title: KCN2

city: New York

first: Maya

middle: Stella

last: Dixon

state: NY

address: 1130 St Nicholas Ave, ICRC Floor 5 Rm 505

institute: Columbia University

description: Library name: CS004

data_processing:
Raw sequencing reads were aligned to the mouse reference genome mm39 and processed into a matrix of unique molecular identifiers (UMIs) per cell barcode and gene using Cell Ranger v5.0.0 (10x Genomics). The resulting files were analyzed with the R v4.3.3 package "Seurat v5.0.3"48. Low-quality cells (defined as those with nCount_RNA < 800, nFeature_RNA < 500, or percent.mt > 10) were excluded. Data from all samples were merged and normalized using the “SCTransform”49 method for variance stabilization. Principal component analysis (PCA) was performed with the “RunPCA” function, followed by clustering using the “FindNeighbors” and “FindClusters” functions. Clusters were visualized with dimensional reduction using the “UMAP” method.
Assembly: mm39
Supplementary files format and content: Processed data is the differentially expresssed genes in the clustering. The file format is csv

source_name: Pancreas

extract_protocol:
Harvested pancreata were rinsed with PBS, minced into 1 mm³ pieces on ice, and transferred to a 20 mL digestion buffer containingCollagenase P (20 mg, Roche, 11213857001), DNase I (200uL 10mg/mL, Roche 10104159001), Fetal Bovine Serum (400 µL), and Rho Kinase inhibitor (Y-27632) (20 µL, Cayman Chemicals,  10005583). The mixture was incubated for 75 minutes at 37°C with continuous rotation. Samples were then passed through a 70 μm cell strainer (Cell Treat,  229483), and the tube was rinsed with 20 mL of ice-cold PBS. Following centrifugation at 700 rpm for 5 minutes at 4°C, the pellet was resuspended in 1 mL of PBS containing 20 mM HEPES, 2 mM EDTA, 5mM MgCl2, 1% FBS, 50ug/mL DNase I, and Rho Kinase inhibitor (Y-27632). Cells were stained with DAPI, and viable cells were sorted using the BC Influx cell sorter. The viability of the cell samples was confirmed to be greater than 80%, and the cells were resuspended in PBS containing 10% FBS at a concentration of 1,000 cells/µL. The resulting single-cell suspension was used for scRNA-seq.
We aimed to profile 10,000 cells per library. All libraries were sequenced on the NovaSeq6000 (Illumina, San Diego, California, USA) or DNBSEQ-G400 (MGI Tech, Shenzhen, China)

value: Pancreas

value: Tissue

value: Acinar and ductal cells

value: Pdx1-Cre; Kras+/LSL-G12D; Nrf2flox/flox


title: TMD8,C, rep2

status: Public on May 17 2025

type: SRA

city: Xiamen

first: jiazhen

last: lin

state: Fujian

address: No. 2000 of Xiang an East road

country: China

institute: Xiamen uniersity

description: Library name: C2 FPKM

library_source: transcriptomic

data_processing:
3.RNAseq analysis method
3.1 Data filtering
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
3.2 RNA identification
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
3.3 Gene Quantification Differential Expression Analysis
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
3.4 Gene Annotation
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: hg38
Supplementary files format and content: processed data excel file include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoma tissue

growth_protocol: The incubator condition was set at 37℃ with 5% CO2. TMD8 cell line was cultured in RPMI-1640 (Hyclone, Thermo Scientific, Logan, UT, USA) adding 10% fetal bovine serum (Gibco, Thermo Scientific, Grand Island, NY, USA).

extract_protocol:
1.1 Cell Sample Lysis
Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells).
1.2 Sample Purification
1.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃.
1.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking；
1.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity).
1.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h.
1.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting.
1.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。
1.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min.
1.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
2.mRNA Library Preparation
2.1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2.2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
2.3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
2.4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
2.5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
2.6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
2.7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
2.8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
2.9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: TMD8 cells were treated with 375nM chidamide, 1µM anlotinib, or 375nM chidamide combined with 1µM anlotinib for 24h, and then first lysed with TRIzol reagent (Invitrogen, NY, USA) and further extracted following the manufacturer's guidelines.

tag: tissue

value: Lymphoma tissue

tag: cell line

tag: cell type

value: Lymphoma cell line

tag: genotype

value: double-hit lymphoma with TP53 mutation

tag: treatment

value: Chidamide

tag: batch


title: Cholinergic neuron-GBM co-culture conditions

city: Philadelphia

first: Yusha

last: Sun

state: PA

address: 415 Curie Boulevard, Clinical Research Building, Room 105

country: USA

institute: University of Pennsylvania Perelman School of Medicine

description:
Library name: Cholinergic-GBM
in-house modified Smart-seq3

library_source: transcriptomic single cell

data_processing:
To process single-cell RNA sequencing data, raw files were demultiplexed with bcl2fastq (Illumina) without adapter trimming and with the option for --create-fastq-for-index-reads. A combined fastq file consisting of a 22-bp cell barcode (composed of 8-bp index 1, 8-bp index 2, and 6-bp barcode) was then generated. Alignment was performed using STARsolo as part of STAR v2.7.10b with GRCh38 as the reference genome and gencode v.41 GTF as the annotation file, and with the following additional parameters: --alignIntronMax 1000000 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --limitOutSJcollapsed 4000000 --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 22 --soloUMIstart 23 --soloUMIlen 8 --soloBarcodeMate 1  --clip5pNbases 30  --soloCBmatchWLtype 1MM_multi  --soloCellFilter EmptyDrops_CR  --soloStrand Reverse. A cell barcode text file was supplied, and multimapping alignments were discarded.
Note that the raw fastq.gz files are structured where the first 22 base pairs are the cell barcode, then the next 8 base pairs the UMI.
Assembly: hg38
Supplementary files format and content: Tab-separated value files, matrix files, and samplesheet csv files with barcode whitelist

molecule: polyA RNA

source_name: human glioblastoma & human iPSC-derived neuron

extract_protocol:
For scRNAseq experiments, at a cholinergic neuron (CW50065) age of 3 weeks in vitro, UP-10072 GBM cells were seeded into plates at a 1:20 tumor cell to neuron ratio for 6 days prior to dissociation for sequencing. We employed four separate conditions: 1) GBM-neuron co-culture, 2) GBM with neuronal conditioned media, 3) GBM cells alone, and 4) neurons alone. For the conditioned media condition, media collected from cholinergic neuron culture from the previous week was used to culture tumor cells alone for the period of 6 days. For all conditions, cells were dissociated via a previously published protocol (dx.doi.org/10.17504/protocols.io.bh32j8qe) from n = 4 distinct coverslips. Cell viability and cell concentration were measured with an automated cell counter (Thermo Fisher Scientific, Countess 3 Automated Cell Counter) with trypan blue staining (Thermo Fisher Scientific, C10312). An ideal cell viability following dissociation is typically > 80%. Cells were then resuspended in FACS pre-sort buffer (BD, 563503) with 0.2 μg/mL DAPI (BD, 564907). Single cells were sorted on a BD Influx (100 μm nozzle) with FACSDiva software into low-profile 96-well PCR plates (USA Scientific, 1402-9500) containing 3 μL of SMART-seq3 lysis buffer (0.5 μL PEG 8000 (40% solution, Sigma Aldrich, P1458), 0.03 μL Triton X-100 (10% solution), 0.02 μL of 100 μM Oligo-dT30VN, 0.2 μL of 10 mM dNTPs (Roche, 50-196-5273), 0.02 μL Protector RNase inhibitor (Sigma Aldrich, 3335402001), 0.02 μL recombinant RNase inhibitor (Takara, 2313B) and 2.21 μL nuclease-free water per reaction (Thermo Fisher Scientific, AM9932)) and 3 μL Vapor-Lock (Qiagen, 981611). Plates after sorting were briefly centrifuged, frozen on dry ice, and stored at -80°C for later processing.
For library preparation, plates were thawed, heated to 72°C for 10 minutes, and subsequently kept at 4°C for cell lysis. 3 μL of RT mix, containing 0.1 μL of 1 M Tris-HCl pH 8.3 (Hampton Research, HR2-900-14), 0.024 μL of 5 M NaCl (Thermo Fisher Scientific, AM9759), 0.01 μL of 1 M MgCl2 (Thermo Fisher Scientific, AM9530G), 0.04 μL of 1 mM GTP (Thermo Fisher Scientific, R1461), 0.32 μL of 100 mM DTT (Millipore Sigma, 3483-12-3), 0.016 μL of nuclease-free water, 0.025 μL Protector RNase inhibitor (Millipore Sigma, C852A14), 0.025 μL recombinant RNase inhibitor (Takara, 2313B), 0.04 μL reverse transcriptase (Thermo Fisher Scientific, EP0753), and 0.4 μL of 20 μM TSO, was added to each well of the 96-well plate. To enable multiplexing and enhance throughput, we designed 48 unique TSOs consisting of an additional 6-bp cell barcode directly adjacent to the 5’-end of the Smart-seq3 UMI. Reverse transcription was performed with the following thermocycling conditions: 42°C for 90 minutes, 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes, 85°C for 5 minutes, and 4°C indefinitely. Next, for cDNA amplification, 6 μL of PCR mix, consisting of 2 μL 5X KAPA HiFi HotStart Buffer (Roche, KK2502), 0.3 μL of 10 mM dNTPs, 0.005 μL of 1 M MgCl2, 0.01 μL of 1mM PCR forward primer, 0.01 μL of 100 μM PCR reverse primer, 3.475 μL of nuclease-free water, and 0.2 μL of KAPA HiFi HotStart polymerase (Roche, KK2502), was added to each well. cDNA amplification was performed with the following thermocycling conditions: 98°C for 3 minutes, 18 cycles of 98°C for 20 seconds then 65°C for 30 seconds then 72°C for 4 minutes, 72°C for 5 minutes, and 4°C indefinitely. cDNA from 48 wells was then pooled together into one sample (2 samples per plate), and samples were then purified twice with 0.6X then 0.8X AMPure XP beads (Thermo Fisher Scientific, A63881) and eluted in 10 μL of nuclease-free water. cDNA was quantified using Qubit dsDNA HS assay kit (Life Technologies, Q32851). Each sample was then tagmented by mixing 2 μL of 0.5 ng/μL cDNA, 4 μL of 2X TD buffer (20 mM Tris pH 8.0, 10 mM MgCl2, 20% dimethylformamide (Sigma, D4551)), and 2 μL of Tn5 (Thermo Fisher Scientific, TNP92110) and incubating at 55°C for 20 minutes with reaction termination upon addition of 2 μL of 0.2% SDS (Invitrogen, 15553-035) at room temperature for 5 minutes. We chose to use i5-only Tn5 to enrich for the 5’-ends of mRNA, although full-length sequencing can be achieved using i5/i7 Tn5. Fragments were amplified by adding 1 μL of 10 μM Nextera i7 primer, 1 μL 10 μM Nextera i5 primer, 5 μL of 5X Phusion Plus Buffer (Thermo Fisher Scientific, F630L), 0.5 μL of 10 mM dNTPs, 0.5 μL of 1% Tween-20, 6.8 μL nuclease-free water, and 0.2 μL of Phusion Plus polymerase (Thermo Fisher Scientific, F630L). Tagmentation PCR was performed with the following thermocycling conditions: 98°C for 3 minutes, 8 cycles of 98°C for 10 seconds then 60°C for 30 seconds then 72°C for seconds, 72°C for 5 minutes, and then indefinitely at 4°C. Resulting DNA was purified twice with 0.8X then 1.0X AMPure XP beads and eluted in 10 μL of 10 mM Tris, pH 8.0. Samples were then quantified by qPCR with library sizes quantified by Bioanalyzer (Agilent). Samples were sequenced on either a NovaSeq 6000 (Illumina) or NextSeq 550 (Illumina) at a final depth of roughly 100K-200K reads/cell.

