title: NF1 KO MCF7 cells biol rep 2

city: Missouri City

first: Zifan

last: Zhao

state: TX

address: 34 Chapparal Ct

department: Breast Center

institute: Baylor College of Medicine

description: Library name: Sample 4

data_processing:
Paired-end 150 bp reads were aligned to hg19 (GRCh37) reference genome using RSEM v1.2.31 and Bowtie 2.
RSEM counts of protein-coding genes were log2-transformed and normalized using the trimmed mean of M values (TMM) method.
Assembly: hg19 (GRCh37)
Supplementary files format and content: Tab-delimited RSEM gene-level expression result files. Each row represents one gene, with columns including gene_id, transcript_id(s), length, effective_length, expected_count, TPM, and FPKM. The expected_count column contains RSEM-estimated gene-level read counts, and TPM/FPKM columns contain normalized gene expression values.

growth_protocol: NF1+ and NF1KO MCF7 cells were cultured in DMEM supplemented with 10% FBS in humidified atmosphere at 5% CO2 and 37C

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen). One µg RNA per sample was submitted to Novogene for RNA quality control (Agilent 2100 Bioanalyzer), library preparation, and next-generation sequencing (Illumina NovaSeq 6000)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. Libraries were generated through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed by Qubit and real-time PCR for quantification and by Bioanalyzer for size distribution. Quantified libraries were pooled and sequenced on an Illumina platform.

tag: cell line

value: NF1 KO


title: Cre-pos-MSR

status: Public on Jun 13 2026

type: SRA

city: Saint Louis

first: Gwendalyn

middle: J

last: Randolph

state: Missouri

address: 660 South Euclid Ave

department: Immunolgoy

country: USA

institute: Washington University in St. Louis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count"
Assembly: mm10-2020-A
Supplementary files format and content: Processed Seurat RDS object

molecule: total RNA

organism: Mus musculus

source_name: mesentery sheet region

extract_protocol:
Whole mesenteries and omenta from eight lipoatrophic AdiponectinCre/+ RosaDTAfl/+ female mice that received fat transplant surgery referred to as distal adipocyte receiving lipoatrophic mice (DARL) and their littermates that have standard fat depots that received sham surgery referred to as peritoneal adipocyte-replete control mice post-sham surgery (PARC) mice 8 weeks post-surgery were pinned on Sylgard dishes and kept hydrated in PBS. The adipose region in PARC mice and the corresponding area in DARL mice were carefully separated from the membranous sheet region for each omentum and mesentery using a scalpel and placed in RPMI with 5% FBS on ice. Each sheet or adipose region collected from each mouse was minced and digested separately using 1 mg/mL collagenase IV,  0.1 mg/mL DNAse, and 0.5% BSA for 30 minutes on a shaker. The samples were centrifuged and resuspended for downstream processing. Following digestion of the omentum and mesentery from PARC and DARL mice, the samples were washed and filtered with 100 m filters and stained for CD45+, DAPI, and TER-119. Samples were kept on ice until sorted on the FACSAria II with a 100-m nozzle (Becton Dickinson). Cells stained with DAPI were gated out during cell sorting to remove dead cells. Similarly, cells stained positive for TER-119 were excluded to remove red blood cells from our cell quantifications to increase the collection of desired cells. Approximately equal quantities of CD45+ and CD45- cells were submitted for 10X Genomics single-cell RNA sequencing via the McDonald Genome Institute Core.
10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit

tag: tissue

value: mesentery sheet region

tag: cell type

value: CD45+/CD45- cells

tag: genotype

value: Adiponectin Cre+/DTA

tag: treatment

value: fat pad transplant


title: Newborn Distal, replicate 1, RNA_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

country: China

institute: Shandong University

description: Library name: ND1

library_source: genomic

data_processing:
Raw sequencing reads were assessed for quality and adapter contamination prior to alignment.
Clean reads were aligned to the mouse reference genome (mm10) using Bowtie2.
Reads with low mapping quality, mitochondrial reads, and PCR duplicates were removed before downstream analysis. Accessible chromatin regions were identified using MACS2 peak calling.
Peak annotations and downstream analyses were performed using standard bioinformatic workflows. Genome-wide accessibility tracks were generated in bigWig format for visualization in IGV.
Assembly: All ATAC-seq sequencing reads were aligned to the official mouse reference genome assembly. The Mus musculus GRCm38 (mm10) genome build was used as the standard reference for genome mapping and subsequent bioinformatics analysis (default standard for mouse intestinal epigenetic research).
Supplementary files format and content: Processed data files include BED files containing ATAC-seq peak coordinates, bigWig files containing normalized chromatin accessibility signal tracks, and tab-delimited text files containing peak annotations and differential accessibility results. BED files report genomic coordinates of accessible chromatin regions identified by MACS2, while bigWig files provide genome-wide accessibility profiles for visualization. Differential accessibility files include genomic coordinates, fold changes, statistical significance values, and associated gene annotations.

molecule: genomic DNA

source_name: colonic epithelial cells

extract_protocol:
Colonic epithelial cells were isolated from mouse tissues and processed immediately for ATAC-seq library preparation. Cells were washed with ice-cold PBS and lysed in a detergent-containing lysis buffer to release intact nuclei. Nuclei were collected by centrifugation, washed, and resuspended in transposition reaction buffer for subsequent tagmentation.
ATAC-seq libraries were prepared using the Novoprotein ATAC Library Prep Kit (Novoprotein, China) according to the manufacturer's instructions. Briefly, purified nuclei were incubated with Tn5 transposase at 37°C for 30 min to simultaneously fragment accessible chromatin and insert sequencing adapters. Following transposition, DNA was purified using magnetic beads and amplified by PCR with indexed primers. Amplified libraries were purified, quantified using Qubit fluorometry, and assessed for fragment size distribution using an Agilent Bioanalyzer. Libraries were sequenced on an Illumina platform with paired-end 150-bp reads (PE150).

value: colonic epithelial cells


title: NF1 KO MCF7 cells biol rep 1

description: Library name: Sample 3

library_source: transcriptomic

organism: Homo sapiens

tag: batch


title: Cre-pos-MFR

description: 10x Genomics

source_name: mesentery fat region

value: mesentery fat region


title: arcZ2, rep1

city: Jena

first: Marcel

last: Sprenger

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

description:
Library name: arcZ2-1
column name arcZ2, rep1

data_processing:
CLC Genomics Workbench v22.0.2
using default parameters for RNA sequencing
Assembly: NCBI accession CP015137.1
Supplementary files format and content: Expression Browser_only arcZ variants.xlsx
Supplementary files format and content: xlsx files include total counts, TPM, CPM and RPKM values

organism: Dickeya solani

growth_protocol: D. solani was grown overnight in LB. The following day bacteria were diluted in fresh media and grown to OD 0.5. RNA samples were collected and transcription was stopped by adding 0.5 volumes of ice-cold methanol.

extract_protocol:
Total RNA was isolated by hot phenol extraction. Prepared RNA was DNAse digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using biotinylated oligo probes for ribosomal RNA (PMID: 32317317). Integrity of the prepared RNA was tested using a Bioanalyzer.
cDNA libraries were prepared using the NEBNext UltraExpress RNA Library Prep Kit for Illumina (NEB, E3330L) according to the manufacturer's instructions. Library quality was assessed on an Agilent 2100 Bioanalyzer and pooled libraries were sequenced on a NextSeq 1000 system with 100 nt single-read mode.

