title: UF1hypo shUHRF1.1

first: Jiongliang

address: 190 Kaiyuan Avenue

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

description: Library name: UF1hypo shUHRF1.1

data_processing:
For removing potential adapters and low-quality reads, Fastp v0.21.0  was used. HISAT2 v2.0.4  was then applied to map the clean reads to human genome of GRCh38 . Raw gene counts and the normalized expression value (TPM, transcripts per kilobase million) were computed by StringTie v2.1.4 .
Assembly: GRCh38
Supplementary files format and content: StringTie output.

source_name: colon

extract_protocol: transcriptome profiling were performed in human HCT116 wild-type cells, HCT116 DNMT1 hypomorphs, and HCT116 UHRF1 hypomorphs. The paired-end RNA-seq on the Illumina platform was employed to obtain comprehensive gene expression profiles.

value: colon

tag: cell line


title: UF1hypo shScr.1

status: Public on Apr 20 2026

type: SRA

city: Guangzhou

last: Wang

state: Guangdong

country: China

description: Library name: UF1hypo shScr.1

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: treatment

value: shScr


title: Sample1 of Run5, Severe Alzheimer's Disease,  Dentate gyrus punch

city: Amsterdam

first: Dilara

last: Ayyildiz

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute For Neuroscience

description:
Library name: S1R5
10x Genomics

library_source: transcriptomic single cell

data_processing:
Paired-end FASTQ files were aligned and quantified with STARsolo123 from STAR v2.7.10b_alpha_230301(--soloFeatures Gene GeneFull_Ex50pAS Velocyto, --soloType CB_UMI_Simple, --soloCBwhitelist 3M-february-2018.txt, --soloUMIlen 12, --soloCellFilter EmptyDrops_CR, --soloMultiMappers EM) using the human reference genome GRCh38 (GENCODE v32/Ensembl98). All downstream steps were performed using the count matrix of GeneFull_Ex50pAS option, unless specified otherwise.
Assembly: GRCh38
Supplementary files format and content: Seurat Object as RDS file

molecule: total RNA

source_name: Dentate gyrus

extract_protocol:
Nuclei were isolated from the frozen punched tissue or sections using an optimized isolation protocol. Briefly, samples were homogenized using a glass Dounce homogenizer (15 gentle strokes) in 1 ml of ice-cold Homogenization Buffer (HB), which contained mM sucrose, 5 mM calcium chloride, 3 mM magnesium acetate, 10 mM Tris, 0.1 mM EDTA, 0.1% Igepal, 0.1 mM PMSF, 1 mM 2-mercaptoethanol, and UltraPure water, along with 5 μl RNasin Plus (Promega, Benelux, Belgium). The homogenate was filtered using a 70 μm strainer and washed with 1.65 mL HB, bringing the final volume to 2.65 ml. An additional 2.65 ml of Gradient Medium (containing 5 mM calcium chloride, 50% OptiPrep (Sigma-Aldrich, Belgium), 3 mM magnesium acetate, 10 mM Tris, 0.2 mM PMSF, and 1 mM 2-mercaptoethanol) was added to achieve a final volume of 5.3 ml. To isolate the nuclei, OptiPrep Diluent Medium (ODM) consisting of 150 mM potassium chloride, 30 mM magnesium chloride, 60 mM Tris, and 250 mM sucrose was prepared. The sample was layered onto a 4 ml 29% cushion (29% Optiprep, ODM) using a P1000 pipette, and the weight was balanced with HB. Centrifugation was carried out at 7,700 rpm for 30 min at 4°C using a SW41Ti rotor. After centrifugation, the  supernatant was removed with a plastic Pasteur pipette, and the lower supernatant was aspirated using a P200 pipette. The nuclei were resuspended in 200 μl of resuspension buffer (1x PBS, 1% BSA, and 0.2 U/μl RNasin Plus), transferred to a fresh tube, and washed again with 100-200 μl of the same buffer. The resuspended solution was pooled, and any clumps were disrupted by pipetting with a P200. The sample was then filtered through a 0.35 μm strainer using a Falcon tube. A 9 μl-aliquot of the sample was mixed with 1 μl of propidium iodide (PI) stain, loaded onto a LUNA-FL slide, and left to settle for 30 seconds. The nuclei were examined under a LUNA-FL Automated Cell Counter to assess numbers and morphology.
Post cDNA amplification cleanup and construction of sample-indexed libraries and their amplification followed manufacturer’s directions (10x Genomics, CG000183_Rev_A), with the amplification step directly dependent on the quantity of input cDNA. In order to reach sequencing saturation of ~65% (~45,000 reads/nucleus), single nucleus libraries were run using paired-end sequencing with single indexing on the NovaSeq6000 platform, following manufacturer’s instructions (10x Genomics, CG000204_Rev_A). To avoid lane bias, multiple uniquely indexed samples were mixed and distributed over several lanes.

value: Dentate gyrus

tag: Sex

value: M

tag: age

tag: group

value: SAD

tag: batch

value: Run 5


title: TN_WD_female_3d_89_liver

city: LAUSANNE

first: Johan

last: Auwerx

address: Station 15

department: SV-IBI

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne EPFL

description: Library name: HDP-019069_liver

data_processing:
Bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced by Alithea Genomics (Switzerland). The raw data was demultiplexed, cleaned, and aligned to the mouse reference genome GRCm39/mm39 using R (version 4.1.a) and START (version 2.7.9a). Count matrices were used for downstream analyses
Assembly: genome GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was extracted from liver and heart tissues using Direct-zol-96 RNA kit (Zymo research)
The generation of bulk RNA Barcoding and sequencing (BRB-seq) libraries was performed using the MERCURIUSTM BRB-seq library preparation kit for Illumina and following the manufacturer’s manual

value: liver


title: No template control

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

country: USA

institute: University of Oklahoma Health Sciences Center

description:
Library name: DSP-1001660008101-A-A01
Technical no-template control from the GeoMx DSP Human Whole Transcriptome Atlas RNA workflow; processed alongside the four experimental slides.
raw_count14.csv
GeoMx_tmm_ruv_normalized_count_linear_S14.csv
sampleAnnoFile_S14.csv

data_processing:
Raw paired-end reads were processed with Bruker GeoMx NGS Pipeline v3.1.0.194 to assign reads to Human Whole Transcriptome Atlas targets and generate gene-level count outputs. Quality control and downstream normalization were performed in R using standR v1.10.0. ROIs were excluded if they failed preset thresholds for minimum segment reads (1000), percent trimmed (80), percent stitched (80), percent aligned (80), percent sequencing saturation (50), maximum no-template-control count (1000), minimum area (1000), and minimum nuclei (50, when available). For slide 5, nuclei-based filtering was not available. Genes with fewer than 5 counts in more than 60% of regions were removed in the discovery cohort. Normalized expression matrices were generated using trimmed mean of M-values normalization and RUV5 correction for slide-level effects; differential expression testing was performed with limma-voom v3.62.2.
Assembly: hg38
Supplementary files format and content: Raw count matrix of slide 1-4: raw_count14.csv  | Raw count matrix of slide 5: raw_count5.csv | Normalized count matrix of slide 1-4: GeoMx_tmm_ruv_normalized_count_linear_S14.csv | Normalized count matrix of slide 5: GeoMx_tmm_ruv_normalized_count_linear_S5.csv | Metadata of slide 1-4: sampleAnnoFile_S14.csv | Metadata of slide 5: sampleAnnoFile_S5.csv
Supplementary files format and content: In Metadata, "library" column  matches the library name above, "SegmentDisplayName" column matches the columns/samples in the raw count matrix, "sampleID" column matches the columns/samples in the normalized count matrix.
Library strategy: Spatial Transcriptomics

organism: synthetic construct

source_name: no template control

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) breast tissues from patients diagnosed with ductal carcinoma in situ (DCIS) or invasive ductal carcinoma (IDC) were obtained from the Department of Pathology at the University of Oklahoma Health Campus (Oklahoma City, OK). A pathologist confirmed the histopathologic diagnosis using routine diagnostic criteria. Patient demographic and clinicopathologic data were abstracted from the medical record, samples were de-identified, and their use was approved under University of Oklahoma IRB 12384. FFPE sections were mounted on Apex BOND Adhesive slides with tissue positioned within the GeoMx imaging area and baked at 60°C for at least 30 minutes. Slides were prepared on the Leica BOND RX using the GeoMx NGS RNA FFPE BOND workflow for breast tissue, including: bake and dewax preparation, ER2 heat-induced epitope retrieval for 10 minutes at 100°C, and Proteinase K digestion at 0.1 μg/mL for 15 minutes. Human Whole Transcriptome Atlas RNA probes containing UV-photocleavable barcoded oligonucleotides were hybridized overnight at 37°C. After stringent washes at 37°C (two 25-minute washes in Stringent Wash solution followed by two 2-minute washes in 2X SSC), slides were blocked in Buffer W for 30 minutes and stained for 1 hour at room temperature with the four-color morphology panel alpha smooth muscle actin (SMA)-647, SYTO 13 nuclear stain, pan-cytokeratin (CK)-532, and leukocyte (CD45)-AF594. Morphology markers guided ROI selection and segmentation of CK+, SMA+, and/or CD45+ compartments. Prepared slides were loaded onto the GeoMx DSP, each ROI was illuminated with UV light, and released oligonucleotides were collected by microcapillary aspiration into separate wells of a 96-well plate.
Region-specific oligonucleotides released on the GeoMx DSP were collected into individual wells of a 96-well plate and converted into sequencing libraries according to the manufacturer’s GeoMx RNA library preparation workflow for the Human Whole Transcriptome Atlas assay. Libraries were indexed according to the GeoMx protocol and sequenced as paired-end 150-bp reads on an Illumina NovaSeq X Plus instrument at the University of Colorado Anschutz Medical Campus shared-resource facility in Aurora, Colorado.

value: no template control

tag: cell type

tag: slide

value: No template control

tag: roi

tag: segment


title: UF1hypo shScr.2

description: Library name: UF1hypo shScr.2


title: Ath_Root_Ctrl_Bulk_R1

city: Stanford

first: Guannan

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

description: Roots from 4-6-day-old seedlings for bulk RNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using Cell Ranger (v5.0.1, 10X Genomics)
Assembly: Arabidopsis (TAIR10) from The Arabidopsis Information Resource (TAIR; https://www.arabidopsis.org/), C. sativa (v2) from Brassicaceae Database (BRAD; http://brassicadb.cn), E. salsugineum (v1.0) and S. parvula (v2.2) from Phytozome 12 (https://phytozome-next.jgi.doe.gov/) (Phytozome ID 574 and 173, respectively), reference genome for S. irio (v1.0) from Brassicaceae Database (BRAD; http://brassicadb.cn) with the updated gene model annotation (Sun et al., 2022) from the CoGe database (https://genomevolution.org/) with the Genome ID 57216.
Supplementary files format and content: tab-separated value files and matrix files; rds files

