title: STEPN-56_Region_2

type: other

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

hyb_protocol: A total of 343 unique genes were included in the analysis of this dataset. 319 genes came from an early version of the Xenium human brain base panel and 100 genes from a custom designed panel. The custom panel was curated based on Ependymoma single cell analysis data (Gojo, Johannes, et al. 2020), selecting for genes useful in programs identification. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation (Davis et al. 2014). Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

data_processing:
During every Xenium Analyzer run, image processing, and decoding are performed real time on-instrument.
Downstream analysis were done using Seurat pipeline and house-made scripts.

molecule: other

source_name: Ependymoma, Recurrence

extract_protocol: For fresh frozen samples, tissue sections were cut at a thickness of 10µM with a Leica CM3050S cryostat and collected onto Fisherbrand™ Superfrost™ Plus microscope slides, 10um tissue sections were placed onto a Xenium slide followed by fixation and permeabilization. For FFPE blocks, 5 µm tissue sections on a Xenium slide underwent deparaffinization and permeabilization. A mix of pre-designed and custom gene expression probe hybridization occurred at 50°C overnight. After multiple washing to remove un-hybridized probes, ligation of probes and annealing of rolling circle amplification (RCA) primer occurred at 37°C for 2 hours. Circularized probes were then enzymatically amplified at 30°C for 2 hours, after which background autofluorescence was quenched chemically. Slide was then loaded into the Xenium Analyzer following nuclei staining.

tag: age

tag: gender

tag: type

value: Fresh frozen in-situ

tag: sampling

value: Recurrence

tag: fusion

value: Ependymoma

tag: subtype

value: ZFTA-RELA


title: 73T-Run5850.2186.2-FOV_22

status: Public on Dec 09 2025

type: RNA

city: Clayton

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

department: Anatomy and developmental biology

country: Australia

institute: Monash University

description:
raw data files:
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_22.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 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.

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

molecule: total RNA

organism: Homo sapiens

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

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

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

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: STEPN-57_Region_2

city: Boston

state: MA

country: USA

value: F


title: colon_infected_d7_rep3

type: SRA

city: Xi'an

first: Shanshan

last: Li

state: Shannxi

address: Chang'an District

country: China

institute: Xi'an Jiaotong University

description: Library name: D7-3

library_source: transcriptomic

data_processing:
Raw reads were cleaned using fastp v0.19.7
Cleaned reads were aligned to the mouse reference genome GRCm39 by STAR v2.7.9a
The resulting BAM files were sorted using samtools v1.13 by coordinate.
The sorted BAM files were analyzed using featureCounts v2.0.0 with the gene annotation file. The gene expression matrix was generated from this step.
Assembly: GRCm39
Supplementary files format and content: raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: colon

extract_protocol:
Transcriptome sequencing (bulk RNA-seq) was performed on the colons of BALB/c on different days after Salmonella Typhimurium gavage (Days 0,1,3,5 and 7, n=3). The colons were washed 5 times with PBS, preserved in RNALater (Beyotime) at -80℃ until further use. The RNA extraction, RNA library preparation and sequencing were carried out by Novogene.
sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs, USA), with index-coded samples clustered according to the manufacturer’s instructions using a cBot Cluster Generation System and the TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Libraries were sequenced using an Illumina NovaSeq 6000 to produce 150 bp paired-end reads.

treatment_protocol: Salmonella infection

value: colon

value: female

tag: treatment

value: infected by Salmonella

value: 6-8 weeks old


title: 64N-Normal_A-FOV_23

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_23.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: caecum

value: RHS


title: colon_uninfected_d0_rep2

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: A8_ctrl
Not infected mice-2

library_source: transcriptomic single cell

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).

