title: 3w, Proximal, M, M9, Rep2

description: Library name: 10005CN46_C2


title: Sample 95 low flow high pressure

status: Public on Aug 14 2025

type: SRA

city: Seattle

first: Samuel

middle: G

last: Rayner

state: WA

address: 850 Republican Street

department: Medicine

country: USA

institute: University of Washington

description:
Library name: 95-LF-HP_S2
GeneCounts1.tsv

library_source: transcriptomic

data_processing:
Raw FASTQ files were quality-checked with FastQC.
Reads were aligned to the GRCh38 human reference genome using STAR aligner.
Gene-level counts were quantified using featureCounts.
Count normalization and differential expression analysis were performed using DESeq2 in R.
Assembly: GRCh38 (GENCODE v38)
Supplementary files format and content: Gene-level counts (raw and normalized) in tab-delimited text files

molecule: polyA RNA

organism: Homo sapiens

source_name: Distal Pulmonary Arteries

growth_protocol: PAECs were cultured within a culture chamber in EGM-2 (Lonza) to confluence, at 37 degrees and 5% CO2

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quality was assessed using an Agilent Bioanalyzer.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina, with polyA selection, following the manufacturer's instructions.

treatment_protocol: Cells were exposed to shear stress (0, 3, or 20 dyn/cm²) and pressure (0 or 60 mmHg) for 24 hours within a resistor-coupled microfluidic platform.

tag: tissue

value: Distal Pulmonary Arteries

tag: cell line

value: Primary Human Cells

tag: cell type

value: Pulmonary artery endothelial cells

tag: disease

value: IPAH

tag: Sex

value: Male

tag: pressure

value: Low

tag: shear

value: High

tag: round


title: Frontal cortex,, batch 2, sham, sample 2

city: East victoria Park

first: Amira

last: Allahham

state: Perth, WA

address: 2/88 Dane st.

country: Australia

institute: Fiona Wood Foundation

description: Library name: E3FC13

data_processing:
The RNA sequencing data was processed on an external Linux server using the sequence shown in Figure 2. Genome data was sent from AGRF, downloaded on the server and processed using MATE Terminal (Version 1.8.0), and R studio version (Version 3.6.1). Poor quality reads were checked using FastQC (Version 0.11.3) where the first 15 base pairs were trimmed using the fastp software (Chen et al., 2018). Raw RNA sequences were aligned with the reference genome Mus musculus GRCm38.102 from Ensembl (Cunningham et al., 2018) (http://asia.ensembl.org/Mus_musculus/Info/Index) using the STAR read aligner (Version 2.7) (Dobin et al., 2013) to generate BAM files to represent the aligned sequences. Rows that have little or no information about gene information were prefiltered from the dataset and a minimal filtering rule was applied where rows of the DESeqDataSet, a subclass of SummarizedExperiment used to store input values, calculations and results of an analysis of differential expression, were removed because they have no counts, or only have a single count across all samples were removed. The quality of data was assessed before the analysis where the distribution of the raw read counts was plotted using a bar plot, then it was transformed using regularised log (rlog) which transforms the count data to the log2 scale in a way that minimizes differences between samples for rows with small counts, normalising it with respect to library size. This was also plotted as box plots for better visualisation. For the analysis, Principal Component Analysis (PCA) and hierarchical clustering methods were performed to explore the similarity of samples by bringing out strong patterns in a dataset and identifying outliers. A heatmap showing the correlations in gene expression for all pairwise combinations of samples in the dataset was created. Using the package DESeq2 (Version 1.24.0) (Love et al., 2014) on R studio (Version 3.6.1), differential gene analysis was performed to quantitate changes in expression levels between the different intervention groups of the samples. The Wald test in DESeq2 was used for significance, and corrections for multiple testing was done by calculating the Benjamini-Hochberg adjusted p-values. A threshold of adjusted p-value (Padj) <0.05 and absolute log2(fold change) >1 were set to identify differentially expressed genes (DEGs). DEG results were visualised using volcano plots and heatmaps using the ggplot, ggrepel and pheatmap packages in R studio. For analysis of functions and pathways, overrepresentation analysis of the DEGS list on gene ontology (GO) terms and Kyoto Encyclopaedia of Genes and Genomes (KEGG) based pathway analysis was run using ClusterProfiler (Version 3.12.0) (Yu et al., 2012). GO pathway significance was set to p-value <0.05, and it included three types of pathways; biological functions (BP), molecular functions (MF), and cell component (CC) pathways. Batch corrections were included in the analysis by making the batch a factor and excluding its effects on the final results.
Assembly: Mus musculus GRCm38.102 from Ensembl
Supplementary files format and content: Mouse_brain_GEO_counts.csv

molecule: total RNA

organism: Mus musculus

source_name: Brain, Frontal cortex

growth_protocol: The RNeasy mini kit (Cat No./ID: 74104, QIAGEN, Germany) was used to harvest the RNA in the brain sections. The samples were first pipetted up and down in the lysis buffer to break down the tissue, vortexed for one minute to homogenise the sample, then 350 µl of 70% ethanol was added to it. 700 µl of sample and the precipitate that formed was transferred to the RNeasy spin column placed in a 2 ml collection tube. The lid was gently closed, and the sample was centrifuged for 15 s at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane and the flow-through was discarded. For the column DNase digestion, 350 µl of Buffer RW1 was added to the RNEasy spin column and centrifuged for 15 s at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane, then the flow through was discarded, 10 µl of DNase 1 stock solution was added to 70 µl of Buffer RDD, mixed gently by inverting the tube, and centrifuged briefly to collect residual liquid. Then, 80 μl of DNase I incubation mix was added to the RNeas spin column membrane, it was incubated at room temperature for 15 mins, 350 μl of buffer RW1 was added to it and it was centrifuged at ≥8000 x g (≥10,000 rpm), then 700 μl buffer RW1 was added to it, and it was centrifuged again at the same setting and the flow-through was discarded. To wash the spin column membrane, 500 μl buffer RPE was added to the RNeasy spin column, and it was centrifuged for 15 mins at ≥8000 x g (≥10,000 rpm) and the flow through was discarded, then another 500 μl of buffer RPE were added and it was centrifuged at the same speed for 2 mins. Finally, the column was placed in a new 2 ml collection tube and centrifuged at full speed for 1 min, placed in another 1.5 ml collection tube and 30-50 μl of RNAse-free water was added directly to the spin column membrane and it was centrifuged at ≥8000 x g (≥10,000 rpm) for 1 min to elute the RNA, and it was stored at -80°C.

extract_protocol: Before analysis, RNA concentration was quantified at OD260 nm by using a NanoDrop-1000 (Thermo Fisher Scientific, USA), and quality control tests were performed on the Bioanalyzer to ensure there is enough RNA. Aliquots of 10 μg were sent for sequencing at the Australian Genome Research Facility (AGRF), where 1 μg of total RNA was used for sequencing via the Illumina Nova-Seq Control Software (Version 1.6.0.). Real Time Analysis (RTA) (Version 3.4.4) for real-time base calling was used, and it produced a 100bp single end run. The Illumina bcl2fastq (Version 2.20.0.422) pipeline was used to generate the primary sequence data.

treatment_protocol: Mice underwent isoflurane anaesthesia through inhalation of vapour liquid isoflurane 100% (v/v), which was administered at a 4 ml/min oxygen rate during the induction in a chamber, and then maintained at a 2 ml/min oxygen rate for the duration of the procedures using a mask. Analgesia of 0.1 mg/kg dose of Buprenorphine was given subcutaneously to the mice while they were under anaesthesia to minimize pain during recovery. Burn procedures were performed on the right dorsal flank, and sham and excision procedures were performed on the medial posterior dorsal side. Both locations were away from the limbs to avoid restriction of movement and discomfort during recovery. In all three groups, the injury site was shaved in preparation for the procedure. In the sham group, the skin was shaved without inducing any injury to the site, which was done to control for the effects of anaesthesia, analgesics and handling. Before the burn procedure, the injury site was cleaned with a 4% chlorhexidine scrub. A brass rod 19 mm in diameter was heated to > 90° C and then applied to the skin for 10 seconds, which created a 7-8% TBSA full thickness burn injury, damaging both skin layers and ablating nerve endings at the site of injury to minimize pain during recovery. For the excision group, the injury site was cleaned with a 4% chlorhexidine scrub and a punch biopsy 12 mm in diameter was used to score the skin and provide a template for the excision. Scissors and forceps were then used to complete the excision, which was also a full-thickness injury. As mouse skin lacks tension, the area created by the excision later expanded to be of the same size as that of the burn. After the procedures, each mouse recovered from anaesthesia in a separate cage and was then returned to its home cage. No dressing was used as it increases discomfort (Sugarbaker & Chang, 1979). Post injury, mice were given drinking water containing 1 mg/mL of Paracetamol for five days to reduce pain during recovery (Taylor et al., 2016). Paracetamol was consumed at a rate of approximately 20 mg per day.

value: Brain, Frontal cortex

value: Mixed brain tissue

tag: genotype

tag: treatment

value: Sham

tag: batch


title: Frontal cortex, batch 2, sham, sample 3

description: Library name: E3FC14


title: Sample 95 high flow high pressure

description:
Library name: 95-HF-HP_S1
GeneCounts1.tsv


title: Sample 95 high flow low pressure

description:
Library name: 95-HFLP_S44
GeneCounts1.tsv


title: Frontal cortex, batch 2, sham, sample 1

description: Library name: E3FC11


title: Frontal cortex, batch 3, burn, sample 1

description: Library name: E5P11

source_name: Brain, Piriform cortex

value: Brain, Piriform cortex

value: Burn


title: Frontal cortex, batch 2, excision, sample 5

description: Library name: E3FC10

value: Excision


title: Frontal cortex, batch 2, burn, sample 1

description: Library name: E3FC1


title: 3w, Distal, F, M8, Rep2

city: Columbia

first: Aidan

last: Daly

state: SC

address: 2230 Rembert Street

institute: New York Genome Center

description: Library name: 10005CN45_E2

data_processing:
ST cDNA libraries were diluted to 4nM and 1.08pm libraries loaded for sequencing on an Illumina NextSeq 550 (Illumina, USA) using paired-end sequencing (R1 30bp, R2 55bp). Samples were sequenced at a mean depth of 65.6 million paired-end reads depth. fastq reads were generated with bcl2fastq2. ST Pipeline155 was used to process the resulting fastq files. Briefly, 5nt trimmed R2 was used for mapping to the mouse genome using STAR156. After that, mapped reads were annotated using HTseq-count157. Spatial barcodes were collapsed using TagGD155,158 modified demultiplexer (k-mer 6, mismatches 2). Then, unique molecular identifiers (UMIs) mapped to the same transcript and spatial barcode were collapsed using naive clustering with one mismatch allowed in the mapping process as described in umi-tools159. The output genes-by-barcode matrix was used in all further processing steps. Average library saturation was 78.3%. To focus on reliably detected genes across spots, genes detected in fewer than 2% of spots were removed, as were spots with fewer than 100 UMIs across all genes. The resulting median number of genes and UMI transcripts per spatial spot was 2,164 (10th percentile was 829 and 90th percentile was 4,370) and 4,343 (10th percentile was 1,246 and 90th percentile was 13,055).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: JPEG-formatted image files containing H&E staining of each Sample

source_name: Distal colon

growth_protocol: C57BL/6J mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and maintained in accordance with ethical guidelines monitored by the Institutional Animal Care and Use Committees (IACUC) established by the Division of Comparative Medicine at the Broad Institute of MIT and Harvard and Columbia University, and consistent with the Guide for Care and Use of Laboratory Animals, National Research Council, 1996 (institutional animal welfare assurance no. A4711-01), with protocols 0122-10-16 and AABI3617, respectively.

