title: postPBS_F2_RRBS_oxRRBS

city: Minneapolis

first: Natalia

last: Tretyakova

state: Minnesota

address: 2231 6th St SE Room 2-147

department: Medicinal Chemistry

institute: University of Minnesota

data_processing:
Trimmomatic for adapter and low-quality base removal
HISAT2 for read mapping
Samtools for alignment sorting and filtering
featureCounts for gene expression quantification
edgeR for gene expression analyses
Assembly: mm10
Supplementary files format and content: CSV with Ensembl identifier, base mean expression, log2(fold change), nominal P-value, and FDR value
Supplementary files format and content: Tab-delimited text matrix with raw fragment counts of gene expression
Supplementary files format and content: BED with extra column for methylation fraction

extract_protocol:
Genomic DNA isolated from Type II alveolar epithelial cells of control and treated A/J mice was prepared for RRBS and oxo-RRBS using the Ovation RRBS Methyl-Seq System with TrueMethyl oxBS module (NuGEN, Redwood City, CA) according to the manufacturer’s protocol. Library amplification was optimized as directed using qPCR, and the libraries were amplified accordingly followed by Agencourt bead clean-up.
reduced representation bisulfite sequencing (RRBS) combined with oxidative-RRBS (oxRRBS)
Alveolar type II epithelial cells (Type II pneumocytes) were isolated according to published procedures. Briefly, the lungs were perfused with 10 mL cold phosphate buffered saline (PBS) before enzymatic digestion with 2 mL of dispase infused into the lung, after which they were removed and incubated in an additional 2 mL of dispase for one hour. The lungs were then manually disintegrated and the resulting cell suspension labeled with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32 (Thermo Fisher Scientific). Samples  were pooled to include three sets of lungs per sample for a total of three samples for FACS separation. Type II pneumocytes were isolated by negative selection and thus identified as the unlabeled cell population. Type II pneumocytes were also gated as sideward scatter high (SSChigh) cell population which minimizes contamination with lymphoid cells by selecting cells with a higher granularity. The cells were separated by fluorescence activated cell sorting (FACS)  using a BD FACS Aria II P07800142 (BSL2) (BD Biosciences, San Jose, CA). Following isolation via FACS, Type II pneumocytes were pelleted by centrifugation. The samples were first centrifuged for 12 min at 200 x g and 4°C and the supernatant was removed, except for the bottom 1 mL, which was transferred to a 1.7 mL Eppendorf tube. To this tube, 500 µL of PBS was added, and the tube was centrifuged for 12 min at 200 x g at 4°C. The supernatant was removed while the bottom 100 μL was saved. One mL of PBS was added to the tube, and the sample was centrifuged for 12 min at 800 x g and 4°C. After this final centrifugation, all supernatant is removed, and the cell pellet was used to isolate DNA and RNA using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Hilden Germany) according to the man-ufacturer’s instructions.

value: Lung

tag: gender

value: Alveolar type II epithelial cells

value: 7 weeks intranasal PBS


title: WT 5mo H3K27ac NEUN-

status: Public on Jun 04 2025

type: SRA

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

country: France

institute: CNRS

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Assembly: mm10
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

molecule: genomic DNA

organism: Mus musculus

source_name: ChIPed DNA obtained from FACS sorted NeuN- nulei from brain of mouse hippocampus

extract_protocol: ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: tisuue

value: brain


title: postPBS_F3_RRBS_oxRRBS

country: USA

source_name: Lung

tag: tissue

value: female

tag: cell type

tag: treatment


title: Brescia Ovarian Tumour - 4

city: Oxford

first: Lena

last: Rai

address: Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: R5
counts.R5

library_source: transcriptomic

data_processing:
Raw sequencing data from Brescia ovarian tumour samples was subjected to adapter trimming using Trim Galore v0.6.5, clipping 12bp from the 5' end of reads and discarding reads that were shorter than 60bp.
Transcript expression was quantified in transcripts per million (TPM) using Kallisto v0.46.2 with cDNA annotations from Ensembl release 75.
Transcript-level abundance from Brescia Ovarian Tumour sequences was imported and summarised at the gene level using tximport v1.14.2. Whole transcriptome data from ovarian tumour epithelial cells were aligned to hg19 using STAR and then counted using FeatureCount tool.
Assembly: GRCh37
Supplementary files format and content: TPM_BresciaSamples contains Transcripts Per Million data for all Brescia ovarian tumour samples. FeatureCounts_TumourEpithelialCells.csv contains Feature counts data for all Ovarian Tumour epithelial cells.

molecule: total RNA

organism: Homo sapiens

source_name: Ovarian Tumour

extract_protocol:
RNA from Brescia Ovarian tumour samples was extracted using Trizol reagent (ThermoFisher Scientific, CA, USA) followed by clean-up with RNeasy MinElute Cleanup Kit (Qiagen, CA, USA) according to manufacturer’s instructions. Single cell RNA purification kit (Norgen Biotek Corp., Canada) was used for extracting RNA from ovarian tumour epithelial cells.
Libraries from total RNA samples from Brescia samples were prepared using NEB Next® Ultra RNA Library Prep Kit for Illumina (NEB, UK) using manufacturer’s recommendations. . SMARTer Stranded total RNA-Seq kit v2 Pico input (Takara Bio USA) was used for ovarian tumour epithelial cells according to manufacturer’s protocol.

value: Ovarian Tumour


title: Brescia Ovarian Tumour - 3

description:
Library name: R4
counts.R4


title: Brescia Ovarian Tumour - 2

description:
Library name: R2
counts.R2


title: CBG05471

type: RNA

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street, Room 1350

department: Terrence Donnelly Centre for Cellular and Biomolecular Research

country: Canada

institute: University of Toronto

description:
raw data file:
A58_2.D.txt
channel:
2
RNCMPT00422

hyb_protocol: Hybridizations were carried out for 20 hours at 42°C and washed for 30 seconds in 6 x SSPE, 0.005% sarcosine and 30 seconds in 0.06x SPE in a HS4800 Pro Hybridization Station (Tecan).

scan_protocol: Arrays were scanned on an microarray scanner at 5 micron resolution (Axon Instruments GenePix 4000B). Images were quantified using Imagene 3.0 or 8.0.

data_processing: The experiment was represented with a matrix where rows correspond to probes and columns are the intensities of the Cy5- or Cy3-labeled RNA from the GST-RBP pulldown assay. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

organism: synthetic construct

source_name: Pulldown RNA labeled with Cy5

label_protocol: Manufacturer's recommended protocol (Kreatech).

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purifyied by phenol-chloroform extraction followed by ethanol precipitation.

tag: protocol

value: GST-tagged RNA-binding protein pulldown

tag: rna binding protein


title: SRSF3_Cy3

description:
raw data file:
A57_2.D.txt
channel:
1
RNCMPT00419

source_name: Pulldown RNA labeled with Cy3


title: bladder_cancer_TURBT_84

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

tag: Sex

value: male

tag: age at randomization

tag: clinical stage


title: NEMVEDRAFT_v1g214798

description:
raw data file:
A58_2.D.txt
channel:
1
RNCMPT00421


title: Y57G11C.36

description:
raw data file:
A59_2.D.txt
channel:
1
RNCMPT00423


title: Brescia Ovarian Tumour - 1

description:
Library name: R1
counts.R1


title: R31981_pure-neural-lep

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

description: Library name: R31981

data_processing:
Raw fastq.gz files were submitted to salmon quantification using the quase-mapping mode with --posBias and --seqBias set --libType A.
Salmon transcript quantification files were then collapsed into genes (ncbi ENTREZID and gene symbol) using the ensembl annotation via the tximport R package.
Data was normalized using the DESeq2's default algorithm with the flag --fitType = "local" set. Normalized counts were exported after converting to log2 space.
Assembly: hg38/salmon_partial_sa_index from RefGenie server
Supplementary files format and content: TAB delimited plain text file with normalized log2 expression for all genes and all samples in rows x columns

source_name: Nerve biopsy

extract_protocol:
Nerve biopsies that had been snap-frozen were thawed on wet ice and homogenized using a Polytron Homogenizer PT3100 (Kinematica AG, Switzerland) in the presence of TRIzol Reagent. RNA extraction was performed according to the standard protocol provided by the manufacturer (Ambion, Thermo Fisher Scientific, MA, USA). Residual DNA contamination was removed using the DNA-free kit, following the manufacturer’s instructions (Thermo Fisher Scientific Inc., MA, USA). The integrity of the isolated RNA was evaluated using 1% agarose gel electrophoresis and the TapeStation RNA ScreenTape system (Agilent Technologies, CA, USA).
RNA sequencing libraries were constructed using the NEBNext Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA), with ribosomal RNA depletion via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA, USA).

