title: Invivo - IL27 Vector; Exvivo - Cabozantinib Rep 1

description:
Library name: IL27CO_Rep1
IL27_Cabo_1


title: Sp100 KO, 12hr IFN, biol rep 3

status: Public on Dec 09 2025

type: SRA

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

country: USA

institute: NIAID

description:
Library name: Sample 15
KO5_12hIFN_3

library_source: transcriptomic

data_processing:
Pipeliner workflow, https://github.com/CCBR/Pipeliner
Reads were trimmed to remove contaminating adapter sequences and low-quality bases using Cutadapt and aligned to the human hg19 reference genome using STAR version 2.6.1.
RSEM v1.3.0 was used for gene-level expression quantification, and limma v 3.50.3 for voom quantile normalization and differential expression analysis.
Only genes with more than 0.5 counts per million were used for downstream analysis.
Assembly: hg19
Supplementary files format and content: BigWig files of RNA-seq transcript expression data.
Supplementary files format and content: csv file includes RPKM counts for genes for all samples.

molecule: polyA RNA

organism: Homo sapiens

source_name: NIKS

growth_protocol: NIKS cells were grown in Rheinwald-Green F medium (3:1 Ham’s F-12/high-glucose Dulbecco’s modified Eagle’s medium [DMEM], 5% fetal bovine serum [FBS], 0.4 µg/ml hydrocortisone, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 2mM glutamine, 6 µg/ml insulin, 100 U/ml penicillin, and 100 µg/ml streptomycin) on a layer of lethally irradiated J2/3T3 mouse fibroblast cells. J2/3T3 fibroblasts were grown in DMEM, 10% newborn calf serum, 2 mM glutamine,100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
Total RNA was isolated with the RNeasy Mini-RNA extraction kit (Qiagen).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep following the vendor’s protocol

treatment_protocol: Cells were untreated or stimulated with 25 ng/mL Human Interferon Alpha 2a (PBL Assay Science) for 12 or 48 hours prior to harvesting total RNA.

tag: cell line

value: NIKS

tag: cell type

value: Normal immortalized keratinocytes

tag: genotype

value: Sp100 knockout

tag: treatment

value: 25 ng/mL Human Interferon Alpha 2a

tag: time

value: 12 hour


title: 92T-10501A-FOV_28

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:
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_28.rds

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

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

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

molecule: total RNA

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

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

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

tag: tissue

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: 73T-Run5850.2186.1-FOV_28

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:
73T-Run5850.2186.1-FOV_28.rds

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

value: M

value: sigmoid

value: pMMR

value: LHS


title: Invivo - IL27 vector; Exvivo - Media Rep 2

city: West Lafayette

first: Harish

last: Kothandaraman

state: Indiana

address: 201S University St

department: Purdue Institute for Cancer Research

institute: Purdue University

description:
Library name: IL270_Rep2
IL27_0_2

data_processing:
Reads were trimmed off adapters, low quality bases using cutadapt, and then mapped to the mouse genome using HISAT2. StringTie and gffCompare were used for building a comprehensive transcriptome.
Differential expression analysis of mRNAs between two groups was performed using the R package DESeq2. The mRNAs with an adjusted p-value below 0.05 and absolute fold change ≥ 1.5 were considered differentially expressed mRNAs.
Assembly: GRCm38
Supplementary files format and content: text file containing gene counts

organism: Mus musculus

source_name: tumor

growth_protocol:
The mouse adenocarcinoma cell line TRAMP-C2-Ras was cultured in DMEM-F12 (Gibco, Waltham, Massachusetts) supplemented with 10% FBS (Hyclone, Cytiva, Marlborough, MA) and 1% antibiotic-antimycotic solution (Gibco). TRAMP-C2 cells (ATCC) were transduced with a lentivirus expressing activated H-rasG12V (Lv-Hras) and described previously (TC2ras)[21]. The plasmid pCpGfree-Lucia (pCpG-Lucia) was purchased from Invivogen (San Diego, CA). To construct the pTSTA-ctrl vector, the components of the TSTA system (GAL4 and VP16) were cloned into pCpGfree-Lucia (VectorBuilder). A duplex encoding two Gly4Ser sequences as a linker (2xG4S) and the pepL sequence (LSLITRL) was synthesized by IDT (Integrated DNA Technologies, Coralville, IA, USA) to have 5′ and 3′ ‘sticky ends’ compatible with XcmI and NheI, respectively. To construct the pTSTA-IL27pepL vector, this duplex was ligated into the pCpGfree-Lucia vector along with the TSTA elements. All vectors were purified using GeneJET plasmid endotoxin free Megaprep kits (Thermo Fisher; Waltham, MA, USA).
Male C57/BL6 mice (8-10 weeks of age) were obtained from Envigo and maintained on a standard chow diet and ad libitum water under standard light/dark cycles.

extract_protocol:
Preservation in RNAlater at 4oC lasted for up to 1 week, following manufacturer’s protocols, to preserve RNA integrity for downstream applications. RNAlater was removed and ‘dried’ tumor tissues were kept in microcentrifuge tubes at -80°C. Total RNA was isolated from sections of these tumors. Briefly, 600 μL of RLT buffer + 10 μL of β-Mercaptoethanol were added to the tumor section, and homogenized with a PRO200 homogenizer (MidSci, ValleyPark, MO, USA) in three brief pulses of 10–15 s each at a mid-power. Lysates were then processed using a Qiagen RNAeasy kit (Qiagen).
Total RNA was sequenced by LC Sciences (Houston, TX) with analysis support. Before sequencing, RNA integrity was checked with an Agilent 2100 Bioanalyzer to ensure a minimum RNA Integrity Number (RIN) of 8. Illumina’s TruSeq-stranded-mRNA protocol was followed to prepare a poly (A) RNA sequencing library and Poly (A) tail-containing mRNAs were purified using oligo-dT magnetic beads. The purified poly (A) RNA was fragmented using divalent cation buffer in elevated temperature. Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip was used to perform quality control analysis and to quantify the sequencing library. Illumina’s NovaSeq 6000 sequencing system was used to perform paired-ended sequencing.

