title: female healthy control, baseline_replicate 5

description: Library name: 2704sHF0

value: T0 (baseline)

value: female


title: Heart_3days_Coronary artery ligation_rep1

status: Public on Apr 30 2025

type: RNA

city: Zhanjiang

first: Fanji

last: Meng

address: 12# Minyou Road, Xiashan District

department: Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University

country: China

institute: Guangdong Medical University

description: tsRNA expression after 3days in coronary artery ligation-induced myocardial infarction in mouse

hyb_protocol: 22.5 uL 2X Hybridization buffer (Agilent) was mixed with the completed labeling reaction to a final volume of 45 uL. The mixture was heated at 100°C for 5 min and chilled immediately to 0°C. 45 uL labeled sample mix was hybridized onto a microarray at 55°C for 20 hrs. The slides were washed at room temperature in 6X SSC with 0.005% Triton X-102 for 10 min, then in 0.1X SSC with 0.005% Triton X-102 for 5 min. The slides were scanned on an Agilent G2505C microarray scanner.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies).After normalization, the probe signals having Present (P) or Marginal (M) QC flags in a certain proportion were retained. Multiple probes from the same small RNA (miRNA/TsRNA (tRF&tiRNA)/pre-miRNA/tRNA/snoRNA) were combined into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds. Hierarchical Clustering heatmaps, scatter plots and volcano plots were plotted to display small RNAs expression pattern among samples by R software.

molecule: total RNA

organism: Mus musculus

label_protocol: For Small RNA Microarray profiling, 100 ng total RNA was firstly dephosphorylated with 3 units T4 polynucleotide kinase (T4 PNK) at 37°C for 40 min to remove both (P) and (cP) chemical groups from the 3' end of RNAs to form a 3-OH end. The reaction was terminated at 70°C for 5 min and cooled immediately to 0°C. 7 uL of DMSO was added and heated to 100°C for 3 min to denature the RNAs and chilled immediately to 0°C. RNA end labeling was performed by adding ligase buffer, BSA, final 50 mM pCp-Cy3, and 15 units T4 RNA ligase in a 28 uL reaction at 16°C overnight.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis.

treatment_protocol: Mice were randomly divided into the sham group and the myocardial infraction (MI) group. Ligation of left anterior descending coronary artery was conducted in the MI group and myocardial ischemia was confirmed withe elevated ST-segment in electrocardiogram. However, string went through the corresponding myocardial region without ligation in the sham group. Finally, heart samples were collected from the infarction area in the MI group and the corresponding region in the sham group. Heart samples were refrigerated at −80°C for further detection.

tag: tissue

value: heart

tag: strain

tag: gender

value: male

tag: age

value: 6-8 weeks

tag: weight


title: Heart_3days_Sham_rep2

description: tsRNA expression after 3days in myocardium of sham mouse


title: WGBS_MbovP202_2

type: SRA

city: Wuhan

first: Doukun

last: Lu

address: Huazhong Agricultural University

institute: National Key Laboratory of Agricultural Microbiology

description: Library name: Sample5

library_source: genomic

data_processing:
We used FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads.
Bismark software (version 0.16.3) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail).
Methylated sites were identified with a binomial test using the methylated counts (mC), totols counts (mC+umC) and the non-conversion rate (r).
Differentially methylated regions (DMRs) were identified using the DSS software.
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/263/795/GCF_002263795.2_ARS-UCD1.3/GCF_002263795.2_ARS-UCD1.3_genomic.fna.gz
Supplementary files format and content: The cx-report.txt.gz file containing statistics for all C sites in each sample

molecule: genomic DNA

organism: Bos taurus

source_name: Bovine peritoneal macrophages

growth_protocol: The BoMac and BoMacMbovP202 cells were grown in RPIM 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
Cells DNA was extracted using the Universal Genomic DNA Extraction Kit from TaKaRa (Shanghai, China).
Accel-NGS® Methyl-Seq DNA Library Kit for illumina

value: Bovine peritoneal macrophages

tag: cell line

value: BoMacMbovP202 cells

tag: cell type

value: Macrophage cells

tag: genotype

value: stable monoclonal cell lines expressing MbovP202


title: female healthy control, baseline_replicate 4

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

country: USA

institute: Nova Southeastern University

description: Library name: 2692sHF0

library_source: transcriptomic

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2, and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Raw counts from HTSeq and STAR were imported into Bioconductor/R package DESeq2, normalized, and tested for differential gene expression. This analysis was done separately for the files produced by each aligner.
Only genes with raw counts equal or more than 50 in all samples in at least one group were used for the differential gene expression analysis
For further analysis, we selected genes and exons that were differentially expressed based on one of the following two criteria: (a) either a fold change (FC) > |1.5| and false discovery rate (FDR) < 0.10 in one out of the three aligners and FC > |1.4| and FDR < 0.15 in the remaining two aligners, OR (b) a FC > |1.5| and FDR < 0.10 in two out of three aligners.
Assembly: GRCh38, release 103
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 50 in all samples in at least one group

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center) according to the manufacturer’s instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent Technologies). All RNA samples had an RNA Integrity number (RIN) above seven.
The libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit

value: peripheral blood mononuclear cells

tag: disease state

value: healthy control

tag: time point_in_exercise

tag: Sex


title: RRBS of Deer Mouse Left Ventricle_wild9

city: Princeton

first: Dhriti

last: Tandon

state: New Jersey

address: 106A Guyot Hall

department: Ecology and Evolutionary Biology

institute: Princeton University

data_processing:
We prepared the reference Peromyscus genome (Pman_2.0) with bowtie2 in BS-Seeker2 for BS-converted reads that were bounded from 50-500bp.
We demultiplexed sequence pools by retaining reads that had a perfect sequence match to the expected barcode sequence tags with an in-house python script. We then trimmed FASTQ files to remove low quality reads (Q<20) and adapter sequences clipped using cutadapt 1.8.1, discarding reads that are <20bp in length.
Trimmed reads were mapped to the reference using the bs-seeker_2-align.py script in BS-Seeker2, which uses bowtie2 to align reads in reduced representation mode by using the -r flag. The lower (-L) and upper (-U) bounds of fragment length were set to 50 and 500, respectively.
To call methylation we used the bs_seeker2-call-methylation.py script in BS-Seeker2, with default settings and the -x flag that removes reads not fully converted by the bisulfite treatment.
Assembly: Pman_2.0
Supplementary files format and content: .CGmap files contain chromosome number in column 1, nucleotide on Watson (+) strand in column 2, position (in bp) in column 3, CpG context (CG/CHG/CHH) in column 4, dinucleotide-context (CA/CC/CG/CT) in column 5, methylation-level = #_of_C / (#_of_C + #_of_T) in column 6, number of C (methylated C, the count of reads showing C here) in column 7, and number of C + number of T (all Cytosines, the count of reads showing C or T here) in column 8. Description taken from https://github.com/BSSeeker/BSseeker2.

organism: Peromyscus maniculatus

source_name: Left Ventricle

growth_protocol: Lowland mice were derived from wild-caught individuals collected in eastern Nebraska (9 mile prairie; Lancaster County, Nebraska, USA; 40°52′ 12′′ N, 96°48′ 20.3′′ W; 430 m above sea level; standard pO2=20.2 kPa). We collected highland mice from the summit of Mt. Evans in the Rocky Mountains (Clear Creek County, Colorado, USA; 39°35′ 18′′ N, 105°38′ 38′′ W; 4,350 m above sea level; standard PO2=12.8 kPa) under permits from Colorado Parks and Wildlife (CO CWP 17TR2168a) and the United States Forest Service (Authorization ID: CLC772).

extract_protocol:
We extracted genomic DNA from left ventricle tissue following Qiagen DNeasy’s protocol (Qiagen). For RRBS, we digested high molecular weight genomic DNA with the Msp1 restriction enzyme. We prepared libraries following the NEBNext sample preparation kit protocol (New England Biolabs), with a spike-in of 1ng of enterobacteria phage DNA to each genomic library as a non-methylated internal control for estimating the efficiency of bisulfite (BS) conversion downstream.
We used AMPure beads for DNA purification and to retain fragments between 100-400bp in size. The resulting fragments were treated with BS to convert unmethylated cytosines following the low DNA input (1ng-2μg) protocol in the Qiagen EpiTect Fast Bisulfite Conversion kit (Qiagen). We then conducted low amplification of the converted DNA with 12 cycles of PCR to enrich for adapter-ligated fragments with MyTaq Mix (Bioline Inc.), during which each sample was also barcoded with unique sequence tags that permitted the pooling of final genomic libraries. We collected single-end (1x100nt) SP sequencing on an Illumina Novaseq6000 in Princeton University’s Lewis Sigler Genomics Core Facility.

treatment_protocol: We exposed 28 laboratory-born and reared highland and lowland deer mice to experimental hypobaric hypoxia to assess population specific methylation responses to hypoxia exposure. We collected data from 11 additional mice captured in lowland and highland habitats.

value: Left Ventricle

tag: population

value: Wild (Lowland habitat)

value: Female


title: 6 Control

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E. 3rd St. Bloomington, IN 47405

institute: Indiana University

description:
Library name: Sample_6
Illumina NovaSeq X

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment, and barcode processing , gene counting, and aggregation were made using Cellranger Multi Pipeline. (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi)
Assembly: Mouse mm10 Human GRC38
Supplementary files format and content: Tab seperated values files and matrix files

source_name: colon tumor

extract_protocol:
For sample preparation, 20-25 mg of fresh TP KO tumors (7 vehicle and 8 BRAFi+EGFRi) or 817 (3 vehicle and 3 BRAFi+EGFRi) were processed using the Tissue Fixation and Dissociation for Chromium Fixed RNA Profiling protocol (CG000553, 10X Genomics) and the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (1000414, 10X Genomics).
Gene expression libraries were prepared at the Indiana University School of Medicine (IUSM) Center for Medical Genomics using the Chromium Fixed RNA Kit, Mouse Transcriptome (1000497, 10x Genomics), in accordance with the user guide (Chromium Fixed RNA Profiling, CG000527- RevD). Briefly, 8,000 cells per sample were targeted for Gel-Beads-in-Emulsion (GEMs) formation after hybridization and pooling equally. The final library was generated and then sequenced using an Illumina NovaSeq X plus with approximately 2500 million reads.

value: colon tumor

value: 817 Organoids

value: Tumor Epithelial Cells

tag: treatment

value: Vehicle


title: WGBS_MbovP202_1

description: Library name: Sample4


title: female healthy control, baseline_replicate 3

description: Library name: 2680sHF0

value: T0 (baseline)

value: female


title: 5 Inhibitor

description:
Library name: Sample_5
Illumina NovaSeq X

value: Encorafenib+Gefitinib


title: 4 Control

description:
Library name: Sample_4
Illumina NovaSeq X


title: RRBS of Deer Mouse Left Ventricle_wild8

value: Wild (Highland habitat)

value: Male


title: RRBS of Deer Mouse Left Ventricle:Highland_hypoxia1

value: Highland

tag: condition

value: Hypoxia


title: WGBS_Control_2

description: Library name: Sample2

value: Bovine peritoneal macrophages

value: BoMac cells

value: Macrophage cells

value: empty vector control


title: RRBS of Deer Mouse Left Ventricle_wild7

value: Left Ventricle


title: female healthy control, baseline_replicate 2

description: Library name: 2656sHF0

value: peripheral blood mononuclear cells

value: healthy control


title: female healthy control, baseline_replicate 7

description: Library name: 2728sHF0


title: WGBS_Control_1

description: Library name: Sample1


title: 22Rv1 cells, BSJ-5-63-NC, replicate-2

city: Boston

first: Li

last: Jia

state: Massachusetts

address: 20 Shattuck Street, Thorn 1529

department: Urology

institute: Brigham and Women's Hospital

data_processing:
Raw RNA-seq reads are aligned to the human genome version hg38 by using STAR aligner.
Gene counts are quantified using HT-seq with REFSEQ annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: 22Rv1 cells were maintained in RPMI medium 1640 supplemented with 10% FBS (Sigma, Cat. F0926) and 1% penicillin-streptomycin solution (Gibco, Cat. 15140122) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit according to the manufacturer's protocol.
RNA-seq library preparaion and next-generation sequencing by Illumina HiSeq were conducte through GENEWIZ services.

treatment_protocol: 22Rv1 cells were treated with DMSO, BSJ-5-63 (100 nM), or BSJ-5-63-NC (100 nM) for 8 hours.

value: prostate cancer cells

value: WT


title: 3 Treated

description:
Library name: Sample_3
Illumina NovaSeq X

value: colon tumor

value: 817 Organoids

value: Tumor Epithelial Cells


title: PA14rpoS-STOP_R3

city: Monterrey

first: Luis

middle: Mauricio

last: Salazar-García

address: Av. Eugenio Garza Sada 2501 Sur

country: Mexico

institute: Tecnológico de Monterrey

description:
Library name: RpoS 3
Replicate 3

data_processing:
Reads were trimmed with fastp (v0.23.2).
Alignment was performed using HISAT2.
Quantification using featureCounts (v2.0.3).
Differential expression analysis was carried out using DESeq2 (v1.40.1).
Assembly: ASM1462v1
Supplementary files format and content: Raw data were processed using Fastp for quality trimming. Further downstream analysis will be published separately.

