title: 92T-10501A-FOV_33

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
92T-10501A-FOV_33.rds

value: Colon tumour,FFPE

value: caecum

value: dMMR

value: RHS


title: Total RNA, biol rep1, glucose replete condition, timepoint 10

status: Public on Dec 09 2025

type: SRA

city: Manchester

first: Christopher

last: Grant

state: Greater Manchester

address: Oxford Rd

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: University of Manchester

description:
Library name: Total_Rep1_Gplus_T10
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gplus, T10

library_source: transcriptomic

data_processing:
Sequence reads were trimmed, quality-filtered, and aligned to the S. cerevisiae W303 genome using NextGenMap. T→C conversions were quantified using the SLAM-DUNK pipeline. All computational steps were executed using a customized Nextflow implementation of nf-core/slamseq.
Count matrices were generated for all samples. For total RNA datasets, time-course profiles were corrected for technical batch effects using an internal batch covariate model. In addition, 4TU-labelling efficiencies were calibrated using a set of ∼100 transcripts not expressed under glucose-replete conditions; their total versus labelled RNA counts were used to derive time-dependent efficiency factors, which were applied to normalize incorporation differences during glucose depletion.
Assembly: S. cerevisiae W303
Supplementary files format and content: xlsx files include labelled readcounts and unlablled readcounts in separate tabs for each sample

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae strains were derivatives of W303-1A (MATa ura3-52 leu2-3 leu2-112 trp1-1 ade2-1 his3-11 can1-100). Cells were maintained in synthetic complete dextrose (SCD) medium (2% glucose, 0.67% yeast nitrogen base) supplemented with amino acids. For glucose starvation conditions, cultures were switched to synthetic complete medium lacking glucose.

extract_protocol:
Total RNA extraction: Cell pellets were snap-frozen and lysed in TRIzol with glass bead disruption, followed by phenol-chloroform extraction, isopropanol precipitation, DNase I treatment, and ethanol purification. RNA quality was assessed by Qubit (RNA HS) and TapeStation 4200.  P-body RNA extraction: Cells were lysed in Blob100 buffer with RNase inhibitors and protease inhibitors. High-molecular-weight complexes were pelleted, and P-bodies were immunoprecipitated using anti-Myc magnetic beads. After stringent Blob500 and Blob100 washes, bound RNA was released by Proteinase K treatment, crosslinks reversed, and RNA extracted using the RiboPure Yeast Kit. DNase I treatment and purification were performed as above.
Incorporated 4TU residues were alkylated with 10 mM iodoacetamide in 30% DMSO at room temperature for 15 min, quenched with DTT, and ethanol-precipitated. Strand-specific 3′ mRNA libraries were prepared using the Lexogen QuantSeq 3′ mRNA-Seq V2 (FWD) kit with Unique Dual Indices. Libraries were amplified (13–15 PCR cycles), purified, quantified, and sized prior to pooling. Sequencing was performed on an Illumina NovaSeq 6000.

treatment_protocol: For SLAM-seq time-course experiments, exponentially growing cells (OD₆₀₀ 0.6–0.8) were harvested, washed, and resuspended in pre-warmed SC (glucose-deplete) or SCD (glucose-replete) medium as appropriate. Newly synthesized RNA was labeled by addition of 2 mM 4-thiouracil (4TU). Samples were collected at 0, 2.5, 5, 10, 20, and 40 minutes. For P-body IP RNA, Dcp1-Myc–expressing strains were 4TU-labelled and crosslinked in 0.8% formaldehyde prior to immunoprecipitation.

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose replete

tag: batch

value: Total, Rep1


title: Hb_suscetibleM3

city: Princeton

first: Adelaide

last: Minerva

state: New Jersey

address: Washington Road

department: Princeton Neuroscience Institute

country: USA

institute: Princeton University

description:
Library name: Hb_suscetibleM3
10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, and gene counting were done using CellRanger software v6.1.1 or v7.1.0 (10X Genomics) using the --include-introns flag
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
For VTA, bilateral punches from two animals of the same sex and condition were pooled together and Dounce homogenized. Pairs were selected randomly from within each sex and condition. Pooling ensured a high enough concentration of nuclei per sample for quality sequencing. The sample was filtered through a 40um strainer and nuclei were isolated via iodixanol gradient centrifugation.  For habenula, a single punch over the midline was taken per animal and each sample contained tissue from only one animal. The sample was filtered through a 40um strainer and nuclei were isolated via pellet centrifugation.  Nuclei from both brain regions were hand-counted using a hemocytometer on an EVOS M5000 microscope and final concentrations were ~1,000 nuclei per ul. The volume of suspension used for library preparation was adjusted in order to load a target of 20,000 nuclei and capture 10,000 nuclei per sample.
Library construction was performed according to the manufacturer's instructions (10X Genomics Chromium v3). Briefly, nuclei were resuspended in the master mix and loaded together with partioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the lysate contained in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequence, unique molecular identifier (UMI), and the 10X barcode. The pooled and barcoded cDNA was then cleaned up with Silance DynaBeads, amplified by PCR, and the appropriate sized fragments were selected qith SPRIselect reagent for subsequent library construction. During library construction the Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

