title: liver_4

city: Columbia

first: John

last: Driver

address: 1201 Rollins Street

institute: University of Missouri

description: Library name: liver_4

data_processing:
The Sscrofa 11.1 genome assembly was used to align sequencing reads to generate gene matrix data by Cell Ranger (v8.0.0).
Assembly: Sscrofa 11.1
Supplementary files format and content: matrix files

organism: Sus scrofa

source_name: liver

extract_protocol:
Fetal liver tissues were weighed and dispersed into single cell suspensions using glass homogenizers. Cells were then filtered using 100 µm cell strainers, washed with PBS, and treated with an ammonium chloride-based lysis buffer to remove red blood cells. After counting, 6 million cells from each liver were Fc-blocked with rat IgG (Sigma Aldrich, St. Louis, MO) and stained with anti-porcine CD45 antibody (ThermoFisher Scientific, Waltham MA). Cells were then stained with the propidium iodine (PI) viability dye and sorted for live CD45+ and CD45- cells using a BD FACS Melody cell sorter (BD Biosciences, Franklin Lakes, NJ). Thymus tissues were incubated in 3 ml of Hanks’ Balanced Salt Solution (HBSS) with 2ul of collagenase Type 1 (Worthington, Lakewood, NJ) at 37°C for 30 minutes after which they were dispersed into single cells using glass homogenizers, washed with PBS, filtered, counted, stained with PI, and finally sorted for live cells. Bone marrow was collected from the scapula, femur, tibia, humerus, ulna, and radius of 47 DG fetuses, from the femur and tibia of 60, 75, and 90 DG fetuses, and from the ribs and sternum of 1 DOA and 7 MOA pigs after they were cut open with scissors. Cells were filtered, washed with DMEM containing 10% FBS, counted, stained with PI, and FACS sorted for live cells.
Gene expression libraries were prepared using the Chromium Next GEM Single Cell 5′ Kit v2 (10× Genomics, Pleasanton, CA) according to the manufacturer’s instructions. V(D)J libraries were enriched for TCR and BCR transcripts with pig-specific primers.

value: liver

value: primary cells


title: House dust mite treated 4

status: Public on Jun 15 2026

type: SRA

city: Durham

first: Hamed

last: Bostan

state: NC

address: 111 TW Alexander Dr

country: USA

institute: NIEHS

description: Library name: HDM4

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

tag: cell type

value: Bone Marrow Derived Macrophages

tag: treatment

value: HDM


title: liver_3

state: MO

description: Library name: liver_3

library_source: transcriptomic single cell

tag: tissue

tag: cell line


title: House dust mite treated 3

description: Library name: HDM3


title: PolyA-RNA_FKT_BamMut No-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_39

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.

molecule: polyA RNA

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

tag: genotype

tag: batch


title: liver_2

description: Library name: liver_2


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

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

description: Library name: 14B_GEX

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

organism: Homo sapiens

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


title: liver_1

description: Library name: liver_1


title: Hose dust mite treated 1

description: Library name: HDM1


title: M7_thymus_3

description: Library name: M7_thymus_3

source_name: Thymus

value: Thymus


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

description: Library name: 14A_GEX

value: treatment-naïve


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 21B

description: Library name: 21B_TCR

source_name: peripheral blood

extract_protocol:
Cryopreserved post-treatment PBMC were thawed, and T cells were isolated using EasySep Human T Cell Isolation Kit (Stemcell) per manufacturer recommendations. Cells were washed in 1× PBS, filtered (70 μm) and quantified using acridine orange/propidium iodide (AO/PI) staining on a Cellometer Auto 2000 (Nexcelom). Cells were concentrated to 1000 cells/μL and loaded onto the Chromium Controller (10X Genomics) with a target of 6,000 cells per sample.
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 6000 system (Illumina) and was sequenced with pair-end reads of 75 bp.

value: peripheral blood

value: bintrafusp alfa + Tri-Ad5


title: [ATAC-Seq] shYT#2_6

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

description: Library name: Sample 11

library_source: genomic

data_processing:
For the ATAC-Seq analysis the nextflow pipeline (https://nf-co.re/atacseq/2.1.2/) was used.
Assembly: mm10
Supplementary files format and content: bigWig files for each sample

molecule: genomic DNA

extract_protocol:
Tumor-bearing livers were minced and digested in 15 mL of 1× PBS containing 7.5 mg Pronase, 7.5 mg Collagenase P, and 1.5 mg DNase I using a C Tube (Miltenyi Biotec) and the gentleMACS Octo Dissociator (Miltenyi) for 45 minutes at 100 rpm and 37 °C. Following digestion, the cell suspension was filtered through a 100 µm cell strainer and washed with an appropriate volume of Advanced DMEM/F12 (AdDMEM/F12) medium. Red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183), followed by debris removal (Miltenyi, #130-109-398) and dead cell removal (Miltenyi, #130-090-101) according to the manufacturer’s protocols. Cells were then incubated with Fc receptor blocking reagent (Miltenyi) for 10 minutes on ice. Tumor cells were labeled with anti-EpCAM-APC antibody (eBioscience, #17-5791-82; 1:100) for 30 minutes on ice. After washing, cells were incubated with anti-APC microbeads (Miltenyi) for an additional 30 minutes. Labeled cells were then loaded onto LS columns (Miltenyi) and processed according to the manufacturer’s instructions. Positively labeled EpCAM⁺ cells were eluted and further processed for downstream applications.
A total of 5 × 10^4 cells were pelleted in a pre-wetted 1.5 mL low-binding tube by centrifugation at 500 × g for 5 minutes at 4°C using a fixed-angle rotor. Cells were resuspended in 50 µL ice-cold ATAC-Resuspension Buffer (RSB: 10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂) supplemented with 0.1% (v/v) NP-40, 0.1% (v/v) Tween-20, and 0.01% (w/v) digitonin. The suspension was pipetted up and down three times and incubated on ice for 3 minutes to lyse the cells. To remove the lysis reagents, 1 mL ice-cold RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and the tube was gently inverted three times. Nuclei were pelleted by centrifugation at 500 × g for 10 minutes at 4°C, and the supernatant was carefully removed. Nuclei were resuspended in 50 µL of transposition reaction mix containing: 25 µL 2× TD buffer (Illumina), 2.5 µL Tn5 transposase (to reach 100 nM final concentration), 16.5 µL 1× PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, 5 µL nuclease-free water. The mix was pipetted up and down six times to ensure homogeneous suspension. Samples were incubated at 37°C for 30 minutes at 1000 rpm using a thermomixer. Following transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 Kit (Zymo Research) according to the manufacturer's instructions and amplified by PCR.

value: shYT


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

description: Library name: 12B_GEX


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 20B

description: Library name: 20B_TCR


title: [ATAC-Seq] shYT#2_5

description: Library name: Sample 10


title: M7_thymus_1

description: Library name: M7_thymus_1


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 19B

description: Library name: 19B_TCR


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

description: Library name: 8B_GEX


title: [ATAC-Seq] shYT#2_4

description: Library name: Sample 9


title: Neonatal_thymus_3

description: Library name: Neonatal_thymus_3


title: Non-proliferating CD4⁺ T-cells, 100uM PCS,HC3

city: Atlanta

first: Souheil

last: Younes

state: Georgia

address: 1750 Haygood Dr NE

department: Pathology and Laboratory Medicine

institute: Emory University

description:
Library name: s024
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

value: 100uM PCS

tag: group

value: Non-proliferating


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 18B

description: Library name: 18B_TCR


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

description: Library name: 8A_GEX


title: Neonatal_thymus_2

description: Library name: Neonatal_thymus_2

value: primary cells


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 17B

description: Library name: 17B_TCR


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

description: Library name: 5B_GEX


title: Neonatal_thymus_1

description: Library name: Neonatal_thymus_1


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 14B

description: Library name: 14B_TCR


title: [ATAC-Seq] shYT#2_1

description: Library name: Sample 6


title: d90_thymus_3

description: Library name: d90_thymus_3


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 12B

description: Library name: 12B_TCR


title: [ATAC-Seq] shRen_5

description: Library name: Sample 5

value: shRen


title: Control primary mouse tubular epithelial cells under TNFα + IFNγ stimulation (replicate 3)

status: Public on Jun 16 2026

city: PHILADELPHIA

first: Yanjuan

last: Hou

state: PA

address: 3400 civic center blvd

department: Perelman School of Medicine, Department of Medicine

institute: university of pennsylvania

description:
Library name: CTR_3
Bulk RNA-seq of primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

data_processing:
Raw sequencing reads were subjected to quality control and adaptor trimming.
Clean reads were aligned to the Mus musculus reference genome (mm10).
Gene-level counts were generated using featureCounts / Salmon quantification.
Expression values were normalized to TPM.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing raw gene counts and TPM-normalized expression values for all samples.

