title: MLE-12 cells, 1 mM glucose, 12 hours, rep3

city: Guangzhou

first: Xiting

last: Lv

state: Guangdong

address: No. 232 East Ring Road, Guangzhou Higher Education Mega Center

institute: Guangzhou University of Chinese Medicine

description: Library name: MLE12_1 mM 3

data_processing:
DESeq2 (v1.16.1)
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Total RNA Extraction Kit 2.0 Plus. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer's instructions.

value: Lung epithelial cells

value: 1 mM glucose, 12 hours


title: HUDEP2 cells; KO_rep3;H3K4me3;ChIP-seq

status: Public on Apr 10 2026

type: SRA

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

country: China

institute: Soochow University

description: Library name: 1345264_PXU030_R1

library_source: genomic

data_processing:
For ChIP-Seq, raw sequencing data were aligned to the mouse genome mm9 and the drosophila genome dm6 using Bowtie2 (ref. 51; v2.3.2). To identify ChIP-enriched regions, SICER52 (v1.1) was used. For ChIP–seq of KMT2D, the window size of 50 bp, the gap size of 50 bp and the false discovery rate (FDR) threshold of 0.05 were used. For ChIP–seq of histone modifications (H3K4me1 and H3K27ac), the window size of 200 bp, the gap size of 200 bp and the FDR threshold of 10−3 were used. Reads on indicated regions were collected to calculate reads per kilobase million as a measure of signal intensity.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: Human bone marrow

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Antibody were added to the sonication samples, followed with gentle rotation for 16 hours at 4°C, Beads added after that,followed with gentle rotation for 6 hours at 4°C. beads transfered to a new tube. Using wash buffer to wash beads, then, samples were incubated in SDS elution buffer for 6 hours. separate beads and supernatant, DNA was in supernatant and then extracted by the phenol/chloroform/isopropanol protocol. Library construction was performed using the DNA Library Prep Kit.

tag: tissue

value: Human bone marrow

tag: cell line

tag: cell type

value: erythroblast cells

tag: treatment

value: KO

tag: antibody

value: H3K4me3(Cell Signaling Tech,C42D8)


title: B12 High treated splenic CD11b+ Cells

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

country: USA

institute: University of Miami

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing and aggregation were made using the Cell Ranger software v2.1.1
Assembly: m38
Supplementary files format and content: Tab-separate values file and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Splenic Cd45.2+CD11b+ Cells

extract_protocol:
Viably frozen single cell suspensions of splenic cells were FACS sorted on CD45.2+CD11b+DAPI. Cells were resuspended in 10% FBS in PBS.
Library preparation was performed according to manufacturer's instruction (single cell 3' v2 protocol, 10x Genomics).

value: Splenic Cd45.2+CD11b+ Cells

value: High B12


title: isl1-cpf1_sib-homeo-2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: isl1-cpf1_sib-homeo-2

library_source: transcriptomic

data_processing:
RNA-seq raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner (version 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (version v1.3.0 ).
ATAC-seq raw reads were aligned using bowtie2 default parameters.
Assembly: danRer11
Supplementary files format and content: RNA-seq processed read count in csv file
Supplementary files format and content: ATAC-seq processed data in bigwig file format

molecule: polyA RNA

organism: Danio rerio

source_name: posterior lateral line

growth_protocol: embryos were raised until 5dpf larval stage in E2 embryo medium.

extract_protocol:
mcherry+ cells were FACsorted after Trypsin larvae dissociation. For RNA-seq, cells were sorted into Trizol and RNA was extracted using phenol/chloroform extraction method. For ATAC-seq, nuclei were extracted and tagmentation performed as described in Buenrostro, Jason D et al., Nat. Methods (2013) and Corces, M. R. et al., Nat. Methods (2017).
RNA libraries for RNA-seq were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing following manufacturer's protocols. For ATAC-seq, DNA fragments were purified using the Monarch PCR & DNA Cleanup Kit following manufacturer's instructions. Libraries were constructed using Illumina Nextera Dual Indexing as described in Corces, M. R. et al., Nat. Methods (2017).

treatment_protocol: 300uM neomycin treatment was done at 5dpf (not in homeostasis samples) for 30min, then samples were extensively washed with E2 embryo medium and let to recover for 1 hr or 3hr depending on the sample.

value: posterior lateral line

value: neuromast cells

tag: genotype

value: isl1apsi97 sibling

value: homeostasis


title: GMD2.B

city: South San Francisco

first: Xinming

last: Tong

state: California

address: 1 DNA Way

institute: Genentech Inv.

description: Library name: SAM24459012

data_processing:
Read count extraction was performed using internal GSNAP-based NGS workflow
Assembly: Genome Reference Consortium Human build 38
Supplementary files format and content: CSV files includes raw counts for each sample

source_name: colon organoid

extract_protocol:
The RNA was isolated using QIAGEN´s RNeasy Plus Mini Kit
Libraries were prepared using the TruSeq RNA Sample Preparation Kit

value: colon organoid


title: isl1-cpf1_sib-homeo-3

description: Library name: isl1-cpf1_sib-homeo-3


title: GMD1.B

description: Library name: SAM24459010


title: MLE-12 cells, 1 mM glucose, 12 hours, rep2

description: Library name: MLE12_1 mM 2


title: GMD2.A

description: Library name: SAM24459011


title: HUDEP2 cells; NT_rep3;H3K4me3;ChIP-seq

description: Library name: 1345260_PXU026_R1

value: NT


title: HUDEP2 cells; dTAG13 treated_rep1

description: Library name: TAG_1

data_processing:
Raw counts of gene transcripts were derived from raw fastq files using the alignment-independent quantification tool, Salmon (https://combine- lab.github.io/salmon/), with standard settings. The raw count matrix was then imported into R-studio and utilized as input for Limma_voom analysis following the vignette of the package for normalization, differential gene expression analysis, and unbiased clustering analysis, including principal component analysis. The output of Limma_voom was used as the input for pre-ranked-based GSEA to enrich functional pathways and gene signatures (https://www.gsea-msigdb.org/gsea/index.jsp).
Assembly: hg19
Supplementary files format and content: Count file

source_name: Blood

extract_protocol:
RNA samples of two biological replicates were extracted from cultured cells, using TRIzol (Ambion by Life technologies, 343,911), following the manufacturer’s instructions. RNA was then sent out for library preparation and next-generation sequencing to a commercial company, Novogene (CA, USA).
According to the manufacturer's instructions, three biologically duplicated RNA samples were extracted from cultured cells using TRIZOL (Ambion by Life technologies, 343911). RNA sample quality was analyzed, and library were prepared and next-generation sequenced by a commercial company, Novogene (California, USA).

value: Blood

value: Human blood


title: GMD1.A

description: Library name: SAM24459009


title: CD8+CD90.1+P4-6CD25high transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 3

city: Nashville

first: Mary

last: Philip

state: TN

address: 777 PRB, 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

description: Library name: E48h-D456-25hi-3

data_processing:
Reads were aligned to the mouse reference genome (GRCm38) with BWA-backtrac. Post alignment filtering was done with samtools v1.656 and Broad Institute’s Picard tools to remove unmapped reads, improperly paired reads, nonunique reads, and duplicates. To identify regions of open chromatin, peak calling was performed with MACS2 v2.2.657. Only peaks with adjusted P values smaller than 0.01 were retained.
Consensus peak sets were generated if a peak was found in at least two replicates. The peak atlas was annotated using the ChIPseeker and TxDb.Mmusculus.UCSC.mm10.knownGene.
Coverage files (BigWig) per replicate normalized for differences in sequencing depths between the different samples were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40 . Blacklisted genomic regions were excluded (https://sites.google.com/site/anshulkundaje/projects/blacklists).
Assembly: GRCm38.p6
Supplementary files format and content: BigWig files

source_name: spleen

extract_protocol:
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition happened at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio.

value: spleen

value: primary cells

value: CD8 T cell

value: Listeria monocytogenes

tag: batch

value: Favret


title: MLE-12 cells, 25 mM glucose, 12 hours, rep3

description: Library name: MLE12_25 mM 3

value: Lung epithelial cells

value: 25 mM glucose, 12 hours


title: MLE-12 cells, 1 mM glucose, 12 hours, rep1

description: Library name: MLE12_1 mM 1

value: 1 mM glucose, 12 hours


title: HUDEP2 cells; KO_rep1;H3K4me3;ChIP-seq

description: Library name: 1480009_PXU010_R1

value: Human bone marrow

value: erythroblast cells

value: KO

value: H3K4me3(Cell Signaling Tech,C42D8)


title: isl1-cpf1_sib-3hneo-3

description: Library name: isl1-cpf1_sib-3hneo-3

value: posterior lateral line

value: neuromast cells

value: isl1apsi97 sibling

value: 30min neomycin (300uM)


title: isl1-cpf1_sib-3hneo-2

description: Library name: isl1-cpf1_sib-3hneo-2


title: MLE-12 cells, 25 mM glucose, 12 hours, rep2

description: Library name: MLE12_25 mM 2


title: isl1-cpf1_sib-homeo-1

description: Library name: isl1-cpf1_sib-homeo-1

value: homeostasis


title: HUDEP2 cells; NT_rep2;H3K4me3;ChIP-seq

description: Library name: 1480012_PXU013_R1

value: NT


title: MLE-12 cells, 25 mM glucose, 12 hours, rep1

description: Library name: MLE12_25 mM 1


title: isl1-cpf1_sib-3hneo-1

description: Library name: isl1-cpf1_sib-3hneo-1


title: CD8+CD90.1+P4-6CD25high transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 2

description: Library name: E48h-D456-25hi-2

value: spleen

value: primary cells


title: CD8+CD90.1+P4-6CD25high transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 1

description: Library name: E48h-D456-25hi-1

value: CD8 T cell

value: Listeria monocytogenes


title: HUDEP2 cells; KO_rep2;H3K4me3;ChIP-seq

description: Library name: 1480013_PXU014_R1


title: HUDEP2 cells; NT_rep1;H3K4me3;ChIP-seq

description: Library name: 1480008_PXU009_R1


title: isl1-cpf1_mut-homeo-3

description: Library name: isl1-cpf1_mut-homeo-3

value: isl1apsi97 mutant


title: Lung tissue collected from hypoglycemic mice with IAV infection for 3 day, rep3

description: Library name: Hypoglycemia_IAV 4

source_name: Lung

value: Lung


title: CD8+CD90.1+P4-6CD25low transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 3

