title: P172_130

description: Library name: P172_130

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

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 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: Williams E medium

value: Sigma-aldrich

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

value: penicillin/streptomycin

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: DRE-null


title: U2 rep1

status: Public on Dec 09 2025

type: SRA

city: Kraków

first: Dominika

last: Wloch-Salamon

state: Małopolskie

address: Gronostajowa 7,, 14

country: Poland

institute: Jagiellonian University

description:
Library name: NQ_III_3_1
NQ3III1

library_source: transcriptomic

data_processing:
Library construction, sequencing, and the subsequent bioinformatic analysis were carried out by Novogene. Lists of differentially expressed genes (DEGs) were created using the DESeq2 R package
Assembly: Saccharomyces cerevisiae
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Saccharomyces cerevisiae S288C

source_name: population

growth_protocol: Clones were incubated shaking overnight in rich medium at 30°C. The following day, 20 μl of liquid culture (of each clone) was transferred to a 20 ml of YPD medium and incubated shaking at 30 °C for 7 days. Yeast cells were then separated into U and L fractions using Percoll centrifugation (as described previously by Allen at all.  2006) and only L fraction quiescent cells were used. Post-centrifugation, quiescent L cells were collected from the bottom of the tubes and subjected to two sequential washes 8 mL of Tris buffer. After each wash, the supernatant was carefully removed.

extract_protocol:
The optical density (OD) of each sample was measured to ensure an extraction efficiency yielding approximately ≥20 ng/µL, corresponding to ~3 × 10⁸ cells. Total RNA was extracted from the isolated Q cells using the Ribo-Pure™-Yeast Kit (Thermo Fisher Scientific), following the manufacturer's protocol. Each samples had two tech-nical repetition (1/2) that were then stored at –70°C.
Library construction, sequencing, and the subsequent bioinformatic analysis were carried out by Novogene.

tag: strain

tag: cell type

value: quiescent cells

tag: genotype

value: prototroph

tag: treatment

value: 15 days starvation, fractionation, lower fraction

tag: batch


title: U1 rep2

description:
Library name: NQ_I_3_2
NQ3I2

value: 8 days starvation, fractionation, lower fraction


title: ACHN Cells, Control replicate 2

city: Seoul

first: Aeryang

last: Jung

address: 222, Banpo-Daero

department: Urology

country: South Korea

institute: The Catholic University, Seoul

description:
Library name: Control_2
Control-3

data_processing:
Raw reads were quality-checked using FastQC. Adapters and low-quality bases were trimmed with Trimmomatic. Reads were aligned to the human reference genome using TopHat. Aligned reads were quantified using ExDEGA (E-Biogen Inc., Seoul, Republic of Korea). Differential expression and pathway enrichment analyses were performed using ExDEGA and DAVID bioinformatics resources.
Assembly: Human reference genome GRCh38 (hg38).
Supplementary files format and content: Processed data are provided as a CSV file (read_counts_matrix.csv) containing raw read counts per gene (rows = genes, columns = samples).

organism: Homo sapiens

source_name: ACHN Cells

growth_protocol: ACHN renal cell carcinoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Thermo Fisher Scientific, USA). RNA integrity was confirmed by Bioanalyzer prior to library construction.
RNA libraries were prepared using the NEBNext Ultra Directional RNA-Seq Kit (New England BioLabs, Rowley, MA, USA) according to the manufacturer’s protocol. Libraries were sequenced on the Illumina HiSeq 2500 platform to generate paired-end 100 bp reads.

treatment_protocol: Cells were treated with vehicle control (DMSO), niclosamide (1 µM), sunitinib (2.5 µM), or the combination of niclosamide (1 µM) and sunitinib (2.5 µM) for the indicated durations prior to RNA extraction.

tag: cell line

value: ACHN Cells

value: wild type

value: DMSO control

value: batch 1


title: P172_129

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

country: USA

institute: Michigan State University

description: Library name: P172_129

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.

