title: P19_T48_HiC_replicate_2

city: Antwerp

first: Valeriya

last: Malysheva

state: Select State

address: Universiteitsplein 1, Building V

country: Belgium

institute: VIB Center for Molecular Neurology

data_processing:
Image analysis and base calling were performed using RTA 1.18.61   and CASAVA 1.8.2.
Raw paired-end sequencing reads were mapped against the mouse genome (mm9) with Bowtie2.
Low quality reads (MAPQ<=10), PCR duplicates and interactions falling within the same restriction fragment were filtered out using an in-house pipeline
Hi-C contact maps were constructed at 5kb resolution, then normalized by matrix balancing using the ICE algorithm.
Statistically significant interactions were identified by Fit-Hi-C
Reproducible between biological replicates interactions we defined using sdef R package
Interactions that appear in both biological replicates, pass the defined by sdef method cut-off and show at least 3 interactions in both replicates were considered as significant and have been used for further integrative analysis and GRN reconstruction
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated txt format files containing reproducible interactions per time point (non-differentiated, 6h ATRA treatment and 48h treatment)

source_name: P19 48h ATRA treatment replicate 2

growth_protocol: F9 EC cells were cultures in Dubelcco’s modified Eagle’s medium supplemented with 10% fetal Calf serum. In a similar manner, P19 cell’s medium was supplemented with 5% fetal Calf serum and 5% delipidated Calf serum. In both cases the medium was complemented with 40ug/ml Gentamicin. F9 or P19 EC cells were cultured in monolayer conditions seeded in gelatine-coated tissue culture plates (0.1%).

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized. DNA was then restricted and the overhangs filled in incorporating a biotinylated dCTP. Free ends were then ligated together. Crosslinks were reversed, the DNA was sheared to 200-400 bp, biotin from non-ligated ends removed and then biotinylated ligation junctions were recovered with streptavidin beads. DNA-bound beads were then used for the library preparation.
NebNext Ultra library prep kit for Illumina has been used. Per PCR reaction 1/5 of DNA-bound beads has been used for amplification (5 cycles). The library was then purified using SPRI beads and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.

treatment_protocol: For cell differentiation induction, ATRA was added to plates in a final concentration of 1x10-6 M at different time points.

value: P19 embryonal carcinoma cells


title: recombinant inbred line (RIL) JY157

status: Public on Sep 30 2025

type: SRA

city: Beijing

first: Xin

last: Lu

address: Zhongguancun South Street,Haidian District

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

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

molecule: genomic DNA

organism: Zea mays

source_name: leaf

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

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

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

tag: tissue

value: leaf


title: experiment_H001AS8_B15_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

organism: Homo sapiens

source_name: hPSC derived cardiomyocytes

growth_protocol: hPSC were differentiated into cardiomyocites with RBA media.

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

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

value: hPSC derived cardiomyocytes

tag: cell line

tag: cell type

value: hPSC derived cardiomyocytes DD23

tag: treatment

value: Tetracycline


title: P19_T48_HiC_replicate_1

organism: Mus musculus

source_name: P19 48h ATRA treatment replicate 1


title: 16-131-Grp5-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

city: Rahway

first: Yuhyun

last: Ji

state: NJ

address: 126 E Lincoln Ave

country: USA

institute: Merck & Co., Inc.

description: Library name: G05_sample05_time03

library_source: transcriptomic

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

molecule: total RNA

organism: Macaca mulatta

source_name: Blood

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

value: Blood

value: Day 7 after prime dose


title: experiment_H001AS8_B14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: P19_T6_HiC_replicate_1

source_name: P19 6h ATRA treatment replicate 1


title: recombinant inbred line (RIL) JY155


title: P19_T6_HiC_replicate_2

source_name: P19 6h ATRA treatment replicate 2


title: 16-131-Grp5-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample05_time02

value: Day 1 after prime dose


title: 16-131-Grp5-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample05_time01

value: Day 0 after prime dose


title: experiment_H001AS8_B13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: P19_T0_HiC_replicate_2

source_name: P19 non-diifferentiated replicate 2


title: HPV071-A14L101-Grp1-D0_PID22718_AID5442_Batch2_Mrk_RNA_Seq_09Apr2024_1712687142355

description: Library name: G06_sample01_time01


title: recombinant inbred line (RIL) JY153


title: experiment_H001AS8_B12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: A14L103-Grp5-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample04_time06

value: Day 7 after boost dose


title: P19_T0_HiC_replicate_1

source_name: P19 non-differentiated replicate 1


title: recombinant inbred line (RIL) JY152


title: experiment_H001AS8_B11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: A14L103-Grp5-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample04_time05

value: Day 1 after boost dose


title: recombinant inbred line (RIL) JY151


title: experiment_H001AS8_B10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: A14L103-Grp5-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample04_time04

value: Day 0 after boost dose


title: recombinant inbred line (RIL) JY150


title: recombinant inbred line (RIL) JY154


title: experiment_H001AS8_B09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY148


title: experiment_H001AS8_B08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: A14L103-Grp5-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample04_time02


title: recombinant inbred line (RIL) JY147


title: A14L103-Grp5-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample04_time01


title: recombinant inbred line (RIL) JY146


title: experiment_H001AS8_B06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY145


title: 17-40-Grp5-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample03_time05


title: 17-40-Grp5-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample03_time06


title: recombinant inbred line (RIL) JY144


title: experiment_H001AS8_B04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: A14L103-Grp5-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample04_time03


title: experiment_H001AS8_B03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 17-40-Grp5-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample03_time04


title: recombinant inbred line (RIL) JY142


title: Col-0_HH_24h4

city: Durham

first: Sheng Yang

last: He

address: 124 Science Drive

institute: Duke University

description: Library name: CO_C1123_60d_S19

data_processing:
The pool was loaded onto two (2) lanes of an Illumina S1 flow cell and sequencing was performed in a 1x100bp single end read format using a NovaSeq v1.5, 100 cycle reagent kit. Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. A summary of the run output is attached below. Basic QC information about  sequence data is provided by FastQC reports. Reads were mapped with TAIR genome using STAR and DEseq2 was used to identifiy  differntially expressed genes.
Sequence reads were trimmed and filtered for adapter sequence and low quality sequence using Trimmomatic (Used adapter file and filtering parameter: $adapterDir/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Alignment: Trimmed sequence reads were mapped to TAIR v10 using STAR aligner.
Read count extraction was performed using Subreads.
Read abundance measurment was performed using normalization function of DEseq2.
Assembly: TAIR version10
Supplementary files format and content: The csv file contains read counts mapped and counted by STAR aligner and Subreads.

organism: Arabidopsis thaliana

source_name: whole leaves

growth_protocol: Arabidopsis plants were placed under 60% relative humidity at the temperature range of 20 °C to 22 °C, and light intensity of 100 µmol m-2 s-1 with a 12-hour light, 12-hour dark photoperiod.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plant mini kit and cleaned up by QIAGEN DNase on-column Kit.
Libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit with IDT for Illumina RNA UD Indexes, following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were pooled in equimolar amounts and the pool quantified using the Invitrogen Collibri Quantification qPCR kit.

treatment_protocol: Arabidopsis plants were placed under 60% or 100% relative humidity at the set temperature range of 20-22°C.

value: whole leaves

tag: genotype

value: high humidity

tag: time


title: experiment_H001AS8_B07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_B02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY141


title: Col-0_HH_24h3

description: Library name: CO_C1123_60c_S14


title: 17-40-Grp5-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample03_time02


title: hiPSC-LO_9 days_rep4

type: RNA

city: Yokohama

first: Tomomi

last: Tadokoro

state: Kanagawa

address: 3-9 Fukuura

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays ( G4845A, G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for micro array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.

source_name: hiPSC-derived liver organoid cultured for 9 days after the fusion of hiPSC-LB_replicate4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: hiPSC-LB is generated by co-culture of hiPSC-derived hepatic endoderm, endothelial cells, and mesenchymal cells using Elplasia plate (Corning) for 1 day under 37ºC, 5% CO2 condition. One day later, hiPSC-LB were placed on cell culture insert and cultured for 9 days.