source_name: primary culture

growth_protocol: Primary mouse renal tubular epithelial cells were isolated and cultured under standard conditions in appropriate growth medium at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were assessed before library preparation.
RNA-seq libraries were prepared using an Illumina-compatible library preparation kit following the manufacturer’s protocol, including mRNA enrichment, cDNA synthesis, adaptor ligation, and PCR amplification.

treatment_protocol: Cells were infected with adenovirus expressing Cre recombinase (AdvCre) to induce ELF3 deletion or with control adenovirus. Following viral transduction, cells were stimulated with TNFα and IFNγ prior to RNA extraction.

value: kidney

value: renal tubular epithelial cells

value: wild type

value: TNFα + IFNγ

value: batch 1


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

description: Library name: 5A_GEX

value: tumor tissue

value: T cells

value: mixed


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 8B

description: Library name: 8B_TCR

value: bintrafusp alfa


title: [ATAC-Seq] shRen_4

description: Library name: Sample 4


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

description: Library name: 2A_GEX

value: treatment-naïve


title: DOX bio rep 3 female

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: DOX4X-4

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

source_name: bone marrow

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: DOX bio rep 2 female

description: Library name: DOX4X-3


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

description: Library name: 2B_GEX


title: d90_thymus_1

description: Library name: d90_thymus_1

value: Thymus


title: PolyA-RNA_FKT_BamMut 18h-heat-shock, bam, rep 2

description: Library name: Sample_44

value: bam mutant ovarian cysts

value: Bulk ovarian cysts


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 5B

description: Library name: 5B_TCR

value: peripheral blood


title: d90_thymus_2

description: Library name: d90_thymus_2

value: primary cells


title: [ATAC-Seq] shRen_3

description: Library name: Sample 3

value: shRen


title: Vehicle 1

description: Library name: Vehicle1

value: Bone Marrow Derived Macrophages

value: Vehicle


title: d75_thymus_3

description: Library name: d75_thymus_3


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

description: Library name: 1B_GEX

value: tumor tissue


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 2B

description: Library name: 2B_TCR

value: T cells


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

description: Library name: 18B_GEX

value: mixed

value: bintrafusp alfa + Tri-Ad5


title: [ATAC-Seq] shRen_2

description: Library name: Sample 2


title: PolyA-RNA_FKT_BamMut 09h-heat-shock, bam, rep 1

description: Library name: Sample_41


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

description: Library name: 1A_GEX

value: treatment-naïve


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

description: Library name: 18A_GEX


title: PolyA-RNA_FKT_BamMut No-Heat-Shock, bam, rep 2

description: Library name: Sample_40


title: d75_thymus_2

description: Library name: d75_thymus_2


title: scVDJ-seq of post-treatment peripheral-blood T cells from HNSCC patients; 1B

description: Library name: 1B_TCR

value: bintrafusp alfa


title: [ATAC-Seq] shRen_1

description: Library name: Sample 1


title: d75_thymus_1

description: Library name: d75_thymus_1


title: Hose dust mite treated 2

description: Library name: HDM2

value: HDM


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 21B

description: Library name: 21B_GEX


title: Riboseq_Low_3

city: Tianjin

first: Xiaoxi

last: Xu

address: No. 154, Anshan Road, Heping District

country: China

institute: Tianjin Medical University General Hospital

description:
Library name: sample6
Low glucose (2.5 mM), biological repeat 3

data_processing:
After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing.
For samples with biological replicates, DESeq2 R package (1.14.1) was used for differential expression analysis. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2 (Fold Change) | > 0 & padj < 0.05 found by DESeq2 were assigned as differentially expressed.
Quantification of mapped results to gene level was carried out using HTSeq(0.9.1). HTSeq is a Python package that calculates the number of mapped reads to each gene[5]. RPKM values were generated to represent the gene expression level of each specific gene. RPKM is the abbreviation of “Reads Per Kilobase of transcript, per Million mapped reads”, which normalizes both sequencing depth and gene length.
Ribo-seq used TopHat2(2.0.12) for genome mapping. TopHat2 is an enhanced version of TopHat, using short read aligner Bowtie to align the RNA-seq reads to mammalian-sized genomes and analyzing the mapping result to identify splice junctions. TopHat2 allows variable-length indels with respect to the reference genome, which give it the ability to accurately align the transcriptomes in the presence of insertions, deletions and gene fusions.
Assembly: mm10
Supplementary files format and content: riboseq_gene_count.xlsx
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

source_name: Primary pancreatic islets

extract_protocol:
Sample was treated with specific lysis buffer with cycloheximide (50mg/mL) to acquire the lysate.
Following PAGE purification, the both ends of RPF were phosphorylated and ligated with 5’ and 3’ adapters respectively. The RNA samples were then treated with rRNA depletion kit（Qiagen,334387） to deplete the samples of as much rRNA contamination as possible. Then the fragments were reversely transcribed to the cDNAs and amplified by PCR[1-2].After library construction（Multiplex Small RNA Library Prep Set for ILLumina (Set1)，NEB，E7300L）,the concentration of library was measured by The Qubit® 2.0 Fluorometer and adjusted to 1ng/μL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once the insert size and concentration of the library was correct, the samples can then be subjected for sequencing.

value: Primary pancreatic islets

value: Low glucose (2.5 mM) 2h


title: shRen_IgG_4

description: Library name: Sample 20

data_processing:
Adapter and quality trimming were performed using Cutadapt. Reads were aligned to the mm10 genome and a repeat-masked E. coli genome (used as spike-in) using Bowtie2. Reads with inserts <120 bp mapped to mm10 were extracted (deepTools), and a scaling factor based on the E. coli spike-in was used to generate normalized bigWig files. Peak calling was performed using Genrich using the following parameters: q 1e-4  -a 700. For cumulative distribution frequency (CDF) analysis, TEAD1 signals at categorized peaks (based on RNA-Seq regulation, downregulated, upregulated or not-regulated) were associated with the nearest TSS using BEDtools, and plotted with ggecdf (ggpubr).
Assembly: mm10
Supplementary files format and content: bigWig files for each sample
Library strategy: CUT&Run