tag: time

value: 0 min


title: Adult Proximal, replicate 2, RNA_seq

description: Library name: AP2


title: NF1+ MCF7 cells biol rep 2

description: Library name: Sample 2

value: WT


title: arcZ1, rep3

description:
Library name: arcZ1-3
column name arcZ1, rep3


title: Cre-neg-OSR

description: 10x Genomics

source_name: omentum sheet region

value: omentum sheet region

value: Adiponectin Cre-/DTA

value: sham surgery


title: Cre-neg-OFR

description: 10x Genomics

source_name: omentum fat region

value: omentum fat region


title: arcZ1, rep2

description:
Library name: arcZ1-2
column name arcZ1, rep2


title: A431-SUZ12

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

description: Library name: A431-SUZ12-1

data_processing:
Reads were trimmed with Trim Galore (v0.6.7) and aligned to the human reference genome (hg38) using Bowtie2 (v.2.2.5). Deduplicated reads were removed using samtools (v.1.14). Peaks were identified using a sliding window method to determine genomic regions with >1.5 mapping read enrichment over IgG control and adjusted p < 0.05. The BAM file for each replicate was converted to a TDF file for Integrative Genomics Viewer (IGV) software.
Assembly: hg38
Supplementary files format and content: TDF, tag density file
Library strategy: CUT&RUN

source_name: skin cancer

extract_protocol:
FACS isolation of epidermal cells from human skin was performed as follows: Skin samples were collected, and the adipose layer was scraped off using a surgical scalpel and washed with PBS. Samples were incubated in the enzymes, followed by the Epidermis Dissociation Kit manufacturer’s protocol (Miltenyi Biotec). The cell pellet was washed twice with DPBS (Thermo Fisher Scientific) before staining with cell-surface markers. The cells were stained with 1:200 PE-CD324(E-cadherin, BD Bioscience) and 1:200 FITC-α6-integrin (Thermo Fisher Scientific) in staining buffer (2% FBS in HBSS (Corning)) for 30 minutes on ice and then washed twice with DPBS before cell sorting. Epidermal cells were sorted as E-cadherin (+) and α6-integrin (+). A431 tumors were collected from the mice and cut into small pieces (< 1mm3) with razor blades in 10cm plate. Chopped tumors were incubated with 0.25% collagenase (Millipore Sigma) in HBSS for 45 minutes. After collagenase incubation, chopped tumors were treated with 1 unit DNase (Millipore Sigma) for 10 minutes. Collect the tumors and medium filtered through 100μm filters and transfer the tumors from filters into 10cm plate. Tumors were incubated 0.25% Trypsin/EDTA (Corning) at 37C for 30 minutes. The A431 cells were stained with 1:200 Alexa fluor 700-β1-integrin (Biolegend), 1:200 APC-Cy7-α6-integrin (Biolegend), and 1:300 APC-CD11b, APC-CD31 and APC-CD45 (Biolegend) in staining buffer for 30 minutes on ice and then washed twice with DPBS before cell sorting. SCC cells were sorted as CD11b, CD31, CD45 (-), β1-integrin (high), and α6-integrin (high).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNext Multiplex Oligos (NEB) for Illumina following the manufacturer’s instructions. PCR-amplified libraries were purified using 1X ratio of Agencourt AMPure-XP Beads (Beckman) and eluted in 15μl TE buffer. All libraries were sequenced on an Illumina NextSeq using 50 bp paired-end reads.

value: skin cancer

value: Epidermal  SCC cells


title: arcZ1, rep1

description:
Library name: arcZ1-1
column name arcZ1, rep1


title: Cre-neg-MSR

description: 10x Genomics


title: Adult Distal, replicate 1, RNA_seq

description: Library name: AD1


title: A431-EED

description: Library name: A431-EED-1

value: EED


title: MJe10

city: Palo Alto

first: Konstantina

last: Stankovic

state: CA

address: Cooper Lane

institute: Stanford University

description:
Library name: UCSD_D20
10x genomics

data_processing:
The 10X Genomics Cell Ranger 2.1.0 pipeline (http://support.10xgenomics.com/) was used to process raw sequence data. Briefly, Cell Ranger utilizes bcl2fastq (https://support.illumina.com/) to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files. These FASTQ files were then aligned to the reference genome using RNA-seq aligner STAR. The aligned reads are traced back to the individual cells, and gene expression levels were quantified based on the number of unique molecular indices (UMIs) detected in each cell. Filtered gene–cell barcode matrices were generated by Cell Ranger for downstream analysis.
Assembly: hg38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: UCSD hiPSCs derived

extract_protocol:
The collected cells were incubated with TrypLE Select in a 37 °C incubator for about 2 minutes, until detachment of the edge of the cells was observed. TrypLE was then removed, and the cells were gently resuspended in DMEM/F12 supplemented with 10% fetal bovine serum (Gibco, 26140079) using a P1000 pipette until no visible aggregates remained. The cell suspension was filtered through a 100 μm cell strainer to eliminate any chunks of cell aggregates. Then, cells were resuspended in 1X phosphate-buffered saline (PBS; Gibco, 14190144) containing 0.04% bovine serum albumin (BSA; SIGMA, A8412). Cell viability was assessed manually using a hemocytometer and confirmed with a BioRad TC20 automated cell counter. The final cell concentration was 1,000 cells/μl, with cell viability exceeding 80%.
Single-cell 3′ RNA-seq was performed using the Chromium single-cell system (10X Genomics) and the NexSeq 2000 (Illumina). Dissociated cells were added to a single-cell master mix targeting 10,000 cells, following the Chromium Single Cell 3' v3 protocol (10X Genomics, G000183, Rev C). Along with the single-cell gel beads and oil partitioned in separate wells of a Single Cell B Chip, the single-cell reaction mixture was loaded to the Chromium Controller for Gel Bead-in-Emulsion generation and barcoding. This was followed by cDNA synthesis and library preparation. At each step, cDNA and library quality were examined by Tape station 4200. The final sequencing library was processed using a custom sequencing program on an Illumina NextSeq 2000, with 28-bp plus 91-bp paired-end sequencing, achieving a reading depth of over 30,000 reads per cell.

value: UCSD hiPSCs derived

value: OPC

value: OPC differentiation


title: Cre-neg-MFR

description: 10x Genomics

value: CD45+/CD45- cells


title: MCOLN3 Y391D #4

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description:
Library name: WR12
column name in RNAseq_counts.tsv: WR12

data_processing:
Reads were aligned to the human transcriptome (Gencode r.28) using kallisto (Bray et al. 2016)
Transcript-level abundance estimates were summarized to gene-level expression values using the lengthScaledTPM method in tximport (Soneson et. al., 2015).
Data was normalized using edgeR’s TMM mormalization
log2CPM values were calculated using voom (from limma)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes raw counts. Samples are identified by the column header.

molecule: polyA RNA

growth_protocol: Human adrenocortical HAC15 cell line was routinely cultured in growth media consisting of Dulbecco’s modified Eagle’s medium (DMEM)-F12 (Gibco) supplemented with 10 % cosmic calf serum (Hyclone), 1 % ITS (insulin-transferrin-selenium; Corning), and antibiotics, 1 % penicillin/streptomycin (Gibco) and 0.1 % gentamicin (Gibco). Cells were grown at 37 °C in a humidified atmosphere of 5 % CO2.

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini kit (Qiagen; Cat#: 74134) and eluted in nuclease-free H2O.
Poly(A) Tail RNA Selection 250-300 bp Insert cDNA Library Strand-Specific Preparation by LC Sciences. Library construction and sequencing is described by LCScience.com as: "Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the paired-end 2×150bp sequencing on an Illumina Hiseq 4000 at LC Sciences following the vendor's recommended protocol.

value: Adrenocortical carcinoma cell


title: A431-EZH2

description: Library name: A431-EZH2-1


title: MJe9

description:
Library name: UCSD_D14
10x genomics

value: Placode


title: HCT116 cells, sh_circRAPGEF5_2

city: Hefei

first: yu

middle: xiang

last: dai

address: No.81 Meishan Road Hefei China

institute: Anhui Medical University

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Colorectal cancer

growth_protocol: Normal growth conditions, according to instructions by provider

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.Kit: mirVana™ miRNA ISOlation Kit, Ambion-1561. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: HCT116 cells were transfected with an sh-RNA knockdown system purchased from Sigma-Aldrich, and after 36 or 48 h of incubation, the cells were collected.

