title: Input_2

status: Public on Aug 07 2026

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

description:
Library name: Input_2
Input_2 (V350145221_L01_total_Input_Rep2.fq.gz): RNA input, replicate 2, WT macrophages, RNA-seq; (serves as RNA-seq reference)

data_processing:
Raw sequencing reads were subjected to adapter trimming and quality control before alignment to the mouse reference genome (GRCm39/mm39) using STAR. For RNA-seq, gene-level read counts were generated and normalized for downstream differential expression analysis. Differentially expressed genes were identified using standard statistical methods. For m6Am-seq, reads from Input, m7G-IP, FTO(+)/m6A-IP, and FTO(-)/m6A-IP libraries were aligned to the mouse reference genome. Enriched m6Am sites and peaks were identified by comparing immunoprecipitated samples with corresponding controls and by evaluating FTO-dependent signal changes. Peak annotation, enrichment analysis, and downstream comparative analyses were performed using custom bioinformatic pipelines. Processed data files include gene expression matrices, differential expression results, m6Am peak annotations, genomic coordinates, and peak enrichment statistics.
Assembly: Mus musculus reference genome mm10
Supplementary files format and content: Bigwig

source_name: macrophages

extract_protocol:
Total RNA was extracted from mouse colon tissues and/or isolated macrophages using TRIzol reagent according to the manufacturer’s instructions. RNA quality and concentration were assessed prior to library preparation. For m6Am-seq, RNA fragments larger than 200 nt were purified and processed as described below.
For m6Am-seq, RNA fragments (>200 nt) were fragmented to approximately 150 nt and subjected to cap-m7G immunoprecipitation using an anti-m7G antibody. Immunoprecipitated RNA was further treated with or without recombinant FTO demethylase, followed by m6A immunoprecipitation using an anti-m6A antibody. Four libraries (Input, m7G-IP, FTO(+)/m6A-IP, and FTO(−)/m6A-IP) were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio) according to the manufacturer's instructions. Due to the strand-specific nature of this kit, cDNA sequence information is captured exclusively in Read 2 (R2); Read 1 (R1) reflects the adapter/primer sequence and was excluded from analysis. Libraries were sequenced on the Illumina HiSeq X Ten platform with paired-end 150-bp reads; only R2 reads were retained and used for downstream analysis.

value: macrophages

tag: sample group

value: Input


title: Input_1

type: SRA

country: China

description:
Library name: Input_1
Input_1 (V350145221_L01_total_Input_Rep1.fq.gz): RNA input, replicate 1, WT macrophages, RNA-seq; (serves as RNA-seq reference);

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type


title: APOE3, Female, 24M, #2

status: Public on Aug 08 2026

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

country: USA

institute: Mayo Clinic

description:
Library name: BU-APOE-17
10x Genomics v3

library_source: transcriptomic single cell

data_processing:
The single cell RNA sequencing data preprocessing was performed using the standard 10x Genomics Cell Ranger Single Cell Software Suite v.3.0.2. Briefly, raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering, and differential expression analyses were performed using Seurat v5.0.1 with default parameter settings unless specified otherwise.
Assembly: mm10
Supplementary files format and content: compressed tab-separated and matrix values

source_name: brain

extract_protocol:
The mice were perfused with phosphate-buffered saline (PBS, pH 7.4) after anesthetization with isoflurane, followed by a quick dissection of cortex from left hemisphere to the HBSS buffer (Gibco, 14025076). The cortices were then dissociated with papain-based the Neural Tissue Dissociation kit (Miltenyi Biotec, 130–092-628) using gentleMACS™ Dissociator (Miltenyi Biotec, 130-093-235) followed by debris removal through filtering with the 70-µm cell strainer. Cell suspensions were then subject to myelin removal (Cat# 130-096-433, Miltenyi Biotec), red cell lysis (Cat# 130-094-183; Miltenyi Biotec) and dead cell removal (Cat# 130-090-101; Miltenyi Biotec) according to the manufacturer’s instructions. Finally, cell pellets were resuspended in Ca/Mg-free PBS supplemented with 0.5% FBS. Cell numbers and viability were determined through trypan blue examination under microscope. More than 90% of the cells were identified viable for all the 24 samples.
The isolated cells were subject to single cell RNA sequencing (scRNAseq) through the chromium platform (10x Genomics) with the 39 gene expression V3 kit, using a targeted input of ∼6,000–9,000 cells per sample. In brief, gel-beads in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10x-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent) analysis and then sequenced on a HiSeq 4000 instrument (Illumina) targeting a depth of 25,000–50,000 reads per cell.

tag: tissue

value: brain

tag: flow cell

tag: apoe genotype

tag: age in_months

tag: Sex

value: Female


title: non_FTO_2

description:
Library name: non_FTO_2
non_FTO_2 (V350145221_L01_non_FTO_Rep2.fq.gz): FTO(−)/m6A-IP, replicate 2, WT macrophages, RIP-seq (m6Am-seq);


title: non_FTO_1

description:
Library name: non_FTO_1
non_FTO_1 (V350145221_L01_non_FTO_Rep1.fq.gz): FTO(−)/m6A-IP, replicate 1, WT macrophages, RIP-seq (m6Am-seq);


title: m7G_IP_2

description:
Library name: m7G_IP_2
m7G_IP_2 (V350145221_L01_m7G_IP_Rep2.fq.gz): cap-m7G IP, replicate 2, WT macrophages, RIP-seq (m6Am-seq);


title: APOE2, Female, 24M, #2

description:
Library name: BU-APOE-16
10x Genomics v3


title: m7G_IP_1

description:
Library name: m7G_IP_1
m7G_IP_1 (V350145221_L01_m7G_IP_Rep1.fq.gz): cap-m7G IP, replicate 1, WT macrophages, RIP-seq (m6Am-seq);


title: F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 1

city: LIMOGES

first: Stéphanie

last: DURAND

address: 2 rue du Dr Marcland

department: UMR 1308 INSERM

country: France

institute: University of Limoges / INSERM

description:
Library name: Sample 1
Column name in Raw_Counts_All_Samples.txt : F1_NTn1

data_processing:
Bioinformatics analysis was conducting by the Beijing Genomics Institute according following analysis pipeline: 1) Raw data obtained from sequencing were filtered using SOAPnuke to remove reads with low quality (reads with a percentage of bases with a quality value less than 15 exceeding 20% of the total bases in the read), adapter contamination, and high content of unknown bases (N) (greater than 0.1%). More of 30 million high-quality (clean) paired reads per sample were obtained after read filtering step, with more 90% of reads with quality greater than Q30 (range: 89.85 to 96.34%). 2) HISAT2 (v2.2.1) was used for aligning clean reads to human reference genome (GRCh38.p14). (3) Gene expression quantification was performed using RSEM3 (v1.3.1) software with Bowtie2 (v2.3.4.3) used as the internal transcriptome aligner. Alignment results show a range of 78.74 to 84.96% of read uniquely mapped to reference. Finally, the average alignment of the gene set was 87.20% and a total of 18856 genes were detected.
SOAPnuke (v1.5.6) parameters : -l 15 -q 0.2 -n 0.001 -G
HISAT2 (v2.2.1) parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Bowtie2 (v2.4.5) parameters: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 20 -N 1
RSEM (v1.3.1) parameters: -p 8 --forward-prob 0
Assembly: Homo_sapiens_NCBI_GCF_000001405.40_GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Homo sapiens

source_name: colon

growth_protocol: The SW480 cell line was purchased from the American Type Culture Collection (ATCC/LGC Promochem, Molsheim, France) and cultured in RPMI 1640 GlutaMAXTM medium (Gibco™, Thermo Fisher, MA, USA) supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and 1 % of penicillin-streptomycin (Thermo Fisher) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA was harvested using the Quick-RNA™ Microprep kit (Zymo Research). Only samples with a concentration of at least 50 ng/µL and an RNA Integrity Number (RIN) greater than 7 were included for further analysis.
RNA sequencing was conducted by the Beijing Genomics Institute, following the manufacturer’s protocol for Rolling-Circle and DNA Nano-Ball (DNB™) technology. Paired-end reads were generated with a length of 150 bases using the DNBSEQ platform.

treatment_protocol: The optimal elution conditions for SdFFF separation were as follows: flow injection through the accumulation wall of a 100 μL SW480 cell suspension (2.5 × 106 cells/mL) ; Flow rate: 1.0 mL/min ; Mobile phase: sterile DEP, pH 7.4 and conductivity 20 mS/m ; External multigravitational field strength: 12 ± 0.2 g (270 rpm) ; Time-dependent fraction collection: F1: 3'20” to 4'30” and F3: 6'00” to 7'50”. A third fraction was also collected, constituting the total eluted population, PT: 3'20 to 7'50, without the void volume as an internal biological control

value: colon

tag: cell line

value: colorectal cancer cell

tag: genotype

value: Wild Type

tag: treatment

value: SdFFF fraction:F1

tag: batch


title: HC11 cells_8h 100nM insulin_biol rep 5

city: Oxford

first: Fadil

middle: M

last: Hannan

state: Oxfordshire

address: Level 3, Women's Centre, John Radcliffe Hospital

department: Nuffield Department of Women's and Reproductive Health

country: United Kingdom

institute: University of Oxford

description:
Library name: INS8h5
INS8h5

data_processing:
The sequencing libraries were multiplexed and loaded on an Illumina NovaSeq 6000 instrument. Samples were sequenced using a 2x150 paired-end (PE) configuration. Image analysis and base calling were conducted on instrument, and raw sequence data were converted into FASTQ files and demultiplexed using Illumina bcl2fastq program version 2.20.
Assembly: HC11: mm9, NCBI Build 37. MCF-12A and MFG: human (hg19, GRCh37).
Supplementary files format and content: CSV files containing raw counts data for each sample; one counts file per dataset.

molecule: polyA RNA

extract_protocol:
HC11 and MCF-12A RNA was extracted using the RNeasy mini plus kit (Qiagen). MFG RNA was extracted using the RNeasy plus universal kit (Qiagen).
HC11 and MCF-12A RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). MFG RNA libraries were prepared using rRNA depletion followed by NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s recommendations.

