title: WT skin P1

first: Maria

last: Genander

address: Tomtebodavägen 16

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

description:
Library name: WT
10x Genomics

data_processing:
Pre-processing of the sequencing reads into count matrices was done with CellRanger 52. Raw count matrices were filtered using CellBender with parameters --expected-cells=10000 and --total-droplets-included=15000. The filtered counts were processed downstream using Scanpy 53. Count matrices of WT and Padi4 cKO were combined and cells following either of these criteria were filtered out: a) >20% of mitochondrial counts, b) <5 or >95 percentile of ribosomal counts, c) more than 1% of haemoglobin, d) <2000 or >60000 total counts, or e) <1000 or >8000 number of genes with positive counts in the cell. Genes were filtered to keep only those a) expressed in at least 5 cells, and b) with at least 5 counts. Counts were log-normalized and the top 1000 highly variable genes were selected for downstream analysis. Cell cycle phase was predicted using Scanpy’s score_genes_cell_cycle function. After performing PCA, the effect of cell cycle phase was corrected using harmony 54. The resulting filtered and processed counts were spatially embedded using UMAP 55 and clustering was performed using the Leiden algorithm 56. Clusters were annotated based on differentially expressed genes found with a Wilcoxon and t-test. For downstream analysis, fibroblasts, melanocytes, and clusters with mixed signature were removed. Diffusion maps of the inner HF clusters were computed using Scanpy’s implementation 57 and its components were selected based on sufficient distinction of the 3 lineages. Pseudotime analysis was performed using diffusion pseudotime 42. Pseudotime values were ordered (ranked pseudotime) and/or binned (50 bins) to visualize cell distributions along differentiation trajectories.
Assembly: Mouse mm10
Supplementary files format and content: Cellranger processed files included

source_name: Back skin

growth_protocol: WT and PADI4 P1 mice

extract_protocol:
At postnatal day 1, K14-Cre Padi4 fl/fl mouse back skins were dissected and and put in 1:1 1xDispase:PBS (from 5x (10mg/ml) Dispase stock) at 4°C overnight with the dermal side facing the enzymatic solution. After incubation the epidermis and dermis were mechanically separated using fine forceps. The dermal fraction, containing the growing hair follicles, was incubated put in HBSS (Thermofisher Scientific (Gibco)) with 20% collagenase (in PBS (Sigma-Aldrich)) at 37°C for 1 h. After incubation, the dermal/hair follicle fraction was scraped off using a scalpel and collected by centrifugation at 300xg for 10 min, after which the pellet was resuspended in trypsin (Thermofisher Scientific (Gibco)) and incubated for 15 min at 37°C. Cell suspensions were then filtered using both 70- and 40-mm filters, washed twice in PBS and pelleted by centrifugation for 5min at 300xg. DAPI was used to exclude dead cells. Epithelial cells were tdTOMATO positive. Using a fluorescence activated cell sorter (BD FACS AriaII), approximately 100,000 sorted tdTOMATO-positive cells from each animal were collected in E-low medium without serum for subsequent single-cell library preparation.
Single-cell libraries were prepared using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits (10x Genomics, PN-1000269) according to the manufacturer’s protocol (CG000315 Rev E). Single-cell suspensions were adjusted to achieve a target recovery of approximately 10,000 cells. Cells were loaded onto a Chromium Next GEM Chip G along with barcoded gel beads, master mix reagents, and partitioning oil to create Gel Beads-in-Emulsion (GEMs) using the Chromium Controller. Each GEM contained a unique 10x barcode and unique molecular identifier (UMI) linked to mRNA transcripts through reverse transcription. GEMs were incubated to perform reverse transcription, after which they were broken, and cDNA was recovered using Dynabeads with Dynabead cleanup buffer (Ref no). First-strand cDNA was amplified by PCR to generate sufficient material for library construction. The amplified cDNA was subjected to enzymatic fragmentation, end-repair, and A-tailing to optimize fragment size. Adapters were ligated, and sample indices were introduced via sample index PCR. Cleanup steps were performed throughout the process to purify and size-select cDNA and libraries. Library quality and concentration were assessed using an Agilent Bioanalyzer with High Sensitivity DNA reagents. The final libraries consisted of paired-end constructs with dual indices. Libraries were pooled and sequenced to obtain paired-end reads, with Read 1 capturing the 10x barcode and UMI information and Read 2 covering the cDNA insert.

treatment_protocol: No relevant treatment protocol

tag: tissue

value: Back skin

tag: cell line

value: No

value: keratinocytes


title: E16.5F PGCs IUHG  bisulfite-seq bio rep3

status: Public on Jul 28 2025

type: SRA

city: Shanghai

first: Jiangshan

last: Cong

address: No.130,Dongan Road

country: China

institute: Fudan University

description: Library name: Sample 24

library_source: genomic

data_processing:
Raw sequencing reads from WGBS were processed using the integrated methylpy software package. First, methylpy indexed the bisulfite-converted genome sequence, and alignment was conducted in paired-end mode using Bowtie2 as the alignment tool. Then, the call-methylation-state function within methylpy was used to calculate the methylation state of all cytosines across the genome, storing results in allc files. Finally, biological replicates from different samples were merged into a single allc file for further analysis.
Assembly: mm39
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: PGCs

growth_protocol: Mice were maintained on a 12h light and 12h dark cycle in a constant temperature (20-25 ℃) and humidity levels (30-70%).

extract_protocol:
The EGFP-positive PGCs obtained through FACS were washed with PBS. DNA was isolated from the cells by using QIAamp® DNA Micro Kit (QIAGEN).
Genomic DNA was subjected to bisulfite conversion using EpiArt® DNA Methylation Bisulfite Kit (Vazyme) following the manufacturer’s instructions. Libraries for sequencing were prepared using 100ng-200ng of genomic DNA by EpiArt® DNA Methylation Library Kit. Libraries were purified for DNA fragments between 100bp-200bp. Library quality was assessed on the Agilent 5400 system (Agilent) and then amplified by PCR system.

treatment_protocol: STZ-induced intrauterine hyperglycemia mice at E3.5 of pregnancy by 120mg/kg STZ (Sigma).  A blood glucose level of more than 14 mM was used as the inclusion criterion for diabetes at E6.5 of pregnancy.

tag: Sex

value: female

tag: developmental stage

tag: cell type

value: PGCs

tag: genotype

value: WT

tag: treatment

value: STZ-induced


title: E16.5F PGCs IUHG  bisulfite-seq bio rep2

description: Library name: Sample 23


title: E16.5M PGCs control  bisulfite-seq bio rep1

description: Library name: Sample 25

value: male

value: control group


title: E16.5F PGCs IUHG  bisulfite-seq bio rep1

description: Library name: Sample 22


title: E16.5F PGCs control  bisulfite-seq bio rep1

description: Library name: Sample 19


title: E16.5F PGCs control  bisulfite-seq bio rep2

description: Library name: Sample 20


title: E16.5F PGCs control  bisulfite-seq bio rep3

description: Library name: Sample 21


title: E13.5M PGCs IUHG  bisulfite-seq bio rep3

description: Library name: Sample 18


title: G217Bura5-DA dbcAMP B-1 (dbcAMP10)

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

country: USA

institute: University of California

library_source: transcriptomic

data_processing:
Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Histoplasma G217B transcriptome (S5 Data of PMID:26177267). Relative abundances (reported as TPM values) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.0. Further analysis was restricted to transcripts with TPM ≥ 10 in at least one sample.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.30.8. Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 1.5x (absolute log2 fold change ≥ 0.585) for a given contrast.
For comparison with previous expression profiling, the above KALLISTO/LIMMA pipeline was applied to the reads from PMID:26177267 (SRA accession SRP058149) and LIMMA fit parameters were taken from S2 Data of PMID:31568523.
The results of the LIMMA analysis are in supplementary file Table_all_genes_2.cdt, an Excel-compatible tab-delimited text file conforming to JavaTreeView extended CDT format.  Each row is a transcript with the UNIQID column giving the systematic gene name from PMID:26177267.  Annotation columns are taken from S4 of PMID:35089059: NAME -- manually curated short gene name; Description; HcG217B_pred -- systematic name from the 9/21/2005 predicted gene set from Washington University; HcG217B_acc -- GenBank accession from GCA_017607445.1; HcG217B_rc -- repeat classification as in fig 4A of PMID:35089059.  ChIP-chip associations (RypX_chip columns) are taken from S2 of PMID:23935449 based on the HcG217B_pred column.  The p(X) columns give limma BH-adjusted p-values for differential expression in each contrast.  Class indicates the differential expression pattern and BGCOLOR gives class-specific hex color codes.  GWEIGHT is a place-holder column for JavaTreeView compatibility.  The final seven columns give the limma fit contrasts as log2(CPM ratio) values; viz., dbcAMP/ddw|1, CPT/ddw|1, and butyrate/ddw|1 give differential expression in response to treatment for samples in batch 1; d8/t=0|Rodriguez and Y/H|Gilmore give comparison contrasts from prior publications (PMID:26177267 and PMID:31568523); and (WT/SG1|2 and dbcAMP/ddw|2) give differential expression in reponse to treatment for samples in batch 2.
Assembly: Version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PMID:26177267)
Supplementary files format and content: tab-delimited text files include TPM and estimated count values for each sample

molecule: polyA RNA

organism: Histoplasma ohiense

source_name: yeast cells

extract_protocol:
Total RNA was extracted from fungal cells using a Qiazol-based RNA extraction protocol. Frozen, resuspended pellets of cells were incubated at RT for 5 minutes to thaw. The lysate was subjected to bead beating (Mini-Beadbeater, Biospec Products, Bartlesville, OK) followed by a chloroform extraction. The aqueous phase was then transferred to an Epoch RNA column where the filter was washed with 3 M NaOAc (pH=5.5) and then with 10 mM TrisCl (pH=7.5) in 80% EtOH. DNase (Purelink, Invitrogen, Carlsbad, CA) treatment was used to remove any residual DNA, and the filters were washed again with NaOAc and TrisCl before eluting the RNA in nuclease-free water.  For each experiment, mRNA was extracted from an equal amount of total RNA (up to 20 μg) of each sample. Total RNA samples and were treated with rDNase I (Ambion). RNA quality was determined with a RNA 6000 Nano Bioanalyzer chip (Agilent Technologies, Santa Clara, CA). mRNA was purified using polyA selection with Oligo-dT Dynabeads (Thermo Fisher, Waltham, MA) as described in the manufacturer’s protocol. Ribosomal RNA depletion was confirmed with an RNA 6000 Nano Bioanalyzer chip.
Libraries for RNAseq were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA). Individual libraries were uniquely barcoded with NEBNext Multiplex Oligos for Illumina sequencing platform (New England Biolabs, Ipswich, MA). Average fragment size and presence of excess adapter was determined with High Sensitivity DNA Bioanalyzer chip from Agilent Technologies (Santa Clara, CA). Libraries had an average fragment length of 300 to 500 bp. The concentration of the individual libraries was quantified using the KAPA library quantification kit. A total of 5 ng of each library was pooled into each final libraries and run on a High Sensitivity DNA Bioanalyzer chip to determine the average fragment size of the final pooled samples. The final libraries were submitted to the UCSF Center for Advanced Technology for sequencing on an Illumina HiSeq 4000 sequencer.