value: Colorectal cancer

value: MT


title: MCOLN3 Y391D #3

description:
Library name: WR11
column name in RNAseq_counts.tsv: WR11


title: MJe8

description:
Library name: SK8-A_D20
10x genomics

source_name: SK8-A hiPSCs derived

value: SK8-A hiPSCs derived


title: A431-H3K27me3

description: Library name: A431-H3K27me3-1


title: HCT116 cells, sh_circRAPGEF5_1


title: Epi-SUZ12

description: Library name: F25-SUZ12

source_name: Skin epidermis

value: Skin epidermis

value: Epidermal cells


title: MJe7

description:
Library name: SK8-A_D14
10x genomics

value: WT


title: MCOLN3 Y391D #1

description:
Library name: WR9
column name in RNAseq_counts.tsv: WR9


title: Epi-EED

description: Library name: F25-EED


title: Purified PEG10 PBNPs

city: Hsinchu

first: Pin-Yan

last: Chen

address: No. 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

country: Taiwan

institute: National Tsing Hua University

description: Library name: Sample 2

library_source: other

data_processing:
RNA sequencing data were processed using a standard pipeline. Raw reads were quality filtered and trimmed using fastp, with quality assessed by FastQC. Clean reads were aligned to the reference genome using HISAT2, and processed with SAMtools. Gene expression was quantified using featureCounts and normalized as transcripts per million (TPM) to account for gene length and sequencing depth, enabling comparison of relative transcript abundance across samples.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel files containing TPM-normalized transcript abundance values of RNAs detected in PBNPs and HEK293T cells by RNA sequencing.

molecule: other

extract_protocol:
Purified PBNPs were first treated with nuclease prior to RNA extraction. RNAs from purified PBNPs and corresponding HEK293T producer cells were extracted using the Direct-zol RNA Microprep Kit (Zymo Research, R2061). Extracted RNAs were subsequently treated with DNase I (Zymo Research, E1011).
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina). mRNA was enriched using oligo(dT)-coupled magnetic beads, fragmented, and reverse-transcribed into first-strand cDNA, followed by double-stranded cDNA synthesis, adaptor ligation, and PCR amplification. Libraries were purified using the AMPure XP system (Beckman Coulter), qualified using the Qsep400 System (BiOptic Inc.), quantified using a Qubit 2.0 Fluorometer (Thermo Fisher), and sequenced on an Illumina NovaSeq platform with 150 bp paired-end reads (Genomics BioSci & Tech, Taiwan).

value: Protein-based nanoparticles (PBNPs)

value: purified PBNPs


title: PEM-3

city: chengdu

first: donghao

last: zhang

address: No. 211, Huimin Road, Wenjiang District, Chengdu City

institute: sichuan agricultural university

description:
Library name: SAMPLES6
PEM-3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 44.25 raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. Then about 41.71 G clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq25. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar. Based on the hypergeometric distribution, GO6, KEGG7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software8-9. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: GRCg6a (GCA_000002315.5)
Supplementary files format and content: A tab-delimited text file containing FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all expressed genes across all samples. Rows represent Ensembl gene IDs or gene symbols, and columns represent individual samples (e.g., PEM-1, SOL-2, etc.). FPKM values were calculated using Cufflinks based on HISAT2-aligned reads to the Gallus gallus reference genome.

organism: Gallus gallus

source_name: pectoralis major muscles

extract_protocol:
Total RNA was extracted from chicken skeletal muscle tissue using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. Briefly, approximately 100 mg of frozen muscle tissue was homogenized in 1 mL of TRIzol using a tissue grinder under liquid nitrogen. After incubation at room temperature for 5 minutes to permit complete dissociation of nucleoprotein complexes, 200 µL of chloroform was added per 1 mL of TRIzol. The samples were shaken vigorously for 15 seconds and then incubated at room temperature for 2–3 minutes. Phase separation was achieved by centrifugation at 12,000 × g for 15 minutes at 4°C. The upper aqueous phase containing RNA was carefully transferred to a new RNase-free microcentrifuge tube, and an equal volume of isopropanol was added to precipitate RNA. After incubation at room temperature for 10 minutes, the mixture was centrifuged at 12,000 × g for 10 minutes at 4°C. The resulting RNA pellet was washed once with 1 mL of 75% ethanol (prepared with DEPC-treated water), followed by centrifugation at 7,500 × g for 5 minutes at 4°C. After discarding the supernatant, the pellet was air-dried at room temperature for 5–10 minutes and then dissolved in 30–50 µL of RNase-free water.  RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: pectoralis major muscles

tag: breed

value: broilers


title: MCOLN3 WT #4

description:
Library name: WR8
column name in RNAseq_counts.tsv: WR8


title: HEK293T producer cells

description: Library name: Sample 1

value: human embryonic kidney cells

value: producer cells


title: Epi-EZH2

description: Library name: F25-EZH2


title: PEM-2

description:
Library name: SAMPLES5
PEM-2


title: Cre-pos-MSR TCR

description: 10x Genomics

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count"
Assembly: mm10-2020-A
Supplementary files format and content: Processed Seurat RDS object
Library strategy: TCR-Seq

value: mesentery sheet region

value: Adiponectin Cre+/DTA

value: fat pad transplant


title: Ctrl Distal, replicate 1, RNA_seq

description: Library name: CD1

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

tag: strain


title: MCOLN3 WT #3

description:
Library name: WR7
column name in RNAseq_counts.tsv: WR7

value: Adrenocortical carcinoma cell


title: patient-3

city: 北京-Beijing

first: QING

last: Liu

state: 北京市

address: Department of Neurology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College (PUMC) & Chinese Academy of Medical Science (CAMS), Beijing, China

description: Library name: sample6

data_processing:
Data were processed using Cell Ranger and analyzed via Seurat (v4.0). Quality control metrics included filtering cells with <200 or >5,000 detected genes and mitochondrial gene expression >20%.
Assembly: GRCh38

source_name: brain

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone SH30256.01) and digested using Trypsin (Hyclone SH30042.01) as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using SeekMate Tinitan Fluorescence Cell Counter (SeekGene M002C) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI-1640 (Gibco 11875119) and then resuspended at 1×106 cells per ml in RPMI-1640 and 2% FBS (Gibco 10100147C).
Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (SeekGene Catalog No.K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42℃ for 90 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index.The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme N411-01), analyzed by Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic Qsep400). The libraries were then sequenced on illumina NovaSeq X Plus with PE150 read length.

value: brain

value: microglia


title: Epi-H3K27me3

description: Library name: F25-H3K27me3


title: Newborn Proximal, replicate 2, RNA_seq

description: Library name: NP2

value: colonic epithelial cells


title: PEM-1

description:
Library name: SAMPLES4
PEM-1


title: MCOLN3 WT #2

description:
Library name: WR6
column name in RNAseq_counts.tsv: WR6


title: Cre-pos-OSR

description: 10x Genomics

value: omentum sheet region

value: CD45+/CD45- cells


title: patient-2

institute: Peking Union Medical College Hospital (PUMCH), Peking Union Medical College (PUMC) & Chinese Academy of Medical Science (CAMS)

description: Library name: sample5


title: SCC-2

description: Library name: set2_Gil_SCC7_H3K27me3

extract_protocol:
Normal human skin samples were washed once in cold 1x PBS, fat layer was removed, and the skin was then incubated in 1.26 U/ml dispase (Gibco) overnight at 4 °C. The epidermis was separated from underlying dermis and kept at liquid nitrogen until use. Human SCC tumor biopsies were freshly collected after surgery and kept at liquid nitrogen until use.   Next, nuclei from frozen human epidermis and SCC tumor samples were isolated. Isolated nuclei were then subjected to CUT&RUN analysis using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNext Multiplex Oligos (NEB) for Illumina following the manufacturer’s instructions. PCR-amplified libraries were purified using 1X ratio of Agencourt AMPure-XP Beads (Beckman) and eluted in 15μl TE buffer. All libraries were sequenced on an Illumina NextSeq using 50 bp paired-end reads.