value: malignant (GBM) & nonmalignant (neuron)


title: CHRUPOST

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

data_processing:
Reads underwent quality check with FastQC (v0.11.9); Kallisto (v0.46.1) was used to map reads to the human reference genome (HomoSapien GRCh38) and to generate transcript counts.
Assembly: HomoSapien GRCh38
Supplementary files format and content: 3col.tsv- Long format of aligned raw gene counts
Supplementary files format and content: GeneCounts_ RAW DATA.xlsx- Wide format of aligned raw gene counts

source_name: Skeletal Muscle

extract_protocol:
RNA was extracted using AllPrep RNA/RNA/miRNA universal kit (Qiagen) according to manufacturer instructions
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol

treatment_protocol: 27 Pre-menopausal, untrained females (aged 23.5 ± 4.8) underwent a 12-week resistance training program. Skeletal muscle biopsies were collected before (PRE) and after (POST) the training program to quantify the effect of resistance training on the transcriptome

value: vastus lateralis muscle

value: Skeletal Muscle

tag: Sex

value: Female

tag: age of_donor

value: POST


title: Cortical neurons, mir-92a, 5d, biol rep 2

city: Berlin

first: Seija

last: Lehnardt

state: Berlin

address: Charitéplatz 1

department: Institute of Cell Biology and Neurobiology, and Department of Neurology

country: Germany

institute: Charité – Universitätsmedizin Berlin

data_processing:
Bulk RNA-seq reads were mapped to the mouse genome (GRCm38) with STAR version-2.7.3a
Reads were assigned to genes using FeatureCounts SUBREAD version-v2.0.0 with the following parameters: -t exon -g gene_id -s 2
Assembly: GRCm38, version M12 (Ensembl 87)
Supplementary files format and content: tab-delimited file includes raw counts for each Sample

organism: Mus musculus

source_name: cortical neurons

growth_protocol: Cortical neurons were maintained in Neurobasal medium supplemented with 2% B27 supplement, 1% L-Glutamine and antibiotics in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA kit according to manufacturer’s instructions.

value: cortical neurons

value: WT

value: miRNA incubation

tag: time

value: 5 d

tag: experiment batch


title: TMD8,C, rep1

description: Library name: C1 FPKM


title: KC2

description: Library name: CS002

value: Pancreas

value: Kras+/LSL-G12D, Pdx1-Cre


title: Cortical neurons, mir-92a, 5d, biol rep 1


title: CHRUPRE

value: PRE


title: Cortical neurons, mir-124, 5d, biol rep 4


title: TMD8,A, rep3

description: Library name: A3 FPKM

value: Anlotinib


title: TMD8,D, rep2

description: Library name: D2 FPKM

value: Lymphoma tissue

value: Chidamide combined with anlotinib


title: CHMAPOST


title: Gmppb-KO C2C12 cells_3

city: shanghai

first: Ziwei

last: fu

address: Road Dongan 130

institute: fudan universidy

data_processing:
FastQC was used to filter out adapter and low-quality reads and Hisat2 was used  to aligned high-quality reads to mouse genome (mm10) .
Expression level of each gene was with default normalized by subread with featureCounts methods
Then we used SVA to remove confounder factors across all samples, and calculated differential expression genes between each two treatments using DESeq2.
Assembly: mm10
Supplementary files format and content: Processed data file is the gene expression profile as xlsx format. The expression value was processed as Count for subsequent analysis.

source_name: skeletal muscle

growth_protocol: C2C12 cell lines were purchased from the American Type Culture Collection (ATCC). To knock out Gmppb in C2C12 cells, we transfected C2C12 cells with CRISPR plasmids PX458-GFP and PX459-puromycine with two sgRNA. Two pairs of sgRNAs are designed to target exons 1 and 5 of Gmppb gene: exon 1 (F: 5’-CACCGAGCACTCCGAAGCCATTGG-3’; R: 5’-AAACCCAATGGCTTCGGAGTGCTC-3’); exon5 (F: 5’- CACCGAGAGCCTTCCAAGTATGGTG-3’; R: 5’- AAACCACCATACTTGGAAGGCTCTC-3’).We tested transfection efficiency through PX458 plasmids with GFP. At 48 h after transfection, the cells were diluted and cultured with puromycine (4 μg/ml) for a two-day resistance screening. The clones were then diluted to a 96-well plate to expand the culture. Finally, expanded monoclonal cells were confirmed by PCR sequencing. The efficacy of guide RNA was determined by western blotting.

extract_protocol:
1ml Trizol was added to a 10cm dish and left to stand for 10min, the cell lysate was collected and then placed in liquid nitrogen for quick freezing.. Samples were sent on dry ice to Novogene Technology Co., Ltd for immediate downstream RNA sequencing. In brief, following RNA isolation with Trizol (catalog #, check with Novogene), a total amount of 2 μg RNA per sample was used as input material for library preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences.

treatment_protocol: Wild-type and Gmppb-KO C2C12 cells were cultured for 2 days

value: skeletal muscle

value: muscle cells

value: Gmppb mutant

value: Gmppb knockout with CRISPR/Cas9


title: TMD8,A, rep2

description: Library name: A2 FPKM

value: Lymphoma cell line

value: double-hit lymphoma with TP53 mutation


title: Cortical neurons, mir-124, 5d, biol rep 3


title: TMD8,A, rep1

description: Library name: A1 FPKM


title: Cortical neurons, mir-124, 5d, biol rep 2


title: KC1

description: Library name: CS001

value: Tissue

value: Acinar and ductal cells


title: BRSTPRE

value: vastus lateralis muscle

value: Skeletal Muscle

value: Female


title: Old_Female_1_DAT

city: Oklahoma City

first: Ana Luiza

last: Drumond-Bock

state: OK

address: 825 NE 13th St.

department: Aging & Metabolism Research Program

institute: Oklahoma Medical Research Foundation

description:
Library name: Old_Female_1_DAT
DAT_NuTRAP.csv, column_J

data_processing:
Using a high-performance computing (HPC) cluster, fastq files were submitted to pre-alignment quality control (QC) analysis (Ewels et al., 2016), after which adaptors were removed and reads were trimmed for poly-G and Q<20 (Krueger et al., 2023).
Reads were aligned to the mouse genome assembly mm39 using STAR v2.7.10b (Dobin, 2022; Dobin et al., 2013) and quantification was performed using featureCounts (Liao et al., 2014), and post alignment QC reports generated.
Assembly: Mus_musculus.GRCm39.111
Supplementary files format and content: Raw feature counts

source_name: Brain

growth_protocol: Experimental mice were aged naturally within our colony.

extract_protocol:
Mice were anesthetized with isoflurane and rapidly decapitated. To minimize activity induced transcriptomic changes, the brain was immediately removed and placed in ice-cold choline chloride cutting solution. 600 µm-thick horizontal brain slices were collected, accounting for the entire rostral-caudal length of the ventral midbrain. Sections were moved onto a pre-chilled collection block, where the surrounding tissue (such as the pons, hippocampus, and cortex) was removed. Remaining bilateral midbrain portions (containing the substantia nigra pars compacta [SNc] and the ventral tegmental area [VTA]) were collected into Eppendorf tubes and flash-frozen for RNA preservation. All samples were stored in -80oC freezer until the time of TRAP and mRNA isolation. midbrain slices were placed in 200 µl of ice-cold homogenization buffer (50mM Tris, pH 7.4; 12mM MgCl2; 100mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1mM DTT) supplemented with 100 μg/mL cycloheximide (Millipore, cat# C4859–1ML), 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor (ThermoFisher, cat# 10777019), and 1× cOmplete, EDTA-free Protease Inhibitor Cocktail (Milipore, cat# 11836170001). Homogenization used a cordless motor pestle (Kimble #749520-0090 and #749540). After initial homogenization, an additional 500 µl of buffer was added to the samples, washing the pestle in between pulses. Homogenate solution volume was then brought to a total of 1.5 ml and centrifuged at 12,000 g for 10 min at 4oC. After centrifugation, 100 µl of the supernatant was removed and set aside on ice (“input fraction”). The remaining supernatant (~900 µl of “positive fraction”) was transferred into a fresh tube and incubated with 1 µl anti-GFP antibody (Abcam, cat# ab290). Both input and positive samples were placed in an end-over-end rotating mixer and incubated for 1 h at 4oC. Pre-washed Dynabeads protein G (Invitrogen, cat# 10003D; 30 µl per sample) were then added to the positive fraction and the final solution incubated overnight (~16 h) in a rotating mixer at 4oC. Positive tubes were then placed in a DynaMag-2 magnet and supernatant removed and saved as the “negative fraction”. The magnetic beads bound with GFP-labelled polyribosomes/mRNAs, were washed with high-salt buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100 μg/ml cycloheximide; 2mMDTT) three times. After the final wash, Dynabeads were separated from the GFP-labelled polyribosomes/mRNAs by adding 350 µl of Buffer RLT (Qiagen) and 3.5 µl of 2-β mercaptoethanol, proceeding with incubation in a benchtop ThermoMixer (Eppendorf) for 10 min at 22oC. The eluted solution (“positive fraction”), free of magnetic beads, was placed in a fresh tube. mRNA isolation was carried out using RNeasy Mini kit (#74104, QIAGEN), following manufacturer’s suggested protocol. Isolated mRNA was then quantified with a Nanodrop spectrophotometer (ThermoFisher, model# ND-ONEC-W) and its quality measured in a 4150 Tapestation analyzer (Agilent, model# G2992AA) using HSRNA ScreenTape (Agilent, cat# 5067-5579).
Directional mRNA libraries were prepared using NEBNext Ultra II Kit for Illumina (NEB, cat# E7760L) in accordance to the manufacturer’s directions, and following previously established protocol (Chucair-Elliott et al., 2020; Ocanas et al., 2022). In summary, each sample of both positive and input fractions (ranging 3.5-35 ng of mRNA) were individually captured by poly-A RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat# NEBE7490L). mRNA was then eluted from oligo-dT beads, fragmented using a thermal cycler at 94°C for 15 min, and first and second strands of cDNA were individually synthesized following manufacturer’s guidance (NEB, cat# E7760L). The final double-stranded cDNA was purified with the use of SPRISelect Beads (Beckman Coulter, cat# B23318) and eluted in 50 µl 0.1x TE buffer. Next, adaptor ligation was performed using 100-fold dilution of the NEBNext adaptor in dilution buffer (NEB, cat# E6609L), and PCR of the ligated products was conducted using the NEBNext Ultra II Q5 Master Mix (NEB, cat#7760L) and unique index primers (NEB, cat# E6609L), both provided with aforementioned kits, in accordance to manufacture’s protocol (14 cycles). Purified libraries were then quantified using HS dsDNA Qubit kit (ThermoFisher, cat# Q33230). Library integrity, verified in a 4150 Tapestation analyzer (Agilent, model# G2992AA) using HS D1000 ScreenTape (Agilent, cat# 5067-5584), revealed an average peak size of 332bp. Libraries for each sample were then pooled at 5 nM concentration and sequenced by the OMRF[Author’s institution] Clinical Genomics Center using the Illumina NovaSeq 6000 system (S4 PE150).

value: Brain

tag: group

value: Old

value: DAT;NuTRAP

tag: age

value: 21 months

tag: cell


title: CHMAPRE

value: PRE


title: Gmppb-KO C2C12 cells_1


title: PFN1_C71G_SKM_amiR_ATXN2-6

city: Cambridge

first: Deborah

last: Kwon

address: 225 Binney Street

institute: Biogen

description:
Library name: PFN1-amiR-MUS-6
PFN1_C71G_SKM_amiR_ATXN2

data_processing:
Fastq files were generated from bcl files using bcl2fastq v2.20 (Illumina).
Assembly: Alignment of reads was done with STAR version 2.7.2d against the mouse genome version GRCm38 with GENECODE annotation version M25. The human PFN1 gene from reference genome GRCh38, GENCODE version v34, as well as the custom-built sequence of the AAV vector were added to the mouse genome as artificial chromosomes.
Supplementary files format and content: Gene expression quantification was carried out using RSEM version 1.3.2. Differential expression analysis was done using the Quickomics pipeline that employed DESeq2 version 1.34.0

source_name: Muscle

extract_protocol:
RNA was isolated from 15 to 20 mg of mouse tissue powder using the Qiagen miRNeasy Mini kit (Qiagen, 217004) and the fully automated QIAcube Connect according to the manufacturer’s guidelines.
RNA sequencing libraries were generated using the Kapa mRNA HyperPrep Kit (Roche, #KK8581). Libraries were sequenced on a NovaSeq 6000 in paired-end mode, 2x100 bp, generating 106 million mapped pairs in average.

value: Muscle

value: male

tag: rin


title: Gmppb-KO C2C12 cells_2

value: skeletal muscle

value: muscle cells


title: KCN1

description: Library name: CS003

value: Pancreas

value: Pdx1-Cre; Kras+/LSL-G12D; Nrf2flox/flox


title: BRGAPOST

value: POST


title: wild-type C2C12 cells_3

value: wild-type

value: NO


title: PFN1_C71G_SKM_amiR_ATXN2-5

description:
Library name: PFN1-amiR-MUS-5
PFN1_C71G_SKM_amiR_ATXN2


title: Cortical neurons, mut.oligo, 5d, biol rep 4

value: cortical neurons

value: WT

value: miRNA incubation

value: 5 d


title: BRGAPRE

value: vastus lateralis muscle

value: Skeletal Muscle

value: Female


title: PFN1_C71G_SKM_amiR_ATXN2-4

description:
Library name: PFN1-amiR-MUS-4
PFN1_C71G_SKM_amiR_ATXN2


title: Cortical neurons, mut.oligo, 5d, biol rep 3


title: BRBOPOST


title: wild-type C2C12 cells_2


title: PFN1_C71G_SKM_amiR_ATXN2-3

description:
Library name: PFN1-amiR-MUS-3
PFN1_C71G_SKM_amiR_ATXN2

value: female


title: Cortical neurons, mut.oligo, 5d, biol rep 2


title: Gmppb-R287Q mice_3, 32-week-old

data_processing:
FastQC was used to filter out adapter and low-quality reads and Hisat2 was used  to aligned high-quality reads to mouse genome (mm10) .
Expression level of each gene was with default normalized by StringTie with Transcripts Per Kilobase (TPM) methods
Then we used SVA to remove confounder factors across all samples, and calculated differential expression genes between each two treatments using DESeq2.
Assembly: mm10
Supplementary files format and content: Processed data file is the gene expression profile as xlsx format. The expression value was processed as TPM for subsequent analysis.