treatment_protocol: Samples were prepared in two separate experiments. In the first experiment, Histoplasma G217Bura5 was grown in liquid HMM culture at 37°C for 2 passages. On the day of chemical addition, the culture was passaged into fresh HMM + GlcNAc at a final OD600 of 0.2, and 10 mM dbcAMP, 4 mM 8-CPT-cAMP, 5 mM of sodium butyrate, or filter-sterilized autoclaved water (vehicle control) were added to the appropriate cultures, with 3 biological replicates for each chemical. Cultures were returned to 37°C growth with shaking. 2 days after the addition of each chemical, a small volume of each culture was fixed by adding paraformaldehyde (final paraformaldehyde concentration 4% v/v), and 10 ml of each culture were harvested by filtration using Nalgene Rapid-Flow Sterile Disposable Bottle Top Filters with SFCA Membrane (Fisher 09-740-22G). Cells were scraped from the filter into tubes containing 1mL of Qiazol (Qiagen) and promptly flash-frozen in liquid nitrogen. In the second experiment, Histoplasma G217Bura5 or the SG1 mutant were grown in liquid HMM culture at 37°C for 2 passages. On the day of dbcAMP addition, the cultures were passaged into fresh HMM + GlcNAc at a final OD600 of 0.2, and 10 mM dbcAMP or filter-sterilized autoclaved water (vehicle control) were added to the appropriate cultures, with 3 biological replicates for each chemical-strain combination. The cultures were treated and samples were collected as described for the first experiment.

value: dbcAMP

tag: replicate

value: B

tag: batch

value: yeast cells


title: E13.5M PGCs IUHG  bisulfite-seq bio rep1

description: Library name: Sample 16


title: E13.5M PGCs control  bisulfite-seq bio rep3

description: Library name: Sample 15


title: G217Bura5-DA 8-CPT-cAMP C-1 (8-CPT-cAMP4)

value: C


title: E13.5M PGCs control  bisulfite-seq bio rep1

description: Library name: Sample 13


title: G217Bura5-DA 8-CPT-cAMP B-1 (8-CPT-cAMP4)


title: G217Bura5-DA 8-CPT-cAMP A-1 (8-CPT-cAMP4)

value: A


title: Control_49

type: genomic

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

data_processing:
Import the CEL files into Axiom Analysis Suite, using Best Practices Workflow from the recommendations of the Axiom Genotyping Solution-Data Analysis Guide. Annotation and library downloaded from Taiwan Biobank (https://www.biobank.org.tw/fd.php)
SNP ID: dbSNP_RS_ID and affy_snp_id; SNP Call: AA, AB, BB, and NoCall; SNP Annotation: Allele_A, Allele_B, Ref_Allele and Alt_Allele; SNP Quality: CR(Call Rate), ConversionType; SNP frequency: n_AA, n_AB, n_BB, n_NC and MinorAlleleFrequency.

label: biotin

organism: Homo sapiens

source_name: peripheral white blood cells

label_protocol: The CAD group comprised individuals demonstrating angiographic evidence showing significant (>75%) coronary artery stenosis post-administration of intracoronary nitroglycerine (50-200 μg), individuals with a history of percutaneous coronary revascularization or individuals who had undergone coronary artery bypass grafting. The high-risk group consisted of individuals whose calculated 10-year and lifetime risk of atherosclerotic cardiovascular disease (ASCVD) equaled or exceeded 20% based on established criteria, but without any history of angina pectoris or myocardial infarction. The criteria for inclusion in the control group encompassed a number of factors, namely the absence of major systemic diseases, various specific fasting measurements including high-density lipoprotein (HDL) levels (>40 mg/dL for males, >50 mg/dL for females), fasting glucose levels (<100 mg/dL), fasting triglyceride (TG) levels (<150 mg/dL), systolic blood pressure (SBP) below 130 mmHg, diastolic blood pressure (DBP) below 85 mmHg, and a waist circumference below 80 cm for females or 90 cm for males.

growth_protocol: Peripheral venous blood was obtained after an overnight fast.

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

tag: disease state

value: Control

tag: gender


title: PADI4 cKO skin P1

city: Stockholm

country: Sweden

description:
Library name: KO
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

value: PADI4 cKO


title: E13.5F PGCs IUHG  bisulfite-seq bio rep3

description: Library name: Sample 12


title: E16.5M PGCs control  bisulfite-seq bio rep3

description: Library name: Sample 27


title: E13.5F PGCs IUHG  bisulfite-seq bio rep2

description: Library name: Sample 11


title: E13.5F PGCs control  bisulfite-seq bio rep3

description: Library name: Sample 9


title: E16.5M PGCs IUHG  bisulfite-seq bio rep2

description: Library name: Sample 29


title: E13.5F PGCs control  bisulfite-seq bio rep2

description: Library name: Sample 8


title: E13.5F PGCs IUHG  bisulfite-seq bio rep1

description: Library name: Sample 10


title: E12.5 PGCs IUHG  bisulfite-seq bio rep3

description: Library name: Sample 6

value: not determined


title: E13.5F PGCs control  bisulfite-seq bio rep1

description: Library name: Sample 7


title: E12.5 PGCs control  bisulfite-seq bio rep3

description: Library name: Sample 3


title: E12.5 PGCs IUHG  bisulfite-seq bio rep1

description: Library name: Sample 4


title: E13.5M PGCs control  bisulfite-seq bio rep2

description: Library name: Sample 14


title: E12.5 PGCs control  bisulfite-seq bio rep2

description: Library name: Sample 2


title: E12.5 PGCs control  bisulfite-seq bio rep1

description: Library name: Sample 1


title: RNA-seq_E16.5M PGCs IUHG  bio rep2

description: Library name: Sample 35

data_processing:
RNA-seq data quality assessment was conducted using FastQC, and adapters along with low-quality sequencing fragments were removed using Trim Galore. The filtered sequencing fragments were aligned to the mouse reference genome (Mm39) using the STAR two-pass mode. Only uniquely mapped fragments were retained for subsequent analyses. Filtering of the mapped fragments was performed using bamtools (https://github.com/pezmaster31/bamtools), retaining only those with both ends mapped to the genome. For differential gene expression analysis, the featureCounts tool generated a gene expression quantification matrix, followed by differential expression analysis using the R package DESeq2, with thresholds set at absolute fold change > 1 and p-value < 0.01. Gene Ontology (GO) enrichment analysis was performed using clusterProfiler and mouse annotation org.Dr.Mm.db, retaining biological processes with p-value < 0.05 for presentation.
Assembly: mm39
Supplementary files format and content: tab-delimited txt files include FPKM value for ezch sample

extract_protocol:
RNA was harvested using Universal RNA Extraction CZ Kit (ONREW) according to the manufacturer's instructions. 1 𝛍g of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by following the TruePrep® DNA Library Prep Kit V2 (Vazyme) following manufacturer's protocols.


title: RNA-seq_E16.5M PGCs IUHG  bio rep3

description: Library name: Sample 36


title: RNA-seq_E16.5M PGCs IUHG  bio rep1

description: Library name: Sample 34


title: RNA-seq_E16.5M PGCs control  bio rep1

description: Library name: Sample 31


title: RNA-seq_E16.5M PGCs control  bio rep3

description: Library name: Sample 33


title: RNA-seq_E16.5M PGCs control  bio rep2

description: Library name: Sample 32


title: RNA-seq_E16.5F PGCs IUHG  bio rep3

description: Library name: Sample 30


title: RNA-seq_E16.5F PGCs IUHG  bio rep2

description: Library name: Sample 29


title: E13.5M PGCs IUHG  bisulfite-seq bio rep2

description: Library name: Sample 17


title: RNA-seq_E16.5F PGCs control  bio rep3

description: Library name: Sample 27


title: RNA-seq_E16.5F PGCs control  bio rep2

description: Library name: Sample 26


title: RNA-seq_E16.5F PGCs control  bio rep1

description: Library name: Sample 25


title: E12.5 PGCs IUHG  bisulfite-seq bio rep2

description: Library name: Sample 5


title: RNA-seq_E13.5M PGCs IUHG  bio rep3

description: Library name: Sample 24


title: RNA-seq_E13.5M PGCs control  bio rep3

description: Library name: Sample 21


title: RNA-seq_E13.5M PGCs control  bio rep2

description: Library name: Sample 20


title: RNA-seq_E13.5M PGCs IUHG  bio rep1

description: Library name: Sample 22


title: RNA-seq_E13.5F PGCs IUHG  bio rep3

description: Library name: Sample 18


title: RNA-seq_E13.5M PGCs control  bio rep1

description: Library name: Sample 19


title: RNA-seq_E13.5M PGCs IUHG  bio rep2

description: Library name: Sample 23


title: RNA-seq_E13.5F PGCs IUHG  bio rep1

description: Library name: Sample 16


title: RNA-seq_E13.5F PGCs control  bio rep3

description: Library name: Sample 15


title: RNA-seq_E12.5 PGCs IUHG  bio rep3

description: Library name: Sample 12


title: RNA-seq_E13.5F PGCs control  bio rep1

description: Library name: Sample 13


title: RNA-seq_E12.5 PGCs IUHG  bio rep1

description: Library name: Sample 10


title: RNA-seq_E12.5 PGCs control  bio rep1

description: Library name: Sample 7


title: RNA-seq_E12.5 PGCs control  bio rep3

description: Library name: Sample 9


title: RNA-seq_E13.5 female gonads IUHG  bio rep2

description: Library name: Sample 5

source_name: ovary

value: ovary


title: RNA-seq_E12.5 PGCs IUHG  bio rep2

description: Library name: Sample 11


title: RNA-seq_E13.5 female gonads control  bio rep2

description: Library name: Sample 2


title: RNA-seq_E13.5 female gonads control  bio rep3

description: Library name: Sample 3


title: E16.5M PGCs IUHG  bio rep3

description: Library name: Sample 30

data_processing:
Adapters and low-quality sequencing fragments from the raw data were removed using Trim Galore. The processed sequencing fragments were aligned to the mouse reference genome using Bowtie2. Duplicate sequencing fragments were eliminated using Picard MarkDuplicates (http://broadinstitute.github.io/picard/), and reads mapped to the mitochondria were also removed. Due to the Tn5 transposase cutting characteristics, reads aligned to the reference genome were offset: 4 bp to the right for forward strand reads and 5 bp to the left for reverse strand reads. Subsequently, ATAC-seq peaks were identified using MACS2 with the following parameters: -q 0.01 --shift -75 --extsize 150 --nomodel --keep-dup all --call-summits. The normalized ATAC-seq signal was generated using bamCoverage with parameters: -binSize 10 --normalizeUsing RPKM -extendReads. Differentially accessible regions (DARs) at various developmental stages were identified using DiffBind, retaining those with FDR < 0.001 for further analysis.
Assembly: mm39
Supplementary files format and content: bigwig

extract_protocol:
The EGFP-positive PGCs obtained through FACS were washed with PBS. 5,000-10,000 cells were collected and lysed using lysis buffer.
ATAC-seq was performed using the Hyperactive ATAC-Seq Library Prep Kit (Vazyme).  The DNA was extracted as starting material for samples. Libraries was amplified using 15 cycles on the thermocycler and were validated using the Equalbit 1 × dsDNA HS Assay Kit (Vazyme)  for sequencing.


