title: 278T-148191A-FOV_11

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
278T-148191A-FOV_11.rds

value: Colon tumour,FFPE

value: rectal

value: LHS


title: Parkinson’s Disease [JM-PK28]

status: Public on Dec 09 2025

type: RNA

city: Sant Joan d'Alacant

first: Marina

last: Guillot Fernández

state: Alicante

address: Av. Don Santiago Ramón y Cajal, s/n

country: Spain

institute: Instituto de Neurociencias

description: Gene expression data

hyb_protocol: Labeled cRNA was hybridized to the Clariom S Array (Human, Affymetrix) following the manufacturer’s guidelines.

scan_protocol: The Clariom S Array (Human, Affymetrix) was scanned using the GeneChip® Scanner 3000 7G according to the manufacturer's instructions

data_processing:
Raw .CEL files were processed using the R computing environment (version 4.4.2) and BioConductor packages. Quality control was performed with the oligo package and the Transcriptome Analysis Console (TAC) software (version 4.0.3, ThermoFisher Scientific). Robust Multi-array Average (RMA) normalization was applied to adjust for background noise and normalize expression levels. Probes not mapping to known genes were excluded, and lowly expressed genes were filtered out. Differential expression analysis was performed using the limma package, with multiple testing correction applied via the False Discovery Rate (FDR) method.
Normalized log2-transformed gene expression values were obtained after RMA normalization and background correction.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Parkinson’s Disease

label_protocol: Biotin-labeled cRNA was generated for hybridization using the standard Affymetrix protocol.

growth_protocol: Not applicable. Human peripheral blood samples were collected from Parkinson’s disease (PD) patients and healthy controls.

extract_protocol: Peripheral Blood Mononuclear Cells (PBMCs) were isolated from whole blood using BD Vacutainer® CPT™ Cell Preparation Tubes with Sodium Heparin, following the manufacturer’s instructions. RNA extraction was performed using TRI Reagent (Applied Biosystems), and RNA integrity was assessed with the Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment was applied. Samples were obtained from de novo and drug-naïve PD patients and age- and sex-matched healthy controls.

value: HGUA

tag: Sex

value: Male

tag: age

tag: Stage


title: 280N-120131-FOV_11

city: Clayton

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

department: Anatomy and developmental biology

country: Australia

institute: Monash University

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280N-120131-FOV_11.rds

hyb_protocol: NanoString®ISH probes were prepared by incubation at 95 °C for 2 min and immediately transferred to ice. The ISH probe mix (1 nM ISH probe, 40% formamide, 2.5% dextran sulfate, 0.2% BSA, 100 μg ml–1 salmon sperm DNA, 2× SSC, 0.1 U μl–1 SUPERase•In (ThermoFisher) in DEPC H2O) was then pipetted into the chamber, and adhesives supplied with the chambers were applied to the chamber ports. Hybridization occurred at 37 °C overnight after sealing the chamber to prevent evaporation. Following ISH probe hybridization, tissue sections were washed twice in a buffer comprising 50% formamide (VWR) in 2× SSC at 37 °C for 25 min, washed twice with 2× SSC for 2 min each at room temperature and then blocked with 100 mM NHS-acetate for 15 min. After blocking, the hydrophobic barrier was removed with a blade and a custom-made flow cell was attached to the slide.

scan_protocol: Slides 6–9 were processed using the CosMx Human Universal Cell Characterization Panel Version 2 at the Central Facility for Genomics, Griffith University. FFPE tissue sections were hybridized with probes targeting 1000 genes. Cell segmentation was performed using DAPI, CD298/B2M, PanCK, CD45, and CD68. Slides were loaded into the CosMx SMI flow cell and washed with 1.5 ml of reporter wash buffer (1× SSPE, 0.5% Tween 20, 0.1 U μl–1 SUPERase•In, 0.1% Proclin 950, DEPC-treated water) to remove bubbles. A low-resolution image of the entire slide was acquired to allow FOV placement. RNA readout was initiated by flowing 100 μl of Reporter 1 at 200 μl min–1 and incubating for 15 minutes, followed by washing with 1 ml of reporter wash buffer at 750 μl min–1. Imaging buffer (80 mM glucose, 0.6 U ml–1 pyranose oxidase, 18 U ml–1 catalase, 1:1,000 Proclin 950, 500 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 20, DEPC-treated water) was applied before acquisition of eight Z-stack images per FOV (800 nm step size). Fluorophores were UV-cleaved (385 nm, 116 J cm–2, 500 ms) and removed using 200 μl of strip wash buffer (0.0033× SSPE, 0.5% Tween 20, 1:1,000 Proclin 950). Sixteen hybridization cycles were performed and repeated multiple times to enhance sensitivity. Morphology staining was completed on the same instrument by incubating with blocking buffer (NanoString buffer W) for 30 minutes, applying a cocktail of CD298, CD45, CD3, and PanCK antibodies for 1 hour, washing with 8 ml of reporter wash buffer, and adding imaging buffer prior to image acquisition.

data_processing:
Flat files generated as described in: He et a., Nature Biotechnology 2022;40(12):1794-806. Each sample/slide/FOV combination is provided as a seurat saved in R Data Serialization (RDS) format. To obtain the metadata provided including cell identites:
Processed data: AtoMx computed gene-level probe counts with corresponding XY coordinates

label_protocol: Tissue was digested with Protease Plus (ACD Bio) spiked with Proteinase K (ThermoFisher), ranging from 1 to 5 μg ml–1 depending on tissue type, at 40 °C for 15–30 min. Tissue sections were rinsed twice with DEPC H2O, incubated in 1:400 diluted fiducials (Bangs Laboratories) in 2× saline sodium citrate and Tween (0.001% Tween 20, Teknova) for 5 min at room temperature and washed with 1× PBS (ThermoFisher) for 5 min. After digestion and fiducial placement, tissue was fixed with 10% neutral-buffered formalin for 1 min to maintain soft tissue morphology, washed twice with Tris-glycine buffer (0.1 M glycine (Sigma), 0.1 M Tris-base (FisherScientific) in DEPC H2O) for 5 min and then washed with 1× PBS for 5 min. Fixed tissue was blocked using 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, ThermoFisher) diluted in NHS-acetate buffer (0.1 M NaP + 0.1% Tween pH 8.0 in DEPC H2O) for 15 min at room temperature and washed in 2× saline sodium citrate (SSC) for 5 min. An adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over tissue.

extract_protocol: To perform in situ hybridization on tissue sections, the slides were baked in an oven overnight at 37 °C and then at 60 °C for at least 2 h. Tissue sections were dewaxed twice in xylene (Millipore) for 5 min, twice in ethanol (Pharmco) for 2 min and then the slides were baked at 60 °C for 5 min. Tissue sections were subjected to the target retrieval step using the RNAscope Target Retrieval kit (ACD Bio) and heated at 100 °C in a pressure cooker for 15–30 min. After target retrieval, tissue sections were rinsed with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O, ThermoFisher), washed in ethanol for 3 min and dried at room temperature for 30 min. On the dried slide, a hydrophobic barrier line was drawn around the tissue section using an ImmEdge Pen (Vector).

treatment_protocol: Tissue microarrays were constructed at the Monash Histology Platform. 2mm cores were dissected from formalin fixed paraffin embedded clinical samples using a Micro Tissue Arrayer, MTA-1 (Beecher Instruments, USA). Core placement was guided by the histopathological annotation of tissue blocks, excluding overly necrotic areas, as defined by an expert anatomical pathologist (Dr David Nickless). Donor cores were arranged into TMA recipient blocks and reannealed at 45 degrees for 3 hours. 4um sections were collected onto slides. To aid in field of view (FOV) placement, the first and last slide in each series of sequential sections was stained with haematoxylin and eosin (H&E) and digitised at 40X magnification on the Aperio AT slide scanner.

tag: tissue

tag: donor

value: F

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: Ca_in

type: SRA

city: Shanxi

first: wenbin

last: ren

address: 56 Xinjian South Road, Yingze District, Taiyuan City

country: China

institute: Shanxi Medical University

library_source: genomic

data_processing:
The raw sequencing data were examined using the illumina analysis pipeline.
Using Bowtie2, the data were aligned to the Mus musculus reference genome (University of California, Santa Cruz, mm10).
The data were further analyzed through the ChIP-seq analysis based on the model (MACS) program (https://github.com/taoliu/MACS).
The enriched binding peaks were identified after normalization with the control input.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Mus musculus

source_name: embryo

growth_protocol: DMEM, UltraPure™ distilled water (Invitrogen, USA), 1 mM glucose, 0.1 mM nonessential amino acids, 0.1 mM glutamate, 15% FBS, 0.1 mM β-mercaptoethanol (Life Technologies, USA), 1000 U/ml leukemia inhibitory factor (Millipore, USA)  Cells were cultured at 37C at 5% CO2.

