title: 142N-Run5850.2186.2-FOV_5

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_5.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: 118T-Tumour_A-FOV_5

status: Public on Dec 09 2025

type: RNA

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:
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_5.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 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.

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

molecule: total RNA

organism: Homo sapiens

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.

value: M

value: caecum

value: pMMR


title: P172_71

type: SRA

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

country: USA

institute: Michigan State University

description: Library name: P172_71

library_source: transcriptomic

data_processing:
Quality control: FASTQC v0.11.3
Removal of adaptors: Trimmomatic v0.39
Read alignment: STAR v2.7
Normalization and analysis: DESeq2
Assembly: GRCm39 (release 104)
Supplementary files format and content: Tab-delimited text files generated by STAR (ReadsPerGene.out.tab), containing raw and strand-specific read counts for each gene.

organism: Mus musculus

source_name: Liver

extract_protocol:
Primary mouse hepatocytes (1 × 106 cells) were plated in 6-well plate for RNA isolation. Medium was removed and cells were rinsed two times with cold PBS. While on ice, 1 mL of TRIzoL reagent was added to each well and plates were scraped. RNA was extracted using an additional 5:1 phenol:chloroform step (Sigma Aldrich, St. Louis, MO). RNA quantity and purity (260/280 ratio) was assessed with a NanoDrop 1000.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions.

treatment_protocol: Hepatocytes were seeded at a density of 1 × 10⁶ cells/well on type I collagen-coated 6-well plates and cultured in WME supplemented with 5% fetal bovine serum (FBS), 1% penicillin/streptomycin, 1% Glutamax, 0.3 mM ascorbic acid, and 100 nM dexamethasone. After a 3-hour attachment period, non-adherent cells were removed and media was replaced with fresh WME containing 1% ITS Premix, antibiotics, Glutamax, ascorbic acid, and dexamethasone with DMSO vehicle or 10 nM TCDD and maintained at 37 °C in a 5% CO₂ incubator for 2, 4, 8, 12, 24, 48, 72, 96 and 120 hours.

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: wild-type

tag: treatment


title: P172_70

description: Library name: P172_70

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor


title: P172_69

description: Library name: P172_69

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: SVF7-74F (OSa2-6)

city: Boston

first: Shazia

last: Ashraf

state: Massachusetts

address: Massachusetts Eye and Ear Inf.

institute: Massachusetts Eye and Ear Infirmary

description: Library name: OSa2-6

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of hg19 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Assembly: hg19
Supplementary files format and content: Read counts for individual genes were produced using HTSeq

source_name: Corneal endothelial cells from FECD patients with non-expanded TCF4 repeats

growth_protocol: Cell lines generated using SV40 immortalization of corneal endothelial cells from normal donor corneas or FECD patient tissues. All cell lines were cultured in Chen's medium supplemented with 8% serum and 0.08% chondroitin sulfate prior to RNA isolation

extract_protocol:
Cells were trypsinized, pelleted, and the total RNA was extracted from the cell lines using RNeasy Micro kit (Qiagen)
Illumina sequencing libraries were constructed from total RNA using polyA selection followed by NEBNext Ultra II Directional RNA Library Prep protocol (New England Biolabs).

tag: disease status

value: FECD with non-expanded TCF4 repeats

tag: number of tcf4 repeats

tag: immortalization

value: SV40 virus

tag: passage


title: CART19 cells, vehicle, CUT&RUN 3

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Sample21

library_source: genomic

data_processing:
Reads were pseudo-aligned to hg38 using kallisto (v0.46.1). Transcript abundances were imported with tximport (v1.32.0) and converted to integer count matrices for DESeq2 (v1.44.0). Genes with duplicated names or with cumulative counts in the lowest 20% were filtered out. Data processing and visualization were performed in R using dplyr, ComplexHeatmap, and ggplot2.
Raw ATAC-seq reads were quality-checked and adapter-trimmed with FastQC, then aligned to the GRCh38/hg38 genome using Bowtie2. Peaks were called with Genrich in ATAC-seq mode using a q-value cutoff of <0.01. Normalized bigWig signal tracks were generated with deepTools (BPM normalization, 10 bp bins, fragment-centered). Signal around peak summits (±2 kb) was used for k-means clustering with deepTools. A consensus peak set was created with DiffBind, and differential accessibility between BHB-treated and control samples was assessed using DESeq2. Peak annotation and motif enrichment were performed with HOMER, and functional enrichment was analyzed using GREAT. Transcription factor footprints were identified using HINT.
CUT&RUN FASTQ files were quality-checked, trimmed, and aligned to the GRCh38/hg38 genome, followed by standard filtering steps. H3K27ac peaks were called with MACS2 (v2.0.1) using matched input controls and a p-value cutoff of 1×10⁻⁹, and peaks overlapping ENCODE blacklisted regions were removed. A consensus peak set was defined using DiffBind, and differential enrichment was assessed using DESeq2.Active enhancers were defined as accessible regions overlapping H3K27ac peaks. Functional annotation and gene ontology enrichment analyses were performed using GREAT.
Assembly: GRCh38/hg38
Supplementary files format and content: Excel workbook - counts for RNA-seq, ATAC-seq, and CUT&Run-seq
Library strategy: CUT&Run

