title: Stereoseq of ileal Swiss roll sample from Yersinia pseudotuberculosis infected B6 female mouse replicate 1

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

description: Library name: Yp1_FFPE_SR

data_processing:
The mouse reference genome assembly GRCm39 (Ensembl Release 115) was utilized. The primary assembly genomic FASTA (Mus_musculus.GRCm39.dna.toplevel.fa.gz) and corresponding gene annotation GTF (Mus_musculus.GRCm39.115.gtf.gz) files were downloaded directly from the Ensembl FTP server. To accurately account for ribosomal RNA contamination in the FFPE Stereo-seq data, custom rRNA reference sequences were compiled. The complete 45S rDNA unit (GenBank: BK000964.3) and mitochondrial rRNAs 12S and 16S (GenBank: NR_003278.3, NR_003279.1) were fetched via NCBI Entrez utilities. These sequences were concatenated into a unified ribosomal database, and FASTA headers were standardized and cleaned using sed to ensure compatibility. The downloaded primary genome, custom rRNA database, and annotation files were integrated into a custom reference directory to configure the Stereo-seq Analysis Workflow (SAW) pipeline. SAW version 8.2.2 was used
Spatial transcriptomics data from mouse small intestine tissue was processed using the Stereo-seq Analysis Workflow (SAW) pipeline (saw count). The pipeline utilized standard paired-end sequencing inputs (PE75_25+59) generated via the Stereo-seq N FFPE V1.0 kit protocol. Reads were mapped using a custom-curated reference library configuration, which integrated the primary mouse genome with tailored ribosomal RNA sequences. The pipeline leveraged a chip-specific mask file (.barcodeToPos.h5) to decode spatial coordinates, performed automated microorganism detection, and aligned the transcriptomic data with corresponding high-resolution tissue morphology images (.tar.gz). The SAW    --microorganism-detect  flag was set and the Kraken PFPlus database was used to test the non-host reads. The output from the microorgaism detection is included with this submission.
Routine Data anlysis was accomplished in R and included filtering the cell-wise data and then simply visualizing the reads across the tissue including host reads and microbial reads.
Assembly: GRCm39 (Ensembl Release 115)
Supplementary files format and content: Y01679L2.barcodeToPos.h5. This file is the Chip mask for OMNI STEREO SEQ performed with Complete Genomics on mouse small intestine Swiss Roll FFPE block section. This file is used to spatially orient sequencing data contained in fastq files
Supplementary files format and content: Y01679L2.tissue.gef. A binary Gene Expression Format (GEF) file containing spatially resolved gene expression data restricted specifically to the detected tissue area.
Supplementary files format and content: Y01679L2.adjusted.cellbin.gef A cell-level GEF file containing single-cell segmented spatial expression data after cell boundary adjustments.
Supplementary files format and content: Y01679L2_ssDNA_mask.tif. A high-resolution TIFF image representing the single-stranded DNA (ssDNA) stain mask used for cell segmentation and tissue morphology identification.
Supplementary files format and content: Y01679L2_microorganism.species.gem. A Gene Expression Matrix (GEM) file detailing the spatial distribution and quantification of detected microorganisms resolved at the species level.
Supplementary files format and content: Y01679L2_microorganism.genus.gem. A Gene Expression Matrix (GEM) file detailing the spatial distribution and quantification of detected microorganisms resolved at the genus level.
Supplementary files format and content: Y01679L2.host_microorganism.raw.gef.  A raw, unfiltered GEF file containing combined spatial expression counts for both the mouse host tissue and the detected microbial sequences.
Supplementary files format and content: Y01679L2.microorganism.raw.gef. A raw, unfiltered GEF file specifically isolating the spatial quantification data for all detected microorganism sequences.
Supplementary files format and content: Y01679L2_microorganism.phylum.gem. A Gene Expression Matrix (GEM) file detailing the spatial distribution and quantification of detected microorganisms resolved at the phylum level
Supplementary files format and content: Y01679L2_microorganism.class.gem. A Gene Expression Matrix (GEM) file detailing the spatial distribution and quantification of detected microorganisms resolved at the class level
Supplementary files format and content: Y01679L2_microorganism.order.gem. A Gene Expression Matrix (GEM) file detailing the spatial distribution and quantification of detected microorganisms resolved at the order level
Supplementary files format and content: Y01679L2_microorganism.family.gem. A Gene Expression Matrix (GEM) file detailing the spatial distribution and quantification of detected microorganisms resolved at the family level
Supplementary files format and content: GRCm39_SuperRef.fa - The custom reference FASTA genome file containing combined sequences of the mouse primary assembly (GRCm39) and the targeted ribosomal RNA transcripts.
Supplementary files format and content: GRCm39_Super_Fixed.gtf - The standardized and corrected gene transfer format (GTF) annotation file mapping coordinates for both host mouse genes and integrated ribosomal RNA features.
Library strategy: Spatial Transcriptomics

source_name: ileum

extract_protocol:
Spatially resolved transcriptomic profiling was carried out using the Complete Genomics Omni protocol. Mice were euthanized and the small intestine isolated and flushed before 5 cm of the terminal ileum was Swiss rolled. Tissues were fixed in 10% neutral buffered formalin for 18-24 hours prior to paraffin embedding. Sections were cut following embedding and placed per manufacturer guidelines.
Per the manufacturer protocols: Following tissue permeabilization, total spatial RNA was captured in situ using random primers coupled to distinct Coordinate Identifiers (CIDs) and Molecular Identifiers (MIDs) on the chip. Reverse transcription was performed directly on the chip to generate cDNA. The spatially barcoded cDNA was subsequently recovered, amplified via PCR, and purified. Whole-transcriptome libraries were finalized by adapter ligation, PCR enrichment, and single-stranded circularization to generate DNA Nanoballs (DNB) for sequencing on the DNBSEQ platform.

value: ileum

tag: sample type

value: fixed and paraffin embedded swiss roll of intestinal tissue

tag: infecting organism

value: Yersinia pseudotuberculosis

tag: infection details

value: clinical isolate strain 32777, serogroup O5

tag: infection dose

value: 1-2e8 CFU

tag: infection route

value: oral gavage

value: female

value: 7.5 weeks

tag: collection date


title: KO, H3K9me3 ChIP, rep3

status: Public on Jun 19 2026

type: SRA

city: Calgary

first: Ankita

last: Ankita

state: AB

address: 3330 Hospital Dr NW

department: Alberta Children’s Hospital Research Institute

country: Canada

institute: University of Calgary

description:
Library name: Sample 9
NextSeq P3 100 cycle

library_source: genomic

data_processing:
FASTQ files were aligned to the mm10 genome build using Bowtie2 (v2.5.4 ). For broad peak calling, MACS2 (v2.2.6) was used with a threshold of --broad-cutoff 0.1 and then DiffBind (v3.16.0) was used to generate consensus peaks.
BAM files were processed to generate bigwig  files using bamCoverage from deepTools (v3.5.6). RPGC (reads per genome coverage) normalisation method  was implemented for conversion. We used ProfileHeatmap from deepTools  to visualize the signal intensity  around consensus peaks of  ChIP and Input samples.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Trophoblast Stem Cells

growth_protocol: TSCs were cultured in Full Medium consisting of 20% fetal bovine serum (FBS) (Wisent 098-150), 1mM sodium pyruvate (ThermoFisher Scientific 11360070), 1x Antibiotic-Antimycotic (Wisent 450-115-EL), 55 μM 2-mercaptoethanol (Gibco 21985023), 37.5 ng/ml bFGF (Cambridge Stem Cell Institute), and 1μg/ml heparin (Sigma H3149) in RPMI 1640 with L-Glutamine (Wisent 350-000-CL), with 70% of the medium pre-conditioned on mouse embryonic fibroblasts.

extract_protocol:
Native ChIP-seq was performed on approximately 250,000 cells per reaction, resuspended to a concentration of ~5,000 cells/µl inl nuclear isolation buffer (Sigma, NUC-101). MNase digestion was carreid out at 21 ◦C for 8 min. Digested chromatin was then suspended in Complete IP buffer [20 mM Tris–HCl (pH 8), 2 mM EDTA, 150 mM NaCl, 0.1% Triton-X100, 1 ×Protease inhibitor cocktail, and 1 mM phenylmethanesulfonyl fluoride (PMSF)]. Following pre-clearing the chromatin on a mix of protein A / protein G beads, and after 10% was set aside for input, IP was performed overnight rotating at 30 rpm, at 4 ◦C, using 250 ng antibodies against H3K9me3 (Abcam, ab8898) and on a subset of samples also for H3K4me3 (Diagenode, C15200152). DNA was washed in low salt and then high salt washes, before eluting in ChIP elution buffer (100 mM NaHCO 3 and 1% SDS).
Libraries were generated with the NEB Ultra II kit and quantitated using a Agilent Bioanalyzer. Libraries were paired-end sequenced on a NextSeq2000 using the P3 100 cycle program.

tag: cell line

value: Trophoblast Stem Cells

tag: cell type

tag: genotype

value: Peg3 KO

tag: treatment

value: NEB ultra II DNA library prep


title: MM4027-D3

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

country: USA

institute: University of Pittsburgh

description:
Library name: MM4027-D3
scRNA-seq

library_source: transcriptomic single cell

data_processing:
We generated feature-barcode count matrix using cellranger count (mapped to GRCh38 human reference genome) for each sample separately. The outputs of the samples from the same donor were aggregated using cellranger aggr. The feature-barcode count matrix was processed using Seurat package.
Assembly: GRCh38
Supplementary files format and content: D3D7_CD14mono.rds, Ma-healthy.rds, Ma-trauma.rds

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: On day 0, cryopreserved PBMCs were thawed and resuspended in complete media (RPMI164+ 10%FBS + penicillin (100U/mL) + streptomycin (100U/mL)) at 5 * 10^5 cell/mL at 37° with 5%CO2 overnight.

extract_protocol:
Blood samples were obtained from human study subjects. PBMCs were isolated by standard Ficoll centrifugation.
Flow isolated monocytes were further proceeded with scRNA libraries using Chromium Single Cell 3' Reagent Kits (v3.1, CG000315)

treatment_protocol: On day 1, GM-CSF (Sigma-Aldrich, Cat# G5035; final concentration: 50 ng/mL) or M-CSF (Sigma-Aldrich, Cat# H6916; final concentration: 50 ng/mL) were added to the media. On day 4, the same amount of fresh complete media with or without cytokines correspondingly were added to the cultured cells. Cells were harvested on day 7 (Accutase: Sigma-Aldrich, Cat# A6964).

tag: tissue

value: PBMC

value: cryoperserved cells after thawing


title: Whole blood, 0.58y, Female, Poodle [ET06021]

type: genomic

city: Jinju-si

first: Jaemin

last: Kim

state: Gyeongsangnam-do

address: 501, Jinji-daero

country: South Korea

institute: Gyeongsang National University

hyb_protocol: Bisulfite-converted genomic DNA was hybridized to the custom Infinium HorvathMammalMethylChip40 array following standard Illumina protocols

scan_protocol: Arrays were scanned using the Illumina iScan System with standard settings.

data_processing: SeSAMe package in R environment

label: biotin

organism: Canis lupus familiaris

source_name: Whole blood

label_protocol: Standard Illumina protocol

extract_protocol: Whole blood samples were collected from the jugular vein of companion dogs and stored in EDTA tubes. Genomic DNA was extracted using the Exgene Blood SV mini kit (GeneAll Biotechnology, Seoul, Republic of Korea) according to the manufacturer’s instructions. DNA quality and purity were assessed using Qubit fluorometer and NanoDrop spectrophotometer; integrity was confirmed by agarose gel electrophoresis.