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

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

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: ACHN Cells, Control replicate 1

description:
Library name: Control_1
Control-2

tag: cell line

tag: genotype

tag: treatment

tag: batch


title: P172_128

description: Library name: P172_128

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

value: Williams E medium

value: Sigma-aldrich

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

value: penicillin/streptomycin

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: DRE-null


title: U1 rep1

description:
Library name: NQ_I_3_1
NQ3I1

tag: strain

tag: cell type

value: quiescent cells

tag: genotype

value: prototroph

tag: treatment

value: 7 days starvation, fractionation, lower fraction

tag: batch


title: P172_127

description: Library name: P172_127

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

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

value: 12-well plate

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_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


title: EP1NS_hiNs (10x)

city: Boston

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description:
Library name: EP1NS_hiNs
scRNA-seq Cell lines 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.

source_name: Ependymoma Cell lines 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 Cell lines single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

tag: Sex

value: F

tag: age

tag: type

value: scRNA-seq

tag: fusion


title: Gc17

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Library name: Sample 26

library_source: genomic

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

molecule: genomic DNA

organism: Giraffa camelopardalis antiquorum

source_name: buccal

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

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

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

tag: cell type

value: buccal


title: Gc18

description: Library name: Sample 27

value: Female


title: T47D,shCUEDC1-3

city: Chongqing

first: Jian

last: Chen

address: 重庆市渝中区医学院路1号

country: China

institute: 重庆医科大学

description:
Library name: Sample6
fpkm_T3

data_processing:
The sequencing data was filtered with SOAPnuke Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio  (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: FPKM,TXT
Supplementary files format and content: readcount,TXT

growth_protocol: T47D cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifired atmosphere  in a 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested

tag: cell line

value: human breast ductal carcinoma cells

tag: genotype

value: CUEDC1 knockdown


title: P172_126

description: Library name: P172_126

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

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

value: Williams E medium

value: Sigma-aldrich

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

value: penicillin/streptomycin

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: DRE-null

tag: treatment


title: T47D,shCUEDC1-2

address: 重庆市渝中区医学院路1号

description:
Library name: Sample5
fpkm_T2

tag: cell line

tag: cell type

tag: genotype


title: VBT242PDX (SMART-Seq2)

description:
Library name: VBT242PDX
snRNA-seq PDX single-cell RNA-seq

source_name: Ependymoma PDX single-cell

tag: tissue

value: Ependymoma PDX single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: Gc16

description: Library name: Sample 25

value: buccal

value: Male


title: Gc15

description: Library name: Sample 24

value: Female


title: VBT242adh (SMART-Seq2)

description:
Library name: VBT242adh
scRNA-seq Cell lines (adherent) single-cell RNA-seq

source_name: Ependymoma Cell lines (adherent) single-cell

value: scRNA-seq


title: P172_124

description: Library name: P172_124

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 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


title: T47D,shCUEDC1-1

address: 重庆市渝中区医学院路1号

description:
Library name: Sample4
fpkm_T1

tag: cell line

tag: cell type

value: human breast ductal carcinoma cells

tag: genotype

value: CUEDC1 knockdown


title: T47D,shNC-3

address: 重庆市渝中区医学院路1号

description:
Library name: Sample3
fpkm_N3

value: Control


title: Gc14

description: Library name: Sample 23

value: buccal

tag: Sex


title: VBT242sph (SMART-Seq2)

description:
Library name: VBT242sph
scRNA-seq Cell lines (spheres) single-cell RNA-seq

source_name: Ependymoma Cell lines (spheres) single-cell

tag: tissue

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

tag: fusion


title: P172_123

description: Library name: P172_123

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age unit

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: 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

value: nanomolar

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: DRE-null

tag: treatment


title: T47D,shNC-2

address: 重庆市渝中区医学院路1号

description:
Library name: Sample2
fpkm_N2

tag: cell line

tag: cell type

value: human breast ductal carcinoma cells

tag: genotype


title: OK-R

description: Library name: Sample 29

organism: Okapia johnstoni

tag: Sex

value: Female


title: Gc13

description: Library name: Sample 22


title: P172_122

description: Library name: P172_122

tag: tissue

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 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

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology


title: OK-A

description: Library name: Sample 28

tag: cell type

value: buccal

tag: Sex


title: BT165adh (SMART-Seq2)

description:
Library name: BT165adh
scRNA-seq Cell lines (adherent) single-cell RNA-seq

tag: tissue

value: Ependymoma Cell lines (adherent) single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

value: scRNA-seq

tag: fusion


title: Gc12

description: Library name: Sample 21


title: v10_28d

city: Stockholm

first: Nik

middle: V

last: Kuznetsov

address: Nobels vag 16

country: Sweden

institute: Karolinska Institute

description: Library name: T50

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

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 4

tag: time


title: Gc11

description: Library name: Sample 20

value: Male


title: v10_21d

description: Library name: T48

value: treated timepoint 3


title: P172_121

description: Library name: P172_121

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 ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