extract_protocol:
After imaging, coverslips were removed in deionized water and permeabilization reactions immediately started. First, tissue samples were permeabilized with 120µl reagent per reaction of collagenase I (200U) in 1x HBSS (both from ThermoFisher Scientific, USA). Pre-permeabilization reagent removal was followed by a 180µl wash in 0.1X Saline Sodium Citrate (SSC, Sigma-Aldrich, USA) at 37°C. Next, tissue was permeabilized with 75µl 0.1% pepsin (pH 1, Sigma-Aldrich, USA) at 37°C for 10min, followed by another wash with 0.1x SCC. Reverse transcription (RT) was performed by the addition of 75µl RT reagents: 50ng/µl actinomycin D (Sigma-Aldrich, USA), 0.5mM dNTPs (ThermoFisher Scientific, USA), 0.20µg/µl BSA, 1X First strand buffer, 5mM DTT, 2U/µl RNaseOUT, 20U/µl Superscript III (all from ThermoFisher Scientific, USA). Tissues were digested from the slide surface by 1h incubation in proteinase K (Qiagen, Germany) at 56°C. Slides were washed as suggested by the slide manufactures (Codelink, Surmodics): 10min 2x SCC with 0.1% SDS (Sigma Aldrich), 1min 0.2x SCC and 1min 0.1X SSC. To remove spatial cDNA:mRNA hybrids from the array surface, Uracil-Specific Excision Reagent (NEB, USA) was used as previously described153.The reaction was run for 2h at 37°C and the resulting spatially barcoded cDNA libraries were collected and libraries prepared
cDNA:RNA hybrids collected from the array surface were used as input in the first part of library preparation reactions. RNA strands were digested and used as primer to make dsDNA using DNA Polymerase I and RNaseH (2.7X First strand buffer, 3.7 U/µl DNA polymerase I and 0.2 U/µl Ribonuclease H (all from ThermoFisher Scientific, USA)) for 2h at 16°C. The material was made into blunt-end dsRNA products with 15U T4 DNA polymerase (NEB, USA) for 20 minutes at 16°C and reactions stopped by addition of 20mM EDTA (pH 8.0, ThermoFisher Scientific, USA). dsDNA was purified using Ampure XP (Beckman Coulter, USA) at a bead to cDNA ratio of 1:1. Next, the material was linearly amplified using a T7 promoter sequencing initially embedding in the oligonucleotides on the array surface by adding 27.8µl of the T7 reaction mix (46.2mM rNTPs, 1.5X T7 reaction buffer, 1.54 U/µl SUPERaseIN inhibitor and 2.3U/µl T7 enzyme; all from ThermoFisher Scientific, USA) for 14h at 37°C. This was followed by a bead cleanup with RNAclean Ampure XP beads (Beckman Coulter, USA) at a beads:aRNA ratio of 1.8:1. 8µl of the eluted aRNA was used as input to the following reactions. 2.5µl of 3µM aRNA adapters [rApp]AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC[ddC] were added to 8µl of aRNA. The reaction was then incubated at 70°C in a PCR machine for 2min and immediately chilled on wet ice. To ligate the adaptors, 4.5µl T4 RNA ligation mix (3.3X T4 RNA ligase buffer, 66U/µl truncated T4 ligase 2 and 13U/µl murine RNAse inhibitor (all from NEB, USA)) were added at 25°C for 1h, followed by an Ampure XP (Beckam Coulter, USA) bead purification at a bead:cDNA ratio of 1.8:1. 1:1 v/v of 20µM GTGACTGGAGTTCAGACGTGTGCTCTTCCGA and 10mM dNTPs were added to the ligated samples and heated to 65°C for 5min. Reverse transcription took place by adding 2.5X First strand buffer, 13mM DTT, 5 U/µl RNaseOUT and 25 U/µl Superscript III (all from Thermo Fisher Scientific, USA). Samples were incubated at 50°C for 1h. 10µl of nuclease-free water were added followed by a final Ampure XP bead purification at bead:cDNA ratio of 1.7:1 with a final elution of 10µl nuclease-free water. qPCR library quantification and indexing were performed as previously described153.

treatment_protocol: Colons were collected within 5 min of death and flushed using ice-cold 1x PBS (Gibco) using a straight gauge needle with a 2.4mm tip (Kent Scientific Corporation, USA) for mice >3 weeks of age or a newborn feeding needle (Cadence Science, USA) for mice ages 3 weeks. The rest of the mice were processed without colon flushing prior to freezing. Tissues were then dried and embedded in Optimal Cutting Temperature (OCT, Fisher Healthcare, USA) in large molds (VWR, USA). Samples were then plunged onto a metal plate pre-chilled and sitting on top of dry ice for 2min or until complete freezing. Samples were transferred and stored at -80°C until use. Cryosections were cut at 10μm thickness onto ST slides, and stored at -80°C for at most 2 days. Approximately 0.5cm of tissue from three different colon regions was placed on a tissue and dried before transfer to a sterile dish to ensure all excess water was gently removed from the sample. Tissues were then placed in a 1.5 mL tube on dry ice and, upon freezing, transferred to −80°C until subsequent tissue processing.