growth_protocol: we generated two Gmppb knock-in mouse models, namely Gmppb-P32L and Gmppb-R287Q mice, as well as one Gmppb knockout (Gmppb-KO) mouse model. The GmppbP32L mouse model was created through the substitution of the DNA base at position 95 of the Gmppb gene from cytosine (C) to thymine (T), resulting in the alteration of the amino acid at position 32 of the GMPPB protein from proline (P) to leucine (L). The GmppbR287Q mouse model was generated by replacing the DNA base at position 860 of the Gmppb gene, changing guanine (G) to adenine (A). Consequently, this alteration led to the substitution of the amino acid at position 287 of the GMPPB protein from arginine (R) to glutamine (Q). The Gmppb-KO mouse genome sequence has deleted exon 2 and 3, resulting in the removal of 303 base pairs by Cas9

extract_protocol:
Collect 100mg of gastrocnemius muscle from anesthetized mice and promptly freeze the muscle tissue in liquid nitrogen. Then samples were sent on ice to Novogene Technology Co., Ltd for immediate downstream RNA sequencing. In brief, following RNA isolation with Trizol (catalog #, check with Novogene), a total amount of 2 μg RNA per sample was used as input material for library preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences.

treatment_protocol: All mice were kept on a standard diet until they reached 32 weeks of age.

value: Homozygous Gmppb-R287Q mutant  mice

value: Genetically engineered mouse models


title: BRBOPRE

value: PRE


title: PFN1_C71G_SKM_amiR_ATXN2-2

description:
Library name: PFN1-amiR-MUS-2
PFN1_C71G_SKM_amiR_ATXN2

value: Muscle


title: Cortical neurons, mut.oligo, 5d, biol rep 1


title: Cortical neurons, mir-124, 5d, biol rep 1


title: PFN1_C71G_SKM_amiR_ATXN2-1

description:
Library name: PFN1-amiR-MUS-1
PFN1_C71G_SKM_amiR_ATXN2


title: Gmppb-R287Q mice_2, 32-week-old

value: skeletal muscle

value: muscle cells


title: PFN1_C71G_SKM_Vehicle-5

description:
Library name: PFN1-Vehicle-MUS-6
PFN1_C71G_SKM_Vehicle

value: Vehicle

value: male


title: ANJAPRE


title: ALORPOST

value: POST


title: Cortical neurons, untreated, 5d, biol rep 3

value: cortical neurons


title: PFN1_C71G_SKM_Vehicle-4

description:
Library name: PFN1-Vehicle-MUS-5
PFN1_C71G_SKM_Vehicle


title: Gmppb-R287Q mice_1, 32-week-old


title: Cortical neurons, untreated, 5d, biol rep 2

value: WT


title: Gmppb-P32L mice_3, 32-week-old

value: Heterozygous Gmppb-P32L mutant  mice


title: ALORPRE


title: Gmppb-P32L mice_2, 32-week-old


title: Day 8 co-culture serum CMO

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
single cell RNA sequencing, 10X genomics
CMO counts are in processed data files on associated GEX sample

data_processing:
Cell Ranger multi (version 7.1.0) was used to demultiplex the replicates, align and quantify gene expression, specifying the chemistry = SC3Pv3 argument. Reads were aligned to a custom reference genome built by adding the mCherry sequence to the prebuilt human reference GRCh38-2020-A (software and data available from 10x genomics).
Assembly: human GRCh38 (reference GRCh38-2020-A from 10x Genomics)
Supplementary files format and content: Cell ranger output files for demultiplexed samples: 10x counts matrix, features and barcode data
Supplementary files format and content: Normalized count matrix and cell annotations of single cell PGA model: PGA_norm_counts.csv.gz, PGA_meta_annotation.csv
Supplementary files format and content: Normalized count matrix and cell annotations of single cell PGA co-culture model: PGA_co_culture_norm_counts.csv.gz, PGA_co_culture_meta_annotation.csv

growth_protocol: hESCs were grown on growth factor-reduced Matrigel and maintained in mTeSR1 media. Following aggregation cells were cultured in Essential-6 media (E6).

extract_protocol:
Cells were dissociated using Trypsin-EDTA (0.25%) (Thermo Fisher, #25200056) to produce a single cell suspension and resuspended in 1% BSA in PBS.
Duplicate samples from biological replicates were multiplexed together using 10x Genomics 3′ Cellplex kit set A (PN-1000261) according to the manufacturer's instructions. Labelled samples were assessed individually for cell number and viability using a LUNA-FX7™ Automated Cell Counter.
20K cells were processed using the 10X 3' (PN-1000121) following manufacturer's instructions  with an estimated  recovery of 10K cells. Libraries were sequenced using NovaSeq 6000 with an average of 50K reads per cell for the mRNA libraries and 5K reads/ cell for the cell plex library.

treatment_protocol: From day 0 to day 2 cells were treated with BMP4 (24h) and CHIR99021 (24h).

value: Embryonic stem cells

value: Combined (WT + H2B-mCherry)

value: E6+30% serum+Modified EUCM

tag: library type

value: CMO

tag: cmo

value: CMO305 (replicate 1), CMO306 (replicate 2)


title: Cortical neurons, untreated, 5d, biol rep 1

value: 5 d


title: PFN1_C71G_SKM_Vehicle-2

description:
Library name: PFN1-Vehicle-MUS-3
PFN1_C71G_SKM_Vehicle

value: female


title: Gmppb-P32L mice_1, 32-week-old

value: Genetically engineered mouse models


title: wild-type C2C12 cells_1

value: wild-type

value: NO


title: Day 8 co-culture serum GEX

description:
single cell RNA sequencing, 10X genomics
GEX (3' mRNA)

value: mRNA


title: Cortical neurons, mir-92a, 6h, biol rep 3

value: miRNA incubation

value: 6 h


title: ANJAPOST

value: vastus lateralis muscle

value: Skeletal Muscle

value: Female

value: POST


title: Cortical neurons, untreated, 5d, biol rep 4

value: cortical neurons

value: WT


title: Day 8 co-culture CMO

value: Embryonic stem cells

value: Combined (WT + H2B-mCherry)

value: CMO303 (replicate 1), CMO304 (replicate 2)


title: FVB_WT_SKM_Vehicle-6

description:
Library name: FVB-Vehicle-MUS-6
FVB_WT_SKM_Vehicle

value: Muscle

value: Vehicle

value: male


title: Cortical neurons, mir-92a, 6h, biol rep 2


title: Day 8 co-culture GEX


title: FVB_WT_SKM_Vehicle-5

description:
Library name: FVB-Vehicle-MUS-5
FVB_WT_SKM_Vehicle


title: PFN1_C71G_SKM_Vehicle-3

description:
Library name: PFN1-Vehicle-MUS-4
PFN1_C71G_SKM_Vehicle


title: Day 8 CMO

value: CMO

value: CMO301 (replicate 1), CMO302 (replicate 2)


title: wild-type mice_3, 32-week-old

value: skeletal muscle

value: muscle cells

value: wild-type

value: NO


title: Gmppb-KO mice_1, 32-week-old

value: Heterozygous Gmppb-KO  mice

value: Genetically engineered mouse models


title: FVB_WT_SKM_Vehicle-4

description:
Library name: FVB-Vehicle-MUS-4
FVB_WT_SKM_Vehicle


title: Cortical neurons, mir-92a, 6h, biol rep 1

value: miRNA incubation

value: 6 h


title: FVB_WT_SKM_Vehicle-3

description:
Library name: FVB-Vehicle-MUS-3
FVB_WT_SKM_Vehicle

value: female


title: wild-type mice_2, 32-week-old


title: wild-type mice_1, 32-week-old


title: Day 8 GEX

value: Embryonic stem cells

value: WT

value: mRNA


title: PFN1_C71G_SKM_Vehicle-1

description:
Library name: PFN1-Vehicle-MUS-1
PFN1_C71G_SKM_Vehicle

value: Muscle


title: Day 5 co-culture GEX

value: Combined (WT + H2B-mCherry)


title: Cortical neurons, mir-92a, 6h, biol rep 4

value: cortical neurons


title: FVB_WT_SKM_Vehicle-2

description:
Library name: FVB-Vehicle-MUS-2
FVB_WT_SKM_Vehicle

value: Vehicle


title: Cortical neurons, mir-124, 6h, biol rep 3


title: FVB_WT_SKM_Vehicle-1

description:
Library name: FVB-Vehicle-MUS-1
FVB_WT_SKM_Vehicle


title: Cortical neurons, mir-124, 6h, biol rep 2


title: Day 5 co-culture CMO

value: CMO

value: CMO303 (replicate 1), CMO304 (replicate 2)


title: Gmppb-KO mice_3, 32-week-old

value: skeletal muscle

value: muscle cells


title: Cortical neurons, mir-124, 6h, biol rep 1


title: Gmppb-KO mice_2, 32-week-old


title: Slc7a5.TKO-3

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
The raw reads in fastq format was generated using cellranger mkfastq and count matrix was generated by cellranger count acording to cellranger v7.1.0
Assembly: mm10
Supplementary files format and content: count matrix files in H5 format

source_name: Tumor

extract_protocol:
Tumor tissues were dissected from mice and digested with collagenase to make single cells.
scRNA-seq libraries were generataed using 10X 3’ single cell mRNAseq V3 reagents according to manufacturer's protocol.

value: Tumor

value: primary cells

value: Epithelial and immune cells

value: Slc7a5 KO

value: injected with AT3 breast tumor cells


title: PFN1_C71G_CTX_amiR_ATXN2-6

description:
Library name: PFN1-amiR-CTX-6
PFN1_C71G_CTX_amiR_ATXN2

source_name: cerebral cortex

value: cerebral cortex

value: male


title: Day 3 co-culture GEX

value: Embryonic stem cells


title: Day 3 co-culture CMO

value: CMO307 (replicate 1), CMO308 (replicate 2)


title: PFN1_C71G_CTX_amiR_ATXN2-5

description:
Library name: PFN1-amiR-CTX-5
PFN1_C71G_CTX_amiR_ATXN2


title: Slc7a5.TKO-2


title: Slc7a5.TKO-1


title: Cortical neurons, mut.oligo, 6h, biol rep 3

value: WT

value: miRNA incubation

value: 6 h


title: Cortical neurons, mut.oligo, 6h, biol rep 4

value: cortical neurons


title: Day 3 CMO

value: CMO

value: CMO305 (replicate 1), CMO306  (replicate 2)


title: PFN1_C71G_CTX_amiR_ATXN2-4

description:
Library name: PFN1-amiR-CTX-4
PFN1_C71G_CTX_amiR_ATXN2


title: Cortical neurons, mut.oligo, 6h, biol rep 2


title: Cortical neurons, mir-124, 6h, biol rep 4


title: Day 3 GEX

value: mRNA


title: PFN1_C71G_CTX_amiR_ATXN2-2

description:
Library name: PFN1-amiR-CTX-2
PFN1_C71G_CTX_amiR_ATXN2

value: female


title: WT1

value: Tumor


title: Cortical neurons, untreated, 6h, biol rep 3


title: Cortical neurons, untreated, 6h, biol rep 4


title: PFN1_C71G_CTX_amiR_ATXN2-1

description:
Library name: PFN1-amiR-CTX-1
PFN1_C71G_CTX_amiR_ATXN2


title: Tumor_CTL_24h_2

data_processing:
RNA-seq reads were aligned using STARv2.5 and reference genome (mm10) and gene model annotation files from Ensembl. Reads were quantified using HTSeqv0.6.1.
Differential gene expression analysis was done using DESeq2 v1.36.
Assembly: mm10
Supplementary files format and content: raw read counts for each sample and gene annotation information in a spreadsheet

source_name: Immune system

growth_protocol: The 2/20 CTLs (1.33 × 10^5 cells/mL) were cultured in RPMI 1640 medium with 10% FBS and AH1 peptide (SPSYVYHQF, 1 μg/mL), recombinant IL-2 protein (10 Units/mL), and lethally irradiated spleen cells of BALB/c mouse (3.3x105 cells/ml) weekly.

