title: BMDM, Enpatoran stimulated, Mouse A3

first: Michael

middle: P

last: Gantier

state: Victoria

address: 27-31 Wright St

department: Centre for Innate Immunity and Infectious Disease

institute: Hudson Institute of Medical Research

description:
Library name: KikaA3Day5Enpatoran
KikaA3Day5Enpatoran

data_processing:
Base calling was performed using Dragen BCLConvert (v3.7.4).
RNA-seq analysis was performed in R (v4.1.0). The scPipe package (v1.14.0) was employed to process and de-multiplex the data. Read alignment was performed on R1 FASTQ files using the Rsubread package (v2.6.1).
An index was built using the Ensembl Mus musculus GRCm39 primary assembly genome file and alignment was performed with default settings. Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Mus musculus GRCm39 v104 GFF3 genome annotation file.
The resulting BAM file was de-multiplexed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each sample was generated using the sc_gene_counting function (with UMI_cor = 1).
Assembly: mm39
Supplementary files format and content: Comma-separated text file contains UMI-corrected counts for each sample

source_name: Bone-marrow-derived macrophages

growth_protocol: Tlr7Y264H C57BL/6NCrl mice (used under Australian National University animal ethics, reference A2021/29) were used in this experiment. These mice have a mutation leading constitutive activation of TLR7 and SLE-like disease.

extract_protocol:
Total RNA was purified from Tlr7Y264H primary BMDMs using the PureLink RNA Mini Kit (Thermo Fisher Scientific) and DNasetreated using the Purelink DNASE set (Thermo Fisher Scientific). 25 ng of total RNA from each sample was used for the construction of sequencing libraries.
Libraries were generated using an in-house multiplex RNA-seq method (version 01/09/2021; Hudson Genomics Facility). 25 ng of total RNA from each sample was tagged with an 8 bp sample index and 10 bp unique molecular identifier (UMI) during initial poly(A) priming with the addition of a template-switching oligo. After cDNA amplification Illumina P5 adaptors with distinct i5 indexes were added by tagmentation by Nextera transposase and PCR. Final libraries were pooled based upon size-adjusted qPCR and single-end sequencing was performed on a NextSeq 2000 run using a P3 50 cycle kit (cDNA reads generated 61 nt).

treatment_protocol: Primary bone marrow derived macrophages from 9-11 week-old Tlr7Y264H heterozygous female mice were extracted and differentiated for 5 days in complete DMEM supplemented with L929 conditioned medium, prior to 24 h incubation with 5 µM GGC-v1 or 100 nM Enpatoran and total RNA purification for RNA sequencing.

tag: cell type

value: Bone-marrow-derived macrophages

value: Tlr7Y264H heterozygous GOF mutant

value: Enpatoran

tag: donor

tag: Sex

value: Female


title: IP RNA, biol rep1, glucose deplete condition, timepoint 20

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: IP_Rep1_T20
Column name in IP_ReadCounts.xlsx: IP, Rep1, Gminus, T20

library_source: other

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: other

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 deplete

tag: batch

value: IP, Rep1


title: 74T-10501A-FOV_39

type: RNA

city: Clayton

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

department: Anatomy and developmental biology

country: Australia

institute: Monash University

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
74T-10501A-FOV_39.rds

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

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

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

molecule: total RNA

organism: Homo sapiens

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

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

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

tag: tissue

value: Colon tumour,FFPE

value: M

tag: age at diagnosis

tag: primary tumour location

value: descending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: LHS


title: P172_15

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

country: USA

institute: Michigan State University

description: Library name: P172_15

library_source: transcriptomic

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

organism: Mus musculus

source_name: Liver

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

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

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: IP RNA, biol rep2, glucose deplete condition, timepoint 10

description:
Library name: IP_Rep2_T10
Column name in IP_ReadCounts.xlsx: IP, Rep2, Gminus, T10