value: Whole blood

tag: Sex

value: Female

tag: age

tag: breed

value: Poodle


title: Whole blood, 0.58y, Female, Beagle [ET06022]

value: Beagle


title: Recurrent Pregnancy Loss Patient 10

city: Varanasi

first: Ashish

last: Ashish

address: Banaras Hindu University

country: India

institute: MRU Lab

description: Genomic DNA extracted from products of conception (RPOC) samples obtained from patients with a history of recurrent pregnancy loss (RPL). Copy number variations (CNVs) were detected using high-resolution array comparative genomic hybridization (aCGH) on Agilent SurePrint G3 Human CGH 4x180K microarrays. Each test sample (Cy5-labeled) was hybridized against pooled genomic DNA from Agilent Human Reference DNA(Cy3-labeled) to identify chromosomal gains, deletions, and amplifications associated with RPL.

hyb_protocol: Equal amounts of Cy5-labeled test DNA and Cy3-labeled reference DNA were combined and hybridized onto Agilent SurePrint G3 Human CGH 4x180K microarrays according to the manufacturer's protocol (Agilent Oligo aCGH/ChIP-on-Chip Hybridization Kit). The hybridization mixture was incubated at 65°C for 24–40 hours in a rotating hybridization oven at 20 rpm. After hybridization, arrays were washed using Agilent Oligo aCGH Wash Buffer Kit and scanned using an Agilent DNA Microarray Scannerand data were processed using the Agilent Feature Extraction 12.1 Software

scan_protocol: Microarrays were scanned using the Agilent SureScan G2600D Microarray Scanner at 3 μm resolution with default laser and PMT settings for two-color arrays.

data_processing: Cytogenomics v4.0.3.003

source_name: Products of Conception (RPOC)

label_protocol: Genomic DNA (500 ng) from test and reference samples was labeled using the Agilent Genomic DNA Labeling Kit according to the manufacturer’s instructions. Test sample DNA was labeled with Cy3-dUTP and reference DNA with Cy5-dUTP. Labeled products were purified using spin columns, and dye incorporation was quantified using a NanoDrop spectrophotometer.

growth_protocol: Not applicable. DNA was extracted directly from uncultured products of conception (RPOC) tissue obtained from spontaneous pregnancy loss. No cell culture or in vitro growth was performed.

extract_protocol: Genomic DNA was extracted from products of conception (RPOC) tissue using the QIAamp DNA Mini Kit (Qiagen), following the manufacturer’s instructions. Tissue samples were homogenized and lysed with proteinase K, followed by purification through silica-membrane columns. DNA concentration and purity were assessed using NanoDrop spectrophotometry and agarose gel electrophoresis.

treatment_protocol: Not Applicable

value: products of conception (RPOC)  disease status:recurrent pregnancy loss

tag: gestational age

value: first trimester (8–12 weeks)

source_name: Agilent Human Reference DNA

value: Agilent Human Reference DNA


title: Recurrent Pregnancy Loss Patient 11


title: Recurrent Pregnancy Loss Patient 12


title: Gsk3b (IEC-/-) ATAC-Seq 2

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

country: China

institute: Soochow University

description:
Library name: Gsk3b (IEC-/-) ATAC-Seq 2
Combined signal track for Gsk3b (IEC-/-)

data_processing:
The original ATAC-Seq reads were trimmed of adapter sequences using fastp. The trimmed reads were then aligned to the reference genome (mm10) using Bowtie2. Subsequently, duplicates, multi mapping reads, and low quality alignments were removed using SAMtools. Mitochondrial reads, chromosome Y alignments, and ENCODE blacklisted genomic regions were excluded. Peaks were called using MACS3 with the settings -f BAMPE -B --nomodel --SPMR --keep-dup 1.
Assembly: mm10
Supplementary files format and content: bigWig signal tracks generated from MACS3 callpeak bedGraph outputs with --SPMR using merged biological replicates for each condition

source_name: colon cancer tissues

extract_protocol:
Each colon cancer tissue sample (weighing about 500 mg) was finely ground and lysed. The nuclei were then isolated through centrifugation at 2000 * g for 5 minutes.
Then, the TruePrep DNA Library Prep Kit V2 for Illumina (TD501; Vazyme Biotech) was utilized for transposition and high-throughput sequencing library preparation. Finally, these ATAC-Seq libraries were then enriched, quantified, and sequenced on a DNBSEQ-T7 platform (BGI, Shenzhen, China) using the PE150 strategy.

value: colon cancer tissues


title: MM4026-D7

description:
Library name: MM4026-D7
scRNA-seq


title: Recurrent Pregnancy Loss Patient 9


title: KO, H3K9me3 ChIP, rep2

description:
Library name: Sample 8
NextSeq P3 100 cycle


title: Gsk3b (IEC-/-) ATAC-Seq 1

description:
Library name: Gsk3b (IEC-/-) ATAC-Seq 1
Combined signal track for Gsk3b (IEC-/-)


title: KO, H3K9me3 ChIP, rep1

description:
Library name: Sample 7
NextSeq P3 100 cycle


title: Gsk3b (IEC+/+) ATAC-Seq 2

description:
Library name: Gsk3b (IEC+/+) ATAC-Seq 2
Combined signal track for Gsk3b (IEC+/+)


title: MM4026-D3

description:
Library name: MM4026-D3
scRNA-seq


title: HC2-MCSF

description:
Library name: HC2-MCSF
scRNA-seq

value: in vitro culture


title: WT, Input 3

description:
Library name: Sample 6
NextSeq P3 100 cycle

value: WT


title: Recurrent Pregnancy Loss Patient 8


title: HC2-GMCSF

description:
Library name: HC2-GMCSF
scRNA-seq


title: Gsk3b (IEC+/+) ATAC-Seq 1

description:
Library name: Gsk3b (IEC+/+) ATAC-Seq 1
Combined signal track for Gsk3b (IEC+/+)


title: WT, Input 2

description:
Library name: Sample 5
NextSeq P3 100 cycle


title: Recurrent Pregnancy Loss Patient 7


title: NR-treated OT-I CD8+ T cells, biol rep 3

city: Guangzhou

first: Lili

address: No. 135, Xingang West Road

institute: Sun Yat-sen University

description:
Library name: N3
PE150

library_source: transcriptomic

data_processing:
Raw sequencing reads were filtered using SOAPnuke (v2.2.1) to remove sequencing adapters, low-quality bases (base quality ≤ 15, ratio > 20%), and unknown bases ('N' ratio > 5%). Clean reads were obtained and stored in FASTQ format.
Clean reads were aligned to the mouse reference genome (GRCm39/mm39) using HISAT2 (v2.2.1) with sensitive parameters.
Gene expression levels were quantified using RSEM (v1.3.1).
Differential expression analysis was performed using DESeq2 (v1.34.0). Genes with Q value ≤ 0.05 and |log2 fold change| > 1 were considered significant.
GO and KEGG enrichment analysis of differentially expressed genes was performed using Phyper based on Hypergeometric test, with Q value ≤ 0.05 as the significance threshold.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file containing gene expression quantification data (FPKM, TPM, and read counts) for all submitted samples. Rows represent genes (Ensembl gene IDs and gene symbols), columns represent samples.

source_name: spleen

growth_protocol: OT-I CD8+ T cells were isolated from spleens of OT-I transgenic mice and activated with OVA257-264 peptide (10 ng/mL) for 72 hours in RPMI 1640 medium supplemented with 10% FBS,  GlutaMAX™, β-Mercaptoethanol, sodium pyruvate, and 100 U/ml recombinant murine IL-2 (T cell culture medium). After activation, CD8+ T cells were cultured in T cell culture medium for 4 days.

extract_protocol:
Total RNA was extracted using TRIzol Reagent. RNA quality was assessed using a Fragment Analyzer.
RNA-seq libraries were prepared using BGISEQ library preparation kit following manufacturer's protocols. Briefly, mRNA was enriched using oligo(dT) magnetic beads, fragmented, reverse transcribed, and ligated with sequencing adapters. Libraries were amplified by PCR and validated.

treatment_protocol: NR administration was started at day 0 with a final concentration of 500 μmol/L in a T cell culture medium.

value: spleen

value: primary cell

value: CD8+ T cells

value: OT-I transgenic

value: NR, 500 μM


title: MM4035-D3

description:
Library name: MM4035-D3
scRNA-seq

value: PBMC


title: HC2-Ctrl

description:
Library name: HC2-Ctrl
scRNA-seq


title: WT, Input 1

description:
Library name: Sample 4
NextSeq P3 100 cycle

value: Trophoblast Stem Cells

value: NEB ultra II DNA library prep


title: Recurrent Pregnancy Loss Patient 6


title: NR-treated OT-I CD8+ T cells, biol rep 2

description:
Library name: N2
PE150


title: Recurrent Pregnancy Loss Patient 5


title: HC1-GMCSFl

description:
Library name: HC1-GMCSFl
scRNA-seq


title: HC1-MCSF

description:
Library name: HC1-MCSF
scRNA-seq


title: NR-treated OT-I CD8+ T cells, biol rep 1

description:
Library name: N1
PE150


title: WT, H3K9me3 ChIP, rep3

description:
Library name: Sample 3
NextSeq P3 100 cycle


title: WT, H3K9me3 ChIP, rep2

description:
Library name: Sample 2
NextSeq P3 100 cycle


title: Control OT-I CD8+ T cells, biol rep 2

description:
Library name: C2
PE150

value: vehicle control


title: Recurrent Pregnancy Loss Patient 4


title: HC1-Ctrl

description:
Library name: HC1-Ctrl
scRNA-seq


title: Control OT-I CD8+ T cells, biol rep 1

description:
Library name: C1
PE150


title: Recurrent Pregnancy Loss Patient 3


title: WT,H3K9me3 ChIP,rep1

description:
Library name: Sample 1
NextSeq P3 100 cycle


title: control embryo, 1dpf_n3

status: Public on Jun 18 2026

city: Hyderabad

first: Megha

last: Kumar

address: F202, Zebrafish facility, CSIR CCMB , HABSIGUDA

institute: CSIR-CCMB

description:
Library name: WT3
wild type replicate 2

data_processing:
Fastq files were checked for quiality using fastqc
Cutadapt was used for trimming adapters and filtering reads for qualiy and minimum length cutoff
Trimmed fastq reads were aligned to GRCz11 genome using STAR aligner, in quant mode inorder to generate count files along with the alignment files.
Read counts extracted, combined and downstream analysis were performed using the DESeq2 paclage in R
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Danio rerio

source_name: embryonic cell

extract_protocol:
The total RNA was extracted from 1dpf control and rapgef1b depleted embryos using an RNA isolation kit (MN; 740955.50). Sequencing libraries were generated using MGIEasy RNA library prep set (MGI) according to the manufacturer’s instructions. Here, 500 ng total RNA was used as starting material, and rRNA was depleted by MGIEasy rRNA depletion Kit. The rRNA-depleted samples were fragmented, reverse transcribed and the second strand was synthesized and converted to cDNA. DNA was then purified using DNA Clean Beads provided in the kit followed by end repair and A-tailing. Barcoding and adaptor ligation were performed and the samples were purified. Samples were amplified using adaptor-specific primers and quantified using a Qubit dsDNA high-sensitivity kit (ThermoScientific). Sample fragment size was determined using 4200 TapeStation (Agilent). 1pMol of the dsDNA library was denatured and circularized to make single-stranded circular DNA. DNA Nano Balls (DNBs) were created using Rolling cycle amplification. DNBs were loaded onto patterned flowcell and sequenced using PE100 recipe on MGISEQ-2000 sequencer (MGI).
Barcoding and adaptor ligation were performed and the samples were purified. Samples were amplified using adaptor-specific primers and quantified using a Qubit dsDNA high-sensitivity kit (ThermoScientific). Sample fragment size was determined using 4200 TapeStation (Agilent). 1pMol of the dsDNA library was denatured and circularized to make single-stranded circular DNA. DNA Nano Balls (DNBs) were created using Rolling cycle amplification. DNBs were loaded onto patterned flowcell and sequenced using PE100 recipe on MGISEQ-2000 sequencer (MGI).

