title: 374_GES11_951_hippocampus_A/J_female


title: S11_D30_VEH_03

status: Public on Sep 30 2025

type: SRA

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

country: USA

institute: Yale University

description: Library name: S11_D30_VEH

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed using cutadapt
Reads were quantified using RSEM
Assembly: GRCh38.113
Supplementary files format and content: raw counts matrix
Supplementary files format and content: tab delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Human iPS cells (SCTi003-A

extract_protocol:
Total RNA was extracted from cell cultures using the RNA Extraction RNeasy Plus Mini-kit (QIAGEN)
200 ng of total RNA was used to generate barcoded RNA sequencing libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Libraries were sequenced with HiSeq2500 (Illumina) to generate 50-nucleotide single reads, with a minimum of eight million reads per sample. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina). Reads were further processed with RTA v1.18.66.3. FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).

tag: cell line

value: Human iPS cells (SCTi003-A

tag: treatment

value: PBS

tag: time


title: 381_GES11_956_hippocampus_A/J_male

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
raw counts quantified by EMASE
Assembly: GRCm39
Supplementary files format and content: hippocampus_ensembl_v105_gene_counts.txt

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Total hippocampal RNA was isolated using the Life Technologies TRIzol Plus RNA purification kit with on-column DNase-digestion step.
RNA-Seq libraries were prepared using the TruSeq kit (Illumina Inc., San Diego, CA) according to the manufacturer’s protocols.

tag: strain

value: A/J

tag: Sex

value: male

tag: tissue

value: hippocampus


title: experiment_H001AS8_M16_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

library_source: transcriptomic single cell

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

molecule: polyA RNA

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 type

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: HTRA1_2

city: Hangzhou

first: Boya

last: Zhang

state: Zhejiang

address: Qingchun East Road

country: China

institute: Department of dermatology,Sir Run Run Shaw Hospital, Zhejiang University, School of Medicine

description: Library name: Sample2

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: skin

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: skin


title: experiment_H001AS8_N01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 373_GES11_950_hippocampus_A/J_female

value: female


title: Hs578T, Lap+I73, 0.1, R1

city: Leiden

first: Bob

last: van de Water

state: Leiden

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

description: Library name: I17-1234-D01-A5

data_processing:
Alignment was performed using the STAR aligner (version 2.4.2a) against the human GRCh38 reference genome.
Marking duplicates, sorting and indexing were performed using Sambamba (version 0.6.6).
Counts per gene were quantified using HTseq based on the ENSEMBL gene annotation for GRCH38 (release 84).
Data was normalized and differential gene expression was determined using DESeq2.
Assembly: GRCh38 (release 84)
Supplementary files format and content: .txt format containing raw counts

growth_protocol: Hs578T cells were maintained in RPMI-1640 medium with L-glutamine and 25 mM HEPES, supplemented with 10% FBS and penicillin/streptomycin

extract_protocol:
RNA was isolated with the RNeasy Plus Mini Kit (Qiagen) following manufacturer's instructions.
DNA libraries were prepared from the samples with the TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Hs578T cells were treated with the negative solvent control DMSO (0.1%) or the inhibitors I-73 (0.1 and 0.316 μM), D10-81 (0.1 μM), Y3-21 (0.1 μM) for 6 hours prior to collection of RNA.  For combination treatments, cells were treated with I-73 (0.1 μM), lapatinib (3.16 μM) and a combination thereof for 6 hours prior to collection of RNA.

value: Breast cancer cell line


title: experiment_H001AS8_M24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_M15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 348_GES11_931_hippocampus_129S1_SvImJ_male


title: BMDM TGFb 5

city: Schlieren

first: Florence

last: Vallelian

address: Wagistrasse 12

department: Department of Internal Medicine

country: Switzerland

institute: University Hospital and University of Zurich

description: Library name: M5_BMDM_TGFb

data_processing:
Read alignment using STAR (version 2.7.11b)
Read summarization using featureCounts (Rsubread version 2.22.1)
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03
Supplementary files format and content: .txt: Contains feature (gene) counts

source_name: BMDM

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 7- to 12-week-old C57BL/6J mice and then passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dishes (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 or 4  with IL-4 (20 ng/ml, PeproTech), IL-10 (100 ng/ml), TGF-β (100 ng/ml), or IFNγ (20 ng/ml, PeproTech). The BM cells were harvested for analysis on day 7 from the temperature-responsive cell culture plates after cooling to room temperature. Cells were washed twice in PBS and centrifuged (300g, 10 min) before processing.

extract_protocol:
RNA was extracted from macrophages using the RNeasy Mini kit (Qiagen) according to the manufacturer's protocol, including on-column DNase I treatment.
RNA quality was validated on an Agilent Technologies 4150 Tapestation using  RNA Screentapes, and only samples with an RNA integrity number (RIN) of > 9 were used for sequencing. cDNA libraries were generated at the Functional Genomics Center Zurich (FGCZ) from RNA samples using the Illumina Stranded mRNA Prep ligation kit following the manufacturer’s instructions. The quality and concentration of the libraries were determined using an Agilent Technologies 4200 Tapestation with DNA Screentapes. The libraries were pooled in equimolar amounts and sequenced on an Illumina NovaSeq X Plus sequencer (paired-end 150 bp) with a depth of at least 20 million reads per sample.

value: BMDM

value: TGFb


title: BMDM Control 4

description: Library name: M4_BMDM_Control

value: Control


title: experiment_H001AS8_M14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_M23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: S19_D30_GMCSG_02

description: Library name: S19_D30_GMCSG

value: GM+CSF


title: BMDM IL10 5

description: Library name: M5_BMDM_IL10


title: experiment_H001AS8_M22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 363_GES11_942_hippocampus_NOD_ShiLtJ_male


title: BMDM IL4 5

description: Library name: M5_BMDM_IL4


title: experiment_H001AS8_M12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 342_GES11_925_hippocampus_129S1_SvImJ_male


title: 361_GES11_940_hippocampus_NOD_ShiLtJ_male


title: experiment_H001AS8_M20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM Control 5

description: Library name: M5_BMDM_Control


title: experiment_H001AS8_M11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_M21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hs578T, LY3, 0.1, R1

description: Library name: I17-1234-C06-A6


title: Hs578T, Lap+I73, 0.1, R3

description: Library name: I17-1234-F03-A5


title: experiment_H001AS8_M10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 353_GES11_933_hippocampus_NOD_ShiLtJ_female


title: experiment_H001AS8_M17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IL10 4

description: Library name: M4_BMDM_IL10


title: BMDM IFNy 4

description: Library name: M4_BMDM_IFNy

value: IFNy


title: experiment_H001AS8_M13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hs578T, Lap+I73, 0.1, R2

description: Library name: I17-1234-E02-A5


title: BMDM TGFb 3

description: Library name: M3_BMDM_TGFb


title: 343_GES11_926_hippocampus_129S1_SvImJ_male


title: Hs578T, Lap, 3.16, R1

description: Library name: I17-1234-A12-A4


title: BMDM IL4 4

description: Library name: M4_BMDM_IL4


title: Hs578T, Lap, 3.16, R2

description: Library name: I17-1234-B11-A4


title: 345_GES11_928_hippocampus_129S1_SvImJ_male


title: Hs578T, I73, 0.316, R3

description: Library name: I17-1234-D09-A3


title: Hs578T, Lap, 3.16, R3

description: Library name: I17-1234-C10-A4


title: BMDM IL4 3

description: Library name: M3_BMDM_IL4


title: 352_GES11_932_hippocampus_NOD_ShiLtJ_female


title: 334_GES11_919_hippocampus_129S1_SvImJ_female


title: experiment_H001AS8_M09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IL10 3

description: Library name: M3_BMDM_IL10


title: Hs578T, I73, 0.1, R3

description: Library name: I17-1234-C04-A2


title: BMDM IFNy 3

description: Library name: M3_BMDM_IFNy


title: 336_GES11_921_hippocampus_129S1_SvImJ_female


title: Hs578T, I73, 0.316, R2

description: Library name: I17-1234-C08-A3


title: BMDM Control 3

description: Library name: M3_BMDM_Control


title: Hs578T, I73, 0.316, R1

description: Library name: I17-1234-B07-A3


title: 332_GES11_917_hippocampus_129S1_SvImJ_female


title: 331_GES11_916_hippocampus_129S1_SvImJ_female


title: Hs578T, I73 0.1, R1

description: Library name: I17-1234-A06-A2


title: Hs578T, I73, 0.1, R2

description: Library name: I17-1234-B05-A2


title: 328_GES11_915_hippocampus_C57BL/6J_male


title: BMDM IL10 2

description: Library name: M2_BMDM_IL10


title: BMDM TGFb 2

description: Library name: M2_BMDM_TGFb


title: 327_GES11_914_hippocampus_C57BL/6J_male


title: experiment_H001AS8_M06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_M08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hs578T, DMSO, R2