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep2


title: P172_14

description: Library name: P172_14

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration


title: IP RNA, biol rep2, glucose deplete condition, timepoint 5

description:
Library name: IP_Rep2_T5
Column name in IP_ReadCounts.xlsx: IP, Rep2, Gminus, T5

tag: cell line

tag: genotype

tag: treatment

tag: batch


title: 73T-Run5850.2186.1-FOV_38

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_38.rds

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

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: BMDM, GGC-v1 stimulated, Mouse A3

description:
Library name: KikaA3Day5GGC_v1
KikaA3Day5GGC_v1

tag: cell type

value: Bone-marrow-derived macrophages

value: Tlr7Y264H heterozygous GOF mutant

value: Female


title: IP RNA, biol rep1, glucose deplete condition, timepoint 5

description:
Library name: IP_Rep1_T5
Column name in IP_ReadCounts.xlsx: IP, Rep1, Gminus, T5

value: IP, Rep1


title: BMDM, Non-treated, Mouse A2

description:
Library name: KikaA2Day5NT
KikaA2Day5NT

value: NT


title: BMDM, Enpatoran stimulated, Mouse A2

description:
Library name: KikaA2Day5Enpatoran
KikaA2Day5Enpatoran

value: Enpatoran


title: 73T-Run5850.2186.2-FOV_38

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_38.rds


title: 142T-3461G-FOV_38

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_38.rds

value: F

value: ascending colon

value: dMMR

value: RHS


title: IP RNA, biol rep1, glucose deplete condition, timepoint 2.5

description:
Library name: IP_Rep1_T2_5
Column name in IP_ReadCounts.xlsx: IP, Rep1, Gminus, T2.5

value: WT

value: Glucose deplete


title: BMDM, GGC-v1 stimulated, Mouse A2

description:
Library name: KikaA2Day5GGC_v1
KikaA2Day5GGC_v1


title: 278N-148191A-FOV_38

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_38.rds

value: Colon tumour,FFPE

value: rectal


title: P172_13

description: Library name: P172_13

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

value: Sigma-aldrich

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

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: P172_12

description: Library name: P172_12

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: genotype

tag: treatment


title: P172_11

description: Library name: P172_11

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: IP RNA, biol rep1, glucose deplete condition, timepoint 0

description:
Library name: IP_Rep1_T0
Column name in IP_ReadCounts.xlsx: IP, Rep1, Gminus, T0

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep1


title: Total RNA, biol rep3, glucose deplete condition, timepoint 40

description:
Library name: Total_Rep3_Gminus_T40
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gminus, T40

molecule: polyA RNA

value: Total, Rep3


title: BMDM, Non-treated, Mouse A3

description:
Library name: KikaA3Day5NT
KikaA3Day5NT

tag: cell type

value: Bone-marrow-derived macrophages

value: Tlr7Y264H heterozygous GOF mutant

value: NT

tag: donor

tag: Sex

value: Female


title: P172_10

description: Library name: P172_10

tag: tissue

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume


title: 170T-120131-FOV_38

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_38.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: BMDM, Enpatoran stimulated, Mouse A1

description:
Library name: KikaA1Day5Enpatoran
KikaA1Day5Enpatoran

tag: cell type

value: Bone-marrow-derived macrophages

tag: genotype

value: Tlr7Y264H heterozygous GOF mutant

tag: treatment

value: Enpatoran

tag: batch


title: P172_09

description: Library name: P172_09

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: 74T-10501A-FOV_38

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_38.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: descending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness


title: Total RNA, biol rep3, glucose deplete condition, timepoint 20

description:
Library name: Total_Rep3_Gminus_T20
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gminus, T20

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: Total, Rep3


title: IP RNA, biol rep1, glucose deplete condition, timepoint 10

description:
Library name: IP_Rep1_T10
Column name in IP_ReadCounts.xlsx: IP, Rep1, Gminus, T10

value: IP, Rep1


title: BMDM, GGC-v1 stimulated, Mouse A1

description:
Library name: KikaA1Day5GGC_v1
KikaA1Day5GGC_v1

tag: cell type

value: Bone-marrow-derived macrophages

value: Tlr7Y264H heterozygous GOF mutant

value: Female


title: 73T-Run5850.2186.2-FOV_37

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_37.rds

value: sigmoid

value: pMMR

value: LHS


title: Total RNA, biol rep3, glucose deplete condition, timepoint 10

description:
Library name: Total_Rep3_Gminus_T10
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gminus, T10