value: skin cancer

value: Epidermal  SCC cells


title: SOL-3

description:
Library name: SAMPLES3
SOL-3

source_name: soleus muscles

value: soleus muscles


title: SCC-1

description: Library name: set1_Gil_SCC8_H3K27me3


title: patient-1

description: Library name: sample4


title: SOL-2

description:
Library name: SAMPLES2
SOL-2


title: MCOLN3 WT #1

description:
Library name: WR5
column name in RNAseq_counts.tsv: WR5


title: control-3

description: Library name: sample3


title: SOL-1

description:
Library name: SAMPLES1
SOL-1


title: Empty vector #3

description:
Library name: WR3
column name in RNAseq_counts.tsv: WR3


title: Epi-1

description: Library name: set1_Gil_CTL_Epi92_H3K27me3

value: Skin epidermis

value: Epidermal cells


title: control-2

description: Library name: sample2


title: Eed iKO-D

city: New York

first: Elena

last: Ezhkova

address: 1428 Maidson Avenue 702

department: Cell, Developmental, and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Eed iKO-D

data_processing:
Samples were sequenced and demultiplexed by Novogene (Novogene, Sacramento, CA) to produce raw fastq files for each sample. For CTRL and KO samples, each sample was sequenced on two independent sequencing runs, and the two sets of fastq files were concatenated directly then mapped with cellranger. Fastq files were mapped to the mm10 mouse genome using the Cellranger (v.8.0) pipeline from 10X Genomics. UMI counts for each gene were quantified per cell to generate feature-barcode counts matrices.
Assembly: mm10
Supplementary files format and content: processed files are filtered cellranger matrix, feature, and barcode output files. Default filtering parameters in cellranger were used

extract_protocol:
Tumors were collected from the Ctrl-D and Eed iKO-D mice and cut into small pieces (< 1mm3) with razor blades in 10cm plate. Chopped tumors were incubated with 0.25% collagenase (Millipore Sigma) in HBSS for 45 minutes. After collagenase incubation, chopped tumors were treated with 1 unit DNase (Millipore Sigma) for 10 minutes. Collect the tumors and medium filtered through 100μm filters and transfer the tumors from filters into 10cm plate. Tumors were incubated 0.25% Trypsin/EDTA (Corning) at 37C for 30 minutes. Dissociated tumor single-cell suspensions were sequentially strained through 100μm and 40μm filters. Viable cells were isolated by Dead Cell Removal kit (Miltenyi Biotec) according to the manufacturer’s instructions.
Library preparation was performed with the Single Cell 10X Chromium 3’v2 kit (10X Genomics) following the manufacturer’s protocol. Target number of captured cells ranged from 8013-19511 cells. Sequencing was performed on a HiSeq 4000 (Illumina, Inc.). Raw sequencing data was processed with the cellranger pipeline (version 2.1.0, 10X Genomics) and mapped to the mouse reference genome (mm10) to generate matrices of cancer cell transcripts by cell barcodes..

treatment_protocol: For hydroxyl-tamoxifen (4OH-Tam) (Sigma-Aldrich) topical treatment, 4OH-Tam was dissolved in absolute ethanol (Sigma-Aldrich) to a final concentration of 20 mg/ml. To induce recombination, 100ul of 4OT-Tam topically applies on shaved back skin of P50 mice once per day for 4 days. For tumor-initiating agents, 15mg of DMBA (7,12-dimethylbenz[a]anthracene, Millipore Sigma) was dissolved in 4.5 mL of acetone to make 100X DMBA. For working 1X DMBA concentration, 150ul of 100X DMBA was diluted in 7ml of acetone. 0.2 mL of 1X DMBA solution was topically applied to the shaved dorsal skin of mice once per week for up to 20 weeks. Mice were monitored weekly. Mice are collected at 5-month-old ages

tag: site

value: Dorsal skin

value: Epidermal cancer cells

value: K14CrERT2;Eed flox/flox

value: hydroxyl-tamoxifen treated+DMBA

tag: age

value: 5 months-old


title: NF1+ MCF7 cells biol rep 1

description: Library name: Sample 1

value: WT


title: Adult Proximal, replicate 1, RNA_seq

description: Library name: AP1


title: IgG

description: Library name: set1_Gil_CTL_Epi92_IgG


title: Ctrl-D

description: Library name: Ctrl-D

value: Eed flox/flox

value: ethanol+DMBA


title: Empty vector #1

description:
Library name: WR1
column name in RNAseq_counts.tsv: WR1

value: Adrenocortical carcinoma cell


title: CD105F

status: Public on Jun 12 2026

city: Guangzhou

first: Ren

last: Mao

address: 58 Zhongshan Road 2nd, Guangzhou

institute: The First Affiliated Hospital, Sun Yat-Sen University

description:
Library name: sample14
10× Genomics

data_processing:
Human mesenteric tissue single-nucleus RNA-seq data were processed using Cell Ranger software (v3.1.0; 10x Genomics). Raw sequencing reads were converted to FASTQ files, aligned to the human reference genome, and quantified to generate gene-barcode expression matrices for each sample. Low-quality barcodes and UMIs were filtered out. Reads uniquely mapped to the transcriptome and intersecting exonic regions were counted. UMI sequences were corrected for sequencing errors, and valid cell/nucleus barcodes were identified for downstream matrix generation. Cell-by-gene count matrices were generated by UMI counting and cell barcode calling. The filtered feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, are provided as processed data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Creeping fat of Mesenteric adipose tissue in Crohn's disease

extract_protocol:
The samples were chopped on ice into 1-2 mm³ pieces, transferred to cryovials, snap-frozen in liquid nitrogen for 5 minutes, and then stored in an ultra-low temperature freezer and liquid nitrogen.. Then transfer the tissue from the cryovial to a Dounce homogenizer and add 500 μl of pre-chilled lysis buffer to thaw. Use a small and a tight pestle to press the tissue 15-20 times and 5-10 times, respectively, to create a homogenate. Add 700 μl of nuclear wash buffer, mix, and filter through a 70 μm cell strainer. Add 1 ml of 50% iodixanol to the filtrate, mix gently, and layer onto a gradient solution of 30% and 33% iodixanol. Centrifuge at 10,000×g for 20 minutes at 4°C. Extract the white nuclear layer at the interface, add nuclear wash buffer, mix, and centrifuge at 500×g for 8 minutes at 4°C. Transfer the supernatant, resuspend the nuclei, and repeat the wash. Filter through a 40 μm filter, centrifuge, resuspend the nuclei, and adjust the concentration to 700-1200 nuclei/μl using a microscope.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and equenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.


title: CD87N

description:
Library name: sample13
10× Genomics

source_name: Normal mesenteric adipose tissue in Crohn's disease


title: CD87F

description:
Library name: sample12
10× Genomics

value: Creeping fat of Mesenteric adipose tissue in Crohn's disease


title: CD88F

description:
Library name: sample10
10× Genomics


title: CD88N

description:
Library name: sample11
10× Genomics

value: Normal mesenteric adipose tissue in Crohn's disease


title: CD95N

description:
Library name: sample9
10× Genomics


title: CD103F

description:
Library name: sample6
10× Genomics


title: RNA_BamMut No-Heat-Shock, white_sh, rep 2

status: Public on Jun 15 2026

city: Risskov

first: Thomas

middle: Høgsbro

last: Grønbæk

address: Broloftet 5, 4.tv

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description:
Library name: Sample_2
control_2 RNA_run19644

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

organism: Drosophila melanogaster

source_name: bam mutant ovarian cysts

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

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

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

value: bam mutant ovarian cysts

value: Bulk ovarian cysts

value: w ;nosP-GAL4-NGT40/+ ; e[1] bam[Delta86], pW20>w_sh[attP2] / bam[Delta86], P{w[+mC]=hs-bam.O}11d


title: CD121F

description:
Library name: sample4
10× Genomics


title: Lung 13

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Library name: Sample 31
Lung nuclei pooled from three Doxorubicin-treated mice, 6 days after treatment – replicate 1

data_processing:
Pre-processing of sequencing results and generation of count matrices was performed using the Cell Ranger version 9.0.0 (10x Genomics) with prebuilt annotation platform GRCm39-2024-A.
Assembly: GRCm39
Supplementary files format and content: filtered_feature_bc_matrix including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files

source_name: Lung

extract_protocol:
Before tissue extraction, lungs were perfused by injecting PBS through the right ventricle. The extracted pieces were frozen in liquid nitrogen. For kidney samples, half of a frozen mouse kidney was minced on dry ice and homogenized in 5 ml of ice-cold homogenization buffer until no visible chunks remained. Samples from 3 mice were pooled. A 200 µl aliquot of the pooled homogenate was mixed with 400 µl of cold lysis buffer from the Minute™ Single Nucleus Isolation Kit (Invent Biotechnologies) and processed according to the manufacturer's protocol. Nuclei were filtered, centrifuged, washed, and resuspended in PBS containing 1% BSA and 0.2 U/µl RNase inhibitor. Nuclei concentration was measured with Trypan Blue and adjusted to 700–1200 nuclei/µl. For lung samples, the protocol was similar, but only ~50 mg of frozen lung tissue was used for homogenization.
The single-nucleus libraries were prepared with Single Cell 3' v4 (polyA) chemistry  (10x Genomics).

