title: 6514_B, snRNA+snATAC

description: Library name: 6514_B_multiome


title: A7r5 cells, siRNALemd3, H3K27ac, Input, replicate 2

status: Public on Apr 01 2025

type: SRA

city: Beijing

first: Yunxi

last: Liao

state: Beijing

address: 38 Xueyuan Rd, Haidian District

country: China

institute: School of Basic Medical Sciences, Peking University

library_source: genomic

data_processing:
Paired ChIP-seq and ATAC-seq raw reads were trimmed with Trim galore (v0.32) and then aligned to rn7 genome using bwa-mem2 (v2.0pre2), and produce to sam files. Sam files were then sorted and converted to bam format using samtools (v1.15.1). PCR duplicates were removed using gatk (v4.2.6.1) MarkDuplicates. Finally, bam files were filtered using samtools view with ‘-f 2 -q 24’ parameters. As for ATAC-seq, we merge three biological replicates using “samtools merge”. We use danpos (v2.4)75 to call peak and genarate nomalized wig files with the parameters “danpos.py dregion --smooth_width 0 -c 25000000 -u 1 --frsz 200 --extend 200 --region_dis 3000 --pheight 1e-10” for ChIP-seq data, and “danpos.py dpeak -c 25000000 -u 1 --frsz 200 -m 1 --smooth_width 0 --pheight 1e-20” for ATAC-seq. We use wigToBigWig (v4) tool form UCSC to convert wig files to bigwig files.
Assembly: rn7
Supplementary files format and content: There are bigwig files of separate samples and pooled two groups.

molecule: genomic DNA

organism: Rattus norvegicus

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched by the addition of glycine to a final concentration of 125 mM for 5 min. The fixed cells were resuspended in lysis buffer containing protease inhibitors, then subjected to 30 cycles (30 s on and off) of sonication (Bioruptor, Diagenode) to generate chromatin fragments of ~300 bp in length. Lysates were diluted in buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, and 20 mM Tris-HCl, pH 8.1) containing protease inhibitors. For immunoprecipitation, the diluted chromatin was incubated with normal IgG (control) or indicated antibodies at 4℃ overnight with constant rotation, followed by incubation with 50 μl of 50% (v/v) protein A/G Sepharose beads for 2 h. Beads were successively washed. The pulled-down chromatin complex eluted by TE (1 mM EDTA and 10 mM Tris-HCl, pH 8.0) and input were de-crosslinked at 55℃ for 16 h in elution buffer (1% SDS and 0.1 M NaHCO3). The DNA was purified with the QIAquick PCR Purification Kit (QIAGEN).
Libraries for ChIP-seq were prepared using VAHTS Universal Pro DNA Library Prep Kit for Illumina following manufacturers's protocols.

tag: cell line

tag: cell type

value: aortic thoracic smooth muscle cells

tag: genotype

value: LEMD3 knockdown

tag: chip antibody


title: RIP_PRMT1_KD_R1_PlusDox

city: Buffalo

first: Laurie

last: Read

state: NY

address: 955 Main Street

department: Department of Microbiology and Immunology

country: USA

institute: University at Buffalo

library_source: transcriptomic

data_processing:
Illumina adaptors were trimmed using Cutadapt (v3.5), reads were mapped using Bowtie2 (v2.4.4) again the T. brucei genome version TriTrypDB-66_TbruceiTREU927 from TryTrypDB.org. After indexing and sorting the BAM files, featureCounts was used to count the reads for each gene_id. featureCounts output was utilized for DESeq2 for differential expression analysis.
Assembly: Trypanosoma brucei brucei TREU927
Supplementary files format and content: 2913_WT_RF_RK_PRMT1_RIPseq_counts.csv
Supplementary files format and content: featureCounts output from RIP-seq experiments

molecule: total RNA

organism: Trypanosoma brucei

source_name: 29-13-derived PF

growth_protocol: The 29-13-derived PF cell line containing a doxycycline-inducible RNAi construct that targets the 3′ UTR of DRBD18 was used in this study, harbouring the doxycycline-inducible N-terminal MYC tagged DRBD18 over-expression and over-expression of its methyl mutants (Triple R to F and triple R to K mutant) generated by site-directed mutagenesis. Cells were grown in standard conditions at 27ºC in SDM-79 medium supplemented with 10% fetal bovine serum and 10U/ml of penicillin/streptomycin. Drug concentrations used in this work were 15 µg/ml of hygromycin (Sigma), 15 µg/ml of neomycin (Sigma), 2.5 µg/mL of phleomycin, 50 µg/ml of puromycin (Invivogen) and 1 µg/ml of doxycycline (Sigma). The 29-13-derived PF cell line containing a doxycycline-inducible PRMT1 RNAi construct. Cells were grown in standard conditions at 27ºC in SDM-79 medium supplemented with 10% fetal bovine serum and 10U/ml of penicillin/streptomycin. Drug concentrations used in this work were 15 µg/ml of hygromycin (Sigma), 15 µg/ml of neomycin (Sigma), 2.5 µg/mL of phleomycin and 2.5 µg/ml of doxycycline (Sigma).

extract_protocol:
UV crosslinked DRBD18-RNA, DRBD18(R→F)-RNA and DRBD18(R→K)-RNA complexes were immunopurified from the lysate using anti-MYC antibodies attached to MYC beads (GE Healthcare). The unbound fraction was also collected; 10% was used for RNA extraction and 2% for western blotting. Beads were washed three times with IP buffer (lysis buffer plus 150 mM NaCl) and treated with DNase 1 (Sigma) followed by proteinase K (Roche) after confirmation by western blot. RNA was extracted from beads with phenol/chloroform 16 and ethanol precipitated. RNA was isolated from the input fractions using Trizol and ethanol precipitation.
Takara ThruPlex DNAseq kit (R400675) for Illumina. Samples were sequenced on a NovaSeq 6000, PE50, XP flow cell.

treatment_protocol: Three biological replicates of the DRBD18 RNAi cells harbouring either N2MYC-DRBD18(WT), N2MYC-DRBD18(R→F), or N2MYC-DRBD18(R→K) were grown in the presence of 1 µg/ml doxycycline for 36 hrs. Three biological replicates of the PRMT1 RNAi cells  were grown in the presence and absence of 2.5 µg/ml doxycycline for 48 hrs.

value: 29-13-derived PF

value: procyclic form

value: PRMT1 KD

tag: treatment

value: No Dox


title: Quercetin sample tested at 33.09 uM (Replicate: 1, Control Batch Id: 1).

type: RNA

city: Mason

first: Bastian

middle: Gregory

last: Selman

state: Ohio

address: 8700 Mason Montgomery Rd

institute: Procter & Gamble

hyb_protocol: 7.5 micrograms of labeled cRNA was fragmented manually and hybridized to Affymetrix Human Genome U219-96 arrays for 16 hr, washed, stained and scanned using an Affymetrix GeneTitan (Santa Clara, CA).

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan (Santa Clara, CA).

data_processing: The data were analyzed using the rma function in the affy package for R. This function uses RMA for background correction, performs probe specific correction, normalizes using quantile normalization and finally applies a median polish. Package citation: Gautier L, Cope L, Bolstad BM, Irizarry RA (2004). “affy—analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics, 20(3), 307–315. ISSN 1367-4803, doi:10.1093/bioinformatics/btg405.

label: biotin

organism: Homo sapiens

source_name: TK6 Human lymphoblastoid cells

label_protocol: Labeled cRNA was synthesized from 250 ng of total RNA using the Affymetrix (Santa Clara, CA) IVT-Express labeling kit according to manufacturer's instructions. Seven and a half micrograms of labeled cRNA was fragmented manually and hybridized to Affymetrix Human Genome U219-96 arrays for 16 hr, washed, stained and scanned using an Affymetrix GeneTitan (Santa Clara, CA).

growth_protocol: TK6 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, CRL-8015). Cells were cultured at 37C with 5% CO2 and 95% humidity in RPMI 1640 with 10% heat-inactivated FBS and 1% pen-strep. Cells were maintained at or below 1E6 cells/ml.

extract_protocol: Total RNA was extracted using Agencourt RNAdvance Tissue XP beads (Beckman Coulter Inc., Danvers, MA) according to the manufacturer's protocol on the cell lysates. RNA integrity was validated using a NanoDrop 8000 Spectrophotometer (Wilmington, DE).

treatment_protocol: All chemicals were tested in triplicate to a top concentration of 10 mM, or the limit of solubility or cytotoxicity. The final concentration of the solvent in these studies was limited to 0.5% (vol/vol) DMSO or water, although in a few isolated cases 1% DMSO or 10% water was used at a top concentration, in accordance with the OECD guidelines.

value: Quercetin

value: sample

tag: solvent

value: DMSO


title: 6514_A, snRNA+snATAC

city: Toronto

first: Federico

last: Gaiti

state: Ontario

address: 101 college street

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: 6514_A_multiome

library_source: other

data_processing:
Sample demultiplexing, cell barcode demultiplexing, read alignment, gene count aggregation were conducted using CellRanger v2.0.0 or v2.0.2
Assembly: hg38
Supplementary files format and content: Matrix files and tab-separated value file
Library strategy: Multiome

molecule: other

source_name: GBM patient brain tissue

extract_protocol:
Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit (10x Genomics). Tissue was dissociated by mechanical grinding and lysed with NP40 lysis buffer. The isolated pellet was repeatedly washed with PBS + 1% BSA + 1U/µl RNase Inhibitor and concentrated by centrifugation and stained with 7-AAD. Approximately 500,000 nuclei were collected and sorted based on cell size and granularity as well as 7-AAD-postive cells to separate out debris. The sorted nuclei were permeabilized in 0.1x lysis buffer, resuspended in Tris-based diluted nuclei buffer, and countered using a cell counter to achieve the corresponding nuclei stock concentration targeting recovery of 10,000 nuclei.
Following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics; CG000338), nuclei suspension was incubated in transposition mix at 37°C for 60 minutes to digest DNA into fragments at open chromatin regions. The transposed nuclei were then loaded onto a Chromium Next GEM Chip J (10x Genomics; PN-1000234) through a Chromium controller (10x Genomics) to generate Gel Bead-In Emulsions (GEM), which partition nuclei with barcoded gel-beads to enable single-nuclei barcoding. Dissolving the gel bead allows to produce barcoded transposed DNA (Illumina® P5 sequence and a 16 nt 10x ATAC barcode added) and cDNA from poly-adenylated capture of mRNA (Illumina® TruSeq Read 1 sequencing primer and a 16 nt RNA 10x barcode added), followed by Dynabeads cleanup and SPRIselect for size selection. The material was pre-amplified with 7 cycles of PCR for separated ATAC and gene expression library construction.  ATAC library was prepared by PT and sample index addition through PCR amplification. Gene expression library was prepared by obtaining cDNA amplicon though PCR amplification, followed by enzymatic fragmentation, end repair, A-tailing, adaptor ligation and PCR for adding P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 primer sequence.

tag: tissue

value: GBM patient brain tissue


title: Input_WT_R3

value: siDRBD18 + N2MYC-DRBD18-induced

value: 1 ug/ml doxycylcine


title: 6509_E, snRNA+snATAC

description: Library name: 6509_E_multiome


title: A7r5 cells, siRNAscramble, H3K27ac, ChIP, replicate 2

value: WT


title: A7r5 cells, siRNALemd3, H3K27ac, ChIP, replicate 1


title: 6509_D, snRNA+snATAC

description: Library name: 6509_D_multiome


title: Sodium Arsenite sample tested at 1.52 uM (Replicate: 3, Control Batch Id: 6).

value: Sodium Arsenite

value: Water


title: Input_WT_R2


title: Input_WT_R1


title: A7r5 cells, siRNAscramble, H3K27ac, ChIP, replicate 1


title: RIP_PRMT1_KD_R1_MinusDox


title: 6509_C, snRNA+snATAC

description: Library name: 6509_C_multiome


title: MC_TotalRNA_D2_24h_Buty

city: Palo Alto

first: Jelle

last: Folkerts

state: CA

address: 1291 Welch Road

department: Center for Clinical Sciences Research

institute: Stanford University

description:
I19-1034-02_D5_24H/ FPKM
D1_D2_0h_24h_rpkm.txt

data_processing:
Alignment: RNA-Seq and ChIP-Seq reads were aligned to the human genome (GRCh38) using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts).
Tag Directory Generation: Tag directories were generated for each sample using HOMER, with the removal of duplicate reads (-tbp 1 option).
Quantification and Normalization: (RNA-Seq) RNA-Seq data were quantified and normalized using HOMER. Differential expression analysis was conducted using DESeq2, identifying significantly differentially expressed genes with an adjusted P value < 0.05 and Log2 fold change greater than (-)0.8.
Peak Identification: (ChIP-Seq) H3K27Ac enriched regions were identified using HOMER's findPeaks function with specific parameters (e.g., -region -size 150 -minDist 370). Differential peaks were calculated using DESeq2.
Visualization and Annotation: Normalized reads (reads per million) were visualized as BedGraph files in the UCSC Genome Browser using HOMER's makeUCSCfile script. Genomic regions were annotated using the ROSE algorithm and HOMER for super-enhancers and typical enhancers identification.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human peripheral blood mononuclear cell-derived mast cells