value: Nerve biopsy


title: postLPS_F3_RRBS_oxRRBS

value: 3 weeks intranasal LPS, followed by 4 weeks intranasal PBS


title: bladder_cancer_TURBT_82


title: bladder_cancer_TURBT_80


title: R31968_pure-neural-lep

description: Library name: R31968


title: bladder_cancer_TURBT_81


title: u2af2b_Cy5

description:
raw data file:
A56_2.D.txt
channel:
2
RNCMPT00418


title: postLPS_F1_RRBS_oxRRBS


title: R31929_vasculitis

description: Library name: R31929


title: 3wPBS_F3_RRBS_oxRRBS

value: 3 weeks intranasal PBS


title: postLPS_F2_RRBS_oxRRBS


title: 3wPBS_F1_RRBS_oxRRBS


title: R31980_vasculitis

description: Library name: R31980


title: R31911_vasculitis

description: Library name: R31911


title: 3wPBS_F2_RRBS_oxRRBS


title: 3wLPS_F3_RRBS_oxRRBS

value: 3 weeks intranasal LPS


title: R31804_vasculitis

description: Library name: R31804


title: Smp_036270

description:
raw data file:
A56_2.D.txt
channel:
1
RNCMPT00417


title: mei2

description:
raw data file:
A54_2.D.txt
channel:
1
RNCMPT00413


title: bladder_cancer_TURBT_77


title: bladder_cancer_TURBT_75


title: bladder_cancer_TURBT_78


title: bladder_cancer_TURBT_79


title: R31801_vasculitis

description: Library name: R31801


title: nrd1

description:
raw data file:
A54_2.D.txt
channel:
2
RNCMPT00414


title: nop12

description:
raw data file:
A53_2.D.txt
channel:
2
RNCMPT00412


title: 3wLPS_F2_RRBS_oxRRBS


title: bladder_cancer_TURBT_76


title: R31771_pure-neural-lep

description: Library name: R31771


title: R31746_pure-neural-lep

description: Library name: R31746


title: R31787_vasculitis

description: Library name: R31787


title: bladder_cancer_TURBT_74


title: PK11774.1

description:
raw data file:
A50_2.D.txt
channel:
1
RNCMPT00403


title: 3wLPS_F1_RRBS_oxRRBS


title: bladder_cancer_TURBT_73


title: R31731_pure-neural-lep

description: Library name: R31731


title: R_700PHE_4

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

institute: INRAE

data_processing:
Genome_build: genome of Populus trichocarpa v4.1
genome mapping and counts of reads by gene locus are done with STAR; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts_noStranded,counts_forwardStrand,counts_reverseStrand

organism: Populus x canadensis

growth_protocol: Media=Soil,80%relative humidity Temperature=22°C during 16h,18°C during 8h Light=200µM photon/m2/s

extract_protocol:
R_700PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 700PHE-abiotic stress-compound addition-phenanthrenequantity 700mg time 4week  phenanthrene concentration in soil in mg/kg soil DW

tag: genotype

value: wild type (hybrid Populus deltoides x nigra)

tag: developmental stage

value: root


title: RBM47

description:
raw data file:
A45_2.D.txt
channel:
2
RNCMPT00394


title: bladder_cancer_TURBT_70


title: Smp_032060

description:
raw data file:
A46_2.D.txt
channel:
2
RNCMPT00396


title: MBNL2

description:
raw data file:
A49_2.D.txt
channel:
1
RNCMPT00401


title: DDB_G0270634

description:
raw data file:
A48_2.D.txt
channel:
1
RNCMPT00399


title: R_700PHE_2

extract_protocol:
R_700PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: R_700PHE_1

extract_protocol:
R_700PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: R_700PHE_3

extract_protocol:
R_700PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_71


title: R31733_pure-neural-lep

description: Library name: R31733


title: R31595_vasculitis

description: Library name: R31595


title: PK14112.1

description:
raw data file:
A44_2.D.txt
channel:
2
RNCMPT00392


title: postPBS_F1_RRBS_oxRRBS


title: R_400PHE_3

extract_protocol:
R_400PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 400PHE-abiotic stress-compound addition-phenanthrenequantity 400mg time 4week  phenanthrene concentration in soil in mg/kg soil DW


title: bladder_cancer_TURBT_69


title: bladder_cancer_TURBT_68


title: R28202_vasculitis

description: Library name: R28202


title: R29490_vasculitis

description: Library name: R29490


title: R_400PHE_2

extract_protocol:
R_400PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: R_400PHE_1

extract_protocol:
R_400PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: scRNA_seq_donor3_V5_TCR

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description: Library name: scRNA_seq_donor3_V5_TCR

library_source: other

data_processing:
The cell ranger pipeline (v.7.1.0) was used to preprocess the 10X sequencing data generated by the sequencer. Illumina files were converted to FASTQ files using the cellranger mkfastq command. Each read from the FASTQ files were then aligned to human reference genome (version: GRCh38-2020-A) using the cellranger count command to generate count matrix. Data was then processed in Seurat (v4.1.3). Data from all three participants were merged into one data set and processed utilizing 10 PCAs for neighbor finding and 10 PCAs for UMAP visualization. mIEL signature was defined based on a subset of genes and score was calculated using UCell (v2.4.0).
Assembly: hg38
Supplementary files format and content: Seurat object (rds)

molecule: other

source_name: breastmilk

extract_protocol:
Human breast milk samples were collected (between 30 to 50 ml) from donors in the morning on the day of experiment and were processed right away to retain high viability of the cells. The expressed milk samples were diluted with a similar volume of PBS before being centrifuged at 400g for 10min at 4C. After centrifugation, the top layer of fat and the supernatant were discarded. Cell pellets were resuspended in 50ml of PBS and underwent centrifugation again at 1350rpm for 5mins at 4C. Next, the cells were stained with human CD3 MicroBeads (Miltenyi Biotec) and enriched for T cells using the LS columns (Miltenyi Biotec). 8,300 – 10,000 cells from the enriched fraction were loaded to a Chromium Single Cell Controller (10X Genomics) to encapsulate cells into droplets. Libraries were prepared using a Chromium Single Cell 5’ Reagent kits following manufacturer’s instructions. Libraries were then sequenced on Illumina NovaSeq 6000 (Illumina).
scRNA-seq

value: breastmilk

tag: time point

value: 3, 10 and 11 months post-partum


title: bladder_cancer_TURBT_67


title: R_200PHE_4

extract_protocol:
R_200PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 200PHE-abiotic stress-compound addition-phenanthrenequantity 200mg time 4week  phenanthrene concentration in soil in mg/kg soil DW


title: PK23842.1

description:
raw data file:
A34_2.D.txt
channel:
2
RNCMPT00372


title: bladder_cancer_TURBT_64


title: scRNA_seq_donor2_V5_TCR

description: Library name: scRNA_seq_donor2_V5_TCR


title: bladder_cancer_TURBT_66


title: bladder_cancer_TURBT_65


title: R31576_pure-neural-lep

description: Library name: R31576


title: scRNA_seq_donor1_V5_TCR

description: Library name: scRNA_seq_donor1_V5_TCR


title: bladder_cancer_TURBT_63


title: PK20300.1

description:
raw data file:
A28_2.D.txt
channel:
2
RNCMPT00360


title: R_200PHE_3

extract_protocol:
R_200PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: PK13173.1

description:
raw data file:
A31_2.D.txt
channel:
2
RNCMPT00366


title: PK15111.1

description:
raw data file:
A32_2.D.txt
channel:
2
RNCMPT00368


title: DDB_G0286331

description:
raw data file:
A23_2.D.txt
channel:
1
RNCMPT00351


title: R_200PHE_1

extract_protocol:
R_200PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: R_200PHE_2

extract_protocol:
R_200PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: scRNA_seq_donor1_V5_GEX

description: Library name: scRNA_seq_donor1_V5_GEX

library_source: transcriptomic single cell


title: R_2000PHE_4

extract_protocol:
R_2000PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 2000PHE-abiotic stress-compound addition-phenanthrenequantity 2000mg time 4week  phenanthrene concentration in soil in mg/kg soil DW


title: PK26404.1

description:
raw data file:
A30_2.D.txt
channel:
2
RNCMPT00364


title: PFI1175c

description:
raw data file:
A38_2.D.txt
channel:
2
RNCMPT00380


title: bladder_cancer_TURBT_60


title: DFD_3

city: Urumchi

first: Chao Bai

middle: Chao

last: Bai

state: Xinjiang

address: 393 Xinyi Road

department: Department of Vascular and Thyroid Surgery

country: China

institute: The First Affiliated Hospital of Xin-	Conflict of Interest Statement:	 jiang Medical University

description: Library name: Sample6

data_processing:
Fragmented RNAs were converted into double-stranded cDNA, followed by end repair, A tailing, and ligation to VAHTS RNA Multiplex Oligos Set 1 for Illumina (N323, Vazyme, China). The ligated products were then amplified, purified, quantified, and stored at -80°C prior to sequencing. The strand marked with dUTP (the 2nd cDNA strand) was not amplified, allowing for strand-specific sequencing.
According to the requirements of various circRNA identification tools, we employed three mapping software for comparison: HISAT2 (Findcirc), STAR (circrna_finder, circexplorer 2), and BWA (CIRI2).
Based on the genome annotation, we first analyzed the splice sites of circRNA. Next, we determined the type and gene of the circRNA. We combined the annotation information from five known circRNA databases: circAltas, circBase, circRNADb, deepbase2, and circpedia2. Finally, we annotated them based on the ID of the candidate circRNA.
For identification of candidate circRNAs, we utilized the R-package FcircSEC (full-length circRNA sequence extraction and classification) to extract circular RNA sequences based on gene annotation and the output of any circRNA prediction tool.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Human foot tissue

extract_protocol:
Each sample underwent treatment with RQ1 DNase (M6101, Promega, USA) to eliminate DNA from total RNAs. Ribosomal RNAs were depleted using the Ribo-off™ rRNA depletion kit (N406, Vazyme, China). VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605, Vazyme, China) was employed for RNA-seq library preparation. Fragmented RNAs were converted into double-stranded cDNA, followed by end repair, A tailing, and ligation to VAHTS RNA Multiplex Oligos Set 1 for Illumina (N323, Vazyme, China). The ligated products were then amplified, purified, quantified, and stored at -80°C prior to sequencing. The strand marked with dUTP (the 2nd cDNA strand) was not amplified, allowing for strand-specific sequencing.
High-throughput sequencing was carried out using the Illumina Novaseq 6000 system with the PE150 model.