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

value: nanomolar

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: EP1NSPDX (SMART-Seq2)

description:
Library name: EP1NSPDX
snRNA-seq PDX single-cell RNA-seq

tag: tissue

value: Ependymoma PDX single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: P172_125

description: Library name: P172_125

value: Liver

tag: cell type

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age unit

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: treatment


title: Gc9

description: Library name: Sample 18

tag: cell type

value: buccal

tag: Sex

value: Female


title: T47D,shNC-1

address: 重庆市渝中区医学院路1号

description:
Library name: Sample1
fpkm_N1

tag: cell line

value: human breast ductal carcinoma cells

tag: genotype

value: Control


title: v10_7d

description: Library name: T44

tag: tissue

value: peripheral blood

value: T lymphocytes

tag: volunteer #

value: treated timepoint 1

tag: time


title: BT165sph (SMART-Seq2)

description:
Library name: BT165sph
scRNA-seq Cell lines (spheres) single-cell RNA-seq

value: Ependymoma Cell lines (spheres) single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

value: scRNA-seq

tag: fusion


title: EP1NSsph (SMART-Seq2)

description:
Library name: EP1NSsph
scRNA-seq Cell lines (spheres) single-cell RNA-seq

value: Recurrence


title: v10_14d

description: Library name: T46

value: treated timepoint 2


title: v10_bg

description: Library name: T42

value: non-treated control


title: P172_118

description: Library name: P172_118

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

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

value: nanomolar

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: DRE-null


title: P172_117

description: Library name: P172_117

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

value: Williams E medium

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

tag: genotype

tag: treatment


title: Gc8

description: Library name: Sample 17

tag: cell type

value: buccal

tag: Sex

value: Female


title: Gc7

description: Library name: Sample 16

value: Male


title: EP1NSadh (SMART-Seq2)

description:
Library name: EP1NSadh
scRNA-seq Cell lines (adherent) single-cell RNA-seq

tag: tissue

value: Ependymoma Cell lines (adherent) single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-RELA

value: F

tag: age

tag: type

value: scRNA-seq

tag: fusion


title: BT165PDX (SMART-Seq2)

description:
Library name: BT165PDX
snRNA-seq PDX single-cell RNA-seq

value: Ependymoma PDX single-cell

value: Primary

value: snRNA-seq


title: P172_120

description: Library name: P172_120

tag: cell type_ontology

tag: tissue ontology

tag: strain

value: Pkm-delta-DRE

tag: age unit

value: day

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

value: Nuaire

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

value: nanomolar

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: STEPN-44 (SMART-Seq2)

description:
Library name: STEPN-44
snRNA-seq Patient single-cell RNA-seq

source_name: Ependymoma Patient single-cell

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

tag: Sex

value: M

tag: age

tag: type

tag: fusion

value: EPN-YAP


title: v9_28d

description: Library name: T49

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 4

tag: time


title: Gc6

description: Library name: Sample 15

value: buccal

value: Female


title: P172_115

description: Library name: P172_115

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

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

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

value: Dimethyl sulfoxide

tag: genotype

value: DRE-null


title: STEPN-43 (SMART-Seq2)

description:
Library name: STEPN-43
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion

value: EPN-YAP


title: v9_21d

description: Library name: T47

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 3

tag: time


title: Gc10

description: Library name: Sample 19

value: buccal

value: Female


title: Gc5

description: Library name: Sample 14


title: STEPN-42 (SMART-Seq2)

description:
Library name: STEPN-42
snRNA-seq Patient single-cell RNA-seq


title: v9_14d

description: Library name: T45

value: treated timepoint 2


title: P172_114

description: Library name: P172_114

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

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

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

value: nanomolar

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: P172_119

description: Library name: P172_119

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

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

value: Williams E medium

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

tag: treatment concentration_unit_ontology

value: Dimethyl sulfoxide

tag: genotype

value: DRE-null

tag: treatment


title: Gc4

description: Library name: Sample 13

tag: cell type

value: buccal

tag: Sex


title: STEPN-41 (SMART-Seq2)

description:
Library name: STEPN-41
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Primary

tag: subtype

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion

value: EPN-YAP


title: P172_113

description: Library name: P172_113

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

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

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

tag: culture additives_concentration

tag: anitibiotic name

tag: antibiotic concentration

tag: treatment addition_volume

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid


title: v9_7d

description: Library name: T43

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 1

tag: time


title: Gc3

description: Library name: Sample 12

value: buccal

tag: Sex

value: Female


title: STEPN-40 (SMART-Seq2)

description:
Library name: STEPN-40
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 4