extract_protocol:
Tumor-bearing livers were minced and digested in 15 mL of 1× PBS containing 7.5 mg Pronase, 7.5 mg Collagenase P, and 1.5 mg DNase I using a C Tube (Miltenyi Biotec) and the gentleMACS Octo Dissociator (Miltenyi) for 45 minutes at 100 rpm and 37 °C. Following digestion, the cell suspension was filtered through a 100 µm cell strainer and washed with an appropriate volume of Advanced DMEM/F12 (AdDMEM/F12) medium. Red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183), followed by debris removal (Miltenyi, #130-109-398) and dead cell removal (Miltenyi, #130-090-101) according to the manufacturer’s protocols. Cells were then incubated with Fc receptor blocking reagent (Miltenyi) for 10 minutes on ice. Tumor cells were labeled with anti-EpCAM-APC antibody (eBioscience, #17-5791-82; 1:100) for 30 minutes on ice. After washing, cells were incubated with anti-APC microbeads (Miltenyi) for an additional 30 minutes. Labeled cells were then loaded onto LS columns (Miltenyi) and processed according to the manufacturer’s instructions. Positively labeled EpCAM⁺ cells were eluted and further processed for downstream applications.
Following EpCAM enrichment, tumor cells were counted and resuspended at a concentration of 2 × 106 cells in wash buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; protease inhibitor cocktail). For each CUT&RUN reaction, 2 × 105 cells were used. Cells were incubated with 10 µL of activated Concanavalin A-coated magnetic beads (Polysciences) for 10 minutes at room temperature on a hula mixer with constant agitation. Following bead binding, samples were placed on a magnetic stand to remove the supernatant. Bead-bound cells were resuspended in 100 µL of antibody buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 0.01% [w/v] digitonin; 2 mM EDTA; protease inhibitor), and primary antibodies were added as follows: anti-YAP1 ( Cell Signaling Technology, #14074), anti-TEAD1 (Cell Signaling Technology, #12292), anti-H3K27Ac (Abcam, ab4729), and anti-H3K4me1 (Cell Signaling Technology, #5326). A species-matched IgG was used as a negative control. Samples were incubated overnight at 4°C on a hula mixer set at a 50° tilt and 1 RPM. The next day, samples were washed twice with digitonin wash buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 0.01% digitonin; protease inhibitor). Protein A/G-MNase (pAG-MNase; 1 µg/mL) was added in digitonin wash buffer, and samples were incubated for 1 hour at 4°C with gentle agitation. After incubation, cells were washed three times with digitonin wash buffer and twice with low-salt buffer (20 mM HEPES, pH 7.5; 0.5 mM spermidine; 0.01% digitonin). Nuclease activation was performed by transferring the samples to calcium-containing buffer (3.5 mM HEPES, pH 7.5; 10 mM CaCl₂; 0.01% digitonin; protease inhibitor) and incubating on ice for 1 hour with continuous mixing. Cleaved DNA fragments were released by incubation at 37°C for 30 minutes in STOP buffer (170 mM NaCl; 20 mM EGTA; 0.01% digitonin; 50 µg/mL RNase A; 25 µg/mL Glycogen Blue). Supernatants were collected, and DNA was purified by phenol-chloroform extraction. Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645) following the manufacturer’s protocol. Library quality was assessed using the Fragment Analyzer (Agilent Technologies), and equimolar pooling of libraries was performed. Pooled libraries were gel purified, quantified on an Agilent 2100 Bioanalyzer, and sequenced as 75 bp single-end reads on an Illumina NextSeq 500 platform.

tag: cut&run antibody

value: Rabbit IgG (Sigma, I5006)


title: Riboseq_Low_2

description:
Library name: sample5
Low glucose (2.5 mM), biological repeat 2


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

description: Library name: 17B_GEX


title: d60_thymus_3

description: Library name: d60_thymus_3

value: Thymus


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 20B

description: Library name: 20B_GEX


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

description: Library name: 17A_GEX


title: shRen_H3K4me1_4

description: Library name: Sample 19

value: anti-H3K4me1 (Cell Signaling Technology, #5326)


title: Riboseq_Low_1

description:
Library name: sample4
Low glucose (2.5 mM), biological repeat 1


title: shRen_H3K27Ac_4

description: Library name: Sample 18

value: anti-H3K27Ac (Abcam, ab4729)


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 19B

description: Library name: 19B_GEX

value: peripheral blood


title: d60_thymus_2

description: Library name: d60_thymus_2

value: primary cells


title: Riboseq_High_3

description:
Library name: sample3
High glucose (25 mM) 2h, biological repeat 3

value: High glucose (25 mM) 2h


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 18B

description: Library name: 18B_GEX


title: shRen_Tead1_4

description: Library name: Sample 17

value: shRen

value: anti-TEAD1 (Cell Signaling Technology, #12292)


title: d60_thymus_1

description: Library name: d60_thymus_1


title: Riboseq_High_2

description:
Library name: sample2
High glucose (25 mM) 2h, biological repeat 2


title: M7_Bone_marrow_3

description: Library name: M7_Bone_marrow_3

value: bone marrow


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 17B

description: Library name: 17B_GEX

value: T cells

value: mixed


title: M7_thymus_2

description: Library name: M7_thymus_2


title: shRen_YAP_4

description: Library name: Sample 16

value: anti-YAP1 ( Cell Signaling Technology, #14074)


title: M7_Bone_marrow_2

description: Library name: M7_Bone_marrow_2


title: Riboseq_High_1

description:
Library name: sample1
High glucose (25 mM) 2h, biological repeat 1


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 14B

description: Library name: 14B_GEX

value: bintrafusp alfa


title: shRen_IgG_3

description: Library name: Sample 15


title: 48hr co-cultued with IL-1b stimulated chondrocyte3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

description: Library name: Long_3

data_processing:
The RNA-seq libraries (4 Gb per sample, 150 bp × 2 paired-end, 3 samples per condition) were sequenced on an Illumina NovaSeq 6000 platform and then trimmed for quality. The resulting fastq files were aligned to the reference genome using HISAT2. Reads were counted (FeatureCount v2.06) and the number of fragments per 1 million bases of the transcription sequence of each gene was calculated based on the gene and read length. Significance was set up using the Benjamini-Hochberg approach as p <0.05 for false discovery rate (FDR) . The gene ontology and pathway enrichment analyses and GSEA were performed on the differential expression data using NovoMagic online tools (Novogene, Singapore).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MLO-Y4 osteocyte cell line (obtained from Professor Lynda F. Bonewald, Indiana Center for Musculoskeletal Health were seed onto a 24-well plate coated with 0.15mg/ml collagen 1 solution. Primary articular chondrocytes were obtained from the cartilage of 5–6-day-old C57BL/6J mice. Cartilage was carefully dissected from the femoral condyles and tibial plateau and subjected to overnight enzymatic digestion at 37 °C in DMEM containing collagenase D. The isolated cells were resuspended in DMEM supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, and 25 mg/L penicillin/streptomycin solution. Experiments were performed within passage 2 primary chondrocytes.

extract_protocol:
Osteocytes RNA was purified using TRIzol Reagent and RNA extraction kit (NucleoSpin®) according to the manufacturere's protocol
The libraries were generated from high-quality RNA (1 μg) of each sample using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) and then subjected for sequencing (Illumina NovaSeq 6000, Illumina, Inc. San Diego, CA, USA). The sequence data of 150 bp × 2 paired ends of 6G bases/sample (3 samples for each condition) were trimmed and mapped via HISAT2 v2.0.5. Reads were counted (FeatureCount v1.55.0-p3) and the number of fragments per 1 million bases of the transcription sequence of each gene was calculated based on the gene and read length. Significance was set up using the Benjamini-Hochberg approach as p <0.05 for false discovery rate (FDR) . The gene ontology and pathway enrichment analyses and GSEA were performed on the differential expression data using NovoMagic online tools (Novogene, Singapore).

treatment_protocol: Chondrocytes were seeded onto 1.0µm cell culture transwell inserts and stimulated by treatment with 10 ng/ml interleukin-1β for 6 hours. Then, MLO-Y4 was co-cultured with the chondrocytes using transwell insert for 24 hours and 48 hours.