value: Human foot tissue

tag: diagnosis

value: diabetic foot ulcer


title: rsp-2

description:
raw data file:
A23_2.D.txt
channel:
2
RNCMPT00352

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purifyied by phenol-chloroform extraction followed by ethanol precipitation.


title: bladder_cancer_TURBT_62

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.


title: SCL30

description:
raw data file:
A39_2.D.txt
channel:
2
RNCMPT00382


title: R_2000PHE_3

extract_protocol:
R_2000PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_58


title: bladder_cancer_TURBT_61


title: bladder_cancer_TURBT_59


title: DFD_2

description: Library name: Sample5


title: scRNA_seq_donor3_V5_GEX

description: Library name: scRNA_seq_donor3_V5_GEX


title: R_2000PHE_2

extract_protocol:
R_2000PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: DFD_1

description: Library name: Sample4


title: R_2000PHE_1

extract_protocol:
R_2000PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: PK23225.1

description:
raw data file:
A33_2.D.txt
channel:
2
RNCMPT00370


title: PK27686.1

description:
raw data file:
A22_2.D.txt
channel:
1
RNCMPT00349


title: NC_3

description: Library name: Sample3

value: healthy


title: scRNA_seq_donor2_V5_GEX

description: Library name: scRNA_seq_donor2_V5_GEX


title: R_1500PHE_4

extract_protocol:
R_1500PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 1500PHE-abiotic stress-compound addition-phenanthrenequantity 1500mg time 4week  phenanthrene concentration in soil in mg/kg soil DW


title: NC_2

description: Library name: Sample2


title: R_1500PHE_3

extract_protocol:
R_1500PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: NC_1

description: Library name: Sample1


title: R_1500PHE_2

extract_protocol:
R_1500PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_55


title: R_1500PHE_1

extract_protocol:
R_1500PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: CM cryopreserved cells

city: Hatfield

first: Floryne

middle: Ottilie

last: Buishand

address: Hawkshead Lane

department: Clinical Science and Service

institute: Royal Veterinary College

description: Library name: CM-cryo

data_processing:
CellRanger (version 7.1.0, 10x Genomics) was used to process raw FASTQ files and to align reads to either the canine CanFam3.1, human GRCh38, murine GRMch38/mm10, or rat mRatBN7.2 genome.
Assembly: CanFam3.1 for canINS-fresh and canINS-cryo, human GRCh38 for CM-fresh and CM-cryo, murine GRMch38/mm10 for MIN6, or rat mRatBN7.2 for INS-1
Supplementary files format and content: Cell Ranger software output files: barcodes.tsv, features.tsv, matrix.mtx

source_name: CM

extract_protocol:
The canine insulinoma cell line canINS was cultured in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 1% penicillin-streptomycin (Invitrogen) and 200 ng/mL growth hormone (GH) (ProSpec). The human insulinoma cell line CM was cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin-streptomycin. The mouse insulinoma cell line MIN6 was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) containing 25 mM glucose, supplemented with 15% FBS, 0.05 mM beta-mercaptoethanol (Life Technologies) and 1% penicillin-streptomycin. The rat insulinoma cell line INS-1 was cultured in RPMI-1640 + Glutamax (Gibco) supplemented with 10% FBS, 1mM sodium pyruvate (Life Tech), 10mM HEPES (Life Tech), and 0.05 mM beta-mercaptoethanol. All cell lines were cultured at 37°C with 5% CO2, and cells were passaged on reaching 70–80% confluence.
Cell cryopreservation
Freezing medium, consisting out of 90% FCS and 10% dimethyl sulfoxide (DMSO) (Sigma-Aldrich) was added to aliquots of 1 x 106 cells/mL of the canINS and CM cell lines and cells were transferred to cryogenic vials. The vials were put into a CoolCell cell freezing vial container (Corning) and stored at -80°C overnight. Vials of the frozen cell lines were then taken out of the CoolCell containers and stored at -80°C for four weeks until use.
Sample preparation
Cryopreserved cells were thawed in a 37 °C water bath, after which they were washed using pre-warmed 1x phosphate-buffered saline (PBS) (Gibco) supplemented with 0.04% bovine serum albumin (BSA) (Sigma-Aldrich). Single cell suspensions of both fresh and cryopreserved cells were created at a concentration of 1 x 106 cells/mL in 1x PBS + 0.04% BSA according to the Cell Preparation for Single Cell Protocols Handbook CG00053 (10x Genomics). Using trypan blue exclusion, all cell suspensions were confirmed to have a viability greater than 90%. Samples were partitioned on a Chromium Controller (10x Genomics) within 30 min of preparation.
Single-cell 3’ gene expression libraries were prepared for each sample using a Chromium NEXT Gem Single Cell 3 v3.1 Kit and dual index library construction kit (10x Genomics) targeting 10,000 cells per sample. Sequencing was performed on a NovaSeq 6000 sequencer (Illumina) using a 28 x 10 x 10 x 90 bp configuration.

tag: cell line

value: CM

value: insulinoma


title: R_400PHE_4

extract_protocol:
R_400PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: ENSMGAG00000016128

description:
raw data file:
A22_2.D.txt
channel:
2
RNCMPT00350


title: bladder_cancer_TURBT_56


title: PK15181.1

description:
raw data file:
A20_2.D.txt
channel:
1
RNCMPT00345


title: bladder_cancer_TURBT_57


title: CBG15837

description:
raw data file:
A19_2.D.txt
channel:
2
RNCMPT00344


title: PK22404.1

description:
raw data file:
A19_2.D.txt
channel:
1
RNCMPT00343


title: bladder_cancer_TURBT_53

value: female


title: bladder_cancer_TURBT_54


title: bladder_cancer_TURBT_52


title: R_100PHE_4

extract_protocol:
R_100PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 100PHE-abiotic stress-compound addition-phenanthrenequantity 100mg time 4week  phenanthrene concentration in soil in mg/kg soil DW


title: PK04894.1

description:
raw data file:
A20_2.D.txt
channel:
2
RNCMPT00346


title: Y59A8B.10

description:
raw data file:
A21_2.D.txt
channel:
1
RNCMPT00347


title: R_100PHE_3

extract_protocol:
R_100PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: EtBr, 24h, rep2

city: Boston

first: Katja

middle: G

last: Hansen

address: 77 Avenue Louis Pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

data_processing:
Fastq files were concatenated to combine data.
Reads were trimmed using cutadapt 2.5 for both ends. 5 prime ends were trimmed for 3 more nucleotides to remove template sqitch bases and 5 more nucleotides were trimmed from the 3 prime end to remove random hexamer priming.
Trimmed reads were filtered after mapping to rRNA using bowtie1 with settings allowing for one internal and one 5′ mismatch.
After filtering, reads were aligned to the GRCh38 human reference genome using STAR 2.7.3 ( --runThreadN 4 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 100)
Read counts for unique reads were quantified using feature counts of the Rsubread package (useMetaFeatures = TRUE, countMultiMappingReads = FALSE, strandSpecific = 1, isPairedEnd = TRUE, nthreads = 4)
Raw counts were then normalized to gene length and library size to gain RPKM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains the raw counts of unique mapped reads
Supplementary files format and content: tab-delimited text file contains the RPKM calculated from the raw counts.

growth_protocol: Cells were grown in DMEM + 10% FBS.

extract_protocol:
Cells were scraped directly in Tryzol for lysis. RNAs were extracted by chloroform and precipitated with isopropanol.
Library preperation was done using the SMARTer Stranded Total RNA HI Mammalian kit (Takara #634873) and according to manufactory protocol.

treatment_protocol: Cells were treated with 2 ug/ml Ethidium bromide or water as a control for 5 or 24 hours.

value: osteosarcoma

value: Ethidium bromide 2ug/ml, 24h


title: PK27672.1

description:
raw data file:
A18_2.D.txt
channel:
2
RNCMPT00342

value: GST-tagged RNA-binding protein pulldown


title: EtBr, 24h, rep1


title: R_100PHE_2

extract_protocol:
R_100PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: EtBr, 5h, rep2

value: Ethidium bromide 2ug/ml, 5h


title: EtBr, 5h, rep1


title: R_1000PHE_4

extract_protocol:
R_1000PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: 1000PHE-abiotic stress-compound addition-phenanthrenequantity 1000mg time 4week  phenanthrene concentration in soil in mg/kg soil DW


title: R_100PHE_1

extract_protocol:
R_100PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_51

value: male


title: bladder_cancer_TURBT_72


title: bladder_cancer_TURBT_50


title: CBG14639

description:
raw data file:
A15_2.N.txt
channel:
1
RNCMPT00331

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purifyied by phenol-chloroform extraction followed by ethanol precipitation.


