title: 118T-Tumour_A-FOV_8

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_8.rds


title: STEPN-25 (SMART-Seq2)

status: Public on Dec 09 2025

type: SRA

city: Boston

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

country: USA

institute: Dana Farber Cancer Institute

description:
Library name: STEPN-25
snRNA-seq Patient single-cell RNA-seq

library_source: transcriptomic single cell

data_processing:
Illumina bcl2fastq 2.20.0.422 and cellranger 7.1.0 were used for demultiplexing
For SMART-Seq2: RNA-seq sequenced reads were mapped to hg19  using hisat2 (2.1.0) with parameters --met 5 -k 10 --mp 1,1 --np 1 --score-min L,0,-0.1 --secondary --no-mixed --no-softclip --no-discordant --rdg 99999999,99999999 --rfg 99999999,99999999 --no-spliced-alignment --seed 12345  For 10x: cellranger counts v7.1.0 was used to generate all output files (matrix, features, and barcodes). A custom GRCh38 + tdTomato sequence reference was used, and for human + rat samples another custom reference was used with GRCh38 + mRatBN7-2 + tdTomato.
For SMART-Seq2: RNA-seq TPM and counts were calculated using RSEM (v1.3.1) with parameters --estimate-rspd --paired-end -sam
Assembly: hg19, GRCh38 and mRatBN7-1
Supplementary files format and content: Tab-separated values with counts matrix files, qc metrics, and 10x cellranger output filtered bc matrix.

molecule: total RNA

organism: Homo sapiens

source_name: Ependymoma Patient single-cell

growth_protocol: ZFTA-RELA patient derived xenografts. EP1NS, BT165 and VBT242 cells (500,000 cells in 3 μL PBS per mouse) were injected stereotactically into the cortex of 6-week-old female NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ, The Jackson Laboratory, RRID:IMSR_JAX:005557), which were treated with 0.05 mg/kg buprenorphine and anesthetized with 2% to 3% isoflurane. The skull of the mouse was exposed through a small skin incision, and a small burr hole was made using a 25-gauge needle at the selected stereotactic coordinates: 1.0 mm X, 1 mm Y and -1.5 mm Z. After injection, mice were checked daily for signs of distress, including seizures, weight loss, or tremors. Tumor size was monitored monthly by small animal MRI and BLI starting 4 weeks after injection. Mice were euthanized as they developed neurologic symptoms, including head tilt, seizures, sudden weight loss, loss of balance, and/ or ataxia. All animal studies were performed according to Dana- Farber Cancer Institute Institutional Animal Care and Use Committee (IACUC)–approved protocols (13-053).  ZFTA-RELA patient-derived cell lines. Cells were grown in “complete Neurobasal medium”, which consisted in Neurobasal™-A Medium (ThermoFisher Scientific, 10888022) supplemented with 1X of Antibiotic-Antimycotic 100X (ThermoFisher Scientific, 15240062), 1X GlutaMAXTM (ThermoFisher Scientific, 35050061), 1 mg/mL Heparin solution (StemCell Technologies, 7980), 1X B-27 (Thermo Fisher Scientific, 12587010), 20 ng/ml recombinant Human FGF-basic (Shenandoah Biotech, 100-146) and 20 ng/ml recombinant Human EGF (Shenandoah Biotech, 100-26). For further passaging, floating cells were centrifuged at 300g for 5 min, dissociated with Accutase (Innovative Cell Technologies, Inc., AT104-500) for 5 min at 37 °C, and washed with PBS (Gibco, 10010023).  In vitro co-culture. Primary cultures of rat cortical neurons and astrocytes were prepared from E19 embryos. They were plated at a density of 90.000 cells/cm2 on 12mm diameter coverslips on 24-well plates that were previously coated with poly-L-lysine. The cells were maintained in neurobasal medium supplemented with B27 supplement (50x, 2% v/v) and L-glutamine (0.5 mM). After 7 days, accutase dissociated, cells from patient-derived ZFTA-RELA cell lines were added and co-cultured (1000 cells/well). For timelapse live-cell imaging or immunohistochemistry, coverslips were used 4-14 days in vitro (DIV) after seeding ZFTA-RELA cells. As a control, in vitro monocultures of ZFTA-RELA cells were established from patient-derived ZFTA-RELA cell lines as follows. 12mm diameter coverslips on 24-well plates were coated using poly-L-lysine and maintained in neurobasal medium supplemented with B27 supplement (50x, 2% v/v) and L-glutamine (0.5 mM). After 7 days, accutase dissociated, ZFTA-RELA cells were added and cultured (1000-10000 cells/well). For timelapse live-cell imaging immunohistochemistry, coverslips were used 4-14 days in vitro (DIV) after seeding ZFTA-RELA cells.