value: Osteocyte


title: M7_Bone_marrow_1

description: Library name: M7_Bone_marrow_1


title: shRen_H3K4me1_3

description: Library name: Sample 14


title: Neonatal_Bone_marrow_3

description: Library name: Neonatal_Bone_marrow_3


title: 48hr co-cultued with IL-1b stimulated chondrocyte2

description: Library name: Long_2


title: shRen_H3K27Ac_3

description: Library name: Sample 13


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 5B

description: Library name: 5B_GEX


title: Neonatal_Bone_marrow_2

description: Library name: Neonatal_Bone_marrow_2


title: shRen_Tead1_3

description: Library name: Sample 12


title: 24hr co-cultued with IL-1b stimulated chondrocyte3

description: Library name: short_3


title: Neonatal_Bone_marrow_1

description: Library name: Neonatal_Bone_marrow_1


title: shRen_YAP_3

description: Library name: Sample 11


title: d90_Bone_marrow_3

description: Library name: d90_Bone_marrow_3


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 1B

description: Library name: 1B_GEX


title: 24hr co-cultued with IL-1b stimulated chondrocyte2

description: Library name: short_2


title: shRen_IgG_2

description: Library name: Sample 10


title: d90_Bone_marrow_2

description: Library name: d90_Bone_marrow_2


title: control co-cultured with no-stimulated chondrocyte 3

description: Library name: cont_3


title: shRen_H3K4me1_2

description: Library name: Sample 9


title: knock down IgG  sample 2 (Cut & Run)

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

description: Library name: KD IgG_2

data_processing:
nf-core chipseq pipeline
Assembly: hg38(human), mm10(mouse)
Supplementary files format and content: peaks file in bed format
Supplementary files format and content: Coverage in bigwig file
Library strategy: CUT&Run

source_name: Placenta

growth_protocol: Cell culture protocol was published earlier (Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell. 2018 Jan 4;22(1):50-63.e6. doi: 10.1016/j.stem.2017.11.004. Epub 2017 Dec 14. PMID: 29249463)

extract_protocol:
Cut&Run experiments was performed according to the published protocol (1, 2). hTSC were cultured in the stem condition following published protocol (3). When cells reached about 70% confluency, cells were washed with room temperature PBS and trypsinized to get single cell suspension. 1000,000 hTSC cells were used per condition. Briefly 100,000 hTSC cells were washed, and CUT & RUN assay was performed using CUT & RUN Assay kit from Cell Signaling technology (#86652). For our experiment primary antibodies against PRMT1 (Cell signaling technology #2449), H4R3Me2a (Active motif #39705)and RNA-Polymerase II (Rbp1 CTD, Cell Signaling Technology #2629S) or IgG (Cell Signaling Technology #66362S). Finally, DNA fragments were purified and used directly for library preparation using the Illumina TruSeq ChIP. (1. Skene PJ, Henikoff JG, Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc. 2018 May;13 (5):1006-1019. doi: 10.1038/nprot.2018.015. Epub 2018 Apr 12. PMID: 29651053. 2. Meers MP, Bryson TD, Henikoff JG, Henikoff S. Improved CUT&RUN chromatin profiling tools. Elife. 2019 Jun 24;8:e46314. doi: 10.7554/eLife.46314. PMID: 31232687; PMCID: PMC6598765. 3. Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell. 2018 Jan 4;22 (1):50-63.e6. doi: 10.1016/j.stem.2017.11.004. Epub 2017 Dec 14. PMID: 29249463.)
For library preparation TruSeq RNA Library Prep Kit v2 was used. 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

value: CT27 human TSC line

value: human TSC


title: d90_Bone_marrow_1

description: Library name: d90_Bone_marrow_1


title: knock down IgG  sample 1 (Cut & Run)

description: Library name: KD IgG_1


title: shRen_H3K27Ac_2

description: Library name: Sample 8


title: shRen_Tead1_2

description: Library name: Sample 7


title: control co-cultured with no-stimulated chondrocyte 1

description: Library name: cont_1


title: d75_Bone_marrow_2

description: Library name: d75_Bone_marrow_2


title: shRen_YAP_2

description: Library name: Sample 6


title: RNAPol2 knock down sample 1 (Cut & Run)

description: Library name: KD RNAPol2_1


title: d75_Bone_marrow_1

description: Library name: d75_Bone_marrow_1


title: shRen_IgG_1

description: Library name: Sample 5

value: Rabbit IgG (Sigma, I5006)


title: d60_Bone_marrow_3

description: Library name: d60_Bone_marrow_3


title: H4R3 knock down sample 2 (Cut & Run)

description: Library name: KD H4R3_2


title: shRen_anti_PD1

description:
Library name: Sample 2
Singleron

data_processing:
Raw sequencing data were processed using the celescope rna pipeline. Downstream analysis was performed using the Seurat R package (v4.3).
Assembly: mm10
Supplementary files format and content: A filtered matrix(barcodes.tsv.gz, genes.tsv.gz, matrix.mtx.gz) file comprising all cells.

source_name: Cholganiocarcinoma

extract_protocol:
Tumor-bearing livers were minced and digested in 15 mL of 1× PBS containing 7.5 mg Pronase, 7.5 mg Collagenase P, and 1.5 mg DNase I using a C Tube (Miltenyi Biotec) and the gentleMACS Octo Dissociator (Miltenyi) for 45 minutes at 100 rpm and 37 °C. Following digestion, the cell suspension was filtered through a 100 µm cell strainer and washed with an appropriate volume of Advanced DMEM/F12 (AdDMEM/F12) medium. Red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183), followed by debris removal (Miltenyi, #130-109-398) and dead cell removal (Miltenyi, #130-090-101) according to the manufacturer’s protocols.
scRNA-Seq libraries were generated using the GEXSCOPE Single Cell RNA Library Kit V2 (Cat. Num. 4180011).

value: Cholganiocarcinoma

value: Anti-mouse PD-1 (cloneRMP1-14)


title: H4R3 knock down sample 1 (Cut & Run)

description: Library name: KD H4R3_1


title: shRen_H3K27Ac_1

description: Library name: Sample 3

value: anti-H3K27Ac (Abcam, ab4729)


title: shRen_ctrl

description:
Library name: Sample 1
Singleron

value: PBS


title: d60_Bone_marrow_1

description: Library name: d60_Bone_marrow_1

value: primary cells


title: PRMT1 knock down sample 3 (Cut & Run)

description: Library name: KD PRMT1_3


title: shYT

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (v6.1.2) (10x Genomics) with the mm10 mouse reference genome for demultiplexing, alignment, and generation of gene-cell count matrices. Downstream analysis was performed using the Seurat R package (v4.3).
Assembly: mm10
Supplementary files format and content: A filtered_feature_bc_matrix.h5 file comprising all cells.

extract_protocol:
Tumor-bearing livers were minced and digested in 15 mL of 1× PBS containing 7.5 mg Pronase, 7.5 mg Collagenase P, and 1.5 mg DNase I using a C Tube (Miltenyi Biotec) and the gentleMACS Octo Dissociator (Miltenyi) for 45 minutes at 100 rpm and 37 °C. Following digestion, the cell suspension was filtered through a 100 µm cell strainer and washed with an appropriate volume of Advanced DMEM/F12 (AdDMEM/F12) medium. Red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183), followed by debris removal (Miltenyi, #130-109-398) and dead cell removal (Miltenyi, #130-090-101) according to the manufacturer’s protocols. Cells were then incubated with Fc receptor blocking reagent (Miltenyi) for 10 minutes on ice. Subsequently, cells were labeled with 1 µg of anti-mouse hashtag antibodies (TotalSeq™-B, BioLegend) for 30 minutes on ice. After labeling, cells were washed twice with PBS and resuspended in 1× PBS. The final cell concentration was adjusted to 1,000 cells/µL for downstream single-cell library preparation. Single-cell encapsulation and barcoding were performed using the 10x Genomics Chromium Controller. The shRen includes four replicates from four different mice using the following hashtags: TotalSeq-B0301, TotalSeq-B0302, TotalSeq-B0303, TotalSeq-B0304. The shYT samples includes 4 samples: 2x shYT#1 (TotalSeq-B0301, TotalSeq-B0302) and 2x shYT#2 (TotalSeq-B0303, TotalSeq-B0304).
Libraries were prepared using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics), according to the manufacturer’s protocol.