tag: tissue

value: Brain

tag: tissue region

value: Hb

value: Wild type

tag: phenotype

value: susceptible

tag: Sex

value: male


title: SAM24386177

city: South San Francisco

first: Dorothee

last: Nickles

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Sequencing data were processed using HTSeqGenie as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed; subsequently reads that passed QC were aligned to the reference genome GRCh38 usingGSNAP.
Assembly: mm10
Supplementary files format and content: raw fastq files are provided, as well as normalized log2 counts in a gene x sample format

molecule: total RNA

source_name: colon

growth_protocol: Cell lines were cultured in RPMI-1640 medium containing 10% heat-inactivated fetal bovine serum (FBS) and 2 mM L-glutamine (Gibco). Cell lines were kept at low passages and tested negative for Mycoplasma.

extract_protocol:
Total RNA was extracted from sorted tumor cells using the Qiagen All Prep nucleic isolation kit (Qiagen, Inc.; catalog number 80204, Valencia, CA) as per the manufacturer’s protocol, including the on-column DNase digestion. Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific catalog#: Q32852) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies catalog#: 5067-5576).
150 picograms of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina catalog#: FC-131-1024). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific catalog#: Q32851) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies catalog#: 5067-5582).Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pairreads for each sample.

value: colon

tag: cell type

value: tumor

value: M1E5 Zfx F5


title: 73N-Run5850.2186.2-FOV_32

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:
73N-Run5850.2186.2-FOV_32.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

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: donor

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: 73T-Run5850.2186.1-FOV_32

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73T-Run5850.2186.1-FOV_32.rds

value: Colon tumour,FFPE


title: Total RNA, biol rep1, glucose replete condition, timepoint 5

description:
Library name: Total_Rep1_Gplus_T5
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gplus, T5


title: Hb_suscetibleM2

description:
Library name: Hb_suscetibleM2
10X Genomics


title: 137T-3461G-FOV_32

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_32.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: F

value: rectal


title: SAM24386176


title: Total RNA, biol rep1, glucose replete condition, timepoint 2.5

description:
Library name: Total_Rep1_Gplus_T2_5
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gplus, T2.5

value: WT

value: Glucose replete


title: SAM24386168

value: M1E5 WT


title: Hb_susceptibleM1

description:
Library name: Hb_susceptibleM1
10X Genomics

value: Brain

value: Hb


title: 278N-148191A-FOV_32

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:
278N-148191A-FOV_32.rds


title: SAM24386175


title: 170T-120131-FOV_32

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170T-120131-FOV_32.rds


title: Total RNA, biol rep1, glucose replete condition, timepoint 0

description:
Library name: Total_Rep1_Gplus_T0
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gplus, T0

value: Total, Rep1


title: Hb_susceptibleF2

description:
Library name: Hb_susceptibleF2
10X Genomics

value: Wild type

value: susceptible

value: female


title: 92T-10501A-FOV_32

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
92T-10501A-FOV_32.rds

value: caecum

value: dMMR

value: RHS


title: Gg9

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Library name: Sample 9

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the Giraffa camelopardalis rothschildi (ASM1759144v1) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized.
Assembly: ASM1759144v1
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

molecule: genomic DNA

organism: Giraffa giraffa angolensis

source_name: buccal

growth_protocol: The collection of giraffe samples was conducted by the Giraffe Conservation Foundation working in collaboration with partners across Namibia and South Sudan. The two giraffe species had samples collected from Okonjati Game Reserve in Namibia (Angolan giraffe Giraffa giraffa angolensis, subspecies of southern giraffe) and the Boma Bandingilo Jonglei Landscape of South Sudan (Kordofan giraffe G. camelopardalis, subspecies of northern giraffe).

extract_protocol:
Genomic DNA was isolated from giraffe buccal cells using a protocol involving proteinase treatment, protein precipitation, and DNA precipitation in isopropanol. Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed. Individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 ºC, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP (immunoprecipitation) buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 ºC. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50 μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 ºC. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2 μl of glycoblue (20 mg/ml), 20 μl of 5M NaCl and 500 μl ethanol were added and mixed well, then precipitated at -20 ºC for 1 hour to overnight. The precipitate was centrifuged at 14,000 rpm for 20 min at 4 ºC and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500 μl cold 70% ethanol in a -20 ºC freezer for 15 min then centrifuged again at 14,000 rpm for 5 min at 4 ºC and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20 μl H2O or TE. DNA concentration was measured in a Qubit device (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: Buccal swab collection brushes (CytoSoft Brush 1 CP-5B, Medical Packaging Corp., Carmillo, CA, USA) were brushed against the inside cheek surfaces of the anesthetized giraffe for one minute. The samples were stored in the buccal cell brush collection tube on ice or refrigerator for transportation and then stored frozen at -20º C at the collection site. The samples were heat-treated at 72-75º C for 30-35 minutes of moist heat to reduce the chance of harboring viral pathogens, then transported frozen to the USA and stored at -80º C until analysis. Buccal swabs were also obtained from two captive Okapis from the White Oak Conservation Centre in Florida, USA. The Material Transfer Agreement (MTA) for the San Diego Zoo and White Oak Conservation Center with Washington State University were arranged and established.