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Primary root tips of seedlings from different species were cut and placed into a 35 mm petri dish containing a 70 um strainer and 4 mL enzyme solution (1.25% [w/v] Cellulase [“ONOZUKA” R-10, Yakult], 0.1%[w/v] Pectolyase [P-3026, Sigma-Aldrich], 0.4 M Mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin). The sample dish was rotated at 85 rpm for 50 min at 25°C. The root tips were then transferred to a slide glass and gently pressed with a cover glass using a pencil rubber to release protoplasts. The tissues were transferred back to the enzyme solution and incubated for another 10 minutes. Then, the protoplast solution was filtered through a 70 μm filter, and then through a 40 μm filter twice using 50 mL conical tubes. The filtered solution was centrifuged at 500g for 10 min at 22°C using a swinging bucket rotor and the supernatant was discarded. Protoplasts were resuspended using 500 μL Solution A (0.4 M Mannitol, 20 mM MES [pH 5.7], 20 mM KCl, 10 mM CaCl2, 0.1% [w/v] bovine serum albumin) and transferred to a 2 mL round bottom tube. After centrifugation at 200g for 6 min, the pelleted protoplasts were resuspended with 30–50 μL Solution A to achieve the desired cell concentration (~1,000 protoplasts/μL).
The protoplast suspension was loaded into Chromium microfluidic chips (Next GEM Single Cell 3’ kit) and barcoded with a 10X Chromium Controller (10X Genomics). mRNA from the barcoded cells were subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ reagent kit v3.1 chemistry dual index (10X Genomics) according to the manufacturer’s instructions.

value: Root

value: 4-6-day-old seedlings

value: Control


title: Naive-LPS-A1

city: jinan

first: zhang

middle: jia

last: min

address: 山东省济南市平阴县

institute: jinan central hospital

description: Library name: Naive-LPS-A1

data_processing:
Raw reads were quality-controlled and adapter-trimmed using fastp.
Trimmed reads were aligned to the hg38 (human) reference genome using Bowtie2.
PCR duplicates were removed using Picard tools.
Peak calling was performed using MACS2 to identify open chromatin regions (ATAC-seq peaks).
Identified peaks were annotated, and transcription factor binding motif analysis was performed using HOMER.
Assembly: hg38
Supplementary files format and content: BAM: Aligned reads after quality control and duplicate removal BED: Called ATAC-seq peaks bigWig: Normalized signal tracks for visualization HOMER output: Peak annotation and motif analysis results

source_name: peripheral blood

growth_protocol:
Isolation, Sorting, and Culture of Primary Human Immune Cells
Peripheral blood mononuclear cells (PBMCs) were isolated from the peripheral blood of healthy volunteers and patients using Polymorphprep density gradient centrifugation. To obtain CD14⁺ monocytes, PBMCs were cultured in medium for 2 hours, and the adherent cells were subsequently collected. CD14⁺ cells were induced to differentiate into macrophages by treatment with M-CSF (50 ng/mL) for 5 days. Cell purity was assessed by flow cytometry. An in vitro model of immune paralysis was established by treating monocytes with 10–100 ng/mL LPS for 24 hours, followed by washing and culturing in RPMI medium supplemented with 10% human serum for 5 days in the presence of M-CSF (50 ng/mL) to allow differentiation into immune-paralyzed macrophages.

extract_protocol:
RNA Extraction and Transcriptome Sequencing
Total RNA was extracted from isolated and purified CD14⁺ monocytes using TRIzol reagent. Following ribosomal RNA (rRNA) depletion, sequencing libraries were constructed according to the Illumina library preparation protocol and subsequently sequenced on the Illumina Genome Analyzer II platform.
ATAC‑seq
A total of 1×10⁵ fresh cells were used for each assay. Libraries were constructed using Tn5 transposase treatment and sequenced on an Illumina platform. Raw reads were subjected to quality control using fastp and aligned to the reference genome with Bowtie2. PCR duplicates were removed using Picard, and MACS2 was used for peak calling to identify open chromatin regions (ATAC‑seq peaks). Identified peaks were annotated with HOMER, followed by transcription factor binding motif analysis.
Chromatin Immunoprecipitation (ChIP)
Log-phase cells were washed with PBS, cross-linked with 1% formaldehyde at room temperature for 10 min, and quenched with glycine. After lysis, chromatin was sonicated to 200–500 bp fragments. Chromatin was incubated with anti-RNA polymerase II antibody or control IgG pre-bound to Protein A/G magnetic beads at 4℃ overnight. After washing, elution, cross-link reversal and proteinase K digestion, DNA was purified and analyzed by qPCR for target region enrichment.

value: peripheral blood

value: monocytes


title: UF1hypo shUHRF1.2

description: Library name: UF1hypo shUHRF1.2


title: RT_WD_male_17w_87_liver

description: Library name: HDP-018876_liver


title: TN_CD_female_9w_86_liver

description: Library name: HDP-018809_liver


title: Csa_Root_Ctrl_scRNAseq_R1

description: Roots from 3-day-old seedlings for scRNA-seq

organism: Camelina sativa

value: 3-day-old seedlings


title: T407NS_CP-673451_1uM

city: New Haven

first: Kevin

middle: C

last: Johnson

state: CT

address: 333 Cedar Street

department: Neurosurgery

institute: Yale University

description: Library name: A15

data_processing:
cellranger-9.0.1 using include-introns parameter set to `True`.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

growth_protocol: Cells were cultured as non-adherent neurospheres in serum-free Neurobasal (ThermoFisher, Gibco 21103049) supplemented with 1x B-27 (ThermoFisher, 17504044), 2 mM UltraGlutamine (Lonza, BE17-605E/U1), 0.1 U/mL heparin (Sigma-Aldrich, H3149), 20 ng/mL bFGF (Miltenyi, 130-093-839), 20 ng/mL EGF (Provitro, 1325960500), and 100 U/mL penicillin–streptomycin at 37 °C, 5% CO₂. Lines were authenticated by short tandem repeat profiling and routinely tested mycoplasma-negative.

extract_protocol:
Neurospheres from each condition were dissociated and subjected to FACS sorting of viable cells for single cell RNA-sequencing.
Samples were FACS-enriched for viable cells and prepared using the 10x Genomics Chromium GEM-X Single Cell 3′ Gene Expression kit (v4). Cells were loaded onto a Chromium chip with a target recovery of ~6,000–8,000 cells and run on the Chromium Controller. Individual cells were encapsulated in gel bead–in–emulsions (GEMs), where reverse transcription and barcode incorporation occurred. Libraries were generated by disrupting the emulsions, pooling the barcoded material, amplifying cDNA, fragmenting it, and adding sample indices and adapters. Library size and concentration were assessed with an Agilent High Sensitivity DNA kit on a Bioanalyzer 2100. The pooled single-cell libraries were sequenced on an Illumina NovaSeq 6000.

treatment_protocol: Based on IC₅₀ determination, 3×106 IDH-mutant neurospheres were seeded per T75 flask in 15 mL NSC medium and treated with either dasatinib or CP-673451 at 1 µM or 5 µM; DMSO served as vehicle control with matched final concentration across all conditions. Neurospheres were exposed continuously for 6 days, after which spheres were dissociated to single cells, washed in PBS, and viability assessed with trypan blue.

value: Brain

value: Glioma

tag: genotype

value: IDH-mutant


title: T407NS_CP-673451_5uM

description: Library name: A16


title: TN_CD_female_27d_84_liver

description: Library name: HDP-019005_liver


title: HCT116 shUHRF1.1

description: Library name: HCT116 shUHRF1.1

value: colon


title: Csa_Root_Ctrl_scRNAseq_R2


title: TN_CD_male_9d_85_liver

description: Library name: HDP-019072_liver


title: T407NS_Dasatinib_5uM

description: Library name: A14


title: T394NS_CP-673451_5uM

description: Library name: A12


title: HCT116 shUHRF1.2

description: Library name: HCT116 shUHRF1.2


title: Ath_Root_Ctrl_Bulk_R3


title: T407NS_Dasatinib_1uM

description: Library name: A13


title: RT_CD_female_17w_83_liver

description: Library name: HDP-018921_liver


title: Ath_Root_Ctrl_Bulk_R2


title: RT_WD_male_17w_82_liver

description: Library name: HDP-018885_liver


title: HCT116 shScr.2

description: Library name: HCT116 shScr.2

value: shScr


title: T394NS_CP-673451_1uM

description: Library name: A11


title: RT_WD_female_17w_81_liver

description: Library name: HDP-018892_liver


title: TN_WD_female_3d_80_liver

description: Library name: HDP-019014_liver


title: Ath_Root_NaCl_scRNAseq_R1

description: Roots from 4-6-day-old seedlings for scRNA-seq

value: 100 mM NaCl treatment


title: HCT116 shScr.1

description: Library name: HCT116 shScr.1


title: Ath_Root_NaCl_scRNAseq_R2


title: Ath_Root_ABA_scRNAseq_R2

value: 5 M ABA treatment


title: T394NS_Dasatinib_1uM

description: Library name: A9


title: mFoxO-TKO_Fasted_4, quadriceps muscle

type: RNA

city: Aichi Prefecture

first: Mamoru

last: Oyabu

address: 7-430 Morioka-cho, Obu-shi

department: Geroscience Research Center

country: Japan

institute: National Center for Geriatrics and Gerontology

description: Gene expression in skeletal muscle of 24 h-fasted mFoxO1,3,4-/- mice (quadriceps, 8 weeks old)

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-028005 Whole Mouse Genome Microarray 8 × 60K G4858A was used.

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner (G2565CA) to detect Cy3 fluorescence.

data_processing: The scanned images were analyzed using Feature Extraction Software 9.5 (Agilent) with default parameters (protocol: GE1_1100_Jul11 and Grid: 028005_D_F_20150604) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction Software as Non-uniform outliers were excluded.

label_protocol: Cy3-labeled cRNA (1.65 μg) was mixed and fragmented according to the Agilent Technologies protocol.

growth_protocol: Skeletal muscle-specific FoxO1,3,4 knockout (mFoxO1,3,4-/-) mice were generated as previously described (PMID: 35061305). All mice were housed at a constant temperature of 24°C under 12 h-light/dark cycle with ad libitum-access to food (CE-2, CLEA, Japan) and water.

extract_protocol: RNA was isolated from quadriceps muscle of fed or 24 h-fasted WT mice and age-matched mFoxO1,3,4-/- mice (male, 8 weeks old) using TRIzol (Thermo Fisher, Cat# 15596018) solution. Extracted RNA was purified using an RNeasy Mini Kit (Qiagen, Cat# 74104). The purity of the RNA was determined by measuring ultraviolet absorbance at 260 and 280 nm, which confirmed that there was no contamination of proteins. RNA was electrophoresed in 1.2% denaturing agarose gel, and the patterns of ribosomes 28S and 18S were observed, confirming that all samples had similar migration patterns, suggesting total RNA was not degraded.

treatment_protocol: Wild type (WT) mice and mFoxO1,3,4-/- mice were fasted in individual cages for 24 h, whereas control mice were fed ad libitum.

value: quadriceps muscle

tag: gender

value: male

value: 8 weeks old

tag: genotyoe

value: TKO


title: T394NS_Dasatinib_5uM

description: Library name: A10


title: Ath_Root_Ctrl_scRNAseq_R2

value: Root


title: RT_CD_male_17w_79_liver

description: Library name: HDP-018952_liver

value: liver


title: T407NS_DMSO_CTR

description: Library name: A8

value: DMSO


title: WT_Fasted_4, quadriceps muscle

description: Gene expression in skeletal muscle of 24 h-fasted WT mice (quadriceps, 8 weeks old)

value: WT


title: Vascular tissue18,Normal aortal tissues from donors

city: Beijing

first: Xiaozheng

last: Zhou

state: beijing

address: Anzhen Road, Cao Yang District, Beijing, China, 100029

institute: Beijing Anzhen Hospital, Capital Medical University

description: Library name: Sample18

data_processing:
Raw reads were quality checked using FastQC v0.11.9.
Quality trimming and adapter removal were performed using Trimmomatic v0.39 with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed sequence reads were aligned to the human reference genome GRCh38 (hg38) using STAR v2.7.9a with parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1.
Gene expression quantification was performed using featureCounts v2.0.3 with parameters: -t exon -g gene_id -s 2, based on GENCODE v38 annotation.
Differential expression analysis was conducted using DESeq2 v1.34.0 with default parameters.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Vascular tissue

growth_protocol: Human vascular cells under different pathological conditions were preserved in liquid nitrogen.

