title: mSCADD4_ATAC

description: Library name: 22L012242

data_processing:
Paired-end sequencing reads were trimmed by cutadapt  (version 3.5) with the parameters -a CTGTCTCTTATA -A CTGTCTCTTATA -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=20.
Reads were mapped to the reference genome (Mus musculus GRCm38 dna primary assembly) using bowtie2  (version 2.5.1).
Mapped reads were filtered by samtools  (version 1.17) with the parameter -q 12.
Coverage (bigwig) files created in R (version 4.1.2) using the Bioconductor packages ShortRead (version 1.52.0) and rtracklayer (version 1.54.0) on the unique fragments (read pairs).
Coverages were normalized by the total number of fragments and multiplied by a million.
Peaks were called using Homer  (version 4.10) findPeaks with parameters -style factor -fragLength 150 -size 400 -F 6 -L 6.
Peaks overlapping black list regions (mm10-blacklist.v2) were filtered out using bedtools (version 2.31.0).
Assembly: GRCm38
Supplementary files format and content: BED peak files
Supplementary files format and content: BW bigwig coverage

extract_protocol:
We followed the Omni-ATAC protocol. We used the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits and started with 20 mg of frozen liver.
Libraries from purified DNA were prepared using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s instructions. After PCR enrichment of adaptor-ligated DNA, libraries were size selected at 150-700 bp in length using AMPure XP beads (Beckman Coulter) following the instructions of SPRIselect User Guide. Libraries were controlled via BioAnalyzer (Agilent) measurements using the High Sensitivity DNA kit.

value: SCADD


title: RNAseq - NPC neuron LV-E105 rep1

status: Public on Jan 13 2026

type: SRA

city: Cambridge

first: Bongmin

last: Bae

state: MA

address: 16 Divinity Ave

country: USA

institute: Harvard University

description:
Library name: RNAseq_E105_1
dif3E105_1.genome1 and dif3E105_1.genome2

library_source: transcriptomic

data_processing:
Adapters sequences were automatically detected and trimmed using TrimGalore. Reads were mapped to CAST SNP-masked GRCm39 genome using STAR –sjdbGTFfile Mus_musculus.GRCm39.110.gtf --sjdbOverhang 149 --alignEndsType EndToEnd. PCR duplicates were removed using Picard MarkDuplicates. Allele-specific reads were parsed using SNPsplit (v 0.6.0). Read counts were performed by featureCounts -p –countReadPairs -t exon -g gene_id -a Mus_musculus.GRCm39.110.gtf and using SNP split bam files. Parental biased read enrichment was assessed in R using DEseq2.
Assembly: GRCm39
Supplementary files format and content: bigwig files

molecule: total RNA

organism: Mus musculus

source_name: NPC-derived neurons

growth_protocol: Cortices from E16 embryos were carefully collected into cortical neuron plating media (Neurobasal supplemented with 2% B27, 2% FBS and 1X glutamine). Tissues were mechanically triturated into the plating media by pipetting up and down with 1000μL micropipette tips. Cell suspensions were filtered through a 40 μm cell strainer. Dissociated cells were plated onto Poly-D-lysine coated plates with plating media. Next day, media was replaced with cortical neuron maintenance media (Neurobasal supplemented with 2% B27 and 1X glutamine) and kept at 37°C with 5% CO2 until use. / NPCs were plated onto Geltrex coated plates at a density of 50,000 cells/mL (e.g. in 12 well plates 50,000 cells with 1 mL media, and in 6 well plates 100,000 cells in 2 mL media), and incubated for 3-4 hours to allow cell adherence. Transduction was performed at 7500 genomic particles per cell. Next day, NPC media was fed to keep multipotent state of the NPCs. After 48h of transduction, cells were replated onto new Geltrex coated plates with blasticidin-supplemented media. The next day, neuron differentiation was induced by replating NPCs onto PDL coated plates with cortical neuron media with blasticidin. The following day, cell culture media was optionally replaced to fresh cortical neuron media to enhance neuronal differentiation. / Mouse ESCs were grown on 0.2% gelatin coated plate in ESC media (DMEM supplemented with 10 mM HEPES, 0.11 mM β-mercaptoethanol, 1× NEAA, 2 mM L-glutamine, 15% FBS, and 1000 U/mL LIF). For drug treatment, 5 μM GSK-3484862 was added to treatment groups and volume matched DMSO was added to controls.

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientifics) method. DNA was removed from the samples using Turbo DNase (Thermo Fisher Scientifics).
Library preparation was performed using rRNA depletion strategy / mESC library preparation was performed using poly(A) selection strategy

tag: cell type

value: NPC-derived neurons

tag: genotype


title: RNAseq - NPC neuron LV-Scrb rep2

description:
Library name: RNAseq_Scrb_2
dif3Scrb_2.genome1 and dif3Scrb_2.genome2


title: MeWo, CBX3::ALK expression, biological replicate#2

city: Taipei City

first: han-ying

last: cheng

address: No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of clincal medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: Library name: MeWo_CBX3-ALK_2

data_processing:
Quality Control & Trimming: Raw reads were processed using CLC Genomics Workbench 25.0.3 (tool: Trim Sequences 3.0). Low-quality bases (limit 0.01) and ambiguous nucleotides (max 2) were trimmed. To remove bias, the first 12 nucleotides were removed from the 5' end. Illumina adapters were automatically trimmed via the "New trim adapter list".
Alignment Strategy (Species-specific): Trimmed reads were mapped using the "RNA-Seq Analysis 2.9" tool with the following references: For Human samples (MeWo): Mapped to Homo sapiens (GRCh38.p14) with annotations from Ensembl release 113. For Mouse samples (3T3): Mapped to Mus musculus (GRCm39) with annotations from Ensembl release 112.
Mapping Parameters: Alignment was performed with consistent parameters for all samples: Mismatch cost = 2, Insertion/Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8. The library was defined as Strand specific (Reverse).
Expression Calculation: Gene expression values were calculated based on unique gene reads. The final processed files contain "Unique gene reads" (raw counts), TPM, and RPKM values.
Assembly: GRCm39, GRCh38.p14
Supplementary files format and content: Tab-delimited text files
Supplementary files format and content: Each file contains gene expression quantification results. Full column list: Name, Chromosome, Region, Expression value, TPM, RPKM, Exons, Gene ID, Gene length, ENSEMBL, Biotype, Unique gene reads, Total gene reads, Transcripts annotated, Uniquely identified transcripts, Exon length, Unique exon reads, Total exon reads, Ratio of unique to total (exon reads), Unique exon-exon reads, Total exon-exon reads, Unique intron reads, Total intron reads, Ratio of intron to total gene reads.

organism: Homo sapiens

source_name: MeWo

extract_protocol:
Total RNA was extracted from cells using TRIzol Reagent (Invitrogen) following the manufacturer's instructions. 1μg of total RNA was used for construction of sequencing liberaries.
RNA liberaries for RNA-seq were prepared by Illumina Stranded mRNA Prep kit following manufeacture's protocals

tag: cell line

value: MeWo

value: CBX3::ALK expression


title: MeWo, CBX3::ALK expression, biological replicate#3

description: Library name: MeWo_CBX3-ALK_3


title: mRNAseq - mESC treated with DMSO rep3

description:
Library name: mRNAseq_DMSO_3
DMSO_3_genome1 and DMSO_3_genome2

molecule: polyA RNA

source_name: F1.2-3 mESC

value: F1.2-3 mESC

tag: treatment

value: DMSO


title: SJCNS018598_201114440058_R07C01

type: genomic

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
201114440058_R07C01
blood from survivor of childhood cancer and control

hyb_protocol: Bisulfite-converted DNA was processed by following the Illumina Infinium Methylation Assay protocol for hybridization to MethylationEPIC BeadChips.

scan_protocol: Scanning used the Illumina HiScan system followed the Illumina Infinium Methylation Assay protocol.

data_processing: Genome-wide DNAm data were generated using Illumina Infinium MethylationEPIC BeadChip v1 (Illumina, San Diego, CA, USA), with DNA extracted from peripheral blood mononuclear cells (PBMCs) or saliva. Preprocessing was conducted using the minfi package in R, following established quality control procedures including a detection p-value ≤ 0.01. CpGs were excluded if they were located on sex chromosomes, contained single nucleotide polymorphisms (SNPs), or were previously identified as cross-reactive or non-specific. Quantile normalization was applied at the probe level to ensure comparability across samples.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA derived from blood samples from survivor of childhood cancer and community control

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (250 ng per sample) were treated with bisulfite using the Zymo EZ DNA Methylation Kit under the following thermos-cycling conditions: 16 cycles: 95 degrees Celsius for 30 sec, 50 degrees Celsius for 1 hour. Following bisulfite treatment, DNA samples were desulphonated, column purified, then eluted using 12 µl of elution buffer (Zymo Research Corp.). Treating DNA with sodium bisulfite selectively converts cytosine to uracil but preserves 5-methylcytosine, which is immune from deamination.

tag: tissue

value: peripheral blood mononuclear cells

tag: age

tag: Sex

value: male

tag: group

value: cancer survivor

tag: age at cancer diagnosis

tag: diagnostic group

value: Central nervous system (CNS)

tag: average dose to whole heart, cgy

tag: race group

value: White

tag: base line visit start date

tag: base line visit finish

tag: age at death


title: SJHL018648_201114440058_R08C01

description:
201114440058_R08C01
blood from survivor of childhood cancer and control

value: female

value: Hodgkin lymphoma


title: SJGCT019231_201114440058_R03C01

description:
201114440058_R03C01
blood from survivor of childhood cancer and control

value: Germ cell tumor


title: Piezo1_FL_CTX_d3_Heart#3

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: Piezo1_FL_CTX_d3_Heart#3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Heart

extract_protocol:
For population-level RNA-seq, samples were double-sorted, and 1,000 MmSCs were collected into 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich) in DNA LoBind tubes (Eppendorf). For whole-tissue RNA-seq, samples were dissected and immediately frozen in liquid nitrogen until all samples were collected. Fresh-frozen tissues were homogenized in TRIzol followed by RNA isolation according to the manufacturer's protocol. 2 ng RNA were resuspended in 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich).
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: Heart


title: mSCADD1_ATAC

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description: Library name: 22L012239

library_source: genomic

source_name: liver

growth_protocol: WT (BALB_cJ) and SCADD (BALB_cBYJ) were maintained on standard chow diet in a temperature-controlled environment on a 12/12 h light-dark cycle. Food and water were available ad libitum.

value: liver

value: 8 weeks


title: mWT3_ATAC

description: Library name: 22L012237

value: WT


title: RNAseq - NPC neuron LV-Scrb rep1

description:
Library name: RNAseq_Scrb_1
dif3Scrb_1.genome1 and dif3Scrb_1.genome2

value: NPC-derived neurons


title: CHiC - CN BxC rep4

description: Library name: CHiC_CN_BxC_4

library_source: other

data_processing:
Mouse genome GRCm39 was prepared using SNPsplit_genome_preparation script to mask all the CAST_EiJ single nucleotide polymorphism positions using mgp_REL2021_snps.vcf.gz from the Mouse Genomes Project. SNP-masked genome was digested at Arima restriction enzyme sequences using HiCUP_digester. Capture Hi-C fastq files were mapped using HiCUP (v0.8.0). This wrapper identified mapped paired-end reads with valid Hi-C di-tags. Allele phasing was performed inputting ‘hicup.bam’ files to SNPsplit (v0.6.0). Read pairs in ‘hicup.G1_G1.bam’ or ‘hicup.G2_G2.bam’ files were converted to ‘prejuicer’ format using HiCUP hicup2juicer script (v0.9.0) with --usemid --digest options. Using a custom script, reads were filtered for the capture regions with MAPQ score > 30 at both ends, and maternal and paternal read pair numbers were normalized by subsampling the deeper allele.
Assembly: GRCm39
Supplementary files format and content: read pair files (medium format)

molecule: other

source_name: Primary cortical neurons

growth_protocol: Mouse ESCs were grown on 0.2% gelatin coated plate in ESC media (DMEM supplemented with 10 mM HEPES, 0.11 mM β-mercaptoethanol, 1× NEAA, 2 mM L-glutamine, 15% FBS, and 1000 U/mL LIF). For drug treatment, 5 μM GSK-3484862 was added to treatment groups and volume matched DMSO was added to controls.  / Cortices from E16 embryos were carefully collected into cortical neuron plating media (Neurobasal supplemented with 2% B27, 2% FBS and 1X glutamine). Tissues were mechanically triturated into the plating media by pipetting up and down with 1000μL micropipette tips. Cell suspensions were filtered through a 40 μm cell strainer. Dissociated cells were plated onto Poly-D-lysine coated plates with plating media. Next day, media was replaced with cortical neuron maintenance media (Neurobasal supplemented with 2% B27 and 1X glutamine) and kept at 37°C with 5% CO2 until use.