value: buccal

value: Female


title: Hb_resilientF2

description:
Library name: Hb_resilientF2
10X Genomics

value: resilient


title: Gg8

description: Library name: Sample 8


title: Hb_resilientF1

description:
Library name: Hb_resilientF1
10X Genomics


title: SAM24386166

value: colon

value: tumor


title: sorted CD3- CD56+ cells from tonsillar explant, HIV-infected

city: Barcelona

first: María José

last: Buzón Gómez

state: Barcelona

address: Passeig Vall d'Hebron, 119-129

department: Infectious Diseases

country: Spain

institute: Vall d'Hebron Research Institute

description:
Library name: L760
10x Genomics

data_processing:
CellRanger software v8.0.1 was used to perform the alignment, filtering, barcode counting, and UMI counting for each library. Available online at: https://support.10xgenomics.com/single-cell-gene-expression/software/
Seurat v4.3 ecosystem was used for single cell count data quality control, analysis and exploration. Available online at: https://satijalab.org/seurat/
SingleR v1.10 was used for reference-based single-cell RNA-seq annotation. Available online at: https://github.com/SingleR-inc/SingleR
slingshot v2.4 was used for trajectory analysis. Available online at: https://github.com/kstreet13/slingshot
During the initial clustering steps, we identified a small cluster (55 cells in L759 and 62 cells in L760) that was automatically annotated as B cells by the SingleR method using the Monaco Immune Data Set as a reference. We excluded these potentially contaminating B cells from subsequent analyses
Assembly: Human reference GRCh38 - 2024-A
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
HIV-1 group M

source_name: Tonsils

extract_protocol:
To prepare tonsillar cell suspensions, 12 tissue blocks were placed into 1.5 mL Eppendorf tubes containing 400 µL of RPMI-1640 medium supplemented with 5% FBS (R5 medium). The tissues were mechanically digested using pestles (Labolan) attached to a handheld homogenizer (Labolan). The resulting cell suspensions were filtered sequentially through 70 µm cell strainers (LabClinics) and 30 µm CellTrics® filters (Sysmex) to remove debris. Filtered cells were washed twice with 1X PBS, and residual red blood cells were lysed using ACK Lysis Buffer (Fisher Scientific). Cell count and viability were evaluated with the LUNA Automated Cell Counter (Logos Biosystems). CD56+ cells were enriched from both HIV-infected and uninfected tissue suspensions using the MagniSort™ Human CD56 Positive Selection Kit. After enrichment, the cells were washed and resuspended in 1X PBS for viability assessment with LIVE/DEAD Viability dye, incubated for 20 minutes. Subsequently, the cells were washed, resuspended in a staining buffer (1X PBS with 3% FBS), and labeled with surface antibodies targeting lineage markers. Finally, the stained cells were washed again in staining buffer and resuspended in PBS containing 0.04% BSA. The CD3-CD56+ cell population was sorted from the tonsillar CD56+ cell suspensions of HIV-infected and uninfected tissue blocks using a FACS instrument (Cytek Aurora CS), achieving a final purity of >95%
The cellular concentration and viability were verified staining the sample with Trypan Blue (Fisher SC) and evaluated by microscopy. Individual cells were partitioned into Gel Bead‑In‑Emulsions with a Target Cell Recovery of 3478 and 5594 total cells, by using the Chromium X System (10X Genomics). Single cell suspensions were converted to barcoded scRNA-seq libraries using the Chromium GEM-X Single Cell 3' Reagent Kits v4 (10X Genomics) following manufacturer's instructions. After cell lysis and barcoded reverse transcription of RNA, cDNA was amplified during 12 cycles and cDNA QC and quantification were performed on an Agilent TapeStation D5000 DNA ScreenTape (Agilent Technologies). cDNA libraries were indexed by PCR during 15 cycles using PN- 3000431 Chromium Dual Index Kit TT Set A. Size distribution and concentration of 3' cDNA libraries were verified on an Agilent TapeStation D5000 DNA ScreenTape (Agilent Technologies). Finally, sequencing cDNA libraries was carried out on a Nova Seq 6000 sequencer (Illumina) to obtain approximately 40,000 paired-end 150 bp reads per cell.

