title: YAPon_LMI_Day3_rep2

description: Library name: FM_5110

data_processing:
Raw sequencing reads were aligned using the 10x Genomics Cloud Analysis platform using Cell Ranger Count v8.0.1 (include introns: true).
Outputs from Cell Ranger were then ran through the CellBender remove-background (v. 0.3.1.dev0) to handle ambient RNA.
Aligned sequencing outputs were analyzed using the Seurat package (5.0.1). Hard cut-offs were applied to remove all nuclei with less than 500 RNA counts or Feature Counts and greater than 2% mitochondrial reads.
Doublets were removed using the DoubletFinder package (v.2.0.4).
Samples were integrated using the Harmony package (v.1.2.3) prior to generation of UMAPs (RunUMAP) and clustering (FindNeighbors/FindClusters).
Assembly: mm10
Supplementary files format and content: RDS, Seurat R objects containing either all cells (FullSet) or just cardiomyocytes (Cardiomyocytes)

growth_protocol: The animals were housed with access to food and water ad libitum on a 12-h light/12-h dark cycle at 21 °C and 50–60% humidity.

extract_protocol:
Nuclei were collected using a Chromium Nuclei Isolation Kit (10x Genomics, PN-1000493).
Single Cell 3′ Reagents Kit (10x Genomics, Chromium Next GEM Single Cell 3′ Kit version 3.1 or GEM-X Single Cell 3' Kit v4)

treatment_protocol: AAV9 virus expressing YAPon or saline was administrated to 6 week old adult mice by retro-orbital injection. Two weeks later, animals were injected with DMSO or LMI070. The apex of the ventricle was separated from the heart 3 days later. Nuclei were isolated from the apex tissue we collected for single nucleus RNA sequencing.

value: GEM-X Single Cell 3' Kit v4


title: ChIP-Seq, Input, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep2

status: Public on Sep 30 2025

type: SRA

city: Wien

first: Birgit

last: Strobl

address: Veterinarplatz 1

department: TZG

country: Austria

institute: VetMedUni

description: Library name: BSMJ011_STAT1AA_M_BM_IFNg_LPS_03h00min_ChIP_Input

library_source: genomic

data_processing:
Raw reads were trimmed using trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using STAR (version 2.7.1)
Gene expression was quantified by counting uniquely aligned reads in exons using the function summarizeOverlaps from the GenomicAlignments package (version 1.6.3) in R (version 3.2.3)
Gene annotations were based on the Ensembl GENCODE Basic set (genome build GRCm38 release 93)
Peaks were called using MACS3 setting the slocal to 500, llocal to 5000 and the q-value threshold to 0.05. Peaks were filtered to exclude regions that overlap with ENCODE blacklisted regions.
Assembly: mm10
Supplementary files format and content: Excel table with peak locations, quantifications and annotations

molecule: genomic DNA

organism: Mus musculus

source_name: Bone Marrow

growth_protocol: Bone marrow derived macrophages (BMDM) were differentiated and cultured from bone marrow of 8 to 12-week-old male mice. BMDM were differentiated for 7-9 days on Petri dishes (Greiner Bio-One) in DMEM (Sigma-Aldrich) supplemented with 10% FCS (Gibco/Thermo Fisher Scientific), 15% L929 cell-conditioned medium, 2 mM L-glutamine (Sigma-Aldrich), 100 U/ml penicillin, 100 µg/ml streptomycin, (Sigma-Aldrich) and 50 µM β-mercaptoethanol (Gibco/Thermo Fisher Scientific) at 37°C and 5% CO2 atmosphere.

extract_protocol:
Cells were crosslinked with 1 % formaldehyde (ThermoFisher Scientific, 28908) in PBS for 10 minutes (min) at room temperature (RT) on a shaker. Cells were quenched with 0.125 M glycine for 20 min at RT. Cells were harvested and washed twice in ice-cold PBS containing 1x protease inhibitor tablets (PI, Sigma-Aldrich, S8820-2TAB) and 1 mM PMSF (Sigma-Aldrich, SLBX4318). Cells were centrifuged for 5 min at 300 × g at 4 °C, pellets were snap-frozen in liquid nitrogen and stored at -80 °C overnight. Pellets were thawed on ice for 30 min and resuspended in 1 mL of sonication buffer (10 mM Tris pH 8.0, 0.25% SDS, 2mM EDTA) supplemented with 1 mM PMSF and 1x PI. Samples were sonicated in 15 mL polypropylene tubes (Falcon, 352099) suitable for the Bioruptor® Pico (Diagenode) for 20 minutes. Sonicated samples were centrifuged for 10 min at 14000 × g at 4 °C and the supernatant was diluted in 1.5 mL equilibration buffer (10 mM Tris, 233 mM NaCl, 1.66 % TritonX-100, 0.166 % DOX, 1 mM EDTA, 1 mM PMSF, PI). 20% and 10% of total chromatin were used for each immunoprecipitation (IP) and input control, respectively. 1 mg of anti-H3K27ac (Diagenode, C15410196) or 2 mg of anti-H3K4me1 (Abcam, 8895) antibody was added to the sonicated chromatin aliquots. All samples were incubated on a rotator overnight at 4°C. Magnetic beads (ThermoFisher Scientific, 10004D) were washed twice in RIPA-LS buffer (10 mM Tris-HCL pH 8.0, 140 mM NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 0.1% sodium deoxycholate, 1% triton X-100) containing 0.1% BSA. The beads were blocked overnight in RIPA-LS buffer containing 0.1% BSA at 4°C. Input control samples were reversed crosslinked overnight at 65°C. The next day 10 μl of the magnetic beads were added and samples were incubated 3 to 4 hours at 4°C (on a rotator). The beads were washed once with RIPA-LS buffer, RIPA-HS buffer (10 mM Tris-HCL pH 8.0, 500 mM NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 0.1% sodium deoxycholate, 1% triton x-100), RIPA- LiCl buffer (10 mM Tris-HCL pH 8.0, 1mM EDTA pH 8.0, 0.5% sodium deoxycholate, 0.5 % NP-40, 250 mM LiCl) and TE buffer (10 mM Tris-HCL pH 8, 1 mM EDTA). The beads were gently resuspended in a 25 mL tagmentation reaction mix. The tagmentation reaction mix contained 5x tagmentation buffer (50 mM Tris pH 8, 0.25% SDS, 2 mM EDTA), 19 mL nuclease-free water and 1x tagment DNA enzyme (Illumina, 15027865). The reaction mix was incubated for 10 min at 37°C. The beads were washed once with RIPA-LS buffer and 10 mM Tris pH8 and then resuspended in 20 mM EDTA. Samples were heated for 30 min at 50°C and 25 mL NEB Next High fidelity 2x master mix (NEB, M0480S) was preheated for 20s at 98°. 10.5 mL 20 mM MgCl2 was added to the master mix and the mixture was added to the samples. The samples were incubated for 5 min at 72°C and 10 min at 95°C and cooled on ice and 2x forward and barcoded reverse primers were added. Primers used for the ChIPseq analysis are listed in Supplementary Table 6. An enrichment PCR was performed with the following program: 98°C for 30s, 15 cycles (98°C for 10s, 63°C for 30s and 72°C for 30s) and 72°C for 1 min. The supernatant was removed using DynamagTM-96 Side Magnet (ThermoFisher Scientific, 12331D) and stored at -80°C. DNA from the input samples were eluted using Qiagen MinElute Kit (Qiagen, 28006). DNA was quantified using Qubit Fluorometer (ThermoFisher Scientific). To 2 ng of input DNA, 12 mL of the tagmentation reaction mix (1 mL of 5X tagmentation buffer, 1 mL of 1:10 diluted Tagment enzyme and nuclease-free water) was added. The tagmented input DNA was purified with a Qiagen MinElute kit. 2x forward, barcoded reverse primers and 20 mL NEBNext High fidelity 2X master mix were added to the eluted input DNA. An enrichment PCR was performed with the abovementioned program, except the cycle number was 12. The libraries of the samples and input controls were purified and the size was selected by adding 2x AMPureXP beads (Beckman Coulter, A63880). The mixture was resuspended and incubated for 10 min at RT. The supernatant was discarded, and the beads were washed twice with 80% EtOH for 5 seconds and air dried for 5 min on the magnet. The beads were removed from the magnet to elute the DNA, and 50 mL of water was added for 10 min at RT. The beads were placed back on the magnet for 5 min, and the supernatant was removed into a new tube. DNA was measured on the Qubit Fluorometer. For quality check, the fragment size of the DNA was analyzed on Agilent High Sensitivity D1000 TapeStation. 4 nM of samples were pooled according to barcode and DNA fragment size.
Library preparation was conducted on 1 ng of cDNA using the Nextera XT DNA Sample Preparation Kit (Illumina) followed by SPRI (Beckman Coulter) size selection. Sequencing was performed by the Bio-medical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50 bp single end configuration.

