title: Whole blood DNA methylation, AA CONTROL, 74yo F, 207097650112_R07C01


title: BJ-T, WT CTR, biol rep 4

status: Public on Jul 10 2026

type: SRA

city: Pozzuoli

first: Davide

last: Cacchiarelli

state: Napoli

address: via campi flegrei,34

country: Italy

institute: TIGEM

description: Library name: BJ-T, WT CTR, biol rep 4

library_source: transcriptomic

data_processing:
Illumina NovaSeq base call (BCL) files were converted into FASTQ files through bcl2fastq. Sequence reads were trimmed using bbduk software (https://sourceforge.net/projects/bbmap/ - bbmap suite 37.31) to remove adapter sequences, poly-A tails, and low-quality end bases (regions with average quality below 6). Alignment was performed with STAR 2.6.0a on GRCh38. The expression levels of genes were determined with htseq-count 0.9.1
Assembly: hg38
Supplementary files format and content: tab-separated count matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: BJ-T

growth_protocol: BJ-T cells were grown in alphamem (Euroclone # ECM0095) supplemented with 10% FBS (Euroclone #ECS0186L), 1x Glutamax (Thermo #35050061)

extract_protocol:
Prior to library preparation, RNA samples were extracted with RNadvance cell V2 kit (Beckman Coulter #A47943) and diluted to 50 ng/μL.
RNA libraries were prepared using or NEGEDIA 3’Digital RNAseq service

treatment_protocol: Two days after transduction, the medium was supplemented with 1 ug/ml puromycin (Thermo #A1113903), for two days. After antibiotic selection, cells were allowed to overexpress exogenous gene for 72h.

tag: cell line

value: BJ-T

tag: cell type

value: Fibroblasts

tag: treatment

value: Lentiviral overexpression


title: Whole blood DNA methylation, NHW AD, 85yo F, 207215820076_R06C01

type: genomic

city: San Francisco

first: Sebastián

last: Cruz-González

state: California

country: USA

institute: UCSF

hyb_protocol: DNA methylation was quantified using the Illumina Infinium MethylationEPIC BeadChip (EPIC v1.0, ~850K CpG sites) according to the manufacturer's standard Infinium HD Assay protocol.

scan_protocol: BeadChips were scanned on an Illumina iScan system to generate raw IDAT files.

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: whole blood

label_protocol: Bisulfite conversion of genomic DNA was performed prior to hybridization following standard protocols for the Illumina Infinium MethylationEPIC BeadChip array. Samples were randomized across plates and chips to ensure that ancestry, age, and sex were not confounded with each batch.

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

tag: Sex

value: Female

tag: disease state

value: Alzheimer's disease

tag: tissue

value: whole blood

tag: ethnicity

value: NHW

tag: cohort

tag: age


title: Whole blood DNA methylation, AA CONTROL, 71yo F, 207215820062_R01C01

value: Healthy control

value: AA

value: REAAADI


title: BJ-T, WT CTR, biol rep 3

description: Library name: BJ-T, WT CTR, biol rep 3


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215820086_R06C01


title: BJ-T, WT CTR, biol rep 2

description: Library name: BJ-T, WT CTR, biol rep 2


title: Whole blood DNA methylation, NHW CONTROL, 78yo F, 207215830118_R02C01


title: BJ-T, WT CTR, biol rep 1

description: Library name: BJ-T, WT CTR, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 68yo F, 207215820097_R06C01


title: iKCs, G297L, biol rep 4

description: Library name: iKCs, G297L, biol rep 4

data_processing:
Illumina NovaSeq base call (BCL) files were converted into FASTQ files through bcl2fastq. Sequence reads were trimmed using bbduk software (https://sourceforge.net/projects/bbmap/ - bbmap suite 37.31) to remove adapter sequences, poly-A tails, and low-quality end bases (regions with average quality below 6). Alignment was performed with STAR 2.6.0a on GRCh38. The expression levels of genes were determined with htseq-count 0.9.1
The evaluation and quantification of mutations in P63 sequence was achieved with the gatk45 (v. 4.3.0) module AnalyzeSaturationMutagenesis with the parameter –min-q set to 15.
Assembly: hg38
Supplementary files format and content: tab-separated count matrix files

source_name: BJ-T converted to iKCs

treatment_protocol: Two days after transduction, the medium was supplemented with 10 ug/ml blasticidin (Thermo #A1113903), for four days. After antibiotic selection, cells were allowed to overexpress exogenous gene for 72h.

value: BJ-T converted to iKCs

value: iKCs conversion


title: Whole blood DNA methylation, NHW CONTROL, 75yo M, 207215830027_R08C01

value: Male


title: Whole blood DNA methylation, AA AD, 76yo F, 207215820048_R04C01


title: Viral IgG PhIP-Seq for participant 27, timepoint w0, replicate 2

status: Public on Jul 11 2026

city: Boston

first: Stephen

last: Elledge

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Library name: Sample_1_192

library_source: other

data_processing:
Seuqencing reads were aligned to library reference files by bowtie.
Read counts were obtained using samtools.
Read counts from multiple samples were merged to generate the read count files.
Assembly: custom peptidome library
Supplementary files format and content: IDs ranging from 1 to 128287 (but 115,753 unique reference sequences reported) vir3_metadata_geo.csv, read counts

molecule: other

source_name: blood

extract_protocol:
Phage display libraries were mixed with human sera to allow antibodies from sera to bind to displayed peptides. These complexes were then immunoprecipitated using Dynabeads coated either with protein A/G (for IgG) or strepavidin conjugated to biotinylated anti-IgA antibody (for IgA). Phage were then lysed and the contained DNA coding for the displayed peptides were amplified and barcoded by PCR, pooled, gel extracted, and prepared for Illumina sequencing.
Peptide libraries tiling across the proteins from viruses that infect humans (VirScan) and the human proteome were packaged in T7 bacteriophage and expanded as described in Xu et al (DOI:10.1126/science.aaa0698) and Larman et al (DOI: 10.1038/nbt.1856).

value: blood

tag: phip isotype

value: IgG

tag: participant id

tag: time point

tag: replicate

tag: run id

value: IgG Vir YL2

tag: outcome

value: birth

tag: series


title: Whole blood DNA methylation, AA AD, 84yo F, 207215830057_R06C01


title: iKCs, G297L, biol rep 3

description: Library name: iKCs, G297L, biol rep 3


title: iKCs, G297L, biol rep 2

description: Library name: iKCs, G297L, biol rep 2


title: Whole blood DNA methylation, AA AD, 93yo F, 207097650075_R01C01


title: iKCs, G297L, biol rep 1

description: Library name: iKCs, G297L, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 73yo M, 207215830074_R07C01


title: Whole blood DNA methylation, AA AD, 84yo M, 207215830074_R04C01


title: iKCs, R311I, biol rep 4

description: Library name: iKCs, R311I, biol rep 4


title: iKCs, R311I, biol rep 3

description: Library name: iKCs, R311I, biol rep 3


title: Whole blood DNA methylation, AA CONTROL, 69yo M, 207219630047_R01C01


title: Whole blood DNA methylation, NHW CONTROL, 77yo M, 207215820013_R01C01


title: Whole blood DNA methylation, NHW AD, 78yo M, 207219630047_R03C01


title: BJ-T, MYOD1 mut, biol rep 2.1

description: Library name: BJ-T, MYOD1 mut, biol rep 2.1

library_source: transcriptomic single cell

data_processing:
Single cell sequencing data were processed using the zUMIs pipeline (v. 2.9.7) for demultiplexing, read alignment, and UMI quantification to generate a gene-level count matrix and a cell-specific bam alignment file for each sample. The output of zUMI was used for both expression analysis and cell-level genotyping of the gene of interest.
Assembly: hg38
Supplementary files format and content: tab-separated files and matrix

extract_protocol:
cells were sorted in 300 nL lysis buffer overlayed with 3 μL Silicon Oil (5 cSt; Sigma-Aldrich) using a CytoFlex SRT sorter (100 μm nozzle; Beckmann Coulter).
reverse transcription was carried out by adding 100 nL reverse transcription master mix. Preamplification of cDNA was performed in 1 μl total volume using SeqAmp polymerase (Takara Bio #) for 14 cycles. Subsequently, amplified cDNA was diluted with 9 μl H2O and we used 1 μl for downstream tagmentation using 0.004 μl TDE1 enzyme per cell. Final, indexed libraries were pooled per 384-well plate, cleaned and equimolarly pooled before sequencing

value: BJ-T

value: transgene overexpresison


title: iKCs, R311I, biol rep 1

description: Library name: iKCs, R311I, biol rep 1


title: iKCs, R311I, biol rep 2

description: Library name: iKCs, R311I, biol rep 2


title: Whole blood DNA methylation, AA CONTROL, 77yo F, 207228480014_R02C01


title: Whole blood DNA methylation, AA AD, 79yo F, 207215820065_R02C01


title: Whole blood DNA methylation, AA CONTROL, 73yo F, 207215820075_R08C01


title: iKCs, G293H, biol rep 3

description: Library name: iKCs, G293H, biol rep 3


title: iKCs, G293H, biol rep 2

description: Library name: iKCs, G293H, biol rep 2


title: Whole blood DNA methylation, AA CONTROL, 70yo M, 207215830027_R04C01


title: iKCs, G293H, biol rep 1

description: Library name: iKCs, G293H, biol rep 1


title: Whole blood DNA methylation, AA AD, 89yo F, 207219770143_R04C01


title: iKCs, G310Q, biol rep 4

description: Library name: iKCs, G310Q, biol rep 4


title: Whole blood DNA methylation, AA CONTROL, 71yo F, 207228480032_R08C01


title: iKCs, G310Q, biol rep 3

description: Library name: iKCs, G310Q, biol rep 3


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207215820094_R02C01


title: Whole blood DNA methylation, AA AD, 83yo F, 207215830113_R06C01


title: BJ-T, WT CTR, biol rep 2

description: Library name: BJ-T, WT CTR, biol rep 2

growth_protocol: BJ-T cells were grown in DMEM/F12 (Euroclone # ECM0095) supplemented with 10% FBS (Euroclone #ECS0186L), 1x Glutamax (Thermo #35050061), 1xNEAA (Thermo #11140035), 1x 2-Mercapto-ethanol (Thermo #21985023)

value: Fibroblasts

value: Lentiviral overexpression


title: iKCs, G310Q, biol rep 2

description: Library name: iKCs, G310Q, biol rep 2


title: iKCs, G310Q, biol rep 1

description: Library name: iKCs, G310Q, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 75yo M, 207097650067_R08C01