title: CBG04067

description:
raw data file:
A18_2.D.txt
channel:
1
RNCMPT00341


title: R_1000PHE_3

extract_protocol:
R_1000PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: H2O, 24h, rep2

value: water, 24h


title: bladder_cancer_TURBT_45

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.


title: H2O, 24h, rep1


title: R_1000PHE_2

extract_protocol:
R_1000PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_46


title: csx1

description:
raw data file:
A12_2.N.txt
channel:
1
RNCMPT00325


title: R_1000PHE_1

extract_protocol:
R_1000PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: H2O, 5h, rep2

value: water, 5h


title: bladder_cancer_TURBT_44


title: CM fresh cells

description: Library name: CM-fresh


title: R_0PHE_4

extract_protocol:
R_0PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

treatment_protocol: no treatment

value: wild type (hybrid Populus deltoides x nigra)


title: RS31A

description:
raw data file:
A14_2.N.txt
channel:
1
RNCMPT00329


title: Y69A2AR.32

description:
raw data file:
A11_2.N.txt
channel:
2
RNCMPT00324


title: spo5

description:
raw data file:
A10_2.txt
channel:
1
RNCMPT00311


title: bladder_cancer_TURBT_48


title: bladder_cancer_TURBT_49


title: PK03611.1

description:
raw data file:
A12_2.N.txt
channel:
2
RNCMPT00326


title: HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 3replicate

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

description:
Library name: 5.30.2.3M
s_5_30_2_3_m

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads.The STAR splice-aware aligner was used to map the reads to the reference genome (GRCh38.88). The Rsamtools package was used to process bam files. FeatureCounts was used to calculate the read counts for gene (Ensembl)  prepared by biomaRt package.
Assembly: GRCh38.88
Supplementary files format and content: tab-delimited text file includes counts for each Sample

extract_protocol:
Total RNA from cells was isolated using Quick-RNA MiniPrep Kit (Zymo Research, USA) according to the manufacturer's instructions. The 3D gels with cells were pre-treated with Collagenase Type II (Gibco, USA) at a concentration of 150 U/ml and kept in a CO2 incubator until the collagen had visually dissolved (approximately 40 minutes).
To obtain mRNA, total RNA were enriched by Poly(A) using VAHTS mRNA Capture Beads (Vazyme Biotech, Сhina). Double-stranded cDNA libraries were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech) according to the manufacturer’s protocol.

treatment_protocol: The glycated gels were prepared using a non-enzymatic post-glycation method. After gel polymerization, the medium was replaced with the same medium supplemented with D-ribose. Cell-laden 3D hydrogels were treated with different doses of ribose for 5 days to ensure cross-linking between the collagen and the reducing sugar. Then, a medium without ribose was used, which was changed every 2-3 days.

value: D-ribose 30mM


title: CBG13971

description:
raw data file:
A11_2.N.txt
channel:
1
RNCMPT00323


title: R_0PHE_3

extract_protocol:
R_0PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

value: root


title: H2O, 5h, rep1


title: R_0PHE_2

extract_protocol:
R_0PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 1replicate

description:
Library name: 5.30.2.1M
s_5_30_2_1_m


title: NCI-H660_PROX1_Sh.01

city: VANCOUVER

first: Yuzhuo

last: Wang

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

data_processing:
PolyA RNA was sequenced on the Illumina NovaSeq 6000 platform (Novogene) with a depth of 20 million paired-end 150 bp reads per sample.
The sequencing reads were aligned to the GRCh38 reference genome using the HISAT2 aligner (version 2.0.5).
Gene expression counts were quantified using featureCounts (v1.5.0-p3) and normalized to Fragments Per Kilobase of transcript per Million mapped reads (FPKM) to account for differences in sequencing depth and gene length.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

molecule: polyA RNA

growth_protocol: NCI-H660 cells were obtained from ATCC, and cultured based on ATCC protocol

extract_protocol:
Total RNA was harvested using RNeasy Plus Mini Kit.
mRNA was purified from total RNA using poly-T oligo attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library.

treatment_protocol: Lentiviral particles delivering tet-plko.shRNA were added to the culture media of NCI-H660,  puromycin was used at 1 μg/ml to select for infected cells and to maintain stable cell populations. 1ug/mL of Doxycycline was used for knockdown (KD) induction

value: Neuroendocrine prostate cancer (NEPC)  cells

value: PROX1 _Knockdown (KD)

value: Doxycycline induction


title: NCI-H660_Sh.Control _Rep 2

value: Negative Control _Knockdown (KD)


title: R_0PHE_1

extract_protocol:
R_0PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: NCI-H660_PROX1_Sh.02


title: bladder_cancer_TURBT_42


title: bladder_cancer_TURBT_43


title: HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 2replicate

description:
Library name: 5.30.2.2M
s_5_30_2_2_m


title: NCI-H660_Sh.Control _Rep 1


title: HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 3replicate

description:
Library name: 5.15.2.3M
s_5_15_2_3_m

value: D-ribose 15mM


title: bladder_cancer_TURBT_40


title: HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 2replicate

description:
Library name: 5.15.2.2M
s_5_15_2_2_m


title: PTBP2

description:
raw data file:
A7_2.txt
channel:
2
RNCMPT00306


title: rnp-2

description:
raw data file:
A5_2.txt
channel:
1
RNCMPT00301


title: bladder_cancer_TURBT_47


title: bladder_cancer_TURBT_39


title: bladder_cancer_TURBT_41


title: 22Rv1_MMC_Method2_4

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description:
Methyl-Micro-C library generated from 22Rv1 cell line
22Rv1_MMC_Method2.HCG.bedGraph
22Rv1_MMC_Method2.hic

data_processing:
Methyl-Micro-C data were processed using bhmem [PMID: 31384045]. Chromatin interaction of Methyl-Micro-C and Micro-C data were processed using 4DN pipeline [PMID: 28905911] as previously done [PMID: 36544209]. To analyze DNA methylation, Methyl-Micro-C, EM-seq, and NOMe-seq data were aligned using bwameth (https://github.com/brentp/bwa-meth) and quantified using biscuit [PMID: 38412294]. Bistools [PMID: 25747664] and IGV [PMID: 22517427] tools were used to visualize DNA methylation signals.
Assembly: hg38
Supplementary files format and content: hic and bedGraph
Library strategy: Methyl-Micro-C

source_name: Prostate

growth_protocol: 22Rv1 (CRL-2505) cells were obtained from ATCC and were cultured according to the suggested protocols using RPMI (Corning, 10-040-CV) supplemented with 10% FBS plus 1% penicillin and 1% streptomycin.

extract_protocol:
Cells were harvested, crosslinked, and lysed to isolate intact nuclei.
Methyl-Micro-C library: Nuclei were treated with MNase and proximity ligation was performed with a biotinylated bridge. Ligated DNA products underwent end preparation (NEB, E7546S) and methylated adapters (NEB, E7165AAVIAL) are added. After enriching ligated products, oxidation of methylated and hydroxy-methylated cytosines and deamination of unprotected unmethylated cytosines were performed using EM-seq conversion module (NEB, E7125S). Methyl-Micro-C library was generated by performing indexing PCR and sequenced using Illumina NovaSeq sequencing systems, following the guidelines of the manufacturer.
EM-seq library: EM-seq library was generated as previously reported (PMID: 34140313), and the library was sequenced with Illumina NovaSeq sequencing platforms.
NOMe-seq library: NOMe-seq library was generated using M.CviPI methyltransferase (NEB, M0227B) to methylate GpCs as previously described [PMID: 29605855]. Bisulfite treatment was used to methylate CpGs, and the library was generated using IDT xGen Methyl-seq kit (IDT, 10009824) and sequenced with Illumina NovaSeq sequencing platforms.

value: Prostate

value: Prostate Cancer Cell


title: L_700PHE_3

extract_protocol:
L_700PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

value: leaf


title: 22Rv1_MMC_Method2_5


title: HdFbs at 12th passage, 5mg/mL collagen, 15mm D-ribose, 17days, 1replicate

description:
Library name: 5.15.2.1M
s_5_15_2_1_m


title: 22Rv1_MMC_Method2_3


title: L_700PHE_2

extract_protocol:
L_700PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_38


title: HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 2replicate

description:
Library name: 5.0.2.2M
s_5_0_2_2_m

value: D-ribose 0mM


title: L_700PHE_4

extract_protocol:
L_700PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: L_700PHE_1

extract_protocol:
L_700PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 1replicate

description:
Library name: 5.0.2.1M
s_5_0_2_1_m


title: 22Rv1_MMC_Method2_1


title: L_400PHE_3

extract_protocol:
L_400PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 22Rv1_MMC_Method2_2


title: bladder_cancer_TURBT_35


title: bladder_cancer_TURBT_36


title: HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 3replicate

description:
Library name: 5.0.2.3M
s_5_0_2_3_m


title: bladder_cancer_TURBT_37


title: 22Rv1_MMC_Method1_2

description:
Methyl-Micro-C library generated from 22Rv1 cell line
22Rv1_MMC_Method1.HCG.bedGraph
22Rv1_MMC_Method1.hic


title: L_400PHE_2

extract_protocol:
L_400PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_34

value: female


title: HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 2replicate

description:
Library name: 5.30.1.2M
s_5_30_1_2_m


title: hnrnpa0l

description:
raw data file:
A17_2.D.txt
channel:
2
RNCMPT00340

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purifyied by phenol-chloroform extraction followed by ethanol precipitation.

