality trimming: Trimmomatic 0.39
alignment to Ensembl 107 GRCm39: STAR with GeneCounts 2.7.10a
generation of RPKM and TMM: edgeR 3.40.1
Assembly: Ensembl 107 GRCm39
Supplementary files format and content: Spreadsheet CSV:RPKM, TMM, Raw Counts, Annotation

source_name: Lung

growth_protocol: The mice used in this study were housed in pathogen-free facilities.

extract_protocol:
TRIzol
Novogene

treatment_protocol: The mice were treated with doxycycline (625 mg/kg in food and 0.5 mg/ml in drinking water) from embryonic day 6.5 to postnatal day 1 to induce Cre expression in lung mesenchhyme.

value: Lung

value: postnatal day 7

value: Wild type


title: mouse T cell rep1


title: UT_22q_F_1

description:
Library name: Sample_1
Column name in gene_fpkm ALL SAMPLES: UT_22q_F_1

value: Brain

value: Primary isolate

value: Endothelial cell


title: Whole heart tissue, Control Sham, rep 5

value: Whole heart tissue

value: Control

value: Sham


title: mouse HSPC rep2


title: WT_P7_2


title: Patient X070

value: HCV


title: C57 HY19636 MRTX1133 resistant 3

description: Treated for 5 weeks

value: Pancreas

value: MRTX1133 resistant


title: Whole heart tissue, Control Sham, rep 2


title: mouse B cell rep2

value: spleen

value: B cell

value: WT

value: in situ amplification of surface RNA


title: Patient X062

value: liver

value: Female

value: no


title: Patient X061

value: HBV

value: Male


title: mouse T cell rep3

value: T cell


title: Patient X060


title: mouse B cell rep3


title: WT_P7_3

value: Lung

value: postnatal day 7

value: Wild type


title: mouse B cell rep1


title: WT_4M_1

value: 4 months


title: C57 HY19636 MRTX1133 resistant 1

description: Treated for 5 weeks


title: Kidney, Hmox1 KO, 20 h Heme treatment, rep 4

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422.
Sequence read quality was assessed by means of the FastQC method (v0.11.5; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimmomatic version 0.36 was used to trim Illumina adapters and poor-quality bases (trimmomatic parameters: leading=3, trailing=3, sliding window=4:15, minimum length=40).
The remaining high-quality reads were used to align against the Genome Reference Consortium mouse genome build 38 (GRCm38).
Mapping was performed by HISAT2 version 2.1.0 with parameters as default.
Count data were generated by means of the HTSeq method and analyzed using the DESeq2 method in the R statistical computing environment.
Assembly: GRCm38
Supplementary files format and content: tab-delimeted text file includes raw counts for each sample

source_name: Kidney

extract_protocol:
Total RNA was extracted using mirVana™ miRNA Isolation Kit (ThermoFisher Scientific).
Libraries were prepared from 500 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) following the manufacturer's instructions (New England Biolabs).

value: Kidney

value: Hmox1 delta/delta (KO)

tag: time point

value: Hemin


title: WT_4M_3


title: tissue

city: Seoul

first: Seungbok

last: Lee

address: 101, Daehak-ro, Jongno-gu

department: Department of Genomic Medicine

country: South Korea

institute: Seoul National University Hospital

description: Library name: CDC_NM146

data_processing:
STAR 2-pass mapping
RSEM
Assembly: GRCh38
Supplementary files format and content: Raw count

source_name: GLUL

extract_protocol:
TRIzol reagent
TruSeq Stranded mRNA kit

value: GLUL

tag: disease

value: patient GLUL variant

value: muscle


title: KO_P7_2

value: Flcn knockout


title: Patient X056

value: liver

tag: virus


title: C57 HY19636 MRTX1133 resistant 2

description: Treated for 5 weeks

value: Pancreas

value: MRTX1133 resistant


title: WT_4M_4

tag: age


title: Kidney, Hmox1 KO, 20 h Heme treatment, rep 2


title: PKC-HY19636 Vehicle

description: Treated for 1 week

value: Vehicle


title: Patient X058

value: HCV

value: Male

value: yes

tag: metavir


title: KO_P7_1

value: Lung

value: postnatal day 7


title: Kidney, Hmox1 KO, 20 h Heme treatment, rep 3


title: MT-3,Tumor,hepatocellular carcinoma

city: Xi'an, Shaanxi Province

first: Yungang

last: Xu

state: Shaanxi

address: Xi'an, Shaanxi Province

institute: Xi'an Jiaotong University

data_processing:
TrimGalore (v0.6.6),STAR (v2.7.4a) ,and StringTie (v2.1.6)
The fastq data were evaluated using FastQC. Quality control was performed using TrimGalore (v0.6.6). In this process, bases overlapping with adapters by three bases, bases with a quality score lower than 25, and reads with a length shorter than 75 bases were removed.
The reference genome index was built using STAR (v2.7.4a), and paired-end clean reads were aligned to the reference genome (GRCh38.p13) using STAR (v2.7.4a).
Gene expression levels for each sample were quantified using StringTie (v2.1.6), the count, TPM(Transcript per million) and FPKMs (Fragments Per Kilobase of transcript per Million mapped reads) were calculated
Assembly: GRCh38.p13
Supplementary files format and content: gene_count_matrix file includes raw counts for each sample

extract_protocol:
RNA extraction: Total RNA was extracted using the TRIzol method. The purity (OD260/280), concentration, and nucleic acid absorption peak of the RNA were assessed using a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was evaluated using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). mRNA was enriched using oligo(dT) magnetic beads. Fragmentation buffer was then added to break the mRNA into short fragments. Using these mRNA fragments as templates, first-strand cDNA was synthesized using random hexamer primers. Second-strand cDNA synthesis was performed using DNA Polymerase I, RNase H, dNTPs, and buffer. The cDNA fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA) to select cDNA fragments of 150-200 bp in length, followed by polymerase chain reaction (PCR) to generate the final cDNA library.