treatment_protocol: TC2ras cells were prepared for implantation by trypsinizing cells and washing with sterile 1x DPBS. The pellet was resuspended in sterile 1x DPBS at an appropriate concentration. For the subcutaneous model, 3x105 TC2Ras cells were injected in each flank in 50 ml. Implantation was performed under isoflurane anesthesia. For gene delivery via sonoporation, the plasmids (pTSTA-ctrl or pTSTA-IL27pepL) were diluted to the concentration of 10 µg per muscle in a 20 µl volume of sterile 1x DPBS. Sonovue microbubbles (Bracco, Milan, Italy) were added to the DNA just before injection (30% of the total volume). Following injection of the pDNA and microbubbles, ultrasound gel (Aquasonic 100) was applied and the 6 mm probe of a KTAC4000 sonoporator (NepaGene, Japan) was used to apply ultrasound to the shaved skin to deliver the stimulus to the tibialis anterior muscle using parameters established by our group of 1 MHz, 50% duty cycle, 2 W/cm2, and for 60 sec.

value: tumor

value: Prostate adenocarcinoma


title: Sp100 KO, 12hr IFN, biol rep 2

description:
Library name: Sample 14
KO5_12hIFN_2


title: Sp100 KO, 12hr IFN, biol rep 1

description:
Library name: Sample 13
KO5_12hIFN_1


title: Invivo - IL27 vector; Exvivo - Media Rep 1

description:
Library name: IL270_Rep1
IL27_0_1


title: Donor AJD3280 Colon LP T cells Gene Expression

city: St. Petersburg

first: Martin

last: Trapecar

state: FL

address: 600 Fifth Street South

department: Medicine and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description:
Library name: 3-LP-G
10x Genomics 5' gene expression library

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger v7.0.0 (10x Genomics) with default parameters
Gene expression data: cellranger count was used to align reads to the human reference genome (GRCh38) and generate gene-cell count matrices
TCR data: cellranger vdj was used to assemble T cell receptor sequences and identify clonotypes
Quality control: Cells with <200 genes or >10% mitochondrial reads were removed
Data integration and downstream analysis performed using Seurat v4.0+ and Scanpy v1.9+
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene expression matrices in h5 format containing UMI counts per gene per cell
Supplementary files format and content: TCR clonotype information in CSV format containing CDR3 sequences and clonotype assignments

source_name: colon lamina propria

growth_protocol: Not applicable - primary human tissue samples

extract_protocol:
Tissue dissociation: Colon and liver tissues were enzymatically dissociated using Collagenase D (Roche), Dispase (Gibco), and DNase I (StemCell Technologies) in RPMI-1640 medium at 37°C with gentle agitation. Blood: PBMCs were isolated using Ficoll-Paque density gradient centrifugation. Cell sorting: Single-cell suspensions were stained with LIVE/DEAD fixable green fluorescent reactive dye (ThermoFisher), anti-CD45-BV510 (BD Bioscience), and anti-CD3-PE (BD Bioscience) antibodies. CD45+CD3+ T cells were sorted using a Cytoflex SRT cell sorter (Beckman Coulter).
Single-cell encapsulation and library preparation were performed using the Chromium Next GEM Single Cell 5' Reagent Kit v2 (10x Genomics) according to manufacturer's protocol. Sorted CD45+CD3+ T cells were loaded onto the Next GEM Chromium Controller (10x Genomics) targeting 10000 cells per sample. TCR libraries were prepared using the Chromium Single Cell V(D)J Enrichment Kit for human T cells (10x Genomics). Libraries were sequenced on an Illumina NextSeq 500.

treatment_protocol: Not applicable - tissues from healthy donors processed immediately upon arrival

value: colon lamina propria

value: Colon lamina propria CD3+ T cells

tag: disease state

value: healthy

value: female

tag: age

tag: bmi


title: mouse AKAP11 conditional knockout_4

city: New York

first: Cong

last: Xiao

state: MA

address: Hess 9th floor,1470 Madison AVE

institute: Icahn School of Medicine-Mt Sinai

description: Library name: AKAP11cKO_4

data_processing:
The raw data was processing with cummer pepline.
The raw data was trimmed for the adaptor with TrimmomaticPE, TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment of reads to genome (HISAT2), ref: Mus_musculus.GRCm39_tran and Mus_musculus.GRCm39.112.gtf
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: tab-delimite txt file containg the raw counts for each sample

source_name: brian

extract_protocol:
RNA was harvested with RNeasy Mini Kit, Qiagen, Cat# 74016, following the manufacturer’s protocol
All the RNA libraries were made and sequenced in Experimental Department in Novogene, USA, Sacramento, CA.

value: brian


title: mouse AKAP11 conditional knockout_3

description: Library name: AKAP11cKO_3


title: WT mouse colon, normal, replicate B

city: Tokyo

first: Itsarapan

last: Fhaikrue

country: Japan

institute: Tokyo University of Agriculture and Technology

description:
Library name: WTB
Colon tissue from Wild-type germ-free C57BL/6J mouse, 8 weeks old, male, untreated

data_processing:
Raw reads were quality-checked using FastQC v0.11.7 and trimmed using Trimmomatic v0.38 (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using HISAT2 v2.1.0 with default parameters.
Gene-level read counts were quantified using StringTie v2.1.3b with Gencode vM25 annotation.
Differential expression analysis was performed using DESeq2 v1.42.1 in R v4.3.2. Genes with adjusted p-value < 0.05 and baseMean > 10 were considered differentially expressed.
Assembly: GRCm38/mm10
Supplementary files format and content: countmatrix3genotype.csv: Comma-separated file containing raw read counts for all genes across 18 samples (columns: Gene_Symbol, sample names)

source_name: colon

growth_protocol: Germ-free C57BL/6J mice were bred and maintained in sterile isolators. Animals were housed under a 12-hour light/dark cycle with free access to sterile food and water. All mice used were 8-week-old males.