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were obtained from buffy coats of healthy blood donors. CD34+ precursor cells were isolated using the EasySep Human CD34 Positive Selection Kit (STEMCELL Technologies). CD34+ cells were cultured in serum-free conditions in StemSpan medium (STEMCELL Technologies) supplemented with recombinant human IL-6 (50 ng/mL, Peprotech), human IL-3 (10 ng/mL, Peprotech), and human Stem Cell Factor (100 ng/mL, Peprotech) for 4 weeks. Post initial culture, cells were maintained in IMDM Glutamax I medium containing sodium pyruvate, 0.1% 2-mercaptoethanol, 0.5% BSA, 1% insulin-transferrin selenium, ciprofloxacin (10 µg/mL), IL-6 (50 ng/mL), and human Stem Cell Factor (100 ng/mL) for 8-12 weeks until maturity.

extract_protocol:
Total RNA was isolated from butyrate-treated and vehicle-treated PBCMCs using the RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer's protocol. Chromatin was extracted from 100K crosslinked PBCMCs, followed by sonication to obtain fragmented chromatin. Immunoprecipitation was performed using antibodies against H3K27Ac (Abcam, Ab4729) and H3K4Me2 (Abcam, Ab32356) with BSA-blocked Protein A agarose beads (Millipore #16-125).
For RNA-Seq, sequencing libraries were prepared from isolated RNA using the TruSeq RNA Library Prep Kit (Illumina). For ChIP-Seq, Illumina sequencing libraries were prepared from immunoprecipitated chromatin using the ThruPLEX DNA-Seq Kit (Rubicon Genomics).

treatment_protocol: Mature PBCMCs were treated with 5 mM butyrate or vehicle for 1, 3, 12 or 24 hours before RNA isolation and chromatin immunoprecipitation (ChIP).

value: 24h butyrate


title: Quercetin sample tested at 16.54 uM (Replicate: 1, Control Batch Id: 1).


title: 6509_B, snRNA+snATAC

description: Library name: 6509_B_multiome


title: Input_RK1_R3

value: siDRBD18 +  N2MYC-DRBD18(R->K) -induced


title: Quercetin sample tested at 16.54 uM (Replicate: 3, Control Batch Id: 1).


title: Quercetin sample tested at 16.54 uM (Replicate: 2, Control Batch Id: 1).


title: Input_RK1_R2


title: 6509_A, snRNA+snATAC

description: Library name: 6509_A_multiome


title: MC_TotalRNA_D1_24h_Buty

description:
I19-1031-04_D2_24H/ FPKM
D1_D2_0h_24h_rpkm.txt

value: human peripheral blood mononuclear cell-derived mast cells


title: Input_RK1_R1


title: Quercetin sample tested at 8.27 uM (Replicate: 3, Control Batch Id: 1).


title: 6467_F, snRNA+snATAC

description: Library name: 6467_F_multiome


title: Input_RF1_R3

value: siDRBD18 +  N2MYC-DRBD18(R->F)-induced


title: MC_TotalRNA_D1_0h_Buty

description:
I19-1031-03_D2_0H/ FPKM
D1_D2_0h_24h_rpkm.txt

value: 0h butyrate


title: 6467_E, snRNA+snATAC

description: Library name: 6467_E_multiome


title: Input_RF1_R2

value: 29-13-derived PF

value: procyclic form


title: Quercetin sample tested at 8.27 uM (Replicate: 1, Control Batch Id: 1).


title: HeLa, GammaRay, Input, MeRIP-seq

first: Yiming

last: Lu

address: Taiping Road

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

data_processing:
Sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR (version 020201) For meRIP-seq data, exomePeak software (version 3.10) was used for m6A peak calling, and m6A peaks were annotated by Homer (version 4.9) Genome_build: hg19 Supplementary_files_format_and_content: bw and FPKM data for RNA-seq samples
Assembly: hg19
Supplementary files format and content: BigWig

source_name: HeLa

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1 × penicillin-streptomycin (Beyotime) and maintained in a 5% CO2 and 95% air incubator [20% (vol/vol) O2].

extract_protocol:
polyA RNA
For meRIP-seq, the libraries were constructed by Truseq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions and quantified by BioAnalyzer High Sensitivity DNA chip, and then deeply sequenced on the Illumina HiSeq X10 to generate 150-bp paired-end reads. For RNA-seq library, mRNA enrichment, cDNA synthesis, adaptor addition, circularization, PCR amplification and library examination were performed on the BGIseq 500 at Beijing Genome Institute (BGI; Shenzhen, China) For meRIP-seq, the libraries were constructed by Truseq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions and quantified by BioAnalyzer High Sensitivity DNA chip, and then deeply sequenced on the Illumina HiSeq X10 to generate 150-bp paired-end reads. For RNA-seq library, mRNA enrichment, cDNA synthesis, adaptor addition, circularization, PCR amplification and library examination were performed on the BGIseq 500 at Beijing Genome Institute (BGI; Shenzhen, China)

treatment_protocol: Total RNA from the indicated samples was extracted using TRIZol reagent (Invitrogen Life Technologies) according to the manufacturer’s instruction. All samples were treated with DNase I to avoid genomic DNA contaminations. poly(A)+ RNA was isolated from total RNA using Oligotex mRNA Kits and subsequently fragmented into around 150 nt fragments using the RNA fragmentation buffer (20 mM Tris-HCl, pH 7.4, 20 mM ZnCl2) at 94 ℃ for 40 s. The reaction was then stopped with 0.05 M EDTA. For m6A-IP, 2 μg fragmented RNA was incubated with 3 μg anti-m6A antibody (Abcam) in immunoprecipitation buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% Igepal CA-630) supplemented with RNase inhibitor for 2 h at 4 ℃. Then the above mixture was incubated with 20 μl protein A/G beads (Thermo Fisher Scientific, #88803) for additional 2 h at 4 ℃ on a rotating wheel. After washing 5 times with immunoprecipitation buffer, bound RNA was extracted by proteinase K digestion, phenol-chloroform extraction followed by standard ethanol precipitation.

value: HeLa

tag: merip antibody

value: N6-methyladenosine (Abcam, ab151230)

value: Gamma ray exposure


title: Input_RF1_R1


title: HeLa, GammaRay, Rep2, IP, MeRIP-seq


title: Paraquat sample tested at 1500 uM (Replicate: 2, Control Batch Id: 8).

value: Paraquat

value: sample


title: Input_PRMT1_KD_R3_MinusDox

value: PRMT1 KD

value: No Dox


title: Input_PRMT1_KD_R3_PlusDox

value: 1 ug/ml doxycylcine


title: Quercetin sample tested at 4.14 uM (Replicate: 2, Control Batch Id: 1).

value: Quercetin

value: DMSO


title: HeLa, GammaRay, Rep3, IP, MeRIP-seq


title: 6467_C, snRNA+snATAC

description: Library name: 6467_C_multiome

value: GBM patient brain tissue


title: MC_TotalRNA_D2_0h_Buty

description:
I19-1034-01_D5_0H/ FPKM
D1_D2_0h_24h_rpkm.txt


title: HeLa, GammaRay, Rep1, IP, MeRIP-seq


title: Quercetin sample tested at 4.14 uM (Replicate: 1, Control Batch Id: 1).


title: 6467_A, snRNA+snATAC

description: Library name: 6467_A_multiome


title: HeLa, Ctrl, Input, MeRIP-seq

value: Control


title: Input_PRMT1_KD_R2_PlusDox


title: 6467_D, snRNA+snATAC

description: Library name: 6467_D_multiome


title: HeLa, Ctrl, Rep3, IP, MeRIP-seq


title: 6434_A, snRNA+snATAC

description: Library name: 6434_A_multiome


title: Input_PRMT1_KD_R2_MinusDox


title: 6425_G, snRNA+snATAC

description: Library name: 6425_G_multiome


title: Paraquat sample tested at 1500 uM (Replicate: 1, Control Batch Id: 8).

value: Water


title: 6467_B, snRNA+snATAC

description: Library name: 6467_B_multiome


title: Paraquat sample tested at 1250 uM (Replicate: 3, Control Batch Id: 8).


title: Paraquat sample tested at 1250 uM (Replicate: 2, Control Batch Id: 8).


title: Paraquat sample tested at 1250 uM (Replicate: 1, Control Batch Id: 8).


title: Paraquat sample tested at 1500 uM (Replicate: 3, Control Batch Id: 8).


title: Input_PRMT1_KD_R1_PlusDox


title: Quercetin sample tested at 4.14 uM (Replicate: 3, Control Batch Id: 1).


title: Quercetin sample tested at 8.27 uM (Replicate: 2, Control Batch Id: 1).


title: HeLa, Ctrl, Rep1, IP, MeRIP-seq


title: Y18: siRAPTOR_replicate #3

city: Houston

first: Tu N

last: Tran

state: Texas

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

data_processing:
We used tophat for obtaining the bw tracks.
Assembly: hg38
Supplementary files format and content: bigwig file

source_name: Skin

extract_protocol:
RNA of human dermal endothelial cells treated with control or RAPTOR siRNA was extracted using an RNeasy Mini Kit (Qiagen) per manufacturer’s instruction.
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and RNA integrity was measured using the RNA Screen Tape on Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA).
The sequencing libraries were multiplexed and clustered on 1 lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions.

value: Skin

value: Primary human dermal lymphatic endothelial cells

value: RAPTOR siRNA

value: RAPTOR siRNA treatment


title: Control_Total_RNA

value: 29-13-derived PF

value: procyclic form


title: Y17: siRAPTOR_replicate #2


title: Input_PRMT1_KD_R1_MinusDox


title: 6425_D, snRNA+snATAC

description: Library name: 6425_D_multiome


title: Paraquat sample tested at 1041.67 uM (Replicate: 1, Control Batch Id: 8).


title: si-TCF7,replicate1,scRNAseq

city: Shanghai

first: Yuan

last: Min

address: 1239 Siping Road

institute: Tongji university

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed using Cell Ranger v.3.1.0 from 10X Genomics. The cellranger count function was used to generate single cell feature counts for a single library. FASTQ files were mapped separately to the GRC38 human reference genome using STAR as part of the cellranger pipeline. Cell barcodes and Unique Molecular Identifiers (UMI) for each sample were filtered and corrected using the default setting.
Further filtering and clustering analysis of these cells was performed using the Seurat v.3.1.0 R package (http://satijalab.org/seurat/).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Endodermal cells differentiated from hiPSCs were digested with TrypLE.
The cell suspension was loaded onto Chromium microfluidic chips with Gel Bead-In-EMulsions (GEMs) using a 10X Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’v3 (version 3.0) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed on Illumina (HiSeq 2000) according to the manufacturer’s instructions (Illumina).

value: stem cell


title: Paraquat sample tested at 1041.67 uM (Replicate: 2, Control Batch Id: 8).

value: Paraquat


title: HeLa, Ctrl, Rep2, IP, MeRIP-seq

value: HeLa

value: N6-methyladenosine (Abcam, ab151230)


title: Y16: siRAPTOR_replicate #1


title: 6425_C, snRNA+snATAC

description: Library name: 6425_C_multiome


title: si-TBXT,replicate1,scRNAseq

description: 10X Genomics


title: 6425_F, snRNA+snATAC

description: Library name: 6425_F_multiome


title: Y15: siCtrl_replicate #3

value: Control siRNA

value: Control siRNA treatment


title: 6425_E, snRNA+snATAC

description: Library name: 6425_E_multiome


title: si-NC,replicate1,scRNAseq

description: 10X Genomics


title: Paraquat sample tested at 868.06 uM (Replicate: 1, Control Batch Id: 8).

value: sample


title: Paraquat sample tested at 868.06 uM (Replicate: 3, Control Batch Id: 8).


title: 6419_D, snRNA+snATAC

description: Library name: 6419_D_multiome


title: Paraquat sample tested at 868.06 uM (Replicate: 2, Control Batch Id: 8).


