title: P172_44

description: Library name: P172_44

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

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

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

value: nanomolar

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: HMG_GFP_1_Input

status: Public on Dec 09 2025

type: SRA

city: Hangzhou

first: Yan

last: Wang

state: Zhejiang

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

department: College of Life Sciences

country: China

institute: Zhejiang University

library_source: genomic

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

molecule: genomic DNA

organism: Oryza sativa

source_name: HMG-GFP transgenic plants, HP contiditions, input, rep1

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

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

treatment_protocol: Seedlings grown under HP conditions for 28 d.

tag: cell line

value: Leaf blades

tag: chip antibody

value: none (input)


title: Ctrl_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

description: Library name: Sample4

library_source: transcriptomic

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

molecule: polyA RNA

organism: Rattus norvegicus

source_name: rat hippocampal region

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

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

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

tag: tissue

value: rat hippocampal region

tag: group

value: Ctrl

tag: strain

value: Sprague-Dawley

tag: Sex

value: male


title: HMG_GFP_3_IP

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

value: GFP (Chromotek, #gtma)


title: HMG_GFP_2_Input

source_name: HMG-GFP transgenic plants, HP contiditions, input, rep2


title: ChryM_3

description: Library name: Sample3

value: ChryM


title: 46T-148191A-FOV_42

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:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
46T-148191A-FOV_42.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.

value: Colon tumour,FFPE

tag: donor

value: F

tag: age at diagnosis

tag: primary tumour location

value: hepatic flexure

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: P172_42

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_42

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

organism: Mus musculus

source_name: Liver

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

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

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: genotype

tag: treatment


title: P172_41

description: Library name: P172_41

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: HMG_GFP_1_IP

source_name: HMG-GFP transgenic plants, HP contiditions, IP, rep1

tag: cell line

value: Leaf blades

tag: chip antibody

value: GFP (Chromotek, #gtma)


title: ChryM_2

description: Library name: Sample2

tag: tissue

value: rat hippocampal region

tag: group

value: ChryM

tag: strain

value: Sprague-Dawley

tag: Sex

value: male


title: P172_40

description: Library name: P172_40

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: genotype

tag: treatment


title: HMG_GFP_2_IP

source_name: HMG-GFP transgenic plants, HP contiditions, IP, rep2

tag: cell line

tag: chip antibody


title: stimulated vector + PBS_21DIV_S3 [DIV21_sti_PBS3_Mock]

city: Philadelphia

first: Shuo

last: Zhang

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
PhP_sti_RNA_table.txt
DIV21_sti_PBS3_Mock

data_processing:
Demultiplexed FASTQs were aligned to the reference genome using STAR
Gene level read counts were prepared using featureCounts or HTSeq.
All DIV9 and DIV21 RNA-seq samples, including unstimulated and stimulated samples, were put together to estimate unwanted variation by RUVr with k=1.
To make pairwise comparisons, reads were subsetted.
Differentially expressed genes were called using DESeq2 with Wald test, controlling for the estimated unwanted variation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Primary hippomcapal neurons

growth_protocol: Primary hippomcapal neurons culture were cultured in neural basal medium with 2% B27, 1x Glutamax, and 1x Penicillin/Streptomycin.

extract_protocol:
Total RNA was extracted using Trizol-chloroform following RNA purification using RNeasy mini-kit, Qiagen.
130 ng input RNA was used to make libraries using the NEB kit E7490.

treatment_protocol: Cells were treated with 1.5xE6 PhP.eb.upACSS2 or PhP.eB-vector at 5DIV for 48 hours before 1x PBS wash on 7DIV and treatment with hAD-tau or PBS. Aged and 10 months old C57BL6 mice were treated with retro-orbital injection of PhP.eb.upACSS2 or PhP.eB-vector. Aged mice treated at 21-22 months of age with 1.5 xE11 viral genome (vg) and tissue harvested 30 min post remote context recall after 2 months of viral treatment. 10 months old mice treated with 1.2 xE11 vg for 2 weeks and tissue harvested 30 min after acquisition of fear conditioning.2.5 month old PS 19 mice were treated with 1.5 xE10 vg PhP.eb.upACSS2 or PhP.eB-vector for 1 month (1mpi) or 6 month (6 mpi) and euthanized 30 min post 24-hour contextual recall.