treatment_protocol: BMDMs were stimulated with 100 U/mL IFNg (Millipore, IF005) and 5 ng/mL LPS (Sigma, Escherichia coli 055: B5) for the times indicated. 1X106 BMDMs were seeded on a 6-well plate (Falcon, 353224) and stimulated with IFNg for 14 hours. IFNg was removed, cells were washed with PBS and LPS was added for the times indicated. Cells were placed on ice and washed with ice-cold PBS before harvesting for further analysis.

tag: tissue

value: Bone Marrow

tag: time

tag: cell type

value: Macrophage

tag: genotype

value: STAT1alpha KI

tag: treatment

value: IFNg + LPS

tag: batch


title: HPV072-Z142-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

city: Rahway

first: Yuhyun

last: Ji

state: NJ

address: 126 E Lincoln Ave

country: USA

institute: Merck & Co., Inc.

description: Library name: G07_sample08_time06

library_source: transcriptomic

data_processing:
RNA sequencing data was normalized to provide consistent and comparable measures of gene expression (mRNA expression) that can be used for performing expression analysis. Log 10-transformation was applied to fragments per kilobase of transcript per million mapped reads (FPKM) with a smoothing addon, pseudo count, of 0.01 for easier visualization and analysis. This small pseudo count (0.01) was to avoid division by zero, and the value was set small enough not to affect the results. Also, we used log10 to symmetrize up/down regulation. We filtered out transformed FPKM values (log(FPKM + 0.01)+0.01) that are below -1 to remove low-intensity data. Among a total number of 35,398 RNA sequencing data, 22,413 data showing low intensity were removed, and 12,985 data were left. 1,663 NHP genes that do not have human equivalents were ignored, and 11,322 gene data were left. We manually selected 1,184 immune-related genes from the remaining gene data for this study. Representative genes and cytokines related to immune-related pathways, including toll-like receptors (TLRs), cytosolic pattern recognition receptors, and C-type lectin receptors, are selected to show RNA expression patterns induced by different adjuvant types.
Assembly: Gene IDs of remaining RNA sequencing data were converted to the human equivalent using the BioMart-Ensemble database (https://mart.ensembl.org).
Supplementary files format and content: We provide fastq files, raw files from the sequencing machine and FPKM values after the polishing steps that we used for the research.

molecule: total RNA

organism: Macaca mulatta

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were collected to profile mRNA and compare adjuvant effects on immune gene expression. Blood draws occurred at six time points: pre-dose, 1 day after each dose, and 7 days after each dose. Whole blood was preserved in PAXgene Blood RNA tubes, and total RNA was isolated using the PAXgene Blood RNA kit (PreAnalytix) following the manufacturer's instructions. RNA quantity and integrity were evaluated on an Agilent Bioanalyzer using the RNA6000 Nano Lab Chip (Agilent Technologies). For samples collected in PAXgene tubes, cells were pelleted by centrifugation at 10,000 g for 6 minutes, the supernatant was discarded, and pellets were washed in 1 mL of dimethylpyrocarbonate (DMPC)-treated water before a second centrifugation at 10,000 g for 6 minutes. For samples from other media, cells were pelleted at 2,000 g for 30 minutes and the supernatant removed. All cell pellets were disrupted by vortexing in the appropriate lysis buffer for the chosen extraction method.
Total RNA was extracted from samples using standard extraction methods ensuring high RNA integrity. RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA Ribo-Zero kit (Illumina) according to the manufacturer's instructions. This kit depletes ribosomal RNA to enrich for coding and non-coding transcripts, preserving strand specificity. Following RNA extraction and library preparation, the libraries were sequenced on an Illumina platform using a paired-end 50 base pair read format. Sequencing depth and multiplexing were adjusted according to experimental design to ensure sufficient coverage for downstream transcriptomic analyses.

value: Blood

value: Day 7 after boost dose


title: Saline_LMI_Day3_rep1

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

description: Library name: FM_5105

library_source: transcriptomic single cell

molecule: polyA RNA

source_name: Ventricular apex

value: Ventricular apex

tag: virus

value: Saline

tag: drug

tag: day


title: experiment_H001AS8_H17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

city: Torino

first: Elisa

last: Balmas

address: via Nizza 52

department: Department of molecular biotechnology and life sciences

country: Italy

institute: University of Torino

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt

data_processing:
Illumina base calls for iPS2-sci-seq were converted to fastq and demultiplexed with bcl2fastq v2.20.0.422, using i7 and i5 PCR indexes.
count data were obtained from fastq files with the catcheR_scicount function  implemented in our catcheR package https://github.com/alessandro-bertero/catcheR
Reads 1 and 2 were concatenated, adaptor trimmed with TrimGalore 0.6.10, aligned with STAR 2.5.1b to human GRCh38 (GENECODE v21/Ensembl77) gene annotation, and filtered to have a MAPQ score equal of higher than 30 with samtools 1.7. Uniquely mapping reads were extracted, and reads with identical UMI, RT index, and tagmentation site were collapsed as PCR duplicates. RT_primers_conditions.txt file was used to demultiplex the first level of indexing.  Samtools and bedtools 2.27.1 were used to calculate the percentage of ribosomal RNA and to assign reads to genes. Reads were finally assigned to nuclei by further demultiplexing with the RT indexes. Cells with less than 500 UMI were filtered out as noise/low quality. The remaining sparse count matrix was converted to a complete count matrix with the sparsetodense function of Monocle 2.22.
shRNA and cell barcodes have been identified with catcheR_scicatch function implemented in our catcheR package https://github.com/alessandro-bertero/catcheR (this allow to link the cell ID to a cell perturbation)
Assembly: custom reference combining human reference genome (hg19), mouse reference genome (mm10), built by UW genome research (Seattle,WA) and used for Cao J et al. 2017 PMID: 28818938
Supplementary files format and content: sci_RNA_cds_monocle_cell_info.txt is the annotation file post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_counts_norm.txt normalized read count post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_counts_prenorm.txt unnormalized read count post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_processed.rds full post QC and processing single cell dataset file

organism: Homo sapiens

source_name: hPSC derived cardiomyocytes

growth_protocol: hPSC were differentiated into cardiomyocites with RBA media.

extract_protocol:
Nuclear extraction by IGEPAL 0.3% ipotonic buffer. PFA fixation. RNAse inhibitors have been used during all steps to avoid RNA degradation.
2-level indexing sci-RNAseq protocol for the gene expression library and the barcode library. shRNA barcodes have been enriched during RT and PCR indexing by a nested PCR binding the TET repressor.
sci-RNASeq 2 levels of combinatorial indexing

treatment_protocol: hPSC tranfected in pool with iPS-2seq plasmids in AAVS1 locus (multiple perturbations in pool). shRNA expression has been induced throughout differentiation with Tetracycline. hPSC derived cardiomyocytes were cultured for 23 days with tetracycline. Then Harvested at single cell suspension and processed for nuclear extraction.