description: Library name: E48h-D456-25lo-3

value: Favret


title: HUDEP2 cells; KO_rep3;H3K4me1;ChIP-seq

description: Library name: 1345263_PXU029_R1

value: Human bone marrow


title: Lung tissue collected from hypoglycemic mice with IAV infection for 3 day, rep2

description: Library name: Hypoglycemia_IAV 3


title: HUDEP2 cells; NT_rep3;H3K4me1;ChIP-seq

description: Library name: 1345259_PXU025_R1

value: erythroblast cells


title: isl1-cpf1_mut-homeo-2

description: Library name: isl1-cpf1_mut-homeo-2


title: isl1-cpf1_mut-homeo-1

description: Library name: isl1-cpf1_mut-homeo-1


title: isl1-cpf1_mut-3hneo-3

description: Library name: isl1-cpf1_mut-3hneo-3


title: CD8+CD90.1+P4-6CD25low transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 1

description: Library name: E48h-D456-25lo-1


title: HUDEP2 cells; KO_rep2;H3K4me1;ChIP-seq

description: Library name: 1480005_PXU006_R1

value: KO


title: CD8+CD90.1+P4-6CD25low transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 2

description: Library name: E48h-D456-25lo-2


title: Lung tissue collected from control mice with IAV infection for 3 day, rep3

description: Library name: Ctrl_IAV 3


title: isl1-cpf1_mut-3hneo-2

description: Library name: isl1-cpf1_mut-3hneo-2


title: Lung tissue collected from control mice with IAV infection for 3 day, rep2

description: Library name: Ctrl_IAV 2


title: isl1-cpf1_mut-3hneo-1

description: Library name: isl1-cpf1_mut-3hneo-1


title: Lung tissue collected from hypoglycemic mice with IAV infection for 3 day, rep1

description: Library name: Hypoglycemia_IAV 1


title: HUDEP2 cells; KO_rep1;H3K4me1;ChIP-seq

description: Library name: 1480001_PXU002_R1


title: HUDEP2 cells; NT_rep2;H3K4me1;ChIP-seq

description: Library name: 1480004_PXU005_R1


title: CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 2

description: Library name: E48h-D123-2


title: live CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 3

description: Library name: E48h-D123-3


title: CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T cells isolated 12h post activation in LMTAG infected spleens, rep 3

description: Library name: E12hr-3


title: Lung tissue, 2 U/kg insulin treatment, 5 day, rep3

description: Library name: Hypoglycemia 3

value: 2 U/kg insulin treatment, 5 day


title: A549 cells, 1.1 mM glucose, 24 hours, rep3

description: Library name: A549_1.1 mM 3

value: Human lung adenocarcinoma cells

value: 1.1 mM glucose, 24 hours


title: CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T cells isolated 12h post activation in LMTAG infected spleens, rep 2

description: Library name: E12hr-2


title: A549 cells, 1.1 mM glucose, 24 hours, rep1

description: Library name: A549_1.1 mM 1


title: HUDEP2 cells; NT_rep1;H3K4me1;ChIP-seq

description: Library name: 1480000_PXU001_R1


title: Lung tissue collected from control mice with IAV infection for 3 day, rep1

description: Library name: Ctrl_IAV 1


title: A549 cells, 1.1 mM glucose, 24 hours, rep2

description: Library name: A549_1.1 mM 2


title: Lung tissue, 2 U/kg insulin treatment, 5 day, rep1

description: Library name: Hypoglycemia 1


title: HUDEP2 cells; 5-Ph-IAA treated_rep3;KMT2D;ChIP-seq

description: Library name: IAA-K2D-R4

value: 5-Ph-IAA treated


title: Lung tissue, 2 U/kg insulin treatment, 5 day, rep2

description: Library name: Hypoglycemia 2


title: CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T cells isolated 12h post activation in LMTAG infected spleens, rep 1

description: Library name: E12hr-1


title: Lung tissue, PBS treatment, 5 day, rep3

description: Library name: Ctrl 3

value: PBS treatment, 5 day


title: A549 cells, 11.1 mM glucose, 24 hours, rep3

description: Library name: A549_11.1 mM 3

value: 11.1 mM glucose, 24 hours


title: CD8+CD90.1+CD44- transgenic TCRTAG CD8 T cells isolated from spleens, rep 3

description: Library name: N-3


title: A549 cells, 11.1 mM glucose, 24 hours, rep2

description: Library name: A549_11.1 mM 2


title: HUDEP2 cells; 5-Ph-IAA treated_rep1;KMT2D;ChIP-seq

description: Library name: H2-IAA_R2


title: Lung tissue, PBS treatment, 5 day, rep2

description: Library name: Ctrl 2


title: HUDEP2 cells; DMSO treated_rep3;KMT2D;ChIP-seq

description: Library name: DMSO-K2D-R4

value: DMSO treated


title: RSL3-3

city: hefei

first: Wentao

last: Zhang

state: anhui

address: meishan road

institute: anhui medical university

description:
Library name: Sample 6
LIU-LSC-1, RSL3 IC20, rep 3

data_processing:
Sequencing data were demultiplexed, quality filtered (allowing up to 5 bp mismatches), and merged using in-house shell scripts. MAGeCK (v0.5.9) was used to count and normalize sgRNA reads (using mageck count), followed by differential analysis (mageck test) between treatment and control conditions. sgRNA abundance and gene enrichment were visualized with MAGeCK’s built-in plotting tools
Assembly: GRCh38
Supplementary files format and content: raw sgRNA counts matrix in txt format
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted from over 3×10⁷ cells per sample using standard phenol-chloroform extraction, followed by ethanol precipitation. DNA quality was assessed using agarose gel electrophoresis, and concentration was quantified using a Qubit fluorometer. At least 3 μg of genomic DNA per sample was used for sgRNA library amplification.
Two-step PCR was performed to amplify sgRNA cassettes. The first PCR used NEB Q5 polymerase to amplify sgRNA regions from genomic DNA (10,000× coverage), followed by magnetic bead purification. A second PCR added Illumina index primers. Libraries were size-selected (~280 bp), quantified (Qubit), and adjusted to 3 ng/μL. Final libraries were pooled and sequenced on Illumina HiSeq Xten or NovaSeq platforms (PE150, paired-end 150 bp).

value: HNSCC cell line

value: wild-type

value: RSL3 IC20


title: HL_G2_3C

city: Giessen

first: Vijay

middle: Kumar

last: Singh

address: Feulgenstrasse 12

department: Department of Pediatric Oncology, Hematology, and Immunodeficiencies

country: Germany

description: Library name: Sample 32

data_processing:
CLC Genomics Workbench - Qiagen Genomic Services
Raw data was de-multiplexed FASTQ files for each sample were generated using the bcl2fastq
Cutadapt (v1.11) extracts adapter and UMI info, then trims adapters and collapses reads by UMI.
Reads were mapped with Bowtie2 (v2.2.2); only perfect matches were kept.
Trimmed sequence reads were mapped to GRCh37 using QIAGEN CLC Genomic service tools. For mapping to the genome, not more than one mismatch is allowed in the first 32 basesof the read. No indels are allowed in mapping.
Read count extraction and normalization were performed using QIAGEN CLC genomic benchwork
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: Serum

extract_protocol:
RNA was isolated using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturers insructions.
small RNA libraries for non coding-seq were prepared using the QIAseq miRNA Library Kit following manufacturer's protocols.

value: Serum

value: Classical Hodgkin Lymphoma

value: Post-Induction

tag: time

value: Day 57


title: HUDEP2 cells; 5-Ph-IAA treated_rep2;KMT2D;ChIP-seq

description: Library name: IAA-K2D-R3

value: Human bone marrow


title: Sort-purified (live CD8+CD90.1+CD44-) transgenic TCRTAG CD8 T cells isolated from spleens, rep 2

description: Library name: N-2

value: spleen

value: primary cells

value: CD8 T cell

value: Favret


title: CD8+CD90.1+CD44- transgenic TCRTAG CD8 T cells isolated from spleens, rep 1

description: Library name: N-1


title: OVSOGA1si3

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

description: Library name: Sanple 6

data_processing:
Bridge amplification. Bridge PCR amplification was performed on the cBot instrument to generate clusters.
The Illumina sequencing platform uses a 2*150 sequencing mode for Sequencing by Synthesis. Four fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the flow cell for amplification. During the extension of the complementary strand in each sequencing cluster, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence. The sequencer captures the fluorescence signals, and computer software converts the light signals into sequencing peaks, thereby obtaining the sequence information of the target fragments.
The image data of sequencing fragments obtained by the high-throughput sequencer are converted into sequence data (reads) through CASAVA base calling, and the files are in fastq format, which mainly contains the sequence information of the sequencing fragments and their corresponding sequencing quality information. The raw data are in fastq format files, which include the base sequences of the reads and their sequencing quality values. Each read is represented by four lines of information: the first line is the unique identifier of the read in Illumina sequencing, the second line is the base sequence, the third line is a + sign followed by the omitted read identifier, and the fourth line is the base quality value.
Assembly: For each sample, the results of reads aligned to the reference genome were used by the StringTie software to assemble transcripts in the sample based on the known transcript location information file as a guide. Transcripts with expression levels equal to 0 were filtered out, and the StringTie-assembled transcripts from all samples were reassembled.
Supplementary files format and content: xls file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from cell samples, and a total of 1 μg of RNA was required for mRNA sequencing library construction.
1.mRNA Enrichment  For eukaryotic mRNA, enrichment was performed using Oligo (dT) magnetic beads to isolate poly(A)-tailed mRNA.  2.mRNA Fragmentation  The enriched mRNA was randomly fragmented into short fragments of approximately 200 bp using chemical or enzymatic methods.  3.Strand-Specific cDNA Synthesis  First-strand cDNA was synthesized using fragmented mRNA as a template and random primers for reverse transcription.  During second-strand cDNA synthesis, dTTP in the dNTP mix was replaced with dUTP to enable strand specificity.  4.Adapter Ligation  Double-stranded cDNA was purified using AMPure XP beads.  The cDNA ends were repaired and A-tailed using an End Repair Mix.  Sequencing adapters were ligated to the A-tailed cDNA.  5.Second-Strand cDNA Digestion  USER enzyme was used to digest the second-strand cDNA (containing dUTP), ensuring the final library contained only first-strand cDNA.  6.PCR Enrichment  The cDNA library was amplified by PCR for approximately 15 cycles using primers complementary to the sequencing adapters to enrich the final library.  7.Library Quality Control and Quantification  The quality of the library was assessed using an Agilent Bioanalyzer or similar instrument to confirm the expected fragment size distribution (~200-500 bp).  The library concentration was quantified using qPCR or a fluorometric method (e.g., Qubit) to ensure optimal concentration for sequencing.