treatment_protocol: HIV infection

value: Tonsils

tag: age

value: 9 years

value: male

value: CD3- CD56+ lymphocytes

tag: infection

value: HIV BaL strain


title: ChIP_OAL_H3K27me3 rep2

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: ChIP-sequencing

data_processing:
cutadapt
BWA-mem alignment
Assembly: mm10
Supplementary files format and content: text file

source_name: Hematopoietic stem cell

extract_protocol:
none provided by the submitter
ChIP-seq pipeline

value: Old


title: Hb_resilientM2

description:
Library name: Hb_resilientM2
10X Genomics

value: Brain

value: Hb

value: Wild type


title: 73T-Run5850.2186.1-FOV_31

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73T-Run5850.2186.1-FOV_31.rds

value: Colon tumour,FFPE

value: M

value: sigmoid

value: pMMR

value: LHS


title: Gg7

description: Library name: Sample 7

value: buccal

value: Male


title: ChIP_OAL_H3K27me3 rep1

description: ChIP-sequencing


title: Gg6

description: Library name: Sample 6

value: Female


title: 137T-3461G-FOV_31

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_31.rds

value: F

value: rectal


title: ChIP_OAL_H3K4me3 rep2

description: ChIP-sequencing


title: Hb_resilientF3

description:
Library name: Hb_resilientF3
10X Genomics

value: resilient

value: female


title: 170T-120131-FOV_31

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170T-120131-FOV_31.rds


title: Hb_resilientM1

description:
Library name: Hb_resilientM1
10X Genomics

value: male


title: Hb_controlF2

description:
Library name: Hb_controlF2
10X Genomics

value: control


title: ChIP_OAL_H3K4me3 rep1

description: ChIP-sequencing

value: Old


title: ATAC_OAL rep4

description: ATAC-sequencing

extract_protocol:
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


title: SAM24386167

value: colon

tag: cell line

value: tumor

value: M1E5 WT


title: Hb_controlF3

description:
Library name: Hb_controlF3
10X Genomics

value: Brain

value: Hb

tag: genotype

value: Wild type


title: Gg4

description: Library name: Sample 4


title: Gg5

description: Library name: Sample 5


title: 73T-Run5850.2186.2-FOV_31

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_31.rds

value: Colon tumour,FFPE

value: M

value: sigmoid

value: pMMR

value: LHS


title: 92T-10501A-FOV_31

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
92T-10501A-FOV_31.rds

value: F

value: caecum

value: dMMR

value: RHS


title: Hb_controlF1

description:
Library name: Hb_controlF1
10X Genomics

value: control

value: female


title: Gg3

description: Library name: Sample 3

value: buccal

value: Female


title: Hb_resilientM3

description:
Library name: Hb_resilientM3
10X Genomics

value: resilient

value: male


title: ATAC_OAL rep3

description: ATAC-sequencing

value: Old


title: Gg2

description: Library name: Sample 2

value: Male


title: 73T-Run5850.2186.2-FOV_30

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_30.rds

value: Colon tumour,FFPE


title: Hb_controlM3

description:
Library name: Hb_controlM3
10X Genomics

value: Brain

value: Hb

value: Wild type


title: Gg1

description: Library name: Sample 1


title: ATAC_OAL rep2

description: ATAC-sequencing


title: Hb_controlM2

description:
Library name: Hb_controlM2
10X Genomics


title: 73T-Run5850.2186.1-FOV_30

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73T-Run5850.2186.1-FOV_30.rds

value: M

value: sigmoid

value: pMMR

value: LHS


title: ATAC_OAL rep1

description: ATAC-sequencing


title: Hb_controlM1

description:
Library name: Hb_controlM1
10X Genomics


title: 278N-148191A-FOV_31

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:
278N-148191A-FOV_31.rds

value: rectal


title: Erwinia.BIM_REP4

city: Guelph

first: Dion

last: Lepp

address: 93 Stone Rd W

country: Canada

institute: Agriculture and Agri-Food Canada

description: Library name: Erwinia.BIM_REP4

data_processing:
Quality control, read mapping and read counting was performed with the nf-core rnaseq v3.0 pipeline.  Differential gene expression analysis was performed with edgeR package in R.
Assembly: Erwinia amylovora Ea1189  GCF_016446415.2
Supplementary files format and content: tsv file with TPM values

organism: Erwinia amylovora

extract_protocol:
RNA was extracted using the Qiagen Rneasy mini kit according to the manufacturer's instructions, and 50ng of Dnase treated RNA was used for library preparation
total RNA samples were Dnase treated and RNASeq libraries were prepared with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Microbiome kit as per manufacturer’s instructions

value: BIM


title: 64N-Normal_A-FOV_30

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_30.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: F