molecule: genomic DNA

source_name: CART19 cells

growth_protocol: CART19 cells were cultured in CD19-coated plates using standard R10 medium (RPMI-1640 supplemented with 10% FBS, 1% Penicillin–Streptomycin, 1% HEPES, and 1% GlutaMAX) at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was purified with the RNeasy Mini Plus Kit (Qiagen). ATAC-seq DNA was prepared using the Active Motif ATAC-Seq Kit following the supplier’s recommended protocol. CUT&RUN DNA was obtained using the Active Motif ChIC/CUT&RUN Assay Kit, including antibody binding, MNase digestion, and DNA recovery steps as instructed.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Library Prep Kit with Illumina DNA/RNA Unique Dual Indices, following the manufacturer’s instructions.ATAC-seq libraries were generated using the Active Motif ATAC-Seq Kit according to the manufacturer’s protocol. CUT&RUN DNA libraries were constructed using the Illumina DNA Library Prep Kit following the supplier’s recommended procedures.

treatment_protocol: During CD19 stimulation, CART19 cells were treated with either vehicle control or 5 mM β-hydroxybutyrate (BHB) for 48 hours prior to collection for ATAC-seq, CUT&RUN, or RNA-seq

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

value: WT

value: Vehicle


title: CART19 cells, BHB, CUT&RUN 3

description: Library name: Sample24

value: BHB


title: CART19 cells, BHB, CUT&RUN 2

description: Library name: Sample23


title: CART19 cells, BHB, CUT&RUN 1

description: Library name: Sample22


title: SVF3-76M (OSa2-4)

description: Library name: OSa2-4


title: SVF4-61F (OSa2-5)

description: Library name: OSa2-5


title: 142N-Run5850.2186.1-FOV_5

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_5.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.

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: P172_68

description: Library name: P172_68

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: CART19 cells, vehicle, CUT&RUN 2

description: Library name: Sample20

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: SVF2-61F (OSa2-3)

description: Library name: OSa2-3

tag: disease status

value: FECD with non-expanded TCF4 repeats

tag: number of tcf4 repeats

tag: immortalization

value: SV40 virus

tag: passage


title: 170N-Normal_A-FOV_5

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_5.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: P172_67

description: Library name: P172_67

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: v1_28d

city: Stockholm

first: Nik

middle: V

last: Kuznetsov

address: Nobels vag 16

country: Sweden

institute: Karolinska Institute

description: Library name: T9

data_processing:
RNA sequencing and data quality control was performed with Illumina HiSeq-PE150 Platform at Novogene (Hongkong).
Sequences were mapped to the reference genome with HISAT2, v.2.0.5.
Reads were aligned to the human reference genome assembly December 2013 (GRCh38/hg38). STAR software was used to accomplish the mapping of clean reads to the reference genome or transcriptome.
Filtering of data, alignment of RNA-seq reads, gene ontology were arranged at Novogene (Hongkong).
DESeq2 in R package was used for DEG analysis. In gene expression analysis, H-cluster, K-means, and SOM were used to cluster the log2 (ratios).
Assembly: GRCh38/hg38 (December 2013)
Supplementary files format and content: Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Supplementary files format and content: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then fpkm of each gene was calculated based on the length of the gene and reads count mapped to this gene.  All fpkm values for each of genes are listed in the excel file "FPKM".