extract_protocol:
C57BL/6 mESCs were seeded into culture dishes precoated with MEFs cultured in DMEM supplemented with 0.1 mM nonessential amino acids, 0.1 mM glutamate, and 10% fetal bovine serum (FBS) (Invitrogen, USA) overnight.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 30 cycles on the thermocycler. Post amplification libraries were size selected at 250-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Folate power (Sigma–Aldrich, USA) was dissolved in Dulbecco’s modified Eagle’s medium (DMEM) 10X without folic acid (Sigma–Aldrich, USA) and with 3.7%. filtered sodium hydrogen carbonate (Beijing ChemicalReagent Company, China). The final concentration of 4 mg/L folate as a normal control while the folatedeficient group was treated simply by DMEM without folate.

value: embryo

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: folate deficiency

tag: treatment

value: neurodevelopment


title: Ca_h3k4_1


title: 74T-10501A-FOV_11

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
74T-10501A-FOV_11.rds

value: M

value: descending colon

value: dMMR


title: M7_vector_Aged [ACSS2.WT.R7]

city: Philadelphia

first: Shuo

last: Zhang

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Demultiplexed FASTQs were aligned to the reference genome using STAR
Gene level read counts were prepared using featureCounts or HTSeq.
Unwanted variation was estimated by RUVr.
Differential expressed genes were called using DESeq2 with Wald test
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: whole Hippocampus

growth_protocol: Primary hippomcapal neurons culture were cultured in neural basal medium with 2% B27, 1x Glutamax, and 1x Penicillin/Streptomycin.

extract_protocol:
Total RNA was extracted using Trizol-chloroform following RNA purification using RNeasy mini-kit, Qiagen.
130 ng input RNA was used to make libraries using the NEB kit E7490.

treatment_protocol: Cells were treated with 1.5xE6 PhP.eb.upACSS2 or PhP.eB-vector at 5DIV for 48 hours before 1x PBS wash on 7DIV and treatment with hAD-tau or PBS. Aged and 10 months old C57BL6 mice were treated with retro-orbital injection of PhP.eb.upACSS2 or PhP.eB-vector. Aged mice treated at 21-22 months of age with 1.5 xE11 viral genome (vg) and tissue harvested 30 min post remote context recall after 2 months of viral treatment. 10 months old mice treated with 1.2 xE11 vg for 2 weeks and tissue harvested 30 min after acquisition of fear conditioning.2.5 month old PS 19 mice were treated with 1.5 xE10 vg PhP.eb.upACSS2 or PhP.eB-vector for 1 month (1mpi) or 6 month (6 mpi) and euthanized 30 min post 24-hour contextual recall.

value: whole Hippocampus

tag: strain

value: 22-23 months old

value: male


title: Con_h3k4_2

value: WT


title: Parkinson’s Disease [JM-PK26]

description: Gene expression data

value: HGUA

value: Female

value: Hoehn I


title: 64T-Tumour_B-FOV_10

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_10.rds

scan_protocol: Slides 1–3 were processed using the CosMx Human Universal Cell Characterization Panel Version 1 under the NanoString Technology Access Program. FFPE tissue sections were hybridized with transcript-specific probes targeting 1000 genes. Cell segmentation was performed using immunofluorescence markers DAPI, CD298/B2M, PanCK, CD45, and CD3. Slides were mounted into the CosMx Spatial Molecular Imager (SMI) flow cell and flushed with 1.5 ml of reporter wash buffer (1× SSPE, 0.5% Tween 20, 0.1 U μl–1 SUPERase•In, 0.1% Proclin 950, DEPC-treated water) to remove air bubbles. A low-resolution whole-slide image was acquired for field-of-view (FOV) placement. RNA detection began with 100 μl of Reporter 1 flowed at 200 μl min–1 for 15 minutes, followed by 1 ml of reporter wash buffer at 750 μl min–1 to remove unbound probes. Imaging buffer (80 mM glucose, 0.6 U ml–1 pyranose oxidase, 18 U ml–1 catalase, 1:1,000 Proclin 950, 500 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 20, DEPC-treated water) was then introduced, and eight Z-stack images (800 nm step size) were acquired per FOV. Fluorophores were UV-cleaved (385 nm, 116 J cm–2, 500 ms) and removed with 200 μl of strip wash buffer (0.0033× SSPE, 0.5% Tween 20, 1:1,000 Proclin 950). This procedure was repeated for 16 reporter pools and cycles, with multiple iterations to enhance sensitivity. Morphology staining was performed on the same instrument using NanoString buffer W for 30 minutes, followed by a 1-hour incubation with an antibody cocktail (CD298, CD45, CD3, PanCK), wash with 8 ml of reporter wash buffer, and final imaging in imaging buffer.

value: Colon tumour,FFPE

value: F

value: caecum


title: 118T-Tumour_A-FOV_10

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118T-Tumour_A-FOV_10.rds

value: pMMR

value: RHS


title: Con_in

value: embryo

value: mouse embryonic stem cells


title: Parkinson’s Disease [JM-PK20]

description: Gene expression data


title: Parkinson’s Disease [JM-PK23]

description: Gene expression data

value: Hoehn II


title: Parkinson’s Disease [JM-PK25]

description: Gene expression data


title: Parkinson’s Disease [JM-PK2]

description: Gene expression data


title: M6_vector_Aged [ACSS2.WT.R6]


title: 67T-Run5850.2186.2-FOV_10

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_10.rds

scan_protocol: Slides 4–5 were processed using the CosMx Human Universal Cell Characterization Panel Version 1 under the NanoString Technology Access Program. FFPE tissue sections were hybridized with probes targeting 1000 genes. Cell segmentation was performed using DAPI, CD298/B2M, PanCK, and CD45. Slides were loaded into the CosMx SMI flow cell and flushed with 1.5 ml of reporter wash buffer (1× SSPE, 0.5% Tween 20, 0.1 U μl–1 SUPERase•In, 0.1% Proclin 950, DEPC-treated water) to remove bubbles. A low-resolution whole-slide image was acquired to guide FOV placement. RNA detection involved flowing 100 μl of Reporter 1 at 200 μl min–1 for 15 minutes, washing with 1 ml of reporter wash buffer at 750 μl min–1, then adding imaging buffer (80 mM glucose, 0.6 U ml–1 pyranose oxidase, 18 U ml–1 catalase, 1:1,000 Proclin 950, 500 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 20, DEPC-treated water) before imaging. Eight Z-stacks were acquired per FOV (800 nm step size), followed by UV cleavage of fluorophores (385 nm, 116 J cm–2, 500 ms) and washing with 200 μl of strip wash buffer (0.0033× SSPE, 0.5% Tween 20, 1:1,000 Proclin 950). This 16-cycle hybridization and imaging process was repeated for improved sensitivity. Morphology staining was performed by incubating with blocking buffer (NanoString buffer W) for 30 minutes, applying a cocktail of CD298, CD45, CD3, and PanCK antibodies for 1 hour, washing with 8 ml of reporter wash buffer, and imaging in imaging buffer.

value: M

value: sigmoid

value: LHS


title: Parkinson’s Disease [JM-PK30]

description: Gene expression data

value: Male


title: Parkinson’s Disease [JM-PK27]

description: Gene expression data


title: Con_h3k4_1

value: neurodevelopment


title: Tei_dsx_neurons

first: Justin

last: Walsh

address: 3740 Hamilton Walk

description:
Library name: Tei_dsxNeurons
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using CellRanger software v7.1.0
Assembly: GCA_000001215.4
Assembly: GCA_016746365.2
Assembly: GCA_016746245.2
Assembly: GCA_016746235.2
Supplementary files format and content: tab-separated value files, matrix files, and Rds files

molecule: polyA RNA

organism: Drosophila teissieri

source_name: central nervous system

extract_protocol:
For each replicate, the central nervous system of approximately 100 doublesex-GAL4 x UAS-nls::tdTomato flies were dissected in ice cold Schneider's medium and digested in a solution containing Liberase DH for 45 mins. The tissue was washed with Schneider's medium and broken apart via pipetting before FACS sorting out the tdTomato+ cells.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol, 10X Genomics)

value: central nervous system

value: neurons

value: male

value: 4-8 days


title: M8_vector_Aged [ACSS2.WT.R8]

value: whole Hippocampus

value: 22-23 months old


title: Parkinson’s Disease [JM-PK21]

description: Gene expression data

value: Female

value: Hoehn III


title: Parkinson’s Disease [JM-PK19]

description: Gene expression data


title: Parkinson’s Disease [JM-PK18]

description: Gene expression data

value: HGUA


title: Parkinson’s Disease [JM-PK16]

description: Gene expression data


title: Control [JM-CT5]

description: Gene expression data

source_name: Control


title: Control [JM-CT6]

description: Gene expression data


title: M3_vector_Aged [ACSS2.WT.R3]


title: San_dsx_neurons

description:
Library name: San_dsxNeurons
10X Genomics

organism: Drosophila santomea


title: 7N-Normal_A-FOV_10

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7N-Normal_A-FOV_10.rds

value: Colon tumour,FFPE

value: ascending

value: pMMR

value: RHS


title: M5_vector_Aged [ACSS2.WT.R5]


title: DNA methylation from IDH mutant medulloblastoma case 3

type: genomic

city: Hamburg

first: Alicia

last: Fürst

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
DNA methylation from IDH mutant medulloblastoma
Case3

hyb_protocol: For subsequent bisulfite conversion, 100-500 ng of DNA were input to the EZ DNA Methylation Kit (Zymo Research). DNA samples were cleaned utilizing the DNA Clean & Concentrator-5 Kit (Zymo Research) and restored by the Infinium HD FFPE DNA Restore Kit (Illumina).