extract_protocol: Total RNA was extracted using PureLink® RNA Mini Kit (ThermoFisher Scientific) with on-column Dnase I treatment. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: hiPSC-derived liver organoid


title: hiPSC-LO_9 days_rep3

source_name: hiPSC-derived liver organoid cultured for 9 days after the fusion of hiPSC-LB_replicate3


title: hiPSC-LO_9 days_rep1

source_name: hiPSC-derived liver organoid cultured for 9 days after the fusion of hiPSC-LB_replicate1


title: hiPSC-LB_1day_rep4

source_name: hiPSC-derived liver bud cultured for 1 day_replicate4

value: hiPSC-derived liver bud


title: 17-40-Grp5-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample03_time01


title: Col-0_HH_24h2

description: Library name: CO_C1123_60b_S30


title: recombinant inbred line (RIL) JY140


title: hiPSC-LB_1day_rep2

source_name: hiPSC-derived liver bud cultured for 1 day_replicate2


title: hiPSC-LB_1day_rep1

source_name: hiPSC-derived liver bud cultured for 1 day_replicate1


title: A13L037-Grp5-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample02_time06


title: recombinant inbred line (RIL) JY143


title: Col-0_HH_24h1

description: Library name: CO_C1123_60a_S3


title: experiment_H001AS8_A23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: hiPSC-LO_9 days_rep2

source_name: hiPSC-derived liver organoid cultured for 9 days after the fusion of hiPSC-LB_replicate2


title: Col-0_HH_60min4

description: Library name: CO_C1123_24d_S38


title: A13L037-Grp5-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample02_time05


title: 17-40-Grp5-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample03_time03


title: recombinant inbred line (RIL) JY138


title: hiPSC-LB_1day_rep3

source_name: hiPSC-derived liver bud cultured for 1 day_replicate3


title: experiment_H001AS8_A22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: A13L037-Grp5-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample02_time04


title: recombinant inbred line (RIL) JY137

source_name: leaf


title: experiment_H001AS8_B01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

source_name: hPSC derived cardiomyocytes


title: Col-0_HH_60min3

description: Library name: CO_C1123_24c_S40


title: experiment_H001AS8_A21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Col-0_HH_60min2

description: Library name: CO_C1123_24b_S27


title: A13L037-Grp5-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample02_time03


title: recombinant inbred line (RIL) JY136


title: A13L037-Grp5-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample02_time02


title: Col-0_HH_60min1

description: Library name: CO_C1123_24a_S22


title: experiment_H001AS8_A20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY135


title: experiment_H001AS8_A24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: A13L037-Grp5-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample02_time01


title: Col-0_HH_15min4

description: Library name: CO_C1123_15d_S18


title: recombinant inbred line (RIL) JY139


title: recombinant inbred line (RIL) JY134


title: experiment_H001AS8_A18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 17-118-Grp5-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample01_time06


title: recombinant inbred line (RIL) JY133


title: Col-0_HH_15min3

description: Library name: CO_C1123_15c_S13


title: experiment_H001AS8_A17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY132


title: experiment_H001AS8_A16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 17-118-Grp5-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample01_time04


title: Col-0_HH_15min1

description: Library name: CO_C1123_15a_S2


title: recombinant inbred line (RIL) JY131


title: Col-0_HH_0min4

description: Library name: CO_C1123_0d_S37


title: recombinant inbred line (RIL) JY130


title: experiment_H001AS8_A15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 17-118-Grp5-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample01_time03


title: experiment_H001AS8_A14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 17-118-Grp5-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample01_time02


title: Col-0_HH_0min3

description: Library name: CO_C1123_0c_S32


title: recombinant inbred line (RIL) JY129


title: experiment_H001AS8_A13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Col-0_HH_0min2

description: Library name: CO_C1123_0b_S26


title: recombinant inbred line (RIL) JY128


title: experiment_H001AS8_A12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY127


title: Col-0_HH_0min1

description: Library name: CO_C1123_0a_S25


title: 17-118-Grp5-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample01_time05


title: experiment_H001AS8_A11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Col-0_HH_15min2

description: Library name: CO_C1123_15b_S8


title: recombinant inbred line (RIL) JY126


title: 17-184-Grp4-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample05_time05


title: 17-184-Grp4-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample05_time04


title: recombinant inbred line (RIL) JY125


title: rat tenocyte H4K16_LA

first: Tong

last: Pan

address: Northern Garden Road

institute: peking university third hospital

description: Library name: H4K16-LA

data_processing:
After the sequencing data is generated: 1) First, use FastQC to perform quality control on the raw sequencing reads (Raw reads). Then, use the cutadapt software to filter the raw sequences (remove adapters, low - quality sequences, short sequences, etc.) to obtain Clean reads. 2) Align the filtered Clean reads to the reference genome using the bowtie2 software. Based on the Mapped reads aligned to the reference genome, statistically analyze the length distribution of the inserted fragment DNA. Use deeptools to analyze the sequence correlation and the distribution characteristics of sequences in gene regions. 3) Next, use MACS2 to perform peak calling for binding sites in each sample respectively. For the significantly enriched peaks, conduct length statistics, motif prediction, peak annotation, and analyze the distribution characteristics of Mapped reads near the peaks.
Assembly: Rat genome rn7.
Supplementary files format and content: bw and narrowPeak format
Library strategy: CUT&Tag

organism: Rattus norvegicus

source_name: tendon

growth_protocol: Tenocytes were cultured by 1640 medium.

extract_protocol:
100000 cells were washed twice gently with Wash Buffer. 10μL Concanavalin A coated magnetic beads were added per sample and incubated for 10min. Remove unbound supernatant and resuspended bead bound cells with Primary Antibody Buffer and a 1:50 dilution of primary antibody (PTM-1419RM, PTM-1415RM, PTM-1417RM) or IgG control antibody (rabbit IgG, CST, 2729S) incubated overnight at 4℃. The primary antibody was removed using magnet stand. Sencondary antibody (Goat anti-rabbit IgG H&L pAb: PTM-6252) was diluted 1:200 in Antibody Buffer and cells were incubated at RT for 60 min. Cells were washed using the magnet stand 2-3 times in Antibody Buffer. A 1:80 dilution of pA-Tn5 adapter complex was prepared in ChiTag Buffer and incubated with cells at RT for 1h. Cells were washed 2–3× for 5 min in ChiTag Buffer. Then cells were resuspended in Tagmentation Buffer and incubated at 37 °C for 1 h. DNA was purified using Tagment DNA Extract Beads. To amplify libraries, 20μL DNA was mixed with 2.5μL of a universal i5 and a uniquely barcoded i7 primer. A volume of 25 μL 2×HiFi AmpliMix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 3 min; 98 °C for 30 s; 13 cycles of 98 °C for 15 s, 63 °C for 8 s, 72 °C for 5 s; final extension at 72 °C for 2 min and hold at 10 °C. Library clean-up was performed by NovoNGS DNA Clean Beads.
CUT&Tag was performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina) (Cat. No.: N259-YH01) following the manufacturer’s protocol.

treatment_protocol: 20 mM lactate

value: tendon

value: tenocyte

value: WT

value: 20 mM lactate

tag: batch


title: rat tenocyte H4K16_ctr

description: Library name: H4K16-ctr


title: 17-184-Grp4-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample05_time03

source_name: Blood


title: experiment_H001AS8_A19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23


title: recombinant inbred line (RIL) JY124

value: leaf


title: experiment_H001AS8_A08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: Tetracycline


title: rat tenocyte H4K8_ctr

description: Library name: H4K8-ctr


title: recombinant inbred line (RIL) JY123


title: 17-118-Grp5-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G05_sample01_time01

value: Blood


title: 17-184-Grp4-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample05_time02

value: Day 1 after prime dose


title: rat tenocyte, H3K9_LA

description: Library name: H3K9-LA


title: 17-184-Grp4-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample05_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY122


title: experiment_H001AS8_A06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 10M167-Grp4-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample04_time06


title: recombinant inbred line (RIL) JY121


title: rat tenocyte H3K9_ctr

description: Library name: H3K9-ctr


title: experiment_H001AS8_A05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY120


title: experiment_H001AS8_A09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 10M167-Grp4-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample04_time05

value: Day 1 after boost dose


title: 10M167-Grp4-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample04_time04

value: Day 0 after boost dose


title: experiment_H001AS8_A04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY119


title: Experiment Group, AAT-ZCG group, Sample 3

city: Chengdu

first: Zhenyu

last: Luo

address: No.37 Guoxue Road

institute: West China Hospital, Sichuan University

description:
Library name: E3
Column name in all.counts.csv : E3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Counts and FPKM in csv files include for each Sample

source_name: BMSCs (Bone Marrow Mesenchymal Stromal Cells)