source_name: peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient centrifugation isolation protocol optimized for Ficoll-Paque™ PLUS (Cytiva). Human T cells were enriched by the positive CD3 cell selection Kit (EasySep™ Human CD3 Positive Selection Kit II, Stem Cell Technology). Total RNA was purified from sorted cells using RNeasy kit and treated with RNAse-free DNAse kit(##74104; 79254 QIAGEN, Hilden, Germany). The total RNA concentration was measured (NanoDrop2000, Thermo Scientific, Wilmington, DE, USA) and RNA integrity and purity was evaluated by gel electrophoresis analysis (1xTAE 1% UltraPureAgarose, #16500500 Invitrogen, Waltham, MA, USA). All selected isolated RNA samples were subjected to and have passed both the internal lab quality control (QC) and the QC performed by sequencing company (Novogene, Hongkong).
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® Ultra™ 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-Toligo-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 150~200 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.

treatment_protocol: In total, five samples of 10ml peripheral blood each were collected in sodium heparin tube from each volunteer at five time points during the time course of simulated microgravity (SMG) study: at 7 days prior to Day 0 of SMG (timepoint “background, bg“), after 7 days (timepoint “7d”), 14 days  (timepoint “14d”), 21 days (timepoint “21d”) in SMG, and another 7 days after the SMG (timepoint “28 days”).

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 4

tag: time


title: SVN3-65M (OSa2-2)

description: Library name: OSa2-2

source_name: Corneal endothelial cells from normal donor corneas

tag: disease status

value: normal without expanded TCF4 repeats

tag: number of tcf4 repeats

tag: immortalization

value: SV40 virus

tag: passage


title: 7T-3461G-FOV_5

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_5.rds

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.

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: CART19 cells, vehicle, CUT&RUN 1

description: Library name: Sample19

tag: cell line

value: CART19 cells

value: T cell

tag: genotype

value: WT

value: Vehicle


title: SVN1-67F (OSa2-1)

description: Library name: OSa2-1


title: P172_66

description: Library name: P172_66

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: CART19 cells, BHB, ATAC-seq 5

description: Library name: Sample18

data_processing:
Reads were pseudo-aligned to hg38 using kallisto (v0.46.1). Transcript abundances were imported with tximport (v1.32.0) and converted to integer count matrices for DESeq2 (v1.44.0). Genes with duplicated names or with cumulative counts in the lowest 20% were filtered out. Data processing and visualization were performed in R using dplyr, ComplexHeatmap, and ggplot2.
Raw ATAC-seq reads were quality-checked and adapter-trimmed with FastQC, then aligned to the GRCh38/hg38 genome using Bowtie2. Peaks were called with Genrich in ATAC-seq mode using a q-value cutoff of <0.01. Normalized bigWig signal tracks were generated with deepTools (BPM normalization, 10 bp bins, fragment-centered). Signal around peak summits (±2 kb) was used for k-means clustering with deepTools. A consensus peak set was created with DiffBind, and differential accessibility between BHB-treated and control samples was assessed using DESeq2. Peak annotation and motif enrichment were performed with HOMER, and functional enrichment was analyzed using GREAT. Transcription factor footprints were identified using HINT.
CUT&RUN FASTQ files were quality-checked, trimmed, and aligned to the GRCh38/hg38 genome, followed by standard filtering steps. H3K27ac peaks were called with MACS2 (v2.0.1) using matched input controls and a p-value cutoff of 1×10⁻⁹, and peaks overlapping ENCODE blacklisted regions were removed. A consensus peak set was defined using DiffBind, and differential enrichment was assessed using DESeq2.Active enhancers were defined as accessible regions overlapping H3K27ac peaks. Functional annotation and gene ontology enrichment analyses were performed using GREAT.
Assembly: GRCh38/hg38
Supplementary files format and content: Excel workbook - counts for RNA-seq, ATAC-seq, and CUT&Run-seq

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: BHB


title: P172_65

description: Library name: P172_65

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration


title: 118N-148191A-FOV_5

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_5.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: SVF6-61M (OSa1-6)

description: Library name: OSa1-6

source_name: Corneal endothelial cells from FECD patients with expanded TCF4 repeats