extract_protocol:
Adherent cells were washed with PBS two times and scraped into 5 mL PBS. / Dissected mouse cortices (two BxC and two CxB) were snap frozen in liquid nitrogen and stored at -80 °C. Frozen tissues were pulverized using Cell crusher in liquid nitrogen.
Samples resuspended in 5 mL PBS and crosslinked in 2% formaldehyde by adding 500 μL of TC buffer and incubating at room temperature for 20 min. Reaction was quenched by adding 289 μL of strop solution I and incubating at RT for 5 min. Crosslinked tissue powder was then centrifuged at 2,000 xg at RT for 15 min and supernatant was discarded. Pellet was stored at -80 C until use. Samples were resuspended in 20 μL lysis buffer, lysed at 4 C for 30 min, conditioned using SDS solution at 62 C for 10 min, and quenched by incubating with 20 μL of stop solution II at 37 C for 15 min. Digestion of extracted chromatin was performed using Arima enzymes by incubating at 37 C 60 min, 65 C 20 min, and 25 C 10 min. Digested chromatin was subject to biotin end repair at RT for 45 min, followed by proximity ligation at RT for 15 min. Crosslinking reversal was performed using proteinase K and incubating at 55 C 30 min, 68 C overnight, and 25 C 10 min. Proximity-ligated DNA was purified using AMPure XP beads. Proximity-ligated DNA was brought to 100 μL in elution buffer and fragmented using Covaris S220 (140 W, 10% duty factor, 200 cycles per burst, 55 sec) to obtain a target fragment of 400 bp. Double sided size selection was performed using 0.6X and 0.25X AMPure XP beads. Biotin enrichment was performed using 300-400 ng of size-selected DNA and 12.5 μL T1 Streptavidin beads in 200 μL binding buffer reaction. Two washes were performed in 200 μL wash buffer at 55 C for 2 min each. Final wash was performed in 100 μL of elution buffer. Washed beads were resuspended in 50 μL of water. On beads end repair was performed by incubating end repair mix at 20 C 15 min 72 C 15 min, followed by adaptor ligation at 20 C 30 min. Samples were cleaned up by magnetizing beads and washing in 200 μL wash buffer at 55 C 2 min and in 100 μL elution buffer. Washed beads were resuspended in 34 μL of water and immediately used for library amplification using Herculase II Fusion polymerase (98 C 2 min / 10X 98 C 30 sec 60 C 30 sec 72 C 1 min / 72 C 5 min). Different index primer combinations were used for each sample. Amplified library was purified using 1X AMPure XP beads. An aliquot of 1.5 μg PCR product in 30 μL elution buffer was pre-cleared of biotin using 50 μL T1 Streptavidin beads in 230 μL reaction. Pre-cleared Hi-C library was resuspended in 14 μL water. Approximately 1 μg of Hi-C library was incubated with custom probes (Agilent Technologies) in thermocycler (95 C 5 min, 65 C 10 min / 60X 65 C 1 min 37 C 3 sec) and purified using 50 μL T1 Streptavidin beads. Vigorous washes were performed six times at 70 C 5 min each. Capture enriched library is amplified using Herculase II polymerase (98 C 2 min / 13X 98 C 30 sec 60 C 30 sec 72 C 1 min / 72 C 5min). Final library purification was performed using 1X AMPure XP beads and resuspended in 25 μL water. Samples were pooled equimolar. Sequencing was performed PE150.

value: Primary cortical neurons

value: F1 BL6xCast


title: Piezo1_FL_CTX_d3_Heart#1

description: Library name: Piezo1_FL_CTX_d3_Heart#1


title: mWT4_ATAC

description: Library name: 22L012238


title: Piezo1_FL_CTX_d3_Heart#2

description: Library name: Piezo1_FL_CTX_d3_Heart#2


title: MeWo, CBX3::ALK expression, biological replicate#1

description: Library name: MeWo_CBX3-ALK_1

value: MeWo

value: CBX3::ALK expression


title: SJNHL017927_201114440058_R01C01

description:
201114440058_R01C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: Non-Hodgkin lymphoma


title: mSCADD3_ATAC

description: Library name: 22L012241

value: male

value: SCADD


title: SJRHB019598_201114440058_R04C01

description:
201114440058_R04C01
blood from survivor of childhood cancer and control

value: cancer survivor

value: Rhabdomyosarcoma

value: White


title: Piezo1_WT_CTX_d3_Heart#3

description: Library name: Piezo1_WT_CTX_d3_Heart#3


title: RNAseq - NPC neuron LV-Scrb rep3

description:
Library name: RNAseq_Scrb_3
dif3Scrb_3.genome1 and dif3Scrb_3.genome2


title: SJAML018554_201114440058_R02C01

description:
201114440058_R02C01
blood from survivor of childhood cancer and control

value: female

value: Acute myeloid leukemia


title: mWT1_ATAC

description: Library name: 22L012235

value: liver


title: SJALL018498_201114440058_R06C01

description:
201114440058_R06C01
blood from survivor of childhood cancer and control

value: Acute lymphoblastic leukemia


title: mWT2_ATAC

description: Library name: 22L012236

value: 8 weeks

value: WT


title: CHiC - CN BxC rep3

description: Library name: CHiC_CN_BxC_3

value: Primary cortical neurons


title: Piezo1_FL_CTX_d0_Liver#4

description: Library name: Piezo1_FL_CTX_d0_Liver#4

source_name: Liver

value: Liver

value: SED


title: IR_6

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

country: France

institute: cea

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped to reference genome mm10 using Bowtie v1.0.0
Assembly: mm10
Supplementary files format and content: Normalized BigWig files were generated using Homer  makeUC- SCfile v4.9.1 with the following parameter ’-norm 3e7 -style dnase’.

source_name: Bone marrow

extract_protocol:
Nuclei were isolated from HSC with lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Igepal) and resuspended in Tn5 transposase mixture (Nextera Tn5 Transposase, 1xTagment DNA buffer (Illumina), and 0.2mg/ml digitonin (Promega). The tagmentation reaction was carried out for 30 minutes at 37°C followed by DNA purification using the MinElute Reaction Cleanup kit (Qiagen).
Tagmented DNA was amplified with NEBNext High-Fidelity PCR Master Mix (NEB) and sequencing primers Ad1_noMX and Ad2.1-6 indexing primers. Libraries were cleaned and size-selected using Spriselect beads (Beckman)

value: Bone marrow

value: HSC


title: CHiC - mESC treated with DNMTi rep3

description: Library name: CHiC_mESC_DNMTi_3

value: F1.2-3 mESC


title: Piezo1_WT_CTX_d3_Heart#4

description: Library name: Piezo1_WT_CTX_d3_Heart#4

value: Heart


title: CHiC - mESC treated with DMSO rep3

description: Library name: CHiC_mESC_DMSO_3

value: DMSO


title: SJRB018826_201114440058_R05C01

description:
201114440058_R05C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: cancer survivor

value: Retinoblastoma


title: SJOS018820_201114440018_R08C01

description:
201114440018_R08C01
blood from survivor of childhood cancer and control

value: female

value: Osteosarcoma

value: Black


title: CHiC - mESC treated with DNMTi rep1

description: Library name: CHiC_mESC_DNMTi_1


title: IR_5


title: Piezo1_WT_CTX_d3_Heart#2

description: Library name: Piezo1_WT_CTX_d3_Heart#2


title: CHiC - mESC treated with DNMTi rep2

description: Library name: CHiC_mESC_DNMTi_2


title: SJALL018469_201114440018_R07C01

description:
201114440018_R07C01
blood from survivor of childhood cancer and control

value: male

value: Acute lymphoblastic leukemia

value: White


title: mSCADD2_ATAC

description: Library name: 22L012240

value: liver

value: 8 weeks

value: SCADD


title: CHiC - mESC treated with DMSO rep2

description: Library name: CHiC_mESC_DMSO_2


title: Piezo1_FL_CTX_d0_Liver#2

description: Library name: Piezo1_FL_CTX_d0_Liver#2

value: Liver

value: SED


title: H3K27ac_CUTRun_4wk_RS_Daxx_cKO_rep2

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: University of California, Davis

description: Library name: H3K27ac_CUTRun_4wk_RS_Daxx_cKO_rep2

data_processing:
For CUT&RUN data processing, we basically follow the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html). Briefly, raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10) were aligned to the mouse (GRCm38/mm10) genome using Bowtie2 (version 2.5.4 ) with options: --end-to-end –very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. E. coli DNA carried along with bacterially-produced pAG-MNase protein brings along a fixed amount of E. coli DNA and can be used as spike-in DNA. For mapping E.coli spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross- mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute. github.io/picard/). To compare replicates, Pearson correlation coefficients were calculated and plotted by multiBamSummary bins, and the plot correlation from deepTools (version 3.5.5). Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli mapping files (the formula used for calculation of scaling factors: 1/ (spike-in reads/100,000)).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: testis

extract_protocol:
Isolation of pachytene spermatocytes and round spermatids using fluorescence-activated cell sorting (FACS) was performed using a SONY SH800S instrument, with Vybrant DyeCycle Violet Stain (DCV) (Invitrogen, V35003) stained testicular single-cell suspensions prepared as described previously (Yeh et al. 2021).  In brief, to prepare single cells suspensions for cell sorting, detangled seminiferous tubules from adult mouse testes were first washed with 1× Hanks’ Balanced Salt Solution (HBSS, Gibco, 14175095) 3 times and then incubated with 1 mg/mL collagenage type 1 (Worthington, CLS1) for 20 min at 35 °C to remove interstitial cells. Then, the tubules were digested in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, 11885076) containing 2% Fetal Bovine Serum (FBS, Gibco, 16000044), 2 mg/mL collagenase type 1, 0.25 mg/mL DNase I (Sigma, D5025), 1.5 mg/mL hyaluronidase (Sigma, H3506) and 700 U/ml recombinant collagenase (FUJIFILM Wako Pure Chemical Corporation, 036-23141) at 35 ℃ for 20–30 min with vigorous pipetting for cell dissociation. The floating germ cell-enriched cell suspension was then collected from plates and washed with 10 mL FACS buffer (PBS containing 2% FBS) 3 times by centrifugation at 300 × g for 5 min and filtered through a 70 µm nylon cell strainer (Falcon, 352350). The resultant single cells were stained with DCV. After 30 min incubation at 35 ℃, cells were filtered into a 5 mL FACS tube through a 35 µm nylon mesh cap (Falcon, 352235). Samples were kept on ice until sorting.
Daxx-ctrl or Daxx-cKO sorted 50,000 PS or 200,000 RS from one individual mouse as one replicate, and two independent biological replicates were used for CUT&RUN library generation as previously described (a step-by-step https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3). The antibodies used were mouse anti-Histone H3.1/3.2 (1/100; Active Motif AM61629), mouse anti-Histone H3.3 (1/100; Active Motif AM91191), rabbit anti-H3K9me3 (1/100; Abcam ab8898), rabbit anti-H3K27ac antibody (1/100; Cell Signaling Technology; 8173), and mouse anti-Histone H3t (1/100; requested from Dr. Yasuyuki Ohkawa, generated from Ueda et al. 2017). Libraries were constructed using NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Prepared CUT&RUN libraries were sequenced on the NovaSeq X Plus system (Illumina) with paired-ended 150-bp reads.