value: hPSC derived cardiomyocytes

tag: cell line

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: Saline_DMSO_Day3_rep1

description: Library name: FM_5104

value: DMSO


title: HPV072-Z142-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample08_time05

value: Day 1 after boost dose


title: experiment_H001AS8_H16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: YAPon_LMI_Day3_rep1

description: Library name: R5109

value: YAPon

value: Chromium Next GEM Single Cell 3′ Kit version 3.1


title: HPV072-Z142-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample08_time04

value: Day 0 after boost dose


title: experiment_H001AS8_H15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z142-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample08_time03

value: Day 7 after prime dose


title: ChIP-Seq, Input, Macrophage, Wild Type, LPS, 3h, rep1

description: Library name: BSMJ010_WTN_M_BM_LPS_03h00min_ChIP_Input

value: Bone Marrow

value: Wild Type

value: Lipopolysaccharide (LPS)


title: HPV072-Z142-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample08_time01

value: Day 0 after prime dose


title: YAPon_LMI_Day3_rep3

description: Library name: FM_5112

value: GEM-X Single Cell 3' Kit v4


title: experiment_H001AS8_H14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-17R126-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample07_time06

value: Blood

value: Day 7 after boost dose


title: ChIP-Seq, Input, Macrophage, Wild Type, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_WTN_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: Macrophage

value: IFNg + LPS


title: experiment_H001AS8_H18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: ChIP-Seq, Input, Macrophage, Wild Type, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_WTN_M_BM_IFNg_14h00min_ChIP_Input

value: Interferon gamma (IFNg)


title: mESC_random_cyto_2

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description:
Library name: 22017FL-22-01-22_S22
Cytoplasm

data_processing:
nf-core rnaseq v3.9 was used to process data
DESeq2 was used to perform differential expression analysis
Assembly: hg38, mm10
Supplementary files format and content: raw counts
Supplementary files format and content: differential expresion output from DESeq2

extract_protocol:
For P-body-seq, RNA was isolated from P-body and cytoplasmic fractions using the miRNeasy Micro Kit (QIAGEN).
For polyA RNA samples, cDNA libraries were constructed using the V4 ultra + Nextera XT kit for Illumina (Takara Bio). For P-body-seq for total RNA samples, libraries were prepared using Snap seq protocol.
Libraries were sequenced with paired-end 150-bp reads.

value: mESC

value: serum-LIF


title: experiment_H001AS8_H13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: YAPon_DMSO_Day3_rep1

description: Library name: R5108

value: Ventricular apex

value: YAPon

value: DMSO

value: Chromium Next GEM Single Cell 3′ Kit version 3.1


title: ChIP-Seq, Input, Macrophage, Wild Type, Untreated, 14h, rep1

description: Library name: BSMJ010_WTN_M_BM_UT_14h00min_ChIP_Input

value: Bone Marrow

value: Wild Type

value: Untreated


title: experiment_H001AS8_H11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, Input, Macrophage, STAT1KO, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_UT_14h00min_ChIP_Input

value: STAT1 KO


title: mESC_random_cyto_1

description:
Library name: 22017FL-22-01-21_S21
Cytoplasm


title: mESC_random_pbody_2

description:
Library name: 22017FL-22-01-20_S20
Pbody


title: ChIP-Seq, Input, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_IFNg_14h00min_ChIP_Input

value: STAT1alpha KI


title: HPV072-17R126-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample07_time05

value: Blood

value: Day 1 after boost dose


title: HPV072-Z142-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample08_time02

value: Day 1 after prime dose


title: ChIP-Seq, Input, Macrophage, STAT1KO, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_LPS_03h00min_ChIP_Input

value: Macrophage

value: Lipopolysaccharide (LPS)


title: experiment_H001AS8_H10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: mESC_random_pbody_1

description:
Library name: 22017FL-22-01-19_S19
Pbody

value: mESC

value: serum-LIF


title: experiment_H001AS8_H12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: HPV072-17R126-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample07_time04

value: Day 0 after boost dose


title: experiment_H001AS8_H09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, Input, Macrophage, STAT1KO, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: IFNg + LPS


title: HPV072-17R126-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample07_time03

value: Day 7 after prime dose


title: tauopathy KO TCR-seq

city: SAINT LOUIS

first: Hao

last: Hu

state: MO

address: 4370 Duncan Ave

department: Neurology

institute: Washington University School of Medicine

description: 10x genomics

data_processing:
10x Genomics CellRanger software version 7.2 was used for gene counting and vdj contig counting
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Cells were isolated from brains and purely sorted by flow cytometry sorter
Libraries for single-cell gene expression and sequencing were prepared at the McDonnell Genome Institute (MGI) at Washington University.  Specifically, cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.

value: brain

tag: strain

value: leukocytes

value: TE4 Irf8d32


title: ChIP-Seq, Input, Macrophage, STAT1KO, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_IFNg_14h00min_ChIP_Input

value: Bone Marrow

value: STAT1 KO

value: Interferon gamma (IFNg)


title: HPV072-17R126-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample07_time02

value: Blood

value: Day 1 after prime dose


title: ChIP-Seq, Input, Macrophage, STAT1beta KI, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_UT_14h00min_ChIP_Input

value: Macrophage

value: STAT1beta KI

value: Untreated


title: non-tauopathy KO TCR-seq

description: 10x genomics

value: WT Ifr8d332


title: tauopathy Control TCR-seq

description: 10x genomics

value: TE4 Control


title: experiment_H001AS8_H07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: ChIP-Seq, Input, Macrophage, STAT1beta KI, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_LPS_03h00min_ChIP_Input

value: Lipopolysaccharide (LPS)


title: experiment_H001AS8_H08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, Input, Macrophage, STAT1beta KI, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: IFNg + LPS


title: HPV072-17R126-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample07_time01

value: Day 0 after prime dose


title: experiment_H001AS8_H06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt


title: HPV072-17R131-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample06_time06

value: Day 7 after boost dose


title: tauopathy KO scRNA-seq

description: 10x genomics

value: brain

value: leukocytes

value: TE4 Irf8d32


title: experiment_H001AS8_H05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-17R131-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample06_time05

value: Blood

value: Day 1 after boost dose


title: ChIP-Seq, Input, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_IFNg_14h00min_ChIP_Input

value: Bone Marrow

value: Macrophage

value: Interferon gamma (IFNg)


title: tauopathy Control scRNA-seq

description: 10x genomics


title: HPV072-17R131-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample06_time04

value: Day 0 after boost dose


title: ChIP-Seq, Input, Macrophage, STAT1alpha KI, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_UT_14h00min_ChIP_Input

value: STAT1alpha KI

value: Untreated


title: experiment_H001AS8_H04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: non-tauopathy KO scRNA-seq

description: 10x genomics

value: WT Ifr8d332


title: experiment_H001AS8_H03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: HPV072-17R131-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample06_time03

value: Day 7 after prime dose


title: non-tauopathy Control TCR-seq

description: 10x genomics

value: WT Control


title: ChIP-Seq, Input, Macrophage, STAT1alpha KI, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_LPS_03h00min_ChIP_Input

value: Lipopolysaccharide (LPS)


title: HPV072-17R131-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample06_time02

value: Day 1 after prime dose


title: peritoneal macrophages, 30% 4T1 DMSO treated

city: Shanghai

first: Xu

last: Jiang

address: 319 Yueyang St

country: China

institute: Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences

data_processing:
Sequence reads were mapped to the mouse reference genome using HiSat2 (version 2.0.5). Normalization and identification of differentially expressed genes were performed using DESeq2. The resulting P values were adjusted using the and Hochberg approach for controlling the false discovery rate.
Assembly: mm 10
Supplementary files format and content: Microsoft Excel  includes gene counts for each sample