value: Mammary epithelial cell

value: WT

value: 100nM insulin


title: FTO_2

description:
Library name: FTO_2
FTO_2 (V350145221_L01_FTO_Rep2.fq.gz): FTO(+)/m6A-IP, replicate 2, WT macrophages, RIP-seq (m6Am-seq);

value: FTO


title: FTO_1

description:
Library name: FTO_1
FTO_1 (V350145221_L01_FTO_Rep1.fq.gz): FTO(+)/m6A-IP, replicate 1, WT macrophages, RIP-seq (m6Am-seq);


title: HC11 cells_8h 100nM insulin_biol rep 4

description:
Library name: INS8h4
INS8h4


title: F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 3

description:
Library name: Sample 7
Column name in Raw_Counts_All_Samples.txt : F3_NTn3

value: SdFFF fraction:F3


title: HC11 cells_8h 100nM insulin_biol rep 3

description:
Library name: INS8h3
INS8h3


title: HC11 cells_8h 100nM insulin_biol rep 2

description:
Library name: INS8h2
INS8h2


title: HC11 cells_8h 100nM insulin_biol rep 1

description:
Library name: INS8h1
INS8h1


title: HC11 cells_8h control_biol rep 5

description:
Library name: Ctrl8h5
Ctrl8h5

value: 0nM insulin


title: HC11 cells_8h control_biol rep 4

description:
Library name: Ctrl8h4
Ctrl8h4


title: HC11 cells_8h control_biol rep 3

description:
Library name: Ctrl8h3
Ctrl8h3


title: HC11 cells_8h control_biol rep 2

description:
Library name: Ctrl8h2
Ctrl8h2


title: HC11 cells_8h control_biol rep 1

description:
Library name: Ctrl8h1
Ctrl8h1


title: Hindpaw skin cells, PTX and MK2i treated

city: Saint Louis

first: Sheila

last: Stewart

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

description:
Library name: PTX MK2
10x Genomics

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

source_name: Hindpaw Skin

extract_protocol:
Following vehicle or PTX treatment, mice were given normal or MK2i chow. At the end of the experimental timeline, skin from the planar surface of the hindpaws was isolated and digested in DMEM F-12 supplimented with 2mg/mL collagenase A, 1mg/mL hyaluronidase and 2U/mL Dnase I for 1 hour at 37ºC. Cell suspensions were washed with FACS buffer and run through a 70um and 40um strainer. Cells were then stained for eFluor 780 Viability Dye and BV510 CD45. Live cells that were CD45- were sorted out using a Sony Synergy Cell Sorter. Cells from hindpaw skin were heat shocked for 60 seconds to serve as Viability Dye single stain controls. Similar skin cells were used for BV510 CD45 single stain controls. Samples were collected in FACS buffer containing 0.04& BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ GEM X protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Hindpaw Skin

tag: strain

value: C57Bl6 J

value: Wildtype

value: PTX and MK2i

tag: age

value: 12 weeks


title: Hindpaw skin cells, Vehicle and MK2i treated

description:
Library name: Veh MK2
10x Genomics

value: Vehicle and MK2i


title: Hindpaw skin cells, PTX treated

description:
Library name: PTX
10x Genomics

value: Female

value: PTX


title: APOE3, Female, 3M, #2

description:
Library name: BU-APOE-14
10x Genomics v3

value: brain


title: Hindpaw skin cells, Vehicle treated

description:
Library name: Vehicle
10x Genomics

value: Vehicle


title: 13893-JF-14

city: San Diego

first: Kellen

last: Cavagnero

state: California

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

description: Library name: 13893-JF-14

data_processing:
Reads were mapped to the mm10 reference genome and count matrices were generated using CellRanger with default parameters. Downstream processing, and analysis was done using Seurat.
Assembly: mm10
Supplementary files format and content: Cell Ranger output matrices

source_name: Skin

extract_protocol:
Samples were incubated in an optimized lysis buffer, which contains proteinase K, to release RNA from the sample sections. This was followed by an incubation at a higher temperature to partially reverse formalin crosslinking of the released nucleic acids and improve RNA yield and quality. This was followed by DNase treatment that was optimized to eliminate all genomic DNA, including very small DNA fragments. The lysate was then mixed with Buffer RBC, and ethanol was added to provide appropriate binding conditions for RNA. The sample was then applied to an RNeasy MinElute spin column, where the total RNA bound to the membrane and contaminants were effectively washed away. RNA was then eluted in 30µl of RNase-free water.
10X Genomics Flex FFPE protocol and were subjected to 28x91bp of sequencing according to the manufacturer’s protocol (Illumina NovaSeq). Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan

value: Skin

value: Whole tissue


title: 13893-JF-15

description: Library name: 13893-JF-15


title: 13893-JF-13

description: Library name: 13893-JF-13


title: 13893-JF-10

description: Library name: 13893-JF-10


title: 13893-JF-11

description: Library name: 13893-JF-11


title: 13893-JF-12

description: Library name: 13893-JF-12


title: 13893-JF-9

description: Library name: 13893-JF-9

value: Control


title: 13893-JF-8

description: Library name: 13893-JF-8


title: 13893-JF-7

description: Library name: 13893-JF-7


title: 13893-JF-6

description: Library name: 13893-JF-6


title: 13893-JF-5

description: Library name: 13893-JF-5


title: 13893-JF-4

description: Library name: 13893-JF-4


title: 13893-JF-1

description: Library name: 13893-JF-1


title: 13893-JF-2

description: Library name: 13893-JF-2


title: 13894-JF-6

description: Library name: 13894-JF-6

value: IMQ


title: 13894-JF-7

description: Library name: 13894-JF-7


title: 13894-JF-2

description: Library name: 13894-JF-2


title: 13894-JF-1

description: Library name: 13894-JF-1


title: 13894-JF-3

description: Library name: 13894-JF-3


title: 13894-JF-15

description: Library name: 13894-JF-15


title: 13894-JF-14

description: Library name: 13894-JF-14


title: 13894-JF-13

description: Library name: 13894-JF-13


title: 13894-JF-12

description: Library name: 13894-JF-12


title: 13894-JF-11

description: Library name: 13894-JF-11


title: 13894-JF-10

description: Library name: 13894-JF-10


title: NKT Bone Marrow

city: Los Angeles

first: Yichen

last: Zhu

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

description:
Library name: 4BM
10x Genomics

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting variable features across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of mouse immune cells were manually merged and annotated based on immune cell lineage markers. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots.
Assembly: Mouse (GRCm39)
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: Bone marrow

extract_protocol:
Using the in vivo CRS model described above, mouse immune cells were subjected to scRNA-seq analysis. At 3 days post–therapeutic cell injection, mice were euthanized, and six tissues were harvested, including peritoneal fluid, blood, liver, lung, spleen, and bone marrow. Single-cell suspensions were prepared from each tissue and subjected to fluorescence-activated cell sorting (FACS). Mouse CD45⁺ immune cells were isolated from all tissues.
Sorted cells were immediately delivered to the UCLA Technology Center for Genomics & Bioinformatics (TCGB) core facility for library preparation and subsequent scRNA-seq analysis. Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 20,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3’ Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: Bone marrow

value: Immune cells


title: NKT Spleen

description:
Library name: 4SP
10x Genomics

source_name: Spleen

value: Spleen


title: NKT Lung

description:
Library name: 4LN
10x Genomics

source_name: Lung

value: Lung


title: NKT Liver

description:
Library name: 4LV
10x Genomics

source_name: Liver

value: Liver


title: NKT Peritoneal Fluid

description:
Library name: 4PF
10x Genomics

source_name: Peritoneal cavity

value: Peritoneal cavity


title: T Bone Marrow

description:
Library name: 3BM
10x Genomics


title: T Spleen

description:
Library name: 3SP
10x Genomics


title: T Lung

description:
Library name: 3LN
10x Genomics


title: NKT Blood

description:
Library name: 4PB
10x Genomics

source_name: Peripheral blood

value: Peripheral blood


title: T Liver

description:
Library name: 3LV
10x Genomics


title: T Blood

description:
Library name: 3PB
10x Genomics


title: T Peritoneal Fluid

description:
Library name: 3PF
10x Genomics


title: Tumor Bone Marrow

description:
Library name: 2BM
10x Genomics


title: Tumor Spleen

description:
Library name: 2SP
10x Genomics


title: Tumor Liver

description:
Library name: 2LV
10x Genomics


title: Tumor Peritoneal Fluid

description:
Library name: 2PF
10x Genomics


title: Blank Spleen

description:
Library name: 1SP
10x Genomics


title: Blank Lung

description:
Library name: 1LN
10x Genomics


title: Tumor Blood

description:
Library name: 2PB
10x Genomics


title: Blank Bone Marrow

description:
Library name: 1BM
10x Genomics


title: Blank Liver

description:
Library name: 1LV
10x Genomics


title: BMDC_Saline_1

city: xiamen

first: YESI

last: SHI

address: xiangan south road

institute: Xiamen University

description:
Library name: Saline_1
DNBSEQ-T7

data_processing:
Raw reads were filtered to remove adaptor sequences, low-quality reads, and reads containing excessive unknown bases.
Clean reads were aligned to the Mus musculus reference genome (GRCm38/mm10).
Gene expression levels were quantified as raw read counts and normalized expression values.
Differential expression analysis and pathway enrichment analyses were performed between treatment groups.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for all samples.
Supplementary files format and content: Microsoft Excel file containing normalized gene expression values for all samples.

growth_protocol: Mouse bone marrow-derived dendritic cells (BMDCs) were isolated from the bone marrow of C57BL/6 mice and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and recombinant GM-CSF under standard culture conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA quality and concentration were assessed prior to library preparation.
RNA libraries were constructed using a poly(A) enrichment strategy and prepared according to the manufacturer's standard protocol. Sequencing was performed on the DNBSEQ  platform.

treatment_protocol: BMDCs were treated with saline, protoscolex-derived antigens (PSA), F127@PSA, or SHIFT-F127@PSA prior to RNA extraction for transcriptome analysis.

value: Bone marrow-derived dendritic cells

value: Wild type

value: Saline


title: tMut-3

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description: Library name: tMut-3

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: mm10
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: Embryo

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until the 2-cell stage (28 hours post insemination: 28 hpi).

extract_protocol:
For RNA-seq analyses, after the removal of zona pellucida in acid Tyrode, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
For RNA-seq analyses, SMART-seq library preparation was performed using SMART-Seq® mRNA HT (634795, Takara). The produced cDNA was amplified by PCR. The amplified cDNA was purified using KAPA HyperPure Beads (KK8011, KAPA Biosystems). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit dsDNA HS Assay kit (Q32854, Thermo Scientific).

treatment_protocol: After insemination, fertilized embryos were collected at 12-14 hpi for mRNA injection. mRNAs were injected using a piezo manipulator (Prime Tech, Tsukuba, Japan).