value: Distal colon

value: F


title: Frontal cortex, batch 3, excision, sample 1

description: Library name: E5P1


title: 3w, Distal, F, M8, Rep1

description: Library name: 10005CN45_E1


title: Sample 92 static

description:
Library name: 92-Static_S34
GeneCounts1.tsv

value: CHD-PAH

value: Female

value: Static


title: Frontal cortex, batch 2, excision, sample 2

description: Library name: E3FC8


title: Hippocampus, batch 2, excision, sample 4

description: Library name: E3_H_9

source_name: Brain, Hippocampus

value: Brain, Hippocampus


title: 3w, Middle, F, M8, Rep2

description: Library name: 10005CN45_D2

source_name: Middle colon

value: Middle colon


title: Hippocampus, batch 2, excision, sample 3

description: Library name: E3_H_8


title: Sample 92 low flow low pressure

description:
Library name: 92-LF-LP_S35
GeneCounts1.tsv

value: Distal Pulmonary Arteries

value: Primary Human Cells

value: Pulmonary artery endothelial cells


title: 3w, Middle, F, M8, Rep1

description: Library name: 10005CN45_D1


title: Hippocampus, batch 2, excision, sample 2

description: Library name: E3_H_7


title: Hippocampus, batch 2, burn, sample 5

description: Library name: E3_H_5


title: 3w, Proximal, F, M8, Rep2

description: Library name: 10005CN45_C2

source_name: Proximal colon

value: Proximal colon


title: Sample 92 low flow high pressure

description:
Library name: 92-LF-HP_S36
GeneCounts1.tsv

value: Low

value: High


title: Hippocampus, batch 2, burn, sample 4

description: Library name: E3_H_4

value: Mixed brain tissue


title: Sample 92 high flow low pressure

description:
Library name: 92-HF-LP_S37
GeneCounts1.tsv


title: 3w, Proximal, F, M8, Rep1

description: Library name: 10005CN45_C1


title: Hippocampus, batch 2, excision, sample 1

description: Library name: E3_H_6


title: Hippocampus, batch 2, burn, sample 3

description: Library name: E3_H_3


title: Hippocampus, batch 2, sham, sample 5

description: Library name: E3_H_15

value: Sham


title: 3w, Distal, F, M7, Rep2

description: Library name: 10005CN44_E2


title: Hippocampus, batch 2, burn, sample 2

description: Library name: E3_H_2

value: Burn


title: Sample 174 static

description:
Library name: 174-static_S25
GeneCounts2.tsv


title: Sample 92 high flow high pressure

description:
Library name: 92-HFHP_S38
GeneCounts1.tsv


title: Hippocampus, batch 2, sham, sample 2

description: Library name: E3_H_12


title: Hippocampus, batch 2, sham, sample 4

description: Library name: E3_H_14


title: Sample 174 low flow low pressure

description:
Library name: 174-low_S26
GeneCounts2.tsv


title: Sample 174 high flow low pressure

description:
Library name: 174-high_S27
GeneCounts2.tsv


title: Hippocampus, batch 2, sham, sample 3

description: Library name: E3_H_13


title: Hippocampus, batch 2, sham, sample 1

description: Library name: E3_H_11


title: Frontal cortex, batch 1, sham, sample 5

description: Library name: E2FC9

value: Brain, Frontal cortex


title: 3w, Middle, F, M7, Rep1

description: Library name: 10005CN44_D1


title: Sample 131 static

description:
Library name: 131-static_S22
GeneCounts2.tsv


title: Hippocampus, batch 2, burn, sample 1

description: Library name: E3_H_1


title: Frontal cortex, batch 1, sham, sample 4

description: Library name: E2FC8


title: Hippocampus, batch 2, excision, sample 5

description: Library name: E3_H_10

value: Excision


title: 3w, Proximal, F, M7, Rep2

description: Library name: 10005CN44_C2

value: F


title: Sample 131 low flow low pressure

description:
Library name: 131-low_S23
GeneCounts2.tsv

value: CHD-PAH


title: Frontal cortex, batch 1, sham, sample 3

description: Library name: E2FC7


title: Frontal cortex, batch 1, sham, sample 2

description: Library name: E2FC6


title: 3w, Proximal, F, M7, Rep1

description: Library name: 10005CN44_C1


title: Sample 131 high flow low pressure

description:
Library name: 131-high_S24
GeneCounts2.tsv

value: Female


title: Frontal cortex, batch 1, excision, sample 5

description: Library name: E2FC5


title: Frontal cortex, batch 1, excision, sample 4

description: Library name: E2FC4


title: 3w, Distal, M, M6, Rep2

description: Library name: 10005CN43_E2

value: Distal colon

value: M


title: 3w, Distal, F, M7, Rep1

description: Library name: 10005CN44_E1


title: Frontal cortex, batch 1, burn, sample 5

description: Library name: E2FC15


title: Frontal cortex, batch 1, excision, sample 2

description: Library name: E2FC2


title: Frontal cortex, batch 1, excision, sample 3

description: Library name: E2FC3


title: Sample 120 low flow low pressure

description:
Library name: 120-low_S20
GeneCounts2.tsv

value: Control Failed Donor

value: Male


title: 3w, Middle, F, M7, Rep2

description: Library name: 10005CN44_D2

value: Middle colon


title: 3w, Middle, M, M6, Rep2

description: Library name: 10005CN43_D2


title: Frontal cortex, batch 1, burn, sample 4

description: Library name: E2FC14


title: 3w, Distal, M, M6, Rep1

description: Library name: 10005CN43_E1


title: Frontal cortex, batch 1, burn, sample 3

description: Library name: E2FC13


title: 3w, Middle, M, M6, Rep1

description: Library name: 10005CN43_D1


title: Frontal cortex, batch 1, sham. sample 5

description: Library name: E2FC10


title: Frontal cortex, batch 1, burn, sample 1

description: Library name: E2FC11


title: Frontal cortex, batch 1, burn, sample 2

description: Library name: E2FC12


title: Frontal cortex, batch 1, excision, sample 1

description: Library name: E2FC1


title: Sample 118 low flow low pressure

description:
Library name: 118-low_S17
GeneCounts2.tsv

value: Distal Pulmonary Arteries

value: Primary Human Cells

value: Pulmonary artery endothelial cells


title: Hippocampus, batch 1, sham, sample 4

description: Library name: E2_H_9

value: Brain, Hippocampus


title: 3w, Proximal, M, M6, Rep1

description: Library name: 10005CN43_C1

value: Proximal colon


title: Hippocampus, batch 1, sham, sample 2

description: Library name: E2_H_6

value: Mixed brain tissue

value: Sham


title: Sample 118 high flow low pressure

description:
Library name: 118-high_S18
GeneCounts2.tsv

value: Low

value: High


title: Sample 120 static

description:
Library name: 120-static_S19
GeneCounts2.tsv

value: Static


title: Hippocampus, batch 1, excision, sample 4

description: Library name: E2_H_4

value: Excision


title: Hippocampus, batch 1, sham, sample 3

description: Library name: E2_H_7


title: 0d, Distal, M, M2, Rep1

description: Library name: 10005CN42_E1


title: Sample 120 high flow low pressure

description:
Library name: 120-high_S21
GeneCounts2.tsv


title: Hippocampus, batch 1, excision, sample 3

description: Library name: E2_H_3


title: Sample 109 high flow low pressure

description:
Library name: 109-high_S15
GeneCounts2.tsv

value: Female


title: Hippocampus, batch 1, excision, sample 2

description: Library name: E2_H_2


title: Hippocampus, batch 1, burn, sample 4

description: Library name: E2_H_14

value: Burn


title: 0d, Middle, M, M2, Rep2

description: Library name: 10005CN42_D2

value: M


title: Sample 109 low flow low pressure

description:
Library name: 109-low_S14
GeneCounts2.tsv

value: Control Failed Donor


title: Sample 108 static

description:
Library name: 108-static_S10
GeneCounts2.tsv

value: IPAH

value: Male


title: Hippocampus, batch 1, burn, sample 3

description: Library name: E2_H_13


title: Sample 118 static

description:
Library name: 118-static_S16
GeneCounts2.tsv

value: Distal Pulmonary Arteries

value: CHD-PAH


title: Hippocampus, batch 1, burn, sample 2

description: Library name: E2_H_12


title: 0d, Middle, M, M2, Rep1

description: Library name: 10005CN42_D1

value: Middle colon


title: 3w, Proximal, M, M6, Rep2

description: Library name: 10005CN43_C2


title: Hippocampus, batch 1, sham. sample 5

description: Library name: E2_H_10

value: Brain, Hippocampus


title: 0d, Proximal, M, M2, Rep1

description: Library name: 10005CN42_C1

value: Proximal colon


title: 0d, Proximal, M, M2, Rep2

description: Library name: 10005CN42_C2


title: Hippocampus, batch 1, burn, sample 1

description: Library name: E2_H_11

value: Mixed brain tissue


title: 0d, Distal, M, M2, Rep2

description: Library name: 10005CN42_E2

value: Distal colon


title: Hippocampus, batch 1, excision, sample 5

description: Library name: E2_H_5


title: Sample 108 high flow low pressure

description:
Library name: 108-high_S12
GeneCounts2.tsv

value: Primary Human Cells

value: Pulmonary artery endothelial cells

value: Low


title: 1w, Distal, M, M5, Rep1

description: Library name: 10005CN41_E2


title: Hippocampus, batch 1, excision, sample 1

description: Library name: E2_H_1

value: Excision


title: Aortic CD45⁺ leukocytes from control group

city: chengdu

first: zeng

last: wanqin

state: chengdu

address: No17 renming

country: China

institute: Sichuan University

description:
Library name: Scr
scRNA-seq of control mouse aorta cells

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were processed using Cell Ranger (v3.1.0, 10× Genomics) to demultiplex, align to the mouse reference genome (mm10), and generate gene-barcode matrices. Downstream quality control, normalization, dimensionality reduction, clustering, and differential gene expression analysis were performed using the Seurat R package (v4.4.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files including genes normalized data.

source_name: Aorta

extract_protocol:
Aortic leukocytes were lysed using TRIzol reagent (Thermo Fisher Scientific) following repeated pipetting to achieve a single-cell suspension without visible clumps, then snap-frozen in liquid nitrogen for RNA extraction.
Single-cell RNA-seq libraries were constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10× Genomics) following the manufacturer’s protocol. Barcoded cDNAs were amplified, purified with the SPRIselect reagent (Beckman Coulter), and assessed for quality using the Agilent 5400 system.

value: Aorta

value: CD45+ leukocytes


title: Sample 109 static

description:
Library name: 109-static_S13
GeneCounts2.tsv

value: Female

value: Static


title: Aortic CD45⁺ leukocytes from ZnDPA@siIRF5-treated group

description:
Library name: IR5
scRNA-seq of treated mouse aorta cell


title: Hippocampus, batch 1, burn, sample 5

description: Library name: E2_H_15

value: Burn


title: eKO_3

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description: Library name: 6

data_processing:
Reads aligned with RBowtie2. SAM/BAM manipulation with Rsamtools
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with normalized counts

source_name: skin

extract_protocol:
Total RNA from hair follicle stem cells derived from Control or GRK2 eKO mice was extracted using RLT reagent (Qiagen) and purified with RNeasy Micro Kit (Qiagen)
Illumina-compatible library

tag: strain

value: skin

value: hair follicle stem cell

value: GRK2 eKO sample 18-month-old

value: FACS-sorted CD34+ α6-integrin+ bulge cell


title: Sample 103 static

description:
Library name: 103-static_S7
GeneCounts2.tsv

value: Distal Pulmonary Arteries

value: Control Failed Donor

value: Male


title: Sample 103 low flow low pressure

description:
Library name: 103-low_S8
GeneCounts2.tsv


title: eKO_2

description: Library name: 5


title: eKO_1

description: Library name: 4


title: Control_3

description: Library name: 3

value: Control sample 18-month-old


title: Control_2

description: Library name: 2


title: Sample 103 high flow low pressure

description:
Library name: 103-high_S9
GeneCounts2.tsv

value: Primary Human Cells

value: High


title: 1w, Middle, M, M5, Rep1

description: Library name: 10005CN41_D1

value: Middle colon

value: M


title: Control_1

description: Library name: 1


title: 1w, Proximal, M, M5, Rep2

description: Library name: 10005CN41_C2

value: Proximal colon


title: Sample 108 low flow low pressure

description:
Library name: 108-low_S11
GeneCounts2.tsv

value: Pulmonary artery endothelial cells

value: IPAH

value: Low


title: Sample 100 static

description:
Library name: 100-static_S4
GeneCounts2.tsv

value: Static


title: 1w, Proximal, M, M5, Rep1

description: Library name: 10005CN41_C1


title: SUCC-KO-aPDL1 rep 2

city: Suzhou

first: Lin

last: Wang

address: No. 100. Chongwen Road

institute: Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Sample 45

data_processing:
RNA-Seq: For each sample, clean reads were aligned to the reference genome hg38 using HISAT2 (v2.2.1) (Kim et al., 2019a) with the parameters "-k 1 -x -S --novel-splicesite-outfile --no-unal --dta --un-conc-gz". Then, the aligned reads were sorted and indexed using Samtools (v1.5) (Li et al., 2009). StringTie (v2.2.1) (Kovaka et al., 2019) was used to calculate the expression level of each gene with mapped reads within them, with the parameters "-t -C -e -B -A -p - G -o". Finally, transcripts per million (TPM) matrices and gene-sample expression count matrices of integrated samples were obtained. For gene differential expression analysis, the R package DESeq2 (v1.28.1) (Love et al., 2014)was used to calculate the P values for each gene between the CR patient group and the PD patient group. The fold change (FC) of gene expression levels was calculated by dividing the mean TPM values of the case group by the mean TPM values of the control group. Gene with a fold change greater than 1.5 or less than 0.67, a P value less than 0.05 were defined as up-regulated or down-regulated genes in the CR patient group, respectively.  CUT&TAG: The reference mouse genome (GRCm39) and corresponding gene transfer format (GTF) annotation file were downloaded from the NCBI website (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/). Fastp (v0.23.2) was used to filter bad reads with the parameters "-q 5 -u 50 -n 15". All clean reads produced by CUT&Tag-seq of H3K4me3 and H3K27me3 were aligned to the reference genome using Bowtie2 (v2.4.1) with the parameters "-k 1 -x --no-unal --un-gz -q --local". Then, the aligned reads were sorted and indexed using Samtools (v1.5). Peaks were called using MACS2 (v2.2.6)  with the parameters "--broad --broad-cutoff 0.05 -f BAMPE -g mm --keep-dup all". Peaks were merged using BEDTools (v2.26.0)  and re-counted using deepTools (v3.5.1)  for H3K4me3 and H3K27me3, respectively. The merged peaks were subsequently annotated with ChIPseeker (v1.38.0), and were visualized using IGV (v2.13) . Finally, for each histone modification, counts per million (CPM) matrices and peak-sample signal count matrices of integrated samples were obtained. For peak differential analysis, the R package DESeq2 (v1.28.1)  was used to calculate the P values and adjusted P values for each peak between the succinate group and the control group. The fold change (FC) of peak signal levels was calculated by dividing the mean CPM values of the succinate group by the mean CPM values of the control group. Peaks with a fold change greater than 2 or less than 0.5, a P value less than 0.05, and an adjusted P value less than 0.1 were defined as up-regulated or down-regulated peaks in the succinate group, respectively.
Assembly: GRCm39

source_name: tumor

extract_protocol:
RNA-Seq: NucleoSpin RNA Columns ( Cat# 740955.50SS) CUT&TAG: TruePrep Index Kit V2 for Illumina(Vazyme, Cat# TD202)
RNA-Seq: Universal Plus mRNA-Seq with NuQuant (TECAN GENOMICS) RNA-Seq: TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) CUT&TAG: Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme)

value: tumor

value: primary

value: CD8+ T cell


title: SUCC-KO-aPDL1 rep 1

description: Library name: Sample 44


title: 2w, Distal, F, M6, Rep2

description: Library name: 10005CN40_E2

value: Distal colon

value: F


title: SUCC-KO rep 3

description: Library name: Sample 43


title: SUCC-KO rep 1

description: Library name: Sample 41


title: SUCC-KO rep 2

description: Library name: Sample 42


title: Sample 89 static

description:
Library name: 89-Static_S1
GeneCounts2.tsv

value: Distal Pulmonary Arteries

value: Female


title: Sample 100 high flow low pressure

description:
Library name: 100-high_S6
GeneCounts2.tsv

value: Male


title: 2w, Distal, F, M6, Rep1

description: Library name: 10005CN40_E1


title: 2w, Middle, F, M6, Rep2

description: Library name: 10005CN40_D2


title: CTRL-WT-aPDL1 rep 2

description: Library name: Sample 39


title: 1w, Middle, M, M5, Rep2

description: Library name: 10005CN41_D2


title: CTRL-WT-aPDL1 rep 1

description: Library name: Sample 38


title: Sample 89 low flow low pressure

description:
Library name: 89-Low_S2
GeneCounts2.tsv

value: Primary Human Cells


title: CTRL-WT rep 2

description: Library name: Sample 36


title: CTRL-WT rep 3

description: Library name: Sample 37


title: SUCC-KO-aPDL1 rep 3

description: Library name: Sample 46


title: Sample 89 high flow low pressure

description:
Library name: 89-High_S3
GeneCounts2.tsv

value: High


title: 2w, Proximal, F, M6, Rep2

description: Library name: 10005CN40_C2


title: 2w, Middle, F, M6, Rep1

description: Library name: 10005CN40_D1

value: Middle colon


title: SUCC.LM-OVA-TCM.D28 rep 2

description: Library name: Sample 34

source_name: spleen

value: spleen


title: CTRL.LM-OVA-TCM.D28 rep 2

description: Library name: Sample 32


title: 2w, Proximal, F, M6, Rep1

description: Library name: 10005CN40_C1

value: Proximal colon


title: O4YRSK, dox, 4 days, rep2

city: San Diego

first: William

last: Tu

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

description:
Library name: O4YRSK_4D_2
Column name in raw_counts_matrix.csv: O4YRSK_4D_2

data_processing:
Raw fastq files were processed using the nf-core/rnaseq pipeline. Raw reads were assessed using FastQC. Adapter sequences and low-quality bases were removed using Trim Galore!. Cleaned reads were aligned to the reference genome GRCh38 using STAR. Transcript quantification was performed using Salmon, followed by gene-level summarization using tximport. Gene count matrices were imported into R and used as input for analysis by DESeq2 (v1.44.0).
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: Skin

growth_protocol: Human dermal fibroblasts from a healthy 96-year old male donor (GM00731, Coriell) were cultured in Minimum Essential Medium (ThermoFisher) with 15% fetal bovine serum (Omega Scientific), and 1× non-essential amino acids solution (ThermoFisher) on 0.1% gelatin.

extract_protocol:
RNA was extracted with the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) using the Kingfisher Apex System (ThermoFisher). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics) following manufacturer's protocols and indexed with primers from xGEN UDI 10nt Primer Plate 5 (IDT).

treatment_protocol: Transgenes were induced with 1 ug/mL doxycycline for 4 days.