value: shYT


title: d45_Bone_marrow-4

description: Library name: d45_Bone_marrow-4


title: PRMT1 knock down sample 2 (Cut & Run)

description: Library name: KD PRMT1_2


title: shRen_YAP_1

description: Library name: Sample 1

value: shRen


title: shRen

description:
Library name: Sample 1
10x Genomics


title: d45_Bone_marrow-2

description: Library name: d45_Bone_marrow-2

value: bone marrow


title: PRMT1 knock down sample 1 (Cut & Run)

description: Library name: KD PRMT1_1


title: shYT#2_2

description: Library name: Sample 8

data_processing:
Sequencing reads were extracted in FASTQ format using bcl2fastq (v1.8.4, Illumina). Adapter trimming, size selection (retaining reads >25 nucleotides), and quality filtering (Phred score >40) of FASTQ files were performed using Cutadapt. Reads were subsequently aligned to the mouse genome (mm10) with Bowtie2 (version 2.2.9) using default settings. Read counts were extracted in R using the countOverlaps function from the GenomicRanges package. Differential gene expression analysis was carried out with DESeq2 (version 3.26.8) using default parameters.
Assembly: mm10
Supplementary files format and content: a .txt file containing all RPKM values

extract_protocol:
Tumor-bearing livers were minced and digested in 15 mL of 1× PBS containing 7.5 mg Pronase, 7.5 mg Collagenase P, and 1.5 mg DNase I using a C Tube (Miltenyi Biotec) and the gentleMACS Octo Dissociator (Miltenyi) for 45 minutes at 100 rpm and 37 °C. Following digestion, the cell suspension was filtered through a 100 µm cell strainer and washed with an appropriate volume of Advanced DMEM/F12 (AdDMEM/F12) medium. Red blood cell lysis was performed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183), followed by debris removal (Miltenyi, #130-109-398) and dead cell removal (Miltenyi, #130-090-101) according to the manufacturer’s protocols. Cells were then incubated with Fc receptor blocking reagent (Miltenyi) for 10 minutes on ice. Tumor cells were labeled with anti-EpCAM-APC antibody (eBioscience, #17-5791-82; 1:100) for 30 minutes on ice. After washing, cells were incubated with anti-APC microbeads (Miltenyi) for an additional 30 minutes. Labeled cells were then loaded onto LS columns (Miltenyi) and processed according to the manufacturer’s instructions. Positively labeled EpCAM⁺ cells were eluted and further processed for downstream applications.
For bulk RNA sequencing, total RNA was additionally purified using the RNeasy Mini Kit (Qiagen) including an on-column DNase I digestion for 15 minutes at room temperature to remove residual genomic DNA. RNA quality and concentration were assessed using the Fragment Analyzer (Agilent Technologies). For library preparation, 1 µg of high-quality RNA was used as input for mRNA enrichment using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). mRNA was then processed into sequencing libraries using the NEBNext Ultra II RNA Library Prep Kit in combination with NEBNext Multiplex Oligos for Illumina (E6440, New England Biolabs), following the manufacturer’s protocol. Final libraries were quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies).


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 12B

description: Library name: 12B_GEX

value: peripheral blood

value: T cells


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 8B

description: Library name: 8B_GEX

value: mixed


title: 48hr co-cultued with IL-1b stimulated chondrocyte1

description: Library name: Long_1


title: cKO osteocytes stimulated by LPS and aluminum 3

description: Library name: KOT3

data_processing:
The sequence data of 150 bp × 2 paired ends of 6G bases/sample (3 samples for each condition) were trimmed and mapped via HISAT2 v2.0.5. Reads were counted (FeatureCount v1.55.0-p3) and the number of fragments per 1 million bases of the transcription sequence of each gene was calculated based on the gene and read length. Significance was set up using the Benjamini-Hochberg approach as p <0.05 for false discovery rate (FDR) . The gene ontology and pathway enrichment analyses and GSEA were performed on the differential expression data using NovoMagic online tools (Novogene, Singapore).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone

growth_protocol: Long bones were harvested from the limbs of mice, and bone marrow was removed by flushing the marrow cavity with PBS. The bones were then cut into fragments approximately 1–2 mm in size and digested with 0.25% trypsin for 20 minutes. Subsequently, the bone fragments were digested with 0.001 g/mL collagenase type II solution at 37°C for 1 hour. The fragments were then suspended in EDTA solution and incubated in a shaking water bath at 37°C for 30 minutes, after which the supernatant was collected. This EDTA digestion step was repeated three times. Cells obtained from these digestions were suspended in medium and cultured at 37°C in a humidified incubator with 5% CO₂ for 7 days prior to use.

treatment_protocol: Osteocytes were swere first stimulated with 10ng/ml lipopolysaccharide for 3h, and then 20ug/ml aluminum hydroxide  for additional 3 h for induction of pyroptosis.

value: Bone

value: cKO

value: stimulated by LPS and aluminum


title: d45_Bone_marrow-1

description: Library name: d45_Bone_marrow-1


title: scRNA-seq of post-treatment peripheral-blood T cells from HNSCC patients; 2B

description: Library name: 2B_GEX

value: bintrafusp alfa


title: IgG Control sample 2 (Cut & Run)

description: Library name: CTRL IgG_2

value: Placenta

value: CT27 human TSC line

value: human TSC


title: shYT#2_1

description: Library name: Sample 7


title: 24hr co-cultued with IL-1b stimulated chondrocyte1

description: Library name: short_1

value: Osteocyte


title: cKO osteocytes stimulated by LPS and aluminum 2

description: Library name: KOT2


title: IgG Control sample 1 (Cut & Run)

description: Library name: CTRL IgG_1


title: CdSeNP-3 3mg/L Treatment

city: Chengdu

first: xiumei

last: luo

address: Shuangliu

department: Institute of Urban Agriculture

institute: Chinese Academy of Agricultural Sciences

description:
Library name: CdSeNP_3
Lettuce leaves co-treated with Cd and SeNPs

data_processing:
Raw sequencing reads were quality-filtered using fastp v0.23.0 (or Trimmomatic) to remove adapter sequences and low-quality bases (Q < 20).
Clean reads were mapped to the Lactuca sativa reference genome (GCF_002870075.4, Lsat_Salinas_v11) using HISAT2 v2.2.1
StringTie v2.2.1 was used to assemble transcripts and estimate expression levels in transcripts per million (TPM) for each sample.
Differential gene expression between treatment groups was identified using DESeq2 v1.34.0 with a false discovery rate (FDR) cutoff of 0.05 and fold-change threshold of 2 (log₂ fold change ≥ 1 or ≤ -1).
Differentially expressed genes were annotated using BLASTP against the NCBI non-redundant protein database and assigned GO terms using InterProScan.
Assembly: Lactuca sativa GCF_002870075.4 (Lsat_Salinas_v11)
Supplementary files format and content: Processed RNA-seq data are provided as gene-level expression matrices. Raw sequencing reads were quality-filtered (as above), and clean reads were mapped to the Lactuca sativa GCF_002870075.4 reference genome. Gene expression levels were quantified as TPM values. The final processed dataset includes a tab-delimited matrix containing gene IDs, TPM expression values for all samples, and corresponding sample annotations for control, Cd, SeNPs, and Cd+SeNP treatments. Raw count matrices used for differential expression are also provided. Differential expression results (log₂ fold change, p-values, and adjusted p-values) are included for comparative analysis between treatment groups.

organism: Lactuca sativa

source_name: leaves

growth_protocol: Lettuce (Lactuca sativa L. cv.‘Red oak-leaf’) seeds were surface sterilized with 5% H₂O₂ for 10 min and rinsed thoroughly with sterile distilled water. Seeds were germinated in darkness at 25°C and transferred to hydroponic culture in 1/4 Hoagland nutrient solution for 7 days, followed by 1/2 strength solution for another 7 days under controlled growth conditions (25°C, 16 h light/8 h dark photoperiod, 400 μmol m⁻² s⁻¹ light intensity, and 75% relative humidity, pH 6.0).

