title: TA_Crush_3d

city: Rome

first: Andrea

last: Bracaglia

address: Via Antonio Scarpa 16

country: Italy

institute: University of Rome La Sapienza

description: Fresh-frozen spatial transcriptome experiment

data_processing:
Raw sequencing data and .json file obtained with Loupe Browser were processed with 10x Genomics spaceranger pipeline
The reads wre aligned to 10mm mouse genome with spaceranger default parameters to generate h5 matrix
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 h5 matrix with barcodes and gene expression count
Supplementary files format and content: V12M21-034.json json file with spatial coordinates
Supplementary files format and content: lam.tif image in tif format of laminin immunofluorescence staining
Supplementary files format and content: col.tif image in tif format of collagen immunofluorescence staining
Supplementary files format and content: btx.tif image in tif format of bungarotoxin staining
Supplementary files format and content: dapi.tif image in tif format of dapi staining
Library strategy: Spatial Transcriptomics

source_name: Spatial transcriptomics of tibialis anterior muscle 3 days after transient denervation (crush)

growth_protocol: C57BL/6 mice were mainated in a pathogen-free animal facility under standard 12h light/12h dark cycle at 21°C with access to red house and to standard chow and water ad libitum

extract_protocol:
Fresh-fozen muscles were embebbed in OCT and 10 μm sections were cut at the cryostat
Spatial transcriptomics sequencing libraries were prepared with 10X Genomics Visium spatial gene expression slides and reagent kit according to manufacturer's instructions

treatment_protocol: Sciatic nerve crush was performed on 3 months old mice and Tibialis anterior and EDL were collected 3 days and 30 days post-denervation

value: Skeletal muscle


title: Rep_late_rep3_H4K20me3

status: Public on Jan 01 2025

type: SRA

city: Tokyo

first: Takeshi

last: Katsuda

address: 7-chōme-3-1 Hongō

department: Department of Chemical System Engineering

country: Japan

institute: University of Tokyo

library_source: genomic

data_processing:
Reads were trimmed using Cutadapt with parameters “-j 4 --nextseq-trim 20 -m 15” before alignment to the mouse genome (mm10) using Bowtie2 with parameters “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 4.” The resulting sequence alignment files were sorted, and duplicates were removed using Picard (https://broadinstitute.github.io/picard/). The BAM files were then converted to BED files using BEDTools (https://bedtools.readthedocs.io/en/latest/)  with the bamtobed function with option “-bedpe.” Data was filtered to keep read pairs on the same chromosome and with a fragment length <1000 bp. For peak calling, the BEDTools genomecov tool was used to generate BedGraph files. For visualization using IGV and deepTools, the BAM files were converted to BigWig files using the bamCoverage function with options “--binSize 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPGC --extendReads" and then replicates were merged using the bigWigMerge function followed by the bedGraphToBigWig function (UCSC tools).
Peak calling was conducted on the individual BedGraph files using SEACR with options “0.01 norm stringent.”  Downstream analysis was conducted DiffBind. Replicates were processed with default counting and normalization parameters with the option “minMembers=2” and the mm10 blacklist was used.
Assembly: mm10
Supplementary files format and content: BED files (for peaks), BigWig files (for genome tracks)
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

growth_protocol: For characterization of the reprogramming stage, 4-5 week-old mice were retro-orbitally injected with AAV:ITR-U6-sgRNA(backbone)-TBG-Cre-WPRE-hGHpA-ITR with 5 × 1011 genome copies/mouse/gene.

extract_protocol:
CUT&Tag was performed following EpiCypher® CUTANA™ CUT&RUN Protocol v1.7 with minor modifications. Cells at different stages of biliary reprogramming were harvested from the Cas9-EGFP mice challenged with 0.1% DDC for 8-9 weeks by FACS (n = 2-3).
The universal i5 primer, barcode i7 primer, and 25CUTANA High Fidelity 2X PCR Master Mix for CUT&Tag (EpiCypher) were used, and PCR was performed (1 cycle of 20 °C for 5 min; 1 cycle of 72 °C for 5 min; 1 cycle of 98 °C for 45 s, 14–21 cycles of 98 °C for 15 s and 60 °C for 10 s; 72 °C for 1 min). The DNA was cleaned up with 1.3× AMPure XP beads.  Sequencing was performed using a NextSeq2000 with 55 bp paired-end reads.

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo). Eight weeks after the DDC challenge, reprogrammed cells and biliary cells were harvested.

tag: tissue

value: Liver

tag: genotype

value: WT

tag: group


title: DFGC_2_ATAC,snMultiome

city: Duarte

first: Zhao

last: Wang

state: CA

address: 1500 E Duarte Rd

department: Diabetes and Cancer Metabolism

country: USA

institute: City of Hope

library_source: genomic single cell

data_processing:
CellRanger arc v2.0.2 count and aggr functions to aggreate RNA and ATAC output from nine samples into a single set of output: filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz, which are used for following Seurat and Signac analysis
Assembly: mm10
Supplementary files format and content: CellRanger arc aggr output:  filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz

source_name: frozen heart

extract_protocol:
The nuclei isolated by different methods were put into sterile PCR tubes containing reagents as per the 10x user guide. GEMs were generated using the 10x Genomics Chromium Controller with Next GEM Chip J single cell kit (10x Genomics Inc., Pleasanton, CA, USA).
After pre-amplification PCR, all libraries are divided into two parts, one part is used to perform snRNA-seq library, while the other is used to perform snATAC-seq library according to CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevA.

value: frozen heart

tag: cell type

value: cardiomyocyte,macrophage, endothelial cell, epicardial cell, fibroblast, et al


title: LA913

city: Stanford

first: Gabor

last: Boross

address: 450 Serra Mall

institute: Stanford University

description: barcode region of lentiviral backbones from genomic DNA from bulk tumor-bearing lungs were PCR-amplified and high-throughput DNA sequenced

data_processing:
For genomic barcoded DNA, the sgIDs (specific for given guideRNA and so genotype of the tumor) and barcodes (specific to tumor) were identified from fastq files and tumor size (cell number) was calculated by normalizing the number of reads to  three benchmarks “spike-in” cell lines with custom R and python scripts.
Assembly: no genome build or mapping to genome was done
Supplementary files format and content: The dual_guide_tumor_sizes.csv file contains all tumor sizes (number of cells) for all tumors/expansions. The mouse genotype, sample title, guideRNA are shown in comma separated text table.
Library strategy: Amplicon-seq

source_name: lung

growth_protocol: Autochthonous lung tumors were initiated in mice below with Lenti-U6BC-sgDbl/Cre lentiviral pool  and harvested after ~3 months.Mice genotypes used: KrasLSL-G12D;R26LSL-Tomato (KT); KT;H11_LSL-Cas9 and KT;H11LSL-Cas9.

extract_protocol:
Following homogenization and overnight protease K digestion, genomicDNA was extracted from the lung lysates using standard phenol-chloroform and ethanolprecipitation methods.
Tuba-seqUltra libraries were generated by isolating genomic DNA from bulk tumor- bearing lung tissue, followed by PCR amplification of the BC-sgRNA1-sgRNA2 region from 32 μg of bulk lung genomic DNA using Q5 Ultra II High-Fidelity 2× Master Mix (New England Biolabs, M0494X). Unique dual-indexed primers were used to amplify each sample followed by purification using Agencourt AMPure XP beads (Beckman Coulter, A63881). The libraries were pooled based on lung weights to ensure even read depth and sequenced (read length 2 × 150 bp) on the Illumina NextSeq 6000 platform.

value: lung


title: Patient R4124 geneexp

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

country: France

institute: Assistance Publique des Hôpitaux de Paris

description:
Patient
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and aligned using GRCh38 genome assembly as reference data.
Further processing was done with Seurat v4.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheric blood

extract_protocol:
NA
Library was prepared using Chromium Single Cell 3ʹ version CG000317 rev B protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ version CG000317 rev B protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA and the antibody-derived tagged cDNAs. For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ version CG000317 rev B protocol (10x Genomics).
Libraries were equimolar pooled to obtain at least 20,000 read pairs per cell and 5,000 read pairs for feature barcode part after sequencing on Illumina Novaseq 6000 (100 cycles cartridge).
OTHER : CITE-seq

value: Peripheric blood

value: PBMC

value: mRNA derived cDNA

tag: treatment

value: Haetopoietic stem cell transplant


title: Rep_late_rep3_H4K20me2


title: DFGC_1_ATAC,snMultiome


title: Patient R4077 geneexp


title: DFGC_3_RNA,snMultiome

molecule: nuclear RNA


title: Rep_late_rep3_H3K4me3


title: DFGC_2_RNA,snMultiome


title: Patient R4064 geneexp


title: HCT116_siCTL_1

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

country: South Korea

institute: Ewha Womans University

library_source: transcriptomic

data_processing:
Sequence reads were mapped with the bowtie2 software tool, which yielded bam files.
Read counts mapped to a mature miRNA sequence were extracted from the alignment file using bedtools v2.25.0 and Bioconductor , which use the R statistical programming language. Read counts were used to determine the expression level of miRNAs.
The CPM+TMM normalization method was used for between-sample comparison.
Assembly: hsa mirBase
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

molecule: total RNA

source_name: colon

extract_protocol:
Exosomal RNA was isolated using the TRIzol LS reagent. RNA quality was assessed by an Agilent 2100 bioanalyzer using the RNA 6000 Pico Chip, and RNA quantification was performed using a NanoDrop 2000 Spectrophotometer system
library construction was performed with a NEBNext Multiplex Small RNA Library Prep kit according to the manufacturer’s instructions.

value: colon

tag: cell line

value: carcinorma cell


title: DFGC_1_RNA,snMultiome


title: FACS_3_ATAC,snMultiome


title: Patient R3986 geneexp


title: Rep_late_rep3_H3K4me1


title: FACS_2_ATAC,snMultiome


title: Patient R4151 geneexp


title: TA_Crush_30d

source_name: Spatial transcriptomics of tibialis anterior muscle 30 days after transient denervation (crush)


title: Patient R3756 geneexp


title: Rep_late_rep3_H3K36me1


title: Patient R3753 geneexp


title: FACS_3_RNA,snMultiome


title: Patient R4093 geneexp


title: FACS_2_RNA,snMultiome


title: Patient R3692 geneexp


title: Rep_late_rep2_H4K20me3


title: Rep_late_rep3_H4K20me1


title: Patient R3882 geneexp


title: FACS_1_RNA,snMultiome


title: Patient R3640 geneexp


title: Rep_late_rep3_H3K27me3


title: Patient R3733 geneexp


title: Rep_late_rep2_H4K20me2


title: Rep_late_rep3_H3K4me2_CUTAC


title: Patient R3570 geneexp


title: Beads_2_ATAC,snMultiome


title: Rep_late_rep2_H4K20me1


title: Patient R3504 geneexp


title: FACS_1_ATAC,snMultiome


title: Beads_1_ATAC,snMultiome


title: Patient R3532 geneexp


title: Rep_late_rep2_H3K4me3


title: Beads_3_RNA,snMultiome


title: Rep_late_rep3_H3K36me3


title: Rep_late_rep2_H3K4me2_CUTAC


title: Patient R3500 geneexp


title: Rep_late_rep2_H3K4me1


title: Patient R3486 geneexp


title: Beads_2_RNA,snMultiome


title: Rep_late_rep3_H3K27ac


title: Rep_late_rep2_H3K36me3


title: Patient R3435 geneexp


title: Beads_1_RNA,snMultiome


title: Rep_late_rep2_H3K36me1


title: Beads_3_ATAC,snMultiome


title: Rep_late_rep2_H3K27me3


title: Patient R3429 geneexp


title: B cell, Naive, 0hr, rep2

city: New York

first: Jayanta

last: Chaudhuri

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-sequencing reads were quantified using Salmon (v1.9.0) with --validateMappings. The mouse GRCm38 (mm10) reference transcriptome served as the basis for indexing. Subsequently, the Salmon quantification files were processed using the R package tximport (v1.28.0).
Assembly: mm10
Supplementary files format and content: tar file containing quanitification results using Salmon (v1.9.0) for each sample
Supplementary files format and content: comma-delimited text file containing the relative abundance of each transcript in units of Transcripts Per Million (TPM) estimated by Salmon