value: Embryo

value: 2-cell embryo

value: mutant tether and anchor mRNA injection


title: Blank Peritoneal Fluid

description:
Library name: 1PF
10x Genomics


title: Blank Blood

description:
Library name: 1PB
10x Genomics


title: CCR10 KO 10 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

city: San Antonio

last: Xiong

state: TX

address: 7703 Floyd Curl

department: MIMG

institute: UT Health Science Center at San Antonio

description: Library name: Sample 9

data_processing:
Reads for each gene by sample are counted by StringTie. R package ‘DESeq’ was used to normalize data and find group-pairwise differential gene expression. Differentially expressed genes (DEGs) are determined based on 3 criteria: At least one sample type has average RPKM > 1, FDR adjusted p-value < 0.05 (may vary) and Fold change (in either way) > 2 (may vary).
Assembly: UCSC/mm10
Supplementary files format and content: XXX

extract_protocol:
E.Z.N.A. Total RNA Kit I from Omega Bio-Tek was used to isolate total RNA from the lung tissue according to manufacturer's instruction. 500ng of RNA was used for RNA-seq library preparation.
stranded mRNAs-eq library prep and sequencing with 100PE

value: CCR10 Knockout

value: Intranasal SARS-CoV-2 MA10 infection


title: CCR10 KO 9 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 8


title: CCR10 KO 7 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 7


title: CCR10 KO 6 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 6


title: CCR10 Het 5 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 5

value: CCR10 Heterozygous


title: CCR10 Het 4 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 4


title: CCR10 Het 3 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 3


title: CCR10 Het 2 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 2


title: Tumor Lung

description:
Library name: 2LN
10x Genomics


title: medial NAc

city: Princeton

first: Jessie

last: Muir

state: NJ

address: 40 Woodlands Wy

department: Princeton Neuroscience Institute

institute: Princeton

description:
Library name: A1
filtered_feature_bc_matrix.tar.gz is the combined data

data_processing:
Libraries were sequenced using a NovaSeq 6000 (Illumina) at a depth of 300 M reads per sample.
Demultiplexing, barcoded processing, gene counting and aggregation were performed using the 10X Genomics Cell Ranger 9.0 software
Assembly: Custom genome for the D3-cre mouse was built from 10x provided GRCm39 genome with the addition of the cre transcript including poly A tail.
Supplementary files format and content: Zipped tar files- unzips to features, barcodes and matrix files which can be imported to scanpy

molecule: nuclear RNA

source_name: brain; NAc

extract_protocol:
Nuclei were isolated using 10x Genomics Chromium Nuclei Isolation Kit according to manufacturer's instructions
Barcoded cDNA was generated using the Chromium Single Cell 3’ v3.1 kit, Chromium Next GEM Chip G and Chromium Controller iX (10x Genomics) with a targeted cell recovery of 10,000 cells/μL and libraries were constructed using the Dual Index and Library Construction kits (10x Genomics) according to manufacturer's instructions.

value: brain; NAc

value: male

value: 8 weeks


title: lateral Nac

description:
Library name: A2
filtered_feature_bc_matrix.tar.gz is the combined data

source_name: brain: NAc


title: Liver, MNX HC, female, rep3

city: Kansas City

first: Emily

last: Schueddig

state: KS

address: 2901 Rainbow Boulevard

department: Department of Biostatistics & Data Science

institute: University of Kansas Medical Center

description: Library name: HC3

data_processing:
Read quality was assessed using FastQC (v0.12.1, RRID:SCR_014583). UMI-tools (v1.1.6, RRID:SCR_017048) was used for UMI and read extraction, then cutadapt (v5.0, RRID:SCR_011841) was used to retain reads with a minimum read length of 14 base pairs and maximum of 100 base pairs. BWA (v0.7.18, RRID:SCR_010910) with the aln algorithm was used for mapping with parameters set for no gaps (-o 0) and no mismatches (-n 0). Reads were aligned to the genomic sequence of aminoacetylated, mature mitochondrial mt-TR. Since there are known SNP in the mt-tRNA-Arg sequence for different mouse strains, each sample was mapped to its respective reference sequence. Aligned reads were deduplicated using UMI-tools. The resulting set of aligned reads were then mapped to the full mouse genome with the UCSC mm10 assembly as the reference using the bowtie (v1.3.1, RRID:SCR_005476) aligner. If the sequence mapped to another location, it was marked as a false positive and removed from downstream analysis. The number of reads for each unique sequence was extracted for each sample.
Assembly: NC_005089.1, CM004255.1, CM004184.1
Supplementary files format and content: counts.txt is a matrix of tRFs x samples that contains the extracted counts of sequences to the mt-tRNA-Arg gene

source_name: liver

extract_protocol:
Tissues were preserved in RNAlater (Invitrogen, AM7024) and frozen prior to RNA extraction. Small RNA was isolated using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific, AM1560) according to the manufacturer’s instructions with one exception: rather than being discarded, the corresponding large RNA fractions of small RNA isolations were retained, washed, and eluted to assess RNA integrity by visualization of 28S and 18S rRNA bands following agarose gel electrophoresis. Intact RNA samples were pooled by sodium acetate-propanol precipitation, followed by resuspension in nuclease-free water. RNA concentration was quantified using the Qubit microRNA Assay Kit (ThermoFisher Scientific, Q32881). Then RNA was pretreated using the rtStar™ tRF & tiRNA Pretreatment Kit (ArrayStar, AS-FS-005) to remove RNA modifications known to interfere with tRF detection, including 3′-aminoacyl groups, 2′,3′-cyclic phosphates, and 5′ hydroxyl termini, as well as m¹A and m³C methylation. Following pretreatment, RNA quality and concentration were assessed using the Agilent TapeStation 2400 with RNA ScreenTape and High Sensitivity RNA ScreenTape assays.
Small RNA libraries were prepared using the QIAseq miRNA UDI Library Kit and indexed with the QIAseq UDI miRNA Index Kit (Qiagen). Libraries were normalized, pooled, and sequenced on a NovaSeq instrument by the University of Kansas Medical Center Genomics Core Facility.

value: liver

value: HC


title: Liver, MNX HC, female, rep1

description: Library name: HC1


title: Liver, MNX CH, female, rep2

description: Library name: CH2

value: CH


title: Liver, MNX CH, female, rep3

description: Library name: CH3


title: Liver, MNX CH, female, rep1

description: Library name: CH1


title: Liver, MNX CF, female, rep3

description: Library name: CF3

value: CF


title: FAPs, KPC- Day 26_biol rep 1

status: Public on Aug 10 2026

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description:
227C3
FAPs_Day_26_raw_counts.txt

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Genes with less than 20 read counts in at least 2 samples were filtered out and differential gene expression analysis and processed using DESeq2 (v1.36.0) in R (version 4.2.1)
Differential expression analysis was performed using DESeq2, and genes with fold-change ≥ 1.5 and p-value < 0.05 were considered as differentially expressed
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw read counts for each sample

source_name: Hindlimb muscle

growth_protocol: KPCY cell line was grown in DMEM media containing L-Glutamine, 4.5g/L Glucose, without Sodium Pyruvate, and 10% Fetal Bovine Serum.

extract_protocol:
FAPs were sorted using an Influx cell sorter (Becton Dickinson) with the following gating strategy: CD31-/ CD45-/ α7-integrin-/ PI-/ SCA-1+/ Hoechst 33342+. RNA of sorted FAPs was isolated using a combination of Qiazol/chloroform, and miRNeasy kit.
Samples with a RIN of 7 and above were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 using the P3 reagents (100 cycle; Illumina) to generate paired-end reads (59 x 59 base pairs).

treatment_protocol: 2 million cells in 50uL were injected into the pancreas. Control mice received sham surgery

value: Hindlimb muscle

value: Freshly sorted FAPs

value: Male

value: Orthotopic implantation of KPCY cells

tag: time

value: Day 26


title: Liver, MNX CF, female, rep2

description: Library name: CF2


title: Liver, MNX CF, female, rep1

description: Library name: CF1


title: Liver, wildtype FF, female, rep2

description: Library name: FF2

value: FF


title: Liver, MNX HC, female, rep2

description: Library name: HC2


title: Liver, wildtype FF, female, rep3

description: Library name: FF3


title: Liver, wildtype HH, female, rep2

description: Library name: HH2

value: HH


title: Liver, wildtype HH, female, rep3

description: Library name: HH3


title: Liver, wildtype FF, female, rep1

description: Library name: FF1


title: Liver, wildtype CC, female, rep3

description: Library name: CC3

value: CC


title: CCR10 Het 1 Lung Tissue SARS-CoV-2 MA10 infected, Day 14

description: Library name: Sample 1

value: Lung

value: Intranasal SARS-CoV-2 MA10 infection


title: Liver, wildtype CC, female, rep2

description: Library name: CC2


title: cardiac outflow tract, E10.5, WT

city: Nanjing

first: haiyue

last: Feng

state: Jiangsu

address: No.22 Hankou Road,Nanjing City

institute: Nanjing University

description: Library name: E10.5_OFT

data_processing:
Raw reads were processed to generate gene expression profiles using aninternal  pipeline in Singleron company (Nanjing, China).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cardiac outflow tract

extract_protocol:
Fresh OFT tissues from 33 E10.5 wild-type hearts were isolated and stored in the GEXSCOPE Tissue Preservation Solution (Singleron Biotechnologies, Nanjing, China) at 2-8 ℃. Tissues were washed with Hank's Balanced Salt Solution (HBSS), minced, and digested (2 ml GEXSCOPE Dissociation Sol., 37 °C, 15 min, agitation) per protocol. Post-digest, 40-μm strainer isolated single cells, which were centrifuged (300 × g, 4 °C, 5 min). Pellets were re-suspended in 1 ml PBS, counted (TC20 Cell Counter Bio-Rad, Shanghai, China), and adjusted to 1×10⁵ cells/mL.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron).Individual libraries were diluted to 4 nM andpooled forsequencing.At last, pools were sequenced on Illumina HiSeq X with 150bp paired end reads.

