title: Male preterm diabetic (PT-D), RNAseq, rep 4

city: Charlottesville

first: Jennifer

last: Charlton

address: 409 Lane Rd. Room 2035

institute: University of Virginia

data_processing:
Sequencing quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Low-quality reads were discarded before the analyses. Obtained reads were adapter trimmed and then aligned to the GRCm38 mouse genome with the gencode M15 gene annotation using the STAR aligner36. Transcripts were quantified using the --quantMode GeneCounts function of the STAR aligner, and normalization was applied, followed by differential expression assessed using the DESeq237. Genes with mean normalized expression <50 reads in all samples were filtered out because these are more likely to represent transcriptional noise. Differentially expressed genes (DEGs) with a p-value adjusted by false discovery rate (FDR) for multiple comparisons of <0.05 and a fold change (FC) of at least 2 were selected to visualize and rank genes. The sequencing data that support the findings is available at GEO.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
One kidney was stored in RNAlater™ Stabilization Solution (Sigma Aldrich, St. Louis, MO). RNA extraction and cleaning were performed using TRIZOL (Invitrogen, Waltham, MA) and RNeasy MinElute Cleanup Kit with RNase-Free DNase (QIAGEN, Hilden, Germany). Extracted RNA was reconstituted with RNase-free water to a final volume of 50 µl and stored at -80°C until analysis. RNA concentration and OD260/280 were measured with a NanoDrop Spectrophotometer (Thermo Fisher, Waltham, MA). Whole kidney RNA-Seq was performed by Novogene, and only samples with high purity (OD260/280>2.0; RIN>4.0) were analyzed.
Whole kidney RNA-Seq was performed by Novogene, and only samples with high purity (OD260/280>2.0; RIN>4.0) were analyzed.

value: Kidney

tag: genotype

tag: treatment

value: Streptozotocin (STZ)


title: miR-769_3

status: Public on Jun 04 2025

type: SRA

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

library_source: transcriptomic

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.25.2 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

molecule: total RNA

organism: Homo sapiens

source_name: WSTIi081-A, EbiSC

growth_protocol: TeSR™-E8™ medium (#05990, STEMCELL™ Technologies) at 37°C and 5% CO2 in a humidified atmosphere

extract_protocol:
Total RNA isolation was performed with the RNA Mini Kit (Bio&Sell) according to the manufacturers protocol. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 500-100ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

treatment_protocol: 250.000 iPSCs were transfected with Lipofectamin RNAiMAX (Cat. No. 13778075) according to the manufacturers protocol (ThermoFisher Scientific). All miRNA precursor transfections were performed with a concentration of 8 nM for 48 h.

tag: cell line

value: WSTIi081-A, EbiSC

tag: cell type

value: iPSCs

value: transfection Ambion® Pre-miR™ miRNA Precursor for hsa-miR-769-5p (Assay ID PM11974, Cat. No. AM17100, ThermoFisher Scientific)


title: Male preterm diabetic (PT-D), RNAseq, rep 5

country: USA

organism: Mus musculus

source_name: Kidney

tag: tissue

value: WT


title: transcriptome of myocardium of a patient with HCMP - id X61H

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

data_processing:
Pipelines was used for data processing.
Pipeline – Ambiguous and low-quality bases were removed from the files obtained during the FASTQ sequencing process. Removal was done with AdapterRemoval V2. The trimmed files were aligned to the human reference genome GRCH38 and GRCH38.92 gene annotation using RSEM with rsem-prepare-reference and rsem-calculate-expression commands  and the -star option to also generate STAR indices.
Assembly: GRCH38
Supplementary files format and content: Processed count files  were obtained using RSEM pseudo counts output from (rsem-calculate-expression) with --star option enabled..

molecule: polyA RNA

source_name: myocardium

extract_protocol:
Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories).
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.

value: myocardium

tag: batch

tag: Sex

value: f

tag: hight

tag: weight

tag: age

value: no

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

value: yes

tag: lightheadedness

value: systolic

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

value: HCMP

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: Male preterm diabetic (PT-D), RNAseq, rep 3

tag: tissue

tag: genotype

tag: treatment


title: liver, WT1

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

description: Library name: 1_s1623-WT_FXR_mm10

library_source: genomic

data_processing:
ChIP-Seq and initial data processing were carried out using the Active Motif analysis pipeline.
The generated 75-nt single-end (SE75) reads were mapped to the Mus musculus genome (mm10) using the BWA algorithm with default parameters, and alignment data for each read was stored in BAM format.
PCR duplicates were removed to ensure data quality. ChIP samples were normalized to their respective input controls and converted to bigWig format for visualization in the Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: liver

extract_protocol:
ChIP-Seq was conducted using 100 mg of liver tissue from 6-month-old Atp7b−/− and WT mice (n=3 mice per group) with an FXR antibody (H-130X, Santa Cruz Biotechnology).
Active motif ChIP-Seq Kit

value: liver

value: wild-type


title: miR-769_2

tag: cell line

tag: cell type


title: miR-769_1


title: miR-197_3

value: transfection Ambion® Pre-miR™ miRNA Precursor for hsa-miR-197-3p (Assay ID PM10354, Cat. No. AM17100, ThermoFisher Scientific)


title: Male preterm diabetic (PT-D), RNAseq, rep 2


title: transcriptome of myocardium of a patient with HCMP - id X5H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

value: CC


title: miR-197_2

tag: cell line

tag: cell type

tag: treatment


title: Male preterm diabetic (PT-D), RNAseq, rep 1

tag: tissue

tag: genotype


title: miR-197_1


title: HFD1

city: Qingdao

first: Xueqiang

last: Wang

state: China

address: 369 Dengyun Road, High-tech Zone

country: China

institute: University of Health and Rehabilitation Sciences

description: Library name: HFD1

data_processing:
CLC Genomics Workbench V11.0.1
Sequence reads were trimmed for adaptor seguence/low-qualty sequence using CLC genomic benchwork (parameter- Qualty limit. 0.05)
Timmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 inseion cost:3 deleion cost:3 length faction:0.8 simlanity fraction:0.8)
Read count extraction and normalization were performed usina CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

growth_protocol: Mouse were fed a HFD 4 weeks of age,then supplemented with allantoin in their drinking water at the concentrations of 0.06 mg/mL and 0.3mg/mL for additional 4 weeks

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5ug of total RNA was uesed for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Allantoin was supplemented  in their drinking water at the concentrations of 0.06 mg/mL and 0.3mg/mL for additional 4 weeks under HFD

value: Liver

value: HFD


title: transcriptome of myocardium of a patient with HCMP - id X63H

tag: batch

tag: Sex

value: m

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: Male preterm non-diabetic (PT-ND), RNAseq, rep 5

tag: tissue

value: Kidney

tag: genotype

tag: treatment


title: Neg-Ctl_3

tag: cell line

value: WSTIi081-A, EbiSC

tag: cell type

value: iPSCs

value: transfection Pre-miR™ miRNA Precursor Negative Control #1 (Cat. No. AM17110, ThermoFisher Scientific)


title: Biotinylated cel-miR-67 rep 3

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Reads were processed using the nf-core rnaseq pipeline v13.4.0 with the GRCh38 reference assembly and the GENCODE release 46 transcript annotation
Transcript quantifications were performed with salmon v1.10.0 in pseudoalignment mode and tabulated by the nf-core pipeline.
The quantification table was read into R v4.3.2 and analysed with DESeq2 v1.42.1, comparing abundance in miR-486-5p vs cel-miR-67 pulldown samples.
A filter was applied to retain genes with a padj value (Benjamini-Hochberg corrected p-value) below 0.01 as having signficant expression changes.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file of pseudocounts from salmon quantification, with Ensembl gene IDs and gene symbols

source_name: HUVEC

growth_protocol: HUVECs were at 37ºC in 5% CO2 in EBM2 medium supplemented with microvascular growth factors and 2% FBS (Lonza, Basel, Switzerland, catalog # CC-3156)

extract_protocol:
Bound RNA was isolated with the miRNeasy micro kit (Qiagen) with modifications to purify RNAs > 200 nucleotides in length.
Ultra II directional RNA kit (New England Biolabs), using 15ng of RNA input

treatment_protocol: HUVECs were transfected with 10 nM 3'-Bi-miR-486-5p or 10 nM 3'-Bi-cel-miR-67 (Horizon Discovery Biosciences) in lipofectamine RNAiMax (Thermofisher). After 24 hr, cells were lysed, and lysate supernatants were incubated with streptavidin magnetic beads (Dynabeads MyOne Streptavidin C1, Thermo Fisher)

value: HUVEC

value: endothelial

value: wt

value: cel-miR-67 transfection


title: Neg-Ctl_2


title: transcriptome of myocardium of a patient with HCMP - id X58H

value: myocardium

tag: batch

tag: Sex

value: f

tag: hight

tag: weight

tag: age

value: no

tag: vss family_history

tag: vss or_hcmp_family_history

value: yes

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: Biotinylated cel-miR-67 rep 2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: transcriptome of myocardium of a patient with HCMP - id X51H

tag: tissue

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

value: systolic

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

value: HCMP

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: Neg-Ctl_1

tag: cell line

tag: cell type

tag: treatment


title: Male preterm non-diabetic (PT-ND), RNAseq, rep 3

tag: tissue

tag: genotype

value: WT


title: Male preterm non-diabetic (PT-ND), RNAseq, rep 4


title: transcriptome of myocardium of a patient with HCMP - id X4H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

value: CC


title: transcriptome of myocardium of a patient with HCMP - id X60H

tag: tissue

tag: batch

value: m

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: Biotinylated miR-486-5p pull-down RNA rep 2