source_name: peritoneal fluid

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen)
Sequencing libraries were generated using the NEBNext Ultra RNA library prep kit for Illumina (NEB), following the manufacturer’s instructions

value: peritoneal fluid

value: macrophage

value: WT

value: 30% 4T1 DMSO treated


title: experiment_H001AS8_H01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, Input, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_IFNg_14h00min_ChIP_Input

value: Bone Marrow

value: Macrophage


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Untreated, 14h, rep2

description: Library name: BSMJ012_WTN_M_BM_UT_14h00_H3K4me1

value: Wild Type


title: experiment_H001AS8_G22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: peritoneal macrophages, 0% 4T1 DMSO treated

value: 0% 4T1 DMSO treated


title: experiment_H001AS8_G23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Fiko, replicate 2, HiC

city: Guangzhou

first: Xiaoling

last: Wang

state: Guangdong

address: No. 195, West Dongfeng Road

institute: Guangzhou Medical University

data_processing:
The raw data was aligned to the mouse mm10 genomes and processed into allValidPairs files using Hic-Pro (v3.0.0). During this process, low-quality, single-and multiple-alignment reads were discarded. Subsequently, reads were assigned to DpnII restriction fragments, well-aligned reads were filtered to construct the Hi-C contact matrices. Validated contact pairs were normalized with KR normalization and saved as .hic files.
Assembly: mm10
Supplementary files format and content: .Hic

source_name: the spleen and lymphoid nodes

extract_protocol:
Treg cells isolated from the spleen and lymphoid nodes
Hi-C sequencing libraries were were used for Hi-C library construction using the EpiTect Hi-C kit (Qiagen, 59971), following the manufacturer’s protocols.

value: the spleen and lymphoid nodes

value: Treg cells from the spleen and lymph nodes

value: CtcfiKO


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_WTN_M_BM_IFNg_LPS_03h00_H3K4me1

value: IFNg + LPS


title: HPV072-17R262-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample05_time05

value: Blood

value: Day 1 after boost dose


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, LPS, 3h, rep3

description: Library name: BSMJ012_WTN_M_BM_LPS_03h00_H3K4me1


title: HPV072-17R262-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample05_time03

value: Day 7 after prime dose


title: Fiko, replicate 1, HiC


title: experiment_H001AS8_G20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: HPV072-17R262-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample05_time04

value: Day 0 after boost dose


title: experiment_H001AS8_G21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_WTN_M_BM_IFNg_14h00_H3K4me1

value: Interferon gamma (IFNg)


title: HPV072-17R262-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample05_time02

value: Day 1 after prime dose


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Untreated, 14h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_UT_14h00_H3K4me1

value: Bone Marrow

value: Untreated


title: Fctr, replicate 2, HiC

value: Control


title: experiment_H001AS8_H02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: non-tauopathy Control scRNA-seq

description: 10x genomics

value: brain

value: leukocytes

value: WT Control


title: peritoneal macrophages, 30% 4T1 CH223191（10 µM）treated

value: peritoneal fluid

value: macrophage

value: WT

value: 30% 4T1 CH223191（10 µM）treated


title: ChIP-Seq, Input, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: Macrophage

value: STAT1alpha KI

value: IFNg + LPS


title: experiment_H001AS8_G19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: HPV072-17R262-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample05_time01

value: Blood

value: Day 0 after prime dose


title: experiment_H001AS8_G24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-17R131-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample06_time01


title: HPV072-17R262-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample05_time06

value: Day 7 after boost dose


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, LPS, 3h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_LPS_03h00_H3K4me1

value: Bone Marrow

value: Wild Type

value: Lipopolysaccharide (LPS)


title: HPV072-17R245-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample04_time06


title: Fctr, replicate 1, HiC

value: the spleen and lymphoid nodes

value: Treg cells from the spleen and lymph nodes

value: Control


title: experiment_H001AS8_G18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: YapON_AAV9XonYAP5SA

data_processing:
Raw sequencing reads were aligned using the 10x Genomics Cloud Analysis platform using Cell Ranger Count v8.0.1 (include introns: true).
Outputs from Cell Ranger were then ran through the CellBender remove-background (v. 0.3.1.dev0) to handle ambient RNA.
Aligned sequencing outputs were analyzed using the Seurat package (5.0.1). Hard cut-offs were applied to remove all nuclei with less than 500 RNA counts or Feature Counts and greater than 2% mitochondrial reads.
Doublets were removed using the DoubletFinder package (v.2.0.4).
Samples were integrated using the Harmony package (v.1.2.3) prior to generation of UMAPs (RunUMAP) and clustering (FindNeighbors/FindClusters).
Assembly: mm10
Supplementary files format and content: data_YAPon_Letter.rds, rds format from R, content is a Seurat_5.0.1 object of the merge Control and YapON sample.

source_name: ventricular apex

extract_protocol:
Nuclei were collected from the entire heart using a Chromium Nuclei Isolation Kit (10x Genomics, PN-1000493).
Single Cell 3′ Reagents Kit (10x Genomics, Chromium Next GEM Single Cell 3′ Kit version 3.1, 1000269)

treatment_protocol: AAV9 virus expressing GFP and Xon-YAP5SA was administrated to P7 mice by intraperitoneal injection. Two weeks later, the apex of the ventricle was separated from the heart. Nuclei were isolated from the apex tissue we collected for single nucleus RNA sequencing.

value: ventricular apex

value: ICR


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_IFNg_LPS_03h00_H3K4me1

value: Macrophage


title: experiment_H001AS8_G17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Control_AAV9GFP


title: peritoneal macrophages, 0% 4T1 CH223191（10 µM）treated

value: peritoneal fluid

value: macrophage

value: WT

value: 0% 4T1 CH223191（10 µM）treated


title: HPV072-17R245-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample04_time05

value: Day 1 after boost dose


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Untreated, 14h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_UT_14h00_H3K4me1

value: Untreated


title: experiment_H001AS8_G15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_IFNg_14h00_H3K4me1

value: Bone Marrow

value: Wild Type

value: Interferon gamma (IFNg)


title: HPV072-17R245-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample04_time03

value: Blood

value: Day 7 after prime dose


title: HPV072-17R245-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample04_time04

value: Day 0 after boost dose


title: experiment_H001AS8_G14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-17R245-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample04_time02

value: Day 1 after prime dose


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_IFNg_LPS_03h00_H3K4me1

value: Macrophage

value: IFNg + LPS


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, LPS, 3h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_LPS_03h00_H3K4me1

value: Lipopolysaccharide (LPS)


title: recombinant inbred line (RIL) JY275

city: Beijing

first: Xin

last: Lu

address: Zhongguancun South Street,Haidian District

institute: Chinese Academy of Agricultural Sciences

data_processing:
To identify SNPs in the RIL population, Burrows-Wheeler Aligner (Li and Durbin 2009) and GATK(McKenna et al. 2010) were used for alignment and SNP identification
The SNPs of the RILs were supported by a minimum of 1 base. ANNOVAR was employed to determine the physical position of each SNP based on the B73 RefGen_V4 sequence.
Assembly: B73
Library strategy: genotyping-by-sequencin(GBS)

organism: Zea mays

source_name: leaf

growth_protocol: Maize plants were planted in the field and hybrids were removed prior to sampling

extract_protocol:
DNA isolation and extraction using the CTAB protocol (Murray and Thompson 1980)
DNA from 275 RILs was processed according to the previously published GBS method (Zhou et al. 2016), in which NlaⅢ (NEB) and EcoRI (NEB) were used for genomic DNA digestion with a TAA site that can be recognized by the restriction enzyme MseⅠ. Universal primers and index primers were employed to purify PCR products using Agencourt AMPure XP (Beckman). Fragments that were 350–400 bp (including adaptors and indexes) were isolated and purified for sequencing