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Co-culture with AAT-ZCG hydrogel


title: 10M167-Grp4-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample04_time03

value: Day 7 after prime dose


title: experiment_H001AS8_A03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Experiment Group, AAT-ZCG group, Sample 1

description:
Library name: E1
Column name in all.counts.csv : E1

value: BMSCs (Bone Marrow Mesenchymal Stromal Cells)


title: rat tenocyte H4K8_LA

description: Library name: H4K8-LA


title: experiment_H001AS8_A07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: recombinant inbred line (RIL) JY118


title: experiment_H001AS8_A02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Control Group, Blank group, Sample 3

description:
Library name: C3
Column name in all.counts.csv : C3

value: Blank


title: 17-184-Grp4-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample05_time01

value: Day 0 after prime dose


title: Control Group, Blank group, Sample 2

description:
Library name: C2
Column name in all.counts.csv : C2


title: 10M167-Grp4-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample04_time01


title: AAVS1_meso_prog_cyto_2

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description: cyto

data_processing:
Mapping using hisat2
Annotating using featureCounts
Assembly: hg38
Supplementary files format and content: Matrix of Raw Counts
Supplementary files format and content: Deseq2 output tables

extract_protocol: none provided


title: experiment_H001AS8_A01_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_counts_prenorm.txt
sci_RNA_cds_monocle_processed.rds


title: recombinant inbred line (RIL) JY116


title: 13M225-Grp4-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample03_time06


title: Control Group, Blank group, Sample 1

description:
Library name: C1
Column name in all.counts.csv : C1


title: recombinant inbred line (RIL) JY115


title: AAVS1_meso_prog_cyto_1

description: cyto


title: Experiment Group, AAT-ZCG group, Sample 2

description:
Library name: E2
Column name in all.counts.csv : E2


title: AAVS1_meso_prog_pbody_1

description: pbody


title: 13M225-Grp4-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample03_time04


title: recombinant inbred line (RIL) JY114


title: J

first: Lan

last: Wang

address: Xinhua South Road

institute: Beijing Luhe Clinical Institute

description: Library name: Sample 4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and FPKM values for each sample

source_name: Human thyroid tissue

growth_protocol: The normal tissues was 2cm adjacent to the carcinoma. Cancer tissues was confirmed by postoperative pathology as papillary thyroid carcinoma. The patients' cancer tissues and normal paracancer tissues were collected and stored in the refrigerator at -80℃ for long-term storage for high-throughput sequencing.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Human thyroid tissue

value: normal thyroid tissues


title: G

description: Library name: Sample 3

value: Hashimoto's thyroiditis


title: recombinant inbred line (RIL) JY113


title: AAVS1_meso_prog_pbody_2

description: pbody


title: D

description: Library name: Sample 2

value: papillary thyroid carcinoma


title: 13M225-Grp4-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample03_time05


title: 13M225-Grp4-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample03_time03


title: recombinant inbred line (RIL) JY112


title: AAVS1_endo_prog_cyto_2

description: cyto


title: 13M225-Grp4-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample03_time02


title: H

description: Library name: Sample 1

value: papillary thyroid carcinoma complicated with Hashimoto's thyroiditis


title: recombinant inbred line (RIL) JY111

value: leaf


title: 10M167-Grp4-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample04_time02


title: recombinant inbred line (RIL) JY117


title: AAVS1_endo_prog_cyto_1

description: cyto


title: 13M225-Grp4-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample03_time01


title: recombinant inbred line (RIL) JY110


title: A12R027-Grp4-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample02_time06


title: 24132XC-05-03

city: New York

first: Won-Min

last: Song

state: NY

address: 1399 Park Avenue

department: Genetics and Genomic Sciences

institute: Icahn school of medicine at Mount Sinai

description:
Library name: 24132XC-05-03
normalized_peaks.SKMEL147.txt
SKMEL147_shZ1_1

data_processing:
Reads were mapped to reference genome hg38 using STAR aligner79. Peaks were called for each sample using the Model-based Analysis of ChIP-seq (MACS)80 (https://github.com/taoliu/MACS/). Quality control (QC) was performed on the samples, such as the percentage of reads in peaks, the number of detected peaks and outlier analysis based on principal component analysis (PCA). Peaks overlap with the “Blacklist” regions by ENCODE16 were removed. Peaks from all samples were integrated into a single list by union operations. Next, peaks were annotated to genome regions and classified into promoters, exons, introns, 5’UTRs, 3’UTRs and intergenic regions. Peaks overlap with promoters and gene bodies were linked to genes. Enrichment analysis of peaks and genomic regions (such as H3K4me1 peaks and transcription factor binding sites (TFBS)) were performed using the R package LOLA81 , in which genomic regions were collected from the ENCODE16, CODEX82, Cistrome83 and ROADMAP84 databases. For the gene-linked peaks, read counts will be called using featureCounts function from the Rsubread package85 to generate a sample-by-peak read count matrix. Scaling normalization were performed on the matrix using trimmed mean of M-values method86. Differential accessible peaks (DAPs) were identified between treatment conditions using the R package limma with FDR < 0.05. Gene ontology enrichment analysis were performed on the genes linked to DAPs to show the functions of the DAPs.
Assembly: GRCh38
Supplementary files format and content: Tab-deliminated sample x peak normalized data

growth_protocol: Cell line SKmel147 was obtained from Dr. Alan Houghton’s laboratory (MSKCC, New York). The A375 and Yumm1.7 cell line were sourced from American type culture collection. A375 and SKmel147 cells were maintained in DMEM (Corning #10-013-CV), while Yumm1.7 cells were cultured in DMEM-F12 (GIBCO #11320-082). Both media were supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin/streptomycin. All cell lines were kept in a humidified incubator at 37°C with 5% CO2 and were regularly tested to confirm the absence of mycoplasma contamination.

extract_protocol:
ATAC-seq was performed as described previously (Corces et al., 2007). In brief, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience, Massachusetts, USA). 50K to 100K nuclei were then centrifugesd at 500g in a pre-chilled centrifuge for 10 min. Supernatant was removed and the nuclei were resuspended in 50 uL tagmentation by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 300 r.p.m., and then cleaned up by MiniElute reaction clean up kit (Qiagen, Hilden, Germany). Tagmentated DNA was amplified with barcode primers . Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 200M PE reads (100M in each direction) per sample.
ATAC-seq was performed as described previously (Corces et al., 2007). In brief, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience, Massachusetts, USA). 50K to 100K nuclei were then centrifugesd at 500g in a pre-chilled centrifuge for 10 min. Supernatant was removed and the nuclei were resuspended in 50 uL tagmentation by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 300 r.p.m., and then cleaned up by MiniElute reaction clean up kit (Qiagen, Hilden, Germany). Tagmentated DNA was amplified with barcode primers . Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 200M PE reads (100M in each direction) per sample.

treatment_protocol: Totally, 4 × 106 HEK293T cells were seeded per 10 cm tissue culture plate and incubated overnight at 37 °C and 5% CO2. After seeding, HEK293T were co-transfected with bacterial glycerol clones PLKO-puro-shNTC (sigma # SHC016-1EA) , ZNF180_shZ1 (shRNA sequence : TGTCCTTGTTGTGCATCAAAG) ZNF180_shZ2 (shRNA sequence : GCTCGACTTATTGTGCATCAA), shZFP180 (shRNA sequence: GAAGTCGTTCATCCAGAGTTA) lentiviral expression constructs (12 μg), viral packaging plasmid (psPAX2, 8 μg), and viral envelope plasmid (VSVG, 4 μg) using Lipofectamine 2000 (Invitrogen # 52887) following manufacturer’s recommendations. Viral supernatant was collected and 0.45 mm filtered at 48 h post-transfection and stored at -80 °C for long-term usage (1-30 days). Cells were transduced with lentivirus in the presence of polybrene   (8 μg/ml) and selected with puromycin (1–2 μg/ml) for 4–6 days.