extract_protocol:
Total RNA was extracted from lettuce leaf tissues using a commercial plant RNA extraction kit following the manufacturer’s instructions. RNA quality and integrity were assessed using agarose gel electrophoresis and a NanoDrop spectrophotometer. High-quality RNA samples were used for cDNA library construction and subsequent Illumina sequencing.
High-quality total RNA was used for cDNA library construction following the Illumina TruSeq RNA sample preparation protocol. mRNA was enriched using poly(A) selection and fragmented into short fragments. First-strand and second-strand cDNA were synthesized, followed by end repair, A-tailing, and adapter ligation. The ligated products were purified and amplified by PCR to generate sequencing-ready libraries. Library quality and fragment size distribution were assessed before sequencing on an Illumina platform.

treatment_protocol: Four-week-old lettuce seedlings were transferred to full-strength Hoagland nutrient solution and exposed to cadmium and selenium nanoparticles under hydroponic conditions. Cadmium stress was applied using 10 mg/L CdCl₂·2.5H₂O after preliminary toxicity screening. Selenium nanoparticle (SeNPs) treatments were applied at 1, 3, and 5 mg/L, both alone and in combination with 10 mg/L Cd. Untreated plants served as the control. All treatments were maintained under controlled growth conditions, and leaf samples were collected at the 6-leaf stage (1.5 months) for RNA sequencing analysis.

value: leaves

value: whole leaf

tag: cultivar

value: Red oak-leaf

value: 10+3 mg/L Cd+SeNPs exposure


title: shYT#1_2

description: Library name: Sample 6

value: shYT


title: d75_Bone_marrow_3

description: Library name: d75_Bone_marrow_3

data_processing:
The Sscrofa 11.1 genome assembly was used to align sequencing reads to generate gene matrix data by Cell Ranger (v8.0.0).
Assembly: Sscrofa 11.1
Supplementary files format and content: matrix files

extract_protocol:
Fetal liver tissues were weighed and dispersed into single cell suspensions using glass homogenizers. Cells were then filtered using 100 µm cell strainers, washed with PBS, and treated with an ammonium chloride-based lysis buffer to remove red blood cells. After counting, 6 million cells from each liver were Fc-blocked with rat IgG (Sigma Aldrich, St. Louis, MO) and stained with anti-porcine CD45 antibody (ThermoFisher Scientific, Waltham MA). Cells were then stained with the propidium iodine (PI) viability dye and sorted for live CD45+ and CD45- cells using a BD FACS Melody cell sorter (BD Biosciences, Franklin Lakes, NJ). Thymus tissues were incubated in 3 ml of Hanks’ Balanced Salt Solution (HBSS) with 2ul of collagenase Type 1 (Worthington, Lakewood, NJ) at 37°C for 30 minutes after which they were dispersed into single cells using glass homogenizers, washed with PBS, filtered, counted, stained with PI, and finally sorted for live cells. Bone marrow was collected from the scapula, femur, tibia, humerus, ulna, and radius of 47 DG fetuses, from the femur and tibia of 60, 75, and 90 DG fetuses, and from the ribs and sternum of 1 DOA and 7 MOA pigs after they were cut open with scissors. Cells were filtered, washed with DMEM containing 10% FBS, counted, stained with PI, and FACS sorted for live cells.
Gene expression libraries were prepared using the Chromium Next GEM Single Cell 5′ Kit v2 (10× Genomics, Pleasanton, CA) according to the manufacturer’s instructions. V(D)J libraries were enriched for TCR and BCR transcripts with pig-specific primers.

value: bone marrow

value: primary cells


title: control co-cultured with no-stimulated chondrocyte 2

description: Library name: cont_2


title: RNAPol2 knock down sample 2 (Cut & Run)

description: Library name: KD RNAPol2_2


title: cKO osteocytes stimulated by LPS and aluminum 1

description: Library name: KOT1


title: CdSeNP-2 3mg/L Treatment

description:
Library name: CdSeNP_2
Lettuce leaves co-treated with Cd and SeNPs


title: RNAPol2 Control sample 2 (Cut & Run)

description: Library name: CTRL RNAPol2_2


title: WT osteocytes stimulated by LPS and aluminum 3

description: Library name: WT3

value: WT


title: shYT#1_1

description: Library name: Sample 5


title: CdSeNP-1 3mg/L Treatment

description:
Library name: CdSeNP_1
Lettuce leaves co-treated with Cd and SeNPs


title: H4R3 knock down sample 3 (Cut & Run)

description: Library name: KD H4R3_3


title: shYT_anti_PD1

description:
Library name: Sample 4
Singleron

value: Cholganiocarcinoma

value: Anti-mouse PD-1 (cloneRMP1-14)


title: RNAPol2 Control sample 1 (Cut & Run)

description: Library name: CTRL RNAPol2_1


title: shRen_4

description: Library name: Sample 4

value: shRen


title: WT osteocytes stimulated by LPS and aluminum 2

description: Library name: WT2

value: Bone

value: stimulated by LPS and aluminum


title: SeNP-3 3mg/L Treatment

description:
Library name: SeNP_3
Lettuce leaves treated with 3mg/L SeNPs only

value: 3 mg/L SeNPs exposure


title: shRen_3

description: Library name: Sample 3


title: H4R3 Control sample 3 (Cut & Run)

description: Library name: CTRL H4R3_3

value: Placenta

value: CT27 human TSC line


title: shRen_H3K4me1_1

description: Library name: Sample 4

value: anti-H3K4me1 (Cell Signaling Technology, #5326)


title: WT osteocytes stimulated by LPS and aluminum 1

description: Library name: WT1

value: Osteocyte


title: shYT_ctrl

description:
Library name: Sample 3
Singleron

value: PBS


title: SeNP-2 3mg/L Treatment

description:
Library name: SeNP_2
Lettuce leaves treated with 3mg/L SeNPs only

value: leaves

value: whole leaf

value: Red oak-leaf


title: H4R3 Control sample 2 (Cut & Run)

description: Library name: CTRL H4R3_2

value: human TSC


title: SeNP-1 3mg/L Treatment

description:
Library name: SeNP_1
Lettuce leaves treated with 3mg/L SeNPs only


title: shRen_2

description: Library name: Sample 2


title: DOX4X bio rep 4 female

description: Library name: DOX4X-4

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 mouse genome vM27 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: GRCm39
Supplementary files format and content: gene count matrix

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 Buffer RLT Plus with 1% beta-mercaptoethanol.
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.

treatment_protocol: For DOX1X group, young adult mice were adminstrated with a single dose of doxorubicin (10 mg/kg, intravenous;Sigma, D1515). For DOX4X group, young adult (8-10 week-old) mice were treated with 4 doses of doxorubucin (5 mg/kg, intravenous), 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: H4R3 Control sample 1 (Cut & Run)

description: Library name: CTRL H4R3_1


title: shRen_1

description: Library name: Sample 1

value: shRen


title: DOX4X bio rep 3 female

description: Library name: DOX4X-3


title: Cd-3 10mg/L Treatment

description:
Library name: Cd_3
Lettuce leaves exposed to 10 mg/L Cd

value: 10 mg/L CdCl₂ exposure


title: d60_Bone_marrow_2

description: Library name: d60_Bone_marrow_2

value: primary cells


title: PRMT1 Control sample 2 (Cut & Run)