extract_protocol:
CTL cells were isolated using anti-CD45 monoclonal antibody-conjugated magnetic bead. Total RNA was isolated using Direct-zol RNA microprep kit according to manufacturer’s instructions (Zymo Research, Irvine CA). .
The strand mRNA squencing libraries were generated by Novogene using manufactor's protocol.

treatment_protocol: The 2/20 CTLs were activated with AH1 peptide (SPSYVYHQF, 1 μg/mL) or co-cultured with 4T1 cells for 4hr and 24hr.

value: Immune system

value: T cells

value: Activation


title: Cortical neurons, mut.oligo, 6h, biol rep 1


title: Day 1 co-culture GEX

value: Combined (WT+H2B-mCherry)


title: PFN1_C71G_CTX_Vehicle-6

description:
Library name: PFN1-Vehicle-CTX-6
PFN1_C71G_CTX_Vehicle

value: cerebral cortex

value: Vehicle


title: Tumor_CTL_24h_1


title: Day 1 GEX

value: Embryonic stem cells


title: Cortical neurons, untreated, 6h, biol rep 2


title: PFN1_C71G_CTX_Vehicle-5

description:
Library name: PFN1-Vehicle-CTX-5
PFN1_C71G_CTX_Vehicle

value: male


title: Ag_CTL_24h_2

value: WT


title: Cortical neurons, untreated, 6h, biol rep 1


title: WT3

value: primary cells

value: Epithelial and immune cells

value: injected with AT3 breast tumor cells


title: PFN1_C71G_CTX_Vehicle-4

description:
Library name: PFN1-Vehicle-CTX-4
PFN1_C71G_CTX_Vehicle


title: Day 0 CMO

description:
single cell RNA sequencing, 10X genomics
CMO counts are in processed data files on associated GEX sample

value: CMO

value: CMO311 (replicate 1), CMO312 (replicate 2)


title: Ag_CTL_24h_1


title: Day 0 GEX

description:
single cell RNA sequencing, 10X genomics
GEX (3' mRNA)

value: mRNA


title: PFN1_C71G_CTX_Vehicle-3

description:
Library name: PFN1-Vehicle-CTX-3
PFN1_C71G_CTX_Vehicle

value: female


title: PFN1_C71G_CTX_amiR_ATXN2-3

description:
Library name: PFN1-amiR-CTX-3
PFN1_C71G_CTX_amiR_ATXN2


title: Tumor_CTL_4h_2


title: PFN1_C71G_CTX_Vehicle-2

description:
Library name: PFN1-Vehicle-CTX-2
PFN1_C71G_CTX_Vehicle


title: Day -2 mTESR CMO

value: CMO309 (replicate 1), CMO310 (replicate 2)


title: WT2

value: Tumor


title: Day 1 co-culture CMO

value: Combined (WT + H2B-mCherry)


title: KBM7 ChIC H3K27me3 (KIN8790.index20)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: KIN8790.index20
kbm7_damchic_controls.h5ad.gz

library_source: genomic

data_processing:
Dam&ChIC data processing is largely based on the workflow and scripts described in Rooijers et al., 2019 and Markodimitraki et al., 2020 (available at: https://github.com/KindLab/scDamAndTools), but adapted to allow for computational separation of scDamID and sortChIC derived reads and further processing of sortChIC reads.
All reads are demultiplexed by comparing their sample barcode (e.g. single-cell barcode) located at the start of each read (R1 in case of paired-end sequenced libraries) conform to the read layout of 5′-[3 nt UMI][8 nt barcode]TC[gDNA]-3′ for scDamID and 5′-[3 nt UMI][8 nt barcode]WN[gDNA]-3′ for sortChIC reads, to a reference list of barcodes and zero mismatches between the observed barcode and reference are allowed. Sample barcodes and UMIs are trimmed off the reads to only retain gDNA sequences. The UMI sequences were appended to the read name for downstream processing. Per sample barcode, scDamID and sortChIC reads remain mixed at this point.
After preprocessing, the reads were aligned to a reference genome using bowtie2 (v. 2.4.1) with parameters: ‘‘--seed 42 --very-sensitive -N 1’’. Before alignment a ‘GA’ dinucleotide was prepended to the reads that has effectively been digested off scDamID fragments during DpnI gDNA digestion. For human samples, reads were aligned to reference genome hg19 (GRCh37) and mouse samples to mm10 (GRCm38). For allele-specific processing for X-chromosome inactivation experiments, data were aligned to reference genomes generated by imputing 129S1/SvImJ and CAST/EiJ single nucleotide polymorphisms obtained from the Sanger Mouse Genomes project (Keane et al., 2011) onto the mm10 reference genome. The reads were assigned to either genotype by aligning reads to both references. Reads that aligned with lower edit distance (SAM tag ‘NM’) or higher alignment score (SAM tag ‘AS’) in case of equal edit distance to one of the genotypes were assigned to that genotype. Reads aligning with equal edit distance and alignment score to both genotypes were considered of ‘ambiguous’ genotype. Reads that yielded an alignment with mapping quality (BAM field ‘MAPQ’) lower than 10 were discarded.
Following read alignment with ‘GA’ prepended dinucleotide, reads were considered scDamID in case of perfect alignment on genomic GATC motifs. Residual reads were considered sortChIC and their original sequences (i.e., without prepended GA dinucleotide) were realigned using hisat2 (v. 2.1.0) with parameters: ‘‘--seed 42 --no-spliced-alignment --mp '2,0' --sp '4,0'”. These sortChIC-considered reads were further pruned given MNase’s strong adenine or thymidine-nucleotide cut preference; only sortChIC reads were kept that lead with an ‘A’ or ‘T’ base. In addition, we observed that a larger fraction of sortChIC reads (i.e., that do not map on a genomic GATC motif) are ‘TC’-dinucleotide leading in Dam&ChIC libraries than in sortChIC libraries and hence decided to exclude TC-leading reads from Dam&ChIC-derived sortChIC libraries.
Assembly: GRCm38
Supplementary files format and content: H5AD

molecule: genomic DNA

source_name: Blood

growth_protocol: Human haploid KBM7 cells were cultured in suspension in IMDM medium (10% FBS and 1% Pen/Strep). Human HT-1080 cells were cultured in DMEM medium (10% FBS and 1% Pen/Strep). Mouse F1 hybrid Cast/EiJ x 129SvJ embryonic stem cells (mESCs; a kind gift from the Joost Gribnau laboratory) were cultured on a monolayer of irradiated feeders (MEFs) in CM+/+ (G-MEM + 10% FBS, 1% Pen/Strep, 1× GlutaMAX (Gibco), 1× NEVitaminC, 1× sodium pyruvate, 0.1 mM 2-ME and 1000 U/ml ESGROmLIF (EMD Millipore, ESG1107))

extract_protocol:
double thymidine block: cells received 2 mM thymidine for 15 hours, followed by 9 hours of release, followed by a second thymidine block for 13 hours.
MN was activated thorugh 2mM CaCl2 for 30min at 4C at inactivated by EGTA addition. Cells were lysed (protK + NP40), fragments end-repaired (Klenow) and adenine methylated sites were cut (DpnI). Dam and ChIC fragemnts are ligated to blunt end adaptors containing a cell barcode and unique molecular identifier and a T7 promoter. After pooling DNA is amplified by in vitro transcription, before rundom hexamer based reverse transcription and final indexing PCR for sequencing.

treatment_protocol: Dam-POI induction: For Kbm7 cells 0.5 nM Shield-1 was added to stabilize the protein at the indicated timepoint. For mESCs 1mM IVitaminC was added 24h prior to induction, to ensure protein degradation.

value: Blood

value: chronic myelogenous leukemia


title: Day 1 CMO


title: Tumor_CTL_4h_1

value: Immune system

value: T cells

value: Activation


title: Day -2 mTESR GEX

value: Embryonic stem cells


title: KBM7 Dam-LMNB1/ChIC H3K9me3 (KIN8790.index13)

description:
Library name: KIN8790.index13
kbm7_damchic_controls.h5ad.gz


title: PFN1_C71G_CTX_Vehicle-1

description:
Library name: PFN1-Vehicle-CTX-1
PFN1_C71G_CTX_Vehicle

value: cerebral cortex

value: Vehicle


title: Ag-CTL_4h_2

value: WT


title: FVB_WT_CTX_Vehicle-5

description:
Library name: FVB-Vehicle-CTX-6
FVB_WT_CTX_Vehicle

value: male


title: Ag-CTL_4h_1


title: KBM7 ChIC H3K9me3 (KIN8790.index10)

description:
Library name: KIN8790.index10
kbm7_damchic_controls.h5ad.gz


title: genomic DNA from normal8

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description:
Normal colon mucosa
SAMPLE 23

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

tag: gender

value: Femal

tag: sample type

value: clinical sample

tag: disease state

value: Normal


title: KBM7 ChIC H3K27me3 (KIN8790.index14)

description:
Library name: KIN8790.index14
kbm7_damchic_controls.h5ad.gz

tag: tissue

tag: cell line

tag: cell type


title: FVB_WT_CTX_Vehicle-4

description:
Library name: FVB-Vehicle-CTX-5
FVB_WT_CTX_Vehicle

tag: genotype

tag: treatment


title: Resting_CTL_2


title: genomic DNA from normal6

description:
Normal colon mucosa
SAMPLE 21


title: KBM7 ChIC H3K9me3 (KIN8790.index04)

description:
Library name: KIN8790.index04
kbm7_damchic_controls.h5ad.gz


title: FVB_WT_CTX_Vehicle-3

description:
Library name: FVB-Vehicle-CTX-4
FVB_WT_CTX_Vehicle

tag: Sex


title: genomic DNA from normal5

description:
Normal colon mucosa
SAMPLE 20


title: KBM7 Dam-LMNB1/ChIC LMNB1 (KIN8433.index01)

description:
Library name: KIN8433.index01
kbm7_damchic_controls.h5ad.gz


title: Resting_CTL_1


title: FVB_WT_CTX_Vehicle-2

description:
Library name: FVB-Vehicle-CTX-2
FVB_WT_CTX_Vehicle

value: female


title: Tumor-CTL-2

data_processing:
The ATACseq analysis was performed on Galaxy server. Adaptor and quality trimming were performed using Trim Glore! Modules (Galaxyv0.4.3.1). Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings. Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ATAC-seq peak calling was performed on Galaxy server using MACS2 v2.1.2 with following command “-q 0.05 --nomodel --shift --100 --extsize 200 -B --SPMR --keep-dup all --call -summits”.
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
CTL cells were isolated using anti-CD45 monoclonal antibody-conjugated magnetic bead. Nuclei were prepared from cultured cell lines using the Omni-ATAC protocol Nat Methods. 2017 Oct; 14(10): 959–962.)
For each sample, 50,000 nuclei prepared from cultured cells were incubated with 2.5 mL Nextera Tn5 transposase (Illumina) in 50mL 1X transposition reaction mixture in a thermocycler at 37 °C for 1hr. The transposition reaction mixtures were purified with a DNA Clean and Concentrator kit (Zymo Research), and amplified for 11-13 cycles using NEBNext High-Fidelity 2X Master Mix (New England Biolabs) and Nextera Index primers (Illumina). The amplified libraries were size-selected by two rounds of AMPure beads purification (0.5X and 1.2X).


title: genomic DNA from normal3

description:
Normal colon mucosa
SAMPLE 18


title: genomic DNA from normal4

description:
Normal colon mucosa
SAMPLE 19


title: KBM7 ChIC H3K27me3 (KIN6062.index15)

description:
Library name: KIN6062.index15
kbm7_damchic_controls.h5ad.gz


title: KBM7 Dam-LMNB1/ChIC H3K27me3 (KIN6062.index14)

description:
Library name: KIN6062.index14
kbm7_damchic_controls.h5ad.gz


title: FVB_WT_CTX_Vehicle-1

description:
Library name: FVB-Vehicle-CTX-1
FVB_WT_CTX_Vehicle


title: Tumor-CTL-1


title: Ag-CTL-2


title: PFN1_C71G_SC_amiR_ATXN2-6

description:
Library name: PFN1-amiR-SC-6
PFN1_C71G_SC_amiR_ATXN2

source_name: spinal cord

value: spinal cord


title: KBM7 ChIC H3K4me3 (KIN10644.index19)

description:
Library name: KIN10644.index19
kbm7_damchic_controls.h5ad.gz


title: genomic DNA from normal7

description:
Normal colon mucosa
SAMPLE 22

value: Male


title: genomic DNA from normal2

description:
Normal colon mucosa
SAMPLE 17


title: KBM7 ChIC H3K4me3 (KIN10162.index21)

description:
Library name: KIN10162.index21
kbm7_damchic_controls.h5ad.gz


title: PFN1_C71G_SC_amiR_ATXN2-5

description:
Library name: PFN1-amiR-SC-5
PFN1_C71G_SC_amiR_ATXN2


title: Ag-CTL-1


title: genomic DNA from normal1

description:
Normal colon mucosa
SAMPLE 16


title: Resting CTL-1


title: Resting CTL-2


title: genomic DNA from PMP15

description:
High grade pseudomyxoma peritonei
SAMPLE 15

value: Female

value: pseudomyxoma peritonei


title: PFN1_C71G_SC_amiR_ATXN2-3

description:
Library name: PFN1-amiR-SC-3
PFN1_C71G_SC_amiR_ATXN2


title: 4-month-old WT control mouse replicate 3

city: Rochester

first: Benjamin

last: Korman

address: 601 Elmwood Avenue, Box 695

institute: AIR

description:
Library name: WT3
single-end 100 bp

data_processing:
Raw FastQ reads were demultiplexed using bcltofastq-2.19.0 and trimmed using Trimmomatic-0.36. Trimmed reads were mapped to mouse GRCm38.p5 reference genom eusing STAR_2.5.2b. Mapped reads were counted by using FeatureCounts at the gene level.
Assembly: GRCm38.p5
Supplementary files format and content: text tab file
Supplementary files format and content: RawCounts

source_name: Lung

extract_protocol:
Lung was harvested from 4-month-old TNF-Tg and WT mice. Total RNA was extracted using QIAGEN Rneasy Plus Kits according to the manufacturer's instructions.
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size.