tag: cell type

value: Primary hippomcapal neurons


title: ChryM_1

description: Library name: Sample1

tag: tissue

tag: group

tag: strain

tag: Sex


title: LV_2313_male_REC

city: Freiburg

first: Achim

last: Lother

state: --- Select One ---

address: Albertstr. 25

department: Institute of experimental and clinical Pharmacology and Toxicology,

country: Germany

institute: University of Freiburg

description:
Library name: LIB-00095
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

library_source: transcriptomic single cell

data_processing:
We ran cellranger using following specifications: Cellranger Version:cellranger-7.0.0; transcriptome:mm10-2020-A; chemistry:SC3Pv3; include-introns=TRUE
R package SoupX (SoupX_1.6.2) was used with custom contamination fractions (LV_2108: 0.25; LV_2109: 0.3; LV_2110: 0.3; LV_2111: 0.2; LV_2112: 0.2; LV_2113: 0.25; LV_2114: 0.35; LV_2115: 0.3; LV_2310: 0.3; LV_2311: 0.15; LV_2312: 0.1; LV_2313: 0.15) to remove ambient RNA signal.
Doublets were called using R package single cell doublet finder (scDblFinder_1.16.0) and removed from analysis.
Seurat pipeline was used for clustering, DEG analysis and data manipulation (Seurat_5.1.0;  SeuratObject_5.0.2). R package Harmony (harmony_1.2.1) was used for integration of data.
Cell-cell interactions were inferred with R package CellChat (CellChat_1.6.1)
Co-expression networks were inferred by R packages WGCNA and hdWGCNA (WGCNA_1.72-5; hdWGCNA_0.3.01)
Assembly: mm10-2020-A
Supplementary files format and content: fastq files contain demultiplexed raw fw and rv reads. rds file contains the final seurat object

molecule: nuclear RNA

source_name: heart, left ventricle free-wall

extract_protocol:
The protocol is based on published work (Hocker, Sci. Adv. 2021 May;7(20)). In short, flash frozen tissue is homogenized via gentleMACS without enzymatic digestion at 4°C. Nuclei are filtered/centrifuged to remove debris and FAN-sorted to further purify the nuclei. Trypan blue staining was used to determine nuclei concentration, and adjusted to load 15,000 nuclei per sample onto the 10x Chromium Controller.
Single-nucleus GEM reactions and libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 kit (10x Genomics) as per manufacturer specifications (v3.1_User_Guide). Samples were amplified during cDNA preparation and library amplification for 12 cycles.

treatment_protocol: Adult male and female C57BL/6N wildtype mice were treated with aldosterone plus salt (ALDO, 500 µg/kg/d from osmotic minipumps, 1 % NaCl with drinking water). For REC, the aldosterone minipump was explanted after 2 weeks and animals were followed for 4 weeks.

value: heart, left ventricle free-wall


title: 130T-10501A-FOV_42

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
130T-10501A-FOV_42.rds

value: Colon tumour,FFPE

tag: donor

value: F

tag: age at diagnosis

tag: primary tumour location

value: rectum upper

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: P172_39

description: Library name: P172_39

tag: cell type_ontology

tag: tissue ontology

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

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

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: wild-type


title: LV_2312_male_REC

description:
Library name: LIB-00094
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

tag: tissue


title: P172_38

description: Library name: P172_38

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

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

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: test article_administration_duration

tag: genotype

tag: treatment


title: 142T-3461G-FOV_41

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_41.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: stimulated vector + PBS_21DIV_S1 [DIV21_sti_PBS1_Mock]

description:
PhP_sti_RNA_table.txt
DIV21_sti_PBS1_Mock

tag: cell type

value: Primary hippomcapal neurons


title: P172_43

description: Library name: P172_43

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

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

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

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

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: LV_2311_female_REC

description:
Library name: LIB-00093
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

tag: tissue

value: heart, left ventricle free-wall


title: 130T-10501A-FOV_43

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
130T-10501A-FOV_43.rds

tag: donor

tag: Sex

tag: age at diagnosis

tag: primary tumour location

value: rectum upper

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: 46T-148191A-FOV_41

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
46T-148191A-FOV_41.rds

value: Colon tumour,FFPE

value: F

value: hepatic flexure


title: LV_2310_female_REC

description:
Library name: LIB-00092
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads


title: stimulated upACSS2 + PBS_21DIV_S3 [DIV21_sti_PBS3_OE]

description:
PhP_sti_RNA_table.txt
DIV21_sti_PBS3_OE

tag: cell type

tag: treatment


title: P172_37

description: Library name: P172_37

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

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: test article_administration_duration

value: Dimethyl sulfoxide

tag: genotype

value: wild-type


title: P172_36

description: Library name: P172_36

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

value: Nuaire

value: Williams E medium

value: Sigma-aldrich

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

value: penicillin/streptomycin

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: treatment


title: stimulated upACSS2 + PBS_21DIV_S2 [DIV21_sti_PBS2_OE]

description:
PhP_sti_RNA_table.txt
DIV21_sti_PBS2_OE

tag: cell type

value: Primary hippomcapal neurons


title: LV_2115_male_CTRL

description:
Library name: LIB-00060
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

tag: tissue

value: heart, left ventricle free-wall


title: 170T-120131-FOV_42

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_42.rds

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: 170T-120131-FOV_41

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_41.rds


title: 130T-10501A-FOV_41

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
130T-10501A-FOV_41.rds

value: rectum upper


title: stimulated upACSS2 + PBS_21DIV_S1 [DIV21_sti_PBS1_OE]

description:
PhP_sti_RNA_table.txt
DIV21_sti_PBS1_OE


title: P172_34

description: Library name: P172_34

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

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: test article_administration_duration

value: Dimethyl sulfoxide

tag: genotype

value: wild-type


title: 142T-3461G-FOV_42

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_42.rds

tag: tissue

tag: donor

tag: Sex

tag: age at diagnosis

tag: primary tumour location

value: ascending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: P172_35

description: Library name: P172_35

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex 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

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

value: penicillin/streptomycin

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: treatment


title: 67T-Run5850.2186.2-FOV_40

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_40.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: LV_2113_male_ALDO

description:
Library name: LIB-00058
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

value: heart, left ventricle free-wall


title: stimulated vector + PBS_21DIV_S2 [DIV21_sti_PBS2_Mock]

description:
PhP_sti_RNA_table.txt
DIV21_sti_PBS2_Mock

tag: cell type

value: Primary hippomcapal neurons


title: P172_33

description: Library name: P172_33

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

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: test article_administration_duration

value: Dimethyl sulfoxide

tag: genotype

value: wild-type


title: 73T-Run5850.2186.1-FOV_40

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_40.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

tag: age at diagnosis

tag: primary tumour location

tag: total cells

tag: mmr status

tag: sidedness


title: stimulated vector + hAD-tau_21DIV_S2 [DIV21_sti_AD2_Mock]

description:
PhP_sti_RNA_table.txt
DIV21_sti_AD2_Mock

tag: cell type

tag: treatment


title: LV_2112_male_ALDO

description:
Library name: LIB-00057
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads


title: 142T-3461G-FOV_40

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_40.rds

value: F

value: ascending colon

value: dMMR

value: RHS


title: P172_32

description: Library name: P172_32

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

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

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: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: stimulated vector + hAD-tau_21DIV_S1 [DIV21_sti_AD1_Mock]

description:
PhP_sti_RNA_table.txt
DIV21_sti_AD1_Mock

tag: cell type

value: Primary hippomcapal neurons

tag: treatment


title: LV_2111_female_ALDO

description:
Library name: LIB-00056
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

tag: tissue

value: heart, left ventricle free-wall


title: P172_31

description: Library name: P172_31

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

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

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: test article_administration_duration

value: Dimethyl sulfoxide

tag: genotype


title: LV_2110_female_ALDO

description:
Library name: LIB-00055
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

tag: tissue


title: stimulated upACSS2 + hAD-tau_21DIV_S2 [DIV21_sti_AD2_OE]

description:
PhP_sti_RNA_table.txt
DIV21_sti_AD2_OE

tag: cell type

tag: treatment


title: 170T-120131-FOV_40

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_40.rds

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: 118N-148191A-FOV_40

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118N-148191A-FOV_40.rds

value: M

value: caecum

value: RHS


title: LV_2109_female_CTRL

description:
Library name: LIB-00054
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

value: heart, left ventricle free-wall


title: P172_29

description: Library name: P172_29

value: Liver

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 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