title: RNA-seq_E13.5 female gonads control  bio rep1

description: Library name: Sample 1


title: RNA-seq_E13.5 female gonads IUHG  bio rep1

description: Library name: Sample 4


title: E16.5M PGCs IUHG  bio rep2

description: Library name: Sample 29


title: E16.5M PGCs control  bio rep3

description: Library name: Sample 27


title: RNA-seq_E13.5F PGCs control  bio rep2

description: Library name: Sample 14


title: E16.5M PGCs control  bio rep1

description: Library name: Sample 25


title: E16.5M PGCs control  bio rep2

description: Library name: Sample 26


title: RNA-seq_E13.5 female gonads IUHG  bio rep3

description: Library name: Sample 6


title: E16.5F PGCs IUHG  bio rep1

description: Library name: Sample 22


title: RNA-seq_E12.5 PGCs control  bio rep2

description: Library name: Sample 8


title: E16.5F PGCs control  bio rep3

description: Library name: Sample 21


title: E16.5F PGCs control  bio rep1

description: Library name: Sample 19


title: E16.5F PGCs IUHG  bio rep3

description: Library name: Sample 24


title: E13.5M PGCs IUHG  bio rep3

description: Library name: Sample 18


title: E13.5M PGCs IUHG  bio rep2

description: Library name: Sample 17


title: RNA-seq_E13.5F PGCs IUHG  bio rep2

description: Library name: Sample 17


title: E13.5M PGCs IUHG  bio rep1

description: Library name: Sample 16


title: E16.5M PGCs IUHG  bio rep1

description: Library name: Sample 28


title: E13.5M PGCs control  bio rep3

description: Library name: Sample 15


title: E13.5M PGCs control  bio rep1

description: Library name: Sample 13


title: E16.5F PGCs IUHG  bio rep2

description: Library name: Sample 23


title: E13.5F PGCs control  bio rep3

description: Library name: Sample 9


title: E13.5F PGCs IUHG  bio rep1

description: Library name: Sample 10


title: E13.5F PGCs IUHG  bio rep3

description: Library name: Sample 12


title: E13.5F PGCs IUHG  bio rep2

description: Library name: Sample 11


title: E12.5 PGCs IUHG  bio rep1

description: Library name: Sample 4


title: E13.5F PGCs control  bio rep1

description: Library name: Sample 7


title: E16.5F PGCs control  bio rep2

description: Library name: Sample 20


title: E12.5 PGCs IUHG  bio rep3

description: Library name: Sample 6


title: E12.5 PGCs control  bio rep3

description: Library name: Sample 3


title: E12.5 PGCs control  bio rep1

description: Library name: Sample 1


title: E12.5 PGCs control  bio rep2

description: Library name: Sample 2


title: PBS

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

description: Library name: sample1

data_processing:
Matrix generated by Cellranger 7.2.0
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

source_name: colon

growth_protocol: Mice were maintained under specific pathogen-free conditions. All animal protocols were reviewed and approved by the Institutional Animal Care and Use Committee of Xiamen University.

extract_protocol:
Isolated lamina propria mononuclear cells, sample from three mice were pooled together and analyzed per condition. For scRNA-seq of Colon CD45+ cells were sorted by BD Arial III. These cells were barcoded with 10x Cellplex oligos before being encapsulated using the 10X Chromium 3′ Reagent Kits v3 according to manufacturer’s instructions.
Illumina standard protocols

treatment_protocol: Mice were i.p. injected with one dose of BG (1 mg) on day -7 (designated day0, D0 ), Then, Mice received 3% indicated DSS (36,000 to 50,000 molecular weight; MP Biomedicals) in their drinking water for 5 days, followed by 2 days(D7).

value: colon

value: Cd45+ cell

value: PBS


title: BG

description: Library name: sample2

value: BG


title: E13.5M PGCs control  bio rep2

description: Library name: Sample 14

value: PGCs

value: WT


title: V-Br-9

city: Vilnius

first: Milda

last: Milčiūtė

address: Antakalnio st. 17, 12th building

country: Lithuania

institute: VUGENE

description:
Library name: V-Br-9
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-9

data_processing:
Initial quality control and pre-processing using fastp (v0.23.2) (S. Chen et al., 2018) for duplicate removal and adapter trimming.
Further quality control with FastQC (v2.13.0) and MultiQC (v1.14.0) (Ewels et al., 2016).
Gene alignment and mapping were performed using STAR (v2.7.9a) with the human reference genome GRCh38 version 44. Key alignment parameters included --outFilterMultimapNmax 100, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNoverReadLmax 0.04 (maximum 4% mismatch rate per read length), and --peOverlapMMp 0.01 (limiting mismatches in paired-end overlaps to 1%).
Initial filtering by expression levels using the filterByExpr function from the edgeR (v3.42.4) R package (Robinson et al., 2010).
Data normalization with the calcNormFactors function (TMM method) using edgeR.
Conversion to Counts per Million (CPM) values using the cpm function and logarithmic transformation of CPM values.
Assembly: GRCh38 version 44.
Supplementary files format and content: raw.csv: This file contains the raw gene counts as outputted by STAR. The format is comma-separated values.
Supplementary files format and content: normalized.csv: This file contains the normalized gene expression values in Counts Per Million (CPM).

source_name: Superior parietal (Brodmann area 7)

extract_protocol:
Total RNA was extracted using the RNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA; cat. no. 74104), according to the manufacturer’s instructions. RNA concentration and purity were initially measured using the NanoDrop 8000 spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA).
Sequencing libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit for Illumina (New England Biolabs, Ipswich, MA, USA), as per the manufacturer’s recommendations. Briefly, RNA samples were fragmented at 94 °C for 15 minutes, followed by first and second-strand cDNA synthesis using primers containing random priming sites. Subsequent steps included end repair and adenylation of cDNA fragments at the 3’ ends, adapter ligation, indexing, and enrichment via limited-cycle PCR. Final sequencing libraries were validated using the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA) and quantified with the Qubit 3.0 Fluorometer and quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Prepared libraries were clustered onto a lane of a NovaSeq flowcell, which was subsequently loaded onto an Illumina NovaSeq sequencing instrument following the manufacturer’s instructions. Sequencing was performed using a paired-end (PE) configuration of 2×150 bp reads. Image analysis and base calling were executed by the instrument’s control software. The raw sequencing output in .bcl file format was converted to FASTQ files and demultiplexed using Illumina’s bcl2fastq software version 2.17, allowing one mismatch during index sequence identification.

value: Superior parietal (Brodmann area 7)

tag: condition

value: VCI

tag: hemisphere

value: Left

value: Male

tag: race

tag: pmi

tag: age


title: V-Br-6

description:
Library name: V-Br-6
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-6

value: Female

value: White


title: V-Br-4

description:
Library name: V-Br-4
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-4


title: V-Br-8

description:
Library name: V-Br-8
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-8


title: V-Br-7

description:
Library name: V-Br-7
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-7


title: E13.5F PGCs control  bio rep2

description: Library name: Sample 8

value: female

value: control group


title: E12.5 PGCs IUHG  bio rep2

description: Library name: Sample 5

value: STZ-induced


title: C15 - Mouse liver hepatocytes, male mouse, septic, mouse 2

city: Calgary

first: Braedon

last: McDonald

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

description: Library name: Sepsis male 2

data_processing:
Alignment
Reads were pseudo-aligned to reference transcriptome GRCm39 using kallisto (v0.46.1).
Assembly: GRCm39
Supplementary files format and content: Raw read counts for each sample

source_name: Liver

extract_protocol:
RNA was harvested from liver hepatocytes using the Rneasy Mini Kit (Qiagen).
Poly-A selection was performed.  Library preparation was performed using the Illumina stranded mRNA prep protocol.

treatment_protocol: Sepsis was induced in C57Bl/6 mice at 8-12 weeks of age by 1 intraperitoneal injection of 1mg/g fecal slurry (total volume 200 uL) into the right lower abdominal quadrant.  Control mice were given an injection of sterile PBS.

value: Liver

value: Hepatocyte

value: FIP

tag: control

value: no


title: C20 - Mouse liver hepatocytes, female mouse, septic, mouse 3

description: Library name: Sepsis female 3

tag: tissue


title: C14 - Mouse liver hepatocytes, male mouse, septic, mouse 1

description: Library name: Sepsis male 1


title: C15-ERCCmix1 - Mouse liver hepatocytes, male mouse, uninfected + ERCC spike-in mix 1

description: Library name: Control male 2 + ERCC 1

value: PBS

value: ERCC spike-in mix 1


title: C16 - Mouse liver hepatocytes, male mouse, septic, mouse 3

description: Library name: Sepsis male 3


title: C15-ERCCmix2 - Mouse liver hepatocytes, male mouse, uninfected + ERCC spike in mix 2

description: Library name: Control male 2 + ERCC 2

value: ERCC spike-in mix 2


title: C17 - Mouse liver hepatocytes, male mouse, septic, mouse 4

description: Library name: Sepsis male 4


title: V-Br-5

description:
Library name: V-Br-5
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-5

value: Control


title: V-Br-38

description:
Library name: V-Br-38
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-38

value: Superior parietal (Brodmann area 7)


title: C19 - Mouse liver hepatocytes, female mouse, septic, mosue 2

description: Library name: Sepsis female 2


title: UTP4 - Mouse liver hepatocytes, male mouse, uninfected, mouse 4

description: Library name: Control male 4


title: V-Br-40

description:
Library name: V-Br-40
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-40


title: V-Br-39

description:
Library name: V-Br-39
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-39

value: VCI


title: C18 - Mouse liver hepatocytes, female mouse, septic, mouse 1

description: Library name: Sepsis female 1


title: V-Br-36

description:
Library name: V-Br-36
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-36

value: Left


title: V-Br-37

description:
Library name: V-Br-37
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-37


title: UTP3 - Mouse liver hepatocytes, male mouse, uninfected, mouse 3

description: Library name: Control male 3


title: V-Br-34

description:
Library name: V-Br-34
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-34


title: V-Br-35

description:
Library name: V-Br-35
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-35


title: UTP2 - Mouse liver hepatocytes, male mouse, uninfected, mouse 2

description: Library name: Control male 2


title: UTP1 - Mouse liver hepatocytes, male mouse, uninfected, mouse 1

description: Library name: Control male 1


title: V-Br-31

description:
Library name: V-Br-31
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-31


title: UTP5 - Mouse liver hepatocytes, female mouse, uninfected, mouse 1

description: Library name: Control female 1


title: UTP7 - Mouse liver hepatocytes, female mouse, uninfected, mouse 3

description: Library name: Control female 3


title: V-Br-33

description:
Library name: V-Br-33
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-33


title: V-Br-30

description:
Library name: V-Br-30
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-30


title: V-Br-32

description:
Library name: V-Br-32
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-32


title: Water - Water control 2

description: Library name: Negative control 2

value: negative


title: V-Br-28

description:
Library name: V-Br-28
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-28

value: Female


title: PDD9

city: Singapore

first: Li

last: Zeng

address: 11 Jln Tan Tock Seng

country: Singapore

institute: National Neuroscience Institute

description: Library name: PDD9

data_processing:
Preprocessing, including debarcoding and unique molecular identifier (UMI) counting, was performed with Cell Ranger version 3.1.0 (10x Genomics). For each sample, the UMI count file was read by Seurat (version 4.1.0) in R and then subjected to sample-wise quality control. Quality control included assessing the feature number, UMI number and mitochondrial gene percentage. Potential doublets were identified and removed using the “scDblFinder” and “DoubletFinder” packages. A total of 2,000 variable features in the RNA assay of each sample were identified using the “vst” method in the Seurat package. Data integration was performed using the scVI method with 5,000 common feature genes across all samples. The 50 latent dimensions output by scVI were utilised for Uniform Manifold Approximation and Projection (UMAP) analysis, followed by clustering. For downstream analysis, the data were normalised using either “log normalisation” or “sctransform”, depending on the specific analysis being performed.
Assembly: GRCh38
Supplementary files format and content: The RDS file contains the integrated gene expression matrix from all samples, along with cell type annotation information.