source_name: Spleen

growth_protocol: Murine primary B cells were cultured in RPMI-1640 + 15% Fetal Bovine Serum + 1% L-Glutamine + 1% Pen/Strep + 50μM β-mercaptoethanol at 37°C, 5% CO2 with humidification

extract_protocol:
Total RNA was extracted using Zymo RNA miniprep kit (ZymoResearch, R1054) following the manufacturer's protocols. 1 μg of total RNA was used for polyA enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490L)
Libraries were constructed using Poly(A)-enriched RNA samples by xGEN Broad-Range RNA Library Preparation kit (IDT, 10009865) and xGEN UDI Primers Plate 2 (IDT, 10009816)

treatment_protocol: Murine primary B cells were stimulated with 1 μg/mL anti-CD40 monoclonal antibody (Clone HM40-3), 12.5 ng/mL IL-4, or 50 ng/mL IL-21

value: Spleen

value: Primary B cells

value: Wild type


title: B cell, Naive, 0hr, rep3


title: Patient R3388 geneexp


title: Rep_late_rep2_H3K27ac


title: B cell, Naive, 0hr, rep1


title: Rep_late_rep1_H4K20me3


title: B cell, aCD40 + IL-4 + IL-21, 24hr, rep3


title: Patient R3353 geneexp


title: Rep_late_rep1_H4K20me2


title: Patient R3338 geneexp


title: B cell, aCD40 + IL-4 + IL-21, 6hr, rep3


title: Patient R3325 geneexp


title: B cell, aCD40 + IL-4 + IL-21, 24hr, rep1


title: Rep_late_rep1_H4K20me1


title: Rep_late_rep1_H3K4me3


title: 3661STDY6113747_D0+12_LD_TD

city: Oxford

first: Henderson

last: Zhu

address: Oxford Vaccine Group, Old Road, Headington, Old Road, Headington

department: Oxford Vaccine Group, Department of Paediatrics

country: United Kingdom

institute: University of Oxford

description:
3661STDY6113747
Paired baseline sample from GSE114033: GSM3131090

data_processing:
Fastq files from the same sample were concatenated, and pre-alignment quality control carried out using FASTQC.
Reads per gene were counted using the STAR GeneCounts mode.
Sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 Gencode version 26, using STAR (version 2.6.1c).
Assembly: GRCh38
Supplementary files format and content: P1RNASeq_Counts.txt: Text file containing normalized abundance measurements.

source_name: whole blood

extract_protocol:
Total RNA was extracted from all samples using the Tempus Spin RNA Isolation kit (Life Technologies).
Libraries were prepared using a poly-A selection step to exclude ribosomal RNA species (read length: 75bp paired-end, stranded).

value: whole blood

tag: infection

value: S. Paratyphi A NVGH308 strain

tag: dose

value: Low

tag: time point

value: 12 hours


title: 3661STDY6113786_D0+12_LD_nTD

description:
3661STDY6113786
Paired baseline sample from GSE114033: GSM3131105

value: WT


title: 3661STDY6113778_D0+12_LD_nTD

description:
3661STDY6113778
Paired baseline sample from GSE114033: GSM3131101


title: B cell, aCD40 + IL-4 + IL-21, 6hr, rep2


title: Patient R3242 geneexp


title: Rep_late_rep1_H3K4me2_CUTAC

value: Liver


title: Patient R3222 geneexp


title: Rep_late_rep1_H3K4me1


title: Patient R3358 geneexp


title: 3661STDY6113731_D0+12_LD_TD

description:
3661STDY6113731
Paired baseline sample from GSE114033: GSM3131082


title: B cell, aCD40 + IL-4 + IL-21, 6hr, rep1


title: 3661STDY6113233_D0+12_HD_TD

description:
3661STDY6113233
Paired baseline sample from GSE114033: GSM3131059

value: High


title: B cell, aCD40 + IL-21, 24hr, rep3


title: Rep_late_rep1_H3K36me3


title: Patient R3195 geneexp


title: 3661STDY6113760_D0+12_LD_TD

description:
3661STDY6113760
Paired baseline sample from GSE114033: GSM3131092


title: Rep_late_rep1_H3K36me1


title: Patient R3182 geneexp


title: Rep_late_rep1_H3K27me3


title: B cell, aCD40 + IL-4 + IL-21, 24hr, rep2


title: B cell, aCD40 + IL-21, 24hr, rep2


title: Patient R3291 geneexp


title: Patient R3086 geneexp


title: B cell, aCD40 + IL-21, 6hr, rep3


title: Patient R3075 geneexp


title: 3661STDY6113723_D0+12_HD_nTD

description:
3661STDY6113723
Paired baseline sample from GSE114033: GSM3131079


title: Rep_interm_rep3_H3K36me3


title: 3661STDY6113266_D0+12_HD_TD

description:
3661STDY6113266
Paired baseline sample from GSE114033: GSM3131069


title: Patient R3052 geneexp


title: B cell, aCD40 + IL-21, 6hr, rep2


title: Rep_interm_rep3_H3K36me1


title: B cell, aCD40 + IL-21, 6hr, rep1


title: 3661STDY6113229_D0+12_HD_nTD

description:
3661STDY6113229
Paired baseline sample from GSE114033: GSM3131053


title: Patient R3008 geneexp


title: B cell, aCD40 + IL-4, 24hr, rep3

value: aCD40 + IL-4


title: Patient R3017 geneexp

value: Peripheric blood


title: Rep_interm_rep2_H4K20me3


title: Rep_interm_rep2_H4K20me2


title: B cell, aCD40 + IL-4, 24hr, rep2


title: Patient R2904 geneexp

value: PBMC


title: 3661STDY6113258_D0+12_HD_TD

description:
3661STDY6113258
Paired baseline sample from GSE114033: GSM3131067


title: B cell, aCD40 + IL-21, 24hr, rep1


title: B cell, aCD40 + IL-4, 24hr, rep1


title: Rep_late_rep1_H3K27ac


title: 3661STDY6113782_D0+12_LD_nTD

description:
3661STDY6113782
Paired baseline sample from GSE114033: GSM3131103


title: Patient R2813 geneexp

value: mRNA derived cDNA


title: Rep_interm_rep2_H3K4me3


title: B cell, aCD40 + IL-4, 6hr, rep3


title: 3661STDY6113802_D0+12_LD_nTD

description:
3661STDY6113802
Paired baseline sample from GSE114033: NA


title: Patient R2807 geneexp

value: Haetopoietic stem cell transplant


title: 3661STDY6113245_D0+12_HD_TD

description:
3661STDY6113245
Paired baseline sample from GSE114033: GSM3131063


title: Patient R2794 geneexp


title: Rep_interm_rep2_H3K4me2_CUTAC


title: B cell, aCD40 + IL-4, 6hr, rep2


title: B cell, aCD40 + IL-4, 6hr, rep1


title: Rep_interm_rep2_H3K4me1


title: 3661STDY6113806_D0+12_LD_nTD

description:
3661STDY6113806
Paired baseline sample from GSE114033: GSM3131113


title: Patient R2718 geneexp


title: 3661STDY6113736_D0+12_LD_TD

description:
3661STDY6113736
Paired baseline sample from GSE114033: GSM3131084


title: B cell, aCD40, 24hr, rep3


title: 3661STDY6113224_D0+12_HD_nTD

description:
3661STDY6113224
Paired baseline sample from GSE114033: GSM3131076


title: B cell, aCD40, 24hr, rep2


title: Rep_interm_rep2_H3K36me1


title: Patient R2700 geneexp

description:
Patient
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: 3661STDY6113793_D0+12_LD_nTD

description:
3661STDY6113793
Paired baseline sample from GSE114033: GSM3131109


title: B cell, aCD40, 24hr, rep1


title: 3661STDY6113816_D0+12_LD_nTD

description:
3661STDY6113816
Paired baseline sample from GSE114033: GSM3131075


title: Patient R2684 geneexp


title: 3661STDY6113774_D0+12_LD_nTD

description:
3661STDY6113774
Paired baseline sample from GSE114033: GSM3131099


title: 3661STDY6113770_D0+12_LD_nTD

description:
3661STDY6113770
Paired baseline sample from GSE114033: NA


title: 3661STDY6113275_D0+12_HD_nTD

description:
3661STDY6113275
Paired baseline sample from GSE114033: GSM3131077


title: Rep_interm_rep1_H4K20me3


title: Rep_interm_rep2_H3K27ac


title: B cell, aCD40, 6hr, rep3


title: Patient R2759 geneexp


title: B cell, aCD40, 6hr, rep2


title: Rep_interm_rep2_H4K20me1


title: Rep_interm_rep1_H4K20me2


title: Patient R2643 geneexp


title: Rep_interm_rep2_H3K36me3


title: Patient R2521 geneexp


title: 3661STDY6113208_D0+12_HD_TD

description:
3661STDY6113208
Paired baseline sample from GSE114033: GSM3131049


title: Patient R2508 geneexp


title: B cell, STAT3 KO, aCD40 + IL-21, IgG1,  rep1

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie2 (v2.4.1) with --dovetail option.
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as control using narrow peak parameters --cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
Tracks shown are bigwig files processed with deepTools (v3.5.1) bamCoverage with --binSize 10. Saccharomyces cerevisiae spike-in DNA scaled bigwig tracks from replicates were then averaged per condition using bigwigAverage function from deepTools with bin size of 10bp.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except INPUT sample)
Library strategy: CUT&RUN

extract_protocol:
Following stimulation, cell were washed thrice with PBS, and resuspended in Antibody Buffer (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 μM Spermidine, 2 μM EDTA in H2O). Cells were then incubated overnight with anti-STAT3 Mouse mAb (124H6, CellSignaling, Cat #9139, dilution 1/100) in Antibody Buffer in a 96 well V-bottom plate at 4°C. Cells were then washed twice with Buffer 1 (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 μM Spermidine in H2O) and resuspended in 50ul of Buffer 1 + 1X pA/G-MNase (Cell Signaling, cat. 57813) and incubated on ice for 1 hour and washed thrice with Buffer 2 (0.05% w/v Saponin, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 μM Spermidine in 1X PBS). After washing, cells were resuspended in calcium Buffer (Buffer 2 + 2 μM CaCl2) for 30 mins on ice to activate the pA/G-MNase reaction, and equal volume of 2X STOP Buffer (Buffer 2 + 20 μM EDTA + 4 μM EGTA) was added along with 1 pg of Saccharomyces cerevisiae spike-in DNA (Cell Signaling, cat. 29987). Samples were incubated for 15 mins at 37°C and DNA was isolated and purified using Qiagen MinElute Kit according to manufacturer’s protocol and subjected to library amplification.
DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (KAPA Biosystems #KK8234) according to the manufacturer’s instructors with <0.001-3.8 ng input DNA and 14 cycles of PCR.

