title: NCMT3

city: Suzhou

first: Wenbo

last: Jia

state: Jiangsu Province

address: No.199 Ren'ai Road

institute: Soochow University

description: Library name: 6

data_processing:
Paired-end reads were obtained from sequencing. fastp software (v0.23.4)was used for data preprocessing, including quality control (Q30) and adaptor-trimming processing, from which high quality reads were obtained.
High-quality reads were aligned to thereference genome using HISAT2 software (v2.2.1).
Gene level raw counts were then obtained as mRNA expression profiles using feature Count software(v2.0.6). Fold change(FC) and P-value between the two sets of samples were normalized and calculated using edgeR software (v4.0.16).
Gene level raw counts were then obtained as mRNA expression profiles using feature Count software(v2.0.6). Fold change(FC) and P-value between the two sets of samples were normalized and calculated using edgeR software (v4.0.16).
After getting differentially expressed(DE) mRNAs by filtering FC and P-value, the DE mRNAs were used for GO functional analysis and KEGG pathwayanalysis.
Assembly: HG38
Supplementary files format and content: counts, cpm, fpkm
Supplementary files format and content: Gene_Expression_Profiling.xlsx

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent
Briefly, total RNA was extracted with Trizol (Invitrogen,Carlsbad,CA,USA), and subjected to mRNA isolation using GenSeq®mRNA Purification Kit(GenSeq,Inc.,Shanghai,China).Then, the purified mRNA wasused for library construction with GenSeq®Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China) by following manufacturer’s recommendations. The mRNA was fragmented into~300nt in length. The first-strand cDNA was synthesized from the RNA fragments by reverse transcriptase and random hexamer primers, and the second-strand cDNA was synthesized in 2nd Strand Synthesis Buffer with dUTP Mix. Then, the double stranded cDNA fragments were subjected to end-repair and dA tailing, followed by adapter ligation. The adapter-ligated DNA samples were PCR amplified and purified to obtain sequencing libraries. Finally, the libraries were sequenced with sequencer on the paired-end 150 bp mode.

value: colon

tag: sample group

value: NCMT


title: NCMT1

status: Public on Jun 15 2026

type: SRA

country: China

description: Library name: 4

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: CA3

description: Library name: 3

value: CA


title: CA2

description: Library name: 2


title: CA1

description: Library name: 1


title: Contrl cell line [scRNA-seq]

city: Houston

first: Fuduan

last: Peng

state: TX

address: 1881 East Rd

country: USA

institute: MD Anderson Cancer Center

description: Library name: CntrlCellline-5GE

library_source: transcriptomic single cell

data_processing:
Raw scRNA-Seq data were pre-processed (demultiplex cellular barcodes, read alignment and generation of gene count matrix) using Cell Ranger Single Cell Software Suite provided by 10X Genomics. For read alignment of human scRNA-Seq data, human reference GRCh38 (hg38) genomes were used. Detailed quality control metrics were generated and evaluated, and cells were carefully and rigorously filtered to obtain high-quality data for downstream analyses. In brief, for basic quality filtering, cells with low-complexity libraries (in which detected transcripts were aligned to <200 genes such as cell debris, empty drops and low-quality cells) were filtered out and excluded from subsequent analyses, and genes detected in less than 3 cells were also excluded. In addition, cells with less than 500 detected genes or with less than 500 reads count or with a mitochondrial gene fraction that is ≥20% were filtered out using Seurat (v4.1.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include barcodes, features/genes, and raw counts for each sample

source_name: Cell-line

extract_protocol:
Fresh tissue samples were promptly submerged in DMEM with 10% FBS at 2-8 °C upon collection. Prior to tissue digestion, the samples were rinsed with Hanks Balanced Salt Solution (HBSS) and sliced into 1-2 mm fragments. Subsequently, the tissue fragments were incubated in 1mg/ml collagenase IV (Thermofisher # 17104019) for 30 minutes and neutralized with HBSS containing 2% FBS. Following filtration through a 70µm cell strainer, the cells were centrifuged and prepared for sequencing without prior sorting. Concurrently, to monitor the decontamination process of our tissue samples, the HT29 cell line (ATCC, # HTB-38™) was employed as a control throughout the sequencing procedure. Cell counts and viabilities were determined using trypan blue exclusion and counted on a Countess 3 FL automated cell counter (Life Technologies). Cell capture processing and gene expression library preparations were performed following 10X Genomics’ guidelines for 5’ scRNA-seq. QC steps after cDNA amplification and library preparation steps were carried out by running ThermoFisher Qubit HS dsDNA Assay along with Agilent (Santa Clara, CA) HS DNA Bioanalyzer for concentration and quality assessments, respectively. Equal library amounts were used for pooling. Library pool concentration was verified using qPCR using a KAPA Biosystems KAPA Library Quantification Kit prior to sequencing. The pool was sequenced using three lanes of a NovaSeq6000 S4-XP, 200-cycle flow cell. The run parameters used were 26 cycles for read 1, 90 cycles for read2, 10 cycles for index1, and 10 cycles for index2 as stipulated in the protocol mentioned above. Sequencing depth targeted was 100,000 reads/cell.
cDNA

value: colorectal


title: Colorectal tumor tissue of patient 3 [scRNA-seq]

description: Library name: 5T-5GE

source_name: Fresh human colorectal tissue


title: Colorectal tumor tissue of patient 2 [scRNA-seq]

description: Library name: 4T-5GE


title: Colorectal tumor tissue of patient 1 [scRNA-seq]

description: Library name: 3T-5GE


title: Non-proliferating CD4⁺ T-cells, 100uM PCS,HC5

city: Atlanta

first: Souheil

last: Younes

state: Georgia

address: 1750 Haygood Dr NE

department: Pathology and Laboratory Medicine

institute: Emory University

description:
Library name: s040
10x Genomics

data_processing:
Raw reads were assessed using FastQC and aligned to the GRCh38 genome using the STAR aligner. Only samples meeting quality control thresholds were included in further analysis, ensuring alignment with expression patterns from traditional bulk RNA sequencing studies.
Assembly: GRCh38
Supplementary files format and content: raw counts for each sample

source_name: Peripheral Blood

growth_protocol: Cells from healthy donors were labeled with CellTrace™ Violet (catalog C34557, Invitrogen) and stimulated for 6 days with 200 ng of purified NA/LE anti-Human CD3 (clone UCHT1, catalog 555329, BD Biosciences) and purified NA/LE anti-Human CD28 (clone CD28.2) in RPMI media (catalog 10-040-CV, Corning) containing 2% human serum (catalog 46026, Innovative Research) and 1% penicillin and streptomycin (catalog 30-002-CI, Corning).

extract_protocol:
After 6 days of stimulation and PCS exposure, CD4 proliferated cells were sorted by BD FACSAria™ II (BD Biosciences), followed by RNA isolation using the RNeasy Kit (catalog 74104, QIAGEN, Venlo, NL) and library preparation.
Library preparation was performed according to the manufacturer’s instructions using the Illumina® Stranded Total RNA Prep with Ribo-Zero Plus Kit (catalog 20040529, Illumina, San Diego, CA, USA), and IDT for Illumina® RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples, catalog 20040553). cDNA library quality was assessed using an Agilent High-Sensitivity DNA Kit (catalog 5067-4626, Agilent Technologies, Santa Clara, CA, USA), yielding a broad peak between 300-800 base pairs.

treatment_protocol: Cells were exposed to different PCS concentrations (catalog A8895, APExBIO): 10 μM, 50 μM, and 100 μM.

value: Peripheral Blood

tag: cell type

value: T cells

tag: treatment

value: 100uM PCS

tag: group

value: Non-proliferating


title: Proliferating CD4⁺ T-cells, 100uM PCS,HC5

description:
Library name: s039
10x Genomics

value: Proliferating


title: Non-proliferating CD4⁺ T-cells, 50uM PCS,HC5

description:
Library name: s038
10x Genomics

value: 50uM PCS


title: Proliferating CD4⁺ T-cells, 50uM PCS,HC5

description:
Library name: s037
10x Genomics


title: Proliferating CD4⁺ T-cells, 10uM PCS,HC5

description:
Library name: s035
10x Genomics

value: 10uM PCS


title: Non-proliferating CD4⁺ T-cells, 10uM PCS,HC5

description:
Library name: s036
10x Genomics


title: Non-proliferating CD4⁺ T-cells, No PCS,HC5

description:
Library name: s034
10x Genomics

value: No PCS


title: Non-proliferating CD4⁺ T-cells, 50uM PCS,HC4

description:
Library name: s030
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 10uM PCS,HC4

description:
Library name: s028
10x Genomics


title: Proliferating CD4⁺ T-cells, 50uM PCS,HC4

description:
Library name: s029
10x Genomics


title: Proliferating CD4⁺ T-cells, 10uM PCS,HC4

description:
Library name: s027
10x Genomics


title: Non-proliferating CD4⁺ T-cells, No PCS,HC4

description:
Library name: s026
10x Genomics


title: Proliferating CD4⁺ T-cells, No PCS,HC4

description:
Library name: s025
10x Genomics


title: Proliferating CD4⁺ T-cells, 50uM PCS,HC3

description:
Library name: s021
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 50uM PCS,HC3

description:
Library name: s022
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 10uM PCS,HC3

description:
Library name: s020
10x Genomics


title: Proliferating CD4⁺ T-cells, 10uM PCS,HC3

description:
Library name: s019
10x Genomics


title: Non-proliferating CD4⁺ T-cells, No PCS,HC3

description:
Library name: s018
10x Genomics


title: Proliferating CD4⁺ T-cells, No PCS,HC3

description:
Library name: s017
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 100uM PCS,HC2

description:
Library name: s016
10x Genomics


title: Proliferating CD4⁺ T-cells, 100uM PCS,HC2

description:
Library name: s015
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 50uM PCS,HC2

description:
Library name: s014
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 10uM PCS,HC2

description:
Library name: s012
10x Genomics


title: Proliferating CD4⁺ T-cells, 50uM PCS,HC2

description:
Library name: s013
10x Genomics


title: Proliferating CD4⁺ T-cells, 10uM PCS,HC2

description:
Library name: s011
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 100uM PCS,HC1

description:
Library name: s008
10x Genomics


title: Proliferating CD4⁺ T-cells, No PCS,HC2

description:
Library name: s009
10x Genomics


title: Proliferating CD4⁺ T-cells, 100uM PCS,HC1

description:
Library name: s007
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 50uM PCS,HC1