value: F

tag: age

tag: type

tag: fusion


title: v9_bg

description: Library name: T41

value: non-treated control


title: Gc2

description: Library name: Sample 11


title: P172_111

description: Library name: P172_111

value: Liver

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

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

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

value: hour

value: Dimethyl sulfoxide

tag: genotype

value: DRE-null


title: STEPN-39 (SMART-Seq2)

description:
Library name: STEPN-39
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

tag: subtype

tag: Sex

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: P172_116

description: Library name: P172_116

tag: cell type

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age unit

value: day

tag: age unit_ontology

value: Male

tag: sex ontology

tag: culture vessel_type

tag: culture vessel_vendor

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

tag: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

tag: treatment


title: P172_112

description: Library name: P172_112

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

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture 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: genotype


title: v8_28d

description: Library name: T40

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 4

tag: time


title: P172_110

description: Library name: P172_110

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

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

tag: culture additives

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

value: penicillin/streptomycin

value: nanomolar

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

value: Dimethyl sulfoxide

tag: vehicle dtxsid

value: DRE-null


title: STEPN-37 (SMART-Seq2)

description:
Library name: STEPN-37
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 4

tag: Sex

value: M

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: Yak3_dsx_neurons

city: Philadelphia

first: Justin

last: Walsh

state: PA

address: 3740 Hamilton Walk

institute: University of Pennsylvania

description:
Library name: Yak3_dsxNeurons
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using CellRanger software v7.1.0
Assembly: GCA_000001215.4
Assembly: GCA_016746365.2
Assembly: GCA_016746245.2
Assembly: GCA_016746235.2
Supplementary files format and content: tab-separated value files, matrix files, and Rds files

molecule: polyA RNA

organism: Drosophila yakuba

source_name: central nervous system

extract_protocol:
For each replicate, the central nervous system of approximately 100 doublesex-GAL4 x UAS-nls::tdTomato flies were dissected in ice cold Schneider's medium and digested in a solution containing Liberase DH for 45 mins. The tissue was washed with Schneider's medium and broken apart via pipetting before FACS sorting out the tdTomato+ cells.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol, 10X Genomics)

value: central nervous system

tag: cell type

value: neurons

value: male

value: 4-8 days


title: v8_14d

description: Library name: T36

value: peripheral blood

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 2

tag: time


title: v8_21d

description: Library name: T38

value: treated timepoint 3


title: STEPN-36 (SMART-Seq2)

description:
Library name: STEPN-36
snRNA-seq Patient single-cell RNA-seq

value: ZFTA-Cluster 3


title: v8_7d

description: Library name: T34

value: treated timepoint 1


title: Yak2_dsx_neurons

description:
Library name: Yak2_dsxNeurons
10X Genomics


title: STEPN-35 (SMART-Seq2)

description:
Library name: STEPN-35
snRNA-seq Patient single-cell RNA-seq


title: P172_108

description: Library name: P172_108

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

value: hour

value: Dimethyl sulfoxide

tag: genotype


title: P172_107

description: Library name: P172_107

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: test article_administration_duration

tag: test article_name

tag: test article_dtxsid

tag: vehicle name

tag: vehicle dtxsid

value: DRE-null

tag: treatment


title: P172_109

description: Library name: P172_109

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: 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: genotype


title: STEPN-34 (SMART-Seq2)

description:
Library name: STEPN-34
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 3

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: 118T-Tumour_A-FOV_9

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:
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_9.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 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.

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.

value: Colon tumour,FFPE

tag: donor

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: v8_bg

description: Library name: T32

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: non-treated control

tag: time


title: P172_106

description: Library name: P172_106

tag: tissue

value: Liver

value: hepatocyte

tag: cell type_ontology

tag: tissue ontology

tag: strain

tag: age unit

tag: age unit_ontology

tag: sex ontology

tag: culture vessel_type

value: 12-well plate

tag: culture vessel_vendor

value: Corning

tag: culture vessel_diameter

tag: culture vessel_diameter_unit

value: millimeter

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

value: square centimeter

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

value: type I collagen

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

value: Nuaire

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

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: v7_28d

description: Library name: T39

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 4

tag: time


title: STEPN-33 (SMART-Seq2)

description:
Library name: STEPN-33
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 3