value: caecum

value: RHS


title: Erwinia.BIM_REP3

description: Library name: Erwinia.BIM_REP3


title: 137T-3461G-FOV_30

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_30.rds


title: VTA_susceptibleF1

description:
Library name: VTA_susceptibleF1
10X Genomics

value: VTA

value: susceptible

value: female


title: VTA_susceptibleF2

description:
Library name: VTA_susceptibleF2
10X Genomics


title: 170T-120131-FOV_30

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170T-120131-FOV_30.rds


title: Donor AJKQ118 Colon LP T cells TCR repertoire

city: St. Petersburg

first: Martin

last: Trapecar

state: FL

address: 600 Fifth Street South

department: Medicine and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description:
Library name: 5-LP-V
10x Genomics VDJ enriched library for TCR sequencing

library_source: other

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

molecule: other

source_name: colon lamina propria

growth_protocol: Not applicable - primary human tissue samples

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

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

value: colon lamina propria

value: Colon lamina propria CD3+ T cells

tag: disease state

value: healthy

value: male

tag: bmi


title: Donor AJKQ118 LiverT cells TCR repertoire

description:
Library name: 5-L-V
10x Genomics VDJ enriched library for TCR sequencing

source_name: liver

tag: tissue

value: liver

value: Liver CD3+ T cells


title: Erwinia.BIM_REP2

description: Library name: Erwinia.BIM_REP2


title: Donor AJKQ118 Blood T cells TCR repertoire

description:
Library name: 5-PB-V
10x Genomics VDJ enriched library for TCR sequencing

source_name: peripheral blood

value: peripheral blood

value: Peripheral blood CD3+ T cells


title: VTA_susceptibleM1

description:
Library name: VTA_susceptibleM1
10X Genomics

value: Brain

tag: tissue region

value: Wild type


title: Erwinia.WT_REP4

description: Library name: Erwinia.WT_REP4

value: WT


title: VTA_resilientF3

description:
Library name: VTA_resilientF3
10X Genomics

tag: phenotype

value: resilient


title: Donor AJG2309 Blood T cells TCR repertoire

description:
Library name: 4-PB-V
10x Genomics VDJ enriched library for TCR sequencing

tag: Sex


title: 92T-10501A-FOV_30

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
92T-10501A-FOV_30.rds

value: Colon tumour,FFPE

value: F

value: caecum

value: dMMR


title: Erwinia.WT_REP3

description: Library name: Erwinia.WT_REP3


title: 73T-Tumour_B-FOV_3

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_3.rds

value: M

value: sigmoid

value: pMMR

value: LHS


title: Donor AJG2309 Liver T cells TCR repertoire

description:
Library name: 4-L-V
10x Genomics VDJ enriched library for TCR sequencing

tag: cell type

value: healthy

value: male


title: 118T-Tumour_A-FOV_3

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_3.rds

tag: donor

value: RHS


title: VTA_resilientF2

description:
Library name: VTA_resilientF2
10X Genomics

value: VTA

value: female


title: Donor AJG2309 Colon LP T cells TCR repertoire

description:
Library name: 4-LP-V
10x Genomics VDJ enriched library for TCR sequencing

value: colon lamina propria

value: Colon lamina propria CD3+ T cells


title: VTA_resilientF1

description:
Library name: VTA_resilientF1
10X Genomics

value: Brain

value: Wild type


title: 142N-Run5850.2186.2-FOV_3

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_3.rds

value: Colon tumour,FFPE

tag: age at diagnosis

value: ascending


title: Erwinia.WT_REP1

description: Library name: Erwinia.WT_REP1

value: WT


title: VTA_resilientM3

description:
Library name: VTA_resilientM3
10X Genomics

value: resilient


title: 278N-148191A-FOV_30

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:
278N-148191A-FOV_30.rds

value: M

tag: primary tumour location

value: rectal


title: VTA_suscetibleM2

description:
Library name: VTA_suscetibleM2
10X Genomics

value: susceptible


title: DKO mouse colon, DSS, replicate C

city: Tokyo

first: Itsarapan

last: Fhaikrue

country: Japan

institute: Tokyo University of Agriculture and Technology

description:
Library name: dsDKOC
Colon tissue from Lao1-/- Il4i1-/- germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

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

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

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

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

value: colon

tag: strain background

tag: treatment


title: Erwinia.BIM_REP1

description: Library name: Erwinia.BIM_REP1

value: BIM


title: DKO mouse colon, DSS, replicate B

description:
Library name: dsDKOB
Colon tissue from Lao1-/- Il4i1-/- germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

value: male


title: 170N-Normal_A-FOV_3

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_3.rds

value: F

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: 142N-Run5850.2186.1-FOV_3

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_3.rds

value: dMMR

value: RHS


title: 7T-3461G-FOV_3

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_3.rds


title: Donor AJD3280 Liver T cells TCR repertoire

description:
Library name: 3-L-V
10x Genomics VDJ enriched library for TCR sequencing