description:
Library name: s006
10x Genomics


title: Non-proliferating CD4⁺ T-cells, 10uM PCS,HC1

description:
Library name: s004
10x Genomics


title: Proliferating CD4⁺ T-cells, 50uM PCS,HC1

description:
Library name: s005
10x Genomics


title: Proliferating CD4⁺ T-cells, 10uM PCS,HC1

description:
Library name: s003
10x Genomics


title: Non-proliferating CD4⁺ T-cells, No PCS,HC1

description:
Library name: s002
10x Genomics


title: Proliferating CD4⁺ T-cells, No PCS,HC1

description:
Library name: s001
10x Genomics


title: CD4⁺ T-cells, PCS High,GIR08

description:
Library name: 8
10x Genomics

data_processing:
Raw sequencing reads were processed using the 10x Genomics Cell Ranger pipeline (v7.1.0). Reads were aligned to the human reference genome (GRCh38), and gene expression matrices were generated using default parameters. Downstream analyses were performed in R (v4.3.2) using Seurat (v5.0.1). Cells with low gene counts, high mitochondrial gene expression (>10%), or doublet signatures were excluded. Data were log-normalized, scaled, and subjected to dimensionality reduction (PCA and UMAP). Clustering was performed using a shared nearest neighbor (SNN) approach. Differential gene expression and pathway analyses were conducted to identify PCS-associated transcriptional programs in CD4⁺ T cells.
Assembly: GRCh38
Supplementary files format and content: The 10x Genomics Cell Ranger pipeline produces multiple output files that, together, describe the processed single cell data. One output, the 'molecule_info.h5' file, is an HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, features, and barcode lists used for the analysis. Further, the pipeline outputs two types of feature-barcode matrices – filtered and raw. There is one type of feature, 'Gene Expression', in either matrix. For a 'Gene Expression' feature, each element in the matrix is the number of UMIs associated with the corresponding feature (row) and barcode (column). With respect to the 'filtered_feature_bc_matrix.tar.gz' files, rows represent genes detected, while the columns consist of all cell-associated barcodes. On the other hand, for the 'raw_feature_bc_matrix.h5' files, rows represent genes detected, while the columns consist of all barcodes that were detected in the experiment with non-zero signal in either modality. A barcode has a non-zero signal if it has at least one read. Both cell-associated and background barcodes are included in this raw feature-barcode matrix. Sample libraries were aggregated using the Cell Ranger aggr pipeline. Using this pipeline, reads from each sample library were subsampled such that all libraries have the same effective sequencing depth, measured in terms of reads that are confidently mapped to the transcriptome or assigned to known features. Additionally, the pipeline received information on which libraries should be aggregated from an input file called the aggregation CSV. In this file, the ‘sample_id’ column contains the unique identifier for each individual sample library to be aggregated, whereas the ‘molecule_h5’ column describes the path to the corresponding ‘molecule_info.h5’ file to be used in the aggregation.

extract_protocol:
Frozen PBMCs were thawed, and total CD4+T-cells were enriched using the EasySep™ Human CD4+T-Cell Enrichment Kit (StemCell Technologies, Vancouver, CA), following the manufacturer’s instructions. Cells were washed with PBS containing BSA 0.04%, and viability was assessed by staining the cells with Trypan blue. Cells were resuspended at the desired concentration to target 10,000 cells per sample.
Single-cell suspensions were prepared using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10x Genomics, Pleasanton, CA) and partitioned into Gel Beads-in-emulsion (GEMs) using the 10x Chromium Controller and Next GEM Chip K. GEMs were visually inspected, and only samples with an opaque and uniform aspect were used for library preparation. Gene Expression (GEX) libraries were generated from the cDNA. Representative traces and quantitation of libraries were determined using Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA). GEX libraries were sequenced on Illumina NovaSeq S4 system, using 10x’s recommended parameters. The 10x Barcodes in the library were used to associate individual reads back to the individual partitions, and thereby, to each single cell.

tag: subject status

value: PLWH with high cell-associated PCS concentrations


title: CD4⁺ T-cells, PCS Low,GIR07

description:
Library name: 7
10x Genomics

value: PLWH with low cell-associated PCS concentrations


title: CD4⁺ T-cells, PCS Low,GIR04

description:
Library name: 4
10x Genomics


title: CD4⁺ T-cells, PCS High,GIR02

description:
Library name: 2
10x Genomics


title: CD4⁺ T-cells, PCS Low,GIR03

description:
Library name: 3
10x Genomics


title: CD4⁺ T-cells, PCS High,GIR24

description:
Library name: 1
10x Genomics


title: PRMT1_low RPL TSC4

city: Kansas city

first: Soumen

last: Paul

state: Kansas

address: Rainbow Blvd

department: Pathology

institute: University of Kansas Medical center

description: Library name: RPL-107_S43

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the subread-2.0.3
count values containing file were obtained using featureCounts of subread-2.0.3
differential expression was obtained using DESeq2
Assembly: UCSC hg38(iGenomes illumina)
Supplementary files format and content: tab-delimited text files of raw count values for each Sample

source_name: Placenta

growth_protocol: Human TSC Cell culture protocol was published earlier (Saha et al. Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17864-17875. doi: 10.1073/pnas.2002449117)

extract_protocol:
For RNA extraction we used Qiagen RNeasy Kit (Catalog#74104) following manufacturer's protocol. For each experimental conditions, 1 million cells were used to isolate total RNA.
For sequencing, libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) designed for transcriptome analysis from samples as small as a single cell.  For library preparation, the mRNA fraction was enriched, fragmented, sized, reverse transcribed into cDNA and ligated with the appropriate adaptors. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

treatment_protocol: No

value: Placenta

tag: cell line

value: PRMT1_low RPL TSC4

value: Human trophoblast stem cells


title: PRMT1_low RPL TSC3

description: Library name: RPL-44_S29

value: PRMT1_low RPL TSC3


title: RC77NE_H3K27ac_R1

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Cancer Biology

institute: University of Southern California

description:
Library name: RC77NE H3K27ac R1
ChIP-seq

library_source: genomic

data_processing:
ChIP-seq data were processed following ENCODE3 guidelines (PMID: 22955616). Briefly, BWA (PMID: 19451168) was used to align the raw sequencing reads to the human reference genome (hg38). Library complexity was computed to determine the PCR bottleneck coefficients, non-redundant fraction, normalized strand cross-correlation coefficient, and relative strand cross-correlation coefficient. PCR duplicates and unaligned reads were removed using Picard (https://github.com/broadinstitute/picard) and samtools (PMID: 19505943). Uniquely mapped reads were used to call peaks using MACS2 (PMID: 18798982) (narrowPeak format).
Assembly: hg38
Supplementary files format and content: .bw

molecule: genomic DNA

source_name: Prostate

growth_protocol: 22Rv1 (CRL-2505) and RWPE-1 (CRL-11609) cells were obtained from the American Type Culture Collection (ATCC). RC-77N/E and RC77T/E cells were received from Johng Sik Rhim. Cells were cultured according to the suggested protocols at 37°C with 5% CO2. 22Rv1 cells were cultured in RPMI 1640 (Corning, #10-040-CV) supplemented with 10% FBS (Avantor Seradigm, #89510-188) and 1% penicillin/streptomycin. RWPE-1, RC-77N/E, and RC77T/E cells were cultured in the Keratinocyte Serum Free Medium kit (Thermo Fisher Scientific, #17005-042).

extract_protocol:
For ChIP-seq, cells were grown to 70%-90% confluence and cross-linked with 1% formaldehyde for 10 minutes and quenched with 125nM glycine for 5 minutes at RT. Nuclei were lysed in nuclei lysis buffer, and performed snap-freeze using liquid nitrogen. Chromain was sonicated to an approximate length of 200 bp - 500 bp using bioruptor sonicator.
ChIP-seq library: Libraries were prepared using the KAPA Hyper Prep Kit from KAPA Biosystems. End-Repair and A-Tailing Buffers, DNA ligase, and ligation buffer were used. Ampure beads were used for post-ligation clean up, and KAPA HiFi HotStart Ready Mix and Nextflex Primer Mix were used for amplification of adapter modified DNA fragments.

value: Prostate

value: prostate cells

tag: batch


title: PRMT1_low RPL TSC2

description: Library name: RPL-139_S55

value: PRMT1_low RPL TSC2


title: PRMT1_high RPL TSC4

description: Library name: RPL-135_S52

value: PRMT1_high RPL TSC4


title: PRMT1_low RPL TSC1

description: Library name: RPL-134_S51

value: PRMT1_low RPL TSC1


title: Alveolus-on-chip, butyrate treated, uninfected, replicate_2

city: Jena

first: Marc Thilo

last: Figge

state: Thuringen

address: Adolf-Reichwein-Straße 23

department: Applied System Biology

country: Germany

institute: HKI-Leibniz

description:
Library name: Control_butyrate_2
10xGenomics

data_processing:
Raw sequencing data from four iPSC-derived lung-on-chip conditions (Control, butyrate-treated control, IAV-infected and IAV-infected butyrate-treated) were processed using Cell Ranger (10x Genomics) against the GRCh38 genome
Assembly: GRCh38
Supplementary files format and content: Cell ranger filtered feature matrices .h5 for each sample

molecule: polyA RNA

source_name: lung

growth_protocol: The iAT2s were first seeded onto the apical side of the membrane and cultured under static conditions until confluence. Once a confluent epithelial monolayer formed, on day 3, endothelial cells were seeded on the basal side of the membrane. Media were exchanged daily, and both cell layers remained under static conditions. As the final cell type, iPSC-derived macrophages were added to the endothelial surface on day 7.

extract_protocol:
At 24 hours post-infection, cells from the chip were washed with PBS -/- and enzymatically dissociated using Accutase, incubated for 15 minutes at 37 °C, then processed for single-cell RNA sequencing on the 10x Genomics Chromium platform. After dissociation, the cells were assessed for viability, and based on cell number and viability, approximately 10,000 cells per condition were pipetted for further experiments.
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 protocol (10xGenomics, PN-1000268). The workflow included three main steps: Step 1 – GEM Generation & Barcoding: A reaction mix was prepared and loaded onto a Chromium Next GEM Chip. The chip was then operated on the Chromium Controller to produce Gel Bead-In-Emulsions (GEMs), which enable cell barcoding. After GEM formation, GEMs were carefully transferred for reverse transcription (GEM-RT) incubation. GEM-RT reactions were incubated as recommended, with interim storage at 4°C for up to 72 hours or at −20°C for up to a week if necessary. Step 2 – Post GEM-RT Cleanup & cDNA Amplification: Following incubation, GEMs were disrupted, and post-GEM-RT cleanup was performed using Dynabeads. Amplification of cDNA was conducted to generate enough material for downstream applications. The amplified cDNA was purified using SPRIselect beads (Beckman Coulter, B23318) and then subjected to quality control (QC) and quantification. cDNA samples could be stored at 4°C for up to 72 hours or at −20°C for up to four weeks before further use. Step 3 – 3ʹ Gene Expression Library Construction: The amplified cDNA was fragmented, end-repaired, and A-tailed. After fragmentation, a double-sided size selection was performed using SPRIselect beads. Adaptors were ligated to the fragmented cDNA, followed by a cleanup with SPRIselect. Samples were then indexed by PCR amplification, and a final double-sided size selection was performed to purify the libraries. The final libraries underwent quality control and quantification before sequencing. Libraries were sequenced on an Illumina NovaSeq 6000, according to the recommendations of 10x Genomics.

treatment_protocol: On day 12, all infected chips were exposed to Influenza A virus A/Wisconsin/588/2019 (H1N1) at an MOI of 0.1. The virus was applied apically for 2 hours under static conditions. Following incubation, the virus was removed, the chips were washed with serum-free medium, and ALI was re-established. Medium containing butyrate (10 µM) was maintained in the vascular channel of the treated group throughout the post-infection period.