value: Epithelial

value: NRAS mutant


title: recombinant inbred line (RIL) JY109


title: AAVS1_endo_prog_pbody_1

description: pbody


title: 24132XC-05-02

description:
Library name: 24132XC-05-02
normalized_peaks.SKMEL147.txt
SKMEL147_shNTC_2

value: shNTC


title: recombinant inbred line (RIL) JY108


title: AAVS1_primed_cyto_2

description: cyto


title: A12R027-Grp4-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample02_time04

value: Blood


title: recombinant inbred line (RIL) JY107


title: 24132-02-06V1

description:
Library name: 24132-02-06V1
normalized_peaks.A375.txt
shzZ3_12999_2

value: BRAF mutant


title: A12R027-Grp4-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample02_time03


title: AAVS1_primed_cyto_1

description: cyto


title: 24132XC-05-01

description:
Library name: 24132XC-05-01
normalized_peaks.SKMEL147.txt
SKMEL147_shNTC_1


title: 24132-02-05V1

description:
Library name: 24132-02-05V1
normalized_peaks.A375.txt
shzZ3_12999_1


title: AAVS1_primed_pbody_2

description: pbody


title: recombinant inbred line (RIL) JY105


title: A12R027-Grp4-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample02_time02

value: Day 1 after prime dose


title: 24132-02-04V1

description:
Library name: 24132-02-04V1
normalized_peaks.A375.txt
shZ1_431070_2


title: A12R027-Grp4-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample02_time01


title: AAVS1_primed_pbody_1

description: pbody


title: recombinant inbred line (RIL) JY104


title: Naive_cyto_2

description: cyto

source_name: Naive

value: Naive


title: 24132XC-05-04

description:
Library name: 24132XC-05-04
normalized_peaks.SKMEL147.txt
SKMEL147_shZ1_2


title: AAVS1_endo_prog_pbody_2

description: pbody


title: experiment_H001AS8_A10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: 16-228-Grp4-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample01_time06

value: Day 7 after boost dose


title: Naive_cyto_1

description: cyto


title: 24132-02-03V1

description:
Library name: 24132-02-03V1
normalized_peaks.A375.txt
shZ1_431070_1


title: 24132-02-02V1

description:
Library name: 24132-02-02V1
normalized_peaks.A375.txt
shNTC_PLKO618_2


title: 16-228-Grp4-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample01_time05

value: Day 1 after boost dose


title: Naive_pbody_2

description: pbody


title: 16-228-Grp4-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample01_time04

value: Day 0 after boost dose


title: 24132-02-01V1

description:
Library name: 24132-02-01V1
normalized_peaks.A375.txt
shNTC_PLKO618_1


title: recombinant inbred line (RIL) JY106


title: Naive_pbody_1

description: pbody


title: 293T_ctrl_cyto_2

description: cyto


title: 16-228-Grp4-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample01_time03

value: Day 7 after prime dose


title: recombinant inbred line (RIL) JY100


title: NAMEC8 A-485 0.3µM Day 7 rep 2

city: Singapore

first: Li Ping

last: Toh

address: 61 Biopolis Drive, Proteos, #06-14

country: Singapore

institute: IMCB

data_processing:
Raw reads were cleaned using TrimGalore, aligned to the hg19 genome using STAR1 and gene counts were quantified using RSEM.
Genes with low expression and non-protein coding genes were filtered out prior to normalization with limma.
Differential expression between DMSO, SGC-CBP30, and A-485 were performed and genes with pvalue < 0.05 and logFC>1 were selected.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each sample .

growth_protocol: NAMEC8 cells were maintained in MEBM Mammary Epithelial Basal Medium (Lonza) supplemented with MEGM SingleQuots Supplements BulletKit (Lonza) and 1% Penicillin-Streptomycin (Gibco) at 37°C in a humidified 5% CO2 incubator (Thermo Fisher Scientific).

extract_protocol:
NAMEC8 cells were  homogenized with TRIzol reagent and total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA-seq library was prepared using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: NAMEC8 cells were treated with DMSO, 1µM SGC-CBP30, or 0.3µM A-485 for 7 days prior to extraction.

value: Mesenchymal cells

value: WT

value: Day 7


title: 16-228-Grp4-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample01_time02


title: recombinant inbred line (RIL) JY099

value: leaf


title: recombinant inbred line (RIL) JY103


title: 16-228-Grp4-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G04_sample01_time01

value: Day 0 after prime dose


title: NAMEC8 DMSO Day 7 rep 2

value: DMSO


title: NAMEC8 A-485 0.3µM Day 7 rep 1


title: recombinant inbred line (RIL) JY097


title: A11L011-Grp3-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample05_time06

value: Blood


title: recombinant inbred line (RIL) JY098


title: METTL3-KO_dox_cyto_2

description: cyto


title: METTL3-KO_dox_cyto_1

description: cyto


title: NAMEC8 SGC-CBP30 1µM Day 7 rep 1


title: recombinant inbred line (RIL) JY102


title: METTL3-KO_no-dox_cyto_2

description: cyto


title: A11L011-Grp3-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample05_time05


title: recombinant inbred line (RIL) JY096


title: A11L011-Grp3-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample05_time04


title: recombinant inbred line (RIL) JY101


title: recombinant inbred line (RIL) JY095


title: METTL3-KO_no-dox_cyto_1

description: cyto


title: NAMEC8 SGC-CBP30 1µM Day 7 rep 2


title: A11L011-Grp3-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample05_time03


title: Input ARDS survivor 10

city: Edinburgh

first: Manuel

middle: Alejandro

last: Sanchez Garcia

state: Midlothian

address: 4 Little France Drive

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw sequencing reads were first quality trimmed using Trim Galore 0.6.7 followed by read mapping with HISAT2 2.2.1 against the human genome (hg19) in paired-end mode.
Reads mapping to blacklisted regions were removed with the bedtools 2.30 intersect tool and sorted by coordinate and indexed using samtools 1.15 sort and index, respectively. duplicated reads were removed using the MarkDuplicates tool from Picard.
Genome-wide H3K4me3 and H3K27me3 profiles were generated using per condition merged BAM files with ngs.plot 2.61 created with samtools., with corresponding input as controls.
H3K4me3 peaks were identified using the MACS3 3.0.0.a6 callpeak function. Differential H3K4me3 peak analysis between conditions and enriched pathway analysis of differential peaks was performed with a custom R 4.2.0 script using the Bioconductor packages DiffBind, ChIPseeker, and ReactomePA.
The BED files generated by MACS3 were first annotated using the HOMER 4.11 annotatePeaks.pl script to obtain the nearest peak IDs and genes (Ensembl gene IDs).
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigwig files
Supplementary files format and content: bed files

source_name: Circulating neutrophils

extract_protocol:
Blood neutrophils were isolated and fixed in 1 % PFA. Chromatin was sheared by sonication and ChIP performed with the antibodies above. RNA and proteins were digested and DNA extracted for library preparation.
Libraries were constructed according to Illumina protocols
Each sample was sequenced over two lanes, using 75bp paired-end reads

tag: condition

value: ARDS survivor

value: Circulating neutrophils

tag: chip antibody

value: Dexamethasone


title: recombinant inbred line (RIL) JY094


title: NAMEC8 DMSO Day 7 rep 1


title: 293T_ctrl_pbody_2

description: pbody


title: Input ARDS survivor 9


title: A11L011-Grp3-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample05_time02

value: Day 1 after prime dose


title: 293T_ctrl_cyto_1

description: cyto


title: recombinant inbred line (RIL) JY093


title: 293T_ctrl_pbody_1

description: pbody


title: Input ARDS survivor 8


title: recombinant inbred line (RIL) JY092


title: A11L169-Grp3-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample04_time06


title: Input ARDS survivor 7


title: METTL3-KO_dox_pbody_2

description: pbody


title: recombinant inbred line (RIL) JY091


title: A11L169-Grp3-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample04_time05


title: A11L011-Grp3-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample05_time01


title: Input ARDS survivor 6

value: No dexamethasone


title: A11L169-Grp3-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample04_time04


title: recombinant inbred line (RIL) JY090


title: METTL3-KO_dox_pbody_1

description: pbody


title: METTL3-KO_no-dox_pbody_1

description: pbody


title: Input ARDS survivor 4


title: recombinant inbred line (RIL) JY088


title: METTL3-KO_no-dox_pbody_2

description: pbody


title: Input ARDS survivor 5


title: Input Healthy donor 3

value: Healthy donor

value: Control


title: A11L169-Grp3-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample04_time02