tag: tissue type

value: Tumor tissue


title: Patient X055

tag: tissue

value: HBV

tag: hcc


title: KO_4M_3

value: 4 months


title: Patient X053

tag: Sex

value: no


title: Kidney, Hmox1 KO, 20 h Heme treatment, rep 1

value: Kidney

value: Hmox1 delta/delta (KO)

value: Hemin


title: KO_4M_2

value: Flcn knockout


title: MT-2,Tumor,hepatocellular carcinoma

value: liver


title: Kidney, WT, 20 h Heme treatment, rep 3

value: Hmox1 fl/fl (WT)


title: MN-3,Normal,hepatocellular carcinoma

value: Normal tissue adjacent to tumor


title: Patient X052


title: Kidney, WT, 20 h Heme treatment, rep 4


title: Patient X050


title: KO_4M_1


title: Patient X044


title: MT-1,Tumor,hepatocellular carcinoma


title: CRC Hepatic Metastasis PDX IKKa KO rep3

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.4.4_dev) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 30 (Phred score).
Trimmed reads were aligned to an in-silico combined reference genome considering (i) human assemby hg38 release 106 from Ensembl and (ii) mouse assembly mm39 release 106 from Ensembl. STAR aligner tool (v2.7.8) was used for alignment and executed with default parameters except for the number of allowed mismatches which was set to 2
Uniquely mapped reads were considered for further analysis.  BAM files were split by organism to separately process them.
Raw gene expression was quantified using featureCounts tool from subRead software (v2.0.1) with exon as feature.
Raw counts matrix was imported into R Statistical software (v4.3.1). Prior to statistical analysis, those genes with less than 5 raw counts across the 6 samples per timepoint were discarded
For visualization purposes, counts were normalized by variance-stabilizing transformation method as implemented in DESeq2 R package (v1.40.2)
Assembly: hg38 + mm39
Supplementary files format and content: Tab-separated value file: RNAseq_RawCounts_PD05_IKKa_Metastatic_Human_KO_CTL.txt: Human data raw expression levels for each gene (61,552 rows) in each individual sample as calculated using featureCounts. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_NormCounts_PD05_IKKa_Metastatic_Human_KO_CTL.txt. Human data normalized expression levels including the expression of 19,812 genes (rows) per all individual samples. Normalization carried out with VST from DESeq2 (v1.40.2)
Supplementary files format and content: Tab-separated value file: RNAseq_RawCounts_PD05_IKKa_Metastatic_Mouse_KO_CTL.txt: Mouse raw expression levels for each gene (55,414 rows) in each individual sample as calculated using featureCounts. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_NormCounts_PD05_IKKa_Metastatic_Mouse_KO_CTL.txt. Mouse normalized expression levels including the expression of 19,644 genes (rows) per all individual samples. Normalization carried out with VST from DESeq2 (v1.40.2)

organism:
Homo sapiens
Mus musculus

source_name: Colorectal Tumoroid - hepatic metastasis

growth_protocol: PDOs cultured in matrigel at 37 °C, 5% CO2 and medium changed every week.

extract_protocol:
Hepatic Metastatic lesions were mechanically disgregated.  Total RNA was extracted from cells using Qiagen RNeasy Mini Kit (#74106) following manufacturer's instructions. RNA quality was measured by Nanodrop and Agarose gel.
Library was prepared according to manufacturer's instructions (PE 50bp paired-end reads)

value: IKKa-/-

value: knock-out untreated


title: Patient X059

value: HCV

value: Male


title: MN-1,Normal,hepatocellular carcinoma


title: Kidney, WT, 20 h Heme treatment, rep 2


title: Patient X042


title: CRC Hepatic Metastasis PDX IKKa KO rep2

value: Colorectal Tumoroid - hepatic metastasis


title: MN-2,Normal,hepatocellular carcinoma


title: Kidney, Hmox1 KO, 12 h Heme treatment, rep 3


title: Kidney, WT, 20 h Heme treatment, rep 1


title: CRC Hepatic Metastasis PDX WT rep3

value: IKKa+/+

value: wildtype untreated


title: CRC Hepatic Metastasis PDX IKKa KO rep1


title: Kidney, Hmox1 KO, 12 h Heme treatment, rep 4


title: Patient X043

value: HBV

value: yes


title: Patient X041

value: Female


title: L3161C PNP KD Rep 3

first: Matthew

last: Krieger

address: 10833 Le Conte Avenue

institute: University of California Los Angeles

description: Library name: Sample 12

data_processing:
Histograms were generated by separating reads in the BED files by strand and normalizing the coverage to the genomic maximum for that sample. Bar graphs were generated by counting all the reads that unambiguously aligned using the FeatureCounts function in the Rsubread package with the following parameters: isGTFAnnotationFile=TRUE, GTF.featureType=c("gene"), GTF.attrType="Name", isLongRead=TRUE, countMultiMappingReads=FALSE, allowMultiOverlap=TRUE, minOverlap=6, useMetaFeatures=FALSE, nthreads=8. Percentages from FeatureCounts for all samples were then used in the creation of bar graphs.
Assembly: NC_005089.1
Supplementary files format and content: readcounts.csv