value: lung

value: epithelial, endothelial, macrophages

value: butyrate


title: PRMT1_high RPL TSC2

description: Library name: RPL-111_S46

value: PRMT1_high RPL TSC2


title: PRMT1_high RPL TSC3

description: Library name: RPL-113_S47

value: PRMT1_high RPL TSC3


title: PRMT1KD replicate2

city: Kansas City

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

description: Library name: Sample2

value: CT27 humanTSCs with PRMT1 knockdown

value: Trophoblast

tag: genotype


title: CT27 replicate2

description: Library name: Sample4

value: CT27 humanTSCs expressing a scrambled shRNA

value: scrambled shRNA


title: CT27 replicate1

description: Library name: Sample3

value: Placenta


title: KG1a, PRMT2 KO, clone 2, replicate 2

city: Dijon

first: Laurent

last: DELVA

address: 7 boulevard Jeanne d’Arc

department: Inserm U1231 (CTM)

country: France

institute: Université de Bourgogne

description: Library name: KG1a_PRMT2_KO2_2

data_processing:
Raw paired-end FASTQ reads were quality-controlled before alignment.
Reads were aligned to the human reference genome GRCh38 using STAR in two-pass mode.
Gene-level read counts were generated from aligned reads.
Differential gene expression analysis was performed in R using DESeq2.
Low-count genes were filtered before analysis, and log₂ fold changes were estimated using apeglm shrinkage. Differentially expressed genes were defined using adjusted statistical thresholds.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for each sample (STAR2 count).
Supplementary files format and content: Comma-separated values file containing RNA-seq expression values as raw counts and TPM values offset by 1 × 10⁻⁴ for each gene.

growth_protocol: KG-1a human acute myeloid leukemia cells were cultured in RPMI 1640 medium supplemented with 20% fetal bovine serum at 37°C in a humidified incubator with 5% CO₂. Cells were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted from KG-1a PRMT2 wild-type and PRMT2 knockout cells using TRIzol reagent according to the manufacturer’s instructions. RNA quality and quantity were assessed before library preparation.
RNA-seq libraries were prepared from total RNA using an Illumina-compatible library preparation workflow GENEWIZ (Azenta Life Sciences). Libraries were sequenced on an Illumina NovaSeq 6000 platform using a paired-end 2 × 150 bp configuration.

treatment_protocol: PRMT2 knockout KG-1a cell lines were generated using CRISPR/Cas9-mediated genome editing. Independent PRMT2 knockout clones and wild-type control cells were expanded under identical culture conditions before RNA extraction. No drug treatment was applied.

value: Acute myeloid leukemia cell line

value: PRMT2 knockout clone 2


title: PRMT1KD replicate1

description: Library name: Sample1


title: PRMT1_high RPL TSC1

description: Library name: RPL-110_S45

value: PRMT1_high RPL TSC1

value: Human trophoblast stem cells


title: Patient 6 Remission

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: Library name: S18

data_processing:
Short-read quality control and trimming were performed using FastQC v0.11.5, MultiQC v1.7, and TrimGalore v0.6.6, respectively. Reads were aligned to GENCODE humangenome v38 using STAR v.2.7.9a, and low-quality alignments (mapq score < 15) were filtered with samtools v1.17. Next, featureCounts v2.0.1 was used to quantify the gene expression from BAM files.
Assembly: hg38
Supplementary files format and content: gene count matrix

source_name: bone marrow

growth_protocol: For expansion of human BM stroma, patient BM aspirates were rapidly thawed at 37°C and washed using 50% Ex vivo media with DNAase I (100 U/mL) in FBS. Cells were resuspended at 2x106/mL in human stroma media (MEMα with GlutaMax [Gibco, 32561037], Pen/Strep, 3.3% Heparin [Sigma-Aldrich, 2106], and 10% human platelet lysate [STEMCELL Technologies, 6960]) and seeded in culture plates with proper size (P0). Following 3d incubation at 37°C, plates were washed twice with PBS, replenished with fresh human stroma media, and cultured until colony formation. Cells were then detached and seeded at 1-3x105 per 10 cm plate until confluence (P1). BM stroma was viably frozen at P1 for RNA-seq analysis.

extract_protocol:
BM stroma was thawed in DMEM with 10% FBS and lysed in Buffer RLT Plus.
Total RNA was extracted with RNeasy Plus Micro Kit (QIAGEN, Cat. # 74034). The cDNA libraries were prepared using SMART-Seq v4 Plus Kit (Takara, Cat. # R400752) following manufacturer’s protocol.

value: bone marrow

value: Stroma

tag: time point

value: Remission


title: NCMT2

description: Library name: 5

value: colon

value: NCMT


title: Patient 6 Diagnosis

description: Library name: S17

value: Diagnosis


title: Patient 5 No response

description: Library name: S14

value: No response


title: Patient 7 No response

description: Library name: S12R


title: Patient 5 Diagnosis

description: Library name: S13


title: Patient 7 Diagnosis

description: Library name: S11


title: Patient 8 Remission

description: Library name: S10R


title: Patient 3 Remission

description: Library name: S8


title: Patient 2 Diagnosis

description: Library name: S5


title: Patient 8 Diagnosis

description: Library name: S9


title: Patient 2 Remission

description: Library name: S6R


title: Patient 3 Diagnosis

description: Library name: S7


title: Patient 1 Diagnosis

description: Library name: S3


title: A21B25-PyMT-Cas9_Day14

first: Zheng

last: Yin

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

institute: Houston Methodist Cancer Center

description:
Library name: D14
PyMT-Cas9 lineage tracing cell line collected 14 days after doxycycline-induced barcode editing. Genomic DNA was extracted and the A21 and B25 hgRNA barcode locus was amplified for mutation profiling.

data_processing:
Raw FASTQ files were demultiplexed and processed using a custom barcode analysis pipeline. Sequencing reads were aligned to the reference A21 and B25 hgRNA barcode sequence and insertions/deletions were identified. Unique barcode alleles and their frequencies were quantified for each sample. Barcode mutation profiles were subsequently analyzed using LINEMAP to infer mutation evolution dynamics and lineage relationships.
Supplementary files format and content: Four excel files summarizes the Barcode mutations identified by LINEMAP, the files defined the mutations of A21 barcodes at Day 5 (d5A21.xlsx) or Day 14 (d14A21.xlsx) and that from B25 barcodes at Day 5 (d5B25.xlsx) or Day 14 (d14B25.xlsx), respectively
Supplementary files format and content: Each row presented one particlular pattern of barcode mutations and the number of times it was quantified from the fastq profile.

organism: Mus musculus

source_name: mammary tumor

growth_protocol: PyMT-Cas9 mammary tumor cells carrying integrated A21 and B25 homing guide RNA (hgRNA) lineage barcodes were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO2. Cells were maintained under standard culture conditions and expanded prior to barcode induction experiments.

extract_protocol:
Genomic DNA was extracted from harvested cells using standard genomic DNA purification procedures. DNA quality and concentration were assessed prior to barcode amplification.
The A21 and B25 hgRNA barcode locus was PCR amplified from genomic DNA using barcode-specific primers. Amplicons were purified and indexed for Illumina sequencing according to standard amplicon sequencing protocols. Sequencing libraries were quantified, pooled, and subjected to paired-end sequencing.

treatment_protocol: Barcode editing was induced by treatment with doxycycline (500 nM). Cells were harvested at day 5 and day 14 following induction to characterize barcode mutation accumulation and lineage evolution.

value: mammary tumor

value: mammary tumor cell

value: PyMT-Cas9 cells carrying integrated A21 and B25 hgRNA lineage barcodes

value: Doxycycline-induced barcode editing, harvested at day 14


title: A21B25-PyMT-Cas9_Day5

description:
Library name: D5
PyMT-Cas9 lineage tracing cell line collected 5 days after doxycycline-induced barcode editing. Genomic DNA was extracted and the A21 and B25 hgRNA barcode locus was amplified for mutation profiling.

value: Doxycycline-induced barcode editing, harvested at day 5


title: Patient 4 Diagnosis

description: Library name: S1


title: AML12 cultured under standard conditions

city: Aachen

first: Ralf

last: Weiskirchen

address: Pauwelsstr. 30

department: IFMPEGKC

institute: RWTH University Hospital Aachen

description: Library name: AML12

data_processing:
Raw base call (BCL) files were demultiplexed using Illumina bcl-convert to generate sample-level FASTQ files. Downstream processing was performed using the nf-core/rnaseq pipeline (version 3.12.0) implemented in Nextflow. Reads were processed using the provided sample sheet, aligned to the GENCODE GRCm39 v35 reference genome with GENCODE gene annotation, and gene-level counts were generated using featureCounts grouped by gene type. The pipeline was executed using the Docker profile with default parameters unless otherwise specified.
Assembly: GRCm39
Supplementary files format and content: AML12_abundences.csv is a comma-separated values (CSV) file containing transcript-level abundance estimates. Columns include transcript identifiers, transcript length and effective length, estimated read counts, transcripts per million (TPM), and associated gene identifiers, gene names, and gene descriptions.

growth_protocol: AML12 cells were obtained from the American Type Culture Collection (CRL-2254, ATCC, Manassas, VA, USA) and maintained in a humidified incubator at 37 ◦C with 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM, high glucose, #D6171-500ML, Sigma-Aldrich, Merck, Taufkirchen, Germany). The medium was supplemented with 2 mM sodium pyruvate solution (#S8636-100ML, Sigma Aldrich), 10% fetal bovine serum (FBS, #F7524, Sigma- Aldrich), 2 mM L-glutamine (#G7513, Sigma-Aldrich) and 1 × penicil-lin-streptomycin antibiotic solution (P0781-100ML, Sigma Life Science, Lonza, Cologne, Germany).

extract_protocol:
The cells were cultured under basal conditions, until they reached approximately 80% confluence. Subsequently they were lysed in guanidine thiocyanate, and total RNA was isolated using a cesium chloride cushion. The isolated RNA was then precipitated with ethanol and resuspended in nuclease-free water.
Libraries were prepared according to the manufacturer’s instructions for the selected library preparation workflow. Library quality and concentration were assessed, and libraries were normalized, pooled, denatured, and diluted following Illumina guidelines. Sequencing was performed on an Illumina MiSeq using the MiSeq Reagent Kit v2 (300 cycles), generating paired-end reads (2 × 150 bp).

treatment_protocol: Cells were isolated at a density of 70-80% without futher treatment.

value: hepatocyte


title: HFF-1 cells, AMmnp3, day 14

city: Chongqing

first: BINGLIN

last: ZHU

address: 313 Jinyue Road

institute: Jinfeng Laboratory

description:
Library name: SAMPLES 6
AMmnp3

data_processing:
Sequencing was performed at the Jinfeng Laboratory Single-Cell Sequencing Center. Raw sequencing data were processed through a standardized bioinformatics pipeline. Clean reads were aligned to the human reference genome (hg38) using HISAT2, and gene-level counts were obtained with featureCounts.
Assembly: human reference genome (hg38)
Supplementary files format and content: txt files include FPKM values for each sample

source_name: HFF-1 cells

growth_protocol: Human skin fibroblast (HFF-1) were maintained in DMEM/F12 supplemented with 10% fetal bovine serum, NEAA, L-glutamine and antibiotics in humidified atmosphere with 5% CO₂ at 37°C

extract_protocol:
Total RNA was extracted from  AMnp- and AMmnp-reprogrammed HFF-1 cells using TRIzol Reagent, following the manufacturer’s protocol.
RNA libraries were prepared with the TruSeq Stranded RNA Library Prep Kit (Illumina) and sequenced using the NovaSeq 6000 SP Reagent Kit on the Illumina NovaSeq 6000 platform, generating 50 bp paired-end reads.

treatment_protocol: HFF-1 cells were transduced with lentiviral AMnp or AMmnp reprogramming factors and cultured in neural induction medium under hypoxia (5% O₂) for 14 days, with untreated cells as controls.