title: KBM7 Dam&ChIC Dam/H3K9me3 (KIN8791_kbm7.index46)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
sc_damchic_human_binsize_100000.h5ad.gz
input_human_binsize_100000.h5ad.gz

data_processing:
Dam&ChIC data processing is largely based on the workflow and scripts described in Rooijers et al., 2019 and Markodimitraki et al., 2020 (available at: https://github.com/KindLab/scDamAndTools), but adapted to allow for computational separation of scDamID and sortChIC derived reads and further processing of sortChIC reads.
All reads are demultiplexed by comparing their sample barcode (e.g. single-cell barcode) located at the start of each read (R1 in case of paired-end sequenced libraries) conform to the read layout of 5′-[3 nt UMI][8 nt barcode]TC[gDNA]-3′ for scDamID and 5′-[3 nt UMI][8 nt barcode]WN[gDNA]-3′ for sortChIC reads, to a reference list of barcodes and zero mismatches between the observed barcode and reference are allowed. Sample barcodes and UMIs are trimmed off the reads to only retain gDNA sequences. The UMI sequences were appended to the read name for downstream processing. Per sample barcode, scDamID and sortChIC reads remain mixed at this point.
After preprocessing, the reads were aligned to a reference genome using bowtie2 (v. 2.4.1) with parameters: ‘‘--seed 42 --very-sensitive -N 1’’. Before alignment a ‘GA’ dinucleotide was prepended to the reads that has effectively been digested off scDamID fragments during DpnI gDNA digestion. For human samples, reads were aligned to reference genome hg19 (GRCh37) and mouse samples to mm10 (GRCm38). For allele-specific processing for X-chromosome inactivation experiments, data were aligned to reference genomes generated by imputing 129S1/SvImJ and CAST/EiJ single nucleotide polymorphisms obtained from the Sanger Mouse Genomes project (Keane et al., 2011) onto the mm10 reference genome. The reads were assigned to either genotype by aligning reads to both references. Reads that aligned with lower edit distance (SAM tag ‘NM’) or higher alignment score (SAM tag ‘AS’) in case of equal edit distance to one of the genotypes were assigned to that genotype. Reads aligning with equal edit distance and alignment score to both genotypes were considered of ‘ambiguous’ genotype. Reads that yielded an alignment with mapping quality (BAM field ‘MAPQ’) lower than 10 were discarded.
Following read alignment with ‘GA’ prepended dinucleotide, reads were considered scDamID in case of perfect alignment on genomic GATC motifs. Residual reads were considered sortChIC and their original sequences (i.e., without prepended GA dinucleotide) were realigned using hisat2 (v. 2.1.0) with parameters: ‘‘--seed 42 --no-spliced-alignment --mp '2,0' --sp '4,0'”. These sortChIC-considered reads were further pruned given MNase’s strong adenine or thymidine-nucleotide cut preference; only sortChIC reads were kept that lead with an ‘A’ or ‘T’ base. In addition, we observed that a larger fraction of sortChIC reads (i.e., that do not map on a genomic GATC motif) are ‘TC’-dinucleotide leading in Dam&ChIC libraries than in sortChIC libraries and hence decided to exclude TC-leading reads from Dam&ChIC-derived sortChIC libraries.
Library strategy: Dam&ChIC

source_name: Blood

growth_protocol: Human haploid KBM7 cells were cultured in suspension in IMDM medium (10% FBS and 1% Pen/Strep). Human HT-1080 cells were cultured in DMEM medium (10% FBS and 1% Pen/Strep). Mouse F1 hybrid Cast/EiJ x 129SvJ embryonic stem cells (mESCs; a kind gift from the Joost Gribnau laboratory) were cultured on a monolayer of irradiated feeders (MEFs) in CM+/+ (G-MEM + 10% FBS, 1% Pen/Strep, 1× GlutaMAX (Gibco), 1× NEVitaminC, 1× sodium pyruvate, 0.1 mM 2-ME and 1000 U/ml ESGROmLIF (EMD Millipore, ESG1107))

extract_protocol:
For Kbm7 cells nuclei were isolated using 0.05% Saponin. MESCs were fixed at -20C using 70% Ethanol and permeablised using 0.05% Tween. ProteinA-MN was targeted using antibodies against IgG, Lamin B1, H3, H3K4me1, H3K4me3, H3K9me3, H3K27me3 or H3K36me3 and cells were FACS sorted into 384 well plates.
MN was activated thorugh 2mM CaCl2 for 30min at 4C at inactivated by EGTA addition. Cells were lysed (protK + NP40), fragments end-repaired (Klenow) and adenine methylated sites were cut (DpnI). Dam and ChIC fragemnts are ligated to blunt end adaptors containing a cell barcode and unique molecular identifier and a T7 promoter. After pooling DNA is amplified by in vitro transcription, before rundom hexamer based reverse transcription and final indexing PCR for sequencing.

treatment_protocol:
Dam-POI induction: For Kbm7 cells 0.5 nM Shield-1 was added to stabilize the protein at the indicated timepoint. For mESCs 1mM IVitaminC was added 24h prior to induction, to ensure protein degradation.
double thymidine block: cells received 2 mM thymidine for 15 hours, followed by 9 hours of release, followed by a second thymidine block for 13 hours.
VitaminC: Cell culture was depleted from MEFs and 24-48 hours later confluent wells were passaged 1:15 in VitaminC differentiation medium (IMDM with 15% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X NEVitaminC, 50 μg/ml VitaminC and 0.1 mM 2ME).

value: Blood

value: chronic myelogenous leukemia


title: Y13: siCtrl_replicate #1


title: Paraquat sample tested at 1041.67 uM (Replicate: 3, Control Batch Id: 8).


title: 6425_A, snRNA+snATAC

description: Library name: 6425_A_multiome

value: GBM patient brain tissue


title: 6419_B, snRNA+snATAC

description: Library name: 6419_B_multiome


title: C296 CART19 + 10 uM Vecabrutinib

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

data_processing:
Binary base call data converted to fastq using Illumina bcl2fastq software
Check quality with FastQC, trim adapters with trimmomatic, and re-check quality with FastQC
Latest human reference genome GRCh38 was downloaded from NCBI and indexed using STAR
Paired end reads were mapped to the genome, and HTSeq was used to generate expression counts for each gene
DeSeq2 was used to calculate differential expression
Assembly: CRCh38
Supplementary files format and content: tab-delimited text files contain the gene expression counts for each sample or DeSeq2 dataset

source_name: T cell

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
TruSeq RNA Library Prep Kit v2
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untransduced, CART19 TNFR2_WT, and CART19 TNFR2_KO were produced on 3 biological replicates of normal donor T cells and total RNA was isolated.

value: T cell


title: KBM7 Dam&ChIC Dam/H3K4me3 (KIN8791_kbm7.index44)


title: C296 CART19 + 1 uM Vecabrutinib


title: KBM7 Dam&ChIC Dam/H3K4me3 (KIN8791_kbm7.index45)


title: Paraquat sample tested at 750 uM (Replicate: 2, Control Batch Id: 7).

value: Water


title: 6419_A, snRNA+snATAC

description: Library name: 6419_A_multiome


title: C296 CART19 + Vehicle


title: KBM7 Dam&ChIC Dam/H3K27me3 (KIN8791_kbm7.index43)


title: KBM7 Dam&ChIC Dam/H3K27me3 (KIN8791_kbm7.index42)


title: Paraquat sample tested at 750 uM (Replicate: 1, Control Batch Id: 7).


title: Y14: siCtrl_replicate #2

value: Skin

value: Primary human dermal lymphatic endothelial cells


title: Paraquat sample tested at 723.38 uM (Replicate: 2, Control Batch Id: 8).


title: KBM7 mitosis Dam&ChIC Dam-LMNB1/LMNB1 (KIN8433_memo.index06)


title: Paraquat sample tested at 750 uM (Replicate: 3, Control Batch Id: 7).


title: GBM-6431_A.2B05, single cell DNA methylation

description: Library name: GBM-6431_A.2B05

data_processing:
The single-cell DNA methylation sequencing data from Scale Biosciences was processed using the ScaleBio Seq Suite: Methylation Workflow (v1.1.0 pre-release) under default parameters.
Assembly: hg38
Supplementary files format and content: h5 files with matrices of DNA methylation status for each cell
Library strategy: sciMet

extract_protocol:
Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. Nuclei were fixed with 16% formaldehyde followed by nucleosome disruption. After gently mixing nucleosome disruption solution with nuclei suspension, nuclei were centrifuged with pellet resuspended for each biological sample. Nuclei inputs were normalized across samples, and the tagmentation-nuclei mix was prepared for each biological sample based on the number of reactions. Nuclei were distributed across the three 96-well Met Tagment Barcode Plates, using a total of 288 unique barcodes for nuclei tagmentation. Tagmented nuclei were gated for positive DNA staining and sorted for 24 nuclei per well on the sorting plate. Bisulfite Conversion Solution was added to each well to convert unmethylated cytosines to uracil and the post-reaction product was cleaned up through elution.
The sequencing library was prepared by adding amplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.


title: 6419_C, snRNA+snATAC

description: Library name: 6419_C_multiome


title: GBM-6431_A.2B03, single cell DNA methylation

description: Library name: GBM-6431_A.2B03


title: C278 CART19 + 1 uM Vecabrutinib


title: KBM7 mitosis Dam&ChIC Dam-LMNB1/LMNB1 (KIN8433_memo.index05)


title: GBM-6431_A.2B04, single cell DNA methylation

description: Library name: GBM-6431_A.2B04


title: C278 CART19 + Vehicle


title: Paraquat sample tested at 723.38 uM (Replicate: 3, Control Batch Id: 8).


title: KBM7 mitosis Dam&ChIC Dam-LMNB1/LMNB1 (KIN8433_memo.index04)


title: Paraquat sample tested at 468.75 uM (Replicate: 3, Control Batch Id: 7).


title: GBM-6431_A.2B06, single cell DNA methylation

description: Library name: GBM-6431_A.2B06


title: GBM-6431_A.2B02, single cell DNA methylation

description: Library name: GBM-6431_A.2B02


title: C267 CART19 + 10 uM Vecabrutinib


title: Paraquat sample tested at 723.38 uM (Replicate: 1, Control Batch Id: 8).


title: GBM-6431_A.2B01, single cell DNA methylation

description: Library name: GBM-6431_A.2B01


title: KBM7 mitosis Dam&ChIC Dam-LMNB1/LMNB1 (KIN8433_memo.index02)


title: GBM-6431_A.2A12, single cell DNA methylation

description: Library name: GBM-6431_A.2A12


title: C267 CART19 + Vehicle


title: C278 CART19 + 10 uM Vecabrutinib


title: KBM7 Dam&ChIC Dam-LMNB1/H3K9me3 (KIN7781.index46)


title: GBM-6431_A.2A11, single cell DNA methylation

description: Library name: GBM-6431_A.2A11


title: C315_UTD_HTcount


title: Paraquat sample tested at 468.75 uM (Replicate: 2, Control Batch Id: 7).


title: Paraquat sample tested at 468.75 uM (Replicate: 1, Control Batch Id: 7).


title: GBM-6431_A.2A10, single cell DNA methylation

description: Library name: GBM-6431_A.2A10


title: Paraquat sample tested at 292.97 uM (Replicate: 2, Control Batch Id: 7).


title: KBM7 Dam&ChIC Dam-LMNB1/H3K4me3 (KIN6668.index22)


title: Paraquat sample tested at 292.97 uM (Replicate: 1, Control Batch Id: 7).


title: C276_TNFR2_KO_CART19_HTcount


title: C315_CART19_HTcount


title: KBM7 Dam&ChIC Dam-LMNB1/H3K9me3 (KIN6668.index19)


title: KBM7 Dam&ChIC Dam-LMNB1/H3K4me3 (KIN6668.index23)


title: GBM-6431_A.2A08, single cell DNA methylation

description: Library name: GBM-6431_A.2A08


title: GBM-6431_A.2A07, single cell DNA methylation

description: Library name: GBM-6431_A.2A07


title: C320_TNFR2_KO_CART19_HTcount


title: C320_CART19_HTcount


title: KBM7 Dam&ChIC Dam-LMNB1/H3K4me3 (KIN6214.index30)


title: KBM7 Dam&ChIC Dam-LMNB1/H3K9me3 (KIN6214.index34)


title: C267 CART19 + 1 uM Vecabrutinib


title: KBM7 mitosis Dam&ChIC Dam-LMNB1/LMNB1 (KIN8433_memo.index03)


title: KBM7 Dam&ChIC Dam-LMNB1/LMNB1 (KIN6062.index21)


title: GBM-6431_A.2A06, single cell DNA methylation

description: Library name: GBM-6431_A.2A06


title: C320_UTD_HTcount


title: GBM-6431_A.2A09, single cell DNA methylation

description: Library name: GBM-6431_A.2A09


title: C276_CART19_HTcount


title: GBM-6431_A.2A05, single cell DNA methylation

description: Library name: GBM-6431_A.2A05


title: Paraquat sample tested at 183.11 uM (Replicate: 1, Control Batch Id: 7).


title: Paraquat sample tested at 183.11 uM (Replicate: 3, Control Batch Id: 7).


title: Paraquat sample tested at 183.11 uM (Replicate: 2, Control Batch Id: 7).