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: miR-486-5p transfection


title: transcriptome of myocardium of a patient with HCMP - id X48H

tag: tissue

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: Male preterm non-diabetic (PT-ND), RNAseq, rep 2

tag: tissue

value: Kidney

tag: genotype

tag: treatment


title: Biotinylated miR-486-5p pull-down RNA rep 1

tag: cell line

tag: cell type


title: Male preterm non-diabetic (PT-ND), RNAseq, rep 1


title: Biotinylated cel-miR-67 rep 1


title: HEK293t, transfection with scramble siRNA and GPR153-MyC plasmid, rep3

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner). Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
The Ensemble annotation was enriched with UniProt data (UniProt Consortium, 2014).
Assembly: hg38
Supplementary files format and content: library-size normlaized counts

extract_protocol:
Extraction of total RNA from HEK cells was performed using an RNeasy Micro kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA concentrations were determined (NanoDrop ND-1000, TFS, Waltham, MA, USA; λ 600 nm)
1µg of total RNA was used as input for VAHTS Stranded mRNA-seq V6 Library preparation following manufacture’s protocol (Vazyme).

value: Human embryonic  kidney 293 cells

value: transfected with scramble siRNA and GPR153-MyC plasmid


title: Male term diabetic (T-D), RNAseq, rep 5

value: Streptozotocin (STZ)


title: HEK293t, transfection with scramble siRNA and GPR153-MyC plasmid, rep2


title: transcriptome of myocardium of a patient with HCMP - id X59H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics

value: CT


title: transcriptome of myocardium of a patient with HCMP - id X47H

tag: tissue

tag: batch

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: HEK293t, transfection with scramble siRNA and GPR153-MyC plasmid, rep1

tag: cell line

tag: cell type

tag: treatment


title: transcriptome of myocardium of a patient with HCMP - id X46H

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: HEK293t, transfection with GPR153 siRNA and Empty vector, rep3

tag: cell line

tag: cell type

tag: treatment

value: transfected withGPR153 siRNA and Empty vector


title: Male term diabetic (T-D), RNAseq, rep 4

tag: tissue

tag: genotype


title: HEK293t, transfection with GPR153 siRNA and Empty vector, rep2


title: transcriptome of myocardium of a patient with HCMP - id X45H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: Male term diabetic (T-D), RNAseq, rep 3

tag: tissue

tag: genotype

tag: treatment


title: HEK293t, transfection with GPR153 siRNA and Empty vector, rep1

tag: cell line

tag: cell type


title: Biotinylated miR-486-5p pull-down RNA rep 3

value: HUVEC

value: endothelial

value: wt


title: HEK293t, transfection with scramble siRNA and Empty vector, rep2

value: transfected with scramble siRNA and Empty vector


title: Male term diabetic (T-D), RNAseq, rep 2


title: HEK293t, transfection with scramble siRNA and Empty vector, rep3


title: HEK293t, transfection with scramble siRNA and Empty vector, rep1


title: transcriptome of myocardium of a patient with HCMP - id X38H

value: myocardium

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

value: no

tag: vss family_history

value: yes

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: HAH6

description: Library name: HAH6

tag: tissue

value: Liver

tag: genotype

value: WT

tag: treatment

value: HFD+allantoin


title: transcriptome of myocardium of a patient with HCMP - id X40H

tag: batch

tag: Sex

value: f

tag: hight

tag: weight

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

value: systolic

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

value: HCMP

value: CC


title: miCon2

city: Lexington

first: Qingding

address: 760 Press Ave

institute: University of Kentucky

description:
Library name: miCon2
raw counts and TPM

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic to remove adapters and low quality bases. Trimmed reads were mapped to the mouse reference genome assembly GRCm38 transcripts annotation using RSEM.
Assembly: GRCm38
Supplementary files format and content: TPM data: tpm_data.csv
Supplementary files format and content: Count data: count_data.csv

source_name: Intestine

growth_protocol: Mouse intestinal crypts were isolated and cultured for growing organoids in mouse IntestiCult™ Organoid Growth Medium (stemcell tech catalog # 06005).

extract_protocol:
RNA was isolated using a total RNA Isolation Kit (Qiagen, Catalog: 74106).
RNA libraries were prepared for sequencing using standard poly A enrichment Illumina protocols

treatment_protocol: The organoids were infected with lentivirus expressing miR-181a-5p mimic (MLMIR0085, Sigma) or miRNA mimic control (NCLMIR002, Sigma). The infected organoids were cultured in the presence of puromycin (2 ug/ml) to select for organoids with stable overexpression of miR-181a-5p.

tag: tissue

value: Intestine

tag: cell type

value: Intestinal epithelium

value: miRNA mimic control


title: Male term diabetic (T-D), RNAseq, rep 1

value: Kidney

tag: genotype

tag: treatment

value: Streptozotocin (STZ)


title: ormiRNA1813

description:
Library name: ormiRNA1813
raw counts and TPM

value: miR-181a-5p mimic


title: ormiRNA1814

description:
Library name: ormiRNA1814
raw counts and TPM


title: miCon1

description:
Library name: miCon1
raw counts and TPM


title: 4T1 cells, PEtracer static barcode benchmarking, lineage tracing cassette library, pool 3

city: Cambridge

first: Kathryn

last: Yost

state: Massachusetts

address: 455 Main St

department: Biology

institute: Whitehead Institute

description: Library name: PEtracer_4T1_barcoding_Pool3_LTC

library_source: transcriptomic single cell

data_processing:
All scRNA-seq data was processed using the Cellranger software package (version 7.1.0). To capture lineage information a custom reference genome was constructed by appending the 2171 lineage tracing cassette sequences to the human hg38 genome build. Both gene expression and lineage tracing cassette libraries were then aligned to this reference using default parameters. Since the reference contains all 2171 30bp barcode sequences the integration barcode (intBC) of each lineage tracing cassette read can be determined based on which element in the reference it aligns to. A custom Python script was used to extract lineage information from the bam alignment file generated by Cellranger. This script iterated through all reads aligned to a tracing cassette sequence. For each read the lineage mark (LM) sequence at each edit site was determined based on the alignment. For each UMI the number of supporting reads was calculated and the LM for each site set to the LM with the most read support (ties broken randomly). UMIs were then aggregated by intBC, cellBC, and the set of LMs detected across the three edit sites to generate a final LM table. scRNA-seq data for puromycin and blasticidin barcode libraries was aligned using Cellranger to a custom reference. This reference included puromycin and blasticidin resistance cassette sequences with ‘N’s indicating the positions of the 10nt random barcodes. A custom Python script was used to extract the barcode sequence from each read aligned to these elements, generate a consensus barcode for each UMI, and aggregate UMIs by barcode for each cell. To separate barcode calls corresponding to real integrations from sequencing errors and ambient RNA, for each 10x capture a Gaussian mixture model was fitted to the distribution of UMIs per barcode per cell. Barcode calls corresponding to the lower peak were excluded as likely errors. pegRNA libraries were processed using the “CRISPR Guide Capture” feature of Cellranger. pegRNA protospacer mismatch calls supported by <3 UMIs were filtered out and careful quality control performed to exclude cells with multiple pegRNA integrations as these cells could confound our estimation of protospacer mismatch kinetics. Cells with multiple pegRNA calls were removed as well as cells with lineage cassette reads where more than one edit site had an LM installed.
Assembly: mm10
Supplementary files format and content: Processed data barcodes/features/matrix and filtered_counts.h5 files contain the filtered_feature_bc_matrix transcript count matrix outputs from Cellranger. BlastBC_counts.csv, PuroBC_counts.csv, allele_counts.csv, and mapping_counts.csv files contain unfiltered static barcode, lineage tracing cassette allele, and intBC mapping count data.

extract_protocol:
Single cell suspensions were washed with PBS + 0.04% BSA and captured using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1
Gene expression libraries were prepared using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1 according to the manufacturer's instructions. Targeted lineage tracing cassette, puromycin/blasticidin barcode, and pegRNA libraries were prepared from amplified cDNA using two or three rounds of PCR with target-specific amplification primers and sample indexing primers.

tag: cell line


title: Male term non-diabetic (T-ND), RNAseq, rep 4


title: 4T1 cells, PEtracer static barcode benchmarking, Puromycin barcode library, pool 3

description: Library name: PEtracer_4T1_barcoding_Pool3_Puro


title: transcriptome of myocardium of a patient with HCMP - id X33H

tag: batch

tag: Sex

value: m

tag: hight

tag: weight

tag: age

tag: vss family_history

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: 4T1 cells, PEtracer static barcode benchmarking, gene expression library, pool 3

description: Library name: PEtracer_4T1_barcoding_Pool3_GEX

tag: cell line

tag: treatment


title: Male term non-diabetic (T-ND), RNAseq, rep 3

tag: tissue

tag: genotype


title: 4T1 cells, PEtracer static barcode benchmarking, Blasticidin barcode library, pool 3

description: Library name: PEtracer_4T1_barcoding_Pool3_Blast


title: Male term non-diabetic (T-ND), RNAseq, rep 2


title: 4T1 cells, PEtracer static barcode benchmarking, Puromycin barcode library, pool 2

description: Library name: PEtracer_4T1_barcoding_Pool2_Puro


title: 4T1 cells, PEtracer static barcode benchmarking, lineage tracing cassette library, pool 2

description: Library name: PEtracer_4T1_barcoding_Pool2_LTC


title: Male term non-diabetic (T-ND), RNAseq, rep 1


title: transcriptome of myocardium of a patient with HCMP - id X31H

value: myocardium

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

value: rough systolic

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: 4T1 cells, PEtracer static barcode benchmarking, Blasticidin barcode library, pool 2