value: testis

value: primary cell

value: Round spermatid

value: DAXX-cKO


title: Piezo1_FL_CTX_d0_Liver#1

description: Library name: Piezo1_FL_CTX_d0_Liver#1


title: CTRL_3

value: Bone marrow

value: HSC


title: H3K27ac_CUTRun_4wk_RS_Daxx_cKO_rep1

description: Library name: H3K27ac_CUTRun_4wk_RS_Daxx_cKO_rep1


title: Piezo1_FL_CTX_d0_Liver#3

description: Library name: Piezo1_FL_CTX_d0_Liver#3


title: SJSTS018869_201114440018_R02C01

description:
201114440018_R02C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: female

value: cancer survivor

value: Soft tissue sarcoma


title: CHiC - mESC treated with DMSO rep1

description: Library name: CHiC_mESC_DMSO_1

value: F1.2-3 mESC

value: DMSO


title: SJGCT019219_201114440018_R04C01

description:
201114440018_R04C01
blood from survivor of childhood cancer and control

value: Germ cell tumor

value: Black


title: CTRL_2


title: IR_4


title: SJGCT018628_201114440018_R05C01

description:
201114440018_R05C01
blood from survivor of childhood cancer and control


title: Piezo1_WT_CTX_d0_Liver#3

description: Library name: Piezo1_WT_CTX_d0_Liver#3


title: CTRL_1


title: H3K27ac_CUTRun_4wk_RS_Daxx_ctrl_rep2

description: Library name: H3K27ac_CUTRun_4wk_RS_Daxx_ctrl_rep2

value: DAXX-ctrl


title: SJHL018649_201114440018_R06C01

description:
201114440018_R06C01
blood from survivor of childhood cancer and control

value: Hodgkin lymphoma


title: H3K27ac_CUTRun_4wk_RS_Daxx_ctrl_rep1

description: Library name: H3K27ac_CUTRun_4wk_RS_Daxx_ctrl_rep1


title: siRNA MYO6 3

city: Sheffield

first: Chris

last: Toseland

address: Medical School

country: United Kingdom

institute: University of Sheffield

description: Library name: Sample1-3

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Assembly: GRch38
Supplementary files format and content: Tab-delimited text files (TSV) include read counts for each sample.

growth_protocol: Full DMEM medium with 10%FBS and Pen/Strep

extract_protocol:
Total RNA was extracted from three replicates of MYO6 KD (siRNA duplex (5′GGUUUAGGUGUUAAUGAAGtt-3′) (Ambion)) and scrambled siRNA (using control siRNA, Qiagen, 1027280) in MCF-7 cells. Ice cold TRIzol reagent was added to each cell culture dish and homogenised. The mixture was incubated at room temperature for 10 minutes. Chloroform was then added to the mixture and incubated at room temperature for 5 minutes. The samples were centrifuged at 8,000 xg. The top, aqueous layer was collected and isopropanol was added. The mixture was then centrifuged at 12, 000 xg for 30 minutes and the supernatant discarded. The pellet was washed in 75% (v/v) ethanol and centrifuged at 7, 500 xg for 5 minutes. The pellet was air dried and resuspended in RNAse-free H2O. RNA concentration and quality was then assessed by measuring absorbance at 260 nm and A260/A280 ratio. RNA samples were stored at -80°C. The following procedures were performed by  Glasgow Polyomics. The RNA-seq libraries were prepared using Poly-A selection. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer and on an Agilent 2100 bioanalyzer. Paired-end sequencing was then performed on an (2x75 bp) on a HiSeq sequencer  (Glasgow Polyomics).
The following procedures were performed by Glasgow Polyomics. The RNA-seq libraries were prepared using Poly-A selection. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer and on an Agilent 2100 bioanalyzer.

treatment_protocol: For MYO6 KD experiments, MCF7 cell monolayers were seeded at 50% confluency and then transfected with MYO6 KD (siRNA duplex (5′GGUUUAGGUGUUAAUGAAGtt-3′)) or scrambled siRNA (using control siRNA, Qiagen, 1027280) using lipofectamine 2000. Cells were harvested at 48hrs.

value: mammary epithelium

value: MYO6  KD by siRNA


title: SJNHL017924_201114440018_R01C01

description:
201114440018_R01C01
blood from survivor of childhood cancer and control

value: male

value: Non-Hodgkin lymphoma

value: White


title: GalNAc‐Mdm2ASO_CDAHFD-10

city: Hung Hom

first: Kenneth King Yip

last: Cheng

state: Kowloon

address: Y948, Lee Shau Kee Building, The Hong Kong Polytechnic University

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University

description:
Library name: Sample 18
Mdm2ASO_CDAHFD-10

data_processing:
Raw reads were mapped against the GRCm39 mouse genome assembly using STAR aligner (v2.7.10b) with the default options.
The number of reads mapped to each of genes was counted by using featureCounts of subread package (v 2.0.3). Parameters: -s 0 -p --countReadPairs -t exon -g gene_id
Assembly: GRCm39
Supplementary files format and content: csv file containing TMM values for each sample

extract_protocol:
RNA was extracted using the RNeasy mini kit (catalog #74104, Qiagen).
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library/Illumina platforms following manufacturer's protocols.

value: Liver

value: MDM2 knockdown

tag: diet

value: CDAHFD


title: Piezo1_WT_CTX_d0_Liver#2

description: Library name: Piezo1_WT_CTX_d0_Liver#2

value: SED


title: siRNA MYO6 2

description: Library name: Sample1-2


title: GalNAc‐Mdm2ASO_CDAHFD-09

description:
Library name: Sample 17
Mdm2ASO_CDAHFD-09


title: SJALL019052_201114440018_R03C01

description:
201114440018_R03C01
blood from survivor of childhood cancer and control

value: peripheral blood mononuclear cells

value: cancer survivor

value: Acute lymphoblastic leukemia


title: Piezo1_FL_CTX_d0_Heart#4

description: Library name: Piezo1_FL_CTX_d0_Heart#4

value: Heart


title: Piezo1_WT_CTX_d0_Liver#1

description: Library name: Piezo1_WT_CTX_d0_Liver#1


title: siRNA MYO6 1

description: Library name: Sample1-1


title: GalNAc‐Mdm2ASO_CDAHFD-08

description:
Library name: Sample 16
Mdm2ASO_CDAHFD-08


title: Piezo1_WT_CTX_d0_Liver#4

description: Library name: Piezo1_WT_CTX_d0_Liver#4


title: H3K9me3_CUTRun_4wk_RS_Daxx_cKO_rep1

description: Library name: H3K9me3_CUTRun_4wk_RS_Daxx_cKO_rep1

value: testis

value: primary cell

value: Round spermatid

value: DAXX-cKO


title: H3K9me3_CUTRun_4wk_RS_Daxx_cKO_rep2

description: Library name: H3K9me3_CUTRun_4wk_RS_Daxx_cKO_rep2


title: Piezo1_FL_CTX_d0_Heart#3

description: Library name: Piezo1_FL_CTX_d0_Heart#3


title: WT Control 2

description: Library name: Control2

value: mammary epithelium

value: scrambled siRNA control


title: H3K9me3_CUTRun_4wk_RS_Daxx_ctrl_rep2

description: Library name: H3K9me3_CUTRun_4wk_RS_Daxx_ctrl_rep2

value: DAXX-ctrl


title: GalNAc‐Mdm2ASO_CDAHFD-07

description:
Library name: Sample 15
Mdm2ASO_CDAHFD-07


title: Piezo1_FL_CTX_d0_Heart#2

description: Library name: Piezo1_FL_CTX_d0_Heart#2


title: WT control 3

description: Library name: Control3


title: WT Control 1

description: Library name: Control1


title: GalNAc‐Mdm2ASO_CDAHFD-06

description:
Library name: Sample 14
Mdm2ASO_CDAHFD-06


title: H33_CUTRun_4wk_RS_Daxx_cKO_rep2

description: Library name: H33_CUTRun_4wk_RS_Daxx_cKO_rep2


title: H3K9me3_CUTRun_4wk_RS_Daxx_ctrl_rep1

description: Library name: H3K9me3_CUTRun_4wk_RS_Daxx_ctrl_rep1


title: Piezo1_WT_CTX_d0_Heart#4

description: Library name: Piezo1_WT_CTX_d0_Heart#4


title: Piezo1_WT_CTX_d0_Heart#3

description: Library name: Piezo1_WT_CTX_d0_Heart#3


title: BCR,Bcells,timepoint7,tube2

city: Daejeon

first: Jeongsoo

last: Lee

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description:
Library name: BCR_T7_G2
BCR-data

data_processing:
Fastq files were processed using cellranger-6.1.2. References for GEX and BCR are GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-5.0.0, respectively
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files
Library strategy: BCR-Seq

source_name: PBMC

extract_protocol:
B cells were sorted by magnetic sorting using anti-CD19 beads from PBMC
The stained cells were sorted into tetramer+ cells and tetramer neg cells and cells from 4 individuals were pooled to be included in a single gem. Tetramer neg cells were titrated up to a total of 100,000 cells, and then mixed with tetramer+ cells. This cell mixture was resuspended in 2% bovine serum albumin (BSA; Bovogen) in PBS for CITE-seq antibody staining. The cells were incubated with Fc receptor blocker (Miltenyi Biotec) at 4°C, and then stained with prepared CITE-seq antibody mixture and incubated at 4°C for 30 minutes. Next, the cells were washed 3 times, and resuspended to 1000 cells/µl, in a volume of 40–100 µl for subsequent library preparation. Transcriptome, antibody-derived tag, and BCR libraries were separately generated using 10X Genomics kits. All samples were sequenced using an Illumina HiSeq 2500, with an average of over 20 million 100-bp paired-end reads.