extract_protocol:
Human vascular tissue samples, encompassing distinct pathological states  were obtained from surgical resections with informed consent under institutional review board approval. Tissues were immediately rinsed in ice-cold phosphate-buffered saline (PBS) and dissected to isolate the vessel wall. Sections were flash-frozen in liquid nitrogen for subsequent nucleic acid extraction.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used forthe construction of sequencing libraries.

value: Vascular tissue

tag: disease state

value: Normal aortal tissues from donors


title: Ath_Root_Ctrl_scRNAseq_R1

value: 4-6-day-old seedlings

value: Control


title: Ath_Root_ABA_scRNAseq_R1


title: TN_WD_male_17w_77_liver

description: Library name: HDP-018751_liver


title: RT_WD_male_17w_78_liver

description: Library name: HDP-018847_liver


title: T394NS_DMSO_CTR

description: Library name: A7

value: Brain

value: Glioma

value: IDH-mutant


title: Vascular tissue17,Normal aortal tissues from donors

description: Library name: Sample17


title: RT_CD_male_17w_76_liver

description: Library name: HDP-018881_liver


title: mFoxO-TKO_Fasted_3, quadriceps muscle


title: Whole blood DNA: S2_11 (follow-up, T2DM)

city: Thiruvananthapuram

first: Gopika

last: Satheesh

state: Kerala

address: Poojappura

department: Cardiovascular Diseases and Diabetes Biology

country: India

institute: BRIC-Rajiv Gandhi Centre for Biotechnology

description:
Library name: LIB_S2_11
follow-up sample from T2DM participant

library_source: genomic

data_processing:
Basecalling using Guppy v6.4.6 (high-accuracy mode). Alignment to GRCh38.p15 using Minimap2 v2.24. Methylation calling using modbam2bed v0.5.23. Annotation using Bedtools v2.31.0 and HOMER. Differential methylation using MethylKit v1.26.0.
Assembly: GRCh38.p15 (hg38)
Supplementary files format and content: Processed files include: differential methylation tables (CpG-level hyper/hypo), CpG island mapping, HOMER annotation, methylation summaries, and gene–pathway mapping results. Files are provided as TXT and XLSX formats within organized ZIP folders.

molecule: genomic DNA

source_name: whole blood

growth_protocol: Not applicable (human whole blood collected in EDTA tubes).

extract_protocol:
Whole blood genomic DNA was extracted using standard high–molecular-weight DNA extraction methods according to the sequencing provider’s protocol (Genotypic Technology Pvt. Ltd.).
High–molecular-weight DNA was fragmented using Covaris g-TUBE, followed by end-repair and A-tailing (NEBNext Ultra II End Repair Kit). PCR-free ligation libraries were prepared using the Oxford Nanopore Ligation Sequencing Kit with native barcoding (SQK-NBD114.96). Barcoded DNA was purified with AMPure XP beads, quantified, pooled, and loaded onto a PromethION flow cell for sequencing.

treatment_protocol: No treatment applied.

value: whole blood

value: PBMC_derived DNA


title: mFoxO-TKO_Fed_3, quadriceps muscle

description: Gene expression in skeletal muscle of fed mFoxO1,3,4-/- mice (quadriceps, 8 weeks old)

value: quadriceps muscle


title: TN_WD_male_9w_75_liver

description: Library name: HDP-018794_liver


title: Whole blood DNA: S2_12 (follow-up, T2DM)

description:
Library name: LIB_S2_12
follow-up sample from T2DM participant


title: WT_Fed_4, quadriceps muscle

description: Gene expression in skeletal muscle of fed WT mice (quadriceps, 8 weeks old)

value: male


title: RT_WD_female_17w_73_liver

description: Library name: HDP-018955_liver


title: mFoxO-TKO_Fed_4, quadriceps muscle

value: 8 weeks old


title: Vascular tissue15,Normal aortal tissues from donors

description: Library name: Sample15


title: Whole blood DNA: S2_9 (follow-up, T2DM)

description:
Library name: LIB_S2_9
follow-up sample from T2DM participant


title: Vascular tissue16,Normal aortal tissues from donors

description: Library name: Sample16


title: WT_Fasted_3, quadriceps muscle


title: TN_WD_male_3d_74_liver

description: Library name: HDP-019004_liver


title: Whole blood DNA: S2_10 (follow-up, T2DM)

description:
Library name: LIB_S2_10
follow-up sample from T2DM participant


title: WT_Fed_3, quadriceps muscle


title: RT_WD_female_17w_72_liver

description: Library name: HDP-018849_liver


title: Whole blood DNA: S2_8 (follow-up, prediabetes)

description:
Library name: LIB_S2_8
follow-up sample from prediabetic participant


title: Vascular tissue13,Normal aortal tissues from donors

description: Library name: Sample13


title: TN_CD_female_17w_71_liver

description: Library name: HDP-018735_liver


title: Vascular tissue14,Normal aortal tissues from donors

description: Library name: Sample14


title: Vascular tissue11, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample11


title: Whole blood DNA: S2_6 (follow-up, prediabetes)

description:
Library name: LIB_S2_6
follow-up sample from prediabetic participant


title: Whole blood DNA: S2_7 (follow-up, prediabetes)

description:
Library name: LIB_S2_7
follow-up sample from prediabetic participant


title: RT_WD_female_17w_70_liver

description: Library name: HDP-018850_liver


title: Vascular tissue12, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample12


title: Vascular tissue10, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample10


title: Whole blood DNA: S2_5 (follow-up, prediabetes)

description:
Library name: LIB_S2_5
follow-up sample from prediabetic participant


title: RT_CD_female_17w_69_liver

description: Library name: HDP-018883_liver


title: WT_Fasted_2, quadriceps muscle


title: Whole blood DNA: S2_4 (follow-up, normoglycemia)

description:
Library name: LIB_S2_4
follow-up sample from normoglycemic participant


title: mFoxO-TKO_Fed_2, quadriceps muscle

value: TKO


title: TN_WD_female_17w_68_liver

description: Library name: HDP-018718_liver


title: Vascular tissue9, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample9


title: TN_CD_female_27d_67_liver

description: Library name: HDP-019006_liver


title: Vascular tissue8, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample8


title: Whole blood DNA: S2_3 (follow-up, normoglycemia)

description:
Library name: LIB_S2_3
follow-up sample from normoglycemic participant


title: mFoxO-TKO_Fed_1, quadriceps muscle


title: mFoxO-TKO_Fasted_1, quadriceps muscle


title: Whole blood DNA: S2_2 (follow-up, normoglycemia)

description:
Library name: LIB_S2_2
follow-up sample from normoglycemic participant


title: mFoxO-TKO_Fasted_2, quadriceps muscle


title: Vascular tissue7, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample7


title: WT_Fasted_1, quadriceps muscle


title: WT_Fed_2, quadriceps muscle


title: WT_Fed_1, quadriceps muscle


title: TN_CD_male_9w_65_liver

description: Library name: HDP-018836_liver


title: MGG152_sgRNA_NTC

description: Library name: MGG152_sgRNA_NTC

extract_protocol:
MGG152 patient-derived cell lines were collected and dissociated into single cells. The single cell suspensions of all four cell lines were  washed individually three times with 0.1% BSA in PBS and resuspended at 1x106 cells/ml.
Single cells were processed through the 10X Chromium 3’ Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits, following the manufacturers protocol. Briefly, 10,000 cells were loaded into each channel of the chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by barcoded reverse transcription of RNA in the droplets. This was followed by amplification, fragmentation, and addition of adaptor and sample index. Libraries from four 10X channels were pooled together (twice) and sequenced on one lane of an Illumina Next-Seq 1000/2000 sequencer with paired end reads.

value: IDH1 R132H

value: non-targeting sgRNA


title: Whole blood DNA: S2_1 (follow-up, normoglycemia)

description:
Library name: LIB_S2_1
follow-up sample from normoglycemic participant


title: Vascular tissue6,  Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample6


title: RT_CD_male_17w_66_liver

description: Library name: HDP-018950_liver

value: liver


title: TN_WD_female_9w_63_liver

description: Library name: HDP-018838_liver


title: Whole blood DNA: S_12 (baseline, T2DM)

description:
Library name: LIB_S_12
baseline sample from T2DM participant


title: MGG152_sgRNA3_CDKN2A

description: Library name: MGG152_sgRNA3_CDKN2A

value: sgRNA targeting CDKN2A


title: Vascular tissue3, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample3

value: Vascular tissue


title: MGG152_sgRNA1_CDKN2A

description: Library name: MGG152_sgRNA1_CDKN2A


title: Whole blood DNA: S_11 (baseline, T2DM)

description:
Library name: LIB_S_11
baseline sample from T2DM participant


title: TN_WD_male_17w_62_liver

description: Library name: HDP-018702_liver


title: Whole blood DNA: S_10 (baseline, T2DM)

description:
Library name: LIB_S_10
baseline sample from T2DM participant


title: TN_WD_female_17w_64_liver

description: Library name: HDP-018738_liver


title: TN_WD_male_9d_61_liver

description: Library name: HDP-019075_liver


title: Vascular tissue4,Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample4


title: MGG152_Parental

description: Library name: MGG152_Parental


title: TN_CD_female_27d_60_liver

description: Library name: HDP-019008_liver


title: Whole blood DNA: S_8 (baseline, prediabetes)

description:
Library name: LIB_S_8
baseline sample from prediabetic participant


title: BV-3-kang3

city: Hangzhou

first: yuanlin

last: qi

address: No. 666, Wusu Street, Lin'an District

department: Donghu Campus

institute: Zhejiang A&F University

description:
Library name: BV-3-kang3
BV-3, Disease resistance, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to B73 RefGen_v4  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files include FPKM value and gene count for each Sample

organism: Zea mays

source_name: whole body

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: whole body


title: Vascular tissue1, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample1


title: Whole blood DNA: S_9 (baseline, T2DM)

description:
Library name: LIB_S_9
baseline sample from T2DM participant


title: Vascular tissue2, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample2


title: BV-3-kang2

description:
Library name: BV-3-kang2
BV-3, Disease resistance, replicate biosample 2


title: Whole blood DNA: S_7 (baseline, prediabetes)

description:
Library name: LIB_S_7
baseline sample from prediabetic participant


title: RT_CD_male_17w_59_liver

description: Library name: HDP-018919_liver


title: BV-3-kang1

description:
Library name: BV-3-kang1
BV-3, Disease resistance, replicate biosample 1


title: TN_CD_female_9w_58_liver

description: Library name: HDP-018823_liver


title: Whole blood DNA: S_6 (baseline, prediabetes)

description:
Library name: LIB_S_6
baseline sample from prediabetic participant


title: HASMC cell, U83836 day1 3

description: Library name: Sample36

data_processing:
CLC Genomics Workbench y 11.0.1
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction:0.8)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8similarity fraction:0.8)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: cell

growth_protocol: Human aortic endothelial cells (HAECs) and human aortic smooth muscle cells(HASMCs) were maintained in DMEM supplemented with 10% fetalbovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Human aortic endothelial cells (HAECs)and human aortic smooth muscle cells(HASMCs)wereobtained fom ATCC(Manassas, VA,USA).HAECSwere cultured inendothelial growth medium,andHASMCs were maintained in Dulbecco's ModifiedEagle's Medium (DMEM), both supplemented with 10%fetal bovine serum (HyClone, Logan, UT, USA),2 mMglutamine,100U/L penicillin,and 100g/mstreptomycin. All cells were cultured at 37 oC in ahumidified atmosphere containing 5% CO,. Cells wererandomly assigned to treatment with either PBS orangiotensin Il (Ang Il, 100 nM)for 24 hours, followedby exposure to DMSO,metabolites (hypoxanthine orpyroglutamic acid,20)，ormetabolites ininhibitors (BCX-combination with pharmacological1777,a hypoxanthine inhibitor,or Pro-GA,apyroglutamic acid inhibitor, 20 μM)for an additional 6hours. Metabolites and pharmacological inhibitors werefrom MedChemExpress (MCE)(Princeton, NI, USA).CCK-8:Cell viability was measured using the CellCounting Kit-8(CCK-8,AqLab,Beijing, China)following themanufacturer's instructions.BrieflyHASMCs were seeded in 96-well plates at a density of 5x 103 cells per well and allowed to adhere overnight.After the indicated treatments, 10 uL of CCK-8 solutionwas added to each well, and the plates were incubated at37 'C for 2 hours. Absorbance at 450 nm was recordedusing a microplate reader. Cell viability was expressed asa percentage relative to untreated control cells.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used forthe construction of sequencing libraries.