value: GST-tagged RNA-binding protein pulldown


title: L_400PHE_4

extract_protocol:
L_400PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 22Rv1_MMC_Method1_1


title: L_400PHE_1

extract_protocol:
L_400PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 1replicate

description:
Library name: 5.30.1.1M
s_5_30_1_1_m


title: 22Rv1_Micro-C_5

description:
Micro-C library genearted from 22Rv1 cell line
22Rv1_MicroC.hic

data_processing:
Methyl-Micro-C data were processed using bhmem [PMID: 31384045]. Chromatin interaction of Methyl-Micro-C and Micro-C data were processed using 4DN pipeline [PMID: 28905911] as previously done [PMID: 36544209]. To analyze DNA methylation, Methyl-Micro-C, EM-seq, and NOMe-seq data were aligned using bwameth (https://github.com/brentp/bwa-meth) and quantified using biscuit [PMID: 38412294]. Bistools [PMID: 25747664] and IGV [PMID: 22517427] tools were used to visualize DNA methylation signals.
Assembly: hg38
Supplementary files format and content: hic and bedGraph
Library strategy: Micro-C


title: 22Rv1_Micro-C_4


title: HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 2replicate

description:
Library name: 5.15.1.2M
s_5_15_1_2_m


title: 22Rv1_Micro-C_3


title: HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 3replicate

description:
Library name: 5.15.1.3M
s_5_15_1_3_m


title: L_200PHE_2

extract_protocol:
L_200PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 3replicate

description:
Library name: 5.30.1.3M
s_5_30_1_3_m


title: bladder_cancer_TURBT_33

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

value: male


title: bladder_cancer_TURBT_31


title: bladder_cancer_TURBT_32


title: HdFbs at 12th passage, 5mg/mL collagen, 15mm D-ribose, 10days, 1replicate

description:
Library name: 5.15.1.1M
s_5_15_1_1_m

extract_protocol:
Total RNA from cells was isolated using Quick-RNA MiniPrep Kit (Zymo Research, USA) according to the manufacturer's instructions. The 3D gels with cells were pre-treated with Collagenase Type II (Gibco, USA) at a concentration of 150 U/ml and kept in a CO2 incubator until the collagen had visually dissolved (approximately 40 minutes).
To obtain mRNA, total RNA were enriched by Poly(A) using VAHTS mRNA Capture Beads (Vazyme Biotech, Сhina). Double-stranded cDNA libraries were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech) according to the manufacturer’s protocol.


title: bladder_cancer_TURBT_29


title: 22Rv1_Micro-C_2


title: L_200PHE_4

extract_protocol:
L_200PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: L_200PHE_1

extract_protocol:
L_200PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: L_2000PHE_4

extract_protocol:
L_2000PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 3replicate

description:
Library name: 5.0.1.3M
s_5_0_1_3_m


title: L_200PHE_3

extract_protocol:
L_200PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 22Rv1_NOMe-seq_3

description:
NOMe-seq library genearted from 22Rv1 cell line
22Rv1_NOMe-seq.HCG.bedGraph
22Rv1_NOMe-seq.GCH.bedGraph

data_processing:
Methyl-Micro-C data were processed using bhmem [PMID: 31384045]. Chromatin interaction of Methyl-Micro-C and Micro-C data were processed using 4DN pipeline [PMID: 28905911] as previously done [PMID: 36544209]. To analyze DNA methylation, Methyl-Micro-C, EM-seq, and NOMe-seq data were aligned using bwameth (https://github.com/brentp/bwa-meth) and quantified using biscuit [PMID: 38412294]. Bistools [PMID: 25747664] and IGV [PMID: 22517427] tools were used to visualize DNA methylation signals.
Assembly: hg38
Supplementary files format and content: hic and bedGraph
Library strategy: NOMe-seq

extract_protocol:
Cells were harvested, crosslinked, and lysed to isolate intact nuclei.
Methyl-Micro-C library: Nuclei were treated with MNase and proximity ligation was performed with a biotinylated bridge. Ligated DNA products underwent end preparation (NEB, E7546S) and methylated adapters (NEB, E7165AAVIAL) are added. After enriching ligated products, oxidation of methylated and hydroxy-methylated cytosines and deamination of unprotected unmethylated cytosines were performed using EM-seq conversion module (NEB, E7125S). Methyl-Micro-C library was generated by performing indexing PCR and sequenced using Illumina NovaSeq sequencing systems, following the guidelines of the manufacturer.
EM-seq library: EM-seq library was generated as previously reported (PMID: 34140313), and the library was sequenced with Illumina NovaSeq sequencing platforms.
NOMe-seq library: NOMe-seq library was generated using M.CviPI methyltransferase (NEB, M0227B) to methylate GpCs as previously described [PMID: 29605855]. Bisulfite treatment was used to methylate CpGs, and the library was generated using IDT xGen Methyl-seq kit (IDT, 10009824) and sequenced with Illumina NovaSeq sequencing platforms.


title: 22Rv1_Micro-C_1


title: L_2000PHE_3

extract_protocol:
L_2000PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 22Rv1_EM-seq

description:
EM-seq library genearted from 22Rv1 cell line
22Rv1_EM-seq.HCG.bedGraph

data_processing:
Methyl-Micro-C data were processed using bhmem [PMID: 31384045]. Chromatin interaction of Methyl-Micro-C and Micro-C data were processed using 4DN pipeline [PMID: 28905911] as previously done [PMID: 36544209]. To analyze DNA methylation, Methyl-Micro-C, EM-seq, and NOMe-seq data were aligned using bwameth (https://github.com/brentp/bwa-meth) and quantified using biscuit [PMID: 38412294]. Bistools [PMID: 25747664] and IGV [PMID: 22517427] tools were used to visualize DNA methylation signals.
Assembly: hg38
Supplementary files format and content: hic and bedGraph
Library strategy: EM-seq


title: 22Rv1_NOMe-seq_2


title: L_2000PHE_1

extract_protocol:
L_2000PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 2replicate

description:
Library name: 5.0.1.2M
s_5_0_1_2_m


title: HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 1replicate

description:
Library name: 5.0.1.1M
s_5_0_1_1_m


title: bladder_cancer_TURBT_30


title: bladder_cancer_TURBT_26


title: HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 2replicate

description:
Library name: 5.30.2.2
s_5_30_2_2_z


title: 22Rv1_NOMe-seq_1


title: bladder_cancer_TURBT_23


title: HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 1replicate

description:
Library name: 5.30.2.1
s_5_30_2_1_z


title: bladder_cancer_TURBT_28


title: bladder_cancer_TURBT_27


title: bladder_cancer_TURBT_25


title: bladder_cancer_TURBT_24


title: L_1500PHE_3

extract_protocol:
L_1500PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 4411_Illumina

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

description: 10X genomics

data_processing:
Assembly: ChGr38
Cellranger
Supplementary files format and content: filtered feature bc matrix

source_name: Breast cancer tissue

extract_protocol:
Tissue extraction and dispersion
Chromium Next GEM Single Cell 3ʹ

value: Breast cancer tissue


title: HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 3replicate

description:
Library name: 5.15.2.3
s_5_15_2_3_z


title: L_2000PHE_2

extract_protocol:
L_2000PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: 4066_Illumina

description: 10X genomics


title: HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 3replicate

description:
Library name: 5.30.2.3
s_5_30_2_3_z


title: bladder_cancer_TURBT_22


title: L_1500PHE_1

extract_protocol:
L_1500PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: L_1500PHE_2

extract_protocol:
L_1500PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 3replicate

description:
Library name: 5.0.2.3
s_5_0_2_3_z


title: L_1500PHE_4

extract_protocol:
L_1500PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 2replicate

description:
Library name: 5.15.2.2
s_5_15_2_2_z


title: L_100PHE_4

extract_protocol:
L_100PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: polysomalRNA_siLSM14A_NT_REP3