description: Library name: I17-1234-B02-A1

value: DMSO


title: BMDM IL4 2

description: Library name: M2_BMDM_IL4


title: 325_GES11_912_hippocampus_C57BL/6J_male


title: BMDM Control 2

description: Library name: M2_BMDM_Control


title: 323_GES11_910_hippocampus_C57BL/6J_male


title: experiment_H001AS8_M04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hs578T, DMSO, R3

description: Library name: I17-1234-C03-A1


title: Hs578T, DMSO, R1

description: Library name: I17-1234-A01-A1


title: experiment_H001AS8_M05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM TGFb 1

description: Library name: M1_BMDM_TGFb


title: BMDM IFNy 2

description: Library name: M2_BMDM_IFNy


title: 318_GES11_907_hippocampus_C57BL/6J_female


title: Hs578T, D81, 0.1, R3

description: Library name: I17-1234-G12-A7


title: experiment_H001AS8_M03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_M02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IL10 1

description: Library name: M1_BMDM_IL10


title: 316_GES11_905_hippocampus_C57BL/6J_female


title: experiment_H001AS8_M07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IL4 1

description: Library name: M1_BMDM_IL4


title: Hs578T, D81, 0.1, R2

description: Library name: I17-1234-F11-A7


title: experiment_H001AS8_L24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hs578T, D81, 0.1, R1

description: Library name: I17-1234-E10-A7


title: 313_GES11_902_hippocampus_C57BL/6J_female


title: BMDM Control 1

description: Library name: M1_BMDM_Control


title: experiment_H001AS8_L23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IFNy 1

description: Library name: M1_BMDM_IFNy


title: BMDM TGFb 5

description: Library name: M5_BMDM_TGFb

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 7- to 12-week-old C57BL/6J mice and then passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dishes (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech) or 20 ng/ml recombinant GM-CSF (PeproTech) as previously described (Vallelian et al. 2022). On day 3, half of the medium was replaced. Cultures were treated on day 3 or 4  with IL-4 (20 ng/ml, PeproTech), IL-10 (100 ng/ml), TGF-β (100 ng/ml), or IFNγ (20 ng/ml, PeproTech). The BM cells were harvested for analysis on day 7 from the temperature-responsive cell culture plates after cooling to room temperature. Cells were washed twice in PBS and centrifuged (300g, 10 min) before processing.


title: experiment_H001AS8_L20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IL10 5

description: Library name: M5_BMDM_IL10


title: experiment_H001AS8_L21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IL4 5

description: Library name: M5_BMDM_IL4


title: Prostate Adenocarcinoma 9 months post tam Replicate 1 Sequencing Run 2

city: Marseille

first: Lionel

last: Spinelli

address: Avenue de Luminy

country: France

institute: CIML

data_processing:
Each library was processed with 10x Genomics CellRanger pipeline with default option values.
Assembly: GRCm38
Supplementary files format and content: Tarballs of the count matrices produced by CellRanger analysis. Each tarball contains the three files provided by CellRanger (Feature, Barcodes, Matrix) for a single library.
Supplementary files format and content: More advanced preprocessed files can be found from the DOI displayed in the GitHub (see article).

source_name: Tumor prostate at Adenocarcinoma stage (mouse age: 11 months)

extract_protocol:
To distinguish circulating immune cells from tissue resident immune cells, mice were injected intravenously with 3μg of anti CD45.2-FITC for 3 minutes prior to euthanasia. The dorsal-lateral-ventral lobes (DLV lobes) of mouse prostates from PTEN(i)pe-/- mice and age-matched PTENL2/L2control littermates at 3months and 9months post tamoxifen (PIN and adenocarcinoma stage respectively) were isolated and dissociated by enzymatic digestion(collagenase 2 / DNase) to generate a single-cell suspension. For surface staining, single cell suspensions were preincubated with blocking anti-Fc receptor antibody (clone 2.4G2) at 4°C for 10 min. Cells were then washed and stained with appropriate fluorescent labeled monoclonal surface antibodies (CD45, CD11b, Ly-6G) at 4oC for 30 min at dark. Prostate samples from three PTEN(i)pe-/- mice at 3 months post tamoxifen were pooled. Similarly, prostate samples from five  sex-matched PTENL2/L2 control littermates at 3 months post-tamoxifen were also pooled. The same approach was applied for the 9 months samples of PTEN(i)pe-/- and control mice respectively. This experimental procedure was repeated twice in order to generate duplicates for each timepoint and sample type to eliminate possible batch effects during the analysis. Next, samples were FACS-sorted using a BD FACSAriaTM Fusion flow cytometer. Cell viability was evaluated using DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride). The control samples were sorted as bulk resident immune cells (CD45.2-CD45+). However, for the tumorous PTEN(i)pe-/- samples, the tissue resident neutrophils (CD45.2-CD45+CD11b+Ly-6G+) were sorted independently from the rest of the immune cells (CD45.2-CD45+CD11b+Ly-6G-). Post sorting, they were re-pooled in a ratio of 30% neutrophils to 70% of rest immune cells.
Trypan blue exclusion assay was used to determine cell number viability of each FACS-sorted sample using a Neubauer Chamber. Samples with a cell viability of >95% were processed with a Chromium Controller (10X Genomics, Leiden, The Netherlands). Sixteen thousand cells were loaded per well in nanoliter-scale Gel Beads-in Emulsion (GEMs). Single-cell 3’ mRNA-seq libraries were generated according to “User guide Chromium Next GEM Single Cell 3 prime Reagent Kits v3.3 (Dual index) (10x Genomics, PN CG000315- Rev.D). Briefly, cells were partitioned into droplets with barcoded gel beads and reverse transcription master mix using Chromium Chip G. After complementary DNA (cDNA) synthesis and barcoding from poly-adenylated mRNA, GEMs were disrupted and pooled before amplification of cDNA by 11 polymerase chain reaction (PCR) cycles. Following enzymatic fragmentation and size selection of cDNA amplicons, sequencing libraries were constructed by adding Illumina P5 and P7 adapters (San Diego, USA) and i5 and i7 sample indexes by end repair, A-tailing, adaprot ligation, and 10 cycles of PCR amplification. Quality control and quantification of libraries was performed with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). The generated libraries were sequenced on NextSeq2000 sequencer using a P3-type flow cell and 100-type cartridge. Two runs of sequencing were performed for each libray. Next, bioinformatic analysis was followed.
scRNA-seq (10x Genomics 3'v3.1)

treatment_protocol: Gene ablation was induced by intraperitoneal injection of Tamoxifen (Tam) performed daily for 5 days (1 mg/mouse) to 8- to 10-week-old mice, to generate the transgenic PTEN(i)pe-/- (pe, prostate epithelium; (i), induced) and the respective control PTENL2/L2mice that did not bear the PSA-Cre-ERT2 transgene. Treatment was applied 3 or 9 months prior analyzis. No further treatment was applied to the mice prior to sequencing.

value: Prostate

tag: age

value: 11 months

tag: genotype

value: PTEN(i)pe-/-

value: 9 mo Tamoxifen


title: Prostate PIN 3 months post tam Replicate 2 Sequencing Run 2

source_name: Tumor prostate at PIN stage (mouse age: 5 months)

value: 5 months

value: 3 mo Tamoxifen


title: Prostate PIN 3 months post tam Replicate 1 Sequencing Run 2


title: experiment_H001AS8_L22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: experiment_H001AS8_L19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: Prostate  Control 9 month post tam Replicate 2 Sequencing Run 2

source_name: WT prostate (mouse age: 11 months)


title: experiment_H001AS8_M01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, Wild Type, LPS, 6h, rep3

city: Wien

first: Birgit

last: Strobl

address: Veterinarplatz 1

department: TZG

country: Austria

institute: VetMedUni

description: Library name: BSMJ008_WTN_M_BM_LPS_06h00min

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)
Assembly: mm10
Supplementary files format and content: csv file of read counts

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:
Total RNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen, 80204) according to the manufacturer's instructions. 500 pg of RNA was used as input.
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.