tag: disease status

value: FECD with expanded TCF4 repeats

tag: number of tcf4 repeats

tag: immortalization

value: SV40 virus

tag: passage


title: 280N-120131-FOV_5

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_5.rds

value: F


title: CART19 cells, BHB, ATAC-seq 4

description: Library name: Sample17

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

tag: treatment


title: CART19 cells, BHB, ATAC-seq 3

description: Library name: Sample16

value: WT

value: BHB


title: 74T-10501A-FOV_5

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_5.rds

value: descending colon

value: dMMR

value: LHS


title: 46T-148191A-FOV_49

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:
46T-148191A-FOV_49.rds

value: hepatic flexure


title: CART19 cells, BHB, ATAC-seq 2

description: Library name: Sample15


title: SVF1-73F (OSa1-4)

description: Library name: OSa1-4


title: P172_63

description: Library name: P172_63

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: SVF5-54F (OSa1-5)

description: Library name: OSa1-5

tag: disease status

value: FECD with expanded TCF4 repeats

tag: number of tcf4 repeats

tag: immortalization

value: SV40 virus

tag: passage


title: CART19 cells, BHB, ATAC-seq 1

description: Library name: Sample14

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: BHB


title: SVN2-67F (OSa1-2)

description: Library name: OSa1-2

value: normal without expanded TCF4 repeats


title: CART19 cells, vehicle, ATAC-seq 5

description: Library name: Sample13

value: Vehicle


title: 142T-3461G-FOV_48

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:
142T-3461G-FOV_48.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: P172_64

description: Library name: P172_64

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: 278T-148191A-FOV_48

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_48.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: rectal

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: P172_61

description: Library name: P172_61

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

value: hour

value: Dimethyl sulfoxide

tag: genotype

value: wild-type

tag: treatment


title: P172_62

description: Library name: P172_62

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

value: Nuaire

value: Williams E medium

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: SVN1-67F (OSa1-1)

description: Library name: OSa1-1

tag: disease status

value: normal without expanded TCF4 repeats

tag: number of tcf4 repeats

tag: immortalization

value: SV40 virus

tag: passage


title: P172_60

description: Library name: P172_60

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

value: nanomolar

tag: genotype

tag: treatment


title: CART19 cells, vehicle, ATAC-seq 3

description: Library name: Sample11

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

value: WT

value: Vehicle


title: Emma 8-19-21 D13 NP

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description: Library name: Emma2-D13-NP

data_processing:
Illumina pipeline software was used for base calling.
Reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Assembly: EquCab3.0 genome assembly with ENSEMBL annotations
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Equus caballus

source_name: Corpus Luteum

growth_protocol: Healthy normal cycling light breed mares were monitored for ovulation.

extract_protocol:
RNA was purified using Trizol reagent (ThremoFisher) according to manufacturer's instructions.
Directional RNA-seq libraries were prepared from 1000 ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Pregnancy status was determined for each mare. Mares were classified as "Pregnant" or "Non-pregnant." Transvaginal luteal biopsy samples were taken at Day 11 and Day 13 post-ovulation

tag: tissue

value: Corpus Luteum

tag: pregnancy status

value: Non-Pregnant

tag: day


title: 142T-3461G-FOV_47

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:
142T-3461G-FOV_47.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: P172_59

description: Library name: P172_59

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: Emma 8-17-21 D11 NP

description: Library name: Emma2-D11-NP

tag: tissue

value: Corpus Luteum

tag: pregnancy status

value: Non-Pregnant

tag: day


title: 142T-3461G-FOV_46

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:
142T-3461G-FOV_46.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: 46T-148191A-FOV_47

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:
46T-148191A-FOV_47.rds

value: hepatic flexure

value: pMMR


title: Cornelia 8-19-21 D13 Preg

description: Library name: Cornelia-D13-Preg

value: Pregnant


title: CART19 cells, vehicle, ATAC-seq 1

description: Library name: Sample9

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: P172_58

description: Library name: P172_58

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid


title: 46T-148191A-FOV_46

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:
46T-148191A-FOV_46.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: hepatic flexure

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: P172_57

description: Library name: P172_57

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: wild-type

tag: treatment


title: CART19 cells, BHB, RNA-seq 4

description: Library name: Sample8

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

value: WT

value: BHB


title: 280T-120131-FOV_46

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:
280T-120131-FOV_46.rds

tag: tissue

tag: donor

tag: Sex

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

tag: sidedness


title: CART19 cells, BHB, RNA-seq 3

description: Library name: Sample7


title: CART19 cells, vehicle, ATAC-seq 4

description: Library name: Sample12

value: Vehicle


title: Kate 6-28-21 D11 NP

description: Library name: Kate2-D11-NP

value: Corpus Luteum

tag: pregnancy status

value: Non-Pregnant

tag: day


title: Kate 6-30-21 D13 NP

description: Library name: Kate2-D13-NP


title: P172_55

description: Library name: P172_55

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid


title: CART19 cells, BHB, RNA-seq 2

description: Library name: Sample6

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment


title: Kiwi 6-27-21 D13 NP

description: Library name: Kiwi-D13-NP

tag: tissue

tag: pregnancy status

tag: day


title: 142T-3461G-FOV_45

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:
142T-3461G-FOV_45.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: CART19 cells, BHB, RNA-seq 1