value: Ovarian cancer


title: CTCF_ChIP-seq_Mesp1-dCas9

city: Boston

first: Wanying

state: MA

address: Karp Family Research Building

department: Hematology

institute: Boston Children's Hospital & Broad Institute

data_processing:
ChIP-seq data were mapped to mouse reference genome mm10 using Bowtie. The first 36 bases of each read were used for mapping. We only use non-redundant reads to eliminate possible duplicates from biased PCR amplification.
Assembly: mm10

growth_protocol: E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x105 cells / cm² by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol: All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

value: embryonic stem cells

value: CTCF-KD

value: dox treatement


title: HUDEP2 cells; DMSO treated_rep2;KMT2D;ChIP-seq

description: Library name: DMSO-K2D-R3

value: erythroblast cells

value: DMSO treated


title: RSL3-2

description:
Library name: Sample 5
LIU-LSC-1, RSL3 IC20, rep 2

value: HNSCC cell line

value: wild-type


title: A549 cells, 11.1 mM glucose, 24 hours, rep1

description: Library name: A549_11.1 mM 1

value: Human lung adenocarcinoma cells

value: 11.1 mM glucose, 24 hours


title: RSL3-1

description:
Library name: Sample 4
LIU-LSC-1, RSL3 IC20, rep 1

value: RSL3 IC20


title: HUDEP2 cells; IAA  treated_24h_rep1

data_processing:
Raw counts of gene transcripts were derived from raw fastq files using the alignment-independent quantification tool, Salmon (https://combine- lab.github.io/salmon/), with standard settings. The raw count matrix was then imported into R-studio and utilized as input for Limma_voom analysis following the vignette of the package for normalization, differential gene expression analysis, and unbiased clustering analysis, including principal component analysis. The output of Limma_voom was used as the input for pre-ranked-based GSEA to enrich functional pathways and gene signatures (https://www.gsea-msigdb.org/gsea/index.jsp).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes Row counts for each sample

extract_protocol:
RNA samples of two biological replicates were extracted from cultured cells, using TRIzol (Ambion by Life technologies, 343,911), following the manufacturer’s instructions. RNA was then sent out for library preparation and next-generation sequencing to a commercial company, Novogene (CA, USA).
According to the manufacturer's instructions, three biologically duplicated RNA samples were extracted from cultured cells using TRIZOL (Ambion by Life technologies, 343911). RNA sample quality was analyzed, and library were prepared and next-generation sequenced by a commercial company, Novogene (California, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly- T oligo- attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M- MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: 1uM 5-Ph-IAA


title: OVSOGA1si1

description: Library name: Sanple 4


title: OVSOGA1si2

description: Library name: Sanple 5


title: DMSO-2

description:
Library name: Sample 2
LIU-LSC-1, DMSO control, rep 2

value: DMSO


title: CTCF_ChIP-seq-Mesp1-WT

value: WT

value: no treatment


title: OVSOGA1sinc3

description: Library name: Sanple 3


title: DMSO-3

description:
Library name: Sample 3
LIU-LSC-1, DMSO control, rep 3


title: 4C_Mesp1-WT

data_processing:
The 4C-Seq data were analyzed using pipe4C to generate bam files(mm10 build) and wig files for visualization
Assembly: mm10
Supplementary files format and content: wig.gz
Library strategy: 4C-seq

extract_protocol:
The fixed cells were then lysed with a cell lysis buffer, which contains 50 mM Tris-Cl pH7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100 and 1x protease inhibitor cocktail (Roche, Cat#11873580001), for 20-30 minutes on ice. After lysing, the nuclei were harvest and washed with 1x restriction enzyme buffer once. The nuclei pellets were then resuspended in 1x restriction enzyme buffer and treated with 0.3% SDS for 1 hour at 37°C under shaking, followed by another hour with 2.5% Triton X-100. Chromatin digestion was then done by incubating the samples with designated restriction enzyme at proper temperature for overnight while rotating in an airbath. The restriction enzymes used for each locus were listed in "VPinfo.txt". After digestion, heat inactivation at 65°C was applied to inactivate the enzymes and the nuclei were then subjected to ligation with 50μl of T4 DNA ligase (Invitrogen, Cat# 15224-090) in a 7ml ligation solution at 16°C for overnight. Reverse-linking was then performed by treating the samples with proteinase K to get the proximity ligated DNA. The purified DNAs were quantified and subjected to the secondary restriction enzyme digestion, roughly 1 unit of restriction enzyme for 1μg DNA, at the suggested temperature for overnight. After inactivation of the restriction enzymes, the samples were then self-ligated with T4 DNA ligase. The ligated DNAs were recovered with Sodium Acetate and ethanol and quantified with Qubit dsDNA HS assay kit (Thermo Fisher, Cat# Q32851).
The 4C-templates were then amplified with designed primers to generate libraries for sequencing. Firstly, the 4C templates were amplified with locus specific primers using 200ng template in each reaction, and we combined 5 reactions for each locus. A 50 μl PCR product aliquots were purified with homemade seramega beads. And one fifth of the purified DNAs were used for the second PCR. The final products were then purified and subjected to sequencing.

tag: locus

tag: primer

value: GAACCCACTGAAGACACTGG

tag: 1st enzyme

value: DpnII

tag: 2nd enzyme

value: NlaIII


title: HUDEP2 cells; IAA treated_12h_rep1


title: OVSOGA1sinc2

description: Library name: Sanple 2

value: Ovarian cancer


title: 4C_Mesp1-dCas9

value: embryonic stem cells

value: CTCF-KD


title: 4C_Cdiptos-dCas9

value: Cdiptos

value: dox treatement

value: CGGTCCTAGAGCTACTCCTGTCTT


title: HUDEP2 cells; IAA  treated_6h_rep1


title: 4C_Cdiptos-WT


title: DMSO-1

description:
Library name: Sample 1
LIU-LSC-1, DMSO control, rep 1

value: HNSCC cell line

value: wild-type


title: HUDEP2 cells; DMSO treated_rep1;KMT2D;ChIP-seq

description: Library name: H2-DMSO_R2

value: Human bone marrow

value: erythroblast cells

value: DMSO treated


title: HUDEP2 cells; DMSO treated_rep1

value: DMSO


title: Healthy individual, Brother, ATACseq control, genomic sequencing

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max Planck Ring 9

department: Chan group

institute: Friedrich Miescher Laboratory of the Max Planck Society

description:
Library name: CTRL_FBL301
301

data_processing:
Raw FASTQ reads  were extracted with bcl2fastq (version 2.20). Tn5 and Truseq adapter sequences, G repeats due to sequencing artefacts, and reads shorter than 20 bp were trimmed and removed using cutadapt (version 4.0).  Reads were then aligned to human reference genome version hg38 or composite genome of hg38 and EBV using bwa mem (Version: 0.7.17-r1188). Duplicates were marked and removed using Picard (version 2.18.25). Prior to calling peaks, mitochondrial reads, reads with a mapping quality lower than 20 and reads in hg38 blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38human/hg38.blacklist.bed.gz) were discarded. ATAC-seq peak calling was performed using MACS2 (version 2.1.1.20160309) with callpeak –format BAMPE --nomodel –min-length 100 narrowPeak parameters. Sample 131, 132 and 301 were treated as the non-Bloom Syndrome group. 24 million reads subsamples from each sample were pooled to call the non-patient peakset. Similarly, 36 million reads were subsampled from the affected individuals 305 and 306 to call the patient peakset.  Then all the subsampled reads were pooled to call a global peak set, which was further supplemented by non-patient specific or patient specific peaks for downstream analysis. The number of fragments in each ATACseq peak was quantified with htseq-count (HTSeq version 0.9.1). Subsequently, the count matrix was normalized and differential analysis was carried out in DESeq2 (version 1.30.1) to identify significantly differential signals (adjusted p-value <0.05).
Assembly: hg38
Supplementary files format and content: bedgraph files generated from the filtered bamfile.
Supplementary files format and content: narrowPeak, ATAC-seq peaksets for all samples called by macs2, which were used in downstream differential anlaysis.
Supplementary files format and content: tab-delimited txt file, number of fragments in each peak quantified by Htseq.
Supplementary files format and content: tab-delimited txt file of results of differential analysis

source_name: ferritin carrying lymphocytes

growth_protocol: Cell lines from Bloom Syndrome and healthy donors were obtained from Coriell Institute (lymphoblastoid cell lines, LCL: GM16375, AG14980; fibroblast cell lines: GM08505, GM00637). LCLs were cultured in RPMI 1640 medium (Gibco, Cat. #21875) supplemented with 15% fetal bovine serum (FBS, Gibco, UK, Cat. #10500), 1% penicillin-streptomycin (P/S, Gibco, US, Cat #15140) and 1% GlutaMAX-I (Gibco, UK, Cat. #35050).  Fibroblast lines were cultured in 1X DMEM (Gibco, UK, Cat. #11960) supplemented with, 1% minimum essential medium non-essential amino acids (MEM NEAA, Gibco, UK, Cat. #11140) and 1% P/S and 10% or 15% FBS, respectively. Cell passaging was performed according to recommendations by Coriell Institute. All cells were cultured at 37°C under 5% CO2.

extract_protocol:
Cryopreserved samples were washed twice with cold 1x Dulbecco's phosphate buffered saline (PBS, Gibco, Cat. #14190) for downstream ATACseq sample preparation.
50, 000 viable cells were subjected to ATACseq preparation essentially as described in Corces, M. et al. (https://doi.org/10.1038/nmeth.4396) with the following modifications. After cell membrane lysis, nuclei were pelleted at 500g for 10min.

