title: Cardiac fibroblast, sham, 8 week, rep 2

value: heart

value: cardiac fibroblast


title: 10d OE 2

status: Public on Dec 14 2023

type: SRA

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: oesophagus in vitro - 10 days

library_source: transcriptomic

data_processing:
Quality checks, UMI identification, alignment to the mouse reference genome and cell calling were performed using the cellranger software (v3.1.0) with default parameters. Violin plots of the distribution of counts, features, mitochondrial and ribosomal RNA were created and upper and lower bounds were introduced to avoid data heterogeneity and exclude potentially problematic cells.
The data was normalised using the Seurat R package (v3.2.2). Dimensionality reductions (PCA and UMAP), as well as clustering were also performed using the Seurat R package, with the number of clusters being the optimal selected by the software. For the subsequent analysis, we focused on the 1000 most abundant genes. Markers for each cluster were identified by testing for differential gene expression, using the Seurat R package. The above steps were performed both for all the cells in the data, but also individually for each sample set (HF_3d, HF_10d, OE_3d, OE_10d).
Clustering stability was evaluated by a PAC analysis (https://doi.org/10.1038/srep06207). Enrichment analysis on the markers identified per cluster was performed using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.8). RNA velocity trajectory analysis was performed with the velocyto software (v0.17.17) and associated R package (v0.6). Pseudotime analysis was performed with the monocle3 R package (v0.2.3.0).  Further analysis was performed with the above tools, focused on sub-clusters of biological interest.
Cells marked with the fluorescent markers eGFP and tdTomato were identified through sequencing. The identity of the unlabelled cells was inferred by using a semi-supervised classifier based on random forests.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: Sparse matrix of raw abundances for each gene, per cell

molecule: total RNA

organism: Mus musculus

source_name: Oesophageal epithelial cells

growth_protocol: 3D organotypic cultures were performed by combining oesophageal epithelium with either oesophageal stroma or skin stroma (tail dermis) in ThinCert™ Cell Culture Inserts (6-well plates with a pore diameter of 0.4μm, Greiner Bio-One), in DMEM High Glucose/DMEM:F12 (1:1) supplemented with FBS 5%, Insulin 5ug/ml, Adenine 25ug/ml and Apotransferrin 10ug/ml.

extract_protocol:
After 3 or 10days in culture, the oesophageal-derived epithelia were harvested and peeled off from the oesophageal stroma or dermis. The epithelial sheet was dissociated into a single cell suspension and FACS sorted to select live singlets. For each sample, 7,000-9,000 cells were submitted for  10X single cell GEX v3 library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols for 10X Single Cell GEX v3

tag: time point

value: 10 days

value: Oesophageal stroma

tag: replicate


title: Cardiac fibroblast, sham, 8 week, rep 1

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

data_processing:
The FastQC was used for the initial quality check of sequencing results.
The reads with low quality were removed with Trimmomatic (PMID: 24695404).
The expression counts of circRNAs were calculated using the STAR aligner (PMID: 23104886) and DCC algorithm (PMID: 26556385).
The expression counts were normalized by the total counts of circRNAs in each sample.
Assembly: mm10
Supplementary files format and content: Tab-delimited circRNA expression counts normalized by the total counts of circRNAs in each sample.

source_name: heart

growth_protocol: Adult male C57BL/6J mice (8-10 weeks old) were purchased from Damul Science (Damul Science, Dajeon,Korea). All animal experiments were approved by the Institutional Review Board of Chonnam National University Medical School Research Institutional Animal Care and Use Committee (CNU-IACUC-H-2021-39 and CNU-IACUC-H-2022-11) and followed the ‘Guide for the Care and Use of Laboratory Animals’ (8th edition, National academies Press, Washington, DC, USA, 2011).

extract_protocol:
TRI Reagent (Molecular Research Center) was used to isolate total RNA in accordance with the manufacturer's protocol. DNase I (Takara) was used to remove residual DNA in RNA samples.
Total RNA was treated with Ribo-Zero Gold rRNA Removal Kit (Illumina) to remove the ribosomal RNAs and applied to TruSeq Stranded Total RNA Kit (Illumina) to construct RNA-seq library.
The library was sequenced by HiSeq 2500 (Illumina) in the paired-end mode with 100 sequencing cycles.

treatment_protocol: Eight-week-old male C57BL/6J mice were anaesthetized by Avertin. The mice were then ventilated and the chest was opened to expose the thymus and aortic arch. A 7-0 silk suture were placed between the innominate and left carotid arteries. A 27-gauge needle put parallel to the transverse aorta and the suture was tied. After ligation, the needle was removed and the rib cage was closed using 4-0 silk suture.

tag: tissue

tag: cell type

tag: genotype

tag: treatment

value: sham

tag: treatment time

value: 8 week


title: atp22R2

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

country: China

institute: Chinese Academy of Sciences

description: atp22Δ cells collected during standard log phase growth

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the C. glabrata CBS138 reference genome using the hisat2 version 2.1.0.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the edgeR version 3.24.3 package. Genes with a p-value < 0.05 and a log2 fold change value > 1 were considered to represent significantly differentially expressed genes (DEGs). The GO analysis of DEGs was performed using the clusterProfiler version 4.7.1 package.
Assembly: C. glabrata CBS138 (GCF_000002545.3)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Nakaseomyces glabratus

source_name: C. glabrata cells

extract_protocol:
Total RNA was extracted using the hot phenol method
Illumina library preparation and sequencing were then performed by Singapore Immunology Network (SIgN) on samples from three independent experiments following standard operating procedures

value: C. glabrata cells

value: ATP22 knockout


title: Cardiac fibroblast, TAC, 8 week, rep 1

institute: Chonnam National University Medical School

value: transverse aortic constriction


title: 3543_OF1B_1-1-B11-G13

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: OF1B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: Cardiac fibroblast, TAC, 4 week, rep 4

value: 4 week


title: 3543_OF1B_1-1-B11-F2


title: atp22R1


title: 72h OE 3

description: oesophagus in vitro - 3 days

value: 3 days


title: 3543_OF1B_1-1-B11-F1


title: 10d OE 1

description: oesophagus in vitro - 10 days


title: atp3R4

description: atp3Δ cells collected during standard log phase growth

value: ATP3 knockout


title: Cardiac fibroblast, TAC, 4 week, rep 2


title: atp3R3


title: Cardiac fibroblast, TAC, 4 week, rep 3


title: 72h OE 2

description: oesophagus in vitro - 3 days


title: 3543_OF1B_1-1-B11-F14


title: 3543_OF1B_1-1-B11-F13


title: 72h OE 1

description: oesophagus in vitro - 3 days


title: Cardiac fibroblast, TAC, 4 week, rep 1


title: atp3R2


title: Cardiac fibroblast, sham, 4 week, rep 5


title: HCT116-Olaparib-2

city: Mannheim

first: Siche

last: Chen

address: Stockhornstrasse 55, 55

department: Dept. of Experimental Surgery - Cancer Metastasis

country: Germany

institute: Medical Faculty Mannheim, Ruprecht-Karls University of Heidelberg

data_processing:
Raw reads were filtered and cleaned by fastp software. Aliments were performed following STAR instruction. analyzeRepeats.pl function were used for counting. R was used for visualization.
Assembly: hg38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: HCT116 cellls were cultured in McCoy's 5A medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol, without the separation step between mRNAs and microRNAs
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: HCT116 cells were plated into 6-well plate 24 h before treated with DMSO and Olaparib.

tag: cell line

value: colorectal cancer

value: Olaparib


title: atp3R1


title: HCT116-Olaparib-1


title: 3543_OF1B_1-1-B11-E2


title: WTR3

description: WT cells collected during standard log phase growth

value: WT


title: Cardiac fibroblast, sham, 4 week, rep 4

value: heart

value: cardiac fibroblast


title: Cardiac fibroblast, sham, 4 week, rep 3


title: HCT116-DMSO-1

value: DMSO


title: Cardiac fibroblast, sham, 4 week, rep 2

value: sham


title: SC_D6_CD34_3

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

description: RC_D6_CD34_vs_SC_D6_CD34_gene_expression

data_processing:
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
RNA identification: Bowtie2[2] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include read counts of each gene for each sample

molecule: polyA RNA

source_name: CD34+ cells from hESCs

extract_protocol:
1 Sample Lysis
1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107).
1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min.
1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column.
1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification.
1.5 Transfer the DNA spin column to the new collection tube for DNA purification.
2 DNA Purification
2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.
2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube.
2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min.
2.5 Centrifuge at 16,000×g for 2 min and collect the DNA.
3 RNA Purification
3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.
3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.
3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.
3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube.
3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min.
3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: CD34+ cells from hESCs

value: baffled flasks without agitation


title: WTR1

value: C. glabrata cells


title: WTR2


title: 3543_OF1B_1-1-B11-E13


title: 3543_OF1B_1-1-B11-E14


title: Cardiac fibroblast, sham, 4 week, rep 1


title: Cardiac fibroblast, TAC, 1 week, rep 4

value: transverse aortic constriction

value: 1 week


title: Cardiac fibroblast, TAC, 1 week, rep 2


title: 3543_OF1B_1-1-B11-D1

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: M-WT-PFF-Microglia

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

data_processing:
Reads mapped to rRNA were removed and raw data was obtained.
The sequencing reads which contained low-quality, adaptor-polluted and high content of unknown base (N) reads processed were removed before downstream analyses.
Clean reads were mapped to reference using Bowtie2, and then gene expression level was calculated for each sample with RSEM
DESeq2 package was used to detect the DEGs, determining at a cutoff of FDR corrected p-value≤0.05 and |log2(fold change)|≥1 as DEGs.
Principal component analysis (PCA) was performed on the Macrophage and Microglia population respectively based on the rlog of dds result from DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain counts and FPKM for each sample

source_name: Brain

growth_protocol: Adult male and female CD163KO (CD163tm1.1(KOMP)Vlcg) mice and WT (C57BL/6N) littermates (3-4 months old) (n=179 total (n=95 males (50 WT + 45 CD163KO); n=84 females (43 WT+ 41 CD163KO)) were used in this study 1. Mice weighted 20-25g (12 weeks old) at the time of the surgery and were housed maximum 4-6 per cage, with ad libitum access to food and water, in a climate-controlled facility under 12h/12h night/daylight cycle.

extract_protocol:
Once sorted, microglia (200000-500000 cells) and macrophage (10000-30000 cells) cell suspensions (>90% purity after sorting) were centrifuged at 4°C and 400xg for 5 minutes, resuspended in RLT Plus Lysis buffer (QIAGEN, Germany) with 1% β-Mercaptoethanol and vortexed for 1 minute for cell lysis. The solution was further homogenized using a 1mL syringe and a 21gag needle. Total RNA was extracted using RNeasy® Mini Kit (QIAGEN) according to the manufacturer’s protocol.
Total purified RNA was sent to BGI Hong Kong where Switching Mechanism at 5’ End of RNA Template (SMART-seq2) sequencing service was requested. Samples were tested for quality control using Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). RNA integrity (RNI) >7 was considered suitable for sequencing.
Gene expression analysis was performed through full population RNA sequencing using the SMART-seq2 method according to BGI’s standard methodology.