value: Lung

value: primary cells


title: 4-month-old WT control mouse replicate 2

description:
Library name: WT2
single-end 100 bp


title: PFN1_C71G_SC_amiR_ATXN2-4

description:
Library name: PFN1-amiR-SC-4
PFN1_C71G_SC_amiR_ATXN2


title: PFN1_C71G_SC_amiR_ATXN2-2

description:
Library name: PFN1-Vehicle-SC-6
PFN1_C71G_SC_amiR_ATXN2


title: genomic DNA from PMP14

description:
Low grade pseudomyxoma peritonei
SAMPLE 14


title: 4-month-old WT control mouse replicate 1

description:
Library name: WT1
single-end 100 bp


title: genomic DNA from PMP13

description:
Low grade pseudomyxoma peritonei
SAMPLE 13


title: Day2_compression_rep4

first: Federica

last: Michielin

address: 30 Guilford Street

department: GOS ICH

institute: University College London

data_processing:
STAR alignment and fastp fastq file preprocessing
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: fetal lung

extract_protocol:
Total RNA was isolated with the RNeasy Micro kit (Qiagen), according to manufacturer’s instructions. Reverse transcription to cDNA was performed using the high-capacity cDNA reverse transcription kit (Thermo Fisher Scientific), according to manufacturer’s instructions.
Libraries were generated with a KAPA mRNA HyperPrep kit (Roche).

value: fetal lung

tag: strain

value: wild type

tag: time

value: Day 2

value: compression


title: PFN1_C71G_SC_amiR_ATXN2-1

description:
Library name: PFN1-Vehicle-SC-5
PFN1_C71G_SC_amiR_ATXN2


title: Day2_compression_rep3


title: genomic DNA from PMP12

description:
Low grade pseudomyxoma peritonei
SAMPLE 12


title: genomic DNA from PMP11

description:
Low grade pseudomyxoma peritonei
SAMPLE 11


title: PFN1_C71G_SC_Vehicle-6

description:
Library name: PFN1-amiR-SC-2
PFN1_C71G_SC_Vehicle

value: Vehicle


title: Day2_compression_rep2


title: 4-month-old TNF transgenic mouse replicate 2

description:
Library name: TNF-Tg2
single-end 100 bp

value: TNF-Tg


title: 4-month-old TNF transgenic mouse replicate 3

description:
Library name: TNF-Tg3
single-end 100 bp


title: PFN1_C71G_SC_Vehicle-5

description:
Library name: PFN1-amiR-SC-1
PFN1_C71G_SC_Vehicle

value: male


title: Day2_compression_rep1


title: genomic DNA from PMP10

description:
Low grade pseudomyxoma peritonei
SAMPLE 10


title: 4-month-old TNF transgenic mouse replicate 1

description:
Library name: TNF-Tg1
single-end 100 bp


title: Day2_control_rep4

value: control


title: PFN1_C71G_SC_Vehicle-4

description:
Library name: PFN1-Vehicle-SC-4
PFN1_C71G_SC_Vehicle


title: PFN1_C71G_SC_Vehicle-3

description:
Library name: PFN1-Vehicle-SC-3
PFN1_C71G_SC_Vehicle


title: 6T-CEM cells, IgG

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

data_processing:
Raw Data of CUT&Tag was aligned to the reference genome (hg38) using bowtie2 (v2.2.5)
Peaks were identified using MACS2 (v2.2.7)
Assembly: hg38
Supplementary files format and content: read coverage in bigwig files and peaks in bed files
Library strategy: CUT&Tag

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

value: T-ALL cells

tag: chip antibody

value: IgG


title: genomic DNA from PMP9

description:
Low grade pseudomyxoma peritonei
SAMPLE 9

value: clinical sample


title: Day2_control_rep3


title: Day2_control_rep2


title: PFN1_C71G_SC_Vehicle-2

description:
Library name: PFN1-Vehicle-SC-2
PFN1_C71G_SC_Vehicle

value: spinal cord

tag: age

value: female


title: genomic DNA from PMP7

description:
Low grade pseudomyxoma peritonei
SAMPLE 7

value: Female


title: Jurkat cells, IgG, replicate 2

source_name: Jurkat

value: Jurkat


title: Day2_control_rep1


title: genomic DNA from PMP6

description:
High grade pseudomyxoma peritonei
SAMPLE 6

value: Male

value: pseudomyxoma peritonei


title: 6T-CEM cells, H3K27ac


title: Jurkat cells, IgG, replicate 1


title: FVB_WT_SC_Vehicle-6

description:
Library name: FVB-Vehicle-SC-6
FVB_WT_SC_Vehicle


title: Day0_control_rep4

value: fetal lung

value: Day 0


title: genomic DNA from PMP5

description:
High grade pseudomyxoma peritonei
SAMPLE 5


title: Jurkat cells, H3K27ac, replicate 2


title: Day0_control_rep3

value: wild type


title: FVB_WT_SC_Vehicle-5

description:
Library name: FVB-Vehicle-SC-5
FVB_WT_SC_Vehicle


title: genomic DNA from PMP4

description:
Low grade pseudomyxoma peritonei
SAMPLE 4


title: Jurkat cells, H3K27ac, replicate 1


title: PFN1_C71G_SC_Vehicle-1

description:
Library name: PFN1-Vehicle-SC-1
PFN1_C71G_SC_Vehicle


title: genomic DNA from PMP3

description:
High grade pseudomyxoma peritonei
SAMPLE 3


title: Day0_control_rep2


title: FVB_WT_SC_Vehicle-4

description:
Library name: FVB-Vehicle-SC-4
FVB_WT_SC_Vehicle


title: Day0_control_rep1


title: Jurkat cells, no treated, replicate 2

data_processing:
Illumina Casava2.19 software used for basecalling.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and expression values of each gene for each sample and differential expression values between treatment group and control group.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: No treated


title: genomic DNA from PMP2

description:
Low grade pseudomyxoma peritonei
SAMPLE 2


title: FVB_WT_SC_Vehicle-3

description:
Library name: FVB-Vehicle-SC-3
FVB_WT_SC_Vehicle

value: Vehicle


title: FVB_WT_SC_Vehicle-2

description:
Library name: FVB-Vehicle-SC-2
FVB_WT_SC_Vehicle


title: CST_R2_001.fastq.gz

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

description: Library name: CST_R1_001.fastq.gz

data_processing:
Raw data of fastq files were aligned to the mm10 mouse reference genome by using the CellRanger software v3.0.1 (10x Genomics).
Assembly: UCSC macFas5
Supplementary files format and content: CellRanger output

organism: Macaca fascicularis

source_name: testis

extract_protocol:
Tissues were minced with a blade and then incubated in dissociation buffer containing 2 mg/ml Collagenase II (#C6885, Sigma-Aldrich), 10 mg/ml Dispase II (#354235, Corning) and 50000 U/ml DNase I (#DN25, Sigma-Aldrich) for up to 30 min at 37 °C in a shaking incubator.To remove undigested tissues, the single-cell suspension was then passed through a 40-μm cell strainer and cells were spun down at 250 g at 4°C for 4 min. Red blood cells (RBC) were removed by using RBC Lysis Buffer (#00-4333, Invitrogen). In order Cell viability was measured by AO/PI solution (#CS2-0106, Nexcelom Bioscience). The quality control criteria for single-cell suspension were cell viability > 80% and the percentage of cell clumps < 10%. The final concentration of single-cell suspension was adjusted to 1000 cells/μl. In order to recover 8000-10000 cells, a volume of 15 µl was loaded into one channel of the ChromiumTM Single Cell B Chip (#1000073, 10x Genomics). Single-cell bar-coding, cDNA synthesis and library preparation were performed by using the Chromium Single Cell 3' Library & Gel Bead Kit v3 (#1000075, 10x Genomics). DNA libraries were then sequenced on an Illumina novaseq 6000 system configured with the paired-end 150-bp protocol for a sequencing depth of approximately 400 million reads per library.
scRNA-seq

value: testis


title: Jurkat cells, no treated, replicate 1


title: genomic DNA from PMP8

description:
Low grade pseudomyxoma peritonei
SAMPLE 8


title: genomic DNA from PMP1

description:
Low grade pseudomyxoma peritonei
SAMPLE 1


title: Jurkat cells, GNE987 treated, 25nmol, replicate 2

value: Treated by GNE987


title: FVB_WT_SC_Vehicle-1

description:
Library name: FVB-Vehicle-SC-1
FVB_WT_SC_Vehicle


title: Jurkat cells, GNE987 treated, 25nmol, replicate 1


title: UAT_R2_001.fastq.gz

description: Library name: UAT_R1_001.fastq.gz


title: Rolipram 8000 nM replicate 2

status: Public on May 16 2025

city: SEOUL

first: Wankyu

last: Kim

country: South Korea

institute: Ewha Womans University

description:
Library name: Rolipram_8000_R2
HDFn treated with Rolipram 8000 nM, replicate 2

data_processing:
The sequencing quliaty of FASTQ raw files was assessed using FastQC.
Adapter and low-quality sequences were trimmed using BBDuk, and trimmed reads were aligned to the human reference genome (GPCR38, version 34) using STAR aligner (v2.7.1a).
Gene-level quantification was performed using HTSeq-count (v2.0.4) to obtain raw read counts.
Assembly: Human genome assembly GPCR38, version 34.
Supplementary files format and content: Processed data files are provided as CSV files containing Ensembl gene identifiers and corresponding expected read counts for each gene.

source_name: skin (dermis)

growth_protocol: Human Primary Dermal Fibroblast, Neonatal (HDFn) cells (ATCC) were cultured in Fibroblast Basal Medium supplemented with the Fibroblast Growth Kit–Low Serum (ATCC).

extract_protocol:
After treatment, cells were lysed in 100 μL of lysis buffer, and total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) following the manufacturer’s instructions. RNA concentration was measured using the Quant-iT™ RiboGreen™ RNA Assay Kit (Invitrogen) and stored at −20°C until further processing.
RNA sequencing libraries were prepared and sequenced using the DNBSEQ-G400 platform (BGI protocol).

treatment_protocol: Cells were treated with four phosphodiesterase (PDE) inhibitors—roflumilast, rolipram, cilostazol, and milrinone—at 11 concentrations ranging from 7.8 nM to 8,000 nM using a 2-fold serial dilution. Treatment duration was 24 hours.