title: P172_08

description: Library name: P172_08

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name


title: MPEC OT-I cell, Rroid2KO, Day 14, replicate2

city: Wien

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

description:
Library name: Sample12
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: KOMPEC14d_2

data_processing:
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403) including trimming of the sequencing adapters.
Reads in fastq format were aligned to the Mus musculus reference genome version GRCm38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Raw reads per gene were counted by STAR.
Assembly: GRCm38
Supplementary files format and content: Tab-separated file includes raw counts for each sample
Supplementary files format and content: Tab-separated file includes the phenodata for each sample (sample description)

source_name: spleen

extract_protocol:
The OT-I cells were FACS-sorted directly into 700ul RTL lysis buffer supplemented with β-mercaptoethanol. RNA isolation was performed using the RNeasy Micro kit (Qiagen, #74004).
RNA-seq libraries were prepared using the SMART-Seq Stranded Kit (#634442) and Unique Dual Index Kit 1–24 (#634756) according to the manufacturer's protocol (Takara Bio).

treatment_protocol: Listeria monocytogenes expressing ovalbumin (LM-OVA) infection

tag: tissue

value: spleen

tag: cell type

value: OT-I cell

tag: genotype

value: Rroid2 KO

tag: treatment

value: LM-OVA infection


title: P172_07

description: Library name: P172_07

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: 73T-Run5850.2186.1-FOV_37

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_37.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: Total RNA, biol rep3, glucose deplete condition, timepoint 5

description:
Library name: Total_Rep3_Gminus_T5
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gminus, T5

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: Total, Rep3


title: MPEC OT-I cell, Rroid2KO, Day 14, replicate1

description:
Library name: Sample11
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: KOMPEC14d_1

value: spleen

tag: cell type

value: OT-I cell


title: BMDM, Non-treated, Mouse A1

description:
Library name: KikaA1Day5NT
KikaA1Day5NT

value: Bone-marrow-derived macrophages

value: Tlr7Y264H heterozygous GOF mutant

value: NT

value: Female


title: 278N-148191A-FOV_37

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_37.rds

value: rectal


title: 142T-3461G-FOV_37

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_37.rds

value: F

value: ascending colon

value: dMMR

value: RHS


title: SLEC OT-I cell, Rroid2KO, Day 7, replicate2

description:
Library name: Sample8
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: KOSLEC7d_2

value: Rroid2 KO

value: LM-OVA infection


title: P172_06

description: Library name: P172_06

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

value: Dimethyl sulfoxide

value: wild-type


title: Total RNA, biol rep3, glucose deplete condition, timepoint 0

description:
Library name: Total_Rep3_Gminus_T0
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gminus, T0

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: Total, Rep3


title: P172_05

description: Library name: P172_05

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: SLEC OT-I cell, Rroid2KO, Day 14, replicate2

description:
Library name: Sample10
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: KOSLEC14d_2

tag: tissue

value: spleen

tag: cell type

value: OT-I cell

tag: genotype

value: Rroid2 KO

tag: treatment

value: LM-OVA infection


title: P172_03

description: Library name: P172_03

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

value: type I collagen

value: Nuaire

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name


title: SLEC OT-I cell, Rroid2KO, Day 7, replicate1

description:
Library name: Sample7
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: KOSLEC7d_1

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Total RNA, biol rep3, glucose deplete condition, timepoint 2.5

description:
Library name: Total_Rep3_Gminus_T2_5
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gminus, T2.5

tag: cell line

value: WT

value: Glucose deplete

tag: batch

value: Total, Rep3


title: 73T-Run5850.2186.2-FOV_36

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_36.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: Total RNA, biol rep3, glucose replete condition, timepoint 20

description:
Library name: Total_Rep3_Gplus_T20
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gplus, T20

value: Glucose replete


title: P172_02

description: Library name: P172_02

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

value: hour

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: MPEC OT-I cell, Rroid2WT, Day 14, replicate2

description:
Library name: Sample6
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: WTMPEC14d_2