value: cardiac outflow tract

tag: developmental stage

value: WT


title: Liver, wildtype CC, female, rep1

description: Library name: CC1


title: Liver, wildtype HH, female, rep1

description: Library name: HH1


title: BMM IFNγ 1

city: Berkeley

first: Stefan

middle: A

last: Fattinger

address: 415 Weill Hall

institute: UC Berkeley

description: Library name: Sample 7

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36. Trimmed reads were mapped to the Mus musculus GRCm38 reference genome with STAR aligner v.2.5.2b. Analysis of raw counts was performed with DESeq2
Assembly: mm10
Supplementary files format and content: csv file including raw counts of each sample

source_name: Bone marrow derived macrphage (BMMs)

growth_protocol: Bone marrow-derived macrophages (BMMs) were differentiated from bone marrow and maintained in DMEM supplemented with 10% FBS, PenStrep, Glutamin, HEPES, and M-CSF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with TRK lysis buffer (Omega Bio-Tek) and 2-mercaptoethanol followed by total RNA isolation using the E.Z.N.A Total RNA Kit I (Omega Bio-Tek)
RNA libraries for RNA-seq were prepared using an Illumina Poly(A) selection kit following manufacturer's protocols.

treatment_protocol: BMMs were left untreated, stimulated with 10ng/ml of IFNβ, IFNγ, TNF, or TGFβ for 6 hours or preexposed to 10ng/ml IFNβ for 24h before adding 10ng/ml IFNγ for 6h.

value: Bone marrow derived macrphage (BMMs)

value: B6 WT

value: IFNγ


title: hepatocytes, 4n-top, subject4

city: Hongo

first: Yusuke

middle: V

last: Watanabe

state: Bunkyo, Tokyo

department: Bioengineering

institute: University of Tokyo

description: Library name: 16-4n-t-4

data_processing:
Raw counts were alinged to the mouse genome GRCm39 using STAR v 2.7.11a.
The gene count matrix was produced by featureCounts in Subread module v 2.0.6.
Supplementary files format and content: Comma-separated values (CSV) file includes count matrix for all samples.
Assembly: GRCm39

growth_protocol: Hepatocytes were isolated from WT adult male mice.

extract_protocol:
RNA was harvested using FastGene RNA basic kit and cleaned up with the Monarch Spin RNA Cleanup Kit. 20 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Takara  SMART-Seq Stranded Kit by GeneWiz.

treatment_protocol: Hepatocytes were sorted by flow cytometry, according to Hoechst fluorescence.

value: Liver

value: Hepatocytes

value: hepatocytes, 4n-top


title: hepatocytes, 4n-top, subject2

description: Library name: 14-4n-t-2


title: flLB1(F454A/L457A)-1

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

extract_protocol:
After the removal of zona pellucida in acid Tyrode, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
SMART-seq library preparation was performed using SMART-Seq® HT Kit (Z4438N, Takara). The produced cDNA was amplified by PCR with 13 cycles. The amplified cDNA was purified using KAPA HyperPure Beads (KK8011, KAPA Biosystems). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit dsDNA HS Assay kit (Q32854, Thermo Scientific).

value: Embryo

value: 2-cell embryo

value: flLB1(F454A/L457A) mRNA injection


title: hepatocytes, 4n-top, subject3

description: Library name: 15-4n-t-3

value: Male


title: hepatocytes, 4n-whole, subject3

description: Library name: 07-4n-w-3

value: hepatocytes, 4n-whole


title: hepatocytes, 4n-whole, subject4

description: Library name: 08-4n-w-4


title: hepatocytes, 4n-whole, subject2

description: Library name: 06-4n-w-2


title: hepatocytes, 4n-bottom, subject4

description: Library name: 12-4n-b-4

value: hepatocytes, 4n-bottom


title: hepatocytes, 4n-bottom, subject3

description: Library name: 11-4n-b-3


title: hepatocytes, 2n-whole, subject4

description: Library name: 04-2n-w-4

value: hepatocytes, 2n-whole


title: hepatocytes, 4n-bottom, subject2

description: Library name: 10-4n-b-2


title: hepatocytes, 4n-whole, subject1

description: Library name: 05-4n-w-1


title: hepatocytes, 2n-whole, subject3

description: Library name: 03-2n-w-3


title: hepatocytes, 4n-bottom, subject1

description: Library name: 09-4n-b-1


title: hepatocytes, 2n-whole, subject2

description: Library name: 02-2n-w-2


title: hepatocytes, 2n-whole, subject1

description: Library name: 01-2n-w-1


title: primary WT macrophages, LTA-treated, 2 hrs, rep3

city: Boston

first: Daniel

last: Fisch

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description:
Library name: WT+LTA_2h_Rep3
column name in raw_counts.txt: WT+LTA_2h_Rep3

data_processing:
Raw reads were filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, Phred quality score >15, and a minimum length >50 bp.
Filtered reads were aligned to the reference genome (GRCm38 [mm10]) using STAR aligner v2.7.11 with non-canonical splice junction removal, followed by coordinate sorting using samtools v1.22.1.
PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0.
Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains EnsemblIDs and raw counts for each sample

source_name: primary bone marrow-derived macrophages, BMDM

growth_protocol: BMDMs were differentiated from whole bone marrow derived from tibia and femurs of C57BL/6J, WT or Ticam2-/- mice. Briefly, bones were surgically removed and cleaned of surrounding muscle and tissue. Bones were washed once in 70% ethanol, washed in PBS + 2.5 mM EDTA + P/S, and stored in PBS + 2.5 mM EDTA + P/S until processing. The ends of the tibia and femurs were cut, and bones were placed into a sterile 0.6 mL tube with holes at the base. The 0.6 mL tube with bones was placed into a sterile 2 mL tube and the nested tubes spun at 10,000 × g for 1 min. Cell pellets were resuspended in PBS + 2.5 mM EDTA and spun at 400 × g for 3 min followed by RBC lysis using ACK buffer for 1 min at room temperature (RT). Lysis was stopped by adding a 10 Vol of PBS + 2.5 mM EDTA and cells were pelleted at 400 × g for 3 min. A total of 4 x 106 cells were seeded per 10 cm suspension culture dish and differentiated in 10 mL cDMEM supplemented with 30% L929 supernatants containing M-CSF for 6 days. Cells were fed with 5 mL additional differentiation medium after 3 days. BMDMs were detached using PBS + 2.5 mM EDTA by incubating for 10 min at RT and re-seeded into 24-well plates with 0.5×106 cells per well in cDMEM supplemented with 10% L929 supernatants. Experiments were performed the following day.

extract_protocol:
RNA was extracted using PureLink™ RNA Mini Kit (12183025, Thermo Fisher Scientific). During purification, on-column DNAse-treatment using PureLink™ DNase (12185010, Thermo Fisher Scientific) was performed to remove contaminating gDNA following the manufacturer’s instructions. BMDMs were derived from three WT and three Ticam2-/- animals representing three independent biological replicates per genotype/treatment condition. RNA quantity and quality was assessed by spectrophotometry.
Library preparation, HTS, demultiplexing and initial QC were performed by Plasmidsaurus.

treatment_protocol: Cells were stimulated with 10 ng/mL LPS or 100 ng/mL LTA for 2 or 6 hours to stimulate TLR signaling. After 6 h, cells were washed with PBS and harvested for RNA extraction.

value: Macrophage

value: LTA 100 ng/mL, 2 hrs


title: primary WT macrophages, LTA-treated, 2 hrs, rep2

description:
Library name: WT+LTA_2h_Rep2
column name in raw_counts.txt: WT+LTA_2h_Rep2

value: primary bone marrow-derived macrophages, BMDM


title: primary WT macrophages, LPS-treated, 2 hrs, rep3

description:
Library name: WT+LPS_2h_Rep3
column name in raw_counts.txt: WT+LPS_2h_Rep3

value: WT

value: LPS 10 ng/mL, 2 hrs


title: primary WT macrophages, LTA-treated, 2 hrs, rep1

description:
Library name: WT+LTA_2h_Rep1
column name in raw_counts.txt: WT+LTA_2h_Rep1


title: primary WT macrophages, rep2

description:
Library name: WT_UT_Rep2
column name in raw_counts.txt: WT_UT_Rep2

value: untreated


title: primary WT macrophages, LPS-treated, 2 hrs, rep1

description:
Library name: WT+LPS_2h_Rep1
column name in raw_counts.txt: WT+LPS_2h_Rep1


title: primary WT macrophages, LPS-treated, 2 hrs, rep2

description:
Library name: WT+LPS_2h_Rep2
column name in raw_counts.txt: WT+LPS_2h_Rep2


title: primary WT macrophages, rep3

description:
Library name: WT_UT_Rep3
column name in raw_counts.txt: WT_UT_Rep3


title: primary WT macrophages, rep1

description:
Library name: WT_UT_Rep1
column name in raw_counts.txt: WT_UT_Rep1


title: primary WT macrophages, LPS-treated, 6 hrs, rep3

description:
Library name: WT_LPS_6h_Rep3
column name in raw_counts.txt: WT_LPS_6h_Rep3

value: LPS 10 ng/mL, 6 hrs


title: primary WT macrophages, LTA-treated, 6 hrs, rep3

description:
Library name: WT_LTA_6h_Rep3
column name in raw_counts.txt: WT_LTA_6h_Rep3

value: LTA 100 ng/mL, 6 hrs


title: primary WT macrophages, LPS-treated, 6 hrs, rep2

description:
Library name: WT_LPS_6h_Rep2
column name in raw_counts.txt: WT_LPS_6h_Rep2


title: primary WT macrophages, LTA-treated, 6 hrs, rep1

description:
Library name: WT_LTA_6h_Rep1
column name in raw_counts.txt: WT_LTA_6h_Rep1


title: primary WT macrophages, LTA-treated, 6 hrs, rep2

description:
Library name: WT_LTA_6h_Rep2
column name in raw_counts.txt: WT_LTA_6h_Rep2


title: primary TRAM (Ticam2) KO macrophages, LTA-treated, 2 hrs, rep3

description:
Library name: Ticam2KO+LTA_2h_Rep3
column name in raw_counts.txt: Ticam2KO+LTA_2h_Rep3


title: primary WT macrophages, LPS-treated, 6 hrs, rep1

description:
Library name: WT_LPS_6h_Rep1
column name in raw_counts.txt: WT_LPS_6h_Rep1


title: primary TRAM (Ticam2) KO macrophages, LTA-treated, 2 hrs, rep2

description:
Library name: Ticam2KO+LTA_2h_Rep2
column name in raw_counts.txt: Ticam2KO+LTA_2h_Rep2


title: primary TRAM (Ticam2) KO macrophages, LPS-treated, 2 hrs, rep3

description:
Library name: Ticam2KO+LPS_2h_Rep3
column name in raw_counts.txt: Ticam2KO+LPS_2h_Rep3


title: primary TRAM (Ticam2) KO macrophages, LTA-treated, 2 hrs, rep1

description:
Library name: Ticam2KO+LTA_2h_Rep1
column name in raw_counts.txt: Ticam2KO+LTA_2h_Rep1