treatment_protocol: Angiotensin II-induced stimulation was initiated by treatment of cells with 100 nM Ang II for 24 hours.

value: cell

value: HASMC

value: Human Aortic Endothelial Cells

value: HASMC cell, U83836

value: SMCM

value: Normalized intensity from raw data


title: BV-3-gan3

description:
Library name: BV-3-gan3
BV-3, Disease susceptibility, replicate biosample 3


title: HASMC cell, U83836 day1 2

description: Library name: Sample35


title: BV-3-gan2

description:
Library name: BV-3-gan2
BV-3, Disease susceptibility, replicate biosample 2


title: Whole blood DNA: S_5 (baseline, prediabetes)

description:
Library name: LIB_S_5
baseline sample from prediabetic participant

value: whole blood

value: PBMC_derived DNA


title: TN_CD_male_17w_57_liver

description: Library name: HDP-018727_liver


title: HAEC cell, U83836 day1 3

description: Library name: Sample33

value: HAEC

value: Human Umbilical Vein Endothelial Cells

value: HAEC cell, U83836

value: ECM medium


title: RT_CD_female_17w_55_liver

description: Library name: HDP-018922_liver


title: Vascular tissue5, Vascular tissue from patients with ascending thoracic aortic dissection and aneurysm

description: Library name: Sample5


title: HAEC cell, U83836 day1 2

description: Library name: Sample32


title: CK-3-801

description:
Library name: CK-3-801
CK, Disease resistance, replicate biosample 3


title: TN_CD_male_9w_56_liver

description: Library name: HDP-018824_liver


title: Whole blood DNA: S_2 (baseline, normoglycemia)

description:
Library name: LIB_S_2
baseline sample from normoglycemic participant


title: Whole blood DNA: S_3 (baseline, normoglycemia)

description:
Library name: LIB_S_3
baseline sample from normoglycemic participant


title: HAEC cell, U83836 day1 1

description: Library name: Sample31


title: BV-3-gan1

description:
Library name: BV-3-gan1
BV-3, Disease susceptibility, replicate biosample 1


title: HASMC cell, U83836 day1 1

description: Library name: Sample34


title: Whole blood DNA: S_4 (baseline, normoglycemia)

description:
Library name: LIB_S_4
baseline sample from normoglycemic participant


title: TN_WD_female_9d_54_liver

description: Library name: HDP-019076_liver


title: TN_CD_female_27d_53_liver

description: Library name: HDP-019019_liver


title: CK-2-801

description:
Library name: CK-2-801
CK, Disease resistance, replicate biosample 2


title: Whole blood DNA: S_1 (baseline, normoglycemia)

description:
Library name: LIB_S_1
baseline sample from normoglycemic participant


title: CK-1-801

description:
Library name: CK-1-801
CK, Disease resistance, replicate biosample 1


title: HASMC cell, pyroglutamic acid day1 2

description: Library name: Sample29

value: HASMC cell, pyroglutamic acid


title: CK-3-986

description:
Library name: CK-3-986
CK, Disease susceptibility, replicate biosample 3


title: TN_WD_male_9w_51_liver

description: Library name: HDP-018826_liver

value: liver


title: TN_CD_male_9d_52_liver

description: Library name: HDP-019071_liver


title: Tolerant-chip1

description: Library name: Tolerant-chip1

value: peripheral blood

value: monocytes


title: CK-2-986

description:
Library name: CK-2-986
CK, Disease susceptibility, replicate biosample 2

value: whole body


title: HASMC cell, pyroglutamic acid day1 1

description: Library name: Sample28

value: cell


title: HASMC cell, pyroglutamic acid day1 3

description: Library name: Sample30

value: HASMC


title: TN_CD_female_17w_50_liver

description: Library name: HDP-018732_liver


title: Tolerant-ATAC1

description: Library name: Tolerant-ATAC1


title: HAEC cell, pyroglutamic acid day1 3

description: Library name: Sample27

value: HAEC cell, pyroglutamic acid


title: naive-chip1

description: Library name: naive-chip1


title: CK-1-986

description:
Library name: CK-1-986
CK, Disease susceptibility, replicate biosample 1


title: TN_WD_male_9w_49_liver

description: Library name: HDP-018828_liver


title: HAEC cell, pyroglutamic acid day1 2

description: Library name: Sample26


title: Naive-ATAC1

description: Library name: Naive-ATAC1


title: Zebrafish ldlr+/+ static flow

city: Boston

first: Aryan

last: Kaveh

state: MA

address: 60 Fenwood Road

department: Medicine

institute: Brigham and Women's Hospital

description: 10x Genomics generated processed data in barcode, feature and matrix files

data_processing:
Processed data files including the mapped barcode, feature and matrix files were generated using CellRanger software (10x Genomics). For zebrafish data processing, cellranger-6.0.1 was used. For HAEC data processing cellranger-4.0.0 was used.
Assembly: hg38 (HAEC) and danRer10 (zebrafish)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Embryonic vascular endothelial cells and non-endothelial cells

extract_protocol:
Tg(flk:GFP) zebrafish embryos were digested using preheated 0.25% Trypsin-EDTA at 28°C for 20 minutes, mechanically aspirating every 5 minutes. Disassociated embryos were subsequently washed with PBS and 1% FBS. Cell pellets were obtained by centrifugation which were resuspended in PBS and 1% FBS in preparation for fluorescence-activated cell sorting of GFP+ endothelial cells and GFP- non-endothelial cells. HAECs were washed in PBS and 0.05% Trypsin-EDTA. Cell pellets were obtained by centrifugation which were resuspended in complete medium prior to scRNA-seq analysis.
The library was constructed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics) for both zebrafish and HAEC datasets.

treatment_protocol: To inhibit cardiac contractility and generate embryonic zebrafish with reduced or static blood flow, tnnt2 morpholino was injected into the single-cell stage at a 1:100 or 1:20 dose respectively. HAECs were stimulated with unimodal shear stress (physiologic flow, 30 dynes/cm2; reduced flow, 2.5dynes/cm2 or static flow, 0 dynes/cm2) for 48 hours.

value: ldlr+/+


title: ChIP_ONECUT1_PP1_2

city: New York

first: Wilfred

last: Wong

state: NY

address: 430 E 67th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Align to hg19 reference genome using bowtie2-2.4.1
Peak calling to generate signal tracks on on individual replicates using macs2 2.2.7.1 with options -B -p 1e-2 -f BAMPE
Assembly: hg19
Supplementary files format and content: Coverage track in bigWig format

source_name: Pancreatic (hPSC derived)

growth_protocol: All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. hESCs were rinsed with 1X DPBS (without Mg2+ and Ca2+) and first differentiated into DE using S1/2 media, supplemented with 100 ng/ml Activin A (Bon Opus Biosciences) for three days and CHIR99021 (Stemgent, 04-0004-10) for two days (1st day, 5 µM; 2nd day, 0.5 µM).  DE cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and 0.25mM vitamin C (Sigma-Aldrich, A4544) for 2 days to reach GT stage. Cells were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1µM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days to reach PP1 stage. The PP1 cells were then harvested for ChIP-seq.

extract_protocol:
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
Library was prepared using NEBNext Ultra II DNA Library Prep Kit (NEB) according to manufacturer’s protocol.

value: Pancreatic (hPSC derived)

value: Early pancreatic progenitor

value: WT

tag: chip antibody

value: anti-Onecut1 (Santa Cruz,sc-13050)


title: TN_WD_male_17w_48_liver

description: Library name: HDP-018695_liver


title: HAEC cell, pyroglutamic acid day1 1

description: Library name: Sample25

value: HAEC

value: Normalized intensity from raw data


title: TN_WD_male_9d_47_liver

description: Library name: HDP-019052_liver


title: TN_WD_male_27d_46_liver

description: Library name: HDP-019016_liver


title: HASMC cell, BCX-1777 day1 3

description: Library name: Sample24

value: Human Aortic Endothelial Cells

value: HASMC cell, BCX-1777

value: SMCM


title: Zebrafish ldlr+/+ reduced flow

value: Embryonic vascular endothelial cells and non-endothelial cells


title: TN_WD_female_3d_45_liver

description: Library name: HDP-019068_liver

value: liver


title: ChIP_Input2


title: Zebrafish ldlr+/+ flow


title: ChIP_ONECUT1_PP1_1


title: Zebrafish ldlr-/- static flow

value: ldlr-/-


title: YZHA-501

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

description: Library name: YZHA-501

data_processing:
Kallisto and tximport were used to align to gencode primary assembly sequence (release 29) and export sequencing data. The edgeR R packages was used to process the count matrices, including TMM normalization and conversion to log2 counts-per-million. Normalized counts were used to compare cadherin expression.
Assembly: gencode primary assembly sequence (release 29)
Supplementary files format and content: csv count matrix with samples in columns and genes in rows
Supplementary files format and content: metadata.txt is a tab-delimited file with columns for sample, patient, IRB, and BOR. Note: both files include counts and metadata that include 15 additional samples from GSE285619

source_name: skin

extract_protocol:
Patients donated a single 18g core biopsy which was either formalin-fixed paraffin-embedded (FFPE) or fresh frozen (FF). RNA was isolated using Qiagen RNeasy FFPE kit (Qiagen, 73504) for FFPE samples, or Qiagen RNeasy kit (Qiagen, 74104) for FF samples.
RNA QC (quality and quantity) was performed using an Agilent 2100 Bio-analyzer using Agilent reagents and protocols. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA stranded library making kits using Illumina protocols. Library QC (quality and quantity) was performed using an Agilent 2100 Bio-analyzer using Agilent reagents and protocols. RNA-SEQ libraries were sequenced with paired-end 100 bp reads using an Illumina HiSEQ40000 with Illumina reagents and protocols.