source_name: brain

extract_protocol:
Nuclei were isolated from frozen postmortem tissues as previously described with modifications. The tissues were homogenised in chilled lysis buffer (10 mM Tris, 10 mM NaCl, 3 mM MgCl2, 0.05% NP40) using a glass Dounce homogeniser, with 10 loose pestle strokes, followed by 5 tight pestle strokes. The homogenates were filtered through a 40 μm strainer and centrifuged for 5 min at 500 × g, 4°C to pellet the nuclear fraction. The pellet was then resuspended in 10 ml of wash buffer (5% BSA, 40 units/ml Protector RNase inhibitor in 0.5× PBS) and centrifuged for 5 min at 500 × g, 4°C. The pellet was then resuspended in 1 ml wash buffer, mixed with an equal volume of 50% OptiPrep solution, and layered on top of 2 ml of 29% OptiPrep solution. The nuclei were separated by centrifugation at 1,000 × g for 30 min at 4°C. The nuclear pellet was washed three times with wash buffer (2% BSA, 40 units/ml Protector RNase inhibitor in 0.5× PBS) and subsequently resuspended in 500 μl wash buffer to yield a clean single-nucleus suspension. For quantification, the collected nuclei were stained with DAPI and counted with Countess II Automated Cell Counter (Life Technologies).
An estimated 10,000 human nuclei were processed using the Chromium Single Cell 3′ v3 Gene Expression Reagent Kits, following the manufacturer’s instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using an Illumina HiSeq 4000 at NovogeneAIT Genomics Singapore Pte Ltd.

value: brain

tag: disease group

value: Parkinson's disease


title: PDD7

description: Library name: PDD7


title: CHGI-NTC - Water control 1

description: Library name: Negative control 1


title: PDD5

description: Library name: PDD5


title: UTP6 - Mouse liver hepatocytes, female mouse, uninfected, mouse 2

description: Library name: Control female 2


title: V-Br-3

description:
Library name: V-Br-3
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-3

tag: Sex

value: Male


title: LSC_HET_RNA Pol II_2

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

description: Library name: Sample4

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
Clean reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.2.9. MarkDuplicates was used to mark PCR duplicate and unmapped reads. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS2 and ChIPseeker package, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: Bone marrow

extract_protocol:
The CUT&Tag assay was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein) according to the manufacturer’s protocol. 5,000-10,000 LSCs were harvested and resuspended in 45 µL wash buffer. Then 6 µL ConA beads were added to the sample and incubated at 37°C for 10 min. Then the supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL antibody buffer (20 mM Hepes, pH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1× PIC).
Then, 0.5 µL antibody was added to the sample and incubated at 4°C overnight. The supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL secondary antibody buffer, containing 0.5 µL goat anti-rabbit IgG antibody. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL ChiTag Buffer, containing 0.5 µL ChiTag transposome. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL tagmentation buffer. Then, 1 µL 10% SDS was added to the sample and incubated at 55°C for 10 min, and DNA was extracted using 2×DNA clean beads (Vazyme) and amplified with i5 and i7 primers (Vazyme) by 17-20 PCR cycles. The libraries were purified by 1.2×DNA clean beads (Vazyme).

treatment_protocol: LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Nup214fl/+ and Nup214fl/+,Tie2-Cre (Nup214-HET) AML mice were sorted, followed by RNA Pol II-CUT&Tag-seq

value: Bone marrow

value: Leukemia stem cell


title: V-Br-26

description:
Library name: V-Br-26
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-26


title: PDD2

description: Library name: PDD2


title: PDD4

description: Library name: PDD4


title: V-Br-29

description:
Library name: V-Br-29
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-29

value: White


title: PDD1

description: Library name: PDD1


title: V-Br-25

description:
Library name: V-Br-25
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-25


title: DLB8

description: Library name: DLB8

value: Dementia with Lewy bodies


title: DLB_7

description: Library name: DLB_7


title: V-Br-24

description:
Library name: V-Br-24
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-24

value: Asian


title: DLB_6

description: Library name: DLB_6


title: DLB_5

description: Library name: DLB_5


title: LSC_HET_RNA Pol II_1

description: Library name: Sample3


title: V-Br-23

description:
Library name: V-Br-23
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-23


title: DLB4

description: Library name: DLB4


title: V-Br-27

description:
Library name: V-Br-27
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-27


title: V-Br-22

description:
Library name: V-Br-22
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-22


title: CTRL_4

description: Library name: CTRL_4

value: control


title: CTRL_7

description: Library name: CTRL_7


title: V-Br-21

description:
Library name: V-Br-21
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-21


title: V-Br-20

description:
Library name: V-Br-20
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-20


title: RNA-seq_E16.5F PGCs IUHG  bio rep1

description: Library name: Sample 28

value: female

tag: developmental stage

value: PGCs

value: WT

value: STZ-induced


title: DLB_2

description: Library name: DLB_2


title: ADD_6

description: Library name: ADD_6

value: Alzheimer's disease


title: ADD_7

description: Library name: ADD_7


title: V-Br-2

description:
Library name: V-Br-2
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-2

value: Superior parietal (Brodmann area 7)

value: Control

value: Left


title: ADD_5

description: Library name: ADD_5

value: brain


title: ADD_4

description: Library name: ADD_4


title: PPPE.170

city: Rochester

first: Sylvie

last: Girard

state: Minnesota

address: 200 First Street

institute: Mayo Clinic

data_processing:
Libraries were sequenced using the HiSeq 4000 system (Illumina, USA) at the “Integrated Clinical Genomics Centre in Pediatrics”at the CHUSJ.
Data were processed using the RosalinD platform
Assembly: hg19
Supplementary files format and content: Individual text files with the raw counts for each sample
Supplementary files format and content: The same tab-seperated values file for the normalized counts

source_name: Placenta

extract_protocol:
mRNA was extracted using the RNeasy mini kit (Qiagen, Canada) following manufacturer instructions.
Libraries were created using the TruSeq RNA Library Kit v2 (Illumina, USA) and fragment size was validated on a Bioanalyzer (Agilent 2100, USA).

value: Placenta

value: PTB

tag: cell type

value: Whole tissue


title: V-Br-18

description:
Library name: V-Br-18
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-18

value: VCI

value: Female


title: PPPE.162

value: RCIU


title: V-Br-19

description:
Library name: V-Br-19
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-19

value: Male


title: CTRL_5

description: Library name: CTRL_5

value: control


title: PPPE.155


title: PPPE.158


title: PPPE.153


title: ATAC_LSC_FL_1

description: Library name: Sample5

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters “-q 10 -length 30 -stringency 5’.”
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 version 2.2.9. Reads that aligned to the mitochondrial genome were filtered, and PCR duplicates were removed with picard MarkDuplicates.
To identify peaks, the bam files containing unique, nonchrM reads were used to call peaks with MACS2 using parameters ‘‘-nomodel-keep-dup all -q 0.01-shift -100-extsize 200-call-summits -g mm’’.
For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATACseq reads were counted by featureCounts.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
About 5,000 cells were resuspended in 50 µL of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin) and incubated on ice for 5 min. After lysis, 950 µL wash buffer was added to the sample. The supernatant was removed by centrifugation (500 g, 10 min).
Then, 4 µLPBS, 0.4 µL 10% Tween 20, 0.4 µL 1% Digitonin, 13.6 µL ddH2O, 20 µl 2×TD buffer, and 1.6 µL Transposome Mix were added to the sample, which was mixed and incubated at 37°C for 30 min. The reaction was terminated by incubating with 10 µL stop buffer. Then the tagment DNA was extracted using 2×DNA Extract Beads (Novoprotein). Total 35 µL DNA was transferred to a 0.2 ml PCR tube, and 2.5 µL N5 primer, 2.5 µL N7 primer, and 10 µL 5×AmpliMix were added. PCR was performed to amplify the library for 13-16 cycles. After the PCR reaction, libraries were purified using the 1.2×DNA Clean Beads (Novoprotein).

treatment_protocol: HSCs (CD48-CD150+LSK) from Nup214fl/+(FL) and Nup214fl/+,Tie2-Cre (HET) mice were sorted, followed by ATAC-seq. LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from Nup214fl/+(FL) and Nup214fl/+,Tie2-Cre (HET) AML mice (MLL-AF9-driven) were sorted, followed by ATAC-seq.

value: Bone marrow

value: Leukemia stem cell

tag: genotype


title: PPPE.152


title: ATAC_HSC_HET_1

description: Library name: Sample3

value: Hematopoietic stem cell


title: ATAC_LSC_HET_1

description: Library name: Sample7


title: ATAC_LSC_FL_2

description: Library name: Sample6


title: ATAC_HSC_HET_2

description: Library name: Sample4


title: ATAC_LSC_HET_2

description: Library name: Sample8


title: PPPE.148


title: V-Br-16

description:
Library name: V-Br-16
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-16


title: ATAC_HSC_FL_2

description: Library name: Sample2


title: V-Br-15

description:
Library name: V-Br-15
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-15


title: LSC_FL_H3K27ac_2

description: Library name: Sample2

treatment_protocol: LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Nup214fl/+ and Nup214fl/+,Tie2-Cre (Nup214-HET) AML mice were sorted, followed by H3K27ac-CUT&Tag-seq


title: LSC_FL_H3K27ac_1

description: Library name: Sample1


title: LSC_HET_H3K27ac_2

description: Library name: Sample4


title: PPPE.144


title: LSC_HET_H3K27ac_1

description: Library name: Sample3


title: PPPE.146

value: CTL


title: ATAC_HSC_FL_1

description: Library name: Sample1


title: V-Br-14

description:
Library name: V-Br-14
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-14

value: Asian


title: PPPE.136


title: PPPE.133


title: PPPE.134


title: V-Br-13

description:
Library name: V-Br-13
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-13

value: Superior parietal (Brodmann area 7)


title: PPPE.130


title: PPPE.124


title: PPPE.121


title: V-Br-11

description:
Library name: V-Br-11
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-11

value: White


title: V-Br-12

description:
Library name: V-Br-12
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-12

value: Control

value: Left


title: PPPE.113

value: Placenta


title: PPPE.122

value: LOPE


title: PPPE.115

value: Whole tissue


title: V-Br-17

description:
Library name: V-Br-17
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-17


title: CTRL_6

description: Library name: CTRL_6

value: brain


title: ILC2s, IL25 treated  Il25-/- mice, mid 2/3 small intestine

first: Victor

middle: S

last: Cortez

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description:
Library name: 5_ILC2_IL25KO_IL25
10x Genomics

data_processing:
For the ILC2 scRNA-seq analysis, single-cell transcripts were aligned to the mouse genome and processed via the 10X Cell Ranger software version 7.0. The R package Seurat (version 4.3) was used for single cell transcriptome analysis. Cells were removed according to the following thresholds: <1000 genes/cell or >6000 genes per cell, >50000 UMIs/cell, 10% mitochondrial content, <0.001% hemoglobin read content to remove red blood cells. Among the ILC2 cells retained, the effects of mitochondrial and ribosomal content were regressed out using the SCTransform v2 normalization method prior to clustering. Genes were excluded from the final dataset if they were expressed in fewer than 3 cells. For differential expression analysis between clusters, genes were detected if they are expressed in at least 10% of cells in a cluster with a log fold change of at least 0.25. For DEG analysis between comparison groups, genes were detected if expressed in at least 5% of cells in the group with a log fold change of at least 0.25
cellranger v7.0
Assembly: mouse mm10
Supplementary files format and content: .h5 files, cellranger raw matrix output