value: PBMC

value: B cells


title: GalNAc‐conASO_CDAHFD-05

description:
Library name: Sample 13
conASO_CDAHFD-05

value: Liver

value: WT

value: GalNAc‐conASO


title: H33_CUTRun_4wk_RS_Daxx_cKO_rep1

description: Library name: H33_CUTRun_4wk_RS_Daxx_cKO_rep1


title: H33_CUTRun_4wk_RS_Daxx_ctrl_rep2

description: Library name: H33_CUTRun_4wk_RS_Daxx_ctrl_rep2


title: GalNAc‐conASO_CDAHFD-04

description:
Library name: Sample 12
conASO_CDAHFD-04

value: CDAHFD


title: BCR,Bcells,timepoint7,tube1

description:
Library name: BCR_T7_G1
BCR-data


title: BCR,Bcells,timepoint6,tube2

description:
Library name: BCR_T6_G2
BCR-data


title: Piezo1_WT_CTX_d0_Heart#2

description: Library name: Piezo1_WT_CTX_d0_Heart#2

value: SED


title: GalNAc‐conASO_CDAHFD-03

description:
Library name: Sample 11
conASO_CDAHFD-03


title: H33_CUTRun_4wk_RS_Daxx_ctrl_rep1

description: Library name: H33_CUTRun_4wk_RS_Daxx_ctrl_rep1


title: Yoda1_6h#3

description: Library name: Yoda1_6h#3

source_name: Muscle

value: Muscle

value: Mesenchymal stromal cells


title: H312_CUTRun_4wk_RS_Daxx_cKO_rep2

description: Library name: H312_CUTRun_4wk_RS_Daxx_cKO_rep2


title: BCR,Bcells,timepoint5,tube2

description:
Library name: BCR_T5_G2
BCR-data


title: GalNAc‐conASO_CDAHFD-02

description:
Library name: Sample 10
conASO_CDAHFD-02


title: BCR,Bcells,timepoint5,tube1

description:
Library name: BCR_T5_G1
BCR-data


title: H312_CUTRun_4wk_RS_Daxx_ctrl_rep2

description: Library name: H312_CUTRun_4wk_RS_Daxx_ctrl_rep2


title: Yoda1_6h#1

description: Library name: Yoda1_6h#1


title: GalNAc‐conASO_CDAHFD-01

description:
Library name: Sample 9
conASO_CDAHFD-01


title: Strep_MIWI_IP_small_RNAseq_4

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: Library name: VI23-3

data_processing:
In vitro slicing: Reads were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were clipped from the reads using cutadapt with only sequences of at least 15 nucleotides and containing adapter sequences left for further analysis (cutadapt parameters: -a AGATCGGAAGAGCACACGTCT -A GATCGTCGGACTGTAGAACTC -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards --trimmed-only -j 5). The reads were then mapped to the sequences of piRNA target RNAs (Perf.fa.gz or Bulge.fa.gz) using bowtie (with parameters: -v 0 -a --best --strata --allow-contain --threads 10). Only first reads of the sequenced read pairs were used for further analysis. Cummulative read abundances (reads per million) were created from all 15,000 target RNAs based on the start and end position of the reads relative to the 5′ end of targeting piRNA (position 0) - file  "meta_rpm_table.csv.gz". piRNA sequencing: Reads were sorted into individual libraries based on the barcodes and only first reads of the sequenced pairs were used in further analysis. The 3′ adapter sequences were clipped from the reads using cutadapt with only sequences of at least 15 nucleotides and containing adapter sequences left for further analysis (cutadapt parameters: -a AGATCGGAAGAGCACACGTCT -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards --trimmed-only -j 5). The reads were mapped to the mouse genome (GRCm39: Ensembl release 104) using STAR (parameters: --runThreadN 10 -outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000). The reads of 25nt-32nt were considered to represent piRNAs and selected for further analysis. To compare the origin of piRNAs, the piRNAs were annotated based on ENSEMBL gene biotypes, positions of tRNAs (tRNAs table from UCSC), repeats (rmsk table from UCSC) and pachytene piRNA clusters (PMID:23523368). piRNA counts were summarized using Rsubread::featureCounts function - file "MIWI_IP_smallRNAseq.xlsx". Gene expression analysis: Reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (GRCm39: Ensembl release 104) using STAR (parameters: --runThreadN 10 -outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000). Reads were annotated based on ENSEMBL gene biotypes, positions of tRNAs (tRNAs table from UCSC), repeats (rmsk table from UCSC) and pachytene piRNA clusters (PMID:23523368). Read counts were summarized using Rsubread::featureCounts function - file "longRNAseq_featureCounts.xlsx". To analyze the gene expression the reads were aligned to the transcriptome reference using salmon 1.3.0. Transcript counts were collapsed into gene counts and DESeq function of the DESeq2 bioconductor package was used to obtain apeglm shrunken log2 fold changes of gene expression and the adjusted p-values.
Assembly: piRNA sequencing and gene expression analysis: GRCm39 In vitro slicing: Two pools: Perfect or Bulge, each consisting of 15,000 sequences: "Perf.fa.gz", "Bulge.fa.gz"
Supplementary files format and content: In vitro slicing: The files "Perf.fa.gz" and "Bulge.fa.gz" contain 15,000 sequences of in vitro transcribed target RNAs which were used for mapping the reads. The bwt files contain the bowtie mappings to individual 15,000 piRNA target sequences in "Perf.fa.gz" or "Bulge.fa.gz".
Supplementary files format and content: In vitro slicing: The "meta_rpm_table.csv.gz" file contains the cummulative abundances (rpm) of cleaved fragments from all 15,000 target RNAs based on the start and end position of the fragment. piRNA sequencing: The file "MIWI_IP_smallRNAseq.xlsx" contains summarized counts of mapped piRNAs (rpm) to individual genomic elements (genes, repeats, pachytene clusters) obtained by Rsubread::featureCounts. Gene expression analysis: The file "longRNAseq_featureCounts.xlsx" contains summarized counts (rpm) of mapped reads to individual genomic elements (genes, repeats, pachytene clusters) obtained by Rsubread::featureCounts. The file "longRNAseq_salmon.xlsx" contains summarized counts of reads mapped to genes by salmon and normalized by DESeq2.

source_name: testes

growth_protocol: piRNA sequencing and gene expression analysis:: We created two Strep-Miwi knock-in lines by inserting the 8-amino acid Strep II tag (WSHPQFEK) into an internal location at the N-terminus of the MIWI protein. We made two separate knock-in mouse lines (RP85 and RP86) with insertions into two separate locations at the N-terminus, which is predicted to be disordered. In vitro slicing: To design the RNA sequences targeted by MIWI bound piRNAs we searched the piRNA libraries from 10 MIWI-bound small RNA datasets (samples MD40, MD42, MD44, MD46, MD48, MD50, MD52, MD54, MD56, MD58 from GEO: GSE219200) for abundant piRNAs.  Based on 28-32 nt 5’U reads  originating from pachytene clusters we identified the unique genome sequences of 32 nt length generating most of the piRNAs.  Top 15,000 of the sequences were selected, which generated ~70% of all genome mapped reads in the datasets, and used to design the antisense RNA targets  for slicer assay. Based on these sequences, we designed the DNA pool of 15,000 individual single-stranded oligonucleotides (Twist Biosciences), each with a 5’ part having the T7 promoter, followed by a sequence antisense to the piRNAs, and a common sequence that will be used for primer-binding to PCR-amplify the library. Beside this pool containing the targets perfectly complementary to the piRNAs (perfect targets), we also designed the pool where for each sequence we introduced 2-nucleotide mismatch to the piRNA nucleotides 10 and 11 (bulged targets). The ssDNA oligo pool for each library (perfect or bulge targets) was PCR-amplified using primers binding to the T7 promoter region and the 3’ common sequence, which is separate for each library. This double-stranded DNA library was used for in vitro transcription with the T7 viral RNA polymerase to generate the pool of 15,000 target RNAs for each set (perfect or bulge targets). These RNA pools were used for in vitro slicer assays.

extract_protocol:
In vitro slicing: The samples containing the in vitro sliced RNAs were phenol-chloroform extracted and precipitated with ethanol. piRNA sequencing: To extract MIWI-bound piRNAs from adult mouse testes, eluted StrepII-MIWI was subjected to a proteinase K treatment. Briefly, two micrograms of StrepII-MIWI were digested with 10 μg of Proteinase K in Proteinase K buffer by incubation at 42°C for 20 min (with shaking at 400 rpm). The reactions were immediately phenol-chloroform extracted as standard and precipitated overnight in ethanol. After centrifugation of the samples to precipitate the piRNAs, the dry pellets were resuspended in 20 μL RNase-free water. Gene expression analysis: Around 500,000 cells from 1n (spermatids) and 4n (spermatocytes) sorted samples from testicular single cell suspensions were used as input for RNA extraction. RNA was extracted using the Allprep DNA/RNA Micro Kit (Qiagen). The extraction was carried out according to the product’s manual. Elution was performed with 15 uL DEPC water.
In vitro slicing: The precipitated RNA samples were used as input for small RNA library preparation (6 μl of the precipitated RNA following phenol-chloroform extraction), about 80 ng starting material. Libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) and sequenced with the Illumina HiSeq 2000 platform (EMBL GeneCore facility, Heidelberg) using the P50 paired-end option. piRNA sequencing: Libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) and sequenced with the Illumina HiSeq 2000 platform (EMBL GeneCore facility, Heidelberg) using the P50 paired-end option. Gene expression analysis: The Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit was used for the library preparation with 100 ng of total RNA as input. The libraries were sequenced on an Illumina NovaSeq 6000 sequencer for paired-end 100 reads.

treatment_protocol: In vitro slicing: Slicer assays were carried out as described (Reuter et al., 2011), but with slight modifications. After MIWI/piRNA complex isolation, as described in this study, beads were washed in Streptactin wash buffer and then in slicer buffer and used for slicer assays. Alternatively, eluted MIWI fractions were used for the assay. Beads-bound MIWI/piRNA complex or eluted MIWI/piRNA complex were incubated in slicer buffer (10 mM Tris/HCl pH 7.5, 100 mM KCl, 2 mM Mg2Cl, 40 U RiboLock) on ice for 10 min, in 1.5 ml Eppendorf tubes. RNA targets were denatured at 65°C for 5 min and then incubated on ice for 10 min. Reactions were started by the addition of the denatured RNA targets. The total volume of the slicer reactions was 20 mL for bead bound material and variant for soluble MIWI. Two micrograms of soluble MIWI were used for cold assays. The reactions were carried out at 35°C for 2 hours in a Thermoshaker (Eppendorf, Cat. No. EP5387000013) with constant changing modes of shaking (1000 rpm, 10 sec) and pause (90 sec). Reactions were then stopped by adding 300uL of a stop buffer [20 mg Proteinase K (Thermo Fisher Scientific, Cat. No. AM2542) in Proteinase K buffer] and incubated at 42 degrees in a thermoshaker for 20 minutes with shaking (400 rpm).

value: Strep1 (RP68)

tag: experiment

value: testes

tag: mapped to


title: H312_CUTRun_4wk_RS_Daxx_cKO_rep1

description: Library name: H312_CUTRun_4wk_RS_Daxx_cKO_rep1

value: testis

value: primary cell

tag: cell type

tag: genotype


title: Yoda1_4h#3

description: Library name: Yoda1_4h#3

tag: treatment


title: BCR,Bcells,timepoint6,tube1

description:
Library name: BCR_T6_G1
BCR-data

tag: tissue


title: H312_CUTRun_4wk_RS_Daxx_ctrl_rep1

description: Library name: H312_CUTRun_4wk_RS_Daxx_ctrl_rep1

tag: cell line

value: Round spermatid


title: BCR,Bcells,timepoint4,tube2

description:
Library name: BCR_T4_G2
BCR-data


title: Strep_MIWI_IP_small_RNAseq_5

description: Library name: VI23-4


title: BCR,Bcells,timepoint4,tube1

description:
Library name: BCR_T4_G1
BCR-data


title: Yoda1_6h#2

description: Library name: Yoda1_6h#2


title: H3K27ac_CUTRun_4wk_PS_Daxx_cKO_rep2

description: Library name: H3K27ac_CUTRun_4wk_PS_Daxx_cKO_rep2

value: Pachytene spermatocyte

value: DAXX-cKO


title: Yoda1_4h#1

description: Library name: Yoda1_4h#1


title: Strep_MIWI_IP_small_RNAseq_3

description: Library name: VI23-2


title: BCR,Bcells,timepoint3,tube2

description:
Library name: BCR_T3_G2
BCR-data


title: Strep_MIWI_IP_small_RNAseq_2

description: Library name: VI23-1


title: Unstim#3

description: Library name: Unstim#3

value: Vehicle


title: H3K27ac_CUTRun_4wk_PS_Daxx_cKO_rep1

description: Library name: H3K27ac_CUTRun_4wk_PS_Daxx_cKO_rep1


title: BCR,Bcells,timepoint3,tube1

description:
Library name: BCR_T3_G1
BCR-data

value: PBMC


title: Yoda1_4h#2

description: Library name: Yoda1_4h#2


title: Unstim#2

description: Library name: Unstim#2


title: H3K27ac_CUTRun_4wk_PS_Daxx_ctrl_rep2

description: Library name: H3K27ac_CUTRun_4wk_PS_Daxx_ctrl_rep2

value: DAXX-ctrl


title: Unstim#1

description: Library name: Unstim#1


title: 2_cell_Control_2

city: Heilongjiang

first: TT

middle: mei

last: Z

address: Health Care Road

country: China

institute: Harbin Medical University

description: Library name: SCNT_Control_2-cell_2

data_processing:
Adapter sequences and low-quality bases were trimmed using Trim Galore.
Clean reads were aligned to the mouse reference genome (GRCm39) using Hisat2 (for RNA-Seq) or Bowtie2 (for CUT&Tag).
For RNA-Seq, gene expression levels were quantified as counts using featureCounts.
For CUT&Tag, peaks were called using MACS2 .
Differential analysis was performed using DESeq2 (for RNA-Seq) or DiffBind (for CUT&Tag) in R.
Assembly: GRCm39
Supplementary files format and content: RNA-Seq: Processed data are provided in FASTQ format containing raw sequencing reads for each sample.CUT&Tag: Processed data are provided in FASTQ format containing raw sequencing reads for each sample.