value: embryonic cell

value: Wild type


title: control embryo, 1dpf_n2

description:
Library name: WT2
wild type replicate 2


title: control embryo, 1dpf_n1

description:
Library name: WT1
wild type replicate 1


title: rapgef1b KD embryo, 1 dpf_n3

description:
Library name: TK3
rapgef1b knocked down replicate 3

value: rapgef1b knockdown


title: Recurrent Pregnancy Loss Patient 1

value: products of conception (RPOC)  disease status:recurrent pregnancy loss

value: first trimester (8–12 weeks)


title: Recurrent Pregnancy Loss Patient 2

value: Agilent Human Reference DNA


title: rapgef1b KD embryo, 1 dpf_n2

description:
Library name: TK2
rapgef1b knocked down replicate 2


title: rapgef1b KD embryo, 1 dpf_n1

description:
Library name: TK1
rapgef1b knocked down replicate 1


title: NMOs_ZNF512B-KO_3

city: Odense M

first: Sanjeeb

middle: Kumar

last: Sahu

address: CAMPUSVEJ 55

department: Department of Molecular Medicine

country: Denmark

institute: University of Southern Denmark

description: Library name: ZNF512B-KO3

data_processing:
Raw sequencing data were quantified against the Ensembl GRCh38 (release 108) reference using alevin-fry to generate gene expression matrices. Downstream analyses were performed in Seurat v5 and visualized using ShinyCell. Low-quality cells with low gene counts or elevated mitochondrial transcript content, as well as scDblFinder predicted doublets were removed. Per-sample counts were normalized with SCTransform and integrated across replicates. Principal component analysis (PCA) and UMAP were computed on the integrated data for dimensionality reduction and visualization, and cell types were annotated based on established marker genes from prior studies.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: H9 ESCs derived

growth_protocol: H9 hESC lines were grown for at least three passages after thawing and after they reached 70% confluency, they were dissociated into single cells using accutase. Single cells were counted using the TC20 Automated Cell Counter (BIO-RAD) and were plated on 35mm dishes coated with Matrigel (BD Bioscience) at a density of 110000 / cm2. The first day the cells were plated in Neuro-mesodermal medium (NMD) supplemented with 10uM Rock inhibitor (Tocris Bioscience), 3uM CHIR99021 (Tocris Bioscience) and 40ng/ml bFGF (Peprotech). NMD medium is a 1:1 medium of Advanced Dulbecco’s Modified Eagle Medium F12 supplemented with 1x N2(GIBCO), and Neurobasal medium(GIBCO) supplemented with 1 x B27(GIBCO), 2mM L-glutamine(GIBCO), 75mg/ml BSA fraction V(Sigma), 0.1mM 2-mercaptoethanol(GIBCO). The next day Rock inhibitor was removed, and the cells were maintained in NMD medium supplemented with 3uM CHIR99021 and 40ng/ml bFGF (Peprotech) until day 3. The medium was changed every day. Neuromesodermal progenitors generated from human PSCs were dissociated using accutase to generate a single cell suspension. On day 0 of organoid formation, NMP cells (9,000/ well) were plated on an ultra-low binding 96-well U plate (Corning) in NMD medium with 50uM Rho-associated protein kinase ROCK inhibitor (Tocris Bioscience), 10ng/ml bFGF and 2ng/ml IGF1 and 2ng/ml HGF (Peprotech). The plates were centrifuged for 2 min at 350g. The initial volume in each well was 100ul. At day 2, 50ul of the medium was removed and 100ul of NMD medium supplemented with 2ng/ml IGF1 and HGF was added. After day 4 the organoids were maintained in NMD medium without the addition of growth factors. On day 10 the organoids were transferred in 60mm dishes (Corning) in 5 mL of medium and after 1 month in 100mm dishes (Corning) with 12 mL NMD medium. At day 50 organoids were collected for detail analysis.

extract_protocol:
Twenty neuromuscular organoids (NMOs) from each condition were randomly pooled and dissociated into single-cell suspensions based on previously published protocols. Briefly, organoids were washed with PBS and incubated in Versene at 37◦C for 10–20 min, followed by gentle trituration to obtain single cells. DNase I was included during dissociation to reduce cell clumping. Cell suspensions were filtered through a 40-μm cell strainer and viability was assessed by trypan blue exclusion, consistently exceeding 95%. Cells were resuspended in PBS containing 0.04% BSA at approximately 700 cells/μL and processed for library preparation using the Chromium Single Cell platform (10x Genomics) according to the manufacturer’s instructions. Single-cell RNA sequencing was performed using three independent biological replicates per condition.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: H9 ESCs derived

value: Neuromuscular organoids

value: ZNF512B knock out

value: Differenciated Neuromuscular organoids


title: NMOs_ZNF512B-KO_2

description: Library name: ZNF512B-KO2


title: NMOs_ZNF512B-KO_1

description: Library name: ZNF512B-KO1


title: NMOs_Control_1

description: Library name: Control-1

value: Control


title: MM196H3k27Ac vazyme REP1

city: Rome

first: Giacomo

last: Corleone

address: via chianesi 43

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

description: Library name: H3K27Ac-REP1-vazyme

data_processing:
Peaks built by applying nextflow standard cut&tag pipeline:  NXF_VER=24.10.0 nextflow run nf-core/cutandrun -r 3.2.1 - -profile docker --normalisation_mode CPM --peakcaller macs2
Assembly: HG38
Supplementary files format and content: MACS2 Command line: callpeak --nomodel --shift -75 --extsize 150 --keep-dup all -q 0.01 --gsize 2.7E+9 --format BAMPE
Library strategy: CUT&Tag

source_name: Bone Marrow

growth_protocol: optimem medium supplemented with 15% FBS inactived, 1% L-Glutamine and 0,1% Gentamicin. Cells were cultured at 37°C, in a humidified atmosphere with 5% CO2 and mycoplasma contamination was periodically checked by polymerase chain reaction (PCR) analysis.

extract_protocol: we followed the experimental procedure of the kits employed.

value: Bone Marrow

value: Plasma Cell CD138+


title: MM196 H3k27Ac vazyme REP2

description: Library name: H3K27Ac-REP2-vazyme


title: MM196 H3k27Ac epicypher REP2

description: Library name: H3k27Ac-REP2-epicypher


title: ctrl human brain

city: Turku

first: Pekka

last: Taimen

address: Kiinanmyllynkatu 10D

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description: Library name: Human Brain Total RNA AM7962 (ThermoFisher Scientific)

data_processing:
quality control and preprocessing, trimming minimum 35bp length
alignment with GRCm38.94 mouse reference genome
data filtered with, normalized
Assembly: alignment with GRCm38.94 mouse reference genome
Supplementary files format and content: LMNA-raw_countdata_final_Males.txt

source_name: human brain

extract_protocol:
mRNA isolation from tissue extracted from left ventricle of mouse heart
Ilumina TruSeq stranded RNA-seq libraries

value: human brain

value: control

tag: batch


title: Honeycomb HIVE scRNA-seq V1 (site 2)

city: Lebanon

first: Fred

middle: W.

last: Kolling IV

state: NH

address: 1 Medical Center Dr

department: Dartmouth Cancer Center

institute: Dartmouth College

description:
Library name: HC-V1-S1
Honeycomb Biotechnologies HIVE scRNA-seq chemistry V1; chemistry-comparison follow-up

data_processing:
10x Chromium FLEX libraries: processed with Cell Ranger multi (cellranger v7.0.1) against refdata-gex-GRCh38-2020-A with the Chromium Human Transcriptome Probe Set v1.0.
10x Chromium 3' Gene Expression libraries: processed with Cell Ranger count against refdata-gex-GRCh38-2020-A.
Honeycomb HIVE libraries: processed with the Honeycomb BeeNet pipeline.
Parse Biosciences libraries: processed with split-pipe v1.0.5 (--kit WT_mini --chemistry v2) against a GRCh38 reference.
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A for 10x; hg38 for Parse/Honeycomb)
Supplementary files format and content: [to be added with processed-data upload]
Supplementary files format and content: count matrices generated by vendor-provided pre-processing pipelines

source_name: Blood

growth_protocol: PBMCs from human donor

extract_protocol:
Human biological samples (fresh or DMSO-cryopreserved) were dissociated/thawed and processed per each platform's recommended workflow prior to single-cell capture.
Three single-cell RNA-seq platforms were compared on the same biological samples: (1) 10x Genomics Chromium Fixed RNA Profiling (FLEX) and Chromium Single Cell 3' Gene Expression v3 following manufacturer instructions; (2) Honeycomb Biotechnologies HIVE scRNA-seq (v1 and v2 chemistries) following manufacturer instructions; (3) Parse Biosciences Evercode WT_mini v2 combinatorial split-pool scRNA-seq following manufacturer instructions. All libraries were sequenced paired-end on an Illumina NovaSeq 6000.

treatment_protocol: RBC depletion using StemCell RBC removal kit

value: Blood

value: PBMCs

value: followup


title: Honeycomb HIVE scRNA-seq V2 (site 2)

description:
Library name: HC-V2-S2
Honeycomb Biotechnologies HIVE scRNA-seq chemistry V2; chemistry-comparison follow-up


title: 10x Chromium 3' Gene Expression v3 (site 2)

description:
Library name: 10X-3P
10x Genomics Chromium Single Cell 3' Gene Expression; chemistry-comparison follow-up


title: Honeycomb HIVE scRNA-seq, sample B (Stored, site 4)

description:
Library name: HC-20
Honeycomb Biotechnologies HIVE scRNA-seq

value: Total leukocytes

value: main


title: 10x Chromium FLEX (site 2)

description:
Library name: 10X-FLEX
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set; chemistry-comparison follow-up


title: Honeycomb HIVE scRNA-seq, sample A (Stored, site 4)

description:
Library name: HC-19
Honeycomb Biotechnologies HIVE scRNA-seq


title: Honeycomb HIVE scRNA-seq, sample B (Stored, site 3)

description:
Library name: HC-18
Honeycomb Biotechnologies HIVE scRNA-seq


title: Honeycomb HIVE scRNA-seq, sample B (Stored, site 2)

description:
Library name: HC-16
Honeycomb Biotechnologies HIVE scRNA-seq


title: Honeycomb HIVE scRNA-seq, sample A (Stored, site 2)

description:
Library name: HC-15
Honeycomb Biotechnologies HIVE scRNA-seq


title: Honeycomb HIVE scRNA-seq, sample B (Fresh, site 2)

description:
Library name: HC-14
Honeycomb Biotechnologies HIVE scRNA-seq


title: Honeycomb HIVE scRNA-seq, sample A (Fresh, site 2)

description:
Library name: HC-13
Honeycomb Biotechnologies HIVE scRNA-seq


title: Honeycomb HIVE scRNA-seq, sample B (Stored, site 1)

description:
Library name: HC-12
Honeycomb Biotechnologies HIVE scRNA-seq


title: 10x Chromium FLEX, sample B (Stored, site 4)

description:
Library name: 10x-30
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample A (Stored, site 3)

description:
Library name: 10x-27
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample B (Stored, site 3)

description:
Library name: 10x-28
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample A (Stored, site 2)

description:
Library name: 10x-25
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample A (Fresh, site 2)

description:
Library name: 10x-23
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample B (Stored, site 1)

description:
Library name: 10x-22
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample B (Fresh, site 2)

description:
Library name: 10x-24
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample A (Stored, site 1)

description:
Library name: 10x-21
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: HT-29 IL-32 KO TNF+IFN, biol rep 2