title: primary TRAM (Ticam2) KO macrophages, LPS-treated, 2 hrs, rep1

description:
Library name: Ticam2KO+LPS_2h_Rep1
column name in raw_counts.txt: Ticam2KO+LPS_2h_Rep1


title: primary TRAM (Ticam2) KO macrophages, rep2

description:
Library name: Ticam2KO_UT_Rep2
column name in raw_counts.txt: Ticam2KO_UT_Rep2


title: primary TRAM (Ticam2) KO macrophages, LPS-treated, 2 hrs, rep2

description:
Library name: Ticam2KO+LPS_2h_Rep2
column name in raw_counts.txt: Ticam2KO+LPS_2h_Rep2


title: primary TRAM (Ticam2) KO macrophages, LTA-treated, 6 hrs, rep3

description:
Library name: Ticam2KO_LTA_6h_Rep3
column name in raw_counts.txt: Ticam2KO_LTA_6h_Rep3


title: primary TRAM (Ticam2) KO macrophages, rep3

description:
Library name: Ticam2KO_UT_Rep3
column name in raw_counts.txt: Ticam2KO_UT_Rep3


title: primary TRAM (Ticam2) KO macrophages, LTA-treated, 6 hrs, rep2

description:
Library name: Ticam2KO_LTA_6h_Rep2
column name in raw_counts.txt: Ticam2KO_LTA_6h_Rep2


title: primary TRAM (Ticam2) KO macrophages, LTA-treated, 6 hrs, rep1

description:
Library name: Ticam2KO_LTA_6h_Rep1
column name in raw_counts.txt: Ticam2KO_LTA_6h_Rep1


title: primary TRAM (Ticam2) KO macrophages, LPS-treated, 6 hrs, rep3

description:
Library name: Ticam2KO_LPS_6h_Rep3
column name in raw_counts.txt: Ticam2KO_LPS_6h_Rep3


title: primary TRAM (Ticam2) KO macrophages, rep1

description:
Library name: Ticam2KO_UT_Rep1
column name in raw_counts.txt: Ticam2KO_UT_Rep1


title: 13893-JF-3

description: Library name: 13893-JF-3

value: Skin

value: Whole tissue


title: primary TRAM (Ticam2) KO macrophages, LPS-treated, 6 hrs, rep2

description:
Library name: Ticam2KO_LPS_6h_Rep2
column name in raw_counts.txt: Ticam2KO_LPS_6h_Rep2


title: primary TRAM (Ticam2) KO macrophages, LPS-treated, 6 hrs, rep1

description:
Library name: Ticam2KO_LPS_6h_Rep1
column name in raw_counts.txt: Ticam2KO_LPS_6h_Rep1


title: 13894-JF-5

description: Library name: 13894-JF-5

value: IMQ


title: iBMDM, untreated control, unsorted pool, rep3

description:
Library name: untreated3
column name in raw_counts.txt: untreated3

data_processing:
Data analysis was performed using Galaxy Server.
Adapter trimming was conducted using Cutadapt (Galaxy version 3.7), applying a minimum read length of 20 bp and Phred quality score >20.
Reads were filtered using fastp (Galaxy Version 1.1.0) with poly-G trimming.
Trimmed paired-end reads were aligned to the mouse reference genome (GRCm38 [mm10]) using HISAT2 (Galaxy Version 2.2.2) in unstranded paired-end mode (mapping rates exceeding 90%).
Gene-level expression quantification was performed using featureCounts (Galaxy Version 2.1.1) with paired-end fragment counting against the reference genome.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains GeneIDs and raw counts for each sample

source_name: iBMDM MyD88-AGF

growth_protocol: iBMDMs were cultured in DMEM supplemented with glutamine, sodium pyruvate, penicillin/streptomycin (P/S) and 10% FBS (cDMEM), at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted following the manufacturer’s instructions using Trizol LS. gDNA was removed using TurboDNAse and RNA re-extracted using phenol:chloroform. RNA quantity and quality was assessed by spectrophotometry and confirmed by Fragment Analysis showing RIN values >7.1 for all samples (performed by Genewiz)
Library preparation, HTS, demultiplexing and initial QC were performed by Genewiz.

treatment_protocol: Cells were stimulated with 10 ng/mL LPS to induce myddosome formation or left untreated. After 6 h, cells were washed with PBS and prepared for sorting. All subsequent steps were carried out at 4°C to arrest further transcriptional changes. First, LPS-stimulated cells were sorted into responder and bystander populations based on SSChi and SSClo bins and 1×10^6 cells for each were collected into 5 mL flow cytometry tubes containing 0.5 mL TRIzol™ LS. Subsequently, LPS-treated cells and untreated control cells were passed through the flow cytometer without any gating to obtain the pooled samples for comparison. 1×10^6 cells for each sample/replicate were collected into 5 mL flow cytometry tubes containing 0.5 mL TRIzol™ LS.

value: iBMDM MyD88-AGF

value: MyD88-AGF WT


title: iBMDM, untreated control, unsorted pool, rep2

description:
Library name: untreated2
column name in raw_counts.txt: untreated2


title: iBMDM, untreated control, unsorted pool, rep4

description:
Library name: untreated4
column name in raw_counts.txt: untreated4


title: iBMDM, untreated control, unsorted pool, rep1

description:
Library name: untreated1
column name in raw_counts.txt: untreated1


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep3

description:
Library name: responders3
column name in raw_counts.txt: responders3


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep2

description:
Library name: responders2
column name in raw_counts.txt: responders2


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep4

description:
Library name: responders4
column name in raw_counts.txt: responders4


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep1

description:
Library name: responders1
column name in raw_counts.txt: responders1


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep2

description:
Library name: bystanders2
column name in raw_counts.txt: bystanders2


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep4

description:
Library name: bystanders4
column name in raw_counts.txt: bystanders4


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep1

description:
Library name: bystanders1
column name in raw_counts.txt: bystanders1


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep4

description:
Library name: LPS-pool4
column name in raw_counts.txt: LPS-pool4


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep3

description:
Library name: bystanders3
column name in raw_counts.txt: bystanders3


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep3

description:
Library name: LPS-pool3
column name in raw_counts.txt: LPS-pool3


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep2

description:
Library name: LPS-pool2
column name in raw_counts.txt: LPS-pool2


title: iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep1

description:
Library name: LPS-pool1
column name in raw_counts.txt: LPS-pool1


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib8

city: Heidelberg

first: Oliver

middle: Till

last: Fackler

address: Im Neuenheimer Feld 344

department: CIID

country: Germany

institute: Universityhospital Heidelberg

description:
Library name: combined_sublib8_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding

data_processing:
sublibraries were sequenced on two sequencing lanes, respectively, and fastq files were concatenated per sublibrary per R1/R2. Concatenated files were uploaded to Trailmaker™ pipeline module (https://app.trailmaker.parsebiosciences.com/; pipeline v1.4.1, Parse Biosciences) provided by Parse Biosciences and processed with inbuilt tools and workflows. Briefly, unfiltered count matrices were uploaded and cells were filtered for a minimum number of transcripts per cell on a per sample basis (min. threshold range 123 to 765). At this step, the set of iDC co-cultures with Ctrl or Nef T cells at 4h (with and without antigen, well IDs A2, A3, A7 and A8) were filtered out since one sample of this set had insufficient cell counts that prevented further analysis. This was due to a technical problem rather than biological variation. Next, a mitochondrial content filter was applied to remove dead or dying cells from further analysis, excluding barcodes with high mitochondrial content (max. 4.25-16.16% cut-off). This was followed by exclusion of outliers that deviated from a spline regression model between number of genes vs number of transcripts (p-values between 0.000133 and 0.001). Lastly, cells with a high probability of being a doublet were filtered out by applying the scDblFinder method (threshold range: 0.38692 to 0.76466). Data normalization (LogNormalize), principal-component analysis (PCA, based on 2000 highly-variable genes, 26 PCs that explain 90.01% of variation) and data integration were performed using Harmony (Seurat analysis tool) on high quality cells.
Fastq files for submission were generated by splitting original fastq files, thereby excluding data (well ID C1-12 and D1-12) unrelated to this project, on a per sample basis based on well-ID. This was achieved using a python code provided by Parse Biosciences for this purpose.
Inbuilt workflow in the Parse biosciences Trailmaker™ module recreated samples from the different sublibraries based on Round 1 well-coordinates according to following annotation: A1 (Ctrl T only_4h), A2 (Ctrl T + iDC 0 nM_4h), A3 (Ctrl T + iDC 100 nM_4h), A4 (Ctrl T + mDC 0 nM_4h), A5 (Ctrl T + mDC 100 nM_4h), A6 (Nef T only_4h), A7 (Nef T + iDC 0 nM_4h), A8 (Nef T + iDC 100 nM_4h), A9 (Nef T + mDC 0 nM_4h), A10 (Nef T + mDC 100 nM_4h), A11 (iDC 100 nM only_4h), A12 (mDC 100 nM only_4h), B1 (Ctrl T only_24h), B2 (Ctrl T + iDC 0 nM_24h), B3 (Ctrl T + iDC 100 nM_24h), B4 (Ctrl T + mDC 0 nM_24h), B5 (Ctrl T + mDC 100 nM_24h), B6 (Nef T only_24h), B7 (Nef T + iDC 0 nM_24h), B8 (Nef T + iDC 100 nM_24h), B9 (Nef T + mDC 0 nM_24h), B10 (Nef T + mDC 100 nM_24h), B11 (iDC 100 nM_24h), B12 (mDC 100 nM_24h)
Assembly: GRCm39
Supplementary files format and content: RDS file containing Seurat objects

source_name: bone-marrow derived Dendritic Cells

growth_protocol: co-cultures were maintained in RPMI 1640, 10%FBS, 1%Penicillin/Streptomycin, 1%non-essential amino acids, 1%sodium pyruvate, 50 µM beta-Mercaptoethanol, 10 mM HEPES

extract_protocol:
co-cultures were pooled per condition and purified over OptiPrep density cushion by centrifugation at 600xg for 15 min. to obtain highly viable cell populations. Cells were counted and viability was assessed using Trypan blue staining, visual inspection by transmitted light microscopy and analysis of zombie violet staining by flow cytometry (viabilities of over 95%). Per condition, 1E06 cells were prepared for fixation and processed for storage using the Evercode™ Cell Fixation v3 kit from Parse Biosciences according to the manufacturer’s instructions, filtering the cells twice over 40 µm cell strainers. Fixed and permeabilized cells were stored in aliquots at -80°C for approximately one and a half months and thawed for downstream processing with Evercode™ WT chemistry version 3 kit
samples were processed with Evercode™ WT chemistry version 3 kit according to the manufacturer’s instructions and split into 8 sublibraries. In short, samples were loaded into 24 wells (A1-A12 and B1-B12) of a barcoding plate in which a sample/well-specific barcode was added during reverse transcription using oligo-dT and random hexamer primers. Samples were then sequentially pooled and split three times in total, at each step adding another well-specific barcode (and Illumina TruSeq R2 sequencing adapter during the 3rd barcoding round). Pooled samples were split across 8 sublibraries, lysed and library prep was performed according to the manufacturer's instructions. Briefly, cDNA was captured with Streptavidin beads, amplified, fragmented, end repaired and A-tailed using SPRI beads for size selection of PCR fragments. Lastly, Illumina Truseq R1 adaptors were ligated to 5' ends, followed by a final round of barcoding with UDIs. The in total four barcoding steps statistically generate single cell-level diversity/resolution.