scan_protocol: The iScan system was used in combination with the Infinium HumanMethylation450 or MethylationEPIC BeadChip Kit (Illumina) to detect the methylation status of 450,000 or 850,000 genome-wide CpG sites, respectively.

data_processing: The package minfi v1.43.1 was used to preprocess and normalize Illumina methylation array data (preprocessIllumina function) and calculate β-values in R programming language. The intersection of detected CpGs across all arrays was used for further analyses. SNP-associated CpGs, cross-hybridising probes as well as CpGs located on sex-chromosomes were excluded from analysis.

label: Cy3 and Cy5

source_name: FFPE

label_protocol: Standard Illumina Protocol

extract_protocol: For the generation of DNA methylation array data, the Maxwell® FFPE DNA Kit (Promega) was used for the extraction of genomic DNA from FFPE tissues.

value: FFPE

tag: age at diagnosis [years]

tag: histology

value: desmoplastic MB

tag: idh mutation


title: 7T-3461G-FOV_10

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_10.rds

tag: Sex

value: M


title: M2_vector_Aged [ACSS2.WT.R2]

tag: age


title: M1_vector_Aged [ACSS2.WT.R1]


title: M4_vector_Aged [ACSS2.WT.R4]


title: NC-148191A-FOV_10

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
NC-148191A-FOV_10.rds

tag: tissue


title: M12_upACSS2_Aged [ACSS2.OE.R12]


title: piwi-1 positive cells

city: Kansas City

first: Alejandro

last: Sánchez Alvarado

institute: Stowers Institute for Medical Research

description:
Library name: piwi_pos_1
processed data column: s_piwi_pos_15

data_processing:
Fastq files were generated with bclconvert (3.10.5) from illumina.
RNA-seq data was aligned to the Schmidtea mediterranea smed_20140614 genome (GEO GSE72389) from the Sánchez Alvarado lab using STAR (2.7.10b) with --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax .1 --outFilterType BySJout --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000.
Read counts were generated using STAR and TPMs were generated using RSEM (1.3.1) with --estimate-rspd
Assembly: smed_20140614 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72389 transriptome assembled with https://github.com/ejrsimr/transcriptome2star
Supplementary files format and content: CSV files of STAR counts and RSEM TPM

organism: Schmidtea mediterranea

source_name: whole worm

growth_protocol: The clonal asexual planarian S. mediterranea, strain CIW-4 (C4), were cultured at 20°C in a recirculating system containing 1X Montjuic water as previously described (Arnold et al., 2016). Animals that were used for in situ hybridization and RNAi were maintained in a recirculating system and fed calf liver twice a week. Prior to use in experiments, worms were transferred to static culture and starved for at least 2 weeks prior to use.

extract_protocol:
ACME dissociation, mRNA purification with AmPure XT beads, Nexterra XT DNA sample preparation kit
Nexterra XT index kit v2 (sets A and D), SMART-seq v4 amplification

treatment_protocol: Approximately 160 wild type worms divided into no probes control, agat label and piwi label were washed one time with fresh planarian water then treated with 7.5% NAC (Millipore-Sigma, A7250) in PBS for 2 minutes. After one more wash in planarian water, worms were then dissociated and fixed with ACME buffer as described (García-Castro et al., 2021) for about 60 minutes at room temperature agitating with a plastic transfer pipette every 20 minutes.  Cells were spun for 5 minutes at 1000 g and washed in 0.1% BSA two times then serially dehydrated to 70% Ethanol and stored at 4 degrees overnight. HCR V3 was performed as described in Molecular Instruments HCR + Flow, Mammalian Cells in Suspension protocol with 1:1000 RNAse inhibitor added to every step longer than 10 minutes (Promega RNasin RNase Inhibitor plus #N2511). Probes for agat-1, agat-2 and agat-3 were designed by Molecular Instruments to detect transcript sequences SMED30018353, SMED30009513 and SMED30019154, respectively and added in equal proportion to the samples. agat-1, agat-2 and agat-3 probes were designed with the B3, B4 and B5 initiator, respectively, but labeled all in the same AlexaFluor-647 hairpins for amplification. Probes for piwi-1 were designed by Molecular Instruments detect the transcript DQ186985.1, had a B1 initiator, and also labeled with an AlexaFluor-647 hairpin. Samples were labeled post-HCR with 0.2mg/mL DAPI for 30 minutes at room temperature during one of the final washes then checked on a fluorescence microscope for reasonable single cell suspension and brightly labeled cells. For sorting, cells were suspended in 1% BSA in PBS with RNAse inhibitor and kept on ice until sorted with a BD FACSymphony S6 flow cytometer. Cells were water bath sonicated for 1 minute then immediately strained with a 70 um Filcon strainer (BD biosciences, 340633) then immediately sorted. The instrument was set up with 0.4x concentrated sheath fluid (Leinco) and kept at 4°C throughout the sort. The control samples were used to set gates for 2N single cells based on FSC/SSC pattern and DAPI signal, as well as to set gates for the Alexa Fluor 647 label while accounting for autofluorescence and background staining. Collection wells were prepared pre-sort with lysis solution (CloneTech).

value: whole worm

tag: hcr probe

tag: facs gate

value: positive


title: M11_upACSS2_Aged [ACSS2.OE.R11]


title: 280N-120131-FOV_10

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280N-120131-FOV_10.rds

tag: donor

value: F

tag: age at diagnosis

tag: primary tumour location

value: caecum


title: Parkinson’s Disease [JM-PK1]

description: Gene expression data

value: Male

tag: Stage


title: Control [JM-CT26]

description: Gene expression data


title: pooled agat positive cells bio rep 4

description:
Library name: agat_pos_4
processed data column: s_agat_pos_3

value: pooled agat-1/2/3


title: 74T-10501A-FOV_10

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
74T-10501A-FOV_10.rds

value: descending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: LHS


title: Control [JM-CT25]

description: Gene expression data


title: M10_upACSS2_Aged [ACSS2.OE.R10]

tag: cell type

value: whole Hippocampus

value: 22-23 months old

value: male

tag: treatment


title: piwi-1 negative cells

description:
Library name: piwi_neg_1
processed data column: s_piwi_neg_15

value: negative


title: 142N-Run5850.2186.1-FOV_10

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_10.rds

value: Colon tumour,FFPE

value: ascending

value: RHS


title: 73T-Tumour_B-FOV_1

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73T-Tumour_B-FOV_1.rds

value: M

value: sigmoid

value: pMMR


title: M9_upACSS2_Aged [ACSS2.OE.R9]

tag: strain


title: 118T-Tumour_A-FOV_1

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118T-Tumour_A-FOV_1.rds


title: pooled agat positive cells bio rep 2

description:
Library name: agat_pos_2
processed data column: s_agat_pos_6_2

value: whole worm

value: positive


title: pooled agat positive cells bio rep 1

description:
Library name: agat_pos_1
processed data column: s_agat_pos_6_1


title: Control [JM-CT23]

description: Gene expression data

value: Male


title: M8_upACSS2_Aged [ACSS2.OE.R8]


title: 142N-Run5850.2186.2-FOV_1

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.2-FOV_1.rds

value: F


title: M7_upACSS2_Aged [ACSS2.OE.R7]


title: pooled agat negative cells bio rep 4

description:
Library name: agat_neg_4
processed data column: s_agat_neg_3

value: pooled agat-1/2/3


title: M5_upACSS2_Aged [ACSS2.OE.R5]


title: 170N-Normal_A-FOV_1

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170N-Normal_A-FOV_1.rds


title: pooled agat negative cells bio rep 1

description:
Library name: agat_neg_1
processed data column: s_agat_neg_6_1


title: 142N-Run5850.2186.1-FOV_1

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_1.rds

value: dMMR


title: pooled agat negative cells bio rep 2

description:
Library name: agat_neg_2
processed data column: s_agat_neg_6_2


title: M3_upACSS2_Aged [ACSS2.OE.R3]