value: ferritin carrying lymphocytes

value: Wildtype

tag: relation to_proband

value: Brother

tag: bloom syndrome_status

value: Wild-type

tag: age of_sampleing_(month)

tag: medical record


title: K562 cells; IAA  treated_24h_rep1

value: 1uM 5-Ph-IAA


title: OVSOGA1sinc1

description: Library name: Sanple 1

value: Ovarian cancer


title: OB3_EVs

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

institute: Drum Tower hospital affiliated to Nanjing university medical school

description: Library name: Sample 6

data_processing:
miRNA sequences, tRNA sequences and piRNA sequences were obtained from miRBase v21(Kozomara and Griffiths-Jones, 2014), GtRNAdb (Chan and Lowe, 2016) and piRNA bank (Lakshmi and Agrawal, 2008), respectively. Bowtie was used to align clean reads to these reference sequences for annotation.
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: adipose tissue

extract_protocol:
EVs were extracted from adipose tissues of healthy weight and obese subjects and processed for RNA extraction by Trizol. All sRNA library construction and deep sequencing were performed by Novogene (Tianjin, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose tissue

value: Obese


title: K562 cells; IAA _treated_12h_rep1


title: OB4_EVs

description: Library name: Sample 7


title: Cortex_Nanopore_directRNA_rep1

city: Acton

first: Muhammad

last: Bilal

state: ACT

address: 131 Garran Road

department: Eccles Institute of Neuroscience, The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
Library name: Cortex_Nanopore_directRNA_rep1
Adult mouse cortex; Nanopore direct RNA-seq; biological replicate 1

data_processing:
Oxford Nanopore raw signal files were basecalled with Dorado (v0.7.0), and reads were aligned using minimap2 (v2.28). Transcript- and gene-level abundance estimates were generated using NanoCount (v1.2.1) and IsoQuant (v3.7.0). Illumina paired-end RNA-seq reads (150 bp; R1 and R2) were adapter-trimmed using FASTX-Clipper (FASTX-Toolkit, Hannon Lab) with default parameters, removing AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC from R1 and AGATCGGAAGAGCGTCGTGTAGGGAAAGA from R2. Trimmed Illumina reads were quantified against a decoy-aware reference using Salmon (v1.10.1).
Gene- and transcript-level TPM values and read counts were summarised across biological replicates. TRP channel–annotated genes were extracted for downstream analysis.
Assembly: Mus musculus reference genome GRCm39 with Ensembl release 115 annotation.
Supplementary files format and content: Processed data files include spreadsheets containing gene- and transcript-level TPM values and raw read counts derived from Oxford Nanopore direct RNA-seq and Illumina RNA-seq, annotated with Ensembl gene identifiers and gene symbols.

source_name: cortex

growth_protocol: Adult male C57BL/6J mice (5–6 weeks old) were group-housed under controlled temperature and a 12:12 h reverse light/dark cycle with food and water ad libitum.

extract_protocol:
Mice were deeply anaesthetised and transcardially perfused with ice-cold artificial cerebrospinal fluid prior to tissue collection. Cerebral cortex and dorsal root ganglia were rapidly dissected, snap-frozen, and stored at −80 °C. Total RNA was extracted using TRI Reagent followed by purification with the Direct-zol™ RNA Microprep Kit, including on-column DNase I treatment.
For Oxford Nanopore sequencing, direct RNA libraries were prepared using the Oxford Nanopore Direct RNA Sequencing Kit (SQK-RNA004), with Induro Reverse Transcriptase and SUPERase·In added during library preparation, and sequenced on MinION or PromethION instruments. For Illumina sequencing, strand-specific poly(A)+ RNA libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit and sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000.

treatment_protocol: No experimental treatment was applied. All samples were obtained from untreated wild-type animals.

value: cortex

tag: Sex

value: Male

tag: developmental stage

value: 5-6 weeks old

value: brain tissue

value: wild type

value: untreated


title: Cortex_Nanopore_directRNA_rep2

description:
Library name: Cortex_Nanopore_directRNA_rep2
Adult mouse cortex; Nanopore direct RNA-seq; biological replicate 2

tag: tissue


title: Bloom Syndrom Affected, Patient 1, ATACseq

description:
Library name: FBL305
305

tag: cell type

value: BLM-/-

value: Patient 1

value: Affected

tag: mutation

value: BLM c.2207_2212delATCTGAinsTAGATTC in exon10

value: Wilm's tumor at 36 months, AML at 72 months, myelodyplastic syndrome at 72 months


title: NFAT5_NaCl

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description: Library name: NFAT5_hypertonic

data_processing:
Remove adapters and low quality reads with fastp version 0.21.0
Align to human genome with bowtie2 version 2.5.2
Convert sam files to position sorted bam files with picard tools version 2.25.0
Deduplicate bam files with picard tools
Create bigWig files with deeptools version 3.3.0
Assembly: mm10
Supplementary files format and content: read coverage bigwig files scaled to human HK2 cell spike-ins and RPGC (reads per genomic content) normalized
Library strategy: CUT&Tag

source_name: kidney

growth_protocol: Murine Inner Medullary Collecting Duct (IMCD) (ATCC) cells were cultured in DMEM/F-12 (Thermo-Fisher) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
DNA was purified using a MinElute PCR Purification Kit (Qiagen)
DNA was PCR amplified using barcoded primers and NEBNext HiFi 2x PCR master mix (NEB). Libraries were purified using AMPure XP beads (Beckman).

treatment_protocol: 100mM NaCl

value: kidney

tag: cell line

value: IMCD

value: inner medula collecting duct

tag: treatment

value: NaCl

tag: antibody


title: OB2_EVs

description: Library name: Sample 5

value: adipose tissue


title: K562 cells; IAA  treated_6h_rep1

tag: genotype

value: 1uM 5-Ph-IAA


title: Bloom Syndrom Affected, Patient 2, ATACseq

description:
Library name: FBL306
306

value: ferritin carrying lymphocytes

value: Patient 2


title: NFAT5_control

description: Library name: NFAT5_isotonic

value: control


title: Bloom Syndrom Carrier, Sister, ATACseq

description:
Library name: FBL302
302

value: BLM+/-

value: Sister

value: Carrier


title: H3K27me3_NaCl

description: Library name: H3K27me3_hypertonic


title: Healthy3_EVs

description: Library name: Sample 3

value: Healthy weight


title: Healthy individual, Brother, ATACseq

description:
Library name: FBL301
301

value: Wildtype

value: Brother

value: Wild-type


title: Bloom Syndrom Carrier, Mother, ATACseq

description:
Library name: FBL132
132

value: Mother

value: BLM c.2207_2212delATCTGAinsTAGATTC in exon10


title: Healthy2_EVs

description: Library name: Sample 2


title: OB1_EVs

description: Library name: Sample 4

value: Obese


title: H3K27me3_control

description: Library name: H3K27me3_isotonic

value: kidney

value: IMCD

value: inner medula collecting duct


title: H3K27ac_NaCl

description: Library name: H3K27ac_hypertonic

value: NaCl


title: Bloom Syndrom Carrier, Father, ATACseq

description:
Library name: FBL131
131

value: ferritin carrying lymphocytes

value: Father


title: RNA from tonsil, donor 2

city: Rennes

first: Samuel

last: Bastos Serra Trinca

address: 2 avenue du professeur Léon Bernard

country: France

institute: University of Rennes

description: Library name: T2_RACE

data_processing:
After sequencing, FASTQ files are processed using MiGEC (for UMI handling, version 1.2.9) and FLASH (to merge R1 and R2 reads, version 1.2.11), generating FASTA files with paired sequences, which are then submitted to IMGT/HighV-QUEST for alignment (IMGT/V-QUEST program version: 3,6,3). Sequences with a productive and usable VDJ were retained.
Assembly: IMGT/V-QUEST reference directory release: 202416-4
Supplementary files format and content: Table of clone counts after hierarchical clustering performed on IMGT outputs using the Scoper package (version 1.3.0)
Library strategy: BCR-Seq

source_name: tonsil

extract_protocol:
RNA extracted from memory B cells obtained by magnetic enrichment from a human tonsil
500 ng of total RNA extracted from memory B cells were subjected to RACE-RepSeq library preparation (RT using Cγ-, Cα- and Cµ-specific primers, followed by two PCR steps)

value: tonsil

value: memory B cells


title: K562 cells; DMSO treated_rep1

value: DMSO


title: RNA from tonsil, donor 3

description: Library name: T3_RACE


title: Healthy1_EVs

description: Library name: Sample 1

value: adipose tissue


title: H3K27ac_control

description: Library name: H3K27ac_isotonic

value: control


title: 207049890123_R04C01

status: Public on Apr 09 2026

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 117-2194 Health Sciences Mall

department: Faculty of Medicine

country: Canada

institute: University of British Columbia

description: Capillary sample from ID_19

hyb_protocol: DNA was bisulfite converted using EZ-96 DNA Methylation kits (Zymo Research, Irvine, CA), hybridized to the MethylationEPIC BeadChip Infinium microarray v2.0  (EPICv2) array using standard Illumina protocol

scan_protocol: Arrays were scanned with an Illumina HiScan

data_processing: Noob, functional normalized, and batch corrected

label: Cy3 and Cy5

source_name: Whole Blood

label_protocol: Standard Illumnia protocol

extract_protocol: Genomic DNA was extracted from whole blood using Qiagen DNeasy Kit according to standard instructions

value: Whole Blood

value: M

tag: age

tag: id_individual sample

tag: id_matched sample

tag: sample type

value: Capillary


title: 207049890123_R05C01

description: Venous sample from ID_18

value: Venous


title: 207049890123_R07C01

description: Capillary sample from ID_15


title: 207049890078_R06C01

description: Venous sample from ID_17

value: F


title: 207049890123_R02C01

description: Venous sample from ID_19


title: 207049890123_R03C01

description: Venous sample from ID_20


title: 207049890123_R06C01

description: Capillary sample from ID_20


title: 207049890078_R04C01

description: Capillary sample from ID_17


title: 207049890050_R08C01

description: Capillary sample from ID_14


title: 207049890123_R01C01

description: Capillary sample from ID_18


title: RNA from tonsil, donor 1

description: Library name: T1_RACE


title: 207049890078_R05C01

description: Venous sample from ID_16


title: 207049890050_R07C01

description: Capillary sample from ID_13


title: 207049890078_R02C01

description: Venous sample from ID_15


title: 207049890050_R05C01

description: Venous sample from ID_14


title: pancreas, CD, 12-week on diet, male, 428

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description:
Library name: CD_M_3
column name in KC_12wk_NormaliizedCounts.csv: CD_M_3

data_processing:
Low-quality bases and adapter sequences were trimmed using Trim Galore (version 0.6.7) and CutAdapt (version 3.5).
Cleaned reads were aligned to the University of California Santa Cruz mouse genome (mm10) using the STAR aligner (version 2.7.9). Gene-level quantification was performed using the -quantMode GeneCounts option in STAR, which generates a matrix of raw read counts for each gene.
Assembly: mm10
Supplementary files format and content: Raw counts processed from sequence-aligned read counts (mm10, gene level) as output from STAR. First row is sample name header, in .txt tab-delimited format. Gene_name is only row descriptor, unsorted by gene, and sample column names are directly from FASTQ file names
Supplementary files format and content: Normalized counts processed from raw counts (mm10, gene level) via DESeq2 in R, in .txt tab-delimited format, absolute normalized counts (linear, not log counts), with UCSC Gene_symbol, ENTREZ_ID as first two columns, first row header contains sample names with simplified name corresponding to GEO sample library name. Genes without any reads are excluded

source_name: pancreas

growth_protocol: All mice were generated by breeding. The original C57BL/6 and 129/Sv mice used to generate the KC and KCO strains were purchased from Jackson Laboratories. KC mice were kept on a C57BL/6 background. KCO were maintained in a hybrid C57BL/6 and 129/Sv background

extract_protocol:
Mouse pancreata were snap frozen in liquid nitrogen and manually pulverized using the BioPulverizer (BioSpec Products 59012MS). Total RNA was extracted from pulverized tissue (20-40 mg), homogenized via QIAshredder column, and purified using the RNeasy Mini Kit (Qiagen) with on column DNAse I digestion, per the manufacturer's protocol.
RNA quality and quantity was assessed using an Agilent Bioanalyzer, and only high-quality RNA samples (RIN>7) were used in downstream analysis. RNA-seq libraries were prepared from mRNA purified from approximately 200ng total RNA with oligo-dT bead polyA selection (Illumina)  and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries are quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.
Sequenced (>25M 100-bp paired-end (2x100) reads on NovaSeq 6000 (Illumina)) with the Yale Center for Genome Analysis (YCGA)

treatment_protocol: All mice were put on indicated diet at 6 weeks of age for indicated time. Diets were changed weekly, and pancreate were at terminal time point.