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

data_processing:
RNA-seq data have been analyzed with the Institut Curie RNA-seq Nextflow pipeline (v3.1.4, https://doi.org/10.5281/zenodo.7443721). Briefly, raw reads were first trimmed with Trimgalor. Reads were aligned on the human reference genome (hg19) using STAR (STAR_2.6.1a_08-27). Genes abundance has been then estimated using STAR (STAR_2.6.1a_08-27). .
Assembly: Hg19
Supplementary files format and content: coma delimited text file includes raw counts for each sample

extract_protocol:
RNA was isolated using the TRIzol-chloroform method and treated with DNase I (TURBO DNA-free; Invitrogen™, #AM1907) according to the manufacturer’s instructions. After DNase treatment, RNA was quantified using a Nanodrop 2000 spectrophotometer (Thermo Scientific™), and 1 μg total RNA was used to synthesize cDNA using SuperScript III Reverse Transcriptase (200 U/μL; Invitrogen™, #18080044) and random hexamer primers (Invitrogen™, #SO142), according to the manufacturer’s instructions.
RNA sequencing libraries were prepared from 500ng to 1µg of total RNA or mRNA-enriched from heavy polysome fractions using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. Nanodrop spectrophotometer was used to assess purity of RNA based on absorbance ratios (260/280 and 260/230) and BioAnalyzer for RNA integrity (RIN>9). A first step of polyA+ selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. The libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche).

value: melanoma

value: NT


title: 4399_Illumina

description: 10X genomics


title: L_100PHE_3

extract_protocol:
L_100PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf

value: wild type (hybrid Populus deltoides x nigra)


title: polysomalRNA_siLSM14A_HU_REP3

value: HU


title: bladder_cancer_TURBT_19

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.


title: HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 2replicate

description:
Library name: 5.0.2.2
s_5_0_2_2_z

extract_protocol:
Total RNA from cells was isolated using Quick-RNA MiniPrep Kit (Zymo Research, USA) according to the manufacturer's instructions. The 3D gels with cells were pre-treated with Collagenase Type II (Gibco, USA) at a concentration of 150 U/ml and kept in a CO2 incubator until the collagen had visually dissolved (approximately 40 minutes).
To obtain mRNA, total RNA were enriched by Poly(A) using VAHTS mRNA Capture Beads (Vazyme Biotech, Сhina). Double-stranded cDNA libraries were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech) according to the manufacturer’s protocol.


title: polysomalRNA_siCTRL_HU_REP3

value: siCTRL


title: HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 1replicate

description:
Library name: 5.0.2.1
s_5_0_2_1_z


title: bladder_cancer_TURBT_21


title: polysomalRNA_siCTRL_NT_REP3


title: L_100PHE_2

extract_protocol:
L_100PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: polysomalRNA_siLSM14A_HU_REP2


title: HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 2replicate

description:
Library name: 5.30.1.2
s_5_30_1_2_z

value: D-ribose 30mM


title: L_1000PHE_4

extract_protocol:
L_1000PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: L_1000PHE_2

extract_protocol:
L_1000PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: L_100PHE_1

extract_protocol:
L_100PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 3replicate

description:
Library name: 5.30.1.3
s_5_30_1_3_z


title: HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 3replicate

description:
Library name: 5.15.1.3
s_5_15_1_3_z


title: bladder_cancer_TURBT_18


title: polysomalRNA_siCTRL_HU_REP2


title: HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 1replicate

description:
Library name: 5.30.1.1
s_5_30_1_1_z


title: L_1000PHE_1

extract_protocol:
L_1000PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: bladder_cancer_TURBT_20


title: bladder_cancer_TURBT_17


title: bladder_cancer_TURBT_16


title: polysomalRNA_siLSM14A_HU_REP1


title: bladder_cancer_TURBT_14


title: L_0PHE_4

extract_protocol:
L_0PHE_4(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: HdFbs at 20th passage, 5mg/mL collagen, 15mm D-ribose, 10days, 1replicate

description:
Library name: 5.15.1.1
s_5_15_1_1_z


title: polysomalRNA_siLSM14A_NT_REP1


title: bladder_cancer_TURBT_11


title: L_0PHE_3

extract_protocol:
L_0PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: polysomalRNA_siLSM14A_NT_REP2


title: HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 3replicate

description:
Library name: 5.0.1.3
s_5_0_1_3_z


title: L_1000PHE_3

extract_protocol:
L_1000PHE_3(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: polysomalRNA_siCTRL_HU_REP1


title: L_0PHE_1

extract_protocol:
L_0PHE_1(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: L_0PHE_2

extract_protocol:
L_0PHE_2(5ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf


title: polysomalRNA_siCTRL_NT_REP2


title: HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 2replicate

description:
Library name: 5.0.1.2
s_5_0_1_2_z


title: HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 2replicate

description:
Library name: 5.15.1.2
s_5_15_1_2_z


title: polysomalRNA_siCTRL_NT_REP1


title: HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 1replicate

description:
Library name: 5.0.1.1
s_5_0_1_1_z


title: bladder_cancer_TURBT_15


title: bladder_cancer_TURBT_10


title: bladder_cancer_TURBT_13


title: bladder_cancer_TURBT_9


title: bladder_cancer_TURBT_12


title: bladder_cancer_TURBT_8


title: bladder_cancer_TURBT_7


title: exp2 4 hours, stored plasma sample

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description: Library name: sample 10

data_processing:
Data was trimmed using fastp default parameters.
trimmed data was aligned to the GENCODE GRCh38 v35 transcriptome usings Salmon 1.4.0 and quantification generated.
Fold change analysis was performed using DESeq2 with salmon quantification as input
Assembly: GRCh38
Supplementary files format and content: Salmon quantification.
Supplementary files format and content: Fold change analysis from DESeq2 full and filtered by significance

source_name: cord blood

growth_protocol: CD34+ cells were enriched by positive immunomagnetic selection

extract_protocol:
RNA was isolated using a PicoPure Kit (Cat# KIT0204, Massachusetts, USA)
cDNA libraries were constructed using TruSeq stranded mRNA protocol (Illumina, San Diego, CA, USA)

treatment_protocol: CD34+ cells were incubated with fresh or stored plasma for 0, 20 mins or 4 hours at 37C.

value: cord blood

value: CD34+ cells

value: cord blood hematopoietic

value: WT

value: 4 hours stored plasma

tag: batch


title: totalRNA_siLSM14A_NT_REP3


title: exp 2, 20 mins, stored plasma sample

description: Library name: sample 9

value: 20 mins stored plasma


title: totalRNA_siCTRL_HU_REP3


title: totalRNA_siLSM14A_HU_REP3


title: IDE-KO hepatome cells, biological rep 4

city: Palencia

first: Sergio

last: Díez-Hermano

state: Palencia

address: C/Felipe II, 10, 2C

country: Spain

institute: University of Valladolid

description: Gene expression data from HepG2 IDE-KO cells

hyb_protocol: Following fragmentation, 1 ug of cRNA wer hybridized for 16h at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the microarray scanner GenePix4000B

data_processing: The data were analysed with R programming language (v4.4.1), using the default RMA calibration parameters in the oligo package and the default contrast parameters for eBayes in the limma package

source_name: IDE-KO HepG2 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: HepG2 cells were cultured in Minimum Essential Medium (MEM) supplemented with 10% FBS, 100 U/mL penicillin and 100 g/mL streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA (1 µg) was subjected to cDNA microarray analysis

treatment_protocol: Cells were collected by conventional means. No treatement  was performed. Four independent RNA replicates were processed and analyzed.

value: Hepatic human tissue

value: Insulin Degrading Enzyme KO


title: exp 2, 4 hours, fresh plasma sample

description: Library name: sample 8

value: 4 hours fresh plasma


title: totalRNA_siLSM14A_HU_REP2


title: exp 2, 20 mins, fresh plasma sample

description: Library name: sample 7

value: 20 mins fresh plasma


title: totalRNA_siCTRL_NT_REP3


title: exp 2, time 0 sample sample

description: Library name: sample 6


title: totalRNA_siLSM14A_NT_REP2


title: totalRNA_siCTRL_HU_REP2


title: Lefamulin-3

city: wuhan

first: wenqi

last: dong

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description: replicate biosample 3

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 gossypium hirsutum 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: H37Rv; NC_000962.3
Supplementary files format and content: rpkm value for each sample

organism: Mycobacterium tuberculosis

source_name: logarithmic growth phase culture

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain

value: M.tb H37Rv

value: logarithmic growth phase culture

value: Lefamulin


title: exp 1, 4 hours, stored plasma sample

description: Library name: sample 5


title: totalRNA_siCTRL_NT_REP2

extract_protocol:
RNA was isolated using the TRIzol-chloroform method and treated with DNase I (TURBO DNA-free; Invitrogen™, #AM1907) according to the manufacturer’s instructions. After DNase treatment, RNA was quantified using a Nanodrop 2000 spectrophotometer (Thermo Scientific™), and 1 μg total RNA was used to synthesize cDNA using SuperScript III Reverse Transcriptase (200 U/μL; Invitrogen™, #18080044) and random hexamer primers (Invitrogen™, #SO142), according to the manufacturer’s instructions.
RNA sequencing libraries were prepared from 500ng to 1µg of total RNA or mRNA-enriched from heavy polysome fractions using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. Nanodrop spectrophotometer was used to assess purity of RNA based on absorbance ratios (260/280 and 260/230) and BioAnalyzer for RNA integrity (RIN>9). A first step of polyA+ selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. The libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche).