title: NC-120131-FOV_1

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
NC-120131-FOV_1.rds


title: Control [JM-CT20]

description: Gene expression data

value: Female


title: M2_upACSS2_Aged [ACSS2.OE.R2]

value: whole Hippocampus


title: 74T-10501A-FOV_1

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
74T-10501A-FOV_1.rds

value: descending colon

value: LHS


title: M6_upACSS2_Aged [ACSS2.OE.R6]

value: 22-23 months old

value: male


title: Astro_18

city: BLOOMINGTON

first: Hui-Chen

last: Lu

state: IN

address: 400 EAST SEVENTH STREET, MULTI-DISCIPLINARY SCIENCE BUILDING 2

department: Gill Institute for Neuroscience

institute: Indiana University Bloomington

description: Library name: Astro_18

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the human reference genome mm10 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p --countReadPairs -Q 10”.
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.4.2.1) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: UCSC mm10
Supplementary files format and content: The excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts

source_name: Brain cortex

extract_protocol:
Qiagen RNeasy Mini Kit
Illumina Total RNAseq

value: Brain cortex

value: astrocytes

tag: genotype

value: cKOB

value: Astrocytes isolation


title: 7T-3461G-FOV_1

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_1.rds

value: Colon tumour,FFPE

value: M

value: ascending

value: pMMR

value: RHS


title: Astro_17

description: Library name: Astro_17


title: pooled agat positive cells bio rep 3

description:
Library name: agat_pos_3
processed data column: s_agat_pos_6_3

value: whole worm

value: pooled agat-1/2/3

value: positive


title: X4PreOvcc_39

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

country: Canada

institute: Université Laval

description: Library name: 4PreOv-cc

data_processing:
FASTQC,TRIMGALORE,STAR,DESEQ2
Assembly: Bos taurus ARS 1.3

organism: Bos taurus

source_name: Cumulus cells

extract_protocol:
using miRNeasy Mini Kit (QIAGEN, Hilden, Germany), RNase-Free DNase Set (QIAGEN, Hilden, Germany; cat #79254)
SMART-Seq HT Kit (Takara Bio Inc), following the manufacturer’s recommendation.cDNA was purified using AMPure XP Beads (Beckman Coulter, the Qubit dsDNA High Sensitivity (ThermoFisher Scientific) and Bioanalyzer High Sensitivity DNA Kit (Agilent) were used to determine the cDNA concentration and profile, respectively. The Nextera XT DNA Library Prep (Illumina) was used to prepare the libraries as recommended by the SMART-Seq HT kit.

value: Cumulus cells

tag: cell line

value: Slaughterhouse

value: Late

tag: batch


title: PBS_21DIV_S3 [RNA_PBS_R3_S19]

source_name: Primary embryonic hippocampal neurons

value: Primary embryonic hippocampal neurons

tag: age

value: 21 days in vitro

tag: Sex

value: PBS


title: Astro_16

description: Library name: Astro_16

tag: tissue

value: Brain cortex

value: astrocytes


title: LM23 PBMCs post-treatment with Abatacept

city: Doha

first: Bernice

last: Lo

address: Al Luqta

department: Research

country: Qatar

institute: Sidra Medicine

description:
Library name: LM23post
10x genomics

data_processing:
Gene counting, demultiplexing, barcode processing, and aggregation were all performed using Cell Ranger 7.0.1 configured with default parameters.
Assembly: human reference  transcriptome refdata-gex-GRCh38-2020-A
Supplementary files format and content: processed seurat objects

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs before and after abatacept treatment from patients CM11 and LM23 were thawed and diluted in complete RPMI1640 medium and centrifuged at 300g for 5 minutes. The pellet was resuspended and counted before being pelleted again and suspended at a density between 700-1200 cells/μL in sterile PBS with 0.04% BSA before being loaded into a Chromium Next GEM Chip G using the Chromium Controller.
Library preparation was done using the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index) (10X Genomics, Pleasanton, CA) according to manufactorer recommendations. Sequencing was performed using Novoseq X plus.

value: PBMC

tag: subject id

value: Post-treatment


title: Astro_15

description: Library name: Astro_15

value: cKOB

value: Astrocytes isolation


title: LM23 PBMCs pre-treatment with Abatacept

description:
Library name: LM23pre
10x genomics

value: Pre-treatment


title: PBS_21DIV_S2 [RNA_PBS_R2_S18]


title: X4PreD_39

description: Library name: 4PreD

source_name: oocyte

value: oocyte

value: Early


title: Parkinson’s Disease [JM-PK17]

description: Gene expression data

value: HGUA


title: Astro_14

description: Library name: Astro_14

value: cKOA


title: pooled agat negative cells bio rep 3

description:
Library name: agat_neg_3
processed data column: s_agat_neg_6_3

value: whole worm

tag: hcr probe

value: pooled agat-1/2/3

tag: facs gate

value: negative


title: X4PreDcc_39

description: Library name: 4PreD-cc

value: Cumulus cells

value: Slaughterhouse


title: X4PreOv_39

description: Library name: 4PreOv

value: Late


title: PBS_21DIV_S1 [RNA_PBS_R1_S17]

value: Primary embryonic hippocampal neurons

value: 21 days in vitro

value: PBS


title: M4_upACSS2_Aged [ACSS2.OE.R4]

value: whole Hippocampus

value: 22-23 months old

value: male


title: Astro_10

description: Library name: Astro_10

value: Brain cortex

value: astrocytes

value: Astrocytes isolation


title: X4PosD_39

description: Library name: 4PosD

value: oocyte


title: hAD-tau_21DIV_S4 [RNA_AD_R4_S16]

value: hAD-tau


title: CM11 PBMCs pre-treatment with Abatacept

description:
Library name: CM11pre
10x genomics

value: PBMC

value: Pre-treatment


title: 118N-148191A-FOV_1

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118N-148191A-FOV_1.rds

value: Colon tumour,FFPE

tag: donor

value: M

tag: age at diagnosis

tag: primary tumour location

value: caecum

value: pMMR

value: RHS


title: X4PosDcc_39

description: Library name: 4PosD-cc

value: Cumulus cells

value: Slaughterhouse

value: Late


title: Control [JM-CT16]

description: Gene expression data

value: Male

tag: Stage


title: CM11 PBMCs post-treatment with Abatacept

description:
Library name: CM11post
10x genomics

value: Post-treatment


title: Control [JM-CT21]

description: Gene expression data


title: Control [JM-CT2]

description: Gene expression data

value: Female


title: Control [JM-CT14]

description: Gene expression data


title: Control [JM-CT13]

description: Gene expression data


title: Control [JM-CT17]

description: Gene expression data


title: Control [JM-CT18]

description: Gene expression data


title: Astro_9

description: Library name: Astro_9

value: Brain cortex

value: astrocytes

value: cKOA


title: Control [JM-CT19]

description: Gene expression data


title: Control [JM-CT15]

description: Gene expression data


title: Control [JM-CT1]

description: Gene expression data


title: M1_upACSS2_Aged [ACSS2.OE.R1]

value: whole Hippocampus

value: 22-23 months old

value: male


title: X4DF1_39

description: Library name: 4DF1

value: oocyte

value: Early


title: Astro_8

description: Library name: Astro_8

value: Astrocytes isolation


title: hAD-tau_21DIV_S3 [RNA_AD_R3_S15]

value: Primary embryonic hippocampal neurons

value: 21 days in vitro

value: hAD-tau


title: hAD-tau_21DIV_S1 [RNA_AD_R1_S13]


title: Astro_7

description: Library name: Astro_7


title: Astro_6

description: Library name: Astro_6


title: X4DF1cc_39

description: Library name: 4DF1-cc

value: Cumulus cells

value: Slaughterhouse


title: vector + PBS_21DIV_S3 [DIV21_unsti_PBS3_Mock]

value: Php.eB.vector + PBS


title: Astro_5

description: Library name: Astro_5


title: X4Ccc_39

description: Library name: 4C-cc

value: CTRL


title: X3PreOv_39

description: Library name: 3PreOv

value: Late


title: Astro_4

description: Library name: Astro_4

value: Brain cortex


title: vector + PBS_21DIV_S1 [DIV21_unsti_PBS1_Mock]


title: X3PreD_39

description: Library name: 3PreD


title: shNT_O3

city: Tampa

first: Ana

middle: P

last: Da Silva Gomes

state: Florida

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: H Lee Moffitt Cancer Center

description: Library name: Sample 12

data_processing:
Raw data cleaned by removing reads containing adapters or ploy-N and low quality reads using Novogene in-house perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: grch38
Supplementary files format and content: xls delimited text file including raw counts for each sample
Supplementary files format and content: xls including FPKM values for each sample
Supplementary files format and content: xsl file including DESeq2 values for each sample

growth_protocol: For in vivo experiments, 5,000 4T1 mNeonGreen cells were injected via the tail vein into Balb/c mice. Four weeks later, 4T1 cells were isolated from lung tissue and sorted using an ARIA Sorp II cell sorter, collecting 100,000 cells per sample. For in vitro IFE treated samples, 4T1 cells were seeded into 6-well plates and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified atmosphere at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and contaminant DNA was digested on column with RNase-free DNase (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size, selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size, selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: For in vitro experiment, 24 hours after seeding, the medium was replaced with serum-free RPMI-1640 containing 25% interstitial fluid extract (IFE) isolated from the lungs of either young or old 4T1 metastasis-bearing mice. Seventy-two hours later, cells were collected for RNA isolation.