value: skin (dermis)

value: HDFn

value: fibroblast

value: Rolipram 8000 nM


title: Rolipram 8000 nM replicate 4

description:
Library name: Rolipram_8000_R4
HDFn treated with Rolipram 8000 nM, replicate 4


title: Rolipram 8000 nM replicate 3

description:
Library name: Rolipram_8000_R3
HDFn treated with Rolipram 8000 nM, replicate 3


title: Rolipram 8000 nM replicate 5

description:
Library name: Rolipram_8000_R5
HDFn treated with Rolipram 8000 nM, replicate 5


title: Rolipram 7.8 nM replicate 4

description:
Library name: Rolipram_7.8_R4
HDFn treated with Rolipram 7.8 nM, replicate 4

value: Rolipram 7.8 nM


title: Rolipram 7.8 nM replicate 5

description:
Library name: Rolipram_7.8_R5
HDFn treated with Rolipram 7.8 nM, replicate 5


title: Rolipram 7.8 nM replicate 3

description:
Library name: Rolipram_7.8_R3
HDFn treated with Rolipram 7.8 nM, replicate 3


title: Rolipram 62.5 nM replicate 5

description:
Library name: Rolipram_62.5_R5
HDFn treated with Rolipram 62.5 nM, replicate 5

value: Rolipram 62.5 nM


title: Rolipram 7.8 nM replicate 1

description:
Library name: Rolipram_7.8_R1
HDFn treated with Rolipram 7.8 nM, replicate 1


title: Rolipram 7.8 nM replicate 2

description:
Library name: Rolipram_7.8_R2
HDFn treated with Rolipram 7.8 nM, replicate 2


title: Rolipram 62.5 nM replicate 3

description:
Library name: Rolipram_62.5_R3
HDFn treated with Rolipram 62.5 nM, replicate 3


title: Rolipram 62.5 nM replicate 2

description:
Library name: Rolipram_62.5_R2
HDFn treated with Rolipram 62.5 nM, replicate 2


title: Rolipram 62.5 nM replicate 1

description:
Library name: Rolipram_62.5_R1
HDFn treated with Rolipram 62.5 nM, replicate 1


title: Rolipram 500 nM replicate 5

description:
Library name: Rolipram_500_R5
HDFn treated with Rolipram 500 nM, replicate 5

value: Rolipram 500 nM


title: Rolipram 500 nM replicate 2

description:
Library name: Rolipram_500_R2
HDFn treated with Rolipram 500 nM, replicate 2


title: Rolipram 500 nM replicate 3

description:
Library name: Rolipram_500_R3
HDFn treated with Rolipram 500 nM, replicate 3


title: Rolipram 500 nM replicate 1

description:
Library name: Rolipram_500_R1
HDFn treated with Rolipram 500 nM, replicate 1


title: Rolipram 4000 nM replicate 5

description:
Library name: Rolipram_4000_R5
HDFn treated with Rolipram 4000 nM, replicate 5

value: Rolipram 4000 nM


title: Rolipram 4000 nM replicate 4

description:
Library name: Rolipram_4000_R4
HDFn treated with Rolipram 4000 nM, replicate 4


title: Rolipram 500 nM replicate 4

description:
Library name: Rolipram_500_R4
HDFn treated with Rolipram 500 nM, replicate 4


title: Rolipram 31.3 nM replicate 5

description:
Library name: Rolipram_31.3_R5
HDFn treated with Rolipram 31.3 nM, replicate 5

value: Rolipram 31.3 nM


title: Rolipram 31.3 nM replicate 2

description:
Library name: Rolipram_31.3_R2
HDFn treated with Rolipram 31.3 nM, replicate 2


title: Rolipram 31.3 nM replicate 3

description:
Library name: Rolipram_31.3_R3
HDFn treated with Rolipram 31.3 nM, replicate 3


title: Rolipram 31.3 nM replicate 4

description:
Library name: Rolipram_31.3_R4
HDFn treated with Rolipram 31.3 nM, replicate 4


title: Rolipram 31.3 nM replicate 1

description:
Library name: Rolipram_31.3_R1
HDFn treated with Rolipram 31.3 nM, replicate 1


title: Rolipram 8000 nM replicate 1

description:
Library name: Rolipram_8000_R1
HDFn treated with Rolipram 8000 nM, replicate 1


title: Rolipram 250 nM replicate 5

description:
Library name: Rolipram_250_R5
HDFn treated with Rolipram 250 nM, replicate 5

value: Rolipram 250 nM


title: Rolipram 62.5 nM replicate 4

description:
Library name: Rolipram_62.5_R4
HDFn treated with Rolipram 62.5 nM, replicate 4


title: Rolipram 250 nM replicate 4

description:
Library name: Rolipram_250_R4
HDFn treated with Rolipram 250 nM, replicate 4


title: Rolipram 250 nM replicate 1

description:
Library name: Rolipram_250_R1
HDFn treated with Rolipram 250 nM, replicate 1


title: Rolipram 2000 nM replicate 5

description:
Library name: Rolipram_2000_R5
HDFn treated with Rolipram 2000 nM, replicate 5

value: Rolipram 2000 nM


title: Rolipram 250 nM replicate 2

description:
Library name: Rolipram_250_R2
HDFn treated with Rolipram 250 nM, replicate 2


title: Rolipram 2000 nM replicate 3

description:
Library name: Rolipram_2000_R3
HDFn treated with Rolipram 2000 nM, replicate 3


title: Rolipram 250 nM replicate 3

description:
Library name: Rolipram_250_R3
HDFn treated with Rolipram 250 nM, replicate 3


title: Rolipram 2000 nM replicate 2

description:
Library name: Rolipram_2000_R2
HDFn treated with Rolipram 2000 nM, replicate 2


title: Rolipram 2000 nM replicate 4

description:
Library name: Rolipram_2000_R4
HDFn treated with Rolipram 2000 nM, replicate 4


title: Rolipram 15.6 nM replicate 5

description:
Library name: Rolipram_15.6_R5
HDFn treated with Rolipram 15.6 nM, replicate 5

value: Rolipram 15.6 nM


title: Rolipram 15.6 nM replicate 3

description:
Library name: Rolipram_15.6_R3
HDFn treated with Rolipram 15.6 nM, replicate 3


title: Rolipram 2000 nM replicate 1

description:
Library name: Rolipram_2000_R1
HDFn treated with Rolipram 2000 nM, replicate 1


title: Rolipram 15.6 nM replicate 2

description:
Library name: Rolipram_15.6_R2
HDFn treated with Rolipram 15.6 nM, replicate 2


title: Rolipram 4000 nM replicate 2

description:
Library name: Rolipram_4000_R2
HDFn treated with Rolipram 4000 nM, replicate 2


title: Rolipram 125 nM replicate 5

description:
Library name: Rolipram_125_R5
HDFn treated with Rolipram 125 nM, replicate 5

value: Rolipram 125 nM


title: Rolipram 15.6 nM replicate 4

description:
Library name: Rolipram_15.6_R4
HDFn treated with Rolipram 15.6 nM, replicate 4


title: Rolipram 125 nM replicate 4

description:
Library name: Rolipram_125_R4
HDFn treated with Rolipram 125 nM, replicate 4


title: Rolipram 4000 nM replicate 1

description:
Library name: Rolipram_4000_R1
HDFn treated with Rolipram 4000 nM, replicate 1


title: Rolipram 15.6 nM replicate 1

description:
Library name: Rolipram_15.6_R1
HDFn treated with Rolipram 15.6 nM, replicate 1


title: Rolipram 125 nM replicate 3

description:
Library name: Rolipram_125_R3
HDFn treated with Rolipram 125 nM, replicate 3


title: Rolipram 1000 nM replicate 1

description:
Library name: Rolipram_1000_R1
HDFn treated with Rolipram 1000 nM, replicate 1

value: Rolipram 1000 nM


title: Rolipram 125 nM replicate 1

description:
Library name: Rolipram_125_R1
HDFn treated with Rolipram 125 nM, replicate 1


title: Rolipram 0 nM replicate 5

description:
Library name: Rolipram_0_R5
HDFn treated with Rolipram 0 nM, replicate 5

value: Rolipram 0 nM


title: Rolipram 0 nM replicate 3

description:
Library name: Rolipram_0_R3
HDFn treated with Rolipram 0 nM, replicate 3


title: Rolipram 1000 nM replicate 4

description:
Library name: Rolipram_1000_R4
HDFn treated with Rolipram 1000 nM, replicate 4


title: Rolipram 0 nM replicate 4

description:
Library name: Rolipram_0_R4
HDFn treated with Rolipram 0 nM, replicate 4


title: Rolipram 1000 nM replicate 2

description:
Library name: Rolipram_1000_R2
HDFn treated with Rolipram 1000 nM, replicate 2


title: Rolipram 125 nM replicate 2

description:
Library name: Rolipram_125_R2
HDFn treated with Rolipram 125 nM, replicate 2


title: Rolipram 1000 nM replicate 3

description:
Library name: Rolipram_1000_R3
HDFn treated with Rolipram 1000 nM, replicate 3


title: Rolipram 0 nM replicate 2

description:
Library name: Rolipram_0_R2
HDFn treated with Rolipram 0 nM, replicate 2


title: Roflumilast 8000 nM replicate 5

description:
Library name: Roflumilast_8000_R5
HDFn treated with Roflumilast 8000 nM, replicate 5

value: Roflumilast 8000 nM


title: Roflumilast 8000 nM replicate 4

description:
Library name: Roflumilast_8000_R4
HDFn treated with Roflumilast 8000 nM, replicate 4


title: Roflumilast 8000 nM replicate 3

description:
Library name: Roflumilast_8000_R3
HDFn treated with Roflumilast 8000 nM, replicate 3


title: Roflumilast 8000 nM replicate 1

description:
Library name: Roflumilast_8000_R1
HDFn treated with Roflumilast 8000 nM, replicate 1


title: Roflumilast 7.8 nM replicate 5

description:
Library name: Roflumilast_7.8_R5
HDFn treated with Roflumilast 7.8 nM, replicate 5

value: Roflumilast 7.8 nM


title: Roflumilast 7.8 nM replicate 4

description:
Library name: Roflumilast_7.8_R4
HDFn treated with Roflumilast 7.8 nM, replicate 4

value: skin (dermis)


title: Roflumilast 7.8 nM replicate 3

description:
Library name: Roflumilast_7.8_R3
HDFn treated with Roflumilast 7.8 nM, replicate 3

value: HDFn


title: Rolipram 1000 nM replicate 5

description:
Library name: Rolipram_1000_R5
HDFn treated with Rolipram 1000 nM, replicate 5

value: fibroblast


title: Roflumilast 62.5 nM replicate 4

description:
Library name: Roflumilast_62.5_R4
HDFn treated with Roflumilast 62.5 nM, replicate 4

value: Roflumilast 62.5 nM


title: Roflumilast 62.5 nM replicate 5

description:
Library name: Roflumilast_62.5_R5
HDFn treated with Roflumilast 62.5 nM, replicate 5


title: Roflumilast 62.5 nM replicate 3

description:
Library name: Roflumilast_62.5_R3
HDFn treated with Roflumilast 62.5 nM, replicate 3


title: Roflumilast 62.5 nM replicate 1

description:
Library name: Roflumilast_62.5_R1
HDFn treated with Roflumilast 62.5 nM, replicate 1


title: Roflumilast 62.5 nM replicate 2

description:
Library name: Roflumilast_62.5_R2
HDFn treated with Roflumilast 62.5 nM, replicate 2


title: Roflumilast 500 nM replicate 5

description:
Library name: Roflumilast_500_R5
HDFn treated with Roflumilast 500 nM, replicate 5

value: Roflumilast 500 nM


title: Roflumilast 500 nM replicate 4

description:
Library name: Roflumilast_500_R4
HDFn treated with Roflumilast 500 nM, replicate 4


title: Roflumilast 500 nM replicate 3

description:
Library name: Roflumilast_500_R3
HDFn treated with Roflumilast 500 nM, replicate 3


title: Roflumilast 500 nM replicate 2

description:
Library name: Roflumilast_500_R2
HDFn treated with Roflumilast 500 nM, replicate 2


title: Roflumilast 4000 nM replicate 5

description:
Library name: Roflumilast_4000_R5
HDFn treated with Roflumilast 4000 nM, replicate 5

value: Roflumilast 4000 nM


title: Roflumilast 500 nM replicate 1

description:
Library name: Roflumilast_500_R1
HDFn treated with Roflumilast 500 nM, replicate 1


title: Roflumilast 4000 nM replicate 3

description:
Library name: Roflumilast_4000_R3
HDFn treated with Roflumilast 4000 nM, replicate 3


title: Roflumilast 4000 nM replicate 4

description:
Library name: Roflumilast_4000_R4
HDFn treated with Roflumilast 4000 nM, replicate 4


title: Roflumilast 4000 nM replicate 2

description:
Library name: Roflumilast_4000_R2
HDFn treated with Roflumilast 4000 nM, replicate 2


title: Rolipram 0 nM replicate 1

description:
Library name: Rolipram_0_R1
HDFn treated with Rolipram 0 nM, replicate 1


title: Roflumilast 31.3 nM replicate 4

description:
Library name: Roflumilast_31.3_R4
HDFn treated with Roflumilast 31.3 nM, replicate 4

value: Roflumilast 31.3 nM


title: Roflumilast 31.3 nM replicate 5

description:
Library name: Roflumilast_31.3_R5
HDFn treated with Roflumilast 31.3 nM, replicate 5


title: Roflumilast 8000 nM replicate 2

description:
Library name: Roflumilast_8000_R2
HDFn treated with Roflumilast 8000 nM, replicate 2


title: Roflumilast 31.3 nM replicate 3

description:
Library name: Roflumilast_31.3_R3
HDFn treated with Roflumilast 31.3 nM, replicate 3