title: recombinant inbred line (RIL) JY089


title: A11L169-Grp3-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample04_time01


title: recombinant inbred line (RIL) JY086


title: neurons_cyto_2

description: cyto

source_name: neurons

value: neurons


title: Input Healthy donor 2


title: neural_prog_cyto_2

description: cyto


title: A11L166-Grp3-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample03_time06

value: Day 7 after boost dose


title: Input Healthy donor 1


title: A11L169-Grp3-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample04_time03

value: Day 7 after prime dose


title: recombinant inbred line (RIL) JY085


title: neural_prog_cyto_1

description: cyto


title: recombinant inbred line (RIL) JY084


title: A11L166-Grp3-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample03_time05

value: Day 1 after boost dose


title: neurons_pbody_2

description: pbody


title: H3K4me3 ARDS survivor 9

value: Cell Signaling, 9751


title: H3K4me3 ARDS survivor 10


title: neurons_pbody_1

description: pbody


title: A11L166-Grp3-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample03_time03


title: A11L166-Grp3-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample03_time04

value: Day 0 after boost dose


title: recombinant inbred line (RIL) JY083

value: leaf


title: H3K4me3 ARDS survivor 8


title: recombinant inbred line (RIL) JY082


title: neurons_cyto_1

description: cyto


title: neural_prog_pbody_2

description: pbody


title: A11L166-Grp3-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample03_time02


title: neural_prog_pbody_1

description: pbody


title: recombinant inbred line (RIL) JY081


title: A11L166-Grp3-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample03_time01

value: Day 0 after prime dose


title: H3K4me3 ARDS survivor 7


title: H3K4me3 ARDS survivor 6


title: recombinant inbred line (RIL) JY080


title: H3K4me3 ARDS survivor 5


title: NHBE cells, HRV16 infected, rep 3

city: Glasgow

first: Sheila

middle: Veronica

last: Graham

state: Glasgow City

address: 464 Bearsden Road, Garscube Estate

department: MRC-UoG CVR

institute: University of Glasgow

description: Primary bronchial epithelial cells, healthy, female, 16 years old

data_processing:
Libraries were pooled in equimolar concentrations and sequenced using an Illumina NextSeq 500 sequencer (Illumina, FC-404). Sequencing was performed at a covering of 21 million pair end reads per sample.
RNA-Seq reads were quality assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
RNA-Seq reads were aligned to the Homo sapiens genome (GRCh38) downloaded via Ensembl using Hisat2 (Kim et al., 2015).
After the alignment, FeatureCount was used to count reads mapping to gene annotation files (Liao et al., 2014).
The edgeR package was used to calculate gene expression level and to analyse differentially expressed genes between sample groups.
Assembly: Human NCBI genome build 38
Supplementary files format and content: Excel, gene ID, Log2fold changes, counts per million

source_name: Primary bronchial epithelial cells

growth_protocol: NHBE cells were maintained first at Pneumacult ExPlus medium and following air:liquid interface at Pneumacult ALI maintenance medium changed every Monday, Wednesday and Friday.

extract_protocol:
Cultures were dissected from transwell inserts, flash-frozen and stored in liquid Nitrogen. For harvesting, samples were added in a 1.5 ml Eppendorf tube containing 600 µl of Qiagen lysis buffer, and vortexed for 30 seconds at maximum speed. This dissociated cells from the membrane which was removed with tweezers. RNA was isolated using the RNeasy Mini Kit in combination with the RNase-free DNase Set as per manufacturer’s instructions. RNA quantitation was performed using Nanodrop 2000 Spectrophotometer.
The Illumina TruSeq Stranded mRNA HT kit (Illumina, 20020594) and SuperScript2 Reverse Transcriptase (Invitrogen, 18064014) as per manufacturer’s instructions.

treatment_protocol: NHBE cells were infected with HRV16 at MOI2, at 4 weeks post air:liquid interface.

tag: gender

value: female

tag: disease state

value: healthy

tag: age

value: 16 years old

value: Primary bronchial epithelial cells

value: HRV16 infected (MOI=2)


title: recombinant inbred line (RIL) JY079


title: NHBE cells, HRV16 infected, rep 2


title: H3K4me3 ARDS survivor 4

value: ARDS survivor

value: Circulating neutrophils


title: recombinant inbred line (RIL) JY078


title: NHBE cells, HRV16 infected, rep 1


title: A11R076-Grp3-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample02_time04

value: Blood


title: A11R076-Grp3-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample02_time05


title: H3K4me3 Healthy donor 3

value: Healthy donor

value: Control


title: recombinant inbred line (RIL) JY077


title: NHBE cells, mock infected, rep 3

value: Mock infected


title: H3K4me3 Healthy donor 2


title: recombinant inbred line (RIL) JY076


title: NHBE cells, mock infected, rep 2


title: H3K4me3 Healthy donor 1


title: A11R076-Grp3-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample02_time02

value: Day 1 after prime dose


title: A11R076-Grp3-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample02_time03

value: Day 7 after prime dose


title: recombinant inbred line (RIL) JY075


title: NHBE cells, mock infected, rep 1


title: recombinant inbred line (RIL) JY074


title: A11R076-Grp3-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample02_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY073


title: 10M011-Grp3-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample01_time06


title: 10M011-Grp3-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample01_time05

value: Day 1 after boost dose


title: recombinant inbred line (RIL) JY087

value: leaf


title: imac_conditioned_media_d7_ (R9427)

first: Raman

last: Sethi

state: Singapore

address: #07-01 Matrix, 30 Biopolis Street

institute: BII, A*STAR

description: Library name: R9427

data_processing:
Paired-end raw reads were mapped to GRCh38 human genome build using STAR aligner. Genes were counted for reads that were mapped to genes using featureCounts based on GENCODEv29 gene annotation.
Log2 transformed counts per million mapped read (log2CPM) and log2 transformed reads per kilobase per million mapped reads (log2RPKM) were computed using edgeR Bioconductor package. Across all samples, genes with log2CPM inter-quartile range (IQR) less than 0.5 were filtered out from subsequent differential expression gene (DEG) analysis.
DEG analyses for culture condition comparisons were all done using edgeR. Selection of DEGs was done with Benjamini-Hochberg  which adjusted P-values <0.05.
R function ‘prcomp’ was used to perform Principal Component Analysis (PCA) on log2RPKM values. The pseudobulk values were calculated using the ‘AverageExpression’ function in Seurat.
The pearson correlation were calculated using the ‘cor’ function in R. The GO enrichment was calculated using the ‘enrichGO‘ function from the ClusterProfiler package.
Assembly: GRCh38/ hg38 human genome
Supplementary files format and content: .xlsx fomat containing log2RPKM values, sample metadata and read depth information

source_name: IMR90 iPSC

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermofisher, KIT0204) according to manufacturer’s protocol. All RNAs were analyzed on Labchip GX system (Perkin Elmer, United States) for quality assessment with median RNA Quality Score of 9.15. cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of Ambion ERCC RNA Spike-in Controls (Thermofisher, 4456740) using the SMARTSeq v2 protocol described with the following modifications: 1. Use of 20mM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Nextera XT kit (Illumina, FC-131).
The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit (Perkin Elmer, CLS60672) on the Labchip GX system (Perkin Elmer). All samples were subjected to an indexed PE sequencing run of 2x51 cycles on HiSeq 2000 (Illumina) at 16 samples per lane.

value: IMR90 iPSC

value: imac


title: KO-YM-D30-2

city: Stockholm

first: Keying

last: Zhu

state: -- select state --

address: L8:04, Center for Molecular Medicine, Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

hyb_protocol: NanoString nCounter system

scan_protocol: NanoString nCounter Digital Analyzer

data_processing: The mRNA reads were normalized with the 13 internal reference genes included in the CodeSet; data normalization and further advanced analyses were performed using the NanoString nSolver Analysis Software following the provided guidelines.