treatment_protocol: Naïve splenic B cells were initially cultured with αCD40 (1 μg/mL, Clone HM40-3) + IL-4 (12.5 ng/mL) for 96 hours and IgM+ and IgG1+ B cells were sorted. 400,000 IgM+ or IgG1+ B cells were stimulated with αCD40 (1 μg/mL) + IL-4 (12.5 ng/mL) or αCD40 + IL-21 (10 ng/mL) for an hour

tag: chip antibody

value: anti-STAT3 Mouse mAb (124H6, CST, Cat #9139)

value: STAT3 KO


title: Rep_interm_rep1_H3K4me3


title: 3661STDY6113199_D0+12_HD_TD

description:
3661STDY6113199
Paired baseline sample from GSE114033: GSM3131046


title: B cell, aCD40, 6hr, rep1

value: Spleen


title: Rep_interm_rep1_H4K20me1


title: B cell, STAT3 KO, aCD40 + IL-21, IgM, rep1

value: Primary B cells


title: Patient R2475 geneexp


title: Patient R2412 geneexp


title: Rep_interm_rep1_H3K4me2_CUTAC


title: B cell, STAT3 KO, aCD40 + IL-4, IgG1,  rep1


title: Rep_interm_rep1_H3K4me1


title: 3661STDY6113187_D0+12_HD_TD

description:
3661STDY6113187
Paired baseline sample from GSE114033: GSM3131042


title: B cell, STAT3 KO, aCD40 + IL-4, IgM, rep1


title: 3661STDY6113765_D0+12_LD_TD

description:
3661STDY6113765
Paired baseline sample from GSE114033: GSM3131096


title: 3661STDY6113752_D0+12_LD_TD

description:
3661STDY6113752
Paired baseline sample from GSE114033: GSM3131088


title: Patient R2268 geneexp


title: 3661STDY6113791_D0+12_LD_nTD

description:
3661STDY6113791
Paired baseline sample from GSE114033: GSM3131108


title: Patient R2315 geneexp


title: Rep_interm_rep1_H3K36me1


title: B cell, WT, aCD40 + IL-21, IgG1, rep2

value: Wild type


title: B cell, WT, aCD40 + IL-21, IgG1,  rep1


title: Patient R2029 geneexp


title: Patient R2122 geneexp


title: B cell, WT, aCD40 + IL-21, IgM, rep2


title: Rep_interm_rep2_H3K27me3


title: 3661STDY6113236_D0+12_HD_nTD

description:
3661STDY6113236
Paired baseline sample from GSE114033: GSM3131072

value: whole blood


title: Rep_interm_rep1_H3K27ac


title: 3661STDY6113239_D0+12_HD_TD

description:
3661STDY6113239
Paired baseline sample from GSE114033: GSM3131061

value: S. Paratyphi A NVGH308 strain


title: 3661STDY6113797_D0+12_LD_nTD

description:
3661STDY6113797
Paired baseline sample from GSE114033: GSM3131074

value: Low


title: Rep_interm_rep1_H3K27me3


title: 3661STDY6113741_D0+12_LD_TD

description:
3661STDY6113741
Paired baseline sample from GSE114033: GSM3131086

value: 12 hours


title: B cell, WT, aCD40 + IL-21, IgM, rep1


title: Patient R2043 geneexp


title: B cell, WT, aCD40 + IL-4, IgG1, rep2


title: Patient R1896 geneexp


title: 3661STDY6113757_D0+12_LD_TD

description:
3661STDY6113757
Paired baseline sample from GSE114033: GSM3131094

value: WT


title: 3661STDY6113232_D0+12_HD_nTD

description:
3661STDY6113232
Paired baseline sample from GSE114033: GSM3131057


title: Rep_early_rep3_H3K36me1

value: Liver


title: B cell, WT, aCD40 + IL-4, IgG1,  rep1


title: Healthy donor number 6 HD6 geneexp

description:
Healthy donor number 6
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: B cell, WT, aCD40 + IL-4, IgM, rep1


title: Rep_early_rep2_H4K20me2


title: Rep_early_rep2_H4K20me3


title: Healthy donor number 5 HD5 geneexp

description:
Healthy donor number 5
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: B cell, WT, aCD40 + IL-4, IgM, rep2


title: 3661STDY6113193_D0+12_HD_TD

description:
3661STDY6113193
Paired baseline sample from GSE114033: GSM3131044

value: High


title: Rep_interm_rep1_H3K36me3


title: Healthy donor number 4 HD4 geneexp

description:
Healthy donor number 4
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: Rep_early_rep3_H3K36me3


title: 3661STDY6113214_D0+12_HD_TD

description:
3661STDY6113214
Paired baseline sample from GSE114033: GSM3131051


title: B cell, Input

value: aCD40 + IL-4


title: Rep_early_rep2_H4K20me1


title: 3661STDY6113810_D0+12_LD_nTD

description:
3661STDY6113810
Paired baseline sample from GSE114033: GSM3131115


title: Healthy donor number 2 HD2 geneexp

description:
Healthy donor number 2
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: Peripheric blood


title: Rep_early_rep2_H3K4me3


title: Rep_early_rep2_H3K4me2_CUTAC


title: 3661STDY6113251_D0+12_HD_TD

description:
3661STDY6113251
Paired baseline sample from GSE114033: GSM3131064


title: C15Ledo replicate 1, scRNAseq

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

description: 10x Genomics (scRNA-seq read pairs per cell per library (Single Cell 3' v3), 28 bp; paired end)

data_processing:
For scRNA-seq analysis, the computer was equipped with Intel i9-14900K 24 Cores, 32 Threads and used as a server using Linux Ubuntu 22.04.5 LTS operating system.
Seurat v5.1.0 was used to do quality control and filtering using standard preprocessing workflow
Assembly: GRCm39.110
Supplementary files format and content: The base call files were demultiplexed, processed to generate FASTQ files with Cell Ranger v7.2.0 (10X Genomics) command mkfastq, and then aligned to the mouse reference genome (GRCm39.110), followed by filtering and barcode and unique molecular identifier (UMI) counting to generate count matrices for each sample.

source_name: Endometrial epithelial organoids

extract_protocol:
Endometrial epithelial organoids (EEO) established from postnatal days (PND) 3 and 15 C57BL6 females were collected after 8 days of culture (n=10 females/biological replicate/PND). EEOs were harvested, enzymatically dissociated using 0.05% trypsin (40 min, 37°C), and centrifuged at 300 × g for 5 min. Cells were resuspended in Advanced DMEM/F12 medium supplemented with 1X Anti-Anti, passed through a 40 µm filter and pelleted (300 × g for 5 min). The cell pellets were then resuspended in 1 mL 0.04% BSA in PBS and counted to assess viability. Single-cell RNA sequencing was conducted at the University of Missouri Genomics Technology Core.
For scRNA-seq analysis: scRNA-seq libraries were performed using the manufacturer’s protocol (10X Genomics). Single-cell droplet formation with a target count of 5000 cells per sample was performed using the 10X Chromium system (10X Genomics; Pleasanton, CA). Sequencing was performed in paired-end mode using NovaSeq 6000 (Illumina).

value: Endometrial epithelial organoids

value: Uterus (endometrial epithelium)

value: Post natal day (PND) 15


title: C3Ledo replicate 1, scRNAseq

value: Post natal day (PND) 3


title: Healthy donor number 3 HD3 geneexp

description:
Healthy donor number 3
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: PBMC

value: mRNA derived cDNA

value: Haetopoietic stem cell transplant


title: Rep_early_rep2_H3K4me1


title: BMDMs, Choline3

city: Wuhan

first: jianhong

last: zhao

state: Hubei

address: Donghu Road, No. 115

country: China

institute: Wuhan University

data_processing:
NCBI_GRCm39
Assembly: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: BMDMs

growth_protocol: For the in vivo tumor growth experiments, 5 × 105 shNC/shChrebp MC38 tumor cells were subcutaneously injected into the flanks of C57BL/6 mice.

extract_protocol:
Total RNA from BMDMs (choline-treated or untreated) or tumor tissues (from shNC/shChrebp MC38-bearing C57BL/6 mice) was extracted using the TRIzol reagent kit (Invitrogen, 15596018CN) following the manufacturer's instructions.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: BMDMs

value: Choline


title: Rep_early_rep2_H3K36me1


title: BMDMs, Choline1


title: MUM2B cells, selamectin, 24 hours, rep2

city: Shanghai

first: Jie

last: He

address: Zhi Zao Ju

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Sequence reads were aligned to the reference human genome, GRCh38 using STAR (2.7.0d).
With the cufflinks program and corresponding sequence reads data we estimated the expression level for each gene for Homo sapiens.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies), then the concentration, quality and integrity of RNA were determined by NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: uveal melanoma cells

value: selamectin, 24 hours


title: BMDMs, Choline2


title: MUM2B cells, selamectin, 24 hours, rep1


title: pSLE-EA-3

first: Yanling

last: Chang

address: Pujian road 160

institute: renji hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: CD8+T cell

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8+T cell

value: EA


title: Rep_early_rep2_H3K36me3

value: Liver

value: WT


title: BMDMs, Ctrl3

value: PBS


title: MUM2B cells, DMSO, 24 hours, rep3

value: DMSO, 24 hours


title: pSLE-EA-2


title: Healthy donor number 1 HD1 geneexp

description:
Healthy donor number 1
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: Peripheric blood


title: 3661STDY6113202_D0+12_HD_TD

description:
3661STDY6113202
Paired baseline sample from GSE114033: GSM3131047

value: whole blood

value: S. Paratyphi A NVGH308 strain

value: High

value: 12 hours


title: BMDMs, Ctrl2


title: pSLE-EA-1


title: MUM2B cells, selamectin, 24 hours, rep3


title: Rep_early_rep1_H4K20me3


title: MC38, shChrebp3

source_name: tumor tissues

value: tumor tissues

value: Chrebp knockdown


title: Rep_early_rep1_H4K20me2


title: MUM2B cells, DMSO, 24 hours, rep2


title: late-onset LUAD 7

city: Shenyang

first: Rui

last: Ma

address: 4 Chongshan East Road

institute: The Fourth Affiliated Hospital of China Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.20.
When N number of single-ended sequencing reads was greater than 3, the paired reads were removed; When the proportion of bases with mass value lower than 5 in the single-ended sequencing reads was greater than 20%, the paired reads were removed; Reads that contain adapter were removed.
Bowtie2 software was used to compare Clean reads to the silva database to remove rRNA, and the remaining Reads were used for subsequent analysis.
FastQC was used to visualize the distribution of mass values of base sequencing and evaluate the degree of base separation.
The Reads were compared with the reference genome using Hisat2 software.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: stage I LUAD tumor