value: Bone Marrow

value: Macrophage

value: Wild Type

value: Lipopolysaccharide (LPS)

tag: batch


title: RNA, Macrophage, Wild Type, IFNg+LPS, 6h, rep3

description: Library name: BSMJ008_WTN_M_BM_IFNg.LPS_06h00min

value: IFNg + LPS


title: RNA, Macrophage, Wild Type, Interferon gamma, 14h, rep3

description: Library name: BSMJ008_WTN_M_BM_IFNg_14h00min

value: Interferon gamma (IFNg)


title: BMDM Control 5

description: Library name: M5_BMDM_Control

value: BMDM

value: Control


title: RNA, Macrophage, Wild Type, Untreated, 14h, rep3

description: Library name: BSMJ008_WTN_M_BM_UT_14h00min

value: Untreated


title: RNA, Macrophage, Wild Type, IFNg+LPS, 3h, rep3

description: Library name: BSMJ008_WTN_M_BM_IFNg.LPS_03h00min


title: RNA, Macrophage, Wild Type, LPS, 3h, rep3

description: Library name: BSMJ008_WTN_M_BM_LPS_03h00min


title: experiment_H001AS8_L18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Prostate Control 9 month post tam Replicate 1 Sequencing Run 2

value: Prostate

value: 11 months


title: 311_GES11_900_hippocampus_C57BL/6J_female

value: female

value: hippocampus


title: RNA, Macrophage, STAT1 KO, Untreated, 14h, rep3

description: Library name: BSMJ008_STAT1KO_M_BM_UT_14h00min

value: STAT1 KO


title: BMDC IL4 5

description: Library name: M5_BMDC_IL4

source_name: BMDC

value: BMDC


title: RNA, Macrophage, STAT1 KO, LPS, 6h, rep3

description: Library name: BSMJ008_STAT1KO_M_BM_LPS_06h00min


title: Prostate Adenocarcinoma 9 months post tam Replicate 2 Sequencing Run 2

value: PTEN(i)pe-/-

value: 9 mo Tamoxifen


title: BMDC IL10 5

description: Library name: M5_BMDC_IL10


title: Prostate Control 3 months post tam Replicate 1 Sequencing Run 2

source_name: WT prostate (mouse age: 5 months)

value: 5 months

value: 3 mo Tamoxifen


title: RNA, Macrophage, STAT1 KO, LPS, 3h, rep3

description: Library name: BSMJ008_STAT1KO_M_BM_LPS_03h00min

value: Bone Marrow

value: Macrophage


title: BMDM TGFb 4

description: Library name: M4_BMDM_TGFb

value: TGFb


title: RNA, Macrophage, STAT1 KO, IFNg+LPS, 6h, rep3

description: Library name: BSMJ008_STAT1KO_M_BM_IFNg.LPS_06h00min

value: IFNg + LPS


title: BMDM IL10 4

description: Library name: M4_BMDM_IL10

value: BMDM


title: experiment_H001AS8_L14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: experiment_H001AS8_L16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_L15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Prostate Control 3 month post tam  Replicate 2 Sequencing Run 2

value: Prostate


title: RNA, Macrophage, STAT1 KO, IFNg+LPS, 3h, rep3

description: Library name: BSMJ008_STAT1KO_M_BM_IFNg.LPS_03h00min


title: Prostate Adenocarcinoma 9 months post tam Replicate 1 Sequencing Run 1

value: 11 months


title: BMDM IFNy 4

description: Library name: M4_BMDM_IFNy

value: IFNy


title: Prostate PIN 3 months post tam Replicate 2 Sequencing Run 1


title: RNA, Macrophage, STAT1 KO, Interferon gamma, 14h, rep3

description: Library name: BSMJ008_STAT1KO_M_BM_IFNg_14h00min

value: STAT1 KO

value: Interferon gamma (IFNg)


title: experiment_H001AS8_L12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_L13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Prostate PIN 3 months post tam Replicate 1 Sequencing Run 1

value: PTEN(i)pe-/-


title: RNA, Macrophage, STAT1beta KI, Untreated, 14h, rep3

description: Library name: BSMJ008_STAT1BB_M_BM_UT_14h00min

value: STAT1beta KI

value: Untreated


title: BMDM IL4 4

description: Library name: M4_BMDM_IL4


title: BMDM Control 4

description: Library name: M4_BMDM_Control

value: Control


title: Prostate  Control 9 month post tam Replicate 2 Sequencing Run 1

value: 9 mo Tamoxifen


title: experiment_H001AS8_L11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_L17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IFNy 5

description: Library name: M5_BMDM_IFNy


title: RNA, Macrophage, STAT1beta KI, LPS, 6h, rep3

description: Library name: BSMJ008_STAT1BB_M_BM_LPS_06h00min

value: Bone Marrow

value: Macrophage

value: Lipopolysaccharide (LPS)


title: BMDC TGFb 4

description: Library name: M4_BMDC_TGFb

value: BMDC

value: TGFb


title: Prostate Control 9 month post tam Replicate 1 Sequencing Run 1


title: RNA, Macrophage, STAT1beta KI, LPS, 3h, rep3

description: Library name: BSMJ008_STAT1BB_M_BM_LPS_03h00min


title: Prostate Adenocarcinoma 9 months post tam Replicate 2 Sequencing Run 1


title: experiment_H001AS8_L09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: RNA, Macrophage, STAT1beta KI, IFNg+LPS, 6h, rep3

description: Library name: BSMJ008_STAT1BB_M_BM_IFNg.LPS_06h00min

value: IFNg + LPS


title: experiment_H001AS8_L08_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: Tetracycline


title: RNA, Macrophage, STAT1beta KI, IFNg+LPS, 3h, rep3

description: Library name: BSMJ008_STAT1BB_M_BM_IFNg.LPS_03h00min


title: Prostate Control 3 months post tam Replicate 1 Sequencing Run 1

value: Prostate

value: 5 months

value: 3 mo Tamoxifen


title: BMDC IFNy 4

description: Library name: M4_BMDC_IFNy

value: IFNy


title: experiment_H001AS8_L07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Rag1KONE1KO2 pro-B cells

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

library_source: genomic

data_processing:
NextSeq 500 with a High Output sequencing flow cell using 2x42 paired end sequencing reactions.
Reads were trimmed and aligned to the mouse (Mus musculus) genome mm10 using BWA MEM(Li, 2013).  UCSC liftover tool was used to convert them to mm9.
Assembly: mm10
Supplementary files format and content: mm10 Bigwig files were generated and converting to mm9 for comparision

molecule: genomic DNA

source_name: BM pro-B cells

growth_protocol: Rag deficient pro-B cells were isolated from murine bone marrow using anti-CD19 magnetic microbeads (MACS, Miltenyi) according to the manufacturer’s instructions. B cells cultured 1x10^6 cells/ml in RPMI, L-glutamine (4 mM), penicillin (200 U/ml)-streptomycin (200 mg/ml), b-mercaptoenthanol (50 mM), supplemented with FCS (10% vol/vol.). Cells were expanded in ex vivo culture with IL7 for 5 days.

extract_protocol: The Illumina Nextera Kit was used for tagmentation. Libraries were cleaned up using the Zymo PCR Clean Up kit. Libraries were amplified 5x and quantified by qPCR and then further amplified if needed. Libraries were again purified with Zymo PCR cleanup. Cutting efficiency was assessed by Agient TapeStation prior to sequencing.

treatment_protocol: Cells were treated with 20U DNaseI in 1xHBSS for 40min at 37C. Cells were washed 2x cold 1xPBS and then lysed with cold C1 buffer.

value: BM derived pro-B cells

value: ex vivo IL7 expansion  5 days


title: RNA, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep3

description: Library name: BSMJ008_STAT1BB_M_BM_IFNg_14h00min

value: STAT1beta KI

value: Interferon gamma (IFNg)


title: RNA, Macrophage, STAT1alpha KI, Untreated, 14h, rep3

description: Library name: BSMJ008_STAT1AA_M_BM_UT_14h00min

value: Bone Marrow

value: STAT1alpha KI

value: Untreated


title: experiment_H001AS8_L05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Rag1KONE1KO1 pro-B cells


title: Rag2KOSiteI.3PrKO2 pro-B cells


title: BMDM TGFb 3

description: Library name: M3_BMDM_TGFb

value: BMDM


title: BMDM IL10 3

description: Library name: M3_BMDM_IL10


title: experiment_H001AS8_L04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1alpha KI, LPS, 6h, rep3

description: Library name: BSMJ008_STAT1AA_M_BM_LPS_06h00min

value: Macrophage

value: Lipopolysaccharide (LPS)


title: Rag2KOSiteI.3PrKO1 pro-B cells


title: RNA, Macrophage, STAT1alpha KI, LPS, 3h, rep3

description: Library name: BSMJ008_STAT1AA_M_BM_LPS_03h00min


title: experiment_H001AS8_L10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: experiment_H001AS8_L03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: BMDM IL4 3

description: Library name: M3_BMDM_IL4


title: BMDC IL10 4

description: Library name: M4_BMDC_IL10

value: BMDC


title: Rag2KO2 pro-B cells


title: BMDM IFNy 3

description: Library name: M3_BMDM_IFNy


title: RNA, Macrophage, STAT1alpha KI, IFNg+LPS, 6h, rep3

description: Library name: BSMJ008_STAT1AA_M_BM_IFNg.LPS_06h00min

value: IFNg + LPS


title: Prostate Control 3 month post tam  Replicate 2 Sequencing Run 1

value: Prostate

value: 5 months

value: 3 mo Tamoxifen


title: experiment_H001AS8_L02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC IL4 4