value: uninfected


title: 67T-Run5850.2186.1-FOV_22

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_22.rds


title: Hh123

city: Kyoto

first: Yoshinori

last: Yoshida

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

country: Japan

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: 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: Hh121


title: colon_infected_d7_rep2

description: Library name: D7-2


title: 64N-Normal_A-FOV_22

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_22.rds


title: colon_infected_d1_rep2

description:
Library name: A27_d1
Mice on the 1st day after Salmonella infection-2

value: infected by Salmonella d1


title: STEPN-58_Region_2

value: Fresh frozen in-situ

value: Recurrence

value: Ependymoma


title: Hh119


title: STEPN-57_Region_1

value: ZFTA-RELA


title: colon_infected_d7_rep1

description: Library name: D7-1


title: 137T-3461G-FOV_22

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_22.rds

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

value: Colon tumour,FFPE

value: rectal


title: Hh118


title: Hh145


title: colon_infected_d5_rep3

description: Library name: D5-3


title: STEPN-58_Region_1


title: 278T-148191A-FOV_22

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_22.rds

value: M

value: pMMR

value: LHS


title: Hh116


title: 280T-120131-FOV_22

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_22.rds

value: F


title: STEPN-56_Region_1


title: colon_infected_d5_rep2

description: Library name: D5-2

value: colon

value: female

value: infected by Salmonella


title: Hh114


title: STEPN-55_Region_2

source_name: Ependymoma, Primary

value: Primary


title: Hh112


title: 64T-Tumour_B-FOV_21

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_21.rds

value: caecum

value: RHS


title: STEPN-48_Region_2


title: colon_infected_d3_rep3

description: Library name: D3-3

value: 6-8 weeks old


title: Hh111

value: Right ventricular septum


title: 150T-Tumour_A-FOV_21

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_21.rds

value: transverse


title: STEPN-54_Region_2

value: Fresh frozen in-situ

value: Ependymoma


title: 67T-Run5850.2186.2-FOV_21

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_21.rds

value: Colon tumour,FFPE

value: sigmoid


title: colon_infected_d3_rep1

description: Library name: D3-1


title: Hh103


title: STEPN-55_Region_1

value: ZFTA-RELA


title: colon_infected_d1_rep3

description: Library name: D1-3


title: STEPN-49_Region_2

value: M


title: 64N-Normal_A-FOV_21

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_21.rds

value: pMMR


title: colon_infected_d1_rep2

description: Library name: D1-2


title: 67T-Run5850.2186.1-FOV_21

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_21.rds

value: LHS


title: STEPN-48_Region_1

value: F


title: Hh100


title: Hh93


title: colon_infected_d5_rep1

description: Library name: D5-1

value: colon

value: female


title: STEPN-54_Region_1

value: Primary


title: 130T-10501A-FOV_22

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_22.rds

value: rectum upper


title: colon_uninfected_d0_rep3

description: Library name: ctrl-3

value: uninfected


title: Hh90


title: 137T-3461G-FOV_21

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_21.rds

value: rectal


title: STEPN-49_Region_1


title: 278T-148191A-FOV_21

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_21.rds


title: colon_infected_d3_rep2

description: Library name: D3-2

value: infected by Salmonella

value: 6-8 weeks old


title: 280T-120131-FOV_21

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_21.rds

value: caecum

value: RHS


title: colon_uninfected_d0_rep2

description: Library name: ctrl-2


title: Hh104

value: Right ventricular septum


title: Hh88


title: Hh80


title: colon_uninfected_d0_rep1

description: Library name: ctrl-1


title: STEPN-52_Region_3

value: Fresh frozen in-situ

value: Ependymoma


title: STEPN-51_Region_4

value: M

value: Recurrence

value: ZFTA-RELA


title: 64T-Tumour_B-FOV_20

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_20.rds

value: Colon tumour,FFPE

value: F

value: pMMR


title: Hh76


title: control group C_3

city: chongqing

first: Wanli

last: Yu

address: 118 Xingguang Avenue, Liangjiang New District, Chongqing

institute: chongqing medical university

description: Library name: sample9

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: cell

tag: cell line

value: HT-22 Mouse Hippocampal Neuronal Cell Line

tag: cell type

value: Hippocampal nerve cells