extract_protocol:
Sorting of cells grown in cocultures. DIV 08 coverslips of mono- and co-culture were incubated with Trypsin for 5 minutes. Next, 10% FBS was added and cells were washed from coverslips. The samples were stained with a DAPI as a dead cell marker to identify the live cell population. The single cell suspension was sorted with a FACSAria Fusion 2 (BD Biosciences). Tumor cells were identified by their tdTomato expression.  Fresh tumor processing. Live cells were isolated from immediately processed fresh tumor tissue acquired at the time of surgery. Fresh tumor tissue was mechanically dissociated and enzymatically digested using the Brain Tumor Dissociation Kit (Miltenyi Biotec, 130-095-942) and gentleMACS dissociator (Miltenyi Biotec, 130-096-427) for 30 min at 37 °C. Single-cell suspensions were filtered through a 70 µm strainer (Fisher Scientific, 03-421-228), centrifuged at 500g for 5 minutes and resuspended in a solution of 1% bovine serum albumin (BSA) (Biolegend, 644710) in phosphate-buffered saline (PBS) for fluorescence activated cell sorting (FACS).  Frozen tumor processing. Nuclei for snRNA-seq were extracted from snap frozen as well as optimal cutting temperature (OCT)- embedded tumor tissues. Snap frozen tumor tissue was cut on ice while OCT-embedded tissue was cut on a cryostat at -20 °C and washed with PBS. Frozen tumor tissue was suspended in CST and dissociated with sterile surgical scissors for 5 minutes until homogenous. Dissociated tissue was filtered through a 70 µm strainer, 1XST was added to the nuclei solution and once more transferred through a 70 µm strainer. The nuclei solution was centrifuged at 500g for 5 min. Single-nuclei suspensions were re-suspended in PBS supplemented with 1% BSA (Smart-seq2), or 0.05% BSA (10X Genomics). All steps were performed at 4 °C.  Live cell sorting. A single cell suspension of 100 uL (kept in a FACS-tube in PBS/BSA at 4°C) was used for all sorting procedures as unstained control. For stained controls 0,75μL Calcein AM (Life technologies, C34851) and 0.5μL TO-PRO3 Iodide (Life technologies, T3605) were added to resuspended cells in 100μL PBS/1%BSA for 10 min at room temperature (RT). Single-cell sorting was performed on a SH700 sorter (Sony). Single viable tumor cells were selected by positive staining for calcein AM as well as negative staining for TO-PRO3 and sorted into pre chilled (4 °C) 96 well plates containing TCL buffer (Qiagen, 1031576) + 1% β-mercaptoethanol (Thermo Fisher. 21985023).  Sorted plates were centrifuged at 1000 x g for 1 minute at 4 °C and frozen on dry ice followed by transfer to a -80°C freezer for long term storage before whole transcriptome amplification, library preparation and sequencing.  Nuclei sorting. Dissociated frozen tumor tissue derived single-nuclei suspensions were resuspended in PBS + 1% BSA and stained with 2.5mM Vybrant DyeCycle Ruby Stain (Life Technology, V10309). Nuclei sorting was performed on a SH700 SONY sorter. Intact nuclei were sorted into pre chilled (4 °C) 96-well plates containing TCL buffer + 1% β-mercaptoethanol. Sorted plates were centrifuged at 1000 x g for 1 minute at 4 °C and frozen on dry ice followed by transfer to a -80°C freezer for long term storage before whole transcriptome amplification, library preparation and sequencing.
Smart-seq2 whole transcriptome amplification, library preparation and sequencing of single cells/nuclei were performed following a modified Smart-seq2 protocol. RNA was purified with RNAClean XP beads (Beckman Coulter, A66514). Next Oligo-dT primed reverse transcription (RT) was performed using Maxima H Minus reverse transcriptase (Life Technologies, EP0753) and a template-switching oligonucleotide (TSO; Qiagen) followed by PCR amplification (20 cycles for scRNA-seq and 22 cycles for snRNA-seq) using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, 07958935001), and by AMPure XP bead (Beckman Coulter, A63882) purification. Libraries were generated using the Nextera XT Library Prep kit (Illumina, FC-131-1096). Libraries from 768 cells with unique barcodes were combined and sequenced using a NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906) on a NextSeq 500 sequencer (Illumina).