title: Whole blood DNA methylation, AA AD, 90yo F, 207215830018_R05C01

value: Female

value: Alzheimer's disease


title: iKCs, R279S, biol rep 4

description: Library name: iKCs, R279S, biol rep 4


title: Whole blood DNA methylation, AA AD, 81yo M, 207215830027_R03C01

value: whole blood


title: Whole blood DNA methylation, AA CONTROL, 70yo F, 207097650070_R03C01

value: Healthy control


title: iKCs, R279S, biol rep 3

description: Library name: iKCs, R279S, biol rep 3


title: BJ-T, EMPTY CTR, biol rep 1

description: Library name: BJ-T, EMPTY CTR, biol rep 1


title: iKCs, R279S, biol rep 2

description: Library name: iKCs, R279S, biol rep 2


title: Whole blood DNA methylation, NHW AD, 89yo F, 207215820132_R05C01

value: NHW


title: iKCs, R279S, biol rep 1

description: Library name: iKCs, R279S, biol rep 1


title: Whole blood DNA methylation, NHW CONTROL, 73yo F, 207215820055_R07C01


title: iKCs, R279Q, biol rep 4

description: Library name: iKCs, R279Q, biol rep 4


title: iKCs, R279Q, biol rep 3

description: Library name: iKCs, R279Q, biol rep 3


title: Whole blood DNA methylation, NHW AD, 79yo M, 207228480080_R03C01


title: Whole blood DNA methylation, AA AD, 72yo F, 207215820131_R02C01

value: AA

value: REAAADI


title: Whole blood DNA methylation, AA AD, 79yo M, 207219740068_R04C01


title: iKCs, R279Q, biol rep 1

description: Library name: iKCs, R279Q, biol rep 1

value: BJ-T converted to iKCs

value: iKCs conversion


title: iKCs, R279Q, biol rep 2

description: Library name: iKCs, R279Q, biol rep 2


title: Whole blood DNA methylation, NHW AD, 68yo M, 207215820076_R01C01

value: Male


title: iKCs, R304T, biol rep 4

description: Library name: iKCs, R304T, biol rep 4


title: ATAC-seq of Mus musculus : old fresh HSCs, rep1

city: Sendai

first: Keiyo

last: Takubo

address: 2-1 Seiryo-machi Aoba-ku

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

description:
Library name: Old_Fresh_HSC_ATACseq_rep1
Old HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to ATAC-seq, rep1

library_source: genomic

data_processing:
Fastq files were trimmed using Trim Galore and aligned to the reference mouse genome (mm10) using bowtie2 with a --very-sensitive and single-read mode. Mitochondrial genome, Y chromosome, and scaffold chromosomes were removed using samtools, and duplicate reads were removed using picard MarkDuplicates. Peak calling was performed using MACS3 for each group with -q = 0.05, --extsize =100, and --shift = 50 with narrow peak mode. All peaks called in each group were merged, and peaks overlapping with blacklist region were excluded, and peaks within a distance smaller than 50bp considered as an identical peak. After further removing peaks with average of log CPM < -1, peak count around +/- 125bp of each summit was performed using csaw package of R.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using Deeptools from BAM files removing duplicated reads after normalized to peak counts, and biological replicates were merged with DeepTools.
Supplementary files format and content: PeakCounts_th0.txt provides a tab-deliminated raw count data, counting reads 250bp around each summit following removal of peaks with low signal.
Supplementary files format and content: Peaks_noBL_th0.bed is a BED file providing a +/- 125bp around summits detected by MACS3 followed by removal of low signal peaks. Problematic regions ("blacklist") were removed.

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Cell suspension of 30000 fresh or cultured HSCs was centrifuged at 600 x g for 10 min at 4°C. Cells were resuspended in 50 uL of cold PBS and centrifuged at 600 x g for 5 min. After removal of supernatant, 100 uL/sample of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 2mM MgCl2, 0.1% IGEPAL CA-630) was added, left 5 min on ice, and centrifuged at 600 x g for 10 min to extract nuclei.
Immediately following removal supernatant, nuclei pellet was resupended in 50 uL transposase mix (25 uL 2x TD buffer, 2.5 uL of transposase, 22.5 uL of Water), and incubated for 30 min at 37°C. Each sample was purified with GIAGEN miniElute kit and elute with 14 uL water. Then, tagmented genomic DNA was amplified by PCR using NEB Next High Fidelity 2x PCR mix with primers containing adaptor and index sequences. PCR product was purified using QIAGEN miniElute kit and elute with 30 uL water.

treatment_protocol: Each replicate (n = 2 biological replicates per group) consisted of a pool of 12 young mice (14 weeks old) and 2 old mice (25 and 28 months old). In each group, 30,000 CD150+CD48-LSK cells were sorted and either immediately subjected to ATAC-seq for the fresh group or cultured for 26 hours under SF-O3 conditions supplemented with 4% BSA, 1 ng/mL SCF, 100 ng/mL TPO, and 1% O₂, followed by ATAC-seq for the culture group.

value: Bone marrow

value: Hematopoietic stem cells (CD150+CD48-LSK cells)

tag: genotype

value: Wild type

value: Freshly isolated


title: ATAC-seq of Mus musculus : young cultured HSCs, rep2

description:
Library name: Young_Cultured_HSC_ATACseq_rep2
Young HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to ATAC-seq, rep2

value: Cultured for 26 hr


title: UPN001, post-ACT lesion (biopsy 2), CD3+ T cells (scRNA-seq + scTCR-seq)

city: Basel

first: Michael

middle: Thomas

last: Sandholzer

address: Hebelstrasse 20

department: Department for Biomedicine

country: Switzerland

institute: University Hospital Basel

description: Library name: UPN001_postACT2

data_processing:
FASTQ generation and demultiplexing (Genomics Facility Basel).
GEX and V(D)J reads aligned/quantified with CellRanger v7.1 (GEX: GRCh38-2020-A; V(D)J: GRCh38 ensembl-7.1.0).
Count matrices processed in R v4.3.0 / Seurat v5.1.0; cells filtered (nFeature>650, nCount>1250, %mito<15, %ribo>5, %hemoglobin<10); TCR-based doublets removed; counts normalized and regressed for cell cycle, %mito and IFN-response genes.
Per-cell TCR contigs integrated using scRepertoire v1.7.2.
Raw UMI counts, cell metadata and per-cell TCR annotation combined into a Seurat v5 object (.rds).
Assembly: GEX: GRCh38 (10x refdata-gex-GRCh38-2020-A); TCR V(D)J: GRCh38 ensembl-7.1.0 (CellRanger v7.1).
Supplementary files format and content: Seurat v5 object (.rds) containing the raw (unnormalized) RNA UMI count matrix, cell-level metadata (patient, timepoint, sex, clinical response, QC metrics, cell-type/cluster annotation) and per-cell TCR alpha/beta clonotype annotation (CDR3, V/D/J genes).

source_name: Melanoma metastasis, post-treatment lesion

extract_protocol:
Resected tumor lesions were mechanically dissociated and enzymatically digested (accutase, collagenase IV, hyaluronidase, DNase I), filtered and cryopreserved. Cells were thawed, Fc-blocked, surface-stained and FACS-sorted for viable CD3+ T cells prior to 10x encapsulation.
Single-cell 5-prime gene expression and TCR V(D)J libraries were prepared with the 10x Genomics Chromium Single Cell V(D)J Reagent Kits v2, loading ~10,000 cells per sample per manufacturer instructions. Libraries sequenced on Illumina NovaSeq 6000 (Genomics Facility Basel).

treatment_protocol: Patients received autologous TIL adoptive cell therapy combined with PD-1 blockade within the phase I BaseTIL trial (NCT04165967).

value: CD3+ T cells (FACS-sorted)

value: male

tag: clinical response

value: PR

value: post-ACT, post-treatment tumor biopsy 2

tag: batch


title: Whole blood DNA methylation, NHW AD, 83yo M, 207219630128_R02C01

value: Alzheimer's disease

value: whole blood


title: Whole blood DNA methylation, NHW AD, 89yo M, 207215820077_R05C01

value: NHW


title: Whole blood DNA methylation, AA AD, 78yo F, 207228480032_R02C01

value: Female

value: AA


title: iKCs, R304T, biol rep 2

description: Library name: iKCs, R304T, biol rep 2

tag: cell line

value: BJ-T converted to iKCs

tag: treatment


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207215820089_R04C01

tag: Sex

tag: disease state

value: Healthy control

value: REAAADI


title: Whole blood DNA methylation, AA CONTROL, 77yo F, 207219740068_R06C01

tag: tissue

tag: ethnicity


title: iKCs, R304Q, biol rep 4

description: Library name: iKCs, R304Q, biol rep 4

value: iKCs conversion


title: iKCs, R304T, biol rep 1

description: Library name: iKCs, R304T, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 67yo M, 207219630048_R01C01

value: Male

tag: cohort

tag: age


title: Whole blood DNA methylation, AA AD, 73yo M, 207097650112_R03C01


title: iKCs, R304Q, biol rep 3

description: Library name: iKCs, R304Q, biol rep 3


title: iKCs, R304Q, biol rep 1

description: Library name: iKCs, R304Q, biol rep 1


title: iKCs, T527I, biol rep 4

description: Library name: iKCs, T527I, biol rep 4


title: Whole blood DNA methylation, AA AD, 66yo M, 207215820077_R07C01


title: Whole blood DNA methylation, AA CONTROL, 69yo M, 207215820086_R03C01


title: iKCs, T527I, biol rep 3

description: Library name: iKCs, T527I, biol rep 3


title: Whole blood DNA methylation, NHW CONTROL, 96yo M, 207215820094_R05C01


title: Whole blood DNA methylation, AA AD, 77yo F, 207215820086_R01C01


title: iKCs, T527I, biol rep 2

description: Library name: iKCs, T527I, biol rep 2


title: iKCs, T527I, biol rep 1

description: Library name: iKCs, T527I, biol rep 1


title: iKCs, R304Q, biol rep 2

description: Library name: iKCs, R304Q, biol rep 2


title: Whole blood DNA methylation, AA CONTROL, 70yo F, 207215830103_R05C01


title: Whole blood DNA methylation, AA CONTROL, 66yo F, 207219630122_R01C01


title: iKCs, H556A, biol rep 4

description: Library name: iKCs, H556A, biol rep 4


title: iKCs, H556A, biol rep 3

description: Library name: iKCs, H556A, biol rep 3


title: Whole blood DNA methylation, NHW CONTROL, 74yo F, 207215820046_R01C01


title: iKCs, H556A, biol rep 2

description: Library name: iKCs, H556A, biol rep 2


title: iKCs, R304T, biol rep 3

description: Library name: iKCs, R304T, biol rep 3


title: Whole blood DNA methylation, AA AD, 69yo F, 207097650075_R03C01


title: Whole blood DNA methylation, AA CONTROL, 67yo M, 207215820065_R08C01


title: iKCs, L531R, biol rep 4

description: Library name: iKCs, L531R, biol rep 4


title: iKCs, H556A, biol rep 1

description: Library name: iKCs, H556A, biol rep 1


title: iKCs, L531R, biol rep 2

description: Library name: iKCs, L531R, biol rep 2


title: iKCs, L531R, biol rep 3

description: Library name: iKCs, L531R, biol rep 3


title: Whole blood DNA methylation, NHW AD, 91yo F, 207215820097_R02C01


title: iKCs, L531R, biol rep 1

description: Library name: iKCs, L531R, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 84yo F, 207215820062_R06C01


title: Whole blood DNA methylation, AA AD, 89yo F, 207228480014_R08C01


title: Whole blood DNA methylation, AA CONTROL, 74yo M, 207215820046_R05C01


title: UPN001, intermediate product (preREP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN001_preREP

source_name: Ex vivo expanded tumor-infiltrating lymphocytes

tag: cell type

value: intermediate product, after preREP expansion


title: IL-4 C1q EV+MAPS

city: Hangzhou

first: Mengying

last: An

state: Zhejiang

address: 西湖区浙大路38号

country: China

institute: Zhejiang University

description:
Library name: SAMPLES4
Single-cell transcriptomic profiling of dissociated cells isolated from the ipsilateral hemisphere at 14 days after ischemic stroke following implantation of IL-4 C1q EV+MAPS at day 5 post-stroke.

data_processing:
Raw BCL files were converted to FASTQ format using bcl2fastq (v5.0.1).
FASTQ files were processed using Cell Ranger (v7.0.0) for read alignment, barcode assignment, UMI counting, and generation of gene-cell count matrices.
Gene expression matrices were imported into Seurat (v4.1.0) for quality control. Cells expressing fewer than 500 genes or containing more than 25% mitochondrial transcripts were excluded.
Expression data were normalized using LogNormalize. Highly variable genes were selected for dimensionality reduction and clustering. PCA was performed and the top 20 principal components were used for graph-based clustering and UMAP visualization.
Cell-type annotation was performed using marker genes and reference databases including SingleR, scCATCH, and LC-Marker. Functional enrichment, AUCell scoring, and cell-cell communication analyses were subsequently conducted.
Assembly: GRCm39
Supplementary files format and content: Processed data include filtered gene-cell UMI count matrices generated by Cell Ranger and used for downstream analyses.