value: Skin

value: Fibroblast

value: WT

value: O4YRSK, dox, 4 days


title: SUCC.LM-OVA-TCM.D28 rep 1

description: Library name: Sample 33


title: Sample 100 low flow low pressure

description:
Library name: 100-low_S5
GeneCounts2.tsv

value: Pulmonary artery endothelial cells

value: IPAH

value: Low


title: O4YRSK, dox, 4 days, rep1

description:
Library name: O4YRSK_4D_1
Column name in raw_counts_matrix.csv: O4YRSK_4D_1


title: 2w, Distal, F, M8, Rep2

description: Library name: 10005CN39_E2

value: Distal colon


title: CTRL.LM-OVA-TCM.D28 rep 1

description: Library name: Sample 31

value: primary

value: CD8+ T cell


title: SUCC.LM-OVA-SLEC.D7 rep 3

description: Library name: Sample 30


title: 2w, Distal, F, M8, Rep1

description: Library name: 10005CN39_E1

value: F


title: SUCC.LM-OVA-SLEC.D7 rep 2

description: Library name: Sample 29


title: O4YRSK, no dox, 4 days, rep1

description:
Library name: O4YRSK_0D_1
Column name in raw_counts_matrix.csv: O4YRSK_0D_1

value: O4YRSK, no dox, 4 days


title: SUCC.LM-OVA-SLEC.D7 rep 1

description: Library name: Sample 28


title: CTRL-WT-aPDL1 rep 3

description: Library name: Sample 40

value: tumor


title: OSK, dox, 4 days, rep2

description:
Library name: OSK_4D_2
Column name in raw_counts_matrix.csv: OSK_4D_2

value: OSK, dox, 4 days


title: CTRL.LM-OVA-SLEC.D7 rep 2

description: Library name: Sample 26


title: 2w, Middle, F, M8, Rep2

description: Library name: 10005CN39_D2

value: Middle colon


title: CTRL.LM-OVA-SLEC.D7 rep 1

description: Library name: Sample 25

value: spleen


title: 2w, Middle, F, M8, Rep1

description: Library name: 10005CN39_D1


title: OSK, dox, 4 days, rep1

description:
Library name: OSK_4D_1
Column name in raw_counts_matrix.csv: OSK_4D_1


title: CTRL-WT rep 1

description: Library name: Sample 35


title: 2w, Proximal, F, M8, Rep2

description: Library name: 10005CN39_C2

value: Proximal colon


title: SUCC.LM-OVA-MPEC.D7 rep 3

description: Library name: Sample 24


title: OSK, no dox, 4 days, rep2

description:
Library name: OSK_0D_2
Column name in raw_counts_matrix.csv: OSK_0D_2

value: Skin

value: OSK, no dox, 4 days


title: SUCC.LM-OVA-MPEC.D7 rep 2

description: Library name: Sample 23


title: OSK, no dox, 4 days, rep1

description:
Library name: OSK_0D_1
Column name in raw_counts_matrix.csv: OSK_0D_1

value: Fibroblast

value: WT


title: CTRL.LM-OVA-MPEC.D7 rep 2

description: Library name: Sample 20


title: SUCC.LM-OVA-MPEC.D7 rep 1

description: Library name: Sample 22


title: CTRL.LM-OVA-MPEC.D7 rep 1

description: Library name: Sample 19


title: H3K27me3-SUCC.vitro.D7 rep 2

description: Library name: Sample 18

library_source: genomic

data_processing:
RNA-Seq: For each sample, clean reads were aligned to the reference genome hg38 using HISAT2 (v2.2.1) (Kim et al., 2019a) with the parameters "-k 1 -x -S --novel-splicesite-outfile --no-unal --dta --un-conc-gz". Then, the aligned reads were sorted and indexed using Samtools (v1.5) (Li et al., 2009). StringTie (v2.2.1) (Kovaka et al., 2019) was used to calculate the expression level of each gene with mapped reads within them, with the parameters "-t -C -e -B -A -p - G -o". Finally, transcripts per million (TPM) matrices and gene-sample expression count matrices of integrated samples were obtained. For gene differential expression analysis, the R package DESeq2 (v1.28.1) (Love et al., 2014)was used to calculate the P values for each gene between the CR patient group and the PD patient group. The fold change (FC) of gene expression levels was calculated by dividing the mean TPM values of the case group by the mean TPM values of the control group. Gene with a fold change greater than 1.5 or less than 0.67, a P value less than 0.05 were defined as up-regulated or down-regulated genes in the CR patient group, respectively.  CUT&TAG: The reference mouse genome (GRCm39) and corresponding gene transfer format (GTF) annotation file were downloaded from the NCBI website (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/). Fastp (v0.23.2) was used to filter bad reads with the parameters "-q 5 -u 50 -n 15". All clean reads produced by CUT&Tag-seq of H3K4me3 and H3K27me3 were aligned to the reference genome using Bowtie2 (v2.4.1) with the parameters "-k 1 -x --no-unal --un-gz -q --local". Then, the aligned reads were sorted and indexed using Samtools (v1.5). Peaks were called using MACS2 (v2.2.6)  with the parameters "--broad --broad-cutoff 0.05 -f BAMPE -g mm --keep-dup all". Peaks were merged using BEDTools (v2.26.0)  and re-counted using deepTools (v3.5.1)  for H3K4me3 and H3K27me3, respectively. The merged peaks were subsequently annotated with ChIPseeker (v1.38.0), and were visualized using IGV (v2.13) . Finally, for each histone modification, counts per million (CPM) matrices and peak-sample signal count matrices of integrated samples were obtained. For peak differential analysis, the R package DESeq2 (v1.28.1)  was used to calculate the P values and adjusted P values for each peak between the succinate group and the control group. The fold change (FC) of peak signal levels was calculated by dividing the mean CPM values of the succinate group by the mean CPM values of the control group. Peaks with a fold change greater than 2 or less than 0.5, a P value less than 0.05, and an adjusted P value less than 0.1 were defined as up-regulated or down-regulated peaks in the succinate group, respectively.
Assembly: GRCm39
Library strategy: CUT&Tag

molecule: genomic DNA


title: CTRL.LM-OVA-MPEC.D7 rep 3

description: Library name: Sample 21


title: 2w, Proximal, F, M8, Rep1

description: Library name: 10005CN39_C1


title: mESC-FLAG-M2_ChIP-seq_control_rep5_330-311

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Library name: mESC-FLAG-M2 ChIP-seq control - Rep 5

data_processing:
Read alignment: Adapter sequences were first trimmed from the paired-end fastq files using fastp (v.0.23.2) (S. Chen et al. 2018). Paired-end reads were aligned using BWA-MEM (v.0.7.17) (Li and Durbin 2010) with parameter -M against the human (hg38) or mouse (mm10) genomes. BAM files were sorted using samtools sort (v.1.16.1) (Li et al. 2009) and duplicate read pairs were marked using Picard MarkDuplicates (v.2.24.1) with arguments REMOVE_DUPLICATES='false' ASSUME_SORTED='true' DUPLICATE_SCORING_STRATEGY='SUM_OF_BASE_QUALITIES' READ_NAME_REGEX='[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.'. BAM files were then filtered to remove reads that are duplicated, unmapped, or not in proper pairs using samtools view (v.1.16.1) with arguments -h -b -f 0x3 -F 0x404.
Peak-finding: Peaks for each individual ChIP-exo sample were determined using ChExMix (v0.52) (Yamada et al. 2018) using the following parameters: --threads 4 --expt ${expt} --ctrl ${ctrl} --format BAM --scalewin 1000 --noread2 --round 3 --minmodelupdateevents 50 --prlogconf -4 --alphascale 1.0 --betascale 0.05 --epsilonscale 0.2 --minroc 0.7 --minmodelupdaterefs 25 --pref -0.1 --numcomps 500 --win 250 --back ${back} --memepath ${memePath} --mememinw 6 --mememaxw 18 --seq ${genome} --exclude ${exclude} --q 0.01 --minfold 1.5. Blacklist files (the ${exclude} argument) were sourced from ENCODE. Background files (the ${back} argument) are 2nd-order Markov models created from the human or mouse genomes. Control samples (the ${ctrl} argument) represent pooled BAM files of all relevant control samples in each cell type, merged using samtools merge (v.1.16.1) (Li et al. 2009). This merger was performed across 13 K562 control samples (totaling 40,362,133 read pairs), 5 HepG2 control samples (13,990,398 read pairs), and 14 mES control samples (93,023,738 read pairs).
Assembly: hg38 and mm10
Supplementary files format and content: BED: ChExMix peak locations in BED format. If a BED file is not provided for a sample, either no peaks were found or peak-finding was not provided on the sample (e.g., for control files)
Supplementary files format and content: BW: bigwig files showing only the read1 5' positions after de-duplication. Only the 5' positions are shown because this reflects the exonuclease digestion stop point and is the most relevant position for ChIP-exo analysis. Positive strand and negative strand reads are separated into different bigwig files.

growth_protocol: K562 (CCL-243) and HepG2 (HB-8065) cells were obtained from the American Type Culture Collection (ATCC) handled and sub-cultured following the manufacturers recommendations. A17 A2Lox.cre mES cells (H2B-GFP_iGFP; iFoxA1.Flag) were cultured as previously described (Bulajić et al. 2020).

extract_protocol:
K562 suspension cells were counted and directly crosslinked in media or pelleted and resuspended for crosslinking in PBS. Adherent cells were washed with PBS, trypsinized, quenched and resuspended in media or PBS for counting and crosslinking. All cell counts were performed with a trypan blue dye exclusion test using a hemocytometer. For MO-ChIP-exo, 10 min of crosslinking with 1% formaldehyde was quenched with a 3M Tris pH 7.8. Variations of the crosslinking time, formaldehyde concentration and quencher were used as reported. Crosslinked cells were washed with PBS + 1X CPI and flash frozen in liquid nitrogen.
Crosslinked cell pellets (10 M cells per reaction) were subjected to cell and nuclear lysis. Lysates were resuspended in PBS + 1X CPI for sonication in a Diagenode Bioruptor Pico. The ‘Go & Shear’ setting was used with the validated parameters on the ‘Easy Mode’ for 30’’ON/OF with increasing cycles (1-11 as described). An aliquot of 15 μL (~0.5 M cells) was used to reverse crosslink and purify the DNA for a sonication assessment using the Agilent Tape Station D5000 kit. The sonicated crosslinked chromatin was pre-cleared before ChIP using high speed centrifugation (14k rpm at 4C for 15 min). ChIP antibodies [Anti-CTCF (Sigma 07-729), Anti-USF1-1B8 (DSHB USF1-1B8-6/13/19), IgG (Sigma i5006), Anti-GATA1 (Santa Cruz Biotechnology  SC-266), Anti-FoxA1 (Santa Cruz Biotechnology SC-101058), Anti-SOX2 (R&D AF2018)] were pre-conjugated to 50 μL Protein A or G Dynabeads (Invitrogen) before an overnight incubation with the antibody of interest at 4C. Bead-bound chromatin was washed and subjected to simultaneous End-repair and A-tailing with a subsequent TA ligation of the first HPLC-purified adapter using the NEBNext® Ultra™ II DNA Library Prep Kit. After washes, a fill-in reaction was performed using Phi29 DNA Polymerase (NEB). This reaction was followed by another wash and Lambda Exonuclease (NEB) digestion. Reverse crosslinking was performed overnight to release the DNA. Released DNA was purified using Mag-Bind® TotalPure NGS beads (Omega Bio-Tek) before ligating the 2nd HPLC-purified adapter using T4 DNA ligase (Qiagen). A DNA cleanup was performed using Mag-Bind® TotalPure NGS beads before PCR enrichment for 12 cycles. This was followed by size selection using SPRI select beads (Beckman Coulter) and an additional DNA cleanup to remove excess adapters. Completed libraries were analyzed in the Tape Station using High Sensitivity D5000 ScreenTape and Reagents. Finally, libraries were individually quantified through qPCR using NEBNext® Library Quantification Kit, For Illumina® (NEB) in an ABI StepOne Plus Real Time PCR System. Completed libraries were pooled for each sequencing run based on their concentration and read allocation with a 1% PhiX spike-in, treated with Illumina’s Free Adapter Blocking Reagent and cleaned up using Mag-Bind® TotalPure NGS beads. Final pool concentration was determined through qPCR using NEB Next® Library Quantification Kit, For Illumina® in an ABI StepOne Plus Real Time PCR System before diluting to 0.65 nM for loading. An Illumina NextSeq 2000 Sequencing System was used with a NextSeq™ 1000/2000 P2 XLEAP-SBS™ Reagent Kit (100 Cycle) for paired-end sequencing with 50 bp each for read1 and read2.