title: KBM7 Dam&ChIC Dam-LMNB1/LMNB1 (KIN6062.index20)


title: Paraquat sample tested at 292.97 uM (Replicate: 3, Control Batch Id: 7).


title: Paraquat sample tested at 114.44 uM (Replicate: 1, Control Batch Id: 7).


title: C315_TNFR2_KO_CART19_HTcount


title: Paraquat sample tested at 114.44 uM (Replicate: 2, Control Batch Id: 7).


title: C276_UTD_HTcount


title: KBM7 Dam&ChIC Dam-LMNB1/LMNB1 (KIN6062.index19)


title: Paraquat sample tested at 114.44 uM (Replicate: 3, Control Batch Id: 7).


title: KBM7 scDamID Dam-LMNB1 (KIN6062.index13)


title: GBM-6431_A.2A02, single cell DNA methylation

description: Library name: GBM-6431_A.2A02


title: ID11.MX5.T24.C_0700761991

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

description:
Peripheral blood
700761991

data_processing:
Encoding Sanger/Illumina 1.9 software used for basecalling.
Quality trimming is performed to remove adapter sequences and polyA tails.  Then trimmed reads were aligned to human genome GRCh38/hg38 (Genome Reference Consortium Human Build 38), INSDC Assembly GCA_000001405.28, Dec 2013) using STAR 2.6.1d and featureCounts v2.0.0 was used to generate the raw counts
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMCs

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)

value: PBMCs

tag: time


title: ID11.MX5.T24.B_0700761981

description:
Peripheral blood
700761981


title: KBM7 sortChIC LMNB1 (KIN6062.index11)


title: GBM-6431_A.2A01, single cell DNA methylation

description: Library name: GBM-6431_A.2A01


title: ID11.MX5.T24.A_0700761971

description:
Peripheral blood
700761971


title: Ochratoxin A sample tested at 22.22 uM (Replicate: 3, Control Batch Id: 8).

value: Ochratoxin A

value: DMSO


title: GBM-6431_A.1H12, single cell DNA methylation

description: Library name: GBM-6431_A.1H12


title: GBM-6431_A.2A04, single cell DNA methylation

description: Library name: GBM-6431_A.2A04


title: Ochratoxin A sample tested at 22.22 uM (Replicate: 2, Control Batch Id: 8).


title: KBM7 Dam&ChIC Dam-LMNB1/H3K27me3 (KIN5917.index43)


title: Ochratoxin A sample tested at 22.22 uM (Replicate: 1, Control Batch Id: 8).


title: KBM7 Dam&ChIC Dam-LMNB1/LMNB1 (KIN6062.index10)


title: ID9.MX3.T24.C_0700761931

description:
Peripheral blood
700761931


title: Ochratoxin A sample tested at 14.81 uM (Replicate: 2, Control Batch Id: 8).


title: Ochratoxin A sample tested at 14.81 uM (Replicate: 3, Control Batch Id: 8).


title: GBM-6431_A.2A03, single cell DNA methylation

description: Library name: GBM-6431_A.2A03


title: GBM-6431_A.1H11, single cell DNA methylation

description: Library name: GBM-6431_A.1H11


title: Ochratoxin A sample tested at 9.88 uM (Replicate: 3, Control Batch Id: 8).


title: KBM7 Dam&ChIC Dam/H3K9me3 (HMF1477.index14)


title: GBM-6431_A.1H09, single cell DNA methylation

description: Library name: GBM-6431_A.1H09


title: KBM7 Dam&ChIC Dam-LMNB1/H3K9me3 (HMF1477.index12)


title: ID7.MX1.T24.C_0700761871

description:
Peripheral blood
700761871


title: ID9.MX3.T24.A_0700761911

description:
Peripheral blood
700761911


title: Ochratoxin A sample tested at 14.81 uM (Replicate: 1, Control Batch Id: 8).


title: ID9.MX3.T24.B_0700761921

description:
Peripheral blood
700761921


title: HGF repl3

city: Kyoto

first: Takeya

last: Otsuki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University.

data_processing:
Obtained reads were mapped to the human GRCh38 genome analyzed by STAR (version 2.7.3a). Annotated reads were counted using RSEM (version 1.3.1).
Expression of transcripts sharing each gene was quantified as transcripts per million (TPM). The differential expression analysis was performed by R package glmmSeq from CRAN (https://cran.r-project.org/) to fit a negative binomial mixed effects model. In the model, the biological batch effect was adjusted as a random effect, while the HGF effect was recognized as a fixed effect.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM (FPKM) values for each sample.

source_name: 201B7 iPSCs

extract_protocol:
total RNAs were extracted using the RNeasy Mini Kit (Qiagen)
Double-stranded cDNA libraries (RNA-seq libraries) were prepared using SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Clontech) and MGIEasy_Universal Library_Conversion Kit (App A) (MGI) according to the manufacturer’s instructions.

value: 201B7 iPSCs

value: hiPSC-NPCs

value: conditioned medium from HGF-NPCs


title: GBM-6431_A.1H08, single cell DNA methylation

description: Library name: GBM-6431_A.1H08


title: Ochratoxin A sample tested at 9.88 uM (Replicate: 1, Control Batch Id: 8).


title: Ochratoxin A sample tested at 9.88 uM (Replicate: 2, Control Batch Id: 8).


title: KBM7 Dam&ChIC Dam-LMNB1/H3K27me3 (KIN5917.index31)


title: ID7.MX1.T24.B_0700761861

description:
Peripheral blood
700761861


title: HGF repl2


title: GBM-6431_A.1H07, single cell DNA methylation

description: Library name: GBM-6431_A.1H07


title: GBM-6431_A.1H06, single cell DNA methylation

description: Library name: GBM-6431_A.1H06


title: GBM-6431_A.1H10, single cell DNA methylation

description: Library name: GBM-6431_A.1H10


title: ID6.ConA.T24.C_0700761841

description:
Peripheral blood
700761841

value: ConA


title: GBM-6431_A.1H05, single cell DNA methylation

description: Library name: GBM-6431_A.1H05


title: ID7.MX1.T24.A_0700761851

description:
Peripheral blood
700761851


title: Control repl3

value: conditioned medium from hiPSC-NPCs


title: GBM-6431_A.1H04, single cell DNA methylation

description: Library name: GBM-6431_A.1H04


title: Ochratoxin A sample tested at 6.58 uM (Replicate: 2, Control Batch Id: 8).


title: Control repl2


title: Ochratoxin A sample tested at 6.58 uM (Replicate: 3, Control Batch Id: 8).


title: ID6.ConA.T24.B_0700761831

description:
Peripheral blood
700761831


title: Ochratoxin A sample tested at 6.58 uM (Replicate: 1, Control Batch Id: 8).


title: ID6.ConA.T24.A_0700761821

description:
Peripheral blood
700761821


title: Control repl1


title: N-ethyl-N-nitrosourea sample tested at 3416 uM (Replicate: 3, Control Batch Id: 2).

value: N-ethyl-N-nitrosourea


title: GBM-6431_A.1H03, single cell DNA methylation

description: Library name: GBM-6431_A.1H03


title: HGF+anti-HGF rep1

description:
HGF.expression_S.220525.H.2
gene_RSEM_count.txt
gene_RSEM_FPKM.txt
gene-HGF.control_HGF.expression_DESeq2.txt

data_processing:
Obtained reads were mapped to the human GRCh38 genome analyzed by STAR (version 2.7.3a). Annotated reads were counted using RSEM (version 1.3.1).
FPKM values were calculated from mapped reads by normalizing to total counts. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM (FPKM) values for each sample.

value: conditioned medium from HGF-NPCs with anti-HGF


title: ID5.LPS.T24.C_0700761811

description:
Peripheral blood
700761811

value: LPS


title: GBM-6431_A.1H02, single cell DNA methylation

description: Library name: GBM-6431_A.1H02


title: HGF repl1


title: GBM-6431_A.1H01, single cell DNA methylation

description: Library name: GBM-6431_A.1H01


title: ID5.LPS.T24.B_0700761801

description:
Peripheral blood
700761801


title: N-ethyl-N-nitrosourea sample tested at 3416 uM (Replicate: 2, Control Batch Id: 2).

value: sample


title: Control rep1

description:
Control_S.220525.C.1
gene_RSEM_count.txt
gene_RSEM_FPKM.txt
gene-Control_HGF.control_DESeq2.txt


title: ID4.CTRL.T24.C_0700761781

description:
Peripheral blood
700761781

value: CTRL


title: GBM-6431_A.1G12, single cell DNA methylation

description: Library name: GBM-6431_A.1G12

value: GBM patient brain tissue


title: ID5.LPS.T24.A_0700761791

description:
Peripheral blood
700761791


title: GBM-6431_A.1G11, single cell DNA methylation

description: Library name: GBM-6431_A.1G11


title: CD34+ shLPIN1#3C

city: Kiel

first: Karin

last: Huber

state: Schleswig-Holstein

address: Arnold-Heller-Straße 3

department: Medical Clinic II

country: Germany

institute: UKSH Kiel

data_processing:
RNA-seq data in fastq format were aligned using STAR v.2.5.2b to GRCh38 assembly from GENCODE release v24 and raw read abundances were estimated internally in STAR using the algorithm of HT-Seq.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts per gene for each Sample.

source_name: human CD34+ umbilical cord blood cells

growth_protocol: OCI-AML3 were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37 °C. CD34+ HSPCs isolated from 8 umbilical cord blood units were thaw in a 37 °C warm waterbath and prestimulated for 48 hours in IMDM supplemented with 20% BIT (bovine serum albumin, insulin, transferrin), 100 ng/mL SCF, 100 ng/mL FLT3L, 50 ng/mL TPO, 10-4 M β-mercaptoethanol  and 50 µg/mL Gentamicin. UM171 was added freshly to the media at a final concentration of 35nM. Cells were incubated in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA samples were extracted using the Qiagen Rneasy mini kit per manufacturer instructions
Libraries were prepared from total RNA using the TruSeq Stranded Total RNA Library Prep Kit per manufacturer instructions
Standard RNA-seq,  single end

treatment_protocol: Prior to lentiviral transduction with shRNA, OCI-AML were prestimulated with 5 µg/ml polybrene and CD34+ HSPCs with 10 µg/ml protamine sulfate, respectively. After 48 hours RNA was extracted.

value: CD34+ umbilical cord blood cells

tag: biological replicate

tag: technical replicate


title: GBM-6431_A.1G10, single cell DNA methylation

description: Library name: GBM-6431_A.1G10


title: ID4.CTRL.T24.B_0700761771

description:
Peripheral blood
700761771


title: CD34+ shLPIN1#3B


title: ID4.CTRL.T24.A_0700761761

description:
Peripheral blood
700761761


title: GBM-6431_A.1G09, single cell DNA methylation

description: Library name: GBM-6431_A.1G09


title: CD34+ shLPIN1#3A


title: CD34+ shLPIN1#1C


title: GBM-6431_A.1G08, single cell DNA methylation

description: Library name: GBM-6431_A.1G08


title: N-ethyl-N-nitrosourea sample tested at 1366 uM (Replicate: 2, Control Batch Id: 2).


title: N-ethyl-N-nitrosourea sample tested at 1366 uM (Replicate: 1, Control Batch Id: 2).


title: GBM-6431_A.1G07, single cell DNA methylation

description: Library name: GBM-6431_A.1G07


title: ZS3-046 treatment replicate 2

city: Tampa

first: Jiandong

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Molecular Oncology Department

institute: Moffitt Cancer Center

description: Library name: Sample 5

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Assembly: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Supplementary files format and content: unique hit counts for each sample: sample.counts.txt

growth_protocol: Molm13 cells were maintained in RPMI medium containing 10% FBS in 5% CO2 at 37˚C.

extract_protocol:
Total RNA samples were prepared using RNeasy min kit (Qiagen).
rRNA depletion, library preparation, multiplexing and cluster generation, sequencing on Illumina HiSeq2500, and differential gene expression initial analysis, were performed by Azenta Life Sciences.

treatment_protocol: Cells were treated with 100 nM compound for 8 hrs.

value: Acute myloid leukemia

value: TAF1 PROTAC (ZS3-046)


title: ZS3-046 treatment replicate 3

description: Library name: Sample 6


title: N-ethyl-N-nitrosourea sample tested at 1366 uM (Replicate: 3, Control Batch Id: 2).


title: CD34+ shLPIN1#1B


title: N-ethyl-N-nitrosourea sample tested at 546.5 uM (Replicate: 3, Control Batch Id: 2).


title: N-ethyl-N-nitrosourea sample tested at 546.5 uM (Replicate: 2, Control Batch Id: 2).


title: ZS3-046 treatment replicate 1

description: Library name: Sample 4


title: N-ethyl-N-nitrosourea sample tested at 546.5 uM (Replicate: 1, Control Batch Id: 2).