value: Lung

tag: Sex

value: male

value: Lung cells

value: Doxo

value: 3 months old


title: CD121N

description:
Library name: sample5
10× Genomics


title: WiDr GSK715 RNA-seq replicate 2

city: Nanjing

first: Mu

last: Xu

address: No.32, Gongqingtuan Road,

department: Nanjing First Hospital

institute: Nanjing Medical University

description:
Library name: WiDr_GSK715_2
Total RNA from WiDr cells treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): widr_gene_count_matrix.tsv.gz.

data_processing:
Short-read RNA-seq: Adapters and low-quality reads were removed with Cutadapt. Clean reads were aligned to GRCh38 using HISAT2, and transcript abundance was quantified as FPKM using StringTie. Differential expression analysis was performed with DESeq2 (adjusted P < 0.05, |log2FC| >= 1).
ONT full-length cDNA sequencing: Raw pod5/fast5 signals were base-called with Dorado (--no-trim) to generate FASTQ reads. Reads passing the basecalling quality filter (Q >= 10) were retained as clean reads. Full-length cDNA reads were identified, oriented and trimmed using Pychopper (-Q 7 -z 50), followed by additional filtering with NanoFilt (-q 7 -l 50). Filtered full-length reads were aligned to GRCh38 using minimap2 (-ax splice -uf -k14). Consensus transcript sets were constructed using Pinfish, and transcript reconstruction and merging were performed with StringTie. Transcript abundance was quantified as TPM using Salmon. Differentially expressed transcripts and genes were identified using DESeq2 (P < 0.05 and |log2FoldChange| > 2). Poly(A) sites were identified, clustered and annotated using QuantifyPoly(A) to analyze 3'-end heterogeneity.
Processed matrices prepared for GEO: hct116_gene_count_matrix.tsv.gz; widr_gene_count_matrix.tsv.gz; ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.
Assembly: GRCh38
Supplementary files format and content: hct116_gene_count_matrix.tsv.gz and widr_gene_count_matrix.tsv.gz are gzip-compressed tab-delimited gene-level count matrices for short-read RNA-seq samples.
Supplementary files format and content: ont_widr_gene_counts_matrix.tsv.gz is a gzip-compressed tab-delimited gene-level count matrix for ONT full-length cDNA sequencing samples; ont_widr_full_length_stats.tsv.gz contains full-length read summary statistics.

growth_protocol: HCT116 and WiDr cells were cultured under standard mammalian cell culture conditions before treatment.

extract_protocol:
Total RNA was extracted from treated cells and assessed for quality before library construction.
Total RNA from WiDr and HCT-116 cells treated with DMSO, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor) for 96 h was subjected to poly(A)-enriched library construction by Lianchuan Biotechnology (Hangzhou) and paired-end sequencing on an Illumina NovaSeq 6000. WiDr cells treated with DMSO or 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h were subjected to Oxford Nanopore Technologies (ONT) full-length cDNA sequencing on a PromethION platform by Benagen (Wuhan).

treatment_protocol: Cells were treated for 96 h with DMSO vehicle control, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor), as applicable.

value: colon

value: WiDr

value: colorectal carcinoma cell line

value: short-read RNA-seq


title: NL101

description:
Library name: sample2
10× Genomics

source_name: Normal mesenteric adipose tissue in Non-IBD control


title: NL89

description:
Library name: sample3
10× Genomics

value: Normal mesenteric adipose tissue in Non-IBD control


title: AS041_V

type: RNA

city: Lørenskog

first: Hilde

middle: Loge

last: Nilsen

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

hyb_protocol: Amplification and labelling efficiency were controlled on the NanoDrop. The cRNA quality was assessed by measuring the RNA absorbance ratio 260nm/280nm. The specific activity of labeled cRNA (pmol Cy3 per ug cRNA) was defined to be 6 or above according to the Agilent recommendations.

scan_protocol: Standard Illumina Protocol

data_processing: Expression signals were normalized with the limma R package. Control probes were removed before processing. Background correction was done with the backgroundCorrect function, using the normexp method and offset 16. Hence the lowest possible normalized expression value is log2(16) = 4. Batch correction was done using the normalizeBetweenArrays function, using the quantile method.

source_name: Gut epithelium, P, Rectum

label_protocol: mRNA amplification, labelling, and hybridization were done following the manufacturer’s instructions (Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling). In short, 50 ng RNA was amplified and labelled with Cy3 using the Low Input Quick Amp Labeling Kit, one-color (product number 5190-2331), and the labelled cRNA was purified using the Qiagen RNeasy Mini Kit.

extract_protocol: Total RNA was isolated using AllPrep kit (Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24 Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was according to the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyser, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 were excluded.

value: gut epithelium

tag: status

value: Progressor

tag: segment

value: Rectum

tag: inflammation

tag: neoplasia


title: Peptidergic cells, sated, biol rep 2

city: Durham

first: Vincent

last: Croset

address: Department of Biosciences, South Road

country: United Kingdom

institute: Durham University

description:
Library name: H2
10X Genomics

data_processing:
Reads were aligned these to the FB2023_06 Drosophila melanogaster genome assembly (v6.52) using CellRanger 7.2.0 to create digital gene expression (DGE) matrices
Assembly: FB2023_06 Drosophila melanogaster genome assembly (v6.52)
Supplementary files format and content: Gene expression matrices H5 archives

source_name: Brain

extract_protocol:
Samples were mechanically dissociated for 30s in 1ml homogenisation buffer (250 mM Sucrose, 10 mM Tris-HCl pH 8.0, 25 mM KCl, 5 mM MgCl2, 0.1% Triton-x 100, 0.5% RNasin Plus, 1X 50X protease inhibitor, 0.1 mM DTT) using a pestle motor (DWK Life Sciences, 7495400000) before being released by 25 strokes of a dounce pestle (DWK Life Sciences, 8855000021). These steps were performed on ice. The homogenate was filtered through a 40µm cell strainer (pluriSelect, 43-10040-50) to remove unlysed tissue and again using a 40µm Flowmi (BelArt, H13680-0040) into a 1.5ml Eppendorf tube. Samples were centrifuged at 1000 x g for 10 mins at 4ºC, supernatant discarded and pellet resuspended in 500µl resuspension buffer (1X PBS, 0.5% BSA, 0.5% RNasin Plus). Samples were filtered once more using 40µm Flowmi into a 5ml FACs tube and incubated with Hoechst-33342 (1:1000, Invitrogen, 11534886) for 15 minutes on ice prior to fluorescent sorting.
mRNA barcoding was performed using 10X Genomics Chromium Single Cell 3’ Reagent Kit v3 according to manufacturer's instructions.

value: Brain

value: Peptidergic

value: Sated


title: WiDr DMSO RNA-seq replicate 3

description:
Library name: WiDr_DMSO_3
Total RNA from WiDr cells treated with DMSO vehicle control for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): widr_gene_count_matrix.tsv.gz.

value: DMSO vehicle control for 96 h


title: WiDr DMSO RNA-seq replicate 1

description:
Library name: WiDr_DMSO_1
Total RNA from WiDr cells treated with DMSO vehicle control for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): widr_gene_count_matrix.tsv.gz.


title: HCT116 GSK715 RNA-seq replicate 3

description:
Library name: HCT116_GSK715_3
Total RNA from HCT116 cells treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: WiDr DMSO RNA-seq replicate 2

description:
Library name: WiDr_DMSO_2
Total RNA from WiDr cells treated with DMSO vehicle control for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): widr_gene_count_matrix.tsv.gz.


title: HCT116 GSK715 RNA-seq replicate 2

description:
Library name: HCT116_GSK715_2
Total RNA from HCT116 cells treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: HCT116 GSK025 RNA-seq replicate 3

description:
Library name: HCT116_GSK025_3
Total RNA from HCT116 cells treated with 10 uM GSK025 (GSK3235025, PRMT5 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: HCT116 GSK025 RNA-seq replicate 2

description:
Library name: HCT116_GSK025_2
Total RNA from HCT116 cells treated with 10 uM GSK025 (GSK3235025, PRMT5 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: HCT116 GSK715 RNA-seq replicate 1

description:
Library name: HCT116_GSK715_1
Total RNA from HCT116 cells treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: HCT116 GSK025 RNA-seq replicate 1

description:
Library name: HCT116_GSK025_1
Total RNA from HCT116 cells treated with 10 uM GSK025 (GSK3235025, PRMT5 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: HCT116 DMSO RNA-seq replicate 3

description:
Library name: HCT116_DMSO_3
Total RNA from HCT116 cells treated with DMSO vehicle control for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: HCT116 DMSO RNA-seq replicate 2

description:
Library name: HCT116_DMSO_2
Total RNA from HCT116 cells treated with DMSO vehicle control for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.