extract_protocol:
Total RNA was extracted from colon tissue using the ISOGEN II Reagent (Nippon Gene). The quality of the isolated total RNA was confirmed and the grade of RNA in all samples was unified.
RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions. Sequencing was performed by Macrogen Japan on Illumina NovaSeqX platform with paired-end 150 bp reads.

treatment_protocol: For DSS treatment, mice received 2.5% dextran sulfate sodium (DSS, MW 36,000-50,000, MP Biomedicals) dissolved in drinking water for 24 hours. Normal condition mice received steriled regular  water. After treatment, mice were euthanized and colon tissues were immediately collected.

value: colon

tag: strain background

value: male

value: Wild-type

value: no treatment


title: WT mouse colon, normal, replicate A

description:
Library name: WTA
Colon tissue from Wild-type germ-free C57BL/6J mouse, 8 weeks old, male, untreated


title: 64T-Tumour_B-FOV_27

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_27.rds

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

value: Colon tumour,FFPE

value: F

value: caecum


title: mouse AKAP11 conditional knockout_2

description: Library name: AKAP11cKO_2


title: 150T-Tumour_A-FOV_27

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:
150T-Tumour_A-FOV_27.rds

value: transverse

value: RHS


title: 73T-Run5850.2186.2-FOV_27

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:
73T-Run5850.2186.2-FOV_27.rds

value: M

value: sigmoid

value: pMMR

value: LHS


title: Invivo - Empty Vector; Exvivo - Cabozanitnib+IL-27 Rep 2

description:
Library name: CtrlCO27_Rep2
ctrl_IL27CO_2

value: tumor

tag: cell line

value: Prostate adenocarcinoma


title: Invivo - Empty Vector; Exvivo - Cabozanitnib+IL-27 Rep 1

description:
Library name: CtrlCO27_Rep1
ctrl_IL27CO_1

tag: cell type


title: 67T-Run5850.2186.1-FOV_27

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:
67T-Run5850.2186.1-FOV_27.rds


title: Sp100 KO, 0hr IFN, biol rep 3

description:
Library name: Sample 12
KO5_0hIFN_3

value: NIKS

value: Normal immortalized keratinocytes

tag: genotype

value: Sp100 knockout

value: Untreated

value: 0 hour


title: 7N-Normal_A-FOV_27

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7N-Normal_A-FOV_27.rds

value: ascending


title: mouse AKAP11 conditional knockout_1

description: Library name: AKAP11cKO_1

value: brian


title: Sp100 KO, 0hr IFN, biol rep 1

description:
Library name: Sample 10
KO5_0hIFN_1

tag: treatment


title: mouse control_3

description: Library name: Control_3


title: Invivo - Empty Vector; Exvivo - Anti-PD-L1 Rep 2

description:
Library name: CtrlPDL1_Rep2
ctrl_PDL1_2


title: 137T-3461G-FOV_27

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:
137T-3461G-FOV_27.rds

value: Colon tumour,FFPE

value: F

value: rectal


title: mouse control_2

description: Library name: Control_2


title: Invivo - Empty Vector; Exvivo - Anti-PD-L1 Rep 1

description:
Library name: CtrlPDL1_Rep1
ctrl_PDL1_1


title: Sp100 WT, 48hr IFN, biol rep 3

description:
Library name: Sample 9
Vec2_48hIFN_3

value: WT

value: 25 ng/mL Human Interferon Alpha 2a

tag: time

value: 48 hour


title: mouse control_1

description: Library name: Control_1

tag: tissue


title: 278T-148191A-FOV_27

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_27.rds

tag: donor

value: M

value: pMMR


title: Invivo - Empty Vector; Exvivo - Docetaxel Rep 2

description:
Library name: CtrlD_Rep2
ctrl_Doce_2

value: tumor


title: Sp100 WT, 48hr IFN, biol rep 1

description:
Library name: Sample 7
Vec2_48hIFN_1


title: 170T-120131-FOV_27

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_27.rds

tag: Sex

value: sigmoid

value: LHS


title: Invivo - Empty Vector; Exvivo - Docetaxel Rep 1

description:
Library name: CtrlD_Rep1
ctrl_Doce_1

value: Prostate adenocarcinoma


title: Sp100 WT, 12hr IFN, biol rep 3

description:
Library name: Sample 6
Vec2_12hIFN_3

value: NIKS

value: Normal immortalized keratinocytes

value: 12 hour


title: LM35, LD

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

description:
Library name: ML35
LM35

data_processing:
Illumina bcl2fastq was used for conversion into Fastq files.
Trimmotatic (version 0.39) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome GRCm39/mm39 with STAR (2.7.10a) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools  (1.7) (Li et al. 2009).
The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands.
The University of California, Santa Cruz (UCSC) known canonical gene set (57,186) were used for annotation, and the reads mapped to the exons were quantified using analyzeRNA.pl script in the Homer software with an option of –rpkm or -noadj for FPKM or raw read counts, respectively
Raw reads and Fragments Per Kilobase per Million mapped reads (FPKM) were calculated using HOMER (v4.11) (Heinz et al. 2010)
Assembly: GRCm39/mm39
Supplementary files format and content: bigWig and tab-delimited text files include raw read counts and FPKM values for each Sample.

source_name: gastrocnemius muscle

growth_protocol: Mice were randomly assigned to LD and ADV groups (n = 16) and housed in individual cages (170 × 350 × 145 mm) with a 120-mm diameter running wheel (SANKO, Osaka, Japan). All mice were kept in light-shielded mouse housing boxes at the room temperature of 25.0 ± 1.5 °C with food and water available ad libitum. The mice were entrained to a 12:12-h light-dark cycle with an 8:00-20:00 light period for 2 weeks, followed by 2 weeks in constant darkness (DD). Two mice in the LD group were censored due to injuries or found dead.

extract_protocol:
The gastrocnemius muscle was incubated with RNAlater (Thermo Fisher Scientific) for several hours according to the manufacturer’s instructions and snap-frozen in liquid nitrogen. Frozen gastrocnemius muscle was homogenized twice for 30 sec in TRIzol reagent (Thermo Fischer Scientific) with 5-mm- and 3-mm-diameter stainless beads using a desktop bead Crusher Shakeman 6 (Bio Medical Science Inc., Tokyo, Japan) at 3500 rpm.
Poly(A)-enriched stranded RNA sequencing was carried out using TruSeq stranded mRNA kit by the NGS core facility at the Research Institute for Microbial Diseases of Osaka University on Illumina NovaSeq X with 101-bp paired-end reads.