value: pancreas

tag: strain

value: KrasLSL-G12D/+; Pdx1-Cre

value: 18 weeks

value: CD, 12 weeks


title: 207049890050_R04C01

description: Capillary sample from ID_12


title: 207049890050_R03C01

description: Venous sample from ID_13


title: 207049890050_R06C01

description: Capillary sample from ID_11


title: 207049890078_R03C01

description: Capillary sample from ID_16


title: 207049890041_R07C01

description: Venous sample from ID_10


title: 207049890050_R01C01

description: Venous sample from ID_11


title: 207049890041_R01C01

description: Capillary sample from ID_8


title: 207049890041_R06C01

description: Venous sample from ID_9


title: 207049890041_R05C01

description: Venous sample from ID_8


title: 207036380118_R04C01

description: Venous sample from ID_7


title: 207049890041_R03C01

description: Capillary sample from ID_10


title: 207049890050_R02C01

description: Venous sample from ID_12


title: 207036380118_R03C01

description: Capillary sample from ID_6


title: 207036380118_R07C01

description: Venous sample from ID_4


title: 207036380118_R08C01

description: Capillary sample from ID_7


title: 207049890041_R02C01

description: Capillary sample from ID_9


title: 207036380118_R05C01

description: Venous sample from ID_6


title: 207036380118_R02C01

description: Capillary sample from ID_5


title: 207036380118_R06C01

description: Venous sample from ID_5


title: 207036380118_R01C01

description: Capillary sample from ID_4


title: 207036380068_R07C01

description: Capillary sample from ID_3


title: 207036380068_R06C01

description: Capillary sample from ID_1


title: 207036380068_R04C01

description: Capillary sample from ID_2


title: 207036380068_R03C01

description: Venous sample from ID_2


title: 207036380068_R05C01

description: Venous sample from ID_3


title: Human meningioma, FFPE [MN97]

city: San Francisco

first: Minh

middle: P

last: Nguyen

institute: University of California, San Francisco

description: Illumina EPICv2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Analysis was performed in R v4.4.0 with the SeSAMe package. Probes were filtered and analyzed using the standard SeSAMe preprocessing pipeline, including normal-exponential out-of-band background correction, nonlinear dye bias correction, p-value with out-of-band array hybridization masking, and beta value calculation
Processed data file represents SeSAMe-computed average beta values

label: Cy5 and Cy3

source_name: meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Meningiomas were removed and mechanically lysed, and DNA was extracted from the lysed tissue using the Qiagen QIAamp DNA FFPE Tissue Kit

value: meningioma

value: Female

tag: tumor grade

tag: age at surgery

tag: outcome

value: censored


title: Human meningioma, FFPE [MN99]

description: Illumina EPICv2

tag: Sex

value: Male


title: Human meningioma, FFPE [MN96]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN95]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN94]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN93]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN92]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN90]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN89]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN98]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN88]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN9]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN91]

description: Illumina EPICv2


title: 207036380068_R01C01

description: Venous sample from ID_1


title: Human meningioma, FFPE [MN85]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN87]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN86]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN82]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN83]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN81]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN84]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN8]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN77]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN79]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN80]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN78]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN68]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN71]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN66]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN75]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN73]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN74]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN70]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN76]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN72]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN65]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN61]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN64]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN67]

description: Illumina EPICv2

value: progression


title: Human meningioma, FFPE [MN7]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN59]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN58]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN6]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN60]

description: Illumina EPICv2


title: CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 1

description: Library name: E48h-D123-1

value: spleen

value: primary cells

value: CD8 T cell

value: Listeria monocytogenes

tag: batch

value: Favret


title: Human meningioma, FFPE [MN51]

description: Illumina EPICv2

tag: tissue


title: pancreas, Safflower, 3-week on diet, male, 3_7

description:
Library name: Safflower_5
column name in KC_3wk_NormaliizedCounts.csv: Safflower_5

value: 9 weeks

value: Safflower diet, 3 weeks


title: Human meningioma, FFPE [MN56]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN54]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN49]

description: Illumina EPICv2


title: HFD_EVs 2

description: Library name: Sample 6

data_processing:
miRNA sequences, tRNA sequences and piRNA sequences were obtained from miRBase v21(Kozomara and Griffiths-Jones, 2014), GtRNAdb (Chan and Lowe, 2016) and piRNA bank (Lakshmi and Agrawal, 2008), respectively. Bowtie was used to align clean reads to these reference sequences for annotation.
Assembly: miRBase v21; GtRNAdb; piRNA bank
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

extract_protocol:
EVs were extracted from adipose tissues of chow-fed and high-fat diet mice and processed for RNA extraction by Trizol. All sRNA library construction and deep sequencing were performed by Novogene (Tianjin, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose tissue

value: HFD diet


title: Human meningioma, FFPE [MN53]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN5]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN52]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN48]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN50]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN46]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN40]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN45]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN47]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN44]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN42]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN62]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN41]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN4]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN37]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN38]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN36]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN39]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN34]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN35]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN31]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN33]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN32]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN30]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN26]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN3]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN20]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN63]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN28]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN29]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN21]

description: Illumina EPICv2


title: HUDEP2 cells;KO_rep3_Input

city: Suzhou

first: Peng

description: Library name: 1345276_PXU042_R1

data_processing:
For ChIP-Seq, raw sequencing data were aligned to the mouse genome mm9 and the drosophila genome dm6 using Bowtie2 (ref. 51; v2.3.2). To identify ChIP-enriched regions, SICER52 (v1.1) was used. For ChIP–seq of KMT2D, the window size of 50 bp, the gap size of 50 bp and the false discovery rate (FDR) threshold of 0.05 were used. For ChIP–seq of histone modifications (H3K4me1 and H3K27ac), the window size of 200 bp, the gap size of 200 bp and the FDR threshold of 10−3 were used. Reads on indicated regions were collected to calculate reads per kilobase million as a measure of signal intensity.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Antibody were added to the sonication samples, followed with gentle rotation for 16 hours at 4°C, Beads added after that,followed with gentle rotation for 6 hours at 4°C. beads transfered to a new tube. Using wash buffer to wash beads, then, samples were incubated in SDS elution buffer for 6 hours. separate beads and supernatant, DNA was in supernatant and then extracted by the phenol/chloroform/isopropanol protocol. Library construction was performed using the DNA Library Prep Kit.

value: Human bone marrow

tag: cell type

value: erythroblast cells

value: KO

value: no


title: Human meningioma, FFPE [MN23]

description: Illumina EPICv2

value: meningioma

value: Female


title: HUDEP2 cells; 5-Ph-IAA_rep1_Input

description: Library name: INPUT-R3


title: Human meningioma, FFPE [MN19]

description: Illumina EPICv2

value: censored


title: Human meningioma, FFPE [MN24]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN27]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN17]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN2]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN16]

description: Illumina EPICv2

value: Male


title: Human meningioma, FFPE [MN15]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN22]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN140]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN14]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN137]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN139]

description: Illumina EPICv2

value: progression


title: Human meningioma, FFPE [MN134]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN132]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN131]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN129]

description: Illumina EPICv2


title: IP-Svi-0 27C Rep2

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

description: Library name: ipsvi-27C_R2

data_processing:
The raw files were checked for quality using FastQC and then mapped against Arabidopsis genome (TAIR10) using Hisat2. The resulting alignment files were further processed using the Cufflinks-Cuffdiff protocol with default parameters. HT-seq was used to make read count files.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Seeds of both genoypes were grown on half strength MS media, straightified for 3 days and then transferred to growth rooms with different temperatures. Samples were collected after 7 days of transfer at 27C, 8 days of transfer at 23C, 12 days of transfer at 16C, and  23 days of transfer at 10C.