title: 130T-10501A-FOV_21

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_21.rds

value: rectum upper

value: LHS


title: STEPN-53_Region_4

tag: age

value: Primary


title: control group C_2

description: Library name: sample8


title: colon_infected_d1_rep1

description: Library name: D1-1

value: colon

value: female

value: infected by Salmonella

value: 6-8 weeks old


title: 67T-Run5850.2186.2-FOV_20

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_20.rds

value: sigmoid


title: control group C_1

description: Library name: sample7


title: Hh74

value: Right ventricular septum


title: intervention group B_2

description: Library name: sample5


title: intervention group B_3

description: Library name: sample6


title: Hh89


title: STEPN-50_Region_3

tag: gender

value: M

value: Fresh frozen in-situ

value: Recurrence

value: Ependymoma


title: 67T-Run5850.2186.1-FOV_20

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_20.rds

value: Colon tumour,FFPE

value: pMMR


title: 64N-Normal_A-FOV_20

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_20.rds

value: F

value: caecum

value: RHS


title: STEPN-51_Region_3

tag: type

value: ZFTA-RELA


title: intervention group B_1

description: Library name: sample4

value: cell

value: HT-22 Mouse Hippocampal Neuronal Cell Line

value: Hippocampal nerve cells


title: STEPN-51_Region_2

tag: sampling


title: 137T-3461G-FOV_20

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_20.rds

value: rectal

value: LHS


title: STEPN-52_Region_2

value: Primary

tag: fusion


title: Hh69

value: Right ventricular septum


title: Hh71


title: experimental group A_3

description: Library name: sample3


title: Hh68


title: 278T-148191A-FOV_20

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_20.rds

value: M


title: 280T-120131-FOV_20

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_20.rds


title: 150T-Tumour_A-FOV_20

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_20.rds

value: transverse


title: experimental group A_2

description: Library name: sample2


title: Hh62


title: STEPN-50_Region_2

value: Fresh frozen in-situ

value: Recurrence

tag: subtype


title: STEPN-51_Region_1

tag: tissue

value: Ependymoma


title: Hh66


title: experimental group A_1

description: Library name: sample1


title: 130T-10501A-FOV_20

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_20.rds

value: Colon tumour,FFPE

tag: donor

value: rectum upper

value: pMMR


title: STEPN-53_Region_2


title: Hh60


title: Hh75


title: CTX_3, CUT&Tag

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

institute: Jinan University

description: Library name: Sample1

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: Cortex

extract_protocol:
Fresh virus-infected cortical regions 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 7 days after virus injection using FACS.
CUT&Tag libraries were prepared using CUT&Tag-IT™ Assay Kit (Active Motif, catalog No. 53160)

treatment_protocol: Adult mice were injected with AAV9 hGFAP::Ngn2-P2A-tdTomato in the cortex

value: Cortex

tag: time

value: 7 dpi

value: Sorted tdTomato+ cells

tag: cut&tag antibody

value: Olig2 (EMD/Millipore, #AB9610)


title: STEPN-53_Region_3

value: ZFTA-RELA


title: STEPN-50_Region_1


title: 118T-Tumour_A-FOV_2

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118T-Tumour_A-FOV_2.rds

tag: Sex

tag: age at diagnosis

tag: primary tumour location

value: caecum

value: RHS


title: Hh59


title: STEPN-52_Region_1

value: F

value: Primary


title: 73T-Tumour_B-FOV_2

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73T-Tumour_B-FOV_2.rds

value: M

value: sigmoid

tag: total cells

tag: mmr status

tag: sidedness

value: LHS


title: 142N-Run5850.2186.2-FOV_2

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.2-FOV_2.rds

value: ascending

value: dMMR


title: Hh57

value: Right ventricular septum


title: Hh55


title: STEPN-53_Region_1

value: Fresh frozen in-situ

value: Ependymoma


title: NC, scRNA-seq

description: Library name: Sample1

data_processing:
Raw reads were processed with fastQC and fastp to remove low quality reads. Poly-A tails and adaptor sequences were removed by Cutadapt. After quality control, reads were mapped to the reference genome using STAR. Gene counts and UMI counts were acquired by FeatureCounts software. Expression matrix files for subsequent analyses were generated based on gene counts and UMI counts.
Assembly: mm10
Supplementary files format and content: matrix.tar containing matrix.mtx, genes.tsv, and barcodes.tsv