description: Library name: Sample5

value: BHB


title: P172_53

description: Library name: P172_53

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: Kiwi 6-25-21 D11 NP

description: Library name: Kiwi-D11-NP

tag: tissue

value: Corpus Luteum

tag: pregnancy status

value: Non-Pregnant

tag: day


title: 46T-148191A-FOV_45

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:
46T-148191A-FOV_45.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: hepatic flexure

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness


title: CART19 cells, vehicle, RNA-seq 4

description: Library name: Sample4

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: CART19 cells, vehicle, ATAC-seq 2

description: Library name: Sample10


title: Gisela 6-15-21 D11 Preg

description: Library name: Gisela-D11-Preg

value: Pregnant


title: P172_52

description: Library name: P172_52

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid


title: 170T-120131-FOV_45

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:
170T-120131-FOV_45.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: Cornelia 8-17-21 D11 Preg

description: Library name: Cornelia-D11-Preg

value: Corpus Luteum

tag: pregnancy status

value: Pregnant

tag: day


title: CART19 cells, vehicle, RNA-seq 3

description: Library name: Sample3

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: P172_51

description: Library name: P172_51

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: CART19 cells, vehicle, RNA-seq 2

description: Library name: Sample2

tag: cell line

value: CART19 cells

tag: cell type

tag: genotype

tag: treatment


title: P172_56

description: Library name: P172_56

tag: tissue

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

value: nanomolar

value: hour

tag: test article_name

tag: test article_dtxsid


title: Kate 6-8-21 D11 Preg

description: Library name: Kate-D11-Preg

tag: tissue

value: Corpus Luteum

tag: pregnancy status

value: Pregnant

tag: day


title: 92T-10501A-FOV_45

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:
92T-10501A-FOV_45.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: Kate 6-10-21 D13 NP

description: Library name: Kate-D13-NP

value: Non-Pregnant


title: 92T-10501A-FOV_46

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:
92T-10501A-FOV_46.rds


title: 142T-3461G-FOV_44

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:
142T-3461G-FOV_44.rds

value: ascending colon


title: P172_50

description: Library name: P172_50

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

value: Williams E medium

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: P172_54

description: Library name: P172_54

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

value: penicillin/streptomycin

value: nanomolar

value: hour

tag: test article_name

tag: test article_dtxsid

value: wild-type


title: Roanie 6-7-21 Day 11 NP

description: Library name: Roanie-D11-NP

tag: tissue

value: Corpus Luteum

tag: pregnancy status

value: Non-Pregnant

tag: day


title: P172_48

description: Library name: P172_48

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: incubator model

tag: incubator co2_percent

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: vehicle name

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: M_3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

country: China

institute: Nissi Biotech

description: Library name: Sample9

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
After that, clean reads were aligned to the rat genome by HISAT2 allowing 1 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The R Bioconductor package DESeq2 was utilized to screen out the differentially expressed genes (DEGs). The pValue < 0.05 and |log2FC| ≥ 0.5 were set as the cut-off criteria for identifying DEGs.
Assembly: rat7.0
Supplementary files format and content: Expression profile with FPKM values for all detected genes.
Supplementary files format and content: Expression profile with raw reads count for all detected genes.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: rat hippocampal region

growth_protocol: Male Sprague-Dawley (SD) rats (6-8 weeks old, SPF grade) were acclimatized for one week under standard laboratory conditions (22±1°C, 12-h light/dark cycle, ad libitum access to food and water).