treatment_protocol: For whole population RNA sequencing, mice (batch 1 and batch 2) received bilateral intrastriatal injection of α-syn MONO (Males WT n=7 & CD163KO n=4*; Females WT n=7 &CD163KO n=5), and α-syn PFF (Males WT n=7, & CD163KO n =5; Females WT n=7 & CD163KO n=5). Triplicates were used for sequencing. Mice were sacrificed 2 months post-surgery, their brains dissected and the immune cells (microglia & macrophages) isolated and FACS sorted for RNA purification and subsequent SMART-seq2 sequencing. *CD163KO-MONO males were excluded from the analysis due to inconsistencies in the technical replicates.

value: Brain

value: primary cells

value: Microglia

value: α-syn PFF


title: 3543_OF1B_1-1-B11-E1

value: nuclear RNA + genomic DNA


title: 3543_OF1B_1-1-B11-D13


title: M-WT-MONO-Microglia

value: WT

value: α-syn MONO


title: SC_D6_CD34_1


title: Cardiac fibroblast, TAC, 1 week, rep 3

value: heart

value: cardiac fibroblast


title: M-KO-PFF-Microglia


title: M-WT-PFF-Macrophages

value: Macrophages


title: HCT116-DMSO-2

value: colorectal cancer

value: DMSO


title: Cardiac fibroblast, TAC, 1 week, rep 1


title: Cardiac fibroblast, sham, 1 week, rep 4

value: sham


title: M-WT-MONO-Macrophages


title: RC_D6_CD34_3

value: CD34+ cells from hESCs

value: baffled flasks with agitation


title: RC_D6_CD34_2


title: 3543_OF1B_1-1-B11-D2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: SC_D6_CD34_2

value: baffled flasks without agitation


title: 3543_OF1B_1-1-B11-D14

value: Female


title: 3543_OF1B_1-1-B11-C1


title: Cardiac fibroblast, sham, 1 week, rep 3

value: 1 week


title: M-KO-PFF-Macrophages

value: Brain

value: primary cells


title: M-KO-MONO-Microglia

value: Microglia


title: Cardiac fibroblast, sham, 1 week, rep 2


title: 3543_OF1B_1-1-B11-C2

value: nuclear RNA + genomic DNA


title: 3543_OF1B_1-1-B11-C14


title: SC3

description: RC_vs_SC_ gene_expression

source_name: megakaryocytes from hESCs

value: megakaryocytes from hESCs


title: SC2

description: RC_vs_SC_ gene_expression


title: RC_D6_CD34_1


title: Cardiac fibroblast, sham, 1 week, rep 1

value: heart


title: SC1

description: RC_vs_SC_ gene_expression


title: 3543_OF1B_1-1-B11-B2


title: RC3

description: RC_vs_SC_ gene_expression


title: 3543_OF1B_1-1-B11-C13


title: M-KO-MONO-Macrophages

value: α-syn MONO


title: F-WT-PFF-Microglia

value: WT

value: α-syn PFF


title: RC2

description: RC_vs_SC_ gene_expression


title: RC1

description: RC_vs_SC_ gene_expression


title: STEM-seq_E6.5_9_heter

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
Base calls were performed using CASAVA version 1.8.
STEM-seq reads were aligned to the mm9 genome using BSseeker2.0.8.
Replicates of same stage were pooled together and methylation values in wiggle files were computed for each single base.
Assembly: mm9
Supplementary files format and content: Single base mCG methylation values. Format: chr pos methylated_crick_count un-methylated_crick_count methylated_watson_count un-methylated watson_count
Supplementary files format and content: Bigwig files counted the number of reads falling on each base
Library strategy: STEM-seq

source_name: E6.5 embryo

extract_protocol:
Mouse embryos at stage E6.5 were collected by mating the Zfp281+/- (129S1/SvImJ) males and females. Embryos were washed with PBS and incubated in lysis buffer.
STEM-seq libraries were constructed following the protocol described in this study (Zhang et al., Nature Genetics, 2018).

tag: strain

value: E6.5 embryo


title: F-WT-MONO-Microglia


title: 3543_OF1B_1-1-B11-B1


title: F-WT-PFF-Macrophages

value: Macrophages


title: F-WT-MONO-Macrophages


title: STEM-seq_E6.5_7_wt


title: 3543_OF1B_1-1-B11-B13


title: STEM-seq_E6.5_8_heter


title: PBMCs, patient/control, scRNAseq

city: Munich

first: Johanna

last: Klughammer

address: Feodor Lynen Str 25

institute: Gene Center LMU

description: 10x Genomics, genetic multiplex

library_source: transcriptomic single cell

data_processing:
Raw data processing was performed using the cellranger v6.1.2 multi pipeline (setting expect-cells = 10000 and include-introns = True).
Genetic demultiplexing was done with with cellsnp-lite (v1.2.2) and vireosnp (v0.5.7), using only cells with at least 40 UMI counts as input.
Assembly: GRCh38
Supplementary files format and content: .h5 file containing raw counts matrix including cell and gene IDs, .tsv file containg the cell-donor assignments

source_name: Blood

extract_protocol:
Frozen PBMCs of 1 patient and 1 control were rapidly thawed at 37°C, immediately resuspended in 1% BSA/PBS, followed by centrifugation at 300 g for 10 min. The number of cells in each sample was assessed using the Invitrogen Countess II Automated Cell Counter and both samples were pooled to contribute the same number of cells. Pooled cells were run on the LeviCell System (LevitasBio) to remove dead cells and debris.
20,000 live cells were loaded onto the Chip G of the Chromium Next Gem Single Cell 3’ Reagent Kit V.3.1 with Dual Indexing (10X Genomics). Following capture and lysis, cDNA was synthesized and amplified (12 cycles) as per the manufacturer’s protocol.

value: Blood

value: PBMC


title: STEM-seq_E6.5_6_homo


title: F-KO-PFF-Microglia


title: STEM-seq_E6.5_11_heter


title: 3543_OF1B_1-1-B11-A2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1B_1-1-B11-A1


title: F-KO-PFF-Macrophages


title: F-KO-MONO-Microglia


title: 3543_OF1B_1-1-B11-A14


title: STEM-seq_E6.5_10_wt


title: 3543_OF1B_1-1-B11-B14


title: 3543_OF1B_1-1-B11-A13


title: HTO reads, scRNA-seq

city: Brisbane

first: Onkar

middle: Rajesh

last: Mulay

state: QLD

address: Carmody Road

country: Australia

institute: University of Queensland

description: 10x Genomics

data_processing:
The sequencing data were further processed to generate FASTQ files and the raw count matrix using the CellRanger pipeline.
The multiplexed samples were demultiplexed by mapping of sample reads to hg38 human reference genome and hashing sequences.
Assembly: hg38
Supplementary files format and content: tsv. Files and mtx. Files

source_name: H9 (hESCs)

extract_protocol:
Frozen PSC-CMs were thawed in the water bath and the content of each vial was transferred to a 50 mL Falcon tube containing RPMI-B27 medium with insulin, 5% FBS, and 10 uM ROCK inhibitor Y-27632. The cell pellet was resuspended with filtered PBS plus 2% BSA. Cells were then incubated at room temperature for 10 mins in blocking buffer containing 5uL of Human TruStain FcX solution plus 100uL of staining buffer (2% BSA + 0.01% Tween20 in filtered PBS). Next, 1uL of hashtag antibody was added to each sample and incubated on ice for 20 mins. Cells were then washed twice with staining buffer and 4 x 105 cells from each stained sample were collected and pooled into a 2 mL Eppendorf tube.
The library was generated and sequenced on a NextSeq 500 instrument

value: H9 (hESCs)

value: hESCs derived day 15 cardiomyocytes

value: contains gCaMP6f fluorescent calcium reporter

value: pooled sample


title: Gene expression reads, scRNA-seq

description: 10x Genomics


title: F-KO-MONO-Macrophages

value: Brain

value: primary cells


title: Treated,biological rep1

type: RNA

city: Kamand

first: Amit

last: Prasad

state: Himachal Pradesh

address: Parashar Road

department: School of Basic Sciences

country: India

institute: Indian Institute of Technology Mandi

description: miRNA

hyb_protocol: 21.5ul of Biotin-lableld sample is added to 110.5ul of hybridization master mix and Incubated at 99°C for 5 minutes, then 45°C for 5 minutes.130ul of hybridized reaction mix was injected into GeneChipTM miRNA 4.0 Array Cartridge Array and Incubatd at 48°C and 60 rpm for 16 to 18 hours. Gene chip were washed and stained with Fluidics Station 450

scan_protocol: Gene Chip were scanned using GeneChip™ Scanner 3000 7G

data_processing: data processing and normalization were done using  Expression Console™ Software and Transcriptome Analysis Console (TAC) Software

label: Biotin

source_name: THP1-human leukemia monocytic cell line

label_protocol: Biotin labelling is performed on 400ng of Poly(A) tialed-RNA samples as per the applied biosystems FlashTagTM Biotin HSR protocol

growth_protocol: THP1 cell line was diffentiated to macrophages and kept at 37°C and 5%CO2

extract_protocol: Total miRNA was extracted using Qiagen miRNA easy mini kit as per manufacturer's instructions

treatment_protocol: Differnetiated macrophages were treatedw ith or without ESP for 24H

value: THP1 differentiated to macrophages

value: ESP treated macrophages


title: Control,biological rep1

description: miRNA

value: PBS treated macrophages


title: Treated,biological rep2

description: miRNA


title: glioma_Recurrence 1 [TCGA-DU-6407-R1-02M-EPC-A7F9D5]

status: Public on Dec 13 2023

type: genomic

city: Detroit

first: Laila

middle: M

last: Poisson

state: MI

address: 2799 W Grand Blvd

institute: Henry Ford Health

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
The raw DNA methylation intensity data files (IDAT) were processed with the minfi package. We performed noob (Normal-exponential convolution using out-of-band probes) background correction and dye bias correction using the minfi package (v 1.36.0). The DNA methylation value for each locus is presented as a beta (β) value (β = (M/(M+U)) in which M and U indicate the mean methylated and unmethylated signal intensities for each locus, respectively. β-values range from zero to one, with scores of zero indicating no DNA methylation and scores of one indicating complete DNA methylation. A detection p-value also accompanies each data point and compares the signal intensity difference between the analytical probes and a set of negative control probes on the array. Any data point with a corresponding p-value greater than 1E-4 is deemed not to be statistically significantly different from background and was thus masked as “NA”.
matrix processed value definition: Average Beta

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified at each institution following standard protocols that ensure high quality DNA.