tag: tissue

value: spleen

tag: cell type

value: OT-I cell

tag: genotype

value: Rroid2 WT

tag: treatment

value: LM-OVA infection


title: 73T-Run5850.2186.1-FOV_36

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_36.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: Total RNA, biol rep3, glucose replete condition, timepoint 5

description:
Library name: Total_Rep3_Gplus_T5
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gplus, T5

tag: cell line

value: WT

value: Glucose replete

tag: batch

value: Total, Rep3


title: Total RNA, biol rep3, glucose replete condition, timepoint 10

description:
Library name: Total_Rep3_Gplus_T10
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gplus, T10


title: MPEC OT-I cell, Rroid2WT, Day 14, replicate1

description:
Library name: Sample5
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: WTMPEC14d_1


title: 7T-3461G-FOV_36

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_36.rds

value: ascending

value: RHS


title: SLEC OT-I cell, Rroid2WT, Day 14, replicate2

description:
Library name: Sample4
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: WTSLEC14d_2


title: KrTB-25 (10w)

city: New York City

first: Jorge

last: Baquero

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

description: Library name: Sample 12

data_processing:
Illumina bcl2fastq2 v2.20 was employed for basecalling.
The sequenced reads underwent trimming to eliminate low-quality bases and adapter sequences using cutadapt. Subsequently, these reads were mapped to the mouse GRCm38 reference genome using STAR v2.5.2b.
The extraction of raw read counts was accomplished through HTSeq-count v0.11.2.
Differential expression analysis was conducted using the DESeq2 v1.6.3 package.
We employed the limma package v3.22.7 to remove batch effects from processing samples from different batches.
Assembly: Mouse GRCm38
Supplementary files format and content: Excel files including gene name, raw counts, and log2fold changes (KrTB-DN (4w) vs. KrTB-N (25w) and KrTB-DN (10w) vs. KrTB-N (25w)) for each gene

source_name: Tongue epithelia tissue

extract_protocol:
Qiagen's RNEasy Micro kit (Cat # 74004)
The preparation of RNA libraries utilized the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA), following the protocols provided by the manufacturer. The libraries were sequenced with pair-end 51bp reads on the NovaSeq6000 sequencer.

treatment_protocol: water+4NQO (50 μg/ml) for 10 weeks and then water only for 15 more weeks (25 weeks total), water+doxycycline+4NQO (2 mg/ml and 50 μg/ml) for 4 weeks, and water+doxycycline+4NQO (2 mg/ml and 50 μg/ml) for 10 weeks

value: Tongue epithelia tissue

tag: strain

value: KrTB-DN (10w)


title: CTX_2, CUT&Tag

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

country: China

institute: Jinan University

description: Library name: Sample1

library_source: genomic

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

molecule: genomic DNA

source_name: Cortex

extract_protocol:
Fresh virus-infected cortical regions were removed with tweezers and then dissociated into single cell suspension using the papain system (Worthington) according to manufacturer’s protocol. TdTomato+ cells were sorted from the brain of animals 7 days after virus injection using FACS.
CUT&Tag libraries were prepared using CUT&Tag-IT™ Assay Kit (Active Motif, catalog No. 53160)

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

value: Cortex

tag: time

value: 7 dpi

value: Sorted tdTomato+ cells

tag: cut&tag antibody

value: Olig2 (EMD/Millipore, #AB9610)


title: Total RNA, biol rep3, glucose replete condition, timepoint 2.5

description:
Library name: Total_Rep3_Gplus_T2_5
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gplus, T2.5


title: SLEC OT-I cell, Rroid2KO, Day 14, replicate1

description:
Library name: Sample9
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: KOSLEC14d_1

value: spleen

value: OT-I cell

value: Rroid2 KO

value: LM-OVA infection


title: 170T-120131-FOV_37

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_37.rds

value: Colon tumour,FFPE

value: F

value: sigmoid

value: pMMR


title: Total RNA, biol rep3, glucose replete condition, timepoint 40

description:
Library name: Total_Rep3_Gplus_T40
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gplus, T40

value: WT

value: Glucose replete

value: Total, Rep3


title: 92T-10501A-FOV_37

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_37.rds

value: caecum

value: dMMR

value: RHS


title: P172_04

description: Library name: P172_04

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: Total RNA, biol rep3, glucose replete condition, timepoint 0

description:
Library name: Total_Rep3_Gplus_T0
Column name in Total_ReadCounts.xlsx: Total, Rep3, Gplus, T0