source_name: Small Intestine

extract_protocol:
Small intestinal single cell suspensions were prepared from the proximal 1/3, mid 2/3, and distal 3/3 of tissue. Luminal contents were flushed with PBS, Peyer’s patches removed, and tissue cut open. Pieces were incubated with epithelial cell extraction buffer (EEB: Ca2+/Mg2+ free HBBS, 3% FCS, 10 mM HEPES, 10 mM EDTA, 10 mM DTT) at 37℃ with gentle shaking for 15 min. Tubes were vortexed at full speed for 30 sec and supernatants discarded. The tissue was placed with fresh EEB at 37℃ for 15 min with gentle shaking, then vortexed for 30 sec and supernatant discarded. Tissue was placed in rinse buffer (Ca2+/Mg2+ sufficient HBBS, 3% FCS, 10 mM HEPES) and incubated at 37℃ with gentle shaking for 5 min. Tissue was placed in GentleMACS C tubes (Miltenyi Biotec) with digestion buffer (DB: Ca2+/Mg2+ sufficient HBBS, 3% FCS, 10 mM HEPES, 30 ug/ml DNase I, 0.1 Wunsch/ml Liberase TM), minced with scissors, and incubated at 37℃ with gentle shaking for 10-15 min. Single-cell suspensions were obtained using a gentleMACS tissue dissociator (Miltenyi Biotec), running program m_intestine_0, and then pouring through a 100 um filter and washing with FACS buffer (PBS, 3% FCS)
Library was performed according to the manufacter's instructions (Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit v3.1, 10x genomics)

value: Small Intestine

tag: treatment

value: IL25 treated


title: V-Br-1

description:
Library name: V-Br-1
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-1

value: VCI

value: Female


title: S.Tm_∆invG_infected_2

city: Uppsala

first: Christopher

last: von Beek

address: Husargatan 3

department: IMBIM

institute: Uppsala University

description:
Library name: XH.4059.EXP.24.CB0468.dinvG2
XH.4059.EXP.24.CB0468.dinvG2

data_processing:
# DELIVERY OF RESULTS FROM RNASEQ ANALYSIS WITH NF-CORE RNASEQ PIPELINE  ## Analysis Samples were analysed with the nf-core rnaseq pipeline release 3.8.1. In short, the pipeline does the following:  The workflow processes raw data from FastQ inputs, aligns the reads, generates counts relative to genes or transcripts and performs extensive quality-control on the results.  For information regarding the pipeline, folder structure and how to interpret results, please refer to the pipeline documentation: [https://nf-co.re/rnaseq/3.8.1](https://nf-co.re/rnaseq/3.8.1)  Detailed information about standard outputs from the pipeline can be found [here](https://nf-co.re/rnaseq/3.8.1/output).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing count matrix of merged gene counts from STAR mapping of all samples (salmon.merged.gene_counts.tsv).
Supplementary files format and content: Tab-delimited text file containing count matrix of merged gene counts adjusted for gene length from STAR mapping of all samples (salmon.merged.gene_counts_length_scaled.tsv).

source_name: LUVA

growth_protocol: LUVA cells were maintained in StemPro, 1% GlutaMAX, 1% PenStrep at 37°C, 5% CO2. Salmonella Typhimurium SL1344 strains were inoculated from crytotubes into 15 ml falcon tube with 3 ml LB 0.3 M NaCl + 50 µg/ml streptomycin. After exactly 12 h incubation at 37 °C on a rotating wheel (20 rpm), cultures were diluted 1:20 into LB 0.3 M NaCl without antibtioics and grown further for 4 h.

extract_protocol:
Total RNA was extracted with the RNeasy Micro Kit (Qiagen, #74004) and stored at -80 °C until submission.
Sequencing libraries were prepared from 500ng total RNA using the TruSeq stranded mRNA library preparation kit (cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20040871, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol (#1000000040498).

treatment_protocol: LUVA cells were washed 2x in DPBS and resuspended in StemPro, 1% GlutaMAX. 900 µl of LUVA cells (0.556 x 10^6 cells) were placed into wells in a 12 well plate, 100 µl of S.Tm (MOI 50), resuspended in the same medium, were added to the cells and the plate was incubated for 30 min at 37 °C, 5% CO2. After 30 min, 50 µl of 20x gentamycin in medium were added to a final conc of 100 µg/ml. Cells were harvested (5 min, 400 x g) 3.5 h later.

tag: cell line

value: LUVA

value: Mast cell

value: WT

value: S.Tm ∆invG infected


title: PPPE.109

value: CTL


title: PPPE.110

value: PTB


title: S.Tm_∆invG_infected_3

description:
Library name: XH.4059.EXP.24.CB0468.dinvG3
XH.4059.EXP.24.CB0468.dinvG3


title: ILC2s, PBS treated Il25-/- mice, distal 3/3 small intestine

description:
Library name: 3_ILC2_IL25KO_PBS
10x Genomics

value: PBS treated


title: S.Tm_∆invG_infected_1

description:
Library name: XH.4059.EXP.24.CB0468.dinvG1
XH.4059.EXP.24.CB0468.dinvG1


title: ILC2s, IL25 treated  Il25-/- mice, proximal 1/3 small intestine

description:
Library name: 4_ILC2_IL25KO_IL25
10x Genomics


title: PPPE.106

value: RCIU


title: PPPE.123


title: V-Br-10

description:
Library name: V-Br-10
Column name in raw and normalized counts raw.csv and normalized.csv: V-Br-10

value: Superior parietal (Brodmann area 7)

value: Left


title: ILC2s, IL25 treated  Il25-/- mice, distal 3/3 small intestine

description:
Library name: 6_ILC2_IL25KO_IL25
10x Genomics


title: PPPE.103

value: Placenta

value: EOPE


title: ILC2s, PBS treated Il25-/- mice, mid 2/3 small intestine

description:
Library name: 2_ILC2_IL25KO_PBS
10x Genomics


title: S.Tm_wt_infected_2

description:
Library name: XH.4059.EXP.24.CB0468.STM2
XH.4059.EXP.24.CB0468.STM2

value: S.Tm wt infected


title: ILC2s, PBS treated Il25-/- mice, proximal 1/3 small intestine

description:
Library name: 1_ILC2_IL25KO_PBS
10x Genomics

value: Small Intestine


title: PPPE.101

value: Whole tissue


title: PPPE.099


title: S.Tm_wt_infected_1

description:
Library name: XH.4059.EXP.24.CB0468.STM1
XH.4059.EXP.24.CB0468.STM1


title: ILC2s, IL25 treated wild type mice, mid 2/3 small intestine

description:
Library name: ILC2_IL25_2
10x Genomics

value: Wild type, C57BL/6J

value: IL25 treated


title: Uninfected_3

description:
Library name: XH.4059.EXP.24.CB0468.C3
XH.4059.EXP.24.CB0468.C3

value: LUVA

value: Uninfected


title: Uninfected_2

description:
Library name: XH.4059.EXP.24.CB0468.C2
XH.4059.EXP.24.CB0468.C2

value: Mast cell

value: WT


title: PPPE.098


title: PPPE.097

value: LOPE


title: ILC2s, IL25 treated wild type mice, proximal 1/3 small intestine

description:
Library name: ILC2_IL25_1
10x Genomics


title: Uninfected_1

description:
Library name: XH.4059.EXP.24.CB0468.C1
XH.4059.EXP.24.CB0468.C1


title: Sample 6_NHA cells, v117.28, biol rep2

city: Tuebingen

first: Laura

middle: Sophia

last: Pfeiffer

address: Auf der Morgenstelle 15

country: Germany

institute: University of Tuebingen

description:
Library name: Sample 6
Ctrl_v117-28_expression_comparison.txt
Same processed file as biol rep 1

data_processing:
Raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 16nt were discarded.
Filtered reads were mapped to hg19 reference genome sequences using STAR v2.4.2a with parameters: --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
RNA editing level was quantified by counting the ratio of the number of G-containing reads over the number of all reads mapped to each loci (as described in PMID: 29022589)
Assembly: hg19
Supplementary files format and content: Tab delimited plain txt with header information, includes TPM, FPKM and log2 fold change values of transcript levels for replicates for each sample
Supplementary files format and content: Information on ISG-induced gene (yes/no) is in the last column

source_name: primary cells

growth_protocol: Normal human astrocytes (NHA, Lonza cat. no. CC-2565) were cultured in ABM Basal Medium (Lonza cat. no. CC-3187) with AGM SingleQuot Kit Supplementary & Growth Factors (Lonza cat. no. CC-4123) at 37°C with 5% CO2 in a water saturated steam atmosphere.

extract_protocol:
RNA was isolated 24 h after transfection with the RNeasy MinElute Kit according to manufacturer’s protocol, treated with DNase I, incubated with an RNA strand reverse complementary to the respective ON and heated to 95 °C for 3 min and purified again with the RNeasy MinElute Kit. 25 µl of purified RNA (≥ 40 ng/µl was used for poly(A)+ mRNA sequencing).
Purified RNA was delivered to CeGaT (Germany) for poly(A)+ mRNA sequencing.The library was prepared from 100 ng RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA) and sequenced with a NovaSeq 6000 (50 Million reads, 2 × 100 bp paired end, Illumina, USA). Each sample was prepared as a biological duplicate.

treatment_protocol: 10^5 cells were seeded into a 24-well per condition. 24 h after seeding, medium was changed and cells were forward transfected with the ONs. Forward transfection of the ONs was achieved by diluting 25 pmol ON/well and 1.5 µl/well Lipofectamine RNAiMAX Reagent (ThermoFisher Scientific) in 50µL OptiMEM each. Empty transfections omitted the ON. Both solutions were combined after 5 min incubation and incubated for an additional 20 min before the transfection mix was distributed evenly into one well. After 24 h, cells were harvested for RNA isolation and sequencing.

value: primary cells

value: normal human astrocytes

value: WT, Lonza cat. no. CC-2565

value: ON transfection

tag: on name

value: GAPDH ORF v117.28


title: Sample 4_NHA cells, v117.19, biol rep2

description:
Library name: Sample 4
Ctrl_v117-19_expression_comparison.txt
Same processed file as biol rep 1

value: GAPDH ORF v117.19


title: Sample 3_NHA cells, v117.19, biol rep1

description:
Library name: Sample 3
Ctrl_v117-19_expression_comparison.txt
Same processed file as biol rep 2


title: Sample 1_NHA cells, ctrl, biol rep1

description:
Library name: Sample 1
Processed file is integrated in Samples 3 - 6

value: empty transfection


title: Sample 5_NHA cells, v117.28, biol rep1

description:
Library name: Sample 5
Ctrl_v117-28_expression_comparison.txt
Same processed file as biol rep 2


title: Sample 2_NHA cells, ctrl, biol rep2

description:
Library name: Sample 2
Processed file is integrated in Samples 3 - 6


title: HEL-Control

city: Guiyang

first: Xiao

last: Xiao

address: Gaohai street

institute: Guizhou Medical University

description:
Library name: sample1
Column name in raw_counts_All_Samples.txt: A

data_processing:
The sequencing data（ Raw data） underwent quality control using fastp (v2.0) to remove adapters, trim low-quality reads (score < 20), and discard reads with an N content exceeding 10%.The resulting processed data is referred to as clean data.
Clean reads were aligned to the reference genome using HISAT2 (v2.1.0), and alignment quality was assessed using RSeQC (v3.0.1).
Expression quantification was performed with StringTie.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: cvs files include FPKM values for each Sample

source_name: cell line

growth_protocol: Erythroleukemia (HEL) was cultured in RPMI, with supplemented with 5%–10% fetal bovine serum.These cells were maintained in a humidified incubator containing 5% CO2 at 37°C.

extract_protocol:
RNA  was harvested using MagZolTM Reagent（Axygen, USA） , adding chloroform, and centrifuging to collect the RNA. Total RNA was usde for the construction of sequencing libraries.
Library preparation simplifies with a kit combining double-strand synthesis, end repair, and dA-tailing. mRNA is enriched with VAHTS mRNA Capture Beads（Vazyme, China）, then fragmented, and used for double-stranded cDNA synthesis. Libraries are quality-checked using the Agilent Bioanalyzer and Qubit.

treatment_protocol: HEL cells treated with L1(1 µM) or 0.5% DMSO for 24 h .