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen). NanoDrop 2000 and Agilent 4200 were used for preliminary and precise quantification of concentration respectively. Qualified RNA (concentration≥40ng/ul, total RNA≥2ug and RINe≥6.5) was used for the construction of sequencing libraries.
The mRNA was enriched with magnetic beads with Oligo (dT) and then broken into short fragments. The first cDNA strand was synthesized by six base random primers using fragmented mRNA as template, and the second cDNA strand was synthesized by adding buffer, dNTPs (dTTP, dATP, dGTP and dCTP) and enzyme. The obtained double-stranded cDNA was purified, terminal repaired, A-tailed and sequenced, and then fragment size selection was performed. Finally, PCR was used to enrich the library.

value: stage I LUAD tumor


title: Rep_early_rep2_H3K27ac


title: BMDMs, Ctrl1

value: BMDMs


title: MUM2B cells, DMSO, 24 hours, rep1

value: uveal melanoma cells


title: pSLE-Control-3

value: Control


title: pSLE-Control-2

value: CD8+T cell


title: MC38, shChrebp2


title: 3661STDY6113729_D0+12_HD_nTD

description:
3661STDY6113729
Paired baseline sample from GSE114033: GSM3131081


title: pSLE-Control-1


title: late-onset LUAD 6


title: Rep_early_rep1_H4K20me1


title: MC38, shChrebp1


title: Rep_early_rep2_H3K27me3


title: Rep_early_rep1_H3K4me3


title: late-onset LUAD 5


title: MC38, shCtrl3


title: Rep_early_rep1_H3K4me2_CUTAC


title: MC38, shCtrl2


title: Rep_early_rep1_H3K4me1


title: late-onset LUAD 4


title: late-onset LUAD 3


title: BJAB_ctrl2

city: Palo Alto

first: Jesse

last: Engreitz

address: 240 Pasteur Drive, BMI 3700

description:
Library name: BJAB_ctrl2
RNA-seq in BJAB cells in condition: no stimulation

data_processing:
We removed reads aligning to highly abundant RNA transcripts, including rRNA, snRNA, and repeat elements defined by RepeatMasker. We aligned all remaining reads to the human transcriptome (RefSeq, Downloaded from UCSC Genome Browser March 6, 2013) and genome (hg19) using Tophat2 and discarded reads with MAPQ < 30.
Assembly: hg19
Supplementary files format and content: TPM.txt files contain 2 columns: Gene Symbol, transcripts per million from TopHat2

source_name: BJAB

growth_protocol: We maintained cells at a density between 100K and 1M per ml in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% heat-inactivated FBS (HIFBS, Thermo Fisher Scientific), 2mM L-glutamine, and 100 units/ml streptomycin and 100 mg/ml penicillin by diluting cells 1:8 in fresh media every three days.

extract_protocol:
Cells were lysed in buffer containing dNTPs and oligo-dT primers (see SmartSeq2 protocol)
RNA libraries were prepared for RNA-seq using SmartSeq2

treatment_protocol: We stimulated BJAB cells with 4 µg/ml anti-CD40 (Invitrogen-140409-82) and 10 µg/ml anti-IgM (Sigma-I0759) for 4 hours. We stimulated Jurkat cells with 5 µg/ml anti-CD3 (Biolegend-317315) and 100 ng/ml phorbol 12-myristate 13-acetate (PMA, Sigma-P1585) for 4 hours. We stimulated U937 cells with 200 ng/ml LPS for 4 hours. We stimulated THP1 cells with 1 µg/ml bacterial lipopolysaccharide (LPS) from E. coli K12 (LPS-EK Invivogen tlrl-peklps) for 4 hours.

value: BJAB

value: B cell line

value: untreated


title: BJAB_stim2

description:
Library name: BJAB_stim2
RNA-seq in BJAB cells in condition: anti-IgM anti-CD40 4hr stimulation

value: WT

value: anti-IgM anti-CD40 4hr


title: BJAB_stim1

description:
Library name: BJAB_stim1
RNA-seq in BJAB cells in condition: anti-IgM anti-CD40 4hr stimulation


title: Rep_early_rep1_H3K36me3

value: Liver


title: BJAB_ctrl1

description:
Library name: BJAB_ctrl1
RNA-seq in BJAB cells in condition: no stimulation


title: late-onset LUAD 2


title: MC38, shCtrl1


title: late-onset LUAD 1


title: Urethral Mesenchyme, E18.5 mus female, rep 3

city: Bengaluru

first: Diya

last: Binoy Joseph

state: Karnataka

address: GKVK - Post, Bellary Rd

country: India

institute: Institute for Stem Cell Science and Regenerative Medicine

description:
E18UrMes_12
E18.5MesCounts.txt

data_processing:
Base calling: Illumina bcl2fastq
Read mapping: hisat2-2.2.1
.sam to .bam: samtools-1.9
bam sort and dedup: samtools-1.9
extract features: subread2.0.6
Assembly: grcm38
Supplementary files format and content: tab-delimited text file contains raw counts for E14.5 samples
Supplementary files format and content: tab-delimited text file contains raw counts for E18.5 samples

source_name: Urethral Mesenchyme

growth_protocol: CD-1 strain mice were time bred to obtain embryonic day (E) 14.5 and E18.5 embryos. Noon of detection of vaginal plug was considered to be E0.5.

extract_protocol:
E14.5 and E18.5 embryos were removed from timed pregnant females and the lower urinary tract comprising the bladder and proximal urethra were collected into ice-cold phosphate buffered saline (PBS). Epithelial-mesenchymal separation was performed as previously described (Joseph et al., 2018). Briefly, dissected lower urinary tracts were placed in sterile 1x Hank’s Basic Salt Solution (HBSS) containing sodium bicarbonate (0.03%), antibiotic-antimycotic (Sigma Aldrich, A5955-20ML) and 1% Trypsin w/v (Sigma Aldrich, T4799-5G). Tissues were incubated in the trypsin solution on ice at 4 C for 45-75 mins. Tissues were washed in 1x HBSS containing sodium bicarbonate and antibiotic-antimycotic and briefly treated with DNase to remove excess genomic DNA from lysed cells. Tissues were then placed in cold 1x PBS and the urethra and bladder were separated with spring scissors. The epithelial and mesenchymal layers of the bladder and urethra of female embryos were mechanically separated with fine forceps and collected separately into RLT plus lysis buffer (Qiagen RNeasy Micro kit # 74004). Tissues from female mice from a litter were pooled and a total of 3 biological replicates (from n=3 independent litters) for each sample type were collected. Tissue samples were lysed in RLT plus lysis buffer homogenized using Qiashredder columns and RNA was isolated according to manufacturer instructions of the Qiagen RNeasy Micro kit.
250 ng of total RNA was used for mRNA library prep. NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490L) was used for mRNA isolation according to manufacturer instructions. NEBNext® Ultra™ II Directional RNA Library Prep kit with Sample Purification Beads (#E7765L) was used for library preparation according to manufacturer instructions. Samples were sequenced using NovaSeq 6000. 100 bp pair-ended reads were obtained.

treatment_protocol: No treatment.

value: Urethral Mesenchyme

value: Mesenchymal

value: Wildtype


title: Jurkat_stim2

description:
Library name: Jurkat_stim2
RNA-seq in Jurkat cells in condition: anti-CD3 PMA 4hr stimulation

source_name: Jurkat

value: Jurkat

value: T cell line

value: anti-CD3 PMA 4hr


title: Rep_early_rep1_H3K36me1


title: Rep_early_rep1_H3K27me3


title: Jurkat_stim1

description:
Library name: Jurkat_stim1
RNA-seq in Jurkat cells in condition: anti-CD3 PMA 4hr stimulation


title: early-onset LUAD 7

value: stage I LUAD tumor


title: Rep_early_rep1_H3K27ac


title: Urethral Mesenchyme, E18.5 mus female, rep 2

description:
E18UrMes_10
E18.5MesCounts.txt


title: Bladder Mesenchyme, E18.5 mus female, rep 3

description:
E18BlMes_11
E18.5MesCounts.txt

source_name: Bladder Mesenchyme

value: Bladder Mesenchyme


title: Jurkat_ctrl2

description:
Library name: Jurkat_ctrl2
RNA-seq in Jurkat cells in condition: no stimulation


title: Urethral Mesenchyme, E18.5 mus female, rep 1

description:
E18UrMes_8
E18.5MesCounts.txt


title: Nsd1_KO_Rep_late_rep2_H3K4me3

source_name: Liver


title: early-onset LUAD 6


title: Jurkat_ctrl1

description:
Library name: Jurkat_ctrl1
RNA-seq in Jurkat cells in condition: no stimulation


title: early-onset LUAD 5


title: Nsd1_KO_Rep_late_rep2_H3K4me1


title: Bladder Mesenchyme, E18.5 mus female, rep 2

description:
E18BlMes_9
E18.5MesCounts.txt


title: early-onset LUAD 4


title: U937_stim2

description:
Library name: U937_stim2
RNA-seq in U937 cells in condition: LPS 4 hr stimulation

value: monocytic cell line

value: LPS 4hr


title: Bladder Mesenchyme, E18.5 mus female, rep 1

description:
E18BlMes_7
E18.5MesCounts.txt


title: Nsd1_KO_Rep_late_rep2_H3K36me3


title: U937_stim1

description:
Library name: U937_stim1
RNA-seq in U937 cells in condition: LPS 4 hr stimulation


title: Nsd1_KO_Rep_late_rep2_H3K36me1


title: Urethral Mesenchyme, E14.5 mus female, rep 3

description:
E14UrMes_6
E14.5MesCounts.txt


title: early-onset LUAD 3


title: U937_ctrl2

description:
Library name: U937_ctrl2
RNA-seq in U937 cells in condition: no stimulation


title: Urethral Mesenchyme, E14.5 mus female, rep 2

description:
E14UrMes_4
E14.5MesCounts.txt


title: early-onset LUAD 1


title: Nsd1_KO_Rep_late_rep2_H3K27me3


title: THP-1_dCas9-KRAB_stim2

description:
Library name: THP-1_dCas9-KRAB_stim2
RNA-seq in THP-1 cells in condition: LPS 4 hr stimulation


title: early-onset LUAD 2


title: U937_ctrl1

description:
Library name: U937_ctrl1
RNA-seq in U937 cells in condition: no stimulation


title: PJS1_TC_polyp_S44

city: La Jolla

first: Daniella

last: Vo

address: 9500 Gilman Dr

department: Pediatrics

institute: UC San Diego

description: PJS1_TC_polyp_S44colon organoid

data_processing:
Kallisto
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM gene values for each Sample
Supplementary files format and content: tab-delimited text files include estimated gene counts for each Sample

growth_protocol: Stem cells were isolated from human colon tissue and cultured as 3D organoids. The organoids were broken into single cells and seeded as a monolayer  plate.