extract_protocol:
Total RNA was extracted using Plant RNA Reagent (Invitrogen)
Libraries were constructed using DNBSEQ Eukaryotic Strand-specific mRNA library according to the manufacturer's manual

treatment_protocol: Seedlings were grown at different temperatures (10C, 16C, 23C, and 27C)

value: whole seedlings

value: IP-Svi-0 background


title: Human meningioma, FFPE [MN13]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN135]

description: Illumina EPICv2


title: IP-Svi-0 23C Rep2

description: Library name: ipsvi-23C_R2


title: Human meningioma, FFPE [MN138]

description: Illumina EPICv2


title: IP-Svi-0 23C Rep3

description: Library name: ipsvi-23C_R3


title: IP-Svi-0 16C Rep3

description: Library name: ipsvi-16C_R3


title: Human meningioma, FFPE [MN136]

description: Illumina EPICv2


title: IP-Svi-0 23C Rep1

description: Library name: ipsvi-23C_R1


title: Human meningioma, FFPE [MN128]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN127]

description: Illumina EPICv2


title: IP-Svi-0 16C Rep2

description: Library name: ipsvi-16C_R2


title: Human meningioma, FFPE [MN126]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN125]

description: Illumina EPICv2


title: IP-Svi-0 10C Rep2

description: Library name: ipsvi-10C_R2


title: Human meningioma, FFPE [MN123]

description: Illumina EPICv2


title: IP-Svi-0 10C Rep1

description: Library name: ipsvi-10C_R1


title: Human meningioma, FFPE [MN124]

description: Illumina EPICv2


title: Col-0 27C Rep2

description: Library name: col-27C_R2

value: Col-0 background


title: Human meningioma, FFPE [MN121]

description: Illumina EPICv2


title: IP-Svi-0 16C Rep1

description: Library name: ipsvi-16C_R1


title: Human meningioma, FFPE [MN122]

description: Illumina EPICv2


title: Col-0 27C Rep1

description: Library name: col-27C_R1


title: IP-Svi-0 10C Rep3

description: Library name: ipsvi-10C_R3


title: Col-0 27C Rep3

description: Library name: col-27C_R3


title: Human meningioma, FFPE [MN119]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN120]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN118]

description: Illumina EPICv2


title: Col-0 23C Rep3

description: Library name: col-23C_R3


title: Col-0 23C Rep1

description: Library name: col-23C_R1


title: Col-0 23C Rep2

description: Library name: col-23C_R2


title: Human meningioma, FFPE [MN117]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN115]

description: Illumina EPICv2


title: Col-0 16C Rep1

description: Library name: col-16C_R1


title: Col-0 16C Rep2

description: Library name: col-16C_R2


title: Human meningioma, FFPE [MN116]

description: Illumina EPICv2


title: Col-0 16C Rep3

description: Library name: col-16C_R3


title: Human meningioma, FFPE [MN114]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN113]

description: Illumina EPICv2


title: Col-0 10C Rep3

description: Library name: col-10C_R3


title: Human meningioma, FFPE [MN112]

description: Illumina EPICv2


title: Col-0 10C Rep2

description: Library name: col-10C_R2


title: Human meningioma, FFPE [MN111]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN11]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN110]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN106]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN107]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN103]

description: Illumina EPICv2


title: Col-0 10C Rep1

description: Library name: col-10C_R1


title: Human meningioma, FFPE [MN108]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN104]

description: Illumina EPICv2


title: miR4488-t48_1

type: RNA

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

description: Gene expression data

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

label: biotin

label_protocol: 100 ng total RNA was taken for microarray analysis. Arrays were processed with Gene Chip WT PLUS reagent kit (REF 902281), according to Affymetrix standard protocols

growth_protocol: Cells were grown in Eagle's Minimum Essential Medium with Earle's salts and non-essential amino acids (01-040-1A, Biological Industries, Israel) supplemented with 2.6 mM L-Glutamine, Ampicillin and Streptomycin and 15% FBS. For routine culturing, cell were split 1:3 or 1:4 every 3-4 days.

extract_protocol: RNA was extracted with Qiazol (Qiagen, Germany)

treatment_protocol: HFF cells were transfected either with miR-CTRL or miR-4488.

value: Human foreskin fibroblasts (HFF) (AG14608)


title: miR4488-t48_2

description: Gene expression data

hyb_protocol: According to Affymetrix standard protocols


title: Human meningioma, FFPE [MN102]

description: Illumina EPICv2


title: miR4488-t0_1

description: Gene expression data


title: miR4488-t0_2

description: Gene expression data


title: miR4488-t0_3

description: Gene expression data


title: Human meningioma, FFPE [MN101]

description: Illumina EPICv2


title: Bone, pth4KO, rep3

city: Vigo

first: Luis

last: Méndez Martínez

address: Eduardo Cabello Nº6

country: Spain

institute: Instituto de Investigaciones Marinas (IIM-CSIC)

description: Library name: Sample 47

data_processing:
Sequence reads were trimmed for adapter sequence/low quality with SoapNuke  v2.1.9 (parameters:  -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 100)
Trimmed sequence reads were mapped to GRCz11 zebrafish genome assembly and gene expression quantified using the STAR aligner v2.7.11b
Read counts were filtered and normalized in R v4.4.0 using EdgeR v4.4
Assembly: Ensembl GRCz11 Danio rerio genome assembly
Supplementary files format and content: CSV includes raw counts for each sample
Supplementary files format and content: CSV includes filtered and normalized CPM counts for each sample

source_name: Bone

extract_protocol:
Total RNA was isolated using TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) and then purified with the RNeasy Mini Kit (Qiagen, Germany) according to manufacturer’s instructions
Libraries were prepared using MGIEasy Fast RNA Library Prep Set by BGI according to manufacturer’s instructions

value: Bone


title: miR4488-t48_3

description: Gene expression data


title: Bone, pth4KO, rep4

description: Library name: Sample 48


title: Human meningioma, FFPE [MN100]

description: Illumina EPICv2


title: Bone, pth4KO, rep2

description: Library name: Sample 46


title: Human meningioma, FFPE [MN10]

description: Illumina EPICv2


title: Human meningioma, FFPE [MN1]

description: Illumina EPICv2


title: Bone, pth4KO, rep1

description: Library name: Sample 45


title: Bone, WT, rep4

description: Library name: Sample 44


title: Mouse limb explant, 96-well, H3, rep4

city: Geneva

first: Hanrong

last: Hu

address: B1 0 266.045 (Campus Biotech bâtiment B1)

department: Brain Mind Institute

country: Switzerland

institute: EPFL

description: Library name: 15102024_KH_M-96-well_H3

data_processing:
Basecalls were performed using bases2fastq version 1.8.0. Nextera adapters were trimmed with minimal read length tolerated post-trimming: 35 bp.
CUT&Tag sequencing data was aligned to a hybrid genome (hg38 and Escherichia phage Lambda spike-in) with the Bowtie2 aligner (v2.4.5). The resulting alignment BAM files were converted to bigwig files using bamCoverage from deepTools (v3.5.6) and subsequently scaled based on the number of reads mapped to the spike-in regions.
Broad peaks were called from the BAM files of each sequencing run using MACS3 (v3.0.1) with the parameters --broad-cutoff 0.1, --nolambda and the corresponding H3 as control
Assembly: hg38 (with Escherichia phage Lambda ViralProj14204 spike-in)
Supplementary files format and content: bigWig (after spike-in normalization), broadPeak (except for H3)
Library strategy: CUT&Tag

source_name: limb explants

extract_protocol:
For each mouse sample, five limbs from ALI or 96-well explant cultures were collected in Protein LoBind tubes (Eppendorf, 0030 108 442). Limbs were washed with 1 ml PBS 1x (Gibco, 10010-015) and incubated in 200 µl 0.25% trypsin-EDTA (Gibco, 25200072) at 37 ºC for 5-6 minutes. Following mechanical dissociation by a P200 pipette, trypsin was deactivated by the addition of 400 µl of FBS-containing media. Each sample was topped up with an additional 600 µl of PBS 1x and centrifuged at 400 rcf for 5 minutes at 4 ºC.  For each xenopus sample, eight limbs from ALI or 96-well explant cultures were collected in Protein LoBind tubes. Limbs were washed with 0.7X PBS and treated with 0.35 mg/mL Liberase solution (Sigma-Aldrich, 05401127001) diluted in 0.7X PBS for 30 minutes at room temperature while gently rotating. Cells were mechanically dissociated by pipetting 10–15 times until visibly dislodged. Next, 1 mL of L15 medium (supplemented with 1% antibiotic-antimycotic, 0.8 mM L706 glutamine, and 20% FBS) was added to the mixture. The cells were then centrifuged at 600 rcf for 5 minutes at room temperature and washed with 1 mL of 0.7X PBS containing 0.04% BSA.
CUT&Tag libraries were prepared as previously reported (Zenk et al., 2023). The centrifuged cells were resuspended in 1 ml of CUT&Tag wash buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, BU-106-75), 150 mM NaCl (Sigma-Aldrich, 71386), 0.5 mM spermidine (Merck, S2626), 5 mM sodium butyrate (Sigma-Aldrich, 303410), and 1x Protease Inhibitor Cocktail (Roche, 11873580001) in UltraPure distilled water (Invitrogen, 10977-035)). Then, a volume of Concanavalin A beads (Polysciences, 86057-3) corresponding to 15 µl per histone mark target was prepared by removing the supernatant on a magnetic rack and washing in 1 ml binding buffer (20 mM HEPES [pH 7.5], 10 mM KCl (Sigma-Aldrich, 60142), 1 mM CaCl2 (Sigma-Aldrich, 21115), and 1 mM MnCl2 (Sigma-Aldrich, M1028) in UltraPure distilled water). The supernatant was removed again, and the beads were resuspended in the original volume (15 µl per sample) of binding buffer.  Beads were added to the cell suspension for binding. Using all cells from the dissociated limbs, this corresponded to 60k-600k live cells per histone mark. After 15 minutes of incubation at room temperature on a rotating wheel, tubes were placed in a magnetic rack, the supernatant was discarded, and cells were permeabilized in wash buffer supplemented with 0.01% Digitonin (Invitrogen, BN2006) until nuclei were visible around the beads via Trypan Blue (Invitrogen, T10282) staining.  The supernatant was discarded again on the magnetic rack, and samples were resuspended in 150 µl wash buffer per histone mark and distributed in separate tubes for antibody binding. Primary antibodies were added as per the manufacturer’s suggested concentration for CUT&Tag (H3K27me3 (Diagenode, C15410195): 1 µg in 150 µl; H3K4me3 (Diagenode, C1541003): 0.5 µg in 150 µl; H3: dilute at 1:150 (Activemotif, 39763) along with 2 mM EDTA (Invitrogen, 15575-038). Samples were incubated overnight at 4 ºC on a nutator.  The next day, the primary antibody solution was removed on a magnetic rack, and the beads were washed twice with 400 µl of CUT&Tag wash buffer, vortexing briefly each time. Beads were resuspended in 150 µl of CUT&Tag wash buffer with 1.5 µl of secondary antibody (Abcam, 46540; Antibodies Online, ABIN101961), and incubated for 1 hour at 4 ºC on a nutator.  Next, the secondary antibody solution was removed on a magnetic rack, and the beads were washed twice with 400 µl of CUT&Tag wash buffer, vortexing briefly each time. Beads were resuspended in 150 µl of high salt wash buffer (20 mM HEPES [pH 7.5], 300 mM NaCl, 0.5 mM spermidine, 5 mM sodium butyrate, and 1x Protease Inhibitor Cocktail in UltraPure distilled water) with 2 µl of homemade Protein A-Tn5, and incubated for 1 hour at room temperature in a thermomixer at 300 rpm.  The Protein A-Tn5 solution was removed on a magnetic rack, and the beads were washed twice with 400 µl of high salt wash buffer. Beads were resuspended in 100 µl CUT&Tag wash buffer supplemented with 10 mM MgCl2 (Invitrogen, AM9530G) for chromatin digestion for 1 hour at 37 ºC in a thermomixer at 300 rpm. The reaction was stopped by adding 4.5 µl of 0.5 M EDTA, 2.76 µl of 20% SDS (Sigma-Aldrich, 05030), and 1 µl of 20 mg/ml Proteinase K (Invitrogen, AM2546), and incubating in a thermomixer at 300 rpm for 30 minutes at 55 ºC, followed by 20 minutes at 70 ºC.  Each sample was then purified using the ChIP DNA Clean & Concentrator kit (Zymo, D5205) as per the manufacturer’s instructions for a 100 µl sample. At the final step, samples were eluted in 25 µl of elution buffer (Qiagen, 19086) containing 2 pg of lambda-DNA (NEB, N3011S; tagmented with Tn5 and cleaned up on columns before use) as a spike-in.  For library preparation, 21 µl of each sample was transferred to PCR tube strips, and 25 µl of Nebnext® High-Fidelity 2X PCR Master Mix (NEB, M0541S) was added, along with 2 µl of each i7 and i5 index primer. The following thermocycler program was used: 1x 5 min at 58 °C (gap filling); 1x 5 min at 72 °C (gap filling), 1x 30 s at 98 °C (denaturation), 14x 10 s at 98 °C (denaturation) plus 30 s at 63 °C (annealing/extension), 1x 1 min at 72 °C (extension), hold 4 °C.  A final clean-up was performed by mixing in 45-55 µl of AMPure XP beads (Beckman Coulter, A63881) and incubating at room temperature for 15 minutes. The supernatant was removed on a magnetic rack, and the beads were washed twice in 400 µl 80% EtOH. Finally, beads were resuspended in 33 µl 0.1x TE buffer and incubated for 5 minutes at room temperature. On a magnetic rack, 28 µl of the supernatant was transferred to a new tube. Quality control was performed using the Qubit dsDNA HS Assay kit (Invitrogen, Q32854) and the Agilent High Sensitivity D5000 ScreenTape system (ScreenTape: Agilent, 5067-5592; Reagents: Agilent, 5067-5593).  An equimolar pool (5-15 nM) of samples was submitted for sequencing.