source_name: Cell Line

extract_protocol:
Cells were seeded to 15cm plates and lysed in NP-40 lysis buffer (Invitrogen) for 30 minutes on ice. Protein A/G beads (Invitrogen) were incubated with J2 antibody overnight at 4°C. Conjugated beads with J2 antibody were then incubated with the lysates for 2 hours at 4°C. The beads were then washed with high-salt PBS buffer (1x PBS, 0.1% Tween, 1M NaCl) once, followed by two washes with a low salt PBS buffer (1x PBS, 0.1% Tween, 0.5M NaCl). The immunoprecipitated samples were eluted from the beads using 1mg/ml Proteinase K (Thermo Fisher) in NP-40 lysis buffer.  The dsRNA was then polyadenylated using the methods provided by E. coli Poly A polymerase ( cat#: M0276L).
PCR-cDNA libraries were prepared from ~100 ng of in vitro polyadenylated dsRNAs using the PCR-cDNA sequencing kit from Oxford Nanopore (ONT, catalog #: SQK-PCB114.24) and pooled as per the manufacturer's instructions. Sequencing was performed using R10.4.1 flow cells on a MinION Mk1B device and sequenced for 24 hours. Basecalling was performed using Dorado (version 7.9.8).

value: Cell Line

tag: cell line

tag: cell type

value: Non-Small Cell Lung Carcinoma

value: PNP KD


title: L3161C PNP KD Rep 2

description: Library name: Sample 11

tag: genotype


title: L3161C PNP KD Rep 1

description: Library name: Sample 10


title: Kidney, Hmox1 KO, 12 h Heme treatment, rep 2

value: Kidney

value: Hmox1 delta/delta (KO)

tag: treatment

value: Hemin


title: Patient X040

value: liver


title: L3161C Rep 3

description: Library name: Sample 9


title: Kidney, Hmox1 KO, 12 h Heme treatment, rep 1


title: CRC Hepatic Metastasis PDX WT rep1


title: Kidney, WT, 12 h Heme treatment, rep 4

value: Hmox1 fl/fl (WT)


title: Patient X039

value: no


title: Patient X037

value: HCV


title: CRC Hepatic Metastasis PDX WT rep2


title: Patient X036


title: Kidney, WT, 12 h Heme treatment, rep 3


title: L3161C Rep 1

description: Library name: Sample 7


title: Kidney, WT, 12 h Heme treatment, rep 2


title: 1969B PNP KD Rep 2

description: Library name: Sample 5


title: Kidney, WT, 12 h Heme treatment, rep 1


title: 1969B PNP KD Rep 3

description: Library name: Sample 6


title: Patient X034

value: Male


title: 1969B Rep 3

description: Library name: Sample 3


title: 1969B PNP KD Rep 1

description: Library name: Sample 4


title: Patient X035


title: Patient X033


title: Kidney, Hmox1 KO, 6 h Heme treatment, rep 3

value: 6 h


title: Kidney, Hmox1 KO, 6 h Heme treatment, rep 4


title: 1969B Rep 2

description: Library name: Sample 2


title: R5T48h

city: Ciudad de México

first: Mariano

last: Guardado Estrada

state: Ciudad de México

address: Circuito de la Investigación SN

country: Mexico

institute: UNAM

description: Gene expression data from skeletal muscle of a male Wistar rat collected at 48 hours of postmortem interval.

hyb_protocol: Labeled targets were hybridized to Clariom S Rat Arrays at 45°C for 16 h using the GeneChip Hybridization Oven 645.

scan_protocol: Arrays were washed and stained on a GeneChip Fluidics Station 450, and scanned using the GeneChip Scanner 3000. Data were acquired with the GeneChip Command Console Software v4.0.

data_processing: Raw .CEL files were processed using Transcriptome Analysis Console v4.0 with default settings. Gene-level expression was summarized using RMA and annotated with Clariom_S_Rat.r1.na36.rn6.a1.transcript.csv (genome version rn6). Differential expression was assessed by one-way ANOVA (fold change ≥ 2.0, p < 0.05).

label: biotin

source_name: Rat skeletal muscle, 48 hours of postmortem interval

label_protocol: 10 ng of total RNA were amplified and biotin-labeled using the GeneChip 3' IVT Pico Kit , following the manufacturer’s instructions.

growth_protocol: Wistar rats (<200 g) were housed under a 12 h light/dark cycle with free access to food and water.

extract_protocol: 50–100 mg of frozen skeletal muscle tissue were homogenized with beads, and total RNA was extracted using TRIzol™ Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: Rats were euthanized by cervical dislocation. Control samples (0 h PMI) were collected immediately. Experimental animals were kept at 25°C for 48 hours postmortem before tissue collection.