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-Cluster 2

tag: Sex

value: M

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: v6_bg

city: Stockholm

first: Nik

middle: V

last: Kuznetsov

address: Nobels vag 16

country: Sweden

institute: Karolinska Institute

description: Library name: T22

library_source: transcriptomic

data_processing:
RNA sequencing and data quality control was performed with Illumina HiSeq-PE150 Platform at Novogene (Hongkong).
Sequences were mapped to the reference genome with HISAT2, v.2.0.5.
Reads were aligned to the human reference genome assembly December 2013 (GRCh38/hg38). STAR software was used to accomplish the mapping of clean reads to the reference genome or transcriptome.
Filtering of data, alignment of RNA-seq reads, gene ontology were arranged at Novogene (Hongkong).
DESeq2 in R package was used for DEG analysis. In gene expression analysis, H-cluster, K-means, and SOM were used to cluster the log2 (ratios).
Assembly: GRCh38/hg38 (December 2013)
Supplementary files format and content: Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Supplementary files format and content: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then fpkm of each gene was calculated based on the length of the gene and reads count mapped to this gene.  All fpkm values for each of genes are listed in the excel file "FPKM".

source_name: peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient centrifugation isolation protocol optimized for Ficoll-Paque™ PLUS (Cytiva). Human T cells were enriched by the positive CD3 cell selection Kit (EasySep™ Human CD3 Positive Selection Kit II, Stem Cell Technology). Total RNA was purified from sorted cells using RNeasy kit and treated with RNAse-free DNAse kit(##74104; 79254 QIAGEN, Hilden, Germany). The total RNA concentration was measured (NanoDrop2000, Thermo Scientific, Wilmington, DE, USA) and RNA integrity and purity was evaluated by gel electrophoresis analysis (1xTAE 1% UltraPureAgarose, #16500500 Invitrogen, Waltham, MA, USA). All selected isolated RNA samples were subjected to and have passed both the internal lab quality control (QC) and the QC performed by sequencing company (Novogene, Hongkong).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: In total, five samples of 10ml peripheral blood each were collected in sodium heparin tube from each volunteer at five time points during the time course of simulated microgravity (SMG) study: at 7 days prior to Day 0 of SMG (timepoint “background, bg“), after 7 days (timepoint “7d”), 14 days  (timepoint “14d”), 21 days (timepoint “21d”) in SMG, and another 7 days after the SMG (timepoint “28 days”).

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: non-treated control

tag: time


title: P172_97

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Library name: P172_97

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

organism: Mus musculus

source_name: Liver

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

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

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null


title: 142N-Run5850.2186.2-FOV_8

type: RNA

city: Clayton

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

department: Anatomy and developmental biology

country: Australia

institute: Monash University

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.2-FOV_8.rds

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

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

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

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

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

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

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: STEPN-24 (SMART-Seq2)

description:
Library name: STEPN-24
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

value: ZFTA-Cluster 1

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: v7_bg

description: Library name: T31

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: non-treated control

tag: time


title: v5_28d

description: Library name: T29

tag: tissue

value: treated timepoint 4


title: P172_96

description: Library name: P172_96

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype


title: 142N-Run5850.2186.1-FOV_8

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_8.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: STEPN-23 (SMART-Seq2)

description:
Library name: STEPN-23
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 1

value: M

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: P172_95

description: Library name: P172_95

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

value: Dimethyl sulfoxide

value: DRE-null

tag: treatment


title: 7N-Normal_A-FOV_8

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7N-Normal_A-FOV_8.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.