value: limb explants


title: Bone, WT, rep2

description: Library name: Sample 42


title: Bone, WT, rep3

description: Library name: Sample 43


title: Bone, WT, rep1

description: Library name: Sample 41


title: Mouse limb explant, 96-well, H3K27ac, rep4

description: Library name: 15102024_KH_M-96-well_H3K27ac


title: Scales, pth4KO, rep4

description: Library name: Sample 40

source_name: Scales

value: Scales


title: Mouse limb explant, 96-well, H3K9me3, rep4

description: Library name: 15102024_KH_M-96-well_H3K9me3


title: Scales, pth4KO, rep3

description: Library name: Sample 39


title: Mouse limb explant, 96-well, H3K4me3, rep4

description: Library name: 15102024_KH_M-96-well_H3K4me3


title: Scales, pth4KO, rep1

description: Library name: Sample 37


title: Mouse limb explant, 96-well, H3K27me3, rep4

description: Library name: 15102024_KH_M-96-well_H3K27me3


title: Scales, WT, rep4

description: Library name: Sample 36


title: Mouse limb explant, ALI, H3K9me3, rep4

description: Library name: 15102024_KH_M-ALI_H3K9me3


title: Mouse limb explant, 96-well, H3, rep3

description: Library name: 15082024_KH_M-96-well_H3


title: Scales, pth4KO, rep2

description: Library name: Sample 38


title: Mouse limb explant, ALI, H3K27ac, rep4

description: Library name: 15102024_KH_M-ALI_H3K27ac


title: Gills, pth4KO, rep4

description: Library name: Sample 32

source_name: Gills

value: Gills


title: Mouse limb explant, ALI, H3K4me3, rep4

description: Library name: 15102024_KH_M-ALI_H3K4me3


title: Mouse limb explant, ALI, H3, rep4

description: Library name: 15102024_KH_M-ALI_H3


title: Scales, WT, rep1

description: Library name: Sample 33


title: Mouse limb explant, ALI, H3K27me3, rep4

description: Library name: 15102024_KH_M-ALI_H3K27me3


title: Scales, WT, rep2

description: Library name: Sample 34


title: Scales, WT, rep3

description: Library name: Sample 35


title: Mouse limb explant, 96-well, H3K27ac, rep3

description: Library name: 15082024_KH_M-96-well_H3K27ac


title: Gills, pth4KO, rep3

description: Library name: Sample 31


title: Gills, pth4KO, rep2

description: Library name: Sample 30


title: Gills, WT, rep3

description: Library name: Sample 27


title: Mouse limb explant, 96-well, H3K27me3, rep3

description: Library name: 15082024_KH_M-96-well_H3K27me3


title: Gills, WT, rep1

description: Library name: Sample 25


title: Mouse limb explant, ALI, H3K27ac, rep3

description: Library name: 15082024_KH_M-ALI_H3K27ac


title: Kidney, pth4KO, rep4

description: Library name: Sample 24

source_name: Kidney

value: Kidney


title: Gills, WT, rep4

description: Library name: Sample 28


title: Mouse limb explant, ALI, H3, rep3

description: Library name: 15082024_KH_M-ALI_H3


title: Mouse limb explant, ALI, H3K4me3, rep3

description: Library name: 15082024_KH_M-ALI_H3K4me3


title: Mouse limb explant, 96-well, H3K4me3, rep3

description: Library name: 15082024_KH_M-96-well_H3K4me3


title: Mouse limb explant, 96-well, H3K9me3, rep3

description: Library name: 15082024_KH_M-96-well_H3K9me3


title: Gills, pth4KO, rep1

description: Library name: Sample 29


title: Mouse limb explant, ALI, H3K9me3, rep3

description: Library name: 15082024_KH_M-ALI_H3K9me3


title: Mouse limb explant, ALI, H3K27me3, rep3

description: Library name: 15082024_KH_M-ALI_H3K27me3


title: Mouse limb explant, 96-well, H3, rep2

description: Library name: 13082024_KH_M-96-well_H3


title: Gills, WT, rep2

description: Library name: Sample 26


title: HUDEP2 cells; DMSO_rep1_Input

last: Xu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

institute: Soochow University

description: Library name: INPUT-R2

source_name: Human bone marrow

value: Human bone marrow

value: erythroblast cells

value: DMSO


title: Human meningioma, FFPE [MN57]

description: Illumina EPICv2

value: meningioma


title: Kidney, pth4KO, rep3

description: Library name: Sample 23


title: Kidney, pth4KO, rep2

description: Library name: Sample 22


title: Mouse limb explant, 96-well, H3K4me3, rep2

description: Library name: 13082024_KH_M-96-well_H3K4me3


title: Kidney, pth4KO, rep1

description: Library name: Sample 21


title: Kidney, WT, rep2

description: Library name: Sample 18


title: Kidney, WT, rep1

description: Library name: Sample 17


title: Mouse limb explant, 96-well, H3K27ac, rep2

description: Library name: 13082024_KH_M-96-well_H3K27ac


title: Mouse limb explant, ALI, H3K27ac, rep2

description: Library name: 13082024_KH_M-ALI_H3K27ac


title: Mouse limb explant, 96-well, H3K9me3, rep2

description: Library name: 13082024_KH_M-96-well_H3K9me3


title: Kidney, WT, rep3

description: Library name: Sample 19


title: Mouse limb explant, ALI, H3K4me3, rep2

description: Library name: 13082024_KH_M-ALI_H3K4me3


title: Kidney, WT, rep4

description: Library name: Sample 20


title: Brain, pth4KO, rep4

description: Library name: Sample 16

source_name: Brain

value: Brain


title: Mouse limb explant, 96-well, H3K27me3, rep2

description: Library name: 13082024_KH_M-96-well_H3K27me3


title: Mouse limb explant, ALI, H3K27me3, rep2

description: Library name: 13082024_KH_M-ALI_H3K27me3


title: Mouse limb explant, 96-well, H3, rep1

description: Library name: 07082024_KH_M-96-well_H3


title: Left Basolateral amygdala Sham 2

city: Lubbock

first: Julian

middle: David

last: Cardenas

state: TX

address: 3601 4th Street

department: Pharmacology and Neurosciences

institute: Texas Tech University Health Science Center

description: Library name: sham_bla_left_2

data_processing:
Read quality was assessed using Fastp (v.0.23.4). Reads with a Phred score below 30 were removed (-q 30), and we trimmed 10 low-quality nucleotides from the ends of the reads (-t 10), resulting in reads with a mean length of 91 bp. To align the reads to the reference genome, we utilized Salmon (v.1.10.2). We created a decoy-aware index using the mRatBN7.2 genome release 111 from Ensembl. After building the index, we used the salmon quant command with the -l A flag to automatically identify the library type and the --validatingMappings flag to quantify transcript expression.
Assembly: mRatBN7.2
Supplementary files format and content: Microsoft Excel Spreadsheet includes raw counts for each sample.

organism: Rattus norvegicus

source_name: BLA

extract_protocol:
At the chronic stage of neuropathic pain (4 weeks post-SNL or -sham surgery), rats (SNL, n = 6; sham, n = 6) were euthanized via decapitation. The brains were rapidly extracted and oxygenated in ice-cold ACSF that contained the following (in mM): 125.0 NaCl, 2.6 KCl, 2.5 NaH2PO4, 1.3 CaCl2, 0.9 MgCl2, 21.0 NaHCO3, and 3.5 glucose. Coronal brain slices (1,000 μM) containing the left and right CeA were prepared using a Vibratome (VT1200S, Leica Biosystems, Nussloch, Germany) as described previously (Hein et al., 2021; Presto & Neugebauer, 2022; Thompson et al., 2018). The left and right CeA and BLA were dissected from freshly harvested slices for bulk RNA sequencing analysis.
RNA library preparation and sequencing were performed at the University of Texas at Austin Genomic Facility. Illumina Tag-Seq of polyA enriched total RNA sequencing was performed (single end, 100 bp).