value: cell line

value: HEL

value: erythroleukemia  cells

value: 0.5% DMSO


title: LSC_FL_RNA Pol II_1

description: Library name: Sample1

value: Bone marrow

value: Leukemia stem cell


title: LSC_FL_RNA Pol II_2

description: Library name: Sample2


title: HEL-L1

description:
Library name: sample2
Column name in raw_counts_All_Samples.txt: D


title: PPPE.096

value: Placenta

value: EOPE

value: Whole tissue


title: ILC2s, PBS treated wild type mice, distal 3/3 small intestine

description:
Library name: ILC2_PBS_3
10x Genomics

value: Small Intestine

value: Wild type, C57BL/6J

value: PBS treated


title: ILC2s, IL25 treated wild type mice, distal 3/3 small intestine

description:
Library name: ILC2_IL25_3
10x Genomics

value: IL25 treated


title: iPSC derived human organoids, 8week, treatment

city: Parkville

first: Samantha

last: Barton

address: Parkville Campus 30 Royal Parade

country: Australia

institute: The Florey

description:
Library name: 18a_8week_LPC
10x Genomics

data_processing:
The Fastq files were processed using cellrnager multi (cellranger-6.1.2).  Per sample fastq files were generated using bamtofastq on the sample_alignments.bam.
Assembly: GRCh38-2020-A
Supplementary files format and content: The Fastq files were processed using cellrnager multi (cellranger-6.1.2).  Per sample fastq files were generated using bamtofastq on the sample_alignments.bam.

source_name: iPSC derived human organoids

extract_protocol:
Single cells were fixed overnight at 4 °C using 4 % PFA (ProSciTech) diluted in Concentrated Fix & Permealisation buffer. After fixation, cells were pelleted at 850 x g for 5 min. Cell pellets were quenched with Quenching and Enhancer buffer (from Chromium Gene Expression Flex Library Prep kit). Glycerol was added to each sample to a final concentration of 25 % prior to storing in -80 °C.  RNA was released and captured in‑GEM using the Chromium Gene Expression Flex Library Prep Kit (10x Genomics PN‑1000414) following the Fixed RNA Profiling Demonstrated Protocol CG000478 and User Guide CG000527; this includes in‑droplet lysis of fixed cells and on‑bead reverse transcription.
Chromium Gene Expression Flex Library Prep Kit  following Fixed RNA Profiling Demonstrated Protocol CG000478 and User Guide CG000527; includes in‑GEM lysis, on‑bead reverse transcription, and cDNA amplification.

value: iPSC derived human organoids

value: iPSC derived organoids cells enriched for mature myelinating olig. and funcitonally reactive microglia


title: Ngru_WGBS

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Library name: WGBS_1

data_processing:
WGBS data was mapped to the reference genome using BS-seeker2 with Bowtie2 as a back-end aligner. The resulting bam file was then deduplicated with Sambamba, and the methylation calling done with CGmapTools.
Assembly: Acanthamoeba castellanii: https://zenodo.org/records/6800059, Naegleria gruberi: https://github.com/AlexdeMendoza/6mA_evolution/blob/main/Genomes/Naegleria_gruberi.medakaRagTag.genome.fasta.gz
Supplementary files format and content: CGmap files are described in the BS-Seeker2 github repository: https://github.com/BSSeeker/BSseeker2?tab=readme-ov-file#44-bs_seeker2-call_methylationpy

organism: Naegleria gruberi

source_name: axenic culture

growth_protocol: Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712. Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034.

extract_protocol:
DNA was extracted using Monarch
Whole Genome Bisulfite sequencing (EZ DNA Methylation-Gold Kits coupled with EM-seq library prep modules). Includes CpG methylated pUC19 control and unmethylated lambda phage genome control.

treatment_protocol: No treatments were performed.

value: axenic culture

value: NEG-M

value: amoeba

value: 30C growth 5 days


title: PPPE.094

value: PTB


title: N_gru_untreated_EMseq

description: Library name: N_gru_untreated_EMseq

data_processing:
The EM-seq libraries were sequenced at NovoGene, using Illumina NovaSeq6000 platform, aiming at coverages >30x for reference methylomes, and 5x for shallow treatment samples. The obtained FASTQ files were mapped to the reference genomes using BS-Seeker2, with BOWTIE2 as backend alignment tool. PCR duplicate reads were removed using Sambamba, and methylation calling was obtained using CGmapTools.
We used HISAT2 to map RNA-seq reads against the reference genomes, obtaining counts on transposable elements and protein-coding genes using the TElocal pipeline (https://github.com/mhammell-laboratory/TElocal).
Assembly: The chromosome-scale genome and annotation for Acanthamoeba castellanii Neff strain was obtained from https://zenodo.org/records/6800059. The genome for Cyanophora paradoxa was downloaded from http://cyanophora.rutgers.edu/cyanophora_v2018/blast.php. The genome of Naegleria gruberi was downloaded from GitHub: https://github.com/AlexdeMendoza/6mA_evolution/tree/main/Genomes.
Supplementary files format and content: The EM-seq is presented as CGmap files, described in: https://github.com/BSSeeker/BSseeker2. The RNA-seq file are counts on genes and transposable elements for each sample as obtained by TElocal.
Library strategy: EM-seq

source_name: axenic cell culture

growth_protocol: A. castellanii Neff strain was grown at 23°C in ATCC medium (712 PYG), using 100 mL ventend flasks. N. gruberi NEG-M was grown at 30°C in 1034 Modified PYNFH medium. DNA from untreated cultures of A. castellanii and N. gruberi were kindly provided by Meritxell Antó of Ruiz-Trillo Lab, Institut de Biología Evolutiva, Barcelona. Purified genomic DNA from Cyanophora paradoxa was purchased from CCAP collection.

extract_protocol:
DNA from drug-treated cultures were extracted using the NEB Monarch Genomic DNA Purification Kit. Total RNA from these cultures were extracted using the Monarch Total RNA Miniprep Kit.
For each library, 100-200 ng of initial gDNA were spiked in with unmethylated lambda genome control and methylated pUC19 plasmid control. These were sheared to 300 bp using a Covaris sonicator, and then used as input for Enzymatic Methyl-Seq kit (New England Biolabs), following manufacturer instructions. We used 200 ng of RNA from treated samples to build mRNA-seq libraries, first enriching for poly-A transcripts with the NEB Magnetic mRNA Isolation Kit S1550S, and then building the libraries with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760L) according to manufacturer's instructions.

treatment_protocol: DNA demethylation drugs 5-Azacytidine (ab142744 Abcam), decitabine (ab120842), and zebularine (ab141264) were dissolved in DMSO as per manufacturer’s instructions. A. castellanii was grown with 0 M, 10 nM, 100 nM, 1 µM, 10 µM, and 100 µM final concentration of each drug in 4ml ATCC (712 PYG) 1% DMSO media in a 6 well plate, and effects were tracked daily for 5 days, in duplicate. No treatments displayed a growth phenotype. A. castellanii DNA and RNA were extracted from cultures grown for 4 days in 3.5 mL ATCC (712 PYG) 1% DMSO media, with or without their respective drug in triplicate, at a final drug concentration of 100µM. N. gruberi DNA and RNA were extracted from cultures grown under the same conditions, with 1034 Modified PYNFH media.

value: axenic cell culture

value: Amoeba

value: No treatment


title: iPSC derived human organoids, 8week, control

description:
Library name: 18a_8week_EtOH
10x Genomics


title: PPPE.093

value: Placenta


title: ILC2s, PBS treated wild type mice, proximal 1/3 small intestine

description:
Library name: ILC2_PBS_1
10x Genomics


title: PPPE.092

value: LOPE


title: N_gru_RNA_Zeb_1

description: Library name: N_gru_RNA_Zeb_1

data_processing:
The EM-seq libraries were sequenced at NovoGene, using Illumina NovaSeq6000 platform, aiming at coverages >30x for reference methylomes, and 5x for shallow treatment samples. The obtained FASTQ files were mapped to the reference genomes using BS-Seeker2, with BOWTIE2 as backend alignment tool. PCR duplicate reads were removed using Sambamba, and methylation calling was obtained using CGmapTools.
We used HISAT2 to map RNA-seq reads against the reference genomes, obtaining counts on transposable elements and protein-coding genes using the TElocal pipeline (https://github.com/mhammell-laboratory/TElocal).
Assembly: The chromosome-scale genome and annotation for Acanthamoeba castellanii Neff strain was obtained from https://zenodo.org/records/6800059. The genome for Cyanophora paradoxa was downloaded from http://cyanophora.rutgers.edu/cyanophora_v2018/blast.php. The genome of Naegleria gruberi was downloaded from GitHub: https://github.com/AlexdeMendoza/6mA_evolution/tree/main/Genomes.
Supplementary files format and content: The EM-seq is presented as CGmap files, described in: https://github.com/BSSeeker/BSseeker2. The RNA-seq file are counts on genes and transposable elements for each sample as obtained by TElocal.

value: Zebularine 100µM + DMSO


title: N_gru_RNA_Zeb_2

description: Library name: N_gru_RNA_Zeb_2


title: iPSC derived human organoids, 24hr,  control

description:
Library name: 18a_24hr_EtOH
10x Genomics


title: iPSC derived human organoids, 24hr, treatment

description:
Library name: 18a_24hr_LPC
10x Genomics


title: N_gru_RNA_DMSO_3

description: Library name: N_gru_RNA_DMSO_3

value: DMSO 1% control


title: ILC2s, PBS treated wild type mice, mid 2/3 small intestine

description:
Library name: ILC2_PBS_2
10x Genomics

value: Small Intestine

value: Wild type, C57BL/6J


title: PPPE.089

value: Whole tissue


title: PPPE.088

value: CTL


title: MCF7-KO-5

city: Perth

first: Pieter

last: Eichhorn

state: WA

address: Kent Street

department: Medical School

institute: Curtin University

description:
Library name: Sample 10
MCF7-USP10KO-P9-2

data_processing:
Quality assessment of the sequencing data was evaluated using FastQC (v0.10.1).
Cutadapt(version 1.9.1)
Assembly: Short-read alignment was performed using Hisat2 (v2.0.1) .GRCh38.p13
Supplementary files format and content: CSV file includes FPKM values for all samples

source_name: Breast

growth_protocol: MCF7 breast cancer  cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)  in humidified atmosphere with 5% CO₂ at 37°C.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1  µg of total RNA was used for the construction of sequencing libraries.
All following steps were perfomed by Azenta.