molecule: total RNA

source_name: ipsilateral brain hemisphere

extract_protocol:
Brain tissues were immediately collected and washed twice with cold RNase-free PBS. Samples were minced and enzymatically dissociated in digestion buffer containing Collagenase IV, Papain, and DNase I for 20 min at 37 °C. Enzymatic digestion was terminated with PBS supplemented with 10% FBS, followed by mechanical trituration. Cell suspensions were filtered through 70 µm and 30 µm strainers. Red blood cells and dead cells were removed using erythrocyte lysis buffer and Dead Cell Removal MicroBeads (MACS), respectively. Live cells were washed and resuspended in PBS containing 0.04% BSA. Only cell suspensions with viability greater than 85% were used for downstream library preparation.
Single-cell suspensions were loaded onto Chromium Single Cell 3′ Chips (10x Genomics, v3) targeting approximately 8,000 cells per sample. Single-cell barcoding, reverse transcription, cDNA amplification, and library construction were performed according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp sequencing.

treatment_protocol: Mice subjected to ischemic stroke received implantation of different hydrogel microsphere formulations into the infarct cavity at 5 days post-stroke. At day 14 after stroke, ipsilateral hemispheres were harvested for single-cell RNA sequencing analysis. Healthy control mice received no treatment.

value: ipsilateral brain hemisphere

value: Wild type

value: Stroke+IL-4 C1q EV+MAPS


title: Whole blood DNA methylation, NHW CONTROL, 82yo F, 207219630047_R04C01


title: iKCs, L531E, biol rep 4

description: Library name: iKCs, L531E, biol rep 4


title: Whole blood DNA methylation, NHW AD, 77yo M, 207228480014_R07C01


title: iKCs, L531E, biol rep 3

description: Library name: iKCs, L531E, biol rep 3


title: iKCs, L531E, biol rep 2

description: Library name: iKCs, L531E, biol rep 2


title: iKCs, L531E, biol rep 1

description: Library name: iKCs, L531E, biol rep 1


title: Whole blood DNA methylation, AA AD, 77yo M, 207215820062_R02C01


title: Whole blood DNA methylation, AA AD, 77yo F, 207215820013_R05C01


title: Whole blood DNA methylation, AA AD, 86yo F, 207215830114_R03C01


title: iKCs, I550D, biol rep 4

description: Library name: iKCs, I550D, biol rep 4


title: Whole blood DNA methylation, NHW CONTROL, 78yo F, 207219630128_R03C01


title: iKCs, I550D, biol rep 3

description: Library name: iKCs, I550D, biol rep 3


title: iKCs, I550D, biol rep 2

description: Library name: iKCs, I550D, biol rep 2


title: Whole blood DNA methylation, AA AD, 85yo F, 207228480079_R03C01


title: iKCs, I550D, biol rep 1

description: Library name: iKCs, I550D, biol rep 1


title: Whole blood DNA methylation, AA AD, 83yo M, 207215830027_R02C01


title: Whole blood DNA methylation, AA AD, 80yo F, 207219630048_R08C01


title: iKCs, L548N, biol rep 4

description: Library name: iKCs, L548N, biol rep 4


title: iKCs, L548N, biol rep 1

description: Library name: iKCs, L548N, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 71yo F, 207097650070_R01C01


title: iKCs, C522D, biol rep 4

description: Library name: iKCs, C522D, biol rep 4


title: Whole blood DNA methylation, AA CONTROL, 74yo F, 207215820047_R03C01


title: Whole blood DNA methylation, AA AD, 79yo F, 207215830126_R02C01


title: Whole blood DNA methylation, NHW CONTROL, 82yo F, 207219770097_R07C01


title: iKCs, C522D, biol rep 3

description: Library name: iKCs, C522D, biol rep 3


title: iKCs, C522D, biol rep 2

description: Library name: iKCs, C522D, biol rep 2


title: iKCs, C522D, biol rep 1

description: Library name: iKCs, C522D, biol rep 1


title: Whole blood DNA methylation, NHW CONTROL, 76yo M, 207215830113_R07C01


title: iKCs, C522G, biol rep 4

description: Library name: iKCs, C522G, biol rep 4


title: iKCs, C522G, biol rep 3

description: Library name: iKCs, C522G, biol rep 3


title: Whole blood DNA methylation, AA CONTROL, 66yo M, 207215820076_R07C01


title: iKCs, C522G, biol rep 2

description: Library name: iKCs, C522G, biol rep 2


title: iKCs, C522G, biol rep 1

description: Library name: iKCs, C522G, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 89yo F, 207215820044_R05C01


title: iKCs, L514D, biol rep 4

description: Library name: iKCs, L514D, biol rep 4


title: iKCs, L514D, biol rep 3

description: Library name: iKCs, L514D, biol rep 3


title: Whole blood DNA methylation, AA AD, 84yo M, 207215830113_R01C01


title: iKCs, L514D, biol rep 2

description: Library name: iKCs, L514D, biol rep 2


title: Whole blood DNA methylation, AA CONTROL, 77yo M, 207215830119_R08C01


title: Whole blood DNA methylation, AA AD, 89yo M, 207215820045_R04C01


title: iKCs, L514F, biol rep 4

description: Library name: iKCs, L514F, biol rep 4


title: Whole blood DNA methylation, AA CONTROL, 68yo M, 207221680026_R04C01


title: iKCs, L514F, biol rep 3

description: Library name: iKCs, L514F, biol rep 3


title: Whole blood DNA methylation, AA AD, 77yo M, 207097650067_R07C01


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215830118_R03C01


title: hPIB-SCR_d6_S_CD45_2

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: hPIB-SCR_d6_S_CD45_2

data_processing:
FASTQ files were preprocessed using the nf-core RNA-seq pipeline (v3.14.0) with default parameters, except for UMI extraction, which was done using the following options: --with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*". Technical replicates were merged together.
Briefly, paired-end reads were aligned to the human genome (Ensembl release 110) using STAR, and transcript quantification was performed with Salmon.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

source_name: skin

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, and penicillin/streptomycin.

extract_protocol:
1000-2000 cells were sorted intro PBS with 2 % FBS, pelleted and frozen at -80 °C. RNA was exracted using TRIzol according to manufacturer's protocol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit by Takara.

treatment_protocol: HDFs were transduced on day -1 with lentiviral vectors encoding for PIB and with lentiviral vectors encoding for miRNA hairpins. Cells were sorted on day 3, 6 or 9. Human dendritic cells were enriched from peripheral blood and sorted for subtype-specific markers.

value: skin

value: human dermal fibroblast

value: WT

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.

tag: time

value: Cells were collected on day 6 of reprogramming.

tag: sorted cells

value: live (DAPI-) and CD45+ HLA-DR-

tag: technical replicates


title: iKCs, L514F, biol rep 2

description: Library name: iKCs, L514F, biol rep 2


title: Whole blood DNA methylation, AA AD, 95yo M, 207215820061_R04C01

value: Alzheimer's disease

value: whole blood


title: iKCs, L514F, biol rep 1

description: Library name: iKCs, L514F, biol rep 1

value: BJ-T converted to iKCs


title: iKCs, GFP CTR, biol rep 4

description: Library name: iKCs, GFP CTR, biol rep 4


title: Whole blood DNA methylation, NHW CONTROL, 77yo M, 207219740068_R01C01

value: Healthy control

value: NHW


title: Whole blood DNA methylation, AA AD, 74yo F, 207215820097_R05C01

value: Female

value: AA

value: REAAADI


title: iKCs, GFP CTR, biol rep 3

description: Library name: iKCs, GFP CTR, biol rep 3

value: iKCs conversion


title: Whole blood DNA methylation, NHW AD, 76yo F, 207215820089_R02C01


title: iKCs, GFP CTR, biol rep 2

description: Library name: iKCs, GFP CTR, biol rep 2


title: Whole blood DNA methylation, NHW CONTROL, 67yo F, 207215820131_R04C01


title: iKCs, GFP CTR, biol rep 1

description: Library name: iKCs, GFP CTR, biol rep 1


title: Whole blood DNA methylation, NHW CONTROL, 72yo F, 207215820132_R03C01


title: iKCs, WT CTR, biol rep 4

description: Library name: iKCs, WT CTR, biol rep 4


title: iKCs, WT CTR, biol rep 3

description: Library name: iKCs, WT CTR, biol rep 3


title: iKCs, WT CTR, biol rep 2

description: Library name: iKCs, WT CTR, biol rep 2


title: Whole blood DNA methylation, AA CONTROL, 67yo M, 207215820065_R06C01

value: Male


title: Whole blood DNA methylation, AA AD, 67yo F, 207215820062_R04C01


title: iKCs, WT CTR, biol rep 1

description: Library name: iKCs, WT CTR, biol rep 1


title: 22Rv1, Control + OICR 9429, Rep4

city: Florence

first: Paola

last: Chiarugi

state: Florence

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

institute: University of Florence

description: Library name: 146764_ID3399_15-4C

data_processing:
Sequence reads were trimmed for adaptor/low quality sequence using fastp
Trimmed sequence reads were mapped to GRCh38 using STAR
Read count extraction was performed using HTSeq count
Differential Expression analysis was performed by DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw count for each sample

growth_protocol: 22Rv1 cells were manteined in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using RNeasy Kit (#74104; Qiagen) and RNA-seq was performed starting from 800 ng of RNA from each sample.
Universal Plus mRNA-Seq kit

treatment_protocol: 22Rv1 cells were treated with Lactate 20 mM and/or OICR-9429 10 μM; RNA was extracted 48h after treatments

value: Epithelial cell line


title: Whole blood DNA methylation, NHW CONTROL, 77yo M, 207219630048_R05C01


title: 22Rv1, Control, Rep4

description: Library name: 146762_ID3399_13-4A

value: Control


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215830065_R04C01


title: Whole blood DNA methylation, AA CONTROL, 77yo F, 207221680059_R07C01


title: 22Rv1, Lactate + OICR 9429, Rep3

description: Library name: 146761_ID3399_12-3D


title: 22Rv1, Control + OICR 9429, Rep3

description: Library name: 146760_ID3399_11-3C


title: 22Rv1, Lactate, Rep3

description: Library name: 146759_ID3399_10-3B

value: Lactate


title: Whole blood DNA methylation, HISPANIC CONTROL, 77yo M, 207215820048_R02C01

value: HISPANIC

value: PRADI


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207228480032_R01C01


title: iKCs, G293H, biol rep 4

description: Library name: iKCs, G293H, biol rep 4


title: 22Rv1, Control, Rep3

description: Library name: 146758_ID3399_9-3A

value: WT


title: 22Rv1, Lactate + OICR 9429, Rep2

description: Library name: 146757_ID3399_8-2D


title: Whole blood DNA methylation, HISPANIC CONTROL, 88yo F, 207215820076_R05C01


title: 22Rv1, Control + OICR 9429, Rep2

description: Library name: 146756_ID3399_7-2C


title: Whole blood DNA methylation, HISPANIC CONTROL, 93yo M, 207215820121_R04C01


title: 22Rv1, Lactate, Rep2

description: Library name: 146755_ID3399_6-2B


title: 22Rv1, Control, Rep2

description: Library name: 146754_ID3399_5-2A


title: Whole blood DNA methylation, HISPANIC CONTROL, 87yo F, 207215820065_R07C01


title: 22Rv1, Lactate + OICR 9429, Rep1

description: Library name: 146753_ID3399_4-1D


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo F, 207096540063_R08C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207219630128_R01C01


title: 22Rv1, Control + OICR 9429, Rep1

description: Library name: 146752_ID3399_3-1C


title: Whole blood DNA methylation, HISPANIC CONTROL, 77yo F, 207215820075_R01C01


title: 22Rv1, Lactate, Rep1

description: Library name: 146751_ID3399_2-1B


title: 22Rv1, Control, Rep1

description: Library name: 146750_ID3399_1-1A


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097650112_R06C01


title: HT-1080 shBCAT1-2

city: Kyoto

first: Yoshiki

last: Yamamoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

institute: Kyoto University

description:
Library name: HT-1080 shBCAT1-2
RNA_counts_HT-1080.csv

data_processing:
CLC Genomics Workbench
Raw quantification output is Total Count for each gene (GE files) or transcript (TE files), for each sample
Mapped reads exported, converted into bedgraph for visualization in UCSC browser
Assembly: hg38
Supplementary files format and content: csv files include raw counts.
Supplementary files format and content: excel files include RPKM.