source_name: embryo

growth_protocol: Mice were housed in a specific pathogen-free facility under standard laboratory conditions with a 12-hour light/dark cycle and ad libitum access to food and water.

extract_protocol:
For RNA-Seq, sample extraction and library preparation were performed by a commercial sequencing provider following standard protocols.For CUT&Tag, nuclei were extracted and processed using the TD903 CUT&Tag Kit (Vazyme Biotech) according to the manufacturer's instructions.
For RNA-Seq, library construction was carried out by a commercial sequencing provider.For CUT&Tag, libraries were prepared using the TD903 CUT&Tag Kit (Vazyme Biotech) according to the manufacturer’s protocol.

treatment_protocol: No additional treatment was applied prior to sample collection. Embryos were generated by ICSI , and generated by SCNT with or without Nr5a2 overexpression.

value: embryo


title: H3K9me3_CUTRun_4wk_PS_Daxx_cKO_rep2

description: Library name: H3K9me3_CUTRun_4wk_PS_Daxx_cKO_rep2


title: H3K27ac_CUTRun_4wk_PS_Daxx_ctrl_rep1

description: Library name: H3K27ac_CUTRun_4wk_PS_Daxx_ctrl_rep1


title: 2_cell_ICSI_2

description: Library name: ICSI_2-cell_2


title: 2_cell_Control_1

description: Library name: SCNT_Control_2-cell_1


title: H3K9me3_CUTRun_4wk_PS_Daxx_cKO_rep1

description: Library name: H3K9me3_CUTRun_4wk_PS_Daxx_cKO_rep1


title: BCR,Bcells,timepoint1,tube2

description:
Library name: BCR_T1_G2
BCR-data

value: B cells


title: Piezo1_KO_SKM_d1#4

description: Library name: Piezo1_KO_SKM_d1#4


title: H3K9me3_CUTRun_4wk_PS_Daxx_ctrl_rep2

description: Library name: H3K9me3_CUTRun_4wk_PS_Daxx_ctrl_rep2


title: Piezo1_KO_SKM_d1#3

description: Library name: Piezo1_KO_SKM_d1#3


title: FB,Bcells,timepoint7,tube2

description:
Library name: FB_T7_G2
Feature barcode data (ADT)

data_processing:
Fastq files were processed using cellranger-6.1.2. References for GEX and BCR are GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-5.0.0, respectively
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein


title: BCR,Bcells,timepoint2,tube2

description:
Library name: BCR_T2_G2
BCR-data


title: Piezo1_KO_SKM_d1#1

description: Library name: Piezo1_KO_SKM_d1#1


title: BCR,Bcells,timepoint2,tube1

description:
Library name: BCR_T2_G1
BCR-data


title: 2_cell_ICSI_1

description: Library name: ICSI_2-cell_1


title: Piezo1_KO_SKM_d1#2

description: Library name: Piezo1_KO_SKM_d1#2


title: BCR,Bcells,timepoint1,tube1

description:
Library name: BCR_T1_G1
BCR-data


title: 2_cell_Nr5a2_2

description: Library name: SCNT_Nr5a2_OE_2-cell_2


title: Strep_MIWI_IP_small_RNAseq_1

description: Library name: VI11-1


title: H3K9me3_CUTRun_4wk_PS_Daxx_ctrl_rep1

description: Library name: H3K9me3_CUTRun_4wk_PS_Daxx_ctrl_rep1


title: H3t_CUTRun_4wk_PS_Daxx_cKO_rep2

description: Library name: H3t_CUTRun_4wk_PS_Daxx_cKO_rep2


title: Piezo1_KO_SKM_d3#3

description: Library name: Piezo1_KO_SKM_d3#3


title: 2_cell_Nr5a2_1

description: Library name: SCNT_Nr5a2_OE_2-cell_1


title: FB,Bcells,timepoint7,tube1

description:
Library name: FB_T7_G1
Feature barcode data (ADT)


title: FB,Bcells,timepoint6,tube2

description:
Library name: FB_T6_G2
Feature barcode data (ADT)


title: CUT_Tag_CON-2

description: Library name: SCNT_Control_2-cell_CUT_Tag_2

data_processing:
Adapter sequences and low-quality bases were trimmed using Trim Galore.
Clean reads were aligned to the mouse reference genome (GRCm39) using Hisat2 (for RNA-Seq) or Bowtie2 (for CUT&Tag).
For RNA-Seq, gene expression levels were quantified as counts using featureCounts.
For CUT&Tag, peaks were called using MACS2 .
Differential analysis was performed using DESeq2 (for RNA-Seq) or DiffBind (for CUT&Tag) in R.
Assembly: GRCm39
Supplementary files format and content: RNA-Seq: Processed data are provided in FASTQ format containing raw sequencing reads for each sample.CUT&Tag: Processed data are provided in FASTQ format containing raw sequencing reads for each sample.
Library strategy: CUT&Tag


title: CUT_Tag_CON-1

description: Library name: SCNT_Control_2-cell_CUT_Tag_1


title: Piezo1_KO_SKM_d3#2

description: Library name: Piezo1_KO_SKM_d3#2


title: FB,Bcells,timepoint6,tube1

description:
Library name: FB_T6_G1
Feature barcode data (ADT)


title: H3t_CUTRun_4wk_PS_Daxx_cKO_rep1

description: Library name: H3t_CUTRun_4wk_PS_Daxx_cKO_rep1


title: Piezo1_KO_SKM_d3#1

description: Library name: Piezo1_KO_SKM_d3#1


title: CUT_Tag_ICSI-2

description: Library name: ICSI_2-cell_CUT_Tag_2


title: Piezo1_KO_SKM_d7#3

description: Library name: Piezo1_KO_SKM_d7#3


title: FB,Bcells,timepoint5,tube2

description:
Library name: FB_T5_G2
Feature barcode data (ADT)


title: H3t_CUTRun_4wk_PS_Daxx_ctrl_rep2

description: Library name: H3t_CUTRun_4wk_PS_Daxx_ctrl_rep2


title: H3t_CUTRun_4wk_PS_Daxx_ctrl_rep1

description: Library name: H3t_CUTRun_4wk_PS_Daxx_ctrl_rep1


title: CUT_Tag_ICSI-1

description: Library name: ICSI_2-cell_CUT_Tag_1


title: FB,Bcells,timepoint5,tube1

description:
Library name: FB_T5_G1
Feature barcode data (ADT)


title: Piezo1_KO_SKM_d7#1

description: Library name: Piezo1_KO_SKM_d7#1


title: FB,Bcells,timepoint4,tube1

description:
Library name: FB_T4_G1
Feature barcode data (ADT)


title: H33_CUTRun_4wk_PS_Daxx_cKO_rep2

description: Library name: H33_CUTRun_4wk_PS_Daxx_cKO_rep2


title: FB,Bcells,timepoint3,tube2

description:
Library name: FB_T3_G2
Feature barcode data (ADT)


title: Piezo1_KO_SKM_d7#2

description: Library name: Piezo1_KO_SKM_d7#2


title: H33_CUTRun_4wk_PS_Daxx_ctrl_rep2

description: Library name: H33_CUTRun_4wk_PS_Daxx_ctrl_rep2


title: CUT_Tag_OE-1

description: Library name: SCNT_Nr5a2_OE_2-cell_CUT_Tag_1


title: Piezo1_WT_SKM_d1#4

description: Library name: Piezo1_WT_SKM_d1#4


title: CUT_Tag_OE-2

description: Library name: SCNT_Nr5a2_OE_2-cell_CUT_Tag_2


title: Mo_Control_2

description: Library name: SCNT_Control_morula_2

value: morula


title: FB,Bcells,timepoint4,tube2

description:
Library name: FB_T4_G2
Feature barcode data (ADT)


title: H33_CUTRun_4wk_PS_Daxx_ctrl_rep1

description: Library name: H33_CUTRun_4wk_PS_Daxx_ctrl_rep1


title: H33_CUTRun_4wk_PS_Daxx_cKO_rep1

description: Library name: H33_CUTRun_4wk_PS_Daxx_cKO_rep1


title: Piezo1_WT_SKM_d1#3

description: Library name: Piezo1_WT_SKM_d1#3


title: FB,Bcells,timepoint3,tube1

description:
Library name: FB_T3_G1
Feature barcode data (ADT)


title: Piezo1_WT_SKM_d1#2

description: Library name: Piezo1_WT_SKM_d1#2


title: Mo_Control_1

description: Library name: SCNT_Control_morula_1


title: Mo_ICSI_2

description: Library name: ICSI_morula_2


title: Mo_ICSI_1

description: Library name: ICSI_morula_1


title: Piezo1_WT_SKM_d1#1

description: Library name: Piezo1_WT_SKM_d1#1


title: Mo_Nr5a2_2

description: Library name: SCNT_Nr5a2_OE_morula_2


title: FB,Bcells,timepoint2,tube1

description:
Library name: FB_T2_G1
Feature barcode data (ADT)


title: H312_CUTRun_4wk_PS_Daxx_ctrl_rep2

description: Library name: H312_CUTRun_4wk_PS_Daxx_ctrl_rep2


title: Piezo1_WT_SKM_d3#2

description: Library name: Piezo1_WT_SKM_d3#2


title: H312_CUTRun_4wk_PS_Daxx_ctrl_rep1

description: Library name: H312_CUTRun_4wk_PS_Daxx_ctrl_rep1


title: FB,Bcells,timepoint1,tube2

description:
Library name: FB_T1_G2
Feature barcode data (ADT)


title: Piezo1_WT_SKM_d3#3

description: Library name: Piezo1_WT_SKM_d3#3


title: RNAseq_4wk_RS_DAXX_cKO_rep2

description:
Library name: RNAseq_4wk_RS_DAXX_cKO_rep2
DD_4wRS_K2

data_processing:
Trim Galore (version 0.6.10) was used to trim raw RNA-seq reads with the --paired parameter prior to alignment to the mouse genome (GRCm38/mm10) using bowtie2 (version 2.5.4) by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea). Raw read-count files were generated using featureCounts (version 2.0.6) (Liao et al. 2014), incorporating UCSC mouse RefGene and ERCC annotated sequences. For ERCC spike-in normalization and analysis, the edgeR (Robinson et al. 2010) and Limma (Ritchie et al. 2015) packages were employed. Normalization factors were calculated from reads mapped to ERCC annotated sequences, followed by the filtering of raw reads such that there were a minimum of two counts in at least one sample. The filtered reads were assessed for library size using normalization factors prior to DESeq2 transformation. To identify differentially expressed genes (DEGs) through the following criteria: Benjamini-Hochberg-adjusted p-value < 0.05 and Log2FoldChange > 2.
Assembly: mm10
Supplementary files format and content: reads count

extract_protocol:
Isolation of pachytene spermatocytes and round spermatids using fluorescence-activated cell sorting (FACS) was performed using a SONY SH800S instrument, with Vybrant DyeCycle Violet Stain (DCV) (Invitrogen, V35003) stained testicular single-cell suspensions prepared as described previously (Yeh et al. 2021).  In brief, to prepare single cells suspensions for cell sorting, detangled seminiferous tubules from adult mouse testes were first washed with 1× Hanks’ Balanced Salt Solution (HBSS, Gibco, 14175095) 3 times and then incubated with 1 mg/mL collagenage type 1 (Worthington, CLS1) for 20 min at 35 °C to remove interstitial cells. Then, the tubules were digested in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, 11885076) containing 2% Fetal Bovine Serum (FBS, Gibco, 16000044), 2 mg/mL collagenase type 1, 0.25 mg/mL DNase I (Sigma, D5025), 1.5 mg/mL hyaluronidase (Sigma, H3506) and 700 U/ml recombinant collagenase (FUJIFILM Wako Pure Chemical Corporation, 036-23141) at 35 ℃ for 20–30 min with vigorous pipetting for cell dissociation. The floating germ cell-enriched cell suspension was then collected from plates and washed with 10 mL FACS buffer (PBS containing 2% FBS) 3 times by centrifugation at 300 × g for 5 min and filtered through a 70 µm nylon cell strainer (Falcon, 352350). The resultant single cells were stained with DCV. After 30 min incubation at 35 ℃, cells were filtered into a 5 mL FACS tube through a 35 µm nylon mesh cap (Falcon, 352235). Samples were kept on ice until sorting.
20,000 PS or 50,000 RS were sorted from independent mice as one replicate, and two independent biological replicates were used for RNA-seq library generation. Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer’s instructions. Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instructions. Prepared RNA-seq libraries were sequenced on the NovaSeq X Plus system (Illumina) with paired-ended 150-bp reads.