value: Embryonic stem cells

value: Anti-FLAG-M2 Sigma F1804 Lot 375541


title: 1w, Distal, F, M9, Rep1

description: Library name: 10005CN38_E1


title: O4YRSK, no dox, 4 days, rep2

description:
Library name: O4YRSK_0D_2
Column name in raw_counts_matrix.csv: O4YRSK_0D_2


title: H3K27me3-CTR.vitro.D7 rep 2

description: Library name: Sample 16


title: mESC-FLAG-M2_ChIP-seq_control_rep4_330-211

description: Library name: mESC-FLAG-M2 ChIP-seq control - Rep 4


title: CTRL.LM-OVA-SLEC.D7 rep 3

description: Library name: Sample 27


title: H3K27me3-SUCC.vitro.D7 rep 1

description: Library name: Sample 17


title: 1w, Middle, F, M9, Rep1

description: Library name: 10005CN38_D1


title: mESC-FLAG-M2_ChIP-seq_control_rep3_330-111

description: Library name: mESC-FLAG-M2 ChIP-seq control - Rep 3


title: H3K4me3-SUCC.vitro.D7 rep 2

description: Library name: Sample 14


title: H3K27me3-CTR.vitro.D7 rep 1

description: Library name: Sample 15


title: H3K4me3-SUCC.vitro.D7 rep 1

description: Library name: Sample 13


title: 1w, Proximal, F, M9, Rep2

description: Library name: 10005CN38_C2


title: mESC-FLAG-M2_ChIP-seq_control_rep2_325-211

description: Library name: mESC-FLAG-M2 ChIP-seq control - Rep 2


title: 1w, Proximal, F, M9, Rep1

description: Library name: 10005CN38_C1


title: H3K4me3-CTR.vitro.D7 rep 1

description: Library name: Sample 11


title: mESC-FLAG-M2_ChIP-seq_control_rep1_325-111

description: Library name: mESC-FLAG-M2 ChIP-seq control - Rep 1


title: CTR.vitro.D7 rep 2

description: Library name: Sample 6


title: 1w, Distal, F, M5, Rep1

description: Library name: 10005CN37_E1


title: SUCC-OVA.vitro.D7 rep 2

description: Library name: Sample 4


title: mESC-FLAG-M2_MO-ChIP-exo_control_rep1_317-111

description: Library name: mESC-FLAG-M2 MO-ChIP-exo control - Rep 1

value: Anti-FLAG-M2 Sigma F1804 Lot SLCK5688


title: CTRL-OVA.vitro.D7 rep 1

description: Library name: Sample 1


title: SUCC.vitro.D7 rep 3

description: Library name: Sample 10


title: SUCC.vitro.D7 rep 1

description: Library name: Sample 8


title: CTR.vitro.D7 rep 3

description: Library name: Sample 7


title: 1w, Middle, F, M9, Rep2

description: Library name: 10005CN38_D2


title: TCF1.delta.LEF1.delta.BCR

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: VDJ_Sophie_4

data_processing:
CellRanger pipeline v.6.0.1 multi run with chemistry parameter = auto, and expect-cells = 5000.
Single-cell RNA sequencing (scRNA-seq) data were processed and analysed using the Seurat package (v5.0.3) in R. Raw gene expression matrices were filtered to exclude low-quality cells based on thresholds for mitochondrial gene content and the number of detected genes per cell, using the PercentageFeatureSet() and subset() functions. The subset function was applied with the following parameters: subset(sce, subset = nFeature_RNA > 500 & nFeature_RNA < 6000 & percent.mt < 5 & nCount_RNA > 1000 & nCount_RNA < 4e4)
Normalisation and integration were performed using the scTransform() workflow. Dimensionality reduction was performed using principal component analysis (PCA) via the RunPCA() function, and the top 20–30 principal components were selected to construct a shared nearest neighbour (SNN) graph using FindNeighbours(). Clustering was carried out using the FindClusters() function. Clusters were visualised using Uniform Manifold Approximation and Projection (UMAP) via the RunUMAP() function. Differential expressed genes for each cluster were identified using the FindAllMarkers() function with test.use set as either “wilcox” or “MAST”.
Assembly: GRCm38
Supplementary files format and content: CellRanger verison 6.0.1 outputs file for expression and BCR .
Library strategy: BCR-Seq

source_name: Peritoneal Cavity

extract_protocol:
Total B cells (CD19+CD3-) from peritoneal cavity of  three 8 weeks old mice were sorted by the FACS Aria II cell sorting system (BD Immunocytometry Systems, San Jose, CA, USA)
According to the manufacturer’s instructions for the Chromium Next GEM Single Cell 5’Kit v2

value: Peritoneal Cavity

value: B cells

tag: age

value: 8 weeks


title: 1w, Middle, F, M5, Rep2

description: Library name: 10005CN37_D2

value: F


title: 1w, Distal, F, M5, Rep2

description: Library name: 10005CN37_E2

value: Distal colon


title: 1w, Proximal, F, M5, Rep1

description: Library name: 10005CN37_C1


title: mESC-IgG_MO-ChIP-exo_control_rep2_238-211

description: Library name: mESC-IgG MO-ChIP-exo control - Rep 2

value: IgG Sigma i5006 Lot SLCB7084


title: mESC-FLAG-M2_MO-ChIP-exo_control_rep2_317-211

description: Library name: mESC-FLAG-M2 MO-ChIP-exo control - Rep 2


title: 1w, Proximal, F, M5, Rep2

description: Library name: 10005CN37_C2


title: mESC-FLAG-M2_ChIP-exo_5.0_control_043-111

description: Library name: mESC-FLAG-M2 ChIP-exo 5.0 control

source_name: AG23205 (MC1 null)

value: AG23205 (MC1 null)


title: SUCC.vitro.D7 rep 2

description: Library name: Sample 9

value: primary

value: CD8+ T cell


title: TCF1.delta.LEF1.delta.EXP

description: Library name: GEX_Sophie_4

data_processing:
CellRanger pipeline v.6.0.1 multi run with chemistry parameter = auto, and expect-cells = 5000.
Single-cell RNA sequencing (scRNA-seq) data were processed and analysed using the Seurat package (v5.0.3) in R. Raw gene expression matrices were filtered to exclude low-quality cells based on thresholds for mitochondrial gene content and the number of detected genes per cell, using the PercentageFeatureSet() and subset() functions. The subset function was applied with the following parameters: subset(sce, subset = nFeature_RNA > 500 & nFeature_RNA < 6000 & percent.mt < 5 & nCount_RNA > 1000 & nCount_RNA < 4e4)
Normalisation and integration were performed using the scTransform() workflow. Dimensionality reduction was performed using principal component analysis (PCA) via the RunPCA() function, and the top 20–30 principal components were selected to construct a shared nearest neighbour (SNN) graph using FindNeighbours(). Clustering was carried out using the FindClusters() function. Clusters were visualised using Uniform Manifold Approximation and Projection (UMAP) via the RunUMAP() function. Differential expressed genes for each cluster were identified using the FindAllMarkers() function with test.use set as either “wilcox” or “MAST”.
Assembly: GRCm38
Supplementary files format and content: CellRanger verison 6.0.1 outputs file for expression and BCR .


title: TCF1.WT.LEF1.WT.BCR

description: Library name: VDJ_Sophie_3


title: 1w, Middle, F, M5, Rep1

description: Library name: 10005CN37_D1

value: Middle colon


title: SUCC-OVA.vitro.D7 rep 1

description: Library name: Sample 3

value: spleen


title: mESC-IgG_MO-ChIP-exo_control_rep1_238-111

description: Library name: mESC-IgG MO-ChIP-exo control - Rep 1


title: CTRL-OVA.vitro.D7 rep 2

description: Library name: Sample 2


title: 0d, Distal, M, M4, Rep2

description: Library name: 10005CN36_E2

value: M


title: TCF1.WT.LEF1.WT.EXP

description: Library name: GEX_Sophie_3


title: mESC-IgG_ChIP-exo_5.0_control_044-111

description: Library name: mESC-IgG ChIP-exo 5.0 control


title: H3K4me3-CTR.vitro.D7 rep 2

description: Library name: Sample 12


title: CTR.vitro.D7 rep 1

description: Library name: Sample 5


title: 0d, Distal, M, M4, Rep1

description: Library name: 10005CN36_E1


title: mandibular lymph nodes, lymphatic endothelial cells, sham, 24h post-surgery

city: Shanghai

first: Jinman

last: Chen

address: South of Wanping Road

department: Institute of Spine

institute: Longhua hospital

description: Library name: SHAM-1

data_processing:
Reads were processed using the Cell Ranger 5.0 pipeline. FASTQs generated from Illumina sequencing output were aligned to the mouse genome mm10 by the STAR algorithm. Gene-Barcode matrices were generated for each individual sample after filtering and which contain the barcoded cells and gene expression counts. The Seurat (v3.0.2) R was used for quality control and downstream analysis of our scRNA-seq data. Low quality of cells were excluded which expres fewer than 200 or greater than 6000 unique genes, as well as cells with more than 10% mitochondrial gene expression. The data was normalized by Seurat package) for extracting variable genes which were identified while controlling for the strong relationship between variability and average expression. Data was integrated from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: mandibular lymph nodes

extract_protocol:
At 24 hours post SAH or sham operation, mandibular LNs were harvest from 20 mice of each group. The LNs were minced with 25G needles, and then digested in a solution containing Dnase (100 μg/ml), Dispase II (800 μg/ml), and collagenase P (200 μg/ml) at 37˚C. The samples were mixed by pipetting gently, and the supernatant was collected and added to RPMI/2mM EDTA/1%FCS after 8 minutes digestion. And then fresh enzyme media was added to the remaining tissue, once the tissue had completely dissolved, the cell suspension was collected and filtered by 70-μm nylon mesh cell strainers (BD bioscience). After centrifuged, cells were stained by CD45-microbeads (130-052-301, Miltenyi biotec) for 15 minutes at 4˚C, followed by pass through the LD columns (Miltenyi biotec) in a magnetic separator. The CD45 negative cells were collected and centrifuged, and followed by incubated with anti-CD31 PE-conjugated antibody and anti-PDPN PE-conjugated antibody for 10 minutes. After wash with FCS buffer, cells were incubated with anti-PE microbeads (130-048-801, Miltenyi biotec) for 15 minutes at 4˚C. Finally, the cell suspension was pass through LS columns (Miltenyi biotec) in a magnetic separator, and the PE positive cells were collected for the further single-cell RNA sequencing.
The sorted cells were loaded onto a 10× Genomics Chromium platform to form Gel Beads-in emulsion (GEM). On cDNA synthesis, each cDNA molecule was tagged on the 5’end with (unique molecular identifier) UMI and cell label. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. The library construction were conducted according to the manufacturer’s instruction (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: mandibular lymph nodes

value: lymphatic endothelial cells


title: mESC-IgG_ChIP-exo_5.0_control_rep2_037-112

description: Library name: mESC-IgG ChIP-exo 5.0 control - Rep 2

value: Embryonic stem cells


title: mandibular lymph nodes, lymphatic endothelial cells, SAH, 24h post-surgery

description: Library name: SAH-2


title: 0d, Middle, M, M4, Rep2

description: Library name: 10005CN36_D2


title: mESC-CTCF_MO-ChIP-exo_rep4_237-311

description: Library name: mESC-CTCF MO-ChIP-exo - Rep 4

value: Anti-CTCF Sigma 07-729 Lot 3905315


title: 3_10_S

city: Lund

first: Peter

last: Ellmark

address: Scheelevägen 2, Medicon Village

country: Sweden

institute: Alligator Bioscience AB

description:
Library name: 3_10_S
ENSG_as_rows_on_per_sample_basis

data_processing:
Sequences were aligned to Mus Musculus genome (GRCm38) using STAR (v5.1) and quantified with SALMON (v1.10)
Assembly: GRCm38
Supplementary files format and content: tsv file with raw counts for each sample