value: Wistar

value: Femoral skeletal muscle

value: wild-type

tag: gender

value: male

tag: time


title: Patient X030

value: yes


title: 1969B Rep 1

description: Library name: Sample 1

value: Cell Line


title: Kidney, Hmox1 KO, 6 h Heme treatment, rep 2


title: Patient X029


title: Patient X028


title: Kidney, WT, 6 h Heme treatment, rep 4


title: Kidney, Hmox1 KO, 6 h Heme treatment, rep 1


title: Mouse brain, Adar1-2KO, circRNA, ONT, rep3

city: Beijing

first: Erika

last: Larrea de Orte

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

institute: Chinese Institute for Brain Research (CIBR)

description:
Total RNA was enriched for circRNAs
Adar1-2KO-3-circRNA-ONT

data_processing:
*library strategy: circRNA-seq
For Illumina sequencing:
Basecalling: Bcl2Fastq
Quality filtering: Fastp (version 0.19.7). (1) Discard paired reads if either one  contains adapter contamination; (2) Discard paired reads if more than 10% of bases are uncertain in either one read; (3) Discard paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one
FASTQ files were mapped to the mouse reference genome (GRCm39) using BWA v0.7.17
CIRI-2 v2.0.6 pipeline was used to call circRNAs and CIRI-quant v1.1.2 for circRNA quantification. For the differential expression analysis Deseq2  2.11.40.8 tool was employed. As input, BSJ reads were used as counts.
FASTQ files were obtained using Guppy v6.1.2. Adapters were trimmed using PoreChop v0.2.4 and reads shorter than 500bp were discarded. For circular RNA identification, CIRIlong v1.0.3 was run using GRCm39 as the reference mouse genome. Circular RNAs occurring in genomic repetitive regionsor encoding ribosomal RNA or shorter than 30nt wereexcluded from subsequent analysis.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files named as "_ciri2.txt" correspond to the CIRI2 output for each sample
Supplementary files format and content: Tab-delimited text files named as "_ciriquant.txt" correspond to the CIRIquant output for each sample
Supplementary files format and content: DEAcircRNAsAdar2vsWT.csv coresponds to the differential expression analysis betweeen Adar2KO samples and WT samples
Supplementary files format and content: DEAcircRNAsAdar1-2vsWT.csv coresponds to the differential expression analysis betweeen Adar1-2KO samples and WT samples
Supplementary files format and content: Bed files correspond to the CIRIlong output after QC filtering

source_name: whole brain

extract_protocol:
Adult mice were euthanized and brains were immediately isolated, quickly washed with ice-cold DPBS and fully homogenized in 3mL TRIzol Reagent using a dounce tissue homogenizer. Total RNA was extracted, treated with DNAseI (0.2U/μg total RNA) and cleaned up with phenol chloroform followed by isopropanol precipitation. 5μg total RNA were used to deplete ribosomal RNA and enrich for circRNAs using RnaseR. Enriched RNA was  reverse transcribed using random hexamers primer with an adaptor sequence allowing a rolling amplification of circRNAs. TdT enzyme was used to add a deoxycytidine tail in the single stranded cDNA molecules. An oligo(dG)12 primer coupled with an adaptor sequence was used for second strand synthesis. Double-stranded cDNA samples were size selected with AMPure XP beads  using a sample-bead ratio of 0.5X. The purified cDNA was PCR amplified for 14 cycles and PCR products size selected again (sample-bead ratio of 0.5X) prior to sequencing library preparations
For Illumina sequencing, 5ng cDNA were used for TruePrep DNA Library Prep Kit V2 for Illumina. After cDNA tagmentation and adaptor ligation, 9 PCR cycles were used followed by size selection using AMPure XP beads to enrich for insert length around 350bp.  PE-150 reads were generated.
For Oxford Nanopore Sequencing, 100ng cDNA were used for Ligation Sequencing Kit V12 (SQK-LS112) and sequenced in FLO-MIN112 flow cells.

value: whole brain

tag: strain

value: 3-4 months


title: R4T48h


title: L3161C Rep 2

description: Library name: Sample 8

value: Non-Small Cell Lung Carcinoma


title: Kidney, WT, 6 h Heme treatment, rep 3

value: Kidney


title: Patient X024

value: HBV

tag: censored time


title: Mouse brain, Adar1-2KO, circRNA, ONT, rep2

description:
Total RNA was enriched for circRNAs
Adar1-2KO-2-circRNA-ONT


title: R4T0h

description: Gene expression data from skeletal muscle of a male Wistar rat collected at 0 hours of postmortem interval.

source_name: Rat skeletal muscle, 0 hours of postmortem interval


title: R2T48h


title: R3T48h


title: R5T0h


title: Patient X026

value: liver


title: Mouse brain, Adar1-2KO, circRNA, ONT, rep1

description:
Total RNA was enriched for circRNAs
Adar1-2KO-1-circRNA-ONT


title: R1T48h


title: SAS, CDDP-exposure, rep3

city: Sendai

first: Yuki

last: Nakayama

address: 2-1 Seiryo-machi,Aoba

department: Biochemistry and Molecular Biology

country: Japan

institute: Tohoku Medical Megabank Organization, Tohoku University

description:
Library name: 88
Column name in txi_counts.csv: 10CR_3

data_processing:
Sequence reads were trimmed for adopter sequence/low-quality sequence using fastp
Read counts data were generated by trimmed sequence reads using Sarmon Quant
Assembly: GRCh38
Supplementary files format and content: txi_counts.csv

source_name: SASCR

growth_protocol: All cell lines were maintained  RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere  with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy plus kit (Qiagen). 11 ng/μL RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA directional library prep kit (MGI) following manufacture's protocol.