description: Library name: M4_BMDC_IL4


title: Rag2KO1 pro-B cells

value: BM derived pro-B cells

value: ex vivo IL7 expansion  5 days


title: RNA, Macrophage, STAT1alpha KI, IFNg+LPS, 3h, rep3

description: Library name: BSMJ008_STAT1AA_M_BM_IFNg.LPS_03h00min


title: BMDM Control 3

description: Library name: M3_BMDM_Control

value: Control


title: BMDC Control 4

description: Library name: M4_BMDC_Control


title: experiment_H001AS8_L01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep3

description: Library name: BSMJ008_STAT1AA_M_BM_IFNg_14h00min

value: Bone Marrow

value: Interferon gamma (IFNg)


title: experiment_H001AS8_K24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC TGFb 3

description: Library name: M3_BMDC_TGFb

value: TGFb


title: experiment_H001AS8_L06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, Wild Type, Untreated, 14h, rep2

description: Library name: BSMJ007_WTN_M_BM_UT_14h00min

value: Wild Type

value: Untreated


title: BMDC IL10 3

description: Library name: M3_BMDC_IL10


title: Arthrobacter sp. AZCC_0090, day 2 control, replicate 2

city: Tucson

first: Paul

last: Carini

state: AZ

address: 1657 E Helen St

institute: University of Arizona

description:
Library name: day2_control_rep2
Day.2.control.rep.2

data_processing:
The reads were mapped to Arthrobacter sp. AZCC_0090 genome using Bowtie2 v2.4.1 with default parameters in paired-end mode. Counts were generated with the featureCounts function in the Rsubread v2.12.3 R Bioconductor package.
Assembly: PRJNA632064
Supplementary files format and content: Processed data are read counts mapped to each CDS

organism: Arthrobacter sp. AZCC_0090

source_name: batch cultured cells

extract_protocol:
Replicate filters were placed into microcentrifuge tubes containing glass disruptor beads, and frozen at -80ºC until extraction. RNA was extracted using a Qiagen RNEasy mini kit, per the manufacturer’s instructions. DNA was removed with Ambion TURBO DNase per the manufacturer’s instructions.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices. Samples were sequenced on a NextSeq2000 giving 2x51bp reads. Demultiplexing, quality control, and adapter trimming was performed with BCL Convert v3.9.3. The quality of generated raw reads was assessed by FastQC v0.73 via Galaxy (galaxy0)

value: batch cultured cells

value: hydrated control

value: day 16


title: RNA, Macrophage, Wild Type, LPS, 6h, rep2

description: Library name: BSMJ007_WTN_M_BM_LPS_06h00min

value: Macrophage

value: Lipopolysaccharide (LPS)


title: BMDC IL4 3

description: Library name: M3_BMDC_IL4

value: BMDC


title: Arthrobacter sp. AZCC_0090, day 16 treatment, replicate 4

description:
Library name: day16_treatment_rep4
Day.16.treatment.rep.4

value: desiccated-rehydrated


title: experiment_H001AS8_K22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: Arthrobacter sp. AZCC_0090, day 2 control, replicate 1

description:
Library name: day2_control_rep1
Day.2.control.rep.1


title: BMDC IFNy 3

description: Library name: M3_BMDC_IFNy

value: IFNy


title: Arthrobacter sp. AZCC_0090, day 16 treatment, replicate 2

description:
Library name: day16_treatment_rep2
Day.16.treatment.rep.2


title: RNA, Macrophage, Wild Type, LPS, 3h, rep2

description: Library name: BSMJ007_WTN_M_BM_LPS_03h00min


title: experiment_H001AS8_K23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, Wild Type, IFNg+LPS, 6h, rep2

description: Library name: BSMJ007_WTN_M_BM_IFNg.LPS_06h00min

value: IFNg + LPS


title: BMDC Control 3

description: Library name: M3_BMDC_Control

value: Control


title: experiment_H001AS8_K21_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: Arthrobacter sp. AZCC_0090, day 16 treatment, replicate 1

description:
Library name: day16_treatment_rep1
Day.16.treatment.rep.1


title: experiment_H001AS8_K20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, Wild Type, IFNg+LPS, 3h, rep2

description: Library name: BSMJ007_WTN_M_BM_IFNg.LPS_03h00min

value: Bone Marrow


title: BMDM TGFb 2

description: Library name: M2_BMDM_TGFb

value: BMDM

value: TGFb


title: Arthrobacter sp. AZCC_0090, day 16 control, replicate 5

description:
Library name: day16_control_rep5
Day.16.control.rep.5

value: day 14


title: experiment_H001AS8_K19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM IL10 2

description: Library name: M2_BMDM_IL10


title: Arthrobacter sp. AZCC_0090, day 2 control, replicate 7

description:
Library name: day2_control_rep7
Day.2.control.rep.7

value: batch cultured cells


title: RNA, Macrophage, STAT1 KO, Untreated, 14h, rep2

description: Library name: BSMJ007_STAT1KO_M_BM_UT_14h00min

value: STAT1 KO

value: Untreated


title: experiment_H001AS8_K18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_K17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, Wild Type, Interferon gamma, 14h, rep2

description: Library name: BSMJ007_WTN_M_BM_IFNg_14h00min

value: Macrophage

value: Wild Type

value: Interferon gamma (IFNg)


title: Arthrobacter sp. AZCC_0090, day 16 control, replicate 3

description:
Library name: day16_control_rep3
Day.16.control.rep.3

value: hydrated control


title: BMDM IL4 2

description: Library name: M2_BMDM_IL4


title: Arthrobacter sp. AZCC_0090, day 16 control, replicate 2

description:
Library name: day16_control_rep2
Day.16.control.rep.2


title: experiment_H001AS8_K16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: BMDM IFNy 2

description: Library name: M2_BMDM_IFNy


title: RNA, Macrophage, STAT1 KO, LPS, 3h, rep2

description: Library name: BSMJ007_STAT1KO_M_BM_LPS_03h00min

value: Lipopolysaccharide (LPS)


title: BMDM Control 2

description: Library name: M2_BMDM_Control


title: Arthrobacter sp. AZCC_0090, day 14 treatment, replicate 5

description:
Library name: day14_treatment_rep5
Day.14.treatment.rep.5

value: desiccated-rehydrated


title: Arthrobacter sp. AZCC_0090, day 14 treatment, replicate 2

description:
Library name: day14_treatment_rep2
Day.14.treatment.rep.2


title: experiment_H001AS8_K15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: RNA, Macrophage, STAT1 KO, IFNg+LPS, 3h, rep2

description: Library name: BSMJ007_STAT1KO_M_BM_IFNg.LPS_03h00min

value: IFNg + LPS


title: RNA, Macrophage, STAT1 KO, IFNg+LPS, 6h, rep2

description: Library name: BSMJ007_STAT1KO_M_BM_IFNg.LPS_06h00min

value: Bone Marrow


title: experiment_H001AS8_K14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arthrobacter sp. AZCC_0090, day 14 treatment, replicate 1

description:
Library name: day14_treatment_rep1
Day.14.treatment.rep.1


title: BMDC IL10 2

description: Library name: M2_BMDC_IL10

value: BMDC


title: Arthrobacter sp. AZCC_0090, day 14 control, replicate 5

description:
Library name: day14_control_rep5
Day.14.control.rep.5

value: day 8


title: RNA, Macrophage, STAT1 KO, Interferon gamma, 14h, rep2

description: Library name: BSMJ007_STAT1KO_M_BM_IFNg_14h00min


title: BMDC IL4 2

description: Library name: M2_BMDC_IL4


title: experiment_H001AS8_K12_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: RNA, Macrophage, STAT1beta KI, Untreated, 14h, rep2

description: Library name: BSMJ007_STAT1BB_M_BM_UT_14h00min

value: STAT1beta KI


title: experiment_H001AS8_K11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC IFNy 2

description: Library name: M2_BMDC_IFNy

value: IFNy


title: RNA, Macrophage, STAT1beta KI, LPS, 6h, rep2

description: Library name: BSMJ007_STAT1BB_M_BM_LPS_06h00min


title: RNA, Macrophage, STAT1 KO, LPS, 6h, rep2

description: Library name: BSMJ007_STAT1KO_M_BM_LPS_06h00min

value: STAT1 KO


title: Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 5

description:
Library name: day8_treatment_rep5
Day.8.treatment.rep.5

value: batch cultured cells


title: Arthrobacter sp. AZCC_0090, day 14 control, replicate 2

description:
Library name: day14_control_rep2
Day.14.control.rep.2


title: BMDM TGFb 1

description: Library name: M1_BMDM_TGFb

value: BMDM

value: TGFb


title: RNA, Macrophage, STAT1beta KI, LPS, 3h, rep2

description: Library name: BSMJ007_STAT1BB_M_BM_LPS_03h00min

value: Macrophage


title: BMDC Control 2

description: Library name: M2_BMDC_Control

value: Control


title: experiment_H001AS8_K09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: experiment_H001AS8_K08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC TGFb 2