description: Library name: PEtracer_4T1_barcoding_Pool2_Blast

tag: cell line

tag: treatment


title: transcriptome of myocardium of a patient with HCMP - id X2H

tag: tissue

tag: batch

tag: Sex

value: no

tag: vss family_history

value: yes

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: 4T1 cells, PEtracer static barcode benchmarking, gene expression library, pool 2

description: Library name: PEtracer_4T1_barcoding_Pool2_GEX

tag: cell line


title: transcriptome of myocardium of a patient with HCMP - id X34H

tag: hight

tag: weight

tag: age

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: HipR9

city: Shanghai

first: Shimin

last: Ren

address: Songtao Road 646

institute: Shanghai Institute of Materia Medica.Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

tag: tissue

value: hippocampus

tag: treatment

value: Sesame Oil


title: mouse iPSCs_miR-769_3

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: mouse inducible pluripotent stem cells

growth_protocol: Mouse embryonic fibroblasts (MEF) were isolated from C57B6 mice and cultured as described previously (Hahner et al. 2022). Isolated mouse embryonic fibroblasts were reprogrammed into induced pluripotent stem cells (iPSCs) using the STEMCCA system (Sommer et al. 2009). Briefly, 20.000 mouse embryonic fibroblast (were seeded into culture dishes. After 24 h cells were infected with STEMCCA virus for 24 h. Media was changed for five consecutive days. Cells were then reseeded on mitomycin (Serva, 10 μg/mL, 3 h) -inactivated feeder cells until murine induced pluripotent colonies emerged. Individual colonies were subsequently picked and expanded. Cells were passaged (DMEM GlutaMAX, #10566016, Gibco; 20 % Knockout Serum Replacement, #10828028, 25 μg mLIF, #250–02, Peprotech; 0.1% β-mercaptoethanol, 200 μM Glutamine, #11539876, Gibco) by 70% before colonies touched and reseeded between 2.5 × 103 and 5 × 103 cells per cm2.

tag: cell line

value: mouse inducible pluripotent stem cells

tag: cell type

value: iPSCs

value: transfection Ambion® Pre-miR™ miRNA Precursor for hsa-miR-769-5p (Assay ID PM11974, Cat. No. AM17100, ThermoFisher Scientific)


title: HipR11

value: DHEA


title: 4T1 cells, PEtracer static barcode benchmarking, Puromycin barcode library, pool 1

description: Library name: PEtracer_4T1_barcoding_Pool1_Puro


title: HipR16


title: transcriptome of myocardium of a patient with HCMP - id X29H

tag: batch

tag: Sex

value: f

tag: hight

tag: weight

tag: vss family_history

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

value: HCMP

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics

value: CC


title: transcriptome of myocardium of a patient with HCMP - id X28H

tag: tissue

tag: age

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: Male term non-diabetic (T-ND), RNAseq, rep 5

value: Kidney

tag: genotype

value: WT

tag: treatment


title: 4T1 cells, PEtracer static barcode benchmarking, Blasticidin barcode library, pool 1

description: Library name: PEtracer_4T1_barcoding_Pool1_Blast

tag: cell line


title: mouse iPSCs_miR-769_2

tag: cell type


title: mouse iPSCs_miR-769_1


title: 4T1 cells, PEtracer static barcode benchmarking, lineage tracing cassette library, pool 1

description: Library name: PEtracer_4T1_barcoding_Pool1_LTC


title: transcriptome of myocardium of a patient with HCMP - id X32H

tag: tissue

tag: batch

tag: Sex

tag: hight

tag: weight

tag: vss family_history

value: systolic

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: HipR10

tag: tissue

tag: treatment


title: mouse iPSCs_miR-197_4

tag: cell line

tag: cell type

value: transfection Ambion® Pre-miR™ miRNA Precursor for hsa-miR-197-3p (Assay ID PM10354, Cat. No. AM17100, ThermoFisher Scientific)


title: 4T1 cells, PEtracer static barcode benchmarking, gene expression library, pool 1

description: Library name: PEtracer_4T1_barcoding_Pool1_GEX


title: mouse iPSCs_miR-197_3


title: HipR7


title: mouse iPSCs_miR-197_2


title: transcriptome of myocardium of a patient with HCMP - id X24H

value: myocardium

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: mouse iPSCs_miR-197_1

tag: cell line

tag: cell type

tag: treatment


title: transcriptome of myocardium of a patient with HCMP - id X26H

tag: tissue

tag: batch

tag: Sex

value: m

tag: hight

tag: vss family_history

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: HipR5

tag: treatment


title: mouse iPSCs_Neg-Ctl_4

tag: cell line

tag: cell type

value: transfection Pre-miR™ miRNA Precursor Negative Control #1 (Cat. No. AM17110, ThermoFisher Scientific)


title: HipR3

tag: tissue


title: transcriptome of myocardium of a patient with HCMP - id X15H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

value: no

tag: vss or_hcmp_family_history

value: yes

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: transcriptome of myocardium of a patient with HCMP - id X27H

tag: tissue

tag: vss family_history

value: rough systolic

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: mouse iPSCs_Neg-Ctl_1

tag: cell line

value: mouse inducible pluripotent stem cells

tag: cell type

tag: treatment


title: transcriptome of myocardium of a patient with HCMP - id X22H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: age

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: HipR4

tag: tissue

value: hippocampus

tag: treatment


title: mouse iPSCs_Neg-Ctl_2

tag: cell line

tag: cell type

value: iPSCs


title: transcriptome of myocardium of a patient with HCMP - id X1H

tag: batch

tag: Sex

tag: hight

tag: weight

tag: vss family_history

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics

value: CT


title: eWAT_RandomFoodRestriction_rep8

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
FASTQ-file generation and demultiplexing was performed using bcl2fastq 4.0.3
Alignment to genome and gene counts were generated with the nfcore-rnaseq pipeline v. 3.10.1 using the STAR->Salmon workflow
Assembly: GRCm38
Supplementary files format and content: CSV file with gene ID, chromosome, start, end, strand, length and read counts for the samples

source_name: eWAT

extract_protocol:
Total RNA was isolated from QUAD with Trizol and RNeasy kit (Qiagen), and its quality was verified with 2100 Bioanalyzer Instrument (Agilent).
Libraries were prepared using the Universal Plus mRNA-seq protocol (Tecan) as recommended by the manufacturer. Libraries were quantified with NuQuant using the Qubit fluorometer (Thermo Fisher Scientific), quality checked using a TapeStation instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina).

tag: tissue

value: eWAT

tag: diet

value: Random Food Restriction

tag: spermatozyte contamination

value: No


title: Hive_patient3

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description: Honeycomb Biotechnologies

data_processing:
The BeeNet pipeline (v1.1, Honeycomb Biotechnologies) application (HIVE Honeycomb) was used to process the raw data into count matrices and demultiplex the BCL files into FASTQ files (Illumina Bcl2Fastq), to perform alignment (to BeeNet human reference genome index from the GRCh38), filtering and unique molecular identifier counting and to produce gene-barcode matrices.
Filtered matrix files were used for further scRNA-seq  analyses with R Bioconductor (3.17) and Seurat
Assembly: GRCh38
Supplementary files format and content: Transcript Count Matrix in tsv format

source_name: Bronchoalveolar lavage

extract_protocol:
Fresh BALF cells were prepared Cell Preservation Solution (Honeycomb Biotechnologies) and loaded into one HIVE Collector (Honeycomb Biotechnologies) per patient
Libraries were generated following the HIVE scRNAseq V1 Processing workflow with a kit High Output.

value: Bronchoalveolar lavage


title: eWAT_RandomFoodRestriction_rep10


title: eWAT_RandomFoodRestriction_rep9


title: transcriptome of myocardium of a patient with HCMP - id X13H

tag: batch

tag: Sex

value: f

tag: hight

tag: age

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid

value: HCMP

value: CC


title: Hive_patient2

description: Honeycomb Biotechnologies

tag: tissue


title: Hive_patient1

description: Honeycomb Biotechnologies


title: Hive_patient4

description: Honeycomb Biotechnologies


title: Infected_sorted_biorep_3

city: Dublin

first: Carsten

last: Kroeger

address: Moyne Institute of Preventive Medicine

department: Microbiology

country: Ireland

institute: Trinity College Dublin

description:
Library name: Sinf_3
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

data_processing:
Bacterial RNA-seq: For calculation of bacterial gene expression, reads were mapped with bowtie2 v. 2.4.2 with the parameters -very-sensitive-local to align sequencing reads to the A. baumannii ABC141 reference genome (Lanmead & Salzberg, 2012). Only reads with the highest mapping quality (MAPQ = 44) were kept and aggregated strand-specifically with featureCounts v2.0.3 on features annotated with the types of CDS, sRNA or ncRNA (Liao et al., 2014). To filter for low expression only genes were kept that showed expression of TPM ≥10 in the majority of replicates in one or more of the sample groups resulting in a set of 3299 genes. Differential gene expression (log2 fold-changes and adjusted p-values) was calculated using DESeq2 v1.46 (Love et al., 2014).
Human RNA-seq: Data files were processed through FastQC for quality control (Andrews, 2010). Short reads were mapped to the human reference genome (hg38) using STAR v2.7.3a (Dobin et al., 2013). Uniquely mapped reads were assigned to genes with featureCounts v2.0.3 using the latest Ensembl annotation (v114) (Dyer et al., 2025). To filter for low expression, only those genes were kept that had an expression value of one or more TPM (transcripts per million) in at least half of their replicates. Differentially expressed genes were determined by DESeq2 v1.46.
Assembly: GRCh38 (human reference sequence), GCF_050269755.1 (Acinetobacter baumannii ABC141 reference sequence)
Supplementary files format and content: Human_RNA_seq.txt is a tab-delimited text file which inlcludes raw counts, TPM, normalised read counts and DESeq2 analysis for each sample (human RNA-seq)
Supplementary files format and content: Bacterial_RNA_seq_ABC141.txt is a tab-delimited text file which inlcludes raw counts, TPM, normalised read counts and DESeq2 analysis for each sample (bacterial RNA-seq)