growth_protocol: All cell lines were maintained at 37 °C in a humidified incubator with 5% CO2 in RPMI1640 media supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Total cellular RNAs were isolated using TRIzol Reagent (Thermo).
Standard: 500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420) • Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420)

value: chondrosarcoma

value: BCAT1 knockdown


title: Whole blood DNA methylation, HISPANIC CONTROL, 80yo F, 207221680026_R08C01

value: whole blood


title: Whole blood DNA methylation, HISPANIC CONTROL, 72yo F, 207215820085_R07C01


title: HT-1080 shBCAT1-1

description:
Library name: HT-1080 shBCAT1-1
RNA_counts_HT-1080.csv


title: HT-1080 shCtrl-2

description:
Library name: HT-1080 shCtrl-2
RNA_counts_HT-1080.csv


title: HT-1080 shCtrl-1

description:
Library name: HT-1080 shCtrl-1
RNA_counts_HT-1080.csv


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207215830126_R01C01


title: TBL62_batch_5_ROI_24_anno_Other

city: Los Angeles

first: Jonathan

last: Perrie

state: CA

address: 610 Charles E Young Dr S

department: Bioinformatics

institute: University of California, Los Angeles

description:
Library name: TBL62_batch_5_ROI_24
None

data_processing:
Analysis began with GeoMx DCC files and followed the pre-processing and normalization steps outlined in the GeoMxWorkflows R vignette.
ROIs were filtered to exclude those detecting less than 5% of total genes from the Whole Transcriptome Atlas. Genes were subsequently filtered to exclude those detected in fewer than 5% of ROIs.
The raw expression matrix was normalized using the 75th percentile normalization.
Assembly: hg38
Supplementary files format and content: DCC files: digital count conversion format per ROI
Supplementary files format and content: geomx_ptb_metadata.csv: ROI attributes after pre-processing
Supplementary files format and content: geomx_ptb_negprobes.csv: negative probe counts
Supplementary files format and content: geomx_ptb_q3_data.csv: quantile normalized counts
Supplementary files format and content: geomx_ptb_raw_data.csv: raw counts
Library strategy: Spatial Transcriptomics

source_name: Lymph

extract_protocol:
Lung FFPE tissue sections were mounted on glass slides, deparaffinized, and rehydrated following the GeoMx DSP manufacturer’s protocol. Slides were hybridized overnight at 37 °C with the GeoMx Human Whole Transcriptome Atlas probe set. Tissue morphology markers were revealed by fluorescent immunostaining to guide the selection of ROIs.
Barcoded oligonucleotide probes were photocleaved from selected ROIs by UV exposure and collected into separate wells. Oligos were uniquely indexed, and paired-end reads were generated by Illumina sequencing, then aligned and quantified using NanoString’s DSP analysis pipeline.

value: Lymph

tag: region

value: Other


title: TBL62_batch_5_ROI_23_anno_Other

description:
Library name: TBL62_batch_5_ROI_23
None


title: TBL62_batch_5_ROI_22_anno_Other

description:
Library name: TBL62_batch_5_ROI_22
None


title: TBL62_batch_5_ROI_21_anno_Other

description:
Library name: TBL62_batch_5_ROI_21
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 76yo F, 207228480032_R07C01

value: Healthy control


title: Whole blood DNA methylation, HISPANIC CONTROL, 78yo M, 207221680011_R01C01


title: TBL62_batch_5_ROI_20_anno_Other

description:
Library name: TBL62_batch_5_ROI_20
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 79yo F, 207215820065_R03C01

value: Female


title: TBL62_batch_5_ROI_19_anno_Other

description:
Library name: TBL62_batch_5_ROI_19
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207228480079_R06C01


title: TBL62_batch_5_ROI_18_anno_Other

description:
Library name: TBL62_batch_5_ROI_18
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 84yo F, 207221680011_R07C01


title: TBL62_batch_5_ROI_17_anno_Other

description:
Library name: TBL62_batch_5_ROI_17
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207215820046_R03C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 80yo F, 207228480080_R02C01


title: TBL62_batch_5_ROI_16_anno_Other

description:
Library name: TBL62_batch_5_ROI_16
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207219630128_R08C01


title: iKCs, L548N, biol rep 3

description: Library name: iKCs, L548N, biol rep 3

value: BJ-T converted to iKCs


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo M, 207215820055_R02C01


title: Whole blood DNA methylation, AA CONTROL, 67yo F, 207215830074_R02C01

value: AA

value: REAAADI


title: Whole blood DNA methylation, AA CONTROL, 67yo F, 207097650112_R02C01


title: iKCs, L548N, biol rep 2

description: Library name: iKCs, L548N, biol rep 2

value: iKCs conversion


title: TBL62_batch_5_ROI_15_anno_Other

description:
Library name: TBL62_batch_5_ROI_15
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo M, 207097650075_R07C01

value: Male


title: TBL62_batch_5_ROI_14_anno_Other

description:
Library name: TBL62_batch_5_ROI_14
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207096540063_R02C01


title: Whole blood DNA methylation, AA AD, 69yo F, 207215830119_R06C01

value: Alzheimer's disease


title: TBL62_batch_5_ROI_13_anno_Other

description:
Library name: TBL62_batch_5_ROI_13
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 86yo F, 207219770143_R06C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 86yo M, 207215830119_R04C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 84yo F, 207215820047_R02C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 74yo F, 207215820048_R08C01


title: TBL62_batch_5_ROI_11_anno_Other

description:
Library name: TBL62_batch_5_ROI_11
None


title: TBL62_batch_5_ROI_12_anno_Other

description:
Library name: TBL62_batch_5_ROI_12
None


title: TBL62_batch_5_ROI_10_anno_Other

description:
Library name: TBL62_batch_5_ROI_10
None


title: iDC-MuV2, Input

first: Mijia

last: Lu

address: 180 Tianmushan Rd

institute: Hangzhou Medical College

description: Library name: SAMPLE12

data_processing:
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 software (v2.0.4). Methylated genes in each sample were then identified using MACS software (1.4.2). Differential methylation gene identification was performed using diffReps software (1.55.6). The peaks located on exons were mRNA or LncRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated mRNA and associated genes of LncRNA origin, respectively. circRNA: High quality reads were compared to the reference genome using STAR (v2.5.1b), and circular RNA was detected and identified using DCC(v0.4.4). circBase database and Circ2Traits were used to annotate the identified circular RNA. The peaks located on circRNA were screened, and the source genes of differentially modified circRNA were analyzed by GO and KEGG.
Assembly: GRch38/hg38
Supplementary files format and content: .xlsx. Column A ~ E: the coordinates of the methylated RNA sites in bed format, please ref http://genome.ucsc.edu/FAQ/FAQformat.html#format1. Column F: the length of the methylated RNA sites Column G ~ H: the transcript id and gene symbol of methylated RNA. Column I ~ K: the enrichment results calculated by MACS. Column L ~ S: the annotation of the methylated gene.

source_name: iDC-MuV2, IP

extract_protocol:
The infected or mock-infected cells was collected at 16 h post-infection (hpi) for total RNA extraction using TRIzol reagent according to the product manual.
The total RNA was subjected to immunoprecipitation using the GenSeq® m6A MeRIP Kit (GenSeq Inc.), following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents.  Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed several times, and then, the captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced.

treatment_protocol: THP1-iDC was infected with rhMPV or rMuV, with the control of DMEM (n=2) for 16 hours.

value: iDC-MuV2, IP

value: MuV-infection


title: iDC-Ctrl1, Input

description: Library name: SAMPLE7

source_name: iDC-Ctrl1, IP

value: iDC-Ctrl1, IP

value: Mock infection


title: bovine_8C_to_16C_ONT

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

description: Library name: Sample2

data_processing:
Mouse and bovine Fast5 files were basecalled using MinKNOW (v6.0.14) or Dorado (v0.6.3 or v0.7.3) to generate FASTQ files. The FASTQ reads were then processed and mapped to reference genomes using the wf-transcriptomes pipeline in EPI2ME (v1.7.1) (https://github.com/epi2me-labs/wf-transcriptomes) to obtain GTF files. The mouse reference genome (mm10) and annotation data were downloaded from Illumina iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn), while the bovine reference genome and annotation data were downloaded from the UCSC Genome Browser database (https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/).
Assembly: mm10 or bosTau9
Supplementary files format and content: GTF files generated by EPI2ME (v1.7.1).

organism: Bos taurus

source_name: 8-cell to 16-cell stage embryo

growth_protocol: Superovulated mouse oocytes (Slc:ICR) were in vitro fertilized and resulting embryos were cultured in KSOM up to late two-cell stage (36 hpi). Bovine oocytes were recovered from the ovaries of Japanese Black or Japanese Black × Holstein F1 bovine. In vitro matured oocytes were subjected to IVF with sperm from a Japanese Black bull. At 72 h post-insemination, 8-cell to 16-cell stage bovine embryos were collected.

extract_protocol:
Total RNA was extracted from approximately 200 embryos per each group, by using TRIzol reagent (Thermo Fisher Scientific Inc.) according to the manufacturer’s manual.
The cDNA-PCR Sequencing Kit (SQK-PCS114; Oxford Nanopore Technologies Plc., Oxford, UK) was used for reverse transcription and library preparation according to the manufacturer's protocol. After reverse transcription, cDNA was amplified using LongAmp Hot Start Taq 2X Master Mix (New England Biolabs) with 14 cycles. Amplified cDNA was purified using AMPure XP beads (Beckman Coulter, Inc., Brea, CA) and quantified using a Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.). Each library was separately loaded into an R10.4.1 flow cell (Oxford Nanopore Technologies Plc.) and sequenced on a MinION sequencer (Oxford Nanopore Technologies Plc.).