value: HFF-1 cells

value: human skin fibroblast

value: AMmnp


title: Pim1-/- oxLDL_3

city: Wauwatosa

first: Yiliang

last: Chen

address: 8727 W Watertown Plank

institute: Versiti

description:
Library name: 12Pim1KOoxldl
Column name in GENE_TPM.xlsx: Pim1KOoxldl-3

data_processing:
Bulk RNA-seq data were aligned to the Mus musculus mm10 genome and quality control was performed using Nextflow pipeline (nf-core/rnaseq) .
Gene expression was quantified at the gene level using Salmon.
RNA-seq libraries were then normalized and genes were tested for differential expression between conditions with DESeq2.
DESeq2 Wald tests were used to determine whether fold changes were significantly different from zero.
Assembly: mm10
Supplementary files format and content: xlsx file include normalized count for samples

source_name: peritoneal  macrophages

growth_protocol: Mφs were cultured in RPMI supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin, and maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total cellular RNA was isolated from peritoneal Mφs using the RNeasy® Mini Kit (Qiagen, Hilden, Germany). RNA quality was evaluated with the Bioanalyzer RNA Nano Assay (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Isolated Mφs were treated with 20 μg/mL oxLDL for 8 hours

value: peritoneal  macrophages

value: oxLDL


title: HFF-1 cells, AMmnp2, day 14

description:
Library name: SAMPLES 5
AMmnp2


title: HFF-1 cells, AMmnp1, day 14

description:
Library name: SAMPLES 4
AMmnp1


title: HFF-1 cells, AMnp3, day 14

description:
Library name: SAMPLES 3
AMnp3

value: AMnp


title: Pim1-/- oxLDL_1

description:
Library name: 10Pim1KOoxldl
Column name in GENE_TPM.xlsx: Pim1KOoxldl-1


title: Pim1-/- oxLDL_2

description:
Library name: 11Pim1KOoxldl
Column name in GENE_TPM.xlsx: Pim1KOoxldl-2


title: Pim1-/- control_3

description:
Library name: 9Pim1KOcontrol
Column name in GENE_TPM.xlsx: Pim1KOcontrol-3

value: PBS


title: HFF-1 cells, AMnp2, day 14

description:
Library name: SAMPLES 2
AMnp2


title: HFF-1 cells, AMnp1, day 14

description:
Library name: SAMPLES 1
AMnp1


title: Pim1-/- control_1

description:
Library name: 7Pim1KOcontrol
Column name in GENE_TPM.xlsx: Pim1KOcontrol-1


title: Pim1-/- control_2

description:
Library name: 8Pim1KOcontrol
Column name in GENE_TPM.xlsx: Pim1KOcontrol-2


title: U2OS_siORCA_IgG

city: Urbana

first: Supriya

last: Prasanth

state: IL

address: 601 S Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois Urbana Champaign

description: Library name: IgG_SiORCA

data_processing:
Trimmed reads were aligned to reference genome UCSC hg38 using Bowtie2 with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10. Also, reads were mapped to the E. coli genome assembly to quantify E. coli spike-in DNA. Low quality reads (MAPQ < 30) were removed using SAMtools.
Peak calling on individual replicates was performed using the bam files using following command macs2 callpeak -t target.bam -c control.bam -q 0.01 -f BAMPE -g hs --keep-dup all -n sample
Bedtools intersect (1 bp overlap) was used to find the high confidence overlapping peaks between two replicates
Signal tracks were generated using deepTools-bamCoverage using RPKM and E.coli Spike-in normalization. Average signal files were generated from two replicates using bigWigAverage command.
Differential peaks of BMI1, RNF2 and EZH2 (up - upregulated; ns - non-significant) were identified by DiffBind-DEseq2, with an FDR < 0.05 and (Fold change) > 1.5 cutoff.
Assembly: Chm13
Supplementary files format and content: bigWig (signal track)
Supplementary files format and content: bed (Macs2-called peaks, except for IgG control)
Supplementary files format and content: bed (DiffBind-DEseq2 results)
Library strategy: CUT&Run

growth_protocol: DMEM, 5% Fetal Bovine Serum, 1% Penicillin/Streptomycin. Cells were cultures at 37C at 5% CO2.

extract_protocol:
Sample preparation was done with CUTANA™ ChIC / CUT&RUN Kit (EpiCypher #14-1048). Cells (500,000) were fixed in culture medium supplemented with 0.1% formaldehyde for 1 min before quenching with 0.125 M glycine. Cells were then permeabilized, bound to concanavalin A magnetic beads and incubated overnight at 4 °C with primary antibodies using a 1:50 dilution. After overnight incubation and washing to remove excess antibodies, protein A/G-MNase was added to the antibody-bound beads and activated with calcium at 4 °C for 2 h to cleave target-bound genomic DNA. After quenching the cleavage reaction, the samples were reverse cross-linked under proteinase K treatment overnight at 55 °C.
CUT&RUN DNA was isolated with column chromatography, and libraries were prepared using an NEBNext Ultra II DNA Library Prep kit for Illumina (New England BioLabs). Libraries were sequenced on an Illumina NovaSeq 6000 with paired-end 150-base pair reads.

treatment_protocol: Cells underwent two rounds of siRNA-mediated ORCA knockdown for 24h each. Cells were collected after 24h.

value: Human osteosarcoma

value: SiORCA

tag: cut&run antibody

value: IgG (EpiCypher 13-0042)


title: threonine-deficient offspring pancreas

type: RNA

city: Tokyo

first: Xuguang

last: Li

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: Tokyo University

description: RNA pooled from pancreas of 10-week-old male threonine-deficient offspring

hyb_protocol: Hybridisation was performed at 45 °C for 16 hours according to the Affymetrix protocol. Chips were then washed and stained automatically.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the MAS5 algorithm. MAS5 signal intensities and detection calls were generated for each probe set. Probe sets with fold change > 1.5 or < 0.67 were used for intergroup comparison, and pathway analysis was performed using IPA.

label: biotin

source_name: pancreas

label_protocol: Biotin-labeled cRNA was prepared using the GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Female C57BL/6J mice were fed control or threonine-deficient diet during embryonic day 12.5 to 14.5. Male offspring were weaned at 3 weeks and provided control diet until 10 weeks.

extract_protocol: Total RNA was extracted from pancreas using TRIzol reagent (Invitrogen) following the manufacturer's protocol.

treatment_protocol: Control and TD groups were defined by the maternal diet during embryonic day 12.5 to 14.5. Offspring were not directly treated after birth.

value: threonine-deficient group


title: WT oxLDL_3

description:
Library name: 6WToxldl
Column name in GENE_TPM.xlsx: WToxldl-3

value: WT


title: U2OS_Control_IgG

description: Library name: IgG_Control

value: Control


title: U2OS_SiORCA_EZH2_replicate2

description: Library name: EZH2_SiORCA_2

value: EZH2 (EpiCypher 13-2026)


title: U2OS_SiORCA_EZH2_replicate1

description: Library name: EZH2_SiORCA_1


title: WT oxLDL_1

description:
Library name: 4WToxldl
Column name in GENE_TPM.xlsx: WToxldl-1


title: WT oxLDL_2

description:
Library name: 5WToxldl
Column name in GENE_TPM.xlsx: WToxldl-2


title: WT control_3

description:
Library name: 3WTcontrol
Column name in GENE_TPM.xlsx: WTcontrol-3


title: U2OS_SiORCA_RNF2_replicate2

description: Library name: RNF2_SiORCA_2

value: RING 1B (Cell signaling 5694)


title: U2OS_SiORCA_RNF2_replicate1

description: Library name: RNF2_SiORCA_1


title: WT control_1

description:
Library name: 1WTcontrol
Column name in GENE_TPM.xlsx: WTcontrol-1


title: U2OS_SiORCA_BMI1_replicate2

description: Library name: BMI1_SiORCA_2

value: Bmi1 (Cell signaling 6964)


title: AGO3_rep2 PAR-CLIP

city: Charlottesville

first: Roger

last: Abounader

state: Virginia

address: 21 Hospital Dr, Room No:4813, PO Box  800733

department: Microbiology, Immunology, Cancer Biology

institute: University of Virginia

description: Library name: AGO3_rep2

data_processing:
Raw sequencing data in BCL format was demultiplexed and converted to FASTQ files using bcl2fastq. Adapter sequences were retained during demultiplexing of barcoded samples using Cutadapt. For libraries with a 5’ adapter barcode, the barcode was anchored to the 5’ end of the read and removed while preserving unique molecular identifiers (UMIs). The remaining reads were aligned to the hg19 reference genome using Bowtie (v1.1.2) with the parameters: -v 2 -m 10 --best --strata. Further pre-processing, including the implementation of PARalyzer, was conducted using PARpipe (https://github.com/ohlerlab/PARpipe).
Assembly: hg19
Supplementary files format and content: tab separated files

growth_protocol: U87 cells were cultured and maintained in Minimal Essential Medium (MEM) supplemented with one mM sodium pyruvate, one mM non-essential amino acids (NEAA), 10 ml of 7.5% sodium bicarbonate, 1% penicillin/streptomycin, and 10% fetal bovine serum. The cells were cultured in a humidified chambe at 370C with 5% CO2.

extract_protocol:
The protein-RNA complexes were separated via SDS-PAGE and subsequently electroeluted. These complexes exhibited a migration pattern at around 100 kDa. The electroeluted samples then underwent digestion with proteinase K to release RNA from the complexes, followed by RNA extraction involving an acid phenol/chloroform mixture and ethanol precipitation.
Flag-tagged Ago1-3 plasmids were introduced into U87 cells via Lipofectamine 2000 transfection. Following transfection, the cells were subjected to puromycin selection at a concentration of 1 µg/ml for 48 hours to generate stable cell lines. Verification of Ago1-3 overexpression was conducted through immunoblot analysis employing Ago1-3 antibodies. The PAR-CLIP methodology was implemented and adapted from the previously established protocol (Hafner et al., 2010). Briefly, AGO1, AGO2,AGO3 stable cell lines were cultured overnight in the presence of 100 µM 4-thiouracil (4SU), to label all cellular nascent RNA. Subsequently, these 4SU-labeled cells were exposed to 365 nm UV light (utilizing a Spectro Linker XL-1500) to effectuate the crosslinking of labeled nascent RNA with RNA binding proteins. Following UV exposure, cells were rinsed twice with 1X PBS, harvested, and lysed using a buffer composed of 50 mM HEPES-KOH (pH 7.5), 150 mM KCl, two mM EDTA (pH 8.0), one mM NaF, 0.5% NP-40, 0.5 mM DTT, and freshly prepared protease inhibitor cocktails. Cell lysates were centrifuged at 15,000Xg for 15 minutes at 40C. The supernatant from the lysed cells was subjected to treatment with RNAse T1 at a concentration of 1 U/µl for 15 minutes at room temperature. Subsequently, the Flag-tagged Ago1-3 cell lysates' supernatant underwent immunoprecipitation, facilitated by an anti-Flag antibody conjugated to Protein G Dynabeads. The immunoprecipitated material was further subjected to digestion with RNase T1, and the resulting beads were subjected to washing with a high salt wash buffer. The washed beads were re-suspended in a dephosphorylation buffer and treated with calf intestinal alkaline phosphatase for 10 minutes at 370C to eliminate phosphate groups from RNA molecules. Next, the dephosphorylated beads were treated with polynucleotide kinase and radioactive [γ-32P]-ATP for 30 minutes at 370C to introduce RNA labeling. The protein-RNA complexes were then separated via SDS-PAGE and subsequently electroeluted. These complexes exhibited a migration pattern at around 100 kDa. The electroeluted samples then underwent digestion with proteinase K to release RNA from the complexes, followed by RNA extraction involving an acid phenol/chloroform mixture and ethanol precipitation. The extracted RNA was then converted into cDNA, and adaptor ligation was executed following previously established protocols (31, 65). The resulting libraries were sequenced, and the generated short reads were mapped against the human genome hg38, mRNA, and miRNA precursor databases and the clustered sequences were identified. The PAR-CLIP clustered sequences were identified by T to C conversion at the 4-thiouridine cross-linked site. The majority of the clustered sequences were found at the 3’-UTR regions. Finally, the true target sites were determined from the clustered sequences based on the list of input miRNA seed sequences.