treatment_protocol: After DD exposure, mice were returned to the normal light condition (8:00-20:00) followed by the same LD condition (light–dark condition with an 8:00–20:00 light period) or the ADV-condition (8-hour phase advance once every 4 days) for 64 weeks.

value: gastrocnemius muscle

tag: strain

value: male

value: Wild-type

value: LD

tag: activity measured

value: WHEEL


title: 92T-10501A-FOV_27

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_27.rds

value: Colon tumour,FFPE

value: F

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

value: dMMR

value: RHS


title: LM36, LD

description:
Library name: ML36
LM36


title: Sp100 WT, 12hr IFN, biol rep 2

description:
Library name: Sample 5
Vec2_12hIFN_2

value: WT

value: 25 ng/mL Human Interferon Alpha 2a


title: mouse control_4

description: Library name: Control_4

value: brian


title: Invivo - Empty Vector; Exvivo - Cabozantinib Rep 1

description:
Library name: CtrlCO_Rep1
ctrl_Cabo_1

value: tumor

value: Prostate adenocarcinoma


title: Invivo - Empty Vector; Exvivo - Cabozantinib Rep 2

description:
Library name: CtrlCO_Rep2
ctrl_Cabo_2


title: 64T-Tumour_B-FOV_26

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_26.rds

tag: mmr status

value: pMMR

tag: sidedness


title: Sp100 KO, 0hr IFN, biol rep 2

description:
Library name: Sample 11
KO5_0hIFN_2

value: NIKS

value: Normal immortalized keratinocytes

value: Sp100 knockout

value: Untreated

value: 0 hour


title: Invivo - Empty Vector; Exvivo - Media Rep 2

description:
Library name: Ctrl0_Rep2
ctrl_0_2


title: 73T-Run5850.2186.2-FOV_26

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:
73T-Run5850.2186.2-FOV_26.rds

value: M

value: sigmoid

value: LHS


title: LM33, LD

description:
Library name: ML33
LM33

value: gastrocnemius muscle

value: male

value: Wild-type

value: LD

value: WHEEL


title: 150T-Tumour_A-FOV_26

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:
150T-Tumour_A-FOV_26.rds

value: Colon tumour,FFPE

value: F

value: transverse

value: RHS


title: Invivo - Empty Vector; Exvivo - Media Rep 1

description:
Library name: Ctrl0_Rep1
ctrl_0_1

value: tumor

value: Prostate adenocarcinoma


title: Sp100 WT, 0hr IFN, biol rep 3

description:
Library name: Sample 3
Vec2_0hIFN_3

value: NIKS

value: Normal immortalized keratinocytes

value: WT


title: LM34, LD

description:
Library name: ML34
LM34


title: Sp100 WT, 48hr IFN, biol rep 2

description:
Library name: Sample 8
Vec2_48hIFN_2

value: 25 ng/mL Human Interferon Alpha 2a

value: 48 hour


title: 67T-Run5850.2186.1-FOV_26

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:
67T-Run5850.2186.1-FOV_26.rds

value: M

value: sigmoid

value: pMMR

value: LHS


title: LM31, LD

description:
Library name: ML31
LM31

value: gastrocnemius muscle

value: male

value: Wild-type

value: LD


title: SOX10_2, CUT&Tag

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

country: China

institute: Jinan University

description: Library name: Sample2

library_source: genomic

data_processing:
Reads were mapped to the reference genome using BWA
Peak calling was performed using MACS2 software with a cutoff value < 0.05
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: whole brain

extract_protocol:
Fresh whole brain of transgenic mice were removed with tweezers and then dissociated into single cell suspension using the papain system (Worthington) according to manufacturer’s protocol. TdTomato+ cells were sorted from the brain of animals 10 days after tamoxifen administration using FACS.
CUT&Tag libraries were prepared using CUT&Tag-IT™ Assay Kit (Active Motif, catalog No. 53160)

treatment_protocol: Adult Sox10-CreERT2 and Ai14 transgenic mice were i.p. injected with tamoxifen for 3 days

value: whole brain

value: 10 days post tamoxifen administration

value: Sorted tdTomato+ cells

tag: cut&tag antibody

value: Olig2 (EMD/Millipore, #AB9610)

value: tamoxifen


title: 64N-Normal_A-FOV_26

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:
64N-Normal_A-FOV_26.rds

value: Colon tumour,FFPE

value: F

value: caecum

value: RHS


title: SOX10_1, CUT&Tag

description: Library name: Sample1


title: LM30, LD

description:
Library name: ML30
LM30

value: WHEEL


title: Sp100 WT, 0hr IFN, biol rep 1

description:
Library name: Sample 1
Vec2_0hIFN_1

value: NIKS

value: Normal immortalized keratinocytes

value: WT

value: Untreated

value: 0 hour


title: Human Monocytes, 4h, 10 µg/ml RTD-1 rep3

city: Los Angeles

first: Prasad

last: Tongaonkar

state: CA

address: 7504 NRT, 1450 Biggy St

department: Pathology and Laboratory Medicine

institute: USC

data_processing:
Partek Flow 11.0.23.1023
Quality trimming of bases from 3'end, minimum read length of 25 using Partek Flow
Partek Flow was used for mapping Trimmed sequences to hg38-GENCODE GENES release 42 using STAR-2.7.8a
Gene Counts determined by Partek Flow Quantify to annotation model (Partek E/M)
Partek Flow was used for Normalization using Poscounts(DESeq2 only)
Assembly: hg38
Supplementary files format and content: tab delimited text file contains gene counts for each sample
Supplementary files format and content: tab delimited text file contains Normalized counts for each sample

source_name: monocyte

growth_protocol: Positively selected CD14+ human monocytes were purchased from Lonza (Cambridge, MA) and Stemcell Technologies (Vancouver, BC).  Cells were thawed in RPMI medium containing 10% heat inactivated (HI) FBS and 1% penicillin/streptomycin (P/S) + 100 μg/ml normocin and harvested by centrifugation at 200 x g for 8 mins.  The cells were then resuspended in RPMI medium containing 1% HI FBS and 1% P/S + 100 μg/ml normocin to a concentration of 1 x 106 cells/ml and equilibrated for 2 h at 37 C and 5% CO2.