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: P. aeruginosa PA14 and its rpoS-STOP mutant were grown in LB broth at 37 °C, 200 rpm.

extract_protocol:
RNA was extracted from mid-log phase cells (8 h) using the Jena Bioscience Total RNA Purification Kit (PP-210S).
The RNA-seq libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Kit following manufacturer´s instructions.

value: bacteria

value: STOP codon (Q157*) in rpoS

value: Extraction from mid-log phase

tag: time


title: 2 Treated

description:
Library name: Sample_2
Illumina NovaSeq X

value: Encorafenib+Gefitinib


title: RRBS of Deer Mouse Left Ventricle_wild5

value: Wild (Lowland habitat)

value: Female


title: PA14rpoS-STOP_R2

description:
Library name: RpoS 2
Replicate 2


title: RRBS of Deer Mouse Left Ventricle_wild4

value: Wild (Highland habitat)


title: 22Rv1 cells, BSJ-5-63-NC, replicate-1


title: 22Rv1 cells, BSJ-5-63, replicate-2


title: 1 Treated

description:
Library name: Sample_1
Illumina NovaSeq X


title: 22Rv1 cells, BSJ-5-63, replicate-1


title: RRBS of Deer Mouse Left Ventricle_wild3

value: Male


title: PA14rpoS-STOP_R1

description:
Library name: RpoS 1
Replicate 1


title: No Template Control

city: Seattle

first: Shreeram

last: Akilesh

state: WA

address: 1959 NE Pacific St, Box 356100

department: Laboratory Medicine and Pathology

institute: University of Washington

library_source: other

data_processing:
Illumina BaseSpace FASTQ Generation
Nanostring GeoMx NGS Pipeline Version 2.0.21
Assembly: Not applicable, sequences mapped to Nanostring directory of probe-gene associations
Supplementary files format and content: .dcc, digital count files for input into GeoMx DSP. Each .dcc file represents counts from one region of interest (ROI)
Supplementary files format and content: A .png overview of the entire slide with ROI outlines and numbers
Library strategy: Spatial Transcriptomics

molecule: other

organism: blank sample

source_name: blank sample

extract_protocol:
Nanostring pretreatment for GeoMx DSP = HIER + proteinase K 1µg/ml
Nanostring GeoMx DSP SeqCode H
Nanostring GeoMx DSP readout (2x27bp with standard 8bp indexes)

value: blank sample

tag: donor

value: Not applicable

tag: geomx dsp_probe_set

value: Human NGS Whole Transcriptome Atlas RNA_1.0

tag: disease

tag: slide number

tag: roi histology


title: RRBS of Deer Mouse Left Ventricle_wild2

tag: tissue

value: Left Ventricle


title: PA14WT_R1

description:
Library name: WT 1
Replicate 1

tag: strain


title: RRBS of Deer Mouse Left Ventricle_wild1


title: 22Rv1 cells, DMSO, replicate-1

tag: cell line

value: prostate cancer cells

value: DMSO


title: human kidney tissues

hyb_protocol: NanoString 1000-plex ISH probes were denatured by incubation at 95°C for 2 min and immediately placed on ice. The 1000-plex probe mix was applied onto the tissue section within the incubation frame. The chamber was sealed and hybridization was performed at 37°C overnight. The following day, the tissue section was rinsed with  were rinsed of excess probes in 2X SSCT for 1 min and were washed twice in 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min at room temperature, and blocked with 100 mM NHS-acetate in the dark for 15 min. In preparation for loading onto the CosMx SMI instrument, a flow cell coverslip was applied to the slide and secured using the Nanostring's flowcell compression apparatus. A secure seal was verified by infusing 2X SSCT into one flowcell port which resulted in flushing out of bubbles and buffer exit at the flowcell port on the opposite end.

scan_protocol: After loading onto the CosMx SMI instrument, a preview scan of the entire flow cell was taken. In the scanning phase, the tissue was labeled with antibodies reactive for pan-cytokeratin, CD45 and cell membranes (cocktail of anti-b2 microglobulin and anti-CD298 antibodies) in order to outline tissue morphology. 205 fields of view (FOVs) in total were placed over all 5 tissue patches on the slide. RNA readout was performed by cycles of a) flowing in fluorescent reporter probes b) washing unbound probes c) imaging each FOV d) removing reporter probes with UV illumination and stripping buffer. 16 rounds of reporter hybridization-imaging are performed and each gene target is encoded by a particular sequence of fluorescent reporters that is generated through these imaging cycles.

data_processing: After run completion, the data were automatically pushed to the Nanostring AtoMx cloud-based storage and analysis platform, where cell segmentation, assignment of transcripts to cells and initial calculation of spatial neighborhoods was performed using default parameters. Semi-supervised cell typing was performed using AtoMx’s InSituType module. We used the Kidney Precision Medicine Project (KPMP) normal kidney reference dataset as input and permitted up to 3 unknown cell type assignments in order to account for tumor cell types not represented in KPMP. Neighborhoods/spatial niches, top marker genes for cell types and cell-cell proximity analysis were also computed using AtoMx’s in built analysis modules. UMAPs and spatial projections of cell type assignments and neighborhoods were generated from the Seurat object in R. Exported processed files required for offline analysis included -polygons.csv, -exprMat_file.csv, -fov_positions_file.csv, -metadata_file.csv, and the -tx_file.csv. The AtoMx portal also exported a full Seurat object (_fullobject.rds).

source_name: human kidney tissues

label_protocol: After digestion, the tissue section was then washed with DEPC water and incubated with 1:2000 dilution of fiducial beads in 2X SSC with 0.001% Tween-20. The tissue was incubated with the fiducials for 5 minutes in the dark. After rinsing off excess fiducials with Tris-glycine buffer and 1x PBS, the tissue was blocked with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate) for 15 minutes at room temperature. After rinsing with 2X SSC, an adhesive incubation frame was applied around the tissue sections.

growth_protocol: Not applicable

extract_protocol: Briefly, a 5µm section was mounted on a charged slide and baked overnight at 60°C. Following deparaffinization, the tissue was subjected to heat-induced epitope retrieval at 100°C for 15 minutes using ER1 epitope retrieval buffer (Tris/EDTA, pH 9.0). The slide was rinsed in DEPC water, dipped in 100% EtOH and then air dried for an hour. After application of an incubation frame around the sample, the tissue was digested with Nanostring's proprietary digestion buffer for 30 minutes at 40°C.

treatment_protocol: Not applicable

value: kidney tumor


title: PA14WT_R2

description:
Library name: WT 2
Replicate 2

tag: cell type

value: WT


title: RNA-seq of Solanum lycopersicum root, infected with Phytophthora cinnamomi, 7 dpi, replicate 3

status: Public on Apr 29 2025

city: Madrid

first: Marta

last: Berrocal-Lobo

state: Madrid

address: Antonio Nováis 10, s/n

department: System and Natural Resources

country: Spain

institute: School of Forestry Engineering and Natural Resources

description:
Library name: Pcinn_7dpi_rep3
Root sample from Marmande tomato, infected with Phytophthora cinnamomi, 7 dpi, replicate 3

data_processing:
Real Time Analysis software (RTA) used for basecalling.
PCR duplicates are removed using Cutadapt software.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
Know genes and transcripts are assembled with StringTie with aligned reads based on reference genome model (SL2.50).
Read count is calculated using featureCounts function from Bioconductor
Assembly: SGN release version SL2.50
Supplementary files format and content: Matrix table with raw gene reads counts for every gene and every sample

organism: Solanum lycopersicum

source_name: root

growth_protocol: Hydroponic culture

extract_protocol:
Tissue was harvested using liquid nitrogen and RNA using NZytech kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tomato four day old seedlings were inoculated with Phytophthora cinnamomi zoospores stock (10exp7 zoospores per ml), or water controls, data were collected after three and seven days

value: root

value: mixed root cells

tag: cultivar

value: Marmande

value: mock

tag: batch


title: RNA-seq of Solanum lycopersicum root, infected with Phytophthora cinnamomi, 7 dpi, replicate 2

description:
Library name: Pcinn_7dpi_rep2
Root sample from Marmande tomato, infected with Phytophthora cinnamomi, 7 dpi, replicate 2


title: RNA-seq of Solanum lycopersicum root, infected with Phytophthora cinnamomi, 7 dpi, replicate 1

description:
Library name: Pcinn_7dpi_rep1
Root sample from Marmande tomato, infected with Phytophthora cinnamomi, 7 dpi, replicate 1


title: PA14WT_R3

description:
Library name: WT 3
Replicate 3

value: bacteria

tag: genotype

value: Extraction from mid-log phase


title: RNA-seq of Solanum lycopersicum root, infected with Phytophthora cinnamomi, 3 dpi, replicate 2

description:
Library name: Pcinn_3dpi_rep2
Root sample from Marmande tomato, infected with Phytophthora cinnamomi, 3 dpi, replicate 2


title: RNA-seq of Solanum lycopersicum root, infected with Phytophthora cinnamomi, 3 dpi, replicate 1

description:
Library name: Pcinn_3dpi_rep1
Root sample from Marmande tomato, infected with Phytophthora cinnamomi, 3 dpi, replicate 1


title: 22Rv1 cells, DMSO, replicate-2


title: RNA-seq of Solanum lycopersicum root, mock-inoculated, 7 dpi, rep 3

description:
Library name: Mock_7dpi_rep3
Root sample from Marmande tomato, mock-inoculated, 7 dpi, replicate 3


title: RNA-seq of Solanum lycopersicum root, infected with Phytophthora cinnamomi, 3 dpi, replicate 3

description:
Library name: Pcinn_3dpi_rep3
Root sample from Marmande tomato, infected with Phytophthora cinnamomi, 3 dpi, replicate 3


title: RRBS of Deer Mouse Left Ventricle_wild6

value: Wild (Lowland habitat)

tag: Sex


title: RNA-seq of Solanum lycopersicum root, mock-inoculated, 7 dpi, rep 2

description:
Library name: Mock_7dpi_rep2
Root sample from Marmande tomato, mock-inoculated, 7 dpi, replicate 2


title: RNA-seq of Solanum lycopersicum root, mock-inoculated, 3 dpi, rep 2

description:
Library name: Mock_3dpi_rep2
Root sample from Marmande tomato, mock-inoculated, 3 dpi, replicate 2


title: RNA-seq of Solanum lycopersicum root, mock-inoculated, 3 dpi, rep 3

description:
Library name: Mock_3dpi_rep3
Root sample from Marmande tomato, mock-inoculated, 3 dpi, replicate 3