value: liver

value: Liver CD3+ T cells

value: healthy

value: female

tag: age


title: DKO mouse colon, DSS, replicate A

description:
Library name: dsDKOA
Colon tissue from Lao1-/- Il4i1-/- germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

tag: genotype


title: 118N-148191A-FOV_3

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_3.rds

value: Colon tumour,FFPE

value: caecum


title: Donor AJD3280 Colon IEL T cells TCR repertoire

description:
Library name: 3-IEL-V
10x Genomics VDJ enriched library for TCR sequencing

source_name: colon epithelium

value: colon epithelium

value: Colon intraepithelial CD3+ T cells

tag: disease state


title: VTA_resilientM2

description:
Library name: VTA_resilientM2
10X Genomics

value: Brain

value: VTA

value: Wild type

value: resilient


title: VTA_controlF3

description:
Library name: VTA_controlF3
10X Genomics

value: control


title: LAO1KO mouse colon, DSS, replicate B

description:
Library name: dsLAO1KOB
Colon tissue from Lao1-/- germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

value: colon

value: male


title: LAO1KO mouse colon, DSS, replicate C

description:
Library name: dsLAO1KOC
Colon tissue from Lao1-/- germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS


title: Donor AJKQ118 Colon IEL T cells TCR repertoire

description:
Library name: 5-IEL-V
10x Genomics VDJ enriched library for TCR sequencing

tag: bmi


title: 280N-120131-FOV_3

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280N-120131-FOV_3.rds

tag: tissue

value: F

value: pMMR


title: Donor AJD3280 Colon LP T cells TCR repertoire

description:
Library name: 3-LP-V
10x Genomics VDJ enriched library for TCR sequencing

value: colon lamina propria

value: Colon lamina propria CD3+ T cells


title: Erwinia.WT_REP2

description: Library name: Erwinia.WT_REP2

tag: cell line

value: WT


title: VTA_controlF1

description:
Library name: VTA_controlF1
10X Genomics

tag: tissue region

tag: phenotype

value: female


title: LAO1KO mouse colon, DSS, replicate A

description:
Library name: dsLAO1KOA
Colon tissue from Lao1-/- germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

tag: Sex


title: Donor AJG2309 Colon IEL T cells TCR repertoire

description:
Library name: 4-IEL-V
10x Genomics VDJ enriched library for TCR sequencing

tag: cell type

value: healthy


title: 74T-10501A-FOV_3

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_3.rds

value: Colon tumour,FFPE

tag: donor

value: M

tag: age at diagnosis

value: descending colon

value: dMMR

value: LHS


title: VTA_controlM3

description:
Library name: VTA_controlM3
10X Genomics

value: Brain

value: VTA

value: Wild type


title: WT mouse colon, DSS , replicate C

description:
Library name: dsWTC
Colon tissue from Wild-type germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

value: colon

tag: strain background

value: Wild-type


title: Donor AJKQ118 Blood T cells Gene Expression

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

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

value: peripheral blood

value: Peripheral blood CD3+ T cells

value: male


title: Donor AJKQ118 Liver T cells Gene Expression

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

value: liver

value: Liver CD3+ T cells


title: VTA_resilientM1

description:
Library name: VTA_resilientM1
10X Genomics

value: resilient


title: 73T-Run5850.2186.2-FOV_29

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_29.rds

tag: primary tumour location

value: sigmoid

value: pMMR


title: Donor AJKQ118 Colon LP T cells Gene Expression

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

value: colon lamina propria

value: Colon lamina propria CD3+ T cells

value: healthy


title: VTA_controlM2

description:
Library name: VTA_controlM2
10X Genomics

value: control


title: Donor AJD3280 Blood T cells TCR repertoire

description:
Library name: 3-PB-V
10x Genomics VDJ enriched library for TCR sequencing

value: female


title: 73T-Run5850.2186.1-FOV_29

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73T-Run5850.2186.1-FOV_29.rds

value: Colon tumour,FFPE

value: M

tag: total cells

value: LHS


title: Donor AJKQ118 Colon IEL T cells Gene Expression

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

value: colon epithelium

value: Colon intraepithelial CD3+ T cells


title: WT mouse colon, DSS , replicate A

description:
Library name: dsWTA
Colon tissue from Wild-type germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

value: colon

value: Wild-type

tag: treatment


title: 73N-Normal_A-FOV_29

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_29.rds

tag: mmr status

tag: sidedness


title: VTA_controlM1

description:
Library name: VTA_controlM1
10X Genomics

value: Brain

value: VTA

tag: genotype

value: Wild type

value: male


title: VTA_controlF2

description:
Library name: VTA_controlF2
10X Genomics


title: DKO mouse colon, normal, replicate C

description:
Library name: DKOC
Colon tissue from Lao1-/- Il4i1-/- germ-free C57BL/6J mouse, 8 weeks old, male, untreated

value: no treatment


title: 278T-148191A-FOV_29

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_29.rds

value: rectal

value: pMMR


title: Donor AJG2309 Blood T cells Gene Expression

description:
Library name: 4-PB-G
10x Genomics 5' gene expression library

value: peripheral blood

value: Peripheral blood CD3+ T cells

tag: disease state

value: healthy

tag: age


title: 137T-3461G-FOV_29

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_29.rds

tag: tissue

value: Colon tumour,FFPE

value: F


title: Donor AJG2309 Liver T cells Gene Expression

description:
Library name: 4-L-G
10x Genomics 5' gene expression library

value: liver

value: Liver CD3+ T cells

tag: bmi


title: Endothelial cells (DAPI-, CD31+, CD45-) from ears of wt mice.