value: skin

tag: patient

tag: best overall_response

value: SD

tag: irb


title: HASMC cell, BCX-1777 day1 1

description: Library name: Sample22

tag: tissue

value: cell

tag: cell line

value: HASMC

tag: treatment


title: TN_CD_female_9w_44_liver

description: Library name: HDP-018822_liver


title: YZHA-500

description: Library name: YZHA-500

value: PR


title: HAEC cell, BCX-1777 day1 3

description: Library name: Sample21

value: Human Umbilical Vein Endothelial Cells

value: HAEC cell, BCX-1777

value: ECM medium


title: TN_CD_female_17w_43_liver

description: Library name: HDP-018716_liver


title: HASMC cell, BCX-1777 day1 2

description: Library name: Sample23


title: Zebrafish ldlr-/- flow


title: HAEC cell, BCX-1777 day1 2

description: Library name: Sample20


title: YZHA-498

description: Library name: YZHA-498


title: TN_CD_male_9w_42_liver

description: Library name: HDP-018814_liver


title: YZHA-489

description: Library name: YZHA-489

value: NE


title: Zebrafish ldlr-/- reduced flow


title: HAEC cell, BCX-1777 day1 1

description: Library name: Sample19

value: HAEC


title: Drosphila S2 CRISPR Neg clone 2 rep 1

city: New York City

first: Christopher

middle: Russell

last: Chin

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: Library name: 15_ATAC_Drosophila_S2_NEG_2_rep1

data_processing:
Trimming by TrimGalore
Alignment by BWA
Filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Assembly: hg38 / mm10
Supplementary files format and content: bed files of MACS2 narrowPeaks

organism: Drosophila melanogaster

source_name: Spleen

extract_protocol:
Omni ATAC-Seq protocol (Corces et al., 2017; Nature Methods)
Amplification with Q5® High-Fidelity 2X Master Mix and Illumina dual indexes.

treatment_protocol: Inhibitor or DMSO treatment for 24h.

value: Spleen

value: WT


title: Drosphila S2 CRISPR Neg clone 1 rep 2

description: Library name: 14_ATAC_Drosophila_S2_NEG_1_rep2


title: TN_WD_male_9d_40_liver

description: Library name: HDP-019053_liver


title: HASMC cell, hypoxanthine day1 3

description: Library name: Sample18

value: Human Aortic Endothelial Cells

value: HASMC cell, hypoxanthine

value: Normalized intensity from raw data


title: HASMC cell, hypoxanthine day1 2

description: Library name: Sample17

value: SMCM


title: Drosphila S2 CRISPR Neg clone 2 rep 2

description: Library name: 16_ATAC_Drosophila_S2_NEG_2_rep2


title: YZHA-482

description: Library name: YZHA-482

value: CR


title: YZHA-487

description: Library name: YZHA-487

value: skin


title: RT_WD_female_17w_38_liver

description: Library name: HDP-018893_liver

value: liver


title: TN_CD_male_27d_39_liver

description: Library name: HDP-018980_liver


title: Drosphila S2 CRISPR Osa clone 2 rep 2

description: Library name: 12_ATAC_Drosophila_S2_Osa_AD_rep2

value: Osa CRISPR


title: HASMC cell, hypoxanthine day1 1

description: Library name: Sample16

value: cell

value: HASMC


title: TN_WD_male_17w_41_liver

description: Library name: HDP-018712_liver


title: YZHA-308

description: Library name: YZHA-308

value: PR


title: YZHA-480

description: Library name: YZHA-480

value: SD


title: Drosphila S2 CRISPR Osa clone 2 rep 1

description: Library name: 11_ATAC_Drosophila_S2_Osa_AD_rep1


title: TN_CD_female_9w_37_liver

description: Library name: HDP-018816_liver


title: Drosphila S2 CRISPR Osa clone 1 rep 2

description: Library name: 10_ATAC_Drosophila_S2_Osa_AB_rep2


title: Drosphila S2 CRISPR Neg clone 1 rep 1

description: Library name: 13_ATAC_Drosophila_S2_NEG_1_rep1


title: HAEC cell, hypoxanthine day1 2

description: Library name: Sample14

value: Human Umbilical Vein Endothelial Cells

value: HAEC cell, hypoxanthine

value: ECM medium


title: TN_WD_male_17w_36_liver

description: Library name: HDP-018710_liver


title: YZHA-307

description: Library name: YZHA-307


title: HAEC cell, hypoxanthine day1 1

description: Library name: Sample13

value: HAEC


title: HAEC cell, hypoxanthine day1 3

description: Library name: Sample15


title: Drosphila S2 CRISPR Osa clone 1 rep 1

description: Library name: 09_ATAC_Drosophila_S2_Osa_AB_rep1

value: Spleen


title: TN_CD_female_9w_35_liver

description: Library name: HDP-018790_liver


title: YZHA-481

description: Library name: YZHA-481


title: HASMC cell, AngII day1 3

description: Library name: Sample12

value: Human Aortic Endothelial Cells

value: HASMC cell, AngII


title: TN_WD_female_17w_34_liver

description: Library name: HDP-018697_liver


title: YZHA-305

description: Library name: YZHA-305

value: PD


title: HASMC cell, AngII day1 2

description: Library name: Sample11

value: SMCM

value: Normalized intensity from raw data


title: YZHA-304

description: Library name: YZHA-304

value: skin


title: HASMC cell, AngII day1 1

description: Library name: Sample10


title: Dox + rep1 (MS330_010)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description:
Library name: Sample4
mCherry-positive receiver cells co-cultured with sender cells, Dox +

data_processing:
Reads were aligned to the mouse reference genome (GRCm38.p6) downloaded from the NCBI FTP site. Because the libraries capture the 3′ ends of transcripts, expression was quantified at the gene level (Entrez Gene IDs) rather than at the transcript level. Read trimming, alignment and quantification were performed with Cutadapt (v1.18), TopHat2 (v2.1.1) and HTSeq (v0.11.0), respectively.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files include read counts and RPM  for each Sample

source_name: mammary gland

extract_protocol:
FACS-sorted cells were lysed, and total RNA was purified with the RNeasy Micro Kit (Qiagen, #74004) according to the manufacturer’s instructions.
cDNA synthesis and library construction followed the SC3-seq protocol (Nakamura et al, 2015; Mizuta et al, 2022). For each sample, 1 ng of total RNA was used for cDNA synthesis, and cDNA was amplified for 14 PCR cycles—the established cycle number for bulk RNA-seq. Libraries were prepared from the amplified cDNA and sequenced on the Illumina NextSeq 500/550 platform (High Output Kit v2, 75 cycles; Illumina, cat. no. FC-404-2005).

value: mammary gland

value: mammary epithelial cells

value: Dox +


title: YZHA-302

description: Library name: YZHA-302


title: Dox - rep2 (MS356_022)

description:
Library name: Sample2
mCherry-positive receiver cells co-cultured with sender cells, Dox -

value: Dox -


title: TN_WD_male_27d_32_liver

description: Library name: HDP-018985_liver

value: liver


title: RT_WD_male_17w_31_liver

description: Library name: HDP-018887_liver


title: Dox + rep3 (MS356_028)

description:
Library name: Sample6
mCherry-positive receiver cells co-cultured with sender cells, Dox +


title: YZHA-301

description: Library name: YZHA-301

value: SD


title: HAEC cell, AngII day1 3

description: Library name: Sample9

value: cell

value: Human Umbilical Vein Endothelial Cells

value: HAEC cell, AngII


title: Dox - rep3 (MS356_026)

description:
Library name: Sample3
mCherry-positive receiver cells co-cultured with sender cells, Dox -


title: YZHA-306

description: Library name: YZHA-306

value: NE


title: Dox + rep2 (MS356_024)

description:
Library name: Sample5
mCherry-positive receiver cells co-cultured with sender cells, Dox +


title: TN_CD_male_17w_30_liver

description: Library name: HDP-018805_liver


title: Dox - rep1 (MS330_008)

description:
Library name: Sample1
mCherry-positive receiver cells co-cultured with sender cells, Dox -


title: TN_CD_female_9d_33_liver

description: Library name: HDP-019055_liver


title: HAEC cell, AngII day1 1

description: Library name: Sample7

value: HAEC

value: ECM medium


title: HAEC cell, AngII day1 2

description: Library name: Sample8


title: YZHA-300

description: Library name: YZHA-300

value: PR


title: YZHA-299

description: Library name: YZHA-299


title: TN_CD_male_17w_29_liver

description: Library name: HDP-018713_liver


title: HASMC cell, Control day0 3

description: Library name: Sample6

value: HASMC

value: Human Aortic Endothelial Cells

value: HASMC cell, Control


title: YZHA-298

description: Library name: YZHA-298

value: skin


title: HASMC cell, Control day0 2

description: Library name: Sample5

value: SMCM

value: Normalized intensity from raw data


title: mSI_org_Lkb1HomCys

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

description: Library name: UMC-AM-s005

data_processing:
Mapping and filtering: The Sharq pipeline was used to process the sequencing data18. Mapping was performed using STAR (version 2.6.1), on the Genome Reference Consortium Mouse built 38 (GRCm38). Read assignment was with feature Counts version 1.5.2 using a gene annotation based on GENCODE version M14. External RNA controls (ERCCS) and transcripts mapping to the mitochondrial genome were removed from all cells. Low quality cell barcodes having either less than 800 unique transcripts, 200 genes 33.3% mitochondrial transcripts or over 4-fold non-exonic to exonic reads were excluded, as well as barcodes with over 100,000 unique transcripts. scRNA-seq analysis: Unique transcript counts were normalized using sctransform19 and analyzed using the Seurat R package (version 4.1.0)20. From the top 3000 variable genes, genes associated with cell cycle phase, dissociation stress (heat shock and chaperone proteins according to GO:0006986), sex (Xist, Tsix, and Y chromosome-specific genes), and activity (ribosomal protein genes according to GO:0022626) were removed from the list of variable genes to avoid biases in cell clustering, as described before21. The first 20 principal components were used both to calculate dimensionality reduction using UMAP and to perform clustering with a resolution of 1, k.param = 10 and the Louvain algorithm.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with raw mapped counts for samples sequenced in run MER3145
Supplementary files format and content: tab-delimited text file with raw mapped counts for samples sequenced in run PLU6264
Supplementary files format and content: tab-delimited text file with raw mapped counts for samples sequenced in run BUG7424

source_name: Small Intestine

growth_protocol: Small intestinal organoids were grown under standard conditions. This includes ENR growth medium: advanced DMEM/F12 (Gibco) supplemented with 1% Penicillin-Streptomycin (Sigma-Aldrich), 10 mM HEPES (Gibco), 1% Ultraglutamine 1 (Lonza), 1x B27 (Sigma-Aldrich), 1x N2 (Sigma-Aldrich) and 1 mM N-acetylcysteine (Sigma- Aldrich). Basal culture medium was further supplemented with 50 ng/mL murine recombinant Egf (Peprotech), 2.5% R-spondin1 (RSPO) conditioned medium (homemade) and 1% Noggin conditioned medium (homemade)

extract_protocol:
After single cell dissociation using TrypLE at 37°C cells were filtered through a 40 µm nylon cell strainer (Falcon). Variable single cells were FACS sorted into 384-well cell capture plated (Single Cell Discoveries). Each well of a cell capture plate contains a small 50nl droplet of barcoded primers and 10µl of mineral (Signa, M8410). After sorting, plates were immediately spun and placed on dry ice. Plated were stored at -80ºC. scRNA-seq was performed by Single Cell Discoveries according to an adapted version of the SORT-seq protocol15 with primers described in earlier. Cells were heat-lysed at 65ºC followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT).
Following amplification, library preparation was done following the CEL-Seq2 protocol17 to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina NextSeq500 at paired-end 60- and 26-bp read length and 75,000 reads per cell.