treatment_protocol: Leaf tissues were collected during the tasseling vegetative stage and freeze-dried at −80 °C or genomic DNA isolation

value: leaf


title: HPV072-17R245-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample04_time01

value: Day 0 after prime dose


title: recombinant inbred line (RIL) JY280


title: experiment_H001AS8_G12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt


title: recombinant inbred line (RIL) JY279


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_IFNg_14h00_H3K4me1


title: HPV072-17R140-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample03_time06

value: Day 7 after boost dose


title: experiment_H001AS8_G13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Untreated, 14h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_UT_14h00_H3K4me1

value: STAT1 KO

value: Untreated


title: recombinant inbred line (RIL) JY273


title: experiment_H001AS8_G16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, LPS, 3h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_LPS_03h00_H3K4me1

value: Bone Marrow


title: experiment_H001AS8_G11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_IFNg_LPS_03h00_H3K4me1


title: HPV072-17R140-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample03_time05

value: Day 1 after boost dose


title: recombinant inbred line (RIL) JY271


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_IFNg_14h00_H3K4me1

value: Interferon gamma (IFNg)


title: recombinant inbred line (RIL) JY270


title: HPV072-17R140-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample03_time03

value: Blood

value: Day 7 after prime dose


title: experiment_H001AS8_G08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-17R140-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample03_time04

value: Day 0 after boost dose


title: recombinant inbred line (RIL) JY272


title: experiment_H001AS8_G10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY274


title: recombinant inbred line (RIL) JY269


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, LPS, 3h, rep2

description: Library name: BSMJ011_WTN_M_BM_LPS_03h00_H3K4me1

value: Macrophage


title: experiment_H001AS8_G07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-17R140-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample03_time01


title: recombinant inbred line (RIL) JY267


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_WTN_M_BM_IFNg_LPS_03h00_H3K4me1

value: IFNg + LPS


title: experiment_H001AS8_G05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY268


title: recombinant inbred line (RIL) JY266


title: experiment_H001AS8_G06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z85-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample02_time06


title: HPV072-Z85-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample02_time05


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_WTN_M_BM_IFNg_14h00_H3K4me1


title: experiment_H001AS8_G09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z85-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample02_time04


title: experiment_H001AS8_G04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_G03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY265


title: experiment_H001AS8_G02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Untreated, 14h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_UT_14h00_H3K4me1


title: experiment_H001AS8_G01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_IFNg_LPS_03h00_H3K4me1


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Untreated, 14h, rep1

description: Library name: BSMJ011_WTN_M_BM_UT_14h00_H3K4me1


title: HPV072-Z85-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample02_time03


title: HPV072-17R140-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample03_time02

value: Day 1 after prime dose


title: recombinant inbred line (RIL) JY264

value: leaf


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_IFNg_14h00_H3K4me1


title: HPV072-Z85-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample02_time02


title: recombinant inbred line (RIL) JY263


title: experiment_H001AS8_F24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z85-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample02_time01

value: Day 0 after prime dose


title: recombinant inbred line (RIL) JY262


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Untreated, 14h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_UT_14h00_H3K4me1

value: STAT1beta KI


title: HPV072-Y194-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample01_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY261


title: experiment_H001AS8_F23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Y194-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample01_time05


title: experiment_H001AS8_F22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, LPS, 3h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_LPS_03h00_H3K4me1

value: Lipopolysaccharide (LPS)


title: HPV072-Y194-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample01_time04


title: recombinant inbred line (RIL) JY259


title: HPV072-Y194-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample01_time03


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_IFNg_LPS_03h00_H3K4me1


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, LPS, 3h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_LPS_03h00_H3K4me1

value: STAT1 KO


title: experiment_H001AS8_F21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: recombinant inbred line (RIL) JY258


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_IFNg_14h00_H3K4me1

value: Bone Marrow


title: experiment_H001AS8_F20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Untreated, 14h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_UT_14h00_H3K4me1

value: Untreated


title: HPV072-Y194-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample01_time02

value: Blood


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, LPS, 3h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_LPS_03h00_H3K4me1


title: HPV072-Y194-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample01_time01


title: experiment_H001AS8_F19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY256


title: experiment_H001AS8_F18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_IFNg_14h00_H3K4me1

value: Interferon gamma (IFNg)


title: recombinant inbred line (RIL) JY260


title: HPV071-A14R044-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample16_time05

value: Day 1 after boost dose


title: experiment_H001AS8_F16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R044-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample16_time04

value: Day 0 after boost dose


title: experiment_H001AS8_F17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_F15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY253


title: HPV071-A14R044-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample16_time03

value: Day 7 after prime dose


title: experiment_H001AS8_F14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY251


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_WTN_M_BM_IFNg_LPS_03h00_H3K4me1

value: Macrophage

value: IFNg + LPS


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_IFNg_LPS_03h00_H3K4me1


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_WTN_M_BM_IFNg_14h00_H3K4me1


title: recombinant inbred line (RIL) JY255

value: leaf


title: HPV071-A14R044-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample16_time02

value: Day 1 after prime dose


title: recombinant inbred line (RIL) JY257


title: experiment_H001AS8_F13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R044-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample16_time06

value: Day 7 after boost dose


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_UT_14h00_H3K4me1

value: STAT1alpha KI


title: recombinant inbred line (RIL) JY250


title: HPV071-A14R044-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample16_time01

value: Day 0 after prime dose


title: experiment_H001AS8_F12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: recombinant inbred line (RIL) JY254


title: recombinant inbred line (RIL) JY249


title: ChIP-Seq, H3K4me1, Macrophage, Wild Type, LPS, 3h, rep1

description: Library name: BSMJ010_WTN_M_BM_LPS_03h00_H3K4me1

value: STAT1beta KI

value: Lipopolysaccharide (LPS)


title: experiment_H001AS8_F11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: HPV071-A18L072-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample15_time06

value: Blood


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_LPS_03h00_H3K4me1

value: Bone Marrow


title: recombinant inbred line (RIL) JY248


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_IFNg_LPS_03h00_H3K4me1


title: recombinant inbred line (RIL) JY247


title: experiment_H001AS8_F10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A18L072-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample15_time05

value: Day 1 after boost dose


title: HPV071-A18L072-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample15_time04

value: Day 0 after boost dose


title: experiment_H001AS8_F09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1KO, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_IFNg_14h00_H3K4me1

value: Interferon gamma (IFNg)


title: recombinant inbred line (RIL) JY246


title: experiment_H001AS8_F08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_LPS_03h00_H3K4me1

value: Macrophage


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_UT_14h00_H3K4me1

value: Untreated


title: recombinant inbred line (RIL) JY245

value: leaf


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_IFNg_LPS_03h00_H3K4me1

value: IFNg + LPS


title: recombinant inbred line (RIL) JY244


title: experiment_H001AS8_F07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY242


title: experiment_H001AS8_F05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K4me1, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_IFNg_14h00_H3K4me1


title: HPV071-A18L086-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample14_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY243


title: experiment_H001AS8_F06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt


title: HPV071-A18L072-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample15_time03

value: Day 7 after prime dose


title: HPV071-A18L072-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample15_time01

value: Day 0 after prime dose


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_UT_14h00_H3K4me1

value: STAT1alpha KI


title: HPV071-A18L086-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample14_time05


title: experiment_H001AS8_F04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: experiment_H001AS8_F03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A18L086-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample14_time04