description: Library name: CTRL PRMT1_2


title: conG7_4

city: Freiburg im Breisgau

first: Sebastian

last: Arnold

address: Albertstraße 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

institute: University Freiburg

data_processing:
Untrimmed fastq rawdata files were mapped to the genome using Rsubread v1.28.1 package in R v3.4.4.
Gene counting was performed applying Rsubread::featureCount function with the iGenomes reference genome gtf file for annotation
(archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCm38).
For differential expression analysis, DESeq2 v1.18.1 was used. First, the counts were normalized by library size (DESeq2::estimateSizeFactors) and by gene-wise dispersion (gene-wise geometric mean over the samples; DESeq2::estimateDispersions), then, the differential expression analysis was performed applying negative vinomial generalized linear model fitting and Wald statistics on the normalized count data (DESeq2::DESeq2).
Subsequently, the results were filtered for adjusted p < 0.05 and the log2FC values, as indicated in the figures.
Assembly: GRCm38/mm10 (iGenomes, Illumina;chromosomes 1-19, X, Y, M; archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38)
Supplementary files format and content: TSV, containing count matrices of samples with gene name

source_name: kidney

growth_protocol: IMCD3 standard DMEM medium with 10% FBS

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CRISPR base editing

value: kidney

value: immortilised

value: control

value: CRISPR

tag: cell subtype

value: ciliated cells


title: PRMT1 Control sample 1 (Cut & Run)

description: Library name: CTRL PRMT1_1

value: Placenta

value: CT27 human TSC line


title: Cd-2 10mg/L Treatment

description:
Library name: Cd_2
Lettuce leaves exposed to 10 mg/L Cd

value: leaves

value: whole leaf


title: conG7_3


title: DOX4X bio rep 1 female

description: Library name: DOX4X-1


title: DOX4X bio rep 2 female

description: Library name: DOX4X-2


title: CT27 TSC with PRMT1 knockdown

description:
Library name: PRMT1 KD
10x Genomics

data_processing:
The demultiplexing, barcodeed processing, gene counting were made using Cell Ranger software v7.2.0(https://www.10xgenomics.com/support/software/cell-ranger/downloads).
Downstream analysis was done using Seurat v5
Assembly: refdata-gex-GRCh38-2024-A
Supplementary files format and content: Feature and barcode files

growth_protocol: Human TSC 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: RNAs from single cell suspension was used to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

treatment_protocol: no treatment

value: CT27 HUMAN TSC with PRMT1 knockdown

value: Single cells obtained from CT27 human TSC with PRMT1 Knockdown


title: conG7_2


title: Cd-1 10mg/L Treatment

description:
Library name: Cd_1
Lettuce leaves exposed to 10 mg/L Cd

value: Red oak-leaf


title: DOX1X bio rep 3 female

description: Library name: DOX1X-3

value: bone marrow

value: mesenchymal stem and progenitor cells

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

value: 1X DOX IV 10 mg/kg


title: conG7_1


title: CT27 TSC control

description:
Library name: Control HTS
10x Genomics

value: CT27 HUMAN TSC

value: Single cells obtained from CT27 human TSC


title: DOX1X bio rep 2 female

description: Library name: DOX1X-2


title: Control-2 Treatment

description:
Library name: CK_2
Control lettuce leaves without Cd or SeNP exposure

value: control (0 mg/L CdCl₂)


title: U2OS, siORCA, Replicate 2, RNA Seq

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: U2OS_siORCA2

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: siORCA


title: conA4_4

value: kidney

value: immortilised

value: control

value: CRISPR

value: ciliated cells


title: Control-1 Treatment

description:
Library name: CK_1
Control lettuce leaves without Cd or SeNP exposure

value: leaves

value: whole leaf


title: DOX1X bio rep 1 female

description: Library name: DOX1X-1

value: bone marrow


title: U2OS, siORCA, Replicate1, RNA Seq

description: Library name: U2OS_siORCA1

value: Batch 1


title: conA4_3


title: H.vulgare, PolyA RNA-seq, Morex, replicate2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

description: Library name: PolyA_RNA-seq_barley_Morex_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: Hordeum vulgare

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: conA4_2


title: U2OS, Control, Replicate 2, RNA Seq

description: Library name: U2OS_Control2


title: PBS bio rep 3 female

description: Library name: C3

value: mesenchymal stem and progenitor cells

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

value: 4X PBS IV


title: H.vulgare, PolyA RNA-seq, Morex, replicate1

description: Library name: PolyA_RNA-seq_barley_Morex_rep1


title: conA4_1


title: PBS bio rep 2 female

description: Library name: C2


title: conH12_4


title: PBS bio rep 1 female

description: Library name: C1


title: U2OS, H3K27me3, Input, ChIP

description: Library name: H3K27me3_Input

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (Illumina).
Trimming of reads was performed with trimmomatic
All sequencing files were aligned to human genome (T2T-CHM13v2.0) using Bowtie2 (v) and the sam files were converted to bam files using SAMtools (v)
Peaks were called using MACS
Assembly: T2T-CHM13v2.0
Supplementary files format and content: broadPeak(except for Input)

extract_protocol:
Cells were fixed with 1% formaldeyde for 10 mins at room temperature. After quenching and cell lysis, chromatin was sonnicated using Bioruptor Power-up (Diagenode)
Sequencing libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina, IP-202-1012) as per manufacturer’s protocol. Libraries were amplified by 8-12 PCR cycles. qPCR was used to measure the concentrations of each library which were then pooled at equimolar concentration for each lane and sequenced for 101 cycles from one end of the fragments on a IlluminaNovaSeq 6000.


title: H.vulgare, Chromatin_Bound(CB) RNA-seq, Morex, replicate1

description: Library name: CB_RNA-seq_barley_Morex_rep1

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: conH12_3


title: U2OS, H3K27me3, siORCA, ChIP

description: Library name: H3K27me3_siORCA


title: DOX4X bio rep 5 female

description: Library name: S2_D3

extract_protocol:
Bone marrow were flushed with centrifugation. The remaining bone tissue were cutted into bone chips and enzymetically digested at 37°C for 25 min. Osteoblasts were sorted based on GFP expression into Buffer RLT Plus with 1% beta-mercaptoethanol.
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.

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

value: osteoblast

value: 4X doxorubicin IV 5 mg/kg


title: U2OS, H3K27me3, Control, ChIP

description: Library name: H3K27me3_Control

value: Human Osteosarcoma


title: PE22_PPE36KO_SO4_3.fastq

city: seattle

first: Ashutosh

middle: P

last: Tripathi

state: Washington

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

description: Library name: PE22_PPE36KO_SO4_3.fastq

data_processing:
Read alignment was performed using the Bowtie 2 custom processing pipeline (https://github.com/robertdouglasmorrison/DuffyNGS, https://github.com/robertdouglasmorrison/DuffyTools), as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Assembly: MT_H37Rv_V3
Supplementary files format and content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis culture

growth_protocol: Wild-type (WT) Mycobacterium tuberculosis H37Rv was cultured in Middlebrook 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% tyloxapol, and 100 µM sodium propionate until an OD₆₀₀ of 0.8 was reached. Cells were then harvested by centrifugation, washed three times with phosphate-buffered saline (PBS), and resuspended in sulfate-free HdB medium. Cultures were incubated for an additional 48 h in the presence or absence of 100 µM sodium sulfate

extract_protocol:
The bacteria were harvested at the indicated timepoint and resuspended in Trizol, and lysed by bead beating for 30 seconds at 6 m/s for 3 cycles, with intermittent cooling on ice. Cell debris was pelleted at 20,000 g for 1 minute, and the supernatant was transferred to a heavy phase-lock gel tube containing 300 μL of chloroform. The tubes were inverted for 2 minutes and centrifuged at 20,000 g for 5 minutes. RNA in the aqueous phase was precipitated with 300 μL of isopropanol and 300 μL of high-salt solution (0.8 M sodium citrate, 1.2 M sodium chloride). RNA was purified using the QIAGEN RNeasy kit, and ribosomal RNA was depleted using a previously published protocol [Culviner, P. H. et al doi:10.1128/mBio.00010-20 (2020)]. Briefly, a biotinylated oligo mixture of 23S, 16S, and 5S was incubated with RNA to anneal to rRNA, followed by incubation with streptavidin beads. mRNA was purified from the supernatant using Ampure XP beads.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and the WT H37RV with and without 100 µM SO4 samples were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit while the WT H37RV and pe22/ppe36 KO in sulphate deplete and 10 mM replete condition samples were sequenced at Fred Hutch with Illumina NovoSeqX+.