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose replete

tag: batch

value: Total, Rep3


title: 278N-148191A-FOV_36

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_36.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: rectal

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: KrTB-19 (10w)

description: Library name: Sample 11

value: Tongue epithelia tissue

tag: strain

value: KrTB-DN (10w)


title: SLEC OT-I cell, Rroid2WT, Day 7, replicate2

description:
Library name: Sample2
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: WTSLEC7d_2

value: spleen

tag: cell type

value: OT-I cell

value: Rroid2 WT

value: LM-OVA infection


title: Total RNA, biol rep2, glucose deplete condition, timepoint 40

description:
Library name: Total_Rep2_Gminus_T40
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gminus, T40

value: Glucose deplete

value: Total, Rep2


title: 92T-10501A-FOV_36

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_36.rds

value: F

value: caecum

value: dMMR

value: RHS


title: SLEC OT-I cell, Rroid2WT, Day 14, replicate1

description:
Library name: Sample3
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: WTSLEC14d_1


title: KrTB-13 (10w)

description: Library name: Sample 10


title: Total RNA, biol rep2, glucose deplete condition, timepoint 20

description:
Library name: Total_Rep2_Gminus_T20
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gminus, T20

value: WT


title: 170T-120131-FOV_36

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_36.rds

value: Colon tumour,FFPE

value: sigmoid


title: 73N-Run5850.2186.2-FOV_35

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_35.rds

value: M

value: pMMR


title: 73T-Run5850.2186.1-FOV_35

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_35.rds

value: LHS


title: P172_01

description: Library name: P172_01

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

value: Dimethyl sulfoxide

value: wild-type


title: SLEC OT-I cell, Rroid2WT, Day 7, replicate1

description:
Library name: Sample1
Instrument model: Illumina NextSeq2000; Column name in raw_counts_Roid2.tsv: WTSLEC7d_1

tag: tissue

value: spleen

tag: cell type

value: OT-I cell

tag: genotype

value: Rroid2 WT

tag: treatment

value: LM-OVA infection


title: Total RNA, biol rep2, glucose deplete condition, timepoint 5

description:
Library name: Total_Rep2_Gminus_T5
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gminus, T5

tag: cell line

value: WT

value: Glucose deplete

tag: batch

value: Total, Rep2


title: KrTB-54 (4w)

description: Library name: Sample 8

value: Tongue epithelia tissue

tag: strain

value: KrTB-DN (4w)


title: LAn6, replicate 6, scRNAseq

city: Omaha

first: MohanKumar

last: Krishnan

address: 985870 Nebraska Medical Center

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

description:
Library name: Sample 12
10x Genomics

library_source: transcriptomic single cell

data_processing:
Data processed with 10x Cell Ranger
Data processed with 10x Seurat
Assembly: Mm10
Supplementary files format and content: Tab-separated values files and matrix files from 10x

growth_protocol: C57BL/6 mice breeders were procured from The Jackson Laboratory (Bar Harbor, ME). Mouse pups were housed in the JHU animal facility with and nursed by the dam throughout the study.