title: RVVC patient neutrophil 3

city: Kunming

first: xiang

middle: wen

last: lan

address: 300 Bailong Temple, Panlong District, Kunming, Yunnan 650224, China

institute: Southwest Forestry University

description: Library name: C_3

data_processing:
Raw reads were filtered using Trimmomatic to remove low-quality bases and adapter sequences.
Assembly: Homo sapiens reference genome build GRCh38 (NCBI assembly: GCA_000001405.29).
Supplementary files format and content: The processed data file 1_genes_fpkm_expression.txt contains gene-level FPKM values for all samples, formatted as a tab-delimited text matrix. The first column contains Ensembl gene IDs, and subsequent columns correspond to each sample’s FPKM expression values.

source_name: Vaginal lavage fluid-derived neutrophils

extract_protocol:
Total RNA was extracted from neutrophils using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and purity were assessed using Agilent 2100 Bioanalyzer and NanoDrop spectrophotometry, with RIN values ≥ 7.0 used for library construction.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Briefly, mRNA was purified from total RNA, fragmented, and reverse-transcribed into cDNA. Adapters were ligated to the cDNA fragments, followed by PCR amplification. Library quality was validated using qPCR and Agilent 2100 before sequencing.

value: Neutrophils

value: RVVC patient


title: RVVC patient neutrophil 2

description: Library name: C_2

value: Vaginal lavage fluid-derived neutrophils


title: RVVC patient neutrophil 1

description: Library name: C_1


title: Healthy+IL-17A neutrophil 3

description: Library name: B_3

value: IL-17A treated


title: Healthy control neutrophil 3

description: Library name: A_3

value: Untreated healthy control


title: Lung 9

description:
Library name: Sample 27
Lung nuclei pooled from three Doxorubicin-treated mice, 2 days after treatment – replicate 3

value: Lung

value: male

value: Lung cells

value: Doxo

value: 3 months old


title: BJ_EV_1

description:
Library name: Sample 17
Cells were transduced with an empty vector lentivirus (MOI: 3) and cultured for 8 days - replicate 1

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

source_name: BJ

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

value: BJ

value: foreskin fibroblasts

value: WT

value: Empty vector (MOI:3)


title: T.aestivum,  Chromatin_Bound(CB) RNA-seq, ChineseSpring, mock, root, replicate2

city: shanghai

first: yijing

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

description: Library name: CB_RNA-seq_ChineseSpring_mock_root_rep2

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

organism: Triticum aestivum

source_name: root

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

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

value: root


title: AS068_III

source_name: Gut epithelium, NP, Descendens

value: gut epithelium

value: Non-progressor

value: Descendens


title: Healthy control neutrophil 2

description: Library name: A_2

value: Neutrophils


title: Healthy control neutrophil 1

description: Library name: A_1

value: Vaginal lavage fluid-derived neutrophils


title: Fibroblast,  Strain 47, replicate 4

city: Vienna

first: Trinh

last: Phan-Canh

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

country: Austria

institute: Medical University of Vienna

description: Library name: FB_47_12h_4

data_processing:
Raw paired-end reads (PE150) were trimmed with fastp to remove adaptors, poly-N sequences, and low-quality reads. Quality metrics (Q20, Q30, GC content) were assessed, and clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.0.5). Gene-level counts were generated with featureCounts (v1.5.0-p3).
Assembly: GRCh38/hg38
Supplementary files format and content: A matrix file are provided raw read count for all sample (column names) with Ensembl ID as row names.

source_name: primary fibroblasts

extract_protocol:
RNA was harvested using the ReliaPrepTM RNA Tissue Miniprep System (Promega, Madison, WI, USA)
Library preparation and bulk RNA-seq were performed by Novogene (Novogene, Cambridge, UK): poly(A)+ mRNA was enriched with poly(dT) beads, converted to double-stranded cDNA libraries, quality-controlled, pooled, and sequenced as 150 bp paired-end reads on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: comparing different clinical strains to PBS control

value: primary fibroblasts


title: Fibroblast,  PBS control, replicate 4

description: Library name: FB_PBS_12h_4

value: PBS


title: Fibroblast,  Strain 47, replicate 3

description: Library name: FB_47_12h_3


title: Fibroblast,  Strain 48, replicate 3

description: Library name: FB_48_12h_3


title: Fibroblast,  PBS control, replicate 3

description: Library name: FB_PBS_12h_3


title: Fibroblast,  Strain 48, replicate 2

description: Library name: FB_48_12h_2


title: Fibroblast,  PBS control, replicate 2

description: Library name: FB_pbs_12h_2


title: Fibroblast,  Strain 47, replicate 1

description: Library name: FB_47_12h_1


title: Fibroblast,  Strain 48, replicate 1

description: Library name: FB_48_12h_1


title: Fibroblast,  PBS control, replicate 1

description: Library name: FB_PBS_12h_1


title: Keratinocyte, Strain 47, replicate 4

description: Library name: KC_47_12h_4

source_name: primary keratinocytes

value: primary keratinocytes


title: Keratinocyte, Strain 48, replicate 4

description: Library name: KC_48_12h_4


title: Keratinocyte, PBS control, replicate 4

description: Library name: KC_PBS_12h_4


title: Keratinocyte, Strain 47, replicate 3

description: Library name: KC_47_12h_3


title: Keratinocyte, Strain 48, replicate 3

description: Library name: KC_48_12h_3


title: Keratinocyte, PBS control, replicate 3

description: Library name: KC_PBS_12h_3


title: Keratinocyte, Strain 48, replicate 2

description: Library name: KC_48_12h_2


title: Keratinocyte, PBS control, replicate 2

description: Library name: KC_PBS_12h_2


title: Keratinocyte, Strain 47, replicate 1

description: Library name: KC_47_12h_1


title: ChIP_Rh30_H3K9ac_BI1347-24hr_rep1

city: Boston

first: Susu

last: Zhang

state: MA

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Library name: ChIP_Rh30_H3K9ac_BI1347-24hr_rep1

data_processing:
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9). Raw FASTQ data were trimmed using Trimmomatic-v0.38 and paired end reads were aligned to human hg38 genome using Bowtie2 (v2.3.5) in very sensitive local mode --dovetail --phred33 -I 0 -X 2000 -N 1 --very-sensitive). Peaks were called using MAXS2 (v2.1.4) with a threshold of q<0.01 and peak were annotated to the nearest TSS using HOMER. Differential analysis was performed using DiffBind and DESeq2. Significantly changed peaks were defined by a 1.5-fold change threshold and FDR<0.05. Bigwig files were normalized and generated using Deeptools. Heatmaps were created by Deeptools using the normalized bigwig files.
Assembly: hg38
Supplementary files format and content: Bigwig file

growth_protocol: Rh30 is cultured in DMEN containing 10% FBS, 1% L-Glutamin, and 1% P.S.

extract_protocol:
ChIPseq+AMPure beads clean up
NEB Next Ultra II library prep kit

treatment_protocol: DMSO or BI1347 were added to cell after adhering.