title: DMSO control replicate 3

description: Library name: Sample 3

value: DMSO control


title: CD34+ shLPIN1#1A


title: GBM-6431_A.1G05, single cell DNA methylation

description: Library name: GBM-6431_A.1G05


title: CD34+ shluciferaseC

value: shluciferase


title: CD34+ shluciferaseB


title: GBM-6431_A.1G04, single cell DNA methylation

description: Library name: GBM-6431_A.1G04


title: DMSO control replicate 1

description: Library name: Sample 1


title: GBM-6431_A.1G03, single cell DNA methylation

description: Library name: GBM-6431_A.1G03


title: GBM-6431_A.1G06, single cell DNA methylation

description: Library name: GBM-6431_A.1G06


title: CD34+ shluciferaseA


title: GBM-6431_A.1G02, single cell DNA methylation

description: Library name: GBM-6431_A.1G02


title: OCI-AML3 shLPIN1#3C

source_name: human acute myeloid leukemia cell line OCI-AML3

value: acute myeloid leukemia cells


title: MC_H3K4Me2_D2_24h_Buty

value: human peripheral blood mononuclear cell-derived mast cells

value: 24h butyrate


title: N-ethyl-N-nitrosourea sample tested at 218.6 uM (Replicate: 2, Control Batch Id: 2).

value: DMSO


title: HGF rep1

description:
HGF.control_S.220525.HC.3
gene_RSEM_count.txt
gene_RSEM_FPKM.txt
gene-Control_HGF.control_DESeq2.txt
gene-HGF.control_HGF.expression_DESeq2.txt

value: 201B7 iPSCs

value: hiPSC-NPCs

value: conditioned medium from HGF-NPCs


title: N-ethyl-N-nitrosourea sample tested at 3416 uM (Replicate: 1, Control Batch Id: 2).

value: N-ethyl-N-nitrosourea


title: N-ethyl-N-nitrosourea sample tested at 87.44 uM (Replicate: 3, Control Batch Id: 2).


title: N-ethyl-N-nitrosourea sample tested at 87.44 uM (Replicate: 1, Control Batch Id: 2).


title: N-ethyl-N-nitrosourea sample tested at 218.6 uM (Replicate: 1, Control Batch Id: 2).


title: N-ethyl-N-nitrosourea sample tested at 87.44 uM (Replicate: 2, Control Batch Id: 2).


title: N-ethyl-N-nitrosourea sample tested at 218.6 uM (Replicate: 3, Control Batch Id: 2).


title: MC_H3K4Me2_D2_3h_Buty

value: 3h butyrate


title: OCI-AML3 shLPIN1#3B


title: OCI-AML3 shLPIN1#3A


title: GBM-6431_A.1F11, single cell DNA methylation

description: Library name: GBM-6431_A.1F11


title: OCI-AML3 shLPIN1#2C


title: Methyl Methanesulfonate sample tested at 68.1 uM (Replicate: 2, Control Batch Id: 1).

value: Methyl Methanesulfonate

value: sample

value: Water


title: GBM-6431_A.1F10, single cell DNA methylation

description: Library name: GBM-6431_A.1F10

value: GBM patient brain tissue


title: GBM-6431_A.1G01, single cell DNA methylation

description: Library name: GBM-6431_A.1G01


title: DMSO control replicate 2

description: Library name: Sample 2

value: Acute myloid leukemia


title: MC_H3K4Me2_D2_0h_Buty

value: 0h butyrate


title: MC_H3K4Me2_D2_12h_Buty

value: 12h butyrate


title: GBM-6431_A.1F12, single cell DNA methylation

description: Library name: GBM-6431_A.1F12


title: Methyl Methanesulfonate sample tested at 68.1 uM (Replicate: 3, Control Batch Id: 1).


title: OCI-AML3 shLPIN1#2B


title: GBM-6431_A.1F08, single cell DNA methylation

description: Library name: GBM-6431_A.1F08


title: MC_H3K4Me2_D1_12h_Buty


title: OCI-AML3 shLPIN1#2A


title: Methyl Methanesulfonate sample tested at 68.1 uM (Replicate: 1, Control Batch Id: 1).


title: MC_H3K4Me2_D1_3h_Buty


title: GBM-6431_A.1F09, single cell DNA methylation

description: Library name: GBM-6431_A.1F09


title: Methyl Methanesulfonate sample tested at 34.05 uM (Replicate: 3, Control Batch Id: 1).


title: OCI-AML3 shLPIN1#1C


title: GBM-6431_A.1F07, single cell DNA methylation

description: Library name: GBM-6431_A.1F07


title: OCI-AML3 shLPIN1#1B


title: MC_H3K27Ac_D2_24h_Buty


title: GBM-6431_A.1F06, single cell DNA methylation

description: Library name: GBM-6431_A.1F06


title: MC_H3K4Me2_D1_24h_Buty


title: MC_H3K4Me2_D1_0h_Buty


title: Methyl Methanesulfonate sample tested at 34.05 uM (Replicate: 2, Control Batch Id: 1).


title: Methyl Methanesulfonate sample tested at 34.05 uM (Replicate: 1, Control Batch Id: 1).


title: OCI-AML3 shLPIN1#1A


title: Methyl Methanesulfonate sample tested at 17.025 uM (Replicate: 3, Control Batch Id: 1).


title: GBM-6431_A.1F05, single cell DNA methylation

description: Library name: GBM-6431_A.1F05


title: Methyl Methanesulfonate sample tested at 17.025 uM (Replicate: 2, Control Batch Id: 1).


title: GBM-6431_A.1F04, single cell DNA methylation

description: Library name: GBM-6431_A.1F04


title: MC_H3K27Ac_D2_12h_Buty


title: OCI-AML3 shluciferaseC

value: shluciferase


title: OCI-AML3 shluciferaseB

value: acute myeloid leukemia cells


title: MC_H3K27Ac_D2_0h_Buty

value: human peripheral blood mononuclear cell-derived mast cells


title: Isobutyraldehyde sample tested at 10000 uM (Replicate: 3, Control Batch Id: 7).

value: Isobutyraldehyde


title: GBM-6431_A.1F02, single cell DNA methylation

description: Library name: GBM-6431_A.1F02


title: GBM-6431_A.1F03, single cell DNA methylation

description: Library name: GBM-6431_A.1F03


title: OCI-AML3 shluciferaseA


title: MC_H3K27Ac_D1_12h_Buty


title: Isobutyraldehyde sample tested at 10000 uM (Replicate: 2, Control Batch Id: 7).


title: Isobutyraldehyde sample tested at 10000 uM (Replicate: 1, Control Batch Id: 7).


title: MC_H3K27Ac_D1_3h_Buty


title: GBM-6431_A.1E12, single cell DNA methylation

description: Library name: GBM-6431_A.1E12


title: GBM-6431_A.1E11, single cell DNA methylation

description: Library name: GBM-6431_A.1E11


title: MC_H3K27Ac_D2_3h_Buty


title: Panc-1-Cell

city: Tokushima

first: Toshihito

last: Tanahashi

address: Kuramotocho 3-18-5

institute: Tokushima University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: Excel files include RPM values for each sample.

growth_protocol: To generate cancer-associated adipocytes (CAA), mature adipocytes were indirectly co-cultured with Panc-1 cells using a Transwell culture system.

extract_protocol:
Total RNA was extracted from the purified exosomes using an RNAqueous-Micro Kit (Thermo Fisher Scientific), and the amount and quality of small RNA in the total RNA samples were determined using an Agilent small RNA kit on an Agilent 2100 Bioanalyzer.
Five ng of small RNAs were subjected to library construction using a SMARTer smRNA-Seq Kit for Illumina (Takara Bio), according to the manufacturer’s protocol.

treatment_protocol: Exosomes were isolated from the conditioned medium (CM) via differential centrifugation according to the Minimal Information for Studies of EVs (MISEV) 2018 guidelines proposed by the International Society for EVs (ISEV).

value: cell line

value: Co-clture with adipocyte


title: GBM-6431_A.1E10, single cell DNA methylation

description: Library name: GBM-6431_A.1E10


title: GBM-6431_A.1E09, single cell DNA methylation

description: Library name: GBM-6431_A.1E09


title: GBM-6431_A.1F01, single cell DNA methylation

description: Library name: GBM-6431_A.1F01


title: Panc-1-CM


title: MC_H3K27Ac_D1_24h_Buty

value: 24h butyrate


title: CAA-CM_3

source_name: adipocyte

value: adipocyte

value: WT

value: Co-clture with cell line


title: GBM-6431_A.1E08, single cell DNA methylation

description: Library name: GBM-6431_A.1E08


title: MC_H3K27Ac_D1_0h_Buty


title: Isobutyraldehyde sample tested at 5000 uM (Replicate: 3, Control Batch Id: 7).


title: CAA-CM_2


title: GBM-6431_A.1E06, single cell DNA methylation

description: Library name: GBM-6431_A.1E06


title: Isobutyraldehyde sample tested at 5000 uM (Replicate: 1, Control Batch Id: 7).


title: Gastric_Cancer_rep 50

city: Madurai

first: Jaishree

last: Pandian

state: Tamil Nadu

address: School of Biological Sciences, Madurai Kamaraj University.

department: Unit of Excellence in Cancer Genetics, Department of Genetics, School of Biological Sciences, MKU, Department of Surgery and Surgical Gastroenterology and Histopathology Division, Department of Laboratory Services, MMHRC.

country: India

institute: Madurai Kamaraj University & Meenakshi Mission Hospital & Research Centre, Madurai.

description: Gene expression data of Gastric_Cancer - Replicate 50

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hr at 45°C with GeneChip® Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip® Scanner 3000.

data_processing: Gene level normalized expression signal intensity data of the HTA 2.0 arrays were calculated from CEL files using Gene Level-SST-RMA method which performs GCCN and SST prior to RMA in Affymetrix Expression Console (v1.4.1.46) .

source_name: Gastric tumor tissue

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

extract_protocol: The total RNA was isolated from the tissues using RNeasy mini kit (Qiagen) following manufacturer's standard protocol. All RNA samples had both 18S and 28S bands with RIN (RNA integrity number) value ≥5 and free of DNA and protein contamination.

tag: disease

value: Gastric Cancer

tag: tissues

value: Male


title: Gastric_Cancer_rep 46

description: Gene expression data of Gastric_Cancer - Replicate 46


title: GBM-6431_A.1E05, single cell DNA methylation

description: Library name: GBM-6431_A.1E05


title: A-CM_3


title: Isobutyraldehyde sample tested at 2500 uM (Replicate: 3, Control Batch Id: 7).

value: sample

value: Water


title: Gastric_Cancer_rep 45

description: Gene expression data of Gastric_Cancer - Replicate 45

value: Female


title: Isobutyraldehyde sample tested at 1250 uM (Replicate: 3, Control Batch Id: 7).


title: Gastric_Cancer_rep 47

description: Gene expression data of Gastric_Cancer - Replicate 47


title: Isobutyraldehyde sample tested at 5000 uM (Replicate: 2, Control Batch Id: 7).


title: Methyl Methanesulfonate sample tested at 17.025 uM (Replicate: 1, Control Batch Id: 1).

value: Methyl Methanesulfonate


title: Gastric_Cancer_rep 49

description: Gene expression data of Gastric_Cancer - Replicate 49


title: Isobutyraldehyde sample tested at 2500 uM (Replicate: 1, Control Batch Id: 7).


title: Isobutyraldehyde sample tested at 2500 uM (Replicate: 2, Control Batch Id: 7).


title: CAA-CM_1


title: Isobutyraldehyde sample tested at 1250 uM (Replicate: 2, Control Batch Id: 7).


title: GBM-6431_A.1E07, single cell DNA methylation

description: Library name: GBM-6431_A.1E07

value: GBM patient brain tissue


title: GBM-6431_A.1E04, single cell DNA methylation

description: Library name: GBM-6431_A.1E04


title: A-CM_1


title: Gastric_Cancer_rep 44

description: Gene expression data of Gastric_Cancer - Replicate 44


title: GBM-6431_A.1E03, single cell DNA methylation

description: Library name: GBM-6431_A.1E03


title: GBM-6431_A.1E02, single cell DNA methylation

description: Library name: GBM-6431_A.1E02


title: Brain_patient_81

city: Pessac

first: Andreas

last: Bikfalvi

address: Allée Geoffroy St-Hilaire

country: France

institute: University of Bordeaux

data_processing:
Read alignment software : Salmon / version 0.8.2 / parameters : --threads : "20" --libType : "A"
Assembly: HG38
processed data files format and content: raw and normalized counts

source_name: Brain

extract_protocol:
RNAs were isolated using RNeasy kit (Qiagen, 74134) and DNA was removed using RNase-free DNase (Qiagen, 79254). Overall, 500 ng was used as input material for a Low Input Ribozero treatment using the Epicentre Ribo-Zero Gold Kit–Low Input (HMR). The integ
The depleted RNA was used as input material for the ScriptSeq v2 RNA-Seq Library Preparation protocol. Following 14 cycles of amplification, the libraries were purified using Ampure XP beads. Each library was quantified using Qubit, and the size distribut

value: Brain

tag: patient id

tag: pet

value: pos

tag: age

tag: Sex

value: female

tag: first intervention

tag: histology

value: Astrocytoma

tag: grade

tag: eor

value: Total

tag: recurrence

tag: adjuvant

tag: type of_adjuvant

tag: lost in_follow_up

tag: recurrence free_survival

tag: os

tag: follow up


title: Gastric_Cancer_rep 48

description: Gene expression data of Gastric_Cancer - Replicate 48

tag: disease


title: Isobutyraldehyde sample tested at 625 uM (Replicate: 3, Control Batch Id: 7).