title: RNA-seq of Solanum lycopersicum root, mock-inoculated, 3 dpi, rep 1

description:
Library name: Mock_3dpi_rep1
Root sample from Marmande tomato, mock-inoculated, 3 dpi, replicate 1


title: No Template Control

data_processing:
Illumina BaseSpace FASTQ Generation
Nanostring GeoMx NGS Pipeline Version 2.0.21
Assembly: Not applicable, sequences mapped to Nanostring directory of probe-gene associations
Supplementary files format and content: .dcc, digital count files for input into GeoMx DSP. Each .dcc file represents counts from one region of interest (ROI)
Supplementary files format and content: A .png overview of the each slide with overlaid ROI outlines and numbers
Library strategy: Spatial Transcriptomics

tag: donor id

value: Human NGS Cancer Transcriptome Atlas RNA_1.0

tag: acquisition day


title: LNCaP_EnzR_NC_Rep1

city: Guangzhou

first: Yifan

last: Zhang

state: Guangdong

address: Department of Urology,Nanfang Hospital,Southern Medical University,Guangzhou,Guangdong,China

description:
Library name: sample6
Column name in LpR_siUHRF1_counts.txt: NC.1_count

data_processing:
RNA-seq reads were mapped to the human reference genome (hg38) human genome assembly using HISAT2 (v2.0.5) with default parameters.
Featurecounts (v1.5.0-p3) was used for counting the read numbers.
Assembly: hg38
Supplementary files format and content: tab-deliminated files include raw gene counts

source_name: LNCaP

growth_protocol: LNCaP, C4-2 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was prepared using TRIzol reagent (Life Technologies) following manufacturer’s protocol
Library preparations were performed using the NEBNext Ultra RNA Library Prep Kit for illumina following manufacturer’s protocol

treatment_protocol: LNCaP or C4-2 cells were initially cultured in media containing 5 µM enzalutamide, and the drug concentration in living cells was increased by 5uM after every 10 passages until the drug concentration reached 40uM and passaged 10 times.

value: LNCaP

value: prostate cancer cell line

tag: treatment

value: LNCaP cells were cultured in increasing concentrations of enzalutamide until the drug concentration reached 40 μM and passaged 10 times. Transfection with siNC.


title: LNCaP_EnzR_NC_Rep3

institute: Department of Urology,Nanfang Hospital,Southern Medical University

description:
Library name: sample8
Column name in LpR_siUHRF1_counts.txt: NC.3_count


title: LNCaP_EnzR_NC_Rep2

description:
Library name: sample7
Column name in LpR_siUHRF1_counts.txt: NC.2_count


title: LNCaP_EnzR_siUHRF1_Rep3

description:
Library name: sample11
Column name in LpR_siUHRF1_counts.txt: siUHRF1.3_count

value: LNCaP cells were cultured in increasing concentrations of enzalutamide until the drug concentration reached 40 μM and passaged 10 times. Transfection with siUHRF1.


title: LNCaP_EnzR_siUHRF1_Rep1

description:
Library name: sample9
Column name in LpR_siUHRF1_counts.txt: siUHRF1.1_count


title: LNCaP_EnzR40_NC_Rep1

description:
Library name: sample4
Column name in EnzR_gene_count.txt: LN_NC1

value: LNCaP cells were initially cultured in media containing 5 µM enzalutamide, and the drug concentration in living cells was increased by 5uM after every 10 passages until the drug concentration reached 40uM and passaged 10 times.


title: LNCaP_EnzR40_NC_Rep2

description:
Library name: sample5
Column name in EnzR_gene_count.txt: LN_NC2


title: C4-2_EnzR40_NC_Rep2

description:
Library name: sample2
Column name in EnzR_gene_count.txt: C4_NC2

value: C4-2 cells were initially cultured in media containing 5 µM enzalutamide, and the drug concentration in living cells was increased by 5uM after every 10 passages until the drug concentration reached 40uM and passaged 10 times.


title: C4-2_EnzR40_NC_Rep1

description:
Library name: sample1
Column name in EnzR_gene_count.txt: C4_NC1


title: LNCaP_EnzR_siUHRF1_Rep2

description:
Library name: sample10
Column name in LpR_siUHRF1_counts.txt: siUHRF1.2_count


title: LNCaP_EnzR5

description:
Library name: sample3
Column name in LNCaP_R5_gene_count.txt: LNCaP_EnzR5

value: LNCaP cells were initially cultured in media containing 5 µM enzalutamide after 10 passages


title: GES-1 cells, H. pylori, replicate 2

city: Changsha

first: Minglin

state: China

address: tongzipo road

department: Department of Gastroenterology

institute: The Third Xiangya Hospital, Central South University

description: Library name: GOE11

data_processing:
Libraries were deeply sequenced on the Illumina Novaseq 6000 according to the activity and expected data volume.
The raw RNA-Seq sequence reads were trimmed using Trimmomatic (version 0.39) to remove low-quality reads and adapters.
Assembly: Trimmed data were first evaluated by the software “FastQC” (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with the default parameter and then aligned with Hisat2 (version 2.1.0) against the human (hg38) genome guided by GENCODE gene annotation (version 34) with the default parameter.
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

growth_protocol: RPMI-1640 mediu mcontaining 10% fetal bovine serum

extract_protocol:
Total RNA was isolated using RNAiso Plus (Total RNA extraction reagent, Thermo Fisher Scientific) according to the manufacturer’s instructions and quantified by the NanoDrop 2000 spectrophotometer.
TruSeq Stranded Total Sample Preparation Kit (Illumina, 20020596) was used for sequencing library construction.

value: gastric epithelial cells

value: H. pylori

value: subculture


title: GES-1 cells, H. pylori, replicate 1

description: Library name: GOE10


title: GES-1 cells, H. pylori, replicate 3

description: Library name: GOE12


title: GES-1 cells, Control, replicate 3

description:
Library name: NC12
Column name in gene_count_matrix.txt: NC12

value: Control


title: GES-1 cells, Control, replicate 1

description:
Library name: NC10
Column name in gene_count_matrix.txt: NC10


title: MKN45 cells, H. pylori, replicate 2

description: Library name: MOE8


title: MKN45 cells, H. pylori, replicate 1

description: Library name: MOE7


title: MKN45 cells, H. pylori, replicate 3

description: Library name: MOE9


title: MKN45 cells, Control, replicate 2

description:
Library name: NC8
Column name in gene_count_matrix.txt: NC8


title: MKN45 cells, Control, replicate 3

description:
Library name: NC9
Column name in gene_count_matrix.txt: NC9


title: MKN45 cells, Control, replicate 1

description:
Library name: NC7
Column name in gene_count_matrix.txt: NC7


title: AGS cells, H. pylori, replicate 3

description: Library name: AOE6

source_name: AGS

value: AGS


title: RNA-seq of Solanum lycopersicum root, mock-inoculated, 7 dpi, rep 1

description:
Library name: Mock_7dpi_rep1
Root sample from Marmande tomato, mock-inoculated, 7 dpi, replicate 1

value: root

value: mixed root cells

value: Marmande

value: mock


title: AGS cells, H. pylori, replicate 2

description: Library name: AOE5


title: AGS cells, H. pylori, replicate 1

description: Library name: AOE4


title: AGS cells, Control, replicate 3

description:
Library name: NC6
Column name in gene_count_matrix.txt: NC6


title: AGS cells, Control, replicate 2

description:
Library name: NC5
Column name in gene_count_matrix.txt: NC5


title: AGS cells, Control, replicate 1

description:
Library name: NC4
Column name in gene_count_matrix.txt: NC4


title: GES-1 cells, Control, replicate 2

description:
Library name: NC11
Column name in gene_count_matrix.txt: NC11


title: HGC27 cells, Control, replicate 1

description:
Library name: NC1
Column name in gene_count_matrix.txt: NC1


title: HGC27 cells, H. pylori, replicate 3

description: Library name: HOE3


title: HGC27 cells, H. pylori, replicate 2

description: Library name: HOE2


title: Ectocervix, Fibroblasts, 7, E2, chip, rep4

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description:
Library name: sample_2301_8_F
Column name in raw_counts_all_samples.csv: sample_2301_8_F

data_processing:
FASTQ files were processed using the nf-core-rnaseq pipeline (v3.12.0) (auto strandedness).
Adapter sequences were removed withTrim Galore.
Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.
Downstream analysis was performed using Pluto Bio software (https://pluto.bio).
Assembly: GRCh38
Supplementary files format and content: CSV file includes raw counts for each sample

molecule: polyA RNA

source_name: Ectocervix

growth_protocol: Endocervix and Ectocervix specimens were anonymously collected from patients undergoing hysterectomy for benign conditions (uterine fibroids, endometriosis, menorrhagia) at the Massachusetts General Hospital under IRB-approved protocol #2015P001859 or obtained from organ donors through the organ donor program at IIAM. Chips were cultured using differentiation medium that contained estradiol (E2) in the basal channel and perfused (intermittent flow) with HBSS+/+ in the apical channel.

extract_protocol:
Cells were harvested from apical and basal channels of the Cervix chips using Buffer RLT plus (Qiagen, 1053393). Lysates were stored at –80 °C prior to processing.
Total RNA was submitted to Genewiz (Azenta Life Sciences) for next generation sequencing (Standard RNA-seq, polyA selection with ERCC spike-in, sequencing using an Illumina HiSeq for 2x150bp, ~350M PE reads, single index).

value: Ectocervix

value: Fibroblasts

tag: condition

value: Control (no added hormones)

tag: drug

tag: chip tissue

value: chip

tag: patient id

tag: patient age_(years)

tag: patient condition

value: Fibroids

tag: patient sex

value: Female

tag: patient ethnicity

value: African


title: Ectocervix, Epithelial, 7, E2, chip, rep3

description:
Library name: sample_2301_7
Column name in raw_counts_all_samples.csv: sample_2301_7

tag: tissue

value: Epithelial


title: Ectocervix, Epithelial, 7, E2, chip, rep1

description:
Library name: sample_2301_5
Column name in raw_counts_all_samples.csv: sample_2301_5

tag: cell type


title: Endocervix, Epithelial, 7, E2, chip, rep4

description:
Library name: sample_2301_4
Column name in raw_counts_all_samples.csv: sample_2301_4

source_name: Endocervix

value: Endocervix


title: HGC27 cells, Control, replicate 2

description:
Library name: NC2
Column name in gene_count_matrix.txt: NC2

tag: cell line

value: gastric epithelial cells


title: HGC27 cells, Control, replicate 3

description:
Library name: NC3
Column name in gene_count_matrix.txt: NC3

value: subculture


title: HGC27 cells, H. pylori, replicate 1

description: Library name: HOE1

value: H. pylori


title: Ectocervix, Epithelial, 7, E2, chip, rep4

description:
Library name: sample_2301_8
Column name in raw_counts_all_samples.csv: sample_2301_8


title: Ectocervix, Epithelial, 7, E2, chip, rep2

description:
Library name: sample_2301_6
Column name in raw_counts_all_samples.csv: sample_2301_6


title: Ectocervix, Fibroblasts, 7, E2, chip, rep3

description:
Library name: sample_2301_7_F
Column name in raw_counts_all_samples.csv: sample_2301_7_F


title: Endocervix, Epithelial, 7, E2, chip, rep2

description:
Library name: sample_2301_2
Column name in raw_counts_all_samples.csv: sample_2301_2


title: Endocervix, Fibroblasts, 7, E2, chip, rep3

description:
Library name: sample_2301_3_F
Column name in raw_counts_all_samples.csv: sample_2301_3_F


title: Endocervix, Fibroblasts, 7, E2, chip, rep2

description:
Library name: sample_2301_2_F
Column name in raw_counts_all_samples.csv: sample_2301_2_F