tag: gender

value: female

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Recurrence

value: IDHmut

value: noncodel

value: G-CIMP-high

value: high grade astrocytoma


title: glioma_Primary [GLSS-LX-0304-TP-01M-EPC-BFEB6C]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Primary

value: IDHwt

value: Classic-like

value: mesenchymal


title: glioma_Recurrence 3 [GLSS-LX-0357-R3-01M-EPC-A63D4B]

value: male

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: G-CIMP-low


title: glioma_Primary [TCGA-DU-6407-TP-02M-EPC-4E5F5E]

value: astrocytoma


title: glioma_Recurrence 1 [GLSS-LX-0357-R1-01M-EPC-1BF185]

value: Astrocytoma, IDH-mutant (WHO grade 3)


title: glioma_Recurrence 2 [GLSS-LX-0357-R2-01M-EPC-6F8AB0]


title: glioma_Recurrence 1 [GLSS-LX-0344-R1-01M-EPC-ECAC06]

value: Mesenchymal-like


title: glioma_Primary [GLSS-LX-0344-TP-01M-EPC-85C722]

value: control


title: glioma_Recurrence 1 [GLSS-LX-0304-R1-01M-EPC-545F1F]

value: female

value: Recurrence


title: glioma_Primary [GLSS-LX-0299-TP-01M-EPC-1F29BA]

value: noncodel


title: glioma_Recurrence 2 [GLSS-LX-0344-R2-01M-EPC-3C63F0]


title: glioma_Recurrence 2 [TCGA-DU-6407-R2-02M-EPC-F64EF7]

value: IDHmut


title: Control,biological rep2

description: miRNA

value: THP1 differentiated to macrophages

value: PBS treated macrophages


title: glioma_Recurrence 1 [GLSS-LX-0299-R1-01M-EPC-B573EC]

value: Glioblastoma, IDH-wildtype (WHO grade 4)


title: glioma_Recurrence 2 [GLSS-LX-0299-R2-01M-EPC-C17044]

value: IDHwt

value: RTK I


title: glioma_Primary [GLSS-LX-0267-TP-01M-EPC-61490B]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Primary

value: G-CIMP-high


title: glioma_Primary [GLSS-LX-0215-TP-01M-EPC-A8603E]

value: mesenchymal


title: glioma_Primary [GLSS-LX-0242-TP-01M-EPC-EB0091]

value: male

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: codel

value: Codel

value: subclass 1p/19q codeleted oligodendroglioma


title: glioma_Recurrence 1 [GLSS-LX-0267-R1-01M-EPC-76260E]

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: Recurrence

value: high grade astrocytoma


title: glioma_Recurrence 1 [GLSS-LX-0242-R1-01M-EPC-D53E3A]

value: IDHmut

value: astrocytoma


title: glioma_Recurrence 1 [GLSS-LX-0200-R1-01M-EPC-BB384B]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: noncodel

value: Mesenchymal-like


title: glioma_Primary [GLSS-LX-0200-TP-01M-EPC-6AF76B]

value: IDHwt

value: Classic-like

value: RTK II


title: glioma_Recurrence 1 [GLSS-LX-0178-R1-01M-EPC-81AFEA]

value: female

value: G-CIMP-low


title: glioma_Recurrence 2 [GLSS-LX-0178-R2-01M-EPC-8AAC50]


title: glioma_Primary [GLSS-LX-0176-TP-01M-EPC-918026]

value: male

value: Primary


title: glioma_Recurrence 1 [GLSS-LX-0176-R1-01M-EPC-910551]

value: no class


title: glioma_Recurrence 1 [GLSS-LX-0170-R1-01M-EPC-9558D1]

value: Unknown

value: control


title: glioma_Primary [GLSS-LX-0170-TP-01M-EPC-8CA2CF]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: G-CIMP-high

value: subclass 1p/19q codeleted oligodendroglioma


title: glioma_Primary [GLSS-LX-0164-TP-01M-EPC-D09F60]

value: mesenchymal


title: glioma_Recurrence 1 [GLSS-LX-0134-R1-01M-EPC-2D1682]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Recurrence


title: glioma_Primary [GLSS-LX-0134-TP-01M-EPC-CDBA63]

value: noncodel


title: glioma_Recurrence 1 [GLSS-LX-0114-R1-01M-EPC-06697C]

value: IDHwt

value: RTK I


title: glioma_Recurrence 2 [GLSS-LX-0083-R2-01M-EPC-07FFAE]

value: Mesenchymal-like


title: glioma_Recurrence 2 [GLSS-LX-0123-R2-01M-EPC-CCC2A5]


title: glioma_Primary [GLSS-LX-0132-TP-01M-EPC-045261]

value: meningioma


title: glioma_Recurrence 1 [GLSS-LX-0123-R1-01M-EPC-76C250]

value: Classic-like

value: RTK II


title: glioma_Primary [GLSS-LX-0114-TP-01M-EPC-7B03DA]

value: female

value: Primary


title: glioma_Primary [GLSS-LX-0072-TP-01M-EPC-57D2CA]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: IDHmut

value: astrocytoma


title: glioma_Recurrence 1 [GLSS-LX-0083-R1-01M-EPC-504A59]

value: male


title: glioma_Recurrence 2 [GLSS-LX-0072-R2-01M-EPC-66DAB8]

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: G-CIMP-high


title: glioma_Recurrence 1 [GLSS-LX-0215-R1-01M-EPC-EA4FD1]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: mesenchymal


title: glioma_Primary [GLSS-LX-0070-TP-01M-EPC-E40053]

value: noncodel


title: glioma_Recurrence 2 [GLSS-LX-0070-R2-01M-EPC-1DA5EB]

value: Recurrence

value: IDHwt


title: glioma_Recurrence 1 [GLSS-LX-0070-R1-01M-EPC-D362E1]


title: glioma_Recurrence 1 [GLSS-LX-0040-R1-01M-EPC-F67FA3]

value: Mesenchymal-like


title: glioma_Recurrence 1 [GLSS-LX-0072-R1-01M-EPC-2E53DF]


title: glioma_Primary [GLSS-LX-0040-TP-01M-EPC-C3889A]


title: glioma_Recurrence 1 [GLSS-LX-0132-R1-01M-EPC-728873]

value: no class


title: glioma_Primary [GLSS-LX-0123-TP-01M-EPC-B9E8D3]

value: Classic-like


title: glioma_Primary [GLSS-LX-0019-TP-01M-EPC-E33533]


title: glioma_Recurrence 1 [GLSS-LX-0015-R1-01M-EPC-25434C]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: Codel


title: glioma_Recurrence 1 [GLSS-LX-0019-R1-01M-EPC-C5E3F5]

value: control


title: glioma_Primary [GLSS-LX-0015-TP-01M-EPC-5C276E]

value: female

value: Primary

value: codel

value: 1p/19q codeleted oligodendroglioma


title: glioma_Recurrence 2 [GLSS-LX-0015-R2-01M-EPC-719AA5]

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: IDHmut


title: glioma_Recurrence 1 [GLSS-LX-0003-R1-01M-EPC-D7E196]

value: Glioblastoma, IDH-wildtype (WHO grade 4)


title: glioma_Primary [GLSS-HK-0003-TP-01M-EPC-6834EA]

value: mesenchymal


title: glioma_Recurrence 1 [GLSS-HK-0003-R1-01M-EPC-AC36CA]

value: noncodel

value: RTK II


title: glioma_Recurrence 1 [GLSS-LX-0164-R1-01M-EPC-C604DC]

value: Recurrence

value: IDHwt


title: glioma_Recurrence 1 [GLSS-HK-0002-R1-01M-EPC-DBE704]

value: G-CIMP-high

value: high grade astrocytoma


title: glioma_Recurrence 2 [GLSS-HF-F922-R2-01M-EPC-D67141]

value: male


title: glioma_Recurrence 3 [GLSS-HF-EE77-R3-01M-EPC-6AF605]

value: Classic-like


title: glioma_Recurrence 1 [GLSS-HF-F922-R1-01M-EPC-00A2E0]

value: Astrocytoma, IDH-mutant and 1p/19q-codeleted (WHO grade 4)


title: glioma_Primary [GLSS-HK-0001-TP-01M-EPC-966D7D]

value: midline


title: glioma_Recurrence 2 [GLSS-HF-EE77-R2-01M-EPC-D9FE3D]

value: female

value: control


title: glioma_Recurrence 1 [GLSS-HF-EE77-R1-01M-EPC-08C083]


title: glioma_Primary [GLSS-HK-0002-TP-01M-EPC-139865]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Primary

value: astrocytoma


title: glioma_Primary [GLSS-HF-EE74-TP-01M-EPC-891CEB]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: RTK I


title: glioma_Primary [GLSS-HF-EDB1-TP-01M-EPC-204754]


title: glioma_Primary [GLSS-LX-0003-TP-01M-EPC-13A6E5]

value: noncodel

value: Mesenchymal-like


title: glioma_Recurrence 1 [GLSS-HF-E6BA-R1-01M-EPC-10A328]

value: Recurrence

value: IDHmut


title: glioma_Recurrence 2 [GLSS-HF-E6BA-R2-01M-EPC-F41EBF]

value: Unknown

value: Codel


title: glioma_Recurrence 1 [GLSS-HF-EDB1-R1-01M-EPC-5D5CEF]

value: RTK II


title: glioma_Primary [GLSS-HF-E362-TP-01M-EPC-F32415]

value: male


title: glioma_Recurrence 1 [GLSS-HF-DF35-R1-01M-EPC-359F1E]

value: IDHwt

value: mesenchymal


title: glioma_Primary [GLSS-HF-DE05-TP-01M-EPC-7B687D]

value: female

value: Classic-like


title: glioma_Recurrence 2 [GLSS-HF-DCED-R2-01M-EPC-114B69]

source_name: GLSS-HF-DCED


title: glioma_Recurrence 2 [GLSS-HF-DE05-R1-01M-EPC-ADC829]


title: glioma_Recurrence 2 [GLSS-LX-0003-R2-01M-EPC-D5E346]


title: glioma_Primary [GLSS-HF-F922-TP-01M-EPC-BED05A]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: codel

value: 1p/19q codeleted oligodendroglioma


title: glioma_Recurrence 1 [GLSS-HF-E362-R1-01M-EPC-4BEF87]

value: Glioblastoma, IDH-wildtype (WHO grade 4)


title: glioma_Primary [GLSS-HF-DF35-TP-01M-EPC-5AA41D]

value: Primary

value: RTK I


title: glioma_Primary [GLSS-HF-D48E-TP-01M-EPC-9D2248]

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: noncodel

value: G-CIMP-high

value: astrocytoma


title: glioma_Recurrence 1 [GLSS-HF-DCED-R1-01M-EPC-8151C0]

value: Recurrence


title: glioma_Recurrence 1 [GLSS-HK-0001-R1-01M-EPC-CBF116]


title: glioma_Recurrence 1 [GLSS-HF-EE74-R1-01M-EPC-5AD560]

value: Mesenchymal-like


title: glioma_Primary [GLSS-HF-BCDE-TP-01M-EPC-064E29]

source_name: GLSS-HF-BCDE

value: male

value: RTK II


title: glioma_Recurrence 2 [GLSS-HF-CB66-R2-01M-EPC-1522F8]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 3)

value: IDHmut

value: Codel


title: glioma_Primary [GLSS-HF-B972-TP-01M-EPC-5A550B]

value: IDHwt

value: mesenchymal


title: glioma_Recurrence 1 [GLSS-HF-D48E-R1-01M-EPC-3D15C5]