title: H312_CUTRun_4wk_PS_Daxx_cKO_rep1

description: Library name: H312_CUTRun_4wk_PS_Daxx_cKO_rep1


title: H312_CUTRun_4wk_PS_Daxx_cKO_rep2

description: Library name: H312_CUTRun_4wk_PS_Daxx_cKO_rep2


title: GEX,Bcells,timepoint7,tube2

description:
Library name: T7_G2
10X GEX data

library_source: transcriptomic single cell

data_processing:
Fastq files were processed using cellranger-6.1.2. References for GEX and BCR are GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-5.0.0, respectively
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files


title: FB,Bcells,timepoint1,tube1

description:
Library name: FB_T1_G1
Feature barcode data (ADT)


title: FB,Bcells,timepoint2,tube2

description:
Library name: FB_T2_G2
Feature barcode data (ADT)


title: RNAseq_4wk_RS_DAXX_cKO_rep1

description:
Library name: RNAseq_4wk_RS_DAXX_cKO_rep1
DD_4wRS_K1


title: Piezo1_WT_SKM_d3#1

description: Library name: Piezo1_WT_SKM_d3#1


title: GEX,Bcells,timepoint7,tube1

description:
Library name: T7_G1
10X GEX data


title: CRISPRoff_NTC_30d

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

description: HEK293T cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridize to human Infinium MethylationEPIC Beadchip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing:
Data analysis was performed using the Illumina default procedure implemented in the Bioconductor minfi package. We have defined a differentially methylated region (DMR) as a consecutive sequence of two CpGs exhibiting a methylation increase of over 10% when they are in a distance less than 1  kb.
processed value definition: Delta beta

label: other

label_protocol: Standard Illumina protocol

growth_protocol: Human embryonic kidney HEK293T cells were maintained in Dulbecco’s Modified Eagle Medium (Sigma Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (Sigma Aldrich), 4 mM L-glutamine (Sigma Aldrich), 100 U/ml penicillin and 100 µg/ml streptomycin (Sigma Aldrich). Cells were incubated at 37◦C in a humidified 5% CO2-containing atmosphere

extract_protocol: To enrich the EGFP+ cells, FACS sorting was performed after 72 h and the sorted cells were subjected directly for DNA, RNA and protein extraction using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Venlo, Netherlands).

treatment_protocol: HEK293T cells were transfected using Lipofectamine 3000 Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Briefly, cells were seeded in 6 well plates and were transfected the day after at around 80% of confluency. The transfection cocktail was prepared as follows: 4µg of the plasmid DNA, 5 µl Lipofectamine™ 3000 Reagent, 5 µl P3000™ Reagent (2 µL/µg DNA) and Opti-MEM™ Medium (Invitrogen).

value: epithelial-like cell


title: dDNMT3a_BACH2_g8_30d

description: HEK293T cell line


title: RNAseq_4wk_RS_DAXX_ctrl_rep2

description:
Library name: RNAseq_4wk_RS_DAXX_ctrl_rep2
DD_4wRS_C2


title: RNAseq_4wk_RS_DAXX_ctrl_rep1

description:
Library name: RNAseq_4wk_RS_DAXX_ctrl_rep1
DD_4wRS_C1


title: RNAseq_4wk_PS_DAXX_cKO_rep2

description:
Library name: RNAseq_4wk_PS_DAXX_cKO_rep2
DD_4wPD_K2


title: RNAseq_4wk_PS_DAXX_cKO_rep1

description:
Library name: RNAseq_4wk_PS_DAXX_cKO_rep1
DD_4wPD_K1


title: mut3A_NTC_30d

description: HEK293T cell line


title: CRISPRoff_BACH2_g8_30d

description: HEK293T cell line


title: Piezo1_WT_SKM_d7#3

description: Library name: Piezo1_WT_SKM_d7#3


title: GEX,Bcells,timepoint5,tube2

description:
Library name: T5_G2
10X GEX data


title: Pdgfra.Cre_Piezo1.FL.SED#2

description: Library name: Pdgfra.Cre_Piezo1.FL.SED#2

value: SED


title: Mo_Nr5a2_1

description: Library name: SCNT_Nr5a2_OE_morula_1


title: Pdgfra.Cre_Piezo1.WT.SED#3

description: Library name: Pdgfra.Cre_Piezo1.WT.SED#3

value: Muscle


title: Piezo1_WT_SKM_d7#2

description: Library name: Piezo1_WT_SKM_d7#2


title: 3A3A_NTC_30d

description: HEK293T cell line


title: GEX,Bcells,timepoint4,tube2

description:
Library name: T4_G2
10X GEX data


title: GEX,Bcells,timepoint6,tube2

description:
Library name: T6_G2
10X GEX data


title: Pdgfra.Cre_Piezo1.FL.SED#1

description: Library name: Pdgfra.Cre_Piezo1.FL.SED#1


title: Pdgfra.Cre_Piezo1.FL.SED#3

description: Library name: Pdgfra.Cre_Piezo1.FL.SED#3


title: 3A3A_BACH2_g8_30d

description: HEK293T cell line


title: Pdgfra.Cre_Piezo1.WT.SED#1

description: Library name: Pdgfra.Cre_Piezo1.WT.SED#1


title: RNAseq_4wk_PS_DAXX_ctrl_rep2

description:
Library name: RNAseq_4wk_PS_DAXX_ctrl_rep2
DD_4wPD_C3


title: RNA_KOCOMP_CD45.1_02

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description: Library name: Sample 7

data_processing:
The bulk RNA-seq analysis was performed using the Seq-N-Slide pipeline;using the rna-star and rna-star-groups-dge routes.
trimmed adapters from .fastq files using Trimmomatic (v0.36)
aligning reads to the mm10 reference genome using Star (v2.7.3a)
aligning reads to probable contaminants using fastq_screen (v0.13.0)
resulting reads are quantified using featureCounts from subread v1.6.3; differential expression is performed using DESeq2 (v1.26.0)
Assembly: mm10
Supplementary files format and content: normalized counts matrix  csv file

source_name: sdLN

extract_protocol:
Cell sorting of fluorescent antibody-labeled cell suspensions was performed on FACSAria II (BD Biosciences) at the Cytometry & Cell Sorting Laboratory at NYUGSoM. 3.3-18.6x103 migDC were sorted per sample. migDC = Live singlets lineage- (CD3- TCR-β- CD19- NK1.1- NKp46- Siglec-F- Ly6G-) CD11c+ MHC-IIhi. RNA was extracted from sort-purified cells using the QIAGEN RNeasy Mini Kit and the accompanying RNase-Free DNase Set according to the manufacturer protocol.
cDNA libraries were prepared using the low input Clontech SMART-Seq HT with Nxt HT kit according to the manufacturer protocol.

treatment_protocol: Irradiated CD45.1 hosts were reconstituted with an equal mixture of competitor CD45.1 BM and BM from either Etv3+/+ or Etv3-/- donors (CD45.2). SdLN (bilateral inguinal and brachial nodes) were collected and LN capsules pierced with sharp forceps. SdLN were digested in 1 mg/ml collagenase D (Roche) in HBSS with calcium and magnesium for 30 min at 37°C. The single cell suspension was passed through a 70 μm filter prior to downstream analysis.

value: sdLN

value: migDC

value: Competitor (Etv3-/- donor)


title: WT.SED#3

description: Library name: WT.SED#3

value: Mesenchymal stromal cells


title: RNAseq_4wk_PS_DAXX_ctrl_rep1

description:
Library name: RNAseq_4wk_PS_DAXX_ctrl_rep1
DD_4wPD_C2

value: testis

value: primary cell


title: GEX,Bcells,timepoint6,tube1

description:
Library name: T6_G1
10X GEX data


title: RNA_KOCOMP_CD45.1_01

description: Library name: Sample 5


title: GEX,Bcells,timepoint5,tube1

description:
Library name: T5_G1
10X GEX data


title: RNA_KO_CD45.2_01

description: Library name: Sample 6


title: WT.SED#2

description: Library name: WT.SED#2


title: 3A3L_BACH2_g8_30d

description: HEK293T cell line


title: mut3A_BACH2_g8_30d

description: HEK293T cell line


title: GEX,Bcells,timepoint3,tube2

description:
Library name: T3_G2
10X GEX data


title: RNA_KO_CD45.2_02

description: Library name: Sample 8


title: mut3A_NTC_7d

description: HEK293T cell line


title: Pdgfra.Cre_Piezo1.WT.SED#2

description: Library name: Pdgfra.Cre_Piezo1.WT.SED#2


title: 3A3L_NTC_30d

description: HEK293T cell line


title: 3A_NTC_30d

description: HEK293T cell line


title: GEX,Bcells,timepoint4,tube1

description:
Library name: T4_G1
10X GEX data


title: 3A_BACH2_g8_30d

description: HEK293T cell line


title: Piezo1_WT_SKM_d7#1

description: Library name: Piezo1_WT_SKM_d7#1


title: RNA_WT_CD45.2_02

description: Library name: Sample 4


title: mut3A_BACH2_g8_7d

description: HEK293T cell line


title: GEX,Bcells,timepoint1,tube2

description:
Library name: T1_G2
10X GEX data


title: GEX,Bcells,timepoint2,tube2

description:
Library name: T2_G2
10X GEX data


title: RNA_WTCOMP_CD45.1_02

description: Library name: Sample 3

value: Competitor (Etv3+/+ donor)


title: GEX,Bcells,timepoint2,tube1

description:
Library name: T2_G1
10X GEX data


title: WT.SED#1

description: Library name: WT.SED#1


title: GEX,Bcells,timepoint3,tube1

description:
Library name: T3_G1
10X GEX data


title: GEX,Bcells,timepoint1,tube1

description:
Library name: T1_G1
10X GEX data


title: WT.EXT#2

description: Library name: WT.EXT#2

value: EXT


title: dDNMT3a_BACH2_g8_7d

description: HEK293T cell line


title: RNA_WT_CD45.2_01

description: Library name: Sample 2


title: CRISPRoff_NTC_7d

description: HEK293T cell line


title: HSPC_6days_20mGy_sample2

type: RNA

description: Gene expression data from murine 20mGy-irradiated LT-HSC at 6 days of culture maintenance in stem cell medium

hyb_protocol: Following fragmentation, 5.5 ug of Labeled ss-cDNA were hybridized with rotation at 60rpm  for 16 hr at 45C on GeneChip Clariom S array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with TAC 4.0.1.36 software, normalized with loess algorithm  and corrected by global scaling. Annotation was performed with mta10transcriptcluster.db.