value: 8-cell to 16-cell stage embryo

value: in vitro produced


title: Whole blood DNA methylation, HISPANIC CONTROL, 81yo F, 207215830074_R06C01

value: whole blood

value: HISPANIC

value: PRADI


title: iDC-hMPV2, Input

description: Library name: SAMPLE10

source_name: iDC-hMPV2, IP

value: iDC-hMPV2, IP

value: hMPV-infection


title: Whole blood DNA methylation, AA CONTROL, 72yo F, 207215820061_R06C01

value: Female

value: Healthy control


title: iKCs, L514D, biol rep 1

description: Library name: iKCs, L514D, biol rep 1

value: BJ-T converted to iKCs


title: TBL62_batch_5_ROI_9_anno_Other

description:
Library name: TBL62_batch_5_ROI_9
None

value: Lymph

value: Other


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207215830065_R06C01


title: TBL62_batch_5_ROI_8_anno_Other

description:
Library name: TBL62_batch_5_ROI_8
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207219740068_R03C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo F, 207215820094_R08C01


title: TBL62_batch_5_ROI_7_anno_Other

description:
Library name: TBL62_batch_5_ROI_7
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 83yo M, 207215830057_R04C01

value: Male


title: TBL62_batch_5_ROI_6_anno_Other

description:
Library name: TBL62_batch_5_ROI_6
None


title: TBL62_batch_5_ROI_5_anno_Other

description:
Library name: TBL62_batch_5_ROI_5
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 88yo F, 207215820034_R07C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 86yo F, 207215820131_R01C01


title: TBL62_batch_5_ROI_4_anno_Other

description:
Library name: TBL62_batch_5_ROI_4
None


title: TBL62_batch_5_ROI_3_anno_Other

description:
Library name: TBL62_batch_5_ROI_3
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 76yo F, 207215830057_R02C01


title: TBL62_batch_5_ROI_2_anno_Other

description:
Library name: TBL62_batch_5_ROI_2
None


title: TBL62_batch_5_ROI_1_anno_Other

description:
Library name: TBL62_batch_5_ROI_1
None


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207215830057_R03C01

value: Alzheimer's disease


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207215820055_R03C01


title: Whole blood DNA methylation, HISPANIC AD, 92yo F, 207215820065_R05C01


title: NTC_batch_5_ROI_NA_anno_NA

description:
Library name: NTC_batch_5_ROI_NA
None

source_name: Control

value: Control


title: EPTB222_batch_5_ROI_24_anno_Other

description:
Library name: EPTB222_batch_5_ROI_24
None

source_name: Abdomen

value: Abdomen


title: Whole blood DNA methylation, HISPANIC AD, 79yo F, 207228480080_R06C01


title: EPTB222_batch_5_ROI_23_anno_Other

description:
Library name: EPTB222_batch_5_ROI_23
None


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207097650075_R06C01


title: EPTB222_batch_5_ROI_21_anno_Other

description:
Library name: EPTB222_batch_5_ROI_21
None


title: Whole blood DNA methylation, HISPANIC AD, 91yo M, 207215830119_R02C01


title: EPTB222_batch_5_ROI_20_anno_Other

description:
Library name: EPTB222_batch_5_ROI_20
None


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207215820044_R02C01


title: EPTB222_batch_5_ROI_19_anno_Other

description:
Library name: EPTB222_batch_5_ROI_19
None


title: Whole blood DNA methylation, HISPANIC AD, 78yo M, 207215830104_R06C01


title: EPTB222_batch_5_ROI_18_anno_Other

description:
Library name: EPTB222_batch_5_ROI_18
None


title: Whole blood DNA methylation, HISPANIC AD, 84yo F, 207215830074_R01C01

value: CuADI


title: EPTB222_batch_5_ROI_17_anno_Other

description:
Library name: EPTB222_batch_5_ROI_17
None


title: Whole blood DNA methylation, AA CONTROL, 70yo M, 207215830074_R08C01

value: AA

value: REAAADI


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo F, 207215820045_R05C01

value: whole blood


title: Whole blood DNA methylation, HISPANIC CONTROL, 67yo F, 207228480032_R03C01

value: HISPANIC


title: EPTB222_batch_5_ROI_15_anno_Other

description:
Library name: EPTB222_batch_5_ROI_15
None


title: EPTB222_batch_5_ROI_14_anno_Other

description:
Library name: EPTB222_batch_5_ROI_14
None


title: Whole blood DNA methylation, HISPANIC AD, 76yo M, 207215820132_R08C01

value: PRADI


title: EPTB222_batch_5_ROI_12_anno_Other

description:
Library name: EPTB222_batch_5_ROI_12
None


title: Whole blood DNA methylation, HISPANIC AD, 75yo F, 207215820076_R08C01


title: Whole blood DNA methylation, HISPANIC AD, 76yo F, 207221680011_R08C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 74yo M, 207097650070_R02C01


title: Whole blood DNA methylation, HISPANIC AD, 76yo F, 207096540063_R03C01


title: EPTB222_batch_5_ROI_10_anno_Other

description:
Library name: EPTB222_batch_5_ROI_10
None


title: Whole blood DNA methylation, HISPANIC AD, 79yo F, 207219630047_R02C01


title: EPTB222_batch_5_ROI_9_anno_Other

description:
Library name: EPTB222_batch_5_ROI_9
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo F, 207228480014_R06C01


title: EPTB222_batch_5_ROI_7_anno_Other

description:
Library name: EPTB222_batch_5_ROI_7
None


title: Whole blood DNA methylation, HISPANIC AD, 71yo F, 207219630047_R07C01


title: EPTB222_batch_5_ROI_6_anno_Other

description:
Library name: EPTB222_batch_5_ROI_6
None


title: Whole blood DNA methylation, HISPANIC AD, 85yo M, 207219630128_R04C01


title: Whole blood DNA methylation, HISPANIC AD, 81yo M, 207228480032_R04C01


title: EPTB222_batch_5_ROI_4_anno_Other

description:
Library name: EPTB222_batch_5_ROI_4
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207219630128_R06C01


title: EPTB222_batch_5_ROI_3_anno_Other

description:
Library name: EPTB222_batch_5_ROI_3
None


title: Whole blood DNA methylation, HISPANIC AD, 79yo F, 207096540017_R07C01


title: EPTB222_batch_5_ROI_2_anno_Other

description:
Library name: EPTB222_batch_5_ROI_2
None


title: EPTB222_batch_5_ROI_1_anno_Other

description:
Library name: EPTB222_batch_5_ROI_1
None


title: Whole blood DNA methylation, HISPANIC CONTROL, 82yo M, 207215820089_R07C01


title: PTB223_batch_4_ROI_15_anno_Alveoli

description:
Library name: PTB223_batch_4_ROI_15
Alveoli | PTB 22.3 | 15

source_name: Lung

value: Lung

value: Alveoli


title: Whole blood DNA methylation, HISPANIC AD, 82yo F, 207219740068_R05C01

value: Female


title: PTB223_batch_4_ROI_14_anno_Alveoli

description:
Library name: PTB223_batch_4_ROI_14
Alveoli | PTB 22.3 | 14


title: SV40-MES-13, Drosha KD, miRNAseq, rep2

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

description:
Library name: DroshaKD_rep2
Drosha_sh_2

data_processing:
Raw FASTQ files were trimmed using fastx_trimmer to remove adapters and aligned to mouse mature miRNA sequences (miRbase release 22.1) using bowtie (version 1.3.1). miRNA abundance was quantified using samtools idxstats command and subsequently normalized to Reads per Million (RPM). Differential expression analysis was performed using the limma R package (version 3.62.0), employing linear models and empirical Bayes methods.
Assembly: mm10
Supplementary files format and content: xlsx file include RPM values for each Sample

extract_protocol:
Total RNA was extracted from the mouse renal mesangial cell line ME13 sv40 (both DROSHA knockdown and control groups) using a standard phenol-chloroform-based method (TRIzol reagent). The protocol involved cell lysis, phase separation with chloroform, RNA precipitation with isopropanol, and washing with ethanol. To specifically enrich for small RNA species (including microRNAs), the total RNA fraction was further processed. Small RNAs (approximately 18-30 nucleotides) were size-selected and purified using a commercial kit (mirVana™ miRNA Isolation Kit or similar) according to the manufacturer's instructions. The final RNA concentration and integrity were assessed using a spectrophotometer (NanoDrop) and a bioanalyzer ( Agilent 2100 Bioanalyzer with the Small RNA Kit), respectively, to ensure high-quality input material for library construction.
Small RNA sequencing libraries were constructed from the enriched small RNA samples using a dedicated commercial kit(NEBNext® Multiplex Small RNA Library Prep Set for Illumina). The protocol typically involved the following key steps: First, 3' and 5' RNA adapters were sequentially ligated to the small RNAs. The adapter-ligated RNA was then reverse-transcribed into cDNA. Following this, the cDNA was amplified via PCR using primers containing unique index sequences to allow for sample multiplexing. The final PCR products, representing the small RNA library, were size-selected to isolate fragments corresponding to the desired library size range (typically ~140-160 bp for mature microRNAs) using gel electrophoresis or magnetic bead-based purification. Library quality and concentration were validated using a High Sensitivity DNA assay on a bioanalyzer or by qPCR, and were then pooled in equimolar amounts for sequencing on an NextSeq  Illumina platform.

value: mouse renal mesangial cell

value: Drosha KD


title: Whole blood DNA methylation, HISPANIC AD, 80yo F, 207215820061_R03C01


title: PTB223_batch_4_ROI_13_anno_Alveoli

description:
Library name: PTB223_batch_4_ROI_13
Alveoli | PTB 22.3 | 13


title: PTB223_batch_4_ROI_12_anno_Alveoli

description:
Library name: PTB223_batch_4_ROI_12
Alveoli | PTB 22.3 | 12


title: PTB223_batch_4_ROI_11_anno_Mantle

description:
Library name: PTB223_batch_4_ROI_11
Mantle | PTB 22.3 | 11

value: Mantle


title: SV40-MES-13, WT, miRNAseq, rep1

description:
Library name: WT_rep1
A475_1

value: WT


title: SV40-MES-13, sh7 Drosha KO, RNAseq, rep2

description: Library name: sh7_Drosha_KO_rep2

data_processing:
Transcript abundances were quantified using the kallisto (version 0.48.0) under default set_x001f_tings. The transcript-level abundance estimates results were then imported into the R package tximport to summarize the gene-level abundance estimates for downstream analysis.
Assembly: GENCODE.vM29
Supplementary files format and content: xlsx file include TPM values for each Sample

growth_protocol: Mouse renal mesangial cells (SV40-MES-13) were cultured in high-glucose DMEM (PM150210, Pricella) and Ham's F-12 (PM150810, Pricella) (3:1 ratio) containing 5% (v/v) FBS and penicillin and streptomycin. HEK293T cells were cultured in high-glucose DMEM containing 10% (v/v) FBS and penicillin and streptomycin. All cells were maintained at 37 ℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
The total RNA of SV40-MES-13 cells was extracted using Ultrapure RNA Kit (CW BIO, CW0581M) and sent to BGI Genomics for library preparation and sequencing (Illumina HiSeq 2500).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 150 bases reads are generated onT7 platform (BGI-Shenzhen, China).

treatment_protocol: Lentivirus vectors For the construction of the lentiviral knockdown plasmid, shRNA sequences targeting Drosha were used: sh-5 Drosha (CCTGGAATATGTCCACACTTT) and sh-7 Drosha (GTGTGCCCATTGAAATAAA). These sequences were cloned into the pLL 3.7 vector (Addgene #11795). For lentivirus packaging, HEK293T cells were co-transfected with lentiviral vectors, psPAX2 (Addgene #12260), pMD2G (Addgene #12259), and the sh-Drosha pLL3.7 construct using PEI (Yeasen, MW40000). The viruses were harvested 48 hours post-transfection after filtering through a 0.45μm membrane, and the viral titer was then determined. The sequences for all the primers used are listed in Supplementary Table 1. Lentivirus infection Lentivirus particles were concentrated using ViralStarsTM LC Lentivirus Concentrate Reagent (LeapWal, LC110R) prior to infection. EnvirusTM-LV diluent (Engreen, 30001-2) was used to enhance the infection efficiency, and SV40-MES-13 cells were infected with the concentrated lentivirus following the manufacture’s guidelines.