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: G-CIMP-low

value: high grade astrocytoma


title: glioma_Recurrence 3 [GLSS-HF-BCDE-R3-01M-EPC-ECF8B2]

value: Glioblastoma, IDH-wildtype (WHO grade 4)


title: glioma_Recurrence 1 [GLSS-HF-CB66-R1-01M-EPC-D91328]

value: female

value: codel

value: 1p/19q codeleted oligodendroglioma


title: glioma_Recurrence 2 [GLSS-HF-B92C-R2-01M-EPC-58A139]

value: noncodel

value: control


title: glioma_Recurrence 1 [GLSS-HF-B972-R1-01M-EPC-9AE184]

value: Recurrence

value: Mesenchymal-like


title: glioma_Recurrence 1 [GLSS-HF-B3DE-R1-01M-EPC-DDF7EA]

value: male


title: glioma_Primary [GLSS-HF-B3DE-TP-01M-EPC-F89A8B]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: Primary


title: glioma_Primary [GLSS-HF-B30B-TP-01M-EPC-077905]

value: Classic-like

value: RTK II


title: glioma_Recurrence 2 [GLSS-HF-B30B-R2-01M-EPC-75D063]

value: IDHwt


title: glioma_Primary [GLSS-HF-AD84-TP-01M-EPC-34B931]

value: Unknown

value: G-CIMP-high

value: astrocytoma


title: glioma_Recurrence 1 [GLSS-HF-AD84-R1-01M-EPC-FAD820]

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: IDHmut


title: glioma_Recurrence 2 [GLSS-HF-9A7A-R2-01M-EPC-A077DA]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: RTK I


title: glioma_Recurrence 1 [GLSS-HF-9A7A-R1-01M-EPC-7D99F6]

value: noncodel


title: glioma_Primary [GLSS-HF-CB66-TP-01M-EPC-256484]

value: female

value: codel

value: Codel

value: 1p/19q codeleted oligodendroglioma


title: glioma_Recurrence 1 [GLSS-HF-8FCD-R1-01M-EPC-7F42B9]

value: Recurrence


title: glioma_Recurrence 1 [GLSS-HF-891E-R1-01M-EPC-DD5035]

value: male

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: G-CIMP-low

value: high grade astrocytoma


title: glioma_Primary [GLSS-HF-887A-TP-01M-EPC-89FB60]

value: Primary

value: Classic-like

value: mesenchymal


title: glioma_Primary [GLSS-HF-891E-TP-01M-EPC-4FE57C]

value: Unknown

value: G-CIMP-high

value: astrocytoma


title: glioma_Primary [GLSS-HF-8FCD-TP-01M-EPC-A16FA0]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: IDHwt

value: Mesenchymal-like


title: glioma_Primary [GLSS-HF-B92C-TP-01M-EPC-C2F257]

value: noncodel

value: RTK II


title: glioma_Recurrence 1 [GLSS-HF-8438-R1-01M-EPC-885AEF]

value: no class


title: glioma_Recurrence 1 [GLSS-HF-887A-R1-01M-EPC-9BA269]

value: Recurrence


title: glioma_Recurrence 2 [GLSS-HF-8438-R2-01M-EPC-A9D6C2]

value: male

value: RTK I


title: glioma_Primary [GLSS-HF-7CAC-TP-01M-EPC-B10748]


title: glioma_Recurrence 3 [GLSS-HF-753F-R3-01M-EPC-C4C6B3]

value: hypothalamus


title: glioma_Recurrence 1 [GLSS-HF-6658-R1-01M-EPC-0EDB01]


title: glioma_Primary [GLSS-HF-9A7A-TP-01M-EPC-E7F59A]


title: glioma_Recurrence 2 [GLSS-HF-753F-R2-01M-EPC-2AF3BB]

value: control


title: glioma_Recurrence 1 [GLSS-HF-630A-R1-01M-EPC-7532E2]

value: female


title: glioma_Primary [GLSS-HF-57AE-TP-01M-EPC-3A1C51]

value: Primary


title: glioma_Recurrence 2 [GLSS-HF-57AE-R2-01M-EPC-8ADA14]

value: mesenchymal


title: glioma_Recurrence 2 [GLSS-HF-891E-R2-01M-EPC-9FE93D]

value: Unknown

value: high grade astrocytoma


title: glioma_Primary [GLSS-HF-53B9-TP-01M-EPC-2ED903]

value: Classic-like


title: glioma_Primary [GLSS-HF-8438-TP-01M-EPC-37E08B]

value: Glioblastoma, IDH-wildtype (WHO grade 4)


title: glioma_Recurrence 1 [GLSS-HF-57AE-R1-01M-EPC-5AC507]

value: IDHwt


title: glioma_Recurrence 1 [GLSS-HF-7CAC-R1-01M-EPC-27477B]


title: glioma_Recurrence 1 [GLSS-HF-6504-R1-01M-EPC-252EE9]

value: Mesenchymal-like


title: glioma_Recurrence 4 [GLSS-HF-753F-R4-01M-EPC-76AAC7]

value: noncodel


title: glioma_Primary [GLSS-HF-630A-TP-01M-EPC-92AEC9]

value: RTK II


title: glioma_Primary [GLSS-HF-6504-TP-01M-EPC-E06884]


title: glioma_Primary [GLSS-HF-6658-TP-01M-EPC-EFC2A0]


title: glioma_Recurrence 2 [GLSS-HF-53B9-R2-01M-EPC-A0A5F3]


title: glioma_Primary [GLSS-HF-4F0A-TP-01M-EPC-840C2F]

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: IDHmut

value: G-CIMP-high

value: astrocytoma


title: glioma_Primary [GLSS-HF-4FBF-R1-01M-EPC-C3406D]

value: male


title: glioma_Primary [GLSS-HF-50F3-TP-01M-EPC-93C210]


title: glioma_Primary [GLSS-HF-4D9A-TP-01M-EPC-C80747]


title: glioma_Recurrence 1 [GLSS-HF-4B46-R1-01M-EPC-455B6E]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 3)

value: Recurrence

value: codel

value: Codel

value: 1p/19q codeleted oligodendroglioma


title: glioma_Recurrence 2 [GLSS-HF-4F0A-R2-01M-EPC-E4FA81]

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: G-CIMP-low

value: high grade astrocytoma


title: glioma_Primary [GLSS-HF-4B46-TP-01M-EPC-A920DE]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: Primary


title: glioma_Recurrence 2 [GLSS-HF-50F3-R2-01M-EPC-6753AA]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: IDHwt

value: noncodel

value: Mesenchymal-like

value: mesenchymal


title: glioma_Recurrence 1 [GLSS-HF-4FBF-R2-01M-EPC-1CEBCD]


title: glioma_Recurrence 1 [GLSS-HF-4F0A-R1-01M-EPC-6642F6]

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: IDHmut

value: G-CIMP-high

value: control


title: glioma_Recurrence 1 [GLSS-HF-4D9A-R1-01M-EPC-AF1FB6]

value: male

value: Recurrence


title: glioma_Primary [GLSS-HF-409D-TP-01M-EPC-62ABD1]

value: female


title: glioma_Recurrence 1 [GLSS-HF-409D-R1-01M-EPC-2AACCA]


title: glioma_Primary [GLSS-HF-38DA-TP-01M-EPC-8199DB]

value: RTK II


title: glioma_Recurrence 1 [GLSS-HF-38DA-R1-01M-EPC-C52925]


title: glioma_Recurrence 1 [GLSS-HF-3162-R1-02M-EPC-109017]


title: glioma_Primary [GLSS-HF-3118-TP-01M-EPC-F7E790]

value: Classic-like


title: glioma_Recurrence 1 [GLSS-HF-3118-R1-01M-EPC-7645C3]


title: glioma_Primary [GLSS-HF-3050-TP-01M-EPC-ACD195]


title: glioma_Recurrence 1 [GLSS-HF-3050-R1-01M-EPC-914E6C]


title: glioma_Primary [GLSS-HF-2DF0-TP-01M-EPC-3CEC1B]


title: glioma_Recurrence 2 [GLSS-HF-3050-R2-01M-EPC-29ACCE]

value: RTK I


title: glioma_Recurrence 1 [GLSS-HF-2548-R1-02M-EPC-280C13]


title: glioma_Primary [GLSS-HF-2548-TP-02M-EPC-F65D55]


title: glioma_Recurrence 2 [GLSS-HF-1E83-R2-01M-EPC-2B7636]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: high grade astrocytoma


title: glioma_Primary [GLSS-HF-1E83-TP-01M-EPC-531D30]

value: Primary

value: astrocytoma


title: glioma_Recurrence 1 [GLSS-HF-1E83-R1-01M-EPC-362E33]

value: noncodel


title: glioma_Recurrence 1 [GLSS-HF-1DDC-R1-01M-EPC-9176F0]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: IDHwt

value: Mesenchymal-like


title: glioma_Primary [GLSS-HF-1DDC-TP-01M-EPC-BC0FE1]

value: mesenchymal


title: glioma_Primary [GLSS-HF-01E6-TP-02M-EPC-272C58]

value: Astrocytoma, IDH-mutant (WHO grade 4)

value: G-CIMP-high


title: glioma_Recurrence 1 [GLSS-HF-01E6-R1-02M-EPC-EF4DDB]

value: G-CIMP-low


title: glioma_Recurrence 1 [GLSS-HF-0EAE-R1-01M-EPC-2367A2]

value: male

value: Recurrence


title: glioma_Recurrence 1 [GLSS-HF-1CCD-R1-01M-EPC-4BC5A1]

value: control


title: glioma_Primary [GLSS-HF-0EAE-TP-01M-EPC-72FBD3]


title: glioma_Primary [GLSS-HF-3162-TP-02M-EPC-4A333F]


title: glioma_Recurrence 2 [GLSS-HF-1CCD-R2-01M-EPC-529132]

value: Classic-like


title: glioma_Recurrence 1 [GLSS-HF-2DF0-R1-01M-EPC-82F06C]

value: female


title: MGC806 H3K27ac

city: Shanghai

first: Li

last: Fangyuan

state: Shanghai

address: Ruijin Er road

institute: Shanghai Jiao Tong University

data_processing:
Peak calling utilized a model-based analysis of ChIP-Seq (MACS) algorithm
ChIP-Seq reads were aligned to the reference human genome 19 using the Bowtie alignment program, and the unique aligned reads were converted to BED format. The overlap analysis, plot of genomic location, peak filtering, sequence extraction, and motif identification were performed using ChIPseek
ChIPseek also employed scripts from BEDtools using a genome binning algorithm used by the UCSC genome browser to sort genomic regions into groups along the length of chromosome.
Integrative genomics viewer was used to visualize data.
Assembly: hg19
Supplementary files format and content: bed, peakfiles

source_name: gastric cancer

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
DNA (20 ng) was quantified by fluorimetry, electrophoresis was resolved, and 40-250 bp factions were extracted. DNA was blunted and phosphorylated with T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. Subsequently, an A nucleotide was added to the 3’ end of the DNA fragments. Adaptor-ligated libraries were amplified by 16 cycles of PCR amplification. A purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and subjected to massively parallel sequencing (Illumina Genome Analyzer IIx) following the manufacturer’s protocols.