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: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

value: wild-type


title: stimulated upACSS2 + hAD-tau_21DIV_S3 [DIV21_sti_AD3_OE]

description:
PhP_sti_RNA_table.txt
DIV21_sti_AD3_OE

tag: cell type

value: Primary hippomcapal neurons

tag: treatment


title: P172_30

description: Library name: P172_30

tag: tissue

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

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

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: test article_administration_duration

value: Dimethyl sulfoxide

tag: genotype


title: LV_2114_male_CTRL

description:
Library name: LIB-00059
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads

tag: tissue

value: heart, left ventricle free-wall


title: stimulated vector + hAD-tau_21DIV_S3 [DIV21_sti_AD3_Mock]

description:
PhP_sti_RNA_table.txt
DIV21_sti_AD3_Mock

tag: cell type

tag: treatment


title: stimulated upACSS2 + hAD-tau_21DIV_S1 [DIV21_sti_AD1_OE]

description:
PhP_sti_RNA_table.txt
DIV21_sti_AD1_OE


title: LV_2108_female_CTRL

description:
Library name: LIB-00053
FANS of viable nuclei, 10XGenomics v3.1 dual index kit, 2x100PE, ~275M reads


title: 74T-10501A-FOV_40

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_40.rds

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

value: LHS


title: P172_28

description: Library name: P172_28

value: Liver

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 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

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: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: P172_27

description: Library name: P172_27

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

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

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: test article_administration_duration

value: hour

tag: genotype

value: wild-type

tag: treatment


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

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_Rep3_T40
Column name in IP_ReadCounts.xlsx: IP, Rep3, Gminus, T40

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

value: WT

value: Glucose deplete

tag: batch

value: IP, Rep3


title: 142N-Run5850.2186.2-FOV_4

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.2-FOV_4.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: ischemia kidney WT6

city: Chapel Hill

first: Jiayi

last: Zhou

state: NC

address: 703, 160 Medical Dr.

department: Pathology and Lab Medicine

institute: University of North Carolina Chapel Hill

description: Library name: S11

data_processing:
These raw sequences were aligned to the ensembl gene database using the SALMON aligner, followed by annotation using Gencode v44. Quantification of gene expression levels was conducted with the Stringtie transcriptome aligner. Utilizing a Python script (prepDE.py) provided by Stringtie, count matrices for genes and transcripts were generated from the output files.
Assembly: ensembl
Supplementary files format and content: text file
Supplementary files format and content: csv. File

source_name: Kidney

extract_protocol:
Total kidney RNA was extracted using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacture’s protocol.
Library preparation and sequencing were performed by High Throughput Sequencing Facility at UNC Chapel Hill. Paired-end raw sequences of 100 bp were acquired by NextSeq 2000 (Illumina, San Diego, CA), and subsequent demultiplexing was performed using bclconvert with a 1-mismatch threshold to segregate reads based on indexes.

value: Kidney

value: Wildtype

value: ischmeia reperfusion injury


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

description:
Library name: IP_Rep3_T20
Column name in IP_ReadCounts.xlsx: IP, Rep3, Gminus, T20


title: ischemia kidney WT5

description: Library name: S10


title: P172_26

description: Library name: P172_26

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

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 concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid


title: 142N-Run5850.2186.1-FOV_4

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_4.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


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

description:
Library name: IP_Rep3_T10
Column name in IP_ReadCounts.xlsx: IP, Rep3, Gminus, T10

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep3


title: 170N-Normal_A-FOV_4

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
170N-Normal_A-FOV_4.rds

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

value: sigmoid

value: pMMR

value: LHS


title: P172_25

description: Library name: P172_25

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

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

value: hour

value: wild-type


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

description:
Library name: IP_Rep3_T5
Column name in IP_ReadCounts.xlsx: IP, Rep3, Gminus, T5