value: Breast

value: Adenocarcinoma

value: USP10 KO


title: N_gru_RNA_DMSO_2

description: Library name: N_gru_RNA_DMSO_2

value: NEG-M


title: MCF7-KO-4

description:
Library name: Sample 9
MCF7-USP10KO-P9-1


title: PPPE.086


title: N_gru_RNA_DMSO_1

description: Library name: N_gru_RNA_DMSO_1


title: N_gru_RNA_Dec_3

description: Library name: N_gru_RNA_Dec_3

value: Decitabine 100µM + DMSO


title: PPPE.085


title: MCF7-KO-3

description:
Library name: Sample 8
MCF7-USP10KO-P8-2


title: Epithelial cells, PBS and IL25 treated mice, small intestine, biol rep 1, lane 1

description:
Library name: A_siEPI_1
10x Genomics

data_processing:
For scRNA-seq analysis of the small intestine epithelium, single-cell transcripts were aligned to the mouse genome and processed via the 10X Cell Ranger software version 5.0.1. The R package Seurat (version 4.3.2) was used for single-cell transcriptome analysis. The MULTIseqDemux function was used to demultiplex samples using the HTO CITE-seq assay data. Cells were removed according to the following thresholds: <200 genes/cell or >5000 genes per cell, >20000 UMIs/cell, 20% mitochondrial content, <0.01% hemoglobin read content. Epithelial cell types were identified by expression of cell-type specific signature genes (tuft cells-Dclk1; goblet cells-Muc2; enteroendocrine cells-Chga; Paneth cells-Lyz1; crypt cells-Lgr5, Mki67; absorptive enterocytes-Slc5a1, Slc15a1, and lack of other cell-type signature genes).
Cellranger v5.0.1
Seurat HTOdemux function
Assembly: mouse mm10
Supplementary files format and content: .h5 files, raw matrices from cellranger

extract_protocol:
For the small intestine epithelial scRNA-seq, cells were isolated from C57BL/6J (a total of 2 IL-2-treated and 2 PBS-treated) mice 49 and 50 days after the last treatment. Cells were collected from both epithelial extraction buffer fractions and the epithelial cells (EpCAM+CD45-) were sorted to >95% purity. Sorted cells from a given region of PBS or IL-25 treated mice were labeled with TotalSeq anti-mouse Hashtag antibodies for 30 minutes at 4℃, followed by 3 washes with FACS buffer, and counting of cells. Equal number of cells from each region were combined and single-cell libraries from a total of 50,000 cells were prepared with the Chromium Next GEM Single Cell 3ʹ v3.1:Dual Index Libraries following the manufacturer’s protocol.
Library was performed according to the manufacter's instructions. Chromium Next GEM Single Cell 3ʹ v3.1:Dual Index Libraries,10x genomics; Biolegend TotalSeq-B barcoding, barcodes 301-310; 301=PBS proximal 1/5 small intestine (SI), 302= PBS mid 2/5 SI, 303= PBS mid 3/5 SI, 304=PBS mid 4/5 SI, 305=PBS distal 5/5 SI; 306=IL25 proximal 1/5 SI, 307=IL25 mid 2/5 SI, 308=IL25 mid 3/5 SI, 309=IL25 mid SI, 310=IL25 distal 5/5 SI

value: Epitheilal Cell

value: PBS treated


title: Epithelial cells, PBS and IL25 treated mice, small intestine, biol rep 1, lane 2

description:
Library name: A_siEPI_2
10x Genomics


title: Epithelial cells, PBS and IL25 treated mice, small intestine, biol rep 2, lane 1

description:
Library name: B_siEPI_1
10x Genomics


title: Epithelial cells, PBS and IL25 treated mice, small intestine, biol rep 2, lane 2

description:
Library name: B_siEPI_2
10x Genomics


title: MCF7-KO-1

description:
Library name: Sample 6
MCF7-USP10KO-P7


title: MCF7-KO-2

description:
Library name: Sample 7
MCF7-USP10KO-P8-1


title: PPPE.084

value: RCIU


title: ILC2s, Hp infected mice, biol rep 3

description:
Library name: locksleyr-Hp_3_3V4_GEM-X
10x Genomics

data_processing:
For the ILC2 scRNA-seq analysis, single-cell transcripts were aligned to the mouse genome and processed via the 10X Cell Ranger software version 7.0. The R package Seurat (version 4.3) was used for single cell transcriptome analysis. Cells were removed according to the following thresholds: <1000 genes/cell or >6000 genes per cell, >50000 UMIs/cell, 10% mitochondrial content, <0.001% hemoglobin read content to remove red blood cells. Among the ILC2 cells retained, the effects of mitochondrial and ribosomal content were regressed out using the SCTransform v2 normalization method prior to clustering. Genes were excluded from the final dataset if they were expressed in fewer than 3 cells. For differential expression analysis between clusters, genes were detected if they are expressed in at least 10% of cells in a cluster with a log fold change of at least 0.25. For DEG analysis between comparison groups, genes were detected if expressed in at least 5% of cells in the group with a log fold change of at least 0.25
Assembly: Mouse mm10
Supplementary files format and content: .h5 files, cellranger raw matrix output

extract_protocol:
Small intestinal single cell suspensions were prepared from the proximal 1/3 of tissue.Luminal contents were flushed with PBS, Peyer’s patches removed, and tissue cut open. Pieces were incubated with epithelial cell extraction buffer (EEB: Ca2+/Mg2+ free HBBS, 3% FCS, 10 mM HEPES, 10 mM EDTA, 10 mM DTT) at 37℃ with gentle shaking for 15 min. Tubes were vortexed at full speed for 30 sec and supernatants discarded. The tissue was placed with fresh EEB at 37℃ for 15 min with gentle shaking, then vortexed for 30 sec and supernatant discarded. Tissue was placed in rinse buffer (Ca2+/Mg2+ sufficient HBBS, 3% FCS, 10 mM HEPES) and incubated at 37℃ with gentle shaking for 5 min. Tissue was placed in GentleMACS C tubes (Miltenyi Biotec) with digestion buffer (DB: Ca2+/Mg2+ sufficient HBBS, 3% FCS, 10 mM HEPES, 30 ug/ml DNase I, 0.1 Wunsch/ml Liberase TM), minced with scissors, and incubated at 37℃ with gentle shaking for 10-15 min. Single-cell suspensions were obtained using a gentleMACS tissue dissociator (Miltenyi Biotec), running program m_intestine_0, and then pouring through a 100 um filter and washing with FACS buffer (PBS, 3% FCS)
Library was performed according to the manufacter's instructions (Chromium GEM-X Single Cell 3’ Kit v4, 10x genomics)

value: Female

value: Hp infected


title: ILC2s, Nb infected mice, biol rep 1

description:
Library name: locksleyr-Nb_1_3V4_GEM-x
10x Genomics

value: Nb infected


title: ILC2s, control mice, biol rep 2

description:
Library name: locksleyr-Ctrl_2_3V4_GEM-X
10x Genomics

value: Naïve


title: ILC2s, Nb infected mice, biol rep 2

description:
Library name: locksleyr-Nb_2_3V4_GEM-x
10x Genomics


title: ILC2s, Nb infected mice, biol rep 3

description:
Library name: locksleyr-Nb_3_3V4_GEM-x
10x Genomics


title: ILC2s, Hp infected mice, biol rep 1

description:
Library name: locksleyr-Hp_1_3V4_GEM-X
10x Genomics


title: N_gru_RNA_Dec_2

description: Library name: N_gru_RNA_Dec_2

value: axenic cell culture

value: Amoeba


title: ILC2s, Hp infected mice, biol rep 2

description:
Library name: locksleyr-Hp_2_3V4_GEM-X
10x Genomics

value: Small Intestine

value: Wild type, C57BL/6J


title: PPPE.078

value: Placenta

value: Whole tissue


title: MCF7- WT-4

description:
Library name: Sample 4
MCF7-WT-P18-1

value: Breast

value: Adenocarcinoma

value: WT


title: ILC2s, control mice, biol rep 1

description:
Library name: locksleyr-Ctrl_1_3V4_GEM-X
10x Genomics


title: N_gru_RNA_Dec_1

description: Library name: N_gru_RNA_Dec_1

value: NEG-M

value: Decitabine 100µM + DMSO


title: N_gru_RNA_Aza_3

description: Library name: N_gru_RNA_Aza_3

value: 5-Azacytidine 100µM + DMSO


title: PPPE.079

value: LOPE


title: MCF7- WT-5

description:
Library name: Sample 5
MCF7-WT-P18-2


title: N_gru_RNA_Aza_2

description: Library name: N_gru_RNA_Aza_2


title: PPPE.076

value: PTB


title: MCF7- WT-3

description:
Library name: Sample 3
MCF7-WT-P17-2


title: PPPE.074


title: N_gru_RNA_Aza_1

description: Library name: N_gru_RNA_Aza_1


title: MCF7- WT-2

description:
Library name: Sample 2
MCF7-WT-P17-1


title: MCF7- WT-1

description:
Library name: Sample 1
MCF7-WT-P16-2


title: PPPE.073

value: RCIU


title: N_gru_EMseq_Zeb_2

description: Library name: N_gru_EMseq_Zeb_2

value: Zebularine 100µM + DMSO


title: PPPE.072


title: Primary 19-004

city: Seattle

first: Sonali

last: Arora

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Library name: 19-004D2_Primary
Primary 19-004

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The RNA sequencing reads were aligned to the Gencode GRCh38.primary_assembly reference genome using STAR29 (v2.7.7a).
Gene-level quantification was conducted with HTSeq30 (v0.11.0) using Gencode V22 primary assembly annotations.
Counts per million ( cpm) reads were calculated using the cpm() function from R package, edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts per million (cpm) values for each Sample.

source_name: Bladder

growth_protocol: Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue samples using the Maxwell RSC RNA FFPE Kit (Promega, Madison, WI, USA) on the automated Maxwell RSC 48 instrument (Promega)

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an P2-100 flow cell.

treatment_protocol: untreated

value: Bladder

value: Primary

value: Flash-frozen


title: PPPE.070

value: EOPE


title: PPPE.067

value: CTL


title: N_gru_EMseq_DMSO_3

description: Library name: N_gru_EMseq_DMSO_3

value: axenic cell culture

value: Amoeba

value: DMSO 1% control


title: N_gru_EMseq_DMSO_2

description: Library name: N_gru_EMseq_DMSO_2


title: Primary 18-016

description:
Library name: 18-016H7_Bladder
Primary 18-016


title: PPPE.066

value: Placenta

value: Whole tissue


title: N_gru_EMseq_DMSO_1

description: Library name: N_gru_EMseq_DMSO_1

value: NEG-M


title: Primary 17-026

description:
Library name: 17-026K4_Bladder
Primary 17-026


title: Primary 17-020

description:
Library name: 17-020P2_Bladder
Primary 17-020


title: PPPE.058


title: Primary 19-007

description:
Library name: 19-007D5_Primary
Primary 19-007


title: N_gru_EMseq_Dec_2

description: Library name: N_gru_EMseq_Dec_2

value: Decitabine 100µM + DMSO


title: PPPE.057


title: N_gru_EMseq_Dec_1

description: Library name: N_gru_EMseq_Dec_1


title: N_gru_EMseq_Aza_3

description: Library name: N_gru_EMseq_Aza_3

value: 5-Azacytidine 100µM + DMSO


title: PPPE.064


title: N_gru_EMseq_Dec_3

description: Library name: N_gru_EMseq_Dec_3


title: RNA-Seq, PBMCs, HFD + L-NAME + NO2-OA 3

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisallee 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

description:
Library name: Sample 13 - BO2196
x

data_processing:
After demultiplexing with bcl2fastq software (Illumina, v2.20), the fastq files underwent trimming and adapter removal using Trim Galore. Read mapping was performed against the respective reference genome (human hg38/mouse mm39) using Hisat2. Gene expression quantification was achieved by read counting using FeatureCounts (R package). The resulting counts were then converted to Transcripts Per Million (TPM) for normalization in R.
Assembly: mouse mm39
Supplementary files format and content: .txt-file containing TPM counts

source_name: murine PBMCs

growth_protocol: Mouse PBMC collection: Mouse blood was collected into syringes pre-loaded with 10 µL of 0.5 M EDTA (pH 8.0) to prevent coagulation. After gentle mixing, the blood was transferred to Eppendorf tubes, and plasma was separated by centrifugation at 500 g for 5 min. The remaining blood was diluted in PBS (1:3 dilution) and layered over Ficoll (Merck, #GE17-5446-02). Samples were centrifuged at 400 g for 30 min at RT without brake. PBMCs were collected from the interphase, washed in PBS supplemented with 0.3 mM EDTA and 2% FBS, and pelleted at 400 g for 8 min. Red blood cells were lysed with erythrocyte lysis buffer (10 min, RT; 0.83% (w/v) NH4Cl, 10 mM Hepes-NaOH, pH 7.4), followed by centrifugation. Cells were resuspended in 100 µL PBS and counted using Trypan Blue. PBMCs were frozen in a 1:1 mixture of resuspension medium (40% FBS in RPMI) and 2× freezing medium (30% DMSO in RPMI containing 40% FBS), transferred to cryovials, and initially stored at −80 °C using a controlled-rate freezing container before long-term storage in liquid nitrogen.