value: Small Intestine

value: mSI organoids


title: mSI_org_Lkb1HomBud

description: Library name: UMC-AM-s004


title: YZHA-297

description: Library name: YZHA-297

value: CR


title: TN_CD_female_17w_28_liver

description: Library name: HDP-018754_liver

extract_protocol:
RNA was extracted from liver and heart tissues using Direct-zol-96 RNA kit (Zymo research)
The generation of bulk RNA Barcoding and sequencing (BRB-seq) libraries was performed using the MERCURIUSTM BRB-seq library preparation kit for Illumina and following the manufacturer’s manual

value: liver


title: TN_CD_male_17w_27_liver

description: Library name: HDP-018700_liver


title: TN_CD_male_9d_26_liver

description: Library name: HDP-019058_liver


title: mSI_org_Lkb1het

description: Library name: UMC-AM-s003


title: HAEC cell, Control day0 3

description: Library name: Sample3

value: cell

value: HAEC cell, Control


title: TN_WD_female_27d_25_liver

description: Library name: HDP-018976_liver


title: mSI_org_WT

description: Library name: UMC-AM-s002

value: WT


title: YZHA-296

description: Library name: YZHA-296

value: SD


title: HAEC cell, Control day0 2

description: Library name: Sample2

value: HAEC

value: Human Umbilical Vein Endothelial Cells


title: YZHA-294

description: Library name: YZHA-294

value: PR


title: TN_WD_female_9w_23_liver

description: Library name: HDP-018808_liver


title: CMML Patient 6 BMMNC timepoint 2 (scATAC-seq)

first: Hayden

middle: L

last: Bell

state: Massachusetts

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: cmml_pt6_timepoint2_ATAC

library_source: genomic single cell

data_processing:
Raw data were demultiplexed, aligned to the human reference genome (hg38), and quantified using the Cell Ranger ARC pipeline (10x Genomics) with default parameters.
Assembly: hg38
Supplementary files format and content: *_atac_fragments.tsv.gz: list of ATAC fragments with genomic coordinates and cell barcodes
Supplementary files format and content: *_atac_fragments.tsv.gz.tbi: index file for ATAC fragments
Supplementary files format and content: *_barcodes.tsv.gz: list of GEX barcodes
Supplementary files format and content: *_features.tsv.gz: list of gene IDs and names
Supplementary files format and content: *_matrix.mtx.gz: gene expression count matrix (sparse format)

source_name: Bone marrow

growth_protocol: Using standard operating procedures, mononuclear cells from two CMML patients enrolled on clinical trial NCT05455294 were isolated from bone marrow aspirates, purified using Ficoll density gradient separation, and cryopreserved in 90% FBS/ 10% DMSO for storage in liquid nitrogen.

extract_protocol:
Cells were thawed using standard operating procedures and single-nuclei syspensions were prepared using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow (PN-1000283).
scATACseq and scRNAseq were performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283). In particular, approximately 11,000 nuclei per sample went through a transposition reaction and were loaded onto a Chromium Chip J (10x Genomics, PN-1000234) before being partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) in the Chromium X machine (10x Genomics). A pool of 10x barcodes were sampled to separately and uniquely index the transposed DNA and cDNA of each individual nucleus. ATAC and gene expression (GEX) libraries were generated from the same pool of pre-amplified transposed DNA/cDNA and sequenced. Following quality control with a Bioanalyzer High Sensitivity DNA Kit (Agilent), scRNAseq libraries were sequenced on a NovaSeq S4 platform (Illumina) with 28nt Read 1, 90nt of Read 2, 10nt of Index 1 and 10nt of Index 2. scATACseq libraries were sequenced on a NovaSeq S2 platform (Illumina) using 50nt Read 1, 49nt of Read 2, 8nt of Index 1 and 24nt of Index 2.

value: Bone marrow

value: Mononuclear cells

tag: age

tag: Sex

value: Female

value: Venetoclax/HMA/Navitoclax

tag: baseline blasts_(%)


title: mSI_org_Lkb1HomCys_2

description: Library name: CL20.ENR2

data_processing:
Single-end RNASeq reads were processed using the UMCU RNASeq pipeline (https://github.com/UMCUGenetics/RNASeq, v2.3.0) with default settings. Read quality was assessed by FastQC (0.11.4) followed by splice-aware alignment against the mouse reference genome (GRCm38) with STAR (2.4.2a). RNA expression quantification was performed with htseq-count (0.6.0) in reverse-stranded mode. Multiple sequence runs were integrated using standardized integration parameters.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with raw mapped counts for samples sequenced in run MER3145
Supplementary files format and content: tab-delimited text file with raw mapped counts for samples sequenced in run PLU6264
Supplementary files format and content: tab-delimited text file with raw mapped counts for samples sequenced in run BUG7424

extract_protocol:
Organoids were lysed in RLT lysis buffer (Qiagen) 3-5 days after passaging. Biological triplicates were employed. To isolate RNA from samples, the “miRNA CT 400” protocol was run on a QIAsymphony isolation robot using the QIAsymphony RNA Kit (931636) on each sample in 400ul of the RLT Plus lysis buffer (1053393). RNA quality was checked with the Agilent Fragment Analyzer 5300 system using the RNA Kit (15nt) (Cat. DNF-471-1000). And RNA quantity was measured with the Invitrogen™ Qubit ™ Fluorometer using the Qubit RNA HS Assay Kit (Cat. Q32855).
100ng of total RNA was used to prepare TruSeq Stranded mRNA libraries (Cat. 20020594) following the manufacturers protocol, with full (WT, Lkb1+/- and Lkb1-/- organoids) or half (Lkb1mut + Apc-/- and Lkb1mut + KrasG12D organoids) the reagents volume. After the library preparation libraries were checked with the Fragment Analyzer system dsDNA 910 Reagent Kit (35-1500bp) (Cat. DNF-910-K1000) and with Qubit dsDNA HS Assay Kit (Cat. Q32854). Sample libraries were pooled equimolar.

tag: cell type

tag: batch


title: mFetalIntestinal_WT

description: Library name: UMC-AM-s001

source_name: Fetal intestine

value: Fetal intestine

value: mFetal intestinal organoids


title: YZHA-293

description: Library name: YZHA-293

value: skin


title: HASMC cell, Control day0 1

description: Library name: Sample4

value: HASMC

value: Human Aortic Endothelial Cells

value: HASMC cell, Control

value: SMCM

value: Normalized intensity from raw data


title: TN_WD_male_9d_24_liver

description: Library name: HDP-019082_liver

data_processing:
Bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced by Alithea Genomics (Switzerland). The raw data was demultiplexed, cleaned, and aligned to the mouse reference genome GRCm39/mm39 using R (version 4.1.a) and START (version 2.7.9a). Count matrices were used for downstream analyses
Assembly: genome GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

value: liver


title: HAEC cell, Control day0 1

description: Library name: Sample1

value: cell

value: HAEC cell, Control

value: ECM medium


title: YZHA-295

description: Library name: YZHA-295

value: PR


title: TN_WD_male_17w_22_liver

description: Library name: HDP-018703_liver


title: mSI_org_Lkb1HomCys_1

description: Library name: CL20.ENR1

value: Small Intestine

value: mSI organoids


title: YZHA-292

description: Library name: YZHA-292

value: SD


title: CMML Patient 6 BMMNC timepoint 1 (scATAC-seq)

description: Library name: cmml_pt6_timepoint1_ATAC

value: Bone marrow

value: Mononuclear cells

value: Female

value: No treatment


title: TN_WD_female_17w_21_liver

description: Library name: HDP-018737_liver


title: YZHA-291

description: Library name: YZHA-291

value: skin


title: mSI_org_Lkb1HomBud_3

description: Library name: CL6.ENR3


title: mSI_org_Lkb1HomCys_3

description: Library name: CL20.ENR3


title: TN_CD_male_17w_20_liver

description: Library name: HDP-018806_liver


title: CMML Patient 6 BMMNC timepoint 1 (scRNA-seq)

description: Library name: cmml_pt6_timepoint1_RNA


title: CMML Patient 6 BMMNC timepoint 2 (scRNA-seq)

description: Library name: cmml_pt6_timepoint2_RNA

value: Venetoclax/HMA/Navitoclax


title: TN_CD_female_3d_19_liver

description: Library name: HDP-019061_liver


title: mSI_org_Lkb1HomBud_2

description: Library name: CL6.ENR2


title: YZHA-288

description: Library name: YZHA-288

value: CR


title: CMML Patient 5 BMMNC timepoint 4 (scATAC-seq)

description: Library name: cmml_pt5_timepoint4_ATAC

value: Male


title: mSI_org_Lkb1HomBud_1

description: Library name: CL6.ENR1


title: CMML Patient 5 BMMNC timepoint 4 (scRNA-seq)

description: Library name: cmml_pt5_timepoint4_RNA


title: RT_WD_male_17w_18_liver

description: Library name: HDP-018963_liver


title: YZHA-290

description: Library name: YZHA-290

value: NE


title: mSI_org_Lkb1Het_3

description: Library name: CL9.ENR3


title: YZHA-262

description: Library name: YZHA-262


title: YZ-225

description: Library name: YZ-225


title: RT_WD_female_17w_17_liver

description: Library name: HDP-018890_liver

value: liver


title: CMML Patient 5 BMMNC timepoint 3 (scRNA-seq)

description: Library name: cmml_pt5_timepoint3_RNA


title: YZ-212

description: Library name: YZ-212

value: PD


title: mSI_org_Lkb1Het_1

description: Library name: CL9.ENR1


title: mSI_org_WT_3

description: Library name: CTRL.ENR3

value: WT


title: YZ-202

description: Library name: YZ-202


title: TN_CD_male_9w_16_liver

description: Library name: HDP-018795_liver


title: TN_WD_male_17w_14_liver

description: Library name: HDP-018733_liver


title: mSI_org_Lkb1Het_2

description: Library name: CL9.ENR2


title: TN_CD_female_9d_15_liver

description: Library name: HDP-019112_liver


title: CMML Patient 5 BMMNC timepoint 3 (scATAC-seq)

description: Library name: cmml_pt5_timepoint3_ATAC


title: YZ-187

description: Library name: YZ-187


title: mSI_org_WT_2

description: Library name: CTRL.ENR2


title: CMML Patient 5 BMMNC timepoint 2 (scRNA-seq)

description: Library name: cmml_pt5_timepoint2_RNA


title: CMML Patient 5 BMMNC timepoint 2 (scATAC-seq)

description: Library name: cmml_pt5_timepoint2_ATAC


title: CMML Patient 5 BMMNC timepoint 1 (scATAC-seq)

description: Library name: cmml_pt5_timepoint1_ATAC


title: mSI_org_WT_1

description: Library name: CTRL.ENR1


title: RT_CD_female_17w_13_liver

description: Library name: HDP-018895_liver


title: YZ-183

description: Library name: YZ-183


title: TN_WD_male_3d_12_liver

description: Library name: HDP-019021_liver


title: YZ-174

description: Library name: YZ-174


title: RNA-Seq of bavachinin-treated SAS: bavachinin3

city: Taoyuan City

first: Chia-Yu

last: Yang

address: No.259, Wenhua 1st Rd., Guishan Dist.

department: Department of Microbiology & Immunology, Chang Gung University

country: Taiwan

institute: NGS Genomics Core Lab

description: Library name: bavachinin-3

data_processing:
Sequence reads were trimmed for adapter and low-quality bases using Cutadapt 1.12 and Partek Flow Trim Bases (Q20; minimum read length 25 bp).
Trimmed reads were aligned to the human reference genome (hg38) using STAR within Partek Flow.
Gene- and transcript-level quantification was performed using the Partek E/M algorithm with Ensembl hg38 release 108 v2 annotation.
Gene-level counts were normalized using CPM, and downstream analyses (GSA and PCA) were performed in Partek Flow.
Assembly: hg38 (Homo sapiens), Ensembl release 108 v2
Supplementary files format and content: Tab-delimited matrix including raw gene-level read counts for all samples, generated by Partek Flow using Ensembl hg38 (release 108 v2) annotation.