description: Library name: M2_BMDC_TGFb


title: RNA, Macrophage, STAT1beta KI, IFNg+LPS, 3h, rep2

description: Library name: BSMJ007_STAT1BB_M_BM_IFNg.LPS_03h00min


title: Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 3

description:
Library name: day8_treatment_rep3
Day.8.treatment.rep.3


title: BMDM IL10 1

description: Library name: M1_BMDM_IL10


title: experiment_H001AS8_K07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep2

description: Library name: BSMJ007_STAT1BB_M_BM_IFNg_14h00min

value: Interferon gamma (IFNg)


title: Arthrobacter sp. AZCC_0090, day 14 control, replicate 3

description:
Library name: day14_control_rep3
Day.14.control.rep.3

value: hydrated control


title: Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 2

description:
Library name: day8_treatment_rep2
Day.8.treatment.rep.2

value: desiccated-rehydrated


title: BMDM IFNy 1

description: Library name: M1_BMDM_IFNy


title: BMDM IL4 1

description: Library name: M1_BMDM_IL4


title: experiment_H001AS8_K13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: experiment_H001AS8_K06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arthrobacter sp. AZCC_0090, day 8 control, replicate 5

description:
Library name: day8_control_rep5
Day.8.control.rep.5

value: day 2


title: experiment_H001AS8_K03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1alpha KI, LPS, 3h, rep2

description: Library name: BSMJ007_STAT1AA_M_BM_LPS_03h00min

value: Bone Marrow

value: STAT1alpha KI

value: Lipopolysaccharide (LPS)


title: BMDC IL10 1

description: Library name: M1_BMDC_IL10

value: BMDC


title: experiment_H001AS8_K10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDM Control 1

description: Library name: M1_BMDM_Control


title: experiment_H001AS8_K05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC TGFb 1

description: Library name: M1_BMDC_TGFb


title: experiment_H001AS8_K04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arthrobacter sp. AZCC_0090, day 2 treatment, replicate 5

description:
Library name: day2_treatment_rep5
Day.2.treatment.rep.5


title: Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 4

description:
Library name: day8_treatment_rep4
Day.8.treatment.rep.4

value: day 8


title: Arthrobacter sp. AZCC_0090, day 8 control, replicate 3

description:
Library name: day8_control_rep3
Day.8.control.rep.3

value: batch cultured cells


title: RNA, Macrophage, STAT1alpha KI, Untreated, 14h, rep2

description: Library name: BSMJ007_STAT1AA_M_BM_UT_14h00min

value: Untreated


title: RNA, Macrophage, STAT1alpha KI, IFNg+LPS, 6h, rep2

description: Library name: BSMJ007_STAT1AA_M_BM_IFNg.LPS_06h00min

value: IFNg + LPS


title: Arthrobacter sp. AZCC_0090, day 8 control, replicate 1

description:
Library name: day8_control_rep1
Day.8.control.rep.1


title: RNA, Macrophage, STAT1beta KI, IFNg+LPS, 6h, rep2

description: Library name: BSMJ007_STAT1BB_M_BM_IFNg.LPS_06h00min

value: Macrophage

value: STAT1beta KI


title: BMDC IL4 1

description: Library name: M1_BMDC_IL4


title: experiment_H001AS8_K02_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: RNA, Macrophage, STAT1alpha KI, IFNg+LPS, 3h, rep2

description: Library name: BSMJ007_STAT1AA_M_BM_IFNg.LPS_03h00min


title: BMDC IFNy 1

description: Library name: M1_BMDC_IFNy

value: IFNy


title: experiment_H001AS8_K01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1alpha KI, LPS, 6h, rep2

description: Library name: BSMJ007_STAT1AA_M_BM_LPS_06h00min


title: RNA, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep2

description: Library name: BSMJ007_STAT1AA_M_BM_IFNg_14h00min

value: Interferon gamma (IFNg)


title: RNA, Macrophage, Wild Type, Untreated, 14h, rep1

description: Library name: BSMJ006_WTN_M_BM_UT_14h00min

value: Wild Type


title: Arthrobacter sp. AZCC_0090, day 2 treatment, replicate 3

description:
Library name: day2_treatment_rep3
Day.2.treatment.rep.3

value: desiccated-rehydrated


title: MSQ43: RNA-seq

city: Novosibirsk

first: Andrey

last: Popov

address: Academician Lavrentiev Avenue, 10

country: Russia

institute: Institute of Cytology and Genetics, SB RAS

data_processing:
ChIP-seq: The quality of raw reads was analyzed using FASTQC (Andrews 2010) and multiQC (Ewels et al. 2016) Illumina adapters were cut using the Cutadapt (Martin 2011) program. Then, raw reads were processed including trimming, aligning, peak calling, filtering, and quality controlling using ENCODE ChIP-seq AQUAS pipeline (https://github.com/kundajelab/chipseq_pipeline). We used AsteI4  as a reference genome. Consistency between replicates was analyzed using functions makeTagDirectory and analyzeRepeats.pl from HOMER Software (Heinz et al. 2010) for computing RPKM values. The obtained RPKM values were correlated using python library scipy.stat for Spearman’s correlation calculation and matplotlib library for hexbin graph plotting.
RNA-seq: Raw reads were processed at usegalaxy.org (The Galaxy Community et al. 2024) using FASTQC (Andrews 2010), multiQC (Ewels et al. 2016) and Trimmomatic (Bolger et al. 2014) tools  for quality control. Trimmed reads were aligned  to the reference genome AsteI4 using Hisat2 (Kim et al. 2019). Transcriptome assembly was done using Stringtie (Pertea et al. 2015) and Stringtie-merge tools. Normalized FPKM values were generated using Stringtie tool and gtf file created by Stringtie-merge. Consistency between replicates and PCA analysis were done using python.
Assembly: AsteI2_V4.fa
Supplementary files format and content: .bigwig files

organism: Anopheles stephensi

source_name: cell line

growth_protocol: Adhesive monolayered MSQ43 cells (Fig. 1, B) were maintained at 28C in 5% CO2 at approximately 60-80% confluence in MEM (Minimum Essential Medium) with Earle′s salts (Sigma Aldrich, #0275) containing 5% heat-inactivated fetal bovine serum (Sigma Aldrich, #F9665), 0.1% D-glucose (Sigma Aldrich, G7021), 1 mM NEAA (Sigma Aldrich, #M7145), 2 mM L-glutamine (Thermo Fisher Scientific, #35050038), 1x vitamin solution (Thermo Fisher Scientific, #11120052), 2.2g/L sodium bicarbonate, and 1% Penicillin/Streptomycin (Sigma Aldrich,#P4333). TripleExpress (Thermo Fisher Scientific, #12604013) was used for harvesting/passaging. 10% DMSO in KSR (Thermo Fisher Scientific, #10828028) was used for freezing.

extract_protocol:
ChIP-Seq: DNA was extracted using ChIP DNA Clean & Concentrator columns (Zymo Research, D5205). RNA-seq: Total RNA was extracted using Aurum™ Total RNA Mini Kit (Bio-Rad, #7326820). 1-2 mln cells were lysed followed by purification on silica membrane in a spin-column format using a spin-mediated protocol, including DNA digestion for 25 minutes.
ChIP-seq libraries were prepared for sequencing using Kapa Hyper Prep Kit (Roche, #KK8504) and a KAPA Single-Indexed Adapter Set A, (Roche, #KK8701). RNA-seq: after purification concentration of RNA was measured with a Qubit 4 spectrophotometer using Qubit RNA HS Assay kit (Thermo Fisher Scientific, #Q32852), then samples were sent for RNA sequencing to the BGI facility (Hong Kong).

value: cell line


title: BMDC Control 1

description: Library name: M1_BMDC_Control

value: Control


title: experiment_H001AS8_J24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: experiment_H001AS8_J23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arthrobacter sp. AZCC_0090, day 2 treatment, replicate 4

description:
Library name: day2_treatment_rep4
Day.2.treatment.rep.4

value: day 2


title: MSQ43: ChIP-seq: H3K27me3


title: BMDC IL10 5

description: Library name: M5_BMDC_IL10

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 7- to 12-week-old C57BL/6J mice and then passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dishes (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 20 ng/ml recombinant GM-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 or 4  with IL-4 (20 ng/ml, PeproTech), IL-10 (100 ng/ml), TGF-β (100 ng/ml), or IFNγ (20 ng/ml, PeproTech). The BM cells were harvested for analysis on day 7 from the temperature-responsive cell culture plates after cooling to room temperature. Cells were washed twice in PBS and centrifuged (300g, 10 min) before processing.