value: melanoma

value: NT


title: exp 1, 4 houurs, fresh plasma sample

description: Library name: sample 3


title: totalRNA_siLSM14A_HU_REP1

value: HU


title: bladder_cancer_TURBT_5

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

value: male


title: IDE-KO hepatome cells, biological rep 3


title: SK-N-AS cells of rs1950834-GG, DX 3

city: Nanjing

first: Yan

last: Kong

address: 87 Dingjiaqiao Road

institute: Southeast University

description: Library name: GD_3

data_processing:
SOAPnuke (v2.1.0)
Assembly: hg38
Supplementary files format and content: CSV files

source_name: Neuroblastoma

extract_protocol:
RNA was harvested using RNeasy min plus kit (Qiagen). 2μg taotal RNA was used for sequencing.
1) Perform mRNA enrichment on total RNA using mRNA enrichment method: Use magnetic beads with Oligo dT to enrich mRNA with polyA tails. 2) Fragment the obtained RNA with fragmentation buffer, reverse transcribe using random N6 primers, and then synthesize cDNA double strands to form double-stranded DNA. 3) Fill in the ends of the synthesized double-stranded DNA, 5' end phosphorylate, form a sticky end with an "A" protruding at the 3' end, and then connect a bubble-shaped adapter with a protruding "T" at the 3' end. 4) The connected products undergo PCR amplification using specific primers. 5) Denature the PCR products into single strands, and then use a bridge primer to circularize the single-stranded DNA to obtain a single-stranded circular DNA library.

value: Neuroblastoma

value: SK-N-AS

value: DX


title: Lefamulin-1

description: replicate biosample 1


title: IDE-KO hepatome cells, biological rep 2


title: IDE-KO hepatome cells, biological rep 1


title: exp 1, 20 mins, fresh plasma sample

description: Library name: sample 2

value: cord blood

value: CD34+ cells

value: cord blood hematopoietic

value: WT


title: bladder_cancer_TURBT_6

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.


title: control hepatome cells, biological rep 2

description: Gene expression data from HepG2 control cells

source_name: Control HepG2 cells

value: Hepatic human tissue

value: Control


title: bladder_cancer_TURBT_4


title: control hepatome cells, biological rep 4


title: control hepatome cells, biological rep 3


title: expt 1, time 0 sample

description: Library name: sample 1


title: DMSO-3

description: replicate biosample 3

value: DMSO


title: bladder_cancer_TURBT_1


title: SK-N-AS cells of rs1950834-GG, DX 2

description: Library name: GD_2


title: totalRNA_siCTRL_HU_REP1

value: siCTRL


title: DNA

city: qingdao

first: chengwen

last: gao

state: shandong

address: Huangdao Qingdao Shandong

institute: Affiliated Hospital of Qingdao University

description: Library name: DNA

data_processing:
*library strategy: modified STARR-seq
Expression data for the SNP fragments were processed by converting raw counts to Transcripts Per Million (TPM) and filtering out low-expressed fragments. Residual log expression normalization and hierarchical clustering were performed to assess sample quality, with outliers identified based on D-statistics and removed from the dataset. Pairwise global alignments compared relevant sequences, summarizing results with alignment scores. The filtered expression data and sequence alignment outputs were saved for further analysis.Enhancer activity analysis followed the method described by Tippens et al.66 Raw sequencing reads were processed using the "voom" function from the R limma package (v3.40.6). Input and output samples were treated as separate experimental conditions, and eSNPs were identified based on significantly higher expression in the output compared to the input. A false discovery rate (FDR)-adjusted p-value less than 0.05 and a fold change greater than 1.5 (log₂FC > 0.585) defined eSNPs (Table S2). SNPs showing significantly reduced expression were classified as candidate silencer SNPs.To identify baaSNPs among the eSNPs, differential allelic regulatory activity was calculated using the mpra package (v1.14.0)43. The analysis employed the `mpralm()` function, which uses a linear model to measure differential regulatory activity between two alleles. This provided summary statistics for each variant, including t-statistics, p-values, log fold changes, B-statistics, and average expression .
Supplementary files format and content: csv files include counts for each cell lines

source_name: DNA

extract_protocol:
Neuro-2a, SH-SY5Y, HEK-293T, and PC-12 cells were cultured to logarithmic growth phase, reaching a density of 2×107 cells on the day of transfection. Transfections were performed using Xfect™ Transfection Reagent (Takara, Cat. No. 631317, China) under optimized conditions established from preliminary experiments. The purified plasmid DNA from the constructed library was transfected into the cells, and each experiment was conducted in triplicate to ensure reproducibility.
Before cell transfection, the plasmid library was used to construct the input sequencing library. For the initial PCR, 100 ng of the plasmid library underwent a one-step PCR. The purified products were then subjected to two additional rounds of PCR with sample index primers. High-fidelity KAPA HiFi HotStart ReadyMix (Roche, Cat. No. KK2601, USA) was used in all PCR steps to ensure accurate amplification. The final products were prepared for paired-end sequencing on the Illumina NovaSeq 6000 platform. After transfection, total RNA was extracted using the E.Z.N.A.® Total RNA Midiprep Kit (Omega Bio-Tek, Cat. No. R6664, USA). Polyadenylated RNA was isolated using VAHTS mRNA Capture Beads (Vazyme, Cat. No. N401, China) and reverse-transcribed with the HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, Cat. No. R312-02, China). The resulting cDNA was treated with RNase A and purified using AMPure XP beads. Two rounds of PCR amplification were performed, with products purified using Agencourt SPRIselect Reagent (Beckman Coulter, Cat. No. B23318, USA). Three biological replicates were prepared for both input and output sequencing libraries, which were then sequenced using paired-end 150 bp reads on the Illumina NovaSeq 6000 platform.

value: DNA


title: exp 1, 20 mins, stored plasma sample

description: Library name: sample 4

value: 20 mins stored plasma


title: SK-N-AS cells of rs1950834-GG, DX 1

description: Library name: GD_1


title: bladder_cancer_TURBT_3

city: San Diego

first: Elai

last: Davicioni

address: 9725 Lusk Blvd

institute: Veracyte, Inc


title: Lefamulin-2

description: replicate biosample 2

value: M.tb H37Rv

value: logarithmic growth phase culture

value: Lefamulin


title: DMSO-2

description: replicate biosample 2


title: SK-N-AS cells of rs1950834-GG, control 3

description: Library name: G_3

value: control


title: DMSO-1

description: replicate biosample 1


title: SK-N-AS cells of rs1950834-GG, control 2

description: Library name: G_2

value: Neuroblastoma


title: N2, TM, rep6

city: Changsha

first: Guolin

last: Li

state: Hunan

address: 177 Lushan Road

department: College of Life Sciences

institute: Hunan Normal University

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Cutadapt(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
HISAT2(https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package was used to align reads of all samples to the reference genome
StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GCF_000002985.6
Supplementary files format and content: xlsx file includes FPKM and count values for each Sample

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencinglibrary. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)(Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module(NEB, cat.e6150, USA) under 94℃ 5-7min).
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used tosynthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR.

value: whole animal

tag: Stage

value: TM


title: SK-N-AS cells of rs1950834-GG, control 1

description: Library name: G_1

value: SK-N-AS


title: SH-SY5Y

description: Library name: SH-SY5Y


title: N2, TM, rep5


title: control hepatome cells, biological rep 1


title: Kasumi1 cells, shRUNX1, 92

city: Beijing

first: Qian

last: Chen

address: Qinghuayuan Stress

institute: Tsinghua University

data_processing:
Adapters and low quality reads were trimmed with fastp v0.20.1 with parameter "-q 20".
Trimmed sequence reads were mapped to hg19 using Hisat2 v2.2.0 with default parameters.
Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools v1.7 with parameter "-Sb -q 20".
FeatureCounts v2.0.1 was applied to calculate the counts per gene under default parameters.
Differentially expressed genes were identified using R package DESeq2 v1.26.0. Please note that the 'Kasumi1_shRUNX1_count.txt' was generated comparing control and shRUNX1 treated RNA abundance using previously published control data (GSE207233; GSM6282809, GSM6282810 and GSM6282811).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts per gene for each Sample

growth_protocol: Cells were cultured in RPMI 1640 medium with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy plus kit (Qiagen) for Kasumi-1 cells and TRIZOL reagent (Invitrogen) for MOLM13 cells.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

treatment_protocol: Kasumi-1 and MOLM13 cells were infected with lentiviruses expressing shRNAs. After 48 h of transduction, puromycin (1 μg/mL) was added into medium for another 48 h to select shRNA expressing cells.

value: Human acute myeloblastic leukemia

value: RUNX1 shRNA


title: totalRNA_siLSM14A_NT_REP1

value: melanoma

value: NT


title: SK-N-AS cells of rs1950834-AA, DX 3

description: Library name: AD_3

value: DX


title: AML cells, METTL3 degrader ZW27941, rep2

city: Gainesville

first: Yutao

last: Zhang

state: FL

address: 2033 Mowry Road, CGRC 285

institute: University of Florida

description:
This study investigates the role of METTL3 in the cell cycle regulation of acute myeloid leukemia (AML) cells. The MOLM-13 cell line was treated with the METTL3 degrader ZW27941. RNA was extracted from treated and control cells, and RNA sequencing was performed using the Illumina NovaSeq 6000 platform
GE-7301_5_Ruki-ZW41_2_i7_i5_L006

data_processing:
hisat2, version 2.2.1-3n
samtools, version 1.19.2
htseq-count, version 2.0.3
Assembly: hg38
Supplementary files format and content: The htseq files are the processed data files after htseq-count. They contain the raw counts for each sample.