value: SASCR

value: Head and neck squamous cell carcinoma

value: CDDP exposure


title: R2T0h


title: SAS, CDDP-exposure, rep2

description:
Library name: 87
Column name in txi_counts.csv: 10CR_2


title: Kidney, WT, 6 h Heme treatment, rep 1

value: Hmox1 fl/fl (WT)

tag: time point

value: Hemin


title: Mouse brain, wild type, circRNA, ONT, rep3

description:
Total RNA was enriched for circRNAs
WT3-circRNA-ONT

value: wild type

value: Male


title: R3T0h

value: Wistar

value: Femoral skeletal muscle

value: wild-type


title: Mouse brain, Adar2KO, circRNA, ONT, rep3

description:
Total RNA was enriched for circRNAs
Adar2KO-3-circRNA-ONT


title: SAS, non-treatment, rep2

description:
Library name: 84
Column name in txi_counts.csv: 10P_2

source_name: SAS

value: SAS

value: No


title: SAS, CDDP-exposure, rep1

description:
Library name: 86
Column name in txi_counts.csv: 10CR_1


title: R1T0h

value: male


title: Kidney, Hmox1 KO, 0 h, rep 4

value: Hmox1 delta/delta (KO)

value: no treatment


title: Kidney, Hmox1 KO, 0 h, rep 1

value: Kidney


title: Patient X023

source_name: liver

value: liver

value: HCV

value: Female

value: no


title: Mouse brain, wild type, circRNA, ONT, rep2

description:
Total RNA was enriched for circRNAs
WT2-circRNA-ONT

value: whole brain

value: 3-4 months


title: Mouse brain, Adar2KO, circRNA, ONT, rep1

description:
Total RNA was enriched for circRNAs
Adar2KO-1-circRNA-ONT


title: Kidney, Hmox1 KO, 0 h, rep 3


title: SAS, non-treatment, rep3

description:
Library name: 85
Column name in txi_counts.csv: 10P_3

value: Head and neck squamous cell carcinoma


title: Kidney, WT, 0 h, rep 4

value: Hmox1 fl/fl (WT)


title: Patient X027

value: HBV

value: yes


title: Patient X021


title: Patient X025

value: Male


title: Kidney, Hmox1 KO, 0 h, rep 2


title: Patient X019


title: Patient X020


title: Kidney, WT, 0 h, rep 2


title: Mouse brain, Adar2KO, circRNA, ONT, rep2

description:
Total RNA was enriched for circRNAs
Adar2KO-2-circRNA-ONT


title: 82_r252

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: Library name: 82_r252

data_processing:
Each FASTQ file gets a quality report generated by FASTQC tool. Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using fastq-mcf. Reads shorter than 15 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/)) with default settings. Feature count table was generated by R package Rsubread_2.10.5
Assembly: Canis_lupus_familiaris.ROS_Cfam_1.0.105
Supplementary files format and content: Excel file, raw count (Rsubread:FeatureCount)

organism: Canis lupus familiaris

source_name: lung

extract_protocol:
Total RNA was isolated using the RNeasy® Micro Kit (Qiagen) according to the manufacturer’s instructions including an on-column DNA digestion.
The RNA sequencing library was generated from 50 ng total RNA using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England BioLabs) according to manufacture´s protocols. The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run) with an average of 3 x10^7 reads per RNA sample.

treatment_protocol: After isolation, cells were seeded at a maximum density of 50 Mio. cells per T75-flask overnight in RPMI 1640 medium containing 10% fetal calve serum, 1% penicillin/streptomycin and 1% sodium pyruvate at 37°C, 5% CO2. After an overnight incubation at 37°C with 5% CO2, cells were seeded at a density of 1 x 105 cells per well in a 24-well plate (Sarstedt) for subsequent infection. Before infection, cells were washed twice, followed by incubation with washing medium containing a multiplicity of infection (MOI) of 1 viral particles. After 3 h of incubation at 37°C and 5% CO2, washing medium was replaced by culture medium and cells were kept until harvesting at 1 day post infection. Cells were carefully scratched from the wells with a cell scraper and cell pellets were rapidly frozen in liquid nitrogen and stored at -80°C until further use.

value: lung

value: primary alveolar macrophages

value: Canine Distemper virus strain R252


title: HSC-4, CDDP-exposure, rep1

description:
Library name: 80
Column name in txi_counts.csv: 8CR_1

value: CDDP exposure


title: Kidney, WT, 0 h, rep 1

value: no treatment


title: 139_r252

description: Library name: 139_r252


title: HSC-4, non-treatment, rep3

description:
Library name: 79
Column name in txi_counts.csv: 8P_3

value: No


title: SAS, non-treatment, rep1

description:
Library name: 83
Column name in txi_counts.csv: 10P_1

value: SAS


title: HSC-4, non-treatment, rep2

description:
Library name: 78
Column name in txi_counts.csv: 8P_2


title: Mouse brain, wild type, circRNA, ONT, rep1

description:
Total RNA was enriched for circRNAs
WT1-circRNA-ONT

value: wild type


title: HSC-4, CDDP-exposure, rep3

description:
Library name: 82
Column name in txi_counts.csv: 8CR_3


title: Patient X010

value: liver


title: Patient X017


title: 138_ond

description: Library name: 138_ond

value: Canine Distemper virus strain OND


title: 4T1_DMSO_rep3

city: Chengdu

first: Yumei

last: Wang

address: 1166 LiuTai

institute: Chengdu University of TCM

data_processing:
Basecalls performed using CASAVA1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38/GRCm39 whole genome using hisat2 with parameters -t -q -x -p 8
Count were calculated using htseq with parameters -f -r -s no -a 10 -i
Assembly: hg38/GRCm39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Breast

growth_protocol: The MDA-MB-231 and 4T1 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol following manufacturer's protocol.
The libraries were constructed by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and following manufacturer's protocol.