treatment_protocol: co-culture of OT-II.2 CD4 T cells and immature or matured (+LPS) BMDCs with or without pulsing of OT-II.2 DCs with OVA323-339

value: CD4 T lymphocytes (memory cells)

value: bone-marrow derived Dendritic Cells

tag: mouse strain

value: male

value: 8 weeks

value: co-culture with and without antigen OVA323-339


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib7

description:
Library name: combined_sublib7_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib6

description:
Library name: combined_sublib6_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib5

description:
Library name: combined_sublib5_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib1

description:
Library name: combined_sublib1_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding


title: A.HHSR.76

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

description: Library name: 107081-001-261

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html, DESeq2-method.32).

source_name: aorta

growth_protocol: Animals were bred and housed at an AAALAC-accredited SPF animal facility (TNO Metabolic Health Research, Leiden, the Netherlands). The Ldlr−/−.Leiden mouse model was chosen because these mice develop characteristics of the metabolic syndrome including obesity, insulin resistance, hyperlipidemia, MASLD with fibrosis and atherosclerosis when fed a high fat diet. Male mice were selected due to their higher susceptibility to obesity and inflammation compared to females. Mice (aged 14-19 weeks) were group-housed in a temperature-controlled room at 50-60% humidity and with a 12h light-dark cycle. Mice had access to food and water ad libitum. Body weight, food intake per cage and clinical signs were monitored regularly. One group of n=8 mice served as healthy control group and received the grain-based chow diet (Ssniff Spezialdiäten, Soest, Germany) and a total of 75 mice received an HFD containing 45 kCal% fat from lard, 35 kCal% carbohydrates and 20 kCal% casein (Research Diets, New Brunswick, NJ, USA) to induce MASH and atherosclerosis.

extract_protocol:
At the study endpoint at t=14 weeks (or at t=0 for the HFD reference group), mice were sacrificed by gradual fill CO2 asphyxiation. Liver tissue, hearts with aortic roots, ascending aortas, perigonadal (pgWAT) and subcutaneous white adipose tissue (scWAT) and brown adipose tissue (BAT) were collected. Left gastrocnemius and soleus muscles were isolated jointly and right gastrocnemius and quadriceps were isolated separately. Tissues were snap-frozen in liquid nitrogen for biochemical/transcriptome analyses. For transcriptomics analysis, snap-frozen tissue of the right liver lobe, right quadriceps femoris, perigonadal WAT and ascending aorta were used. RNA was extracted using the RNA-Stat60 total RNA isolation kit (Amsbio) for liver, muscle and aorta and using the Ambion RNAqueous total RNA isolation kit (ThermoFisher Scientific, Waltman, MA, USA) for WAT.
mRNA was isolated from total RNA with oligo-dT magnetic beads. Next, cDNA was synthesized and subsequently ligated with sequencing adapters and amplified by PCR and was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 v1.5 sequencer (Illumina, San Diego) with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-30 million read counts per sample. Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: At t=0, after a 20-week run-in period on the HFD, mice were matched based on body weight, age and glucose, cholesterol and triglyceride levels into equal groups of n=15 mice each. Group sizes were calculated by power analysis (GPower), using a minimal effect size of 30%, two-sided t-test with 95% confidence interval, 90% power and α of 0.05. One group served as HFD reference group and was sacrificed at t=0 to indicate the histological severity (in particular MASH and atherosclerosis) at the start of the intervention period and determine whether the interventions affected parameters beyond levels at the start of the intervention period or merely blocked further progression. Another group on HFD received daily subcutaneous saline injections (HFD vehicle control) for 14 weeks. The third group on HFD received daily subcutaneous semaglutide injections (100 µL; Ozempic®, Novo Nordisk, Bagsværd, Denmark). To acclimatize to the final semaglutide dosage (0.12 mg/kg body weight/day), the dose was escalated over the course of five days at a rate of 0.024 (20%) 0.048 (40%) 0.072 (60%), 0.096 (80%) mg/kg body weight/day until the final dose was reached that was maintained for 14 weeks. Doses were adjusted based on weekly individual body weights. For the fourth group of mice on HFD, a running wheel (Mouse Igloo+Fast Trac, Datesand, Bredbury, UK) was added into the cage, to which the mice had unlimited access and which has been shown to increase voluntary movement in these mice12. The last group on HFD received both subcutaneous semaglutide injections and a running wheel in the cage.

value: aorta

value: HHSR

tag: treatmdescript

tag: animalnr


title: A.HHSR.82

description: Library name: 107081-001-267


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib3

description:
Library name: combined_sublib3_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding

tag: cell type


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib4

description:
Library name: combined_sublib4_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding


title: A.HHSR.70

description: Library name: 107081-001-256

tag: tissue


title: A.HHSR.81

description: Library name: 107081-001-266


title: OT-II.2 CD4 T cell-BMDC co-culture_sublib2

description:
Library name: combined_sublib2_group_Fackler
Parse Evercode WT kit, split-pool combinatorial barcoding


title: A.HHSR.74

description: Library name: 107081-001-259


title: A.HHSR.79

description: Library name: 107081-001-264


title: A.HHSR.77

description: Library name: 107081-001-262


title: A.HHR.68

description: Library name: 107081-001-254

value: HHR


title: A.HHR.66

description: Library name: 107081-001-252


title: A.HHR.64

description: Library name: 107081-001-250


title: A.HHR.63

description: Library name: 107081-001-249


title: A.HHR.56

description: Library name: 107081-001-242


title: A.HHR.54

description: Library name: 107081-001-240


title: A.HHS.49

description: Library name: 107081-001-235

value: HHS


title: A.HHR.60

description: Library name: 107081-001-246


title: A.HHS.47

description: Library name: 107081-001-233


title: A.HHS.41

description: Library name: 107081-001-227


title: A.HHR.57

description: Library name: 107081-001-243


title: A.HHS.39

description: Library name: 107081-001-225


title: A.HHS.48

description: Library name: 107081-001-234


title: A.HHS.52

description: Library name: 107081-001-238


title: A.HHR.55

description: Library name: 107081-001-241


title: A.HHS.45

description: Library name: 107081-001-231


title: A.HH.37

description: Library name: 107081-001-223

value: HH


title: A.HHS.43

description: Library name: 107081-001-229


title: A.HH.35

description: Library name: 107081-001-221


title: A.HH.27

description: Library name: 107081-001-213

source_name: aorta (excess fat removed)

value: aorta (excess fat removed)