organism:
Acinetobacter baumannii
Homo sapiens

extract_protocol:
Total RNA from infected cells, non-infected cells and ABC141 inocula was extracted following a previously described method (Kröger et al., 2018). For cultures, bacteria were lysed with 2/5 volume of ice-cold 5% (v/v) phenol, 95% (v/v) ethanol ultra-pure solution for 1 h on ice. The same lysis process was applied to the total of infected cells and mock-infected cells sorted by FACS. A centrifugation at 3220 x g for 10 min at 4°C pelleted the sample, which was resuspended with 1 mL ice-cold TRIzol and transferred into a Phase-Lock-Tube (VWR, #2302830). 400 µL of chloroform was added and the solution was shaken (without vortexing) for 10 s, followed by a 3 min incubation at RT. The tubes were centrifuged at 12000 x g at 4 °C for 15 min. Then, the aqueous phase was transferred to a new 1.5 mL tube. 450 µL of isopropanol was added and mixed before a 30 min incubation at RT. A new centrifugation at full speed for 30 min preceded three washes of the pellet with 350 µL of ethanol 75%, a 10 min incubation at RT and a 10 min centrifugation at full speed. The last supernatant was discarded and the pellet air dried before resuspension with 25 µL of RNAse-free water, followed by a 5 min incubation at 65 °C at 900 rpm. The RNA extraction quality was verified with a 1/10 dilution using the 4200 TapeStation (Agilent Technologies).
Total RNA was sent to Core Unit Systems Medicine (SysMed) sequencing facility for RNA-seq (University of Würzburg, Germany), where DNase I digestion and rRNA depletion (RiboCop) was performed. Library for the sequencing was prepared using the NEBNext Multiplex Small RNA Library Prep kit. Sequencing was performed on the Illumina NextSeq-500 Mid Output KT v2.5 (150 cycles).

tag: cell line

tag: cell type

value: somatic cell hybrid, endothelial


title: transcriptome of myocardium of a patient with HCMP - id X37H

value: myocardium

tag: batch

tag: Sex

value: m

tag: weight

tag: vss family_history

value: systolic

tag: bisoprolol

tag: amlodipin

tag: eks

tag: rin

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: Infected_sorted_biorep_2

description:
Library name: Sinf_2
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

tag: cell line


title: Infected_sorted_biorep_1

description:
Library name: Sinf_1
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

tag: cell type


title: Infected_sorted_biorep_4

description:
Library name: Sinf_4
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: transcriptome of myocardium of a patient with HCMP - id X12H

tag: tissue

tag: batch

tag: hight

tag: age

value: no

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

value: yes

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: eWAT_RandomFoodRestriction_rep7

tag: diet

tag: spermatozyte contamination

tag: rin


title: transcriptome of myocardium of a patient with HCMP - id X10H

tag: tissue

tag: batch

tag: Sex

tag: weight

tag: vss family_history

value: rough systolic

tag: bisoprolol

tag: amlodipin

tag: eks

tag: disease

tag: bmi

tag: dyspnea

tag: diuretics

tag: statins

tag: anticoagulants

tag: antiarrytmics


title: transcriptome of myocardium of a patient with HCMP - id X11H

tag: hight

tag: age

tag: vss or_hcmp_family_history

tag: syncopation

tag: lightheadedness

tag: interruptions

tag: ischemia

tag: hypertension

tag: hypertension level

tag: hypertension stage

tag: perindopril

tag: spironolacton

tag: torasemid


title: Infected_not_sorted_biorep_3

description:
Library name: Inf_5
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.

tag: cell line

tag: cell type


title: Infected_not_sorted_biorep_4

description:
Library name: Inf_6
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: mouse iPSCs_Neg-Ctl_3

value: mouse inducible pluripotent stem cells

tag: treatment

value: transfection Pre-miR™ miRNA Precursor Negative Control #1 (Cat. No. AM17110, ThermoFisher Scientific)


title: Infected_not_sorted_biorep_2

description:
Library name: Inf_4
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: eWAT_RandomFoodRestriction_rep6

tag: tissue

tag: diet

tag: spermatozyte contamination

tag: rin


title: Infected_not_sorted_biorep_1

description:
Library name: Inf_3
The human data is in Human_RNA_seq.txt.The bacterial data is in Bacterial_RNA_seq_ABC141.txt. Column names labelled "raw" are raw readcounts, column names labelled as "normalised" are normalised read counts and column names labelled with TPM are TPM values for each entry and sample. Biological replicates are indicated after the underscore (e.g., ABC141_1 is experiment 1, ABC141_2 is experiment 2 etc.). Columns labelled ABC141 are data from the inoculum, S-inf are data from infected cells sorted, Inf are data from infected cells unsorted, Neg are data from uninfected and unsorted cells and S-Neg are data from uninfected and sorted cells.


title: Wt + PBS lung day14_3

city: Chiba

first: Jun

last: Ikari

state: Chiba

address: 1-8-1 Inohana Chuo-ku Chiba, Chiba, Japan

country: Japan

institute: Chiba University

description: Library name: DK24248_07

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). The poly A tail and adapter sequences obtained from LEXOGEN were used for references.
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample.
Supplementary files format and content: Excel file includes RPM values for each sample.

source_name: lung

growth_protocol: Male C57BL/6 mice were purchased from Japan SLC (Shizuoka, Japan) and CLEA Japan (Tokyo, Japan). PAD4 -/- mice with a C57BL/6 background were purchased from Jackson Laboratory (ME, USA).

extract_protocol:
We used the right lung stored at −80°C after resection with Allprotect Tissue Reagent (QIAGEN; Venlo, Netherlands, cat. 76405) to purify RNA using the RNeasy Plus Mini Kit (QIAGEN; Venlo, Netherlands, cat. 74134) according to the manufacturer’s protocol. The quality and concentration of the RNA were verified using a Qubit fluorometer (Life Technologies, CA, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).
Purified total RNA (500 ng) was used to prepare RNA libraries using the Quant Seq 3’ mRNA-seq library preparation kit FWD of Illumina (LEXOGEN, Vienna, Austria) following the instructions provided by the manufacturer. RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nt-long reads.

treatment_protocol: Pancreatic porcine ELS were purchased from Elastin Products Company (MO, USA, cat. EC134). ELS was dissolved in glycerol and 50% 0.02M NaOAc pH5 and stored at −20℃. At the time of use, ELS was adjusted to 3 U/100 µL with PBS. The 8–12-week-old mice were used in the study. Intratracheal administration of 3 U/100 µL ELS (ELS group) and 100 µL PBS (the control group) was performed and animals were categorised into two groups accordingly.

value: lung

tag: Sex

value: Male

tag: strain

tag: genotype

value: Wild type

value: PBS

tag: time point


title: KO + ELS lung day14_3

description: Library name: DK24248_06

value: PAD4 KO

value: ELS


title: Wt + ELS lung day14_3

description: Library name: DK24248_08


title: eWAT_Control_rep10

value: eWAT

value: Control

value: Yes


title: eWAT_Control_rep8


title: Wt + ELS lung day1_3

description: Library name: DK24248_04


title: Wt + PBS lung day1_3

description: Library name: DK24248_03


title: eWAT_Control_rep6

value: No


title: KO + PBS lung day1_3

description: Library name: DK24248_01


title: eWAT_Control_rep9


title: AML12: scRNAseq from bone marrow cells from AML patient

city: New York

first: Joy

last: Fan

address: 520 West 120th Street

institute: Columbia University

description:
Library name: AML12_scRNA
10x Genomics

data_processing:
scRNA-seq raw reads were processed using 10X Genomics CellRanger and SEQC pipelines. Filtered count matrices were loaded into AnnData objects using Scanpy v1.7.2. Cells were filtered based on library size using a histogram knee-point threshold. Normalization was performed using sc.pp.normalize_per_cell, and doublet detection was done with DoubletDetection (25 iterations). For scATAC-seq, FASTQ files were processed into cell-by-peak matrices using the CellRanger ATAC pipeline with modifications described in [158]. A median of 10,504 cells/sample and 5,165 molecules/cell were retained after filtering.
Assembly: Human Hg38
Supplementary files format and content: CSV files containing counts and metadata for each RNA sample; fragments files for each ATAC sample

source_name: Bone Marrow

extract_protocol:
Cryopreserved bone marrow mononuclear cells were thawed in prewarmed FACS buffer (PBS + fetal bovine serum). Cells were pelleted and washed, then blocked with Human TruStain FcX™ (Biolegend #422301) for 15 minutes at 4°C. Antibodies against CD34 (Clone 561; FITC Biolegend 343603) and CD133 (Clone 7; PE Biolegend 372803) were added and incubated for 15 minutes at 4°C. Cells were washed, stained with DAPI, and sorted on a Sony SH800 cell sorter to enrich for immature populations (e.g., CD34+ or PROM+). Unsorted mononuclear cells were also used for sequencing.
All samples and sorted populations were profiled using 10X Genomics Chromium Single Cell 3’ v3 (for scRNA-seq) and the 10X Genomics Single Cell ATAC Reagent Kits v1.1 (for scATAC-seq). For scATAC-seq, nuclei were isolated and subjected to a transposition reaction at 37°C for 60 minutes before encapsulation with the 10X Chromium Controller targeting ~5,000 nuclei. Libraries were constructed per manufacturer instructions (10X Genomics; CG000168 RevA), assessed via Bioanalyzer High-Sensitivity DNA Kit (Agilent), and sequenced on Illumina HiSeq 2500 and NovaSeq platforms.