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

description: Library name: 36

data_processing:
Transcript-level quantification was performed using Kallisto v0.50.1 against the Homo sapiens GRCh38 release 108 transcriptome index.
Transcript counts were summarized to gene level using tximport.
Genes with at least 1 CPM in 2 or more samples were retained.
Raw counts were normalized using the voom method from the limma Bioconductor package (log2-CPM).
Assembly: GRCh38.108
Supplementary files format and content: comma-separated text file includes raw gene-level counts for each sample
Supplementary files format and content: comma-separated text file includes voom-normalized log2-CPM values for each sample

growth_protocol: The HT-29 intestinal epithelial cell (IEC) line (ATCC HTB-38) was grown in McCoy's medium (ATCC 30-2007), supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin (GIBCO), at 37 degrees C and 5% CO2. Cells were seeded in 75 cm2 flasks and harvested at confluence (~95%) using 0.05% trypsin/EDTA. Experiments were conducted with cells between passage 3 and 10.

extract_protocol:
Cells were harvested and total RNA was extracted using the All Prep DNA/RNA/miRNA Universal Kit (#80224, Qiagen, MD, USA).
polyA-enriched stranded RNA libraries were prepared. 100 bp paired-end sequencing (PE100, 25M reads) was performed on an Illumina NovaSeq 6000 at the McGill University and Genome Quebec Innovation Centre (Montreal, QC, Canada).

treatment_protocol: CRISPR-Cas9-edited (IL32 KO) or control HT-29 IEC were plated in 48-well plates (10^5 cells/well) and exposed to human recombinant cytokines: hrTNF-a (10 ng/mL) and/or hrIFN-b1a (50 U/mL) (R&D Systems), or medium alone, for 18 hours.

tag: crispr

value: IL-32 CRISPR

tag: stimulation

value: TNF-a+IFN-b


title: HT-29 IL-32 KO IFN-I, biol rep 2

description: Library name: 35

value: IFN-b


city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: sciplex_TTNhet_TTNhom_PB10.5WT_hiPSC_cardiac_monolayers

data_processing:
Sequenced read were processed, aligned to human genome (GRCh38.96/hg38), counted and filtered using sci-RNA-seq3 method (Srivatsan SR et al., Science, 2020)
Assembly: GRCh38.96/hg38
Supplementary files format and content: Three RDS files: 1) Seurat object for TTN heterozygous (TTNhet) with PB10.5 (WT) and 2) Seurat object for TTN homozygous (TTNhom) with PB10.5 (WT) hiPSC-derived cardiac monolayers and 3) a Seurat object prior to gene filtering.

molecule: nuclear RNA

source_name: TTN heterozygous(TTNhet), TTN homozygous(TTNhom), and PB10.5 (WT) hiPSC-derived cardiac monolayers

extract_protocol:
Single-nucleus isolation and single-nucleus RNA-seq libraries were generated using three-level single-nucleus combinatorial indexing RNA sequencing (sci-RNA-seq) across TTN heterozygous, TTN homozygous, and PB10.5 (WT) conditions. Nuclei were hashed and pooled prior to sci-RNA-seq using a nuclear barcoding strategy, in which fixed barcodes carrying well-specific oligonucleotides were assigned to individual technical replicates (Srivatsan et al., Science, 2020)
Single-nucleus RNA-seq libraries were generated using three-level single-nucleus combinatorial indexing RNA sequencing (sci-RNA-seq) (Srivatsan SR et al., Science, 2020)

value: Cardiomyocte, Proliferative Cardiomyocyte and Fibroblast

value: TTN heterozygous (TTNhet), TTN homozygous (TTNhom), and PB10.5 (WT)


title: HT-29 IL-32 KO TNF, biol rep 2

description: Library name: 34

value: TNF-a


title: HT-29 IL-32 KO MEDIUM, biol rep 2

description: Library name: 33

value: Medium


title: HT-29 CTL IFN-I, biol rep 2

description: Library name: 31

value: CTL CRISPR


title: HT-29 CTL TNF, biol rep 2

description: Library name: 30


title: HT-29 CTL MEDIUM, biol rep 2

description: Library name: 29


title: HT-29 IL-32 KO TNF+IFN, biol rep 1

description: Library name: 20


title: HT-29 IL-32 KO IFN-I, biol rep 1

description: Library name: 19


title: HT-29 IL-32 KO MEDIUM, biol rep 1

description: Library name: 17


title: HT-29 IL-32 KO TNF, biol rep 1

description: Library name: 18


title: HT-29 CTL IFN-I, biol rep 1

description: Library name: 15


title: HT-29 CTL TNF, biol rep 1

description: Library name: 14


title: MiaPaCa2_PPP2R1A_KD_3

city: Göttingen

first: Nignjun

last: Duan

address: Robert-Koch-Straße 40

country: Germany

institute: Universitätsmedizin Göttingen

description: Library name: C-KD-22-1

data_processing:
Raw read quality was checked with FastQC, mapping to the reference gemone with STAR, and quantified with Stringtie.
Assembly: GCRH38
Supplementary files format and content: The processed file is a CSV file contains raw counts of each sample.

growth_protocol: To obtain mRNA for RNA sequencing, cells were seeded into 6-well plates in 2 mL of respective medium per well. The seeding number was adjusted to ensure that the cells reached a maximum of 60% confluency after 2 days of incubation at cell culture conditions.

extract_protocol:
The cells were lysed by adding 100 μL of RL Lysis Buffer from the innuPREP RNA Mini Kit 2.0 to each well. Cell lysates were processed by the manufacturer’s instructions from the kit mentioned above. RNA concentrations were measured using the DS-11+ Spectrophotometer (DeNovix). The samples were then stored at -80°C until further use.
RNA-seq library is constructed with a TruSeq RNA library preparation kit following relevant protocol.

value: pancreatic cancer cell line

value: KD


title: MiaPaCa2_PPP2R1A_KD_1

description: Library name: C-KD-8-1


title: MiaPaCa2_CCRX_ctrl_3

description: Library name: CCRX-22-1

value: WT


title: Dam_54h_Sample41_batch2

city: Newton

first: Matt

last: Kanke

state: MA - Massachusetts

address: 112 Harding Street

institute: Amgen

description: Library name: 30165_C_Colon_Adcrcnma_Trtd

data_processing:
Raw sequencing reads were aligned to the human genome reference (Human.B38) using the OSA aligner (Qiagen Omicsoft). Aligned reads were collapased into gene-level counts using Omicsoft’s RSEM implementation and the genomic locations in the GENCODE v33 gene model. Data analysis was performed using the Ingenuity Pathway Analysis (IPA) package (Qiagen).
Assembly: Human.B38 Gencode v33
Supplementary files format and content: batch1_primary_count_gene.Counts.Table.txt
Supplementary files format and content: batch2_primary_count_gene.Counts.Table.txt

growth_protocol: The human colorectal adenocarcinoma cell line Caco-2 expressing Cas9 was purchased from UBIGENE Biosciences Co., Ltd (Guangzhou, China). Cells were maintained in 77% minimum essential media (Gibco) supplemented with 20% heat inactivated fetal bovine serum (Sigma Aldrich), 1% Glutamax, 1% Sodium pyruvate, 1% non-essential amino acids (Gibco) and 100 μg/ml hygromycin (Gibco) in a humidified atmosphere (37⁰C and 5% CO2). For differentiation, cells were seeded at 8x104 cells/200μl on 0.4μm pores polyester HTS transwell membrane (Corning-Costar, Acton, MA) and grown as monolayers.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and 800ng of RNA was reverse transcribed with cDNA synthesis master mix (Legene Biosciences,CA, USA).
Sequencing libraries were constructed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) and IDT for Illumina-TruSeq RNA UD Indexes. Libraries were sequenced on a NovaSeqX to a minimum depth of 35 million reads.

treatment_protocol: After 12 days, recombinant human TNF-α and human IFN-γ were treated to both apical and basal chamber for 0h (N = 4 per group), 6h (N=7~8 per group), 9h (N=7 per group), 18h (N=4 per group), 30h (N=8 per group) and 54h (N=8 per group). For 3D microfluidic model system, OrganoReady Colon Caco-2 (Mimetas BV, The Netherlands) comprising 64 ready-to-use Caco-2 seeded against collagen I was used.


title: Dam_54h_Sample43_batch2

description: Library name: 30166_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample38_batch2

description: Library name: 30164_C_Colon_Adcrcnma_Trtd


title: Dam_30h_Sample36_batch2

description: Library name: 30163_C_Colon_Adcrcnma_Trtd


title: Dam_30h_Sample34_batch2

description: Library name: 30162_C_Colon_Adcrcnma_Trtd


title: Con_30h_Sample32_batch2

description: Library name: 30161_C_Colon_Adcrcnma_Trtd


title: Dam_18h_Sample28_batch2

description: Library name: 30159_C_Colon_Adcrcnma_Trtd


title: Dam_18h_Sample25_batch2

description: Library name: 30157_C_Colon_Adcrcnma_Trtd


title: Con_18h_Sample23_batch2

description: Library name: 30156_C_Colon_Adcrcnma_Trtd


title: Con_18h_Sample21_batch2

description: Library name: 30155_C_Colon_Adcrcnma_Trtd


title: Dam_18h_Sample27_batch2

description: Library name: 30158_C_Colon_Adcrcnma_Trtd


title: Dam_9h_Sample19_batch2

description: Library name: 30154_C_Colon_Adcrcnma_Trtd


title: Dam_9h_Sample18_batch2

description: Library name: 30153_C_Colon_Adcrcnma_Trtd


title: Dam_9h_Sample17_batch2

description: Library name: 30152_C_Colon_Adcrcnma_Trtd


title: Con_9h_Sample16_batch2

description: Library name: 30151_C_Colon_Adcrcnma_Trtd


title: Con_9h_Sample14_batch2

description: Library name: 30150_C_Colon_Adcrcnma_Trtd


title: Dam_6h_Sample12_batch2

description: Library name: 30149_C_Colon_Adcrcnma_Trtd


title: Con_6h_Sample8_batch2

description: Library name: 30147_C_Colon_Adcrcnma_Trtd


title: Dam_6h_Sample10_batch2

description: Library name: 30148_C_Colon_Adcrcnma_Trtd


title: Con_6h_Sample6_batch2

description: Library name: 30146_C_Colon_Adcrcnma_Trtd


title: Con_0h_Sample1_batch2

description: Library name: 30143_C_Colon_Adcrcnma_Trtd


title: Dam_54h_Sample44_batch2

description: Library name: 30142_C_Colon_Adcrcnma_Trtd


title: Dam_54h_Sample42_batch2

description: Library name: 30141_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample40_batch2

description: Library name: 30140_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample39_batch2

description: Library name: 30139_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample37_batch2

description: Library name: 30138_C_Colon_Adcrcnma_Trtd


title: Dam_30h_Sample35_batch2

description: Library name: 30137_C_Colon_Adcrcnma_Trtd


title: Dam_30h_Sample33_batch2

description: Library name: 30136_C_Colon_Adcrcnma_Trtd


title: Con_30h_Sample31_batch2

description: Library name: 30135_C_Colon_Adcrcnma_Trtd


title: NMOs_Control_3

description: Library name: Control-3

value: H9 ESCs derived

value: Neuromuscular organoids

value: Control

value: Differenciated Neuromuscular organoids


title: NMOs_Control_2

description: Library name: Control-2


title: MM196 H3k27Ac epicypher REP1

description: Library name: H3k27Ac-REP1-epicypher

value: Bone Marrow

value: Plasma Cell CD138+


title: Con_6h_Sample5_batch2

description: Library name: 30145_C_Colon_Adcrcnma_Trtd


title: Con_30h_Sample29_batch2

description: Library name: 30134_C_Colon_Adcrcnma_Trtd


title: Con_0h_Sample3_batch2

description: Library name: 30144_C_Colon_Adcrcnma_Trtd


title: Parse Biosciences Evercode WT_mini v2 (site 2)