treatment_protocol: Flag-tagged AGO1, AGO2, and AGO3 plasmids were introduced into U87 cells using Lipofectamine 2000 transfection. Following transfection, cells underwent puromycin selection (1 µg/mL) for 48 hours to establish stable cell lines. These stable cell lines were then cultured overnight in medium supplemented with 100 µM 4-thiouridine (4SU) and subsequently irradiated with 365 nm UV light before harvesting.

value: Glioblastoma


title: U2OS_SiORCA_BMI1_replicate1

description: Library name: BMI1_SiORCA_1


title: AGO3_rep1 PAR-CLIP

description: Library name: AGO3_rep1


title: U2OS_Control_EZH2_replicate1

description: Library name: EZH2_Control_1


title: AGO2_rep1 PAR-CLIP

description: Library name: AGO2_rep1


title: U2OS_Control_RNF2_replicate2

description: Library name: RNF2_Control_2


title: AGO2 _rep2 PAR-CLIP

description: Library name: AGO2_rep2


title: AGO1_rep2 PAR-CLIP

description: Library name: AGO1_rep2


title: U2OS_Control_RNF2_replicate1

description: Library name: RNF2_Control_1


title: AGO1_rep1 PAR-CLIP

description: Library name: AGO1_rep1


title: Hh188

city: Kyoto

first: Yoshinori

last: Yoshida

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

institute: Kyoto University

data_processing:
For the computational analyses, we trimmed adapter sequences by using cutadapt, remove the reads mapped to ribosomal RNA by using bowtie2 and samtools.
The STAR index was constructed from the genome index, and RNA-seq single-end reads were aligned to the genome using STAR
Using the bam files produced by the alignment tool, use the modules in RseQC to evaluate the quality of the RNA-seq data with the reference files.
HTSeq was used to count reads mapping to individual genes by processing the sorted bam files with accepted read quality.
Counts generated by HTSeq-count were normalized using DESeq2. This normalization utilized the size factor derived from the count data of all 58 DCM samples and 12 controls.
Assembly: Hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files includes raw counts values for each sample
Supplementary files format and content: tab-delimited text files includes normalized counts for each sample

source_name: Right ventricular septum

extract_protocol:
Sample homogenization was performed using 700 μL of QIAZOL (QIAGEN) either by manual crushing with a pestle or with a gentleMACS Dissociator (Miltenyi Biotec). After homogenization, two supernatants were collected in new 1.5 mL RNase-free microcentrifuge tubes. RNA extraction was carried out using the miRNeasy Micro Kit with a Rnase-Free Dnase Set (QIAGEN).
The cDNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit and protocol from Illumina (Illumina Inc., San Diego, CA).

value: Right ventricular septum


title: Hh184


title: U2OS_Control_BMI1_replicate1

description: Library name: BMI1_Control_1


title: Hh183


title: Hh180


title: U2OS, Control, Replicate 2, RNA-Seq

description:
Library name: U2OS_Control2
all_counts_U2OS_siEZH2_NCBI.txt

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
RNA-seq FASTQ files were aligned to the T2T star index using STAR aligner version 2.7.10b
Aligned reads were subsequently sorted and indexed using samtools (v1.17)
Read counts per gene for control and siORCA conditions were computed using the featureCount function from the subread package.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: Read counts in .txt file

source_name: Bone

growth_protocol: DMEM, 5% Fetal Bowin serum, 1X Penicillin and Streptomycin. Cells were cultured at 37 C at 5% CO2

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit and DNA was removed using DNase I
Ribosomal RNA was removed with the Ribozero HMR Gold kit (Illumina). The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand.

treatment_protocol: Cells were transfected with control (gl3) or siORCA.

value: Bone

value: Human Osteosarcoma

value: Batch 2


title: U2OS, Control, Replicate 1, RNA-Seq

description:
Library name: U2OS_Control1
all_counts_U2OS_siEZH2_NCBI.txt


title: Hh170


title: Hh171


title: WI38, siORCA, Replicate1, RNA-Seq

description:
Library name: WI38_siORCA1
all_counts_WI38_NCBI.txt

source_name: Lung

value: Lung

value: Human Lung Fibroblast

value: siORCA

value: Batch 1


title: Hh165


title: WI38, Control, Replicate 2, RNA-Seq

description:
Library name: WI38_Control2
all_counts_WI38_NCBI.txt


title: Hh162


title: Hgc27, SG21, LPDS, biol rep3

city: Istanbul

first: Burcu

last: Yucel

address: Unalan Mah.

department: Medical Faculty

country: Turkey

institute: Istanbul Medeniyet University

description: Library name: Hgc27_SG21_LPDS_rep3

data_processing:
All samples were processed and sequenced within the same flow cell to minimize batch effects. Raw BCL files obtained from the sequencer were converted into FASTQ format using bcl2fastq. Quality control and trimming were performed with Sickle, retaining reads with a minimum Phred quality score of 28 and a minimum length of 100 bp to ensure selection of high-quality mRNA reads.
Assembly: Reads were aligned to the human reference genome (hg38) using STAR aligner with the corresponding GTF annotation file.
Supplementary files format and content: Tab-delimited text files containing raw read counts for each gene. The first column represents gene names (symbols) and the second column represents the integer read counts.

source_name: Stomach

growth_protocol: TMEM97 KO and WT HGC27 gastric carcinoma cell lines cultured with FBS containing or LPDS containing high glucose DMEM medium.

extract_protocol:
Total RNA was isolated using Qiagen Rneasy mini kit.
Isolated RNA samples were quality checked, and RNA integrity numbers (RIN) were assessed with an RNA ScreenTape assay kit on the 4200 TapeStation system (Agilent Technologies). Quantification of RNA samples was determined with the Qubit RNA Broad Range Assay Kit using Qubit Flex Fluorometer (Invitrogen). 100 ng of total RNA input was subjected to library construction with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina).

treatment_protocol: Cells cultured in LPDS containing medium.

value: Stomach

value: Epithelial

value: TMEM97 Knockout

value: LPDS


title: Hh155


title: Hh153


title: Hh147


title: Hgc27, SG21, LPDS, biol rep2

description: Library name: Hgc27_SG21_LPDS_rep2


title: Hh145


title: Hgc27, SG21, LPDS, biol rep1

description: Library name: Hgc27_SG21_LPDS_rep1


title: Hgc27, SG21, FBS, biol rep3

description: Library name: Hgc27_SG21_FBS_rep3

value: FBS


title: Hgc27, SG21, FBS, biol rep2

description: Library name: Hgc27_SG21_FBS_rep2


title: Hh141


title: Hgc27, SG21, FBS, biol rep1

description: Library name: Hgc27_SG21_FBS_rep1


title: Hgc27, SG12, LPDS, biol rep3

description: Library name: Hgc27_SG12_LPDS_rep3


title: Hh130


title: Hgc27, SG12, LPDS, biol rep2

description: Library name: Hgc27_SG12_LPDS_rep2


title: Hh127


title: Hh125


title: Hgc27, SG12, FBS, biol rep3

description: Library name: Hgc27_SG12_FBS_rep3


title: Hh123


title: Hgc27, SG12, FBS, biol rep2

description: Library name: Hgc27_SG12_FBS_rep2


title: Hh121


title: Hgc27, SG12, FBS, biol rep1

description: Library name: Hgc27_SG12_FBS_rep1


title: Hgc27, SGCTRL, LPDS, biol rep3

description: Library name: Hgc27_SGCTRL_LPDS_rep3

value: SG Control, WT


title: Hh118


title: Patient 1 Remission

description: Library name: S4

value: bone marrow

value: Stroma

value: Remission


title: Hgc27, SG12, LPDS, biol rep1

description: Library name: Hgc27_SG12_LPDS_rep1


title: Patient 4 Relapse

description: Library name: S2

value: Relapse


title: Hgc27, SGCTRL, LPDS, biol rep2

description: Library name: Hgc27_SGCTRL_LPDS_rep2


title: Patient01 12weeks treatment

status: Public on Jun 16 2026

type: protein

city: Shimamoto-cho, Mishima-gun

first: Keiichi

last: Minami

state: OSAKA

address: 3-1-1 Sakurai

department: Minase Research Institute

institute: Ono Pharmaceutical

hyb_protocol: In this study, SOMAscan was used, and the measurements were outsourced. (SomaLogic Operating Co., Inc.)

label: SOMAmer

molecule: protein

source_name: CIPN

growth_protocol: Patient-derived samples were used in this study.

value: Plasma


title: control offspring pancreas

description: RNA pooled from pancreas of 10-week-old male control offspring

value: control group


title: Hh116

value: Right ventricular septum


title: Hgc27, SGCTRL, LPDS, biol rep1

description: Library name: Hgc27_SGCTRL_LPDS_rep1


title: Hh114


title: Hgc27,SGCTRL, FBS, biol rep3

description: Library name: Hgc27_SGCTRL_FBS_rep3


title: Hh112


title: Hh111


title: Hgc27,SGCTRL, FBS, biol rep1

description: Library name: Hgc27_SGCTRL_FBS_rep1


title: Hgc27,SGCTRL, FBS, biol rep2

description: Library name: Hgc27_SGCTRL_FBS_rep2


title: Hh104


title: WT control_2

description:
Library name: 2WTcontrol
Column name in GENE_TPM.xlsx: WTcontrol-2

value: peritoneal  macrophages

value: WT

value: PBS


title: Hh103


title: Hgc27, LPDS, biol rep3

description: Library name: Hgc27_LPDS_rep3

value: Parental


title: U2OS_Control_EZH2_replicate2

description: Library name: EZH2_Control_2

value: Human osteosarcoma

value: Control

value: EZH2 (EpiCypher 13-2026)


title: Hgc27, LPDS, biol rep2

description: Library name: Hgc27_LPDS_rep2

value: Stomach

value: Epithelial

value: LPDS


title: Hh100


title: Hh119


title: Hgc27, LPDS, biol rep1

description: Library name: Hgc27_LPDS_rep1


title: Hh93


title: Hgc27, FBS, biol rep3

description: Library name: Hgc27_FBS_rep3

value: FBS


title: Hh90


title: Hgc27, FBS, biol rep2

description: Library name: Hgc27_FBS_rep2


title: U2OS_Control_BMI1_replicate2

description: Library name: BMI1_Control_2

value: Bmi1 (Cell signaling 6964)


title: Hh89


title: U2OS, siEZH2, Replicate 1, RNA-Seq

description:
Library name: U2OS_siEZH2_1
all_counts_U2OS_siEZH2_NCBI.txt

value: Bone

value: Human Osteosarcoma

value: Batch 2


title: Hgc27, FBS, biol rep1

description: Library name: Hgc27_FBS_rep1


title: U2OS, siEZH2, Replicate 2, RNA-Seq

description:
Library name: U2OS_siEZH2_2
all_counts_U2OS_siEZH2_NCBI.txt


title: Hh88


title: IgG

city: Wuhan

first: Tian

last: Xuezhang

address: Donghu Road

institute: Wuhan University

description: Library name: samples2

data_processing:
raw data was filtered using Trim Galore (v.0.6.2) and mapped to the human genome (hg 38) using Bowtie2 (v.2.5.2) with default parameters. Then, the unmapped clean data was mapped to HSV-1 genome (KOS strain, GenBank: JQ673480.1) with default parameters. The CUT&Tag peaks were called using SEACR (v1.3) software
Assembly: hg38,  HSV-1 genome (KOS strain, GenBank: JQ673480.1)
Supplementary files format and content: bedgraph
Library strategy: CUT&Tag

source_name: cell line

extract_protocol:
The CUT&Tag experiment was performed by using CUT&Tag 4.0 High-Sensitivity Kit (Novoprotein, Suzhou, China) according to the manufacturer’s guidelines.
DNA was extracted using Tagment DNA Extract Beads (Novoprotein, Suzhou, China) according to the manufacturer’s instructions and then amplified to generate Illumina sequencing libraries.