source_name: sorted

extract_protocol:
PureLink RNA Mini Kit and Mouse RiboPure
Illumina® Stranded mRNA Prep, Ligation (20040534, Illumina)

value: sorted


title: 3_9_S

description:
Library name: 3_9_S
ENSG_as_rows_on_per_sample_basis


title: 3_6_S

description:
Library name: 3_6_S
ENSG_as_rows_on_per_sample_basis


title: mESC-CTCF_MO-ChIP-exo_rep3_275-211

description: Library name: mESC-CTCF MO-ChIP-exo - Rep 3


title: 0d, Middle, M, M4, Rep1

description: Library name: 10005CN36_D1


title: 3_5_L

description:
Library name: 3_5_L
ENSG_as_rows_on_per_sample_basis

source_name: lymph

value: lymph


title: 3_5_B

description:
Library name: 3_5_B
ENSG_as_rows_on_per_sample_basis

source_name: blood

value: blood


title: 3_4_T

description:
Library name: 3_4_T
ENSG_as_rows_on_per_sample_basis

value: tumor


title: 3_4_B

description:
Library name: 3_4_B
ENSG_as_rows_on_per_sample_basis


title: 3_4_L

description:
Library name: 3_4_L
ENSG_as_rows_on_per_sample_basis


title: mESC_(Frozen_Chromatin)-IgG_ChIP-exo_5.0_rep1_038-111

description: Library name: mESC (Frozen Chromatin)-IgG ChIP-exo 5.0 - Rep 1


title: 0d, Proximal, M, M4, Rep2

description: Library name: 10005CN36_C2

value: Proximal colon


title: mESC-CTCF_MO-ChIP-exo_rep2_275-111

description: Library name: mESC-CTCF MO-ChIP-exo - Rep 2


title: mESC-CTCF_MO-ChIP-exo_rep1_237-411

description: Library name: mESC-CTCF MO-ChIP-exo - Rep 1


title: mESC-IgG_ChIP-exo_5.0_rep1_037-111

description: Library name: mESC-IgG ChIP-exo 5.0 - Rep 1


title: 0d, Proximal, M, M4, Rep1

description: Library name: 10005CN36_C1


title: 0d, Distal, F, M6, Rep1

description: Library name: 10005CN35_E1

value: Distal colon

value: F


title: 3_3_B

description:
Library name: 3_3_B
ENSG_as_rows_on_per_sample_basis


title: 3_3_T

description:
Library name: 3_3_T
ENSG_as_rows_on_per_sample_basis


title: 3_2_T

description:
Library name: 3_2_T
ENSG_as_rows_on_per_sample_basis


title: 3_3_L

description:
Library name: 3_3_L
ENSG_as_rows_on_per_sample_basis


title: mESC_(Frozen_Chromatin)-SOX2_ChIP-exo_5.0_rep1_036-111

description: Library name: mESC (Frozen Chromatin)-SOX2 ChIP-exo 5.0 - Rep 1

value: AG23205 (MC1 null)

value: Anti-SOX2 R&D AF2018 Lot KOY0419101


title: 3_5_T

description:
Library name: 3_5_T
ENSG_as_rows_on_per_sample_basis


title: 3_1_T

description:
Library name: 3_1_T
ENSG_as_rows_on_per_sample_basis


title: 0d, Middle, F, M6, Rep1

description: Library name: 10005CN35_D1


title: 0d, Proximal, F, M6, Rep2

description: Library name: 10005CN35_C2


title: 3_2_L

description:
Library name: 3_2_L
ENSG_as_rows_on_per_sample_basis


title: 3_1_B

description:
Library name: 3_1_B
ENSG_as_rows_on_per_sample_basis


title: mESC-SOX2_ChIP-exo_5.0_(SPRI_Beads)_rep1_034-111

description: Library name: mESC-SOX2 ChIP-exo 5.0 (SPRI Beads)- Rep 1


title: mESC-SOX2_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_035-111

description: Library name: mESC-SOX2 ChIP-exo 5.0 (Std Desalting Adapters)- Rep 1


title: 0d, Proximal, F, M6, Rep1

description: Library name: 10005CN35_C1


title: 2_7_S

description:
Library name: 2_7_S
ENSG_as_rows_on_per_sample_basis

value: CD40 mAb


title: mESC_(Frozen_Chromatin)-CTCF_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_032-111

description: Library name: mESC (Frozen Chromatin)-CTCF ChIP-exo 5.0 (Std Desalting Adapters) - Rep 1

value: Anti-CTCF Sigma 07-729 Lot 3515588


title: 2_5_L

description:
Library name: 2_5_L
ENSG_as_rows_on_per_sample_basis


title: 2w, Proximal, F, M5, Rep1

description: Library name: 10005CN29_E1


title: 2_6_S

description:
Library name: 2_6_S
ENSG_as_rows_on_per_sample_basis


title: 0d, Distal, F, M6, Rep2

description: Library name: 10005CN35_E2


title: 2w, Proximal, F, M5, Rep2

description: Library name: 10005CN29_E2


title: 2_10_S

description:
Library name: 2_10_S
ENSG_as_rows_on_per_sample_basis


title: 2_4_T

description:
Library name: 2_4_T
ENSG_as_rows_on_per_sample_basis


title: 2_5_T

description:
Library name: 2_5_T
ENSG_as_rows_on_per_sample_basis


title: mESC-SOX2_ChIP-exo_5.0_rep1_033-111

description: Library name: mESC-SOX2 ChIP-exo 5.0 - Rep 1


title: 2_5_B

description:
Library name: 2_5_B
ENSG_as_rows_on_per_sample_basis


title: mESC_(Frozen_Chromatin)-CTCF_ChIP-exo_5.0_(SPRI_Beads)_rep1_031-111

description: Library name: mESC (Frozen Chromatin)-CTCF ChIP-exo 5.0 (SPRI Beads)- Rep 1


title: mESC_(Frozen_Chromatin)-CTCF_ChIP-exo_5.0_rep1_030-111

description: Library name: mESC (Frozen Chromatin)-CTCF ChIP-exo 5.0 - Rep 1


title: 2w, Distal, F, M5, Rep2

description: Library name: 10005CN29_D2


title: 3_1_L

description:
Library name: 3_1_L
ENSG_as_rows_on_per_sample_basis


title: 2_4_L

description:
Library name: 2_4_L
ENSG_as_rows_on_per_sample_basis


title: 2_3_L

description:
Library name: 2_3_L
ENSG_as_rows_on_per_sample_basis


title: 2_3_B

description:
Library name: 2_3_B
ENSG_as_rows_on_per_sample_basis


title: 2w, Distal, F, M5, Rep1

description: Library name: 10005CN29_D1


title: 2_4_B

description:
Library name: 2_4_B
ENSG_as_rows_on_per_sample_basis


title: 2_3_T

description:
Library name: 2_3_T
ENSG_as_rows_on_per_sample_basis


title: mESC-CTCF_ChIP-exo_5.0_(Std_Desalting_Adapters)_rep1_029-111

description: Library name: mESC-CTCF ChIP-exo 5.0 (Std Desalting Adapters)- Rep 1


title: 2w, Middle, F, M5, Rep2

description: Library name: 10005CN29_C2

value: Middle colon


title: 2_2_T

description:
Library name: 2_2_T
ENSG_as_rows_on_per_sample_basis


title: 1_10_S

description:
Library name: 1_10_S
ENSG_as_rows_on_per_sample_basis

value: Vehicle


title: Batch2_Replicate_2_Hash

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

country: Germany

institute: University Hospital Würzburg

description:
Library name: Replicate_2_Hash
10x Genomics

data_processing:
The reads of the sequenced libraries were mapped using CellRanger version 7.0.0 (10x Genomics) to the mouse mm10-3.0.0 reference genome (10x Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Colon

extract_protocol:
Mice colon was harvested and immediately preserved in ice-cold HBSS. Shortly after, tissue was incubated for 20min at 37°C in PBS containing 2% FCS and 5 mM DTT. Supernatant was discarded, colon was cut into small pieces and again incubated at 37°C for 30min in RPMI 1640 containing Liberase (2.5mg/ml) and DNase (50 U/ml) with shaking. Supernatant was then collected and centrifuged for 10min at 4 °C and 400g. The resulting pellet was washed three times with PBS containing 10%FCS. After the last washing step, pellet was resuspended in 1ml PBS containing 10 % FCS. Per experimental condition, single cells were tagged using TotalSeq-B anti-mouse Hashtags (Biolegend; #155831, #155833, #155835, #155837) at 25 µg/ml for 30 min at 4°C following the manufacturer’s instructions. The different experimental conditions were tagged as follows: wildtype mice, TotalSeq-B0301 anti-mouse Hashtag 1 antibody; JUP-KO mice, TotalSeq-B0302 anti-mouse Hashtag 2 antibody; DSS-treated WT mice, TotalSeq-B0303 anti-mouse Hashtag 3 antibody; DSS-treated JUP-KO mice, TotalSeq-B0304 anti-mouse Hashtag 4 antibody. For each batch, single cells from the different experimental conditions were pooled and flow-sorted on a BD FACS Aria II to purify viable single cells. The subsequent processing of cells was performed using the 10x Chromium Next GEM Single Cell 3’ v3.1 with cell surface barcode technology (dual index). Approximately 23,000 – 25,000 pooled cells were loaded to capture about 14,000 cells per batch. The DNA libraries for gene expression analysis and barcodes were pooled and sequenced paired-end on an Illumina NextSeq 2000 instrument with a P3 flow cell and 100 cycles, generating approximately 1,200 million reads.
scRNA-seq was performed using the 10x Chromium Next GEM Single Cell 3’ v3.1 with cell surface barcode technology (dual index).

value: Colon


title: Batch2_Replicate_2_GEX

description:
Library name: Replicate_2_GEX
10x Genomics
features.tsv.gz


title: 2_1_T

description:
Library name: 2_1_T
ENSG_as_rows_on_per_sample_basis


title: 2_2_L

description:
Library name: 2_2_L
ENSG_as_rows_on_per_sample_basis


title: 2w, Proximal, M, M4, Rep3

description: Library name: 10005CN27_E2

value: M


title: 2_2_B

description:
Library name: 2_2_B
ENSG_as_rows_on_per_sample_basis


title: 2w, Distal, M, M4, Rep1

description: Library name: 10005CN27_E1


title: 2_1_B

description:
Library name: 2_1_B
ENSG_as_rows_on_per_sample_basis


title: 2w, Middle, M, M4, Rep2

description: Library name: 10005CN27_D2


title: Batch1_Replicate_1_Hash

description:
Library name: Replicate_1_Hash
10x Genomics


title: 1_5_T

description:
Library name: 1_5_T
ENSG_as_rows_on_per_sample_basis


title: Batch1_Replicate_1_GEX

description:
Library name: Replicate_1_GEX
10x Genomics
features.tsv.gz


title: 1_9_S

description:
Library name: 1_9_S
ENSG_as_rows_on_per_sample_basis


title: 2w, Middle, M, M4, Rep1

description: Library name: 10005CN27_D1


title: 1_7_S

description:
Library name: 1_7_S
ENSG_as_rows_on_per_sample_basis


title: 2w, Middle, F, M5, Rep1

description: Library name: 10005CN29_C1


title: 1_6_S

description:
Library name: 1_6_S
ENSG_as_rows_on_per_sample_basis


title: mESC-CTCF_ChIP-exo_5.0_(SPRI_Beads)_rep1_028-111

description: Library name: mESC-CTCF ChIP-exo 5.0 (SPRI Beads)- Rep 1

value: Embryonic stem cells


title: mESC-CTCF_ChIP-exo_5.0_rep1_027-111

description: Library name: mESC-CTCF ChIP-exo 5.0 - Rep 1


title: 1_5_L

description:
Library name: 1_5_L
ENSG_as_rows_on_per_sample_basis


title: 2w, Proximal, M, M4, Rep2

description: Library name: 10005CN27_C2


title: 1_4_L

description:
Library name: 1_4_L
ENSG_as_rows_on_per_sample_basis


title: 6w, Distal, F, M7, Rep2

description: Library name: 10005CN24_E2


title: HEK293 untransfected, 18 h after transfection, rep 3

city: Bielefeld

first: Niklas

last: Kraemer

address: Alte Verler Strasse 1

institute: Sartorius Xell GmbH

description: Library name: NT3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence. The RNA-Seq data mapping was performed using the STAR mapper tool on the Galaxy web platform (Galaxy Version 2.7.10b+galaxy4) using default parameters..
Assembly: GRCh38, primary assembly, and evidence-based annotations of the human genome (GRCh38, GENCODE release 40, Ensembl release 106)
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

extract_protocol:
For total RNA isolation, 1E7 cells were harvested at 18 h after transient transfection and centrifuged at 800 x g and 4 °C for 7 min. The pellet was lysed in 1 mL of TRI Reagent (Zymo Research) followed by addition of 200 µL of chloroform. The mixture was vortexed for 15 s, incubated at room temperature for 3 min, and centrifuged at 12,000 x g at 4 °C for 15 min. To precipitate the RNA, isopropanol was added (1:1) and the tube was inverted 3 times. After an incubation of 10 min at room temperature, the mixture was centrifuged at 12,000 x g at 4 °C for 10 min. The RNA pellet was washed twice with ethanol (75%) and centrifuged at 7,500 x g at 4 °C for 5 min each time. The ethanol was discarded, and the pellet was dried for 10 min. The RNA was solubilized in 50 µL of RNase-free water. The concentration was determined using a NanoDrop One (Thermo Fisher Scientific). A 75 nt paired-end, stranded sequencing approach was performed on a NextSeq system (Illumina).
RNA libraries for RNA-seq were prepared using a TruSeq Stranded Total RNA kit (Illumina) following manufacturer's protocols.