extract_protocol:
RNA was extracted using Quick RNA Miniprep kit (Zymo Research)
Libraries were prepared using Kapa Stranded RNA seq kit as per manufacturer.

treatment_protocol: Cells were treated with vehicle (0.01% acetic acid) or 10 µg/ml RTD-1 for 4 h at 37 C and 5% CO2. Cells were then harvested at 200 xg for 8 min.

value: monocyte

value: wildtype


title: 137T-3461G-FOV_26

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:
137T-3461G-FOV_26.rds

value: rectal

value: pMMR

value: LHS


title: TA Muscle, PBM Sedentary, 6

city: Boston

first: Nashwa

last: Cheema

address: 55 Fruit St

institute: Massachusetts General Hospital

description: Library name: 23263XR-02-12

data_processing:
Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. STAR Aligner version 2.7.1a was used to align the reads. Picard tools (version 2.20.4) was applied to mark duplicates of mapping. The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts.
Assembly: GRCm38
Supplementary files format and content: The featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

source_name: muscle

extract_protocol:
TA tissue was shipped on dry ice to Admera Health who processed the samples and performed mRNA extraction, sequencing, and analysis. Total RNA was quantified by Qubit RNA HS Assay (ThermoFisher) and RNA integrity was determined by Bioanalyzer 2100 Eukaryote Total RNA Nano (Agilent Technologies, CA, USA) with  RNA integrity numbers (RINs) of ≥ 7.7.
PolyA selection and cDNA libraries were constructed using the NEB Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc., Massachusetts, USA). Samples were sequenced on an Illumina NovaSeq (Illumina, California, USA) with a read length configuration of 150 PE for 60M paired-end reads per sample (30M in each direction).

value: muscle


title: 278T-148191A-FOV_26

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_26.rds

value: M


title: LM29, LD

description:
Library name: ML29
LM29

value: gastrocnemius muscle

value: male

value: Wild-type

value: LD


title: TA Muscle, PBM Sedentary, 5

description: Library name: 23263XR-02-11


title: Human Monocytes, 4h, vehicle rep3

value: vehicle


title: Human Monocytes, 4h, 10 µg/ml RTD-1 rep2


title: Sp100 WT, 12hr IFN, biol rep 1

description:
Library name: Sample 4
Vec2_12hIFN_1

value: NIKS

value: 25 ng/mL Human Interferon Alpha 2a

value: 12 hour


title: 170T-120131-FOV_26

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_26.rds

value: Colon tumour,FFPE

value: F

value: sigmoid


title: LM27, LD

description:
Library name: ML27
LM27

value: WHEEL


title: LM32, LD

description:
Library name: ML32
LM32


title: TA Muscle, PBM Sedentary, 4

description: Library name: 23263XR-02-10

value: WT


title: Human Monocytes, 4h, vehicle rep2

value: monocyte

value: wildtype


title: LM23, LD

description:
Library name: ML23
LM23


title: TA Muscle, PBM Sedentary, 2

description: Library name: 23263XR-02-08

value: muscle


title: 130T-10501A-FOV_26

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:
130T-10501A-FOV_26.rds

value: rectum upper

value: pMMR

value: LHS


title: 64T-Tumour_B-FOV_25

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_25.rds

value: caecum

value: RHS


title: Human Monocytes, 4h, 10 µg/ml RTD-1 rep1


title: Human Monocytes, 4h, vehicle rep1

value: vehicle


title: Sp100 WT, 0hr IFN, biol rep 2

description:
Library name: Sample 2
Vec2_0hIFN_2

value: NIKS

value: Normal immortalized keratinocytes

value: Untreated

value: 0 hour


title: TA Muscle, PBM Sedentary, 1

description: Library name: 23263XR-02-07


title: LM22, LD

description:
Library name: ML22
LM22

value: gastrocnemius muscle

value: male

value: Wild-type

value: LD


title: SF558 Fibrosis+AZ4547 [SF558-3]

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

data_processing:
For the computational analyses, we trimmed adapter sequences by using cutadapt, remove the reads mapped to ribosomal RNA by using bowtie2 and samtools.
The STAR index was constructed from the genome index, and RNA-seq single-end reads were aligned to the genome using STAR
Using the bam files produced by the alignment tool, use the modules in RseQC to evaluate the quality of the RNA-seq data with the reference files.
HTSeq was used to count reads mapping to individual genes by processing the sorted bam files with accepted read quality.
Counts generated by HTSeq-count were normalized using DESeq2. This normalization utilized the size factor derived from the count data of all 58 DCM samples and 12 controls.
Assembly: Hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files includes raw counts values for each sample
Supplementary files format and content: tab-delimited text files includes normalized counts for each sample

source_name: cardiac organoid

growth_protocol: Day 14 hiPSC-derived epicardial cells (GFP+) and day 14 hiPSC-derived ventricular cardiomyocytes were dissociated into single cells and then mixed in a 1:1 ratio of 20,000 cells in total in a 96-well polyheme-coated round bottom plate. These aggregates are named cardiac organoids. These organoids were cultured for 10 days in StemPro-34 based medium containing retinol (2 μM, Sigma). At day 10, organoids were cultured in maturation medium (DMEM containing low glucose (2 g/L) with palmitic acid (200  μM, Sigma), dexamethasone (100 ng/ml, Sigma), T3 hormone (4 nM, Sigma) and GW7647 (PPARA agonist, 1  μM, Merck)) for the following 11 days and then for another 3 days in DMEM containing low glucose (2 g/L) with palmitate (200  μM) alone, to generate mature ventricular organoids.