extract_protocol:
The mouse liver tissues were surgically removed and first washed with Dulbecco’s phosphate-buffered saline (DPBS) without calcium and magnesium to wash away blood and preservation medium, transferred into a petri dish and diced into small pieces (roughly 1 cm2 for resections and 0.25 cm2 for biopsies) using a scalpel. The liver tissue was dissociated for single-cell preparation using the mouse liver dissociation kit (Cat #130-105-807, Miltenyi Biotech, Auburn, CA) and gentleMACS Dissociator (Cat #130-093-235, Miltenyi Biotech, Auburn, CA.). Briefly, the tissue was distributed evenly into four gentleMacs C Tubes, then each tube received 5 ml of Liberase enzymatic digestion solution (0.2 Wünsch/ml) reconstituted in HepatoZYME media (without growth factors, which may influence the downstream scRNA-seq) containing DNAse I (2000 U/ml). The mixture was warmed to 37 °C for optimal enzymatic activity. The enzymatic digestion occurred in an incubating shaker at 37 °C and 200 RPM for 30 mins. The partially degraded extracellular tissue matrix in each C tube was mechanically dissociated by running two “B” cycles in the gentleMACS Dissociator. A 1:1 ratio of 20% FBS (Fetal Bovine Serum) to 80% DPBS was added to neutralize the enzymatic reaction and the cell suspensions were filtered through 70 um filters to remove large pieces of debris, gently mashing pieces through the filter. Cells dissociated from liver tissues were purified by centrifuging the cell suspensions at 50 x g, 4 °C for 5 mins to pelletize the cells; dissociated single cells were then stained for viability assessment using 0.05% trypan blue (Cat #T6146, Millipore Sigma, St. Louis, MA) in PBS on a Cellometer AutoT4 cell counter (Nexcelom Bioscience, Waltham, MA).
Library constructed according to 10x Genomics single cell 3’ v2 protocol

treatment_protocol: C57BL/6 mice from each litter were randomly assigned to two study groups: (a) naive control and (b) phlebotomy-induced anemia. Phlebotomy-induced anemia was performed in mouse pups by facial vein phlebotomy to remove 20µL blood/g body weight on P2, P4, P6, P8, and P10 to reduce the hematocrit (Hct) index from an initial 45-60% range, down to 20-24%. Hematocrits and RBC indices were measured at each phlebotomy; 5 µL blood was diluted 1:20 in Cellpak reagent (Sysmex America, Mundelein, IL; catalog #DCL-310A), and analyzed in the Sysmex XT-2000iV veterinary hematology analyzer. Non-phlebotomized control animals were handled similarly to phlebotomized animals with a daily non-phlebotomizing needle stick. Pups were weighed daily to determine the volume of blood to be drawn. The animals were euthanized 24 h (P11) later, and the liver tissue was processed for scRNA sequencing.

value: Liver

value: single cells

value: Phlebotomy-induced anemia


title: LAn5, replicate 5, scRNAseq

description:
Library name: Sample 11
10x Genomics


title: Total RNA, biol rep2, glucose deplete condition, timepoint 2.5

description:
Library name: Total_Rep2_Gminus_T2_5
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gminus, T2.5


title: 137T-3461G-FOV_35

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_35.rds

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: rectal

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: KrTB-31 (4w)

description: Library name: Sample 6


title: LAn4, replicate 4, scRNAseq

description:
Library name: Sample 10
10x Genomics


title: KrTB-37 (4w)

description: Library name: Sample 7


title: 278N-148191A-FOV_35

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_35.rds

value: M


title: 170T-120131-FOV_35

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_35.rds

value: sigmoid


title: Total RNA, biol rep2, glucose deplete condition, timepoint 0

description:
Library name: Total_Rep2_Gminus_T0
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gminus, T0


title: KrTB-29 (4w)

description: Library name: Sample 5


title: Total RNA, biol rep2, glucose replete condition, timepoint 40

description:
Library name: Total_Rep2_Gplus_T40
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gplus, T40

value: Glucose replete


title: LAn3, replicate 3, scRNAseq

description:
Library name: Sample 9
10x Genomics


title: Total RNA, biol rep2, glucose deplete condition, timepoint 10

description:
Library name: Total_Rep2_Gminus_T10
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gminus, T10


title: LAn2, replicate 2, scRNAseq

description:
Library name: Sample 8
10x Genomics


title: 92T-10501A-FOV_35

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_35.rds

value: caecum

value: dMMR

value: RHS


title: KrTB-12 (10w)

description: Library name: Sample 9

value: KrTB-DN (10w)