data_processing: The data were analyzed using the rma function in the affy package for R. This function uses RMA for background correction, performs probe specific correction, normalizes using quantile normalization and finally applies a median polish. Package citation: Gautier L, Cope L, Bolstad BM, Irizarry RA (2004). “affy—analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics, 20(3), 307–315. ISSN 1367-4803, doi:10.1093/bioinformatics/btg405.

value: Isobutyraldehyde

tag: solvent


title: Brain_patient_146

tag: tissue

tag: patient id

value: Oligodendroglioma


title: Isobutyraldehyde sample tested at 1250 uM (Replicate: 1, Control Batch Id: 7).


title: Brain_patient_30

tag: pet

tag: age

value: male

value: Subtotal


title: GBM-6431_A.1E01, single cell DNA methylation

description: Library name: GBM-6431_A.1E01


title: GBM-6431_A.1D12, single cell DNA methylation

description: Library name: GBM-6431_A.1D12


title: Gastric_Cancer_rep 43

description: Gene expression data of Gastric_Cancer - Replicate 43

tag: tissues


title: Brain_patient_27

tag: Sex

tag: first intervention

tag: histology


title: Brain_patient_96

tag: grade

tag: eor

tag: recurrence


title: Gastric_Cancer_rep 41

description: Gene expression data of Gastric_Cancer - Replicate 41


title: GBM-6431_A.1D11, single cell DNA methylation

description: Library name: GBM-6431_A.1D11


title: Hydroquinone sample tested at 22.7 uM (Replicate: 2, Control Batch Id: 1).

value: Hydroquinone


title: Hydroquinone sample tested at 22.7 uM (Replicate: 3, Control Batch Id: 1).


title: GBM-6431_A.1D09, single cell DNA methylation

description: Library name: GBM-6431_A.1D09


title: Isobutyraldehyde sample tested at 625 uM (Replicate: 2, Control Batch Id: 7).


title: Gastric_Cancer_rep 39

description: Gene expression data of Gastric_Cancer - Replicate 39

value: Gastric Cancer


title: Gastric_Cancer_rep 42

description: Gene expression data of Gastric_Cancer - Replicate 42


title: Gastric_Cancer_rep 40

description: Gene expression data of Gastric_Cancer - Replicate 40

value: Male


title: Hydroquinone sample tested at 11.35 uM (Replicate: 3, Control Batch Id: 1).

value: sample


title: Isobutyraldehyde sample tested at 625 uM (Replicate: 1, Control Batch Id: 7).

value: Water


title: GBM-6431_A.1D10, single cell DNA methylation

description: Library name: GBM-6431_A.1D10


title: Gastric_Cancer_rep 37

description: Gene expression data of Gastric_Cancer - Replicate 37


title: Gastric_Cancer_rep 38

description: Gene expression data of Gastric_Cancer - Replicate 38

value: Female


title: GBM-6431_A.1D08, single cell DNA methylation

description: Library name: GBM-6431_A.1D08


title: Brain_patient_15

tag: proteomic id

tag: adjuvant

tag: type of_adjuvant

tag: lost in_follow_up


title: Hydroquinone sample tested at 22.7 uM (Replicate: 1, Control Batch Id: 1).


title: Brain_patient_42

value: RT

tag: recurrence free_survival

tag: os

tag: follow up


title: GBM-6431_A.1D07, single cell DNA methylation

description: Library name: GBM-6431_A.1D07

tag: tissue

value: GBM patient brain tissue


title: Gastric_Cancer_rep 36

description: Gene expression data of Gastric_Cancer - Replicate 36

tag: disease


title: Brain_patient_138

value: Brain

tag: patient id

tag: pet

value: neg

tag: age


title: Brain_patient_62

value: pos

tag: Sex

tag: first intervention

value: Partial


title: GBM-6431_A.1D06, single cell DNA methylation

description: Library name: GBM-6431_A.1D06


title: GBM-6431_A.1D05, single cell DNA methylation

description: Library name: GBM-6431_A.1D05


title: Brain_patient_37

value: female

tag: histology

value: Astrocytoma

tag: grade

value: Total


title: Hydroquinone sample tested at 11.35 uM (Replicate: 2, Control Batch Id: 1).

tag: solvent


title: GBM-6431_A.1D04, single cell DNA methylation

description: Library name: GBM-6431_A.1D04


title: Brain_patient_105

tag: proteomic id

value: male

value: Oligodendroglioma

tag: eor

tag: recurrence

value: CT


title: GBM-6431_A.1D03, single cell DNA methylation

description: Library name: GBM-6431_A.1D03


title: GBM-6431_A.1D02, single cell DNA methylation

description: Library name: GBM-6431_A.1D02


title: Gastric_Cancer_rep 32

description: Gene expression data of Gastric_Cancer - Replicate 32

value: Gastric Cancer

tag: tissues


title: Hydroquinone sample tested at 11.35 uM (Replicate: 1, Control Batch Id: 1).

value: Hydroquinone


title: Hydroquinone sample tested at 5.68 uM (Replicate: 2, Control Batch Id: 1).

value: sample


title: GBM-6431_A.1D01, single cell DNA methylation

description: Library name: GBM-6431_A.1D01


title: Hydroquinone sample tested at 5.68 uM (Replicate: 3, Control Batch Id: 1).

value: Water


title: Gastric_Cancer_rep 35

description: Gene expression data of Gastric_Cancer - Replicate 35

value: Female


title: Gastric_Cancer_rep 34

description: Gene expression data of Gastric_Cancer - Replicate 34


title: Brain_patient_35

tag: adjuvant

tag: lost in_follow_up

tag: recurrence free_survival


title: Hydroquinone sample tested at 5.68 uM (Replicate: 1, Control Batch Id: 1).


title: Brain_patient_98

tag: tissue

tag: os

tag: follow up


title: Gastric_Cancer_rep 33

description: Gene expression data of Gastric_Cancer - Replicate 33

tag: disease

value: Male


title: Hydrogen peroxide sample tested at 15 uM (Replicate: 3, Control Batch Id: 2).

value: Hydrogen peroxide


title: Gastric_Cancer_rep 31

description: Gene expression data of Gastric_Cancer - Replicate 31


title: GBM-6431_A.1C11, single cell DNA methylation

description: Library name: GBM-6431_A.1C11

value: GBM patient brain tissue


title: Hydrogen peroxide sample tested at 15 uM (Replicate: 2, Control Batch Id: 2).


title: Brain_patient_111

value: Brain

tag: patient id

tag: pet

value: neg

tag: age

value: Subtotal

tag: type of_adjuvant


title: Brain_patient_71

tag: Sex

tag: first intervention

tag: histology

tag: grade


title: Gastric_Cancer_rep 29

description: Gene expression data of Gastric_Cancer - Replicate 29


title: Hydrogen peroxide sample tested at 15 uM (Replicate: 1, Control Batch Id: 2).

tag: solvent


title: Hydrogen peroxide sample tested at 7.13 uM (Replicate: 3, Control Batch Id: 2).


title: Gastric_Cancer_rep 27

description: Gene expression data of Gastric_Cancer - Replicate 27

tag: tissues


title: Brain_patient_94

tag: proteomic id

tag: eor

tag: recurrence

tag: adjuvant


title: Hydrogen peroxide sample tested at 7.13 uM (Replicate: 2, Control Batch Id: 2).


title: Gastric_Cancer_rep 28

description: Gene expression data of Gastric_Cancer - Replicate 28


title: Gastric_Cancer_rep 25

description: Gene expression data of Gastric_Cancer - Replicate 25


title: GBM-6431_A.1C10, single cell DNA methylation

description: Library name: GBM-6431_A.1C10

tag: tissue


title: Gastric_Cancer_rep 26

description: Gene expression data of Gastric_Cancer - Replicate 26


title: Gastric_Cancer_rep 24

description: Gene expression data of Gastric_Cancer - Replicate 24


title: Brain_patient_56

value: pos

tag: lost in_follow_up

tag: recurrence free_survival

tag: os

tag: follow up


title: GBM-6431_A.1C12, single cell DNA methylation

description: Library name: GBM-6431_A.1C12


title: Brain_patient_158

tag: patient id

tag: pet

tag: age

value: Astrocytoma


title: GBM-6431_A.1C09, single cell DNA methylation

description: Library name: GBM-6431_A.1C09


title: Brain_patient_80

tag: Sex

value: female

tag: first intervention

value: Total

tag: type of_adjuvant


title: GBM-6431_A.1C08, single cell DNA methylation

description: Library name: GBM-6431_A.1C08


title: Gastric_Cancer_rep 23

description: Gene expression data of Gastric_Cancer - Replicate 23

tag: disease


title: GBM-6431_A.1C07, single cell DNA methylation

description: Library name: GBM-6431_A.1C07


title: Brain_patient_82

value: male

tag: histology

value: Oligodendroglioma

tag: grade


title: Brain_patient_79

tag: proteomic id

tag: eor


title: GBM-6431_A.1C06, single cell DNA methylation

description: Library name: GBM-6431_A.1C06


title: GBM-6431_A.1C05, single cell DNA methylation

description: Library name: GBM-6431_A.1C05


title: GBM-6431_A.1C04, single cell DNA methylation

description: Library name: GBM-6431_A.1C04


title: Brain_patient_86

tag: recurrence

tag: adjuvant

value: CT


title: A-CM_2

tag: cell type

value: adipocyte

tag: genotype

value: WT

tag: treatment

value: Co-clture with cell line

tag: time


title: Brain_patient_112

tag: tissue

tag: patient id

tag: lost in_follow_up

tag: recurrence free_survival

tag: os

tag: follow up


title: GBM-6431_A.1C03, single cell DNA methylation

description: Library name: GBM-6431_A.1C03


title: Hydrogen peroxide sample tested at 3.39 uM (Replicate: 2, Control Batch Id: 2).

value: sample

tag: solvent

value: Water


title: Hydrogen peroxide sample tested at 3.39 uM (Replicate: 3, Control Batch Id: 2).

value: Hydrogen peroxide


title: Hydrogen peroxide sample tested at 7.13 uM (Replicate: 1, Control Batch Id: 2).


title: Gastric_Cancer_rep 22

description: Gene expression data of Gastric_Cancer - Replicate 22

tag: disease

value: Gastric Cancer

tag: tissues

value: Male


title: Eugenol sample tested at 300 uM (Replicate: 1, Control Batch Id: 6).

value: Eugenol

value: DMSO


title: Brain_patient_49

value: Brain

tag: proteomic id

tag: pet

value: neg

tag: age

tag: Sex

tag: first intervention

tag: histology

tag: grade

tag: type of_adjuvant


title: Brain_patient_148

tag: tissue

tag: eor

value: Subtotal

tag: recurrence

tag: adjuvant


title: Eugenol sample tested at 300 uM (Replicate: 2, Control Batch Id: 6).


title: GBM-6431_A.1C02, single cell DNA methylation

description: Library name: GBM-6431_A.1C02

value: GBM patient brain tissue


title: Hydrogen peroxide sample tested at 3.39 uM (Replicate: 1, Control Batch Id: 2).


title: Gastric_Cancer_rep 21

description: Gene expression data of Gastric_Cancer - Replicate 21


title: GBM-6431_A.1C01, single cell DNA methylation

description: Library name: GBM-6431_A.1C01


title: Gastric_Cancer_rep 19

description: Gene expression data of Gastric_Cancer - Replicate 19


title: Brain_patient_58

tag: patient id

value: pos

value: female

value: Total

tag: lost in_follow_up

tag: recurrence free_survival

tag: os


title: Gastric_Cancer_rep 17

description: Gene expression data of Gastric_Cancer - Replicate 17

tag: disease

tag: tissues


title: Gastric_Cancer_rep 18

description: Gene expression data of Gastric_Cancer - Replicate 18


title: Eugenol sample tested at 150 uM (Replicate: 1, Control Batch Id: 6).