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep3


title: P172_24

description: Library name: P172_24

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

value: Sigma-aldrich

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

value: penicillin/streptomycin

value: nanomolar

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid


title: 7T-3461G-FOV_4

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_4.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: ischemia kidney WT2

description: Library name: S7

value: Kidney

tag: genotype

value: Wildtype

tag: treatment

value: ischmeia reperfusion injury


title: P172_23

description: Library name: P172_23

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

value: wild-type


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

description:
Library name: IP_Rep3_T0
Column name in IP_ReadCounts.xlsx: IP, Rep3, Gminus, T0

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep3


title: 118N-148191A-FOV_4

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118N-148191A-FOV_4.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


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

description:
Library name: IP_Rep3_T2_5
Column name in IP_ReadCounts.xlsx: IP, Rep3, Gminus, T2.5


title: 118T-Tumour_A-FOV_4

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118T-Tumour_A-FOV_4.rds


title: 280N-120131-FOV_4

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280N-120131-FOV_4.rds

value: F


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

description:
Library name: IP_Rep2_T40
Column name in IP_ReadCounts.xlsx: IP, Rep2, Gminus, T40

value: IP, Rep2


title: ischemia kidney HH5

description: Library name: S5

value: Kidney

value: Elmo1 HH

value: ischmeia reperfusion injury


title: P172_22

description: Library name: P172_22

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

value: nanomolar

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid


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

description:
Library name: IP_Rep2_T20
Column name in IP_ReadCounts.xlsx: IP, Rep2, Gminus, T20

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep2


title: P172_21

description: Library name: P172_21

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

value: Williams E medium

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

value: wild-type


title: ischemia kidney HH4

description: Library name: S4

tag: tissue

value: Kidney

tag: genotype

value: Elmo1 HH

tag: treatment

value: ischmeia reperfusion injury


title: P172_20

description: Library name: P172_20

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

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

value: type I collagen

value: Nuaire

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: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: 73T-Run5850.2186.2-FOV_39

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_39.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: 74T-10501A-FOV_4

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_4.rds

value: descending colon

value: dMMR


title: ischemia kidney HH3

description: Library name: S3

value: Kidney

tag: genotype

value: Elmo1 HH

tag: treatment


title: P172_19

description: Library name: P172_19

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 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

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 final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

value: Dimethyl sulfoxide

value: wild-type


title: ischemia kidney WT4

description: Library name: S9

tag: tissue

tag: genotype

value: Wildtype

tag: treatment

value: ischmeia reperfusion injury


title: 73T-Run5850.2186.1-FOV_39

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_39.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: ischemia kidney WT3

description: Library name: S8

value: Kidney


title: ischemia kidney HH2

description: Library name: S2

value: Elmo1 HH


title: 142T-3461G-FOV_39

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_39.rds

value: F

value: ascending colon

value: dMMR

value: RHS


title: P172_18

description: Library name: P172_18

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: strain ontology

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

value: penicillin/streptomycin

tag: treatment addition_volume

tag: treatment stock_concentration

value: nanomolar

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


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

description:
Library name: IP_Rep2_T2_5
Column name in IP_ReadCounts.xlsx: IP, Rep2, Gminus, T2.5

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep2


title: ischemia kidney HH1

description: Library name: S1

tag: tissue

value: Kidney

value: Elmo1 HH

value: ischmeia reperfusion injury


title: ischemia kidney WT1

description: Library name: S6

value: Wildtype


title: P172_17

description: Library name: P172_17

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

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: anitibiotic name

tag: antibiotic concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

value: Dimethyl sulfoxide

value: wild-type


title: 278N-148191A-FOV_39

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_39.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: IP RNA, biol rep2, glucose deplete condition, timepoint 0

description:
Library name: IP_Rep2_T0
Column name in IP_ReadCounts.xlsx: IP, Rep2, Gminus, T0

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Glucose deplete

tag: batch

value: IP, Rep2


title: 170T-120131-FOV_39

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_39.rds

value: F

value: sigmoid


title: P172_16

description: Library name: P172_16

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 ontology

tag: culture vessel_type

tag: culture vessel_vendor

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

value: nanomolar

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


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

description:
Library name: IP_Rep1_T40
Column name in IP_ReadCounts.xlsx: IP, Rep1, Gminus, T40

tag: cell line

tag: genotype

value: WT

tag: treatment

tag: batch

value: IP, Rep1