city: New York

first: Vanessa

last: Cristaldi

state: NY

address: 522 First Avenue

department: Dermatology

institute: NYU Langone Health

description:
Library name: Naïve_Ecs
10X Genomics

data_processing:
The barcoded processing, gene counting were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
Ears were collected and after digested with10mg/ml of collagenase IV (Invitrogen, 17104019) and 50 U/ml of  DNASE I (Sigma-Aldrich, 04536282001) for 30 min at 37°C. Digests were then passed through a metallic mesh and a 70-μm pore filter. Single cell suspensions were stained for Live/Dead with DAPI, CD45 (FITC), CD31(PE)
Libraries were prepared using single cell 3′ reagent kits v3.1 (Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121; 10x Genomics)

value: Skin

value: Endothelial cell

value: wild-type


title: Invivo - Empty Vector; Exvivo - IL27 Rep 2

city: West Lafayette

first: Harish

last: Kothandaraman

state: Indiana

address: 201S University St

department: Purdue Institute for Cancer Research

institute: Purdue University

description:
Library name: Ctrl_IL27_Rep2
IL27_IL27_2

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

source_name: tumor

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

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

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

value: tumor

tag: cell line

value: Prostate adenocarcinoma


title: DKO mouse colon, normal, replicate B

description:
Library name: DKOB
Colon tissue from Lao1-/- Il4i1-/- germ-free C57BL/6J mouse, 8 weeks old, male, untreated

value: colon


title: 170T-120131-FOV_29

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170T-120131-FOV_29.rds

value: sigmoid

value: LHS


title: Donor AJG2309 Colon LP T cells Gene Expression

description:
Library name: 4-LP-G
10x Genomics 5' gene expression library

value: colon lamina propria

value: Colon lamina propria CD3+ T cells

value: male


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

description:
Library name: Ctrl_IL27_Rep1
IL27_IL27_2


title: DKO mouse colon, normal, replicate A

description:
Library name: DKOA
Colon tissue from Lao1-/- Il4i1-/- germ-free C57BL/6J mouse, 8 weeks old, male, untreated

value: no treatment


title: Donor AJG2309 Colon IEL T cells Gene Expression

description:
Library name: 4-IEL-G
10x Genomics 5' gene expression library

value: colon epithelium

value: Colon intraepithelial CD3+ T cells

value: healthy


title: 92T-10501A-FOV_29

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
92T-10501A-FOV_29.rds

value: Colon tumour,FFPE

value: F

value: caecum

value: dMMR

value: RHS


title: Invivo - IL27 Vector; Exvivo - IL-27 Rep 2

description:
Library name: IL27_IL27_Rep2
IL27_IL27_2

value: tumor


title: LAO1KO mouse colon, normal, replicate C

description:
Library name: LAO1KOC
Colon tissue from Lao1-/- germ-free C57BL/6J mouse, 8 weeks old, male, untreated


title: WT mouse colon, DSS , replicate B

description:
Library name: dsWTB
Colon tissue from Wild-type germ-free C57BL/6J mouse, 8 weeks old, male, 24h 2.5% DSS

value: Wild-type


title: LAO1KO mouse colon, normal, replicate B

description:
Library name: LAO1KOB
Colon tissue from Lao1-/- germ-free C57BL/6J mouse, 8 weeks old, male, untreated

value: colon


title: Donor AJD3280 Blood T cells Gene Expression

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

value: peripheral blood

value: Peripheral blood CD3+ T cells

value: female


title: 64T-Tumour_B-FOV_28

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_28.rds

value: pMMR


title: 73T-Run5850.2186.2-FOV_28

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_28.rds

value: M

value: sigmoid

value: LHS


title: LAO1KO mouse colon, normal, replicate A

description:
Library name: LAO1KOA
Colon tissue from Lao1-/- germ-free C57BL/6J mouse, 8 weeks old, male, untreated