value: BMDC


title: RNA, Macrophage, Wild Type, LPS, 3h, rep1

description: Library name: BSMJ006_WTN_M_BM_LPS_03h00min

value: Bone Marrow

value: Lipopolysaccharide (LPS)


title: BMDC TGFb 4

description: Library name: M4_BMDC_TGFb

value: TGFb


title: RNA, Macrophage, Wild Type, LPS, 6h, rep1

description: Library name: BSMJ006_WTN_M_BM_LPS_06h00min


title: experiment_H001AS8_J22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_J21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC IL4 5

description: Library name: M5_BMDC_IL4


title: BMDC IL10 4

description: Library name: M4_BMDC_IL10


title: BMDC IL4 4

description: Library name: M4_BMDC_IL4


title: MSQ43: ChIP-seq: H3K27ac


title: RNA, Macrophage, Wild Type, IFNg+LPS, 6h, rep1

description: Library name: BSMJ006_WTN_M_BM_IFNg.LPS_06h00min

value: IFNg + LPS


title: experiment_H001AS8_J19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_J20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC IFNy 4

description: Library name: M4_BMDC_IFNy


title: MSQ43: ChIP-seq: H2AK119Ubiq


title: RNA, Macrophage, Wild Type, IFNg+LPS, 3h, rep1

description: Library name: BSMJ006_WTN_M_BM_IFNg.LPS_03h00min

value: Macrophage


title: RNA, Macrophage, STAT1 KO, Untreated, 14h, rep1

description: Library name: BSMJ006_STAT1KO_M_BM_UT_14h00min

value: STAT1 KO

value: Untreated


title: HPV072-Z149-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

city: Rahway

first: Yuhyun

last: Ji

state: NJ

address: 126 E Lincoln Ave

institute: Merck & Co., Inc.

description: Library name: G08_sample04_time06

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.

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: RNA, Macrophage, Wild Type, Interferon gamma, 14h, rep1

description: Library name: BSMJ006_WTN_M_BM_IFNg_14h00min

value: Wild Type

value: Interferon gamma (IFNg)


title: HPV072-Z149-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample04_time05

value: Day 1 after boost dose


title: HPV072-Z149-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample04_time04

value: Day 0 after boost dose


title: MSQ43: ChIP-seq: H3K9me3

value: cell line


title: experiment_H001AS8_J15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: MSQ43: ChIP-seq: H3K4me3


title: BMDC IL4 3

description: Library name: M3_BMDC_IL4

value: BMDC


title: RNA, Macrophage, STAT1 KO, IFNg+LPS, 6h, rep1

description: Library name: BSMJ006_STAT1KO_M_BM_IFNg.LPS_06h00min

value: Bone Marrow


title: HPV072-Z149-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample04_time02

value: Day 1 after prime dose


title: BMDC IFNy 3

description: Library name: M3_BMDC_IFNy

value: IFNy


title: RNA, Macrophage, STAT1 KO, IFNg+LPS, 3h, rep1

description: Library name: BSMJ006_STAT1KO_M_BM_IFNg.LPS_03h00min

value: Macrophage

value: IFNg + LPS


title: RNA, Macrophage, STAT1 KO, Interferon gamma, 14h, rep1

description: Library name: BSMJ006_STAT1KO_M_BM_IFNg_14h00min

value: STAT1 KO


title: HPV072-Z149-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample04_time01

value: Blood

value: Day 0 after prime dose


title: HPV072-Z67-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample03_time06

value: Day 7 after boost dose


title: experiment_H001AS8_J18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC Control 4

description: Library name: M4_BMDC_Control

value: Control


title: RNA, Macrophage, STAT1beta KI, LPS, 6h, rep1

description: Library name: BSMJ006_STAT1BB_M_BM_LPS_06h00min

value: STAT1beta KI

value: Lipopolysaccharide (LPS)


title: experiment_H001AS8_J17_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: experiment_H001AS8_J11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC TGFb 3

description: Library name: M3_BMDC_TGFb

value: TGFb


title: experiment_H001AS8_J16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: BMDC IL10 3

description: Library name: M3_BMDC_IL10


title: RNA, Macrophage, STAT1 KO, LPS, 3h, rep1

description: Library name: BSMJ006_STAT1KO_M_BM_LPS_03h00min


title: RNA, Macrophage, STAT1beta KI, LPS, 3h, rep1

description: Library name: BSMJ006_STAT1BB_M_BM_LPS_03h00min


title: experiment_H001AS8_J12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23


title: experiment_H001AS8_J10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: RNA, Macrophage, STAT1 KO, LPS, 6h, rep1

description: Library name: BSMJ006_STAT1KO_M_BM_LPS_06h00min


title: BMDC IL4 2

description: Library name: M2_BMDC_IL4

value: BMDC


title: BMDC Control 3

description: Library name: M3_BMDC_Control


title: HPV072-Z149-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample04_time03

value: Day 7 after prime dose


title: experiment_H001AS8_J13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1beta KI, IFNg+LPS, 6h, rep1

description: Library name: BSMJ006_STAT1BB_M_BM_IFNg.LPS_06h00min

value: Bone Marrow


title: experiment_H001AS8_J14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z67-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample03_time05

value: Day 1 after boost dose


title: HPV072-Z67-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample03_time02

value: Day 1 after prime dose


title: BMDC TGFb 2

description: Library name: M2_BMDC_TGFb


title: BMDC Control 2

description: Library name: M2_BMDC_Control


title: HPV072-Z67-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample03_time01


title: experiment_H001AS8_J06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z67-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample03_time04

value: Day 0 after boost dose


title: RNA, Macrophage, STAT1beta KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ006_STAT1BB_M_BM_IFNg_14h00min

value: Macrophage

value: Interferon gamma (IFNg)


title: BMDC IL10 2

description: Library name: M2_BMDC_IL10


title: HPV072-Z195-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample02_time06

value: Blood


title: experiment_H001AS8_J07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1beta KI, Untreated, 14h, rep1

description: Library name: BSMJ006_STAT1BB_M_BM_UT_14h00min

value: Untreated


title: BMDC IFNy 2

description: Library name: M2_BMDC_IFNy

value: IFNy


title: HPV072-Z67-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample03_time03


title: RNA, Macrophage, STAT1alpha KI, Untreated, 14h, rep1

description: Library name: BSMJ006_STAT1AA_M_BM_UT_14h00min

value: STAT1alpha KI


title: BMDC TGFb 1

description: Library name: M1_BMDC_TGFb


title: BMDC IL10 1

description: Library name: M1_BMDC_IL10


title: experiment_H001AS8_J09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: BMDC IL4 1

description: Library name: M1_BMDC_IL4


title: RNA, Macrophage, STAT1alpha KI, LPS, 3h, rep1

description: Library name: BSMJ006_STAT1AA_M_BM_LPS_03h00min

value: Lipopolysaccharide (LPS)


title: experiment_H001AS8_J08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z195-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample02_time05


title: BMDC IFNy 1

description: Library name: M1_BMDC_IFNy


title: experiment_H001AS8_J05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1beta KI, IFNg+LPS, 3h, rep1

description: Library name: BSMJ006_STAT1BB_M_BM_IFNg.LPS_03h00min

value: STAT1beta KI

value: IFNg + LPS


title: RNA, Macrophage, STAT1alpha KI, LPS, 6h, rep1

description: Library name: BSMJ006_STAT1AA_M_BM_LPS_06h00min


title: HPV072-Z195-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample02_time04


title: experiment_H001AS8_J03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: experiment_H001AS8_J02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: HPV072-Z195-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample02_time02


title: HPV072-Z195-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample02_time03

value: Day 7 after prime dose


title: BMDC Control 1

description: Library name: M1_BMDC_Control

value: BMDC

value: Control


title: experiment_H001AS8_J04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1alpha KI, IFNg+LPS, 3h, rep1

description: Library name: BSMJ006_STAT1AA_M_BM_IFNg.LPS_03h00min

value: Bone Marrow


title: 18mo mouse, bulk retina, suppl, rep3

city: Irvine

first: Emily

last: Tom

state: CA

address: 847 Health Sciences Quad, FLF Lab #6131A

institute: University of California, Irvine

description:
Library name: 18mo_mouse_bulk_retina_SUPPL_replicate_3
Column in RAWCOUNTS_18mo_VEHvsSUPPL.txt: 18mo_supp_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter and low quality reads from raw data.
All clean-reads were mapped to Mus musculus reference genome mm10 by HISAT2 (2.2.1)
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.42.0). The threshold of significant differential expression：padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bulk retina

extract_protocol:
RNA was extracted from fresh retinas using TRIzol Reagent (15596026, Invitrogen)
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strandcDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Thelibrary was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: For supplementation experiments, 0.36nmol 24:5 was unilaterally supplemented via intravitreal injection in 18-month-old mice, with the contralateral eye serving as a vehicle-injected control. Retinas were collected 5 days following injection for RNAsequencing.