extract_protocol:
Sample homogenization was performed using 700 μL of QIAZOL (QIAGEN) by manual crushing with a pestle. After homogenization, two supernatants were collected in new 1.5 mL RNase-free microcentrifuge tubes. RNA extraction was carried out using the miRNeasy Micro Kit with a Rnase-Free Dnase Set (QIAGEN).
The cDNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit and protocol from Illumina (Illumina Inc., San Diego, CA).

treatment_protocol: To induce cardiac injury and fibrotic changes, mature organoids were cultured in DMEM containing low glucose (2 g/L) with palmitate (200  μM) supplemented by isoproterenol (100 μM, Sigma) and TGFB1 (3ng/ml, Sigma) and AZD4547 (5uM) or DMSO in hypoxic condition (5 % O2, 5 % CO2, 37 ℃) for 1 week.

value: cardiac organoid

value: iPSC

value: wild type

value: Fibrotic condition treated with AZD4547


title: 73T-Run5850.2186.2-FOV_25

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:
73T-Run5850.2186.2-FOV_25.rds

value: Colon tumour,FFPE

value: M

value: sigmoid

value: pMMR


title: TA Muscle, Sedentary, 6

description: Library name: 23263XR-02-06

value: muscle

value: WT


title: LM21, LD

description:
Library name: ML21
LM21

value: WHEEL


title: 150T-Tumour_A-FOV_25

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:
150T-Tumour_A-FOV_25.rds

value: F

value: transverse

value: RHS


title: LM28, LD

description:
Library name: ML28
LM28

value: gastrocnemius muscle

value: male


title: SF558 Fibrosis+DMSO [SF558-2]

value: Fibrotic condition


title: TA Muscle, Sedentary, 5

description: Library name: 23263XR-02-05


title: 67T-Run5850.2186.1-FOV_25

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:
67T-Run5850.2186.1-FOV_25.rds

value: LHS


title: SF558 control [SF558-1]

value: cardiac organoid

value: iPSC

value: control


title: AM35, ADV

description:
Library name: MA35
AM35

value: Wild-type

value: ADV


title: TA Muscle, Sedentary, 4

description: Library name: 23263XR-02-04


title: AM36, ADV

description:
Library name: MA36
AM36


title: 64N-Normal_A-FOV_25

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:
64N-Normal_A-FOV_25.rds

value: Colon tumour,FFPE

value: caecum


title: TA Muscle, PBM Sedentary, 3

description: Library name: 23263XR-02-09

value: muscle


title: TA Muscle, Sedentary, 3

description: Library name: 23263XR-02-03

value: WT


title: AM34, ADV

description:
Library name: MA34
AM34

value: WHEEL


title: SF521 Fibrosis+AZ4547 [SF521-3]

value: wild type

value: Fibrotic condition treated with AZD4547


title: 137T-3461G-FOV_25

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:
137T-3461G-FOV_25.rds

value: F

value: rectal

value: pMMR


title: TA Muscle, Sedentary, 2

description: Library name: 23263XR-02-02


title: LM26, LD

description:
Library name: ML26
LM26

value: gastrocnemius muscle

value: male

value: LD


title: 278T-148191A-FOV_25

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_25.rds

value: M

value: LHS


title: SF521 Fibrosis+DMSO [SF521-2]

value: cardiac organoid

value: iPSC

value: Fibrotic condition


title: SF521 control [SF521-1]

value: control


title: TA Muscle, Sedentary, 1

description: Library name: 23263XR-02-01

value: muscle


title: 170T-120131-FOV_25

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_25.rds

value: Colon tumour,FFPE

value: sigmoid


title: AM32, ADV

description:
Library name: MA32
AM32

value: Wild-type

value: ADV

value: WHEEL


title: TA Muscle, PBM Fatigue, 6

description: Library name: 23263XR-01-12

value: WT


title: 130T-10501A-FOV_25

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:
130T-10501A-FOV_25.rds

value: F

value: rectum upper

value: pMMR


title: SF520 Fibrosis+DMSO [SF520-2]

value: wild type


title: AM31, ADV

description:
Library name: MA31
AM31

value: gastrocnemius muscle

value: male


title: TA Muscle, PBM Fatigue, 5

description: Library name: 23263XR-01-11


title: 64T-Tumour_B-FOV_24

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_24.rds

value: caecum

value: RHS


title: 150T-Tumour_A-FOV_24

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:
150T-Tumour_A-FOV_24.rds

value: transverse


title: SF520 control [SF520-1]

value: cardiac organoid

value: iPSC

value: control


title: TA Muscle, PBM Fatigue, 4

description: Library name: 23263XR-01-10

value: muscle


title: AM29, ADV

description:
Library name: MA29
AM29

value: Wild-type


title: 73T-Run5850.2186.2-FOV_24

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:
73T-Run5850.2186.2-FOV_24.rds

value: Colon tumour,FFPE

value: M

value: sigmoid

value: LHS


title: TA Muscle, PBM Fatigue, 3

description: Library name: 23263XR-01-09

value: WT


title: Hh188

source_name: Right ventricular septum

extract_protocol:
Sample homogenization was performed using 700 μL of QIAZOL (QIAGEN) either by manual crushing with a pestle or with a gentleMACS Dissociator (Miltenyi Biotec). After homogenization, two supernatants were collected in new 1.5 mL RNase-free microcentrifuge tubes. RNA extraction was carried out using the miRNeasy Micro Kit with a Rnase-Free Dnase Set (QIAGEN).
The cDNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit and protocol from Illumina (Illumina Inc., San Diego, CA).