treatment_protocol: Cells were treated with 1 µmol/L ponatinib or DMSO for 24 h.

value: Breast

value: epithelial cell

value: WT

value: DMSO


title: Patient X008

data_processing:
Clustering and DNA sequencing using the Illumina cBot and HiSeq 4000 was performed according to manufacturer's protocols. A concentration of 1.0 nM of DNA was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.7.7 and Bcl2fastq v2.17. Raw sequencing reads were trimmed with fastp using default settings. Reads were subsequently aligned to the gencode v38 human reference genome primary assembly with STARv2.7.8a using default settings and --sjdbOverhang 150. STAR was also used to generate per sample count tables in parallel (--quantMode GeneCounts).
Assembly: gencode v38 human reference genome
Supplementary files format and content: training_raw_counts.txt: Tab-delimited text file showing raw read counts.
Supplementary files format and content: training_RPM.txt: Tab-delimited text file showing RPM normalized reads.

extract_protocol:
Total RNA was extracted from 5 to 10 slides of 10 micron each per liver biopsy using the RNeasy FFPE Kit (Qiagen).
The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina".

value: HBV

value: no


title: Kidney, WT, 0 h, rep 3

value: Kidney

value: Hmox1 fl/fl (WT)


title: 86_r252

description: Library name: 86_r252

value: lung

value: primary alveolar macrophages


title: HSC-4, CDDP-exposure, rep2

description:
Library name: 81
Column name in txi_counts.csv: 8CR_2

value: Head and neck squamous cell carcinoma

value: CDDP exposure


title: 4T1_DMSO_rep2


title: Ca9-22, CDDP-exposure, rep1

description:
Library name: 74
Column name in txi_counts.csv: 7CR_1


title: 135_ond

description: Library name: 135_ond


title: Patient X016

value: HCV

value: Male


title: Patient X006

value: yes


title: 4T1_DMSO_rep1


title: Patient X012

value: liver


title: Ca9-22, non-treatment, rep3

description:
Library name: 73
Column name in txi_counts.csv: 7P_3

value: No


title: 4T1_Ponatinib_rep3

value: Breast

value: Ponatinib


title: 136_r252

description: Library name: 136_r252

value: Canine Distemper virus strain R252


title: Patient X011


title: 4T1_Ponatinib_rep2

value: epithelial cell

value: WT


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-4

city: Xi’an

first: Ping

last: Zhu

address: Changle Xi Road

institute: Fourth Military Medical University

description:
Library name: MPZ_3E8_4
10x genomics

data_processing:
For rhesus macaques data, spaceranegr (v1.2.1) was used to process spatial sequencing data for mapping to reference genome. SCTransform function in Seurat (v4.1.0) was used to process the gene expression matrix. The pathologists preliminarily divided the pathological areas of the sections in virus-infected group, integrated the matrix and gene expression matrix after stlearn sorted out the H&E sections, and then performed dimensionality reduction clustering, which was defined according to the data of pathological spots in each cluster.
For mouse data, spaceranegr (v1.3.1) was used to process mouse spatial sequencing data for mapping to reference genome. SCTransform function in Seurat (v4.1.0) was used to process the gene expression matrix. Spots with SARS-CoV-2 genes was defined as infected spots; otherwise, defined as uninfected spots. On this basis, the two uninfected positions closest to the infected positions are defined as border positions. runRCTD function in spacexr (v2.2.1) was used for assigning single cell types to spatial transcriptomics spots and defining a spot where the proportion of a certain cell type exceeds 50% as that cell type.
Assembly: macaque reference Ensembl_release105 and mouse reference Ensembl_release111
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: tissue images.gz
Library strategy: Spatial Transcriptomics

organism: Macaca mulatta

extract_protocol:
The spatial transcriptome sequencing was performed by Genedenovo Biotechnology Co., Ltd. The lung tissues of rhesus macaques (Healthy, n=4; Ctrl, n=4; MPZ, n=4; 3E8, n=4; MPZ+3E8, n=4; at 7dpi) and virus-infected hCD147 mice (n=4; at 3dpi) were used to perform spatial transcriptome sequencing. The tissues were embedded in the OCT-filled mold and cut into slices by cryo-sectional technology. Subsequently, the samples were barcoded through 10× Genomics Platform using Visium Spatial Tissue Optimization Reagent Kit and Slide Kit (PN-1000192, PN-1000191, 10× Genomics), Visium Spatial Gene Expression Reagent Kit and Slide Kit (PN-1000189, PN-1000188, 10× Genomics), Library Construction Kit (PN-1000196, 10× Genomics), and Dual Index Kit (PN-1000215, 10× Genomics). Each sequencing library was sequenced using Illumina sequencing platform.
10× Genomics Visium Spatial

value: 3-4 years

value: male

value: SARS-CoV-2 (Beta strain)