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_LPS_03h00_H3K4me1

value: Lipopolysaccharide (LPS)


title: recombinant inbred line (RIL) JY240


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_IFNg_LPS_03h00_H3K4me1


title: HPV071-A18L072-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample15_time02

value: Day 1 after prime dose


title: experiment_H001AS8_F02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: recombinant inbred line (RIL) JY239


title: ChIP-Seq, H3K4me1, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_IFNg_14h00_H3K4me1

value: Bone Marrow


title: HPV071-A18L086-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample14_time02

value: Blood


title: HPV071-A18L086-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample14_time01


title: experiment_H001AS8_F01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Untreated, 14h, rep3

description: Library name: BSMJ012_WTN_M_BM_UT_14h00_H3K27ac

value: Wild Type


title: recombinant inbred line (RIL) JY238


title: experiment_H001AS8_E24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-16-36-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample13_time06


title: HPV071-16-36-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample13_time05

value: Day 1 after boost dose


title: recombinant inbred line (RIL) JY236


title: recombinant inbred line (RIL) JY241


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, LPS, 3h, rep3

description: Library name: BSMJ012_WTN_M_BM_LPS_03h00_H3K27ac

value: Macrophage


title: recombinant inbred line (RIL) JY234


title: recombinant inbred line (RIL) JY235


title: HPV071-A18L086-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample14_time03


title: experiment_H001AS8_E22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_WTN_M_BM_IFNg_LPS_03h00_H3K27ac


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_WTN_M_BM_IFNg_14h00_H3K27ac

value: Interferon gamma (IFNg)


title: HPV071-16-36-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample13_time04

value: Day 0 after boost dose


title: experiment_H001AS8_E21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-16-36-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample13_time03


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Untreated, 14h, rep2

description: Library name: BSMJ011_WTN_M_BM_UT_14h00_H3K27ac

value: Untreated


title: experiment_H001AS8_E20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-16-36-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample13_time02


title: experiment_H001AS8_E23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY233

value: leaf


title: recombinant inbred line (RIL) JY232


title: experiment_H001AS8_E19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, LPS, 3h, rep2

description: Library name: BSMJ011_WTN_M_BM_LPS_03h00_H3K27ac


title: recombinant inbred line (RIL) JY237


title: recombinant inbred line (RIL) JY231


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_WTN_M_BM_IFNg_LPS_03h00_H3K27ac

value: IFNg + LPS


title: experiment_H001AS8_E18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14L102-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample12_time06

value: Day 7 after boost dose


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_WTN_M_BM_IFNg_14h00_H3K27ac


title: experiment_H001AS8_E17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY230


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Untreated, 14h, rep1

description: Library name: BSMJ010_WTN_M_BM_IFNg_14h00_H3K27ac


title: recombinant inbred line (RIL) JY229


title: experiment_H001AS8_E16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14L102-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample12_time04


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, LPS, 3h, rep1

description: Library name: BSMJ010_WTN_M_BM_LPS_03h00_H3K27ac


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_WTN_M_BM_IFNg_LPS_03h00_H3K27ac


title: HPV071-A14L102-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample12_time03

value: Day 7 after prime dose


title: recombinant inbred line (RIL) JY227


title: ChIP-Seq, H3K27ac, Macrophage, Wild Type, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_WTN_M_BM_UT_14h00_H3K27ac


title: experiment_H001AS8_E15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt

value: hPSC derived cardiomyocytes


title: HPV071-A14L102-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample12_time01

value: Day 0 after prime dose


title: HPV071-A14L102-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample12_time02

value: Day 1 after prime dose


title: recombinant inbred line (RIL) JY226


title: experiment_H001AS8_E14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23


title: recombinant inbred line (RIL) JY228


title: experiment_H001AS8_E13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: HPV071-16-36-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample13_time01


title: recombinant inbred line (RIL) JY225


title: experiment_H001AS8_E12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R032-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample11_time06


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, LPS, 3h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_LPS_03h00_H3K27ac

value: Bone Marrow

value: STAT1 KO

value: Lipopolysaccharide (LPS)


title: recombinant inbred line (RIL) JY224


title: experiment_H001AS8_E11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14L102-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample12_time05

value: Blood

value: Day 1 after boost dose


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_IFNg_LPS_03h00_H3K27ac

value: Macrophage


title: recombinant inbred line (RIL) JY223


title: experiment_H001AS8_E10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R032-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample11_time04

value: Day 0 after boost dose


title: recombinant inbred line (RIL) JY222


title: experiment_H001AS8_E09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY221


title: experiment_H001AS8_E08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R032-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample11_time02


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Untreated, 14h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_UT_14h00_H3K27ac

value: Untreated


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, LPS, 3h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_LPS_03h00_H3K27ac


title: recombinant inbred line (RIL) JY220

value: leaf


title: HPV071-A14R032-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample11_time01


title: experiment_H001AS8_E06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_IFNg_LPS_03h00_H3K27ac

value: IFNg + LPS


title: recombinant inbred line (RIL) JY219


title: recombinant inbred line (RIL) JY218


title: HPV071-A14R032-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample11_time05


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_UT_14h00_H3K27ac


title: HPV071-A18L067-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample10_time05


title: recombinant inbred line (RIL) JY217


title: experiment_H001AS8_E04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_IFNg_14h00_H3K27ac

value: Interferon gamma (IFNg)


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_STAT1KO_M_BM_IFNg_14h00_H3K27ac


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_LPS_03h00_H3K27ac


title: HPV071-A18L067-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample10_time04


title: recombinant inbred line (RIL) JY216


title: experiment_H001AS8_E05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_E03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A18L067-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample10_time03

value: Day 7 after prime dose


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_IFNg_LPS_03h00_H3K27ac


title: recombinant inbred line (RIL) JY215


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Untreated, 14h, rep2

description: Library name: BSMJ011_STAT1KO_M_BM_UT_14h00_H3K27ac


title: HPV071-A14R032-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample11_time03


title: experiment_H001AS8_E07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: experiment_H001AS8_E02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A18L067-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample10_time02


title: experiment_H001AS8_E01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1KO, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1KO_M_BM_IFNg_14h00_H3K27ac


title: HPV071-A18L067-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample10_time01

value: Day 0 after prime dose


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Untreated, 14h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_UT_14h00_H3K27ac

value: STAT1beta KI


title: HPV071-A18L067-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample10_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY214


title: recombinant inbred line (RIL) JY213


title: experiment_H001AS8_D24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, LPS, 3h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_LPS_03h00_H3K27ac

value: Bone Marrow


title: HPV071-A14R028-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample09_time06


title: experiment_H001AS8_D23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY212


title: HPV071-A14R028-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample09_time05


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_IFNg_LPS_03h00_H3K27ac


title: HPV071-A14R028-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample09_time04


title: experiment_H001AS8_D22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_STAT1BB_M_BM_IFNg_14h00_H3K27ac


title: HPV071-A14R028-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample09_time03


title: experiment_H001AS8_D21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt


title: recombinant inbred line (RIL) JY209


title: recombinant inbred line (RIL) JY211


title: recombinant inbred line (RIL) JY210


title: HPV071-A14R028-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample09_time02

value: Day 1 after prime dose


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Untreated, 14h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_UT_14h00_H3K27ac


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, LPS, 3h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_LPS_03h00_H3K27ac

value: Lipopolysaccharide (LPS)


title: recombinant inbred line (RIL) JY208


title: experiment_H001AS8_D19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_D20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_IFNg_LPS_03h00_H3K27ac


title: recombinant inbred line (RIL) JY207


title: HPV071-A14R028-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample09_time01

value: Blood


title: HPV071-A13L116-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample08_time06


title: recombinant inbred line (RIL) JY206


title: HPV071-A13L116-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample08_time05

value: Day 1 after boost dose


title: experiment_H001AS8_D17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_UT_14h00_H3K27ac

value: Macrophage


title: experiment_H001AS8_D18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_D16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A13L116-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample08_time04

value: Day 0 after boost dose


title: recombinant inbred line (RIL) JY204

value: leaf


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_LPS_03h00_H3K27ac


title: recombinant inbred line (RIL) JY203


title: HPV071-A13L116-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample08_time03


title: HPV071-A13L116-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample08_time02