extract_protocol:
All cells were lysed using TRI-Reagent and RNA was isolated using Zymo Research: Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: No infection or treatment

tag: sample type

value: colon organoid

tag: disease type

value: PJS


title: Bladder Mesenchyme, E14.5 mus female, rep 3

description:
E14BlMes_5
E14.5MesCounts.txt


title: Nsd1_KO_Rep_late_rep1_H3K4me3


title: Lynch_2_TCNI_S43

description: Lynch_2_TCNI_S43colon organoid

value: LYNCH


title: Nsd1_KO_Rep_late_rep2_H3K27ac


title: Bladder Mesenchyme, E14.5 mus female, rep 2

description:
E14BlMes_3
E14.5MesCounts.txt


title: THP-1_dCas9-KRAB_stim1

description:
Library name: THP-1_dCas9-KRAB_stim1
RNA-seq in THP-1 cells in condition: LPS 4 hr stimulation


title: Nsd1_KO_Rep_late_rep1_H3K4me1


title: Lynch1_no_PF_S51

description: Lynch1_no_PF_S51colon organoid


title: THP-1_dCas9-KRAB_ctrl2

description:
Library name: THP-1_dCas9-KRAB_ctrl2
RNA-seq in THP-1 cells in condition: no stimulation

value: untreated


title: Nsd1_KO_Rep_late_rep1_H3K36me3


title: THP-1_dCas9-KRAB_ctrl1

description:
Library name: THP-1_dCas9-KRAB_ctrl1
RNA-seq in THP-1 cells in condition: no stimulation


title: Nsd1_KO_Rep_late_rep1_H3K36me1


title: FAP_7_polyp_S46

description: FAP_7_polyp_S46colon organoid

value: FAP


title: Bladder Mesenchyme, E14.5 mus female, rep 1

description:
E14BlMes_1
E14.5MesCounts.txt


title: FAP4_polyp_S42

description: FAP4_polyp_S42colon organoid


title: HK-2 cells, cisplatin (20μM)6

city: jilin

first: hu

last: jianqiang

address: changchun

institute: jilin University

description:
Library name: Sample 6
Nfe2l1-OE_3_FPKM

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster
Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Kidney tissue

growth_protocol: HK-2 cells were cultured in DME/F-12 (10% FBS and 1% penicillin/streptomycin)

extract_protocol:
2 μg total RNAs were used for the constructlon of sequencing libraries.
RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina®  following the manufacturer’s instruction.

treatment_protocol: cisplatin (20μM)

value: Kidney tissue

value: Nfe2l1 overexpression

value: Renal tubular epithelial cells

value: cisplatin (20μM)


title: HK-2 cells, cisplatin (20μM)5

description:
Library name: Sample 5
Nfe2l1-OE_2_FPKM


title: Nsd1_KO_Rep_late_rep1_H3K27me3

data_processing:
Reads were trimmed using Cutadapt with parameters “-j 4 --nextseq-trim 20 -m 15” before alignment to the mouse genome (mm10) using Bowtie2 with parameters “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 4.” The resulting sequence alignment files were sorted, and duplicates were removed using Picard (https://broadinstitute.github.io/picard/). The BAM files were then converted to BED files using BEDTools (https://bedtools.readthedocs.io/en/latest/)  with the bamtobed function with option “-bedpe.” Data was filtered to keep read pairs on the same chromosome and with a fragment length <1000 bp. For peak calling, the BEDTools genomecov tool was used to generate BedGraph files. For visualization using IGV and deepTools, the BAM files were converted to BigWig files using the bamCoverage function with options “--binSize 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPGC --extendReads" and then replicates were merged using the bigWigMerge function followed by the bedGraphToBigWig function (UCSC tools).
Peak calling was conducted on the individual BedGraph files using SEACR with options “0.01 norm stringent.”  Downstream analysis was conducted DiffBind. Replicates were processed with default counting and normalization parameters with the option “minMembers=2” and the mm10 blacklist was used.
Assembly: mm10
Supplementary files format and content: BED files (for peaks), BigWig files (for genome tracks)
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed following EpiCypher® CUTANA™ CUT&RUN Protocol v1.7 with minor modifications. Cells at different stages of biliary reprogramming were harvested from the Cas9-EGFP mice challenged with 0.1% DDC for 8-9 weeks by FACS (n = 2-3).
The universal i5 primer, barcode i7 primer, and 25CUTANA High Fidelity 2X PCR Master Mix for CUT&Tag (EpiCypher) were used, and PCR was performed (1 cycle of 20 °C for 5 min; 1 cycle of 72 °C for 5 min; 1 cycle of 98 °C for 45 s, 14–21 cycles of 98 °C for 15 s and 60 °C for 10 s; 72 °C for 1 min). The DNA was cleaned up with 1.3× AMPure XP beads.  Sequencing was performed using a NextSeq2000 with 55 bp paired-end reads.

value: Liver


title: Urethral Epithelium, E18.5 mus female, rep 2

description:
E18UrEp_12
E18.5EpiCounts.txt

source_name: Urethral Epithelium

extract_protocol:
E14.5 and E18.5 embryos were removed from timed pregnant females and the lower urinary tract comprising the bladder and proximal urethra were collected into ice-cold phosphate buffered saline (PBS). Epithelial-mesenchymal separation was performed as previously described (Joseph et al., 2018). Briefly, dissected lower urinary tracts were placed in sterile 1x Hank’s Basic Salt Solution (HBSS) containing sodium bicarbonate (0.03%), antibiotic-antimycotic (Sigma Aldrich, A5955-20ML) and 1% Trypsin w/v (Sigma Aldrich, T4799-5G). Tissues were incubated in the trypsin solution on ice at 4 C for 45-75 mins. Tissues were washed in 1x HBSS containing sodium bicarbonate and antibiotic-antimycotic and briefly treated with DNase to remove excess genomic DNA from lysed cells. Tissues were then placed in cold 1x PBS and the urethra and bladder were separated with spring scissors. The epithelial and mesenchymal layers of the bladder and urethra of female embryos were mechanically separated with fine forceps and collected separately into RLT plus lysis buffer (Qiagen RNeasy Micro kit # 74004). Tissues from female mice from a litter were pooled and a total of 3 biological replicates (from n=3 independent litters) for each sample type were collected. Tissue samples were lysed in RLT plus lysis buffer homogenized using Qiashredder columns and RNA was isolated according to manufacturer instructions of the Qiagen RNeasy Micro kit.
60 ng of total RNA was used for mRNA library prep. NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490L) was used for mRNA isolation according to manufacturer instructions. NEBNext® Ultra™ II Directional RNA Library Prep kit with Sample Purification Beads (#E7765L) was used for library preparation according to manufacturer instructions. Samples were sequenced using NovaSeq 6000. 100 bp pair-ended reads were obtained.

value: Urethral Epithelium

value: Epithelial

value: Wildtype


title: FAP1_polyp_S41

description: FAP1_polyp_S41colon organoid


title: Nsd1_KO_Rep_late_rep1_H3K27ac


title: Urethral Epithelium, E18.5 mus female, rep 1

description:
E18UrEp_10
E18.5EpiCounts.txt


title: Urethral Mesenchyme, E14.5 mus female, rep 1

description:
E14UrMes_2
E14.5MesCounts.txt

value: Urethral Mesenchyme

value: Mesenchymal


title: FAP1_NI_S40

description: FAP1_NI_S40colon organoid


title: Bladder Epithelium, E18.5 mus female, rep 3

description:
E18BlEp_13
E18.5EpiCounts.txt

source_name: Bladder Epithelium

value: Bladder Epithelium


title: HK-2 cells, cisplatin (20μM)3

description:
Library name: Sample 3
Con-3_FPKM

value: WT


title: Nsd1_KO_Rep_interm_rep2_H3K4me1


title: HK-2 cells, cisplatin (20μM)2

description:
Library name: Sample 2
Con-2_FPKM


title: Nsd1_KO_Rep_interm_rep2_H3K36me3


title: Patient R2632 geneexp

description:
Patient
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

source_name: Peripheric blood

value: Peripheric blood

value: PBMC

value: mRNA derived cDNA

value: Haetopoietic stem cell transplant


title: Urethral Epithelium, E18.5 mus female, rep 3

description:
E18UrEp_14
E18.5EpiCounts.txt


title: Urethral Epithelium, E14.5 mus female, rep 4

description:
E14UrEp_8
E14.5EpiCounts.txt


title: Nsd1_KO_Rep_interm_rep2_H3K36me1


title: Lyn1-sig_colon_S46

description: Lyn1-sig_colon_S46colon tissue

source_name: colon

value: colon tissue

value: LYNCH


title: Nsd1_KO_Rep_interm_rep2_H3K27me3


title: DU145_siDNMT3B-L

city: Guangzhou

first: Qianghua

last: Zhou

address: Urology

institute: Sun yat-sen memorial hospital

data_processing:
Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4  --barcode-mismatches 0
Adaptor contamination was remove from reads (the number of bases contaminated by the adaptor in reads is greater than 5bp. For pair-end sequencing, if one end is contaminated by the adaptor, the Reads at both ends are removed)；Remove low-quality reads (Reads with more than 50% of the total bases are bases with a mass value of Q ≤ 19 . For pair-end sequencing, if one pair is low-quality reads, the both reads will be removed)；Remove the reads with N rate greater than 5%  (For pair-end sequencing, if one pair contains more than 5% N, the both reads will be removed)
Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
Assembly: hg19(ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
Supplementary files format and content: excel files include normalize values for each Sample

source_name: prostate cancer

growth_protocol: DU145 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.

value: prostate cancer

value: prostate cancer cell line

value: DNMT3B-L knockdown

value: siDNMT3B-L targeting DNMT3B-L were transfected in the cell


title: Urethral Epithelium, E14.5 mus female, rep 3

description:
E14UrEp_6
E14.5EpiCounts.txt

value: Urethral Epithelium


title: DU145_siPTBP1#2

value: PTBP1 knockdown

value: siPTBP1#2 targeting PTBP1 were transfected in the cell


title: JPS_1_TC_POLYP_S56

description: JPS_1_TC_POLYP_S56colon tissue

value: JPS


title: HK-2 cells, cisplatin (20μM)4

description:
Library name: Sample 4
Nfe2l1-OE_1_FPKM

value: Kidney tissue

value: Nfe2l1 overexpression

value: Renal tubular epithelial cells

value: cisplatin (20μM)


title: Nsd1_KO_Rep_interm_rep2_H3K27ac

first: Takeshi

last: Katsuda

address: 7-chōme-3-1 Hongō

value: Liver


title: Nsd1_KO_Rep_interm_rep2_H3K4me3


title: DU145_siPTBP1#1

value: siPTBP1#1 targeting PTBP1 were transfected in the cell


title: Urethral Epithelium, E14.5 mus female, rep 1

description:
E14UrEp_2
E14.5EpiCounts.txt

value: Epithelial

value: Wildtype


title: Urethral Epithelium, E14.5 mus female, rep 2

description:
E14UrEp_4
E14.5EpiCounts.txt


title: Nsd1_KO_Rep_interm_rep1_H3K4me3


title: Nsd1_KO_Rep_interm_rep1_H3K4me1


title: Bladder Epithelium, E18.5 mus female, rep 2

description:
E18BlEp_11
E18.5EpiCounts.txt

value: Bladder Epithelium


title: Bladder Epithelium, E18.5 mus female, rep 1

description:
E18BlEp_9
E18.5EpiCounts.txt


title: HK-2 cells, cisplatin (20μM)1

description:
Library name: Sample 1
Con-1_FPKM

value: WT


title: DU145_Control

value: prostate cancer

value: prostate cancer cell line

value: Negetive control


title: Bladder Epithelium, E14.5 mus female, rep 4

description:
E14BlEp_7
E14.5EpiCounts.txt


title: PJS2_SIG_NI_S54

description: PJS2_SIG_NI_S54colon tissue

value: colon tissue

value: PJS


title: PJS2__TC_NI_S53

description: PJS2__TC_NI_S53colon tissue


title: FAP-7_DC_NI_S51

description: FAP-7_DC_NI_S51colon tissue

value: FAP


title: Lynch2-sig_colon_S47

description: Lynch2-sig_colon_S47colon tissue

value: LYNCH


title: JEG-3 cells, sgAPC,rep3

city: Cambridge

first: Bowen

last: Gu

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology Department

institute: Harvard University

data_processing:
The quality of the sequence reads were accessed by FastQC and the fastq files were quantified with Salmon (version 1.5.2)
Differentially expressed genes were determined by estimating fold change and dispersion using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of TPM for each sample