source_name: SAS

extract_protocol:
SAS cells were exposed to bavachinin (20 μM) for 24 hours, or left untreated as a control. Following treatment, the cells were harvested, and total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA pellet was subsequently dissolved in RNase-free water and stored at –80°C for future use.
RNA sequencing (RNA-seq) libraries were constructed using the MGIEasy RNA Directional Library Prep Set (MGI, Cat. No.: 1000006385, China), in accordance with the manufacturer's guidelines. For each library, 200 ng of total RNA was fragmented using fragmentation buffer, and the resulting RNA fragments underwent reverse transcription followed by second strand synthesis. DNA adapters were then ligated to the fragments. After purification using DNA Clean Beads, the adapter-ligated products were amplified by PCR with the provided enzyme mix and primer mix. The quantity and size distribution of the PCR products were evaluated using the Agilent 2100 Bioanalyzer with the High-Sensitivity DNA Kit (Agilent Technologies, 5067-462, USA). The PCR products were then denatured, circularized into single-stranded DNA, and subjected to enzymatic digestion. Finally, the libraries were normalized to the same concentration and sequenced on the DNBSEQ-G400 PE150 platform.

value: SAS


title: TN_WD_female_9d_11_liver

first: Johan

address: Station 15

institute: Ecole Polytechnique Fédérale de Lausanne EPFL

description: Library name: HDP-019087_liver


title: CMML Patient 5 BMMNC timepoint 1 (scRNA-seq)

description: Library name: cmml_pt5_timepoint1_RNA


title: Astrocyte, 8 h, rep3

city: Niigata-shi

first: Tokiharu

last: Sato

state: Niigata

address: 1-757 Asahimachidori, Chuo-ku

department: Department of System Pathology for Neurological Disorders

institute: Niigata University, Brain Research Institute

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-24

data_processing:
Raw sequence reads were trimmed and their quality was assessed by Trimmomatic (version 0.39) and FastQC (version 0.11.9) programs, respectively. Trimmed reads were then aligned to the mouse genome (GRCm39/m32) by the STAR aligner (version 2.7.9a) with default parameters. Read counts and transcript per million (TPM) values were calculated using RSEM program (version 1.3.1) at default setting.
Assembly: GRCm39/m32
Supplementary files format and content: tab-delimited text file including raw counts for each sample.

source_name: Cervical cord

extract_protocol:
mRNA extractions were performed by RiboTag-HA based immunoprecipitation and Rneasy Plus Micro kit (Qiagen).
cDNA libraries were prepared by the SMART-seq v4 Ultra Low Input RNA kit (TAKARA) and Nextera XT DNA Library Preparation kit (Illumina) according to manufacture’s instructions.

value: Cervical cord

value: After 8 hours


title: Astrocyte, 8 h, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-23


title: YZ-17

description: Library name: YZ-17


title: RT_CD_female_17w_10_liver

city: LAUSANNE

last: Auwerx

description: Library name: HDP-018884_liver


title: RNA-Seq of bavachinin-treated SAS: bavachinin2

description: Library name: bavachinin-2


title: YZ-162

description: Library name: YZ-162

value: PR


title: TN_CD_female_17w_8_liver

description: Library name: HDP-018698_liver


title: Astrocyte, 4 h, rep3

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-21

value: After 4 hours


title: RNA-Seq of bavachinin-treated SAS: bavachinin1

description: Library name: bavachinin-1


title: YZ-158

description: Library name: YZ-158


title: TN_WD_female_17w_9_liver

description: Library name: HDP-018792_liver


title: YZ-169

description: Library name: YZ-169

value: SD


title: Astrocyte, 4 h, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-20


title: RNA-Seq of SAS: control3

description: Library name: control-3


title: YZ-156

description: Library name: YZ-156


title: Astrocyte, 4 h, rep1

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-19


title: TN_WD_male_9w_7_liver

description: Library name: HDP-018797_liver


title: Astrocyte, 8 h, rep1

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-22


title: Astrocyte, 2 h, rep3

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-18

value: After 2 hours


title: TN_CD_female_17w_6_liver

description: Library name: HDP-018717_liver


title: Astrocyte, 2 h, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-17


title: RNA-Seq of SAS: control1

description: Library name: control-1


title: YZ-155

description: Library name: YZ-155


title: TN_WD_female_3d_5_liver

description: Library name: HDP-019011_liver


title: RNA-Seq of SAS: control2

description: Library name: control-2


title: RT_CD_female_17w_4_liver

description: Library name: HDP-018965_liver


title: YZ-008

description: Library name: YZ-008


title: Astrocyte, 2 h, rep1

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-16


title: 8128-JF-2

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 8128-JF-2

data_processing:
The CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: hg19
Supplementary files format and content: cell ranger output format

extract_protocol:
Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE [https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf]
Tissue Sections;  https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: skin cells


title: 8128-JF-4

description: Library name: 8128-JF-4


title: MSKB57

source_name: patient tumor

growth_protocol: OCT embedded patinet PDAC tumors

extract_protocol:
Archival patient PDAC samples from two 50um sections of OCT embedded tumors were broken up using razor blades in petri dish on ice in 1 ml NST-DAPI solution. The crude nuclei preparation was then subjected to FACS on a BD FACSAria Flow Cytometer Cell Sorter to isolate 2N, 4N and aneuploid nuclei.Duplicates of sorted samples were used to confirm KRAS variant allele frequency. Approximately 10,000-50,000 nuclei from either aneuploid or 4N populations were carefully pelleted for ATAC-seq library prep.
ATAC libraries were prepared for sequencing using standard Illumina Nextera DNA Library Preparation protocols.

tag: tissue type

value: Pancreatic ductal adenocarcinoma

value: patient tumor

tag: kras allele

tag: status

value: NED

tag: os

tag: dfs

tag: Stage

value: Stage I-III


title: MSKB60


title: RT_CD_male_17w_3_liver

description: Library name: HDP-018879_liver


title: TN_CD_female_3d_2_liver

description: Library name: HDP-019118_liver


title: MSKB43

value: DOD


title: 8128-JF-3

description: Library name: 8128-JF-3

value: skin


title: V2a, 8 h, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-23

tag: genotype


title: TN_CD_male_17w_1_liver

description: Library name: HDP-018701_liver

value: liver


title: 8128-JF-1

description: Library name: 8128-JF-1


title: MSKB42


title: MSKB34


title: Liver Ercc1 d/- AL 7wks #4

first: Wilbert

last: Vermeij

address: Heidelberglaan 25

institute: Princess Máxima Center

description: Library name: IG24

data_processing:
Processing of raw sequencing reads was performed on an in house-generated data analysis pipeline. Removal of sequence adaptors, tRNA, and rRNA from both mRNA- and Ribo-seq and truncation of mRNA reads was performed using Trimmomatic (version 0.39). Trimmed reads were aligned to the coding region (CDS) of the mouse reference genome (annotation: gencode.vM20.annotation.gtf; genome: GRCm38.p6.genome.fa; http://gencodegenes.org/mouse/release_M20.html) using STAR (version 2.7.0f). Read counts for each gene were obtained using FeatureCounts (as part of SubRead version 1.6.4).
Assembly: GRCm38.p6.genome.fa gencode.vM20.annotation.gtf
Supplementary files format and content: Tab-delimited count files produced by featureCounts

source_name: Liver

growth_protocol: Animals were housed individually in ventilated cages under specific pathogen-free conditions, in carefully controlled environments (20–22 °C, 12h light:12h dark cycle). All animals were bred and maintained on AIN93G synthetic pellets (Research Diet Services B.V., Wijk bij Duurstede, The Netherlands; gross energy content 4.9 kcal/g dry mass, digestible energy 3.97 kcal/g). On average, 6-16 week old Ercc1Δ/− mice ate 2.3 g food per day. The animals that were given dietary restriction (DR) were so from 7 weeks of age, when development was largely completed, starting with 10% restriction. DR was gradually increased weekly with 10%, until 30% DR (1.6 g/day), which was provided from 9 weeks of age onward as previously published. Adult WT mice ate on average 3.0 g food per day, resulting in 2.1 g/day for 30% DR. To avoid alterations in the biological clock, food was provided to the animals just before the start of the dark (active) period, Zeitgeber Time (ZT) 12:00, except for the day of sacrifice, when no food was given prior to collect.

extract_protocol:
Snap-frozen liver specimens were lysed in QIAzol lysis reagent with the TissueLyser LT (QIAGEN) and RNA was isolated using the miRNeasy mini kit (QIAGEN; 217004) according to manufacturer’s protocol with optional on column DNase I treatment (QIAGEN; 79254). RNA quality and quantity were assessed using the NanoDrop One (Thermo Fisher Scientific, USA) and Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA; G2939BA), respectively.
RNA library was prepared by Novogene from ≥ 200 ng RNA.

treatment_protocol: See growth protocol.

tag: strain

value: F1 Hybrid C57BL6J/FVBN

value: Liver

value: Male

value: Ercc1 d/-


title: V2a, 8 h, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-22

value: Cervical cord

value: After 8 hours


title: 10082-JF-11

description: Library name: 10082-JF-11


title: V2a, 8 h, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-24


title: Liver Ercc1 d/- AL 16wks #4

description: Library name: IG23


title: MSKB30


title: 10082-JF-8

description: Library name: 10082-JF-8


title: 10082-JF-9

description: Library name: 10082-JF-9


title: V2a, 4 h, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-21

value: After 4 hours


title: MSKB31


title: 10082-JF-10

description: Library name: 10082-JF-10


title: Liver Ercc1 d/- 30% DR 16wks #4

description: Library name: IG21


title: 9260-JF-16

description: Library name: 9260-JF-16


title: V2a, 4 h, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-20


title: V2a, 2 h, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-18


title: MSKB10


title: Liver Ercc1 d/- 30% DR 16wks #3

description: Library name: IG20


title: 9260-JF-6

description: Library name: 9260-JF-6


title: V2a, 4 h, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-19


title: Liver Ercc1 +/+ AL 104wks #4

description: Library name: IG22

value: Ercc1 +/+

value: AL/104 wks


title: Liver Ercc1 +/+ AL 104wks #3

description: Library name: IG19


title: V2a, 2 h, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-17

value: After 2 hours


title: MSKB7

value: Pancreatic ductal adenocarcinoma


title: MSKB5

value: patient tumor


title: MSKB4

value: ND

value: NED


title: Liver Ercc1 +/+ AL 16wks #4

description: Library name: IG18


title: V2a, 2 h, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-16


title: Liver Ercc1 d/- 30% DR 16wks #2

description: Library name: IG17


title: Microglia, Day 28, rep3

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-15

value: Day 28


title: 9260-JF-4

description: Library name: 9260-JF-4

value: skin

value: skin cells


title: Microglia, Day 28, rep2

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-14


title: 9260-JF-3

description: Library name: 9260-JF-3


title: 9260-JF-5

description: Library name: 9260-JF-5


title: MSKB3

value: Stage I-III


title: Liver Ercc1 +/+ 30% DR 16wks #4

description: Library name: IG16

value: F1 Hybrid C57BL6J/FVBN

value: Liver


title: 9260-JF-2

description: Library name: 9260-JF-2


title: Liver Ercc1 d/- AL 7wks #3

description: Library name: IG15

value: Male

value: Ercc1 d/-


title: 9260-JF-1

description: Library name: 9260-JF-1


title: Microglia, Day 14, rep3

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-12

value: Cervical cord

value: Day 14


title: MSKB1

value: DOD


title: Microglia, Day 28, rep1

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-13


title: Liver Ercc1 +/+ 30% DR 16wks #3

description: Library name: IG14

value: Ercc1 +/+


title: KCP_H3K27Ac_CR_

data_processing:
Cut&Run Tools was used to align reads and call peaks
Resulting pileup files were used to generate bigwigs from default macs2 settings in Cut&Run Tools.
Assembly: hg19
Supplementary files format and content: bigwig coverage tracks
Library strategy: CUT&RUN

growth_protocol: POs were suspended in 30 ul of Matrigel dome and applied to the bottom of each well of non-tissue culture treated 48 well plate to solidify. The Matrigel dome was overlaid with 0.4 ml of DMEM-F12 base medium supplied with Glutamax, Penicillin/Streptomycin, B27TM supplement, 1mM N-acetyle-L-cystein, 10mM Nicotinamide, 0.5uM A83-01, 100ng/ml hNoggin, 50ng/ml hEGF, 10nM hGastrin I, 100ng/ml hFGF10, 500ng/ml Rsp1.