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_IFNg_LPS_03h00_H3K27ac

value: IFNg + LPS


title: recombinant inbred line (RIL) JY202


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Untreated, 14h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_UT_14h00_H3K27ac

value: STAT1alpha KI

value: Untreated


title: HPV071-A13L116-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample08_time01


title: experiment_H001AS8_D13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_STAT1BB_M_BM_IFNg_14h00_H3K27ac

value: Interferon gamma (IFNg)


title: HPV071-W61-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample07_time06


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, LPS, 3h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_LPS_03h00_H3K27ac


title: recombinant inbred line (RIL) JY200


title: recombinant inbred line (RIL) JY201


title: experiment_H001AS8_D11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_D12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY205


title: HPV071-W61-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample07_time04


title: experiment_H001AS8_D10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY199


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_IFNg_14h00_H3K27ac


title: recombinant inbred line (RIL) JY198


title: HPV071-W61-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample07_time03

value: Day 7 after prime dose


title: experiment_H001AS8_D15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_D14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Untreated, 14h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_UT_14h00_H3K27ac


title: ChIP-Seq, H3K27ac, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1BB_M_BM_IFNg_14h00_H3K27ac

value: STAT1beta KI


title: recombinant inbred line (RIL) JY197


title: HPV071-W61-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample07_time02


title: recombinant inbred line (RIL) JY196


title: experiment_H001AS8_D07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23


title: HPV071-W61-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample07_time01

value: Day 0 after prime dose


title: experiment_H001AS8_D06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, LPS, 3h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_LPS_03h00_H3K27ac

value: Bone Marrow


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep3

description: Library name: BSMJ012_STAT1AA_M_BM_IFNg_LPS_03h00_H3K27ac


title: HPV071-A14R029-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample06_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY194


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_IFNg_14h00_H3K27ac


title: recombinant inbred line (RIL) JY193


title: HPV071-A14R029-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample06_time04

value: Blood


title: experiment_H001AS8_D05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_D04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-W61-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample07_time05

value: Day 1 after boost dose


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep2

description: Library name: BSMJ011_STAT1AA_M_BM_IFNg_LPS_03h00_H3K27ac

value: Macrophage


title: experiment_H001AS8_D09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt


title: recombinant inbred line (RIL) JY195


title: recombinant inbred line (RIL) JY192


title: experiment_H001AS8_D03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R029-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample06_time05


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Untreated, 14h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_UT_14h00_H3K27ac


title: experiment_H001AS8_D08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY191


title: experiment_H001AS8_D02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_IFNg_14h00_H3K27ac


title: HPV071-A14R029-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample06_time03


title: HPV071-A14R029-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample06_time02

value: Day 1 after prime dose


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, LPS, 3h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_LPS_03h00_H3K27ac

value: Lipopolysaccharide (LPS)


title: ChIP-Seq, H3K27ac, Macrophage, STAT1alpha KI, Interferon gamma + LPS, 3h, rep1

description: Library name: BSMJ010_STAT1AA_M_BM_IFNg_LPS_03h00_H3K27ac

value: IFNg + LPS


title: experiment_H001AS8_D01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY190

value: leaf


title: 19NA9

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I St NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

data_processing:
The Empirical Analysis of Digital Gene Expression Data in R (EdgeR) package [46, 48, 49] in Bioconductor (version 3.40.1) was applied for differential expression analysis between M1 and M0, and between M2 and M0 in vehicle and NextA treatments. The weighted likelihood empirical Bayes method was used to control the p-values and the false discovery rate (FDR) [50]. The significance of gene expression was set at a threshold with p-value< -1.5, or log2-fold-change>1.5.
Assembly: GRCm39/mm39
Supplementary files format and content: Comma-separated values files; input and output for EdgeR

source_name: bone marrow

extract_protocol:
Murine bone marrow-derived macrophages (BMDMs) and THP-1 human monocytic cells were cultured in RPMI-1640 complete medium.
RNA-seq analysis of vehicle or HDAC6i, NextA treated BMDMs was performed as follows. FastQC (http://www. bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to evaluate the quality of the raw reads from M0, M1, and M2 samples in triplicates. The reverse and forward reads per sample were also assessed for paired-ended sequencing. Transcript quantification was performed with SALMON transcript quantification tool [47]. The reference genome served as the input index for the SALMON algorithm to report transcripts per mapped reads (TPM) per sample.

treatment_protocol: For adoptive cell therapy (ACT), BMDMs were isolated for intratumor transplantation from C57BL/6-Tg (UBCGFP)30Scha/J (Jax Strain #004353) (UBC-GFP) to distinguish between endogenous TAMs and transplanted macrophages. BMDMs were also isolated from wild-type C57BL/6 mice wherever necessary. Isolated bone marrow cells were cultured in RPMI-1640 complete medium as mentioned above and incubated in 5% CO2 at 37 °C. For isolating BMDMs, bone marrow from the femur and tibia bones was flushed, resuspended, and cultured in 10  cm culture plates with murine recombinant M-Csf (20ng/ mL). On day 4, undifferentiated and floating cells were washed with PBS and replaced with fresh RPMI media. BMDMs were allowed to incubate for another day with fresh medium. On day 6, macrophages were pretreated with 5µM of HDAC6 inhibitor NextA or vehicle prior to adding M1 polarizing factors; murine recombinant interferon-gamma (IFNγ) (50ng/mL), and bacterial lipopolysaccharide (LPS) (100ng/mL) for 24  h. The macrophages were harvested, washed thoroughly with PBS, and resuspended to a cell density of 1×106 cells in 100uL of PBS for intratumor implantation. M2 macrophages were obtained with recombinant murine cytokines IL-4 (20ng/ mL) and IL-13 (20ng/mL). For the macrophage repolarization experiments, BMDMs were polarized to M1 for 24 h in the presence of vehicle or 5µM NextA as previously described. Subsequently, M1 macrophages were repolarized to M2 through stimulation with IL-4 and IL-13. These samples were evaluated 24 h after the repolarization step

value: bone marrow

value: murine bone marrow-derived macrophages

value: NextA (HDAC6 inhibitor)


title: recombinant inbred line (RIL) JY189


title: 18NA8

growth_protocol: Murine bone marrow-derived macrophages (BMDMs) and THP-1 human monocytic cells were cultured in RPMI-1640 complete medium.


title: recombinant inbred line (RIL) JY188


title: HPV071-A14R013-Grp2-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample05_time06


title: experiment_H001AS8_C23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: 17NA7


title: HPV071-A14R013-Grp2-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample05_time05


title: recombinant inbred line (RIL) JY187


title: experiment_H001AS8_C22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R013-Grp2-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample05_time04

value: Day 0 after boost dose


title: 15NA5


title: recombinant inbred line (RIL) JY186


title: HPV071-A14R013-Grp2-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample05_time03

value: Day 7 after prime dose


title: experiment_H001AS8_C20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23


title: experiment_H001AS8_C21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: 14NA4


title: experiment_H001AS8_C19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY184


title: 13NA3


title: HPV071-A14R013-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample05_time01

value: Day 0 after prime dose


title: HPV071-A14R013-Grp2-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample05_time02


title: recombinant inbred line (RIL) JY183


title: experiment_H001AS8_C18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R029-Grp2-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample06_time01


title: HPV071-A14R045-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample04_time06

value: Day 7 after boost dose


title: experiment_H001AS8_C24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 12NA2


title: experiment_H001AS8_C17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R045-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample04_time05

value: Blood


title: 11NA1


title: 16NA6


title: recombinant inbred line (RIL) JY181


title: experiment_H001AS8_C16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY185


title: 9V9

value: Vehicle


title: HPV071-A14R045-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample04_time04