description:
Library name: PARSE
Parse Biosciences Evercode WT_mini v2 combinatorial split-pool scRNA-seq; one sublibrary multiplexing 12 biological samples (well positions A1-A12); processed with split-pipe v1.0.5

value: Blood

value: PBMCs

value: followup


title: Dam_18h_Sample26_batch2

description: Library name: 30133_C_Colon_Adcrcnma_Trtd


title: Honeycomb HIVE scRNA-seq, sample A (Stored, site 3)

description:
Library name: HC-17
Honeycomb Biotechnologies HIVE scRNA-seq

value: Total leukocytes

value: main


title: Con_18h_Sample22_batch2

description: Library name: 30131_C_Colon_Adcrcnma_Trtd


title: Con_9h_Sample15_batch2

description: Library name: 30129_C_Colon_Adcrcnma_Trtd


title: Con_18h_Sample24_batch2

description: Library name: 30132_C_Colon_Adcrcnma_Trtd


title: Dam_9h_Sample20_batch2

description: Library name: 30130_C_Colon_Adcrcnma_Trtd


title: Dam_6h_Sample11_batch2

description: Library name: 30127_C_Colon_Adcrcnma_Trtd


title: Dam_6h_Sample9_batch2

description: Library name: 30126_C_Colon_Adcrcnma_Trtd


title: Con_9h_Sample13_batch2

description: Library name: 30128_C_Colon_Adcrcnma_Trtd


title: 10x Chromium FLEX, sample B (Stored, site 2)

description:
Library name: 10x-26
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: 10x Chromium FLEX, sample A (Stored, site 4)

description:
Library name: 10x-29
10x Genomics Chromium Fixed RNA Profiling (FLEX), human probe set


title: Honeycomb HIVE scRNA-seq, sample A (Stored, site 1)

description:
Library name: HC-11
Honeycomb Biotechnologies HIVE scRNA-seq


title: Con_6h_Sample7_batch2

description: Library name: 30125_C_Colon_Adcrcnma_Trtd


title: Con_0h_Sample4_batch2

description: Library name: 30124_C_Colon_Adcrcnma_Trtd


title: Con_0h_Sample2_batch2

description: Library name: 30123_C_Colon_Adcrcnma_Trtd


title: Dam_54h_Sample28_batch1

description: Library name: 19774_C_Colon_Adcrcnma_Trtd


title: Dam_54h_Sample27_batch1

description: Library name: 19773_C_Colon_Adcrcnma_Trtd


title: Dam_54h_Sample29_batch1

description: Library name: 19775_C_Colon_Adcrcnma_Trtd


title: Dam_54h_Sample26_batch1

description: Library name: 19772_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample25_batch1

description: Library name: 19771_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample24_batch1

description: Library name: 19770_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample23_batch1

description: Library name: 19769_C_Colon_Adcrcnma_Trtd


title: Dam_30h_Sample21_batch1

description: Library name: 19767_C_Colon_Adcrcnma_Trtd


title: Con_54h_Sample22_batch1

description: Library name: 19768_C_Colon_Adcrcnma_Trtd


title: HT-29 CTL TNF+IFN, biol rep 2

description: Library name: 32

value: TNF-a+IFN-b


title: Dam_30h_Sample20_batch1

description: Library name: 19766_C_Colon_Adcrcnma_Trtd


title: Dam_30h_Sample19_batch1

description: Library name: 19765_C_Colon_Adcrcnma_Trtd


title: Dam_30h_Sample18_batch1

description: Library name: 19764_C_Colon_Adcrcnma_Trtd


title: Con_30h_Sample17_batch1

description: Library name: 19763_C_Colon_Adcrcnma_Trtd


title: Con_30h_Sample16_batch1

description: Library name: 19762_C_Colon_Adcrcnma_Trtd


title: Con_30h_Sample15_batch1

description: Library name: 19761_C_Colon_Adcrcnma_Trtd


title: Con_30h_Sample14_batch1

description: Library name: 19760_C_Colon_Adcrcnma_Trtd


title: Dam_9h_Sample13_batch1

description: Library name: 19759_C_Colon_Adcrcnma_Trtd


title: Dam_9h_Sample11_batch1

description: Library name: 19757_C_Colon_Adcrcnma_Trtd


title: Dam_9h_Sample12_batch1

description: Library name: 19758_C_Colon_Adcrcnma_Trtd


title: Con_9h_Sample10_batch1

description: Library name: 19756_C_Colon_Adcrcnma_Trtd


title: Con_9h_Sample9_batch1

description: Library name: 19755_C_Colon_Adcrcnma_Trtd


title: 22531-72

city: North Brunswick Township

first: Jia

last: Xu

state: NJ

address: 675 US Highway One

institute: Genomic Prediction, Inc.

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #22 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

data_processing:
Affymetrix UK Biobank Axiom Array Manufacturer's Protocol
Primary data description: DNA copy number and genotyping

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day d4

growth_protocol: Thawing of human 2PN zygotes was performed using the Qinn's Advantage warming kit or using a one-step protocol with GMOPS-plus depending on the method of cryopreservation. Donated oocytes were warmed using the Cryotech warming kit. Embryos were cultured in Global total.

extract_protocol: Single cells, single polar bodies, or cytoplasmic fragments were placed into single PCR tubes containing 2 ul of Genomic Prediction's loading Buffer. Genomic DNA amplification was performed using amplification kit as indicated for each sample.

treatment_protocol: Cas9 or ABE ribonucleoprotein complex was assembled in vitro and injected at fertilization or at the 1-cell stage of embryo development. Zygotes were either at the 2PN stage or at the entry into the first mitosis.

value: Preimplantation embryo


title: HT-29 CTL TNF+IFN, biol rep 1

description: Library name: 16

value: CTL CRISPR


title: male, normal diet, replicate 4

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

description: Library name: MNC4

data_processing:
Raw sequence data were processed using the nf-core RNA-Seq pipeline (version 3.19.0). Reads were aligned to the GRCm39 mouse reference genome using the STAR aligner and gene quantification was performed against the GENCODE vM37 primary assembly annotation with RSEM to obtain gene expression counts.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file that includes counts/TPM for each gene and sample

source_name: liver

extract_protocol:
Total RNA was isolated from approximately 20 mg of homogenized whole-liver powder using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
1 µg of total RNA per sample was submitted to Azenta Life Sciences for library preparation using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) followed by sequencing on the NovaSeq platform (Illumina).

treatment_protocol: Male and female C57BL/6J mice (Jackson Laboratory, #000664) were obtained at 6 weeks of age and assigned to either a normal chow (NC; LabDiet 5053; 4.5% of calories from fat) or a high fat (HF; Research Diets, D12492; 60% of calories from fat) diet for 10 weeks. Mice were group-housed in a temperature-controlled room with ad libitum access to food and water under a 12 h light/12 h dark cycle (lights on at 07:00, Zeitgeber time 0).

value: liver

value: wt

value: normal diet


title: 22531-69

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #19 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

hyb_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4


title: HT-29 CTL MEDIUM, biol rep 1

description: Library name: 13

value: Medium


title: Con_9h_Sample8_batch1

description: Library name: 19754_C_Colon_Adcrcnma_Trtd


title: 22531-70

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #20 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

scan_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol


title: Tumor, Tall Cell Variant

city: Los Angeles

first: Anthony

last: Nguyen

address: 8700 Beverly Blvd, Department of Radiation Oncology

institute: Cedars-Sinai Medical Center

description: Library name: 1B

data_processing:
Demultiplexed fastq files for gene expression libraries were processed by Cellranger (v4.0.0)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Cell Ranger output files : filtered_feature_bc_matrix.h5

source_name: Tumor

extract_protocol:
Following CD45-positive selection, samples were diluted to 1000 cells/uL and processed according to the Single Cell 3’ v1 assay (10x Genomics) with a targeted 10,000 cell recovery.
Gene expression libraries were prepared according to the Single Cell 3’ v1 protocol (10x Genomics) and were sequenced using paired-end 150bp reads on the Novaseq 6000 (Illumina) through the CSMC Applied Genomics, Computation & Translational Core

value: Tumor


title: Dam_6h_Sample7_batch1

description: Library name: 19753_C_Colon_Adcrcnma_Trtd


title: Dam_6h_Sample6_batch1

description: Library name: 19752_C_Colon_Adcrcnma_Trtd


title: MiaPaCa2_PPP2R1A_KD_2

description: Library name: C-KD-15-1

value: pancreatic cancer cell line

value: KD


title: Con_6h_Sample4_batch1

description: Library name: 19750_C_Colon_Adcrcnma_Trtd


title: Dam_6h_Sample5_batch1

description: Library name: 19751_C_Colon_Adcrcnma_Trtd


title: Con_6h_Sample3_batch1

description: Library name: 19749_C_Colon_Adcrcnma_Trtd


title: Con_6h_Sample2_batch1

description: Library name: 19748_C_Colon_Adcrcnma_Trtd


title: MiaPaCa2_CCRX_ctrl_2

description: Library name: CCRX-15-1

value: WT


title: Con_6h_Sample1_batch1

description: Library name: 19747_C_Colon_Adcrcnma_Trtd


title: PANC1 Day14 replicate 3

city: Heidelberg

first: Gong

last: Chen

state: Baden-Württemberg

address: Im Neuenheimer Feld 420

department: Department of General, Visceral & Transplant Surgery

institute: University of Heidelberg

description:
Library name: PANC1_D14_3
Bulk RNA-seq after 14 days osteogenic induction

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapter trimming and quality filtering were performed using TrimGalore.
Assembly: GRCh38 (GENCODE annotation). Raw reads were aligned to the human reference genome, and gene-level expression values were derived for downstream analysis.
Supplementary files format and content: Excel files containing gene-level
Supplementary files format and content: expression matrices (log2 CPM) derived from bulk RNA-seq analysis.

source_name: pancreas

growth_protocol: Pancreatic cancer cell lines (Capan-2, PANC-1) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit 21 days post-induction. Samples with an A260/A280 ratio between 1.8-2.0 as determined by NanoDrop were selected for subsequent experiments. cDNA was synthesized using the High-Capacity cDNA Reverse Transcription Kit.
mRNA was enriched using oligo(dT) magnetic beads followed by fragmentation. First- and second-strand cDNA synthesis was performed, and sequencing libraries were constructed using the Illumina TruSeq mRNA Library Preparation Kit following the manufacturer’s protocol. Libraries were subjected to PCR amplification and size selection prior to sequencing.

treatment_protocol: Cells were cultured in osteogenic induction medium (NH OsteoDiff medium, Miltenyi Biotec, Bergisch Gladbach, Germany) for 7 or 14 days. Control groups were maintained in standard culture medium without osteogenic supplements.