value: bulk retina

value: 18 months

value: WT

value: intravitreal 24:5 suppl


title: experiment_H001AS8_J01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RNA, Macrophage, STAT1alpha KI, Interferon gamma, 14h, rep1

description: Library name: BSMJ006_STAT1AA_M_BM_IFNg_14h00min

value: Macrophage

value: Interferon gamma (IFNg)


title: 18mo mouse, bulk retina, suppl, rep2

description:
Library name: 18mo_mouse_bulk_retina_SUPPL_replicate_2
Column in RAWCOUNTS_18mo_VEHvsSUPPL.txt: 18mo_supp_2


title: experiment_H001AS8_I24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 18mo mouse, bulk retina, suppl, rep1

description:
Library name: 18mo_mouse_bulk_retina_SUPPL_replicate_1
Column in RAWCOUNTS_18mo_VEHvsSUPPL.txt: 18mo_supp_1


title: HPV072-Z185-Grp4-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample01_time06

value: Blood

value: Day 7 after boost dose


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

description: Library name: BSMJ012_WTN_M_BM_UT_14h00min_ChIP_Input

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

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.

value: Wild Type

value: Untreated


title: HPV072-Z195-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample02_time01

value: Day 0 after prime dose


title: experiment_H001AS8_I23_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: HPV072-Z185-Grp4-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample01_time05

value: Day 1 after boost dose


title: 18mo mouse, bulk retina, vehicle, rep3

description:
Library name: 18mo_mouse_bulk_retina_VEH_replicate_3
Column in RAWCOUNTS_18mo_VEHvsSUPPL.txt: 18mo_veh_3

value: intravitreal vehicle


title: experiment_H001AS8_I22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: RNA, Macrophage, STAT1alpha KI, IFNg+LPS, 6h, rep1

description: Library name: BSMJ006_STAT1AA_M_BM_IFNg.LPS_06h00min

value: Bone Marrow

value: STAT1alpha KI

value: IFNg + LPS


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

description: Library name: BSMJ012_WTN_M_BM_IFNg_LPS_03h00min_ChIP_Input


title: HPV072-Z185-Grp4-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample01_time03

value: Day 7 after prime dose


title: experiment_H001AS8_I21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z185-Grp4-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample01_time04

value: Day 0 after boost dose


title: 18mo mouse, bulk retina, vehicle, rep1

description:
Library name: 18mo_mouse_bulk_retina_VEH_replicate_1
Column in RAWCOUNTS_18mo_VEHvsSUPPL.txt: 18mo_veh_1

value: bulk retina

value: 18 months

value: WT


title: 18mo mouse, bulk retina, vehicle, rep2

description:
Library name: 18mo_mouse_bulk_retina_VEH_replicate_2
Column in RAWCOUNTS_18mo_VEHvsSUPPL.txt: 18mo_veh_2


title: experiment_H001AS8_I20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


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

description: Library name: BSMJ012_WTN_M_BM_IFNg_14h00min_ChIP_Input

value: Macrophage

value: Interferon gamma (IFNg)


title: 18mo mouse, bulk retina, WT, rep4

description:
Library name: 18mo_mouse_bulk_retina_WT_replicate_4
Column in FPKM_12movs18mo_Elovl2.txt: WT4_18mo


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

description: Library name: BSMJ012_STAT1KO_M_BM_LPS_03h00min_ChIP_Input

value: STAT1 KO

value: Lipopolysaccharide (LPS)


title: HPV072-Z185-Grp4-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample01_time01

value: Blood

value: Day 0 after prime dose


title: experiment_H001AS8_I18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: 18mo mouse, bulk retina, WT, rep3

description:
Library name: 18mo_mouse_bulk_retina_WT_replicate_3
Column in FPKM_12movs18mo_Elovl2.txt: WT3_18mo


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

description: Library name: BSMJ012_STAT1KO_M_BM_UT_14h00min_ChIP_Input

value: Untreated


title: HPV072-Z185-Grp4-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G08_sample01_time02

value: Day 1 after prime dose


title: experiment_H001AS8_I19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: experiment_H001AS8_I17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 18mo mouse, bulk retina, WT, rep1

description:
Library name: 18mo_mouse_bulk_retina_WT_replicate_1
Column in FPKM_12movs18mo_Elovl2.txt: WT1_18mo


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

description: Library name: BSMJ012_STAT1KO_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: Bone Marrow

value: IFNg + LPS


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

description: Library name: BSMJ012_STAT1KO_M_BM_IFNg_14h00min_ChIP_Input


title: HPV072-17R19-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample12_time05

value: Day 1 after boost dose


title: experiment_H001AS8_I16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


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

description: Library name: BSMJ012_WTN_M_BM_LPS_03h00min_ChIP_Input

value: Wild Type


title: HPV072-17R19-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample12_time04

value: Day 0 after boost dose


title: HPV072-17R19-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample12_time06

value: Day 7 after boost dose


title: 18mo mouse, bulk retina, WT, rep2

description:
Library name: 18mo_mouse_bulk_retina_WT_replicate_2
Column in FPKM_12movs18mo_Elovl2.txt: WT2_18mo

value: bulk retina

value: 18 months

value: WT


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

description: Library name: BSMJ012_STAT1BB_M_BM_UT_14h00min_ChIP_Input

value: Macrophage

value: STAT1beta KI


title: experiment_H001AS8_I15_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: 12mo mouse, bulk retina, Elovl2, rep3

description:
Library name: 12mo_mouse_bulk_retina_Elovl2_replicate_3
Column in FPKM_12movs18mo_Elovl2.txt: Mut3_12mo

value: 12 months


title: 12mo mouse, bulk retina, Elovl2, rep2

description:
Library name: 12mo_mouse_bulk_retina_Elovl2_replicate_2
Column in FPKM_12movs18mo_Elovl2.txt: Mut2_12mo


title: HPV072-17R19-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample12_time02

value: Blood


title: HPV072-17R19-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample12_time03

value: Day 7 after prime dose


title: experiment_H001AS8_I14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


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

description: Library name: BSMJ012_STAT1BB_M_BM_IFNg_LPS_03h00min_ChIP_Input


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

description: Library name: BSMJ012_STAT1BB_M_BM_IFNg_14h00min_ChIP_Input

value: Interferon gamma (IFNg)


title: 12mo mouse, bulk retina, Elovl2, rep1

description:
Library name: 12mo_mouse_bulk_retina_Elovl2_replicate_1
Column in FPKM_12movs18mo_Elovl2.txt: Mut1_12mo


title: experiment_H001AS8_I13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


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

description: Library name: BSMJ012_STAT1AA_M_BM_UT_14h00min_ChIP_Input

value: Bone Marrow

value: STAT1alpha KI

value: Untreated


title: 12mo mouse, bulk retina, WT, rep3

description:
Library name: 12mo_mouse_bulk_retina_WT_replicate_3
Column in FPKM_12movs18mo_Elovl2.txt: WT3_12mo


title: experiment_H001AS8_I12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 12mo mouse, bulk retina, WT, rep2

description:
Library name: 12mo_mouse_bulk_retina_WT_replicate_2
Column in FPKM_12movs18mo_Elovl2.txt: WT2_12mo


title: HPV072-17R19-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample12_time01

value: Day 0 after prime dose


title: experiment_H001AS8_I11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z138-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample11_time05

value: Day 1 after boost dose


title: experiment_H001AS8_I10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-Z138-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample11_time04

value: Day 0 after boost dose


title: HPV072-Z138-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample11_time03


title: experiment_H001AS8_I09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


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

description: Library name: BSMJ012_STAT1AA_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: IFNg + LPS


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

description: Library name: BSMJ012_STAT1AA_M_BM_LPS_03h00min_ChIP_Input

value: Lipopolysaccharide (LPS)