value: cell line

value: human osteosarcoma

value: wild type

value: HSV-1 ICP0 RFm


title: Hh80

value: Right ventricular septum


title: SMCHD1

description: Library name: samples1


title: Hh76


title: RPL4

description:
Library name: RPL4
NovaSeqS1_101PE

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the subread-2.0.3
count values containing file were obtained using featureCounts of subread-2.0.3
differential expression was obtained using DESeq2
tab-delimited text files of raw count values for all samples
Assembly: UCSC hg38 (iGenomes illumina)
Supplementary files format and content: RPL_vs_CTRL_count_file.csv
Supplementary files format and content: DESeq2Out_RPL_vs_Normal.csv

growth_protocol: No Cell culture was involved

extract_protocol:
Whole placental villi were used for RNA extraction using Qiagen RNeasy Kit (Catalog#74104) following manufacturer's protocol.
For sequencing, libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) designed for transcriptome analysis from samples as small as a single cell. For library preparation, the mRNA fraction was enriched, fragmented, sized, reverse transcribed into cDNA and ligated with the appropriate adaptors. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

value: Placenta

value: RPL

tag: Sex

value: Female

tag: age

value: 8 weeks


title: Hh75


title: Hh178


title: RPL3

description:
Library name: RPL3
NovaSeqS1_101PE

value: Male

value: 9 weeks


title: Hh74


title: WI38, siORCA, Replicate 2, RNA-Seq

description:
Library name: WI38_siORCA2
all_counts_WI38_NCBI.txt

value: Lung

value: Human Lung Fibroblast

value: siORCA


title: RPL1

description:
Library name: RPL1
NovaSeqS1_101PE

value: 14 weeks 6 days


title: Normal4

description:
Library name: Normal4
NovaSeqS1_101PE

value: Normal

value: 5 weeks


title: RPL2

description:
Library name: RPL2
NovaSeqS1_101PE

value: 12 weeks 3 days


title: Hh71


title: Hh69


title: Hh68


title: Normal3

description:
Library name: Normal3
NovaSeqS1_101PE

value: 5 weeks 6 days


title: Hh66


title: Normal2

description:
Library name: Normal2
NovaSeqS1_101PE

value: 6 weeks 4 days


title: Hh62


title: Hh60


title: Normal1

description:
Library name: Normal1
NovaSeqS1_101PE

value: 6 weeks1 day


title: PC9 cells WT- IgG-Osimertinib

first: Ge

last: Sun

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

description: Library name: Sample23

data_processing:
RNA-Seq sequenced reads were aligned to the GRCh38 human reference genome using Hisat2. The number of reads mapped to each annotated gene was counted using featureCounts (using GENCODE v25 annotations). The CUT&Tag sequencing reads were aligned to the pig reference genome (hg38) using Bowtie2 v2.3.4.
Supplementary files format and content: hg38
Supplementary files format and content: bigwig, counts
Library strategy: CUT&Tag

extract_protocol:
All experiments were performed according to the manufacturer’s instructions. Total RNA was extracted and purified from cells using the TRIzol reagent from Invitrogen, ethanol and isopropanol from Sinopharm. cDNA synthesis was performed using the HiScript II Q RT SuperMix for qRT-PCR (+gDNA wiper) kit from Vazyme. qRT-PCR reactions were prepared using the ChamQ Universal SYBR qRT-PCR Master Mix kit from Vazyme. For protein MS, after treating with DMSO or Osimertinib for 48 hours, PC9 cells were collected for protein analysis. Protein concentration was determined using the BCA Protein Assay Kit. Proteins were digested into peptides by trypsin, and then analyzed by LC-MS/MS system to generate a comprehensive protein profile.For metabolic MS, cells were treated with DMSO and 1 μM Osimertinib for 48 hours, and collected for mass spectrometry analysis.
The library construction procedure was strictly carried out in accordance with the instructions of the corresponding experiment.

value: Non-small cell lung cancer cell

value: Wild type cell

value: Osimertinib


title: WI38, Control, Replicate1, RNA-Seq

description:
Library name: WI38_Control1
all_counts_WI38_NCBI.txt


title: Hh59

value: Right ventricular septum


title: PC9 cells WT- IgG-DMSO

description: Library name: Sample22

value: DMSO


title: Hh57


title: PC9 cells WT- H3K9me3-DMSO

description: Library name: Sample19


title: PC9 cells-sgPKM2#2-Osimertinib

description: Library name: Sample6

data_processing:
RNA-Seq sequenced reads were aligned to the GRCh38 human reference genome using Hisat2. The number of reads mapped to each annotated gene was counted using featureCounts (using GENCODE v25 annotations). The CUT&Tag sequencing reads were aligned to the pig reference genome (hg38) using Bowtie2 v2.3.4.
Supplementary files format and content: hg38
Supplementary files format and content: bigwig, counts


title: PC9 cells WT- H3K9me3-Osimertinib

description: Library name: Sample20


title: PC9 cells WT- H3K4me3-Osimertinib

description: Library name: Sample18


title: Hh55


title: PC9 cells-sgPKM2#1-Osimertinib

description: Library name: Sample5


title: PC9 cells WT- H3K4me3-DMSO

description: Library name: Sample17


title: Hh54


title: PC9 cells-sgCtrl-Osimertinib

description: Library name: Sample4

value: sgCtrl


title: PC9 cells WT- H3K4me1-Osimertinib

description: Library name: Sample16


title: PC9 cells WT- H3K4me1-DMSO

description: Library name: Sample15


title: Hh53


title: PC9 cells WT- KDM1A-Osimertinib

description: Library name: Sample14


title: PC9 cells WT- KDM1A-DMSO

description: Library name: Sample13


title: Hh52


title: All_Patient_omentum

city: St Louis

first: Jichang

last: Han

state: MO

address: 4905 Children's PI

institute: Washington University in St Louis

description:
Library name: Sample1
10x Genomics

data_processing:
Raw gene expression matrices were processed using the Seurat package in R (V5.1.0). Count matrices from each library were read in with Read10X and converted to Seurat objects using CreateSeuratObject (min.cells = 3, min.features = 200). Cells were renamed to ensure unique barcodes across samples by removing trailing “-1” suffixes, and individual Seurat objects were merged into a single object for joint analysis. The percentage of mitochondrial gene expression was calculated using PercentageFeatureSet(pattern = "^MT-"), and cells were filtered based on quality control metrics: only cells with fewer than 25,000 total counts, more than 500 and fewer than 6,000 detected features, and less than 10% mitochondrial reads were retained. Filtered data were normalized with NormalizeData, and the top 3,000 highly variable genes were identified using FindVariableFeatures. Data were scaled with ScaleData while regressing out nCount_RNA and percent.mt, and principal component analysis was performed with RunPCA. The first 25 principal components—accounting for approximately 88% of variance—were used to construct a shared‐nearest‐neighbor graph (FindNeighbors, dims = 1:25) and to perform graph‐based clustering across resolutions 0.1 to 1.5 (FindClusters). UMAP embeddings were computed on these 25 PCs (RunUMAP, dims = 1:25) to visualize cell populations. Cluster identities and original sample labels (orig.ident) were preserved in metadata for downstream interpretation. UMAP plots were generated for each clustering resolution as well as grouped by orig.ident, and the fully processed Seurat object was saved for subsequent analyses.
Assembly: Raw sequencing data were processed using Cell Ranger (versions 3.1.0, 6.1.1, or 7.0.1) with the GRCh38 human reference genome to produce gene expression matrices from single-cell 5′ RNA-seq data.
Supplementary files format and content: normalized gene expression across all cells and cell metadata

source_name: omentum

extract_protocol:
Using a scalpel, the tissue was dissected into omentum sheet and fat regions, which were then minced separately and transferred into tubes for enzymatic digestion. Digestion media consisted of RPMI 1640 supplemented with 1 mg/mL collagenase IV and 0.1 mg/mL DNase, and samples were incubated for 45 minutes at 150 rpm. Digestion was then stopped by adding chilled FACS buffer, and the cell suspension was passed through a 70 µm filter before centrifugation at 500 g for 5 minutes at 4 °C. Cell pellets were resuspended in FACS buffer containing DAPI, and DAPI-negative (live) cells were sorted. All sorted live cells were then submitted for single-cell RNA sequencing.
RNA libraries were prepared using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics, #1000263) according to the manufacturer’s instructions. In brief, cells were encapsulated into droplets, barcoded during reverse transcription, and the emulsions were broken to enable cDNA amplification via PCR, following the V(D)J enrichment protocol (10x Genomics, #1000252). Libraries were prepared following 10x Genomics guidelines and sequenced on an Illumina NovaSeq6000 platform, with samples pooled and barcoded to ensure sufficient read depth. Raw sequencing data were processed using Cell Ranger (versions 3.1.0, 6.1.1, or 7.0.1) with the GRCh38 human reference genome to produce gene expression matrices from single-cell 5′ RNA-seq data.

value: omentum

value: whole digested cells


title: PC9 cells-sgPKM2#1-Vehicle

description: Library name: Sample2


title: scVDJ-seq of HNSCC-infiltrating T cells; 21B

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

description: Library name: 21B_TCR

data_processing:
The resulting fastq files were processed using cellranger multi (version 7.1.0).
Supplementary files format and content: Cellranger output files:  sample_id_filtered_feature_bc_matrix.h5, sample_id_clonotypes.csv, sample_id_filtered_contig_annotations.csv, sample_id_vdj_contig_info.pb

source_name: tumor tissue

extract_protocol:
Fresh pre- and post-treatment tumor biopsies were digested using the Human Tumor Dissociation Kit and the gentleMACS Dissociator (Miltenyi Biotec) per manufacturer recommendations. Single cell tumor suspensions were washed with RPMI-1640, passed through a 70-m filter, stained with TruStain FcX (Biolegend), primarily-conjugated anti-human CD3 antibody (clone SK7, Biolegend) and the viability marker Sytox Blue (Thermo) and viable CD3-positive cells were isolated using fluorescent activated cell sorting (FACSAria III, BD Biosciences).
Cells were mixed with barcoded gelbeads and 5′ GEM Kit v2 reagents (10X Genomics), and single-cell capture was performed. Following reverse transcription, cDNA was amplified, and gene expression libraries were constructed according to the manufacturer’s recommendations. Each fragmented DNA library was loaded into a sequencing lane on a NovaSeq or HiSeq system (Illumina) and was sequenced with pair-end reads of 75 bp.