title: double knockout (MLPKO-cRADKO) mouse heart 4, 16 weeks of age

city: Lexington

first: Jonathan

last: Satin

state: KY

address: 741 S. Limestone

department: Physiology

institute: University of Kentucky

description: Library name: 16_dKO_4

data_processing:
Each FASTQ file was processed using FastQC to assess the quality of the reads. Subsequently, the reads were aligned to the GRCm39 genome assembly using the STAR alignment software. The total successfully assigned alignments ranged from 64% to 74%. Raw counts were calculated with the featureCounts package.
Assembly: GRCm39
Supplementary files format and content: .csv file includes raw counts for all samples

source_name: heart, left ventricle

extract_protocol:
RNA was extracted from rapid-freeze clamped apical halves of cardiac ventricle (N=5 per group). The manufacturers protocol Qiagen RNeasy Fibrous Tissue Mini Kit (50) (Qiagen 74704, Venlo, Netherlands) was followed. RNA with RIN>9 was submitted to Novogene (Sacramento, CA) for sequencing.
Novogene carried out mRNA enrichment "using polyA selection (Kit) and prepared using a library kit".

treatment_protocol: All mice were administered a single dose of tamoxifen (100 mg/kg intraperitoneal) at 10 weeks of age (2.5 months).

value: heart, left ventricle

tag: age

value: 16 weeks of age

value: MLPKO-cRADKO

value: 1 month post tamoxifen


title: LAn1, replicate 1, scRNAseq

description:
Library name: Sample 7
10x Genomics

value: Liver

value: single cells

value: Phlebotomy-induced anemia


title: Total RNA, biol rep2, glucose replete condition, timepoint 20

description:
Library name: Total_Rep2_Gplus_T20
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gplus, T20

value: WT

value: Total, Rep2


title: double knockout (MLPKO-cRADKO) mouse heart 5, 16 weeks of age

description: Library name: 16_dKO_5


title: 73T-Run5850.2186.1-FOV_34

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_34.rds

value: Colon tumour,FFPE

value: pMMR

value: LHS


title: 73N-Run5850.2186.2-FOV_34

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_34.rds

value: M

value: sigmoid


title: 142T-3461G-FOV_34

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_34.rds

value: F

value: ascending colon

value: dMMR


title: LC6, replicate 6, scRNAseq

description:
Library name: Sample 6
10x Genomics

value: No


title: Total RNA, biol rep2, glucose replete condition, timepoint 5

description:
Library name: Total_Rep2_Gplus_T5
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gplus, T5

value: Glucose replete


title: LC4, replicate 4, scRNAseq

description:
Library name: Sample 4
10x Genomics


title: double knockout (MLPKO-cRADKO) mouse heart 2, 16 weeks of age

description: Library name: 16_dKO_2

value: heart, left ventricle

value: 16 weeks of age

value: MLPKO-cRADKO


title: double knockout (MLPKO-cRADKO) mouse heart 1, 16 weeks of age

description: Library name: 16_dKO_1

value: 1 month post tamoxifen


title: double knockout (MLPKO-cRADKO) mouse heart 3, 16 weeks of age

description: Library name: 16_dKO_3


title: Total RNA, biol rep2, glucose replete condition, timepoint 0

description:
Library name: Total_Rep2_Gplus_T0
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gplus, T0


title: 278N-148191A-FOV_34

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_34.rds

value: rectal


title: Total RNA, biol rep2, glucose replete condition, timepoint 2.5

description:
Library name: Total_Rep2_Gplus_T2_5
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gplus, T2.5

value: WT


title: LC5, replicate 5, scRNAseq

description:
Library name: Sample 5
10x Genomics

value: Liver

value: single cells


title: LC3, replicate 3, scRNAseq

description:
Library name: Sample 3
10x Genomics


title: MLPKO mouse heart 5, 16 weeks of age

description: Library name: 16_MLPKO_5

value: MLPKO


title: Total RNA, biol rep1, glucose deplete condition, timepoint 40

description:
Library name: Total_Rep1_Gminus_T40
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gminus, T40