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

description: Library name: BSMJ012_STAT1BB_M_BM_LPS_03h00min_ChIP_Input

value: Macrophage


title: 12mo mouse, bulk retina, WT, rep1

description:
Library name: 12mo_mouse_bulk_retina_WT_replicate_1
Column in FPKM_12movs18mo_Elovl2.txt: WT1_12mo

value: bulk retina

value: WT


title: Wdr4^cKO.input

city: Wuhan City

first: JIe

last: Liu

state: Hubei

address: No.299 Bayi Road, Wuchang District

institute: Wuhan University

description: Library name: Sample9

data_processing:
For input RNA, raw reads generated from sequencing were filtered using fastp (v0.18.0) to obtain high-quality clean reads. Filtering steps included: removing reads containing adapter sequences; removing reads with more than 10% unknown nucleotides (N); removing reads in which more than 50% of bases had low quality removing reads in which more than 50% of bases had low quality (Q-value less than or equal to 20). For footprint RNA, low-quality reads were also filtered using fastp. Reads with more than 50% low-quality bases or more than 10% N bases were removed. Adapter sequences were trimmed, and reads of 20–40 bp in length were retained for further analysis. Clean reads were mapped to rRNA reference databases (GenBank and Rfam) using Bowtie2, and reads aligned to rRNA, tRNA, snRNA, snoRNA, or miRNA were excluded.
Assembly: Mus musculus, Ensembl_release111
Supplementary files format and content: txt files include TPM values for each Sample

source_name: TAMs sorted from Hepa1-6 orthotopic tumor

extract_protocol:
For input RNA, total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, cells were lysed in TRIzol, followed by the addition of chloroform and centrifugation to separate the aqueous and organic phases. Under acidic conditions, RNA partitions into the aqueous phase, which was collected and precipitated with isopropanol to recover RNA.  For footprint RNA, ribosome profiling was performed based on a standard protocol with minor modifications. Cell lysates were mechanically sheared, clarified by centrifugation, and treated with RNase I and DNase I to digest unprotected RNA and DNA. Digestion was stopped with SUPERase·In, and ribosome-protected fragments (RFs) were purified using MicroSpin S-400 HR columns and size-selected (>17 nt) with the RNA Clean & Concentrator-25 kit (Zymo Research). rRNA was depleted by hybridization with antisense DNA probes followed by RNase H and DNase I digestion. Final RFs were purified using magnetic beads (Vazyme).
For input RNA, mRNA was enriched using mRNA Capture Beads, followed by heat-induced fragmentation. First-strand cDNA synthesis was performed using a reverse transcription enzyme mix, and during second-strand synthesis, end repair and A-tailing were completed. Adaptors were then ligated, and target fragments were selected using Hieff NGS® DNA Selection Beads. PCR amplification was performed to generate the final libraries, which were sequenced on the Illumina NovaSeq X Plus platform.  For footprint RNA, libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (E7300S/L). Adapters were ligated to both ends of ribosome-protected fragments (RFs), followed by reverse transcription and PCR amplification. PCR products of 140–160 bp were size-selected and used to generate cDNA libraries, which were sequenced on the Illumina NovaSeq X Plus platform by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: macrophages


title: experiment_H001AS8_I08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


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

description: Library name: BSMJ011_WTN_M_BM_UT_14h00min_ChIP_Input

value: Wild Type


title: HPV072-Z138-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample11_time02

value: Blood

value: Day 1 after prime dose


title: HPV072-Z138-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample11_time01


title: experiment_H001AS8_I07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: Wdr4^ff.input

description: Library name: Sample7

value: TAMs sorted from Hepa1-6 orthotopic tumor


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

description: Library name: BSMJ011_WTN_M_BM_LPS_03h00min_ChIP_Input

value: Bone Marrow


title: HPV072-Z138-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample11_time06

value: Day 7 after boost dose


title: Wdr4^ff.ribo

description: Library name: Sample8

library_source: other

data_processing:
For input RNA, raw reads generated from sequencing were filtered using fastp (v0.18.0) to obtain high-quality clean reads. Filtering steps included: removing reads containing adapter sequences; removing reads with more than 10% unknown nucleotides (N); removing reads in which more than 50% of bases had low quality removing reads in which more than 50% of bases had low quality (Q-value less than or equal to 20). For footprint RNA, low-quality reads were also filtered using fastp. Reads with more than 50% low-quality bases or more than 10% N bases were removed. Adapter sequences were trimmed, and reads of 20–40 bp in length were retained for further analysis. Clean reads were mapped to rRNA reference databases (GenBank and Rfam) using Bowtie2, and reads aligned to rRNA, tRNA, snRNA, snoRNA, or miRNA were excluded.
Assembly: Mus musculus, Ensembl_release111
Supplementary files format and content: txt files include TPM values for each Sample
Library strategy: Ribo-Seq

molecule: other


title: experiment_H001AS8_I06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


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

description: Library name: BSMJ012_STAT1AA_M_BM_IFNg_14h00min_ChIP_Input

value: STAT1alpha KI

value: Interferon gamma (IFNg)


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

description: Library name: BSMJ011_WTN_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: IFNg + LPS


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

description: Library name: BSMJ011_WTN_M_BM_IFNg_14h00min_ChIP_Input


title: experiment_H001AS8_I05_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: HPV072-17R236-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample10_time05

value: Day 1 after boost dose


title: HPV072-17R236-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample10_time04

value: Day 0 after boost dose


title: experiment_H001AS8_I04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Wdr4^cKO.ribo

description: Library name: Sample10


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

description: Library name: BSMJ011_STAT1KO_M_BM_UT_14h00min_ChIP_Input

value: Macrophage

value: STAT1 KO

value: Untreated


title: sgWdr4-2.input

description: Library name: Sample5

source_name: iBMDM

value: iBMDM

value: macrophages


title: experiment_H001AS8_I03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: HPV072-17R236-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample10_time03

value: Blood

value: Day 7 after prime dose


title: experiment_H001AS8_I02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: sgWdr4-1.input

description: Library name: Sample3


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

description: Library name: BSMJ011_STAT1KO_M_BM_LPS_03h00min_ChIP_Input

value: Bone Marrow

value: Lipopolysaccharide (LPS)


title: HPV072-17R236-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample10_time02

value: Day 1 after prime dose


title: WT.ribo

description: Library name: Sample2


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

description: Library name: BSMJ011_STAT1KO_M_BM_IFNg_14h00min_ChIP_Input


title: experiment_H001AS8_I01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: WT.input

description: Library name: Sample1


title: sgWdr4-1.ribo

description: Library name: Sample4


title: HPV072-17R236-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample10_time01

value: Day 0 after prime dose


title: HPV072-Z54-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample09_time06

value: Day 7 after boost dose


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

description: Library name: BSMJ011_STAT1BB_M_BM_UT_14h00min_ChIP_Input

value: STAT1beta KI


title: LMI_MI

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: LMI_MI

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 individual cell types (Cardiomyocytes, Fibroblasts, or Myeloid)

source_name: Ventricular apex

growth_protocol: 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)

treatment_protocol: AAV9 virus expressing YAPon was administrated to P7 ICR mice by intraperitoneal injection. At 6 weeks of age, animals were injected with DMSO or LMI070. Two weeks later, left anterior descending (LAD) ligation was performed ("MI") or sham surgery ("Sham"). Ventricular tissue below the suture was separated from the heart 7 days following surgery.

value: Ventricular apex

tag: virus

value: YAPon

tag: drug

value: LMI

tag: surgery

value: MI

tag: day


title: HPV072-Z54-Grp3-W24-1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample09_time05

value: Day 1 after boost dose


title: HPV072-Z54-Grp3-W24_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample09_time04

value: Day 0 after boost dose


title: experiment_H001AS8_H22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

source_name: hPSC derived cardiomyocytes


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

description: Library name: BSMJ011_STAT1BB_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: Macrophage

value: IFNg + LPS


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

description: Library name: BSMJ011_STAT1BB_M_BM_LPS_03h00min_ChIP_Input


title: LMI_Sham

description: Library name: LMI_Sham

value: Sham

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


title: experiment_H001AS8_H21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: experiment_H001AS8_H24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: DMSO_MI

description: Library name: DMSO_MI

value: DMSO


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

description: Library name: BSMJ011_STAT1BB_M_BM_IFNg_14h00min_ChIP_Input

value: Bone Marrow

value: Interferon gamma (IFNg)


title: HPV072-17R236-Grp3-W24-7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample10_time06

value: Blood

value: Day 7 after boost dose


title: sgWdr4-2.ribo

description: Library name: Sample6

value: iBMDM

value: macrophages


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

description: Library name: BSMJ011_STAT1KO_M_BM_IFNg_LPS_03h00min_ChIP_Input

value: STAT1 KO


title: HPV072-Z54-Grp3-D7_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample09_time03

value: Day 7 after prime dose


title: experiment_H001AS8_H20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


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

description: Library name: BSMJ011_STAT1AA_M_BM_UT_14h00min_ChIP_Input

value: STAT1alpha KI

value: Untreated


title: HPV072-Z54-Grp3-D1_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample09_time02

value: Day 1 after prime dose


title: DMSO_Sham

description: Library name: DMSO_Sham

value: Ventricular apex

value: YAPon

value: Sham


title: experiment_H001AS8_H19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: HPV072-Z54-Grp3-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G07_sample09_time01

value: Day 0 after prime dose


title: experiment_H001AS8_H23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


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

description: Library name: BSMJ011_STAT1AA_M_BM_LPS_03h00min_ChIP_Input

value: Bone Marrow

value: Macrophage

value: Lipopolysaccharide (LPS)