value: Mouse renal mesangial cells

value: Drosha KO


title: Whole blood DNA methylation, HISPANIC CONTROL, 68yo F, 207228480080_R07C01

value: Healthy control


title: SV40-MES-13, sh7 Drosha KO, RNAseq, rep1

description: Library name: sh7_Drosha_KO_rep1


title: SV40-MES-13, sh5 Drosha KO, RNAseq, rep1

description: Library name: sh5_Drosha_KO_rep1


title: PTB223_batch_4_ROI_10_anno_Core

description:
Library name: PTB223_batch_4_ROI_10
Core | PTB 22.3 | 10

value: Core


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097650070_R08C01


title: SV40-MES-13, Empty vector, RNAseq, rep2

description: Library name: EV_rep2


title: PTB223_batch_4_ROI_9_anno_Core

description:
Library name: PTB223_batch_4_ROI_9
Core | PTB 22.3 | 09


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo F, 207215830126_R03C01


title: TMAO+IR-3

first: Chongbin

last: Zhong

address: No 253, Middle Gongye Avenue

department: Department of Cardiology

institute: Zhujiang Hospital, Southern Medical University

description: Library name: sample6

data_processing:
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0). Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts

source_name: heart sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
Eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis and PCR amplified.

value: heart sample

value: wt

value: TMAO preconditioning+ ischemia-reperfusion (IR) models


title: SV40-MES-13, Empty vector, RNAseq, rep1

description: Library name: EV_rep1


title: PTB223_batch_4_ROI_8_anno_Mantle

description:
Library name: PTB223_batch_4_ROI_8
Mantle | PTB 22.3 | 08


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207097650067_R04C01

source_name: whole blood

value: whole blood


title: TMAO+IR-2

description: Library name: sample5


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207215820034_R04C01

value: HISPANIC


title: IR-3

description: Library name: sample3

value: ischemia-reperfusion (IR) models


title: Whole blood DNA methylation, HISPANIC AD, 85yo F, 207215830074_R03C01

value: Alzheimer's disease

value: PRADI


title: PTB223_batch_4_ROI_7_anno_Core

description:
Library name: PTB223_batch_4_ROI_7
Core | PTB 22.3 | 07

value: Lung


title: TMAO+IR-1

description: Library name: sample4


title: PTB223_batch_4_ROI_6_anno_Core

description:
Library name: PTB223_batch_4_ROI_6
Core | PTB 22.3 | 06


title: IR-1

description: Library name: sample1


title: Whole blood DNA methylation, HISPANIC CONTROL, 74yo F, 207096540017_R01C01

value: Female


title: Fenofibrate_50_3

city: Beijing

first: Yang

last: Liu

address: No. 49, Huayuan North Road, Haidian District, Beijing

institute: Peking University Third Hospital

description:
Library name: FF_3
F503_FPKM

data_processing:
Raw sequencing reads were processed using the following steps: 1 Quality Control: Adapter sequences were removed using Seqtk, followed by trimming of 3’-end bases with Q-scores <20 (error rate <0.01; Q=-10log₁₀(error_ratio)). Reads shorter than 25 bp or aligned to ribosomal RNA were discarded. 2 Alignment: Filtered reads were mapped to the reference genome using HISAT2 (v2.0.4) with spliced alignment mode. 3 Quantification: Gene-level fragment counts were generated by StringTie (v1.3.0) and normalized via the TMM method. 4 FPKM Calculation: Normalized FPKM values were computed using a Perl script.
Assembly: GRCm39 (Genome Reference Consortium Mouse Build 39)
Supplementary files format and content: processed data file_FPKM.txt File type: Tab-delimited text file (.txt) Content: Gene expression matrix in FPKM units Normalization: FPKM calculated using StringTie (v1.3.0) with TMM((trimmed mean of M values)) normalization

source_name: B16F15 melanoma cell line

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Purified total RNA was subjected to mRNA enrichment, fragmentation, and cDNA synthesis (first- and second-strand). The resulting double-stranded cDNA underwent end repair, 3'-end adenylation, and adapter ligation. Libraries were then enriched by PCR amplification and quantified using a Qubit® 2.0 Fluorometer with the Qubit™ dsDNA HS Assay Kit.

value: B16F15 melanoma cell line


title: PTB223_batch_4_ROI_5_anno_Core

description:
Library name: PTB223_batch_4_ROI_5
None


title: Fenofibrate_50_2

description:
Library name: FF_2
F502_FPKM

source_name: B16F14 melanoma cell line

value: B16F14 melanoma cell line


title: Whole blood DNA methylation, HISPANIC AD, 78yo F, 207215820006_R06C01

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).


title: Fenofibrate_50_1

description:
Library name: FF_1
F501_FPKM

source_name: B16F13 melanoma cell line

value: B16F13 melanoma cell line


title: PTB223_batch_4_ROI_4_anno_Mantle

description:
Library name: PTB223_batch_4_ROI_4
Mantle | PTB 22.3 | 04

value: Mantle


title: Ctrl_3

description:
Library name: Ctrl_3
Ctrl3_FPKM

source_name: B16F12 melanoma cell line

value: B16F12 melanoma cell line


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207221680059_R05C01

value: Healthy control


title: Ctrl_2

description:
Library name: Ctrl_2
Ctrl2_FPKM

source_name: B16F11 melanoma cell line

value: B16F11 melanoma cell line


title: PTB223_batch_4_ROI_3_anno_Mantle

description:
Library name: PTB223_batch_4_ROI_3
Mantle | PTB 22.3 | 03


title: Ctrl_1

description:
Library name: Ctrl_1
Ctrl1_FPKM

source_name: B16F10 melanoma cell line

value: B16F10 melanoma cell line


title: Whole blood DNA methylation, HISPANIC AD, 98yo F, 207215820131_R05C01


title: BC0141

city: Stanford

first: Laura

last: Amaya

address: 269 Campus Drive

institute: Stanford University

description: Library name: BC0141

data_processing:
Adapters were trimmed using cutadapt, and reads were mapped to the hg38 genome using bowtie2 with a maximum fragment length of 2000bp. Filtering criteria included non-mitochondrial reads, mapq > 20, and properly paired reads. Duplicates were removed using Picard tools. Peak calling was performed using macs2 with specific parameters (--shift -75 --extsize 150 --nomodel --call-summits --nolambda -p 0.01 -B –SPMR) on Tn5 insertion sites.
ChrAccR (https://github.com/GreenleafLab/ChrAccR) was utilized for differential accessibility analysis between sorted T cell populations.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Blood

growth_protocol: Tr1 and non-Tr1 cells were isolated from T-allo10 cell products, and Teff isolated from T-allo cell products at day 10 of culture by FACS. CD4+ T cells, CD4+ T cells were isolated using FACS from cryopreserved PBMC from the first cohort of patients with hematological malignancies infused with 1 x 106 T-allo10 cells/kg a day before their unmanipulated allo-HSCT (ClinicalTrials.gov ID: NCT03198234) at day 35, 90 and 300 post-treatment (n = 3), and four healthy donors.

extract_protocol:
DNA was tagmented and libraries prepared following the OMNI-ATAC protocol
DNA was tagmented and libraries prepared following the OMNI-ATAC protocol

value: Blood

value: Healthy

value: No treatment

value: TimeNA


title: PTB223_batch_4_ROI_2_anno_Core

description:
Library name: PTB223_batch_4_ROI_2
Core | PTB 22.3 | 02

value: Core


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207215830103_R08C01

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

value: Male

value: Alzheimer's disease

value: whole blood

value: HISPANIC


title: HD

description: Library name: HD


title: BC3826

description: Library name: BC3826


title: PTB223_batch_4_ROI_1_anno_Mantle

description:
Library name: PTB223_batch_4_ROI_1
Mantle | PTB 22.3 | 01

value: Lung


title: BC2800

description: Library name: BC2800


title: Whole blood DNA methylation, HISPANIC CONTROL, 80yo M, 207215820076_R03C01

value: PRADI


title: Pt3_D300

description: Library name: Pt3_D300

value: Patient

value: Tallo

value: Day 300


title: PTB221_batch_4_ROI_26_anno_Alveoli

description:
Library name: PTB221_batch_4_ROI_26
Alveoli | PTB 22.1 | 26

value: Alveoli


title: IR-2

description: Library name: sample2

value: heart sample

value: wt

value: ischemia-reperfusion (IR) models


title: Pt2_D300

description: Library name: Pt2_D300

value: Blood


title: Whole blood DNA methylation, HISPANIC AD, 80yo F, 207215820089_R08C01

value: Female


title: Pt1_D300

description: Library name: Pt1_D300


title: PTB221_batch_4_ROI_25_anno_Alveoli

description:
Library name: PTB221_batch_4_ROI_25
Alveoli | PTB 22.1 | 25


title: Pt3_D90

description: Library name: Pt3_D90

value: Day 90


title: Whole blood DNA methylation, HISPANIC CONTROL, 77yo F, 207221680026_R01C01

value: Healthy control


title: Pt2_D90

description: Library name: Pt2_D90


title: Whole blood DNA methylation, HISPANIC CONTROL, 76yo F, 207215820132_R02C01


title: EPTB222_batch_5_ROI_22_anno_Other

description:
Library name: EPTB222_batch_5_ROI_22
None

value: Abdomen

value: Other


title: Pt1_D90

description: Library name: Pt1_D90


title: PTB221_batch_4_ROI_24_anno_Alveoli

description:
Library name: PTB221_batch_4_ROI_24
Alveoli | PTB 22.1 | 24


title: Pt3_D35

description: Library name: Pt3_D35

value: Day 35


title: Whole blood DNA methylation, HISPANIC CONTROL, 68yo F, 207215820048_R05C01