title: experiment_H001AS8_C15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 8V8


title: recombinant inbred line (RIL) JY180


title: HPV071-A14R045-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample04_time03


title: recombinant inbred line (RIL) JY178


title: experiment_H001AS8_C13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14R045-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample04_time02


title: 7V7


title: recombinant inbred line (RIL) JY179


title: HPV071-A14R04-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample04_time01


title: experiment_H001AS8_C12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 6V6


title: recombinant inbred line (RIL) JY176


title: recombinant inbred line (RIL) JY177


title: 5V5


title: experiment_H001AS8_C11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-17-185-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample03_time06


title: recombinant inbred line (RIL) JY182


title: HPV071-17-185-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample03_time05

value: Day 1 after boost dose


title: 4V4


title: recombinant inbred line (RIL) JY175


title: experiment_H001AS8_C10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 3V3


title: experiment_H001AS8_C09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY174


title: experiment_H001AS8_C14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 2V2


title: recombinant inbred line (RIL) JY173


title: HPV071-17-185-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample03_time03


title: experiment_H001AS8_C08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 1V1


title: recombinant inbred line (RIL) JY172


title: experiment_H001AS8_C07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY171


title: HPV071-17-18-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample03_time01


title: HPV071-A14L097-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample02_time06


title: experiment_H001AS8_C06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Zygote_RNA_Rep1

city: Kolkata

first: ZHUMUR

last: GHOSH

address: EN 80, Sector V, Bidhan Nagar

country: India

institute: Bose Institute

data_processing:
Linux and R
Read quality was assessed for each samples (both long and small RNAseq data) using FastQC and low-quality reads (quality <32) were removed using Cutadapt3.4.
The trimmed long RNA reads were mapped to the Mouse mm10 reference genome retrieved from Ensembl using spliced aligner tool Hisat2 2.1.0. SAMtools 0.1.19 was used to sort and index the BAM files. Transcript counts were generated using FeatureCounts, followed by batch correction with ComBat-seq and Diffrential analysis with DESeq2.
For miRNA detection, for both online and in-house datasets, the trimmed small RNA reads were aligned with mature mouse miRNA sequences retrieved from miRBase Release 22 using Megablast. In-house custom scripts have been used to detect the general profile for each group followed by differential analysis using DESeq2.
Assembly: mm10
Supplementary files format and content: tab delimited text files include transcript counts for each sample

source_name: Zygote (1 cell stage)

extract_protocol:
Total RNA was isolated Qiagen using miRNeasy Mini Kit according to manufacturer's protocol.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® UltraTM II Directional RNA Library Prep Kit (New England BioLabs, MA, USA), according to manufacturer’s instructions, at Genotypic Technology Pvt. Ltd., Bangalore, India.
Small RNA sequencing (SmRNA) library for oocyte and sperm was prepared using the NEXTflexTM Small RNA-Seq Kit v3 (Bioo Scientfic Corporation, Austin, Texas, U.S.A.), at Genotypic Technology Pvt. Ltd., Bangalore, India, following manufacturer’s instructions.
Small RNA sequencing (smRNA) libraries for zygote was prepared with QIAseq® miRNA Library Kit (Cat: 331502) protocol (Qiagen, Maryland, U.S.A.) at Genotypic Technology Pvt. Ltd., Bangalore, India.

value: Zygote (1 cell stage)

value: Balb/c


title: recombinant inbred line (RIL) JY170


title: experiment_H001AS8_C05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Oocyte_RNA_Rep2

source_name: Oocyte

value: Oocyte


title: HPV071-A14L097-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample02_time05


title: Zygote_RNA_Rep2


title: recombinant inbred line (RIL) JY169

value: leaf


title: experiment_H001AS8_C04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Oocyte_RNA_Rep1


title: recombinant inbred line (RIL) JY168


title: HPV071-A14L097-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample02_time04


title: HPV071-17-185-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample03_time04


title: experiment_H001AS8_C03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Sperm_RNA_Rep2

source_name: Sperm

value: Sperm


title: HPV071-A14L097-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample02_time03


title: HPV071-17-185-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample03_time02

value: Day 1 after prime dose


title: recombinant inbred line (RIL) JY166


title: HPV071-A14L097-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample02_time02


title: experiment_H001AS8_C02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY167


title: Sperm_RNA_Rep1


title: experiment_H001AS8_C01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14L097-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample02_time01


title: experiment_H001AS8_B24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV071-A14L101-Grp1-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample01_time06


title: Control-rep3

city: JiNan

first: Anda

last: Shi

address: Culture West Road num 107

institute: Qilu Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: mice CCA tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mice CCA tissue

value: LD-1 cell line

value: CCA cell line


title: Control-rep2


title: experiment_H001AS8_B23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: recombinant inbred line (RIL) JY165


title: Control-rep1


title: HPV071-A14L101-Grp1-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample01_time05


title: recombinant inbred line (RIL) JY163


title: experiment_H001AS8_B22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23


title: experiment_H001AS8_B21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: recombinant inbred line (RIL) JY162


title: HGF-rep3


title: HPV071-A14L101-Grp1-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample01_time03

value: Day 7 after prime dose


title: HGF-rep2


title: HPV071-A14L101-Grp1-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample01_time04

value: Day 0 after boost dose


title: recombinant inbred line (RIL) JY161


title: HPV071-A14L101-Grp1-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample01_time02

value: Blood


title: experiment_H001AS8_B20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HGF-rep1


title: recombinant inbred line (RIL) JY160


title: experiment_H001AS8_B19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY159


title: pdac

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description: Leukocytes isolated from blood and multiples tissues from naïve and cancer bearing mice

data_processing:
Rhapsody processing pipeline
Assembly: GRCm38
Supplementary files format and content: Seurat r object containing raw counts and metadata

source_name: mixed sample (non-demultiplexed)

growth_protocol: All experiments were performed on 6–24-week-old C57BL/6 background mice. Chow and water were available ad libitum

extract_protocol:
For the generation of single-cell whole-transcriptomes we used a BD Rhapsody system according to manufacture instructions. 60,000 sorted live cells were loaded into a Rhapsody Single Cell Analysis System cartridge. Cell capture and cDNA synthesis were performed according to manufacturer’s instructions; cells were isolated into nanowells by gravity, then cells lysed and mRNA, AbSeq oligos and Sample tags oligos were released and captured by beads present in the nanowells
Two separated indexed libraries were prepared for whole transcriptome analysis and Sample Tag demultiplexing following manufacturer’s instructions. The average size of the libraries was calculated using the 2100 Bioanalyzer (Agilent) and the concentration was determined using the Qubit fluorometer (Thermofisher). Finally, libraries were combined and sequenced together in a paired end run (60x42) using a NextSeq 2000 system (Illumina) and a P2 flowcell. Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).

treatment_protocol: For the generation of single-cell whole-transcriptomess tissues were dissected and dissociated into a single-cell suspension by enzyme digestion. Cell strainer-filtered single-cell solution were sorted in BD Aria Cell Sorter as DAPI-CD11b+Ly6G+ cells and loaded into a BD Rhapsody cartridge

value: mixed sample (non-demultiplexed)

value: Pancreatic_tumor:100000 tumor cells from the pancreatic adenocarcinoma FC1242 cell line were injected in the pancreas


title: 16-131-Grp5-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample05_time06

value: Day 7 after boost dose


title: LPS

description: Leukocytes isolated from blood and multiples tissues from naïve and LPS-treated mice

value: 400ng of LPS i.v. and samples harvested 24h


title: recombinant inbred line (RIL) JY164


title: recombinant inbred line (RIL) JY158


title: experiment_H001AS8_B17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 16-131-Grp5-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample05_time05

value: Day 1 after boost dose


title: 16-131-Grp5-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample05_time04


title: experiment_H001AS8_B16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY156

value: leaf