value: Bone Marrow

value: Bone marrow mononuclear cells


title: BM_control: scRNAseq from a healthy bone marrow reference sample

description:
Library name: BM_control_scRNA
10x Genomics


title: AML9: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML9_scRNA
10x Genomics


title: LTG016

description: Library name: WK2915

data_processing:
Sequencing quality and adapter contamination were assessed using FastQC
Any adapter sequences were trimmed using Cutadapt
Reads were aligned to Mus musculus genome (mm10) reference genome using STAR
Assembly: mm10
Supplementary files format and content: Excel spreadsheet with raw RNA-seq gene count data

extract_protocol:
Trizol followed by Dnase treatment and Qiagen clean-up
RNA-Seq kit

value: liver

value: Atp7b KO


title: AML14: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML14_scRNA
10x Genomics


title: eWAT_Control_rep7


title: AML13: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML13_scRNA
10x Genomics


title: KO + PBS lung day14_3

description: Library name: DK24248_05


title: LTG015

description: Library name: WK1636


title: AML11: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML11_scRNA
10x Genomics


title: LTG014

description: Library name: WK0993


title: AML8: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML8_scRNA
10x Genomics


title: KO +  ELS lung day1_3

description: Library name: DK24248_02


title: LTG012

description: Library name: WK2921

value: WT


title: eWAT_RandomFoodRestriction_rep5

value: Random Food Restriction


title: LTG013

description: Library name: WK0992


title: eWAT_RandomFoodRestriction_rep4


title: AML7: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML7_scRNA
10x Genomics


title: LTG011

description: Library name: WK1631


title: LTG010

description: Library name: WK2913


title: eWAT_RandomFoodRestriction_rep2


title: LTG009

description: Library name: WK1474


title: eWAT_RandomFoodRestriction_rep1


title: AML4:  scRNAseq from CD34+ sorted bone marrow cells from AML patient

description:
Library name: AML4_scRNA
10x Genomics


title: Wt + PBS lung day14_2

description: Library name: DK24091_06


title: eWAT_Control_rep5


title: KO + ELS lung day14_2

description: Library name: DK24091_04


title: KO + PBS lung day14_2

description: Library name: DK24091_02


title: eWAT_Control_rep4


title: eWAT_Control_rep3


title: AML5:  scRNAseq from bone marrow cells from AML patient

description:
Library name: AML5_scRNA
10x Genomics


title: KO + PBS lung day14_1

description: Library name: DK24091_01


title: AML1: scRNAseq from CD34+ sorted bone marrow cells from AML patient

description:
Library name: AML1_scRNA
10x Genomics


title: Wt + PBS lung day1_2

description: Library name: DK24106_06


title: eWAT_RandomFoodRestriction_rep3


title: eWAT_Control_rep2


title: new_8

city: changchun

first: Yan

state: jilin

address: 1163 Xinmin Street

institute: Jilin University

description:
Library name: Sample 16
Column name in genes_fpkm_expression.xlsx:FPKM.new_8

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs and lncRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups. The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: peripheral blood

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented (NEBNext® Magnesium RNA Fragmentation Module, cat.E6150S, USA) into short fragments using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: disease

value: newly diagnosed, untreated type 2 diabetes

value: peripheral blood


title: Wt + PBS lung day1_1

description: Library name: DK24106_05

value: lung


title: KO + ELS lung day14_1

description: Library name: DK24091_03


title: AML2: scRNAseq from CD34+ sorted bone marrow cells from AML patient

description:
Library name: AML2_scRNA
10x Genomics


title: AML6: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML6_scRNA
10x Genomics


title: new_6

description:
Library name: Sample 14
Column name in genes_fpkm_expression.xlsx:FPKM.new_6


title: Wt + ELS lung day1_1

description: Library name: DK24106_07

value: Wild type


title: Wt + PBS lung day14_1

description: Library name: DK24091_05

value: PBS


title: eWAT_Control_rep1


title: new_5

description:
Library name: Sample 13
Column name in genes_fpkm_expression.xlsx:FPKM.new_5


title: KO + PBS lung day1_1

description: Library name: DK24106_01

value: PAD4 KO


title: KO + PBS lung day1_2

description: Library name: DK24106_02


title: new_7

description:
Library name: Sample 15
Column name in genes_fpkm_expression.xlsx:FPKM.new_7


title: KO + ELS lung day1_1

description: Library name: DK24106_03

value: ELS


title: Male preterm non-diabetic (PT-ND), scRNAseq, rep 1

description: 10x Genomics

data_processing:
The filtered gene barcode matrix files were further analyzed using Seurat (v 5.1.0). Genes detected in fewer than three cells and cells with fewer than 200 expressed genes were excluded from the analysis. Cells with mitochondrial gene expression exceeding 50% were deemed injured or apoptotic and were similarly excluded. A higher mitochondrial gene cutoff was used to account for the inherently elevated baseline mitochondrial content of the kidney and increased vulnerability to mitochondrial injury in proximal tubules associated with diabetic kidney disease38. Also, parameters such as UMI counts per cell (nCount RNA), genes detected per cell (nFeature RNA) and low complex cells (log10GenesPerUMI > 0.80) were used to eliminate poor quality cells resulting in 17,374 genes across 9,247 cells. scTransform was used for performing normalization and variance stabilization to address technical variability and for effective integration of samples and downstream analysis. To build the K-nearest neighbor graph, the initial 30 principal components derived from principal-component analysis were included in FindNeighbor. Subsequently, we conducted an unsupervised clustering analysis using the Louvain algorithm, set to a resolution of 1.4, with the FindClusters followed by FindSubCluster with a resolution of 0.2. For dimensionality reduction and visualization, UMAP coordinates were computed with the RunUMAP, based on the same 30 principal components. Finally, cell type-specific marker genes were determined through FindAllMarkers, using the Wilcoxon rank-sum test for statistical significance. Differential gene expression analysis was performed between cells from groups using FindMarkers. Genes with avg Log2 fold change ≥2 (or) ≤−2 and multiple testing adjusted p-value ≤0.05 were considered significantly (up or down) regulated for further analysis. The gene ontology (GO) enrichment for the significantly differentially expressed genes was analyzed by clusterProfiler (v 4.12.1)39 and GO terms with p and q values ≤0.05 were considered significant. For enhanced visualization of UMAPs, clustered dot plots reported in this study were generated using scCustomize40.
Assembly: mm10
Supplementary files format and content: CellRanger output file: h5 file

extract_protocol:
The kidneys were directly perfused via the left ventricle with 0.9% saline. The kidneys were rapidly dissected, moved to ice-cold PBS, then minced on ice using a scalpel. Each minced kidney was transferred into a 15 mL centrifuge tube with 2.0 mL of the protease solution for each half of the kidney (protease solution: ice-cold: 25 mM CaCl2, 10 mg/mL B. Licheniformis protease, 125 U/mL DNase I, 1xDPBS). Samples were digested on ice and triturated using p1000 tip for 15 seconds every 2 minutes for a total of 20 minutes. The digestion was stopped by adding 3 mL of ice-cold PBS + 10% FBS and centrifuged at 1200g for 5 min at 4°C. The pellet was resuspended in 2 mL of PBS + 10% FBS, and cells were filtered through a 70-μm cell strainer and rinsed with 2 mL of PBS + 0.01% BSA. Next, cells were centrifuged and resuspended in 5 mL of PBS +0.01% BSA. Cells were filtered the second time through a 40-μm cell strainer and rinsed with 2 mL of PBS + 0.01% BSA, centrifuged, and resuspended in 1 mL of 1x RBC Lysis Buffer. Red blood cell lysis was performed for 5 minutes with occasional shaking, at room temperature. The reaction was stopped by adding 20 mL of 1xPBS, cells were centrifuged at 1200g for 5 min at 4°C and resuspended in PBS + 0.04% BSA. Cell suspension was stained with Propidium Iodide (Thermo Fisher #P1304MP), and live cells were sorted using the BD FACSMelody cell sorter. Sorted cells were centrifuged at 1200g for 5 min at 4°C and resuspended in 50μl of PBS + 0.04% BSA.
Samples were processed and prepared for scRNA sequencing at University of Virginia, School of Medicine University of Virginia - UVA Genome Analysis and Technology Core (RRID:SCR_018883, 5P30CA044579). Single-cell suspensions were introduced into a multi-channel microfluidics chip within the Chromium Controller (10x Genomics Inc., Pleasanton, CA, USA) to generate Gel Beads in Emulsion (GEMs), aiming for a cell recovery target of 5,000 to 10,000 cells. The single-cell suspension was processed using the 10x Genomics Chromium Single Cell System (10x Genomics, Inc.). Gene expression libraries were prepared with the Chromium™ Next GEM Single Cell 3' Kit v3.1, 16 rxns (PN-1000268), the Chromium™ Next GEM Chip G Single Cell Kit, 48 rxnt (PN-1000120), and the Chromium™ Dual Index Kit TT Set A 96 rxns (for 3' and 5' Gene Expression, TCR/BCR and Multiome) (PN- 1000215).  A small portion of the prepared library was sequenced on the MiSeq to perform initial quality control, including checking cell count, assessing the quality of the library, and performing rapid cluster analysis, later the sequencing was performed on the NextSeq 500 sequencer. Raw sequence data were processed using CellRanger (10x Genomics, Inc) and Bcl2fastq (https://support.illumina.com), generating sample-specific FASTQ files. The fastq files were aligned to the mm10 (version 2020-A) reference transcriptome using the ‘cell ranger count’ function from Cell Ranger pipeline (v 7.0.1), resulting in a total of 17,326 cells estimated across all samples (3,727 cells in T-ND, 3,810 in PT-ND, 5,065 in T-D, and 4,742 in PT-D).