value: tumor tissue

value: T cells

value: mixed

value: bintrafusp alfa + Tri-Ad5


title: Hh51


title: Hh142


title: scVDJ-seq of HNSCC-infiltrating T cells; 21A

description: Library name: 21A_TCR

value: treatment-naïve


title: PC9 cells-sgCtrl-Vehicle

description: Library name: Sample1


title: Hh48


title: scVDJ-seq of HNSCC-infiltrating T cells; 20A

description: Library name: 20A_TCR


title: scVDJ-seq of HNSCC-infiltrating T cells; 20B

description: Library name: 20B_TCR


title: O.sativa, PolyA RNA-seq, ZH11, replicate2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

description: Library name: PolyA_RNA-seq_rice_ZH11_rep2

data_processing:
PolyA RNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
StringTie (v2.1.7) were used for transcript assembly and gene abundance estimation.
Assembly: Triticum urartu (AA, IGDB version 1.0), Aegilops tauschii (DD, Aet_v4.0), Triticum aestivum (AABBDD, IWGSC version 1.0), Hordeum vulgare (HH, IBSC_v2), Secale cereale (Weining.v1.0) , Zea mays (B73_RefGen_v4) and Oryza sativa (MSU7.0)
Supplementary files format and content: tab-delimited text files include locus, FPKM and TPM for transcripts in each sample

organism: Oryza sativa

source_name: 9-day-old seedling

growth_protocol: Seedlings (above-ground) of common wheat (Triticum aestivum cultivars ‘Chinesespring’‘AK58’ and ‘Fielder’), barley (Hordeum vulgare cultivar ‘Morex’), rye (Secale cereale cultivar ‘Weining’), maize (Zea mays cultivar ‘B73’) and rice (Oryza sativa cultivars ‘ZH11’ and ‘Jap’) were harvested after 9-day growth. The roots, leaf and embryos of three wheat species (Triticum aestivum cultivar ‘Chinese Spring’, Triticum urartu cultivar ‘G1812’ and Aegilops tauschii cultivar ‘AL8-78’) were collected as follows: roots in the Hoagland solution were harvested after 9-day growth; the fresh immature embryos were isolated 14 days post anthesis; leaf were were harvested after 9-day growth.

extract_protocol:
Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.
RNA-seq

value: 9-day-old seedling


title: scVDJ-seq of HNSCC-infiltrating T cells; 19B

description: Library name: 19B_TCR


title: Hh46


title: Hh133


title: scVDJ-seq of HNSCC-infiltrating T cells; 19A

description: Library name: 19A_TCR


title: O.sativa, PolyA  RNA-seq, ZH11, replicate1

description: Library name: PolyA_RNA-seq_rice_ZH11_rep1


title: scVDJ-seq of HNSCC-infiltrating T cells; 18B

description: Library name: 18B_TCR


title: Hh39


title: scVDJ-seq of HNSCC-infiltrating T cells; 18A

description: Library name: 18A_TCR


title: O.sativa, PolyA RNA-seq, Jap, replicate2

description: Library name: PolyA_RNA-seq_rice_Jap_rep2


title: Hh38


title: scVDJ-seq of HNSCC-infiltrating T cells; 17B

description: Library name: 17B_TCR


title: scVDJ-seq of HNSCC-infiltrating T cells; 17A

description: Library name: 17A_TCR


title: Hh36


title: scVDJ-seq of HNSCC-infiltrating T cells; 14B

description: Library name: 14B_TCR

value: bintrafusp alfa


title: O.sativa, PolyA RNA-seq, Jap, replicate1

description: Library name: PolyA_RNA-seq_rice_Jap_rep1


title: PC9 cells-sgPKM2#2-Vehicle

description: Library name: Sample3


title: scVDJ-seq of HNSCC-infiltrating T cells; 14A

description: Library name: 14A_TCR


title: O.sativa, Chromatin_Bound(CB) RNA-seq, ZH11, replicate2

description: Library name: CB_RNA-seq_rice_ZH11_rep2

library_source: other

data_processing:
CB RNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
For each species, all CB RNA samples were subsampled to match the read count of each sample with the lowest number of reads. The subsampled data were then merged in each species for further analysis. Peak calling were conducted using MACS2 as described for ChIP-seq data processing.
Assembly: Triticum urartu (AA, IGDB version 1.0), Aegilops tauschii (DD, Aet_v4.0), Triticum aestivum (AABBDD, IWGSC version 1.0), Hordeum vulgare (HH, IBSC_v2), Secale cereale (Weining.v1.0) , Zea mays (B73_RefGen_v4) and Oryza sativa (MSU7.0)
Supplementary files format and content: bw files

molecule: other

extract_protocol:
Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.
Chromatin-bound(CB) RNA-seq


title: scVDJ-seq of HNSCC-infiltrating T cells; 12B

description: Library name: 12B_TCR


title: Hh30


title: scVDJ-seq of HNSCC-infiltrating T cells; 12A

description: Library name: 12A_TCR


title: scVDJ-seq of HNSCC-infiltrating T cells; 8B

description: Library name: 8B_TCR


title: O.sativa, Chromatin_Bound(CB) RNA-seq, ZH11, replicate1

description: Library name: CB_RNA-seq_rice_ZH11_rep1


title: Hh24


title: scVDJ-seq of HNSCC-infiltrating T cells; 8A

description: Library name: 8A_TCR


title: scVDJ-seq of HNSCC-infiltrating T cells; 5B

description: Library name: 5B_TCR


title: O.sativa, Chromatin_Bound(CB) RNA-seq, Jap, replicate2

description: Library name: CB_RNA-seq_rice_Jap_rep2


title: Vehicle 6

city: Durham

first: Hamed

last: Bostan

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Library name: Vehicle6

data_processing:
Raw sequencing reads were assessed using FastQC v0.12.1. Adapter trimming and quality filtering were performed using Trim Galore v0.6.10, which uses Cutadapt v4.5. Trimmed reads were aligned to the Mus musculus reference genome (GRCm38) using STAR v2.6.0c. Gene-level counts were generated using featureCounts v2.0.6 from the Subread package, with gene annotations based on RefSeq/NCBI Reference v39.
FASTQ files were quality‑checked using FastQC and trimmed for adapters and low‑quality bases using TrimGalore.
Reads were aligned to the mouse reference genome (mm39) using STAR version 2.6.0c with default parameters.
Gene‑level quantification was performed using featureCounts version 2.0.6 (Subread) to generate raw integer read counts.
Processed data consist of a single gene‑by‑sample raw count matrix; downstream normalization and analysis were performed in R using standard Bioconductor workflows.
Assembly: mm39
Supplementary files format and content: count

source_name: Bone Marrow Derived Macrophages

extract_protocol:
Total RNA was isolated from mouse bone marrow derived macrophages using the RNeasy Mini Kit (Qiagen), with on-column DNase I digestion to remove residual genomic DNA. RNA concentration and integrity were evaluated using a Qubit Fluorometer (Thermo Fisher Scientific) and an Agilent TapeStation 4200 (D1000 ScreenTape; TapeStation Analysis Software v4.1, Agilent Technologies).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacture's protocol

value: Bone Marrow Derived Macrophages

value: Vehicle


title: scVDJ-seq of HNSCC-infiltrating T cells; 5A

description: Library name: 5A_TCR


title: O.sativa, Chromatin_Bound(CB) RNA-seq, Jap, replicate1

description: Library name: CB_RNA-seq_rice_Jap_rep1


title: Vehicle 5

description: Library name: Vehicle5


title: scVDJ-seq of HNSCC-infiltrating T cells; 2B

description: Library name: 2B_TCR


title: scVDJ-seq of HNSCC-infiltrating T cells; 2A

description: Library name: 2A_TCR


title: scVDJ-seq of HNSCC-infiltrating T cells; 1A

description: Library name: 1A_TCR


title: Vehicle 4

description: Library name: Vehicle4


title: scVDJ-seq of HNSCC-infiltrating T cells; 1B

description: Library name: 1B_TCR


title: scRNA-seq of HNSCC-infiltrating T cells; 21B

description: Library name: 21B_GEX


title: Vehicle 3

description: Library name: Vehicle3


title: DOX bio rep 1 female

first: Soheil

last: Jahangiri

address: 610 University Ave

institute: University Health Network

description: Library name: DOX4X-2

data_processing:
Short-read quality control and trimming were performed using FastQC v0.11.5, MultiQC v1.7, and TrimGalore v0.6.6, respectively. Reads were aligned to the UCSC mm10 mouse reference genome using Bowtie2 v2.4.5, and uniquely mapped reads were extracted by sambamba v0.7.0. Subsequently, alignment coordinates were adjusted by shifting forward and reverse strand reads by +4 and -5 bp, respectively, to correct for the asymmetric cleavage of Tn5 transposase. Duplicate reads were identified and removed using Picard v2.10.9 to eliminate PCR artifacts. Post-alignment quality control was performed using the ATACseqQC v1.20.2 R package, and peak calling was done using MACS2 v2.2.7.1. Differential binding analysis was conducted using DiffBind v3.16.0 R package. First, peaks overlapping with the ENCODE mm10 black list were filtered. Next, read counts were obtained for the peaks overlapping in at least three samples. Finally, differential binding analysis was performed using the built-in DESEQ2 method and RLE normalization.
Assembly: mm10
Supplementary files format and content: narrow peaks

extract_protocol:
Total bone marrow were flushed out by centrifugation, followed by enzymatic digestion at 37°C for 25 min. Bone marrow mesenchymal stem and progenitor cells were sorted based on tdTomato expression into 50% fetal bovine serum in PBS.
Nucleus extraction and library preparation were performed following the low-put Omni protocol by  Princess Margaret Genomic Center.

treatment_protocol: Young adult (8-10 week-old) mice were treated with 4 doses of doxorubucin (5 mg/kg, intravenous;Sigma, D1515) or PBS, one week interval between each injection. Animals were euthanized at 8w post treatment.