label: single target-specific color-coded probes

source_name: spinal cord homogenate

extract_protocol: TRIzol

value: Male

value: KO

tag: Stage


title: imac_co-culture_d7_ (R9425)

description: Library name: R9425


title: KO-YM-D30-3

label_protocol: single target-specific color-coded probes


title: imac_co-culture_d3_ (R9424)

description: Library name: R9424


title: 10M011-Grp3-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample01_time04

value: Day 0 after boost dose


title: recombinant inbred line (RIL) JY071


title: recombinant inbred line (RIL) JY072


title: 10M011-Grp3-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample01_time03


title: recombinant inbred line (RIL) JY070


title: KO-YM-D30-1


title: imac_only_d0_ (R9423)

description: Library name: R9423


title: 10M011-Grp3-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample01_time02


title: KO-YF-D30-3

value: Female


title: KO-YF-D30-2


title: recombinant inbred line (RIL) JY069


title: 10M011-Grp3-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample01_time01

value: Day 0 after prime dose


title: A11R076-Grp3-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G03_sample02_time01


title: recombinant inbred line (RIL) JY068


title: hepatocyte_only_d7_ (R9422)

description: Library name: R9422

value: ihepatocyte


title: imac_non-conditioned_media_d7_ (R9426)

description: Library name: R9426


title: hepatocyte_co-culture_d7_ (R9421)

description: Library name: R9421


title: hepatocyte_co-culture_d3_ (R9420)

description: Library name: R9420


title: recombinant inbred line (RIL) JY067


title: 17-12-Grp2-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample05_time06

value: Blood


title: WT-YM-3

value: WT


title: hepatocyte_only_d0_ (R9419)

description: Library name: R9419


title: WT-YM-2


title: imac_conditioned_media_d7_ (R9418)

description: Library name: R9418


title: 17-12-Grp2-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample05_time05


title: recombinant inbred line (RIL) JY064


title: 17-12-Grp2-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample05_time04


title: recombinant inbred line (RIL) JY065


title: imac_non-conditioned_media_d7_ (R9417)

description: Library name: R9417


title: 17-12-Grp2-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample05_time02


title: WT-YM-1


title: WT-YF-3


title: WT-YF-4


title: KO-YF-D30-1


title: recombinant inbred line (RIL) JY063


title: imac_co-culture_d7_ (R9416)

description: Library name: R9416


title: 17-12-Grp2-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample05_time01


title: recombinant inbred line (RIL) JY062


title: imac_co-culture_d3_ (R9415)

description: Library name: R9415


title: 17-120-Grp2-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample04_time06


title: WT-YF-2


title: WT-YF-1


title: recombinant inbred line (RIL) JY061


title: imac_only_d0_ (R9414)

description: Library name: R9414


title: 17-120-Grp2-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample04_time05


title: WT-OM-3


title: recombinant inbred line (RIL) JY060


title: recombinant inbred line (RIL) JY066


title: 17-12-Grp2-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample05_time03


title: WT-OM-2


title: 17-120-Grp2-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample04_time04


title: hepatocyte_co-culture_d7_ (R9412)

description: Library name: R9412


title: hepatocyte_only_d7_ (R9413)

description: Library name: R9413


title: recombinant inbred line (RIL) JY059


title: 17-120-Grp2-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample04_time03


title: recombinant inbred line (RIL) JY058


title: KO-OM-D30-4


title: 17-120-Grp2-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample04_time02


title: hepatocyte_co-culture_d3_ (R9411)

description: Library name: R9411


title: hepatocyte_only_d0_ (R9410)

description: Library name: R9410


title: WT-OM-1


title: 17-120-Grp2-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample04_time01


title: recombinant inbred line (RIL) JY057


title: KO-OM-D30-3


title: imac_conditioned_media_d7_ (R9409)

description: Library name: R9409


title: 16-52-Grp2-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample03_time06


title: recombinant inbred line (RIL) JY055


title: KO-OM-D30-2


title: imac_non-conditioned_media_d7_ (R9408)

description: Library name: R9408


title: 16-52-Grp2-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample03_time05


title: KO-OM-D30-1


title: recombinant inbred line (RIL) JY054


title: 16-52-Grp2-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample03_time04


title: imac_co-culture_d7_ (R9407)

description: Library name: R9407


title: recombinant inbred line (RIL) JY053


title: imac_co-culture_d3_ (R9406)

description: Library name: R9406


title: KO-OF-D30-3


title: 16-52-Grp2-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample03_time03


title: KO-OF-D30-2


title: recombinant inbred line (RIL) JY051


title: imac_only_d0_ (R9405)

description: Library name: R9405


title: hepatocyte_only_d7_ (R9404)

description: Library name: R9404


title: 16-52-Grp2-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample03_time01


title: recombinant inbred line (RIL) JY056


title: KO-OF-D20-4


title: hepatocyte_co-culture_d7_ (R9403)

description: Library name: R9403


title: KO-OF-D30-1


title: A11R075-Grp2-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample02_time06


title: recombinant inbred line (RIL) JY050


title: KO-OF-D20-3


title: hepatocyte_co-culture_d3_ (R9402)

description: Library name: R9402


title: recombinant inbred line (RIL) JY049


title: A11R075-Grp2-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample02_time05


title: recombinant inbred line (RIL) JY048


title: A11R075-Grp2-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample02_time04


title: KO-OF-D20-2


title: imac_conditioned_media_d7_ (R9400)

description: Library name: R9400


title: recombinant inbred line (RIL) JY047


title: recombinant inbred line (RIL) JY046


title: 16-52-Grp2-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample03_time02


title: KO-OF-D10-3


title: imac_non-conditioned_media_d7_ (R9399)

description: Library name: R9399


title: A11R075-Grp2-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample02_time02


title: recombinant inbred line (RIL) JY052


title: KO-OF-D10-2


title: A11R075-Grp2-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample02_time03


title: 18-06-Grp2-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample01_time06


title: KO-OF-D10-1


title: A11R075-Grp2-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample02_time01


title: WT-OF-5


title: recombinant inbred line (RIL) JY043


title: imac_only_d0_ (R9396)

description: Library name: R9396


title: hepatocyte_only_d0_ (R9401)

description: Library name: R9401


title: WT-OF-4


title: 18-06-Grp2-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample01_time05


title: recombinant inbred line (RIL) JY042


title: KO-OF-D20-1


title: hepatocyte_only_d7_ (R9395)

description: Library name: R9395


title: 18-06-Grp2-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample01_time04


title: recombinant inbred line (RIL) JY041


title: hepatocyte_co-culture_d7_ (R9394)

description: Library name: R9394


title: 18-06-Grp2-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample01_time03


title: WT-OF-3


title: imac_co-culture_d7_ (R9398)

description: Library name: R9398


title: 18-06-Grp2-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample01_time02


title: BY4741 shocked Rep 2

city: Bangalore

first: Purusharth

middle: I

last: Rajyaguru

state: Karnataka

address: CV Raman road

department: Biochemistry

country: India

institute: Indian Institute of Science Bangalore

description: Library name: Sample 12

data_processing:
The raw reads were processed using FastQC for quality assessment and pre-processing using TrimGalore. The pre-processed high-quality data was aligned to the Saccharomyces cerevisiae reference genome using Hisat2.
Featurecounts4 tool was used to estimate and calculate transcript abundance. Absolute counts for transcripts were estimated. TPM (Transcripts Per Million) normalized read count was performed for all samples.
DESeq25 was used to calculate the differentially expressed transcripts.
Transcripts were functionally annotated based on homology using BLAST5 tool.
Pathway analysis was done on KAAS6 server using Saccharomyces cerevisiae as the reference organism for pathway identification for all samples.
Assembly: NCBI (GCA_000146045.2 Saccharomyces cerevisiae BY4741 S288C)
Supplementary files format and content: xlsz files containing differential expression data

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown until OD600 0.4-0.5 in Ura- media at 30 degrees celsius (180rpm)

extract_protocol:
RNA was isolated using the hot-phenol method.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs, MA, USA) at Genotypic Technology Pvt. Ltd., Bangalore, India.

treatment_protocol: Continous 100mM NaClO4 treatment supplemented in Ura-media till OD600 0.4-0.5 at 30 degrees celsius (Sample 3,4,7,8) ; 5.6 Mach Intensity shock exposed cells grown in Ura-media till OD600 0.4-0.5 at 30 degrees celsius (Sample 10,12).