value: pancreas

value: epithelial cell

value: wild-type


title: PANC1 Day14 replicate 2

description:
Library name: PANC1_D14_2
Bulk RNA-seq after 14 days osteogenic induction


title: PANC1 Control replicate 3

description:
Library name: PANC1_con_3
Bulk RNA-seq of PANC1 control

value: Control


title: PANC1 Day7 replicate 2

description:
Library name: PANC1_D7_2
Bulk RNA-seq after 7 days osteogenic induction


title: PANC1 Day7 replicate 1

description:
Library name: PANC1_D7_1
Bulk RNA-seq after 7 days osteogenic induction


title: PANC1 Day7 replicate 3

description:
Library name: PANC1_D7_3
Bulk RNA-seq after 7 days osteogenic induction


title: PANC1 Control replicate 2

description:
Library name: PANC1_con_2
Bulk RNA-seq of PANC1 control


title: Capan-2 Day14 replicate 3

description:
Library name: Capan2_D14_3
Bulk RNA-seq after 14 days osteogenic induction


title: Capan-2 Day14 replicate 2

description:
Library name: Capan2_D14_2
Bulk RNA-seq after 14 days osteogenic induction


title: PANC1 Control replicate 1

description:
Library name: PANC1_con_1
Bulk RNA-seq of PANC1 control


title: Capan2 Control replicate 3

description:
Library name: Capan2_con_3
Bulk RNA-seq of Capan-2 control


title: Capan-2 Day7 replicate 2

description:
Library name: Capan2_D7_2
Bulk RNA-seq after 7 days osteogenic induction


title: Capan-2 Day7 replicate 3

description:
Library name: Capan2_D7_3
Bulk RNA-seq after 7 days osteogenic induction


title: Capan-2 Day7 replicate 1

description:
Library name: Capan2_D7_1
Bulk RNA-seq after 7 days osteogenic induction


title: Capan2 Control replicate 2

description:
Library name: Capan2_con_2
Bulk RNA-seq of Capan-2 control


title: N/P(14) rep2

city: Taipei

first: Tsung-Han

last: Hsieh

address: XinYi dist.,WuXing Street, No.250.

country: Taiwan

institute: Taipei Medical University

description: Library name: sample 4

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using STAR v2.7.2b
Reads number were calculated using RSEM v1.3.1.
Assembly: Hg19
Supplementary files format and content: Matrix table with raw count for every gene and every sample

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Life Technologies, Invitrogen, Carlsbad, CA), according to the manufacturer's instructions
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA protocols

value: untreat


title: Capan2 Control replicate 1

description:
Library name: Capan2_con_1
Bulk RNA-seq of Capan-2 control


title: HUVEC premature senescence replicate 1

city: Kyoto

first: Tomoya

last: Kitani

address: 465 Kajii-cho Kawaramachi-Hirokoji Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description:
Library name: HUVEC_PreSen_1
premature senescence

data_processing:
Reads were trimmed using Trim Galore, aligned to the GRCh38 genome using STAR, and quantified using featureCounts.
Assembly: GRCh38 (GENCODE release 44)
Supplementary files format and content: Gene-level count matrix with one column per sample and one row per gene.

source_name: HUVEC

growth_protocol: HUVECs were cultured in EGM-2 medium at 37°C and 5 percent CO2.

extract_protocol:
Total RNA was extracted with the Zymo Quick-RNA Miniprep Kit according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Exome kit.

treatment_protocol: Premature senescence was induced by retroviral overexpression of TRF2ΔBΔM. Replicative senescence was generated by repeated passaging until growth arrest.

value: HUVEC

value: endothelial cell

value: TRF2 mutant overexpression


title: HUVEC premature senescence replicate 2

description:
Library name: HUVEC_PreSen_2
premature senescence


title: HUVEC young replicate 3

description:
Library name: HUVEC_Young_3
young control


title: HUVEC young replicate 2

description:
Library name: HUVEC_Young_2
young control


title: HUVEC young replicate 1

description:
Library name: HUVEC_Young_1
young control


title: HUVEC replicative senescence replicate 3

description:
Library name: HUVEC_RepSen_3
replicative senescence

value: replicative senescence


title: HUVEC replicative senescence replicate 2

description:
Library name: HUVEC_RepSen_2
replicative senescence


title: VCaP_DALTAC_3_3h_ERG

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

description: Library name: SI_42209

data_processing:
ChIP-seq reads were trimmed using Trimmomatic (v0.39, settings TruSeq3-PE-2.fa:2:30:10, minlen 50). Alignment was then performed separately to both the human genome (hg38) and the drosophila genome (dm6) using BWA (v0.7.17 “bwa mem”, options -5S -T0, version 0.7.17-r1198-dirty). Low-quality and duplicate reads were filtered with SAMtools and Picard, respectively. Normalization ratios were calculated based on the lowest amount of uniquely aligned reads per ChIP target to each genome as reccomended in ActiveMotifs protocols. Reads were then downsampled per the normalization ratios. P300 Samples did not have this normalization step. Then peak calling was performed with MACS2 using narrow or broad settings depending on the target, and blacklisted genomic regions were removed using BEDTools with the ENCODE exclusion list. MACS was run with a bam vcap IgG control. Processed data were converted to BigWig format using UCSC wigToBigWig for visualization. Read density heatmaps and average enrichment profiles were generated using deepTools. For histone marks, signals were plotted within ±2.5 kb of the reference point, and for other transcriptome factors within ±1 kb. The parameters --skipZeros, --averageType mean, and --plotType se were applied. ENCODE blacklist regions (ENCFF356LFX) were excluded from analysis.
Assembly: hg38
Supplementary files format and content: .bed: peak locations from macs bed calling with blacklist removed; .bw: signal files

source_name: VCaP

growth_protocol: VCaP cells were maintained in DMEM GlutaMAX supplemented with 10% FBS (Thermo Fisher Scientific).

extract_protocol:
In brief, cells were crosslinked in 1% formaldehyde, quenched with glycine, and lysed for chromatin extraction. Chromatin was sheared to 200–600 bp fragments using a Bioruptor (Diagenode) and subjected to immunoprecipitation with antibodies against transcription factors (AR, FOXA1, p300, ERG and BRD4) or histone marks (H3K27ac, H2BK20ac, and RNA Pol II) using the iDeal ChIP-seq Kit (Diagenode). Drosophila spike-in chromatin (Active Motif, 53083) and spike-in antibody (Active Motif, 61686) were added during the overnight incubation. After reverse crosslinking and DNA purification, sequencing libraries were prepared and sequenced on an Illumina HiSeq 2500 platform.
ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: The cells were treated with 100 nM DALTAC-1 or p300i+ARi for 1 and 3 hours

value: VCaP

value: prostate cancer

value: 100 nM DALTAC-1 3h


title: VCaP_DALTAC_3_1h_ERG

description: Library name: SI_42208

value: 100 nM DALTAC-1 1h


title: VCaP_DMSO_ERG

description: Library name: SI_42205

value: DMSO


title: Vehicle-treated BMDN Input ChIP-Seq 2

city: Suzhou

first: Xiaoqin

last: Yang

address: NO. 199 Renai Road

institute: Soochow University

description: Library name: Vehicle-treated BMDN Input ChIP-Seq 2

data_processing:
Reads were aligned to the reference genome (mm10) using Bowtie2. Subsequently, duplicates, multi mapping reads, and low quality alignments were removed using SAMtools. Mitochondrial reads, chromosome Y alignments, and ENCODE blacklisted genomic regions were excluded. Peaks were called using MACS3 with the settings -f BAMPE -B --nomodel --SPMR --keep-dup 1. For histone modification ChIP-Seq, peak calling was performed  with --broad option enabled.
Assembly: mm10
Supplementary files format and content: bigWig signal tracks generated from MACS3 callpeak bedGraph outputs with --SPMR using merged biological replicates for each condition (except for Input samples)

source_name: neutrophil

extract_protocol:
The chromatin immunoprecipitation (ChIP) protocol was performed to analyze histone modifications. Briefly, cells were collected and treated with 1% formaldehyde for 10 minutes at room temperature to induce crosslinking. After sonication, an anti-H3K36me2 antibody was used for immunoprecipitation, and then the DNA was extracted and purified using the Universal DNA Purification Kit.
Libraries were constructed from ChIP samples using the VAHTS Universal DNA Library Prep Kit for Illumina V3 and then sequenced on the NovaSeq X platform by Annoroad Gene Tech (Beijing) Co., Ltd.

value: neutrophil


title: VCaP_100nM_DALTAC_1_1h_BRD4

description: Library name: SI_41276


title: VCaP_100nM_DALTAC_1_3h_BRD4

description: Library name: SI_41278


title: VCaP_100nM_DALTAC_1_1h_POL2

description: Library name: SI_41146


title: VCaP_100nM_DALTAC_1_3h_POL2

description: Library name: SI_41147


title: VCaP_100nM_DALTAC_1_3h_AR

description: Library name: SI_41141


title: VCaP_DMSO_AR

description: Library name: SI_41139


title: VCaP_100nM_DALTAC_1_1h_FOXA1

description: Library name: SI_40690


title: NTUB1 rep1

description: Library name: sample 1


title: VCaP_DMSO_FOXA1

description: Library name: SI_40689


title: VCaP_100nM_DALTAC_1_3h_FOXA1

description: Library name: SI_40692


title: VCaP_100nM_DALTAC_1_3h_P300

description: Library name: SI_40570


title: VCaP_100nM_DALTAC_1_3h_H2BK20ac

description: Library name: SI_40565


title: VCaP_100nM_P300i_ARi_3h_H2BK20ac

description: Library name: SI_40566


title: VCaP_100nM_DALTAC_1_1h_H2BK20ac

description: Library name: SI_40563


title: VCaP_100nM_p300i_ARi_1h_H2BK20ac

description: Library name: SI_40564


title: VCaP_100nM_P300i_ARi_3h_H3K27ac

description: Library name: SI_40561


title: VCaP_DMSO_H2BK20ac

description: Library name: SI_40562


title: VCaP_100nM_P300i_ARi_1h_H3K27ac

description: Library name: SI_40559


title: VCaP_DMSO_P300

description: Library name: SI_34976


title: VCaP_100nM_DALTAC_1_1h_H3K27ac

description: Library name: SI_40558


title: VCaP_100nM_ARi_p300i_24hr_Rep2

description: Library name: SI_40729

data_processing:
Alignment was  performed using kalliso (v0.46.1) quant to human (hg38/GRCh38) reference (Homo_sapiens.GRCh38.96.gtf gene reference). Read counts were adjusted for normalization then filtered in R via package EdgeR. Package Limma-Voom (vlimma_3.53.10) was involved for differential expression analysis. GSEA analysis and corresponding heatmaps and figures were created using R package fgsea (vfgsea_1.24.0), ComplexHeatmap and ggplot2.
Assembly: hg38
Supplementary files format and content: Counts Matrix

extract_protocol:
Total RNA was extracted from cells using QIAzol Lysis Reagent (QIAGEN). Initially, 1x10^6 cells were lysed with 700 µL of QIAzol. The lysates were incubated at room temperature for 5 minutes to dissociate nucleoproteins, then mixed with 140 µL chloroform and centrifuged at 12,000 g for 15 minutes at 4°C to achieve phase separation. The aqueous phase was then mixed with 1.5x volume of ethanol and applied to a RNeasy Mini spin column (QIAGEN) for RNA purification, following the miRNeasy Mini Kit protocol. The RNA was then eluted in RNase-free water, and its concentration and purity assessed using a NanoDrop spectrophotometer.
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. PolyA+ RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2 × 100 nucleotide read length) with sequence coverage to 15–20M paired reads.