value: Right ventricular septum


title: 67T-Run5850.2186.1-FOV_24

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:
67T-Run5850.2186.1-FOV_24.rds

value: pMMR


title: AM28, ADV

description:
Library name: MA28
AM28

value: gastrocnemius muscle

value: ADV

value: WHEEL


title: AM27, ADV

description:
Library name: MA27
AM27

value: male


title: Hh184


title: Hh183


title: TA Muscle, PBM Fatigue, 2

description: Library name: 23263XR-01-08


title: TA Muscle, PBM Fatigue, 1

description: Library name: 23263XR-01-07


title: AM26, ADV

description:
Library name: MA26
AM26


title: AM25, ADV

description:
Library name: MA25
AM25


title: TA Muscle, Fatigue, 6

description: Library name: 23263XR-01-06


title: SF520 Fibrosis+AZ4547 [SF520-3]

value: wild type

value: Fibrotic condition treated with AZD4547


title: Hh180


title: Hh178


title: AM30, ADV

description:
Library name: MA30
AM30


title: TA Muscle, Fatigue, 5

description: Library name: 23263XR-01-05


title: 278T-148191A-FOV_24

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_24.rds

value: rectal


title: AM24, ADV

description:
Library name: MA24
AM24


title: TA Muscle, Fatigue, 4

description: Library name: 23263XR-01-04


title: Hh171


title: AM23, ADV

description:
Library name: MA23
AM23


title: 280T-120131-FOV_24

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_24.rds

value: F

value: caecum

value: RHS


title: TA Muscle, Fatigue, 3

description: Library name: 23263XR-01-03

value: muscle


title: Hh165


title: 130T-10501A-FOV_24

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:
130T-10501A-FOV_24.rds

value: Colon tumour,FFPE

value: rectum upper


title: 64T-Tumour_B-FOV_23

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_23.rds


title: Hh170


title: AM22, ADV

description:
Library name: MA22
AM22

value: Wild-type


title: AM21, ADV

description:
Library name: MA21
AM21


title: 137T-3461G-FOV_24

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:
137T-3461G-FOV_24.rds

value: LHS


title: TA Muscle, Fatigue, 1

description: Library name: 23263XR-01-01

value: WT


title: 150T-Tumour_A-FOV_23

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:
150T-Tumour_A-FOV_23.rds

value: transverse

value: pMMR


title: Hh155

value: Right ventricular septum


title: Hh162


title: 73T-Run5850.2186.2-FOV_23

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:
73T-Run5850.2186.2-FOV_23.rds

value: M

value: sigmoid


title: colon_infected_d7_rep2

city: Xi'an

first: Ruifen

last: Zhang

state: Shaanxi

address: No. 28, Xianning West Road, Pengkang Building, Xingqing Campus, Xi'an Jiaotong University

department: School of Life Sciences

institute: xjtu

description:
Library name: A6_d7
Mice on the 7th day after Salmonella infection-2

data_processing:
Cell × gene count matrices were generated for each sample using the "count" workflow of Kallisto/bustools (KB) v0.28.2 in combination with the parameter “--filter bustools”, and its transcriptomic index was constructed based on the mouse genome GRCm39 (downloaded from Ensembl v111).
For each sample, we also only retained those cells with > 1000 genes, > 2000 UMIs and where the percentage of total reads from mitochondrial genes was < 10%, as well as only retaining those genes that could be detected (i.e., having one or more reads) in at least 3 cells.
Each count matrix was processed using Seurat v5.0.1 with the SCTransform normalisation workflow
Doublets were then predicted using DoubletFinder v2.0.4 with a set clustering resolution for modelling homotypic doublets (0.3) and a set proportion of expected doublets (7.5%) per sample; only cell barcodes classified as ‘singlet’ were retained for further analysis
Assembly: GRCm39 genome
Supplementary files format and content: All_obj.rds: Seurat object of all samples and all cell types.
Supplementary files format and content: Epithelial.rds: Seurat object of all samples and epithalial cells.
Supplementary files format and content: Fibroblast.rds: Seurat object of all samples and fibroblast cells.
Supplementary files format and content: Immune.rds: Seurat object of all samples and immune cells.

extract_protocol:
Tissues were gently cleaned, cut into pieces of approx. 3-5mm3, and incubated on ice at 4°C. Infiltrates were pre-cooled to 4°C with PBS, and allowed to settle for 10-50s before discarding the supernatant. The dissociative enzyme was transferred into the centrifuge tube, which was sealed with film, placed in a 37°C constant temperature oscillating water bath and incubated for 15 min at 100rpm/min. Digestion was terminated by placing the sample on ice at 4°C, adding an appropriate amount of DMEM, and letting it stand and settle for 2 min. The resulting cell suspensions were filtered through a 40 μm nylon cell strainer.
scRNA-seq library preparation and sequencing was then performed by Genergy Bio (Shanghai, China) using the 10x Chromium single cell-platform with version 3 reaction chemistry, in accordance with manufacturer’s instructions. Single-cell suspensions were prepared as barcoded scRNA-seq libraries using a Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics, Shanghai, China), with libraries sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, USA).

treatment_protocol: Salmonella infection

value: colon

value: infected by Salmonella d7


title: 64N-Normal_A-FOV_24

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:
64N-Normal_A-FOV_24.rds


title: FlareTSLP+cells in the large intestine, scRNAseq

city: San Francisco

first: Richard

last: Locksley

address: 513 Parnassus Avenue

institute: University of California, San Francisco

data_processing:
Sample demultiplexing, alignments and UMI counts were performed using the 10x Genomics CellRanger pipeline (v 8.1.0) with a custom reference based on the latest mouse genome (mm39), including the tdTomato sequence.
Assembly: mm39
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: large intestine, lamina propria