title: Endocervix, Fibroblasts, E, E2, chip, rep3

description:
Library name: sample_23_6_19_b
Column name in raw_counts_all_samples.csv: sample_23_6_19_b

value: E

value: Mixed


title: Endocervix, Epithelial, 7, E2, chip, rep3

description:
Library name: sample_2301_3
Column name in raw_counts_all_samples.csv: sample_2301_3


title: Endocervix, Epithelial, E, E2, chip, rep3

description:
Library name: sample_23_6_19_a
Column name in raw_counts_all_samples.csv: sample_23_6_19_a


title: Endocervix, Fibroblasts, E, E2, chip, rep2

description:
Library name: sample_23_6_18_b
Column name in raw_counts_all_samples.csv: sample_23_6_18_b


title: Endocervix, Epithelial, E, E2, chip, rep2

description:
Library name: sample_23_6_18_a
Column name in raw_counts_all_samples.csv: sample_23_6_18_a


title: Ectocervix, Fibroblasts, 7, E2, chip, rep1

description:
Library name: sample_2301_5_F
Column name in raw_counts_all_samples.csv: sample_2301_5_F


title: Endocervix, Fibroblasts, E, E2, chip, rep1

description:
Library name: sample_23_6_17_b
Column name in raw_counts_all_samples.csv: sample_23_6_17_b


title: Endocervix, Epithelial, 7, E2, chip, rep1

description:
Library name: sample_2301_1
Column name in raw_counts_all_samples.csv: sample_2301_1


title: Endocervix, Epithelial, E, E2, chip, rep1

description:
Library name: sample_23_6_17_a
Column name in raw_counts_all_samples.csv: sample_23_6_17_a


title: Endocervix, Fibroblasts, A, E2, chip, rep3

description:
Library name: sample_23_6_06_b
Column name in raw_counts_all_samples.csv: sample_23_6_06_b

value: A

value: Abnormal uterine bleeding

value: Hispanic


title: Ectocervix, Fibroblasts, 7, E2, chip, rep2

description:
Library name: sample_2301_6_F
Column name in raw_counts_all_samples.csv: sample_2301_6_F

value: Ectocervix


title: Endocervix, Epithelial, A, E2, chip, rep2

description:
Library name: sample_23_6_05_a
Column name in raw_counts_all_samples.csv: sample_23_6_05_a


title: Endocervix, Epithelial, A, E2, chip, rep3

description:
Library name: sample_23_6_06_a
Column name in raw_counts_all_samples.csv: sample_23_6_06_a


title: Endocervix, Fibroblasts, A, E2, chip, rep1

description:
Library name: sample_23_6_04_b
Column name in raw_counts_all_samples.csv: sample_23_6_04_b

value: Fibroblasts


title: Endocervix, Fibroblasts, A, E2, chip, rep2

description:
Library name: sample_23_6_05_b
Column name in raw_counts_all_samples.csv: sample_23_6_05_b

value: Control (no added hormones)


title: Endocervix, Fibroblasts, 7, E2, chip, rep4

description:
Library name: sample_2301_4_F
Column name in raw_counts_all_samples.csv: sample_2301_4_F

value: chip


title: Endocervix, Epithelial, A, E2, chip, rep1

description:
Library name: sample_23_6_04_a
Column name in raw_counts_all_samples.csv: sample_23_6_04_a


title: Endocervix, Fibroblasts, 7, E2, chip, rep1

description:
Library name: sample_2301_1_F
Column name in raw_counts_all_samples.csv: sample_2301_1_F

value: Fibroids


title: On-CAR-T chip

city: Brooklyn

first: Weiqiang

last: Chen

state: New York

address: 6 MetroTech Center

institute: New York University

description:
Library name: Sample 1
Hashtag 1: GTCAACTCTTTAGCG, Leukemia chip treated with Healthy donor derived CAR T cells;
Hashtag 2: TGATGGCCTATTGGG, Leukemia chip treated with Patient derived CAR T cells;
Hashtag 3: TTCCGCCTCTCTTTG, Leukemia chip treated with Healthy donor derived Mock T cells;
Hashtag 4: AGTAAGTTCAGCGTA, Leukemia chip treated without treatment

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software.
Hashtag oligo (HTO) counts were quantified using CITE-seq-count.
HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells and demultiplexed using the HTODemux function in Seurat.
Assembly: hg38/GRCh38
Supplementary files format and content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

source_name: Cells on CAR-T chip

growth_protocol: The bioengineered leukemia bone marrow niche samples (designated as leukemia chip)as reported. The leukemia chips were cultured a mixture of SFEM-II (STEMCELL Technologies), EGM-2, RMPI1640 at a ratio of 1:2:1 and supplement with a cytokine cocktail [Thrombopoietin (TPO, Cat#300-18, Peprotech), Interleukin-6 (IL-6, Cat#200-06, Peprotech), Interleukin-3 (IL-3,Cat#200-03, Peprotech), FMS-like tyrosine kinase 3 ligand (Flt3-L, Cat#300-19, Peprotech) and Stem cell factor (SCF, Cat#300-07, Peprotech), all at 12.5 ng/mL] and recombinant human VEGF-165/VEGFA (Cat#230-00012-10, RayBiotech) at 10 ng/mL.

extract_protocol:
The leukemia samples (designated as HD CAR, PD CAR, Mock, None) were engineered and cultured on-chip for 7 days as described above followed by 2-day treatment with CAR T cell, PD CAR T cell, Mock T cell or left untreated. Single‐cell suspensions of leukemia samples were prepared by off-chip recovery with nattokinase, pre-labeled with different anti-human hashtag antibodies (TotalSeq, BioLegend), i.e., Hashtag1-GTCAACTCTTTAGCG, Cat#394601; Hashtag2-TGATGGCCTATTGGG, Cat#394603, Hashtag3-TTCCGCCTCTCTTTG, Cat#394605, Hashtag4-AGTAAGTTCAGCGTA, Cat#394607, and mixed into one sample. Correspondingly, freshly thawed HD CAR T cell, PD CAR T cell, Mock T cell, and bone marrow mononuclear cells were pre-labeled with different anti-human hashtag antibodies, mixed into one sample, and used controls. The libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3): Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075), Single Cell 3′ Chip Kit v3 (PN-1000073) and i7 Multiplex Kit (PN-120262) (10x Genomics) and following the Single Cell 3′ Reagent Kits (v3) User Guide (manual part no. CG000183 Rev B). Libraries were then run on an Illumina NovaSeq 6000 using 28bp read 1, 8bp i7 index, and 91bp read 2.  The raw sequencing results from the 10x Genomics platform were processed using CellRanger (version 3.1). In brief, CellRanger was used to generate a count matrix by aligning output reads, filtering the empty dropouts, and counting unique molecular identifiers (UMIs). We used Ensemble hg38/GRCh38 as the reference genome for read alignment. Further analyses including quality control and data filtering, the identification of highly variable genes, dimensionality reduction, standard unsupervised clustering algorithms, and the discovery of differentially expressed genes were performed using the R package Seurat (version 4.1.1)
Single Cell 3’ Reagent Kits: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000075; Single Cell 3’ Chip Kit v3 PN-1000073 and i7 Multiplex Kit PN-120262 (10x Genomics). Samples were tagged with cell hashing oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions.

value: Cells on CAR-T chip


title: Off-CAR-T chip

description:
Library name: Sample 2
Hashtag 1: GTCAACTCTTTAGCG, Healthy donor derived CAR T cells;
Hashtag 2: TGATGGCCTATTGGG, Patient derived CAR T cells;
Hashtag 3: TTCCGCCTCTCTTTG, Healthy donor derived Mock T cells;
Hashtag 4: AGTAAGTTCAGCGTA, Human bone marrow mononucelar cells

source_name: Cells off CAR-T chip

value: Cells off CAR-T chip


title: Ileal organoids, differentiation control

city: Basel

first: Gray

last: Camp

address: Grenzacherstraße 183

department: Institute of Human Biology

country: Germany

institute: Roche Pharma Research and Early Development

description:
Library name: IHBDECO082_001_ctr_2_3
Single-cell RNA sequencing (10xGenomics Chromium)

data_processing:
The STARsolo pipeline (https://doi.org/10.1101/2021.05.05.442755 ) was used to align to the GRCh38 genome and Ensembl 98 gene annotation.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: CellRanger output tab-delimited text file listing the barcodes appearing in the matrix.mtx filtered barcodes x features count matrix.
Supplementary files format and content: features.tsv.gz: CellRanger output tab-delimited text file listing the features appearing in the matrix.mtx filtered barcodes x features count matrix.
Supplementary files format and content: matrix.mtx.gz: CellRanger output matrix market file containing the filtered barcodes x features count matrix.

source_name: Ileal organoid

growth_protocol: Human intestinal tissue samples were obtained and experimental procedures performed within the framework of the non-profit foundation HTCR (Munich, Germany) including informed patient’s consent. Ileal organoids were derived and maintained according to previously published culture conditions (https://doi.org/10.1016/j.stem.2018.11.016).

extract_protocol:
After the indicated treatment durations, organoids were dissociated for single cell RNA sequencing using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec). First, culture medium was removed and organoids were incubated in Cell Recovery Solution (Corning) for 40 minutes at 4°C. Next, organoids were transferred to 1% BSA-coated tubes using HBSS-1% BSA buffer while pipetting thoroughly to fragmentize the organoids. Organoid fragments were centrifuged at 500g, 5 min, 4°C. Each cell pellet was resuspended in pre-warmed buffer X mixed with 25 μL of enzyme P. Cells were incubated for 15 minutes at 37°C combined with mechanical dissociation by pipetting every 5 minutes. Next, 5 μL of enzyme A in 10 μL buffer Y were added to the digest and incubated for a further 10 minutes combined with pipetting every 5 minutes. Cells were subsequently washed twice with HBSS-1% BSA buffer, and filtered through a 40 μm filter coated with 1% BSA. Single cells were counted using a Countess 3 FL Automated Cell Counter (Invitrogen) and kept on ice.
Dilutions of ~1000 cells/μL in 50 - 60 μL HBSS-1% BSA buffer were prepared and immediately processed using the 10x Chromium Next GEM Single Cell 3´ v3.1 Kit according to the manufacturer's instructions. Libraries were sequenced on Illumina’s NovaSeq6000.

treatment_protocol: For the cytokine treatments, organoids were dissociated into 5-10 cell fragments using TrypLE (Invitrogen) and reseeded in matrigel. After 6 days, organoids were treated for 6 days by supplementing the culture medium with 50 ng/mL TNFα and 200 ng/mL RANKL (Acro Biosystems) for TNF treatment or with 400 ng/mL IL-4 and 40 ng/mL IL-13 (Acro Biosystems) for IL13 and IL4 treatment. To model host cell responses to viral infection, organoids were treated for 1 day with 1 ng/mL IFNα, 1 ng/mL IFNγ (Acro Biosystems) and 5 ng/mL IFNβ (PeproTech)33. To model acute pathogenic inflammation, organoids were treated for 1 day with 10 ng/mL TNFα, 10 ng/mL IL-6, 500 ng/mL IL-17A, 1 ng/mL IFNγ (Acro Biosystems), 50 ng/mL IL-18, 100 ng/mL OSM (Biolegend), and 100 ng/mL SCF (MedChemExpress)34–36. After the indicated treatment durations, organoids were dissociated for single cell RNA sequencing using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) as described previously23. First, culture medium was removed and organoids were incubated in Cell Recovery Solution (Corning) for 40 minutes at 4°C. Next, organoids were transferred to 1% BSA-coated tubes using HBSS-1% BSA buffer while pipetting thoroughly to fragmentize the organoids. Organoid fragments were centrifuged at 500g, 5 min, 4°C. Each cell pellet was resuspended in pre-warmed buffer X mixed with 25 μL of enzyme P. Cells were incubated for 15 minutes at 37°C combined with mechanical dissociation by pipetting every 5 minutes. Next, 5 μL of enzyme A in 10 μL buffer Y were added to the digest and incubated for a further 10 minutes combined with pipetting every 5 minutes. Cells were subsequently washed twice with HBSS-1% BSA buffer, and filtered through a 40 μm filter coated with 1% BSA. Single cells were counted using a Countess 3 FL Automated Cell Counter (Invitrogen) and kept on ice. Dilutions of ~1000 cells/μL in 50 - 60 μL HBSS-1% BSA buffer were prepared and immediately processed using the 10x Chromium Next GEM Single Cell 3´ v3.1 Kit according to the manufacturer's instructions. Libraries were sequenced on Illumina’s NovaSeq6000.