title: Roflumilast 7.8 nM replicate 2

description:
Library name: Roflumilast_7.8_R2
HDFn treated with Roflumilast 7.8 nM, replicate 2


title: Roflumilast 31.3 nM replicate 1

description:
Library name: Roflumilast_31.3_R1
HDFn treated with Roflumilast 31.3 nM, replicate 1


title: Roflumilast 250 nM replicate 4

description:
Library name: Roflumilast_250_R4
HDFn treated with Roflumilast 250 nM, replicate 4

value: Roflumilast 250 nM


title: Roflumilast 31.3 nM replicate 2

description:
Library name: Roflumilast_31.3_R2
HDFn treated with Roflumilast 31.3 nM, replicate 2


title: Roflumilast 7.8 nM replicate 1

description:
Library name: Roflumilast_7.8_R1
HDFn treated with Roflumilast 7.8 nM, replicate 1


title: Roflumilast 250 nM replicate 1

description:
Library name: Roflumilast_250_R1
HDFn treated with Roflumilast 250 nM, replicate 1


title: Roflumilast 250 nM replicate 5

description:
Library name: Roflumilast_250_R5
HDFn treated with Roflumilast 250 nM, replicate 5


title: Roflumilast 2000 nM replicate 4

description:
Library name: Roflumilast_2000_R4
HDFn treated with Roflumilast 2000 nM, replicate 4

value: Roflumilast 2000 nM


title: Roflumilast 2000 nM replicate 5

description:
Library name: Roflumilast_2000_R5
HDFn treated with Roflumilast 2000 nM, replicate 5


title: Roflumilast 250 nM replicate 3

description:
Library name: Roflumilast_250_R3
HDFn treated with Roflumilast 250 nM, replicate 3


title: Roflumilast 2000 nM replicate 2

description:
Library name: Roflumilast_2000_R2
HDFn treated with Roflumilast 2000 nM, replicate 2


title: Roflumilast 15.6 nM replicate 3

description:
Library name: Roflumilast_15.6_R3
HDFn treated with Roflumilast 15.6 nM, replicate 3

value: Roflumilast 15.6 nM


title: Roflumilast 15.6 nM replicate 5

description:
Library name: Roflumilast_15.6_R5
HDFn treated with Roflumilast 15.6 nM, replicate 5


title: Roflumilast 125 nM replicate 5

description:
Library name: Roflumilast_125_R5
HDFn treated with Roflumilast 125 nM, replicate 5

value: Roflumilast 125 nM


title: Roflumilast 125 nM replicate 2

description:
Library name: Roflumilast_125_R2
HDFn treated with Roflumilast 125 nM, replicate 2


title: Roflumilast 125 nM replicate 3

description:
Library name: Roflumilast_125_R3
HDFn treated with Roflumilast 125 nM, replicate 3


title: Roflumilast 15.6 nM replicate 4

description:
Library name: Roflumilast_15.6_R4
HDFn treated with Roflumilast 15.6 nM, replicate 4


title: Roflumilast 1000 nM replicate 5

description:
Library name: Roflumilast_1000_R5
HDFn treated with Roflumilast 1000 nM, replicate 5

value: Roflumilast 1000 nM


title: Roflumilast 4000 nM replicate 1

description:
Library name: Roflumilast_4000_R1
HDFn treated with Roflumilast 4000 nM, replicate 1


title: Roflumilast 15.6 nM replicate 2

description:
Library name: Roflumilast_15.6_R2
HDFn treated with Roflumilast 15.6 nM, replicate 2


title: Roflumilast 15.6 nM replicate 1

description:
Library name: Roflumilast_15.6_R1
HDFn treated with Roflumilast 15.6 nM, replicate 1


title: Roflumilast 2000 nM replicate 1

description:
Library name: Roflumilast_2000_R1
HDFn treated with Roflumilast 2000 nM, replicate 1


title: Roflumilast 1000 nM replicate 4

description:
Library name: Roflumilast_1000_R4
HDFn treated with Roflumilast 1000 nM, replicate 4


title: Roflumilast 125 nM replicate 1

description:
Library name: Roflumilast_125_R1
HDFn treated with Roflumilast 125 nM, replicate 1


title: Roflumilast 1000 nM replicate 1

description:
Library name: Roflumilast_1000_R1
HDFn treated with Roflumilast 1000 nM, replicate 1


title: Roflumilast 1000 nM replicate 2

description:
Library name: Roflumilast_1000_R2
HDFn treated with Roflumilast 1000 nM, replicate 2


title: Roflumilast 0 nM replicate 3

description:
Library name: Roflumilast_0_R3
HDFn treated with Roflumilast 0 nM, replicate 3

value: Roflumilast 0 nM


title: Roflumilast 0 nM replicate 4

description:
Library name: Roflumilast_0_R4
HDFn treated with Roflumilast 0 nM, replicate 4


title: Roflumilast 0 nM replicate 2

description:
Library name: Roflumilast_0_R2
HDFn treated with Roflumilast 0 nM, replicate 2


title: Roflumilast 1000 nM replicate 3

description:
Library name: Roflumilast_1000_R3
HDFn treated with Roflumilast 1000 nM, replicate 3


title: Roflumilast 0 nM replicate 1

description:
Library name: Roflumilast_0_R1
HDFn treated with Roflumilast 0 nM, replicate 1


title: Milrinone 8000 nM replicate 4

description:
Library name: Milrinone_8000_R4
HDFn treated with Milrinone 8000 nM, replicate 4

value: Milrinone 8000 nM


title: Milrinone 8000 nM replicate 2

description:
Library name: Milrinone_8000_R2
HDFn treated with Milrinone 8000 nM, replicate 2


title: Milrinone 8000 nM replicate 5

description:
Library name: Milrinone_8000_R5
HDFn treated with Milrinone 8000 nM, replicate 5


title: Roflumilast 250 nM replicate 2

description:
Library name: Roflumilast_250_R2
HDFn treated with Roflumilast 250 nM, replicate 2


title: Milrinone 8000 nM replicate 1

description:
Library name: Milrinone_8000_R1
HDFn treated with Milrinone 8000 nM, replicate 1


title: Roflumilast 2000 nM replicate 3

description:
Library name: Roflumilast_2000_R3
HDFn treated with Roflumilast 2000 nM, replicate 3


title: Roflumilast 125 nM replicate 4

description:
Library name: Roflumilast_125_R4
HDFn treated with Roflumilast 125 nM, replicate 4


title: Milrinone 7.8 nM replicate 5

description:
Library name: Milrinone_7.8_R5
HDFn treated with Milrinone 7.8 nM, replicate 5

value: Milrinone 7.8 nM


title: Milrinone 7.8 nM replicate 4

description:
Library name: Milrinone_7.8_R4
HDFn treated with Milrinone 7.8 nM, replicate 4


title: Milrinone 7.8 nM replicate 3

description:
Library name: Milrinone_7.8_R3
HDFn treated with Milrinone 7.8 nM, replicate 3


title: Milrinone 62.5 nM replicate 4

description:
Library name: Milrinone_62.5_R4
HDFn treated with Milrinone 62.5 nM, replicate 4

value: Milrinone 62.5 nM


title: Milrinone 7.8 nM replicate 1

description:
Library name: Milrinone_7.8_R1
HDFn treated with Milrinone 7.8 nM, replicate 1


title: Milrinone 62.5 nM replicate 1

description:
Library name: Milrinone_62.5_R1
HDFn treated with Milrinone 62.5 nM, replicate 1


title: Milrinone 7.8 nM replicate 2

description:
Library name: Milrinone_7.8_R2
HDFn treated with Milrinone 7.8 nM, replicate 2


title: Milrinone 500 nM replicate 5

description:
Library name: Milrinone_500_R5
HDFn treated with Milrinone 500 nM, replicate 5

value: Milrinone 500 nM


title: Milrinone 500 nM replicate 3

description:
Library name: Milrinone_500_R3
HDFn treated with Milrinone 500 nM, replicate 3

value: skin (dermis)


title: Milrinone 62.5 nM replicate 2

description:
Library name: Milrinone_62.5_R2
HDFn treated with Milrinone 62.5 nM, replicate 2

value: HDFn


title: Milrinone 62.5 nM replicate 3

description:
Library name: Milrinone_62.5_R3
HDFn treated with Milrinone 62.5 nM, replicate 3

value: fibroblast


title: Milrinone 4000 nM replicate 5

description:
Library name: Milrinone_4000_R5
HDFn treated with Milrinone 4000 nM, replicate 5

value: Milrinone 4000 nM


title: Milrinone 8000 nM replicate 3

description:
Library name: Milrinone_8000_R3
HDFn treated with Milrinone 8000 nM, replicate 3


title: Milrinone 500 nM replicate 2

description:
Library name: Milrinone_500_R2
HDFn treated with Milrinone 500 nM, replicate 2


title: Milrinone 500 nM replicate 4

description:
Library name: Milrinone_500_R4
HDFn treated with Milrinone 500 nM, replicate 4


title: Milrinone 31.3 nM replicate 5

description:
Library name: Milrinone_31.3_R5
HDFn treated with Milrinone 31.3 nM, replicate 5

value: Milrinone 31.3 nM


title: Milrinone 4000 nM replicate 2

description:
Library name: Milrinone_4000_R2
HDFn treated with Milrinone 4000 nM, replicate 2


title: Milrinone 500 nM replicate 1

description:
Library name: Milrinone_500_R1
HDFn treated with Milrinone 500 nM, replicate 1


title: Milrinone 31.3 nM replicate 4

description:
Library name: Milrinone_31.3_R4
HDFn treated with Milrinone 31.3 nM, replicate 4


title: Milrinone 31.3 nM replicate 3

description:
Library name: Milrinone_31.3_R3
HDFn treated with Milrinone 31.3 nM, replicate 3


title: Milrinone 4000 nM replicate 4

description:
Library name: Milrinone_4000_R4
HDFn treated with Milrinone 4000 nM, replicate 4


title: Milrinone 250 nM replicate 4

description:
Library name: Milrinone_250_R4
HDFn treated with Milrinone 250 nM, replicate 4

value: Milrinone 250 nM


title: Milrinone 31.3 nM replicate 2

description:
Library name: Milrinone_31.3_R2
HDFn treated with Milrinone 31.3 nM, replicate 2


title: Milrinone 31.3 nM replicate 1

description:
Library name: Milrinone_31.3_R1
HDFn treated with Milrinone 31.3 nM, replicate 1


title: Milrinone 250 nM replicate 5

description:
Library name: Milrinone_250_R5
HDFn treated with Milrinone 250 nM, replicate 5


title: Milrinone 62.5 nM replicate 5

description:
Library name: Milrinone_62.5_R5
HDFn treated with Milrinone 62.5 nM, replicate 5


title: Milrinone 250 nM replicate 1

description:
Library name: Milrinone_250_R1
HDFn treated with Milrinone 250 nM, replicate 1


title: Milrinone 250 nM replicate 3

description:
Library name: Milrinone_250_R3
HDFn treated with Milrinone 250 nM, replicate 3


title: Milrinone 250 nM replicate 2

description:
Library name: Milrinone_250_R2
HDFn treated with Milrinone 250 nM, replicate 2


title: Milrinone 2000 nM replicate 5

description:
Library name: Milrinone_2000_R5
HDFn treated with Milrinone 2000 nM, replicate 5

value: Milrinone 2000 nM


title: Milrinone 4000 nM replicate 3

description:
Library name: Milrinone_4000_R3
HDFn treated with Milrinone 4000 nM, replicate 3


title: Milrinone 15.6 nM replicate 3

description:
Library name: Milrinone_15.6_R3
HDFn treated with Milrinone 15.6 nM, replicate 3

value: Milrinone 15.6 nM


title: Milrinone 15.6 nM replicate 2

description:
Library name: Milrinone_15.6_R2
HDFn treated with Milrinone 15.6 nM, replicate 2


title: Milrinone 125 nM replicate 3

description:
Library name: Milrinone_125_R3
HDFn treated with Milrinone 125 nM, replicate 3

value: Milrinone 125 nM


title: Milrinone 2000 nM replicate 3

description:
Library name: Milrinone_2000_R3
HDFn treated with Milrinone 2000 nM, replicate 3


title: Milrinone 2000 nM replicate 1

description:
Library name: Milrinone_2000_R1
HDFn treated with Milrinone 2000 nM, replicate 1


title: Milrinone 4000 nM replicate 1

description:
Library name: Milrinone_4000_R1
HDFn treated with Milrinone 4000 nM, replicate 1


title: Milrinone 1000 nM replicate 2

description:
Library name: Milrinone_1000_R2
HDFn treated with Milrinone 1000 nM, replicate 2

value: Milrinone 1000 nM


title: Milrinone 15.6 nM replicate 1

description:
Library name: Milrinone_15.6_R1
HDFn treated with Milrinone 15.6 nM, replicate 1