title: A.HH.33

description: Library name: 107081-001-219


title: A.CC.3

description: Library name: 107081-001-204

value: CC


title: W.HHSR.74

description: Library name: 107081-001-192

source_name: perigonal WAT = pgWAT

value: perigonal WAT = pgWAT


title: W.HHSR.80

description: Library name: 107081-001-198


title: W.HHSR.73

description: Library name: 107081-001-191


title: A.CC.1

description: Library name: 107081-001-202


title: A.HH.25

description: Library name: 107081-001-211


title: A.HH.28

description: Library name: 107081-001-214


title: W.HHSR.83

description: Library name: 107081-001-201


title: W.HHSR.82

description: Library name: 107081-001-200


title: A.CC.7

description: Library name: 107081-001-208


title: W.HHSR.81

description: Library name: 107081-001-199


title: W.HHSR.71

description: Library name: 107081-001-190


title: W.HHSR.70

description: Library name: 107081-001-189


title: W.HHR.68

description: Library name: 107081-001-187


title: W.HHR.65

description: Library name: 107081-001-184


title: W.HHR.64

description: Library name: 107081-001-183


title: W.HHR.63

description: Library name: 107081-001-182


title: W.HHR.62

description: Library name: 107081-001-181


title: W.HHR.60

description: Library name: 107081-001-179


title: W.HHR.59

description: Library name: 107081-001-178


title: W.HHR.58

description: Library name: 107081-001-177


title: W.HHR.56

description: Library name: 107081-001-175


title: W.HHS.51

description: Library name: 107081-001-170


title: W.HHR.57

description: Library name: 107081-001-176


title: W.HHS.50

description: Library name: 107081-001-169


title: W.HHS.44

description: Library name: 107081-001-163


title: W.HHS.43

description: Library name: 107081-001-162


title: W.HHS.41

description: Library name: 107081-001-160


title: W.HHS.40

description: Library name: 107081-001-159


title: W.HHS.39

description: Library name: 107081-001-158


title: W.HH.37

description: Library name: 107081-001-156


title: W.HH.36

description: Library name: 107081-001-155


title: W.HH.34

description: Library name: 107081-001-153


title: W.HH.33

description: Library name: 107081-001-152


title: W.HH.32

description: Library name: 107081-001-151


title: W.HH.31

description: Library name: 107081-001-150


title: W.HH.30

description: Library name: 107081-001-149


title: W.HH.28

description: Library name: 107081-001-147


title: W.HH.27

description: Library name: 107081-001-146


title: W.HH.24

description: Library name: 107081-001-143


title: W.CC.8

description: Library name: 107081-001-142


title: W.CC.7

description: Library name: 107081-001-141


title: W.CC.6

description: Library name: 107081-001-140


title: W.CC.5

description: Library name: 107081-001-139


title: W.CC.4

description: Library name: 107081-001-138


title: W.CC.1

description: Library name: 107081-001-135


title: M.HHSR.83

description: Library name: 107081-001-134

source_name: Muscle, quadriceps right

value: Muscle, quadriceps right


title: M.HHSR.82

description: Library name: 107081-001-133


title: M.HHSR.81

description: Library name: 107081-001-132


title: W.CC.2

description: Library name: 107081-001-136


title: M.HHSR.80

description: Library name: 107081-001-131


title: M.HHSR.78

description: Library name: 107081-001-129


title: M.HHSR.79

description: Library name: 107081-001-130


title: M.HHSR.77

description: Library name: 107081-001-128


title: M.HHSR.76

description: Library name: 107081-001-127


title: M.HHSR.75

description: Library name: 107081-001-126


title: M.HHSR.74

description: Library name: 107081-001-125


title: M.HHSR.73

description: Library name: 107081-001-124


title: M.HHSR.71

description: Library name: 107081-001-123


title: M.HHSR.69

description: Library name: 107081-001-121


title: M.HHR.68

description: Library name: 107081-001-120


title: M.HHSR.70

description: Library name: 107081-001-122


title: M.HHR.67

description: Library name: 107081-001-119


title: M.HHR.66

description: Library name: 107081-001-118


title: M.HHR.64

description: Library name: 107081-001-116


title: M.HHR.65

description: Library name: 107081-001-117


title: M.HHR.63

description: Library name: 107081-001-115


title: M.HHR.62

description: Library name: 107081-001-114


title: M.HHR.61

description: Library name: 107081-001-113


title: M.HHR.60

description: Library name: 107081-001-112


title: M.HHR.59

description: Library name: 107081-001-111


title: M.HHR.58

description: Library name: 107081-001-110


title: M.HHR.57

description: Library name: 107081-001-109


title: M.HHR.55

description: Library name: 107081-001-107


title: M.HHS.53

description: Library name: 107081-001-105


title: M.HHR.56

description: Library name: 107081-001-108


title: M.HHS.52

description: Library name: 107081-001-104


title: M.HHR.54

description: Library name: 107081-001-106


title: M.HHS.50

description: Library name: 107081-001-102


title: M.HHS.51

description: Library name: 107081-001-103


title: M.HHS.49

description: Library name: 107081-001-101


title: M.HHS.48

description: Library name: 107081-001-100


title: M.HHS.47

description: Library name: 107081-001-099


title: M.HHS.46

description: Library name: 107081-001-098


title: M.HHS.45

description: Library name: 107081-001-097


title: M.HHS.44

description: Library name: 107081-001-096


title: M.HHS.42

description: Library name: 107081-001-094


title: M.HHS.43

description: Library name: 107081-001-095


title: M.HHS.41

description: Library name: 107081-001-093


title: M.HH.38

description: Library name: 107081-001-090


title: M.HHS.39

description: Library name: 107081-001-091


title: M.HHS.40

description: Library name: 107081-001-092


title: M.HH.36

description: Library name: 107081-001-088


title: M.HH.37

description: Library name: 107081-001-089


title: M.HH.35

description: Library name: 107081-001-087


title: M.HH.33

description: Library name: 107081-001-085


title: M.HH.34

description: Library name: 107081-001-086


title: M.HH.32

description: Library name: 107081-001-084


title: M.HH.31

description: Library name: 107081-001-083


title: M.HH.30

description: Library name: 107081-001-082


title: M.HH.29

description: Library name: 107081-001-081


title: M.HH.28

description: Library name: 107081-001-080


title: M.HH.27

description: Library name: 107081-001-079


title: 16S In-vitro transcribed

city: El Paso

first: Eda

last: Kocui

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

description:
Library name: Sanple 12
In-vitro transcribed 16S; We do not have a processed data file for 16S IVT since it was used as control for all 30S ribosomal particles, which contain the 16S ribosomal RNA. In other words, processes data for this sample is incorporated into all processed data files for samples where 16S ribosomal RNA is present.

library_source: other

data_processing:
Basecalling was done using the Guppy, a software provided by Oxford Nanopore Technologies, version 6.4.2+97a7f06, from Oxford Nanopore Technologies Community.
Post-basecalling, FASTQ files, were merged and aligned using Minmap2 to rrlB gene or rrsB gene. A dictionary for reference genes was built using the Picard tool. This reference dictionary was required for alignment optimization by EpiNano, the program we employed to determine the RNA modifications. Subsequently, the BAM file was indexed using SAMtools. The indexed BAM files were used by EpiNano (version 1.2.2) to obtain Z scores and the sum of errors (SE). We combined the Z scores and the sum of errors to detect modifications and determine their extent in various ribosomal particles.
To determine the extents of correctly processed and unprocessed 5S and 23S rRNA molecules at their 3’ end, first we needed to extract the read depths for 3’end positions of 5S and 23S rRNA. The read depths were extracted by running SAMtools mpileup function.
Assembly: Escherichia coli BL21(DE3): B21_04498 (rrlB) ; Escherichia coli BL21(DE3): B21_04496 (rrsB) ; Escherichia coli BL21(DE3): ECD_r00019 (rrfB). Additionally, the gene sequences for 5S and 23S were added 15 and 20 nucleotides in the 3' ends, respectively, to study their processing composition. The sequence were part of the non-processed rRNA sequences of the E.coli genome.
Supplementary files format and content: Processed files are in comma separated(.csv) and tab(.tsv) separated formats. Files are output from Epinano and SAMTools mpileup for the prediction of RNA modifications and analysis of 3' ends, respectively.

molecule: other

organism: Escherichia coli

source_name: In-vitro transcribed

growth_protocol: The cells were grown at 37ºC in 200 mL of media containing 10 g/L sodium chloride, 10g/L tryptone, 1g/L yeast extract, 100μg/mL carbenicillin, and 34μg/mL chloramphenicol. When the cell reached an optical density at 600 nm of about 0.3, the cell growth was arrested by adding 200 ml of ice.

extract_protocol:
The ribosomal particles were isoalate using a  20-40% gradients were made in a buffer consisting of 20mM HEPES KOH pH 7.5, 150mM NH4Cl, 1mM MgCl2 and 4mM BME. Gradient peaks were then collected for particles of the same sedimentation coefficient and RNA was purified using RNeasy kit. Additionally, 23S rRNA was expressed from pCW1 plasmid and The DNA coding sequence of 16S rRNA was inserted into the KpnI and XbaI restriction enzyme sites of pUC19.
RNAs were poly-adenylated using the NEB Poly(A) polymerase protocol. The library preparations were performed following the directions of Oxford Nanopore Technologies Direct RNA Sequencing Kit, SQK-RNA002

value: In-vitro transcribed


title: M.HH.26

description: Library name: 107081-001-078


title: M.HH.25

description: Library name: 107081-001-077


title: M.HH.24

description: Library name: 107081-001-076


title: 23S In-vitro transcribed

description:
Library name: Sample 11
In-vitro transcribed 23S


title: M.CC.8

description: Library name: 107081-001-075


title: 30S wild-type Replicate 2

description:
Library name: Sample 10
16S rRNA from 30S

source_name: BLR(DE3) Delta dbpA:  Kan, expressing wild-type DbpA pET-3a

value: Bacteria

value: BLR(DE3) Delta dbpA: Kan


title: 30S wild-type Replicate 1

description:
Library name: Sample 9
16S rRNA from 30S

value: BLR(DE3) Delta dbpA: Kan, expressing wild-type DbpA pET-3a


title: M.CC.7

description: Library name: 107081-001-074


title: M.CC.6

description: Library name: 107081-001-073


title: 35S from R331A DbpA-expressing cells Replicate 2

description:
Library name: Sample 8
23S and 5S rRNA from 50S

source_name: BLR(DE3) Delta dbpA:  Kan, expressing R331A DbpA pET-3a


title: M.CC.4

description: Library name: 107081-001-071


title: M.CC.5

description: Library name: 107081-001-072


title: 35S from R331A DbpA-expressing cells Replicate 1

description:
Library name: Sample 7
23S and 5S rRNA from 50S

value: BLR(DE3) Delta dbpA: Kan, expressing R331A DbpA pET-3a


title: M.CC.3

description: Library name: 107081-001-070


title: 45S from R331A DbpA-expressing cells Replicate 2

description:
Library name: Sample 6
23S and 5S rRNA from 50S


title: M.CC.2

description: Library name: 107081-001-069


title: M.CC.1

description: Library name: 107081-001-068


title: L.HHSR.83

description: Library name: 107081-001-067

source_name: Liver, dexter lobe

value: Liver, dexter lobe


title: 50S from R331A DbpA-expressing cells Replicate 2

description:
Library name: Sample 4
23S and 5S rRNA from 50S


title: 45S from R331A DbpA-expressing cells Replicate 1

description:
Library name: Sample 5
23S and 5S rRNA from 50S


title: 50S from R331A DbpA-expressing cells Replicate 1

description:
Library name: Sample 3
23S and 5S rRNA from 50S


title: 50S wild-type Replicate 1

description:
Library name: Sample 1
23S and 5S rRNA from 50S


title: 50S wild-type Replicate 2

description:
Library name: Sample 2
23S and 5S rRNA from 50S


title: L.HHSR.81

description: Library name: 107081-001-065


title: L.HHSR.80

description: Library name: 107081-001-064


title: L.HHSR.82

description: Library name: 107081-001-066


title: L.HHSR.77

description: Library name: 107081-001-061


title: L.HHSR.79

description: Library name: 107081-001-063


title: L.HHSR.78

description: Library name: 107081-001-062


title: B;p38α CD45- (tumor/stroma) population, biological rep 3

type: RNA

city: Barcelona

first: Paula

last: Granado Martínez

state: Barcelona

address: Passeig de la Vall d'Hebron 129

department: eCore Cancer

country: Spain

institute: Vall d'Hebron Research Institute (VHIR)

description: Gene expression data from CD45- (tumor/stroma) population from UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA;p38α-/- melanoma mouse model. CD45- cells from digested fresh mouse tumor samples were negatively selected using the MagniSort Mouse CD45 Positive Selection Kit (Invitrogen) following the manufacturer’s protocol.

hyb_protocol: The hybridization protocol was performed using GeneChipTM Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific)

scan_protocol: Scannig was performed using aGene-Chip scanner 3000 7G

data_processing: RMA

label: Biotin

source_name: tumor/stroma (CD45-) from melanoma mouse tumor, B;p38α

label_protocol: After generating the cDNA using WT PLUS Reagent kit-HT (Thermo Fisher scientific, Waltham, MA, USA) 5,5 ng of cDNA (sense strand) were fragmented and biotin labeled with FlashTag Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific).