treatment_protocol: The cells were treated with 100 nM DALTAC-1 or p300i+ARi for 4, 12 and 24 hours


title: VCaP_DMSO_H3K27ac

description: Library name: SI_40557


title: VCaP_100nM_DALTAC_1_24hr_Rep2

description: Library name: SI_40727


title: VCaP_100nM_ARi_p300i_12hr_Rep2

description: Library name: SI_40725


title: VCaP_100nM_ARi_p300i_24hr_Rep1

description: Library name: SI_40728


title: VCaP_100nM_DALTAC_1_24hr_Rep1

description: Library name: SI_40726


title: VCaP_100nM_DALTAC_1_12hr_Rep1

description: Library name: SI_40722


title: NTUB1 rep2

description: Library name: sample 2


title: VCaP_100nM_DALTAC_1_4hr_Rep2

description: Library name: SI_40719


title: VCaP_100nM_p300i_ARi_4hr_Rep2

description: Library name: SI_40721


title: VCaP_DMSO_Rep2

description: Library name: SI_40717


title: VCaP_100nM_DALTAC_1_4hr_Rep1

description: Library name: SI_40718


title: sorted Tscm cells, RA6

city: Seoul

first: Eun Bong

last: Lee

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University Hospital

description: Library name: RA6

data_processing:
The fastq files were aligned to the human reference genome (GRCh38-2020-A) by using the CellRanger count command (version 7.1.0).
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using density gradient centrifugation. Cells were washed with PBS, stained with Tscm marker dye (CD3, CCR7, CD45RA, CD27, CD95), washed and resuspended in FACS buffer (1% v/v FBS in PBS). Tscm cells were sorted (CD3+CCR7+CD45RA+CD27+CD95high) by fluorescence-activated cell sorting (FACS) using a FACSAria III instrument (BD Biosciences). The sorted Tscm cells were washed in FACS buffer and subsequently used for single-cell RNA sequencing.
Cells were loaded into a Chromium Single Cell Controller (10x Genomics) using either the Chromium Single Cell 5′ Reagent Kit v1.1 or v2.0, targeting for a cell recovery of 10,000 cells per sample. Gel bead-in-emulsion (GEM) generation, barcoding, reverse transcription, and cDNA amplification were performed according to the manufacturer’s protocol to construct 5′ gene expression libraries. Libraries were sequenced on an Illumina NovaSeq 6000 platform. Raw base call files were converted to FASTQ format using bcl2fastq2.

value: Blood

value: sorted Tscm cells

tag: individual

value: female

tag: disease state

value: Rheumatoid Arthritis

value: JAK inhibitor


title: VCaP_DMSO_Rep1

description: Library name: SI_40716


title: sorted Tscm cells, RA4

description: Library name: RA4


title: sorted Tscm cells, RA3

description: Library name: RA3


title: sorted Tscm cells, HC5

description: Library name: HC5

value: Healthy control


title: sorted Tscm cells, HC4

description: Library name: HC4


title: U87MG cells, S/G(-)_1

status: Public on Jun 20 2026

city: Busan

first: Jong-Ho

address: 37 Nakdong-daero 550 Beon-gil

institute: Dong-A University

data_processing:
ExDEGA  GraphicPlus_v2.1
Bowtie2
Supplementary files format and content: Read Count.xlsx

growth_protocol: U87MG epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: U87MG epithelial cells were cultured with serine/glycine-containing complete media or equivalent media lacking serine/glycine for 24h.

value: glioblastoma cell line

tag: cell state

value: Naïve

value: without serine and glycine DMEM

tag: time

value: Day 1


title: sorted Tscm cells, RA1

description: Library name: RA1


title: sorted Tscm cells, HC3

description: Library name: HC3


title: sorted Tscm cells, HC2

description: Library name: HC2

value: male


title: sorted Tscm cells, HC1

description: Library name: HC1


title: sorted Tscm cells, RA2

description: Library name: RA2


title: SiHa LNM2-3

city: Guangzhou

first: Li

last: Yuan

address: 58, Zhongshan 2nd road

institute: sun yat-sen university

description: Library name: Sample 12

data_processing:
The libraries were quality controlled with Agilent 2200 and sequenced by  Illumina NovaSeq 6000 on a 150 bp paired-end run.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to genome using the Hisat2.
HTseq was used to get gene expression.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: SiHa cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qjagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

value: SiHa cells

value: cervical cancer cells

value: highly lymph node metastatic cervical cancer cell lines


title: SiHa LNM2-2

description: Library name: Sample 11


title: SiHa LNM2-1

description: Library name: Sample 10


title: SiHa PR-2, parental conteraparts

description: Library name: Sample 8

value: parental conteraparts


title: HeLa LNM2-3

description: Library name: Sample 6

source_name: HeLa cells

value: HeLa cells


title: SiHa PR-1, parental conteraparts

description: Library name: Sample 7


title: HeLa LNM2-2

description: Library name: Sample 5


title: HeLa LNM2-1

description: Library name: Sample 4


title: HeLa PR-2

description: Library name: Sample 2


title: HeLa PR-1

description: Library name: Sample 1


title: SY-OENC-3

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

description:
Library name: SY-OENC-3
SY-OENC-3

data_processing:
Raw sequencing reads were trimmed for adapters using Skewer, and quality control was performed with FastQC (v0.11.2). Clean reads were aligned to the human reference genome (hg38) using STAR. Transcript assembly was conducted with StringTie (v1.3.1c), and expression levels were quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using Perl.
Assembly: hg38
Supplementary files format and content: xls file include FPKM values for each sample

growth_protocol: SK-N-BE(2) and SH-SY5Y cells were cultured Minimum Essential Medium (Gibco) containing 10% fetal bovine serum (Gibco), supplemented with sodium glutamate (Gibco), pyruvate (Gibco), and a mixture of non-essential amino acids (Gibco), and maintained in a humidified incubator at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen), and RNA concentration was measured with NanoDrop 2000 spectrophotometer (Thermo Scientific).
Strand-specific libraries were prepared from three biological replicates using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA), and sequencing was carried out on the Illumina NovaSeq 6000 platform.

treatment_protocol: Lentiviral vectors containing the full-length human NDUFS6 coding sequence and short hairpin RNAs (shRNAs) targeting NDUFS6 were constructed to generate stable overexpression (OE) and knockdown (KD) cell lines, respectively. Corresponding empty vectors were used as negative controls. Cells were incubated with lentiviral particles in culture medium supplemented with 5 μg/mL polybrene (sigma TR-1003) for 16 hours. Selection with 2 μg/mL puromycin (A1113803) began 48 hours post-infection and continued for approximately one week.

value: Neuroblastoma

value: Control for NDUFS6-overexpression


title: SY-OENC-1

description:
Library name: SY-OENC-1
SY-OENC-1


title: SY-OE-3

description:
Library name: SY-OE-3
SY-OE-3


title: SY-OE-2

description:
Library name: SY-OE-2
SY-OE-2


title: ATAC, Ctrl, WT, rep 4

city: Toronto

first: Giacomo

last: Furlan

state: ONTARIO

address: 25 Orde St

institute: Lunenfeld-Tanenbaum Research Institute

description:
Library name: Sample 4
WT_D

data_processing:
Read quality was assessed using FastQC. Paired-end reads were trimmed using Trim Galore, and only high-quality reads passing these steps were retained for downstream analysis.
Reads were aligned to the Mus musculus reference genome (mm10) using Bowtie2 (v2.4.1). Unaligned reads, mitochondrial reads, and PCR duplicates were removed at this stage.
Peak calling was performed with MACS3 (v3.0.3), using --nomodel and --nolambda parameters. Peaks overlapping with mouse ENCODE blacklist regions were excluded.
Differential accessibility analysis was performed in R using the DiffBind package (v3.16.0). Regions were considered significantly differentially accessible with a false discovery rate (FDR) < 0.05 and an absolute log₂ fold change > 1.
Genomic regions were annotated to nearby genes using GREAT (McLean et al., 2010), with the following settings: proximal = ±5 kb from transcription start site (TSS); distal = up to 1000 kb.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing normalized counts for all peaks in all samples

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in standard serum/LIF medium consisting of DMEM GlutaMAX supplemented with sodium pyruvate, 15% fetal bovine serum, 0.1 mM non-essential amino acids, 50 U mL-1 penicillin–streptomycin, 0.1 mM 2-mercaptoethanol, and 1,000 U mL-1 ESGRO LIF.

extract_protocol:
50,000 live cells were collected and resuspended in cold resuspension buffer (RSB: 10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂) supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Following lysis, nuclei were washed in RSB containing 0.1% NP-40 and subjected to tagmentation using the transposition mixture: 25 μL of 2× TD buffer, 2.5 μL of Tn5 transposase (100 nM final concentration), 16.5 μL of 1× PBS, 0.5 μL of 1% digitonin, 0.5 μL of 10% Tween-20, and 5 μL of nuclease-free water. After transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 Kit.
Library amplification was carried out as per protocol (Corces et al., 2017). Amplified libraries were purified using AMPure XP beads with a double-sided size selection to remove both primer dimers and large fragments (>1000 bp). Final libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit, pooled at equimolar concentrations, and sequenced on a NovaSeq X platform with a 10B flow cell, generating 150 bp paired-end reads.

treatment_protocol: To induce in vitro pausing, 200nM of the mTOR inhibitor INK128 was added to the culture medium for 12 hours.

value: embryonic stem cells

value: WT

value: Ctrl


title: SY-OE-1

description:
Library name: SY-OE-1
SY-OE-1


title: SY-KDNC-2

description:
Library name: SY-KDNC-2
SY-KDNC-2

value: Control for NDUFS6-knockdown


title: SY-KDNC-3

description:
Library name: SY-KDNC-3
SY-KDNC-3


title: sorted cortical microglia, from MG-srgap2f/f mice, rep4 (mouse 1109)

city: New Yiork

first: Carlos

last: Diaz-Salazar

address: Jerome L Greene Science Center, 3227 Broadway, L8 Quad A

department: Zuckerman Institute

institute: Columbia University

description:
Library name: cKO_109.bam
Column name in "WT_vs_cKO.counts.csv" : 1109

data_processing:
Reads were aligned to the GRCm39 mouse genome using BaseSpace DRAGEN RNA app (Illumina). Differential gene expression analysis was performed with pyDESeq2 81,82. Genes with less than 10 read counts in total were filtered out. ERT2 expression from the Tmem119creERT2 locus was mapped to the Esr1 gene and was thus filtered out
Assembly: GRCm39
Supplementary files format and content: csv file contains raw count matrix for all seven samples. Column header is each mouse ID.

source_name: mouse cortex

growth_protocol: srgap2-deficient microglia were generated by crossing the inducible, microglia-specific Tmem119creErt2 mouse line with the srgap2f/f line (MG-Srgap2F/F mice), and inducing sgrap2 deletion by tamoxifen gavage at P8. WT mice (srgap2f/f mice) also received tamoxifen gavage.

extract_protocol:
Fresh cortices from ice-cold PBS-perfused anesthetized P30 mice were quickly homogenized made into a single-cell suspension by passing it through a 100 mm filter. Immune cells were isolated by centrifuging a brain homogenate on a 40% Percoll gradient at 2000 rpm for 5 min at 4ºC. Myelin and fat debris were removed, cells washed with PBS, and incubated (2% FBS in PBS) with the following antibodies for 30 min at 4ºC: CD11b-APC (1:200,Tonbo), CD45-APCCy7 (1:200 Tonbo), Cx3Cr1-PECy7 (1:200 Biolegend). After washing twice, microglia (~100,000 cells / cortex) were sorted directly into TRIzol (Thermo Fisher Scientific) as CD11b+, CD45low, CX3CR1+ cells on a Sony MA900 (SONY) sorter with a 100 mm microfluidic chip. TRIzol containing the cell lysates was mixed with chloroform at a 5/1 ratio, shaken and spun at 12,000 g for 15 min at 4ºC. Clear supernatant was transferred to a fresh tube and washed with 70% ethanol. RNA cleanup was performed on a RNeasy Mini (Qiagen) according to manufacturer instructions. RNA quantity and quality was assessed with a 2100 Bioanalyzer (Agilent).
cDNA Libraries were prepared from samples with >8.5 RIN using the NEBNext Ultra II RNA Library Prep quit, the NEBNext Poly(A) mRNA Magnetic Isolation beads, and the NEBNex Multiplex Oligos for Illumina (all New England Biolabs), all according to manufacturer’s instructions.