value: Kidney


title: KO + ELS lung day1_2

description: Library name: DK24106_04


title: Phenformin

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

data_processing:
The 10x Genomics Cell Ranger pipeline (v3.1.0) was used to trim, demultiplex, align and count unique transcripts for the reference genome mm10 v1.2.0 and the Ensembl v84 gene annotation.
Assembly: mm10/GRCm38
Supplementary files format and content: *features.tsv.gz, *barcodes.tsv.gz, *matrix.mtx.gz: compressed filtered features (genes), barcodes and expression matrices generated by Cell Ranger.

source_name: Murine breast tumor (FVB)

extract_protocol:
CD45+ Cells enrichment was performed on dissociated Day 4 MT tumors, via MACS, from treatment groups as indicated.
10000 cells per condition (>90% enriched for CD31-EpCam-CD45+) were subjected to the 10XGenomics Single Cell 3' transcriptome library preparation.

value: Murine breast tumor (FVB)

value: Saline+Phenformin


title: Wt + ELS lung day1_2

description: Library name: DK24106_08


title: Wt + ELS lung day14_1

description: Library name: DK24091_07


title: new_4

description:
Library name: Sample 12
Column name in genes_fpkm_expression.xlsx:FPKM.new_4


title: PolyIC

value: Poly I:C+PBS


title: Control

value: Saline+PBS


title: Male preterm diabetic (PT-D), scRNAseq, rep 1

description: 10x Genomics

value: Streptozotocin (STZ)


title: Male term diabetic (T-D), scRNAseq, rep 1

description: 10x Genomics


title: new_3

description:
Library name: Sample 11
Column name in genes_fpkm_expression.xlsx:FPKM.new_3


title: Combination

value: Poly I:C+Phenformin


title: new_2

description:
Library name: Sample 10
Column name in genes_fpkm_expression.xlsx:FPKM.new_2


title: Male term non-diabetic (T-ND), scRNAseq, rep 1

description: 10x Genomics


title: MT-PIC-4

data_processing:
Trimmomatic (v0.32.48) was used to trim reads, removing adaptors and other Illumina-specific sequences in palindrome mode.
A four-nucleotide sliding window was used to remove bases when the quality within the window was < 30 and reads shorter than 30 base pairs were dropped.
Reads were aligned to the mouse reference genome build mm10 using STAR (v2.3.0) with default settings.
Reads were counted for exonic regions defined by ensGene annotation set from Ensembl (GRCm38, n = 39,017 genes), using featureCounts (v1.4.4).
Assembly: mm10/GRCm38
Supplementary files format and content: raw counts for each sample

source_name: Murine breast tumor (BALBc)

extract_protocol:
RNA extraction was performed using RNeasy columns (74104, Qiagen) following cell pellet lysis or flash frozen tissue homogenization
Libraries for RNA-seq were prepared according to strand-specific Illumina TruSeq protocols

value: Murine breast tumor (BALBc)


title: MT-PIC-3

value: WT


title: MT-PIC-2


title: Neonate_Spleen_CD8+_T_cell_RNA_4

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
The paired end reads (from four independent biological replicates for each developmental stage and age) were processed using trim galore and fastq files were aligned using STAR 2.7.10a with mm10 mouse genome assembly 129. To assess gene body coverage, a gene body coverage python package (RseQC geneBody_coverage.py) was utilized. Reads mapped to annotated features were counted using featureCounts130.
Assembly: mm10 mouse genome assembly
Supplementary files format and content: Raw counts file are text files.

source_name: Spleen

extract_protocol:
Thymi and spleens from adult or neonatal mice were collected in RPMI+10% FBS and mashed through a 40µM cell strainer to create a single-cell suspension. Spleens and thymi underwent magnetic enrichment with CD8a and CD4 MicroBeads (Miltenyi Biotec; cat# 130-117-044; cat# 130-117-043), respectively, per the manufacturer’s instructions. The bound thymic fraction was sorted for double positive thymocytes, while the eluted fraction underwent CD8a magnetic enrichment as described previously, after which the bound fraction was sorted for SP8 thymocytes, while the eluted fraction was sorted for DN thymocytes. Thymocyte counts were taken by diluting a single-cell thymus suspension and counting on a MoxiZ cell counter.
To extract RNA, sorted cells were resuspended in 1ml of Trizol (Thermo #15596018). 200ul of chloroform was added to 1ml of trizol lysates. After vigorous shaking, samples were centrifuged at 16000x g at 4C. During the spin, phase lock gel tubes were prepared by a pre-spin 12000xg at room temperature. 600ul chloroform was added to these pre-spun tubes. The aqueous phase of trizol-chloroform mixture was added to the phase lock tube containing chloroform. After vigorously shaking these phase lock tubes were centrifuged at 12000xg at 4 C. The aqueous phase from the phase lock tubes was added to isopropanol and glycoblue containing precipitation tubes. These precipitation tubes were mixed, incubated for 1 hour, and spun at 16,000 x g at 4o c. The supernatant was discarded and the pellets washed with ice-cold ethanol. Pellets were further centrifuged at 16000xg at 4 c. The supernatant was discarded, and the pellet air-dried and resuspended in RNAase-free water. RNA sample quality was confirmed using a Qubit (RNA HS kit; Thermo Fisher) to determine the concentration and with a Fragment Analyzer (Agilent) to determine RNA integrity. PolyA+ RNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). TruSeq-barcoded RNAseq libraries was generated with the NEBNext Ultra II Non-Directional RNA Library Prep Kit (New England Biolabs). Each library was quantified with a Qubit (dsDNA HS kit; Thermo Fisher) and the size distribution was determined with a Fragment Analyzer (Agilent) prior to pooling.

value: Spleen

value: CD8+ T cells

value: C57BL/6 mice


title: ctrl_8

description:
Library name: Sample 8
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_8

value: healthy

value: peripheral blood


title: MT-PIC-1


title: new_1

description:
Library name: Sample 9
Column name in genes_fpkm_expression.xlsx:FPKM.new_1

value: newly diagnosed, untreated type 2 diabetes


title: MT-PHEN-3


title: MT-PHEN-2


title: ctrl_7

description:
Library name: Sample 7
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_7


title: Neonate_Spleen_CD8+_T_cell_RNA_2


title: Neonate_Spleen_CD8+_T_cell_RNA_1


title: MT-CTRL-4


title: MT-CTRL-3


title: ctrl_6

description:
Library name: Sample 6
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_6


title: MT-CTRL-1


title: MT-PHEN-1


title: MT-CTRL-2


title: Neonate_Thymus_Single_Positive_RNA_4

source_name: Thymus

value: Thymus

value: Single Positive


title: ctrl_5

description:
Library name: Sample 5
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_5


title: Neonate_Thymus_Single_Positive_RNA_3


title: MT-COMBO-3


title: Neonate_Spleen_CD8+_T_cell_RNA_3


title: MT-COMBO-4


title: MT-PHEN-4


title: Neonate_Thymus_Single_Positive_RNA_2


title: ctrl_4

description:
Library name: Sample 4
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_4


title: Neonate_Thymus_Single_Positive_RNA_1


title: MT-COMBO-2


title: Wt + ELS lung day14_2

description: Library name: DK24091_08

value: lung

value: Wild type

value: ELS


title: ctrl_3

description:
Library name: Sample 3
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_3


title: 4T1-PIC-4

value: Murine breast tumor (FVB)

value: Poly I:C+PBS


title: ctrl_2

description:
Library name: Sample 2
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_2


title: Neonate_Thymus_Double_Positive_RNA_4

value: Double Positive


title: 4T1-PIC-2


title: 4T1-PIC-3


title: MT-COMBO-1

value: Poly I:C+Phenformin


title: Neonate_Thymus_Double_Positive_RNA_3


title: FFPE_003_72H_rRNA_depletion

city: Hong Kong

first: Xin

address: 30-32 Ngan Shing Street, Shatin, New Territories

department: Department of Surgery

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: Sample 8

data_processing:
Sequence reads were preprocessed for adaptor sequence/low-quality sequence using fastp with default parameyers.
Preprocessed reads were mapped to the UCSC human reference genome (GRCh38) using STAR (version 2.7.3a) with default parameters.
Gene expression was quantified using RNA-seq by expectation maximization (RSEM).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

source_name: primary tumor resection

extract_protocol:
Total RNA was extracted using the PureLink™ RNA Mini Kit (Thermo Fisher Scientific, catalog number: 12183018A) and the PureLink™ FFPE RNA Isolation Kit (Thermo Fisher Scientific, catalog number: K156002) for FF and FFPE tissues, respectively, according to manufacturer’s protocols.
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Hong Kong, China).