tag: solvent


title: Brain_patient_134

tag: proteomic id

tag: pet

tag: age

value: Oligodendroglioma

tag: follow up


title: Gastric_Cancer_rep 20

description: Gene expression data of Gastric_Cancer - Replicate 20

value: Female


title: Eugenol sample tested at 150 uM (Replicate: 2, Control Batch Id: 6).


title: Eugenol sample tested at 300 uM (Replicate: 3, Control Batch Id: 6).


title: GBM-6431_A.1B12, single cell DNA methylation

description: Library name: GBM-6431_A.1B12


title: Eugenol sample tested at 75 uM (Replicate: 3, Control Batch Id: 6).


title: Gastric_Cancer_rep 16

description: Gene expression data of Gastric_Cancer - Replicate 16


title: Eugenol sample tested at 75 uM (Replicate: 2, Control Batch Id: 6).


title: Brain_patient_1

tag: Sex

value: male

tag: first intervention

tag: histology

tag: grade


title: Gastric_Cancer_rep 15

description: Gene expression data of Gastric_Cancer - Replicate 15


title: Eugenol sample tested at 150 uM (Replicate: 3, Control Batch Id: 6).

value: sample


title: Brain_patient_16

tag: tissue

tag: eor

tag: recurrence


title: Gastric_Cancer_rep 13

description: Gene expression data of Gastric_Cancer - Replicate 13


title: GBM-6431_A.1B07, single cell DNA methylation

description: Library name: GBM-6431_A.1B07


title: Eugenol sample tested at 75 uM (Replicate: 1, Control Batch Id: 6).


title: GBM-6431_A.1B08, single cell DNA methylation

description: Library name: GBM-6431_A.1B08


title: Brain_patient_25

tag: patient id

tag: adjuvant

tag: lost in_follow_up


title: GBM-6431_A.1B09, single cell DNA methylation

description: Library name: GBM-6431_A.1B09


title: Brain_patient_124

tag: type of_adjuvant

tag: recurrence free_survival

tag: os


title: Brain_patient_95


title: GBM-6431_A.1B06, single cell DNA methylation

description: Library name: GBM-6431_A.1B06


title: Brain_patient_17

tag: proteomic id


title: GBM-6431_A.1B05, single cell DNA methylation

description: Library name: GBM-6431_A.1B05


title: Gastric_Cancer_rep 12

description: Gene expression data of Gastric_Cancer - Replicate 12

tag: disease

tag: tissues


title: GBM-6431_A.1B11, single cell DNA methylation

description: Library name: GBM-6431_A.1B11


title: Brain_patient_44

tag: pet

tag: age

value: Astrocytoma

tag: follow up


title: Eugenol sample tested at 37.5 uM (Replicate: 2, Control Batch Id: 6).

tag: solvent


title: Eugenol sample tested at 18.75 uM (Replicate: 3, Control Batch Id: 6).


title: Eugenol sample tested at 37.5 uM (Replicate: 3, Control Batch Id: 6).


title: Gastric_Cancer_rep 11

description: Gene expression data of Gastric_Cancer - Replicate 11


title: Gastric_Cancer_rep 9

description: Gene expression data of Gastric_Cancer - Replicate 9


title: Eugenol sample tested at 18.75 uM (Replicate: 2, Control Batch Id: 6).


title: GBM-6431_A.1B04, single cell DNA methylation

description: Library name: GBM-6431_A.1B04


title: Brain_patient_59

tag: Sex

tag: first intervention

tag: histology

tag: grade

value: RT


title: Gastric_Cancer_rep 7

description: Gene expression data of Gastric_Cancer - Replicate 7

value: Gastric Cancer


title: Eugenol sample tested at 37.5 uM (Replicate: 1, Control Batch Id: 6).


title: Gastric_Cancer_rep 6

description: Gene expression data of Gastric_Cancer - Replicate 6

value: Male


title: Eugenol sample tested at 18.75 uM (Replicate: 1, Control Batch Id: 6).

value: Eugenol


title: GBM-6431_A.1B10, single cell DNA methylation

description: Library name: GBM-6431_A.1B10

tag: tissue


title: GBM-6431_A.1B03, single cell DNA methylation

description: Library name: GBM-6431_A.1B03


title: Gastric_Cancer_rep 8

description: Gene expression data of Gastric_Cancer - Replicate 8


title: Brain_patient_93

tag: patient id

tag: eor

tag: recurrence

tag: adjuvant


title: GBM-6431_B.2E10, single cell DNA methylation

description: Library name: GBM-6431_B.2E10


title: Brain_patient_152

tag: lost in_follow_up

tag: recurrence free_survival

tag: os


title: Gastric_Cancer_rep 5

description: Gene expression data of Gastric_Cancer - Replicate 5

tag: disease

tag: tissues


title: Brain_patient_104

tag: proteomic id

tag: pet

tag: age

tag: type of_adjuvant


title: Gastric_Cancer_rep 4

description: Gene expression data of Gastric_Cancer - Replicate 4


title: GBM-6431_A.1B02, single cell DNA methylation

description: Library name: GBM-6431_A.1B02


title: Brain_patient_34

tag: Sex

tag: first intervention

tag: follow up


title: Gastric_Cancer_rep 10

description: Gene expression data of Gastric_Cancer - Replicate 10


title: D-Mannitol sample tested at 10000 uM (Replicate: 2, Control Batch Id: 2).

value: D-Mannitol

tag: solvent

value: Water


title: Brain_patient_110

tag: tissue

value: Brain

tag: patient id

value: neg

tag: histology

tag: grade


title: Gastric_Cancer_rep 30

description: Gene expression data of Gastric_Cancer - Replicate 30


title: Gastric_Cancer_rep 2

description: Gene expression data of Gastric_Cancer - Replicate 2


title: D-Mannitol sample tested at 2500 uM (Replicate: 1, Control Batch Id: 2).


title: Cyclohexanone sample tested at 10000 uM (Replicate: 2, Control Batch Id: 2).

value: Cyclohexanone


title: D-Mannitol sample tested at 10000 uM (Replicate: 3, Control Batch Id: 2).


title: GBM-6431_B.2E09, single cell DNA methylation

description: Library name: GBM-6431_B.2E09

value: GBM patient brain tissue


title: Gastric_Cancer_rep 3

description: Gene expression data of Gastric_Cancer - Replicate 3


title: D-Mannitol sample tested at 10000 uM (Replicate: 1, Control Batch Id: 2).


title: D-Mannitol sample tested at 2500 uM (Replicate: 3, Control Batch Id: 2).


title: D-Mannitol sample tested at 2500 uM (Replicate: 2, Control Batch Id: 2).


title: Cyclohexanone sample tested at 10000 uM (Replicate: 1, Control Batch Id: 2).


title: GBM-6431_B.2E08, single cell DNA methylation

description: Library name: GBM-6431_B.2E08


title: Brain_patient_74

tag: eor

tag: recurrence

tag: adjuvant

tag: lost in_follow_up


title: GBM-6431_B.2E07, single cell DNA methylation

description: Library name: GBM-6431_B.2E07


title: GBM-6431_B.2E04, single cell DNA methylation

description: Library name: GBM-6431_B.2E04


title: Cyclohexanone sample tested at 10000 uM (Replicate: 3, Control Batch Id: 2).


title: Brain_patient_130

tag: recurrence free_survival

tag: os


title: Brain_patient_5

tag: proteomic id

tag: pet

value: female


title: Gastric_Cancer_rep 1

description: Gene expression data of Gastric_Cancer - Replicate 1

tag: disease

tag: tissues


title: GBM-6431_B.2E06, single cell DNA methylation

description: Library name: GBM-6431_B.2E06


title: Brain_patient_39

value: pos

tag: age

tag: Sex

tag: first intervention

value: Total


title: Brain_patient_2

tag: tissue

value: Oligodendroglioma

tag: follow up


title: Brain_patient_65

tag: patient id

tag: histology


title: Cyclohexanone sample tested at 2500 uM (Replicate: 1, Control Batch Id: 2).

tag: solvent


title: Gastric_Normal_rep 12

description: Gene expression data of Gastric_Normal - Replicate 12

source_name: Adjacent gastric normal tissue

value: Normal

value: Female


title: Gastric_Normal_rep 9

description: Gene expression data of Gastric_Normal - Replicate 9


title: GBM-6431_B.2E05, single cell DNA methylation

description: Library name: GBM-6431_B.2E05


title: Gastric_Normal_rep 8

description: Gene expression data of Gastric_Normal - Replicate 8


title: Cyclohexanone sample tested at 625 uM (Replicate: 1, Control Batch Id: 2).

value: sample


title: GBM-6431_B.2D11, single cell DNA methylation

description: Library name: GBM-6431_B.2D11


title: Gastric_Cancer_rep 14

description: Gene expression data of Gastric_Cancer - Replicate 14


title: Gastric_Normal_rep 14

description: Gene expression data of Gastric_Normal - Replicate 14


title: GBM-6431_B.2E03, single cell DNA methylation

description: Library name: GBM-6431_B.2E03


title: Gastric_Normal_rep 13

description: Gene expression data of Gastric_Normal - Replicate 13


title: Gastric_Normal_rep 11

description: Gene expression data of Gastric_Normal - Replicate 11


title: Brain_patient_73

value: Astrocytoma

tag: grade

tag: eor

tag: recurrence

tag: type of_adjuvant


title: Gastric_Normal_rep 6

description: Gene expression data of Gastric_Normal - Replicate 6


title: Brain_patient_32

tag: adjuvant

tag: lost in_follow_up

tag: recurrence free_survival

tag: os


title: Cyclohexanone sample tested at 2500 uM (Replicate: 3, Control Batch Id: 2).


title: Gastric_Normal_rep 15

description: Gene expression data of Gastric_Normal - Replicate 15

tag: disease

tag: tissues


title: Brain_patient_19

tag: proteomic id

tag: pet

tag: age

tag: Sex


title: Curcumin sample tested at 16.3 uM (Replicate: 2, Control Batch Id: 1).

value: Curcumin

value: DMSO


title: GBM-6431_B.2E02, single cell DNA methylation

description: Library name: GBM-6431_B.2E02

tag: tissue


title: Gastric_Normal_rep 10

description: Gene expression data of Gastric_Normal - Replicate 10


title: GBM-6431_B.2E01, single cell DNA methylation

description: Library name: GBM-6431_B.2E01


title: Brain_patient_77

tag: patient id

value: male

tag: first intervention

tag: histology

tag: follow up


title: GBM-6431_B.2D12, single cell DNA methylation

description: Library name: GBM-6431_B.2D12


title: Cyclohexanone sample tested at 2500 uM (Replicate: 2, Control Batch Id: 2).

tag: solvent


title: Cyclohexanone sample tested at 625 uM (Replicate: 2, Control Batch Id: 2).


title: Brain_patient_60

tag: grade

tag: eor

tag: recurrence

tag: type of_adjuvant


title: Curcumin sample tested at 8.15 uM (Replicate: 3, Control Batch Id: 1).


title: GBM-6431_B.2D06, single cell DNA methylation

description: Library name: GBM-6431_B.2D06


title: Cyclohexanone sample tested at 625 uM (Replicate: 3, Control Batch Id: 2).


title: Curcumin sample tested at 16.3 uM (Replicate: 3, Control Batch Id: 1).


title: Brain_patient_47

tag: adjuvant

tag: lost in_follow_up

tag: recurrence free_survival

tag: os


title: GBM-6431_B.2D05, single cell DNA methylation

description: Library name: GBM-6431_B.2D05


title: Reh_CTRL_2

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

institute: Vitalité Health Network

data_processing:
Adaptor removal with cutadapt
Mapping with bowtie2
feature quantification with featureCounts v2.0.1
DGE analysis with DESeq2 v1.30.1
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix with fold-change and statistics

source_name: Reh Cells

growth_protocol: The REH (CRL-8286) and Raji (CCL-86) cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). B cell lines were maintained in Roswell Park Memorial Institute (RPMI-1640) medium supplemented with 10% Foetal Bovine Serum and L-glutamine (2 mM). Cell culture media, FBS and L-glutamine were provided from Wisent Bioproducts (Saint-Jean-Baptiste, QC, Canada).