extract_protocol:
Fresh virus-infected cortical regions were removed with tweezers and then dissociated into single cell suspension using the papain system (Worthington) according to manufacturer’s protocol. The cell suspension was injected into the SCOPE-chip™ microfluidic chip to complete the separation of single cells based on the principle of "Poisson distribution". Cells fell into specially customized chip microwells under the influence of gravity, ensuring that only one cell fell into each microwell.
The magnetic beads in the chip were collected, and the mRNA captured by the magnetic beads was reverse transcribed into cDNA and amplified. After cDNA fragmentation, adapter ligation and other necessary steps, a sequencing library suitable for the Illumina sequencing platform was constructed.

treatment_protocol: Adult mice were injected with AAV9 hGFAP::Ngn2-P2A-tdTomato+scramble shRNA or +Olig2 shRNA in the cortex

value: Cortex

tag: cell type

value: Brain cells

tag: stain

tag: treatment

value: AAV9-GFAP::Ngn2-P2A-tdTomato + AAV9-U6::scramble shRNA


title: 142N-Run5850.2186.1-FOV_2

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_2.rds

value: Colon tumour,FFPE


title: STEPN-47_Region_3

tag: age

tag: gender

tag: type

value: ZFTA-RELA


title: Hh54


title: STEPN-47_Region_2

tag: sampling

tag: fusion

tag: subtype


title: WT aneurysm tissue d7_1

city: Cologne

first: Patrik

last: Schelemei

address: Kerpener Str. 62

department: Internal Med III

country: Germany

institute: University Hospital Cologne

description:
Library name: WT1
Column name in Olfr2_AAA_d7_gene_counts.txt: A291WT
A291WT

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

source_name: Abdominal Aorta

extract_protocol:
Aortas were homogenized in Trizol buffer and RNA was extracted using the RNeasy micro plus kit (Qiagen).
RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. The cDNA samples were then fragmented, end-repaired, A-tailed, and ligated with Illumina adaptors. After size selection and PCR enrichment, the library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

tag: tissue

value: Abdominal Aorta

tag: genotype

value: WT

value: day 7 after aneurysm induction


title: Hh53


title: STEPN-47_Region_1

value: Primary


title: 118N-148191A-FOV_2

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118N-148191A-FOV_2.rds

tag: donor

tag: Sex

value: M

value: caecum

value: pMMR

value: RHS


title: NC-3461G-FOV_2

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:
NC-3461G-FOV_2.rds

tag: age at diagnosis

tag: primary tumour location


title: Hh52


title: STEPN-46_Region_2


title: Olfr2 KO aneurysm tissue d7_3

description:
Library name: KO3
Column name in Olfr2_AAA_d7_gene_counts.txt: A599KO
A599KO

value: Olfr2 KO


title: STEPN-46_Region_1


title: Olfr2 KO aneurysm tissue d7_2

description:
Library name: KO2
Column name in Olfr2_AAA_d7_gene_counts.txt: A580KO
A580KO


title: Hh51

value: Right ventricular septum


title: NC-120131-FOV_2

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
NC-120131-FOV_2.rds

tag: total cells

tag: mmr status


title: Hh48


title: Olfr2 KO aneurysm tissue d7_1

description:
Library name: KO1
Column name in Olfr2_AAA_d7_gene_counts.txt: A527KO
A527KO