value: bone marrow

value: mesenchymal stem and progenitor cells

value: Lepr-Cre;LSL-tdTomato+/-

value: 4X doxorubicin IV 5 mg/kg


title: scRNA-seq of HNSCC-infiltrating T cells; 20B

description: Library name: 20B_GEX


title: Vehicle 2

description: Library name: Vehicle2


title: scRNA-seq of HNSCC-infiltrating T cells; 21A

description: Library name: 21A_GEX


title: PBS bio rep 3 female

description: Library name: C4

value: 4X PBS IV


title: scRNA-seq of HNSCC-infiltrating T cells; 20A

description: Library name: 20A_GEX


title: PolyA-RNA_FKT_BamMut 18h-heat-shock, bam, rep 1

city: Risskov

first: Thomas

middle: Høgsbro

last: Grønbæk

address: Broloftet 5, 4.tv

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: Library name: Sample_43

data_processing:
RNA and sRNAseq: RNA reads were demultiplexed and trimmed for standard illumina adapter sequences including 4 random nucleotides from each end.
cutntag: Paired-end illumina reads were adapter-trimmed using Trim Galore for standard illumina adapters.
Assembly: dm6, r6.63
Supplementary files format and content: SLX-19644_totalRNA_RNAseq_GeTMM_TE_sense.xlsx, R17585_TOsK_MZ-piwiaub_dKD_TE_GeTMM_sense.xlsx, R18168_GeTMM_gene.xlsx,  R18168_GeTMM_TE_sense.xlsx, SLX-17461_GeTMM_gene.xlsx. All xlsx file with RNAseq reads mapping to TE consensus sequences in sense orientation or to whole transcriptiome. Mapped to the Drosophila transcriptome using STAR, allowing 2 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: R16775_1kb_tiles_RNA_mappers_sum-PlusMinus.xlsx. xlsx file, Small RNAseq mapping to 1kb tiles. Not accounting for orientation (summed). Reads were mapped to the Drosophila genome using Bowtie allowing 0 MM and only uniquely mapping reads. Read coverage was quantified over non-overlapping 1 kb genomic windows using bedtools and normalized to 10 million uniquely mapping reads.
Supplementary files format and content: CutnTag_avg_GeTMM_TE_consensus_unistrand.xlsx. Xlsx file, cutntag reads mapping to TE consensus sequence unistrand. Mapped to the Drosophila transcriptome using Bowtie, allowing 0 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: CutnTag_bam_Table_for_heatmap_log2CPMadd1_single_TE_insertions.xlsx. Xlsx table of cutntag reads mapping to 50bp windows 500bp +/- to all identified single TE insertions in log2 counts per million (CPM). Reads were mapped to in-house ONT long-read assembled D. melanogaster genome from MTD-GAL4; white-sh fly cross using Bowtie2 with concordant-only alignment. The resulting alignments were coordinate-sorted and duplicate marking was done using samtools. Finally reads were filtered for only paired alignments with MAPQ ≥ 30 and no duplicates. Bigwig tracks (all mappers and unique mappers) were generated per sample using deeptools bamCoverage (bin size 10 bp, CPM normalization). Bigwig tracks were intersected with TE insertion coordinates (CutnTag_single_TE_insertions_table.xlsx) from long read DNA sequencing and Cut&Tag data for info on how these were called).
Supplementary files format and content: CutnTag_single_TE_insertions_table.xlsx. Xlsx file of single TE insertions and genome coordinates. TE annotation in long-read genome assembly was done using EDTA v. 2.2 with Drosophila consensus TE library supplied as the reference. TE annotation with CUT&Tag data was done using ngs_te_mapper2 v. 1.0.2. Briefly, the reads from CUT&Tag experiments were used to search for TE insertions by means of finding reads spanning TE consensus sequence and flanking long-read genome assembly sequence at candidate insertion sites. To call an insertion, we required the detection of reads spanning the TE and the flanking genome at both ends of the TE. Insertions identified this way were then pooled for the same fly line and then we analyzed only TE insertions present – but not necessarily homozygous – across every experimental cross in our CUT&Tag analyses.

organism: Drosophila melanogaster

source_name: bam mutant ovarian cysts

growth_protocol: D. melanogaster strains were crossed and reared for experiments at 25°C and 70% humidity with 12:12 hrs light/dark cycle in vials containing standard medium. Before dissection, the flies were fed extra yeast and kept with 3-5 males to support ovary development. The day before dissection, the flies were transferred to a fresh vial to provide the females ample space for egg-laying, preventing egg accumulation in the ovaries.

extract_protocol:
Bulk ovary RNA and small-RNA: 6-8 Ovary pairs from 3-4 days old females were dissected into ice-cold Phosphate-buffered saline (PBS) for bam mutant flies. Bam mutant and heat-shock bam ovarian cysts: 30 ovarian cysts were collected for each sample to compensate for their significantly smaller size.  RNA isolation for RNAseq and small-RNAseq: Samples were subjected to homogenization in TRIzolTM using handheld elecrtric pestle. After 5 minutes incubation Chloroform was added and samples were shaken vigorously and incubated for 3 minutes at RT, then centrifuged at 12,000g and 4°C for 15 minutes. The aqueous phase was transferred to a clean tube and the RNA was subsequently purified first using isopropanol and pelleting the RNA then 75% ethanol. The RNA was resuspended in Rnase-free water and concentrations were measured by spectrophotometry. The samples were stored at -70°C if not immediately used for RNA or small-RNA sequencing library preparation.  Cut&tag: approximately 150 whole ovaries were dissected into Drosophila Ringers buffer for 512C nurse cell nuclei FACS sorting. the ovaries were digested in 5mg/mL collagenase for 15 minutes at RT with continous shaking and intermittent pipetting. Cell suspension was collected by centrifugation 3min at 500rcf and rinced buffort adding nuclear isolation buffer. We disrupted cells with 10 strokes in a Dounce homogenizer with the B pestle and the homogenate was filtered twice through 100µM Nitex mesh. The filtered homogenate was placed on a sucrose step gradient of 2.2 M, 1.6 M, and 0.8 M sucrose and centrifuged for 20 min at 20,000 x g. After centrifugation the sucrose gradient was removed and the pellet was resuspended in nuclear isolation buffer. Hoechst was added to the homogenate at a concentration of 0.5 mg/ml. Nuclei were stored on ice until FACS. Approximately 400 ovaries from Vasa-GFP, bam-/- ovarian cysts, were dissected into Schneider’s insect medium supplemented with 10% fetal bovine serum. GSC-like cells were collected based GFP positive staining. Vasa-GFP, bam –/– ovaries were dissociated in 0,5% trypsin–0,05% EDTA and 5 mg/mL collagenase for 15 min at room temperature, with continuous shaking and intermittent pipetting. Ovarian cell suspension is then filtered through a 70µM Nitex mesh to remove aggregates or debris. The filter was rinsed with S-FBS and cells were collected by centrifugation 5min at 400g, 4ºC. Cells were stored on ice and GFP-positive germline cells were elected from the suspension via fluorescence-activated cell sorting (FACS).
RNAseq: RNA Sample of 2 µg were DNaseI treated and purified using the RNA clean & ConcentratorTM-5 kit (ZYMO #R1013). mRNA were isolated by polyA-RNA enrichment using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S). For total RNAseq, Ribosomal RNA was removed by hybridisation to standard 50nt DNA oligos covering relevant regions in the rRNA precursor and mitochrondrial genome in ratio 1µg RNA : 4µg oligomix and subsequent digestion using thermostable RNAse H (NEB #M0523S). Libraries were cloned using the NEBNextTM Ultra II directional RNA library prep kit for illumina (NEB # E7760) following the instructions. libraries were amplified by PCR using Q5 high-fidelity DNA polymerase with unique dual barcoded primers. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads. Samples were multiplexed in equal amounts and sequenced by VBCF NGS facility on an illumina NovaSeq X flowcell single- or paried-end or an illumina HiSeq 4000 flowcell paired-end or at the CRUK facility in cambridge on an illumina NovaSeq 6000 flowcell singleRead.  Small-RNA: Argonaute bound small RNAs were isolated using the Trans-kingdom, rapid, affordable Purification of RISCs (TRAPR) isolation technique specified in the punlication: Grentzinger et al. 2020. “A Universal Method for the Rapid Isolation of All Known Classes of Functional Silencing Small RNAs.” Nucleic Acids Research 48 (14): e79. sRNA libraries were generated based on protocol from:  Jayaprakash et al. 2011. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39 (21): e141. In brief, 3’ linker ligation was performed by adding uniquely barcoded 3’RNA linkers to the samples. Ligation was performed O/N using T4 RNA ligase 2, truncated K227Q (NEB #M0242). The samples were then multiplexed into sub-multiplexes of individually barcoded samples (biological replicates together), and purified using ZYMO RNA clean and concentrator-5 kit (ZYMO #R1013).  Then the samples were recovered and size selected for 52-63 nt reads (18-29nt RNAs + 3’linker) using PAGE purification. To follow exact size selection on the gel, fluorescently labeled oligos migrating similar to 40 and 60-nucleotide single-stranded RNA was added to samples prior to gel electrophoresis. PAGE purification was performed using ZYMO small-RNATM PAGE Recovery Kit (ZYMO #R1070). 5’ RNA linkers were added to samples, and ligation was performed O/N using T4 RNA ligase (NEB #M0204). The samples were subjected to SPRI purification. The sRNA libraries were then reverse transcribed using Superscript II (InvitrogenTM #18064014) following the manufacturer's instructions using the illumina_RvnTxn primer. Libraries were amplified by PCR using Q5 High-Fidelity DNA Polymerases (NEB #M0491) and unique dual-barcoded primers. Samples were then inspected and purified from a 2% low-melt agarose gel using the Zymoclean gel DNA recovery kit (ZYMO #D4001). Concentrations were measured using QubitTM DNA HS kit (InvitrogenTM Q32851) and sub-multiplexes were multiplexed in equal amounts and sequenced by VBCF NGS facility on a NovaSeqX XP flowcell singleRead.  Cut&tag: Library preparation were conduced on freshly FACS-isolated cells or nuclei in duplicates following the published protocol with minor modifications Kaya-Okur et al. 2019. “CUT&Tag for Efficient Epigenomic Profiling of Small Samples and Single Cells.” Nature Communications 10 (1): 1930. Around 40,000 GSCs sorted-cells (40,000 2C cells) and 500-800 512C sorted-nuclei  (128,000-200,000 2c nuclei) were used for each CUT&Tag reaction. The cells or nuclei were bound to 10µL of concanavalin A-coated beads (Polysciences,  86057-10) by incubation 15min at room temperature . The unbound supernatant was removed and bead-bound cells/nuclei were resuspended in Wash Buffer (WB150 : 20 mM HEPES pH 7.9; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2 mM EDTA and 0,1% BSA with the appropriate primary antibody (listed in the Reagent Table). Primary antibody incubation was performed on a rotating platform overnight at 4 °C. Secondary antibodies were then added (1:100 dilution in WB150) and incubate for 1h at room temperature. Protein A–Tn5 transposase (gift from the Joan Barau laboratory), pre-loaded with MEDS adaptors (see Oligonucleotide Table), was added at a 1:200 dilution in WB150 with adapted 0,01% Digitonin (WB300). Following an incubation of 1h at room temperature, cells/nuclei and beads were washed with WB300 and mixed in a tagmentation buffer (10 mM MgCl2 in WB300). The tagmentation was performed 1h at 37ºC and stoped by adding 10µL a Digest solution ( 90mM EDTA, 1,2% SDS, 3mg/mL Proteinase K) and incubate 1h at 55ºC. DNA was extracted using the DNA Clean & Concentrator kit and libraries were amplified by Q5 high-fidelity DNA polymerase with unique dual barcoded primers for 10-15 amplification cycles. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads and DNA quality was assessed using the 5200 Fragment Analyzer system. Pooled  libraries  were  sequenced by the VBCF NGS facility on an Illumina NextSeq 2000 sequencing device.

treatment_protocol: For heat-shock bam experiments: Heat-shock treatment was performed on 3-4 day old females as described in (Samuels et al. 2024). The treatment involved 1 hour at 37°C followed by 2 hours at 34°C. The 'hours after HS' is defined as starting immediately after this 3-hour treatment.

value: bam mutant ovarian cysts

value: Bulk ovarian cysts


title: PBS bio rep 2 female

description: Library name: C3


title: scRNA-seq of HNSCC-infiltrating T cells; 19B

description: Library name: 19B_GEX


title: House dust mite treated 6

description: Library name: HDM6

value: HDM


title: PolyA-RNA_FKT_BamMut 09h-heat-shock, bam, rep 2

description: Library name: Sample_42


title: scRNA-seq of HNSCC-infiltrating T cells; 19A

description: Library name: 19A_GEX

value: tumor tissue


title: PBS bio rep 1 female

description: Library name: C2


title: House dust mite treated 5

description: Library name: HDM5