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: ChIP_Rh30_H3K9ac_DMSO_rep2

description: Library name: ChIP_Rh30_H3K9ac_DMSO_rep2


title: ChIP_Rh30_MED1_BI1347-24hr_rep1

description: Library name: ChIP_Rh30_MED1_BI1347-24hr_rep1


title: ChIP_Rh30_MED1_DMSO_rep2

description: Library name: ChIP_Rh30_MED1_DMSO_rep2


title: ChIP_Rh30_MED1_DMSO_rep1

description: Library name: ChIP_Rh30_MED1_DMSO_rep1


title: Patient P101 plasma cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease 1 of 2

city: New Haven

first: Darin

last: Dolezal

address: 310 Cedar Street

department: Pathology

institute: Yale School of Medicine

description: Library name: P101_LMD1_PLASMA_EPIC

data_processing:
Sequencing reads were processed to generate fragment-level methylation profiles.
Assembly: Sequencing libraries included lambda phage DNA as a spike-in control. Reads were processed relative to the human reference genome GRCh37 (hg19).
Supplementary files format and content: Differentially methylated fragments (DMFs) were quantified and aggregated into matrices for downstream analysis.

source_name: Human plasma

extract_protocol:
Cell-free DNA (cfDNA) was extracted from plasma and cerebrospinal fluid using standard protocols. Tumor genomic DNA was extracted from FFPE tissue sections.
Libraries were prepared using the PredicineEPIC platform for genome-wide methylation profiling.

value: Human plasma

value: Non-small cell lung carcinoma


title: Patient P054 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P054_CRANI1_PLASMA_EPIC


title: HCT116 DMSO RNA-seq replicate 1

description:
Library name: HCT116_DMSO_1
Total RNA from HCT116 cells treated with DMSO vehicle control for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): hct116_gene_count_matrix.tsv.gz.

source_name: colon

value: colon

value: colorectal carcinoma cell line

value: DMSO vehicle control for 96 h

value: short-read RNA-seq


title: A.tauschii, ChIP-seq, H3K9ac, AL8-78, seedling

description: Library name: DD_AL8-78_Seedling_ChIP-seq_H3K9ac

data_processing:
The sequencing reads were trimmed with fastp (0.22.0).
The clean reads were aligned with bwa program (version 0.7.17-r1188).
Peaks were called using MACS (v2.1.0.20150731).
Assembly: Aegilops tauschii (DD, Aet_v4.0), Secale cereale (Weining.v1.0)
Supplementary files format and content: peak files

organism: Aegilops tauschii

source_name: 9-day-old seedling

growth_protocol: Seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C.The germinated seeds with residual endosperm were transferred to soil  and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.

extract_protocol:
The 9-day-old seedlings (above-ground parts) were harvested and directly vacuum-infiltrated with a formaldehyde cross-linking solution for ChIP-seq. More than 10 ng of ChIP DNA extracted from each sample was used to prepare the sequencing samples.
ChIP-seq

value: 9-day-old seedling

tag: chip antibody

value: H3 acetyl-Lys 9 (Upstate)


title: Fibroblast,  Strain 48, replicate 4

description: Library name: FB_48_12h_4


title: Fibroblast,  Strain 47, replicate 2

description: Library name: FB_47_12h_2


title: Patient P052 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P052_CRANI1_PLASMA_EPIC


title: Patient P051 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P051_CRANI1_PLASMA_EPIC


title: Patient P050 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P050_CRANI1_PLASMA_EPIC


title: Patient P049 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P049_CRANI1_PLASMA_EPIC


title: Patient P048 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P048_CRANI1_PLASMA_EPIC


title: Patient P047 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P047_CRANI1_PLASMA_EPIC


title: A.tauschii, ChIP-seq, H3K4me3, AL8-78, seedling

description: Library name: DD_AL8-78_Seedling_ChIP-seq_H3K4me3

value: H3 trimethyl-Lys 4 (Abcam)


title: AS050_V

source_name: Gut epithelium, NP, Rectum

value: gut epithelium

value: Non-progressor

value: Rectum

value: Chronic active


title: Keratinocyte, Strain 47, replicate 2

description: Library name: KC_47_12h_2


title: Patient P046 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P046_CRANI1_PLASMA_EPIC


title: Patient P045 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P045_CRANI1_PLASMA_EPIC


title: Keratinocyte, PBS control, replicate 1

description: Library name: KC_PBS_12h_1

value: PBS


title: ChIP_Rh30_H3K9ac_BI1347-24hr_rep2

description: Library name: ChIP_Rh30_H3K9ac_BI1347-24hr_rep2

tag: cell line


title: Patient P044 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P044_CRANI1_PLASMA_EPIC

tag: tissue


title: Keratinocyte, Strain 48, replicate 1

description: Library name: KC_48_12h_1

tag: cell type

value: primary keratinocytes


title: Patient P043 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P043_CRANI1_PLASMA_EPIC


title: Patient P042 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P042_CRANI1_PLASMA_EPIC


title: Patient P041 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P041_CRANI1_PLASMA_EPIC


title: Patient P040 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P040_CRANI1_PLASMA_EPIC


title: Patient P039 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P039_CRANI1_PLASMA_EPIC


title: ChIP_Rh30_MED1_BI1347-24hr_rep2

description: Library name: ChIP_Rh30_MED1_BI1347-24hr_rep2

value: Rhabdomyosarcoma

tag: genotype


title: Patient P038 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P038_CRANI1_PLASMA_EPIC


title: ChIP_Rh30_H3K9ac_DMSO_rep1

description: Library name: ChIP_Rh30_H3K9ac_DMSO_rep1

value: PAX3::FOXO1 fusion


title: Patient P037 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy 1 of 2

description: Library name: P037_CRANI1_PLASMA_EPIC

value: Human plasma


title: Patient P036 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P036_CRANI1_PLASMA_EPIC

value: Non-small cell lung carcinoma


title: Patient P035 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P035_CRANI1_PLASMA_EPIC


title: Patient P037 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy 2 of 2

description: Library name: P037_CRANI2_PLASMA_EPIC


title: Patient P034 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P034_CRANI1_PLASMA_EPIC


title: Patient P033 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P033_CRANI1_PLASMA_EPIC


title: Patient P031 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P031_CRANI1_PLASMA_EPIC


title: Patient P032 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P032_CRANI1_PLASMA_EPIC


title: Patient P101 plasma cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease 2 of 2

description: Library name: P101_LMD2_PLASMA_EPIC


title: Patient P030 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P030_CRANI1_PLASMA_EPIC


title: Patient P029 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P029_CRANI1_PLASMA_EPIC


title: Patient P026 plasma cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease

description: Library name: P026_LMD1_PLASMA_EPIC


title: WT_3, (boe16 dataset)

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (GRCm38) with STAR 2.6.1d (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.21.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: heart

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 500ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq500 platform (Illumina) using P3 flowcell with 75bp single-end setup.

value: heart

value: WT


title: WT_2, (boe16 dataset)

description: Library name: Sample 5


title: Patient P026 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P026_CRANI1_PLASMA_EPIC


title: Patient P025 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P025_CRANI1_PLASMA_EPIC


title: WT_1, (boe16 dataset)

description: Library name: Sample 4


title: KO_3, (boe16 dataset)

description: Library name: Sample 3

value: trdn-as KO


title: Patient P055 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P055_CRANI1_PLASMA_EPIC


title: KO_2, (boe16 dataset)

description: Library name: Sample 2


title: KO_1, (boe16 dataset)

description: Library name: Sample 1


title: Patient P024 plasma cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease

description: Library name: P024_LMD1_PLASMA_EPIC


title: Patient P023 plasma cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease

description: Library name: P023_LMD1_PLASMA_EPIC


title: Th0_48hr_2

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: Library name: Th0_48hr_2

data_processing:
Base-calling was performed by RTA v2.4.11, and the BCL files were translated to fastqs using bcl2fastq2 v2.20.0.
Reads were aligned to reference mouse annotation mm10 using Bowtie2, and filtered for duplicated and mitochondrial reads. Peak-calling was performed using MACS2. Read counts per peak were computed using bedtools multicov tool for each sample and then column combined into a matrix.
Assembly: mm10
Supplementary files format and content: Tab-delimited files (.txt) include count values for each peak in each sample.
Supplementary files format and content: Bigwig files (.bw) containing the read coverage data.

source_name: Spleen and lymph nodes

growth_protocol: For the in vitro differentiation of naive CD4+ T cells, naive CD4+ CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines.

extract_protocol:
6,000 viable cells were sorted into PBS/2% FCS and were stored in BambankerTM cell freezing media at -80°C.
For bulk ATAC-seq, cells were thawed at 37°C. Subsequently, cells were lysed and tagmented in 1X TD Buffer, 0.2l TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS at 37°C for 30 min at 300 rpm. DNA purification was performed with the MinElute PCR purification kit (QIAGEN). The complete eluate was pre-amplified with 5 PCR cycles using indexed primers with NEBNext High-Fidelity 2X PCR Master Mix (NEB) and the number of additional cycles was determined by SYBR Green quantitative PCR. After DNA purification, library quantification and quality control were performed with the Kapa Library Quantification Kit (Kapa Biosystems) and a Qubit dsDNA HS Assay kit (Invitrogen). Libraries were sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.