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: v5_21d

description: Library name: T27

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 3

tag: time


title: STEPN-22 (SMART-Seq2)

description:
Library name: STEPN-22
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 1

value: M

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: P172_94

description: Library name: P172_94

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: v5_14d

description: Library name: T25

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 2

tag: time


title: P172_93

description: Library name: P172_93

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

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

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

value: nanomolar

value: hour

value: Dimethyl sulfoxide

value: DRE-null


title: 118N-148191A-FOV_8

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_8.rds

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

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: STEPN-21 (SMART-Seq2)

description:
Library name: STEPN-21
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 1

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: STEPN-20 (SMART-Seq2)

description:
Library name: STEPN-20
scRNA-seq Patient single-cell RNA-seq

value: ZFTA-RELA

value: F

value: scRNA-seq


title: v5_7d

description: Library name: T23

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 1

tag: time


title: v6_14d

description: Library name: T26

tag: tissue

value: treated timepoint 2


title: P172_92

description: Library name: P172_92

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null


title: 280T-120131-FOV_8

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280T-120131-FOV_8.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: v5_bg

description: Library name: T21

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: non-treated control

tag: time


title: STEPN-19 (SMART-Seq2)

description:
Library name: STEPN-19
scRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

value: M

tag: age

tag: type

value: scRNA-seq

tag: fusion


title: P172_98

description: Library name: P172_98

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype


title: v4_28d

description: Library name: T20

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 4

tag: time


title: 74T-10501A-FOV_8

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_8.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_91

description: Library name: P172_91

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

value: Dimethyl sulfoxide

value: DRE-null


title: STEPN-18 (SMART-Seq2)

description:
Library name: STEPN-18
scRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 2

tag: Sex

tag: age

tag: type

value: scRNA-seq

tag: fusion


title: P172_90

description: Library name: P172_90

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

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

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

value: nanomolar

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: v4_21d

description: Library name: T18

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 3

tag: time


title: 118T-Tumour_A-FOV_7

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_7.rds

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: STEPN-15 (SMART-Seq2)

description:
Library name: STEPN-15
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: v4_14d

description: Library name: T16

tag: treatment

value: treated timepoint 2


title: P172_89

description: Library name: P172_89

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

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

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null


title: P172_88

description: Library name: P172_88

tag: tissue

value: Liver

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

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

tag: basal medium

value: penicillin/streptomycin

value: nanomolar

tag: treatment


title: 7T-3461G-FOV_8

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_8.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: v4_7d

description: Library name: T14

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 1

tag: time


title: 142N-Run5850.2186.1-FOV_7

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_7.rds

value: F

value: dMMR


title: v4_bg

description: Library name: T12

value: non-treated control


title: 7T-3461G-FOV_7

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_7.rds


title: STEPN-12 (SMART-Seq2)

description:
Library name: STEPN-12
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-RELA

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: STEPN-11 (SMART-Seq2)

description:
Library name: STEPN-11
snRNA-seq Patient single-cell RNA-seq


title: P172_86

description: Library name: P172_86

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null

tag: treatment


title: P172_85

description: Library name: P172_85

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

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

tag: basal medium

tag: basal medium_vendor

value: nanomolar


title: P172_87

description: Library name: P172_87

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age

tag: age unit

value: day

tag: age unit_ontology

tag: Sex

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture 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: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: v3_21d

description: Library name: T17

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 3

tag: time


title: P172_84

description: Library name: P172_84

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age

tag: age unit

tag: age unit_ontology

tag: Sex

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

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration


title: 118N-148191A-FOV_7

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_7.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: STEPN-10 (SMART-Seq2)

description:
Library name: STEPN-10
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: STEPN-09 (SMART-Seq2)

description:
Library name: STEPN-09
snRNA-seq Patient single-cell RNA-seq


title: 142N-Run5850.2186.2-FOV_7

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_7.rds

value: ascending

value: dMMR


title: 170N-Normal_A-FOV_7

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_7.rds

value: sigmoid

value: LHS


title: v3_7d

description: Library name: T13

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 1

tag: time


title: P172_83

description: Library name: P172_83

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null


title: 74T-10501A-FOV_7

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_7.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: M

tag: age at diagnosis

tag: primary tumour location

value: descending colon

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: LHS


title: STEPN-08 (SMART-Seq2)

description:
Library name: STEPN-08
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: v3_bg

description: Library name: T11

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: non-treated control

tag: time


title: P172_82

description: Library name: P172_82

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: genotype


title: STEPN-07 (SMART-Seq2)

description:
Library name: STEPN-07
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

value: ZFTA-RELA

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: P172_81

description: Library name: P172_81

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

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

value: nanomolar

value: hour

value: Dimethyl sulfoxide

value: DRE-null

tag: treatment


title: 118T-Tumour_A-FOV_6

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_6.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: STEPN-14 (SMART-Seq2)