growth_protocol: Tumors were generated in Tyr::CreERT2;BrafCA/CA (B) and Tyr::CreERT2;BrafCA/CA;p38αlox/lox (B;p38α) mice by topical administration of 4-hydroxytamoxifen (5 mg/ml in acetone) at postnatal days 2.5 and 3.5 to induce BrafV600E expression (and p38α deletion in the second model). On postnatal day 3.5, mice received a single UVB irradiation dose (6.24 kJ/m²) to promote tumor development. Mice were maintained under standard housing conditions and monitored regularly until tumors reached ethical endpoint size, at which point tumors were excised and processed for RNA extraction.

extract_protocol: For RNA purification Direct-Zol RNA kit (Zymo Research, Irvine, CA, USA) was used. The isolation procedure was performed according to the manufacturer's recommendations. RNA was analyzed with a 2100 Bioanalyzer (Agilent) to confirm amount and integrity of the sample. Only high-quality samples were used for following applications.

treatment_protocol: Prior to RNA extraction, mice received topical 4-hydroxytamoxifen (4-OHTx, 5 mg/ml in acetone) at postnatal days 2.5 and 3.5 to induce BrafV600E expression and p38α deletion in melanocytes, followed by irradiation with a single dose of UVB (6.24 kJ/m²) on postnatal day 3.5. Tumors were collected at endpoint. For separated populations, tumors were mechanically and enzymatically dissociated, and CD45⁺ (immune) and CD45⁻ (tumor/stroma) cell populations were isolated using the MagniSort Mouse CD45 Positive Selection Kit (Invitrogen) prior to RNA extraction. No additional treatments were applied to the animals or samples before processing.

value: tumor/stroma cells


title: L.HHSR.76

description: Library name: 107081-001-060


title: B;p38α CD45- (tumor/stroma) population, biological rep 1


title: L.HHSR.75

description: Library name: 107081-001-059


title: B;p38α CD45- (tumor/stroma) population, biological rep 2


title: B CD45- (tumor/stroma) population, biological rep 3

description: Gene expression data from CD45- (tumor/stroma) population from UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA melanoma mouse model. CD45- cells from digested fresh mouse tumor samples were negatively selected using the MagniSort Mouse CD45 Positive Selection Kit (Invitrogen) following the manufacturer’s protocol.

source_name: tumor/stroma (CD45-) from melanoma mouse tumor, B


title: B CD45- (tumor/stroma) population, biological rep 2


title: B CD45- (tumor/stroma) population, biological rep 1


title: L.HHSR.74

description: Library name: 107081-001-058


title: B;p38α CD45+ (immune) population, biological rep 3

description: Gene expression data from CD45+ (immune) population from UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA;p38α-/- melanoma mouse model. CD45+ cells from digested fresh mouse tumor samples were positively selected using the MagniSort Mouse CD45 Posit

source_name: intra-tumoral immune cells (CD45+) from melanoma mouse tumor, B;p38α

value: intra-tumoral immune cells


title: L.HHSR.73

description: Library name: 107081-001-057


title: L.HHSR.70

description: Library name: 107081-001-055


title: L.HHSR.71

description: Library name: 107081-001-056


title: B;p38α CD45+ (immune) population, biological rep 1

description: Gene expression data from CD45+ (immune) population from UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA;p38α-/- melanoma mouse model. CD45+ cells from digested fresh mouse tumor samples were positively selected using the MagniSort Mouse CD45 Positive Selection Kit (Invitrogen) following the manufacturer’s protocol.


title: B;p38α CD45+ (immune) population, biological rep 2


title: L.HHSR.69

description: Library name: 107081-001-054


title: B CD45+ (immune) population, biological rep 2

description: Gene expression data from CD45+ (immune) population from UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA melanoma mouse model. CD45+ cells from digested fresh mouse tumor samples were positively selected using the MagniSort Mouse CD45 Positive Sele

source_name: intra-tumoral immune cells (CD45+) from melanoma mouse tumor, B


title: B CD45+ (immune) population, biological rep 3


title: L.HHR.67

description: Library name: 107081-001-052


title: B CD45+ (immune) population, biological rep 1

description: Gene expression data from CD45+ (immune) population from UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA melanoma mouse model. CD45+ cells from digested fresh mouse tumor samples were positively selected using the MagniSort Mouse CD45 Positive Selection Kit (Invitrogen) following the manufacturer’s protocol.


title: B;p38α complete tumor, biological rep 3

description: Gene expression data from complete UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA;p38α-/- melanoma mouse model

source_name: mouse melanoma tumor, B;p38α

value: melanoma tumor


title: A.HH.31

description: Library name: 107081-001-217

value: aorta


title: L.HHR.68

description: Library name: 107081-001-053

value: HHR


title: L.HHR.66

description: Library name: 107081-001-051


title: B;p38α complete tumor, biological rep 2


title: L.HHR.65

description: Library name: 107081-001-050


title: L.HHR.63

description: Library name: 107081-001-048


title: B complete tumor, biological rep 5

description: Gene expression data from complete UVB-induced melanoma tumor from Tyr::CreERT2;BrafCA/CA melanoma mouse model

source_name: mouse melanoma tumor, B


title: A.CC.6

description: Library name: 107081-001-207


title: L.HHR.64

description: Library name: 107081-001-049


title: B;p38α complete tumor, biological rep 1


title: L.HHR.61

description: Library name: 107081-001-046


title: L.HHR.60

description: Library name: 107081-001-045


title: B complete tumor, biological rep 3


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B6). gRNA

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
Library name: validation_moi1_5_rep02_b6_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_5_rep02_b6_filtered_feature_bc_matrix.h5

data_processing:
We aligned reads to transcripts and identified cells using the 10x Genomics Cell Ranger Count v9. For the guides, we input the guide FASTQ files as CRISPR Guide Capture libraries and the feature_reference file containing the guide sequences.
Assembly: human hg38
Supplementary files format and content: .h5 files from Cellranger

source_name: WTC11 (human iPSC line)

extract_protocol:
Cells were collected using centrifugation, washed with PBS+BSA and subjected to 10x Genomics 3' scRNA-seq
Libraries were constructed accroding to the protocol detailed in Ray et al 2025 (dx.doi.org/10.17504/protocols.io.3byl4z7drvo5/v1)

value: WTC11 (human iPSC line)

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.5, replicate 2, channel B6


title: B complete tumor, biological rep 4


title: L.HHR.62

description: Library name: 107081-001-047


title: B complete tumor, biological rep 1


title: B complete tumor, biological rep 2


title: L.HHR.59

description: Library name: 107081-001-044


title: L.HHR.58

description: Library name: 107081-001-043


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B6). mRNA

description:
Library name: validation_moi1_5_rep02_b6_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_5_rep02_b6_filtered_feature_bc_matrix.h5


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B5). gRNA

description:
Library name: validation_moi1_5_rep02_b5_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_5_rep02_b5_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.5, replicate 2, channel B5


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B5). mRNA

description:
Library name: validation_moi1_5_rep02_b5_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_5_rep02_b5_filtered_feature_bc_matrix.h5


title: L.HHR.56

description: Library name: 107081-001-041


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B4). gRNA

description:
Library name: validation_moi1_5_rep02_b4_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_5_rep02_b4_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.5, replicate 2, channel B4


title: L.HHR.57

description: Library name: 107081-001-042


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B3). gRNA

description:
Library name: validation_moi1_5_rep02_b3_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_5_rep02_b3_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.5, replicate 2, channel B3


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B4). mRNA

description:
Library name: validation_moi1_5_rep02_b4_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_5_rep02_b4_filtered_feature_bc_matrix.h5


title: L.HHR.54

description: Library name: 107081-001-039


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B3). mRNA

description:
Library name: validation_moi1_5_rep02_b3_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_5_rep02_b3_filtered_feature_bc_matrix.h5


title: L.HHS.52

description: Library name: 107081-001-037

value: HHS


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B2). gRNA

description:
Library name: validation_moi1_5_rep02_b2_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_5_rep02_b2_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.5, replicate 2, channel B2


title: L.HHR.55

description: Library name: 107081-001-040


title: L.HHS.53

description: Library name: 107081-001-038


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B2). mRNA

description:
Library name: validation_moi1_5_rep02_b2_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_5_rep02_b2_filtered_feature_bc_matrix.h5


title: L.HHS.51

description: Library name: 107081-001-036


title: L.HHS.50

description: Library name: 107081-001-035


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B1). gRNA

description:
Library name: validation_moi1_5_rep02_b1_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_5_rep02_b1_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.5, replicate 2, channel B1


title: L.HHS.49

description: Library name: 107081-001-034


title: Validation DC-TAP-seq for 203 genes at MOI 1.5 (replicate 2, channel B1). mRNA

description:
Library name: validation_moi1_5_rep02_b1_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_5_rep02_b1_filtered_feature_bc_matrix.h5


title: L.HHS.47

description: Library name: 107081-001-032


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A6). gRNA

description:
Library name: validation_moi1_1_rep01_a6_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_1_rep01_a6_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A6


title: L.HHS.46

description: Library name: 107081-001-031


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A6). mRNA

description:
Library name: validation_moi1_1_rep01_a6_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_1_rep01_a6_filtered_feature_bc_matrix.h5


title: L.HHS.45

description: Library name: 107081-001-030


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A5). gRNA

description:
Library name: validation_moi1_1_rep01_a5_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_1_rep01_a5_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A5


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A5). mRNA

description:
Library name: validation_moi1_1_rep01_a5_mRNA
3' mRNA (10x Genomics Direct-Capture TAP-seq): read1 contains cell barcode and UMI; read2 contains transcript sequence
validation_moi1_1_rep01_a5_filtered_feature_bc_matrix.h5


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A4). gRNA

description:
Library name: validation_moi1_1_rep01_a4_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_1_rep01_a4_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A4


title: L.HHS.41

description: Library name: 107081-001-026

value: Liver, dexter lobe


title: Validation DC-TAP-seq for 203 genes at MOI 1.1 (replicate 1, channel A3). gRNA

description:
Library name: validation_moi1_1_rep01_a3_gRNA
Guide-derived oligonucleotide (GDO): read1 contains cell barcode and UMI; read2 contains captured gRNA sequence
validation_moi1_1_rep01_a3_filtered_feature_bc_matrix.h5

value: sgOpti-CS 582-guide DC-TAP-seq library (482 targeting 30 candidate elements + 100 non-targeting); MOI 1.1, replicate 1, channel A3


title: L.HHS.44

description: Library name: 107081-001-029