value: BLA


title: Brain, pth4KO, rep1

description: Library name: Sample 13


title: Brain, pth4KO, rep3

description: Library name: Sample 15


title: Brain, pth4KO, rep2

description: Library name: Sample 14


title: Brain, WT, rep3

description: Library name: Sample 11


title: Mouse limb explant, 96-well, H3K9me3, rep1

description: Library name: 07082024_KH_M-96-well_H3K9me3


title: Brain, WT, rep1

description: Library name: Sample 9


title: Mouse limb explant, ALI, H3, rep1

description: Library name: 07082024_KH_M-ALI_H3


title: Mouse limb explant, 96-well, H3K4me3, rep1

description: Library name: 07082024_KH_M-96-well_H3K4me3


title: IP-Svi-0 27C Rep3

description: Library name: ipsvi-27C_R3


title: Lung tissue, PBS treatment, 5 day, rep1

city: Guangzhou

first: Xiting

last: Lv

address: No. 232 East Ring Road, Guangzhou Higher Education Mega Center

institute: Guangzhou University of Chinese Medicine

description: Library name: Ctrl 1

data_processing:
DESeq2 (v1.16.1)
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using Total RNA Extraction Kit 2.0 Plus. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer's instructions.

value: Lung

value: PBS treatment, 5 day


title: Human meningioma, FFPE [MN25]

description: Illumina EPICv2

value: Female

value: censored


title: Brain, WT, rep2

description: Library name: Sample 10


title: Intestine, pth4KO, rep4

description: Library name: Sample 8

source_name: Intestine

value: Intestine


title: Mouse limb explant, ALI, H3K9me3, rep2

description: Library name: 13082024_KH_M-ALI_H3K9me3


title: Intestine, pth4KO, rep2

description: Library name: Sample 6


title: Mouse limb explant, 96-well, H3K27me3, rep1

description: Library name: 07082024_KH_M-96-well_H3K27me3


title: IP-Svi-0 27C Rep1

description: Library name: ipsvi-27C_R1

value: whole seedlings

value: IP-Svi-0 background


title: Mouse limb explant, ALI, H3K9me3, rep1

description: Library name: 07082024_KH_M-ALI_H3K9me3

value: limb explants


title: Brain, WT, rep4

description: Library name: Sample 12


title: Mouse limb explant, 96-well, H3K27ac, rep1

description: Library name: 07082024_KH_M-96-well_H3K27ac


title: Intestine, pth4KO, rep3

description: Library name: Sample 7


title: Intestine, pth4KO, rep1

description: Library name: Sample 5


title: Mouse limb explant, ALI, H3K4me3, rep1

description: Library name: 07082024_KH_M-ALI_H3K4me3


title: Inguinal Subcutaneus White Adipose Tissue, 70 days post 33.3 Gy CONV irradiation, rep 3

city: Pisa

first: Giulia

last: Furini

address: Via Giuseppe Moruzzi 1

department: Institute of Clinical Physiology (IFC)

country: Italy

institute: National Research Council (CNR)

description: Library name: 10C_AT

data_processing:
Dragen BCLConvert (for demultiplexing): raw data
Kallisto 0.5.0
Assembly: mm10
Supplementary files format and content: tsv from kallisto, gene counts

extract_protocol:
Total RNA was extracted from 10–15 mg of frozen Inguinal Subcutaneus White Adipose Tissue, collected from the left hindlimb of both control and irradiated mice. Homogenization was performed with a Qiagen TissueLyser II in 700 µL of TRIzol reagent using stainless steel beads at 30 Hz for 5×30 sec. The aqueous phase obtained after chloroform addition (1/5 volume) and centrifugation (12000 × g for 15 min at 4 °C) was loaded onto Direct-zol RNA Microprep columns (Zymo Research,) and RNA eluted in 15 uL RNAse-free water, as indicated by the manufacturer protocol.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus

treatment_protocol: C57BL/6J mice were exposed to 33.3 Gy electron irradiation using the ElectronFlash linear accelerator (Linac) available at the Centro Pisano FLASH Radiotherapy (CPFR). The instrument was set on either FLASH or conventional (CONV) modality.  Sham, not irradiated mice served as controls.

value: WT


title: Inguinal Subcutaneus White Adipose Tissue, 70 days post 33.3 Gy CONV irradiation, rep 2

description: Library name: 8C_AT


title: Intestine, WT, rep3

description: Library name: Sample 3


title: Human meningioma, FFPE, [MN24-1]

description: Nanostring nCounter

hyb_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.

scan_protocol: Cartridges were scanned on the nCounter Digital Analyzer with a FOV setting of 550

data_processing:
Samples here are unique meningiomas included in the study. Counts were positive control normalized using the spike-in positive control probes in the nSolver solftware, as per recommendations from the manufacturer (Nanostring).
Nanostring_IncidentalMeningioma_Processed_Data_Matrix.xls represents Positive control normalized counts

source_name: FFPE meningioma

extract_protocol: Total RNA was extracted from frozen or FFPE meningioma tumor samples using Qiagen AllPrep or Qiagen FFPE RNAeasy kits.

value: FFPE meningioma

tag: disease


title: Inguinal Subcutaneus White Adipose Tissue, 70 days post 33.3 Gy FLASH irradiation, rep 4

description: Library name: 6F_AT

value: FLASH-RT


title: Human meningioma, FFPE, [MN22-1]

description: Nanostring nCounter

label_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.

value: Male


title: Inguinal Subcutaneus White Adipose Tissue, 70 days post 33.3 Gy FLASH irradiation, rep 1

description: Library name: 3F_AT


title: Inguinal Subcutaneus White Adipose Tissue, 70 days post 33.3 Gy FLASH irradiation, rep 2

description: Library name: 4F_AT


title: Inguinal Subcutaneus White Adipose Tissue, 70 days post 33.3 Gy CONV irradiation, rep 1

description: Library name: 7C_AT


title: Human meningioma, FFPE, [MN21-1]

description: Nanostring nCounter


title: Intestine, WT, rep2

description: Library name: Sample 2


title: Mouse limb explant, ALI, H3K27ac, rep1

description: Library name: 07082024_KH_M-ALI_H3K27ac


title: Human meningioma, FFPE, [MN23-1]

description: Nanostring nCounter

value: progression


title: Human meningioma, FFPE, [MN20-1]

description: Nanostring nCounter


title: Inguinal Subcutaneus White Adipose Tissue, 70 days not irradiated, rep 2

description: Library name: 2CNT_AT

value: sham


title: Intestine, WT, rep1

description: Library name: Sample 1


title: Inguinal Subcutaneus White Adipose Tissue, 70 days not irradiated, rep 1

description: Library name: 1CNT_AT


title: Human meningioma, FFPE, [MN19-1]

description: Nanostring nCounter

value: meningioma


title: Intestine, WT, rep4

description: Library name: Sample 4


title: Inguinal Subcutaneus White Adipose Tissue, 70 days post 33.3 Gy FLASH irradiation, rep 3

description: Library name: 5F_AT


title: Inguinal Subcutaneus White Adipose Tissue, 70 days not irradiated, rep 3

description: Library name: 4CNT_AT


title: Human meningioma, FFPE, [MN18-1]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN16-1]

description: Nanostring nCounter


title: Mutant Mouse, Heart 2

city: Iowa City

first: Jared

middle: M.

last: McLendon

state: Iowa

address: 180 South Grand Ave, CPB 554

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

description:
Library name: 1678_S824_GX
FFPE Spatial Sequencing

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline (v4.0.1) to generate FASTQ files.
Data were aligned to the mm10-2020-A mouse genome using Space Ranger's default settings.
Gene expression level of coding genes was analyzed with Seurat v5.
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: ####.tif: high-res image of tissue
Supplementary files format and content: ####.json: sequencing metadata and demultiplexing summary
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
Fresh tissue was fixed in 10% neutral buffered formalin, embedded in paraffin, and 5 um section were cut.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides and Reagent kit according to the manufacturers instructions.

value: Heart

tag: background

value: male


title: Human meningioma, FFPE, [MN13-1]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN12-1]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN11-1]

description: Nanostring nCounter


title: Mutant Mouse, Heart 3

description:
Library name: 1680_S825_GX
FFPE Spatial Sequencing

value: female


title: WT Mouse, Heart 3

description:
Library name: 1671_S821_WT
FFPE Spatial Sequencing


title: Human meningioma, FFPE, [MN10-1]

description: Nanostring nCounter


title: Mutant Mouse, Heart 1

description:
Library name: 1677_S823_GX
FFPE Spatial Sequencing


title: Human meningioma, FFPE, [MN15-1]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN8-1]

description: Nanostring nCounter


title: WT Mouse, Heart 2

description:
Library name: 1669_S820_WT
FFPE Spatial Sequencing


title: WT Mouse, Heart 1

description:
Library name: 1665_S819_WT
FFPE Spatial Sequencing


title: OE-2_FKDL210361465-1a

city: Shanghai

first: Juanjuan

last: Shi

address: 160 Pujian Rd Shanghai 200127 P. R. China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

description: Library name: Ly6D OE-2

data_processing:
ATACseq reads were trimmed by Trim Galore (v0.6.7) to remove adaptor sequences. The trimmed reads were aligned to mm10 Bowtie2 (v.2.4.2) with the parameters —very-sensitive-local —nounal —no-mixed —no-discordant —phred33 -I 10 -X 700. Peaks were first called for each replicate using MACS2 (v.2.2.7.1) with the parameters --nomodel --shift -100 --extsize 200.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: KPC1199 overexpress Ly6D cells.

extract_protocol:
Ly6D low and high cells were sorted from orthotopical models transplanted with KPC1199 WT cells. Ly6D WT cells and Ly6D overexpression cells were sorted from orthotopical models transplanted with KPC1199 Ly6D WT and KPC1199 Ly6D overexpression cell.
For ATAC-seq experiments, 50,000 cells of KPC1199 cells were tagmented according to manufacturer’s instructions (Vazyme, TD501)

value: cell line

tag: cell line

value: Pancreatic cancer cells


title: Human meningioma, FFPE, [MN7-1]

description: Nanostring nCounter

value: Female

value: censored


title: Human meningioma, FFPE, [MN6-1]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN9-1]

description: Nanostring nCounter


title: pxpr-2_FKDL210361463-1a

description: Library name: Ly6D WT-2

source_name: KPC1199 WT cells


title: low-2_FKDL210395132-1a

description: Library name: Ly6D low-2

source_name: ly6d low express from KPC1199 WT cells


title: pxpr-1_FKDL210361462-1a

description: Library name: Ly6D WT-1


title: OE-1_FKDL210361464-1a

description: Library name: Ly6D OE-1


title: Human meningioma, FFPE, [MN5-1]

description: Nanostring nCounter


title: high-1_FKDL210395129-1a

description: Library name: Ly6D hi-1

source_name: ly6d hi express from KPC1199 WT cells


title: low-1_FKDL210395131-1a

description: Library name: Ly6D low-1


title: Human meningioma, FFPE, [MN3-1]

description: Nanostring nCounter


title: high-2_FKDL210395130-1a

description: Library name: Ly6D hi-2