value: mammary carcinoma

value: Old IFE treated

value: in vitro


title: shNT_O2

description: Library name: Sample 11


title: X3PreOvcc_39

description: Library name: 3PreOv-cc


title: shNT_O1

description: Library name: Sample 10


title: hAD-tau_21DIV_S2 [RNA_AD_R2_S14]


title: vector + PBS_9DIV_S3 [DIV9_unsti_PBS3_Mock]

value: 9 days in vitro


title: X3PreDcc_39

description: Library name: 3PreD-cc


title: vector + PBS_9DIV_S2 [DIV9_unsti_PBS2_Mock]


title: X4C_39

description: Library name: 4C


title: shNT_Y3

description: Library name: Sample 9

value: Young IFE treated


title: vector + PBS_9DIV_S1 [DIV9_unsti_PBS1_Mock]


title: X3PosD_39

description: Library name: 3PosD

value: oocyte


title: vector + PBS_21DIV_S2 [DIV21_unsti_PBS2_Mock]


title: upACSS2 + PBS_21DIV_S3 [DIV21_unsti_PBS3_OE]

value: PhP.eB.upACSS2 + hAD-tau


title: shNT_Y2

description: Library name: Sample 8


title: X3PosDcc_39

description: Library name: 3PosD-cc


title: upACSS2 + PBS_21DIV_S2 [DIV21_unsti_PBS2_OE]


title: shNT_Y1

description: Library name: Sample 7


title: X3DF1_39

description: Library name: 3DF1

value: Early


title: upACSS2 + PBS_21DIV_S1 [DIV21_unsti_PBS1_OE]

value: Primary embryonic hippocampal neurons


title: upACSS2 + PBS_9DIV_S3 [DIV9_unsti_PBS3_OE]


title: GFP_Pos_O3

description: Library name: Sample 6

value: Old mouse

value: in vivo


title: X3DF1cc_39

description: Library name: 3DF1-cc

value: Cumulus cells


title: X3C_39

description: Library name: 3C

value: Slaughterhouse


title: X3Ccc_39

description: Library name: 3C-cc


title: upACSS2 + PBS_9DIV_S2 [DIV9_unsti_PBS2_OE]


title: GFP_Pos_O1

description: Library name: Sample 4


title: X2PreOv_39

description: Library name: 2PreOv


title: GFP_Pos_Y3

description: Library name: Sample 3

value: Young mouse


title: vector + hAD-tau_21DIV_S3 [DIV21_unsti_AD3_Mock]

value: 21 days in vitro

value: Php.eB.vector + PBS


title: GFP_Pos_Y2

description: Library name: Sample 2


title: upACSS2 + PBS_9DIV_S1 [DIV9_unsti_PBS1_OE]


title: X2PreOvcc_39

description: Library name: 2PreOv-cc

value: Late


title: GFP_Pos_O2

description: Library name: Sample 5

value: mammary carcinoma


title: vector + hAD-tau_21DIV_S2 [DIV21_unsti_AD2_Mock]


title: GFP_Pos_Y1

description: Library name: Sample 1


title: X2PreD_39

description: Library name: 2PreD


title: colon_infected_d5

city: Xi'an

first: Shanshan

last: Li

state: Shannxi

address: Chang'an District

institute: Xi'an Jiaotong University

description: Library name: d5

data_processing:
Raw sequencing data were processed using the BSTMatrix pipeline to generate FASTQ files
Sequences were aligned to GRCm39 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantifed using Space Ranger's default settings
The DAPI-stained image was used for cell segmentation using the watershed algorithm implanted in the cellpose v2.2.3
Assembly: GRCm39 genome
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: barcodes_pos.tsv.gz: list of location of  the barcode type on the chip
Supplementary files format and content: d0.cell.single_seruat.Rds.gz: Seurat object after day0 cell segmentation
Supplementary files format and content: day0.png.gz: Day0 HE stained images of tissue
Library strategy: Spatial Transcriptomics

source_name: colon

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with chilled BMKMANU S1000 Tissue Optimization Slides and BMKMANU S1000 Gene Expression Slides according to manufacturer's construction

treatment_protocol: Salmonella infection

value: colon

value: female

value: infected by Salmonella

value: 6-8 weeks old


title: vector + hAD-tau_9DIV_S3 [DIV9_unsti_AD3_Mock]

value: 9 days in vitro


title: HIP_LEP_7

city: Palma

first: Paula

last: Oliver

address: Cra. Valldemossa km 7.5

institute: University of the Balearic Islands

hyb_protocol: After 16 h hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned at 0.7 μm resolution using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Normalization and data analysis were executed by the “Bioinformatics and Biostatistics Unit” from the “Príncipe Felipe Research Center” (Valencia, Spain). The raw data background was corrected following Robust Multichip Average (RMA). All statistical analyses were performed with R version 4.0.4 and R Studio version 1.4.1717 software. Differences in expression were calculated with a moderate t statistic of the limma package, and the contrasts studied were HF vs CTRL, LEP vs CTRL and LEP vs HF group.

organism: Rattus norvegicus

source_name: Hippocampus

label_protocol: Probing of Affymetrix GeneChip Rat Clariom S microarrays 10+30 (Affymetrix UK Ltd., High Wycombe, UK) was performed as described in the manufacturer’s protocols. The probes were prepared from aliquots of 100 ng total RNA by the instructions supplied with the Affymetrix WT PLUS Reagent Kit.

extract_protocol: Total RNA from the PBMC and hippocampus samples of young 3.5-month-old animals were isolated using Tripure reagent (Roche Diagnostics Barcelona, Spain) following the manufacturer’s protocol. Before analysis, RNA integrity and purity were determined using the RNA Nano 6000 Chip on an Agilent Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA). RNA integrity numbers (RIN) were evaluated using a Bioanalyzer (Agilent Technologies Inc.) and were between 7 and 10 for all the samples.

treatment_protocol: Two-month-old virgin female Wistar rats were mated with male rats. After matching, females were placed in individual cages with free access to water and food. On day 1 after delivery, excess pups in each litter were removed to keep 10 pups per dam. Male pups from a total of 8 litters were randomly assigned into 2 groups receiving different experimental treatments from day 1 to day 20 of lactation during the first 2 h of the beginning of the light cycle: Control (n = 16), leptin (n = 10). All treatments were administered orally. A solution of recombinant murine leptin (PeproTech, London, UK) dissolved in Captisol® was administered to leptin group. The amount of leptin administered to the animals was calculated as five times the average amount of daily leptin intake from breast milk; the Control group received the same volume of the vehicle, Captisol®. On day 21, after weaning, male rats were single-caged and kept on a normolipidic control balanced diet (D12450B, Research Diets). On day 23, the Control group rats were randomly assigned to two groups: normal-weight, CTRL group (n = 8), fed ad libitum a standard chow diet with 10% calories from fat (D12450B, Research Diets); and MONW, HF group (n = 8), fed a chow diet with 60% calories from fat (D12492, Research Diets), administered under isocaloric conditions to CTRL, to prevent development of obesity. Moreover, the leptin treated group, LEP group (n=10) received the same hyperlipidic diet as the HF group, also administered under isocaloric conditions relative to the CTRL group.