value: gastric cancer

tag: chip antibody

value: Genomic DNA


title: MGC805 H3K4me3


title: MGC803 Input


title: MGC803 BPTF

value: BPTF (no. ab72036, Abcam)


title: A_2.6.T

city: Melbourne

first: Joel

middle: Jeffrey Duncan

last: Moffet

state: Victoria

address: 1G Royal Parade

institute: WEHI

data_processing:
Raw counts from the two separate experimental batches were grouped into a single dataset. AOIs were removed if their nuclei count was below 100 nuclei, as provided by NanoString. Genes were filtered out unless above limit of quantitation in 5 % of remaining AOIs, calculated for each AOI as the geometric mean of all negative probes multiplied by the geometric standard deviations of the negative probes to the second power. Remaining genes were normalized by upper quartile normalization
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing matrix of upper quartile normalized gene counts for each sample

source_name: primary high grade glioma

extract_protocol:
Formalin fixed paraffin embedded (FFPE) tissue were sectioned at 5 μm thickness and mounted onto Superfrost Plus slides within one month of spatial transcriptomics analysis. Slides were stored at 4 degrees Celsius with desiccator and shipped to NanoString (Seattle, USA) for Technology Access Program (TAP) processing for GeoMx DSP.
Pathology review was performed on all the six cases. The tissue sections demonstrated distinct morphological features and were assessed using the cellularity of the tumor cells, nuclear pleomorphisms, presence of mitoses, necrosis, and microvascular proliferation. The five anatomic features proposed by The Ivy Glioblastoma Atlas Project (Ivy GAP) were used to annotate the tumors into regions. These included: Leading edge (LE): the outermost part of tumour with the least tumor cell density and bordering on the normal tissue area; Cellular tumor (CT): the core of the tumor with highest cell density; Infiltrating tumor (IT): the zone interposed between LE and CT with moderate tumour cell density; Microvascular proliferation (MVP): Areas with endothelial proliferation; Pseudopalisading cells around necrosis (PAN): dense tumour cells geographically fenced around core necrosis. Other features recognized are regions of large non-palisaded necrosis (NEC) and normal brain tissue (N). Annotations were performed by two pathologists.
After baking the slides for 2 hours for paraffin removal, slides were loaded onto a Leica BOND RX for tissue rehydration, heat-induced epitope retrieval (ER2 for 20 minutes at 100 °C) and proteinase K treatment (0.1 μg/ml for 15 minutes at 37 °C). The tissue sections were then hybridized with the Human WTA probes overnight. Following 2 x 5 min stringent washes (1:1 4x SSC buffer & formamide), the slides were blocked and then incubated morphology marker antibodies: GFAP (488 channel, NBP2-3318AF488, Novus), CD45 (594 channel, 13917BF, Cell Signaling Technologies), and Ki67 (647 channel, 9027BF, Cell Signaling Technologies). Syto83 (532 channel, S11364, Invitrogen) was used as a nuclear stain. Tissue sections were then loaded into the GeoMx platform and Regions of interest (ROIs) were selected guided by the immunofluorescence of the morphology markers antibodies listed above. Segmentation was used in some ROIs used to enrich for Ki67+ and/or CD45+ populations. UV light was then directed by the GeoMx at each AOI and released the RNA ID and UMI-containing oligonucleotide tags from the WTA probes for collection and sequencing preparation. Illumina i5 and i7 dual indexing primers were added to the oligonucleotide tags during PCR to uniquely index each AOI. AMPure XP beads (Beckman Coulter) were used for PCR purification. Library concentration as measured using a Qubit fluorometer (Thermo Fisher Scientific) and quality was assessed using a Bioanalyzer (Agilent). Sequencing was performed on an Illumina NovaSeq 6000 and .fastq files were processed into gene count data for each AOI using the GeoMx® NGS Pipeline.

value: anaplastic astrocytoma

tag: sample

tag: id simple

tag: region

tag: id sample

tag: class

value: A

value: F

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

tag: classification

value: Tumour

tag: infiltration

value: High

tag: ivygap

value: Cellular Tumour

value: negative

tag: roi type

value: tumor

tag: tumor location

value: Right parietal

value: Mutated

tag: atrx

value: Intact

tag: ki67 percentage

tag: cytology

tag: who grade

tag: comments

tag: loq


title: A_3.1.T

tag: tissue

tag: sample

tag: id simple

tag: region

tag: id sample

tag: Sex

value: M

value: Ki67- Border

value: Low

tag: age

value: Right frontal

value: Pre-treated:radiation, temozolomide


title: A_2.5.T

tag: class

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

tag: classification

value: Border

tag: infiltration

value: positive


title: A_2.6.K

value: anaplastic astrocytoma

value: A

tag: ivygap

tag: roi type

tag: tumor location

tag: atrx

tag: ki67 percentage

tag: cytology

tag: who grade


title: A_2.6.I

tag: tissue

tag: sample

tag: id simple

tag: region

tag: id sample

value: F

value: Tumour

value: non

tag: comments

tag: loq


title: A_2.4.T

tag: class

tag: Sex

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

value: Infiltrating Tumour

value: negative

tag: age


title: A_2.3.T

tag: classification

tag: infiltration

tag: ivygap

value: Cellular Tumour

tag: roi type

value: tumor

tag: tumor location

value: Right parietal

tag: atrx

tag: ki67 percentage


title: A_2.5.I

tag: tissue

tag: sample

tag: id simple

tag: region

tag: id sample

value: Mutated

value: Intact

tag: cytology

tag: who grade


title: DNA from CTC-MCC-5D cell line (Passage 14)

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

description: DNA from CTC-MCC-5D cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: RnBeads package in R environment (v4.1.1)

label: Cy5 and Cy3

source_name: CTC-MCC-5D cell line (P14)

extract_protocol: DNA was extracted from cell lines samples using  a standard high salt method based on SDS/Proteinase K.

tag: gender

value: Male

tag: disease

value: Colorectal adenocarcinoma (Circulating Tumor Cell from peripheral blood)


title: DNA from CTC-MCC-5D cell line (Passage 13)

description: DNA from CTC-MCC-5D cell line

source_name: CTC-MCC-5D cell line (P13)


title: A_2.1.T

tag: class

tag: Sex

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

value: Low

tag: age

tag: comments

tag: loq


title: A_2.2.I

tag: tissue

tag: sample

tag: classification

value: Ki67- Border

tag: infiltration

tag: ivygap

tag: roi type

tag: tumor location

tag: atrx

tag: ki67 percentage


title: DNA from CTC-MCC-5E cell line (Passage 10)

description: DNA from CTC-MCC-5E cell line

source_name: CTC-MCC-5E cell line (P10)

tag: gender

tag: disease


title: DNA from CTC-MCC-5F cell line (Passage 10)

description: DNA from CTC-MCC-5F cell line

source_name: CTC-MCC-5F cell line (P10)


title: GBM_1.6.T

value: glioblastoma

value: JJ98 GBM

tag: id simple

tag: region

tag: id sample

tag: class

value: GBM

tag: Sex

value: M

tag: batch

value: Pilot

tag: lib size

value: Normal

value: Tumour Leading Edge

value: Right temporo-occipital

value: Mosaic

tag: cytology

tag: who grade

value: MGMT methylated


title: A_2.2.T

tag: tissue

value: anaplastic astrocytoma

tag: sample

value: A

value: F

tag: immune border

tag: aoinucleicount

tag: classification

tag: infiltration

value: Cellular Tumour

value: negative

value: tumor

tag: age

value: Right parietal

tag: comments

tag: loq


title: DNA from CTC-MCC-5B cell line (Passage 11)

description: DNA from CTC-MCC-5B cell line

source_name: CTC-MCC-5B cell line (P11)

tag: gender

value: Male

tag: disease

value: Colorectal adenocarcinoma (Circulating Tumor Cell from peripheral blood)


title: GBM_1.5.T

value: glioblastoma

value: JJ98 GBM

tag: id simple

tag: region

tag: id sample

tag: class

value: GBM

value: Ki67- Border

value: Low

tag: ivygap

value: Infiltrating Tumour

value: non

tag: roi type

tag: tumor location

value: Intact

tag: atrx

tag: ki67 percentage


title: DNA from CTC-MCC-41.4 cell line (Passage 12)

description: DNA from CTC-MCC-41.4 cell line

source_name: CTC-MCC-41.4 cell line (P12)


title: DNA from CTC-MCC-5G cell line (Passage 11)

description: DNA from CTC-MCC-5G cell line

source_name: CTC-MCC-5G cell line (P11)


title: DNA from CTC-MCC-5E cell line (Passage 12)

description: DNA from CTC-MCC-5E cell line

source_name: CTC-MCC-5E cell line (P12)


title: DNA from CTC-MCC-5F cell line (Passage 12)

description: DNA from CTC-MCC-5F cell line

source_name: CTC-MCC-5F cell line (P12)


title: DNA from CTC-MCC-41.4 cell line (Passage 10)

description: DNA from CTC-MCC-41.4 cell line

source_name: CTC-MCC-41.4 cell line (P10)


title: DNA from CTC-MCC-5D cell line (Passage 12)

description: DNA from CTC-MCC-5D cell line

source_name: CTC-MCC-5D cell line (P12)


title: DNA from CTC-MCC-5F cell line (Passage 11)

description: DNA from CTC-MCC-5F cell line

source_name: CTC-MCC-5F cell line (P11)


title: DNA from CTC-MCC-5E cell line (Passage 11)

description: DNA from CTC-MCC-5E cell line

source_name: CTC-MCC-5E cell line (P11)


title: DNA from CTC-MCC-5B cell line (Passage 10)

description: DNA from CTC-MCC-5B cell line

source_name: CTC-MCC-5B cell line (P10)


title: GBM_1.3.I

tag: tissue

tag: sample

tag: Sex

value: M

tag: batch

value: Pilot

tag: lib size

tag: immune border

tag: aoinucleicount

value: Tumour

value: High

value: Right temporo-occipital

value: Mosaic

tag: cytology

tag: who grade

value: MGMT methylated


title: GBM_1.3.K

tag: id simple

tag: region

tag: classification

tag: infiltration

value: Cellular Tumour

value: positive

tag: age

tag: comments

tag: loq


title: DNA from CTC-MCC-5A cell line (Passage 11)

description: DNA from CTC-MCC-5A cell line

source_name: CTC-MCC-5A cell line (P11)