description:
Library name: STEPN-14
NA Patient single-cell RNA-seq

tag: sampling

value: Recurrence

tag: subtype

tag: age

tag: type

tag: fusion


title: STEPN-13 (SMART-Seq2)

description:
Library name: STEPN-13
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

value: Primary


title: v2_28d

description: Library name: T10

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 4

tag: time


title: v3_28d

description: Library name: T19

tag: treatment


title: v2_21d

description: Library name: T8

tag: tissue

value: treated timepoint 3


title: STEPN-06 (SMART-Seq2)

description:
Library name: STEPN-06
snRNA-seq Patient single-cell RNA-seq

value: ZFTA-RELA

value: snRNA-seq


title: v3_14d

description: Library name: T15

value: treated timepoint 2


title: 280N-120131-FOV_7

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_7.rds

tag: donor

value: F


title: P172_80

description: Library name: P172_80

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null


title: STEPN-05 (SMART-Seq2)

description:
Library name: STEPN-05
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

value: ZFTA-RELA

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: 142N-Run5850.2186.2-FOV_6

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_6.rds

value: Colon tumour,FFPE

tag: donor

tag: age at diagnosis

tag: primary tumour location

value: ascending

tag: total cells

tag: mmr status

value: dMMR

tag: sidedness

value: RHS


title: STEPN-04 (SMART-Seq2)

description:
Library name: STEPN-04
snRNA-seq Patient single-cell RNA-seq

value: Primary


title: P172_79

description: Library name: P172_79

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

tag: test article_name

tag: test article_dtxsid

tag: treatment


title: v2_14d

description: Library name: T6

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 2

tag: time


title: P172_78

description: Library name: P172_78

tag: cell type_ontology

tag: tissue ontology

tag: strain

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

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

value: penicillin/streptomycin

value: nanomolar

value: hour

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null


title: v2_bg

description: Library name: T2

tag: tissue

tag: cell type

tag: volunteer #

tag: treatment

value: non-treated control

tag: time


title: 7T-3461G-FOV_6

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_6.rds

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: 142N-Run5850.2186.1-FOV_6

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_6.rds

value: F

value: dMMR


title: 73T-Tumour_B-FOV_6

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73T-Tumour_B-FOV_6.rds

value: sigmoid

value: LHS


title: STEPN-03 (SMART-Seq2)

description:
Library name: STEPN-03
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

value: ZFTA-RELA

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: 170N-Normal_A-FOV_6

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_6.rds

tag: tissue


title: v2_7d

description: Library name: T4

value: peripheral blood

tag: cell type

value: T lymphocytes

value: treated timepoint 1


title: STEPN-02 (SMART-Seq2)

description:
Library name: STEPN-02
snRNA-seq Patient single-cell RNA-seq

value: Primary

value: SYVN1::MAJIN; NFIB::VPS51


title: 118N-148191A-FOV_6

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_6.rds

value: Colon tumour,FFPE

value: caecum


title: STEPN-01 (SMART-Seq2)

description:
Library name: STEPN-01
snRNA-seq Patient single-cell RNA-seq


title: v1_21d

description: Library name: T7

tag: volunteer #

value: treated timepoint 3


title: 280N-120131-FOV_6

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_6.rds

value: pMMR


title: P172_75

description: Library name: P172_75

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

value: DRE-null

tag: treatment


title: P172_74

description: Library name: P172_74

tag: tissue

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

tag: basal medium

tag: basal medium_vendor


title: STEMdiff™ Kidney Organoid Kit, CloneR™2, 3D, rep1

city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

country: Canada

institute: STEMCELL Technologies

description:
Library name: Illumina-Kidney-CloneR2-3D
scRNA-seq data of kidney organoids differentiated in STEMdiff™ Kidney Organoid Kit and generated in 3D with CloneR™2 and Y-27632

data_processing:
The barcoded processing, gene counting and aggregation were made using the Fluent BioSciences PIPSeeker software v3.3.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Kidney