value: Hippocampus

tag: gender

value: male

tag: diet

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: HIP_LEP_8


title: X2PosD_39

description: Library name: 2PosD

value: oocyte

tag: cell type

tag: treatment


title: colon_infected_d3

description: Library name: d3


title: HIP_LEP_4


title: colon_infected_d1

description: Library name: d1


title: vector + hAD-tau_21DIV_S1 [DIV21_unsti_AD1_Mock]

value: Primary embryonic hippocampal neurons

tag: strain


title: X2PreD-cc_39

description: Library name: 2PreD-cc

value: Cumulus cells

tag: cell line

tag: genotype

value: Early


title: HIP_LEP_3


title: vector + hAD-tau_9DIV_S1 [DIV9_unsti_AD1_Mock]

tag: age


title: X2PosD-cc_39

description: Library name: 2PosD-cc

value: Slaughterhouse

tag: batch


title: X2DF1_39

description: Library name: 2DF1

tag: tissue


title: upACSS2 + hAD-tau_21DIV_S3 [DIV21_unsti_AD3_OE]

value: 21 days in vitro

tag: Sex

value: PhP.eB.upACSS2 + hAD-tau


title: HIP_LEP_5


title: KO_Ly6Chigh_monocytes_4

city: Cologne

first: Patrik

last: Schelemei

address: Kerpener Str. 62

department: Internal Med III

institute: University Hospital Cologne

description:
Library name: Sample 8
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: KO_1775

data_processing:
Raw data (raw reads) of fastq format were firstly processed to obtain clean data (clean reads) by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. Clean reads were mapped to the mus musculus GRCm38 reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCm38
Supplementary files format and content: text-delimited file contains raw counts for each sample

source_name: spleen

extract_protocol:
FACS sorted Ly6Chigh monocytes were sorted into Triziol LS. RNA was extracted using the Rneasy Micro Plus Kit (Qiagen)
Total RNA was reverse transcribed into cDNA by selecting mRNA with oligo dT primer and SMART-Seq v4 oligonucleotides for template switching at the 5’ end of the transcript. The double-strand cDNA was synthesized by LD-PCR amplification with the SMART-Seq® v4 Ultra® Low Input RNA Kit, followed by purification with AMPure XP beads and quantification with Qubit. cDNA was fragmented, end-repairment performed, A-tailed, and ligated with Illumina adaptors. After size selection and PCR enrichment, the library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: spleen

value: Ly6Chigh monocytes

value: Olfr2 KO

value: day 7 after aneurysm induction


title: HIP_LEP_10


title: X2DF1-cc_39

description: Library name: 2DF1-cc


title: colon_uninfected_d0

description: Library name: ctrl

value: colon

value: female

value: uninfected


title: HIP_LEP_1

value: Hippocampus


title: HIP_HF_8

value: male


title: upACSS2 + hAD-tau_21DIV_S2 [DIV21_unsti_AD2_OE]


title: KO_Ly6Chigh_monocytes_3

description:
Library name: Sample 7
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: KO_1784


title: X2C_39

description: Library name: 2C

value: CTRL


title: HIP_LEP_6

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: HIP_LEP_2


title: upACSS2 + hAD-tau_21DIV_S1 [DIV21_unsti_AD1_OE]

value: Primary embryonic hippocampal neurons


title: KO_Ly6Chigh_monocytes_2

description:
Library name: Sample 6
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: KO_1626


title: upACSS2 + hAD-tau_9DIV_S3 [DIV9_unsti_AD3_OE]

value: 9 days in vitro


title: KO_Ly6Chigh_monocytes_1

description:
Library name: Sample 5
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: KO_1627


title: HIP_HF_7


title: X1PreOv_39

description: Library name: 1PreOv

value: oocyte

value: Late


title: X2Ccc_39

description: Library name: 2C-cc

value: Cumulus cells

value: Slaughterhouse


title: upACSS2 + hAD-tau_9DIV_S2 [DIV9_unsti_AD2_OE]

value: PhP.eB.upACSS2 + hAD-tau


title: HIP_HF_6


title: X1PreOvcc_39

description: Library name: 1PreOv-cc


title: WT_Ly6Chigh_monocytes_4

description:
Library name: Sample 4
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: WT_1780

value: spleen

value: Ly6Chigh monocytes

value: WT


title: upACSS2 + hAD-tau_9DIV_S1 [DIV9_unsti_AD1_OE]


title: HIP_HF_5


title: HIP_HF_4


title: X1PreD_39

description: Library name: 1PreD

value: Early


title: WT_Ly6Chigh_monocytes_3

description:
Library name: Sample 3
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: WT_1782

value: day 7 after aneurysm induction


title: aortic dissection-4

city: Tianjin

first: chao

last: chang

address: South Taierzhuang Road

institute: Tianjin University,Tianjin Chest Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1.0 BeadChip(850K) using

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

data_processing: BeadStudio software v3.2

source_name: Aortic wall tissue

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: Aortic wall tissue

tag: sample group

value: TAAD case


title: WT_Ly6Chigh_monocytes_2

description:
Library name: Sample 2
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: WT_1615


title: PBS_H3K27ac_rep2

data_processing:
Unaligned paired-end CUT&RUN data were pooled across NextSeq lanes, then aligned using bowtie2 v2.3.4.1 (command-line parameters --local -X 1000).
Data were then filtered for poor alignments using samtools v1.1 (samtools view -h -bS -f 2 -F 256 -q 5) and sorted by tag position (samtools sort -n) then PCR de-duplicated using PICARD MarkDuplicates v2.21.3-SNAPSHOT (command-line parameters REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname).
Resulting aligned tags were processed for differential peaks using RGT-THOR v0.13.2, contrasting AD Tau-injected cells with PBS-injected cells and using matching IgG samples as background control.
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: Cut&Run-seq

extract_protocol:
Total RNA was extracted using Trizol-chloroform following RNA purification using RNeasy mini-kit, Qiagen.
10 ng input DNA was used to make libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: Cells were treated with 1.5xE6 PhP.eb.upACSS2 or PhP.eB-vector at 5DIV for 48 hours before 1x PBS wash on 7DIV and treatment with hAD-tau or PBS.

value: 21 days in vitro

value: PBS

tag: chip antibody


title: HIP_HF_3

value: Hippocampus

value: male

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: X1PreDcc_39

description: Library name: 1PreD-cc


title: control-1

value: control


title: control-4


title: control-6


title: PBS_IgG_rep2

value: Primary embryonic hippocampal neurons

value: IgG


title: aortic dissection-2


title: WT_Ly6Chigh_monocytes_1

description:
Library name: Sample 1
Column name in Monocyte_Seq_Olfr2_AAA_counts.txt: WT_1603


title: aortic dissection-3


title: X1PosD_39

description: Library name: 1PosD

value: oocyte

value: Slaughterhouse

value: Late


title: HIP_HF_2


title: hAD-tau_H3K27ac_rep2

value: hAD-tau


title: PS19 mice and TAM treatment (PCfD-TAM)

city: St Louis

first: George

middle: Travis

last: Tabor

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

description:
Library name: PS19_TAM
10X Genomics Chromium GEM-X Single Cell 3’ V4

data_processing:
FATSQ files are aligned to GRCm39 using Cell Ranger v8.0.1. 2.0
Assembly: GRCm39
Supplementary files format and content: compressed gzip archives containing filtered 10x outputs (features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz)

molecule: nuclear RNA

source_name: brain

extract_protocol:
Nuclei isolation and sorting of microglia via fluorescence-activated nuclei sorting (FANS) were performed as previously described. Hippocampi from three individual mice per experimental group were pooled for nuclei isolation. Dissected hippocampi were homogenized in nuclei isolation buffer (0.5% Triton X-100, 0.1M Sucrose, 5mM MgCl2, 1mM EDTA, 10mM Tris-HCl) supplemented with 40U/μl RNasin using a Dounce homogenizer. Nuclei were pelleted (700 g for 5 minutes at 4C), resuspended in 2 mL of nuclei isolation buffer with RNasin, and incubated for 10 minutes on ice. Following incubation, nuclei were pelleted (700 g for 5 minutes at 4C), washed once with sort buffer (1X HBSS, 10% bovine serum albumin, 1mM EDTA, and 40U/μl RNasin) and then resuspended in 260 μL of sort buffer with RNAsin. Nuclei were stained for 30 minutes on ice with the following antibodies: anti-PU.1-PE (1:100, BioLegend, 681308) and anti-Olig2-647 (1:2500, Abcam, ab225100) for microglia and oligodendrocytes, respectively. Nuclei were labeled with DAPI (1:1000, BioLegend, 422801). Following staining, nuclei were pelleted (700 g for 5 minutes at 4C), resuspended in 500 μL of sort buffer with RNAsin, and strained through a 70 μm mesh strainer. PU.1+ singlets were sorted on a Beckman Coulter Mo-Flo Astrios EQ into sort buffer with RNasin.
After sorting, BSA was added to a final concentration of 1%. Nuclei were pelleted at 800 g for 10 minutes at 4C and then resuspended in PBS with 1% BSA. Individual nuclei were then coupled to beads using the 10X Genomics Chromium controller. Single nuclei sequencing libraries were prepared following the 10X Genomics Chromium GEM-X Single Cell 3’ V4 kit protocol. Libraries were paired end sequenced on an Illumina NovaSeq X Plus platform (28X10X10X90X) to a minimum depth of 100,000 reads per nuclei.