title: STEPN-45_Region_2

value: Fresh frozen in-situ


title: 74T-10501A-FOV_2

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
74T-10501A-FOV_2.rds

value: descending colon

value: dMMR

tag: sidedness

value: LHS


title: 64T-Tumour_B-FOV_19

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_19.rds

value: F


title: Hh46


title: STEPN-45_Region_1

value: Ependymoma


title: 150T-Tumour_A-FOV_19

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_19.rds

value: Colon tumour,FFPE

value: transverse


title: 170N-Normal_A-FOV_2

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170N-Normal_A-FOV_2.rds

value: sigmoid


title: WT aneurysm tissue d7_3

description:
Library name: WT3
Column name in Olfr2_AAA_d7_gene_counts.txt: A778WT
A778WT

value: Abdominal Aorta

value: WT

value: day 7 after aneurysm induction


title: STEPN-15_Region_1

value: Recurrence

value: ZFTA-RELA


title: ChIP_OCR_PU.1_rep1

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description:
Library name: Sample 46
ChIP_Spi1_Thermo_OCR

data_processing:
cutadapt
STAR alignment (RNA-seq)
BWA-mem alignment (ATAC-seq, ChIP-seq)
featureCount, gene-level extraction (RNA-seq), macs2 peak-calling (ATAC-seq,ChIP-seq)
Assembly: mm10
Supplementary files format and content: text file

source_name: Bone marrow

extract_protocol:
RNA was purified with TRIzol TM Reagent (Invitrogen, 15596026) and Direct-zol RNA microprep (Zymo R2060)
RNA-seq libraries were constructed using SMARTer Standard total RNA-seq kit v2
The engineered hyperactive Tn5 transposase that is preloaded with DNA adapters thus removing the need for a separate annealing step.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

tag: cell type

value: Hematopoietic stem cell

value: CR treatment


title: ChIP_OWT_PU.1_rep1

description:
Library name: Sample 47
ChIP_Spi1_Thermo_OWT

tag: treatment

value: control


title: WT aneurysm tissue d7_2

description:
Library name: WT2
Column name in Olfr2_AAA_d7_gene_counts.txt: A292WT
A292WT


title: ChIP_OCRRF_PU.1_rep1

description:
Library name: Sample 45
ChIP_Spi1_Thermo_OCRRF

value: CR refeed


title: Hh36

value: Right ventricular septum


title: ChIP_OCR_H3K4me3_rep2

description:
Library name: Sample 44
ChIP_OCR_H3K4me3_rep2


title: 67T-Run5850.2186.1-FOV_19

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_19.rds

value: M

value: pMMR

value: LHS


title: STEPN-10_Region_3

tag: age

value: F

value: Fresh frozen in-situ

value: Primary

value: Ependymoma


title: Hh30


title: ChIP_OCR_H3K4me3_rep1

description:
Library name: Sample 43
ChIP_OCR_H3K4me3_rep1

value: WT


title: 64N-Normal_A-FOV_19

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_19.rds

value: Colon tumour,FFPE

value: caecum

value: RHS


title: Hh24


title: ChIP_OCR_H3K27me3_rep2

description:
Library name: Sample 42
ChIP_OCR_H3K27me3_rep2

value: Bone marrow


title: STEPN-06_Region_5

tag: gender

value: ZFTA-RELA


title: 137T-3461G-FOV_19

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_19.rds

value: rectal


title: STEPN-06_Region_4

tag: type


title: Hh39


title: 278T-148191A-FOV_19

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_19.rds


title: CD8 T cell, DMSO, 02

city: Melbourne

first: Rachel

last: Pascoe

state: VIC

address: 792 Elizabeth Street

department: Microbiology and Immunology

institute: University of Melbourne

data_processing:
Bulk sequencing reads were aligned to the GRCh38 reference genome and transcriptome using the STAR aligner (version 2.7.8a)
Aligned read files were sorted and indexed using samtools
Indexed Bam files were gene counted using featureCounts (version 2.0.0)
Assembly: Ensembl GRCh38/107
Supplementary files format and content: tab delimited text
Supplementary files format and content: Differential_analysis_donors.txt contains the data on the differential gene expression for each donor, shown as pomalidomide-treated conditon relative to DMSO-treated condition.