value: whole blood

value: HISPANIC


title: PTB221_batch_4_ROI_23_anno_Alveoli

description:
Library name: PTB221_batch_4_ROI_23
Alveoli | PTB 22.1 | 23

value: Lung


title: Whole blood DNA methylation, HISPANIC AD, 89yo F, 207215820077_R08C01

value: Alzheimer's disease

value: PRADI


title: EPTB222_batch_5_ROI_16_anno_Other

description:
Library name: EPTB222_batch_5_ROI_16
None


title: Whole blood DNA methylation, HISPANIC AD, 82yo M, 207215820075_R04C01

value: Male


title: Pt2_D35

description: Library name: Pt2_D35

value: Patient

value: Tallo


title: Pt1_D35

description: Library name: Pt1_D35


title: EPTB222_batch_5_ROI_13_anno_Other

description:
Library name: EPTB222_batch_5_ROI_13
None


title: PTB221_batch_4_ROI_22_anno_Alveoli

description:
Library name: PTB221_batch_4_ROI_22
Alveoli | PTB 22.1 | 22

value: Alveoli


title: JJ012-1 shBCAT1-3

description:
Library name: JJ012-1 shBCAT1-3
JJ012_RPKM.xlsx

value: chondrosarcoma

value: BCAT1 knockdown


title: Whole blood DNA methylation, HISPANIC AD, 84yo M, 207215830118_R01C01


title: JJ012-1 shBCAT1-2

description:
Library name: JJ012-1 shBCAT1-2
JJ012_RPKM.xlsx


title: PTB221_batch_4_ROI_21_anno_Mantle

description:
Library name: PTB221_batch_4_ROI_21
Mantle | PTB 22.1 | 21

value: Mantle


title: EPTB222_batch_5_ROI_11_anno_Other

description:
Library name: EPTB222_batch_5_ROI_11
None


title: EPTB222_batch_5_ROI_8_anno_Other

description:
Library name: EPTB222_batch_5_ROI_8
None


title: Whole blood DNA methylation, HISPANIC AD, 82yo F, 207215830018_R04C01

value: Female


title: JJ012-1 shCtrl-3

description:
Library name: JJ012-1 shCtrl-3
JJ012_RPKM.xlsx

value: WT


title: PTB221_batch_4_ROI_20_anno_Core

description:
Library name: PTB221_batch_4_ROI_20
Core | PTB 22.1 | 20

value: Core


title: JJ012-1 shBCAT1-1

description:
Library name: JJ012-1 shBCAT1-1
JJ012_RPKM.xlsx


title: JJ012-1 shCtrl-2

description:
Library name: JJ012-1 shCtrl-2
JJ012_RPKM.xlsx


title: Whole blood DNA methylation, HISPANIC AD, 87yo F, 207097650070_R05C01


title: JJ012-1 shCtrl-1

description:
Library name: JJ012-1 shCtrl-1
JJ012_RPKM.xlsx


title: PTB221_batch_4_ROI_19_anno_Core

description:
Library name: PTB221_batch_4_ROI_19
Core | PTB 22.1 | 19


title: NDCS-1 shBCAT1-3

description:
Library name: NDCS-1 shBCAT1-3
NDCS-1_RPKM.xlsx


title: EPTB222_batch_5_ROI_5_anno_Other

description:
Library name: EPTB222_batch_5_ROI_5
None

value: Abdomen

value: Other


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207215830103_R02C01

value: whole blood


title: NDCS-1 shBCAT1-2

description:
Library name: NDCS-1 shBCAT1-2
NDCS-1_RPKM.xlsx


title: PTB221_batch_4_ROI_18_anno_Core

description:
Library name: PTB221_batch_4_ROI_18
Core | PTB 22.1 | 18


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207096540017_R03C01

value: HISPANIC


title: NDCS-1 shBCAT1-1

description:
Library name: NDCS-1 shBCAT1-1
NDCS-1_RPKM.xlsx


title: NDCS-1 shCtrl-3

description:
Library name: NDCS-1 shCtrl-3
NDCS-1_RPKM.xlsx


title: PTB221_batch_4_ROI_17_anno_Core

description:
Library name: PTB221_batch_4_ROI_17
Core | PTB 22.1 | 17

value: Lung


title: NDCS-1 shCtrl-2

description:
Library name: NDCS-1 shCtrl-2
NDCS-1_RPKM.xlsx


title: Whole blood DNA methylation, HISPANIC AD, 90yo F, 207215830057_R08C01

value: Alzheimer's disease


title: Whole blood DNA methylation, HISPANIC AD, 84yo F, 207221680011_R05C01

value: PRADI


title: PTB221_batch_4_ROI_16_anno_Core

description:
Library name: PTB221_batch_4_ROI_16
Core | PTB 22.1 | 16


title: NDCS-1 shCtrl-1

description:
Library name: NDCS-1 shCtrl-1
NDCS-1_RPKM.xlsx


title: YD10B_8Gy

city: Cheonan

first: Jihye

last: Park

address: 119 Dan-daero, Dongnam-gu

country: South Korea

institute: Dankook University

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

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

source_name: oral tongue

label_protocol: Standard Illumina protocol

growth_protocol: Ca9-22  cells were maintained in MEM/EBSS medium; OSC20 cells were cultured in a 1:1 mixture of Dulbecco's Modified Eagle's Medium and Ham's F-12 Nutrient Mixture (DMEM/F12); and YD10B cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) (all from HyClone, Logan, UT, USA). All media were supplemented with 10% fetal bovine serum (FBS; HyClone) and 1% antibiotic-antimycotic solution (Gibco, Grand Island, NY, USA). Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Genomic DNA was extracted from all cell lines using a standard phenol-chloroform extraction method. Bisulfite conversion of extracted DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructions. Methylation-specific PCR (MSP) was carried out to assess the methylation status of candidate gene promoter regions using primer pairs spanning the putative transcriptional start site within the 5′ CpG island, as previously described {Herman, 1996 #139}. Each MSP reaction was performed using 1 μl of bisulfite-converted DNA as template and JumpStart™ REDTaq® DNA Polymerase (Sigma-Aldrich, St. Louis, MO, USA) for amplification.

treatment_protocol: The cells were exposed to gamma rays through the aircenter mode after changing to fresh media. All irradiations were performed using a 137Cs-ray source (Eckert & Ziegler) at a dose rate of 2.6 Gy/min. Following irradiation at doses of 4 and 8 Gy, the cells were incubated for 3 days at 37°C in a humid incubator with 5% CO2.

value: oral tongue

value: epithelial

value: irradiated 8 Gy


title: Whole blood DNA methylation, HISPANIC AD, 80yo F, 207228480079_R01C01


title: YD10B_4Gy

value: irradiated 4 Gy


title: YD10B_0Gy


title: PTB221_batch_4_ROI_15_anno_Mantle

description:
Library name: PTB221_batch_4_ROI_15
Mantle | PTB 22.1 | 15


title: Whole blood DNA methylation, HISPANIC AD, 82yo F, 207215830057_R05C01


title: Whole blood DNA methylation, HISPANIC AD, 83yo F, 207215820013_R04C01


title: OSC20_8Gy

source_name: oral

value: oral

value: epithelial-like


title: OSC20_0Gy


title: PTB221_batch_4_ROI_14_anno_Core

description:
Library name: PTB221_batch_4_ROI_14
Core | PTB 22.1 | 14


title: OSC20_4Gy


title: Whole blood DNA methylation, HISPANIC AD, 87yo F, 207215820086_R07C01


title: PTB221_batch_4_ROI_13_anno_Core

description:
Library name: PTB221_batch_4_ROI_13
Core | PTB 22.1 | 13


title: SV40-MES-13, Drosha KD, miRNAseq, rep1

description:
Library name: DroshaKD_rep1
Drosha_sh_1

value: mouse renal mesangial cell

value: Drosha KD


title: Ca9-22_8Gy

source_name: head & neck

value: head & neck


title: Whole blood DNA methylation, HISPANIC AD, 89yo F, 207215820034_R03C01

value: Female


title: Ca9-22_4Gy


title: Ca9-22_0Gy


title: SV40-MES-13, WT, miRNAseq, rep2

description:
Library name: WT_rep2
A475_2

value: WT


title: PTB221_batch_4_ROI_12_anno_Mantle

description:
Library name: PTB221_batch_4_ROI_12
Mantle | PTB 22.1 | 12

value: Mantle


title: Whole blood DNA methylation, HISPANIC CONTROL, 74yo F, 207097420032_R04C01

value: Healthy control

value: whole blood


title: PTB221_batch_4_ROI_11_anno_Core

description:
Library name: PTB221_batch_4_ROI_11
Core | PTB 22.1 | 11

value: Lung

value: Core


title: stamen from stage3 N.colorata floral bud repeat3

city: Shanghai

first: Chang

address: Xinjiangwancheng street, Yangpu District, Shanghai

institute: Fudan University

description:
Library name: S3_St_3
bulk RNA sequencing of stamens of  N.colorata floral bud

data_processing:
Raw paired‑end reads were quality‑filtered using fastp, aligned to the reference genome with HISAT2, and then transcript assembly and quantification were performed with StringTie, generating gene‑level read count tables and transcript annotation files (GTF)
Assembly: Nymphaea colorata v1.2 from Phytozome (https://phytozome-next.jgi.doe.gov/info/Ncolorata_v1_2)
Supplementary files format and content: TSV file containing gene‑level raw read counts for all samples, with gene identifiers in rows and sample IDs in columns.
Supplementary files format and content: GTF file containing assembled transcript structures (exon coordinates) and expression abundance estimates (FPKM/TPM) produced by StringTie.

organism: Nymphaea colorata

source_name: flower

extract_protocol:
Total RNA was extracted from water lily floral bud tissues using TRIzol reagent. RNA concentration and purity were assessed with a Nanodrop 2000 spectrophotometer, integrity was evaluated by agarose gel electrophoresis, and the RIN value was determined using an Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit, which includes poly(A) mRNA enrichment, fragmentation, reverse transcription, adapter ligation, and PCR amplification; the libraries were sequenced as 150‑bp paired‑end reads on an Illumina platform.

value: flower

value: stamen

tag: group


title: inner tepal from stage3 N.colorata floral bud repeat3

description:
Library name: S3_Pe_3
bulk RNA sequencing of inner tepals of  N.colorata floral bud

value: tepal

value: inner tepal


title: Whole blood DNA methylation, HISPANIC AD, 84yo F, 207080920105_R08C01

first: Sebastián

value: Alzheimer's disease

value: HISPANIC

value: PRADI


title: outer tepal from stage3 N.colorata floral bud repeat3

description:
Library name: S3_Se_3
bulk RNA sequencing of outer tepals of  N.colorata floral bud

value: outer tepal


title: Whole blood DNA methylation, HISPANIC AD, 82yo F, 207097420040_R01C01

value: PERUVIAN


title: PTB221_batch_4_ROI_10_anno_Mantle

description:
Library name: PTB221_batch_4_ROI_10
Mantle | PTB 22.1 | 10


title: stamen from stage3 N.colorata floral bud repeat2

description:
Library name: S3_St_2
bulk RNA sequencing of stamens of  N.colorata floral bud


title: inner tepal from stage3 N.colorata floral bud repeat2

description:
Library name: S3_Pe_2
bulk RNA sequencing of inner tepals of  N.colorata floral bud


title: outer tepal from stage3 N.colorata floral bud repeat2

description:
Library name: S3_Se_2
bulk RNA sequencing of outer tepals of  N.colorata floral bud


title: PTB221_batch_4_ROI_9_anno_Core

description:
Library name: PTB221_batch_4_ROI_9
None


title: Whole blood DNA methylation, HISPANIC AD, 92yo F, 207097420015_R02C01


title: stamen from stage3 N.colorata floral bud repeat1

description:
Library name: S3_St_1
bulk RNA sequencing of stamens of  N.colorata floral bud


title: Whole blood DNA methylation, NHW CONTROL, 72yo F, 207228480014_R01C01

value: NHW


title: PTB221_batch_4_ROI_8_anno_Core

description:
Library name: PTB221_batch_4_ROI_8
Core | PTB 22.1 | 08


title: inner tepal from stage3 N.colorata floral bud repeat1

description:
Library name: S3_Pe_1
bulk RNA sequencing of inner tepals of  N.colorata floral bud


title: Whole blood DNA methylation, HISPANIC AD, 88yo F, 207097420061_R01C01

value: Female


title: outer tepal from stage3 N.colorata floral bud repeat1

description:
Library name: S3_Se_1
bulk RNA sequencing of outer tepals of  N.colorata floral bud


title: PTB221_batch_4_ROI_7_anno_Mantle

description:
Library name: PTB221_batch_4_ROI_7
None


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207097420047_R05C01


title: TC32_VTP50469_tumor_rep2

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

description:
Library name: KB53
Raw counts for samples in batch 3

data_processing:
The quality of the sequencing data was analyzed with FastQC.
Adaptor fragments, low quality ends and short sequences were removed with Trim Galore.
Trimmed sequences were aligned to the reference genome, GRCh38, and gene counts generated with STAR (Batches 1-2, 4) or Salmon (Batch 3).
Additional quality control was performed with MultiQC.
Differentially expressed genes were identified with DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab delimited raw count files using STAR for read counts for batches 1,2 and 4
Supplementary files format and content: Tab delimited raw count files using Salmon for read counts for batch 3

source_name: tumor

growth_protocol:
All cell lines were grown in RPMI1640 + 10% FBS + 2 mM L-glutamine.
1e6 A673 MEN1-KO (A673 gMEN1 1-3, A673 gMEN1 5-1, gMEN1 5-2) or A673 control (A673 gControl 1) cells were injected subcutaneously in NSG mice and tumors were collected 28 days later and flash frozen.

extract_protocol:
Total RNA was collected using a Qiagen RNeasy kit
The polyA enrichment library was prepared using NEBNext Ultra II RNA Library Prep kit and sequencing with the Illumina Novaseq6000 or NovaSeq X Plus sequencer utilizing a paired-end 150 bp (PE150) sequencing strategy

treatment_protocol:
A673 and TC32 cells were treated with 10 µM VTP50469 or 0.1% DMSO (control) for 72 hours.
5e4 A673 and TC32 cells were injected into the tail vein of NSG mice and treated for 5 or 6 weeks respectively with 0.1% VTP50469 mouse chow compared to control mouse chow and liver tumors were flash frozen.

value: tumor

value: Ewing sarcoma cell line

tag: genotype

value: 0.1% VTP50469 mouse chow


title: 22Rv1, Lactate + OICR 9429, Rep4

description: Library name: 146765_ID3399_16-4D

value: Epithelial cell line

value: WT


title: TC32_VTP50469_tumor_rep3

description:
Library name: KB54
Raw counts for samples in batch 3


title: PTB221_batch_4_ROI_6_anno_Mantle

description:
Library name: PTB221_batch_4_ROI_6
None

value: Lung

value: Mantle


title: TC32_VTP50469_tumor_rep1

description:
Library name: KB52
Raw counts for samples in batch 3


title: Whole blood DNA methylation, HISPANIC CONTROL, 67yo M, 207097320052_R05C01

last: Cruz-González

institute: UCSF

value: Male

value: Healthy control

value: whole blood


title: Whole blood DNA methylation, AA AD, 83yo F, 207215820045_R03C01

value: Alzheimer's disease

value: AA

value: REAAADI


title: PTB221_batch_4_ROI_5_anno_Core

description:
Library name: PTB221_batch_4_ROI_5
Core | PTB 22.1 | 05

value: Core


title: TC32_control_tumor_rep2

description:
Library name: KB50
Raw counts for samples in batch 3

value: standard mouse chow


title: Whole blood DNA methylation, HISPANIC CONTROL, 69yo M, 207097420153_R08C01

value: HISPANIC

value: CuADI


title: TC32_control_tumor_rep1

description:
Library name: KB49
Raw counts for samples in batch 3

value: tumor


title: TC32_control_tumor_rep3

description:
Library name: KB51
Raw counts for samples in batch 3

value: Ewing sarcoma cell line


title: PTB221_batch_4_ROI_4_anno_Mantle

description:
Library name: PTB221_batch_4_ROI_4
Mantle | PTB 22.1 | 04


title: A673_VTP50469_tumor_rep3

description:
Library name: KB48
Raw counts for samples in batch 3

value: 0.1% VTP50469 mouse chow


title: Whole blood DNA methylation, HISPANIC AD, 78yo F, 207080910104_R07C01

value: Female

value: PRADI


title: A673_VTP50469_tumor_rep2

description:
Library name: KB47
Raw counts for samples in batch 3


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207097420047_R08C01


title: A673_control_tumor_rep3

description:
Library name: KB45
Raw counts for samples in batch 3


title: Whole blood DNA methylation, HISPANIC AD, 79yo F, 207080910061_R02C01


title: PTB221_batch_4_ROI_2_anno_Core

description:
Library name: PTB221_batch_4_ROI_2
Core | PTB 22.1 | 02

value: Lung


title: A673_control_tumor_rep2

description:
Library name: KB44
Raw counts for samples in batch 3


title: PTB221_batch_4_ROI_3_anno_Core

description:
Library name: PTB221_batch_4_ROI_3
Core | PTB 22.1 | 03


title: PTB221_batch_4_ROI_1_anno_Other

description:
Library name: PTB221_batch_4_ROI_1
None

value: Other


title: A673_control_tumor_rep1

description:
Library name: KB43
Raw counts for samples in batch 3


title: Whole blood DNA methylation, HISPANIC AD, 75yo F, 207097320021_R05C01

value: PERUVIAN


title: IGROV-1/CP cisplatin + nelfinavir biol replicate 2

city: Montreal

first: Benjamin

last: Forgie

state: Quebec

address: 3775 Rue University

country: Canada

institute: McGill University

description: Library name: CN2_MPS12351762_A09

data_processing:
Base calling and demultiplexing were performed using BCL Convert v4.2.4 to generate FASTQ files.
FASTQ files were processed using the DRAGEN RNA-seq pipeline.
For samples requiring additional sequencing to reach the requested read depth, FASTQ files from the initial and repeat sequencing read sets were combined during DRAGEN analysis to generate the final gene-level count matrix.
Assembly: GRCh38
Supplementary files format and content: CSV file containing a gene-level normalized count matrix for all 12 IGROV-1/CP RNA-seq samples. Rows correspond to genes and columns correspond to individual biological replicate samples.

growth_protocol: IGROV-1/CP platinum-resistant ovarian cancer cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and antibiotics at 37°C with 5% CO2. Cells were cultured under standard adherent mammalian cell culture conditions prior to treatment and RNA collection.

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy Plus Universal Mini Kit according to the manufacturer’s instructions. Briefly, QIAzol lysis reagent was added to the cell samples, and homogenization was performed by passing the lysate 15 times through a 20-gauge needle attached to a sterile 3 mL syringe. RNA was eluted in 35 uL of the buffer provided with the extraction kit. Total RNA was quantified and RNA integrity was assessed using the 5K/RNA/Charge Variant Assay LabChip and RNA Assay Reagent Kit.
Libraries were generated from 250 ng of total RNA using the Illumina Stranded mRNA Prep Kit, including mRNA enrichment, according to the manufacturer’s recommendations. Libraries were quantified using the KAPA Library Quantification Kit, and average fragment size was determined using a Fragment Analyzer 5300. Libraries were normalized, pooled, denatured in 0.02 N NaOH, neutralized with pre-load buffer, and loaded at 170 pM onto an Illumina NovaSeq X Plus 25B lane for 2 x 100 bp paired-end sequencing. A PhiX control library was spiked in at 1%.

treatment_protocol: IGROV-1/CP cells were treated with vehicle, 10 uM cisplatin (CDDP) for 3 h followed by culture in drug-free medium until 24 h, 20 uM nelfinavir (NFV) for 24 h, or 10 uM CDDP for 3 h followed by culture in medium containing 20 uM NFV until 24 h. Cell pellets were then collected and submitted to Genome Quebec for RNA extraction, library preparation, and sequencing.

value: ovarian cancer cell

value: Not genetically modified

value: cisplatin + nelfinavir


title: NTC_batch_4_ROI_NA_anno_NA

description:
Library name: NTC_batch_4_ROI_NA
None

source_name: Control

value: Control


title: Whole blood DNA methylation, HISPANIC AD, 63yo M, 207097420192_R01C01

value: Male

value: Alzheimer's disease

value: whole blood


title: IGROV-1/CP cisplatin + nelfinavir biol replicate 1

description: Library name: CN1_MPS12351762_H08


title: TBL60_batch_3_ROI_12_anno_Other

description:
Library name: TBL60_batch_3_ROI_12
None

source_name: Lymph

value: Lymph


title: IGROV-1/CP nelfinavir biol replicate 2

description: Library name: NFV2_MPS12351762_F08

value: nelfinavir


title: IGROV-1/CP nelfinavir replicate 1

description: Library name: NFV1_MPS12351762_E08


title: Whole blood DNA methylation, HISPANIC AD, 69yo M, 207097420015_R04C01

value: HISPANIC


title: IGROV-1/CP cisplatin biol replicate 2

description: Library name: CDDP2_MPS12351933_H08

value: cisplatin


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097420153_R05C01

value: Healthy control


title: IGROV-1/CP cisplatin biol replicate 1

description: Library name: CDDP1_MPS12351762_B08


title: IGROV-1/CP vehicle biol replicate 3

description: Library name: Veh3_MPS12351762_A08

value: vehicle


title: TBL60_batch_3_ROI_10_anno_Other

description:
Library name: TBL60_batch_3_ROI_10
None


title: TBL60_batch_3_ROI_9_anno_Other

description:
Library name: TBL60_batch_3_ROI_9
None


title: IGROV-1/CP vehicle biol replicate 2

description: Library name: Veh2_MPS12351762_H07


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207219770097_R02C01


title: 293_ML60218_rep3

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

description: Library name: 293_ML60218_rep3

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq v2.20 conversion software. Reads were subsequently trimmed with TrimGalore, mapped to the hg38 transcriptome, and quantified using Salmon. Differentially expressed genes were identified using DESeq2.
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: raw counts, and Transcribe per milion in CSV format

source_name: cell line

growth_protocol: HEK293Tcells were obtained from ATCC (CRL-3216, Batch#70049877) and grown in 10 cm BioLite™   Cell Culture   Treated   Dishes   (Catalog# 12-556-002 Thermo   Scientific)   in Dulbecco’s Modified Eagle Medium, high glucose (Catalog# 11965092, Gibco). HEK293T experiments were conducted on cells between passage 10-25. THP-1 monocytes were obtained from ATCC (TIB-202 Batch# 62454382) and propagated in T-75 flasks between 0.2 and 1 × 10e6 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP-1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
E.Z.N.A.® Total RNA Kit I (Catalog# R6834-01, Omega), with 100% ethanol instead of 70% at the binding step to enrich small RNA.
Libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) and sequenced on two 25B lanes for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

treatment_protocol: siRNA and ASO transfected using Lipofectamine® RNAiMax (cat # 13778150) with standard protocol, Overexpression sample are transfected using Lipofectamine 3000 (cat #L3000015)

value: cell line


title: Whole blood DNA methylation, HISPANIC CONTROL, 67yo F, 207097420079_R07C01

city: San Francisco

value: Female


title: 293_ML60218_rep2

description: Library name: 293_ML60218_rep2


title: TBL60_batch_3_ROI_7_anno_Other

description:
Library name: TBL60_batch_3_ROI_7
None

value: Other


title: 293_ML60218_rep1

description: Library name: 293_ML60218_rep1


title: Whole blood DNA methylation, HISPANIC CONTROL, 77yo M, 207097420048_R08C01

value: PERUVIAN


title: TBL60_batch_3_ROI_6_anno_Other

description:
Library name: TBL60_batch_3_ROI_6
None


title: IGROV-1/CP vehicle biol replicate 1

description: Library name: Veh1_MPS12351762_G07

value: ovarian cancer cell


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo M, 207080920090_R03C01


title: 293_DMSO_rep2

description: Library name: 293_DMSO_rep2

value: DMSO


title: 293_DMSO_rep1

description: Library name: 293_DMSO_rep1


title: TBL60_batch_3_ROI_5_anno_Other

description:
Library name: TBL60_batch_3_ROI_5
None


title: Hek293T_siPOLR3A_rep3

description: Library name: Hek293T_siPOLR3A_rep3


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo F, 207080920090_R07C01


title: Hek293T_siPOLR3A_rep2

description: Library name: Hek293T_siPOLR3A_rep2


title: Hek293T_siPOLR3A_rep1

description: Library name: Hek293T_siPOLR3A_rep1


title: Hek293T_siControl_rep3

description: Library name: Hek293T_siControl_rep3

value: siControl


title: Whole blood DNA methylation, HISPANIC CONTROL, 81yo M, 207080910104_R08C01

value: PRADI


title: Hek293T_siControl_rep1

description: Library name: Hek293T_siControl_rep1


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207097420192_R02C01

value: CuADI


title: Hek293T_siControl_rep2

description: Library name: Hek293T_siControl_rep2


title: TBL60_batch_3_ROI_2_anno_Other

description:
Library name: TBL60_batch_3_ROI_2
None


title: TBL60_batch_3_ROI_3_anno_Other

description:
Library name: TBL60_batch_3_ROI_3
None


title: Whole blood DNA methylation, HISPANIC AD, 80yo M, 207097420049_R08C01

value: Male

value: Alzheimer's disease