treatment_protocol: Male mice were weaned into cages designated for treatment with TAM or OIL to avoid fighting. Tamoxifen (‘TAM,’ Sigma, T5648) was dissolved in corn oil (‘OIL’, Sigma, C8267) at a concentration of 20 mg/mL by shaking at 37C overnight. Aliquots were frozen at -20C and thawed just before use. A given aliquot was stored at 4C between treatment days for up to one month or until precipitation was observed. Mice were gavaged with 200 mg/kg TAM (10 uL per gram bodyweight) or OIL once per day for 5 days in a row at 3 months of age using bent 20G or 22G metal feeding needles. Mice were sacrified and tissues were harvested after perfusion at 9.5 months of age. Hippocampi were flash frozen on dry ice and stored at -80C until processing for snRNAseq analysis.

value: brain

value: microglia

value: PS19; DGAT1 fl/fl; DGAT2 fl/fl; Cx3cr1-CreERT2+/-

value: tamoxifen


title: X1PosDcc_39

description: Library name: 1PosD-cc

value: Cumulus cells


title: HIP_CTRL_8

value: Standard chow diet with 10% calories from fat (D12450B, Research Diets)


title: PS19 mice and Oil treatment (PCfD-OIL)

description:
Library name: PS19_Oil
10X Genomics Chromium GEM-X Single Cell 3’ V4

value: oil


title: X1DF1_39

description: Library name: 1DF1

value: Early


title: WT mice and TAM treatment (CfD-TAM)

description:
Library name: WT_TAM
10X Genomics Chromium GEM-X Single Cell 3’ V4

value: WT; DGAT1 fl/fl; DGAT2 fl/fl; Cx3cr1-CreERT2+/-


title: aortic dissection-5

value: Aortic wall tissue

value: TAAD case


title: X1DF1cc_39

description: Library name: 1DF1-cc


title: hAD-tau_IgG_rep2

value: Primary embryonic hippocampal neurons

value: 21 days in vitro


title: PBS_IgG_rep1

value: PBS

value: IgG


title: WT mice and Oil treatment (CfD-OIL)

description:
Library name: WT_Oil
10X Genomics Chromium GEM-X Single Cell 3’ V4


title: X1C_39

description: Library name: 1C

value: oocyte

value: Slaughterhouse

value: CTRL


title: hAD-tau_H3K27ac_rep1

value: hAD-tau


title: aortic dissection-1


title: hAD-tau_IgG_rep1


title: hepatocyte_Mttp_KO_CM_4

city: Mineola

first: M. Mahmood

last: Hussain

state: New York

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

data_processing:
Raw data in fastq format were processed by Novogene using their in-house Perl scripts  to obtain clean reads by removing adapter sequences, reads with poly-N, and low-quality reads.
Trimmed sequence reads were mapped to GRCm39/mm39 using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm39
Supplementary files format and content: tab-limited text file includes raw counts for each sample
Supplementary files format and content: tab-limited text file includes FPKM values for each sample

source_name: Hepatocytes

growth_protocol: Stromal vascular fraction (SVF) was isolated from inguinal adipose tissue collected in PBS as described previously26 from male Mttpf/f and A-Mttp–/– mice (n=3) fed an obesogenic diet for 6 months. The minced tissue was incubated with digestion buffer (1.5 U/mL of collagenase D, 2.4 U/mL of dispase II, and 10mM CaCl2) for 30 min to 1 h until the tissue and digestion buffer became homogeneous. The digestion was stopped by adding an equal volume of PBS containing 0.5 % BSA and centrifuged at 300 g for 5 min at room temperature. The cell pellet was resuspended in PBS containing 0.5% BSA and passed through a 100 µM cell strainer. The flow through was centrifuged again at 300 g for 5 min at room temperature and the pellet was re-suspended in PBS containing 0.5% BSA and passed through 40 µM cell strainer. The flow through was centrifuged at 300 g for 5 min and the resultant pellet was re-suspended in DMEM containing 10% FBS supplement with 1% antibiotics (penicillin and streptomycin) and transferred to a T75 flask. The media was changed the next day. The cells were either used for experiment or cryo-frozen in freezing media (90% FBS, and 10% DMSO). Mouse SVF was differentiated using a differentiation cocktail containing 500 μM IBMX, 5 μg/mL insulin, 1 μM dexamethasone, 200 μM indomethacin and 1 µM rosiglitazone. Cells were maintained in a differentiation cocktail media for 3 days. Differentiation media was replaced with media containing insulin 5μg/ml and maintained for 2 days. Further adipocytes were maintained DMEM containing 10% FBS supplement with 1% antibiotics (penicillin and streptomycin) for 2 days. Mice were anesthetized and sacrificed by cervical dislocation. The vena cava was canulated using 24 G butterfly syringe and connected to a peristaltic pump. A small cut was made in the portal vein and the liver was perfused with 35 mL of PBS containing 1% penicillin/streptomycin mix. The liver was further perfused with 35 mL liver perfusion medium (Gibco, #17701038) containing 1% penicillin/streptomycin mix followed by 35 mL liver digestion media (Gibco, #17703034) containing 0.25 % collagenase II (Thermo Fisher Scientific, #17101015). The liver was collected and minced in digestion media and incubated in rotor at 37 °C till the liver tissue and liver digestion media became homogenous. An equal volume of hepatocyte culture media (Gibco, #17705-021) containing 10% FBS was added to neutralize the action of collagenase and centrifuged at 300g for 10 mins. The resultant pellet was washed with hepatocyte wash buffer and again centrifuged at 300g for 10 mins. The supernatant was discarded, and the pellet was resuspended in hepatocyte culture media and filtered through 100 µM cell strainer (Thermo Fisher Scientific, Catalog No #431752). The flow through was collected, and centrifuged at 300g for 10 mins. The resultant pellet was resuspended in hepatocyte culture media and seeded in collagen coated 6 well plates (Corning #356400). The next day the media was replaced with fresh hepatocyte culture media and proceeded for experiment as mentioned in results and figure legends.

extract_protocol:
Total RNA was isolated from different organs using a TRIZOL reagent. The RNA was purified using  RNA purification kit. RNA concentrations were measured using NanoDrop (Thermo Scientific™, USA, #ND-2000).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Wild type hepatocytes were treated over night with condition media from overnight starved Mttpflox and Mttp KO adipocytes.

value: Hepatocytes

value: Mttp KO conditioned media


title: control-5

value: control


title: Skeletal Muscle, Male D2W-2, snATAC-Seq

city: Cincinnati

first: Douglas

last: Millay

state: OH

address: 3333 Burnet Ave Cincinnati, OH 45229

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital and Medical Center

description: Library name: D2W-Male2

library_source: genomic single cell

data_processing:
Raw read sequences were demultiplexed using cut adapt and aligned to the mm10 build of the mouse genome using snap tools. Aligned bam files were converted to snap file format then to sorted fragment files using snap tools snappre and dump fragment functions, respectively.
Quality control, data normalization,  dimensionality reduction, integration, was performed using ArchR v1.0.3. Peak calling was performed using MACS2, and a final peak set was generated using the ArchR iterative overlap peak merging procedure.
Assembly: mm10
Supplementary files format and content: TSV
Supplementary files format and content: GZ

source_name: Skeletal muscle

extract_protocol:
Frozen tibialis anterior muscles were cryosectioned on dry ice and homogenized using a gentleMACS Dissociator (Miltenyi; “Protein_01_01” program) in MACS buffer consisting of 5 mM CaCl₂, 2 mM EDTA, protease inhibitor (Roche), 3 mM magnesium acetate, 10 mM Tris-HCl (pH 8.0), and 0.6 mM DTT. The homogenate was passed through a 30 μm CellTrics filter (Sysmex) and collected in 15 ml tubes. Nuclei were pelleted by centrifugation at 500 × g for 5 min at 4°C, resuspended in Nuclear Permeabilization Buffer (PBS containing 5% BSA, 0.2% IGEPAL CA-630, 1 mM DTT, and protease inhibitors), and incubated for 5 min at 4°C on a rotating platform. After a second centrifugation at the same settings, nuclei were transferred into a high-salt tagmentation buffer (36.3 mM Tris-acetate, 72.6 mM potassium acetate, 11 mM magnesium acetate, and 17.6% DMF), counted with a hemocytometer, and diluted to a concentration of 1,000 nuclei in 9 μl.
Aliquots of 1,000 nuclei were dispensed into four 96-well plates (384 wells total). Barcoded Tn5 transposomes (1 μl per well) were added using a BenchSmart 96 (Mettler Toledo), and tagmentation was carried out at 37°C for 90 min with shaking at 900 rpm. The reaction was terminated with 2.5 μl of 100 mM EDTA (20 mM final) followed by an additional 15 min incubation at 37°C. Each well then received 6 μl of 3× sort buffer (PBS supplemented with 3% BSA and 3 mM EDTA). All wells were pooled, stained with Draq7 (1:500; Cell Signaling), and sorted on a Sony SH800. Eighty nuclei were deposited per well into four new 96-well plates containing 8 μl of primer mix (15 pmol i7, 15 pmol i5, 200 ng BSA, and 0.027% SDS).
Plates were incubated at 65°C for 25 min, followed by the addition of 4 μl of 1.33% Triton X-100 to neutralize SDS. Each well received 11 μl of Q5 PCR master mix (5 μl 5× buffer, 0.5 μl 10 mM dNTPs, 0.25 μl Q5 polymerase, and 5.25 μl water), and amplification was performed with the following cycling parameters: 72°C for 4 min; 98°C for 30 s; 12 cycles of 98°C for 10 s, 60°C for 30 s, and 72°C for 45 s; and a final hold at 4°C. PCR products were pooled and purified using the Zymo DNA Clean & Concentrator-5 kit. Fragments between 200–600 bp were size-selected on a 1.5% agarose gel and recovered with the Zymo Gel DNA Recovery kit. Library concentration was measured with the Qubit 1× dsDNA HS assay (Invitrogen), and fragment size distribution and nucleosomal periodicity were evaluated using a High Sensitivity D1000 TapeStation (Agilent).
Next-generation sequencing of snATAC libraries was performed on the DNBSEQ G400 platform using paired-end sequencing, 50-bp reads for each end, generating approximately 5,000-10,000 raw reads per cell