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional RNA-seq library preparation by VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (N605) for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads (Vazyme, N401). Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to VAHTS RNA Multiplex Oligos Set 1 for Illumina (N323), the ligated products were amplified, purified, quantified, and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.

treatment_protocol: Rats were then randomly assigned to a normal control group and a diabetes mellitus (DM) model group. The DM model group received high-fat diet feeding for 4 weeks followed by a single intraperitoneal (i.p.) injection of streptozotocin (STZ, 50 mg·kg⁻¹ in citrate buffer, pH 4.5). Animals with sustained hyperglycemia (FBG ≥16.7 mmol·L⁻¹) were considered successful DM models. Subsequently, DM rats underwent chronic unpredictable mild stress (CUMS) for 5 weeks to induce depression-like phenotypes.

tag: tissue

value: rat hippocampal region

tag: group

value: Model

tag: strain

value: Sprague-Dawley

tag: Sex

value: male


title: Emma 6-7-21 D13 Preg

description: Library name: Emma-D13-Preg

tag: pregnancy status

value: Pregnant

tag: day


title: CART19 cells, vehicle, RNA-seq 1

description: Library name: Sample1

tag: cell line

value: CART19 cells

tag: cell type

value: T cell

value: WT

value: Vehicle


title: 170T-120131-FOV_44

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:
170T-120131-FOV_44.rds

value: Colon tumour,FFPE

tag: donor

value: F

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: 46T-148191A-FOV_44

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:
46T-148191A-FOV_44.rds

value: hepatic flexure

value: RHS


title: P172_49

description: Library name: P172_49

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: M_2

description: Library name: Sample8

tag: tissue

value: rat hippocampal region

tag: group

value: Model

tag: strain

value: Sprague-Dawley

tag: Sex

value: male


title: Emma 6-5-21 D11 Preg

description: Library name: Emma-D11-Preg

value: Corpus Luteum

tag: pregnancy status

value: Pregnant

tag: day


title: 92T-10501A-FOV_44

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:
92T-10501A-FOV_44.rds

value: Colon tumour,FFPE

tag: donor

value: F

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: P172_47

description: Library name: P172_47

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: genotype

tag: treatment


title: M_1

description: Library name: Sample7

tag: tissue

value: rat hippocampal region

tag: group

value: Model

tag: strain

value: Sprague-Dawley

tag: Sex

value: male


title: P172_46

description: Library name: P172_46

value: Liver

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: penicillin/streptomycin

value: nanomolar

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: HMG_GFP_3_Input

city: Hangzhou

first: Yan

last: Wang

state: Zhejiang

address: 866 Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province, China

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Basecalls were performed using bcl2fastq v2.19
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Clean data were aligned to the rice reference genome using Bowtie2 v2.4.1. Only uniquely mapping reads with at most two mismatches were retained.
Peak calling was performed using MACS2 v2.1.2 with the significance cut-off q-value <0.05
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. Comma-separated values files including peak information were generated using MACS v2 with default settings.
Assembly: MSU v7.0
Supplementary files format and content: bigWig and comma-separated values files include all peaks information  (except for Input sample)

organism: Oryza sativa

source_name: HMG-GFP transgenic plants, HP contiditions, input, rep3

growth_protocol: Plants were grown in a greenhouse under a 12-h light (30°C) /12h dark (22°C) photoperiod, ~200 μmol m-2 s-1 photon densities, and ~60% humidity.

extract_protocol:
Collected leaves were cross-linked with 1% (v/v) formaldehyde for 30 min under vacuum, and then stopped by adding 0.125 M Glycine. The nuclei was extracted and lysed, and the chromatin solution was sonicated to shear DNA.
ChIP-seq libraries were prepared using DNAs obtained from the ChIP experiments using the TruSeq DNA LT/HT Sample Prep Kit (Illumina), following the manufacturer’s instructions.

treatment_protocol: Seedlings grown under HP conditions for 28 d.

tag: cell line

value: Leaf blades

tag: chip antibody

value: none (input)


title: 142T-3461G-FOV_43

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:
142T-3461G-FOV_43.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: Ctrl_3

description: Library name: Sample6

value: rat hippocampal region

tag: group

value: Ctrl

tag: strain


title: P172_45

description: Library name: P172_45

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

value: fetal bovine serum;Glutamax;ascorbic acid;dexamethasone

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: genotype

tag: treatment


title: 170T-120131-FOV_43

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:
170T-120131-FOV_43.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: Ctrl_2

description: Library name: Sample5

value: rat hippocampal region

tag: group

value: Ctrl

tag: strain

value: Sprague-Dawley

value: male


title: 46T-148191A-FOV_43

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:
46T-148191A-FOV_43.rds

value: hepatic flexure

value: RHS