tag: gender

value: Male

tag: disease

value: Colorectal adenocarcinoma (Circulating Tumor Cell from peripheral blood)


title: GBM_1.3.T

tag: tissue

value: glioblastoma

tag: sample

value: JJ98 GBM

tag: id sample

tag: class

value: GBM

tag: ivygap

value: negative

tag: roi type

value: tumor

tag: tumor location

tag: atrx

tag: ki67 percentage


title: DNA from CTC-MCC-5G cell line (Passage 10)

description: DNA from CTC-MCC-5G cell line

source_name: CTC-MCC-5G cell line (P10)


title: GBM_1.2.T

source_name: primary high grade glioma

tag: id simple

tag: region

tag: Sex

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

value: Intact

tag: cytology

tag: who grade


title: GBM_1.2.I

tag: tissue

tag: sample

value: M

tag: classification

tag: infiltration

value: non

tag: age

tag: comments

tag: loq


title: GBM_1.2.K

tag: id sample

tag: class

value: Pilot

value: Tumour

tag: ivygap

tag: roi type

tag: tumor location

tag: atrx

tag: ki67 percentage


title: DNA from CTC-MCC-5C cell line (Passage 16)

description: DNA from CTC-MCC-5C cell line

source_name: CTC-MCC-5C cell line (P16)

tag: gender

tag: disease


title: GBM_1.1.I

tag: id simple

tag: region

tag: Sex

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

value: High

value: Cellular Tumour + Microvascular Proliferation

value: Right temporo-occipital

tag: cytology

tag: who grade


title: DNA from CTC-MCC-5C cell line (Passage 15)

description: DNA from CTC-MCC-5C cell line

source_name: CTC-MCC-5C cell line (P15)


title: A_1.4.I

tag: tissue

value: oligodendroglioma

tag: sample

value: JJ93 A

tag: id sample

tag: class

value: A

value: F

tag: classification

tag: infiltration

value: Cellular Tumour

tag: age

value: Left frontal

value: Mutated

value: A*

tag: comments

tag: loq


title: A_1.5.T

tag: id simple

tag: region

value: Ki67- Border

value: Low

tag: ivygap

value: negative

tag: roi type

value: tumor

tag: tumor location

tag: atrx

tag: ki67 percentage


title: DNA from CTC-MCC-5C cell line (Passage 14)

description: DNA from CTC-MCC-5C cell line

source_name: CTC-MCC-5C cell line (P14)

tag: gender

value: Male

tag: disease

value: Colorectal adenocarcinoma (Circulating Tumor Cell from peripheral blood)


title: DNA from CTC-MCC-5G cell line (Passage 12)

description: DNA from CTC-MCC-5G cell line

source_name: CTC-MCC-5G cell line (P12)


title: DNA from CTC-MCC-5A cell line (Passage 10)

description: DNA from CTC-MCC-5A cell line

source_name: CTC-MCC-5A cell line (P10)


title: A_1.3.T

tag: tissue

tag: sample

tag: Sex

tag: batch

value: Pilot

tag: lib size

tag: immune border

tag: aoinucleicount

value: Tumour

value: High

value: Intact

tag: cytology

tag: who grade


title: DNA from CTC-MCC-41 cell line (Passage 12) 2

description: DNA from CTC-MCC-41 cell line

source_name: CTC-MCC-41 cell line (P12)


title: DNA from CTC-MCC-5B cell line (Passage 9)

description: DNA from CTC-MCC-5B cell line

source_name: CTC-MCC-5B cell line (P9)


title: A_1.4.T

value: oligodendroglioma

value: JJ93 A

tag: id simple

tag: region

tag: id sample

tag: class

tag: classification

tag: infiltration

value: non

tag: age

tag: comments

tag: loq


title: GBM_1.1.K

tag: tissue

value: glioblastoma

tag: sample

value: JJ98 GBM

value: GBM

value: M

tag: ivygap

value: Cellular Tumour + Microvascular Proliferation

value: positive

tag: roi type

tag: tumor location

value: Right temporo-occipital

tag: atrx

value: Mosaic

tag: ki67 percentage

value: MGMT methylated


title: GBM_1.1.T

tag: Sex

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

value: negative

value: tumor

tag: cytology

tag: who grade


title: A_1.2.I

tag: id simple

tag: region

tag: id sample

tag: class

value: A

value: F

value: Pilot

tag: classification

value: Tumour

tag: infiltration

value: Cellular Tumour

tag: age

value: Left frontal

value: Mutated

value: A*


title: DNA from CTC-MCC-41 cell line (Passage 14) 2

description: DNA from CTC-MCC-41 cell line

source_name: CTC-MCC-41 cell line (P14)

tag: gender

value: Male

tag: disease

value: Colorectal adenocarcinoma (Circulating Tumor Cell from peripheral blood)


title: A_1.3.K

tag: tissue

value: oligodendroglioma

tag: sample

value: JJ93 A

value: High

tag: ivygap

tag: roi type

tag: tumor location

tag: atrx

value: Intact

tag: ki67 percentage

tag: comments

tag: loq


title: A_1.2.T

tag: id simple

tag: region

tag: Sex

tag: batch

tag: lib size

tag: immune border

tag: aoinucleicount

tag: cytology

tag: who grade


title: DNA from CTC-MCC-5A cell line (Passage 12)

description: DNA from CTC-MCC-5A cell line

source_name: CTC-MCC-5A cell line (P12)

tag: gender

tag: disease


title: DNA from CTC-MCC-41.4 cell line (Passage 11)

description: DNA from CTC-MCC-41.4 cell line

source_name: CTC-MCC-41.4 cell line (P11)


title: DNA from CTC-MCC-41 cell line (Passage 13) 2

description: DNA from CTC-MCC-41 cell line

source_name: CTC-MCC-41 cell line (P13)


title: A_1.1.T

tag: tissue

tag: sample

tag: id sample

tag: class

tag: classification

value: Border

tag: infiltration

value: Low

tag: ivygap

value: positive

tag: roi type

tag: age


title: A_1.2.K

tag: id simple

tag: region

value: A

tag: Sex

tag: batch

tag: tumor location

tag: atrx

tag: ki67 percentage

tag: comments

tag: loq


title: 9_75_pct_PEDOT_3_1

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

description: 9.75% (w/w PEDOT/PVA) PEDOT:PSS , biological replicate 3, technical replicate 1

data_processing:
Quality of sequencing data was assessed using FASTQC.
Reads were aligned to the human reference genome hg38 using STAR and gene counts were determined using featureCounts.
Log2 fold changes of differentially expressed genes (DEGs) were determined with DESeq2 via a paired model of non-conductive versus conductive substrates and including biological replicates as a covariate.
Top DEGs were filtered with a log2 fold change greater than or equal to 0.25 and p-value less than or equal to 0.05 and used to construct a volcano plot via EnhancedVolcano, an MA plot via ggpubr’s ‘ggmaplot’ function, as well as to determine gene ontology (GO) terms via g:Profiler.
For generating a principal component analysis (PCA) plot and heatmap, normalization of sequencing data into log2 counts per million (cpm) was performed with edgeR.
Batch effect corrections due to biological replicates was performed with the sva package’s ‘ComBat’ function after averaging technical replicates.
Normalized data with batch correction were used to generate a PCA plot via ggplot and heat map via pheatmap.
Assembly: hg38
Supplementary files format and content: Text file containing raw counts from featureCounts.

growth_protocol: RUES2 hPSC-CMs were maintained in RPMI + B27 with insulin at 37C with 5% CO2.

extract_protocol:
hPSC-CMs on 8% PVA or conductive scaffolds were dissociated with 0.5 mL 0.25% Trypsin-EDTA and pelleted via centrifugation at 1500 RPM for 5 minutes. The cells were resuspended in DPBS, repelleted, and lysed with 1mL QIAzol (Qiagen, 79306) for 5 minutes. Chloroform was added 1:5 to QIAzol, shaken for 15 seconds, and allowed to sit for 3 minutes. The samples were centrifuged for 10 minutes at 15,000 RPM and 4C and the aqueous phase containing the RNA was transferred to new tubes. An equal volume of isopropanol was added and the samples were allowed to rest for 10 minutes, followed by a 10 minute centrifugation at 15,000 RPM at 4C. The supernatant was then removed and the RNA pellet was resuspended in 1 mL of cold 75% molecular grade ethanol in diethylpyrocarbonate (DEPC) water. The samples were repelleted at 15,000 RPM at 4C, decanted, and resuspended in 100 µL of DEPC water. An RNeasy Mini kit (Qiagen, 74104) was used to purify the RNA following the manufacturer’s protocol.
Illumina Total RNA Prep (Ribodepletion)

treatment_protocol: Day 50 RUES2 hPSC-CMs were cultured on either 8% PVA (non-conductive control) or 9.75% PEDOT:PSS/PVA (conductive) electrospun scaffolds for 3 days.

tag: cell line

tag: cell type

value: Human ESC - cardiomyocyte

tag: genotype

value: WT

tag: treatment

value: 9.75% (w/w PEDOT/PVA) PEDOT:PSS


title: 9_75_pct_PEDOT_3_3

description: 9.75% (w/w PEDOT/PVA) PEDOT:PSS , biological replicate 3, technical replicate 3


title: 9_75_pct_PEDOT_2_1

description: 9.75% (w/w PEDOT/PVA) PEDOT:PSS , biological replicate 2, technical replicate 1


title: GBM_1.4.T

tag: tissue

value: glioblastoma

tag: sample

value: JJ98 GBM

tag: id sample

tag: class

value: GBM

value: M

value: Pilot

tag: lib size

tag: immune border

tag: aoinucleicount

tag: classification

tag: infiltration

value: Cellular Tumour

value: non

value: tumor

value: Right temporo-occipital

value: Mosaic

tag: cytology

tag: who grade

value: MGMT methylated


title: 8_pct_PVA_2_3

description: 8% PVA substrate, biological replicate 2, technical replicate 3

value: 8% PVA


title: 8_pct_PVA_3_1

description: 8% PVA substrate, biological replicate 3, technical replicate 1


title: 9_75_pct_PEDOT_1_2

description: 9.75% (w/w PEDOT/PVA) PEDOT:PSS , biological replicate 1, technical replicate 2


title: 8_pct_PVA_3_3

description: 8% PVA substrate, biological replicate 3, technical replicate 3


title: 8_pct_PVA_1_3

description: 8% PVA substrate, biological replicate 1, technical replicate 3


title: 8_pct_PVA_1_2

description: 8% PVA substrate, biological replicate 1, technical replicate 2


title: 8_pct_PVA_2_2

description: 8% PVA substrate, biological replicate 2, technical replicate 2


title: MOLM-13, DMSO, rep 3

city: Hannover

first: Tina

middle: M.