source_name: PBMC from HIV-negative individual

growth_protocol: Cells were cultured for 13 days in supplemented RPMI, in the presence of 10 U/mL IL-2, 1 uM raltegravir. Media was changed every 48 hours.

extract_protocol:
RNA was harvested using Qiagen RNeasy Plus Micro kit (Cat. 74034), per manufacturer's conditions.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Library Prep Kit following manufacturers protocols.

treatment_protocol: PBMC were treated with either pomalidomide (0.25 uM) or DMSO vehicle control. Half media changes were performed every 48 hours to maintain drug exposure.

value: PBMC from HIV-negative individual

value: CD8+ T cells

value: No treatment


title: 280T-120131-FOV_19

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_19.rds


title: CD8 T cell, DMSO, 01


title: ATAC_OCR_rep4

description:
Library name: Sample 40
ATAC_OCR_rep4

value: Hematopoietic stem cell

value: CR treatment


title: ChIP_OCR_H3K27me3_rep1

description:
Library name: Sample 41
ChIP_OCR_H3K27me3_rep1


title: Hh38

value: Right ventricular septum


title: STEPN-01_Region_2

value: F

tag: sampling


title: ATAC_OCR_rep3

description:
Library name: Sample 39
ATAC_OCR_rep3


title: STEPN-01_Region_3

value: Fresh frozen in-situ

tag: fusion


title: 67T-Run5850.2186.2-FOV_19

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_19.rds

value: M

value: sigmoid

value: pMMR

value: LHS


title: 130T-10501A-FOV_19

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_19.rds

value: Colon tumour,FFPE

value: rectum upper


title: STEPN-12_Region_4

value: Primary

value: Ependymoma

tag: subtype


title: HIV-specific CD8 T cell, Pom, PRA009

source_name: PBMC from person living with HIV on suppressive ART

tag: tissue

value: HIV-specific CD8+ T cells

value: Pom


title: STEPN-01_Region_1

value: ZFTA-RELA


title: HIV-specific CD8 T cell, DMSO, PRA009

value: PBMC from person living with HIV on suppressive ART

value: DMSO


title: 150T-Tumour_A-FOV_18

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_18.rds

value: transverse

value: RHS


title: sh, scRNA-seq

description: Library name: Sample2

value: Cortex

tag: time

value: Brain cells

tag: stain

value: AAV9-GFAP::Ngn2-P2A-tdTomato + AAV9-U6::Olig2 shRNA1-U6::Olig2 shRNA2-U6::Olig2 shRNA3


title: STEPN-16_Region_1

value: F

value: FFPE in-situ


title: ATAC_OCR_rep2

description:
Library name: Sample 38
ATAC_OCR_rep2

value: Bone marrow

value: Hematopoietic stem cell

tag: genotype

value: WT

value: CR treatment


title: ATAC_OCR_rep1

description:
Library name: Sample 37
ATAC_OCR_rep1


title: 67T-Run5850.2186.2-FOV_18

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_18.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