treatment_protocol: With and without 100 µM SO4 in HdB media. In SO4 repletion experiment with and without 10 mM SO4 after 48 h of starvation in sulphate free modified Sauton's media.

tag: strain

value: M. tuberculosis culture

value: Repleted with 10 mM of SO4 for 24 h post 48 h of starvation


title: conH12_2

value: kidney

value: immortilised


title: DOX4X bio rep 4 female

description: Library name: S2_D2

value: bone


title: PE22_PPE36KO_SO4_2.fastq

description: Library name: PE22_PPE36KO_SO4_2.fastq


title: conH12_1

value: control

value: CRISPR

value: ciliated cells


title: WI38_OIS_4

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Library name: Sample 190
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 4

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts

extract_protocol:
Total RNA was extracted using TriPure™ Isolation Reagent (Sigma-Aldrich), following the manufacturer's instructions with phenol-chloroform extraction.
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).

value: Lung fibroblasts

value: WT

value: RasV12 (MOI:3)


title: PE22_PPE36KO_SO4_1.fastq

description: Library name: PE22_PPE36KO_SO4_1.fastq


title: conD8_4


title: DOX4X bio rep 2 female

description: Library name: S1_D3


title: PE22_PPE36KO_w_o_SO4_3.fastq

description: Library name: PE22_PPE36KO_w_o_SO4_3.fastq


title: WI38_OIS_2

description:
Library name: Sample 188
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 2


title: conD8_3


title: DOX4X bio rep 1 female

description: Library name: S1_D1


title: WI38_OIS_1

description:
Library name: Sample 187
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 1


title: PE22_PPE36KO_w_o_SO4_2.fastq

description: Library name: PE22_PPE36KO_w_o_SO4_2.fastq


title: conD8_2


title: PBS bio rep 3 female

description: Library name: S2_C2


title: PE22_PPE36KO_w_o_SO4_1.fastq

description: Library name: PE22_PPE36KO_w_o_SO4_1.fastq


title: WI38_EV_4

description:
Library name: Sample 186
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 4

value: Empty vector (MOI:3)


title: conD8_1


title: PBS bio rep 2 female

description: Library name: S2_C1


title: WTRv_SO4_3.fastq

description: Library name: WTRv_SO4_3.fastq

value: Starved for SO4 in modified Sauton's for 72 h


title: WI38_EV_3

description:
Library name: Sample 185
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 3


title: WDR60_4

value: homoz mutant


title: PBS bio rep 1 female

description: Library name: S1_C3

value: osteoblast

value: 4X PBS IV


title: Control-3 Treatment

description:
Library name: CK_3
Control lettuce leaves without Cd or SeNP exposure

value: leaves

value: whole leaf

value: Red oak-leaf

value: control (0 mg/L CdCl₂)


title: WI38_EV_2

description:
Library name: Sample 184
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 2


title: WDR60_3

value: kidney

value: immortilised


title: DOX female pooled two bio rep

description: Library name: DOX

data_processing:
Single-cell gene counts were acquired by mapping the raw reads to mouse genome mm10 using 10x Genomics Cell Ranger v7.2.0
Assembly: mm10
Supplementary files format and content: Filtered feature bc matrix (h5 file)

source_name: bone marrow+bone

extract_protocol:
Total bone marrow was flushed with centrifugation. The remaing bone tissue was cutted into bone chips. Bone marrow and bone chips were digested at 37°C for 25 min individually and pooled together for following processess. Hematopoietic cells were depleted using AutoMACS through two rounds of depletion: first round lineage (B220, CD3, CD4, CD8, CD11b, Gr1, Ter119, CD71) deletion, second round progenitor (CD45, cKit). The remaining non-hematopoeitic cells were subjected to scRNA-seq library preparation.
Droplet-based separation of bone marrow non-hematopoietic cells were performed using the Chromium X platform (10X Genomics). The cDNA libraries were prepared using Chromium Next GEM Single Cell 3ʹ Kit v3.1.

value: bone marrow+bone

value: non-hematopoietic cell

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

value: 4X doxorubicin IV 5 mg/kg


title: WTRv_SO4_1.fastq

description: Library name: WTRv_SO4_1.fastq

value: M. tuberculosis culture


title: WTRv_SO4_2.fastq

description: Library name: WTRv_SO4_2.fastq


title: WI38_EV_1

description:
Library name: Sample 183
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 1

value: Lung fibroblasts

value: WT


title: WDR60_2

value: CRISPR

value: ciliated cells


title: PBS female pooled two bio rep

description: Library name: PBS


title: DOX bio rep 1 female

description: Library name: C4

value: bone marrow

value: mesenchymal stem and progenitor cells


title: WTRv_w_o_SO4_3.fastq

description: Library name: WTRv_w_o_SO4_3.fastq

value: Starved for SO4 in modified Sauton's for 72 h


title: Proliferating CD4⁺ T-cells, 100uM PCS,HC3

description:
Library name: s023
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

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.

value: Peripheral Blood

value: T cells

value: 100uM PCS

value: Proliferating


title: U2OS, Control, Replicate1, RNA Seq

description: Library name: U2OS_Control1

value: bone

value: Human Osteosarcoma


title: WI38_OSIS_4

description:
Library name: Sample 182
Cells were treated with 0.75 mM H2O2 for 2 hours and cultured for 8 days - replicate 4

value: Oxidative stress-induced senescence (8 days 0.75 mM H2O2)


title: IgG mEPC control  sample 2 (Cut & Run)

description: Library name: mEPC_IgG_2

data_processing:
nf-core chipseq pipeline
Assembly: hg38(human), mm10(mouse)
Supplementary files format and content: peaks file in bed format
Supplementary files format and content: Coverage in bigwig file
Library strategy: CUT&Run

source_name: Ectoplacental cone

extract_protocol:
Cut&Run experiments was performed according to the published protocol (1, 2). hTSC were cultured in the stem condition following published protocol (3). When cells reached about 70% confluency, cells were washed with room temperature PBS and trypsinized to get single cell suspension. 1000,000 hTSC cells were used per condition. Briefly 100,000 hTSC cells were washed, and CUT & RUN assay was performed using CUT & RUN Assay kit from Cell Signaling technology (#86652). For our experiment primary antibodies against PRMT1 (Cell signaling technology #2449), H4R3Me2a (Active motif #39705)and RNA-Polymerase II (Rbp1 CTD, Cell Signaling Technology #2629S) or IgG (Cell Signaling Technology #66362S). Finally, DNA fragments were purified and used directly for library preparation using the Illumina TruSeq ChIP. (1. Skene PJ, Henikoff JG, Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc. 2018 May;13 (5):1006-1019. doi: 10.1038/nprot.2018.015. Epub 2018 Apr 12. PMID: 29651053. 2. Meers MP, Bryson TD, Henikoff JG, Henikoff S. Improved CUT&RUN chromatin profiling tools. Elife. 2019 Jun 24;8:e46314. doi: 10.7554/eLife.46314. PMID: 31232687; PMCID: PMC6598765. 3. Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell. 2018 Jan 4;22 (1):50-63.e6. doi: 10.1016/j.stem.2017.11.004. Epub 2017 Dec 14. PMID: 29249463.)
For library preparation TruSeq RNA Library Prep Kit v2 was used. 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: Ectoplacental cone

value: Primary trophoblast progenitors

value: mouse EPC


title: WDR60_1

value: kidney

value: immortilised

value: homoz mutant


title: WTRv_w_o_SO4_2.fastq

description: Library name: WTRv_w_o_SO4_2.fastq

value: M. tuberculosis culture