last: Schnoeder

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

description:
readcounts_norm_ATACseq_MOLM-13_PR957vsDMSO.txt
DARs_down_ATACseq_MOLM-13_PR957vsDMSO.txt
DARs_up_ATACseq_MOLM-13_PR957vsDMSO.txt

data_processing:
ATAC-seq reads were trimmed using Trimmomatic v0.39 with following parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Aligment was performed using bowtie2 v2.2.5 against the human reference genome hg38
Duplicated reads were removed using picard v2.27.1 and sorting and indexing of bam files was done using samtools v1.7
Narrow peaks were called using MACS2 v2.2.7.1
bigWig files were generated using bamCoverage v3.5.1
Normalization and differential accesible regions analysis were performed using the DESeq2 R package
Assembly: hg38
Supplementary files format and content: bigWig, tab-delimited matrix table (.txt)

growth_protocol: MOLM-13 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Nuclear fraction was extracted from the cells and tagmented using  Illumina Tagment DNA TDE1 Enzyme and Buffer Kit. Subsequently, DNA was extracted using the DNA Clean & Concentrator-5 from Zymo Research.
ATAC libraries were amplified from tagmented DNA isolates using 7 cycles on the thermocycler. Post amplification libraries were size selected using SPRI-select beads from Beckman Coulter. Library fragment lenght was checked by HSD5000 Tape and DNA concentration by Qubit.

treatment_protocol: MOLM-13 cells were treated for 48hours with 100nM of the immunoproteasome inhibitor PR-957 (ONX-0914) or DMSO as a diluent control

value: acute myeloid leukemia

value: DMSO control

tag: time


title: MOLM-13, PR-957, rep 1


title: MOLM-13, DMSO, rep 2


title: MOLM-13, PR-957, rep 2


title: MOLM-13, DMSO, rep 1


title: MOLM-13, PR-957, rep 3


title: MOLM-13, MI-503 + PR-957, rep 1

description:
DEG_RNAseq_MOLM-13_CombivsDMSO-new.txt
Comb_MI_DMSO_readscounts-new

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39
Trimmed sequence reads were aligned to the UCSC hg38 genome using STAR v2.7.10a.
Read count extraction was performed using featureCounts v2.0.1
Normalization and differential gene expression analysis were performed using the DESeq2 R package
Assembly: hg38
Supplementary files format and content: tab-delimited matrix table (.txt)

extract_protocol:
RNA was harvested using RNeasy MinElute Cleanup Kit (Qiagen). 5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's instructions.

treatment_protocol: MOLM-13 cells were treated for 72hours with 1μM MI-503, 1μM MI-503 and 100nM PR-957 (ONX-0914) or DMSO as a diluent control


title: MOLM-13, MI-503 + PR-957, rep 4


title: MOLM-13, MI-503 + PR-957, rep 2


title: MOLM-13, MI-503, rep 3

description:
DEG_RNAseq_MOLM-13_MIvsDMSO-new.txt
Comb_MI_DMSO_readscounts-new


title: MOLM-13, MI-503, rep 1


title: MOLM-13, DMSO, rep 4

description:
DEG_RNAseq_MOLM-13_MIvsDMSO-new.txt
DEG_RNAseq_MOLM-13_CombivsDMSO-new.txt
Comb_MI_DMSO_readscounts-new


title: MOLM-13, MI-503, rep 2


title: MOLM-13, DMSO, rep 1


title: MOLM-13, MI-503, rep 4


title: MOLM-13, DMSO, rep 3


title: 9_75_pct_PEDOT_2_2

description: 9.75% (w/w PEDOT/PVA) PEDOT:PSS , biological replicate 2, technical replicate 2

value: Human ESC - cardiomyocyte


title: 9_75_pct_PEDOT_1_3

description: 9.75% (w/w PEDOT/PVA) PEDOT:PSS , biological replicate 1, technical replicate 3

value: WT


title: MOLM-13, PR-957, rep 4

description:
DEG_RNAseq_MOLM-13_PR957vsDMSO.txt
Counts-RNAseq_MOLM-13_PR957vsDMSO.txt

treatment_protocol: MOLM-13 cells were treated for 72hours with 100nM of the immunoproteasome inhibitor PR-957 (ONX-0914) or DMSO as a diluent control


title: MOLM-13, PR-957, rep 2


title: MOLM-13, PR-957, rep 3


title: MOLM-13, PR-957, rep 1


title: MOLM-13, DMSO, rep 4


title: MOLM-13, DMSO, rep 2


title: MOLM-13, DMSO, rep 3


title: MOLM-13, DMSO, rep 1


title: Leiomyosarcoma_14

city: Pohang

first: Sarah

address: 558, Handong-ro, Buk-gu

institute: Handong Global University

data_processing:
The adapter sequences and the ends of reads less than Phred quality score 20 were trimmed, and simultaneously, reads shorter than 50 bp were removed using cutadapt v.2.8.
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a. (parameters - quantMode: TranscriptomeSAM)
Gene expression estimation was performed using RSEM v.1.3.1. (parameters - strandedness: reverse, estimate-rspd)
Assembly: hg38
Supplementary files format and content: comma separated text file including log2(FPKM+0.001) values for each sample

source_name: Uterus

extract_protocol:
mRNA molecules were purified and fragmented from 1 μg of total RNA using oligo (dT) magnetic beads.
The libraries were prepared for 151 bp paired-end sequencing using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA)

value: Uterus

tag: disease state

value: Leiomyosarcoma


title: Leiomyosarcoma_13


title: Leiomyosarcoma_16


title: Leiomyosarcoma_15


title: Leiomyosarcoma_11


title: Leiomyosarcoma_10


title: MOLM-13, DMSO, rep 2

tag: cell line


title: Leiomyoma_16

value: Leiomyoma


title: Leiomyosarcoma_17


title: Leiomyoma_17


title: Leiomyoma_15


title: Leiomyosarcoma_12


title: Leiomyoma_12


title: Leiomyoma_14


title: Leiomyoma_10


title: Leiomyosarcoma_8


title: Leiomyoma_13


title: Leiomyoma_9


title: Leiomyosarcoma_6


title: Leiomyoma_7


title: Leiomyosarcoma_7


title: Leiomyosarcoma_18


title: Leiomyoma_8


title: Leiomyoma_6


title: Leiomyoma_5


title: Leiomyosarcoma_3


title: Leiomyosarcoma_2


title: Leiomyoma_3


title: Leiomyoma_2


title: Leiomyoma_1


title: ip_CD34_3

city: Chengdu

first: ya

last: zhou

state: Sichuan

address: huacai road No.26, chenghua district

institute: Institute of blood transfusion

description: CD34+ umbilical cord blood HSPCs co-cultured with hiPSC-nMSC for 7 days

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: umbilical cord

extract_protocol:
Strand-specific RNA-seq (ssRNA-seq) libraries were prepared according the manufacturer's instructions using the Illumina Standard RNA sample library preparation kit (Illumina, San Diego, CA, USA).
After quantification using the Agilent 2100 bioanalyzer (Agilent, Santa Clara, CA, USA), the strand-specific libraries were sequenced on an Illumina HiSeq X ten instrument that generatedpaired-end reads of 150 nucleotides.

value: umbilical cord

tag: cell type

value: umbilical cord blood cells


title: Leiomyosarcoma_1

last: Kim


title: Leiomyoma_4


title: N_CD34_3

description: CD34+ umbilical cord blood HSPCs co-cultured without MSC for 7 days


title: Leiomyoma_11


title: ip_CD34_2

value: CD34+ umbilical cord blood HSPCs co-cultured with hiPSC-nMSC for 7 days


title: N_CD34_4

value: CD34+ umbilical cord blood HSPCs co-cultured without MSC for 7 days


title: ip_CD34_4


title: H1_CD34_2

description: CD34+ umbilical cord blood HSPCs co-cultured with H1-nMSC for 7 days


title: Leiomyosarcoma_9


title: H1_CD34_3

value: CD34+ umbilical cord blood HSPCs co-cultured with H1-nMSC for 7 days


title: C_CD34_4

description: CD34+ umbilical cord blood cells co-cultured with UC-MSC for 7 days


title: C_CD34_3

value: CD34+ umbilical cord blood cells co-cultured with UC-MSC for 7 days


title: C_CD34_2


title: H1_CD34_4


title: Leiomyosarcoma_5


title: ip9_NM_1

description: Mesenchymal stem cells isolated from hiPSCs derived brain organoid named hiPSC-nMSCs

value: Mesenchymal stem cells


title: Leiomyosarcoma_4


title: ip9_NM_2

source_name: Mesenchymal stem cells isolated from hiPSCs derived brain organoid named hiPSC-nMSCs


title: H1_NM_3

description: Mesenchymal stem cells isolated from H1 hESCs derived brain organoid named H1 nMSCs

source_name: Mesenchymal stem cells isolated from H1 hESCs derived brain organoid named H1-nMSCs

value: Mesenchymal stem cells isolated from H1-hESCs derived brain organoid named H1-nMSCs


title: ip9_NM_3

value: Mesenchymal stem cells isolated from hiPSCs derived brain organoid named hiPSC-nMSCs


title: H1_NM_2

value: Mesenchymal stem cells isolated from H1 hESCs derived brain organoid named H1-nMSCs


title: C_M_3

description: Mesenchymal stem cells derieved  from umbilical cord (UC-MSCs)


title: H1_NM_1


title: C_M_2

value: Mesenchymal stem cells derieved  from umbilical cord (UC-MSCs)


title: N_CD34_2


title: C_M_1


title: ip002_2

description: human induced pluripotent stem cells (hiPSCs)

source_name: human induced pluripotent stem cells

value: human induced pluripotent stem cells

value: hiPSCs were maintained on Matrigel-coated plates in mTeSR1 medium


title: ip002_3


title: H1_3

description: H1 human embryonic stem cells (H1 hESCs)

source_name: H1 human embryonic stem cells

value: H1 human embryonic stem cells

value: H1 hESCs were maintained on Matrigel-coated plates in mTeSR1 medium


title: ip002_1


title: H1_2


title: H1_1


title: M_D_2

first: Yanmeng

last: Tao

address: #5 Yiheyuan Road

department: Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies

institute: Peking University

description:
M_D_2
RNAseq_3_gene_count.xls

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.