value: sigmoid

value: pMMR

value: LHS


title: HIV-specific CD8 T cell, DMSO, PRA007

value: PBMC from person living with HIV on suppressive ART

value: HIV-specific CD8+ T cells

value: DMSO


title: ATAC_OCRRF_rep2

description:
Library name: Sample 36
ATAC_OCRRF_rep2

value: CR refeed


title: STEPN-19_Region_1

value: Recurrence

value: Ependymoma

value: ZFTA-RELA


title: HIV-specific CD8 T cell, Pom, PRA004

value: Pom


title: ATAC_OCRRF_rep1

description:
Library name: Sample 35
ATAC_OCRRF_rep1

value: Bone marrow


title: 137T-3461G-FOV_18

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_18.rds

value: F

tag: primary tumour location

value: rectal

tag: total cells

tag: mmr status


title: 73N-Normal_A-FOV_18

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:
73N-Normal_A-FOV_18.rds

tag: sidedness


title: STEPN-14_Region_1

tag: age

value: FFPE in-situ


title: STEPN-12_Region_3

tag: gender

value: Fresh frozen in-situ

value: Primary


title: 278T-148191A-FOV_18

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_18.rds

value: Colon tumour,FFPE

value: M


title: mRNAseq_GFP_Scramble_rep1

description:
Library name: Sample 33
mRNAseq_GFP_Scramble_rep1

tag: cell type

value: Hematopoietic stem cell

tag: treatment

value: control


title: STEPN-12_Region_1

tag: type

tag: sampling

tag: fusion


title: HIV-specific CD8 T cell, Pom, LKA12

tag: tissue

value: PBMC from person living with HIV on suppressive ART

value: HIV-specific CD8+ T cells


title: mRNAseq_GFP_Scramble_rep2

description:
Library name: Sample 34
mRNAseq_GFP_Scramble_rep2


title: mRNAseq_GFP_Kdr_shRNA_rep4

description:
Library name: Sample 32
mRNAseq_GFP_Kdr_shRNA_rep4


title: HIV-specific CD8 T cell, Pom, PRA007


title: HIV-specific CD8 T cell, DMSO, PRA004

value: DMSO


title: 130T-10501A-FOV_18

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_18.rds

value: rectum upper

value: pMMR

value: LHS


title: HIV-specific CD8 T cell, Pom, UCSF-3162

value: Pom


title: HIV-specific CD8 T cell, DMSO, LKA12


title: STEPN-12_Region_2

value: Ependymoma

tag: subtype

value: ZFTA-RELA


title: STEPN-19_Region_2

value: Recurrence


title: HIV-specific CD8 T cell, DMSO, UCSF-3162


title: mRNAseq_GFP_Kdr_shRNA_rep2

description:
Library name: Sample 30
mRNAseq_GFP_Kdr_shRNA_rep2

value: Bone marrow

tag: genotype


title: 64T-Tumour_B-FOV_17

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_17.rds

tag: donor

value: F

value: caecum

value: RHS


title: mRNAseq_GFP_Kdr_shRNA_rep3

description:
Library name: Sample 31
mRNAseq_GFP_Kdr_shRNA_rep3


title: STEPN-10_Region_1

value: Fresh frozen in-situ

value: Primary


title: mRNAseq_GFP_Kdr_shRNA_rep1

description:
Library name: Sample 29
mRNAseq_GFP_Kdr_shRNA_rep1

value: Hematopoietic stem cell

value: control


title: 150T-Tumour_A-FOV_17

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_17.rds

value: Colon tumour,FFPE

tag: Sex

value: transverse


title: 67T-Run5850.2186.1-FOV_18

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_18.rds

value: M

tag: age at diagnosis

value: sigmoid


title: HIV-specific CD8 T cell, DMSO, UCSF-2651

value: PBMC from person living with HIV on suppressive ART

value: HIV-specific CD8+ T cells

value: DMSO


title: 280T-120131-FOV_18

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_18.rds

tag: primary tumour location

value: pMMR


title: 67T-Run5850.2186.2-FOV_17

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_17.rds

tag: total cells

value: LHS


title: STEPN-06_Region_2

value: Ependymoma

value: ZFTA-RELA


title: mRNAseq_Double_Scramble_rep2

description:
Library name: Sample 28
mRNAseq_Double_Scramble_rep2

value: Bone marrow


title: 67T-Run5850.2186.1-FOV_17

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_17.rds

tag: mmr status


title: CSE-treated3

city: Daejeon

first: Heerim

last: Yeo

address: 99, Daehak-ro, Yuseong-gu

country: South Korea

institute: Chungnam National University

description: Library name: SM3

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: MC38 tumor tissue

growth_protocol: MC38 cells were grown in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/ml streptomycin at 37°C in a humidified atmosphere containing 5% CO2. MC38 tumor-bearing mice were established by injecting MC38 cells into the right flank subcutaneously of specific pathogen-free 6-week-old female C57BL/6 mice. Mice were housed under controlled environmental conditions of temperature (23°C), humidity (50%), and a 12-h light/dark cycle. The animals were fed a standard chow diet and provided free access to drinking water.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The mice were administrated 100 mg/kg of CSE daily via oral gavage, while control mice received the same volume of 1% CMC in DW.