value: MPZ, 5 mg/kg; 3E8, 5 mg/kg


title: Ca9-22, non-treatment, rep2

description:
Library name: 72
Column name in txi_counts.csv: 7P_2


title: 121_r252

description: Library name: 121_r252

value: lung

value: primary alveolar macrophages


title: HSC-4, non-treatment, rep1

description:
Library name: 77
Column name in txi_counts.csv: 8P_1

value: Head and neck squamous cell carcinoma


title: 4T1_Ponatinib_rep1


title: 118_r252

description: Library name: 118_r252


title: Ca9-22, CDDP-exposure, rep3

description:
Library name: 76
Column name in txi_counts.csv: 7CR_3

value: CDDP exposure


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-2

description:
Library name: MPZ_3E8_2
10x genomics


title: Ca9-22, CDDP-exposure, rep2

description:
Library name: 75
Column name in txi_counts.csv: 7CR_2


title: HO1-u-1, CDDP-exposure, rep3

description:
Library name: 70
Column name in txi_counts.csv: 6CR_3


title: Patient X013

value: HBV

value: Male

value: no


title: WT-MOCK2-IP

city: Suzhou

first: Anqi

last: Dong

address: 199 Ren'ai Road

institute: Soochow university

description: Library name: sample16

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Raw reads would be processed to get high quality clean reads according to four stringent filtering standards: i Removing reads containing adapters; ii Removing reads containing more than 10% of unknown nucleotides (N); iii Removing reads that are all A bases；ⅳ Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The rRNA removed reads of each sample were then mapped to reference genome, respectively.
MACS2 (version: 2.1.2) software was used to identify read-enriched regions from MeRIP-seq data. Dynamic Poisson Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when q-value<0.05.
The distribution of peak on different function regions, such as 5’UTR, CDS and 3’UTR, was performed.
All peak related genes were mapped to GO terms in the Gene Ontology database.
Pathway enrichment analysis identified significantly enriched metabolic pathways or signal transduction pathways in peak related genes comparing with the whole genome background.
MEME suit (http://meme-suite.org/) and DREME (http://memesuite.org/tools/dreme) were used to detect the significant sequence motif in the transcript sequence associated with peaks.
The DiffBind (version 2.8) software was used to combine peaks of every group, and obtained the union of peaks among groups. Peak abundance was shown by calculating rpm-values of each sample.
Peaks distant from peak-related gene (which locates farther upstream than 2k or downstream 300bp) were removed, and the remaining peak related genes were used for subsequent GO and KO enrichment analysis.
The DiffBind (version 2.8) software was used to analysis RNA methylation rate between groups.
Assembly: GRCm39
Supplementary files format and content: all_samples.expression.Annot.xls includes raw counts for each sample
Library strategy: MeRIP-Seq

source_name: peritoneal cavity

growth_protocol: Peritoneal macrophages (PMs) were isolated from WT and Adap-/- mice via peritoneal lavage using 5 ml of phosphate-buffered saline (PBS), 3 days after injection of 3% thioglycolate. The PMs were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin-streptomycin.

extract_protocol:
Total RNA was extracted and purified with TRIzol reagent (Invitrogen, USA) following the manufacturer’s procedure. The RNA amount and purity were examined using a Nanodrop 2000 (Thermo Fisher Scientific, USA).
After total RNA was extracted, the enriched RNA was fragmented into short fragments (about 100nt) by using fragmentation buffer. RNA was divided into two parts, one of which was used as the input (no IP experiment was performed). The other RNA was enriched with m6A specific antibody. The enriched RNA was reverse transcripted into cDNA with random primers. Next, the cDNA fragments was end repaired, and ligated to Illumina sequencing adapters. Finally we got qualified library for sequencing, sequenced using Illumina HiSeqTM 4000 (or other platforms) by Gene Denovo Biotechnology Co. (Guangzhou, China)

treatment_protocol: PMs isolated from WT and Adap-/- mice were treated or untreated with 1 ug/ml LPS for 6 h.

value: peritoneal cavity

value: primary cell

value: peritoneal macrophage

value: mock


title: 43_non

description: Library name: 43_non


title: Patient X005

first: Nicolaas

last: Van Renne

institute: Laboratory of Experimental Medicine and Pediatrics (LEMP)

value: liver

value: HCV

value: yes


title: 120_ond

description: Library name: 120_ond

value: Canine Distemper virus strain OND


title: Patient X009


title: WT-MOCK2-INPUT

description: Library name: sample15

value: WT


title: 117_ond

description: Library name: 117_ond


title: 48_non

description: Library name: 48_non


title: Ca9-22, non-treatment, rep1

description:
Library name: 71
Column name in txi_counts.csv: 7P_1

value: No


title: Patient X001


title: WT-MOCK1-IP

description: Library name: sample14


title: SARS-CoV-2 infection, 3E8 treatment-3

description:
Library name: 3E8_3
10x genomics

value: lung

value: 3-4 years

value: male

value: SARS-CoV-2 (Beta strain)