value: Spleen and lymph nodes


title: Patient P023 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P023_CRANI1_PLASMA_EPIC


title: Th0_48hr_1

description: Library name: Th0_48hr_1


title: Patient P022 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P022_CRANI1_PLASMA_EPIC


title: Th0_48hr_3

description: Library name: Th0_48hr_3


title: Patient P022 plasma cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease

description: Library name: P022_LMD1_PLASMA_EPIC


title: Cyp11a1-KO-CNS-6

description:
Library name: Cyp11a1-KO-CNS-6
KO-CNS-6

data_processing:
Base-calling was performed using NextSeq Control Software 2.2.0.4 (RTA 2.4.11) and the BCL files were demultiplexed into fastq files using bcl2fast2 v2.20.0.422. Data were then preprocessed using the Cumulus SMART-Seq2v2.6.1 workflow on Terra (https://terra.bio/). The workflow employs histat2 v2.1.0 to align read to mm10 mouse genome, and the RSEM v1.3.3 to calculate raw counts and TPM. The workflow computes the TPM-normalized count for each gene, defined as TPM_i / 10^6 * c rounded to the nearest integer, where TPM_i is the TPM for gene i, and c is the total number of reads achieved for the sample.
Assembly: mm10
Supplementary files format and content: comma-separated values (CSV) files include TPM-normalized count for every gene (rows)  in every sample (columns)

source_name: CNS

extract_protocol:
For the CYP11A1 WT vs. cKO and GR WT vs. cKO experiments, EAE mice were euthanized and perfused intracardially with ice-cold PBS. The brain and spinal cord were finely minced using a razor blade and digested with 2.5 mg/ml collagenase D (Roche Diagnostics) at 37°C for 20 minutes. The digested tissue was then passed through a 70-μm strainer. Mononuclear cells were isolated by density gradient centrifugation using a Percoll (Amersham Biosciences) gradient of 37% and 70%. The mononuclear cells were collected from the interphase for further analysis. 2,000 CNS-infiltrating 2D2+ cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).  For the in vitro Dex and TGF-β1 treatment experiment, in vitro–differentiated Th17Inf cells were treated with dexamethasone (Dex), TGF-β1, or a combination of both for 2 days. 2,000 live Th17 cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).
Libraries were prepared using a modified SMART-Seq2 protocol, including RNA secondary structure denaturation at 72 °C for 3 min, reverse transcription with Maxima Reverse Transcriptase (Thermo Fischer Scientific) and whole-transcriptome amplification using KAPA HiFi HotStart ReadyMix 2× (KAPA Biosystems) for 12 cycles. Whole-transcriptome amplification product quality was confirmed with a High Sensitivity DNA Chip run on a Bioanalyzer 2100 (Agilent, G2939BA) and quantified using a Qubit dsDNA HS Assay kit (Thermo Scientific). Libraries were prepared with a Nextera XT DNA Library Preparation kit (Illumina) and sequenced using a high-output V2 75 cycle kit (Illumina) on a NextSeq 500 sequencer (Illumina) with 2 × 38 paired-end reads.

value: CNS

value: T cell


title: Patient P021 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P021_CRANI1_PLASMA_EPIC


title: Patient P020 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P020_CRANI1_PLASMA_EPIC


title: Cyp11a1-KO-CNS-5

description:
Library name: Cyp11a1-KO-CNS-5
KO-CNS-5


title: Patient P018 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P018_CRANI1_PLASMA_EPIC


title: Cyp11a1-KO-CNS-4

description:
Library name: Cyp11a1-KO-CNS-4
KO-CNS-4


title: Patient P016 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P016_CRANI1_PLASMA_EPIC


title: Patient P019 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P019_CRANI1_PLASMA_EPIC


title: Cyp11a1-KO-CNS-1

description:
Library name: Cyp11a1-KO-CNS-1
KO-CNS-1


title: Cyp11a1-KO-CNS-2

description:
Library name: Cyp11a1-KO-CNS-2
KO-CNS-2


title: Cyp11a1-WT-CNS-4

description:
Library name: Cyp11a1-WT-CNS-4
WT-CNS-4


title: Cyp11a1-WT-CNS-3

description:
Library name: Cyp11a1-WT-CNS-3
WT-CNS-3


title: Patient P017 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P017_CRANI1_PLASMA_EPIC


title: Patient P014 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P014_CRANI1_PLASMA_EPIC


title: Cyp11a1-KO-CNS-3

description:
Library name: Cyp11a1-KO-CNS-3
KO-CNS-3


title: Patient P015 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P015_CRANI1_PLASMA_EPIC


title: Patient P013 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P013_CRANI1_PLASMA_EPIC


title: Patient P053 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P053_CRANI1_PLASMA_EPIC


title: Cyp11a1-WT-CNS-2

description:
Library name: Cyp11a1-WT-CNS-2
WT-CNS-2


title: Patient P011 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P011_CRANI1_PLASMA_EPIC


title: Patient P009 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P009_CRANI1_PLASMA_EPIC


title: Cyp11a1-WT-CNS-1

description:
Library name: Cyp11a1-WT-CNS-1
WT-CNS-1


title: Patient P012 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P012_CRANI1_PLASMA_EPIC


title: Patient P010 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P010_CRANI1_PLASMA_EPIC


title: KO_Dex_7

description: Library name: KO_Dex_7

source_name: in vitro; originally from spleen and dLN

extract_protocol:
For the CHD1 WT vs. cKO and GR WT vs. cKO experiments, EAE mice were euthanized and perfused intracardially with ice-cold PBS. The brain and spinal cord were finely minced using a razor blade and digested with 2.5 mg/ml collagenase D (Roche Diagnostics) at 37°C for 20 minutes. The digested tissue was then passed through a 70-μm strainer. Mononuclear cells were isolated by density gradient centrifugation using a Percoll (Amersham Biosciences) gradient of 37% and 70%. The mononuclear cells were collected from the interphase for further analysis. 2,000 CNS-infiltrating 2D2+ cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich). At the same time, draining lymph nodes (dLNs) cells were obtained by mechanically dispersing the organs through a 70-μm strainer. 2,000 2D2+ cells were sorted from dLN by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).  For the in vitro Dex treatment experiment, naive T cells from WT or IL-23R KO mice were differentiated into Th17Inf cells in vitro and treated with or without dexamethasone (Dex) for two days. 2,000 live Th17 cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).
Libraries were prepared using a modified SMART-Seq2 protocol, including RNA secondary structure denaturation at 72 °C for 3 min, reverse transcription with Maxima Reverse Transcriptase (Thermo Fischer Scientific) and whole-transcriptome amplification using KAPA HiFi HotStart ReadyMix 2× (KAPA Biosystems) for 12 cycles. Whole-transcriptome amplification product quality was confirmed with a High Sensitivity DNA Chip run on a Bioanalyzer 2100 (Agilent, G2939BA) and quantified using a Qubit dsDNA HS Assay kit (Thermo Scientific). Libraries were prepared with a Nextera XT DNA Library Preparation kit (Illumina) and sequenced using a high-output V2 75 cycle kit (Illumina) on a NextSeq 500 sequencer (Illumina) with 2 × 38 paired-end reads.


title: KO_Dex_6

description: Library name: KO_Dex_6

value: in vitro; originally from spleen and dLN


title: KO_Dex_8

description: Library name: KO_Dex_8


title: Patient P008 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P008_CRANI1_PLASMA_EPIC


title: KO_Dex_5

description: Library name: KO_Dex_5


title: Patient P007 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P007_CRANI1_PLASMA_EPIC


title: WT_Dex_4

description: Library name: WT_Dex_4


title: WT_Dex_3

description: Library name: WT_Dex_3


title: Patient P006 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P006_CRANI1_PLASMA_EPIC


title: Patient P005 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P005_CRANI1_PLASMA_EPIC


title: WT_Dex_2

description: Library name: WT_Dex_2


title: Patient P004 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy 1 of 2

description: Library name: P004_CRANI1_PLASMA_EPIC


title: KO_Ctrl_8

description: Library name: KO_Ctrl_8


title: Patient P004 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy 2 of 2

description: Library name: P004_CRANI2_PLASMA_EPIC


title: WT_Dex_1

description: Library name: WT_Dex_1