value: primary tumor resection


title: 4T1-PHEN-4

value: WT

value: Saline+Phenformin


title: Neonate_Thymus_Double_Positive_RNA_2


title: 4T1-PHEN-1


title: Neonate_Thymus_Double_Positive_RNA_1


title: FFPE_003_24H_polyA

description: Library name: Sample 6


title: 4T1-CTRL-3

value: Saline+PBS


title: 4T1-CTRL-2


title: FF_003_polyA

description: Library name: Sample 3


title: FFPE_003_24H_rRNA_depletion

description: Library name: Sample 5


title: FF_003_rRNA_depletion

description: Library name: Sample 2


title: Neonate_Thymus_Double_Negative_RNA_4

value: Double Negative

value: C57BL/6 mice


title: Neonate_Thymus_Double_Negative_RNA_2


title: 4T1-COMBO-4


title: 4T1-CTRL-1


title: Ad-NEXN+high-Pi, rep4

city: Guangzhou

first: Canzhao

last: Liu

address: Gongye Street

institute: Southern Medical University

description: Library name: sample 8

data_processing:
Step 1: Use Fastp software (https://github.com/OpenGene/fastp) to filter out reads with adapter contamination, low quality, and undetermined bases, and verify sequence quality.
Step 2: Employ HISAT2 (https://ccb.jhu.edu/software/hisat2) for read mapping to the Homo sapiens GRCh38 reference genome.
Step 3: Use StringTie (https://ccb.jhu.edu/software/stringtie) to assemble the mapped reads and merge transcriptomes across samples to reconstruct a comprehensive transcriptome, which was further refined using gffcompare (https://github.com/gpertea/gffcompare/).
Step 4: Estimate expression levels with StringTie, calculating FPKM values for mRNAs.
Step 5: Conduct differential expression analysis with edgeR, identifying mRNAs with a |log2(FC)|>1 (fold change > 2 or < 0.5) and a P - value < 0.05 from parametric F - tests.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: human aortic isolated SMCs (HASMCs)

growth_protocol: Primary human aortic smooth muscle cells (HASMCs) were sourced from iCell Bioscience Inc. (catalog number: HUM-iCell-c010) and cultured in proprietary low-serum medium (PriMed-iCell-004) in strict adherence to the manufacturer's guidelines. These cells were meticulously cultivated under controlled conditions in a humidified incubator at a temperature of 37°C, with an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted and purified using TRIzol Reagent (Invitrogen, 15596026). Its quantity and purity were measured with a NanoDrop ND - 1000. RNA integrity was ensured with a RIN score above 7.0, assessed by Bioanalyzer 2100 and agarose gel electrophoresis. Poly(A) RNA was selected from total RNA using Dynabeads Oligo (dT) 25 - 61005.
The selected poly(A) RNA fragments were reverse - transcribed into cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649). Then, it was converted into U - labeled second - stranded DNAs. An A - base was added to the ends for adapter ligation. Indexed adapters were ligated to the A - tailed DNA, and products were size - selected with AMPureXP beads. After UDG enzyme (NEB, cat.m0280) treatment, the products were amplified by PCR. The final cDNA library had an average insert size of 300±50 bp.

treatment_protocol: HASMCs were pre-transfected with NC or Ad-NEXN. and then followed by high-Pi stimulation.

value: human aortic isolated SMCs (HASMCs)

value: Pre - transfect with Ad-NEXN, then stimulate with high-Pi


title: Neonate_Thymus_Double_Negative_RNA_3

value: Thymus


title: 4T1-CTRL-4


title: ctrl_1

description:
Library name: Sample 1
Column name in genes_fpkm_expression.xlsx:FPKM.ctrl_1

value: healthy

value: peripheral blood


title: 4T1-COMBO-3


title: 4T1-PIC-1


title: Neonate_Thymus_Double_Negative_RNA_1


title: 4T1-PHEN-2


title: Adult_Spleen_CD8+_T_cell_RNA_4

value: Spleen

value: CD8+ T cells


title: Ctrl_16hr-PHS

type: RNA

first: Jongmin

middle: J

last: Kim

address: 930 Campus Road

department: Biomedical Sciences

hyb_protocol: Fragmented cRNA was hybridized to the Drosophila genome 2.0 arrays (Affymetrix, Cat# 900532). All microarray experiments were performed by the Stanford Protein and Nucleic Acid (PAN) facility.

scan_protocol: Affymetrix

data_processing: All the raw CEL files were background adjusted and quantile normalized together by using R/BioConductor (v3.0.2) package GCRMA. Gene annotation was based on the Affymetrix file: Drosophila_2.na32.annot.csv.

label: biotin

organism: Drosophila melanogaster

source_name: Drosophila melanogaster testes

label_protocol: Reverse transcription was performed with oligo(dT)24 primer with a T7 promoter using ~200 ng of total RNA per Affymetrix protocol. The second strand was synthesized from the cDNA, and cRNA was produced by in vitro transcription.

growth_protocol: Flies were raised on molasses food at 25C.

extract_protocol: RNA was extracted from about 30 pairs of dissected testes without accessory glands using Trizol (Invitrogen).

treatment_protocol: For the heat shock timecourse, flies were raised at 25˚C until there were mid- and late-stage pupa. Then bottles were placed in a 37˚C water bath for 30 minutes to induce heat shock and returned to 25˚C, as spelled out in Kim et al., (PMID: 28522526)

tag: time course

value: 16 hours after 30 minutes heat shock but no Bam expression


title: Ctrl_24hr-PHS

description: This sample data is used in our previous publication (PMID: 28522526), and uploaded to GEO (GSM2374952)

value: 24 hours after 30 minutes heat shock but no Bam expression


title: Ad-NEXN+high-Pi, rep2

description: Library name: sample 6


title: 4T1-COMBO-2

value: Murine breast tumor (FVB)


title: Ad-NEXN+high-Pi, rep1

description: Library name: sample 5


title: 4T1-COMBO-1

value: Poly I:C+Phenformin


title: Ctrl_32hr-PHS

value: 32 hours after 30 minutes heat shock but no Bam expression


title: Adult_Spleen_CD8+_T_cell_RNA_2


title: NC+high-Pi, rep3

description: Library name: sample 3

value: Pre - transfect with NC, then stimulate with high-Pi


title: Adult_Spleen_CD8+_T_cell_RNA_1


title: NK (N to N)_Vehicle_#4 (Native kidney_Vehicle_16-R)

city: Toyama

first: Jun-Dal

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 10.1.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 10.1.1 (Qiagen).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Mouse kidney

extract_protocol:
Eight- to 12-week-old male mice that expresses human CD25 limited to the podocytes (NEP25 mice: http://www.informatics.jax.org/allele/MGI:3762500) were used in this study. We performed kidney transplantation between NEP25 mice and their wild-type littermates which have the same genetic background (C57BL/6N). Then anti-human CD25 antibodies (LMB2, 1.75 ng/g per body weight) or vehicle was injected into tail vein. Kidneys were harvested at day 8. Samples were frozen in liquid nitrogen and were crushed into powder with a Multi-beads Shocker (Yasui Kikai Co.). Total RNA was extracted from powdered kidney samples using ISOGEN II reagent (Nippon Gene). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and then converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Kidney

value: Male


title: Ctrl_noHS

description: This sample data is used in our previous publication (PMID: 28522526), and uploaded to GEO (GSM2374951)

value: no Bam expression


title: NK (N to N)_Vehicle_#2 (Native kidney_Vehicle_14-R)


title: Adult_Thymus_Single_Positive_RNA_4

value: Single Positive

value: C57BL/6 mice


title: NC+high-Pi, rep2

description: Library name: sample 2

value: human aortic isolated SMCs (HASMCs)


title: NK (N to N)_Vehicle_#1 (Native kidney_Vehicle_13-R)


title: hs-Bam_48hr-PHS

description: This sample data is used in our previous publication (PMID: 28522526), and uploaded to GEO (GSM2474164)

value: hs-bam; bam[1]/bam[86]

value: 48 hours after Bam pulse expression by 30 minutes heat shock


title: NC+high-Pi, rep1

description: Library name: sample 1


title: Adult_Spleen_CD8+_T_cell_RNA_3


title: hs-Bam_40hr-PHS

value: 40 hours after Bam pulse expression by 30 minutes heat shock


title: Adult_Thymus_Single_Positive_RNA_2

value: Thymus


title: NK (N to N)_LMB2_#4 (Native kidney_LMB2_12-R)


title: NC+high-Pi, rep4

description: Library name: sample 4


title: iSLK cells, delta_circ-vIRF4 mutant virus, lytic infection, 72 hours, biol rep 3

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 1200 Newell Dr.