treatment_protocol: mice received two doses (75 ug/g BW) of tamoxifen at P8 and P10

value: mouse cortex

value: microglia

value: Tamoxifen at P8


title: VCaP_100nM_DALTAC_1_3h_H3K27ac

description: Library name: SI_40560

value: VCaP

value: prostate cancer


title: SY-KD-1_3

description:
Library name: SY-KD-1_3
SY-KD-1_3


title: SY-KDNC-1

description:
Library name: SY-KDNC-1
SY-KDNC-1


title: SY-KD-1_2

description:
Library name: SY-KD-1_2
SY-KD-1_2


title: BE2_OENC_3

description:
Library name: BE2_OENC_3
BE2_OENC_3


title: SY-KD-1_1

description:
Library name: SY-KD-1_1
SY-KD-1_1


title: BE2_OENC_2

description:
Library name: BE2_OENC_2
BE2_OENC_2


title: BE2_OENC_1

description:
Library name: BE2_OENC_1
BE2_OENC_1


title: BE2_OE_2

description:
Library name: BE2_OE_2
BE2_OE_2


title: BE2_OE_1

description:
Library name: BE2_OE_1
BE2_OE_1


title: BE2_KDNC_3

description:
Library name: BE2_KDNC_3
BE2_KDNC_3


title: BE2_KDNC_2

description:
Library name: BE2_KDNC_2
BE2_KDNC_2


title: BE2_KDNC_1

description:
Library name: BE2_KDNC_1
BE2_KDNC_1


title: BE2_KD_3

description:
Library name: BE2_KD_3
BE2_KD_3


title: BE2_KD_2

description:
Library name: BE2_KD_2
BE2_KD_2


title: BE2_KD_1

description:
Library name: BE2_KD_1
BE2_KD_1


title: SiHa PR P4HA3-2

description: Library name: Sample 5

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: Uterine smooth muscle (2.0 × 0.5 × 0.5 cm3) was cut from the site of incision at the lower edges of the uterus during cesarean section. Samples were then washed three times with ice-cold sterile phosphate-buffered saline(PBS), and then stored in liquid nitrogen.

extract_protocol:
mRNA libraries were prepared for sequencing using standard Illumina protocols
mRNA-Seq

treatment_protocol: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.


title: SiHa PR P4HA3-1

description: Library name: Sample 4


title: SiHa PR-2

description: Library name: Sample 2


title: SiHa PR-1

description: Library name: Sample 1


title: TPC-1-Len replicate 1

first: jun

middle: Yun

last: Wang

address: Fudan University Shanghai Cancer Center, 270 Dong'an Road, Xuhui District, Shanghai, China

department: Head and Neck Surgery

institute: Fudan University Shanghai Cancer Center

description: Library name: tpc_lenv_res1

data_processing:
aw sequencing reads were filtered to remove low-quality reads and adapter sequences.
Assembly: GRCh38
Supplementary files format and content: A tab-delimited text file containing a matrix of raw, un-normalized integer counts. Rows correspond to genes, identified by gene symbols, and columns correspond to the samples listed above.

source_name: thyroid epithelial

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10 % fetal bovine serum and 1 % penicillin-streptomycin at 37 °C with 5 % CO₂.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Thermo Fisher, 15596026) following the manufacturer’s instructions. RNA integrity (RIN ≥ 8) was confirmed with Agilent 2100 Bioanalyzer.
Poly(A)-selected stranded mRNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) according to the vendor’s protocol.

treatment_protocol: Lenvatinib-resistant sub-line (TPC-1-Len) was generated by continuous exposure to 6 µM lenvatinib for >3 months; parental TPC-1 cells were maintained drug-free. No drug was present during RNA harvest.

value: thyroid epithelial

value: papillary thyroid carcinoma cell line


title: TPC-1 parental replicate 3

description: Library name: tpc_blank3


title: TPC-1 parental replicate 2

description: Library name: tpc_blank2


title: TPC-1 parental replicate 1

description: Library name: tpc_blank1


title: UC8-3

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Library name: Het3

data_processing:
fastp (version 0.18.0)
short reads alignment tool Bowtie2 (version 2.2.8)
HISAT2. 2.4
StringTie v1.3.1
RSEM software
Assembly: GRCH38 ensemble release100
Supplementary files format and content: raw counts and  FPKM values for each Sample

source_name: retinal organoids

extract_protocol:
Total RNA was extracted by Trizol reagent (Sigma), mRNA was enriched by Oligo(dT) beads.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols, then transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB, #7530,New England Biolabs, Ipswich, MA, USA).

value: retinal organoids

value: UC8 hiSPCs

value: differentiated retinal cells

value: remove the central dark core layer


title: UC8-2

description: Library name: Het2


title: UC8-1

description: Library name: Het1


title: UC7-3

description: Library name: Hom3

value: UC7 hiSPCs


title: UC7-2

description: Library name: Hom2


title: UC7-1

description: Library name: Hom1


title: UC3-3

description: Library name: Conrtol3

value: UC3 hiSPCs


title: UC3-2

description: Library name: Conrtol2


title: UC3-1

description: Library name: Conrtol1


title: Lenvatinib-resistant TPC-1 cells with KRT15 knockdown, replicate 3

description:
Library name: Sample_JZ25085113-sh-KRT15-TPC-1-Len-3
kd-3

source_name: thyroid gland

growth_protocol: Lenvatinib-resistant TPC-1 cells (TPC-1-Len) were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL Penicillin-Streptomycin, and maintained under continuous exposure to 10 μM lenvatinib to preserve their resistant phenotype.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Thermo Fisher) following the manufacturer's protocol.
Following RNA extraction, sequencing libraries were constructed by OE Biotech (Shanghai, China) using standard protocols for the Illumina platform. This involved mRNA purification, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: TPC-1-Len cells were seeded and transfected with either a non-targeting control shRNA (sh-NC) or an shRNA targeting KRT15 (sh-KRT15) using hieff-TransTM liposomal-transfection reagent according to the manufacturer's instructions. Cells were harvested for RNA extraction after transfection.

value: thyroid gland

value: epithelial cell

value: transfection with shRNA targeting KRT15


title: Lenvatinib-resistant TPC-1 cells with KRT15 knockdown, replicate 1

description:
Library name: Sample_JZ25085111-sh-KRT15-TPC-1-Len-1
kd-1


title: Lenvatinib-resistant TPC-1 cells with sh-NC, replicate 3

description:
Library name: Sample_JZ25085110-NC-TPC-1-Len-3
con-3

value: NC


title: Lenvatinib-resistant TPC-1 cells with KRT15 knockdown, replicate 2

description:
Library name: Sample_JZ25085112-sh-KRT15-TPC-1-Len-2
kd-2


title: Lenvatinib-resistant TPC-1 cells with sh-NC, replicate 2

description:
Library name: Sample_JZ25085109-NC-TPC-1-Len-2
con-2


title: Lenvatinib-resistant TPC-1 cells with sh-NC, replicate 1

description:
Library name: Sample_JZ25085108-NC-TPC-1-Len-1
con-1


title: PANC1 Day14 replicate 1

description:
Library name: PANC1_D14_1
Bulk RNA-seq after 14 days osteogenic induction

value: pancreas

value: wild-type


title: SiHa PR P4HA3-3

description: Library name: Sample 6

value: SiHa cells

value: cervical cancer cells


title: Capan-2 Day14 replicate 1

description:
Library name: Capan2_D14_1
Bulk RNA-seq after 14 days osteogenic induction


title: T24 cells, siUSP43-2

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

description:
Library name: sample5
Column name in All.fpkm_anno.txt: siUSP43-2

data_processing:
Raw sequencing reads were quality-filtered using Cutadapt (version 2.6). Cleaned reads were aligned to the Homo sapiens reference genome (GRCh38, NCBI) with subsequent quantification of exonic reads mapped to annotated genes using Hisat2(v2.2.1).
Assembly: GRCh38
Supplementary files format and content: .txt file includes raw counts and FPKM values for each Sample

growth_protocol: T24 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods. A total of 2 μg of high-quality RNA was used for the construction of sequencing libraries.
VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech, cat. NO NR60502) following the manufacturer’s instruction

value: bladder cancer cell

value: USP43 knockdown


title: T24 cells, siUSP43-3

description:
Library name: sample6
Column name in All.fpkm_anno.txt: siUSP43-3


title: T24 cells, siUSP43-1

description:
Library name: sample4
Column name in All.fpkm_anno.txt: siUSP43-1


title: T24 cells, siNC-2

description:
Library name: sample2
Column name in All.fpkm_anno.txt: NC-2

value: WT


title: TPC-1-Len replicate 2

description: Library name: tpc_lenv_res2

value: thyroid epithelial

value: papillary thyroid carcinoma cell line


title: N/P(14) rep1

description: Library name: sample 3

value: untreat


title: P7503_dpa113

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

description: Library name: P7503

data_processing:
Illumina adapter sequences were trimmed off from the raw reads using Cutadapt and only reads with minimum 30bp were kept for downstream analysis.  Trimmed reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function.  CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 20 -min-sample 1.0.
Assembly: GRCh38
Supplementary files format and content: tab-separated file of methylation levels per CpG locus (row) for all samples (column)

extract_protocol:
Genomic DNA was extracted from PBMCs using phenol-chloroform method.
500ng genomic DNA was sheared and subject to end-repair, A-tailing and ligated with methylated adaptors.  Purified libraries were hybridized to biotinylated probes and subjected for bisulfite conversion (Zymo Cat# D5030).  Captured DNA was PCR amplified with KAPA HiFi HotStart Uracil+ (Cat# KK2801) into a final TBS-seq library.  Library quality was evaluated using TapeStation with the high-sensitivity D1000 tape (Agilent Cat# 5067- 5584).

value: Blood

value: PBMC

value: Male

tag: trajectory group

tag: days post_admission


title: T24 cells, siNC-1

description:
Library name: sample1
Column name in All.fpkm_anno.txt: NC-1

tag: cell line

tag: cell type


title: P7502_dpa008

description: Library name: P7502


title: P7403_dpa197

description: Library name: P7403

value: Female


title: P7203_dpa306

description: Library name: P7203


title: P7302_dpa144

description: Library name: P7302


title: P7202_dpa013

description: Library name: P7202


title: P7102_dpa103

description: Library name: P7102


title: P7201_dpa002

description: Library name: P7201


title: P7002_dpa186

description: Library name: P7002


title: P7101_dpa068

description: Library name: P7101


title: P7001_dpa005

description: Library name: P7001


title: P6902_dpa009

description: Library name: P6902


title: P6903_dpa272

description: Library name: P6903


title: P6901_dpa005

description: Library name: P6901


title: P6803_dpa213

description: Library name: P6803


title: P6802_dpa213

description: Library name: P6802


title: P6703_dpa008

description: Library name: P6703


title: P6701_dpa003

description: Library name: P6701


title: P6702_dpa003

description: Library name: P6702


title: P6601_dpa002

description: Library name: P6601


title: P6602_dpa005

description: Library name: P6602


title: P6502_dpa264

description: Library name: P6502


title: P6402_dpa009

description: Library name: P6402


title: P6401_dpa002

description: Library name: P6401


title: P6302_dpa389

description: Library name: P6302


title: P6301_dpa002

description: Library name: P6301


title: P6203_dpa009

description: Library name: P6203


title: P6202_dpa002

description: Library name: P6202