extract_protocol:
Prior to circPax-5 precipitation, 100 uL of streptavidin-conjugated magnetic beads (New England Biolabs) were initially washed twice in co-immunoprecipitation (CoIP) buffer (20 mM Tris-Cl (pH 7,5); 150 mM NaCl; 1 mM EDTA; 0,5 % NP-40; RNAseOUT RNAse inhibitor (50 U/mL, Invitrogen); and Protease Inhibitor Cocktail IIITM (1000X, Sigma-Aldrich)) and incubated in 100 uL of CoIP buffer containing yeast tRNA (1 ug/mL, Sigma-Aldrich) and bovine serum albumin/BSA (1 ug/mL, Sigma-Aldrich) for 2 hours on an orbital shaker at room temperature. Beads were then washed twice with 500 uL of CoIP buffer and mixed with cell lysates/probe mixture. Lysate/probe mixture was prepared using cells (6x107) lysed in 500 uL of CoIP buffer and incubated 2 hours with 400 pmol of biotin-labelled DNA probe on an orbital shaker at room temperature. CircPax-5 precipitations were performed by mixing 500uL of the lysate mixture with the prepared beads on an orbital shaker at room temperature for 1 hour. Precipitation mixtures were then washed twice with 500 uL of CoIP buffer thereafter, magnetic pellets were submitted to RNA extractions using the MirVana total RNA extraction kit (ThermoFisher). RNA quantification and integrity were evaluated (TapeStation, Agilent) and processed for RNA sequencing.
Small RNA library was prepared from 150ng of RNA. For each individual library, RNA was ligated to chemically modified adapters to supress adapter dimer formation. Modified adapters were added to both 3′ and 5′ ends following manufacturer recommended conditions. Adapter ligated RNA was reverse transcribed using Ion Torrent specific primer. cDNA was then amplified using Ion convert barcode primers containing a unique index to allow libraries to be pooled during Ion Torrent sequencing (Life Technologies). Library QC was assayed on Agilent Tape Station using D1000 screen tape. Equally-pooled libraries (7pmol) were clonally amplified onto Ion Sphere™ Particles (ISPs supplied by Ion HiQ OT2 Kit) and sequenced on Ion PI v3 chip on Ion Torrent Proton sequencer.

treatment_protocol: To profile co-interacting microRNAs with circPax-5, we isolated endogenous circPax_2-5 complexes from each cell line (Raji and Reh) using biotin-labelled DNA probes (40nt) targeting the complementary sequence corresponding to the exon junction created by RNA circularization. DNA probes were pre-incubated with cell lysates whereas streptavidin-conjugated magnetic beads were washed and treated with blocking agents (tRNA and BSA) prior to circPax-5 precipitations. Control samples consisted of non-specific probes with scrambled sequences and submitted to the same methodology in parallel. Samples were all submitted in biological triplicates.

tag: condition

value: CONTROL


title: GBM-6431_B.2D10, single cell DNA methylation

description: Library name: GBM-6431_B.2D10


title: GBM-6431_B.2D03, single cell DNA methylation

description: Library name: GBM-6431_B.2D03


title: Brain_patient_107

tag: proteomic id

tag: pet

tag: age

value: CT


title: GBM-6431_B.2D09, single cell DNA methylation

description: Library name: GBM-6431_B.2D09

tag: tissue


title: Curcumin sample tested at 4.08 uM (Replicate: 2, Control Batch Id: 1).

extract_protocol: Total RNA was extracted using Agencourt RNAdvance Tissue XP beads (Beckman Coulter Inc., Danvers, MA) according to the manufacturer's protocol on the cell lysates. RNA integrity was validated using a NanoDrop 8000 Spectrophotometer (Wilmington, DE).


title: Curcumin sample tested at 4.08 uM (Replicate: 3, Control Batch Id: 1).


title: Curcumin sample tested at 16.3 uM (Replicate: 1, Control Batch Id: 1).


title: Curcumin sample tested at 4.08 uM (Replicate: 1, Control Batch Id: 1).


title: Gastric_Normal_rep 3

description: Gene expression data of Gastric_Normal - Replicate 3

tag: disease

tag: tissues


title: Gastric_Normal_rep 4

description: Gene expression data of Gastric_Normal - Replicate 4


title: Curcumin sample tested at 2.04 uM (Replicate: 2, Control Batch Id: 1).


title: GBM-6431_B.2D08, single cell DNA methylation

description: Library name: GBM-6431_B.2D08


title: Reh_PAX5_1


title: Brain_patient_46

value: Brain

tag: patient id

tag: Sex

tag: first intervention

tag: histology

tag: follow up


title: Gastric_Normal_rep 7

description: Gene expression data of Gastric_Normal - Replicate 7

value: Male


title: GBM-6431_B.2C12, single cell DNA methylation

description: Library name: GBM-6431_B.2C12


title: Brain_patient_157

tag: grade

tag: eor

value: Subtotal

tag: recurrence

tag: type of_adjuvant


title: Raji_CTRL_3

source_name: Raji Cells


title: WMH_7

city: Qingdao

first: Xiang

last: Xu

address: 127 Siliunan Road

institute: The Affiliated Qingdao Central Hospital of Qingdao University

data_processing:
the indexed coded samples were clustered on a cBot clustering system using TruSeq PE Cluster Kit V3-CBOT-HS (Illumina).
the libraries were sequenced on an Illumina HiSeq 2500 platform, and 125 bp paired-end reads were obtained
Supplementary files format and content: ab-delimited text files include FPKM values for each Sample …

source_name: plasma exosomes

extract_protocol:
Total RNA was isolated from exosomes using the miRNeasy Serum/Plasma Advanced kit according to the manufacturer’s protocol.A total of 20 ng RNA per sample was used as the input material for RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma exosomes

tag: disease state

value: white matter hyperintensities (WMH)


title: Curcumin sample tested at 8.15 uM (Replicate: 2, Control Batch Id: 1).

first: Bastian

last: Selman

address: 8700 Mason Montgomery Rd

institute: Procter & Gamble

source_name: TK6 Human lymphoblastoid cells

tag: solvent


title: Curcumin sample tested at 8.15 uM (Replicate: 1, Control Batch Id: 1).


title: Reh_CTRL_3

tag: condition


title: Gastric_Normal_rep 5

description: Gene expression data of Gastric_Normal - Replicate 5


title: Gastric_Normal_rep 2

description: Gene expression data of Gastric_Normal - Replicate 2


title: GBM-6431_B.2C10, single cell DNA methylation

first: Federico

last: Gaiti

address: 101 college street

institute: Princess Margaret Cancer Centre

description: Library name: GBM-6431_B.2C10

source_name: GBM patient brain tissue

value: GBM patient brain tissue


title: Raji_CTRL_1


title: Brain_patient_3

tag: proteomic id

tag: pet

value: pos

value: Total

tag: adjuvant

tag: lost in_follow_up

tag: recurrence free_survival

tag: os


title: Cadmium Chloride sample tested at 3.56 uM (Replicate: 3, Control Batch Id: 8).

value: Cadmium Chloride

value: Water


title: WMH_4

tag: tissue


title: GBM-6431_B.2D04, single cell DNA methylation

description: Library name: GBM-6431_B.2D04


title: GBM-6431_B.2C09, single cell DNA methylation

description: Library name: GBM-6431_B.2C09


title: Reh_CTRL_1


title: GBM-6431_B.2D07, single cell DNA methylation

description: Library name: GBM-6431_B.2D07


title: WMH_3


title: Raji_PAX5_2


title: Brain_patient_89

tag: patient id

tag: age

tag: Sex

tag: first intervention

value: Oligodendroglioma


title: Reh_PAX5_3


title: GBM-6431_B.2D02, single cell DNA methylation

description: Library name: GBM-6431_B.2D02


title: GBM-6431_B.2C07, single cell DNA methylation

description: Library name: GBM-6431_B.2C07


title: Reh_PAX5_2


title: Gastric_Normal_rep 1

description: Gene expression data of Gastric_Normal - Replicate 1

tag: disease

value: Normal

tag: tissues

value: Female


title: Brain_patient_57

value: female

tag: histology

value: Astrocytoma

tag: grade

tag: eor

tag: recurrence

tag: follow up


title: Curcumin sample tested at 2.04 uM (Replicate: 3, Control Batch Id: 1).

value: Curcumin

value: sample

tag: solvent

value: DMSO


title: WMH_1

tag: disease state


title: GBM-6431_B.2D01, single cell DNA methylation

description: Library name: GBM-6431_B.2D01


title: Brain_patient_114

value: Brain

tag: proteomic id

tag: pet

tag: adjuvant

tag: lost in_follow_up


title: Cadmium Chloride sample tested at 2.37 uM (Replicate: 3, Control Batch Id: 8).


title: GBM-6431_B.2C05, single cell DNA methylation

description: Library name: GBM-6431_B.2C05

tag: tissue


title: MMP19KO-2

city: Beijing

first: Baihui

last: Ma

address: 167 Beilishi Road

institute: Fuwai Hospital

description: Library name: Sample 6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: aorta tissue

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell type

value: aorta tissue

tag: genotype


title: controls_3

value: plasma exosomes

value: healthy control


title: GBM-6431_B.2C11, single cell DNA methylation

description: Library name: GBM-6431_B.2C11

value: GBM patient brain tissue


title: Raji_CTRL_2

tag: condition

value: CONTROL


title: WMH_5

value: white matter hyperintensities (WMH)


title: WMH_6


title: Curcumin sample tested at 2.04 uM (Replicate: 1, Control Batch Id: 1).

city: Mason


title: Cadmium Chloride sample tested at 3.56 uM (Replicate: 2, Control Batch Id: 8).

value: Cadmium Chloride


title: Cadmium Chloride sample tested at 1.58 uM (Replicate: 3, Control Batch Id: 8).

value: Water


title: Cadmium Chloride sample tested at 1.58 uM (Replicate: 2, Control Batch Id: 8).


title: GBM-6431_B.2C08, single cell DNA methylation

city: Toronto

description: Library name: GBM-6431_B.2C08


title: Wt-4

description: Library name: Sample 4


title: controls_1


title: Raji_PAX5_3


title: GBM-6431_B.2C04, single cell DNA methylation

description: Library name: GBM-6431_B.2C04


title: Cadmium Chloride sample tested at 3.56 uM (Replicate: 1, Control Batch Id: 8).


title: Raji_PAX5_1


title: Wt-2

description: Library name: Sample 2


title: GBM-6431_B.2C06, single cell DNA methylation

description: Library name: GBM-6431_B.2C06


title: MMP19KO-3

description: Library name: Sample 7


title: GBM-6431_B.2C03, single cell DNA methylation

description: Library name: GBM-6431_B.2C03


title: controls_4


title: Cadmium Chloride sample tested at 1.05 uM (Replicate: 3, Control Batch Id: 8).


title: Cadmium Chloride sample tested at 2.37 uM (Replicate: 1, Control Batch Id: 8).


title: Ovariectomized rat treated with DAPM 39

city: Baton Rouge

first: Tammy

middle: R

last: Dugas

state: LA

address: Skip Bertman Drive

department: Comparative Biomedical Sciences

institute: LSU School of Veterinary Medicine

description: miRNA profiling was done in isolated RNA from pulmonary artery using NanoString nCounter Tumor Signaling 360 Panel.

hyb_protocol: An overnight hybridization was performed, followed by a two-step magnetic bead-based purification. The purified target/probes complexes were immobilized on the catridge for data collection in nCounter SPRINT Profiler.

scan_protocol: Digitial images were taken from immobilized target/probes complex and color-coded barcode were counted.

data_processing: Run files in RCC format were analyzed using nSolver software. Raw counts for mRNA were subjected to background substraction, followed by normalization using positive control normalization and CodeSet Content Normalization. Data were analyzed using two-way ANOVA to determine significance between groups and significant interactions between groups.

label: Biotin

source_name: Pulmonary artery

label_protocol: 10 ng of tissue RNA were ligated with unique oligonucleotide tags. Then, tagged miRNA were labeled using oligonucleotide probes with color-coded signal in 5' end and biotin on its 3' end.

extract_protocol: RNA was extracted from pulmonary arteries with a miRNeasy mini kit (Qiagen).

tag: strain

value: Sprague Dawley

tag: Sex

tag: age

value: 11-15 weeks


title: WMH_2


title: GBM-6431_B.2B10, single cell DNA methylation

description: Library name: GBM-6431_B.2B10


title: GBM-6431_B.2B09, single cell DNA methylation

description: Library name: GBM-6431_B.2B09


title: GBM-6431_B.2C02, single cell DNA methylation

description: Library name: GBM-6431_B.2C02


title: Wt-3

description: Library name: Sample 3


title: Ovariectomized rat treated with DAPM 40

value: Female


title: controls_2


title: GBM-6431_B.2B12, single cell DNA methylation

description: Library name: GBM-6431_B.2B12


title: MMP19KO-1

description: Library name: Sample 5


title: GBM-6431_B.2B08, single cell DNA methylation

description: Library name: GBM-6431_B.2B08


title: Wt-1

description: Library name: Sample 1


title: GBM-6431_B.2B11, single cell DNA methylation

description: Library name: GBM-6431_B.2B11


title: Cadmium Chloride sample tested at 2.37 uM (Replicate: 2, Control Batch Id: 8).


title: Azidothymidine sample tested at 3740 uM (Replicate: 3, Control Batch Id: 7).

value: Azidothymidine