value: Wild-type

value: Shocked


title: hepatocyte_co-culture_d3_ (R9393)

description: Library name: R9393


title: recombinant inbred line (RIL) JY045


title: recombinant inbred line (RIL) JY039


title: hepatocyte_only_d0_ (R9392)

description: Library name: R9392


title: recombinant inbred line (RIL) JY044


title: WT-OF-1


title: imac_co-culture_d3_ (R9397)

description: Library name: R9397


title: 18-06-Grp2-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G02_sample01_time01


title: BY4741 unshocked Rep 2

description: Library name: Sample 11

value: Unshocked


title: imac_conditioned_media_d7_ (R9391)

description: Library name: R9391


title: BY4741 shocked Rep 1

description: Library name: Sample 10


title: recombinant inbred line (RIL) JY037


title: recombinant inbred line (RIL) JY036


title: 17-51-Grp1-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample05_time05


title: BY4741 unshocked Rep 1

description: Library name: Sample 9


title: imac_co-culture_d7_ (R9389)

description: Library name: R9389


title: 17-51-Grp1-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample05_time04


title: WT-OF-2


title: edc3∆lsm4∆C NaClO4 treated Rep 2

description: Library name: Sample 8

value: edc3 deletion and Lsm4p C terminus Q/N-rich domain deletion

value: NaClO4 treated


title: recombinant inbred line (RIL) JY040


title: imac_co-culture_d3_ (R9388)

description: Library name: R9388


title: recombinant inbred line (RIL) JY035


title: 17-51-Grp1-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample05_time03

value: Day 7 after prime dose


title: BY4741 NaClO4 treated Rep 2

description: Library name: Sample 7


title: recombinant inbred line (RIL) JY034

value: leaf


title: edc3∆lsm4∆C untreated Rep 2

description: Library name: Sample 6

value: Untreated


title: recombinant inbred line (RIL) JY033


title: 17-51-Grp1-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample05_time02

value: Day 1 after prime dose


title: hepatocyte_only_d7_ (R9386)

description: Library name: R9386

value: IMR90 iPSC


title: imac_only_d0_ (R9387)

description: Library name: R9387

value: imac


title: 17-51-Grp1-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample05_time01


title: recombinant inbred line (RIL) JY038


title: BY4741 untreated Rep 2

description: Library name: Sample 5

value: Untretaed


title: recombinant inbred line (RIL) JY032


title: edc3∆lsm4∆C NaClO4 treated Rep 1

description: Library name: Sample 4


title: imac_non-conditioned_media_d7_ (R9390)

description: Library name: R9390


title: 17-51-Grp1-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample05_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY031


title: hepatocyte_co-culture_d3_ (R9384)

description: Library name: R9384


title: T214-Grp1-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample04_time05

value: Day 1 after boost dose


title: recombinant inbred line (RIL) JY030


title: hepatocyte_only_d0_ (R9383)

description: Library name: R9383

value: ihepatocyte


title: BY4741 NaClO4 treated Rep 1

description: Library name: Sample 3


title: T214-Grp1-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample04_time04

value: Blood

value: Day 0 after boost dose


title: edc3∆lsm4∆C untreated Rep 1

description: Library name: Sample 2


title: recombinant inbred line (RIL) JY029


title: imac_conditioned_media_d7_eb (R9382)

description: Library name: R9382


title: recombinant inbred line (RIL) JY028


title: BY4741 untreated Rep 1

description: Library name: Sample 1

value: Wild-type


title: imac_non-conditioned_media_d7_eb (R9381)

description: Library name: R9381


title: T214-Grp1-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample04_time02


title: imac_co-culture_d3 (R9380)

description: Library name: R9380


title: recombinant inbred line (RIL) JY027


title: T214-Grp1-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample04_time01

value: Day 0 after prime dose


title: LND_8_rep3

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

country: Germany

institute: University of Würzburg

data_processing:
Quality assessment of fastq reads was performed using FastQC (V.0.12.0; Barbraham Institute).
Trimming of sequencing reads to eliminate low quality reads and technical sequences was performed using BBDuk based on a phred score quality threshold of <10.
The sequenced genome of MRSA strain 101588 was annotated with Prokka (Seemann, 2014) and used for assigning reads later.
mapping was done with the BBMap software (V.38.84).
resulting alignments were assigned to both coding sequences and sRNAs using the featureCounts methods of the Subread package.
Assembly: Staphylococcus aureus strain 101588
Supplementary files format and content: counttable.tsv contains tab delimited table with raw counts for all CDS and sRNAs
Supplementary files format and content: files ending with .bw are bigwig files
Supplementary files format and content: file “sa101588_curated_sRNAs.gff” contains tab-separated gff annotation file with newly added annotation of small RNAs

organism: Staphylococcus aureus

growth_protocol: Five microliters of MHB cultures in biological triplicates were prepared and incubated overnight. Cell densities were adjusted to OD600 = 0.05 in 60 ml culture volume in 250 ml flasks and re-incubated.

extract_protocol:
The phenol-chloroform method was used for total RNA extraction. Cell pellets were thawed on ice and suspended in 750μl Tris EDTA (TE) buffer (Sigma Aldrich, Missouri – USA). Cell suspensions were lysed in Lysing Matrix E tubes on a FastPrep machine (both from MP Biomedicals, Irvine, California – USA) at a maximum force of 6.5 for two cycles of 30 sec each. After a 30 sec centrifugation at 4° C, 500μl of the supernatant was transferred into a fresh 2 ml tube to which 60μl of 10% w/v sodium dodecyl sulphate (SDS) was added with mixing. The tubes were incubated at 640C for 2 min followed by addition of 66μl of 1M Sodium acetate (NaOAc) with mixing. Roti‐Aqua phenol (750μl per sample) (Carl Roth, Baden-Wurttemberg, Germany) was added to the samples followed by mixing. The tubes were incubated for 10 min at 64°C with inversion at 2-min intervals followed by centrifugation for 15 min at 4°C. The aqueous portion was added to PLG heavy tubes (MP Biomedicals, Irvine, California – USA) containing 750μl chloroform followed by shaking for 2 min. The tubes were centrifuged for 12 min at 15°C. RNA was precipitated with 600μl isopropanol, washed with 500μl ice cold 70% ethanol (EtOH), air-dried at room temperature, and eluted on ice with 30μl of RNAse-free water (Ambion, Austin, Texas, USA). A Nanodrop spectrophotometer (DeNovix Inc, Wilmington, Delaware – USA) was used for quantification and quality assessment and RNA extracts were frozen at ‐80°C. All centrifugation steps were performed at 13,000 rpm on a 5424R centrifuge (Eppendorf, Hamburg, Germany).
RNA extracts were subjected on DNAse digestion to eliminate potential DNA contamination. Ribosomal RNA (rRNA) depletion was performed with RiboCOP‐Meta rRNA depletion (Vienna, Austria) following manufacturer guidelines. Briefly, rRNA-specific magnetic beads are mixed with total RNA, and the mixture denatured where beads are allowed to bind to rRNA followed by magnetic separation and purification of rRNA-free RNA. Lexogen’s Corall Library Prep (Vienna, Austria) kit and protocol was used following manufacturer recommendations. In this fragmentation-free, Illumina-compatible library preparation protocol, proprietary Displacement Strand Priming (DSP) is used for reverse transcription followed by 3’ Linker Oligo ligation, second strand complementary DNA (cDNA) generation and PCR amplification of the cDNA libraries. All cleaning steps in the protocol are performed using magnetic bead-based approaches. Libraries were checked for quality with Bioanalyzer RNA assay. The pooled sequencing library (1.8 pM) was loaded onto an Illumina NextSeq 500 MidOutput machine (130 M with 1 x 150 cycle single-end sequencing).

treatment_protocol: At OD600 = 0.5, the three, 60 ml cultures were split into three technical replicates of 15 ml each in 100 ml flasks yielding nine flasks for different treatments. Cells were challenged with low- (8 µg/ml) and high- (16 µg/ml) dose treatments of linezolid (reconstituted in dimethyl sulfoxide (DMSO), (Sigma Aldrich, Missouri, USA)). From each biological replicate, one set was left untreated, one was subjected to low dose and the other to high dose treatments for 10 min. All incubation steps were performed at 370C with shaking (200 rpm). To halt transcription, 2 ml STOP Mix solution (20:1 ratio of 100% Ethanol to Roti Aqua Phenol) was used. Cultures were centrifuged at 3500 rpm for 10 min at 40C (Thermo Scientific, Massachusetts – USA) after which the supernatant was discarded, and cell pellets frozen at -800C, pending RNA extraction.