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: Gc1

description: Library name: Sample 10

value: buccal

value: Female


title: 142N-Run5850.2186.1-FOV_9

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_9.rds

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

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: v7_21d

description: Library name: T37

tag: tissue

value: treated timepoint 3


title: STEPN-38 (SMART-Seq2)

description:
Library name: STEPN-38
snRNA-seq Patient single-cell RNA-seq

value: ZFTA-Cluster 4


title: P172_105

description: Library name: P172_105

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

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-32 (SMART-Seq2)

description:
Library name: STEPN-32
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-Cluster 3

tag: Sex

value: F

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: v7_14d

description: Library name: T35

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 2

tag: time


title: P172_104

description: Library name: P172_104

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

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


title: 7N-Normal_A-FOV_9

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_9.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: v7_7d

description: Library name: T33

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 1

tag: time


title: STEPN-31 (SMART-Seq2)

description:
Library name: STEPN-31
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 3

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: P172_103

description: Library name: P172_103

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

tag: culture vessel_diameter_unit_ontology

tag: culture vessel_sufacearea

tag: culture vessel_sufacearea_unit

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

tag: culture vessel_seeding_cell_density

tag: culture vessel_cell_density

tag: incubator vendor

tag: incubator model

tag: incubator co2_percent

tag: incubator o2_percent

tag: incubator temperature

tag: basal medium

value: Williams E medium

tag: basal medium_vendor

value: Sigma-aldrich

tag: culture additives

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

tag: culture additives_concentration

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment 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-30 (SMART-Seq2)

description:
Library name: STEPN-30
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Recurrence

tag: subtype

value: ZFTA-Cluster 3

tag: Sex

tag: age

tag: type

tag: fusion


title: 64T-Tumour_B-FOV_9

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_9.rds

value: Colon tumour,FFPE

tag: donor

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: 7T-3461G-FOV_9

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_9.rds

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

value: M

value: ascending


title: NC-148191A-FOV_9

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:
NC-148191A-FOV_9.rds


title: 280N-120131-FOV_9

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_9.rds


title: v6_28d

description: Library name: T30

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

tag: treatment

value: treated timepoint 4

tag: time


title: STEPN-29 (SMART-Seq2)

description:
Library name: STEPN-29
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: snRNA-seq


title: P172_102

description: Library name: P172_102

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

tag: vehicle dtxsid

tag: genotype


title: P172_101

description: Library name: P172_101

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: Dimethyl sulfoxide

value: DRE-null

tag: treatment


title: STEPN-28 (SMART-Seq2)

description:
Library name: STEPN-28
snRNA-seq Patient single-cell RNA-seq

tag: tissue

value: Ependymoma Patient single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-Cluster 2

tag: Sex

tag: age

tag: type

value: snRNA-seq

tag: fusion


title: P172_100

description: Library name: P172_100

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

tag: culture vessel_sufacearea_unit_ontology

tag: culture vessel_coating_substrate

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: vehicle name

tag: vehicle dtxsid

tag: genotype


title: STEPN-27 (SMART-Seq2)

description:
Library name: STEPN-27
snRNA-seq Patient single-cell RNA-seq

tag: tissue

tag: sampling

tag: subtype

tag: Sex

value: M

tag: age

tag: type

tag: fusion

value: CCND1::RP11; KDM2A::POLA2


title: 67T-Run5850.2186.2-FOV_9

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_9.rds

value: Colon tumour,FFPE

tag: donor

tag: age at diagnosis

tag: primary tumour location

value: sigmoid

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: LHS


title: 74T-10501A-FOV_9

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_9.rds

value: descending colon

value: dMMR


title: P172_99

description: Library name: P172_99

value: Liver

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

tag: anitibiotic name

value: penicillin/streptomycin

tag: antibiotic concentration

tag: treatment addition_volume

tag: treatment stock_concentration

tag: treatment final_concentration

tag: treatment concentration_unit

value: nanomolar

tag: treatment concentration_unit_ontology

tag: test article_administration_duration

value: hour

tag: test article_name

tag: test article_dtxsid

value: Dimethyl sulfoxide

value: DRE-null

tag: treatment


title: v6_21d

description: Library name: T28

tag: tissue

value: peripheral blood

tag: cell type

value: T lymphocytes

tag: volunteer #

value: treated timepoint 3

tag: time


title: 64T-Tumour_B-FOV_8

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_8.rds

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: v6_7d

description: Library name: T24

value: treated timepoint 1


title: STEPN-26 (SMART-Seq2)

description:
Library name: STEPN-26
snRNA-seq Patient single-cell RNA-seq

value: Ependymoma Patient single-cell

tag: sampling

value: Primary

tag: subtype

value: ZFTA-Cluster 2

value: M

tag: age

tag: type

value: snRNA-seq

tag: fusion