extract_protocol:
Intestine tissues were harvested and flushed with ice-cold PBS. After removing the Peyer’s patches, gut tissues were opened and washed with PBS to remove lumen content and mucus.  Segments were incubated while rocking for 15 min at 37 °C in 20 ml HBSS (Ca2+- and Mg2+-free) containing 5% FCS, 10 mM HEPES, 10 mM EDTA and 10 mM dithiothreitol. Tissue segments were vortexed vigorously for 30 s to remove the epithelial fraction. The remaining tissue segments were incubated a second time while rocking for 15 min at 37 °C in 10 ml of the same HBSS/FBS/EDTA/DTT media and then vortexed for 30 sec. The tissue segments were transferred to a new tube and incubated while rocking for 5 min at 37 °C in 20 ml HBSS (with Ca2+ and Mg2+) containing 2% FCS and 10 mM HEPES before transferring to new tubes containing 5 ml HBSS (with Ca2+ and Mg2+), 3% FCS, 10 mM HEPES, 30 µg/ml DNase and 0.1 unit/ml Liberase TM, followed by processing with gentleMax Octo Dissociator program “intestine”. Lamina propria cells were pelleted, washed and filtered with 70 µM cell strainers before staining for flow cytometry.  Standard surface and/or intracellular staining protocols were used followed by DAPI staining for dead cell exclusion. Samples were processed using BD FACSAria™.
Live cells were purified via FACS based on tdTomato expression and subsequently labeled with unique barcoded H-2/CD45 TotalSeq-B anti-mouse hashtag antibodies for multiplexing. The cells were processed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell  3′ Kit v3.1. Briefly, cell counts were performed using a hemacytometer, and the desired number of cells was injected into microfluidic chips to create Gel Beads-in-Emulsion (GEMs) with the 10X Chromium controller. Reverse transcription (RT) was performed on the GEMs, followed by purification and amplification of the RT products. Cell multiplexing oligo (CMO) DNA was separated from cDNA using size selection with SPRIselect beads. Gene expression (GEX) libraries and CMO libraries were generated separately and profiled using the Bioanalyzer High Sensitivity DNA kit. Prior to sequencing, the GEX and corresponding CMO libraries were mixed in a 4:1 ratio. Sequencing of the mixed libraries was conducted on the Illumina NovaSeq X platform.

value: large intestine, lamina propria


title: FlareTSLP+cells in the cecum, scRNAseq

source_name: cecum, lamina propria

value: cecum, lamina propria


title: 67T-Run5850.2186.1-FOV_23

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:
67T-Run5850.2186.1-FOV_23.rds


title: FlareTSLP+cells in the distal small intestine, replicate 2, scRNAseq

source_name: distal ileum, lamina propria

value: distal ileum, lamina propria


title: colon_infected_d7_rep1

description:
Library name: A4_d7
Mice on the 7th day after Salmonella infection-1


title: Hh147


title: Hh153


title: colon_infected_d5_rep2

description:
Library name: d5_2
Mice on the 5th day after Salmonella infection-2

value: infected by Salmonella d5


title: FlareTSLP+cells in the distal small intestine, replicate 1, scRNAseq


title: FlareTSLP+cells in the proximal small intestine, replicate 2, scRNAseq

source_name: proximal jejunum, lamina propria

value: proximal jejunum, lamina propria


title: colon_infected_d5_rep1

description:
Library name: A19_d5
Mice on the 5th day after Salmonella infection-1


title: TA Muscle, Fatigue, 2

description: Library name: 23263XR-01-02

value: muscle


title: AM33, ADV

description:
Library name: MA33
AM33

value: gastrocnemius muscle

value: male

value: ADV

value: WHEEL


title: 278T-148191A-FOV_23

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_23.rds

value: Colon tumour,FFPE

value: rectal

value: LHS


title: Hh142

value: Right ventricular septum


title: FlareTSLP+cells in the proximal small intestine, replicate 1, scRNAseq


title: colon_infected_d3_rep2

description:
Library name: A29_d3
Mice on the 3rd day after Salmonella infection-2

value: infected by Salmonella d3


title: Hh141


title: 280T-120131-FOV_23

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_23.rds

value: F

value: caecum

value: pMMR

value: RHS


title: Hh133


title: colon_infected_d3_rep1

description:
Library name: A23_d3
Mice on the 3rd day after Salmonella infection-1

value: colon


title: Human lung COPD TMA4

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

hyb_protocol: Target-specific Xenium probes were hybridized in situ to released RNA transcripts according to the manufacturer’s protocol.

scan_protocol: Slides were imaged on the Xenium Analyzer.

data_processing: Following hybridization, the slides were imaged and processed using the standard pipeline of the Xenium Analyzer (v3.2.0), with transcript assignment to individual cells performed using the 10x Genomics multimodal segmentation algorithm. Quality control thresholds included Phred Q > 20 for transcripts; cells required nFeature > 5, nCounts > 9, and nuclear area 6–80 µm². Downstream analysis was performed in Seurat v5.0.1 including normalization, PCA, neighbor graph construction, clustering, and UMAP.

label: Xenium Human Lung 480-gene panel (hLung_480g, design ID EM2BNX, v1.0.0)

source_name: lung

label_protocol: Enzymatic probe extension for signal generation was performed following in situ hybridization. Multimodal staining was then performed using the Xenium Multi-Tissue Stain Mix, including membrane and interior antibody labeling, a universal 18S interior stain, and DAPI nuclear staining.

extract_protocol: FFPE sections (5 µm) were processed on Xenium slides following manufacturer protocols (CG000578, Rev C) with a custom 480-gene panel (hLung_480g, design ID EM2BNX, v1.0.0). FFPE tissue sections were deparaffinized by incubating slides at 60°C, followed by sequential immersion in xylene, ethanol (100%, 96%, 70%), and nuclease-free water. Slides were then dried, assembled into Xenium Cassettes, and treated with a Decrosslinking Buffer. The assembled cassettes were incubated at 80°C in a thermal cycler to release RNA from the tissue.

value: lung

tag: disease

value: COPD

tag: material

value: FFPE

tag: sample type

value: TMA core


title: 130T-10501A-FOV_23

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:
130T-10501A-FOV_23.rds

value: rectum upper


title: Human lung COPD TMA3


title: Human lung COPD TMA2


title: 64T-Tumour_B-FOV_22

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_22.rds


title: Hh130


title: 150T-Tumour_A-FOV_22

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:
150T-Tumour_A-FOV_22.rds

value: transverse


title: Hh127


title: Hh125


title: 137T-3461G-FOV_23

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:
137T-3461G-FOV_23.rds


title: Human lung COPD TMA1


title: colon_uninfected_d0_rep1

description:
Library name: A11_ctrl
Not infected mice-1

value: uninfected


title: colon_infected_d1_rep1

description:
Library name: A17_d1
Mice on the 1st day after Salmonella infection-1

value: infected by Salmonella d1