value: Ileal organoid

value: Mixed ileal cell types

value: Control


title: Ileal organoids, added IL-4 and IL-13

description:
Library name: IHBDECO082_003_Tuft_cells
Single-cell RNA sequencing (10xGenomics Chromium)

value: IL-4 and IL-13


title: Ileal organoids, added TNFα + IL-6 + IL-17A + IFNγ + IL-18 + OSM + SCF, simulated inflammation

description:
Library name: IHBDECO082_005_inflammation
Single-cell RNA sequencing (10xGenomics Chromium)


title: Ileal organoids, added TNFα + RANKL

description:
Library name: IHBDECO082_002_M_cells
Single-cell RNA sequencing (10xGenomics Chromium)

value: TNFα + RANKL


title: MIA PaCa-2 si LINC01963-1 input

city: Beijing

first: Qixian

last: Liu

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus)

institute: Peking Union Medical College Hospital

description: Library name: MIA PaCa-2 si LINC01963-1 input

data_processing:
Quality control：Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11)[1]. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: ensembl_homo_sapiens_grch38_106
Supplementary files format and content: Excel (XLSX)  Differentially methylated peaks (DMPs) between siNC and siLINC01963 groups. Contains: - Peak coordinates (chr, start, end) - Log2 fold change (siLINC01963/siNC) - p-value, FDR (adjusted p-value) - Methylation level (IP/Input ratio) - Nearest gene annotations.

source_name: MIA PaCa-2

extract_protocol:
To determine the m6A levels of c-Myc mRNA, total RNA was extracted and fragmented using NEBNext® Magnesium RNA Fragmentation Module (NEB; Ipswich, MA, USA), followed by cleaning with Monarch® RNA Cleanup Kits (NEB). Then, short RNA fragments were removed and mRNA was fragmented into approximately 200 nt nucleotides. Methylated RNA immunoprecipitation (MeRIP) was performed according to the instructions of the EpiMark® N6-Methyladenosine Enrichment Kit (NEB). The co-precipitated RNA was converted to cDNA for sequencing library construction and sequenced on Illumina NovaSeq 6000 (Novogene; Beijing, China).
Library preparation: The mRNA m6A was sequenced by MeRIP-seq at Novogene (Beijing, China). Briefly, a total of 30 µg RNAs were extracted from treated cells. The integrity and concentration of extracted RNAs were detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare), respectively. Fragmented mRNA (~100 nt) was incubated for 2 hr at 4℃ with antim6A polyclonal antibody (Synaptic Systems) in the immunoprecipitation experiment. Then, immunoprecipitated mRNAs or Input was used for library construction with NEB Next® Ultra™ RNA Library Prep Kit (New England Biolabs). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols.

value: MIA PaCa-2

value: pancreatic cancer cell

value: LINC01963 knockdown

value: treated with siLINC01963 for 48h


title: MIA PaCa-2 si NC-2 input

description: Library name: MIA PaCa-2 si NC-2 input

value: WT

value: treated with siNC for 48h


title: MIA PaCa-2 si NC-1

description: Library name: MIA PaCa-2 si NC-1


title: MIA PaCa-2 si LINC01963-1

description: Library name: MIA PaCa-2 si LINC01963-1


title: MIA PaCa-2 si NC-2

description: Library name: MIA PaCa-2 si NC-2


title: MIA PaCa-2 si LINC01963-2

description: Library name: MIA PaCa-2 si LINC01963-2


title: MIA PaCa-2 si NC-1 input

description: Library name: MIA PaCa-2 si NC-1 input


title: MIA PaCa-2 si LINC01963-2 input

description: Library name: MIA PaCa-2 si LINC01963-2 input


title: cortical, HTT KO RUES2 cells, replicate 4

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

description:
Library name: HTTKO_4
Column name in CHDI_Cortical_Counts_Merged.csv: HTTKO_4

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence using Trimmomatic.
Reads were aligned using HISAT2 using an index created from Ensembl GRCh38 release 104.
Gene counts were quantified using featureCounts using the gtf annotation from the same reference as the alignment.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file including raw count data for all samples.

growth_protocol: Pluripotent cells were dissociated to single cells and replated in mTeSR1 plus rock inhibitor (RI) (Peprotech # 1293823) at a density of 4x106 cells in laminin (Biolamina #LN521) coated T25 flasks. T25 flasks were fed mTeSR1 for no more than 2 days until they reached >80% confluence at which point mTeSR was replaced with CM1o consisting of Base C media plus 10 µM SB 431542 (Stem Cell Technologies #17502048), 200nM LDN193189 (Stem Cell Technologies, #72147) and 5 µM Cyclopamine (Stem Cell Technologies #72074). Base C media consists of 0.5X DMEM/F12 (Thermo Fisher, #10565042), 0.5X Neuraobasal (Thermo Fisher #21103049), 0.5% N2 (Thermo Fisher # 17502048) and 1% B27(Thermo Fisher #17504-044). From this timepoint (day 0), the cells were fed daily with 10 ml of CM1 until day 8. At d8, cells were passaged 1:2 using cell scraping and gentile trituration onto Poly-ornithine (Sigma # P4957) and 20 ug/mL laminin (Sigma Aldrich #L2020) coated T25 flasks. The cells (at this stage, referred to as NPCs) were then fed everyday with CM2o composed Base C media plus 2.5ug/ml Insulin (Thermo Fisher #12585-014), 0.5% NEAA (Thermo Fisher #11140050), 5 uM Cyclopamine and 20ng/mL FGF-2 (Peprotech #100-18B). On d15, neural progenitors were dissociated using Accutase and banked in CryoStor CS10. Banked progenitors for all lines were thawed in parallel, one batch at a time (4 batches per line), onto Poly-ornithine/laminin 6 well plates at a density of 4x106 cells/well in CM3o comprised of Base media C plus 2.5ug/ml Insulin (Thermo Fisher #12585-014), 0.5% NEAA (Thermo Fisher #11140050) plus 2 uM Cyclopamine, 10 ng/ml BDNF (Peprotech #450-02), and 10 ng/ml GDNF (Peprotech # 450-10). ). At this point, the cells were considered early-stage cortical neurons (es-CNs) and were fed every day for 6 days. At d21, cells were dissociated using Accutase and replated for final maturation onto Poly-D-lysine (Sigma Aldrich #P6407) coated 12 well plates, at a density of 2-2.5 x106 cells per well. D21 eCNs were fed every other day for 2 weeks in CM4o comprised of CM3o supplemented with 10 µM DAPT, 20 ng/mL BDNF, and 20 ng/mL GDNF. At day35, eCNs were washed 3x with PBS (Thermo Fisher # 10010023), harvested using a cell scraper, and centrifuged to pellet.

extract_protocol:
RNA was extracted using Rneasy mini extraction kit (QIAGEN) and 250 ng of RNA was used for library preparation
Library construction was performed using TruSeq RNA stranded kit with rRNA reduction (RiboZero)

value: differentiatied cortical neuron

value: HTT KO


title: Ileal organoids, added IFNα + IFNγ and IFNβ, simulated viral response

description:
Library name: IHBDECO082_004_viral
Single-cell RNA sequencing (10xGenomics Chromium)

value: IFNα + IFNγ and IFNβ


title: cortical, HTT KO RUES2 cells, replicate 3

description:
Library name: HTTKO_3
Column name in CHDI_Cortical_Counts_Merged.csv: HTTKO_3


title: cortical, 56CAG RUES2 cells, replicate 3

description:
Library name: 56CAG_3
Column name in CHDI_Cortical_Counts_Merged.csv: 56CAG_3

value: Expanded CAG


title: cortical, 72CAGn1 RUES2 cells replicate 3

description:
Library name: 72CAGn1_3
Column name in CHDI_Cortical_Counts_Merged.csv: 72CAGn1_3


title: cortical, 20CAGn2 RUES2 cells, replicate 3

description:
Library name: 20CAGn2_3
Column name in CHDI_Cortical_Counts_Merged.csv: 20CAGn2_3


title: cortical, HTT KO RUES2 cells, replicate 2

description:
Library name: HTTKO_2
Column name in CHDI_Cortical_Counts_Merged.csv: HTTKO_2


title: cortical, 20CAGn1 RUES2 cells (parental line), replicate 3

description:
Library name: 20CAGn1_3
Column name in CHDI_Cortical_Counts_Merged.csv: 20CAGn1_3


title: cortical, 72CAGn1 RUES2 cells replicate 2

description:
Library name: 72CAGn1_2
Column name in CHDI_Cortical_Counts_Merged.csv: 72CAGn1_2


title: cortical, 56CAG RUES2 cells replicate 2

description:
Library name: 56CAG_2
Column name in CHDI_Cortical_Counts_Merged.csv: 56CAG_2


title: cortical, 20CAGn2 RUES2 cells, replicate 2

description:
Library name: 20CAGn2_2
Column name in CHDI_Cortical_Counts_Merged.csv: 20CAGn2_2


title: cortical, 20CAGn1 RUES2 cells (parental line), replicate 2

description:
Library name: 20CAGn1_2
Column name in CHDI_Cortical_Counts_Merged.csv: 20CAGn1_2


title: cortical, HTT KO RUES2 cells, replicate 1

description:
Library name: HTTKO_1
Column name in CHDI_Cortical_Counts_Merged.csv: HTTKO_1


title: Ileal organoids, perturbation control

description:
Library name: IHBDECO082_006_ctr_4_5
Single-cell RNA sequencing (10xGenomics Chromium)


title: cortical, 72CAGn1 RUES2 cells replicate 1

description:
Library name: 72CAGn1_1
Column name in CHDI_Cortical_Counts_Merged.csv: 72CAGn1_1


title: cortical, 56CAG RUES2 cells, replicate 1

description:
Library name: 56CAG_1
Column name in CHDI_Cortical_Counts_Merged.csv: 56CAG_1


title: cortical, 20CAGn2 RUES2 cells, replicate 1

description:
Library name: 20CAGn2_1
Column name in CHDI_Cortical_Counts_Merged.csv: 20CAGn2_1


title: cortical, 20CAGn1 RUES2 cells (parental line), replicate 1

description:
Library name: 20CAGn1_1
Column name in CHDI_Cortical_Counts_Merged.csv: 20CAGn1_1


title: 72CAGn1 RUES2 cells replicate 3

description:
Library name: 72CAGn1_3
Column name in CHDI_Pluripotent_Counts_Merged.csv: 72CAGn1_3

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence using Trimmomatic.
Reads were aligned using HISAT2 using an index created from Ensembl GRCh38 release 84.
Gene counts were quantified using featureCounts using the gtf annotation from the same reference as the alignment.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file including raw count data for all samples.