value: untransfected


title: 1_5_B

description:
Library name: 1_5_B
ENSG_as_rows_on_per_sample_basis


title: 1_4_T

description:
Library name: 1_4_T
ENSG_as_rows_on_per_sample_basis


title: 1_4_B

description:
Library name: 1_4_B
ENSG_as_rows_on_per_sample_basis


title: 2w, Proximal, M, M4, Rep1

description: Library name: 10005CN27_C1


title: 6w, Distal, F, M7, Rep1

description: Library name: 10005CN24_E1


title: HEK293 untransfected, 18 h after transfection, rep 2

description: Library name: NT2


title: 1_2_T

description:
Library name: 1_2_T
ENSG_as_rows_on_per_sample_basis


title: 1_3_L

description:
Library name: 1_3_L
ENSG_as_rows_on_per_sample_basis


title: 1_2_L

description:
Library name: 1_2_L
ENSG_as_rows_on_per_sample_basis


title: HEK293 untransfected, 18 h after transfection, rep 1

description: Library name: NT1


title: HEK293 transfected, 18 h after transfection, rep 3

description: Library name: PM3

value: transfected


title: 6w, Middle, F, M7, Rep2

description: Library name: 10005CN24_D2


title: 1_3_B

description:
Library name: 1_3_B
ENSG_as_rows_on_per_sample_basis


title: HEK293 transfected, 18 h after transfection, rep 2

description: Library name: PM2


title: 1_1_L

description:
Library name: 1_1_L
ENSG_as_rows_on_per_sample_basis

value: lymph


title: 1_1_T

description:
Library name: 1_1_T
ENSG_as_rows_on_per_sample_basis


title: HEK293 transfected, 18 h after transfection, rep 1

description: Library name: PM1


title: 6w, Middle, F, M7, Rep1

description: Library name: 10005CN24_D1


title: 1_1_B

description:
Library name: 1_1_B
ENSG_as_rows_on_per_sample_basis

value: blood


title: 6w, Proximal, F, M7, Rep2

description: Library name: 10005CN24_C2


title: RNA-seq, MOC1-esc1 in vitro, sgNfrkb, IFNγ, Replicate 3

city: Cambridge

first: Robert

last: Manguso

state: MA

address: 415 Main Street

institute: Broad Institute

description: Library name: sgNfrkb_IFNg_Rep3

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Transcript counts were quantified by pseudoalignment of trimmed reads to mm10 using Kallisto (v0.46.0)
Gene counts were aggregated from transcript counts using the tximport (v1.24.0) R package
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample

source_name: HNSCC

growth_protocol: Mouse MOC1-esc1 cell line (sgCtrl and sgNfrkb) were cultured in IMDM/Hams-F12 (2:1) supplemented with 5% heat-inactivated FBS, 100 U/mL penicillin–streptomycin, 5 ng/mL EGF, 40 ng/mL hydrocortisone, and 5 mg/mL insulin.

extract_protocol:
Single-cell suspensions from cells cultured in a monolayer were homogenized in 600 μl RNA lysis buffer. RNA was extracted from homogenized samples using the RNA Miniprep Plus Kit in accordance with the manufacturer’s suggested protocol.
The library was constructed by Takara SMARTer Stranded Total RNA-Seq Kit v2

treatment_protocol: The MOC1-esc1 cell line were treated for 24h with either DMSO or 10ng/ml IFNγ. Cells were collected for RNA-seq after 24h treatment.

value: HNSCC

value: tumor cells

value: Known:TP53V170E; HRASQ61L; FAT1E2054D

value: IFNγ


title: RNA-seq, MOC1-esc1 in vitro, sgNfrkb, IFNγ, Replicate 2

description: Library name: sgNfrkb_IFNg_Rep2


title: HEK293 untransfected, 18 h after transfection, replicate 3

description: Library name: NT3


title: 6w, Proximal, F, M7, Rep1

description: Library name: 10005CN24_C1

value: Proximal colon

value: F


title: RNA-seq, MOC1-esc1 in vitro, sgNfrkb, IFNγ, Replicate 1

description: Library name: sgNfrkb_IFNg_Rep1


title: RNA-seq, MOC1-esc1 in vitro, sgNfrkb, DMSO, Replicate 3

description: Library name: sgNfrkb_DMSO_Rep3

value: DMSO


title: RNA-seq, MOC1-esc1 in vitro, sgNfrkb, DMSO, Replicate 2

description: Library name: sgNfrkb_DMSO_Rep2


title: RNA-seq, MOC1-esc1 in vitro, sgNfrkb, DMSO, Replicate 1

description: Library name: sgNfrkb_DMSO_Rep1


title: HEK293 untransfected, 18 h after transfection, replicate 1

description: Library name: NT1


title: 6w, Distal, F, M6, Rep1

description: Library name: 10005CN23_E1

source_name: Distal colon

value: Distal colon


title: Non-leukocyte kidney cells of low potassium diet

city: Shimotsuke

first: Takanori

last: Komada

state: Tochigi

address: 3311-1, Yakushiji

department: Center for Molecular Medicine

country: Japan

institute: Jichi Medical University

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw unique molecular identifier (UMI)-based data files were mapped against the mm10 reference genome and mapped reads were counted using the Cell Ranger package (10X Genomics) with default parameters.
The Seurat package in R was used to analyze the scRNA-seq data.
Clusters were detected using FindClusters and annotated based on the feature genes according to known mouse markers.
Differentially expressed genes (DEGs) were identified using FindAllMarkers.
Assembly: mm10
Supplementary files format and content: HDF5 file continaing a feature barcode matrix. This file can be loaded into R using Seurat.

source_name: Kidney

extract_protocol:
To obtain non-leukocyte kidney cells, whole kidneys of mice were minced and incubated within the collagenase P solution described in the flow cytometry section. The tissue chunks were further digested by pipetting and passing through thin syringe needles multiple times. After enriching the cells using the Percoll gradient method, cells were incubated with Hoechst33342 at 37 °C for 15 min and then labeled with PE/Cy7-conjugated anti-CD45 antibody. Hoechst33342+CD45–Sytox– cells, as live non-leukocytes, were sorted using FACSAria II (BD). Cells were resuspended in Cell Banker 1 (Zenogen Pharma, Koriyama, Japan) and stored at -80 °C until ready for the gel bead emulsion process. Samples with high viability were utilized, yielding either normal K+ (N) or low-K+ (L) (n=2 for each), and were processed using a dead cell removal kit (Miltenyi, Bergisch Gladbach, Germany). Cells were processed using the 10x Genomics Chromium controller and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following manufacturer's instructions. Each treatment group cell mixture (N or L, n=1 for each) was loaded, aiming for a targeted cell recovery of 6,000 cells.
The library was prepared using 10xGenomics's Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and dual index kit following manufacturer's instructions.  Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.  Sequencing was conducted by Azenta (Leipzig, Germany) using a NovaSeq 6000 (Illumina, San Diego, CA, USA).

treatment_protocol: Male C57BL/6J WT mice were fed a normal-K+ or low-K+ diet for 4 weeks (n=3 for each group).

value: Kidney

value: kidney cells

value: WT

value: Low potassium diet


title: 6w, Middle, F, M6, Rep2

description: Library name: 10005CN23_D2

source_name: Middle colon

value: Middle colon


title: 6w, Distal, F, M6, Rep2

description: Library name: 10005CN23_E2


title: Non-leukocyte kidney cells of normal potassium diet

description:
Library name: Sample 1
10x Genomics

value: Normal potassium diet


title: HEK293 transfected, 18 h after transfection, replicate 2

description: Library name: PM2

value: transfected


title: Infected_Mec_003

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description:
Library name: E77
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.

data_processing:
Illumina NovaSeq for sequencing
HISAT2 (v2.2.1) was used for indexing the reference genome
SAMTOOLS (v1.15.1) was used to sort and convert the sam files to bam files
stringtie(v.2.2.1) was used to calculate the raw read counts per gene
Normalisation and differential gene expression analysis was done using edgeR (genes with atleast 10 reads across replicates in any samples, were selected for each comparative analysis)
Assembly: Reference genome used : Mus Musculus (GRCm38, mm10) , accession number : NCBI:GCA_000001635.8
Supplementary files format and content: tab separated value .tsv files containing raw reads count and comparison of genes’ expression for sample pairs

source_name: Bone marrow-derived macrophages (BMDMs)

growth_protocol: Bone marrow derived macrophages (BMDMs) were cultured in DMEM medium supplemented with 10% FBS, 2mM L-Glutamine, 1mM sodium pyruvate, 10mM HEPES buffer and 30ng/ul macrophage colony stimulating factor (MCSF) for 6 days.

extract_protocol:
Total RNA was extracted from macrophages and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for 10 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina NovaSeq6000 sequencer using the paired end sequencing format.

treatment_protocol: MCSF differentiated bone marrow-derived macrophages (BMDMs)  were infected with log phase culture of Mycobacterium tuberculosis H37Rv expressing the biosensor Mrx1-roGFP2 at moi 10. After 3 hours, extracellular bacteria were removed by washing thrice with pre-warmed DPBS. Infected cells were incubated for 24 hours at 37 degrees Celcius in 5% CO2 treated either with 20uM meclizne or solvent control (0.2% DMSO). At 24 hours post-infection, infected macrophages were flow sorted using BD FACS Aria where infected cells were defined as those showing GFP positive signal.

value: Bone marrow-derived macrophages (BMDMs)

value: Treated with 20uM Meclizine


title: Infected_Mec_001

description:
Library name: E75
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: Infected_Mec_002

description:
Library name: E76
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: 1_2_B

description:
Library name: 1_2_B
ENSG_as_rows_on_per_sample_basis

value: blood

value: Vehicle


title: HEK293 transfected, 18 h after transfection, replicate 1

description: Library name: PM1


title: 6w, Middle, F, M6, Rep1

description: Library name: 10005CN23_D1


title: Infected_DMSO_003

description:
Library name: E65
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.