value: MC38 tumor tissue

tag: cell line

value: Tumor cells


title: mRNAseq_Double_KdrBmpr_shRNA2_rep2

description:
Library name: Sample 26
mRNAseq_Double_KdrBmpr_shRNA2_rep2


title: STEPN-06_Region_1

tag: age

value: Fresh frozen in-situ

value: Primary


title: STEPN-10_Region_2

tag: gender

value: F


title: mRNAseq_Double_Scramble_rep1

description:
Library name: Sample 27
mRNAseq_Double_Scramble_rep1

tag: cell type

value: Hematopoietic stem cell

value: control


title: CSE-treated2

description: Library name: SM2


title: 73N-Normal_A-FOV_17

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:
73N-Normal_A-FOV_17.rds

value: Colon tumour,FFPE

value: M

tag: sidedness


title: STEPN-17_Region_1

tag: type

value: FFPE in-situ

value: Recurrence


title: 137T-3461G-FOV_17

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_17.rds

value: rectal


title: CSE-treated1

description: Library name: SM1


title: 278T-148191A-FOV_17

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_17.rds

value: pMMR


title: mRNAseq_Double_KdrBmpr_shRNA2_rep1

description:
Library name: Sample 25
mRNAseq_Double_KdrBmpr_shRNA2_rep1

tag: treatment


title: Control3

description: Library name: CON4


title: ST-deltamsbB-2

city: College Station

first: Ling

last: Yang

state: TX

address: 206 Olsen Blvd, Reynolds HSC  Rm159

institute: Texas A&M university

description: Library name: msbB2

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: S. Typhimurium 14028 reference genome (NC_016856.1)
Supplementary files format and content: TSV files include FPKM values for each Sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: ATCC 14028S mutant

growth_protocol: Single coloby of each bacteria strain was innoclated in 5mL fresh LB, and cultured at 37℃ overnignt

extract_protocol:
RNA were extracted by using QIANGEN Rneasy mini kit following the manufacturing guidelines
libraries were prepared with the TruSeq Stranded Total RNA kit

tag: strain

value: deltamsbB


title: Control2

description: Library name: CON3

tag: tissue


title: ST-deltamsbB-1

description: Library name: msbB1


title: ST-wildtype-2

description: Library name: WT2

source_name: ATCC 14028S

value: wildtype


title: STEPN-06_Region_3

tag: sampling

tag: fusion

value: Ependymoma

tag: subtype

value: ZFTA-RELA


title: mRNAseq_Double_KdrBmpr_shRNA1_rep1

description:
Library name: Sample 23
mRNAseq_Double_KdrBmpr_shRNA1_rep1

value: Bone marrow

tag: genotype


title: HIV-specific CD8 T cell, Pom, UCSF-2651

value: PBMC from person living with HIV on suppressive ART

value: HIV-specific CD8+ T cells

value: Pom


title: mRNAseq_Double_KdrBmpr_shRNA1_rep2

description:
Library name: Sample 24
mRNAseq_Double_KdrBmpr_shRNA1_rep2


title: Control1

description: Library name: CON1

value: MC38 tumor tissue

value: Tumor cells


title: 280T-120131-FOV_17

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_17.rds

tag: donor

tag: Sex

value: F

tag: age at diagnosis

value: caecum

value: RHS


title: 130T-10501A-FOV_17

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_17.rds

value: Colon tumour,FFPE

tag: primary tumour location

value: rectum upper

tag: total cells

tag: mmr status

value: LHS


title: mRNAseq_OAL_rep4

description:
Library name: Sample 22
mRNAseq_OWT_rep4

value: Hematopoietic stem cell

value: WT

value: control