source_name: heart

growth_protocol: Cells were cultured in reprogramming medium (DMEM/M199 (4:1) supplemented with 10% FBS,10% KnockOut Serum Replacement, 1% MEM Non-Essential Amino Acids, 1% GlutaMAX, 1% penicillin-streptomycin, 2 µg/mL Doxycycline hyclate)

extract_protocol:
Performed according to RNeasy Plus Mini Kit (QIAGEN, Cat#74134)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.  In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: Cells were treated with Ctrl (DMSO) or 2C (SB431542 and Baricitinib)

value: heart

value: NHCF (Lonza, Cat#CC2904)

value: Cardiac fibroblasts

tag: genotype

value: WT

value: MYOCD+2C for 5 weeks


title: M_C_2

description:
M_C_2
RNAseq_3_gene_count.xls

tag: treatment

value: MYOCD+Ctrl for 5 weeks


title: BPTF-KO-MGC803

data_processing:
The raw sequencing reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. The clean reads were then separately aligned to the reference genome by using TopHat (http://tophat.cbcb.umd.edu/, version2.0.0) software. The bowtie mapping criteria were as follows: reads should be uniquely matched to the genome allowing up to 2 mismatches, without insertions or deletions.
DEGs (differential expression genes) between two different samples (BPTF/MGC803-KO vs. MGC803/BPTF-NC) were identified by calculating the expression level of each transcript according to the fragments per kilobase of exon per million mapped reads (FRKM) method.
R statistical package software EdgdR (Empirical Analysis of Digital Gene Expression in R, (http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis. GO functional enrichment and KEGG pathway analysis was carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: gastric cancer

extract_protocol:
Total RNA was extracted from the  MGC803/BPTF-KO cells using TRIzol Reagent (Life Technologies) according the manufacturer’s instructions and genomic DNA was removed using DNase I (Takara)
RNA-seq transcriptome library was prepared by using 1 μg of total RNA following the TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA). Messenger RNA was isolated according to the polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer. Double-stranded cDNA was then synthesized utilizing a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). The synthesized cDNA was then subjected to end-repair, phosphorylation, and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were further size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 16 PCR cycles.

tag: tissue

value: gastric cancer

value: BPTF-KO

value: BPTF-Knock out


title: BPTF-NC-MGC803

value: Negative control

value: BPTF-NC


title: Bone metastatic castration-resistant prostate cancer [H-6259]

city: Boston

first: Sean

last: Lawler

state: MA

address: 75 Francis St

institute: Brigham and Women's Hospital

description: RNA isolated from pure neutrophil isolations using Zymogen Direct-zol RNA isolation kit

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to hg38 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output
Normalized fpkm values calculated with cufflinks
Genome_build: hg38

source_name: Blood

extract_protocol:
Neutrophils were isolated from blood using the Stem Cell Human Neutrophil Isolation kit
Libraries were prepared using  Kapa mRNA Hyper Prep reagent kits from 200ng of purified total RNA according to manufacturers' protocols.

tag: disease progression stage

tag: tissue/cell type

value: Peripheral blood neutrophil


title: M_C_1

description:
M_C_1
RNAseq_3_gene_count.xls


title: M_D_1

description:
M_D_1
RNAseq_3_gene_count.xls


title: Vec_2

description:
Vec_2
RNAseq_3_gene_count.xls

value: Vector+Ctrl for 5 weeks


title: Bone metastatic castration-resistant prostate cancer [H-3713894]


title: Localized prostate cancer [H-3711966]

value: Localized prostate cancer


title: Bone metastatic castration-resistant prostate cancer [H-3350550]


title: Healthy male donor [H-320974]

value: Healthy male donor


title: Healthy male donor [H-3224168]


title: Healthy male donor [H-334728]


title: Healthy male donor [H-2512220]


title: Localized prostate cancer [H-3158761]


title: Bone metastatic castration-resistant prostate cancer [H-214884]


title: Bone metastatic hormone-senstitive prostate cancer [H-1404067]


title: Bone metastatic hormone-senstitive prostate cancer [H-1153640]


title: Localized prostate cancer [H-1102755]


title: 13019_YF1B_8-6-D8-P23

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

source_name: YF1B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: 13019_YF1B_8-6-D8-P12


title: Bone metastatic hormone-senstitive prostate cancer [H-96144785]


title: Vec_1

description:
Vec_1
RNAseq_3_gene_count.xls

value: heart

value: NHCF (Lonza, Cat#CC2904)


title: 13019_YF1B_8-6-D8-P11


title: 13019_YF1B_8-6-D8-O24


title: 13019_YF1B_8-6-D8-O23


title: 13019_YF1B_8-6-D8-O12


title: 13019_YF1B_8-6-D8-N23


title: 13019_YF1B_8-6-D8-N11


title: 13019_YF1B_8-6-D8-M24


title: 13019_YF1B_8-6-D8-O11


title: 13019_YF1B_8-6-D8-N24


title: 13019_YF1B_8-6-D8-M12


title: Localized prostate cancer [H-3124010]


title: 13019_YF1B_8-6-D8-M11


title: 13019_YF1B_8-6-D8-M23


title: Bone metastatic castration-resistant prostate cancer [H-2478651]


title: 13019_YF1B_8-6-D8-L24


title: 13019_YF1B_8-6-D8-L23


title: 13019_YF1B_8-6-D8-L12


title: 13019_YF1B_8-6-D8-N12


title: 13019_YF1B_8-6-D8-K23


title: 13019_YF1B_8-6-D8-L11


title: 13019_YF1B_8-6-D8-K24


title: 13019_YF1B_8-6-D8-K11


title: 13019_YF1B_8-6-D8-P24


title: 13019_YF1B_8-6-D8-J23


title: 13019_YF1B_8-6-D8-J12


title: 13019_YF1B_8-6-D8-J11


title: 13019_YF1B_8-6-D8-I12


title: 13019_YF1B_8-6-D8-I23


title: 13019_YF1B_8-6-D8-I24


title: 13019_YF1B_8-6-D8-H24


title: 13019_YF1B_8-6-D8-I11


title: 13019_YF1B_8-6-D8-H23


title: 13019_YF1B_8-6-D8-H12


title: 13019_YF1B_8-6-D8-G11


title: 13019_YF1B_8-6-D8-G23


title: 13019_YF1B_8-6-D8-G24


title: 13019_YF1B_8-6-D8-H11


title: 13019_YF1B_8-6-D8-F12


title: 13019_YF1B_8-6-D8-F23


title: 13019_YF1B_8-6-D8-F24


title: 13019_YF1B_8-6-D8-E12


title: 13019_YF1B_8-6-D8-F11


title: 13019_YF1B_8-6-D8-E23


title: 13019_YF1B_8-6-D8-E24


title: 13019_YF1B_8-6-D8-D23


title: 13019_YF1B_8-6-D8-D12


title: 13019_YF1B_8-6-D8-K12


title: 13019_YF1B_8-6-D8-E11


title: 13019_YF1B_8-6-D8-D11


title: 13019_YF1B_8-6-D8-C24


title: 13019_YF1B_8-6-D8-C23


title: 13019_YF1B_8-6-D8-C11


title: 13019_YF1B_8-6-D8-B24


title: 13019_YF1B_8-6-D8-C12


title: 13019_YF1B_8-6-D8-B23


title: 13019_YF1B_8-6-D8-G12


title: 13019_YF1B_8-6-D8-A23


title: 13019_YF1B_8-6-D8-B12


title: 13019_YF1B_8-5-D8-P9


title: 13019_YF1B_8-6-D8-A24


title: 13019_YF1B_8-6-D8-A11


title: 13019_YF1B_8-6-D8-B11


title: 13019_YF1B_8-5-D8-P22


title: 13019_YF1B_8-5-D8-P21


title: 13019_YF1B_8-6-D8-D24


title: 13019_YF1B_8-5-D8-O9


title: 13019_YF1B_8-5-D8-O10


title: 13019_YF1B_8-5-D8-O22


title: 13019_YF1B_8-5-D8-O21


title: 13019_YF1B_8-5-D8-N22


title: 13019_YF1B_8-5-D8-N9


title: 13019_YF1B_8-5-D8-M22


title: 13019_YF1B_8-5-D8-M9


title: 13019_YF1B_8-5-D8-M10


title: 13019_YF1B_8-5-D8-N10


title: 13019_YF1B_8-5-D8-L9


title: 13019_YF1B_8-5-D8-L22


title: 13019_YF1B_8-5-D8-M21


title: 13019_YF1B_8-5-D8-N21


title: 13019_YF1B_8-6-D8-A12


title: 13019_YF1B_8-5-D8-K22


title: 13019_YF1B_8-5-D8-K21


title: 13019_YF1B_8-5-D8-P10


title: 13019_YF1B_8-5-D8-J9


title: 13019_YF1B_8-5-D8-I22


title: 13019_YF1B_8-5-D8-J22


title: 13019_YF1B_8-5-D8-J10


title: 13019_YF1B_8-5-D8-I21


title: 13019_YF1B_8-5-D8-I9


title: 13019_YF1B_8-5-D8-I10


title: 13019_YF1B_8-5-D8-J21


title: 13019_YF1B_8-5-D8-H9


title: 13019_YF1B_8-5-D8-H22


title: 13019_YF1B_8-5-D8-H10


title: 13019_YF1B_8-5-D8-H21


title: 13019_YF1B_8-5-D8-G10


title: 13019_YF1B_8-5-D8-G9


title: 13019_YF1B_8-5-D8-G22


title: 13019_YF1B_8-5-D8-F9


title: 13019_YF1B_8-5-D8-E22


title: 13019_YF1B_8-5-D8-F22


title: 13019_YF1B_8-5-D8-L10


title: 13019_YF1B_8-5-D8-G21


title: 13019_YF1B_8-5-D8-L21


title: 13019_YF1B_8-5-D8-E9


title: 13019_YF1B_8-5-D8-K10


title: 13019_YF1B_8-5-D8-F10


title: 13019_YF1B_8-5-D8-E21


title: 13019_YF1B_8-5-D8-D21


title: 13019_YF1B_8-5-D8-D9


title: 13019_YF1B_8-5-D8-D22


title: 13019_YF1B_8-5-D8-C22


title: 13019_YF1B_8-5-D8-C9


title: 13019_YF1B_8-5-D8-C21


title: 13019_YF1B_8-5-D8-B9


title: 13019_YF1B_8-5-D8-F21


title: 13019_YF1B_8-5-D8-B21


title: 13019_YF1B_8-5-D8-E10


title: 13019_YF1B_8-5-D8-B22


title: 13019_YF1B_8-5-D8-C10


title: 13019_YF1B_8-5-D8-D10


title: 13019_YF1B_8-5-D8-A22


title: 13019_YF1B_8-5-D8-B10


title: 13019_YF1B_8-5-D8-A9


title: 13019_YF1B_8-4-D8-O7


title: 13019_YF1B_8-4-D8-P7


title: 13019_YF1B_8-5-D8-A10


title: 13019_YF1B_8-5-D8-A21


title: 13019_YF1B_8-4-D8-O8


title: 13019_YF1B_8-4-D8-P20


title: 13019_YF1B_8-4-D8-N7


title: 13019_YF1B_8-4-D8-O19


title: 13019_YF1B_8-4-D8-N8


title: 13019_YF1B_8-4-D8-O20


title: 13019_YF1B_8-4-D8-P19


title: 13019_YF1B_8-4-D8-N20


title: 13019_YF1B_8-4-D8-M8


title: 13019_YF1B_8-4-D8-N19


title: 13019_YF1B_8-4-D8-M19


title: 13019_YF1B_8-4-D8-M7


title: 13019_YF1B_8-4-D8-L8


title: 13019_YF1B_8-4-D8-L7


title: 13019_YF1B_8-4-D8-L20


title: 13019_YF1B_8-4-D8-M20


title: 13019_YF1B_8-4-D8-K8


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