value: Glucose deplete

value: Total, Rep1


title: 170T-120131-FOV_34

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_34.rds

value: Colon tumour,FFPE

value: sigmoid

value: pMMR

value: LHS


title: MLPKO mouse heart 4, 16 weeks of age

description: Library name: 16_MLPKO_4


title: Total RNA, biol rep2, glucose replete condition, timepoint 10

description:
Library name: Total_Rep2_Gplus_T10
Column name in Total_ReadCounts.xlsx: Total, Rep2, Gplus, T10

value: Total, Rep2


title: LC2, replicate 2, scRNAseq

description:
Library name: Sample 2
10x Genomics

value: No


title: 73N-Run5850.2186.2-FOV_33

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_33.rds

value: M


title: LC1, replicate 1, scRNAseq

description:
Library name: Sample 1
10x Genomics


title: 92T-10501A-FOV_34

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_34.rds

value: F

value: caecum

value: dMMR

value: RHS


title: Total RNA, biol rep1, glucose deplete condition, timepoint 20

description:
Library name: Total_Rep1_Gminus_T20
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gminus, T20

value: WT


title: MLPKO mouse heart 2, 16 weeks of age

description: Library name: 16_MLPKO_2

value: heart, left ventricle

value: 16 weeks of age

value: 1 month post tamoxifen


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

description:
Library name: Total_Rep1_Gminus_T10
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gminus, T10

value: Glucose deplete


title: SAM24417410

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

source_name: colon

growth_protocol: female mice 6-10-week-old were inoculated subcutaneously in the right flank with 1 x 106 tumor cells resuspended in 50% Hank’s balanced salt solution (HBSS) and 50% Matrigel (Corning). Tumors were collected in RPMI-1640, minced and enzymatically digested with 0.2 mg/ml Collagenase P (Roche), 0.8 mg/ml Dispase (Life Technologies) and 0.1 mg/ml DNase I (Roche) in RPMI-1640 at 37°C for 45 min. After tumor digestion cells were washed with RPMI-1640 containing 10% FBS and filtered with a 70-µm cell strainer.

extract_protocol:
Total RNA was extracted from FACS 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

value: tumor

value: MC-38 M1E5-Zfx-KO-Thy1.2


title: MLPKO mouse heart 3, 16 weeks of age

description: Library name: 16_MLPKO_3

value: MLPKO


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

description:
Library name: Total_Rep1_Gminus_T5
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gminus, T5

value: Total, Rep1


title: 142T-3461G-FOV_33

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_33.rds

value: Colon tumour,FFPE

value: ascending colon


title: SAM24417409


title: 73T-Run5850.2186.1-FOV_33

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_33.rds

value: M

value: sigmoid

value: pMMR

value: LHS


title: SAM24417408


title: MLPKO mouse heart 1, 16 weeks of age

description: Library name: 16_MLPKO_1


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

description:
Library name: Total_Rep1_Gminus_T0
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gminus, T0


title: 278N-148191A-FOV_33

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_33.rds

value: rectal


title: Hb_susceptibleF3

city: Princeton

first: Adelaide

last: Minerva

state: New Jersey

address: Washington Road

department: Princeton Neuroscience Institute

institute: Princeton University

description:
Library name: Hb_susceptibleF3
10X Genomics

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

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.

value: Brain

tag: tissue region

value: Hb

value: Wild type

tag: phenotype

value: susceptible

value: female


title: 170T-120131-FOV_33

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_33.rds

tag: tissue

value: F


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

description:
Library name: Total_Rep1_Gminus_T2_5
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gminus, T2.5

value: WT

value: Glucose deplete


title: SAM24417406

value: colon

tag: cell type

value: tumor

value: MC-38 M1E5-Zfx-KO-Thy1.2


title: Total RNA, biol rep1, glucose replete condition, timepoint 20

description:
Library name: Total_Rep1_Gplus_T20
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gplus, T20

tag: genotype

value: Glucose replete

value: Total, Rep1


title: Hb_susceptibleF1

description:
Library name: Hb_susceptibleF1
10X Genomics


title: Total RNA, biol rep1, glucose replete condition, timepoint 40

description:
Library name: Total_Rep1_Gplus_T40
Column name in Total_ReadCounts.xlsx: Total, Rep1, Gplus, T40

tag: treatment


title: SAM24417407

tag: cell line


title: SAM24417405