extract_protocol:
PBMCs were thawed according to 10x Genomics demonstrated protocol #CG00039. RNA was purified from cells using the miRNeasy kit (Qiagen, #217004) according to manufacturer’s instructions with additional DNase (Qiagen, #79254) digestion.
Quality control and quantification of the isolated RNA were performed using Fragment Analyzer 5200 (Agilent) using the High Sensitivity RNA quantification kit and Fragment Analyzer Controller Software (Agilent v3.1.0.12). Random primed library preparation was started with 150 ng of total RNA using the Watchmaker RNA library prep kit with Polaris depletion (Watchmaker Genomics) according to the instructions of the manufacturer. The barcoded libraries were purified and quantified using Qubit Fluorometric Quantification (ThermoFisher Scientific). Size distribution of the library DNA was analyzed using the Fragment Analyzer 5200 (Agilent). Sequencing of 2x150 bp was performed with an Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA).

value: murine PBMCs


title: RNA-Seq, PBMCs, HFD + L-NAME 4

description:
Library name: Sample 9 - BO2190
x


title: RNA-Seq, PBMCs, HFD + L-NAME 1

description:
Library name: Sample 6 - BO2219
x


title: RNA-Seq, PBMCs, HFD + L-NAME + NO2-OA 6

description:
Library name: Sample 16 - BO2187
x


title: RNA-Seq, PBMCs, HFD + L-NAME + NO2-OA 1

description:
Library name: Sample 11 - BO2200
x


title: RNA-Seq, PBMCs, HFD + L-NAME + NO2-OA 5

description:
Library name: Sample 15 - BO2195
x


title: RNA-Seq, PBMCs, NO2-OA [3µM] + IL-1β 3

description:
Library name: Sample 18 - JK_5194
x

data_processing:
After demultiplexing with bcl2fastq software (Illumina, v2.20), the fastq files underwent trimming and adapter removal using Trim Galore. Read mapping was performed against the respective reference genome (human hg38/mouse mm39) using Hisat2. Gene expression quantification was achieved by read counting using FeatureCounts (R package). The resulting counts were then converted to Transcripts Per Million (TPM) for normalization in R.
Assembly: human hg38
Supplementary files format and content: .txt-file containing TPM counts

source_name: human PBMCs

growth_protocol: PBMCs were isolated from buffy coats of healthy blood donors by density gradient centrifugation. In particular, blood was diluted in PBS (ThermoFisher, #10010023) containing 0.3 mM EDTA and layered onto Ficoll® Paque (Cytiva, #17144003). Tubes were centrifuged for 20 min at RT, 2,030 rpm, brake 4 and PBMCs were collected from the interphase between Ficoll® Paque and plasma. PBMCs were washed multiple times with PBS containing 0.3 mM EDTA and 0.2% BSA and used for further experiments.

extract_protocol:
PBMCs were harvested by centrifugation and washed with ice-cold PBS. RNA was purified from cells using the miRNeasy kit (Qiagen, #217004) according to manufacturer’s instructions with additional DNase (Qiagen, #79254) digestion.
Quality control and quantification of the isolated RNA were performed using Fragment Analyzer 5200 (Agilent) using the High Sensitivity RNA quantification kit and Fragment Analyzer Controller Software (Agilent v3.1.0.12). Random primed library preparation was started with 150 ng of total RNA using the Watchmaker RNA library prep kit with Polaris depletion (Watchmaker Genomics) according to the instructions of the manufacturer. The barcoded libraries were purified and quantified using Qubit Fluorometric Quantification (ThermoFisher Scientific). Size distribution of the library DNA was analyzed using the Fragment Analyzer 5200 (Agilent). Sequencing of 2x150 bp was performed with an Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA).

treatment_protocol: Human primary PBMCs were seeded in cell culture plates in RPMI-1640 medium (Merck, #R8758) supplemented with 10% fetal bovine serum (FBS; Gibco, #10500064). Nitro-oleic acid (50:50 mix of (E)-9- and 10-nitrooctadec-9-enoic acid; NO2-OA) was added for a final concentration of 1 µM or 3 µM. After 2.5 h pre-treatment, PBMCs were treated for an additional 4.5 h with IL-1β (10 ng/mL; Sigma-Aldrich, #H6291-10UG).

value: human PBMCs

value: NO2-OA [3µM] + IL-1β [10 ng/ml]


title: RNA-Seq, PBMCs, NO2-OA [3µM] + IL-1β 2

description:
Library name: Sample 17 - JK_5179
x


title: RNA-Seq, PBMCs, chow 5

description:
Library name: Sample 5 - BO2193
x


title: N_gru_EMseq_Aza_2

description: Library name: N_gru_EMseq_Aza_2


title: N_gru_EMseq_Zeb_1

description: Library name: N_gru_EMseq_Zeb_1

value: Zebularine 100µM + DMSO


title: RNA-Seq, PBMCs, HFD + L-NAME + NO2-OA 2

description:
Library name: Sample 12 - BO2218
x


title: RNA-Seq, PBMCs, HFD + L-NAME 3

description:
Library name: Sample 8 - BO2191
x


title: RNA-Seq, PBMCs, NO2-OA [3µM] + IL-1β 1

description:
Library name: Sample 16 - JK_5164
x


title: RNA-Seq, PBMCs, HFD + L-NAME 5

description:
Library name: Sample 10 - BO2216
x


title: RNA-Seq, PBMCs, HFD + L-NAME + NO2-OA 4

description:
Library name: Sample 14 - BO2184
x


title: PPPE.056


title: S.Tm_wt_infected_3

description:
Library name: XH.4059.EXP.24.CB0468.STM3
XH.4059.EXP.24.CB0468.STM3

value: LUVA

value: Mast cell

value: WT

value: S.Tm wt infected


title: Primary 16-079

description:
Library name: 16-079P4_Bladder
Primary 16-079

value: Bladder

value: Primary

value: Flash-frozen


title: PPPE.053

value: EOPE


title: PPPE.051

value: Placenta

value: LOPE


title: PPPE.048

value: CTL

value: Whole tissue


title: RNA-Seq, PBMCs, chow 4

description:
Library name: Sample 4 - BO2192
x


title: RNA-Seq, PBMCs, NO2-OA [1µM] + IL-1β 3

description:
Library name: Sample 15 - JK_5193
x

value: NO2-OA [1µM] + IL-1β [10 ng/ml]


title: N_gru_EMseq_Aza_1

description: Library name: N_gru_EMseq_Aza_1

value: axenic cell culture

value: NEG-M

value: Amoeba

value: 5-Azacytidine 100µM + DMSO


title: PPPE.040


title: RNA-Seq, PBMCs, chow 1

description:
Library name: Sample 1 - BO2210
x

value: murine PBMCs


title: RNA-Seq, PBMCs, Vehicle + IL-1β 3

description:
Library name: Sample 12 - JK_5192
x

value: human PBMCs

value: Vehicle + IL-1β [10 ng/ml]


title: RNA-Seq, PBMCs, NO2-OA [1µM] + IL-1β 1

description:
Library name: Sample 13 - JK_5163
x


title: PPPE.037


title: RNA-Seq, PBMCs, NO2-OA [1µM] + IL-1β 2

description:
Library name: Sample 14 - JK_5178
x


title: RNA-Seq, PBMCs, Vehicle + IL-1β 2

description:
Library name: Sample 11 - JK_5177
x


title: RNA-Seq, PBMCs, chow 2

description:
Library name: Sample 2 - BO2211
x


title: PPPE.034


title: PPPE.028


title: PBMCs, HFD + L-NAME 2

description:
Library name: Sample 4 - 2216
10x Genomics

data_processing:
Fastq files generated by bcl2fastq were processed with cellranger count against the mouse mm39 reference.
Assembly: Reference transcriptome: mouse mm39
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single cell preparation and barcoding: PBMCs were thawed according to 10x Genomics demonstrated protocol #CG00039 and a cell concentration of 700 to 1,200 PBMCs per µl of PBS + 0.04% BSA was set. Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #PN-1000128, Chip G: #1000127) was used to generate GEMs, reverse transcribe RNA and amplify cDNA according to manufacturer’s instructions. Targeted cell recovery was 10,000.
Library construction and sequencing: After cleanup (step 2.3), 2 µl of the cDNA was used for quality control on the Agilent fragment analyzer (DNF-473 Standard Sensitivity NGS Fragment Kit). In addition, 10 µl of the cDNA was used as input for step 3 of the Chromium Next GEM Single Cell 3´ Reagent Kit to perform fragmentation, end-repair, A-tailing and adapter-ligation. The finished library was monitored again using the fragment analyzer and the DNF-473 Standard Sensitivity NGS Fragment Kit. Equimolar amounts of each sample were plexed at 1.25 nmol/l. Sequencing was performed as paired-end 2x150bp (S4-Flowcell) on a Novaseq 6000 (Illumina).


title: PBMCs, HFD + L-NAME 1

description:
Library name: Sample 3 - 2190
10x Genomics


title: RNA-Seq, PBMCs, chow 3

description:
Library name: Sample 3 - BO2188
x


title: PPPE.030

data_processing:
Libraries were sequenced using the HiSeq 4000 system (Illumina, USA) at the “Integrated Clinical Genomics Centre in Pediatrics”at the CHUSJ.
Data were processed using the RosalinD platform
Assembly: hg19
Supplementary files format and content: Individual text files with the raw counts for each sample
Supplementary files format and content: The same tab-seperated values file for the normalized counts


title: PPPE.026


title: RNA-Seq, PBMCs, NO2-OA [3µM] + untreated 2

description:
Library name: Sample 8 - JK_5173
x

value: NO2-OA [3µM]


title: PBMCs, chow 2

description:
Library name: Sample 2 - 2210
10x Genomics


title: PPPE.023


title: PBMCs, HFD + L-NAME + NO2-OA 1

description:
Library name: Sample 5 - 2218
10x Genomics


title: PBMCs, chow 1

description:
Library name: Sample 1 - 2188_original2088
10x Genomics


title: RNA-Seq, PBMCs, HFD + L-NAME 2

description:
Library name: Sample 7 - BO2186
x


title: RNA-Seq, PBMCs, NO2-OA [3µM] + untreated 1

description:
Library name: Sample 7 - JK_5158
x


title: PPPE.019


title: RNA-Seq, PBMCs, Vehicle + IL-1β 1

description:
Library name: Sample 10 - JK_5162
x


title: RNA-Seq, PBMCs, NO2-OA [1µM] + untreated 2

description:
Library name: Sample 5 - JK_5169
x

value: NO2-OA [1µM]


title: PPPE.020


title: PPPE.017


title: RNA-Seq, PBMCs, NO2-OA [1µM] + untreated 3

description:
Library name: Sample 6 - JK_5184
x


title: KO iBAT 2

city: Iowa City

first: Renata

middle: O

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

institute: University of Iowa

description: Library name: S2-16

data_processing:
psuedoalignment and quantification performed using Kallisto (v0.45.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with transcripts per million

source_name: brown adipose tissue

extract_protocol:
Total RNA was extracted from tissues with TRIzol reagent (Invitrogen) and purified with the RNeasy kit (Qiagen Inc).
Illumina TruSeq mRNA Stranded kit

value: brown adipose tissue

value: KO

value: male

value: 12 weeks of 60% high fat diet


title: RNA-Seq, PBMCs, NO2-OA [1µM] + untreated 1

description:
Library name: Sample 4 - JK_5154
x