growth_protocol: JEG-3 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) with high glucose, 10% fetal bovine serum, and 1x Antibiotic-Antimycotic

extract_protocol:
Cells grown at 60-90% confluency were harvested, and total RNA were extracted by RNeasy Mini Kit.
RNA-seq library was prepared by NEBNext Ultra RNA Library Prep Kit for Illumina

value: APC knockout


title: Nsd1_KO_Rep_interm_rep1_H3K36me3

city: Tokyo

institute: University of Tokyo


title: JEG-3 cells, sgAPC,rep2


title: Bladder Epithelium, E14.5 mus female, rep 3

description:
E14BlEp_5
E14.5EpiCounts.txt


title: FAP-6_TC_polyp_S50

description: FAP-6_TC_polyp_S50colon tissue


title: Nsd1_KO_Rep_interm_rep1_H3K36me1


title: JEG-3 cells, sgAPC,rep1


title: Bladder Epithelium, E14.5 mus female, rep 2

description:
E14BlEp_3
E14.5EpiCounts.txt


title: FAP-4_Cecum_NI_S49

description: FAP-4_Cecum_NI_S49colon tissue


title: FAP-1_sig_S48

description: FAP-1_sig_S48colon tissue


title: Nsd1_KO_Rep_interm_rep1_H3K27ac


title: JEG-3 cells, Wildtype,rep2


title: Nsd1_KO_Rep_interm_rep1_H3K27me3


title: Bladder Epithelium, E14.5 mus female, rep 1

description:
E14BlEp_1
E14.5EpiCounts.txt


title: JPS1_REC_NI_S55

description: JPS1_REC_NI_S55colon tissue

value: JPS


title: JEG-3 cells, Wildtype,rep3


title: 786-O parental Dur treated replicate 3 [7_DUR3]

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Trimmed reads were aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0,-0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000).
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (GENCODE version 33; Ensembl version 99).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene counts for each Sample

growth_protocol: Two human advanced renal cell carcinoma cell lines A498 and 786-O were purchased from ATCC. They were cultured in DMEM growth media containing 25mM glucose and glutamine supplemented with 10% heat-inactivated foetal bovine serum and 1% penicillin-streptomycin at 37⁰C in a humidified atmosphere of 5% CO2. Sunitinib (SU11248) malate was purchased from Selleckchem. For the development of sunitinib-resistant cells, parental cells were exposed to increasing concentrations of sunitinib. In brief, the RCC cell lines were treated with varying concentrations of sunitinib (0, 1, 2, 3, 4, 5, 7, 10, 20, and 50μM). With the passage of time of every four days, it has been observed that A498 cells showed stable growth and eventually became confluent at a concentration of 2µM, while 798-O cells showed stable growth to confluence at a concentration of 4µM. It can be assumed that cells that grew to confluence had developed stable sunitinib-resistance after a period of four months or >20 passages. The cells were constantly in sunitinib containing medium throughout the selection process.

extract_protocol:
Total RNA was isolated from cultured cells according to the QIAGEN RNeasy mini kit protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Sample prep kit.

treatment_protocol: Cells were treated with either Atezolizumab (AT), Avelumab (Av), or Durvalumab (Dur), at a concentration of 10mg/mL for 24 hours.

value: advanced clear cell renal cell carcinoma (ccRCC)

tag: drug resistance

value: Durvalumab

tag: batch


title: FAP-7_TC_NI_S52

description: FAP-7_TC_NI_S52colon tissue


title: Nsd1_KO_Rep_early_rep2_H3K4me3

value: Liver


title: JEG-3 cells, Wildtype,rep1


title: 786-O parental Dur treated replicate 2 [7_DUR2]


title: YIF_short

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

description: 10 x Genomics

data_processing:
Samples from Young animals; MUC8408, MUC8409, MUC8410, MUC8411, MUC8412, MUC8413: FASTQ files were aligned to the mm10 mouse genome with Ensembl release 94 annotations and pre-processed using the CellRanger software v2.1.1 (10x Genomics) for downstream analyses. Samples  from middle old and old animals; MUC28169, MUC28170, MUC28171, MUC28172: FASTQ files were aligned to the GRCm38 mouse genome with Ensembl release 101 annotations and pre-processed using the CellRanger software v3.1.0 (10x Genomics) for downstream analyses.
Assembly: mm10
Supplementary files format and content: demultiplexed h5 files with counts

source_name: pancreas

extract_protocol:
For islet acquisition, mice were anesthetized with an intraperitoneal injection of ketamine (300-360 mg/kg) and xylazine (30-40 mg/kg). The peritoneal cavity was exposed for clamping of the pancreatic main duct to the intestine and cannulation in situ via the common bile duct. Collagenase was injected in a 5 milliliters/min flow, and the pancreas was removed. Islets were separated and gently washed, passed through a sterile 40 mesh stainless steel screen, and centrifuged at 300 x G for 3 minutes at room temperature. The pellet was mixed in a density gradient cell separation medium of Ficoll and sodium diatrizoate and centrifuged at 300 x G for 3 minutes at room temperature, the islets were collected, sedimented, and washed through a sterile 40 μm mesh cell strainer with Hank’s buffered salt solution (HBSS). After the cleaning, islets were cultivated with Connaught Medical Research Laboratories (CMRL)-based media containing 2 mM glutamine, 10% fetal bovine serum (FBS), and 1% penicillin and streptozotocin solution, and stored in a 37◦C culture chamber containing 5% CO2. (PMID: 19876025)
Samples from Young animals; MUC8408, MUC8409, MUC8410, MUC8411, MUC8412, MUC8413: Libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v2 (10x Genomics) according to the manufacturer’s instructions. Libraries were pooled and sequenced on an Illumina HiSeq4000 with a target read depth of 50000 reads/cell. Samples  from middle old and old animals; MUC28169, MUC28170, MUC28171, MUC28172: Libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were pooled and sequenced on an Illumina NovaSeq6000 with a target read depth of 50000 reads/cell.

treatment_protocol: Old, middle-aged, and young mice were randomly grouped into ad libitum (AL) and intermittent fasting (IF) groups. Before starting the IF intervention, all mice were housed in a threesome for two weeks to allow for acclimation to the animal facility. In the IF group, the food was removed from midnight to the following day (24 hours later), we employed the intermittent fasting protocol 1:2, which consists of 24 hours of food starvation for 48 hours of free access to a chow diet (PMID: 29039412). Mice in the AL group were handled but with unrestricted chow diet access. For all groups, water was offered without restriction. Food intake was measured every three days, in the IF group we calculated the difference between the amount of food offered at the beginning of the food offer phase with the rest at the end of the phase. The experimental design is demonstrated in Figure 1a. All groups, independently of age, were exposed to 4-5 weeks or 9-10 weeks of IF regimen and euthanized by cervical dislocation forty-eight hours after the last IF cycle.

value: pancreas

tag: age

value: young

value: pancreatic islets

value: intermittent fasting


title: Nsd1_KO_Rep_early_rep2_H3K4me1


title: T-HESCs, siNC5

first: Yan

address: 197 Ruijin 2nd Road

department: Department of Reproductive Medical Center

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
fastp; hisat2;rsem
Assembly: GRCh38.p14
Supplementary files format and content: table-delimited text file includes raw counts, normalized counts, fpkm, tpm  for each Sample

source_name: T-HESCs

extract_protocol:
normal (to be updated)
Mustseq  (to be updated)

value: T-HESCs

value: immortalized human endometrial stromal cells

value: WT

value: siNC


title: Nsd1_KO_Rep_early_rep2_H3K36me3


title: Ybaseline

description: 10 x Genomics

value: baseline


title: 786-O parental Dur treated replicate 1 [7_DUR1]


title: T-HESCs, siNC3


title: T-HESCs, siNC4


title: YAL

description: 10 x Genomics

value: ad libitum


title: 786-O parental Av treated replicate 3 [7_AV3]

value: Avelumab


title: Nsd1_KO_Rep_early_rep2_H3K27ac


title: T-HESCs, siNC1


title: Nsd1_KO_Rep_early_rep2_H3K36me1


title: T-HESCs, siSCG5

value: SCGB2A1 knockdown

value: siSCG


title: YIF_AL

description: 10 x Genomics

value: intermittent fasting and ad libitum


title: Nsd1_KO_Rep_early_rep1_H3K4me1


title: 786-O parental Av treated replicate 2 [7_AV2]

value: advanced clear cell renal cell carcinoma (ccRCC)


title: Nsd1_KO_Rep_early_rep2_H3K27me3


title: YIF

description: 10 x Genomics


title: T-HESCs, siSCG4


title: 786-O parental At treated replicate 1 [7_AT1]

value: Atezolizumab


title: YAL_short

description: 10 x Genomics


title: Nsd1_KO_Rep_early_rep1_H3K4me3

value: Liver


title: 786-O parental At treated replicate 3 [7_AT3]


title: OIF

description: 10 x Genomics

value: pancreas

value: Old


title: Nsd1_KO_Rep_early_rep1_H3K36me1


title: T-HESCs, siNC2


title: 786-O Sunitinib-resistant Dur treated replicate 3 [74Dur3]

value: Sunitinib

value: Durvalumab


title: OAL

description: 10 x Genomics

value: pancreatic islets


title: Nsd1_KO_Rep_early_rep1_H3K36me3


title: MIF

description: 10 x Genomics

value: middle-aged

value: intermittent fasting


title: 786-O parental Av treated replicate 1 [7_AV1]


title: T-HESCs, siSCG2

value: T-HESCs

value: immortalized human endometrial stromal cells


title: T-HESCs, siSCG3


title: 786-O parental At treated replicate 2 [7_AT2]


title: MAL

description: 10 x Genomics

value: ad libitum


title: Nsd1_KO_Rep_early_rep1_H3K27me3


title: R235MI_B2sal

city: Charleston

first: Allison

last: Trouten

state: SC

address: 173 Ashley Ave Room BSB 642

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

data_processing:
Raw fastq files were aligned using STAR 2.7.10a aligner
Differential expression analysis run using DEseq2 1.44.0
Heatmaps created using pheatmap (1.0.12)
Other plots made via ggplot2 3.5.1
Gene ontology assessment via fgsea 1.30.0
Assembly: mm10
Supplementary files format and content: Tab delimited CSV file includes normalized raw counts for each sample
Supplementary files format and content: Compressed fastq files include raw unaligned sequencing files

source_name: Left ventricular

extract_protocol:
Standard Trizol phenol chloroform extraction
Total RNA samples were sent to Novogene for library prep and sequencing (mRNA library preparation poly A enrichment)

treatment_protocol: Daily injection P0-P1 of high dose HEPES saline-buffered NAC (25mM HEPES 140mM NaCl) or saline control. LAD-O or sham procedure on P2, sacrifice at P3.