source_name: cells

growth_protocol: All RUES2 cells were maintained in MTeSR1 media (Stem Cell Technologies) with daily feeds on growth factor reduced Matrigel basement membrane (Corning) in humid environment with 5% CO2 at 37 degrees

extract_protocol:
RNA was extracted using Rneasy mini extraction kit (QIAGEN) and 1 ug of RNA was used for library preparation
Library construction was performed using TruSeq RNA stranded kit with rRNA reduction (RiboZero)

value: cells

value: Pluripotent


title: 56CAG RUES2 cells, replicate 3

description:
Library name: 56CAG_3
Column name in CHDI_Pluripotent_Counts_Merged.csv: 56CAG_3


title: HTT KO RUES2 cells, replicate 3

description:
Library name: HTTKO_3
Column name in CHDI_Pluripotent_Counts_Merged.csv: HTTKO_3


title: 20CAGn2 RUES2 cells, replicate 3

description:
Library name: 20CAGn2_3
Column name in CHDI_Pluripotent_Counts_Merged.csv: 20CAGn2_3


title: 72CAGn1 RUES2 cells replicate 2

description:
Library name: 72CAGn1_2
Column name in CHDI_Pluripotent_Counts_Merged.csv: 72CAGn1_2


title: 20CAGn2 RUES2 cells, replicate 2

description:
Library name: 20CAGn2_2
Column name in CHDI_Pluripotent_Counts_Merged.csv: 20CAGn2_2


title: 20CAGn1 RUES2 cells (parental line), replicate 2

description:
Library name: 20CAGn1_2
Column name in CHDI_Pluripotent_Counts_Merged.csv: 20CAGn1_2


title: 20CAGn2 RUES2 cells, replicate 1

description:
Library name: 20CAGn2_1
Column name in CHDI_Pluripotent_Counts_Merged.csv: 20CAGn2_1


title: HTT KO RUES2 cells, replicate 2

description:
Library name: HTTKO_2
Column name in CHDI_Pluripotent_Counts_Merged.csv: HTTKO_2


title: 56CAG RUES2 cells replicate 2

description:
Library name: 56CAG_2
Column name in CHDI_Pluripotent_Counts_Merged.csv: 56CAG_2


title: 72CAGn1 RUES2 cells replicate 1

description:
Library name: 72CAGn1_1
Column name in CHDI_Pluripotent_Counts_Merged.csv: 72CAGn1_1


title: DU145, SOX11 overexpression 3

city: Derio

first: Arkaitz

last: Carracedo

state: Biscay

address: Parque Científico Tecnológico de Bizkaia building 801A

department: Cancer Cell Signaling And Metabolism Lab

institute: CIC bioGUNE

data_processing:
Reads were trimmed for Illumina universal adapter using cutadapt: cutadapt -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" -A "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" -j 0 -q 10 -m 30 ).
Assembly: After QC using fastQC we mapped the reads to the human genome (Ensmbl GRCh38.v94) using STAR version=2.7.0e with parameters: -- outFilterMultimapNmax 1 -- twopassMode Basic.
Supplementary files format and content: Raw counts .txt file

source_name: brain metastasis

growth_protocol: DU145 cells were cultured in growth media (DMEM plus 10% FBS, 1% P/S) and used as control and overpressed cells.  Cells were passaged approximately once per week and plated at 4x10e5 cells.

extract_protocol:
Maxwell® RSC simplyRNA Cell Kit (Catalog number selected: AS1390)
Sequencing libraries were prepared using the TruSeq Stranded mRNA LibraryPrep kit (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate  (Illumina Inc. Cat. # 20019792).

value: brain metastasis

value: epithelial cells

value: SOX11 overexpression


title: 56CAG RUES2 cells, replicate 1

description:
Library name: 56CAG_1
Column name in CHDI_Pluripotent_Counts_Merged.csv: 56CAG_1


title: DU145, SOX11 overexpression 4


title: 20CAGn1 RUES2 cells (parental line), replicate 1

description:
Library name: 20CAGn1_1
Column name in CHDI_Pluripotent_Counts_Merged.csv: 20CAGn1_1

value: Control


title: DU145, SOX11 overexpression 1


title: DU145, control 4

value: control


title: DU145, control 3


title: DU145, SOX11 overexpression 2


title: DU145, control 2


title: Localized prostate cancer, patient 32

data_processing:
Reads were trimmed for Illumina universal adapter using cutadapt: cutadapt -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" -A "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" -j 0 -q 10 -m 30 ).
Assembly: After QC using fastq.gzC we mapped the reads to the human genome (Ensmbl GRCh38.v94) using STAR version=2.7.0e with parameters: -- outFilterMultimapNmax 1 -- twopassMode Basic.
Supplementary files format and content: Raw counts .txt file

source_name: prostatectomy

extract_protocol:
snap frozen OCT primary tumors.
Sequencing libraries were prepared following “TruSeqStrandedmRNASamplePreparationGuide (Part#15031058Rev.E)” using the “TruSeq®StrandedmRNALibraryPrep” kit (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792).

value: prostatectomy

tag: disease

value: Localized prostate cancer

tag: age


title: DU145, control 1

tag: genotype


title: Localized prostate cancer, patient 31


title: Localized prostate cancer, patient 30


title: Localized prostate cancer, patient 27


title: Localized prostate cancer, patient 28


title: Localized prostate cancer, patient 29


title: Localized prostate cancer, patient 26


title: Localized prostate cancer, patient 24


title: Localized prostate cancer, patient 23


title: Localized prostate cancer, patient 25


title: HTT KO RUES2 cells, replicate 1

description:
Library name: HTTKO_1
Column name in CHDI_Pluripotent_Counts_Merged.csv: HTTKO_1


title: 20CAGn1 RUES2 cells (parental line), replicate 3

description:
Library name: 20CAGn1_3
Column name in CHDI_Pluripotent_Counts_Merged.csv: 20CAGn1_3


title: Localized prostate cancer, patient 22


title: Localized prostate cancer, patient 17


title: Localized prostate cancer, patient 18


title: Localized prostate cancer, patient 21


title: Localized prostate cancer, patient 19


title: Localized prostate cancer, patient 16


title: Localized prostate cancer, patient 20


title: metastatic hormone naïve prostate cancer biopsy, patient 15

source_name: prostate gland biopsy

value: prostate gland biopsy

value: metastatic hormone naive prostate cancer


title: metastatic hormone naïve prostate cancer biopsy, patient 13


title: metastatic hormone naïve prostate cancer biopsy, patient 10


title: metastatic hormone naïve prostate cancer biopsy, patient 12


title: metastatic hormone naïve prostate cancer biopsy, patient 9


title: metastatic hormone naïve prostate cancer biopsy, patient 14


title: metastatic hormone naïve prostate cancer biopsy, patient 11


title: metastatic hormone naïve prostate cancer biopsy, patient 6


title: metastatic hormone naïve prostate cancer biopsy, patient 7


title: metastatic hormone naïve prostate cancer biopsy, patient 3


title: metastatic hormone naïve prostate cancer biopsy, patient 8


title: metastatic hormone naïve prostate cancer biopsy, patient 4


title: metastatic hormone naïve prostate cancer biopsy, patient 605

data_processing:
Based on the library specifications and read length of 150bp, reads were specifically trimmed for 3 specific nucleotides using cutadapt v3.5 sotfware as follows. First, we removed the first 3 nucleotides of R2 (cutadapt -U 3 --pair-filter=any --minimum-length=30), then removed adapters from both reads using TruSeq adapters (cutadapt -b file:cutadapt_TruSeq_CD_R1.fa -B file:cutadapt_TruSeq_CD_R2.fa --minimum-length=30  --pair-filter=any) and finally remove the last 3 nucleotides in R1 (cutadapt -u -3 -q 10 --pair-filter=any --minimum-length=30).
Assembly: After QC using fastQC we mapped the reads to the human genome (Ensmbl GRCh38.v94) using STAR version=2.7.0e with parameters: -- outFilterMultimapNmax 1 -- twopassMode Basic.
Supplementary files format and content: Raw counts .txt file

extract_protocol:
formalin-fixed paraffin-embedded (FFPE) specimens derived from primary tumours in patients presenting localized and metastatic prostate cancer at the time of diagnosis
Sequencing libraries were prepared using SMARTer Stranded Total RNA-seq Kit v2 – Pico Input Mammalian kit (Takara Bio USA, Cat.# 634411) and following the user manual (Rev. 063017).


title: metastatic hormone naïve prostate cancer biopsy, patient 1512


title: metastatic hormone naïve prostate cancer biopsy, patient 1544


title: metastatic hormone naïve prostate cancer biopsy, patient 1510


title: metastatic hormone naïve prostate cancer biopsy, patient 2 [Validation dataset]


title: metastatic hormone naïve prostate cancer biopsy, patient 1509


title: metastatic hormone naïve prostate cancer biopsy, patient 1 [Validation dataset]


title: metastatic hormone naïve prostate cancer biopsy, patient 1505


title: metastatic hormone naïve prostate cancer biopsy, patient 1504


title: metastatic hormone naïve prostate cancer biopsy, patient 1503


title: metastatic hormone naïve prostate cancer biopsy, patient 1500


title: metastatic hormone naïve prostate cancer biopsy, patient 1499


title: metastatic hormone naïve prostate cancer biopsy, patient 1502


title: metastatic hormone naïve prostate cancer biopsy, patient 1495


title: metastatic hormone naïve prostate cancer biopsy, patient 1498


title: metastatic hormone naïve prostate cancer biopsy, patient 5


title: metastatic hormone naïve prostate cancer biopsy, patient 1494


title: metastatic hormone naïve prostate cancer biopsy, patient 1493


title: metastatic hormone naïve prostate cancer biopsy, patient 1444


title: metastatic hormone naïve prostate cancer biopsy, patient 1430


title: metastatic hormone naïve prostate cancer biopsy, patient 1427


title: metastatic hormone naïve prostate cancer biopsy, patient 1424


title: metastatic hormone naïve prostate cancer biopsy, patient 1416


title: metastatic hormone naïve prostate cancer biopsy, patient 1390


title: metastatic hormone naïve prostate cancer biopsy, patient 1397


title: metastatic hormone naïve prostate cancer biopsy, patient 1423


title: metastatic hormone naïve prostate cancer biopsy, patient 1511


title: metastatic hormone naïve prostate cancer biopsy, patient 1380


title: metastatic hormone naïve prostate cancer biopsy, patient 1382


title: Localized prostate cancer biopsy, patient 96


title: Localized prostate cancer biopsy, patient 50


title: Localized prostate cancer biopsy, patient 88


title: Localized prostate cancer biopsy, patient 70


title: Localized prostate cancer biopsy, patient 41


title: metastatic hormone naïve prostate cancer biopsy, patient 1497


title: metastatic hormone naïve prostate cancer biopsy, patient 1383


title: Localized prostate cancer biopsy, patient 38


title: Localized prostate cancer biopsy, patient 35


title: Localized prostate cancer biopsy, patient 31


title: Localized prostate cancer biopsy, patient 30


title: Localized prostate cancer biopsy, patient 260


title: Localized prostate cancer biopsy, patient 242


title: metastatic hormone naïve prostate cancer biopsy, patient 1371


title: Localized prostate cancer biopsy, patient 224


title: Localized prostate cancer biopsy, patient 250


title: metastatic hormone naïve prostate cancer biopsy, patient 1428


title: Localized prostate cancer biopsy, patient 213


title: Localized prostate cancer biopsy, patient 209


title: Localized prostate cancer biopsy, patient 186


title: Localized prostate cancer biopsy, patient 18


title: Localized prostate cancer biopsy, patient 156


title: Localized prostate cancer biopsy, patient 141


title: Localized prostate cancer biopsy, patient 165


title: Localized prostate cancer biopsy, patient 13


title: Localized prostate cancer biopsy, patient 104


title: Localized prostate cancer biopsy, patient 114


title: Localized prostate cancer biopsy, patient 199


title: Localized prostate cancer biopsy, patient 87


title: Localized prostate cancer biopsy, patient 52


title: Localized prostate cancer biopsy, patient 51


title: Localized prostate cancer biopsy, patient 32


title: Localized prostate cancer biopsy, patient 44


title: Localized prostate cancer biopsy, patient 295


title: Localized prostate cancer biopsy, patient 356


title: Localized prostate cancer biopsy, patient 245


title: Localized prostate cancer biopsy, patient 351


title: Localized prostate cancer biopsy, patient 333


title: Localized prostate cancer biopsy, patient 325


title: metastatic hormone naïve prostate cancer biopsy, patient 1458


title: Localized prostate cancer biopsy, patient 309


title: Localized prostate cancer biopsy, patient 303


title: Localized prostate cancer biopsy, patient 286


title: Localized prostate cancer biopsy, patient 228


title: Localized prostate cancer biopsy, patient 226


title: Localized prostate cancer biopsy, patient 223


title: Localized prostate cancer biopsy, patient 183


title: metastatic hormone naïve prostate cancer biopsy, patient 2

description: 10x Genomics

data_processing:
The sequenced data was processed for analysis with Cell Ranger (version 7.0.1), “cellranger count” was used to perform the alignment analysis using human reference genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: The alignment, filtering, barcode counting, and UMI counting was done using the Cell Ranger software v7.0.1