extract_protocol:
Organoids were extracted from the matrigel by cell recovery solution, trypsinized into single cell suspension. 500,000 cells were used per CUT&RUN assay.
CUT&RUN library was prepared with no more than 10 ng CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit (NEB) according to manufacturer’s protocol.

treatment_protocol: In case of ERK inhbitor treatment,  LY3214996 was used at 1uM and POs were incubated for 4 days. DMSO was used as control.

value: Pancreatic (hPSC derived)

value: Pancreatic progenitor organoid

value: KCP


title: KCP_JUNB_CR_2


title: MSKB2

value: Pancreatic ductal adenocarcinoma

value: patient tumor

value: AWD


title: 8911-JF-15

description: Library name: 8911-JF-15

value: skin


title: Liver Ercc1 +/+ AL 16wks #3

description: Library name: IG13


title: Microglia, Day 14, rep2

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-11


title: 8911-JF-16

description: Library name: 8911-JF-16

value: skin cells


title: Microglia, Day 14, rep1

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-10


title: Liver Ercc1 +/+ AL 104wks #2

description: Library name: IG12

value: AL/104 wks


title: Liver Ercc1 d/- AL 7wks #2

description: Library name: IG11

value: F1 Hybrid C57BL6J/FVBN


title: KCP_JUNB_CR_1


title: Microglia, Day 7, rep3

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-09

value: Day 7


title: Microglia, Day 7, rep2

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-08


title: KCP_FOSL2_CR_2


title: 8911-JF-13

description: Library name: 8911-JF-13


title: Liver Ercc1 +/+ 30% DR 16wks #2

description: Library name: IG10

value: Liver

value: Male


title: ChIP_TET1_PP1_2

value: Early pancreatic progenitor

value: WT

tag: chip antibody

value: anti-V5-tag (Cell Signaling Technologies, #13202, lot#7)


title: KCP_FOSL2_CR_1

tag: tissue


title: Liver Ercc1 +/+ AL 16wks #2

description: Library name: IG9

value: Ercc1 +/+


title: Microglia, Day 7, rep1

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-07

value: Cervical cord


title: 8911-JF-14

description: Library name: 8911-JF-14


title: KCP_FOS_CR_2

value: Pancreatic (hPSC derived)

tag: cell line

value: Pancreatic progenitor organoid


title: ChIP_TET1_PP1_1


title: Microglia, Day 3, rep3

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-06

tag: treatment

value: Day 3


title: Microglia, Day 3, rep2

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-05


title: KCP_FOS_CR_1

value: KCP


title: Liver Ercc1 d/- AL 16wks #2

description: Library name: IG7

value: Ercc1 d/-


title: ChIP_Input1


title: Microglia, Day 3, rep1

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-04


title: KCP_LY_RNA-seq_2

data_processing:
Transcriptome alignment by Salmon
Tximport to obtain transcript level quantification before gene summarization.
Differential expression by DESeq2 1.16.1
Assembly: hg19
Supplementary files format and content: tar of Salmon quantification

growth_protocol: Pancreatic progenitor cells grown in PO condition were suspended in 30 ul of Matrigel dome and applied to the bottom of each well of non-tissue culture treated 48 well plate to solidify. The Matrigel dome was overlaid with 0.4 ml of DMEM-F12 base medium supplied with Glutamax, Penicillin/Streptomycin, B27TM supplement, 1mM N-acetyle-L-cystein, 10mM Nicotinamide, 0.5uM A83-01, 100ng/ml hNoggin, 50ng/ml hEGF, 10nM hGastrin I, 100ng/ml hFGF10, 500ng/ml Rsp1.

extract_protocol:
Total RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: POs were treated with doxycycline to introduce mutations. RNA was extracted from POs at paired passages across genotypes. In case of ERK inhbitor treatment,  LY3214996 was used at 1uM and POs were incubated for 4 days. DMSO was used as control.  KCP POs transduced with lentivirus coding the sgRNA against AP-1 factors were indicated.

value: KCP PO P29 treated with ERKi


title: KCP_LY_RNA-seq_1

value: KCP PO P28 treated with ERKi


title: KCPS_Methyl_1

data_processing:
*library strategy: EPIC Methyl Capture
Raw reads alignment and CpG methylation call were performed by Bismark v0.15.0.
Assembly: hg19
Supplementary files format and content: methylcall files are in .bw format.

extract_protocol:
POs in culture were directly lysed and gDNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen).
gDNA was submitted to the MSKCC Integrated Genomics Operation Core to be processed with the TruSeq Methyl Capture EPIC Library Prep Kit from Illumina.

value: pancreatic progenitor organoid

value: KCPS


title: Liver Ercc1 +/+ 30% DR 16wks #1

description: Library name: IG6

value: F1 Hybrid C57BL6J/FVBN


title: Microglia, Control, rep3

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-03

value: Control


title: Liver Ercc1 d/- AL 16wks #3

description: Library name: IG8

value: Liver

value: Male


title: KCP_DMSO_RNA-seq_1

value: KCP PO P28 treated with DMSO


title: Liver Ercc1 +/+ AL 104wks #1

description: Library name: IG5

value: AL/104 wks


title: Microglia, Control, rep2

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-02


title: KCP_Methyl_1


title: KCP_DMSO_RNA-seq_2

value: KCP PO P29 treated with DMSO


title: KCP_Methyl_2


title: Liver Ercc1 d/- AL 7wks #1

description: Library name: IG4


title: KCPS_RNA-seq_3

value: KCPS PO P22


title: KCPS_Methyl_2

value: Pancreatic (hPSC derived)


title: Astrocyte, Day 28, rep3

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-15

value: Cervical cord

value: Day 28


title: Microglia, Control, rep1

description:
2 × 75 bp paired-end
Cx3cr1.txt
Cx3cr1-01


title: Liver Ercc1 d/- AL 16wks #1

description: Library name: IG3


title: KP_Methyl_2

value: KP


title: Liver Ercc1 +/+ AL 16wks #1

description: Library name: IG2

value: Ercc1 +/+


title: KCPS_RNA-seq_2

value: Pancreatic progenitor organoid

value: KCPS PO P21


title: Astrocyte, Day 28, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-14


title: KP_Methyl_1

value: pancreatic progenitor organoid


title: KC_Methyl_2

value: KC


title: Liver Ercc1 d/- 30% DR 16wks #1

description: Library name: IG1

value: F1 Hybrid C57BL6J/FVBN

value: Ercc1 d/-


title: Astrocyte, Day 28, rep1

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-13


title: KCPS_RNA-seq_1

value: KCPS

value: KCPS PO P20


title: Astrocyte, Day 14, rep3

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-12

value: Day 14


title: KC_Methyl_1


title: KCP_JUND_KO_RNA-seq_3

value: KCP with AP-1 KO

value: KCP at P8 were transduced with JUND sgRNA and harvested 8 weeks later at P8+8


title: KCP_RNA-seq_3

value: KCP

value: KCP PO P22


title: KCP_RNA-seq_2

value: Pancreatic (hPSC derived)

value: KCP PO P21


title: Heart, Control, Male, 9183, Infarct

city: Aachen

first: Julia

last: Wollenhaupt

address: Pauwelsstraße 30

department: Institute for Molecular Cardiovascular Research

country: Germany

institute: Uniklinik RWTH Aachen

description: Library name: JUW03_43

data_processing:
Raw sequences from fastq files were aligned to the Ensembl reference mouse cDNA (GRCm39 v109) by kallisto (v0.48.0)
The transcript read counts were assembled to gene level using the R package tximport (v1.22.0) based on the Ensembl gene annotation GTF file (v109).
Only protein-coding genes and transcripts were included for further analysis based on the Ensembl gene annotation GTF file (v109).
Genes with an average count no more than 5 were filtered out.
Assembly: GRCm39 v109
Supplementary files format and content: Expression_read_counts.tsv
Supplementary files format and content: Tab-delimited text file includes read count values for each sample.

source_name: Heart infarct

growth_protocol: All animals were fed with a western type diet for 4 weeks. Then the Chronic kidney disease (CKD) group was fed with a western type diet containing 0.3% adenine for 10 days followed by a western type diet containing 0,15% adenine for additional 11 days (4 days before MI induction and 7 days post-MI). The control group received a western type diet for the entire period.

extract_protocol:
RNA was extracted by using the Qiagen RNeasy Micro Kit with inclusion of a DNAse-treatment step, all according to manufacturer's instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Cardiac tissue was rinsed with ice-cold PBS and snap-frozen in liquid nitrogen directly after organ explantation, after which it was stored at -80°C until RNA extraction.

value: Heart infarct

value: Male

value: ApoE-/-

value: Control


title: KP_RNA-seq_3

value: Pancreatic progenitor organoid

value: KP

value: KP PO P22


title: Astrocyte, Day 14, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-11

value: Cervical cord


title: Heart, Control, Male, 9184, Infarct

description: Library name: JUW03_44


title: KCP_RNA-seq_1

value: KCP PO P20


title: Astrocyte, Day 7, rep3

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-09

value: Day 7


title: Heart, Chronic kidney disease (CKD), Male, 9179, Infarct

description: Library name: JUW03_39

value: CKD


title: Heart, Control, Male, 9182, Infarct

description: Library name: JUW03_42


title: KCP_JUND_KO_RNA-seq_1

value: KCP with AP-1 KO

value: KCP at P8 were transduced with JUND sgRNA and harvested 6 weeks later at P8+6


title: KCP_JUNB_KO_RNA-seq_3

value: KCP at P8 were transduced with JUNB sgRNA and harvested 8 weeks later at P8+8


title: Astrocyte, Day 14, rep1

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-10

value: Day 14


title: Heart, Control, Male, 9180, Infarct

description: Library name: JUW03_40


title: KP_RNA-seq_1

value: Pancreatic (hPSC derived)

value: KP PO P20


title: KCP_JUNB_KO_RNA-seq_2

value: KCP at P8 were transduced with JUNB sgRNA and harvested 7 weeks later  at P8+7


title: KP_RNA-seq_2

value: KP PO P21


title: Astrocyte, Day 7, rep1

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-07


title: KCP_JUND_KO_RNA-seq_2

value: KCP at P8 were transduced with JUND sgRNA and harvested 7 weeks later at P8+7


title: Astrocyte, Day 7, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-08


title: Heart, Chronic kidney disease (CKD), Male, 9177, Infarct

description: Library name: JUW03_37

value: Heart infarct

value: Male

value: ApoE-/-


title: Astrocyte, Day 3, rep3

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-06

value: Day 3


title: Heart, Chronic kidney disease (CKD), Male, 9178, Infarct

description: Library name: JUW03_38


title: Heart, Chronic kidney disease (CKD), Male, 9176, Infarct

description: Library name: JUW03_36


title: KC_RNA-seq_3

value: Pancreatic progenitor organoid

value: KC

value: KC PO P22


title: Astrocyte, Day 3, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-05

value: Cervical cord


title: KCP_FOSL2_KO_RNA-seq_3

value: KCP with AP-1 KO

value: KCP at P8 were transduced with FOSL2 sgRNA and harvested 8 weeks later at P8+8


title: KC_RNA-seq_1

value: KC PO P20


title: KC_RNA-seq_2

value: KC PO P21