value: Left ventricular

value: cardiomyocytes

value: wild type

value: saline

value: MI surgery


title: 786-O Sunitinib-resistant Dur treated replicate 1 [74Dur1]

value: advanced clear cell renal cell carcinoma (ccRCC)


title: Nsd1_KO_Rep_early_rep1_H3K27ac

value: Liver


title: 786-O Sunitinib-resistant Dur treated replicate 2 [74Dur2]


title: 786-O Sunitinib-resistant Av treated replicate 2 [74Av2]

value: Avelumab


title: PEM-seq_HEK293T_control_AGBL1

city: Beijing

first: Changchang

last: Xin

state: Beijing

address: No.5 Yiheyuan Road Haidian District,Beijing,P.R.China

institute: Peking University

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg38
Supplementary files format and content: tab file
Library strategy: PEM-seq

extract_protocol:
Followed the PEM-seq protocol that described in Yin et al., 2019.
Followed the PEM-seq protocol that described in Yin et al., 2019.

treatment_protocol: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.

value: Human embryonic kidney

value: WT

value: plasmid transfection

tag: crispr-cas nuclease

value: control

tag: editing site


title: Kdm2a_KO_Rep_interm_rep3_H3K36me3

tag: tissue


title: R230MI_D2sal

tag: genotype


title: R230MI_B2sal


title: R230MI_C2NAC

value: NAC


title: 786-O Sunitinib-resistant Av treated replicate 3 [74Av3]

value: Sunitinib


title: Kdm2a_KO_Rep_interm_rep2_H3K4me3

tag: group


title: R235MI_A3NAC

tag: cell type


title: PEM-seq_HEK293T_AsCpf1_AGBL1

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the AGBL1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.

tag: treatment


title: PEM-seq_HEK293T_SpCas9_AGBL1

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting AGBL1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.

tag: cell line


title: 786-O Sunitinib-resistant At treated replicate 3 [74At3]

value: Atezolizumab


title: 786-O Sunitinib-resistant At treated replicate 2 [74At2]


title: PEM-seq_HEK293T_CasMINI_AGBL1

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the AGBL1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: CasMINI


title: Kdm2a_KO_Rep_interm_rep3_H3K36me1


title: PEM-seq_HEK293T_ISDra2_AGBL1

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the AGBL1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: Kdm2a_KO_Rep_interm_rep2_H3K36me3


title: R207_C_2sal_sham

value: Sham surgery


title: R235MI_A2NAC

value: Left ventricular


title: 786-O Sunitinib-resistant Av treated replicate 1 [74Av1]


title: Kdm2a_KO_Rep_interm_rep2_H3K36me1


title: T-HESCs, siSCG1

value: T-HESCs

value: immortalized human endometrial stromal cells

value: SCGB2A1 knockdown

value: siSCG


title: PEM-seq_HEK293T_Nme2-C.NR_AGBL1

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the AGBL1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: PEM-seq_HEK293T_ISYmu1_AGBL1

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the AGBL1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: R207_D_2sal_sham

value: cardiomyocytes

value: wild type

value: saline


title: Kdm2a_KO_Rep_interm_rep2_H3K4me1

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo). Eight weeks after the DDC challenge, reprogrammed cells and biliary cells were harvested.

value: Liver


title: 786-O Sunitinib-resistant At treated replicate 1 [74At1]

value: advanced clear cell renal cell carcinoma (ccRCC)


title: A498 parental Dur treated replicate 3 [4_DUR3]

value: Durvalumab


title: PEM-seq_HEK293T_control_MAPK8

value: Human embryonic kidney

value: WT

value: plasmid transfection

value: control


title: A498 parental Dur treated replicate 1 [4_DUR1]


title: Kdm2a_KO_Rep_interm_rep2_H3K27me3


title: B_3NAC_sham

value: NAC


title: R219_A_3sal_sham

value: Sham surgery


title: PEM-seq_HEK293T_ISAam1_AGBL1

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the AGBL1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: Kdm2a_KO_Rep_interm_rep2_H3K27ac


title: Kdm2a_KO_Rep_interm_rep1_H3K4me1


title: A498 parental Av treated replicate 3 [4_AV3]

value: Avelumab


title: R207_A_2NAC_sham

value: Left ventricular


title: SHF_AngII

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

data_processing:
cDNA libraries were sequenced by NovaSeq 6000 (Illumina) in a paired-end fashion to reach more than 1.5M reads. Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to the mouse genome mm10 using STAR (v2.5, mismatch=2) and quantified using HTSeq (v0.6.1, -m union).
Assembly: mm10
Supplementary files format and content: Comma separtated values list including read counts of genes for each cell.

source_name: Aorta

extract_protocol:
Aortic tissues were cut into small pieces and digested in enzyme cocktails. Live singlet cells were collected by flow cytometry and sorted based on lineage tracking. Cells were then submitted to a 10x Chromium System.
Indexed single cell libraries were constructed using a Chromium Single Cell 3’ v3 Reagent Kit (10x Genomics).

treatment_protocol: Aortic samples were harvested from male mice either at baseline or after 3 days of AngII infusion.

value: Aorta

tag: strain

tag: Sex

value: Male

value: AngII

tag: time

value: 3 days


title: PEM-seq_HEK293T_AsCpf1_MAPK8

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the MAPK8 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: Kdm2a_KO_Rep_interm_rep1_H3K4me3


title: Kdm2a_KO_Rep_interm_rep1_H3K36me3


title: CNC_AngII


title: PEM-seq_HEK293T_Nme2-C.NR_MAPK8

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the MAPK8 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: SHF_Baseline

value: Baseline


title: A498 parental Av treated replicate 1 [4_AV1]


title: Kdm2a_KO_Rep_interm_rep1_H3K36me1


title: A498 parental Av treated replicate 2 [4_AV2]


title: A498 parental Dur treated replicate 2 [4_DUR2]


title: CNC_Baseline


title: PEM-seq_HEK293T_CasMINI_MAPK8

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the MAPK8 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: CasMINI


title: A498 parental At treated replicate 3 [4_AT3]

value: Atezolizumab


title: Kdm2a_KO_Rep_interm_rep1_H3K27me3

value: Liver


title: PEM-seq_HEK293T_ISDge10_MAPK8

treatment_protocol: The cells were transfected with the gRNA-ISDge10 plasmid targeting the MAPK8 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDge10 plasmid) on Day 3.


title: A_3NAC_sham

value: cardiomyocytes

value: wild type


title: A498 parental At treated replicate 2 [4_AT2]

treatment_protocol: Cells were treated with either Atezolizumab (AT), Avelumab (Av), or Durvalumab (Dur), at a concentration of 10mg/mL for 24 hours.

value: advanced clear cell renal cell carcinoma (ccRCC)


title: APAP and a-CD41, exp3

city: Kunming

first: Xue

middle: Ruo

last: Yang

address: Wujiaying Street, Chenggong District, Kunming, Yunnan

institute: Yunnan university

description:
count CD-3
IgG_and_CD41.xls

data_processing:
Raw data (raw reads) in fastq format were processed using in-house Perl scripts. Clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. Quality metrics such as Q20, Q30, GC-content, and sequence duplication levels were calculated for the clean data. All downstream analyses were based on high-quality clean data. Reads were mapped against the reference genome and transcript annotation (GRCm38) using Hisat2 software
Assembly: GRCm38(Mus musculus)
Supplementary files format and content: tab-delimited text file includes raw count for each Sample

source_name: liver

extract_protocol:
Wild-type C57BL/6J mice were anesthetized using a CO2 chamber. To avoid contamination of the peritoneal cavity with fur, the skin and peritoneum were opened separately. The inferior vena cava was clamped with forceps, and a catheter was inserted into the superior vena cava via the right atrium. The portal vein was then cut once the buffer started to perfuse into the liver. The liver was perfused with 1x Hank's Balanced Salt Solution (HBSS) containing 53.6 mM KCl, 4.4 mM KH2PO4, 1367.5 mM NaCl, 3.36 mM NaHPO4, 55.5 mM D-Glucose, and 100 mL 1 M HEPES (pH 7.2-7.4) for 3-5 minutes until it appeared clear. Subsequently, the buffer was switched to a collagenase digestion solution (1xHBSS with 1.25 mM MgSO4, 4 mM CaCl2, Collagenase Type I, and 50 μg/mL DNase) for 15-20 minutes of digestion. Post-digestion, the liver was dissected and placed in chilled 1xHBSS in a Petri dish to keep it cool until further processing. The gallbladder was removed, and the liver was chopped into 2-3 mm pieces and incubated in 10-20 mL digestion buffer at 37°C for 15 minutes. The liver tissue was then mashed using a 70 μm cell strainer placed over a 50 mL tube and rinsed with 1xHBSS to a final volume of 50 mL. The suspension was centrifuged at 50xg for 5 minutes (acceleration/brake = 0) to remove hepatocytes, with the resulting supernatant containing nonparenchymal cells (NPCs). The supernatant was further centrifuged at 450xg for 5 minutes (acceleration/brake ≥ 5), and the pellet, containing hepatic NPCs, was resuspended in 4 mL of 20% OptiPrep solution diluted with 1xHBSS. This suspension was carefully layered with 5 mL of 1xHBSS buffer in a 15 mL tube and centrifuged at 3000 rpm for 17 minutes (acceleration/brake = 0). The cell fraction between the 20% OptiPrep and 1xHBSS layers, containing Kupffer cells (KCs) and liver endothelial sinusoidal cells (LESCs), was collected and washed with 1xHBSS.To isolate KCs, the cell fraction was incubated in a cell culture dish at 37°C for 10 minutes. KCs adhered to the plate, while LESCs remained in suspension. The adhered KCs were then collected for subsequent experiments. The purity and viability of isolated KCs reached 90% and 80%, respectively, which was confirmed by staining with anti-Timd4 antibodies or trypan blue.
Mice were treated according to different experimental protocols. Kupffer cells (KCs) were isolated and lysed in 1 mL RNAiso Plus reagent (TaKaRa, Cat #9109). RNA concentration and purity were measured using a NanoDrop 2000 (Thermo Fisher Scientific), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies). A total of 1 μg RNA per sample was used for RNA sample preparation. Sequencing libraries were generated using the NEB Next Ultra™ RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations. Index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions

value: liver

value: Kupffer cell

value: macrophage

value: WT

value: acteminophen and anti-CD41 antibody treated


title: APAP and a-CD41, exp2

description:
count CD-2
IgG_and_CD41.xls


title: PEM-seq_HEK293T_ISDra2_MAPK8

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the MAPK8 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.

value: Human embryonic kidney

value: plasmid transfection


title: PEM-seq_HEK293T_SpCas9_MAPK8

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting MAPK8 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: A498 parental At treated replicate 1 [4_AT1]


title: Kdm2a_KO_Rep_interm_rep1_H3K27ac


title: PEM-seq_HEK293T_ISAam1_MAPK8

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the MAPK8 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: APAP and a-CD41, exp1

description:
count CD-1
IgG_and_CD41.xls


title: APAP and IgG,exp3

description:
count Ig-3
IgG_and_CD41.xls

value: acteminophen and contrl IgG antibody treated


title: Kdm2a_KO_Rep_early_rep3_H3K36me3


title: PEM-seq_HEK293T_control_LSD1

treatment_protocol: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.