extract_protocol:
Single Cell Dissociation of 3D Organoids: Day 18 3D kidney organoid were harvested from Aggrewell HT into a 1.5 mL tube using a wide bore pipette and washed twice with PBS. 1 mL of cold Trypsin-EDTA (0.05%) and Dnase (1:50) were added and the organoids were incubated at 37°C for 10 minutes then triturated 2X with a P1000 pipette. The organoids were again incubated for another 10 minutes then triturated 5X to generate a single cell suspension. FACS buffer was added to the suspension to deactivate the trypsin. Single cells were centrifuged at 300g for 5 mins, then the supernatant was discarded and 1 mL of pre-warmed Cell Suspension Buffer was added. Cell concentration, viability and percent of clumps were determined using a Nucleocounter.  Single Cell Dissociation of 2D Organoids: On day 18, 2D monolayers were washed with PBS and kidney tubules were first enriched by a crude removal of the mesenchymal monolayer. This was done by incubating the monolayers at 37°C for 10 minutes after adding cold Trypsin-EDTA (0.05% and Dnase (1:50). Then with a P1000 pipette and medium force, the trypsin-Dnase mixture was sprayed onto the cells 5X to detach the mesenchymal cells. This trypsin-Dnase-single cell suspension mixture was removed from the well and discarded. Fresh trypsin and Dnase were added to the remaining tubules in the well and the plate was incubated at 37°C for 20 minutes. The tubules were then triturated 5X with a P1000 then incubated again for 5 minutes. A single cell suspension was generated after another round of 6X trituration and FACS buffer was added to the suspension to deactivate the trypsin. Single cells were centrifuged at 300g for 5 mins, then the supernatant was discarded and 1 mL of pre-warmed Cell Suspension Buffer was added. Cell concentration, viability and percent of clumps were determined using a Nucleocounter.  PIPseq V Cell Preparation: After the cell counts, both 2D and 3D samples were then centrifuged at 200g for 3 minutes (RT), followed by aspiration of the supernatant. 200-400uL of cold cell suspension buffer is added to the pellet and gently mixed 10-15 times to resuspend. The single cell concentration was determined using both the Nucleocounter and the Luna Fx7 Automated Cell Counter. A suspension of 2,500 live cells/uL is prepared in a cell suspension buffer to achieve an input volume of 4uL (10,000 live cells/uL) into a PIP reaction.
Library preparation was performed according to the manufacturer’s instructions (Illumina Single Cell 3′ RNA Prep, T10, Illumina). Briefly, single cells were combined with Particle-templated Instant Partitions (PIPs) and barcoded beads to generate emulsified partitions. Following chemical lysis, mRNA released from each partition was reverse transcribed into barcoded cDNA. The cDNA was then amplified by whole transcriptome amplification, isolated from PIPs, and purified using magnetic beads. Quality control included Qubit quantification and fragment analysis. For library construction, cDNA underwent fragmentation, end repair and A-tailing, adapter ligation, and sample index PCR to add Illumina P5, P7, and index sequences. Final libraries were cleaned with magnetic beads and prepared for sequencing on Illumina platforms.

tag: tissue

value: Kidney

tag: cell line

tag: treatment


title: v1_14d

description: Library name: T5

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 2

tag: time


title: 74T-10501A-FOV_6

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_6.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: STEMdiff™ Kidney Organoid Kit, CloneR™2, 2D, rep1

description:
Library name: Illumina-Kidney-CloneR2-2D
scRNA-seq data of kidney organoids differentiated in STEMdiff™ Kidney Organoid Kit and generated in 2D with CloneR™2 and Y-27632


title: 278T-148191A-FOV_51

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
278T-148191A-FOV_51.rds

value: rectal

value: pMMR


title: v1_7d

description: Library name: T3

value: treated timepoint 1


title: P172_73

description: Library name: P172_73

tag: cell type_ontology

tag: tissue ontology

tag: strain

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

value: Williams E medium

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype


title: 46T-148191A-FOV_50

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_50.rds

tag: tissue

value: Colon tumour,FFPE

tag: donor

tag: Sex

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: v1_bg

description: Library name: T1

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: non-treated control

tag: time


title: P172_77

description: Library name: P172_77

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

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

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

value: DRE-null


title: P172_76

description: Library name: P172_76

tag: tissue

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

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

value: Nuaire

tag: incubator model

value: Williams E medium

value: Sigma-aldrich

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

value: penicillin/streptomycin

value: nanomolar

value: hour

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

tag: genotype

tag: treatment


title: P172_72

description: Library name: P172_72

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: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

tag: test article_name

value: wild-type