source_name: Cell line

growth_protocol: MOLM13 cells were cultured in RPMI 1640 medium (Gibco) supplemented with 10% (vol/vol) fetal bovine serum, and 1% penicillin-streptomycin (Sigma). Cell lines were maintained in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
Total RNAs were isolated using Trizol Reagent. RNA quality and quantity were accessed using a DeNovix DS-11 FX + spectrophotometer (DeNovix Inc., Wilmington, DE, USA). Isolated RNA was then subjected to quality control and quantification using an Agilent TapeStation Bioanalyzer. Total RNAs were used for RNA-seq
The library constructions and sequencing were done with 50M raw reads/sample using the Illumina NovaSeq 6000 S4 2x150 platform at the Interdisciplinary Center for Biotechnology Research, University of Florida.

treatment_protocol: MOLM13 cells were cultured and treated with DMSO or ZW27941 (1 μM) for 24 h.

value: Cell line

value: AML cell line (MOLM-13)

value: acute myeloid leukemia

value: FLT3 internal tandem duplication (FLT3-ITD) mutation, t(9;11)(p22;q23) translocation

value: 1 µM ZW27941 for 24 hours


title: Kasumi1 cells, shRUNX1, 59


title: AML cells, METTL3 degrader ZW27941, rep1

description:
This study investigates the role of METTL3 in the cell cycle regulation of acute myeloid leukemia (AML) cells. The MOLM-13 cell line was treated with the METTL3 degrader ZW27941. RNA was extracted from treated and control cells, and RNA sequencing was performed using the Illumina NovaSeq 6000 platform
GE-7301_4_Ruki-ZW41_1_i7_i5_L006


title: AML cells, DMSO, rep3

description:
This study investigates the role of METTL3 in the cell cycle regulation of acute myeloid leukemia (AML) cells. The MOLM-13 cell line was treated with the METTL3 degrader ZW27941. RNA was extracted from treated and control cells, and RNA sequencing was performed using the Illumina NovaSeq 6000 platform
GE-7301_3_Ruki-DMSO_3_i7_i5_L006

value: 1 µM DMSO  for 24 hours


title: N2, TM, rep4


title: SK-N-AS cells of rs1950834-AA, DX 2

description: Library name: AD_2


title: N2, TM, rep3


title: Kasumi1 cells, shRUNX1, 28


title: AML cells, DMSO, rep2

description:
This study investigates the role of METTL3 in the cell cycle regulation of acute myeloid leukemia (AML) cells. The MOLM-13 cell line was treated with the METTL3 degrader ZW27941. RNA was extracted from treated and control cells, and RNA sequencing was performed using the Illumina NovaSeq 6000 platform
GE-7301_2_Ruki-DMSO_2_i7_i5_L006


title: SK-N-AS cells of rs1950834-AA, DX 1

description: Library name: AD_1


title: KG1, JMJD1C

data_processing:
Adapters and low-quality bases were trimmed with trim_galore v0.6.4 with parameter "-q 20 --length 20 --stringency 2”.
Trimmed reads were aligned to the hg19 genome with Bowtie2 v2.3.5.1 with default parameters.
Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools v1.7.
Peaks were called using MACS2 v2.1.1.
RPKM normalized bigwig files were generated using bamCoverage of deepTools v3.3.0.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated and inbubated with antibody/beads. DNA/protein complexes were then eluted and reverse crosslinked at 65 °C for 6 h. DNA was next purified using phenol/chloroform extraction and ethanol precipitation.
ChIP-seq libraries were prepared using End-It DNA End-Repair Kit, Klenow Fragment (3´→ 5´ exo-) and Quick Ligation kit. Libraries were amplified using 16 cycles on the thermocycler and then subjected for size selection using AMPure XP beads.

treatment_protocol: For RUNX1 KD ChIP-seq, MOLM13 and Kasumi-1 cells were infected with lentiviruses expressing shRNAs. After 48 h of transduction, puromycin (1 μg/mL) was added into medium for another 48 h to select shRNA expressing cells.

tag: antibody


title: N2, TM, rep2

tag: tissue


title: SK-N-AS cells of rs1950834-AA, control 3

description: Library name: A_3

tag: cell type


title: N2, TM, rep1

tag: treatment


title: N2, DMSO, rep6

value: DMSO


title: SK-N-AS cells of rs1950834-AA, control 2

description: Library name: A_2

value: control


title: AML cells, METTL3 degrader ZW27941, rep3

description:
This study investigates the role of METTL3 in the cell cycle regulation of acute myeloid leukemia (AML) cells. The MOLM-13 cell line was treated with the METTL3 degrader ZW27941. RNA was extracted from treated and control cells, and RNA sequencing was performed using the Illumina NovaSeq 6000 platform
GE-7301_6_Ruki-ZW41_3_i7_i5_L006


title: MOLM13, input


title: MV4_11, input


title: HdFbs at 20th passage, 5mg/mL collagen, 15mm D-ribose, 17days, 1replicate

description:
Library name: 5.15.2.1
s_5_15_2_1_z

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads.The STAR splice-aware aligner was used to map the reads to the reference genome (GRCh38.88). The Rsamtools package was used to process bam files. FeatureCounts was used to calculate the read counts for gene (Ensembl)  prepared by biomaRt package.
Assembly: GRCh38.88
Supplementary files format and content: tab-delimited text file includes counts for each Sample

extract_protocol:
Total RNA from cells was isolated using Quick-RNA MiniPrep Kit (Zymo Research, USA) according to the manufacturer's instructions. The 3D gels with cells were pre-treated with Collagenase Type II (Gibco, USA) at a concentration of 150 U/ml and kept in a CO2 incubator until the collagen had visually dissolved (approximately 40 minutes).
To obtain mRNA, total RNA were enriched by Poly(A) using VAHTS mRNA Capture Beads (Vazyme Biotech, Сhina). Double-stranded cDNA libraries were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech) according to the manufacturer’s protocol.

value: D-ribose 15mM


title: SK-N-AS cells of rs1950834-AA, control 1

description: Library name: A_1

value: Neuroblastoma


title: B_APIG1

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: PE150 high throughout data

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome (UCSC GRCh38/hg38) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Human prostate

growth_protocol: Primary normal human prostate stromal cell line (PSC27) was routinely cultured in PSCC media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) at 50 μg/ml and/or apigenin at 10 μM, individually.

extract_protocol:
Cells from both culture conditions were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Cells were allowed to stay in culture with appropriate media change until 7-10 days later when they were exposed to apigenin at 10 μM for 2-3 days, then lysed or immediately collected for lysis.

value: Human prostate

value: Human PSC27 prostate stromal cell

value: Stromal

value: Wild type

value: Bleomycin/apigenin


title: AML cells, DMSO, rep1

description:
This study investigates the role of METTL3 in the cell cycle regulation of acute myeloid leukemia (AML) cells. The MOLM-13 cell line was treated with the METTL3 degrader ZW27941. RNA was extracted from treated and control cells, and RNA sequencing was performed using the Illumina NovaSeq 6000 platform
GE-7301_1_Ruki-DMSO_1_i7_i5_L006


title: MV4_11, JMJD1C

value: Human acute myeloblastic leukemia


title: CMK, input

source_name: CMK

value: CMK


title: B_APIG2

description: PE150 high throughout data


title: WFS1 KO + Inh, scRNA-seq_bead_merging_files

first: Xiangyi

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

description:
DNBelab C4
This sample includes raw files that only serve the auxiliary role of merging beads,they only provide information about the combination of two different types of beads.Due to previous research findings, the use of microfluidic technology inevitably results in the phenomenon of multiple beads entering the same oil droplet, leading to a situation where one cell corresponds to multiple cell barcodes. Therefore, MGISEQ-2000RS employ the technology to identify the presence of multiple beads in a single oil droplet (based on the extremely low probability of repetition of the combination of two types of beads in each droplet)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBelab_C4_scRNA_v2.3
Assembly: GRCH38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: hES-derived islet organoid

extract_protocol:
SC-islets were dissociated into single cells with TrypLE and resuspended with DPBS with 0.5% fat-acid -free BSA. Added DNase I to eliminate the DNA released form the dead cells to prevent cell caking and placed the tubes containing cells on ice for preservation.
DNBelab C Series High-throughput Single-Cell RNA Library (MGI, #940-000047-00) was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 250-400 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the MGISEQ-2000RS with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index.

value: hES-derived islet organoid

value: Inhibitor treated for 48h


title: WFS1 KO + Inh, scRNA-seq_GEX

description: DNBelab C4


title: MOLM13, JMJD1C


title: BLEO3

description: PE150 high throughout data

value: Bleomycin


title: N2, DMSO, rep3

value: whole animal


title: B_APIG3

description: PE150 high throughout data


title: N2, DMSO, rep5


title: BLEO2

description: PE150 high throughout data


title: N2, DMSO, rep2


title: CMK, JMJD1C