value: control


title: Kdm2a_KO_Rep_early_rep3_H3K36me1


title: Kdm2a_KO_Rep_early_rep2_H3K4me3


title: 5hmC_Seal SEQ23000

first: Yixiang

last: Shi

address: Room 303, Building #1, 928 Shenhong Road

institute: Accrete Covenant (AC) (Shanghai) Medical Technology Co., Ltd.

data_processing:
raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Assembly: hg19
Supplementary files format and content: 5hmC_Count_Matrix.csv
Library strategy: 5hmC-Seal

source_name: Plasma

extract_protocol:
Blood samples were prospectively collected for analysis at before the first cycle of chemotherapy. Approximately ~5 mL blood was collected for each patient. Plasma was separated within 2 hrs after blood draw, followed by extraction of circulating cfDNA using the Qiagen Circulating DNA Isolation Kit. DNA quality and quantity was examined with standard molecular protocols. High-quality cfDNA samples were frozen at -80C before library construction for the 5hmC-Seal pull-down.
Tagmentation reactions were performed in a 50ml solution with 1X tagmentation buffer from Nextera DNA Sample Preparation Kit (FC-121-1031). The input DNA ranged from 5 ng to 50 ng. Reactions were performed and purified according to the manufacturer’s instruction. In brief, the fragmentation reaction was performed in 50 ml solutions containing 25 ml 23 tagmentation buffer, gDNA, and 0.5-5 X l Tagmentase, at 55℃ for 5 min. The fragmented DNA was eluted into 17.5 ml ddH2O. The glucosylation reactions were performed in a 20 ml solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, purified DNA, 100 mM N3-UDP-Glc, and 1 mM bGT, at 37℃ for 1 hr. After the reaction, 2 ml DBCO-PEG4-DBCO (Click Chemistry Tools, 20 mM stock in DMSO) was added to the reaction mixture, and the mixture was incubated at 37℃ for 2 hr. Next, the modified DNA was purified by a Micro Bio-Spin 30 Column (Bio-Rad). The purified DNA was incubated with 5 ml C1 Streptavidin beads (Life Technologies) in 23 buffer (13 buffer: 5 mM Tris [pH 7.5], 0.5 mM EDTA, and 1 M NaCl) for 15 min according to the manufacture’s instruction. The beads were subsequently undergone six 5 min washes with 1X buffer. All binding and washing were done at room temperature with gentle rotation. The captured DNA fragments were amplified with 12–17 cycles of PCR amplification using the enzyme mix supplied in the Nextera kit. The PCR products were purified using AMPure XP beads according to the manufacture’s instruction. Separate input libraries were made by direct PCR from fragmented DNA without labeling and capture according to the manufacture’s instruction in the Nextera kit.
Briefly, each cfDNA sample was first prepared and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (“Click”) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for DNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) on the Illumina Next-Seq 500 platform at Shanghai Epican Genetech, Ltd. (Shanghai, China).

tag: population

value: Chinese

tag: patient id

value: Plasma


title: 5hmC_Seal SEQ23050


title: PEM-seq_HEK293T_SpCas9_LSD1

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting LSD1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: Kdm2a_KO_Rep_early_rep2_H3K4me1


title: 5hmC_Seal SEQ23114


title: APAP and IgG,exp2

description:
count Ig-2
IgG_and_CD41.xls


title: Kdm2a_KO_Rep_early_rep2_H3K36me3


title: Kdm2a_KO_Rep_early_rep2_H3K36me1


title: PEM-seq_HEK293T_AsCpf1_LSD1

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the LSD1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: 5hmC_Seal SEQ23057


title: C2C12 Myotubes Sardomozide 72h 3

city: Rome

first: Andrea

last: Bracaglia

address: Via Antonio Scarpa 16

institute: University of Rome La Sapienza

data_processing:
Base calling, demultiplexing and adapter masking were carried out with BCL Converter v3.9.3. Low quality bases and adapters were then removed by ERNE software
Reads were aligned to transcriptome GRCm38 (mm10) using STAR with default parameters
The software Stringtie, with default parameters, was used to assemble and quantify full-length transcripts representing multiple spliced variants for each gene locus
RSeqQC was used for the Quality control of read distribution along transcripts. Count tables were generated in R using the package DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: C2C12 myoblasts were growth in DMEM -pyruvate supplemented with 10% FBS and 1% Penicillin/Streptomycin. Differentiation into myotubes was induced shifting cells into differentiation medium, composed of DMEM -pyruvate supplemented with 2% horse serum and 1% Penicillin/Streptomycin

extract_protocol:
Total RNA from C2C12 myotubes was extracted using Qiagen RNeasy mini kits following the manufacturer’s protocol
The libraries for sequencing were prepared using the Illumina kit and sequenced with Illumina NovaSeq (paired end 150pb)

treatment_protocol: Totally differentiated myotubes were treated with Sardomozide dihydrochloride 10μm or DMSO for 72 hours

value: mouse myoblasts

value: Sardomozide 10um


title: PEM-seq_HEK293T_Nme2-C.NR_LSD1

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the LSD1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.


title: PEM-seq_HEK293T_ISYmu1_MAPK8

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the MAPK8 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: APAP and IgG,exp1

description:
count Ig-1
IgG_and_CD41.xls


title: C2C12 Myotubes Sardomozide 72h 2


title: Kdm2a_KO_Rep_early_rep2_H3K27me3

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo). Eight weeks after the DDC challenge, reprogrammed cells and biliary cells were harvested.

value: Liver


title: 5hmC_Seal SEQ22999


title: 5hmC_Seal SEQ23101


title: 5hmC_Seal SEQ23010


title: Kdm2a_KO_Rep_early_rep2_H3K27ac


title: PEM-seq_HEK293T_CasMINI_LSD1

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the LSD1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: CasMINI


title: PEM-seq_HEK293T_ISDra2_LSD1

treatment_protocol: The cells were transfected with the gRNA-ISDra2 plasmid targeting the LSD1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISDra2 plasmid) on Day 3.


title: C2C12 Myotubes DMSO 72h CTR3

value: DMSO


title: C2C12 Myotubes Sardomozide 72h 1


title: 5hmC_Seal SEQ23055


title: Kdm2a_KO_Rep_early_rep1_H3K4me3


title: C2C12 Myotubes DMSO 72h CTR1


title: PEM-seq_HEK293T_ISYmu1_LSD1

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the LSD1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.


title: Kdm2a_KO_Rep_early_rep1_H3K36me1


title: PEM-seq_HEK293T_control_MLH1


title: 5hmC_Seal SEQ23112


title: 5hmC_Seal SEQ23072


title: Kdm2a_KO_Rep_early_rep1_H3K4me1


title: SOD_150_days_biol_rep2

city: Paris

first: Lorenzo

last: Giordani

address: 105 bld de l'hôpital

department: Centre de Recherche en Myologie - UMRS974 Sorbonne Université

institute: INSERM

description:
Frozen Spatial Transcriptome sequencing
ID3215_C1_SOD_150_2

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
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: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots

source_name: skeletal-muscle- Tibialis Anterior and Extensor Digitorum Longus

extract_protocol:
TA and EDL muscles were isolated, embedded in OCT (VWR), and flash frozen in liquid nitrogen
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

value: SOD1G93A  (B6.Cg-Tg(SOD1 G93A)1Gur/J)

value: 150 days


title: PEM-seq_HEK293T_ISAam1_LSD1

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the LSD1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: Kdm2a_KO_Rep_early_rep1_H3K36me3


title: PEM-seq_HEK293T_SpCas9_MLH1

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting MLH1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: Kdm2a_KO_Rep_early_rep1_H3K27me3


title: 5hmC_Seal SEQ23086

city: Shanghai


title: PEM-seq_HEK293T_AsCpf1_MLH1

treatment_protocol: The cells were transfected with the AsCpf1 plasmid targeting the MLH1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-AsCpf1 plasmid) on Day 3.


title: 5hmC_Seal SEQ23109


title: SOD_75_days_biol_rep3

description:
Frozen Spatial Transcriptome sequencing
ID3215_B1_SOD_75_3

value: skeletal-muscle- Tibialis Anterior and Extensor Digitorum Longus

value: 75 days


title: PEM-seq_HEK293T_Nme2-C.NR_MLH1

treatment_protocol: The cells were transfected with the Nme2-C.NR plasmid targeting the MLH1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: WT


title: 5hmC_Seal SEQ23066


title: Hep_rep3_H3K36me3

value: Hep


title: SOD_75_days_biol_rep2

description:
Frozen Spatial Transcriptome sequencing
ID3215_A1_SOD_75_2


title: PEM-seq_HEK293T_CasMINI_MLH1

treatment_protocol: The cells were transfected with the gRNA-CasMINI plasmid targeting the MLH1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-CasMINI plasmid) on Day 3.

value: Human embryonic kidney


title: 5hmC_Seal SEQ23078


title: SOD_150_days_biol_rep1

description:
Frozen Spatial Transcriptome sequencing
ID2237_D1_SOD_150_1


title: Hep_rep3_H3K36me1


title: 5hmC_Seal SEQ23003


title: C2C12 Myotubes DMSO 72h CTR2


title: Hep_rep2_H4K20me3


title: SOD_75_days_biol_rep1

description:
Frozen Spatial Transcriptome sequencing
ID2237_C1_SOD_75_1


title: PEM-seq_HEK293T_ISYmu1_MLH1

treatment_protocol: The cells were transfected with the gRNA-ISYmu1 plasmid targeting the MLH1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISYmu1 plasmid) on Day 3.

value: plasmid transfection


title: 5hmC_Seal SEQ23048


title: WT 150 days

description:
Frozen Spatial Transcriptome sequencing
ID2237_B1_WT_150_1


title: Hep_rep2_H4K20me2


title: PEM-seq_HEK293T_ISAam1_MLH1

treatment_protocol: The cells were transfected with the gRNA-ISAam1 plasmid targeting the MLH1 locus and subsequently sorted for mCherry-positive cells (marked on the gRNA-ISAam1 plasmid) on Day 3.


title: 5hmC_Seal SEQ23067


title: Nsd1KO_Late_Reprogrammed_Rep3

data_processing:
Reads were aligned to the mouse genome (GRCm39) using STAR aligner with default parameters
Gene-count matrices were produced by featureCounts.
Assembly: GRCm39
Supplementary files format and content: BAM files (sequencing reads and alignment), Counts table

extract_protocol:
RNA was isolated with Nucleospin RNA kit (Takara)
Libraries were prepared and sequenced by Novogene (Sacramento, CA)

treatment_protocol: One week later, induction of biliary reprogramming was started by initiating a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet (Envigo).

tag: phenotype

value: Late Reprogrammed


title: Kdm2a_KO_Rep_early_rep1_H3K27ac


title: Hep_rep2_H4K20me1


title: 5hmC_Seal SEQ23042


title: Nsd1KO_Early_Reprogrammed_Rep3

value: Early Reprogrammed


title: Hep_rep2_H3K4me2_CUTAC


title: PEM-seq_HEK293T_SpCas9_VEGFA

treatment_protocol: The cells were transfected with gRNA-SpCas9 plasmid targeting VEGFA locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.

value: VEGFA


title: Hep_rep2_H3K4me3


title: Nsd1KO_Late_Reprogrammed_Rep2


title: 5hmC_Seal SEQ23023

value: Chinese

value: Plasma


title: Nsd1KO_Early_Reprogrammed_Rep2


title: Hep_rep2_H3K4me1


title: 5hmC_Seal SEQ23033