title: 45_non

description: Library name: 45_non

value: primary alveolar macrophages


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-3

description:
Library name: MPZ_3E8_3
10x genomics

value: MPZ, 5 mg/kg; 3E8, 5 mg/kg


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-1

description:
Library name: MPZ_3E8_1
10x genomics


title: HO1-u-1, non-treatment, rep3

description:
Library name: 67
Column name in txi_counts.csv: 6P_3

value: Head and neck squamous cell carcinoma


title: HO1-u-1, CDDP-exposure, rep2

description:
Library name: 69
Column name in txi_counts.csv: 6CR_2

value: CDDP exposure


title: Patient X003

value: Male


title: 140_non

description: Library name: 140_non


title: WT-MOCK1-INPUT

description: Library name: sample13

value: peritoneal cavity

value: primary cell

value: peritoneal macrophage


title: SARS-CoV-2 infection, 3E8 treatment-2

description:
Library name: 3E8_2
10x genomics


title: Kidney, WT, 6 h Heme treatment, rep 2

value: Kidney

value: Hmox1 fl/fl (WT)

value: 6 h

value: Hemin


title: SARS-CoV-2 infection, 3E8 treatment-1

description:
Library name: 3E8_1
10x genomics


title: HO1-u-1, non-treatment, rep2

description:
Library name: 66
Column name in txi_counts.csv: 6P_2

value: No


title: HO1-u-1, non-treatment, rep1

description:
Library name: 65
Column name in txi_counts.csv: 6P_1


title: LP09015_PRS

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

description:
Library name: Sample5
Column name in raw_counts_All_Samples.tsv: LP09015

data_processing:
Reads in FASTQ format were generated using the Illumina bcl2fastq command-line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long, unique, dual indices. Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N's, and trim bases with a quality of less than 30 from the 3' ends of the reads. On average, 8.9 million reads were left after this procedure. Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using the STAR aligner version 2.6.1a in 2-pass mode. STAR counted raw reads per gene. Differential gene expression was calculated using DESeq2 version 1.44.0.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: raw_counts_All_Samples.tsv contains a matrix with raw gene counts, gene symbols, and gene types for each sample.

source_name: human gingiva

growth_protocol: Gingival fibroblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich, St. Louis, MO, USA) containing penicillin, streptomycin (Sigma Aldrich, St. Louis, MO), and 10% fetal bovine serum (Bio&Sell GmbH, Nuremberg, Germany).

extract_protocol:
Total RNA was extracted using the GeneMATRIX Universal RNA Purification Kit (EURX, Gdańsk, Poland) with rDNase set (Macherer-Nagel, Düren, Germany ).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3' FWD protocol version 2 with unique dual indices (Lexogen GmbH, Vienna, Austria). Seventeen PCR cycles were used for library preparation, as determined by quantitative PCR (qPCR) according to the library preparation manual.

treatment_protocol: Gingival fibroblasts of low passage were seeded at 3 × 10^4/cm^2 the day before being exposed to 30% PRS in serum-free medium for an additional 16 hours at 37 °C, 5% CO2, and 95% humidity, followed by the isolation of RNA.

value: human gingiva

value: gingival fibroblast

value: treated with PRS


title: LP09023_PRS

description:
Library name: Sample6
Column name in raw_counts_All_Samples.tsv: LP09023


title: HO1-u-1, CDDP-exposure, rep1

description:
Library name: 68
Column name in txi_counts.csv: 6CR_1


title: HSC-3, CDDP-exposure, rep3

description:
Library name: 58
Column name in txi_counts.csv: 3CR_3


title: WT-LPS2-IP

description: Library name: sample12

value: WT

value: LPS stimulation (1ug/ml, 6h)


title: SARS-CoV-2 infection, 3E8 treatment-4

description:
Library name: 3E8_4
10x genomics

value: lung

value: 3-4 years

value: male

value: SARS-CoV-2 (Beta strain)


title: WT-LPS2-INPUT

description: Library name: sample11

value: peritoneal cavity


title: WT-LPS1-IP

description: Library name: sample10

value: primary cell


title: LP09007_PRS

description:
Library name: Sample4
Column name in raw_counts_All_Samples.tsv: LP09007


title: LP09009_untreated

description:
Library name: Sample2
Column name in raw_counts_All_Samples.tsv: LP09009

value: untreated


title: LP09017_untreated

description:
Library name: Sample3
Column name in raw_counts_All_Samples.tsv: LP09017


title: SARS-CoV-2 infection, Meplazumab treatment-4

description:
Library name: MPZ_4
10x genomics

value: MPZ, 10 mg/kg


title: SARS-CoV-2 infection, Meplazumab treatment-3

description:
Library name: MPZ_3
10x genomics


title: LP09001_untreated

description:
Library name: Sample1
Column name in raw_counts_All_Samples.tsv: LP09001


title: AKO-MOCK2-IP

description: Library name: sample8

value: peritoneal macrophage

value: ADAP knockout

value: mock


title: HSC-3, CDDP-exposure, rep2

description:
Library name: 57
Column name in txi_counts.csv: 3CR_2

value: Head and neck squamous cell carcinoma

value: CDDP exposure


title: WT-LPS1-INPUT

description: Library name: sample9


title: HSC-3, non-treatment, rep3

description:
Library name: 47
Column name in txi_counts.csv: 3P_3

value: No


title: AKO-MOCK2-INPUT

description: Library name: sample7


title: HSC-3, CDDP-exposure, rep1

description:
Library name: 48
Column name in txi_counts.csv: 3CR_1


title: SARS-CoV-2 infection, Meplazumab treatment-2

description:
Library name: MPZ_2
10x genomics


title: SARS-CoV-2 infection, Meplazumab treatment-1

description:
Library name: MPZ_1
10x genomics


title: HSC-3, non-treatment, rep2

description:
Library name: 46
Column name in txi_counts.csv: 3P_2