value: Treated with solvent control (0.2% DMSO)


title: 6w, Proximal, F, M6, Rep2

description: Library name: 10005CN23_C2

source_name: Proximal colon


title: HEK293 untransfected, 18 h after transfection, replicate 2

description: Library name: NT2

value: untransfected


title: Infected_DMSO_002

description:
Library name: E64
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: Infected_DMSO_001

description:
Library name: E63
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: 6w, Proximal, F, M6, Rep1

description: Library name: 10005CN23_C1

value: Proximal colon


title: Tg(myl7:ATF3), 12mpf, rep3

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

description:
Library name: Tg12mpf_S3
QuantSeq

data_processing:
Raw Quant-seq reads were quality-filtered and trimmed to remove adapter sequences and low-quality bases using Trim Galore. The processed reads were then aligned to the GRCz11.108 reference genome using STAR. Transcript assembly, abundance estimation, and differential gene expression analysis were performed using RSEM. Feature counting was conducted to obtain FPKM values, and differential expression analysis was carried out using DESeq2.
Assembly: GRCz11.108.ensembl
Supplementary files format and content: xlsx, expression table

organism: Danio rerio

source_name: Cardiac tissue

extract_protocol:
Total RNA was extracted from zebrafish cardiac tissue using TRIzol reagent (Invitrogen), followed by purification with the Direct-zol RNA MiniPrep Kit (Zymo Research) according to the manufacturer's instructions.
RNA-seq libraries were generated using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the manufacturer's instructions. Briefly, library preparation was initiated by oligo-dT priming for first-strand synthesis without prior poly(A) enrichment or rRNA depletion. After RNA template removal, second-strand synthesis was carried out using random priming. Illumina-specific adapter sequences and external barcodes were introduced during library amplification. The resulting strand-specific libraries, corresponding to the sense strand of the original RNA, were sequenced as 75 bp single-end reads on an Illumina NextSeq 500.

value: Cardiac tissue


title: Tg(myl7:ATF3), 12mpf, rep2

description:
Library name: Tg12mpf_S2
QuantSeq


title: RRBS of mouse fat tissue under high fat diet

city: Atlanta

first: Jia

last: Jing

state: GA

address: Decatur St. SE

department: Biology

institute: Georgia State University

description: Library name: FAT-H-1

data_processing:
The RRBS data analysis including Differentially Methylated Regions (DMRs), methylation rate and pathway analysis were conducted by BGI Bioinformatics Center. The methylation level at each CpG site was determined based on the number of sequences containing methylated CpGs versus the total number of sequences analyzed. For the comparison of DNA methylation rate differences between the HFD- and LFD-fed mice, data were summarized based on genomic features to generate tag density plots around transcription start and termination sites, exon-intron boundaries, CpG islands, and repeat elements and the data were uploaded to University of California Santa Cruz (UCSC) Genome Browser on Mouse (NCBI37/mm9). For RNA-seq, firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. Then we map those clean reads onto reference genome(mm10), followed with novel gene prediction, SNP & INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
Assembly: mm10

source_name: epididymal adipose tissue

extract_protocol:
For RRBS, genomic DNA from the mouse epididymal white fat was extracted by the phenol-chloroform method and commercially sequenced by Beijing Genomics Institute (BGI) (Shenzhen, China). According to the instruction provided by the company, the genomic DNA was digested with the methylation-insensitive restriction enzyme MspI, ligated to sequencing adaptors, treated with sodium bisulfite, PCR-amplified for library construction and sequenced. For RNA-seq,  white fat pad were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using BGISEQ-500.

value: epididymal adipose tissue

value: high fat diet


title: mNPC, Kmt2a KO, H3K4me1, rep4

city: Reykjavik

first: Tinna

last: Reynisdottir

state: Ísland

address: Sturlugata 8

country: Iceland

institute: University Of Iceland

data_processing:
Fastq sample files were aligned to the mouse mm10 genome using Bowtie2 (version 2.4.4)
For vizulising H3K4me1 peaks in UCSC, bam files for all samples for each genotype were merged with SAMtools. They were then converted to bigwig files with deepTools (version 3.5.1) and normalized to 1x mouse genome with --normalizeUsing RPGC .
Peaks were called for merged genotypes against the merged IgG samples for each genotype using MACS3 (version 3.0.0)
Differential peak analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: bigWig file for each sample
Library strategy: CUT&Run

source_name: Neuronal progenitor cells

extract_protocol:
CUT&RUN was performed according to CUTANA™ CUT&RUN Protocol (v.1.7 EpiCypher) from 160.000 cells per sample
Library preparation was done using TruSeq RNA CD Index plate (Illumina, 20019792).

value: Neuronal progenitor cells

tag: cut&run antibody

value: H3K4me1, Abcam, ab8895


title: Tg(myl7:ATF3), 12mpf, rep1

description:
Library name: Tg12mpf_S1
QuantSeq


title: HEK293 transfected, 18 h after transfection, replicate 3

description: Library name: PM3


title: RRBS of mouse fat tissue under low fat diet

description: Library name: FAT-C-1

value: low fat diet


title: Reduced 3

description:
Library name: reduced3
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.

data_processing:
fastp (0.20.1) for quality control (trimming and adapter removal, q>=36)
STAR (2.7.3a) was used for indexing the reference genome (Hg38) and aligning the reads
SAMTOOLS (0.1.13) was used to filter out multiply mapped reads
HTSeq (2.0.8) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using DESeq2
Assembly: Reference genome used : Mus Musculus (GRCm38, mm10) , accession number : NCBI:GCA_000001635.8
Supplementary files format and content: tab separated value .tsv files containing raw reads count (raw_counts.tsv) and comparison of genes’ expression for sample pairs

treatment_protocol: MCSF differentiated bone marrow-derived macrophages (BMDMs)  were infected with log phase culture of Mycobacterium tuberculosis H37Rv expressing biosensor Mrx1-roGFP2 at moi 10. After 3 hours, extracellular bacteria were removed by washing thrice with pre-warmed DPBS. Infected cells were incubated for 24 hours at 37 degrees Celcius in 5% CO2. At 24 hours post-infection, infected macrophages were flow sorted using BD FACS Aria into three bins (based on the Mrx1-roGFP2 excitation ratio read-out) viz. macrophages harboring EMSH-reduced (mycothiol redox potential around -300 mV) and those harboring EMSH-oxidized (mycothiol redox potential around -240 mV). For uninfected control, macrophages were cultured parallely and were mock sorted through the flow sorter without infection.

value: BMDMs infected with Mtb showing EMSH in the reduced range.


title: mNPC, wild-type, IgG, rep1

value: IgG, EpiCypher, 23613-0042


title: Control, 12mpf, rep3

description:
Library name: Con12mpf_S3
QuantSeq

value: wild type


title: Control, 12mpf, rep2

description:
Library name: Con12mpf_S2
QuantSeq


title: mNPC, wild-type, H3K4me1, rep3


title: Reduced 1

description:
Library name: reduced1
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: mNPC, nestin cre wt, H3K4me1, rep4

value: nes-cre+/-


title: NB4, ATRA TREATED, REP2

city: Stockholm

first: Sören

last: Lehmann

address: Blickagången 16

department: the Department of Medicine

institute: Karolinska Institute

description:
Library name: NB4_ATRA_2
other

data_processing:
The bulk RNA-seq data was processed by the nf-core rnaseq pipeline (v1.4.2). In detail, the raw sequencing data were processed by the analysis pipeline nfcore rnaseq 1.4.2. It used FastQC (v0.11.8) and MultiQC (v1.7) for quality control; Trim Galore!(v0.6.4) for adapter trimming; STAR (vSTAR_2.6.1d)  for mapping reads to the human reference genome hg19; featureCounts (v1.6.4)  gene level quantification. The human reference genome annotation GENCODEv39 (gencode.v39lift37.annotation.gtf) was used for gene expression quantification. Differential expression analysis was implemented by DESeq2.
Assembly: hg19
Supplementary files format and content: NB4_ATRA_72hr_RNAseq.csv, raw read count.

source_name: Hematopoietic system

growth_protocol: NB4 cell line was cultivated with RPMI (Thermo Fisher Scientific CAT# 11554526), Fetal Bovine Serum 10% (Fisher Scientific CAT# 11550356) and PenStrep (Gibco CAT# 15140-122), at 37°C, CO2 5% and 95% of humidity.

extract_protocol:
Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina Nextseq 2000 P2 100 cycles kit sequencing run, generating 58 base paired end reads with dual index 10+10 base pairs. Basecalling and demultiplexing was performed using bcl2fastq (v2.20.0) software with default settings generating Fastq files for further downstream mapping and analysis.
Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina Nextseq 2000 P2 100 cycles kit sequencing run, generating 58 base paired end reads with dual index 10+10 base pairs. Basecalling and demultiplexing was performed using bcl2fastq (v2.20.0) software with default settings generating Fastq files for further downstream mapping and analysis.

treatment_protocol: Treatment of NB4 cells for 72 hs with DMSO 0,01 % as control (Sigma-Aldrich CAT# D8418), ATRA 1uM (Sigma-Aldrich CAT# R2625-50MG). Reagent used for measure viability was CellTiter-Glo® 2.0 (Promega CAT# G9243). Values measured with CLARIO STAR Luminescence equipment.

value: Hematopoietic system

value: Promyelocytic leukemia cells

value: carry the t(15;17) PML-RARA fusion gene

value: all-trans retinoic acid (ATRA)


title: NB4, ATRA TREATED, REP3

description:
Library name: NB4_ATRA_3
other


title: Oxidized 3

description:
Library name: oxidized3
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.

value: Bone marrow-derived macrophages (BMDMs)

value: BMDMs infected with Mtb showing mycothiol redox ptential  (EMSH) in the oxidized range.


title: NB4, ATRA TREATED, REP1

description:
Library name: NB4_ATRA_1
other


title: NB4, UNTREATED, REP3

description:
Library name: NB4_UN_3
other


title: Oxidized 2

description:
Library name: oxidized2
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: Tg(myl7:ATF3), 4mpf, rep3

description:
Library name: Tg4mpf_S3
QuantSeq


title: mNPC, nestin cre wt, IgG, rep3


title: mNPC, nestin cre wt, H3K4me1, rep3


title: Tg(myl7:ATF3), 4mpf, rep2

description:
Library name: Tg4mpf_S2
QuantSeq


title: Oxidized 1

description:
Library name: oxidized1
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: NB4, UNTREATED, REP2

description:
Library name: NB4_UN_2
other


title: mNPC, Kmt2a KO, H3K4me1, rep3


title: Bystander 3

description:
Library name: bystander3
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.

value: BMDMs growing in the same milieu as infected macrophages but did not get infected with Mtb.


title: Tg(myl7:ATF3), 4mpf, rep1

description:
Library name: Tg4mpf_S1
QuantSeq

value: Cardiac tissue


title: NB4, UNTREATED, REP1

description:
Library name: NB4_UN_1
other


title: Bystander 2

description:
Library name: bystander2
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: Control, 4mpf, rep3

description:
Library name: Con4mpf_S3
QuantSeq


title: PBMCs from human control replicate3

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

description: Library name: Human_UT_3

data_processing:
To ensure high data quality, Trim Galore was used in paired-end mode to remove low-quality base pairs and adaptor sequences from the libraries. Subsequently, sequencing reads were aligned to their respective reference genomes using the STAR aligner.
Assembly: GCF_000001405.40_GRCh38, GCF_000001635.27_GRCm39, ASM359739v1 and rGopEvg1_v1.p, ASM1834038v1, and bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Tab-separated count matrix

source_name: PBMC

extract_protocol:
RNA harvested using Rneasy mini plus kit (Qiagen) was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit

value: PBMC

value: PBMCs from human control


title: Reduced 2

description:
Library name: reduced2
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: Bystander 1

description:
Library name: bystander1
BMDMs infected with Mtb H37Rv exprerssing the Mrx1-roGFP2 biosensor.


title: Control, 4mpf, rep2

description:
Library name: Con4mpf_S2
QuantSeq


title: mNPC, Kmt2a KO, H3K4me1, rep2

value: Neuronal progenitor cells


title: mNPC, wild-type, H3K4me1, rep2

value: H3K4me1, Abcam, ab8895


title: Control, 4mpf, rep1

description:
Library name: Con4mpf_S1
QuantSeq


title: Control, 12mpf, rep1

description:
Library name: Con12mpf_S1
QuantSeq


title: Uninfected 3

description:
Library name: uninfected3
Mock-sorted uninfected BMDMs

value: BMDMs never infected or exposed to Mtb.


title: mNPC, nestin cre Kmt2a KO, H3K4me1, rep4


title: Uninfected 2

description:
Library name: uninfected2
Mock-sorted uninfected BMDMs


title: PBMCs from human control replicate1

description: Library name: Human_UT_1