extract_protocol:
Prostate tissue from prostate cancer patients. The biopsy was kept in MACS medium, tissue storage solution until dissociation. The tumor was washed with cold phosphate-buffered saline (PBS; GIBCO) and minced into fragments under 0.4 mm. The tissue was chemically dissociated in a sterilized filter with Liberase TH solution (2.5mg/ml; REF QZY-5401135001, Thomas Scientific) in complete media composed of Advanced DMEM/F-12 (REF 12-634-010, Fisher Scientific), Pen/strep (REF 15-140122, GIBCO), MgCl2 (5mM, REF M4880, Sigma Aldrich), DNAse I (200 μg/ml, REF 11284932001, Sigma Aldrich) and Y-27632 dihydrochloride (10 μM; AbMole) at 37ºC shaking at 800 r.p.m for 40 minutes. The tissue solution was manually disaggregated with a pipette every 10 min during the incubation followed by centrifugation at 2400xg for 5 min. Next, a second chemical dissociation was performed with TrypLE (REF 12605010, Thermo Scientific) supplemented with Y-27632 dihydrochloride under constant pipetting for 2 minutes. The inactivation of TrypLE was done by adding FBS (GIBCO) and centrifuged at 2400xg for 5 minutes. The cell pellet was resuspended in PBS, filtered through 40 μm filter and washed with PBS. The suspension was centrifuged at 2400xg for 5 minutes and resuspended in 200ul of PBS. Cells were counted on a Neubauer chamber and 20000 cells were then centrifuged at 2400xg for 5 minutes and resuspended in PBS for scRNAseq analysis according to manufacturers´ indications.
Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127, “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3 ’ Reagent Kits v3.1 (Dual Index) User Guide” (Document number CG000315).


title: Localized prostate cancer biopsy, patient 54


title: Localized prostate cancer biopsy, patient 1

description: 10x Genomics


title: Healthy Control 02, pbmc_16, Post-Vaccination, scRNAseq

city: New Haven

first: Jennifer

last: VanOudenhove

state: CT

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

institute: Yale University

description:
Y4312_HHT
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

data_processing:
The demultiplexed fastq files were run through the Cell Ranger multi pipeline (10X Genomics) to generate the gene expression count matrix, T cell V(D)J and B-cell V(D)J analysis files. The data files from each sample were then combined and normalized by running through the Cell Ranger aggr pipeline. These aggregated data matrices were then used for downstream analyses. Gene expression data analysis was performed using R (v4.3) and the Seurat package (v5) following a standard workflow
Assembly: GRCh38
Supplementary files format and content: Gzipped Tab separated files for features and barcodes for scRNA-seq (barcode-1--barcode-16 correspond to pbmc_01--pbmc_16). Comma separated value files for TCR and BCR corresponding data, and Gzipped matrix file

source_name: Human Blood Mononuclear Cells

extract_protocol:
Human peripheral blood was separate using a ficol gradient, to generate mononuclear cells that were then bead enriched for CD3 and CD19 positive cells at time points pre and post two doses of the SARVS-CoV-2 Vaccine and Surrounding SARS-CoV-2 Infection.
Single cell libraries were made using 10X Chromium Next GEM Single Cell 5' Kit v2 also using the Chromium Single Cell Human TCR and BCR Amplification Kits
5' scRNAseq + TCR +BCR

value: Human Blood Mononuclear Cells

tag: individual

value: Healthy Control 02

tag: time

value: Post-Vaccination

tag: library type

value: GEX


title: Healthy Control 03, pbmc_15, Pre-Vaccination, scRNAseq

description:
Y4257_HHT
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

value: Healthy Control 03

value: Pre-Vaccination


title: Healthy Control 03, pbmc_14, Post-Vaccination, BCR

description:
Y4352_BCR
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv

data_processing:
The demultiplexed fastq files were run through the Cell Ranger multi pipeline (10X Genomics) to generate the gene expression count matrix, T cell V(D)J and B-cell V(D)J analysis files. The data files from each sample were then combined and normalized by running through the Cell Ranger aggr pipeline. These aggregated data matrices were then used for downstream analyses. Gene expression data analysis was performed using R (v4.3) and the Seurat package (v5) following a standard workflow
Assembly: GRCh38
Supplementary files format and content: Gzipped Tab separated files for features and barcodes for scRNA-seq (barcode-1--barcode-16 correspond to pbmc_01--pbmc_16). Comma separated value files for TCR and BCR corresponding data, and Gzipped matrix file
Library strategy: scBCR-seq

value: BCR


title: Healthy Control 03, pbmc_14, Post-Vaccination, TCR

description:
Y4352_TCR
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv

data_processing:
The demultiplexed fastq files were run through the Cell Ranger multi pipeline (10X Genomics) to generate the gene expression count matrix, T cell V(D)J and B-cell V(D)J analysis files. The data files from each sample were then combined and normalized by running through the Cell Ranger aggr pipeline. These aggregated data matrices were then used for downstream analyses. Gene expression data analysis was performed using R (v4.3) and the Seurat package (v5) following a standard workflow
Assembly: GRCh38
Supplementary files format and content: Gzipped Tab separated files for features and barcodes for scRNA-seq (barcode-1--barcode-16 correspond to pbmc_01--pbmc_16). Comma separated value files for TCR and BCR corresponding data, and Gzipped matrix file
Library strategy: scTCR-seq

value: TCR


title: Healthy Control 03, pbmc_14, Post-Vaccination, scRNAseq

description:
Y4352_HHT
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Healthy Control 02, pbmc_13, Pre-Vaccination, scRNAseq

description:
Y4144_HHT
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Healthy Control 02, pbmc_13, Pre-Vaccination, TCR

description:
Y4144_TCR
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Healthy Control 02, pbmc_16, Post-Vaccination, BCR

description:
Y4312_BCR
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Healthy Control 03, pbmc_15, Pre-Vaccination, TCR

description:
Y4257_TCR
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Healthy Control 01, pbmc_12, Pre-Vaccination, scRNAseq

description:
JV34
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

value: Healthy Control 01


title: Healthy Control 01, pbmc_12, Pre-Vaccination, BCR

description:
B-JV34
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Localized prostate cancer biopsy, patient 174


title: Localized prostate cancer biopsy, patient 160


title: Patient P27, pbmc_11, Post-Infection, BCR

description:
B-JV33
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv

value: Patient P27

value: Post-Infection


title: Localized prostate cancer biopsy, patient 24


title: Healthy Control 02, pbmc_13, Pre-Vaccination, BCR

description:
Y4144_BCR
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P27, pbmc_11, Post-Infection, scRNAseq

description:
JV33
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Patient P27, pbmc_10, Post-Vaccination, scRNAseq

description:
JV32
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Patient P27, pbmc_10, Post-Vaccination, BCR

description:
B-JV32
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Localized prostate cancer biopsy, patient 296


title: metastatic hormone naïve prostate cancer biopsy, patient 1

description: 10x Genomics


title: Patient P27, pbmc_09, Pre-Vaccination, TCR

description:
T-JV31
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Localized prostate cancer biopsy, patient 2

description: 10x Genomics


title: Patient P27, pbmc_09, Pre-Vaccination, BCR

description:
B-JV31
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Healthy Control 02, pbmc_16, Post-Vaccination, TCR

description:
Y4312_TCR
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Healthy Control 03, pbmc_15, Pre-Vaccination, BCR

description:
Y4257_BCR
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P27, pbmc_09, Pre-Vaccination, scRNAseq

description:
JV31
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Healthy Control 01, pbmc_12, Pre-Vaccination, TCR

description:
T-JV34
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Healthy Control 01, pbmc_08, Post-Vaccination, scRNAseq

description:
JV19
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Patient P28, pbmc_07, Post-Infection, TCR

description:
T-JV18
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv

value: Patient P28


title: Healthy Control 01, pbmc_08, Post-Vaccination, BCR

description:
B-JV19
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P28, pbmc_07, Post-Infection, BCR

description:
B-JV18
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P27, pbmc_11, Post-Infection, TCR

description:
T-JV33
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P28, pbmc_06, Post-Vaccination, BCR

description:
B-JV17
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P28, pbmc_06, Post-Vaccination, TCR

description:
T-JV17
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P28, pbmc_06, Post-Vaccination, scRNAseq

description:
JV17
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Patient P28, pbmc_05, Pre-Vaccination, BCR

description:
B-JV16
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P28, pbmc_05, Pre-Vaccination, scRNAseq

description:
JV16
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Patient P27, pbmc_10, Post-Vaccination, TCR

description:
T-JV32
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P19, pbmc_04, Post-Vaccination, BCR

description:
B-JV4
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv

value: Patient P19


title: Patient P19, pbmc_04, Post-Vaccination, scRNAseq

description:
JV4
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Patient P28, pbmc_05, Pre-Vaccination, TCR

description:
T-JV16
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P19, pbmc_03, Pre-Vaccination, TCR

description:
T-JV3
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P19, pbmc_03, Pre-Vaccination, BCR

description:
B-JV3
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P19, pbmc_03, Pre-Vaccination, scRNAseq

description:
JV3
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Patient P19, pbmc_04, Post-Vaccination, TCR

description:
T-JV4
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P7, pbmc_02, Post-Vaccination, scRNAseq

description:
JV2
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

value: Patient P7


title: Patient P7, pbmc_02, Post-Vaccination, BCR seqeuncing

description:
B-JV2
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P7, pbmc_02, Post-Vaccination, TCR seqeuncing

description:
T-JV2
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P7, pbmc_01, Pre-Vaccination, BCR sequencing

description:
B-JV1
vdj_b_filtered_contig_annotations.csv
vdj_b_clonotypes.csv


title: Patient P7, pbmc_01, Pre-Vaccination, TCR sequencing

description:
T-JV1
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: Patient P7, pbmc_01, Pre-Vaccination, scRNAseq

description:
JV1
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Healthy Control 01, pbmc_08, Post-Vaccination, TCR

description:
T-JV19
vdj_t_clonotypes.csv
vdj_t_filtered_contig_annotations.csv


title: AC16, linear PVT1 siRNA, rep3

city: Milan

first: Fabio

last: Martelli

address: Via Olgettina 58

country: Italy

institute: IRCCS Policlinico San Donato

data_processing:
Base calling and demultiplexing was performed with Bcl2Fastq 2.20.
Adapters and low quality bases were removed with combined use of Cutadapt v1.11 and ERNE (Del Fabbro C, et al., 2013).
Splice-aware alignment to the human genome (hg38) was performed using STAR with default parameters.
StringTie was utilized for quantification (default parameters).
Differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: Default StringTie quantification results are provided as processed files; they include gene-level quantification results (i.e., Gene ID/Name, chr, strand, gene-start, gene-end, coverage, FPKM and TPM) per-sample.