tag: strain

value: 10 minutes 8 µg/ml Linezolid


title: imac_only_d0_eb (R9379)

description: Library name: R9379


title: recombinant inbred line (RIL) JY026

first: Xin

last: Lu

address: Zhongguancun South Street,Haidian District

institute: Chinese Academy of Agricultural Sciences

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

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


title: hepatocyte_only_d7_eb (R9378)

description: Library name: R9378


title: LND_8_rep1


title: LND_16_rep3

value: 10 minutes 16 µg/ml Linezolid


title: hepatocyte_co-culture_d7_ (R9385)

description: Library name: R9385


title: recombinant inbred line (RIL) JY024


title: LND_16_rep1


title: LND_8_rep2


title: hepatocyte_co-culture_d7_eb (R9377)

description: Library name: R9377


title: A12L073-Grp1-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample03_time06


title: recombinant inbred line (RIL) JY025


title: T214-Grp1-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample04_time06


title: hepatocyte_only_d0_eb (R9375)

description: Library name: R9375


title: A12L073-Grp1-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample03_time03


title: A12L073-Grp1-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample03_time05


title: recombinant inbred line (RIL) JY022


title: A12L073-Grp1-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample03_time02


title: T214-Grp1-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample04_time03


title: recombinant inbred line (RIL) JY021


title: LND_0_rep3

value: 10 minutes untreated


title: LND_0_rep2


title: A12L073-Grp1-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample03_time01


title: recombinant inbred line (RIL) JY020


title: A12L073-Grp1-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample03_time04


title: LND_16_rep2


title: hepatocyte_co-culture_d3_eb (R9376)

description: Library name: R9376


title: A11L175-Grp1-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample02_time06


title: recombinant inbred line (RIL) JY019


title: A11L175-Grp1-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample02_time05


title: recombinant inbred line (RIL) JY023


title: recombinant inbred line (RIL) JY018


title: LND_0_rep1


title: Brain_47 ND2_9

city: Dunedin

first: Caroline

last: Beck

state: Otago

address: 340 Great King Street, North Dunedin

department: Zoology

country: New Zealand

institute: University of Otago

description: Library name: S08

data_processing:
Trimmed and mapped to Xenopus laevis genome (DRAGEN)
Assembly: XENLA_10.1 (Xenbase)
Supplementary files format and content: Read counts made with FEATURE COUNTS, not normalised. Gene_id in col1, matrix of all samples

organism: Xenopus laevis

source_name: Whole Brain

growth_protocol: Tadpoles raised from injected fertilised eggs in 0.1 x MMR

extract_protocol:
Qiagen Rneasy mini kit for total RNA with on column DNaseI
TruSeq stranded mRNA kit

value: Whole Brain

value: Stage NF 47

value: NeuroD2 CRISPant Fo mosiac


title: Brain_47 ND2_4

description: Library name: S06


title: recombinant inbred line (RIL) JY016

value: leaf


title: A11L175-Grp1-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

first: Yuhyun

last: Ji

address: 126 E Lincoln Ave

institute: Merck & Co., Inc.

description: Library name: G01_sample02_time03

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.

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: Day 7 after prime dose


title: Brain_47 ND2_7

description: Library name: S07


title: A11L175-Grp1-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample02_time02

value: Day 1 after prime dose


title: recombinant inbred line (RIL) JY017


title: A11L175-Grp1-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample02_time04


title: LSS1-input

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

description: Library name: SAMPLE 10

data_processing:
Total RNA qualification and quantification
RNA fragmentation (~100 nt)
m6A immunoprecipitation with anti-m6A antibody
RNA purification and library construction using NEBNext® Ultra RNA Library Prep Kit
RNA purification and library construction using NEBNext® Ultra RNA Library Prep Kit
High-throughput sequencing on Illumina platform
Assembly: hg38
Supplementary files format and content: bedGraph or BigWig files for genome browser visualization, BED files for peak coordinates, and tab-delimited count matrices for each sample

source_name: hVECs

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed by Agilent 2100 Bioanalyzer.
For acRIP-seq, 300 µg of total RNA was fragmented into ~100 nt fragments using RNA fragmentation buffer. Fragmented RNA was incubated with anti-AC antibody (e.g., Synaptic Systems, 202003) and immunoprecipitated with Protein A/G magnetic beads. The AC-enriched RNA and corresponding input RNA were used to construct sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit (NEB) following the manufacturer’s protocol.

value: hVECs


title: Brain_47 ND2_3

description: Library name: S05


title: A11L175-Grp1-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample02_time01


title: recombinant inbred line (RIL) JY015


title: OSS1-input

description: Library name: SAMPLE 7


title: LSS3-input

description: Library name: SAMPLE 12


title: LSS2-input

description: Library name: SAMPLE 11


title: OSS3-input

description: Library name: SAMPLE 9


title: recombinant inbred line (RIL) JY014


title: OSS2-input

description: Library name: SAMPLE 8


title: Brain_47_Cas9_5

description: Library name: S04

value: Wildtype


title: LSS3-ip

description: Library name: SAMPLE 6

value: anti-m6A antibody


title: LSS2-ip

description: Library name: SAMPLE 5


title: Brain_47_Cas9_4

description: Library name: S03


title: A4X018-Grp1-Week25_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample01_time06

value: Day 7 after boost dose


title: recombinant inbred line (RIL) JY013


title: A4X018-Grp1-Wk24-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample01_time05

value: Blood

value: Day 1 after boost dose


title: Brain_47_Cas9_2

description: Library name: S02


title: LSS1-ip

description: Library name: SAMPLE 4


title: recombinant inbred line (RIL) JY012


title: A4X018-Grp1-Wk24-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample01_time04

value: Day 0 after boost dose


title: Brain_47_Cas9_1

description: Library name: S01


title: OSS1-ip

description: Library name: SAMPLE 1


title: OSS3-ip

description: Library name: SAMPLE 3


title: OSS2-ip

description: Library name: SAMPLE 2


title: A4X018-Grp1-Day0-7d_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample01_time03


title: A4X018-Grp1-Day0-Pre_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample01_time01

value: Day 0 after prime dose


title: recombinant inbred line (RIL) JY010


title: recombinant inbred line (RIL) JY011


title: recombinant inbred line (RIL) JY008


title: TIGR4∆lctO_2

city: Jackson

first: Jorge

middle: Eugenio

last: Vidal

state: MS

address: 2500 North State Street, Jackson MS 39216

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

description:
Library name: Sample 8
column name in P1600_Normalized_counts_STAR.cvs:

data_processing:
fastqc version v0.11.9, STAR version 2.7.10a_alpha_220818, featureCounts version 2.0.6 and R version 4.4.2; Fastq files were mapped using STAR and generated raw read using featureCounts. Normalization was performed on raw read counts using DESeq2
Assembly: Homo sapiens: Ensembl/Hg38 (GRCh38)
Supplementary files format and content: CSV file containing normalized expression values for each gene and sample.

source_name: Lung

extract_protocol:
RNA was extracted using the Pure Link RNA Mini Kit from archived samples (Invitrogen) according to manufacturer instructions and assessed for quality control parameters of minimum concentration and fidelity (i.e. 18S and 28S bands, RIS >8) through the UMMC Molecular and Genomics Core Facility (MGCF).
Libraries were prepared for RNA sequencing per detailed protocols from Illumina mRNA stranded kit. Briefly, a pooled library was prepared from using n=12-24 samples per group using TruSeq mRNA Stranded Library Prep Kit (Set-A-indexes),
Libraries were assessed for quality and size Qiagen QIAxcel Advanced System or Agilent TapeStation. The library was sequenced using the NextSeq 2000 using P3 (200 cycles, paired end 100bp) on the Illumina NextSeq 2000 platform.

value: Lung

value: Epithelial cells

tag: s. pneumoniae_strain

value: Spn-infected 4 h


title: TIGR4∆spxB_2

description:
Library name: Sample 7
column name in P1600_Normalized_counts_STAR.cvs:


title: recombinant inbred line (RIL) JY009

city: Beijing


title: recombinant inbred line (RIL) JY007


title: A4X018-Grp1-Day0-24h_PID22718_AID5442_Batch1_Mrk_RNA_Seq_20Mar2023_1679340942963

description: Library name: G01_sample01_time02


title: TIGR4_2

description:
Library name: Sample 6
column name in P1600_Normalized_counts_STAR.cvs: