title: Non-diabetic, myocardial biopsy from patient, biol rep 21


title: PD-NC4 clone A1 young

status: Public on Jun 26 2026

type: SRA

city: Pittsburgh

first: Megan

last: Mahlke

state: Pennsylvania

address: 5115 Centre Ave

country: USA

institute: UPMC

description:
Library name: PD-NC4 clone A1 young
This data was aligned to the PDNC4 chromosome 4 assembly.

library_source: genomic

data_processing:
aligned to PD-NC4 or T2T assembly with Bwa, Peak calling with MACS2
Assembly: T2T CHM13 v 2.0 (GCF_009914755.1), PD-NC4 Chr4 assembly (https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1.full)
Supplementary files format and content: bigwig, CENP-A read pileup
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
ChIP-seq or CUT&RUN antibody-directed DNA isolation
NEB Next Ultra II

tag: cell line

tag: cell type

value: fibroblast

tag: treatment


title: Non-diabetic, myocardial biopsy from patient, biol rep 20

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

library_source: transcriptomic

data_processing:
Illumina
Base Calling and quality assessement were performes using NCS v4.0.1 & RTA v2.4.11. demultiplexing was realized usign Bxl2fastq v2.17.1.14.Quality Analysis was performed using FastQC tool v0.11.9. Sequenced reads were trimmed for adapters using cutadapt v4.0 with default parameters. Mapping to Homo Sapiens GRCHh38  was performed using STAR v2.7.5a.  Gene count Table was realized using STAR v2.7.5a
raw Reads
Assembly: GRCHh38
Supplementary files format and content: tab-delimited text files include raw count for each sample

molecule: total RNA

source_name: Left cardiac ventricular biopsy from patient

extract_protocol:
Total RNA extraction was performed using miRNeasy mini kit (Qiagen) following manufacturer’s instructions
100ng of total RNA were used for library construction using Lexogen QuantSeq 3 mRNA seq Library Prep kit (Illumina) following manufacturer's instruction
RNA-Seq SingleEnd 75bp with Illumina NextSeq500

tag: tissue

value: Left Ventricular myocardial biopsy

tag: disease state

value: Non  diabetic


title: lung alveolar organoid, Tigit knockout, plate1-1 well D07

city: South San Francisco

first: Anne

last: Biton

state: CA

address: 1 DNA way

institute: Genentech

description: Library name: 1-1_D07_TIGIT

data_processing:
The sequencing reads in each fastq file were first split between mouse and human using Xenome (Conway et al., 2012). Only reads unambiguously assigned to either mouse or human were kept and respectively aligned to their reference genome (mouse: GRCm38.p5, human: GRCh38.p10) through the HTSeqGenie v4.35 Bioconductor package (Pau and Reeder, 2012, https://doi.org/10.18129/B9.bioc.HTSeqGenie). First, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. Then, reads were aligned using GSNAP (Wu et al., 2010; Wu et al., 2016) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (human: GENCODE 27, mouse: GENCODE M15). Reads unambiguously mapping to exons were counted to get gene-level read counts.
Assembly: GRCm38.p5, GRCh38.p10
Supplementary files format and content: gene_counts.xlsx provides gene-level counts of reads unambiguously mapping to exons. There is one table for the reads assigned by Xenome to the Mus Musculus genome (originating from the mouse alveolar type 2 cells of the organoids in the well), and one table for the reads assigned to the Homo Sapiens genome (originating from the human fibroblasts of the organoids in the well).
Supplementary files format and content: plate_design.csv contains the sgRNA sequences used to target each gene and their location on the four plates.
Supplementary files format and content: imaging_outputs.csv contains the main outputs of the image analysis performed on each well at day 7 and day 14, in terms of number or organoids in the well, average area of the organoids in the well, and estimate of the percentage of the well covered by organoids.
Supplementary files format and content: xenome_stats.csv contains the summary of the sequencing read assignment made by Xenome (Conway et al., 2012).

organism:
Homo sapiens
Mus musculus

source_name: lung mouse alveolar type 2 cells and primary human fibroblasts

extract_protocol:
Libraries were prepared from extracted RNA using a modified Smart-seq3 protocol ( Hagemann-Jensen, M., Ziegenhain, C., Chen, P. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat Biotechnol 38, 708–714 (2020). https://doi.org/10.1038/s41587-020-0497-0) Annealing reaction was performed with 4ul purified RNA, 0.8 ul 40% PEG 8000, 0.08 ul RNAse Inhibitor, 0.04 ul Smart-seq3 oligo dT (100µM), 0.3 ul dNTP (25mM each) and 1 ul water per 384 well reaction. 10 ul mineral oil was added on top to prevent evaporation. Reaction was sealed, spun and incubated at 70˚C for 10 min. Reverse translation was performed by adding 2 ul of RT mix (0.2ul Tris HCl, pH8.0 (1M), 0.24 ul NaCl (1M), 0.2 ul MgCl2 (100mM), 0.08 ul GTP (10mM), 0.64 ul DTT (100mM), 0.16 ul TSO (100µM), 0.08 ul Maxima H Minus RTase and 0.4 ul water) to each 384 well reaction. The RT reaction was incubated at 42°C for 90 min and repeated the following steps for 10 cycles: 50˚C for 2 min and 42˚C for 2 min, and was terminated at 85°C for 5 min.
cDNA amplification was performed by adding 12ul of PCR mix (0.1 ul cDNA fwd (100µM), 0.02 ul cDNA rev (100µM), 0.1 ul MgCl2 (100mM), 10 ul 2X Kapa HiFi Hotstart Readymix  and 1.78 ul water) to the RT reaction for a total of 20 ul. Reaction was thermal cycled at 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 4 min] x 14 cycles, 72 °C 4min. cDNA was diluted 1:10 in water. 1 ul of each sample was transferred to a new 384 well plate to perform tagmentation. 3 ul of tagmentation mix (0.8 ul 5X TAPS Mg buffer, 0.1 ul Tn5 enzyme, 2.1 ul water) was added to each sample on ice. Plate was sealed, vortexed for 15 seconds and spun. The reaction mixture was incubated at 55 °C for 10 min. Reaction was quenched by adding 0.5µl of 0.2% SDS to each well, sealing, vortexing for 15 seconds, and spinning the plate. The plate was  incubated at room temperature for 5 min. Libraries were indexed by added 3.5 ul of PCR mix and 2 ul indexing primers  to each sample.  Reaction was thermal cycled at 72°C for 5 min, 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 30 sec] x 10 cycles, 72 °C 4min. Libraries were pooled and sequenced on an Illumina NovaSeq X Plus system, targeting 8M reads per library.

tag: genotype

value: Tigit CRISPR/Cas9 knockout

tag: batch


title: Non-diabetic, myocardial biopsy from patient, biol rep 19


title: lung alveolar organoid, Ttf1 knockout, plate1-1 well D06

description: Library name: 1-1_D06_TTF1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Ttf1 CRISPR/Cas9 knockout


title: Non-malignant cfRRBS Patient #55

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description:
Library name: L-NM-7
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

library_source: other

data_processing:
The preprocessing of raw cfRRBS data began with quality assessment using a QC tool developed by Wingett and Andrews (2018) to ensure suitability for downstream analysis. Adapter sequences were then removed using Trim Galore (Krueger), resulting in cleaner reads for alignment.   These cleaned reads were aligned to the human reference genome (GRCh37/hg19) using Bismark (Krueger and Andrews, 2011), generating BAM files that contain detailed alignment information.  Reference genome sequences and RefSeq gene annotations were obtained from the UCSC Genome Browser  (hg19 version) to support read interpretation.   To extract methylation-relevant features from the BAM files,we used the Pysam library (Li et al., 2009). Each BAM file included information such as chromosome, start and end positions, bisulfite-converted read sequence, methylation call string (XM tag), and strand alignment.  For each read, we extracted the corresponding genomic sequence and methylation counts (methylated and unmethylated cytosines) along with other relevant information, and stored the output in a structured text file to facilitate downstream quantification.  For each candidate region, we computed MM (Mean Methylation) to quantify average methylation levels, and MHL (Methylation Haplotype Load) to capture the distribution of methylation patterns across cfDNA fragments.  The final output for each region included the following fields: Sample name, Chromosome number, Start Position, End Position,  DNA reference sequence, Methylation Pattern Summary, Sequence Length, Number of CpGs, Coverage, Mean Methylation Value, Methylation Haplotype Load Value, and Number of Haplotype Patterns.
Assembly: GRCh37/hg19
Supplementary files format and content: .txt format (contains Sample name, Chromosome number, Start Position, End Position,  DNA reference sequence, Methylation Pattern Summary, Sequence Length, Number of CpGs, Coverage, Mean Methylation Value, Methylation Haplotype Load Value, and Number of Haplotype Patterns.

molecule: other

source_name: Plasma

extract_protocol:
cfDNA was extracted using Qiagen ccfDNA Midi Kit
Cell-free DNA was extracted from 2-5 mLs of plasma using the QIAamp MinElute ccfDNA Midi Kit according to the manufacturer's instructions. cfDNA was quantified using the Qubit 4 fluorometer according to the Qubit dsDNAhigh-sensitivity assay kit protocol. An Agilent 2100 Bioanalyser instrument was used to assess the cfDNA quality to rule out possible genomic DNA contamination.
4-10 ng of cfDNA was dephosphorylated using recombinant shrimp alkaline phosphatase (rSAP). This was followed by endonuclease digestion suing the MspI restriction enzyme, then enr-repair and adenylation of the 3' ends. Followiing the ligation of custom adapters, exonucleases were used to degrade unligated and partially ligated DNA fragments. This was followed by the cleavage of adaptor hairpin using antarctic thermolabile UDG and endonuclease VII, thus generating single-stranded DNA required for bisultte conversion. The DNA was bisulfite-converted twice using the Epitect plus bisulfite kit. This was followed by PCR amplification and 2.5x Ampure bead purification. The purified DNA was assessed for quality using a Qubit 4 fluorometer (Thermofisher Scientific, USA) and BioAnalyser (Agilent, USA).

value: Plasma

tag: extract molecule

value: cell-fee DNA


title: breast cancer_SM134

type: RNA

city: Houston

first: William

middle: Fraser

last: Symmans

state: TX

address: 2130 W Holcombe Blvd #11.4000

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 600 breast cancer specific genes.

label: biotin

source_name: breast cancer sample

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Patients consented to future tissue-based research sample collections from either prospective biopsy or surgical resection.

tag: er status

value: P

tag: pr status

tag: her2 status

value: N

tag: ajcc stage

value: I

tag: sample collection type

value: Tissue

tag: setting of sample collection

value: Needle Biopsy Sample


title: Non-diabetic, myocardial biopsy from patient, biol rep 18


title: lung alveolar organoid, Tns1 knockout, plate1-1 well D05

description: Library name: 1-1_D05_TNS1

value: Tns1 CRISPR/Cas9 knockout


title: breast cancer_SM133

value: IIA

value: Surgical Tissue Sample


title: Non-malignant cfRRBS Patient #53

description:
Library name: L-NM-5
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Non-diabetic, myocardial biopsy from patient, biol rep 16


title: lung alveolar organoid, Npnt knockout, plate1-1 well D03

description: Library name: 1-1_D03_NPNT

value: Npnt CRISPR/Cas9 knockout


title: Non-malignant cfRRBS Patient #52

description:
Library name: L-NM-4
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM129


title: lung alveolar organoid, Ror1 knockout, plate1-1 well D02

description: Library name: 1-1_D02_ROR1

value: Ror1 CRISPR/Cas9 knockout


title: Non-malignant cfRRBS Patient #51

description:
Library name: L-NM-3
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM128


title: Non-diabetic, myocardial biopsy from patient, biol rep 14

value: Left Ventricular myocardial biopsy


title: lung alveolar organoid, Pla2g15 knockout, plate1-1 well C11

description: Library name: 1-1_C11_PLA2G15

value: Pla2g15 CRISPR/Cas9 knockout


title: Non-malignant cfRRBS Patient #50

description:
Library name: L-NM-2
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM127

value: III


title: Non-diabetic, myocardial biopsy from patient, biol rep 13

value: Non  diabetic


title: lung alveolar organoid, Bmp10 knockout, plate1-1 well C10

description: Library name: 1-1_C10_BMP10

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Bmp10 CRISPR/Cas9 knockout


title: Non-diabetic, myocardial biopsy from patient, biol rep 12


title: lung alveolar organoid, Tigit knockout, plate1-1 well C09

description: Library name: 1-1_C09_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: Lung cancer cfRRBS Patient #48

description:
Library name: L-LS-41
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

tag: Stage

value: Stage IV

value: Plasma

value: cell-fee DNA


title: breast cancer_SM119

value: P

value: N

value: I

value: Tissue


title: Non-diabetic, myocardial biopsy from patient, biol rep 11


title: lung alveolar organoid, Prkn knockout, plate1-1 well C08

description: Library name: 1-1_C08_PRKN

value: Prkn CRISPR/Cas9 knockout


title: Lung cancer cfRRBS Patient #47

description:
Library name: L-LS-40
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III


title: breast cancer_SM117

value: Surgical Tissue Sample


title: Non-diabetic, myocardial biopsy from patient, biol rep 10

value: Left Ventricular myocardial biopsy


title: lung alveolar organoid, Il1a knockout, plate1-1 well C07

description: Library name: 1-1_C07_IL1A

value: Il1a CRISPR/Cas9 knockout


title: breast cancer_SM114

value: IIA


title: Non-diabetic, myocardial biopsy from patient, biol rep 9

value: Non  diabetic


title: Non-malignant cfRRBS Patient #49

description:
Library name: L-NM-1
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: lung alveolar organoid, Trp63 knockout, plate1-1 well C06

description: Library name: 1-1_C06_TRP63

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Trp63 CRISPR/Cas9 knockout


title: breast cancer_SM123


title: Lung cancer cfRRBS Patient #45

description:
Library name: L-LS-38
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM113

value: U


title: Non-diabetic, myocardial biopsy from patient, biol rep 8


title: lung alveolar organoid, Sftpd knockout, plate1-1 well C05

description: Library name: 1-1_C05_SFTPD

value: Sftpd CRISPR/Cas9 knockout


title: breast cancer_SM112

value: Cytology


title: Lung cancer cfRRBS Patient #44

description:
Library name: L-LS-37
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Plasma

value: cell-fee DNA


title: Non-diabetic, myocardial biopsy from patient, biol rep 7


title: lung alveolar organoid, Huwe1 knockout, plate1-1 well C04

description: Library name: 1-1_C04_HUWE1

value: Huwe1 CRISPR/Cas9 knockout


title: PD-NC4 clone C4 young

description:
Library name: PD-NC4 clone C4 young
This data was aligned to the PDNC4 chromosome 4 assembly.

data_processing:
aligned to PD-NC4 or T2T assembly with Bwa, Peak calling with MACS2
Assembly: T2T CHM13 v 2.0 (GCF_009914755.1), PD-NC4 Chr4 assembly (https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1.full)
Supplementary files format and content: bigwig, CENP-A read pileup

value: fibroblast


title: Lung cancer cfRRBS Patient #46

description:
Library name: L-LS-39
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV


title: breast cancer_SM140

value: P

value: N

value: I

value: Tissue


title: breast cancer_SM110

value: Surgical Tissue Sample


title: Lung cancer cfRRBS Patient #43

description:
Library name: L-LS-36
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III


title: Non-diabetic, myocardial biopsy from patient, biol rep 6

value: Left Ventricular myocardial biopsy

value: Non  diabetic


title: Non-diabetic, myocardial biopsy from patient, biol rep 23


title: lung alveolar organoid, Mecom knockout, plate1-1 well C03

description: Library name: 1-1_C03_MECOM

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Mecom CRISPR/Cas9 knockout


title: breast cancer_SM138

value: L

value: IIA


title: lung alveolar organoid, Tfeb knockout, plate1-1 well D09

description: Library name: 1-1_D09_TFEB

value: Tfeb CRISPR/Cas9 knockout


title: breast cancer_SM137

value: Cytology


title: breast cancer_SM108

value: IIB

value: Needle Biopsy Sample


title: Lung cancer cfRRBS Patient #42

description:
Library name: L-LS-35
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Plasma

value: cell-fee DNA


title: Non-diabetic, myocardial biopsy from patient, biol rep 5


title: breast cancer_SM135

value: P

value: N


title: lung alveolar organoid, Tead1 knockout, plate1-1 well C02

description: Library name: 1-1_C02_TEAD1

value: Tead1 CRISPR/Cas9 knockout


title: breast cancer_SM136

value: Tissue


title: Lung cancer cfRRBS Patient #41

description:
Library name: L-LS-34
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV


title: breast cancer_SM106

value: III

value: Surgical Tissue Sample


title: Non-diabetic, myocardial biopsy from patient, biol rep 4

value: Left Ventricular myocardial biopsy

value: Non  diabetic


title: lung alveolar organoid, Gdf2 knockout, plate1-1 well B11

description: Library name: 1-1_B11_GDF2

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Gdf2 CRISPR/Cas9 knockout


title: Lung cancer cfRRBS Patient #40

description:
Library name: L-LS-33
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III


title: Non-diabetic, myocardial biopsy from patient, biol rep 3


title: lung alveolar organoid, Ccbe1 knockout, plate1-1 well B10

description: Library name: 1-1_B10_CCBE1

value: Ccbe1 CRISPR/Cas9 knockout


title: Non-malignant cfRRBS Patient #54

description:
Library name: L-NM-6
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM101

value: I


title: Non-diabetic, myocardial biopsy from patient, biol rep 17


title: Lung cancer cfRRBS Patient #39

description:
Library name: L-LS-32
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Non-diabetic, myocardial biopsy from patient, biol rep 2


title: Lung cancer cfRRBS Patient #38

description:
Library name: L-LS-31
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM099

value: U

value: Needle Biopsy Sample


title: breast cancer_SM132

value: IIA


title: Non-diabetic, myocardial biopsy from patient, biol rep 1


title: lung alveolar organoid, Eif2ak3 knockout, plate1-1 well B09

description: Library name: 1-1_B09_EIF2AK3

value: Eif2ak3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Rnf43 knockout, plate1-1 well D04

description: Library name: 1-1_D04_RNF43

value: Rnf43 CRISPR/Cas9 knockout


title: breast cancer_SM104

value: P

value: N


title: lung alveolar organoid, Pink1 knockout, plate1-1 well B08

description: Library name: 1-1_B08_PINK1

value: Pink1 CRISPR/Cas9 knockout


title: breast cancer_SM098

value: III

value: Cytology


title: Lung cancer cfRRBS Patient #37

description:
Library name: L-LS-30
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Plasma

value: cell-fee DNA


title: lung alveolar organoid, Acp6 knockout, plate1-1 well B07

description: Library name: 1-1_B07_ACP6

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Acp6 CRISPR/Cas9 knockout


title: Lung cancer cfRRBS Patient #36

description:
Library name: L-LS-29
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III


title: breast cancer_SM095

value: Tissue


title: lung alveolar organoid, Trp53 knockout, plate1-1 well B06

description: Library name: 1-1_B06_TRP53

value: Trp53 CRISPR/Cas9 knockout


title: RWPE1

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Library name: RWPE1

data_processing:
The Illumina adapters and low-complexity adapters were removed from the reads using Trim Galore! (version 0.6.7), cutadapt (version 4.1), and an in-house bash script.
Then the reads were mapped to the human genome hg38 using the bisulfite converted read mapper Bismark (version v0.16.3) and Bowtie2 (version 2.1.0).
After deduplication using the deduplicate_bismark script from Bismark, methylation percentages for CpG sites were calculated using the bismark_methylation_extractor script from Bismark.
Assembly: hg38
Supplementary files format and content: Methylation calling files in methylkit input format for all destranded CpG sites.
Supplementary files format and content: Columns include a unique cytosine ID (chrBase), chromosome (chr), 1-based genomic coordinate (base), strand (strand), total read coverage (coverage), and the percentage of methylated (freqC) and unmethylated (freqT) reads at that position.

source_name: prostate

extract_protocol:
Phenol-chloroform
WGBS libraries were prepared from one microgram of genomic DNA. In brief, dDNA was fragmented in water-bath sonicator to an average 300bp. Following end-repair and A-tailing, Illumina-compatible cytosine-methylated adaptor were ligated to gDNA . The product was then subjected to bisulfite-conversion, and final library preparation was done by PCR amplification. Pooled libraries were sequenced on an Illumina instrument.

value: prostate

value: normal


title: breast cancer_SM094

value: Surgical Tissue Sample


title: Lung cancer cfRRBS Patient #35

description:
Library name: L-LS-28
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV


title: PWR1E

description: Library name: PWR1E


title: breast cancer_SM093

value: IIB

value: Needle Biopsy Sample


title: Lung cancer cfRRBS Patient #34

description:
Library name: L-LS-27
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: lung alveolar organoid, Tdtomato knockout, plate1-1 well B05

description: Library name: 1-1_B05_TDTOMATO

value: Tdtomato CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate1-1 well B04

description: Library name: 1-1_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: Lung cancer cfRRBS Patient #33

description:
Library name: L-LS-26
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM092

value: P

value: N

value: IIA


title: LNCAP

description: Library name: LNCAP

value: LNCaP clone FGC

value: carcinoma


title: Lung cancer cfRRBS Patient #32

description:
Library name: L-LS-25
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Plasma

value: cell-fee DNA


title: breast cancer_SM091

value: Tissue


title: lung alveolar organoid, Met knockout, plate1-1 well B02

description: Library name: 1-1_B02_MET

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Met CRISPR/Cas9 knockout


title: Du145

description: Library name: Du145

value: prostate


title: breast cancer_SM090

value: L

value: III


title: Lung cancer cfRRBS Patient #31

description:
Library name: L-LS-24
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV


title: Early-stage filamentous C. albicans cells, untreated, biological replicate 4

city: Szeged

first: Krisztián

last: Laczi

address: 52. Közép Fasor

department: Biotechnology and Microbiology

country: Hungary

institute: University of Szeged

description: Library name: CaU4

data_processing:
Quality filtering was done with Trimmomatic 0.39
The quality filtered reads were mapped on the reference with STAR
Rsubread's featureCounts module was used to compute read numbers
Assembly: C. albicans: GCF_000182965.3, C. auris: GCF_003013715.1
Supplementary files format and content: tab delimited text format containing the read counts of the individual samples

organism: Candida albicans

source_name: Early-stage filamentous

extract_protocol:
Early-stage filamentous C. albicans cells were thawed, refrozen in liquid nitrogen, and resuspended in lysis buffer in bashing lysis tubes, followed by mechanical disruption using a Tissuelyser LT (Qiagen) for 20 min at 50 Hz. C. auris pseudohyphae were ground for 1 min with nuclease-free sand using a microcentrifuge tube–compatible glass pestle, frozen again in liquid nitrogen, and reground in lysis buffer. Lysates were centrifuged (9,000 × g, 2 min), and total RNA was purified using the Quick-RNA Plant Miniprep Kit (Zymo Research, Tustin, CA, USA) according to the manufacturer’s instructions.
total RNA library preparation protocol for Illumina NovaSeq X Plus 2x150 nt: Novogene NGS library preparation kit

value: Early-stage filamentous

value: Untreated


title: Curcumin_Sulforaphane_Replicate_4

city: Novato

first: Nathan

middle: D

last: Price

state: California

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: Library name: D4

data_processing:
Raw fastq reads were processed to remove adapter sequences, reads containing >10% ambiguous nucleotides (N), and low-quality reads (Phred score ≤ 5 for over 50% of bases).
Clean paired-end reads were mapped to the C. elegans reference genome using HISAT2 (v2.0.5).
Aligned reads were assembled with StringTie (v1.3.3b).
Gene-level raw counts were generated using FeatureCounts (v1.5.0-p3) and normalized to Fragments Per Kilobase Million (FPKM) values.
Differential expression analysis was performed using DESeq2 (v1.20.0).
Assembly: WBcel235
Supplementary files format and content: gene_count.txt contains the raw read counts mapped to each gene for all samples.
Supplementary files format and content: gene_fpkm.txt contains the expression values normalized to FPKM for all samples.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole Organism

growth_protocol: SS104 glp-4(bn2) strain was maintained at 15°C and moved to 24°C at the L2/L3 stage to induce sterility. All worms were maintained on Defined Medium (DM) plates seeded with Escherichia coli OP50 as a food source.

extract_protocol:
Following treatment, worms were harvested on Day 3 of adulthood, washed twice in cold M9 buffer, and resuspended in 10–20 µL residual buffer. RNA was extracted using QIAzol lysis reagent and a freeze-thaw method following RNeasy Universal Mini Kit (QIAGEN) guidelines, with final elution in RNAse-free water.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis. The library was finalized after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: On Day 0, L4 (fourth larval stage) worms were picked onto assay plates. The bacterial lawns were overlaid with either Curcumin Phytosome (5 mg/mL), Sulforaphane (0.625 mg/mL), a combination of both, or an untreated control, and allowed to dry overnight prior to worm transfer.

value: Whole Organism

value: Curcumin + Sulforaphane


title: breast cancer_SM089

value: P

value: N

value: Needle Biopsy Sample


title: Lung cancer cfRRBS Patient #30

description:
Library name: L-LS-23
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Early-stage filamentous C. albicans cells, untreated, biological replicate 3

description: Library name: CaU3


title: Curcumin_Sulforaphane_Replicate_3

description: Library name: D3


title: breast cancer_SM086

value: IIB

value: Surgical Tissue Sample


title: Curcumin_Sulforaphane_Replicate_2

description: Library name: D2


title: breast cancer_SM085

value: IIA

value: Cytology


title: Early-stage filamentous C. albicans cells, untreated, biological replicate 1

description: Library name: CaU1


title: Curcumin_Sulforaphane_Replicate_1

description: Library name: D1


title: breast cancer_SM082

value: Tissue


title: Lung cancer cfRRBS Patient #27

description:
Library name: L-LS-20
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III

value: Plasma

value: cell-fee DNA


title: Early-stage filamentous C. albicans cells, 1.56 µg mL−1 NFAP2 treated, biological replicate 4

description: Library name: CaT4


title: Sulforaphane_Replicate_4

description: Library name: C4

value: Sulforaphane 0.625 mg/ml


title: Lung cancer cfRRBS Patient #26

description:
Library name: L-LS-19
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM081


title: Early-stage filamentous C. albicans cells, 1.56 µg mL−1 NFAP2 treated, biological replicate 3

description: Library name: CaT3


title: Sulforaphane_Replicate_3

description: Library name: C3


title: breast cancer_SM080


title: Early-stage filamentous C. albicans cells, 1.56 µg mL−1 NFAP2 treated, biological replicate 1

description: Library name: CaT1


title: breast cancer_SM079

value: I


title: Sulforaphane_Replicate_1

description: Library name: C1


title: Lung cancer cfRRBS Patient #23

description:
Library name: L-LS-16
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV


title: breast cancer_SM077


title: Immune_cells

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

description:
CD45_cells
10X single-cell RNA-seq

library_source: transcriptomic single cell

data_processing:
The 10x GEM-X library reads were mapped to mm10 reference genome using CellRanger v8.0.1. Seurat objects were created in R v4.3.2 with RNA matrix files using Seurat v5.0.3
Quality control was performed by filtering cells with the following criteria: total RNA counts between 100 and 15,000 and total RNA feature counts between 200 and 7500. The filtered data was further processed with DoubletFinder v2.0.4 to remove doublets.
Assembly: mm10
Supplementary files format and content: Tab separated matrix files for scRNA.

organism: Mus musculus

source_name: Peyer’s patches

extract_protocol:
mice consisted of CD45+lineage-CD90.2+RORgt-GFP+ cells (ILC3, 2,118 cells ) that were mixed with CD45+GFP- cells (4,000 cells) and processed in one well of GEM-X 3' Chip.
Library preparation was performed using the Chromium GEM-X Single Cell 3' Reagent Kit v4 kit according to the CG000731 Rev A protocol.
10x GEM-X Single Cell 3' Reagent Kit v4

value: Peyer’s patches

value: CD45+ cells


title: Curcumin_Replicate_4

description: Library name: B4

value: Whole Organism

value: Curcumin 5mg/ml


title: breast cancer_SM076

value: P

value: N


title: M_cells

description:
M_cells
10X single-cell RNA-seq

value: Epithelial cells


title: Lung cancer cfRRBS Patient #22

description:
Library name: L-LS-15
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Curcumin_Replicate_3

description: Library name: B3


title: Lung cancer cfRRBS Patient #21

description:
Library name: L-LS-14
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM074

value: Surgical Tissue Sample


title: UPF2 RNAi vector (UPF2) transformed Medicago truncatula (A17) roots, biological replicate 3

first: Peter

last: Kalo

address: Temesvari krt. 62.

department: Institute of Plant Biology

institute: HUN-REN Biological Research Centre

description: Library name: UPF2_biol_rep_3

data_processing:
Raw sequencing data in fastq format were processed using fastp software to generate clean data by removing reads containing adapters, poly-N sequences, and low-quality reads. The cleaned reads had a quality score of Q30>99.9%. The clean paired-end reads were aligned to the M. truncatula reference genome (ensembl_60_medicago_truncatula_mtruna17r5_0_anr_toplevel) using Hisat2 v2.0.5, which was selected for its capability to generate a splice junction database based on gene model annotations. The mapping efficiency of reads exceeded 93% for all samples, and more than 98% of mapped reads were localized to exonic regions. Mapped reads were subsequently assembled using StringTie (v1.3.3b) via a reference-based approach to predict novel transcripts. Gene expression levels were quantified using feature Counts v1.5.0-p3 to count reads mapped to each gene. To normalize for sequencing depth and gene length, the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) was calculated for each gene.
Assembly: ensembl_60_medicago_truncatula_mtruna17r5_0_anr_toplevel
Supplementary files format and content: Raw count file (xlsx)
Supplementary files format and content: FPKM normalized count file (xlsx)

organism: Medicago truncatula

source_name: root

growth_protocol: M. truncatula Jemalong A17 genotype was used for gene-editing and RNA silencing (RNAi) experiments. Plants were grown in zeolite-based substrate in controlled growth chambers at 24 °C under 16/8 h light/dark photoperiod without rhizobia inoculation.

extract_protocol:
RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Following fragmentation, first-strand cDNA was synthesized using random hexamer primers. The resulting cDNA underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification to generate the final libraries. Library quality was validated using Qubit and real-time PCR for quantification, while size distribution was checked using a Bioanalyzer. Libraries were sequenced on an Illumina platform using a "Sequencing by Synthesis" approach. More than 40 million reads were sequenced for each sample.

treatment_protocol: Generation of UPF1 and UPF2 silenced plants: RNAi constructs were generated by cloning PCR fragments derived form the coding regions of  M. truncatula UPF1 (134 bp), UPF2 (128 bp)  into the pDONR201 vector using Gateway cloning. The fragments were subsequently transferred into the destination vector pKGW-RR_IR to generate RNAi constructs expressing transcripts containing inverted repeats separated by a 342 bp stuffer region. An empty vector was used as a control.The constructs were introduced into wild-type M. truncatula A17 roots by Agrobacterium rhizogenes-mediated hairy root transformation using a slightly modified version of a previously published protocol (Boisson-Dernier et al., 2001). Briefly, seedling root tips were excised, and the cut surfaces were immersed into a culture of A. rhizogenes strain Arqua-1. Seedlings were then grown on agar plates containing Fahraeus medium. After one week, they were transferred to the same mediium supplemented with kanamycin (25 mg ml-1) for two weeks. RNA samples were isolated from pooled transgenic roots prior inoculation; transformed roots were identified using the DsRed fluorescent protein transformatiion marker.

value: root

value: line A17, UPF2 RNAi vector


title: Curcumin_Replicate_2

description: Library name: B2


title: Lung cancer cfRRBS Patient #20

description:
Library name: L-LS-13
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: UPF2 RNAi vector (UPF2) transformed Medicago truncatula (A17) roots, biological replicate 2

description: Library name: UPF2_biol_rep_2


title: breast cancer_SM071

value: IIB

value: Tissue


title: Curcumin_Replicate_1

description: Library name: B1


title: Lung cancer cfRRBS Patient #19

description:
Library name: L-LS-12
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III

value: Plasma


title: breast cancer_SM069


title: Control_Replicate_4

description: Library name: A4

value: Untreated


title: UPF2 RNAi vector (UPF2) transformed Medicago truncatula (A17) roots, biological replicate 1

description: Library name: UPF2_biol_rep_1


title: Lung cancer cfRRBS Patient #29

description:
Library name: L-LS-22
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: cell-fee DNA


title: breast cancer_SM066

value: I


title: UPF1 RNAi vector (UPF1) transformed Medicago truncatula (A17) roots, biological replicate 3

description: Library name: UPF1_biol_rep_3

value: line A17, UPF1 RNAi vector


title: Control_Replicate_3

description: Library name: A3


title: Lung cancer cfRRBS Patient #17

description:
Library name: L-LS-10
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Lung cancer cfRRBS Patient #16

description:
Library name: L-LS-9
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Control_Replicate_2

description: Library name: A2


title: breast cancer_SM064

value: IIA


title: UPF1 RNAi vector (UPF1) transformed Medicago truncatula (A17) roots, biological replicate 2

description: Library name: UPF1_biol_rep_2


title: UPF1 RNAi vector (UPF1) transformed Medicago truncatula (A17) roots, biological replicate 1

description: Library name: UPF1_biol_rep_1


title: Early-stage filamentous C. albicans cells, 1.56 µg mL−1 NFAP2 treated, biological replicate 2

description: Library name: CaT2

value: Early-stage filamentous


title: Lung cancer cfRRBS Patient #24

description:
Library name: L-LS-17
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM063


title: Lung cancer cfRRBS Patient #15

description:
Library name: L-LS-8
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV


title: Control_Replicate_1

description: Library name: A1

value: Whole Organism


title: Empty vector (EV) transformed Medicago truncatula (A17) roots, biological replicate 3

description: Library name: EV_biol_rep_3

value: line A17, empty vector


title: Lung cancer cfRRBS Patient #14

description:
Library name: L-LS-7
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Mouse 8-7 Aspirin

city: New Haven

first: Matthew

last: McConnell

state: Connecticut

address: PO Box 208019, 300 Cedar St

institute: Yale University

description:
Library name: 8-7 Aspirin
37HJWM_6_Aspirin_8-7

data_processing:
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.
Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Alignment to the appropriate reference genome (GRCm39_114) using STAR aligner v2.7.* with non-canonical splice junction removal and output of unmapped reads.
comma separated variable, includes raw counts for each sample
Coordinate sorting of BAM files using samtools v1.21. UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0. Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RustQC v0.2.1. Generation of comprehensive QC report using MultiQC v1.33. Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCm39_114
Supplementary files format and content: tab separated variable, includes raw counts for each sample

source_name: Liver

extract_protocol:
RNA was extractued using the RNEasy Plus Micro Kit (Qiagen)
RNA was converted to complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification by Plasmidsaurus

value: Liver

value: primary tissue

value: Total Liver


title: breast cancer_SM059

value: P

value: N

value: Surgical Tissue Sample


title: Empty vector (EV) transformed Medicago truncatula (A17) roots, biological replicate 2

description: Library name: EV_biol_rep_2

value: root


title: Mouse 8-6 Aspirin

description:
Library name: 8-6 Aspirin
37HJWM_5_Aspirin_8-6


title: breast cancer_SM058

value: L

value: III

value: Tissue


title: Lung cancer cfRRBS Patient #13

description:
Library name: L-LS-6
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III

value: Plasma

value: cell-fee DNA


title: Mouse 8-5 Aspirin

description:
Library name: 8-5 Aspirin
37HJWM_4_Aspirin_8-5


title: Empty vector (EV) transformed Medicago truncatula (A17) roots, biological replicate 1

description: Library name: EV_biol_rep_1


title: Lung cancer cfRRBS Patient #12

description:
Library name: L-LS-5
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM057

value: IIB

value: Cytology

value: Needle Biopsy Sample


title: MDA-MB-231 cells, NANOG EGFP positive, Rep3

city: Dalian city

first: Yujie

last: Zeng

state: Liaoning province

address: No. 9, West Section, Lvshun South Road

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

description: Library name: NANOG EGFP_positive_3

data_processing:
Raw reads were processed to generate gene-level expression matrices, including raw counts and FPKM values.
Assembly: hg38 is used for read alignment.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: breast

extract_protocol:
Total RNA was extracted from harvested cells using a standard RNA isolation protocol according to the manufacturer’s instructions. RNA quality was assessed prior to library preparation.
Strand-specific poly(A)-selected RNA-seq libraries were prepared according to the manufacturer’s protocol and sequenced on the Illumina NovaSeq X Plus platform to generate paired-end 150 bp reads.

value: breast

value: Epithelial cell

value: WT

value: FACS-sorted EGFP+


title: Mouse 8-3 PBS

description:
Library name: 8-3 PBS
37HJWM_3_PBS_8-3

value: Liver

value: primary tissue

value: Total Liver


title: Lung cancer cfRRBS Patient #11

description:
Library name: L-LS-4
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV


title: MDA-MB-231 cells, NANOG EGFP positive, Rep2

description: Library name: NANOG EGFP_positive_2


title: breast cancer_SM056

value: P

value: N


title: Mouse 8-2 PBS

description:
Library name: 8-2 PBS
37HJWM_2_PBS_8-2


title: breast cancer_SM055

value: IIA

value: Tissue

value: Surgical Tissue Sample


title: Lung cancer cfRRBS Patient #10

description:
Library name: L-LS-3
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Plasma

value: cell-fee DNA


title: MDA-MB-231 cells, NANOG EGFP positive, Rep1

description: Library name: NANOG EGFP_positive_1


title: Lung cancer cfRRBS Patient #18

description:
Library name: L-LS-11
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Mouse 8-1 PBS

description:
Library name: 8-1 PBS
37HJWM_1_PBS_8-1


title: Lung cancer cfRRBS Patient #9

description:
Library name: L-LS-2
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM053

value: I


title: MDA-MB-231 cells, NANOG EGFP negative, Rep3

description: Library name: NANOG EGFP_negative_3

value: FACS-sorted EGFP-


title: Mouse 6-8 Aspirin

description:
Library name: 6-8 Aspirin
LZ4CMP_7_Aspirin_6_8


title: breast cancer_SM065


title: breast cancer_SM050


title: Lung cancer cfRRBS Patient #8

description:
Library name: L-LS-1
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: MDA-MB-231 cells, NANOG EGFP negative, Rep2

description: Library name: NANOG EGFP_negative_2

value: breast


title: Mouse 6-7 Aspirin

description:
Library name: 6-7 Aspirin
LZ4CMP_6_Aspirin_6_7


title: Lung cancer cfRRBS Patient #7

description:
Library name: L-ES-7
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage I


title: breast cancer_SM048


title: Mouse 6-6 Aspirin

description:
Library name: 6-6 Aspirin
LZ4CMP_5_Aspirin_6_6


title: MDA-MB-231 cells, NANOG EGFP negative, Rep1

description: Library name: NANOG EGFP_negative_1

value: Epithelial cell

value: WT


title: breast cancer_SM046

value: Cytology


title: Lung cancer cfRRBS Patient #6

description:
Library name: L-ES-6
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Lung cancer cfRRBS Patient #5

description:
Library name: L-ES-5
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: Mouse 6-5 Aspirin

description:
Library name: 6-5 Aspirn
LZ4CMP_4_Aspirin_6_5

value: Liver

value: primary tissue


title: CBNK-4

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

description: Library name: CBNK-4

data_processing:
Sequencing raw data were converted into fastq files by running Illumina’s bcl2fastq. The data were aligned to reference genome (GRCh38-2024-A) using Cell Ranger (10x Genomics Cell Ranger 9.0.1). After mapping, Seurat was used as the primary R package for quality control, transformation and most of the visualization of the gene expression data (PMID: 29608179). Quality control steps were first carried out using GEX assay whereby cells not expressing a minimum of 500 genes and genes expressed less than 3 cells were removed. The number of genes expressed, and the percentage of mitochondrial reads mapped were capped at 7500 and 5%, respectively.
Assembly: GRCh38
Supplementary files format and content: 10X Genomics Cell Ranger (9.0.1) output

source_name: primary cord blood

extract_protocol:
NK cells were isolated from thawed CBUs after purification of CBMCs via Ficoll gradient centrifugation, as described above. The isolated NK cells were then subjected to FACS to obtain purified NK cell subsets. First, Fc receptors were blocked using Human TruStain FcX (BioLegend; 1:50) for 15 min at 4 °C. Cells were then stained for 30 min at 4 °C with the following fluorochrome-conjugated antibodies: anti-human CD45-Krome Orange (Beckman Coulter; 1:40), DAPI (ThermoFisher; 1:1000), anti-human CD56-BV510 (Biolegend; 1:200), anti-human CD16-FITC (Biolegend; 1:100), anti-human CD161-APC (Miltenyi Biotec; 1:100), anti-human CD3-PE (Biolegend; 1:200), anti-human CD33-PE (Biolegend; 1:200), anti-human CD14-PE (Biolegend; 1:200). Live CD56+CD3-CD33-CD14- NK cells were sorted to subsets expressing both CD16 and CD161, denoted as the double positive (DP) NK cell subset; or subsets that lacked both CD16 and CD161 expression, denoted as the double negative (DN) NK cell subset. Sorted NK cell subsets were expanded by co-culture with uAPCs and exogenous IL-2 (200 U/ml) for two weeks. DP/DN-derived NK cells were then stained with combinations of the following nucleotide barcode-labeled antibodies (BioLegend) for epitope labeling: TotalSeq-C1290 anti-human CD3 (HIT3a; 1:200), TotalSeq-C0168 anti-human CD57 (QA17A04; 1:200), TotalSeq-C0166 anti-human CD66b (6/40c; 1:200) , TotalSeq-C0100 anti-human CD20 (2H7; 1:200), TotalSeq-C0083 anti-human CD16 (3G8; 1:200), TotalSeq-C0051 anti-human CD14 (63D3; 1:200), TotalSeq-C0050 anti-human CD19 (HIB19; 1:200), TotalSeq-C0251 anti-human Hashtag 1 (2M2; 1:200), TotalSeq-C0252 anti-human Hashtag 2 (2M2; 1:200), TotalSeq-C0253 anti-human Hashtag 3 (2M2; 1:200), TotalSeq-C0254 anti-human Hashtag 4 (2M2; 1:200), TotalSeq-C0052 anti-human CD33 (P67.6; 1:150), TotalSeq-C0048 anti-human CD45 (2D1; 1:150), TotalSeq-C5100-custom-CD161 (REA631; 1:150), TotalSeq-C0047 anti-human CD56 (5.1H11; 1:150), TotalSeq-C0149 anti-human CD161 (HP-3G10; 1:150). As described in the GEM-X Flex gene expression protocols provided by the manufacturer (10x Genomics), cells were fixed with fixation buffer overnight in 4°C. Fixation was quenched with additive C and quenching buffer. Cells were then washed twice with quenching buffer and counted, 500,000 cells from each sample were loaded.
Libraries were prepared using the GEM-X Flex Gene Expression Reagent Kit (10x Genomics, Chromium Human Transcriptome Probe Set v1.1.0) following the manufacturer’s instructions. Briefly, each sample was subjected to probe hybridization for their gene expression (GEX) and TotalSeq antibody-derived epitope tags (ADT), respectively. Samples were then pooled for GEM generation and library preparation of both GEX and ADT fractions. Library size and quality were determined using a Fragment Analyzer (Agilent TapeStation Traces) before fragmentation and after final purification. Final library concentrations were measured on a Qubit 2.0 fluorometer (Thermo Fisher). For each sequencing reaction, pooling was performed with the aim to yield ~30,000 reads per cell for the GEX libraires and ~10,000 reads per cell for the ADT libraries. The pooled GEM-X Flex libraries were sequenced on the Illumina NovaSeq X Plus instrument using R1-i7-i5-R2 parameters of 28+10+10+90 cycles. For primary cord blood samples, 10x Genomics Chromium Next GEM Single Cell 3′ scRNA-seq protocol was used. Freshly dissociated or cryopreserved cells were resuspended in PBS containing 0.04% BSA. Cell viability was assessed using 0.4% Trypan Blue staining with the Countess™ II FL automated cell counter. Cells were diluted or concentrated to the recommended range of 500–1,000 cells/µL and loaded at a volume targeting the recovery of 7,000–10,000 cells per sample for single-cell RNA sequencing (scRNA-seq). Single-cell capture, barcoding, and library preparation were performed according to the 10x Genomics Chromium Next GEM Single Cell 3′ v3.1 Reagent Kits protocol (CG000204 Rev D). Ten libraries were pooled to a final concentration of 10 nM. The pooled libraries were further quantified by qPCR prior to sequencing. Sequencing was performed on an Illumina NovaSeq 6000 using an S2 100-cycle flow cell, with 28 cycles for Read 1, 8 cycles for the i7 index, and 91 cycles for Read 2. Sequencing was conducted at the ATGC Core Facility at MD Anderson.

value: primary cord blood

value: whole blood


title: breast cancer_SM045

value: P

value: N

value: Needle Biopsy Sample


title: Mouse 6-3 PBS

description:
Library name: 6-3 PBS
LZ4CMP_3_PBS_6_3

value: Total Liver


title: CBNK-3

description: Library name: CBNK-3


title: CA9

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description:
Library name: CA9
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 with --expect-cells=5000 --nosecondary commands.
Assembly: GRCm39
Supplementary files format and content: Integrated .vloupe object
Library strategy: BCR-Seq

source_name: spleen

extract_protocol:
Spleen and lymph nodes from immunized mice were harvested on day 23 for memory B cells isolation using a magnetic positive selection kit (Miltenyi Biotec, Cat. 130-095-838). Approximately 10,000 memory B cells were loaded on a Chromium Next GEM Chip K for single-cell lysis and cDNA first-strand synthesis according to the manufacturer’s protocol, flowed by cDNA amplification.
To construct BCR repertoire libraries, 2 μL of amplified cDNA was subjected to two rounds of target enrichment using nested custom primer pairs specific for BCR constant regions. The library was profiled and quantified using the D1000 ScreenTape assay (Agilent) for the TapeStation system and sequenced by paired-end sequencing (26 x 91 bp) on an Illumina MiSeq, aiming to identify CA9-reactive BCRs with a targeted sequencing depth of 5,000 read pairs per cell. Single-cell BCR-seq data were converted to demultiplexed FASTQ files by the Illumina Miseq controller.

value: spleen

value: memory B cell

value: mRNA-LNP


title: Lung cancer cfRRBS Patient #4

description:
Library name: L-ES-4
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage II

value: Plasma

value: cell-fee DNA


title: breast cancer_SM042

value: I

value: Tissue

value: Surgical Tissue Sample


title: Mouse 6-2 PBS

description:
Library name: 6-2 PBS
LZ4CMP_2_PBS_6_2

value: Liver


title: breast cancer_SM041

value: III


title: Lung cancer cfRRBS Patient #3

description:
Library name: L-ES-3
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage I


title: CBNK-1

description: Library name: CBNK-1

value: primary cord blood

value: whole blood


title: Mouse 6-1 PBS

description:
Library name: 6-1 PBS
LZ4CMP_1_PBS_6_1

value: primary tissue


title: Lung cancer cfRRBS Patient #2

description:
Library name: L-ES-2
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.


title: breast cancer_SM039

value: P

value: L

value: N

value: IIB


title: CBNK-2

description: Library name: CBNK-2


title: PC3

description: Library name: PC3

value: prostate

value: adenocarcinoma; Grade IV


title: DPNK-6

description: Library name: DPNK-6

source_name: ex vivo expanded cord blood NK cells

extract_protocol:
NK cells were isolated from thawed CBUs after purification of CBMCs via Ficoll gradient centrifugation, as described above. The isolated NK cells were then subjected to FACS to obtain purified NK cell subsets. First, Fc receptors were blocked using Human TruStain FcX (BioLegend; 1:50) for 15 min at 4 °C. Cells were then stained for 30 min at 4 °C  with the following fluorochrome-conjugated antibodies: anti-human CD45-Krome Orange (Beckman Coulter; 1:40), DAPI (ThermoFisher; 1:1000), anti-human CD56-BV510 (Biolegend; 1:200), anti-human CD16-FITC (Biolegend; 1:100), anti-human CD161-APC (Miltenyi Biotec; 1:100), anti-human CD3-PE (Biolegend; 1:200), anti-human CD33-PE (Biolegend; 1:200), anti-human CD14-PE (Biolegend; 1:200). Live CD56+CD3-CD33-CD14- NK cells were sorted to subsets expressing both CD16 and CD161, denoted as the double positive (DP) NK cell subset; or subsets that lacked both CD16 and CD161 expression, denoted as the double negative (DN) NK cell subset. Sorted NK cell subsets were expanded by co-culture with uAPCs and exogenous IL-2 (200 U/ml) for two weeks. DP/DN-derived NK cells were then stained with combinations of the following nucleotide barcode-labeled antibodies (BioLegend) for epitope labeling: TotalSeq-C1290 anti-human CD3 (HIT3a; 1:200), TotalSeq-C0168 anti-human CD57 (QA17A04; 1:200), TotalSeq-C0166 anti-human CD66b (6/40c; 1:200) , TotalSeq-C0100 anti-human CD20 (2H7; 1:200), TotalSeq-C0083 anti-human CD16 (3G8; 1:200), TotalSeq-C0051 anti-human CD14 (63D3; 1:200), TotalSeq-C0050 anti-human CD19 (HIB19; 1:200), TotalSeq-C0251 anti-human Hashtag 1 (2M2; 1:200), TotalSeq-C0252 anti-human Hashtag 2 (2M2; 1:200), TotalSeq-C0253 anti-human Hashtag 3 (2M2; 1:200), TotalSeq-C0254 anti-human Hashtag 4 (2M2; 1:200), TotalSeq-C0052 anti-human CD33 (P67.6; 1:150), TotalSeq-C0048 anti-human CD45 (2D1; 1:150), TotalSeq-C5100-custom-CD161 (REA631; 1:150), TotalSeq-C0047 anti-human CD56 (5.1H11; 1:150), TotalSeq-C0149 anti-human CD161 (HP-3G10; 1:150). As described in the GEM-X Flex gene expression protocols provided by the manufacturer (10x Genomics), cells were fixed with fixation buffer overnight in 4°C. Fixation was quenched with additive C and quenching buffer. Cells were then washed twice with quenching buffer and counted, 500,000 cells from each sample were loaded.
Libraries were prepared using the GEM-X Flex Gene Expression Reagent Kit (10x Genomics, Chromium Human Transcriptome Probe Set v1.1.0) following the manufacturer’s instructions. Briefly, each sample was subjected to probe hybridization for their gene expression (GEX) and TotalSeq antibody-derived epitope tags (ADT), respectively. Samples were then pooled for GEM generation and library preparation of both GEX and ADT fractions. Library size and quality were determined using a Fragment Analyzer (Agilent TapeStation Traces) before fragmentation and after final purification. Final library concentrations were measured on a Qubit 2.0 fluorometer (Thermo Fisher). For each sequencing reaction, pooling was performed with the aim to yield ~30,000 reads per cell for the GEX libraires and ~10,000 reads per cell for the ADT libraries. The pooled GEM-X Flex libraries were sequenced on the Illumina NovaSeq X Plus instrument using R1-i7-i5-R2 parameters of 28+10+10+90 cycles.

value: ex vivo expanded cord blood NK cells

value: NK cells


title: MC3T3-E1 treated with 10μM Yoda1 for 24h (Replicate 4)

city: Harbin

first: Haoran

last: Zhang

state: Heilongjiang

address: 246 Xuefu Road

institute: Harbin Medical University

description: Library name: MC3T3-Yoda1-Rep4

data_processing:
Raw reads were quality-controlled and adapters trimmed using default Illumina protocols.
Transcript-level quantification was performed using Salmon in quasi-mapping mode against the transcriptome index built from GENCODE vM30 (mouse) annotations.
Tximport was used to summarize transcript-level abundance to gene-level counts based on consistent annotation files.
Differential expression analysis was conducted using DESeq2, with significance defined as adjusted p-value < 0.05 and |log2 fold change| > 0.5.
Variance stabilizing transformation (VST) normalization was applied before downstream visualization (PCA, heatmaps, volcano plots) using ggplot2, pheatmap, and factoextra.
Assembly: GRCm39 (GENCODE vM30 annotation)
Supplementary files format and content: Processed data files include gene-level count matrices (CSV or XLSX) from tximport and normalized expression data (TPM matrices, XLSX format). Differential expression results for pairwise group comparisons are provided as XLSX files, including gene identifiers, log2 fold change, p-values, adjusted p-values, and gene symbols. Visualization outputs (PCA plots, heatmaps, volcano plots) are provided as PDF files.

source_name: Osteoblastic cell line

growth_protocol: MC3T3-E1 subclone 14 cell line was cultured in α-MEM supplemented with 10% FBS and 1% penicillin/streptomycin mix.

extract_protocol:
RNA was harvested using RNAeasy Animal RNA Isolation Kit (Byotime, Cat# R0027). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

treatment_protocol: MC3T3-E1 were cultured until reaching approximately 80% confluence, then treated with 10μM Yoda1 (10mM Yoda1 dissolved in DMSO, 1:1000) for 24 hours.

value: Osteoblastic cell line

value: MC3T3-E1 subclone 14

value: 10 μM Yoda1 for 24 h


title: breast cancer_SM036

value: Tissue

value: Surgical Tissue Sample


title: lung alveolar organoid, Glis3 knockout, plate1-1 well B03

description: Library name: 1-1_B03_GLIS3

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Glis3 CRISPR/Cas9 knockout


title: MC3T3-E1 treated with 10μM Yoda1 for 24h (Replicate 3)

description: Library name: MC3T3-Yoda1-Rep3


title: DPNK-5

description: Library name: DPNK-5


title: PC eCLIP#2

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

description:
Library name: PC2IP_eCLIP
IP, control endothelial cells under pulsatile shear flow#2

data_processing:
FASTQ files were aligned to the GRCh37 reference genome using Kallisto and quantified to gene-level counts. Counts were normalized using edgeR.
Supplementary Files: Comma-delimited text file containing raw and normalized gene counts for each sample.
Assembly: GRCh37
Supplementary files format and content: excel files include TPM values for each Sample
Library strategy: iCLIP

source_name: HUVEC

growth_protocol: HUVECs was maintained in DMEM (Sigma-Aldrich) supplemented with 10% Clonetics Endothelial Growth Medium (Lonza), 10% FBS (Gibco), 1% L-glutamate, and 1% sodium pyruvate.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Plus Kit (Qiagen) following the manufacturer's instructions.
RNA libraries for circRNA sequencing were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina, with modifications to enrich for circRNAs following RNase R treatment. Libraries were constructed according to the manufacturer's protocols.

treatment_protocol: Cells were collected and resuspended in electroporation buffer, followed by the addition of plasmid or siRNA. Electroporation was performed using the A-034 program on an Amaxa Nucleofector device (Lonza), and cells were subsequently seeded onto collagen I–coated slides or culture plates.

value: HUVEC

value: Endothelial cells

value: WT


title: breast cancer_SM035

value: P

value: IV

value: Needle Biopsy Sample


title: DPNK-4

description: Library name: DPNK-4


title: breast cancer_SM034

value: L

value: N

value: IIA


title: MC3T3-E1 treated with 10μM Yoda1 for 24h (Replicate 2)

description: Library name: MC3T3-Yoda1-Rep2


title: DPNK-3

description: Library name: DPNK-3

value: ex vivo expanded cord blood NK cells

value: NK cells


title: MC3T3-E1 treated with 10μM Yoda1 for 24h (Replicate 1)

description:
Library name: MC3T3-Yoda1-Rep1
Raw RNA-seq data generated; excluded from final analysis due to batch variation.

value: Osteoblastic cell line

value: MC3T3-E1 subclone 14


title: breast cancer_SM032

value: IIB

value: Tissue


title: Lung cancer cfRRBS Patient #28

description:
Library name: L-LS-21
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage III

value: Plasma

value: cell-fee DNA


title: DPNK-1

description: Library name: DPNK-1


title: OM eCLIP#2

description:
Library name: OM2IP_eCLIP
IP, METTL3 knockdown endothelial cells under oscillatory flow#2

value: HUVEC

value: Endothelial cells

value: METTL3 knockdown


title: MC3T3-E1 treated with DMSO for 24h (Replicate 3)

description:
Library name: MC3T3-DMSO-Rep3
Raw RNA-seq data generated; excluded from final analysis due to batch variation.

value: DMSO


title: MC3T3-E1 treated with DMSO for 24h (Replicate 4)

description: Library name: MC3T3-DMSO-Rep4


title: breast cancer_SM033

value: P

value: I

value: Surgical Tissue Sample


title: DPNK-2

description: Library name: DPNK-2


title: breast cancer_SM031

value: N

value: IIA


title: DNNK-6

description: Library name: DNNK-6

value: ex vivo expanded cord blood NK cells

value: NK cells


title: PC eCLIP#1

description:
Library name: PC1IP_eCLIP
IP, control endothelial cells under pulsatile shear flow#1

value: WT


title: Early-stage filamentous C. albicans cells, untreated, biological replicate 2

description: Library name: CaU2

value: Early-stage filamentous

value: Untreated


title: PC input#1

description:
Library name: PC1inp_eCLIP
RNA input, control endothelial cells under pulsatile shear flow#1


title: MC3T3-E1 treated with DMSO for 24h (Replicate 2)

description: Library name: MC3T3-DMSO-Rep2

value: Osteoblastic cell line

value: MC3T3-E1 subclone 14


title: OM input#2

description:
Library name: OM2inp_eCLIP
RNA input, METTL3 knockdown endothelial cells under oscillatory flow#2


title: breast cancer_SM030

value: Tissue


title: Lung cancer cfRRBS Patient #25

description:
Library name: L-LS-18
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

value: Stage IV

value: Plasma

value: cell-fee DNA


title: DNNK-5

description: Library name: DNNK-5


title: Sulforaphane_Replicate_2

description: Library name: C2

value: Whole Organism

value: Sulforaphane 0.625 mg/ml


title: MC3T3-E1 treated with DMSO for 24h (Replicate 1)

description: Library name: MC3T3-DMSO-Rep1

value: DMSO


title: OM eCLIP#1

description:
Library name: OM1IP_eCLIP
IP, METTL3 knockdown endothelial cells under oscillatory flow#1

value: HUVEC

value: Endothelial cells

value: METTL3 knockdown


title: breast cancer_SM028

value: P

value: N

value: IIA

value: Surgical Tissue Sample