growth_protocol: DMEM/F12, 12,5% fetal bovine serum, 2 mM L-Glutamine, 1X Penicillin-Streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was isolated with TRIzol reagent (Thermo Fisher Scientific Inc., MA, USA), followed by RNA purification using the Zymo RNA Clean & Concentrator™ kit (Euroclone, Milan, Italy) according to the manufacturer’s instructions. RNA was eluted in RNAse-free water.
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) was used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand). Libraries were sequenced on 150bp PE mode.

treatment_protocol: AC16 cells were transfected with siRNA targeting circPVT1, linear PVT1 or a non-targeting siRNA control at a final concentration of 50 nM. siRNA transfection reagent supplied by Santa Cruz Biotechnology (Dallas, TX, USA) was used for cell transfections according to the manufacturer’s protocol. 72h post-transfection, cells were harvested.

value: Ventricular cardiomyocytes

tag: treatment

value: linear PVT1 siRNA


title: AC16, linear PVT1 siRNA, rep4


title: AC16, linear PVT1 siRNA, rep2


title: Patient P28, pbmc_07, Post-Infection, scRNAseq

description:
JV18
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: AC16, linear PVT1 siRNA, rep1


title: AC16, circPVT1 siRNA, rep4

value: circPVT1 siRNA


title: AC16, circPVT1 siRNA, rep3


title: AC16, circPVT1 siRNA, rep2


title: AC16, circPVT1 siRNA, rep1


title: AC16, Non-targeting control siRNA, rep4

value: Non-targeting control siRNA


title: AC16, Non-targeting control siRNA, rep3


title: AC16, Non-targeting control siRNA, rep2


title: AC16, Non-targeting control siRNA, rep1


title: Mid-Trimester_Female_AA_s105029

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_AA_Trisect_vs_Term_full_DESeq2_results.txt

data_processing:
Adapter sequences in raw reads were trimmed out using Trimmomatic (v.0.32)
STAR (v.2.5.2b) was used to align trimed sequencing reads to the hg38 human reference genome.
HTSeq (v.0.6.1) was used to quantify gene-level abundance corresponding to the hg38 human reference transcriptome file.
DESeq2 (v.1.18.1) was used to perform differential expression analysis to compare transcriptomic changes in (1) Preterm versus Term and (2) Mid-Trimester versus Term in sex- and race-specific samples.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include mapped read values per gene for each sample that passed QC (Placenta_htseq_gene.txt) and gene level-based differential expression results in 8 files for the  (1) Preterm versus Term and (2) Mid-Trimester versus Term stratified by sex and race.

source_name: placenta

extract_protocol:
Total RNA was extracted from frozen placenta using TRIzol® Reagent (Invitrogen), followed by Qiagen RNeasy® Mini Columns following manufacturer’s instructions.
Multiplexed libraries were created using Agilent SureSelect strand-specific RNA library preparation kit following manufacturer’s instructions. Illumina unique dual indexes (UDI) were used.

value: placenta

tag: status

value: Mid-Trimester

tag: Sex

value: Female

tag: race

value: AA

value: CGGCTATG

value: ATAGAGGC


title: Mid-Trimester_Female_AA_s105028

value: ATTCAGAA


title: Mid-Trimester_Male_AA_s105027

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_AA_Trisect_vs_Term_full_DESeq2_results.txt

value: Male

value: ATTACTCG


title: Preterm_Female_AA_s105024

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_AA_Preterm_vs_Term_full_DESeq2_results.txt

value: Preterm

value: TAATGCGC


title: Preterm_Male_AA_s105021

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_AA_Preterm_vs_Term_full_DESeq2_results.txt

value: CGCTCATT


title: Preterm_Female_AA_s105025

value: AGCGATAG


title: Preterm_Male_AA_s105022

value: TATAGCCT


title: Term_Female_AA_s105019

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_AA_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Female_AA_Trisect_vs_Term_full_DESeq2_results.txt

value: Term

value: TCTCGCGC


title: Term_Male_AA_s105018

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_AA_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Male_AA_Trisect_vs_Term_full_DESeq2_results.txt

value: GAGATTCC


title: Mid-Trimester_Female_White_s105016

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_White_Trisect_vs_Term_full_DESeq2_results.txt

value: placenta

value: White

value: CTGAAGCT

value: CCTATCCT


title: Mid-Trimester_Male_White_s105013

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_White_Trisect_vs_Term_full_DESeq2_results.txt

value: Mid-Trimester

value: GAATTCGT


title: Mid-Trimester_Female_White_s105014

value: Female


title: Mid-Trimester_Male_White_s105012

value: Male

value: TCCGGAGA


title: Preterm_Female_White_s105011

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_White_Preterm_vs_Term_full_DESeq2_results.txt

value: Preterm


title: Term_Female_AA_s105020

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_White_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Female_White_Trisect_vs_Term_full_DESeq2_results.txt

value: AA

value: ATTACTCG


title: Term_Male_AA_s105017


title: Preterm_Female_White_s105010


title: Preterm_Male_White_s105009

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_White_Preterm_vs_Term_full_DESeq2_results.txt

value: ATAGAGGC


title: Term_Female_White_s105006


title: Term_Male_White_s105003

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_White_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Male_White_Trisect_vs_Term_full_DESeq2_results.txt

value: TCCGCGAA

value: TATAGCCT


title: Preterm_Male_White_s105007

value: AGCGATAG


title: Term_Male_White_s105002

value: Term

value: ATTCAGAA


title: Term_Female_White_s105005

value: placenta

value: White

value: TCTCGCGC


title: Preterm_Male_White_s105008


title: Mid-Trimester_Male_AA_s105026

value: Mid-Trimester

value: CCTATCCT


title: Preterm_Female_AA_s105023

value: Female


title: Mid-Trimester_Female_White_s104748

value: GTATGTTC

value: AACAGGAA


title: Term_Female_AA_s104746

value: AGTACTCC

value: AACCTGTT


title: Term_Male_White_s104744

value: Male

value: GATCTATC

value: ATGAGGCT


title: Preterm_Female_AA_s104743

value: Preterm

value: AA

value: AACAGGTT

value: ATACCAAG


title: Mid-Trimester_Female_AA_s104747

value: placenta

value: CTGCTTCC

value: GATAGATC


title: Preterm_Male_AA_s104745

value: TTCCTGTT

value: AGTATCTT


title: Term_Female_White_s104742

value: Term

value: Female

value: White

value: AAGATACT

value: ACTTACAT


title: Preterm_Male_White_s104735

value: Male

value: GGTCACGA

value: GTATTATG


title: Term_Male_AA_s104739

value: ATGTAAGT

value: ACTCTATG


title: Preterm_Male_AA_s104732

value: Preterm

value: AA

value: CATAATAC

value: TTCTAACG


title: Term_Female_AA_s104740

value: placenta

value: CTTGGTAT

value: CCAAGTCC


title: Mid-Trimester_Male_White_s104741

value: Mid-Trimester

value: AGCCTCAT

value: AGTAGAGA


title: Preterm_Female_AA_s104733

value: Female

value: GTGTCGGA

value: GCTTGCGC


title: Mid-Trimester_Female_AA_s104730

value: GCGCAAGC

value: TCACGCCG


title: Term_Female_White_s104736

value: Term

value: White

value: CGCTATGT

value: TCCGACAC


title: Preterm_Female_White_s104738

value: Preterm

value: TCTCTACT

value: CGCGGTTC


title: Preterm_Male_White_s104737

value: placenta

value: Male

value: GGACTTGG

value: CGCAGACG


title: Term_Male_AA_s104729

value: AA

value: CGTTAGAA

value: TTCAGGTC


title: Mid-Trimester_Female_White_s104725

value: Mid-Trimester

value: Female

value: TTATAACC

value: GATATCGA


title: Term_Male_AA_s104726

value: Term

value: GACCTGAA

value: TTGGTGAG


title: Mid-Trimester_Male_AA_s104734

value: TGGCCGGT

value: TAGAGCGC


title: Preterm_Male_White_s104728

value: Preterm

value: White

value: GTCGGAGC

value: GGTTATAA


title: Term_Female_AA_s104727

value: placenta

value: CGGCGTGA

value: GCGCCTGT


title: Mid-Trimester_Male_White_s104724

value: Male

value: TATCGCAC

value: CTTAGTGT


title: Preterm_Male_AA_s104720

value: AA

value: TGCGGCGT

value: CCTCGGTA


title: Preterm_Male_AA_s104722

value: CAATTAAC

value: CGAGATAT


title: Term_Male_White_s104723

value: Term

value: AACTGTAG

value: ACGCCGCA


title: Preterm_Female_White_s104721

value: Preterm

value: Female

value: White

value: ACACTAAG

value: ATCCATAT


title: Term_Male_White_s105004

value: placenta

value: GAGATTCC

value: ATAGAGGC


title: HEK293T_Nanopore_004_dRNAseq

first: Yingyuan

last: Xie

state: GuangDong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
raw signals were basecalled using dorado (v0.7.2) with default parameters and converted into fastq format
Reads that passed the quality threshold (7) and had a length greater than 25bp were then aligned to the reference genome using Minimap2 (v2.22-r1101)
f5c (v1.4) eventalign module was used to align raw signals to 5mer bases with the parameter settings "--scale-events --samples --signal-index".
sam2tsv was used to extract bases quality and alignment results for each read from bam files
In-house python scripts were used to extract and organize current features and base quality features for each 39 motif within each read.
These features were then used as inputs for SingleMod for training or prediction.
Assembly: hg38 (HEK293T_Nanopore_004_dRNAseq), IRGSP-1.0 (Rice_Nanopore_004_dRNAseq)
Supplementary files format and content: tab-delimited text file, methylation rate of all As in 39 motifs predicted by SingleMod

extract_protocol:
After extracting total RNA from the samples using TRIzol (Thermo Fisher Scientifific, 15596026), mRNA was isolated via a Dynabeads mRNA Purifification Kit (Thermo Fisher Scientifific, 61006) with genomic DNA removal using TuRBO DNase kit (Thermo Fisher, AM2238).
Nanopore direct RNA sequencing was conducted following instructions provided by Oxford Nanopore Technologies (Oxford, UK) using DRS kits (SQK-RNA004) and PromethION flowcells (FLO-PRO004).


title: Rice_GLORI_rep2

data_processing:
Raw reads were preprocessed using cutadapt (v4.1), seqkit (v0.8.1) rmdup module and fastp (v0.21.0) for adaptor trimming, deduplication and quality control as well as UMI trimming, respectively.
Then, the clean data were processed using the RNA-m5C pipeline developed by Huang T et al., 2022, with some modifications described.
All A sites with signal greater than 0.9 (representing the ratio of reads with no more than 3 non-converted A to all reads) and coverage greater than 20 after discarding non-converted reads were retained for methylation rate calculation
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text file, quantification of m6A in all As with coverage >= 15.

organism: Oryza sativa

extract_protocol:
After extracting total RNA from the samples using TRIzol (Thermo Fisher Scientifific, 15596026), mRNA was isolated via a Dynabeads mRNA Purifification Kit (Thermo Fisher Scientifific, 61006) with genomic DNA removal using TuRBO DNase kit (Thermo Fisher, AM2238).
GLORI experiments were conducted following instructions provided in Cong Liu et al., 202214, with an adjusted incubation temperature in deamination step of 25 ℃.

value: root


title: Mid-Trimester_Female_AA_s104718

value: Mid-Trimester

value: AA

value: ATATGGAT

value: CTGTATTA


title: Mid-Trimester_Female_White_s104719

value: ATATCTCG

value: ATCTTAGT


title: Mid-Trimester_Male_White_s104731

value: Male

value: GCGCTCTA

value: GCTCCGAC


title: Mid-Trimester_Female_White_s105015

value: Female

value: TCCGGAGA


title: Preterm_Female_White_s104438

value: Preterm

value: White

value: GTGAATAT

value: TCTCATTC


title: Mid-Trimester_Male_AA_s104714

value: placenta

value: AGTTCAGG

value: CCAACAGA


title: Preterm_Female_White_s104715

value: TAATACAG

value: ATATTCAC