treatment_protocol: 200 ug intrperitoneal injection of tamoxifen were given to the mice at prenatal day 6.

value: Skeletal muscle

value: Mymk LacZ/loxP; Pax7CreER

tag: genetic modification

value: Mymk sckO

tag: tissue type

value: Tibialis Anterior

value: Male

value: 200 ug intrperitoneal injection of tamoxifen at prenatal day 6.


title: control-3

value: Aortic wall tissue


title: X1Ccc_39

description: Library name: 1C-cc

value: Cumulus cells


title: control-2


title: PBS_H3K27ac_rep1

value: Primary embryonic hippocampal neurons

value: 21 days in vitro

value: PBS


title: aortic dissection-6

value: TAAD case


title: HIP_CTRL_5

value: Hippocampus

value: male

value: Standard chow diet with 10% calories from fat (D12450B, Research Diets)


title: HIP_CTRL_7


title: HIP_CTRL_6


title: hepatocyte_Mttp_KO_CM_3

value: Hepatocytes

value: Mttp KO conditioned media


title: RNA-seq, (20)S-APPT treated cells, replicate3

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

description: Library name: RNA-seq_(20)S-APPT_3

data_processing:
RNA-seq data sets were trimmed and aligned to mouse genome build mm10 using STAR.
Duplicate reads of all RNA-seq SAMtools.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: hg19
Supplementary files format and content: The processed BigWig (.bw) coverage files were generated using deeptools bamCoverage (Version 3.3.1)

source_name: Liver

extract_protocol:
1,000,000 fresh cells were collected for each RNA-seq sample. Total RNA was extracted using the TRIzol reagent (Invitrogen, USA).
RNA quantification and qualification: RNA degradation and contamination was monitored on 1% agarose gels; RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA); RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Library preparation for Transcriptome sequencing: A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Liver

value: Liver cancer cell

value: WT

value: (20)S-APPT (in DMSO)


title: Skeletal Muscle, Male D2W-1, snATAC-Seq

description: Library name: D2W-Male1

value: Skeletal muscle

value: Mymk loxP/loxP; Pax7CreER

value: Mymk scKO

value: Tibialis Anterior

value: Male


title: HIP_CTRL_3


title: HIP_CTRL_4


title: HIP_HF_1

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: hepatocyte_Mttp_KO_CM_2


title: RNA-seq, Control cells, replicate3

description: Library name: RNA-seq_Ctrl_3

value: DMSO


title: Skeletal Muscle, Female D2W-2, snATAC-Seq

description: Library name: D2W-Female2

value: Mymk LacZ/loxP; Pax7CreER

value: Female

value: 200 ug intrperitoneal injection of tamoxifen at prenatal day 6.


title: Skeletal Muscle, Female D2W-1, snATAC-Seq

description: Library name: D2W-Female1


title: RNA-seq, (20)S-APPT treated cells, replicate2

description: Library name: RNA-seq_(20)S-APPT_2


title: RNA-seq, Control cells, replicate2

description: Library name: RNA-seq_Ctrl_2


title: hepatocyte_Mttp_flox_CM_5

value: Mttp flox conditioned media


title: Skeletal Muscle, Male Control-2, snATAC-Seq

description: Library name: Ctrl-Male2

value: Mymk loxP/loxP


title: RNA-seq, (20)S-APPT treated cells, replicate1

description: Library name: RNA-seq_(20)S-APPT_1


title: Skeletal Muscle, Male Control-1, snATAC-Seq

description: Library name: Ctrl-Male1

value: Mymk LacZ/loxP


title: vector + hAD-tau_9DIV_S2 [DIV9_unsti_AD2_Mock]

data_processing:
Demultiplexed FASTQs were aligned to the reference genome using STAR
Gene level read counts were prepared using featureCounts or HTSeq.
Unwanted variation was estimated by RUVr.
Differential expressed genes were called using DESeq2 with Wald test
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

extract_protocol:
Total RNA was extracted using Trizol-chloroform following RNA purification using RNeasy mini-kit, Qiagen.
130 ng input RNA was used to make libraries using the NEB kit E7490.

value: Primary embryonic hippocampal neurons

value: 9 days in vitro

value: Php.eB.vector + PBS


title: PBMC_LEP_10

value: PBMC

value: male


title: HIP_CTRL_2

value: Hippocampus

value: Standard chow diet with 10% calories from fat (D12450B, Research Diets)


title: hepatocyte_Mttp_flox_CM_4

value: Hepatocytes


title: RNA-seq, Control cells, replicate1

description: Library name: RNA-seq_Ctrl_1

value: Liver

value: Liver cancer cell

value: WT


title: PBMC_LEP_8

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: HIP_CTRL_1


title: hepatocyte_Mttp_flox_CM_3


title: Skeletal Muscle, Female Control, snATAC-Seq

description: Library name: Ctrl-Female

value: Skeletal muscle

value: Tibialis Anterior

value: Female


title: hepatocyte_Mttp_flox_CM_2

value: Mttp flox conditioned media


title: PBMC_LEP_7


title: PBMC_LEP_6


title: MRL/lpr_17W_3

city: Beijing

first: Zhiying

last: Gao

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing,China 100730

department: Department of Nephrology

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences

description: Library name: SAMPLES_6

data_processing:
V2-Dr.TOM Ⅱ
Data filtering: The raw sequencing data are called raw tags. We obtained clean tags using the SOAPnuke[1]. The filtering rules were as follows: removed low quality tags; removed tags with 5’ primer contaminants; remove tags without 3’ primer; removed tags without insertion; removed tags with poly A; removed tags shorter than 15nt.
Small RNA Annotation and miRNA Identification: After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2[2]. Particularly, cmsearch[3] was performed for Rfam mapping. In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA. The miRDeep-P2 [4] or miRDeep2[5] package was used to identify potentially novel miRNAs. The potentially novel miRNAs and were named novel_mirXXX, in which XXX is a unique number specified for each novel miRNA candidate.
miRNA quantification: The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers [11]. The expression formula is:C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
Differential Expression Analysis: Differential expression analysis was performed using the DEGseq [12] (or DESeq2[13] or PoissonDis[14]) on Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com). Q value≤ 0.05 (or FDR value≤0.001) was used to judge the significance of expression difference.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: txt files include TPM values for each Sample

source_name: Kidney

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, Carlsbad, California, USA). 2 ug of total RNA was used for the construction of sequencing libraries.
The library was constructed using the MGIEasy MiRNA Library Prep Kit (BGI-Shenzhen). RNA was sequentially ligated with 3' and 5' adapters, followed by reverse transcription into cDNA and amplification via PCR. Fragment size selection was performed using polyacrylamide gel electrophoresis to ensure quality control. The single-stranded library was then denatured and circularized, with uncyclized linear DNA molecules removed. The circularized DNA was amplified through phi29 and rolling circle amplification (RCA) to generate DNA nanoballs (DNBs), each containing over 300 copies of the original single-stranded circularized molecule. DNA nanoballs (DNBs) were deposited onto a patterned nanoarray, and paired-end 50-base sequencing reads were generated using the G400 platform (BGI-Shenzhen, China).

value: Kidney

value: MRL/MpJ-Fas<lpr>/J


title: hepatocyte_Mttp_flox_CM_1


title: hepatocyte_Mttp_KO_CM_1

value: Mttp KO conditioned media


title: MRL/lpr_17W_2

description: Library name: SAMPLES_5