label: biotin

label_protocol: Biotinylated cDNA were prepared according to the GeneChip whole Transcript (WT) Pico Reagent Kit protolcol (Affymetrix).

growth_protocol: Mouse hematopoietic stem and progenitor cells (HSPC) at 6 days of culture from non- and 20mGy-irradiated LT-HSC

extract_protocol: Total RNA was extracted according to the protocol of RNeasy Plus Micro Kit (QIAGEN) and The RNA integrity (RNA Integrity Score≥7.0) was checked on the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: ND

value: Bone marrow


title: RNA_WTCOMP_CD45.1_01

description: Library name: Sample 1


title: WT.MmSCs.Yoda1.2h#2

description: Library name: WT.MmSCs.Yoda1.2h#2


title: HSPC_6days_20mGy_sample1

source_name: hematopoietic stem and progenitor cells (HSPC)


title: CRISPRoff_BACH2_g8_7d

description: HEK293T cell line


title: WT.MmSCs.Yoda1.2h#1

description: Library name: WT.MmSCs.Yoda1.2h#1


title: 3A3L_NTC_7d

description: HEK293T cell line


title: WT.EXT#1

description: Library name: WT.EXT#1


title: CUTRUN_H3K4me3_ETV3WT_02

description: Library name: Sample 2

data_processing:
CUT&RUN reads were processed using the Seq-N-Slide pipeline (https://doi.org/10.5281/zenodo.5550459).
Sequences were aligned to the Mus musculus reference genome (mm10/GRCm38) using Bowtie2 (version 2.3.4.1). Alignment output was generated in SAM format and subsequently converted to BAM format using Sambamba (version 0.6.8).
Samtools (version 1.9) was used to filter the aligned reads based on mapping quality.
Duplicate reads were removed from the aligned BAM files using Sambamba (version 0.6.8).
BigWig files were generated from BAM files using deepTools (version 3.5.1) with bins per million mapped reads (BPM) normalization.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: GM-BMDC cultures

growth_protocol: Primary mouse bone marrow cells were plated at a density of 1x107 cells per well in 4 ml of RPMI supplemented with 10% FBS, 1% L-glutamine, 1% penicillin-streptomycin, 55 μM 2-mercaptoethanol, 20 ng/ml GM-CSF and 5 ng/ml IL-4 in 6-well plates. Cells were cultured at 37°C for 6 days. On days 2 and 3 of differentiation, 2 ml and 4 ml media respectively were replaced with fresh cytokines.

extract_protocol:
CUT&RUN was performed on ~2.5x105 cells using the CUT&RUN Assay Kit (Cell Signaling Technology) according to the manufacturer protocol. Briefly, cells were washed and immobilized with Concanavalin A beads. 2 µL of H3K4me3 (C42D8) Rabbit mAb was added to each sample and incubated overnight. The tubes were washed, pAG-MNase enzyme was added, and activated with calcium chloride. DNA was purified using DNA Purification Buffers and Spin Columns (Cell Signaling Technology).
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer protocol.

treatment_protocol: GM-BMDC cultures were established from both Etv3+/+ and Etv3-/- mice. DCs were magnetically enriched by negative selection. Briefly, cell suspensions were stained with biotinylated antibodies against CD115, incubated with streptavidin microbeads (Miltenyi Biotec) and passed through LD columns attached to MidiMACS or QuadroMACS separators (Miltenyi Biotec) according to manufacturer protocol.

value: GM-BMDC cultures

value: DC


title: CUTRUN_H3K4me3_ETV3KO_02

description: Library name: Sample 4


title: WT.MmSCs.Yoda1.0h#3

description: Library name: WT.MmSCs.Yoda1.0h#3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

value: Vehicle


title: HSPC_6days_0Gy_sample3

description: Gene expression data from murine non-irradiated LT-HSC at 6 days of culture maintenance in stem cell medium


title: HSPC_6days_0Gy_sample2


title: IL-1R antagonist treated, CD45 positive cells

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: Library name: IL1RA_45_pos

data_processing:
Alignment with Cell Ranger v6
QC and filtering with Seurat v4
Unsupervised clustering with Seurat v4
Assembly: mm10
Supplementary files format and content: .rds object

source_name: lung

extract_protocol:
Chromium Single Cell 3ʹ Reagent v3.1 kit from 10X Genomics
Chromium Single Cell 3ʹ Reagent v3.1 kit from 10X Genomics

value: lung

value: Lung transplant + IL-1R antagonist


title: IL-1R antagonist treated, CD45 negative cells

description: Library name: IL1RA_45_neg


title: WT.MmSCs.Yoda1.0h#2

description: Library name: WT.MmSCs.Yoda1.0h#2


title: CUTRUN_H3K4me3_ETV3KO_01

description: Library name: Sample 3


title: WT.EXT#3

description: Library name: WT.EXT#3


title: 3A_NTC_7d

description: HEK293T cell line

value: epithelial-like cell


title: 3A3A_NTC_7d

description: HEK293T cell line


title: WT.MmSCs.Yoda1.0h#1

description: Library name: WT.MmSCs.Yoda1.0h#1


title: HSPC_6days_0Gy_sample1


title: 3A3A_BACH2_g8_7d

description: HEK293T cell line


title: mut3A_NTC_3d

description: HEK293T cell line


title: CUTRUN_H3K4me3_ETV3WT_01

description: Library name: Sample 1


title: sf3b1 MO + As2S2, rep2

city: Shanghai

first: Fan

last: Wu

address: DongFang road 1881

institute: Shanghai Municipal Hospital of Traditional Chinese Medicine

description: Library name: Sample8

data_processing:
Samples were sequenced on the Illumina platform to generate image files, which were converted into raw sequencing data in FASTQ format by the platform’s built-in software. Low-quality reads and adapter sequences in the raw data were filtered using fastp (version 0.22.0) to obtain clean data for downstream analysis. Clean reads were aligned to the zebrafish reference genome (GRCz11), and differential gene expression analysis was performed using the DESeq2 R package.
Assembly: GRCz11 (danRer11)
Supplementary files format and content: xlsx file including raw read counts of each gene for all samples
Supplementary files format and content: xlsx file including differentially expressed genes with log2 fold change, p-value and adjusted p-value

organism: Danio rerio

source_name: Trunk tissue

extract_protocol:
Total RNA extraction was performed with FastPure Complex Tissue/Cell Total RNA Isolation Kit (Vazyme).
RNA-seq library was constructed by polyA-tailed mRNA selection using NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Trunk tissue

value: Embryonic trunk tissue cells


title: 3A_BACH2_g8_7d

description: HEK293T cell line


title: Control (PBS) treated, CD45 negative cells

description: Library name: PBS_45_neg

value: Lung transplant + Control (PBS)


title: 3A3L_BACH2_g8_7d

description: HEK293T cell line


title: sf3b1 MO + As2S2, rep3

description: Library name: Sample9


title: Pdgfra.CRE_Piezo1.FL_CTX.d1#3

description: Library name: Pdgfra.CRE_Piezo1.FL_CTX.d1#3

value: Muscle


title: Pdgfra.CRE_Piezo1.FL_CTX.d1#1

description: Library name: Pdgfra.CRE_Piezo1.FL_CTX.d1#1


title: mut3A_BACH2_g8_3d

description: HEK293T cell line


title: HSPC_6days_20mGy_sample3


title: sf3b1 MO, rep3

description: Library name: Sample6


title: Pdgfra.CRE_Piezo1.WT_CTX.d1#2

description: Library name: Pdgfra.CRE_Piezo1.WT_CTX.d1#2


title: 20mGy_plus_4PBA

data_processing:
Image analysis and base calling is performed using Illumina Real Time Analysis (3.4.4) with default parameters.
Assembly: mm10
Supplementary files format and content: Raw methylation calling, CGmap

source_name: bone marrow

extract_protocol:
Genomic DNA was extracted with QIAamp® DNA Micro Kit (Qiagen). Genomic DNA is incubated with 200U MspI (New England Biolabs) at 37°C for 2h. Digested product is then end-repaired, A-tailed and ligated to methylated Illumina adaptors with the NEB Next Ultra II kit (New England Biolabs) following provider recommandations. After ligation step, DNA fragments are purified and size-selected with a two step SPRI beads purification in order to select fragments from 40bp to 400bp. Clean-up ligated DNA is eluted in Low TE buffer. Bisulfite conversion is performed following provider recommandations (Zymo EZ-lightning kit). Converted product is finally amplified by PCR using polymerase Kapa HiFi Hotstart U+ Ready mix 2X in a final volume of 50 μL. Indexed libraries with Illumina primers are PCR amplified with 13 cycles following provider incubation protocol. PCR product is then purified by 1.2X SPRI beads clean-up and controlled by capillary electrophoresis on Fragment Analyzer.
Diagenode Premium RRBS kit

value: bone marrow

value: HSC


title: sf3b1 MO, rep2

description: Library name: Sample5


title: Control (PBS) treated, CD45 positive cells

description: Library name: PBS_45_pos


title: sf3b1 MO + As2S2, rep1

description: Library name: Sample7


title: CRISPRoff_NTC_3d

description: HEK293T cell line


title: sf3b1 MO, rep1

description: Library name: Sample4


title: 3A3L_NTC_3d

description: HEK293T cell line


title: Pdgfra.CRE_Piezo1.FL_AEXd1#3

description: Library name: Pdgfra.CRE_Piezo1.FL_AEXd1#2

extract_protocol:
For population-level RNA-seq, samples were double-sorted, and 1,000 MmSCs were collected into 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich) in DNA LoBind tubes (Eppendorf). For whole-tissue RNA-seq, samples were dissected and immediately frozen in liquid nitrogen until all samples were collected. Fresh-frozen tissues were homogenized in TRIzol followed by RNA isolation according to the manufacturer's protocol. 2 ng RNA were resuspended in 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich).
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: Mesenchymal stromal cells

value: AEX


title: control MO, rep1

description: Library name: Sample1


title: Pdgfra.CRE_Piezo1.FL_AEXd1#2

description: Library name: Pdgfra.CRE_Piezo1.FL_AEXd1#1


title: Pdgfra.CRE_Piezo1.FL_CTX.d1#2

description: Library name: Pdgfra.CRE_Piezo1.FL_CTX.d1#2


title: Pdgfra.CRE_Piezo1.WT_CTX.d1#1

description: Library name: Pdgfra.CRE_Piezo1.WT_CTX.d1#1


title: dDNMT3a_BACH2_g8_3d

description: HEK293T cell line


title: Pdgfra.CRE_Piezo1.WT_CTX.d1#3

description: Library name: Pdgfra.CRE_Piezo1.WT_CTX.d1#3


title: 0_Gy_plus_4PBA


title: Pdgfra.CRE_Piezo1.WT_SED#1

description: Library name: Pdgfra.CRE_Piezo1.FL_AEXd1#3


title: CRISPRoff_BACH2_g8_3d

description: HEK293T cell line


title: RNA_WT_CpGA6h_02

data_processing:
Seq-N-Slide
Illumina bcl2fastq
Sequence reads adapter and quality trimmed using Trimmomatic
Trimmed reads aligned to mm10/GrCM38 using STAR
Count extraction performed using featureCounts
Count normalization and differential expression testing using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: FL-BMDC

growth_protocol: Primary mouse bone marrow cells were plated in DMEM supplemented with 10% FBS, 10% B16-Flt3L supernatant, 1% L-glutamine, 1% sodium pyruvate, 1% MEM-NEAA, 1% penicillin-streptomycin, and 55 μM 2-mercaptoethanol. Cells were cultured at 37°C for 8 days without replating and collected by scraping the bottom of the well.

extract_protocol:
RNA was extracted from 1x106 FL-BMDCs using the QIAGEN RNeasy Mini Kit, QIAshredder homogenization columns and the accompanying RNase-Free DNase Set according to the manufacturer protocol.
cDNA libraries were prepared using the low input Clontech SMART-Seq HT with Nxt HT kit according to the manufacturer protocol.