title: Milrinone 15.6 nM replicate 5

description:
Library name: Milrinone_15.6_R5
HDFn treated with Milrinone 15.6 nM, replicate 5


title: Milrinone 1000 nM replicate 4

description:
Library name: Milrinone_1000_R4
HDFn treated with Milrinone 1000 nM, replicate 4


title: Milrinone 0 nM replicate 5

description:
Library name: Milrinone_0_R5
HDFn treated with Milrinone 0 nM, replicate 5

value: Milrinone 0 nM


title: Milrinone 15.6 nM replicate 4

description:
Library name: Milrinone_15.6_R4
HDFn treated with Milrinone 15.6 nM, replicate 4


title: Milrinone 125 nM replicate 5

description:
Library name: Milrinone_125_R5
HDFn treated with Milrinone 125 nM, replicate 5


title: Milrinone 0 nM replicate 3

description:
Library name: Milrinone_0_R3
HDFn treated with Milrinone 0 nM, replicate 3


title: Milrinone 0 nM replicate 2

description:
Library name: Milrinone_0_R2
HDFn treated with Milrinone 0 nM, replicate 2


title: Milrinone 1000 nM replicate 3

description:
Library name: Milrinone_1000_R3
HDFn treated with Milrinone 1000 nM, replicate 3


title: Milrinone 0 nM replicate 1

description:
Library name: Milrinone_0_R1
HDFn treated with Milrinone 0 nM, replicate 1


title: Cilostazol 7.8 nM replicate 2

description:
Library name: Cilostazol_7.8_R2
HDFn treated with Cilostazol 7.8 nM, replicate 2

value: Cilostazol 7.8 nM


title: Cilostazol 8000 nM replicate 2

description:
Library name: Cilostazol_8000_R2
HDFn treated with Cilostazol 8000 nM, replicate 2

value: Cilostazol 8000 nM


title: Cilostazol 62.5 nM replicate 1

description:
Library name: Cilostazol_62.5_R1
HDFn treated with Cilostazol 62.5 nM, replicate 1

value: Cilostazol 62.5 nM


title: Cilostazol 8000 nM replicate 1

description:
Library name: Cilostazol_8000_R1
HDFn treated with Cilostazol 8000 nM, replicate 1


title: Cilostazol 7.8 nM replicate 1

description:
Library name: Cilostazol_7.8_R1
HDFn treated with Cilostazol 7.8 nM, replicate 1


title: Milrinone 2000 nM replicate 4

description:
Library name: Milrinone_2000_R4
HDFn treated with Milrinone 2000 nM, replicate 4


title: Milrinone 2000 nM replicate 2

description:
Library name: Milrinone_2000_R2
HDFn treated with Milrinone 2000 nM, replicate 2


title: Cilostazol 62.5 nM replicate 2

description:
Library name: Cilostazol_62.5_R2
HDFn treated with Cilostazol 62.5 nM, replicate 2


title: Milrinone 1000 nM replicate 5

description:
Library name: Milrinone_1000_R5
HDFn treated with Milrinone 1000 nM, replicate 5


title: Milrinone 125 nM replicate 1

description:
Library name: Milrinone_125_R1
HDFn treated with Milrinone 125 nM, replicate 1


title: Cilostazol 500 nM replicate 1

description:
Library name: Cilostazol_500_R1
HDFn treated with Cilostazol 500 nM, replicate 1

value: Cilostazol 500 nM


title: Milrinone 1000 nM replicate 1

description:
Library name: Milrinone_1000_R1
HDFn treated with Milrinone 1000 nM, replicate 1


title: Cilostazol 4000 nM replicate 2

description:
Library name: Cilostazol_4000_R2
HDFn treated with Cilostazol 4000 nM, replicate 2

value: Cilostazol 4000 nM


title: Cilostazol 4000 nM replicate 1

description:
Library name: Cilostazol_4000_R1
HDFn treated with Cilostazol 4000 nM, replicate 1


title: Cilostazol 250 nM replicate 2

description:
Library name: Cilostazol_250_R2
HDFn treated with Cilostazol 250 nM, replicate 2

value: Cilostazol 250 nM


title: Cilostazol 15.6 nM replicate 2

description:
Library name: Cilostazol_15.6_R2
HDFn treated with Cilostazol 15.6 nM, replicate 2

value: skin (dermis)

value: Cilostazol 15.6 nM


title: Cilostazol 31.3 nM replicate 1

description:
Library name: Cilostazol_31.3_R1
HDFn treated with Cilostazol 31.3 nM, replicate 1

value: HDFn

value: fibroblast

value: Cilostazol 31.3 nM


title: Cilostazol 15.6 nM replicate 1

description:
Library name: Cilostazol_15.6_R1
HDFn treated with Cilostazol 15.6 nM, replicate 1


title: Cilostazol 31.3 nM replicate 2

description:
Library name: Cilostazol_31.3_R2
HDFn treated with Cilostazol 31.3 nM, replicate 2


title: Cilostazol 250 nM replicate 1

description:
Library name: Cilostazol_250_R1
HDFn treated with Cilostazol 250 nM, replicate 1


title: Cilostazol 2000 nM replicate 2

description:
Library name: Cilostazol_2000_R2
HDFn treated with Cilostazol 2000 nM, replicate 2

value: Cilostazol 2000 nM


title: Cilostazol 125 nM replicate 1

description:
Library name: Cilostazol_125_R1
HDFn treated with Cilostazol 125 nM, replicate 1

value: Cilostazol 125 nM


title: Cilostazol 2000 nM replicate 1

description:
Library name: Cilostazol_2000_R1
HDFn treated with Cilostazol 2000 nM, replicate 1


title: Cilostazol 1000 nM replicate 2

description:
Library name: Cilostazol_1000_R2
HDFn treated with Cilostazol 1000 nM, replicate 2

value: Cilostazol 1000 nM


title: Cilostazol 0 nM replicate 2

description:
Library name: Cilostazol_0_R2
HDFn treated with Cilostazol 0 nM, replicate 2

value: Cilostazol 0 nM


title: Cilostazol 0 nM replicate 1

description:
Library name: Cilostazol_0_R1
HDFn treated with Cilostazol 0 nM, replicate 1


title: Cilostazol 1000 nM replicate 1

description:
Library name: Cilostazol_1000_R1
HDFn treated with Cilostazol 1000 nM, replicate 1


title: Bbs5_5 wks_mut_E6

first: Naila

last: Haq

state: London

address: Room HB4.2E, 2nd Floor, Hodgkin Building, Guy's Campus, London Bridge,

institute: King's College London

description: Library name: Sample 10

data_processing:
TopHat and Bowtie
SAMtools
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw conts for each samples
Supplementary files format and content: tab-delimited text files include RPKM for each samples
Supplementary files format and content: excel files for analyses

source_name: Hypothalamic tissue

growth_protocol: No growth protocol

extract_protocol:
Core hypothalamic tissues of 12 weeks old Bbs5 male (3 knockouts and 2 controls littermates) mice were isolated using brain tissue slicer and micro-puncher (Integra-Miltex).
Sample libraries were prepared with the NEBNext® UltraTM Directional RNA Library Prep for Illumina® kit (New England Biolabs, Inc.).

treatment_protocol: no treatment protocol

value: Hypothalamic tissue

value: neuronal

value: Bbs5_5 wks_mut(E6)

value: no treatment


title: Bbs5_5 wks_mut_E5

description: Library name: Sample 9

value: Bbs5_5 wks_mut(E5)


title: Bbs5_5 wks_mut_E4

description: Library name: Sample 8

value: Bbs5_5 wks_mut(E4)


title: Cilostazol 500 nM replicate 2

description:
Library name: Cilostazol_500_R2
HDFn treated with Cilostazol 500 nM, replicate 2

value: Cilostazol 500 nM


title: WT_E3

description: Library name: Sample 7


title: WT_E1

description: Library name: Sample 6


title: Bbs5_12 wks_mut_B5

description: Library name: Sample 4

value: Bbs5_12 wks_mut(B5)


title: Bbs5_12 wks_mut_B4

description: Library name: Sample 3

value: Bbs5_12 wks_mut(B4)


title: WT_B3

description: Library name: Sample 2


title: WT_B1

description: Library name: Sample 1


title: Multiome_snATAC-seq, HGSOC_Unenriched_Tumor

city: Chicago

first: Mazhar

last: Adli

state: IL

address: 303 E. Superior St

department: Department of Obstetrics & Gynecology

institute: Northwestern University

description:
Library name: HGSOC_Unenriched_Tumor_snATAC-seq
10X Genomics

library_source: genomic single cell

data_processing:
FASTQ files were demultiplexed using 10X Genomics' Cellranger
FASTQ files were aligned to GRCh38 using 10X Genomics' Cellranger-arc v. 2.0.2 using default settings
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, atac_fragments.tsv.gz

source_name: High grade serous ovarian cancer

extract_protocol:
The fresh tissues were washed with cold PBS and first mechanically disrupted to generate small pieces. Then, they were subjected to enzymatic digestion with the Tissue Dissociation Kit (Miltenyi Biotec, 130-095-929) following the manufacturer’s instructions. Enzymatic digestion was carried out for 2 hours at 37° C with shaking at 350 rpm. The digested samples were then filtered through 70 micron cell strainers and subjected to the red-blood cell lysis using RBC lysis buffer (eBioScience, 00-4333-57).
The isolated nuclei were immediately used for transposition, followed by GEM generation and barcoding, cleanup and library pre-amplification PCR following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide (10X Genomics, Rev E). The pre-amplified samples were used to generate ATAC library construction and cDNA amplification for Gene Expression library construction.

value: High grade serous ovarian cancer


title: Multiome_snRNA-seq, HGSOC_Unenriched_Tumor

description:
Library name: HGSOC_Unenriched_Tumor_snRNA-seq
10X Genomics

molecule: nuclear RNA


title: si-NEXN+PDGF-BB, rep3

first: Hanyan

last: Yang

address: Zhujiang Hospital, Southern Medical University, Haizhu District, Guangzhou City, Guangdong Province

institute: Southern Medical University

description:
Library name: sample 6
1_genes_fpkm_expression.txt

data_processing:
Step 1: Use Fastp software (https://github.com/OpenGene/fastp) to filter out reads with adapter contamination, low quality, and undetermined bases, and verify sequence quality.
Step 2: Employ HISAT2 (https://ccb.jhu.edu/software/hisat2) for read mapping to the Homo sapiens GRCh38 reference genome.
Step 3: Use StringTie (https://ccb.jhu.edu/software/stringtie) to assemble the mapped reads and merge transcriptomes across samples to reconstruct a comprehensive transcriptome, which was further refined using gffcompare (https://github.com/gpertea/gffcompare/).
Step 4: Estimate expression levels with StringTie, calculating FPKM values for mRNAs.
Step 5: Conduct differential expression analysis with edgeR, identifying mRNAs with a |log2(FC)|>1 (fold change > 2 or < 0.5) and a P - value < 0.05 from parametric F - tests.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: human aortic isolated SMCs (HASMCs)

growth_protocol: Primary human aortic smooth muscle cells (HASMCs) were sourced from iCell Bioscience Inc. (catalog number: HUM-iCell-c010) and cultured in proprietary low-serum medium (PriMed-iCell-004) in strict adherence to the manufacturer's guidelines. These cells were meticulously cultivated under controlled conditions in a humidified incubator at a temperature of 37°C, with an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted and purified using TRIzol Reagent (Invitrogen, 15596026). Its quantity and purity were measured with a NanoDrop ND - 1000. RNA integrity was ensured with a RIN score above 7.0, assessed by Bioanalyzer 2100 and agarose gel electrophoresis. Poly(A) RNA was selected from total RNA using Dynabeads Oligo (dT) 25 - 61005.
The selected poly(A) RNA fragments were reverse - transcribed into cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649). Then, it was converted into U - labeled second - stranded DNAs. An A - base was added to the ends for adapter ligation. Indexed adapters were ligated to the A - tailed DNA, and products were size - selected with AMPureXP beads. After UDG enzyme (NEB, cat.m0280) treatment, the products were amplified by PCR. The final cDNA library had an average insert size of 300±50 bp.

treatment_protocol: HASMCs were pre-transfected with NC or si-NEXN. and then followed by PDGF-BB stimulation for 24h.

value: human aortic isolated SMCs (HASMCs)

value: Pre - transfect with si-NEXN, then stimulate with PDGF - BB for 24 h


title: Cilostazol 125 nM replicate 2

description:
Library name: Cilostazol_125_R2
HDFn treated with Cilostazol 125 nM, replicate 2

value: skin (dermis)

value: HDFn

value: fibroblast


title: NC+PDGF-BB, rep3

description:
Library name: sample 3
1_genes_fpkm_expression.txt

value: Pre - transfect with NC, then stimulate with PDGF - BB for 24 h