institute: University of Florida

description:
Library name: iSLK delta_circ-vIRF4, lytic, biol rep 3
test_lytic.deseq2.results.tsv

data_processing:
Paired-end RNA-seq reads were filtered of rRNA using SortMeRNA (v4.3.2) using the “sensitive” database (v4.3.4) with additional (RNA45SN2) transcript sequence
Read quality was assessed using FASTQC (v0.11.7)
Fastq reads were aligned to a combined human (GRCh38.p13; Ensembl release 103) and KSHV (HHV8; NC\_009333) reference genome using STAR (v.2.5.2a)
Abundance estimates of human and KSHV transcripts were generated using Kallisto (v0.46.0)
Differential expression testing was performed using DESeq2 (v1.32.0) and gene set enrichment analysis was performed using GSEA (v.3.0).
Assembly: Combined human (GRCh38.p13; Ensembl release 103) and KSHV (HHV8; NC\_009333) reference genome
Supplementary files format and content: tsv files containing TPM values for each sample

source_name: iSLK

extract_protocol:
RNA was extracted with RNA-Bee (phenol-chloroform extraction) according to the manufacturer’s protocol. 1 ug of total RNA was used as input to construct sequencing libraries
Lytic libraries were prepared by the authors using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L); Latent libraries were prepared by University of Florida ICBR using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: iSLK


title: NK (N to N)_LMB2_#3 (Native kidney_LMB2_11-R)


title: Adult_Thymus_Single_Positive_RNA_1


title: NK (N to N)_Vehicle_#3 (Native kidney_Vehicle_15-R)


title: Adult_Thymus_Double_Positive_RNA_4

value: Double Positive


title: Adult_Thymus_Single_Positive_RNA_3


title: iSLK cells, delta_circ-vIRF4 mutant virus, lytic infection, 72 hours, biol rep 1

description:
Library name: iSLK delta_circ-vIRF4, lytic, biol rep 1
test_lytic.deseq2.results.tsv


title: hs-Bam_8hr-PHS

value: 8 hours after Bam pulse expression by 30 minutes heat shock


title: hs-Bam_16hr-PHS

description: Column name: H16

data_processing:
Raw fastq reads were trimmed using trim_galore (version 0.4.3) to remove low-quality (Phred score 20) and adapter-containing (stringency 1) reads (29). Trimmed reads were mapped to the Drosophila melanogaster genome (BDGP6.46) with default parameters using STAR (version 2.5.3) (30). Mapped reads with quality scores smaller than 10 (-q 10) or not properly paired reads (-f 2) were discarded using SAMtools (version 1.4.1) (31). Counts per gene were obtained using the featureCounts function of the subread package (version 1.5.0) (32). Expression levels in different time points were TMM-normalized (Trimmed Mean of M-values), assuming the majority of housekeeping genes have the same expression levels in different time points using the R (version 4.1.0) package edgeR (version 3.34.0) (33). Analyses scripts are available in: https://github.com/jongminkmg/HeldOutWings2024
Assembly: Drosophila melanogaster genome (BDGP6.46)
Supplementary files format and content: Normalized CPM

source_name: Testes

extract_protocol:
10~20 μg of total RNA was extracted from ~100 pairs of testes for each time point using Trizol (Invitrogen) followed by RNeasy cleanup (Qiagen) according to kit instructions.
PolyA-tailed RNA was purified using the Oligotex mRNA kit (Qiagen, Cat#70022). Purified PolyA RNA was fragmented in the presence of random hexamer primers in first strand synthesis buffer (Invitrogen, Cat# 18080093) at 85˚C for 8 minutes. Fragmented RNAs were reverse transcribed using Superscript III reverse transcriptase (Invitrogen, Cat# 18080093) in the presence of RNaseOUT (Invitrogen Cat#  10777019) at 50˚C for one hour. From this step, we followed the directions in the NEBNext mRNA Library Prep Master Mix Set for Illumina (E6110s) to make libraries. DNA was purified using a QIAquick PCR purification kit (Qiagen Cat# 28104) after second strand synthesis, end repair, dA tailing, and adapter ligation. After adapter ligation, 300~500 bp fragments were size-selected by gel extraction (1.5% low-melt NUSIEVE gel in TBE).

value: Testes

value: Not a cell line

value: Primarily germ cells

value: 16hrs post heat shock expression of Bam


title: iSLK cells, wild-type virus, lytic infection, 72 hours, biol rep 3

description:
Library name: iSLK WT BAC16, lytic, biol rep 3
test_lytic.deseq2.results.tsv


title: Adult_Thymus_Double_Positive_RNA_3


title: hs-Bam_8hr-PHS

description: Column name: H08

value: 8hrs post heat shock expression of Bam


title: iSLK cells, wild-type virus, lytic infection, 72 hours, biol rep 2

description:
Library name: iSLK WT BAC16, lytic, biol rep 2
test_lytic.deseq2.results.tsv


title: hs-Bam_32hr-PHS

value: 32 hours after Bam pulse expression by 30 minutes heat shock


title: hs-Bam_noHS

description: This sample data is used in our previous publication (PMID: 28522526), and uploaded to GEO (GSM2374954)

value: no Bam expression


title: hs-Bam_24hr-PHS

description: This sample data is used in our previous publication (PMID: 28522526), and uploaded to GEO (GSM2374956)

value: 24 hours after Bam pulse expression by 30 minutes heat shock


title: NK (W to N)_Vehicle_#3 (Native kidney_Vehicle_7-R)

value: Kidney

value: Male


title: hs-Bam_32hr-PHS

description: Column name: H32

value: hs-bam; bam[1]/bam[86]

value: 32hrs post heat shock expression of Bam


title: iSLK cells, wild-type virus, lytic infection, 72 hours, biol rep 1

description:
Library name: iSLK WT BAC16, lytic, biol rep 1
test_lytic.deseq2.results.tsv


title: Adult_Thymus_Double_Negative_RNA_4

description: Pooled DN1-DN3

value: Double Negative

value: C57BL/6 mice


title: Adult_Thymus_Double_Positive_RNA_2

value: Thymus


title: iSLK cells, delta_circ-vIRF4 mutant virus, latent infection, biol rep 2

description:
Library name: iSLK delta_circ-vIRF4, latent, biol rep 2
test_latent.deseq2.results.tsv

value: iSLK


title: Adult_Thymus_Double_Positive_RNA_1

value: Double Positive


title: AML10: scRNAseq from bone marrow cells from AML patient

description:
Library name: AML10_scRNA
10x Genomics

value: Bone Marrow

value: Bone marrow mononuclear cells


title: NK (N to N)_LMB2_#2 (Native kidney_LMB2_10-R)


title: hs-Bam_24hr-PHS

description: Column name: H24

value: Testes

value: Not a cell line

value: Primarily germ cells

value: 24hrs post heat shock expression of Bam


title: NK (N to N)_LMB2_#1 (Native kidney_LMB2_9-R)


title: NK (W to N)_Vehicle_#1 (Native kidney_Vehicle_5-R)


title: Adult_Thymus_Double_Negative_RNA_3

description: Pooled DN1-DN3


title: iSLK cells, delta_circ-vIRF4 mutant virus, latent infection, biol rep 1

description:
Library name: iSLK delta_circ-vIRF4, latent, biol rep 1
test_latent.deseq2.results.tsv


title: iSLK cells, wild-type virus, latent infection, biol rep 2

description:
Library name: iSLK WT BAC16, latent, biol rep 2
test_latent.deseq2.results.tsv

value: wild-type virus, latent infection


title: AML3: scRNAseq from CD34+ sorted bone marrow cells from AML patient

description:
Library name: AML3_scRNA
10x Genomics


title: Adult_Thymus_Double_Negative_RNA_2

description: Pooled DN1-DN3


title: NK (W to N)_Vehicle_#4 (Native kidney_Vehicle_8-R)


title: NK (W to N)_LMB2_#4 (Native kidney_LMB2_4-R)


title: Neonate_Spleen_CD8+_T_cell_4

data_processing:
Fastq files were aligned to the mouse mm10 reference genome with bwa. Unmapped, unpaired, and mitochondrial reads were removed usingsamtools. PCR duplicates were removed using Picard. Peak calling was performed on four replicates with MACS2 with a FDR q-value< 0.05. A union peak list of each data set was created by combining all peaks in all samples, merging overlapping peaks using MACS2 and keeping peaks that were called in more than one sample as a saf file. The number of reads in each peak was determined with featurecounts subread package130. Peaks were annotated using HOMER. Each peak was assigned to the nearest gene based on the shortest distance between the peak and gene’s promoter, on either strand; promoters were defined as 1 kb upstream and 100 bp downstream of annotated transcription start site (TSS). Each gene was assigned to a peak cluster that had the greatest number of gene associated peaks; for ties, genes were randomly assigned to one of the tied clusters.
Assembly: mouse mm10 reference genome
Supplementary files format and content: Peak calls are provided in .saf file,Peak visualization can be done using .bedGraph files, Peak read counts for three replicates are provided as a .txt file

extract_protocol:
Thymi and spleens from adult or neonatal mice were collected in RPMI+10% FBS and mashed through a 40µM cell strainer to create a single-cell suspension. Spleens and thymi underwent magnetic enrichment with CD8a and CD4 MicroBeads (Miltenyi Biotec; cat# 130-117-044; cat# 130-117-043), respectively, per the manufacturer’s instructions. The bound thymic fraction was sorted for double positive thymocytes, while the eluted fraction underwent CD8a magnetic enrichment as described previously, after which the bound fraction was sorted for SP8 thymocytes, while the eluted fraction was sorted for DN thymocytes. Thymocyte counts were taken by diluting a single-cell thymus suspension and counting on a MoxiZ cell counter.
The ATAC-seq libraries were prepared based on the Omni-ATAC-seq protocols  with some minor modifications. Briefly, 100,000 FACS-sorted cells were used to prepare nuclei. The transposition reaction was performed by incubating 25,000 nuclei with Nextera Tn5 transposase (Illumina) at 37°C for 1 hour. The transposition mixture was purified using a Zymo DNA Clean and Concentrator kit. The ATAC libraries were amplified for 11 cycles using NEBNext 2X MasterMix and Nextera Index primers. The amplified libraries were size-selected using AMPure beads, to remove large DNA fragments.

value: CD8+ T cells


title: NK (W to N)_LMB2_#3 (Native kidney_LMB2_3-R)

value: Kidney


title: iSLK cells, wild-type virus, latent infection, biol rep 1

description:
Library name: iSLK WT BAC16, latent, biol rep 1
test_latent.deseq2.results.tsv


title: NK (W to N)_Vehicle_#2 (Native kidney_Vehicle_6-R)

value: Male