value: male

value: no treatment


title: Invivo - IL27 Vector; Exvivo - Cabozanitnib+IL-27 Rep 1

description:
Library name: IL27CO27_Rep1
IL27_IL27CO_1

value: Prostate adenocarcinoma


title: Invivo - IL27 Vector; Exvivo - Cabozanitnib+IL-27 Rep 2

description:
Library name: IL27CO27_Rep2
IL27_IL27CO_2


title: Donor AJD3280 Liver T cells Gene Expression

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

value: liver

value: Liver CD3+ T cells

value: healthy


title: WT mouse colon, normal, replicate C

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


title: 7N-Normal_A-FOV_28

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7N-Normal_A-FOV_28.rds

value: Colon tumour,FFPE

value: ascending

value: RHS


title: Invivo - IL27 Vector; Exvivo - Anti-PD-L1 Rep 2

description:
Library name: IL27PDL1_Rep2
IL27_PDL1_2

value: tumor


title: Donor AJD3280 Colon IEL T cells Gene Expression

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

value: colon epithelium

value: Colon intraepithelial CD3+ T cells


title: Invivo - IL27 Vector; Exvivo - Anti-PD-L1 Rep 1

description:
Library name: IL27PDL1_Rep1
IL27_PDL1_1


title: 142T-3461G-FOV_28

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142T-3461G-FOV_28.rds

value: F

value: ascending colon

value: dMMR


title: Invivo - IL27 Vector; Exvivo - Docetaxel Rep 2

description:
Library name: IL27D_Rep2
IL27_Doce_2


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

description:
Library name: IL27D_Rep1
IL27_Doce_1


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

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

institute: NIAID

description:
Library name: Sample 18
KO5_48hIFN_3

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

source_name: NIKS

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

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

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

value: NIKS

value: Normal immortalized keratinocytes

value: Sp100 knockout

value: 25 ng/mL Human Interferon Alpha 2a

tag: time

value: 48 hour


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

description:
Library name: Sample 17
KO5_48hIFN_2


title: 278T-148191A-FOV_28

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_28.rds

tag: Sex

value: M

value: rectal

value: pMMR

value: LHS


title: scRNA-Seq of SPP1nAB treated muscle cells: S100GFP-pos

city: Ann Arbor

first: Susan

middle: V

last: Brooks

state: Michigan

address: 109 Zina Pitcher Pl

department: Molecular and Integrative Physiology

institute: University of Michigan

description: Library name: SPP1nAB_7dpi

data_processing:
Gene expression count matrices were generated using the count command from Cell Ranger v8.0.0 with the --include-introns=true argument, aligning reads to the GRCm39 mouse reference genome. Default parameters were used unless otherwise specified.
Assembly: GRCm39
Supplementary files format and content: barcodes, features, and mtx files

source_name: skeletal muscle

extract_protocol:
For tissue collection, mice were anesthetized with 3% isoflurane, then euthanized by cervical dislocation, bilateral pneumothorax, and removal of the heart. Hind limb muscles (TA and GTN) of control and experimental mice were quickly harvested using sterile surgical tools and placed in separate plastic petri dishes containing cold phosphate-buffered saline (PBS). Using surgical scissors, muscle tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution (2.5 U/mL Dispase II and 0.2% [~1000 U/mL] Collagenase Type II, 1 mg/mL of hyaluronidase in Dulbeccos modified Eagle medium [DMEM] per mouse). Samples were incubated on a rocker placed in a 37 C incubator for 60 min with manual pipetting the solution up and down to break up tissue every 30 min using an FBS-coated 10 mL serological pipette. Once the digestion was completed, 20 mL of F12 media containing 20% heat inactivated FBS was added into each sample to inactivate enzyme activity. The solution was then filtered through a 70 mm cell strainer into a new 50 mL conical tube and centrifuged again at 300g for 5 min. Live cells were sorted from the suspension via addition of 1 g of propidium iodide (PI) stain into each experimental sample and all samples were filtered through 70 mm cell strainers before the FACS. Cell sorting was done using a BD FACS S8 Sorter (BD Biosciences, San Jose, CA). GFP+ PI- and GFP- PI- cells were sorted into 0.02% BSA PBS solution for immediate processing.
Library preparation and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan. Cells were loaded into the 10X Genomics chromium single cell controller for each sample and captured into nanoliter-scale gel bead-in-emulsions. cDNAs were prepared using the single cell protocol as per manufacturer’s instructions.

value: skeletal muscle

tag: strain

value: SPP1 neutralizing antibody


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

description:
Library name: Sample 16
KO5_48hIFN_1

tag: cell type


title: 170T-120131-FOV_28

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170T-120131-FOV_28.rds

value: Colon tumour,FFPE

tag: donor

tag: age at diagnosis

value: sigmoid


title: scRNA-Seq of IgG treated muscle cells: S100GFP-pos

description: Library name: IgG_Control_7dpi

value: goat anti-mouse IgG


title: Invivo - IL27 Vector; Exvivo - Cabozantinib Rep 2

description:
Library name: IL27CO_Rep2
IL27_Cabo_2

value: tumor

value: Prostate adenocarcinoma