treatment_protocol: FL-BMDCs were stimulated with 1 μM CpG-A/ODN2216 (InvivoGen) or left unstimulated as a control for 6 hours.

value: FL-BMDC

value: bulk DC

value: Control

value: CpG-A (6h)


title: control MO, rep3

description: Library name: Sample3


title: Pdgfra.CRE_Piezo1.FL_AEXd1#1

description: Library name: Pdgfra.CRE_Piezo1.FL_SED#3

value: SED


title: RNA_ETB2ETB4DKO_CpGA6h_02


title: Pdgfra.CRE_Piezo1.FL_SED#3

description: Library name: Pdgfra.CRE_Piezo1.FL_SED#2


title: 3A3L_BACH2_g8_3d

description: HEK293T cell line


title: Mouse, OPC-ITAN & OPC-LacZ, 20-28W, GEX, multiplexing

first: Jeong Ho

address: Daehak-ro

description:
10X Genomics
mouse_IDH-mut_glioma_model.h5ad

data_processing:
Cell Ranger (v.8.0.0) (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: A custom transcriptome reference, based on rhe mouse reference genome (GRCm39), using Cell Ranger mkrefs, adding the Cas9-EGFP sequence.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Four mice IDH-mutant glioma models (OPC-ITAN, 26 to 38-weeks-old-age) and a control mouse (OPC-LacZ, 20-weeks-old-age) were euthanized by trans-cardiac perfusion with 20ml cold DPBS without Ca2+/Mg2+ under isoflurane anesthesia. GFP-positive areas in brain were micro-dissected with a scalpel blade and pooled for digestion using the Adult Brain Dissociation Kit, mouse and rat (#130-107-677, Miltenyi Biotec), kept cold on ice. After manual gentle tissue dissociation, cell debris in the single cell suspension were removed by a gradient centrifugation (3000×g for 10min) at 4℃. The single cell suspension was labeled with immune cell markers, for example, CD11b-APC (1:100 dilution; #101212, BioLegend) and CD45-APC-Cy7 (1:100 dilution; #103116, BioLegend), in flow cytometry buffer. DAPI (0.5μg-1; #422801, BioLegend) stained single cell suspension, to discriminate dead cells from live cells, were isolated with FACSAria Fusion (BD). Except for the "mouse4", all samples were labled with CellPlex kit (10X Genomics).
RNA libraries for single-cell RNA-seq Chromium Single Cell 3' kit v3.1 (10X Genomics) following manufacturer's instructions.

value: brain

tag: strain

value: Idh1R132H, Trp53, Atrx, Nf1 (OPC-ITAN) & Idh1wildtype (OPC-LacZ)

tag: mouse id_1

value: mouse1, OPC-ITAN, 26W, CMO312

tag: mouse id_2

value: mouse2, OPC-ITAN, 28W, CMO307

tag: mouse id_3

value: mouse3, OPC-ITAN, 28W, CMO309

tag: mouse id_4

value: control, OPC-LacZ, 20W, CMO305


title: 3A3A_NTC_3d

description: HEK293T cell line

value: epithelial-like cell


title: control MO, rep2

description: Library name: Sample2

value: Trunk tissue

value: Embryonic trunk tissue cells


title: HumanBrain-PeritumoralTissue-2

description: Xenium data from CASE2

scan_protocol: Xenium library imaging  The prepared samples, along with buffers and decoding consumables, were loaded into a Xenium analyzer (10X Genomics). The run was initiated in accordance with the manufacturer’s guidance. Fluorescent reporters hybridized to their respective complementary regions within barcoded circularized cDNA were imaged. Finally, H&E staining was performed on the same region after the run was complete. All of image data from Xenium and corresponding H&E staining was integrated and generated by Xenium Explorer (10X Genomics, v.3.2.0).

data_processing: Xenium dataset processing  Spatial transcriptomic data were process using Squidpy (v1.6.1)(93), with cell segmentation performed using Xenium’s default nuclear segmentation. Subsequent processing steps were carried out according to a previous report(94). Briefly, gene expression values were normalized based on library size (total size = 100), followed by log transformation and scaling. A k-nearest neighbors’ graph was constructed using all principal components with 16 neighbors, and Louvain clustering was applied for cell grouping.

label: in situ pedlock probe

source_name: Patient-derived peritumoral tissue

extract_protocol:
Xenium probe design  Custom Xenium gene and mutation probes were designed using Xenium Panel Designer(https://cloud.10xgenomics.com/xenium-panel-designer) according to the manufacturer’s instructions. For instance, the IDH1R132H mRNA-capture probe was designed by curating 21-bp sequences flanking the targeted transcribed variant site from the Ensembl canonical transcript (NM_005896.4(IDH1):c.395G>A (p.Arg132His). All possible ligation junctions, including both wildtype and mutant alleles, were evaluated. To ensure binding specificity, an additional IDH1 wildtype probe was included to compete with the mutant probe. Variant sites containing only non-preferred junctions (CG, CT,GG and GC) were excluded. The two bases forming the ligation junction sequence corresponded to the last base of the RNA binding domain (RBD) 5 and the first base of the RBD3 probe. Undesirable conditions, such as hairpin structures, homopolymer regions, dimer formation, or unfavorable annealing temperatures, were carefully avoided. The probe lengths for RBD5 and RBD3 were then adjusted from the initial 21-bp sequence to achieve melting temperature between 50 ℃ and 70 ℃ per probe (overall target 68 ℃ and 82 ℃).
Xenium library preparation  For each case, two serial sections (5 μm thick) from FFPE block were placed on a standard slide for DAB(3,3’-diaminobenzidine) staining and a Xenium slide, following the FFPE Tissue Preparation guide (10X Genomics, CG000578, Rev E). Those slides underwent a series of xylene and ethanol washes for deparaffinization. The DAB slide was incubated overnight with mouse anti-IDH1R132H antibody (1:20 dilution after heat-induced epitope retrieval; #DIA-H09, Dianova). Meanwhile, the Xenium slide was treated with decrosslinking buffer, using the FFPE tissue enhancer, as outlined (10X Genomics, CG000578, Rev E). Overnight in situ probe hybridization was performed using 266 probes from the pre-designed Xenium Human Brain Panel along with 73 additional custom probes (table S8). Following hybridization, the probes were ligated, and sample underwent rolling circle amplification. Autofluorescence was quenched using a specialized mixture, and nuclei were stained with DAPI to facilitate sample tracking and approximate cell boundary identification (10X Genomics, CG000582, Rev G).

tag: patient diagonsis

tag: tissue diagnosis

value: Normal Peritumoral tissue

tag: age

value: 42 years


title: 0_Gy

value: bone marrow

value: HSC


title: HumanBrain-PeritumoralTissue-5

description: Xenium data from CASE5

value: 61 years


title: Pdgfra.CRE_Piezo1.FL_SED#1

description: Library name: Pdgfra.CRE_Piezo1.WT_AEXd1#3

value: Muscle

value: Mesenchymal stromal cells


title: 3A3A_BACH2_g8_3d

description: HEK293T cell line


title: Mouse, OPC-ITAN, 38W, GEX, no_multiplexing

value: Idh1R132H, Trp53, Atrx, Nf1


title: HumanBrain-PeritumoralTissue-3

description: Xenium data from CASE3

value: 48 years


title: RNA_ETB2ETB4DKO_CpGA6h_01

value: FL-BMDC

value: bulk DC

value: CpG-A (6h)


title: HumanBrain-PeritumoralTissue-1

description: Xenium data from CASE1

value: 29 years


title: 3A_BACH2_g8_3d

description: HEK293T cell line


title: Pdgfra.CRE_Piezo1.FL_SED#2

description: Library name: Pdgfra.CRE_Piezo1.FL_SED#1

value: SED


title: 20mGy


title: Setd8KO_ATAC_2

city: Ikoma

first: Kanae

last: Matsuda-Ito

state: 奈良県

address: 8916-5, Takayama-cho

country: Japan

institute: Nara Institute of Science and Techn

description: Library name: Sample19

data_processing:
RNA-seq was performed with 150-bp pair-end sequencing by an Illumina HiSEqX Ten. Obtained reads were processed with fastp to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence. Processed reads were mapped to the mouse genome mm10 genome using STAR. DESeq2 package was used for differential gene expression analysis.
Sequencing reads for ATAC-seq were mapped to the mouse reference genome (mm10) from the University of California, Santa Cruz (UCSC) Genome Browser using Bowtie2 (v2.2.4). Open chromatin regions were analyzed using MACS2 software (v2.1.0.20141030) against BAM data compiled by BEDTools.
Assembly: mm10
Supplementary files format and content: bw (ATAC-seq)
Supplementary files format and content: raw counts (RNA-seq)

source_name: Retina

extract_protocol:
mRNAs were collected using a Dynabeads mRNA DIRECT Micro Kit (Invitrogen), and the purified mRNAs were subjected to cDNA library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocols. ATAC-seq was performed as previously described by Buenrostro, et al. (PMID:2559105). After transpisition reaction with transposase enzyme in Illumina Nextra DNA Preparetion Kit (#FC-121-1030).
Llibraries were prepared for sequencing following standard Illumina protocols

value: Retina

value: Retinal cells


title: HumanBrain-Tumor-Oligodendroglioma

description: Xenium data from CTRL1

source_name: IDH-mutant glioma

value: Tumor


title: Pdgfra.CRE_Piezo1.WT_AEXd1#2

description: Library name: Pdgfra.CRE_Piezo1.WT_AEXd1#1


title: M.SssI NTC_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1028
TMS_CXCR4_Pannel

data_processing:
Data were analyzed using the QIAGEN CLC Genomics Workbench (QIAGEN, Aarhus, Denmark) and if the coverage of the context was less than 10X, we assigned methylation values to "missing".
Assembly: hg38
Supplementary files format and content: Comma-delimited file includes Methylation level

extract_protocol:
To enrich the EGFP+ cells, FACS sorting was performed after 72 h and the sorted cells were subjected directly for DNA, RNA and protein extraction using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Venlo, Netherlands).
we employed QIAseq Targeted Methyl Panel technology. The primer panels to enrich these regions were designed by QIAGEN (Hilden, Germany) both for the BACH2 (258 CpGs, 33 loci, 22,768 bp) and CXCR4 (212 CpGs, 13 loci, 10,871 bp) gRNAs (Supple. Table 2). Briefly, 110 ng DNA was bisulfite converted using EpiTect Fast Bisulfite Conversion Kit according to the manufacturer’s instructions. Converted DNA fragments were attached to unique molecular identifier (UMI) and libraries were created using the QIAseq Targeted Methyl Panel protocol and were amplified for 18 cycles.

value: epithelial-like cell

value: dCas9_M.SssI, non targeted guide RNA (NTC), day3, run on CXCR4 TMS panel


title: Pdgfra.CRE_Piezo1.WT_AEXd1#1

description: Library name: Pdgfra.CRE_Piezo1.WT_SED#3


title: 3A_NTC_3d

description: HEK293T cell line


title: RYGB_CL

city: Seoul

first: Hyeonuk

last: Jeon

address: 50-1, Yonsei-ro, Seodaemun-gu

department: College of Medicine

institute: Yonsei University

description:
Library name: Sample_4
RYGB-5-9-CL

data_processing:
Raw sequencing data underwent quality assessment using FastQC. After quality control, reads were processed with Cell Ranger (v6.0.0, 10x Genomics) using the Rnor_6.0 rat reference genome. Gene expression matrices containing unique molecular identifier (UMI) counts per gene and per barcode were generated with the cellranger count pipeline.
Further analysis was performed using Seurat (v3.1.2). Cell Ranger–derived matrices were normalized with SCTransform, and datasets were integrated using SelectIntegrationFeatures, FindIntegrationAnchors, and IntegrateData. Dimensionality reduction was conducted with RunPCA and RunUMAP, and cell clustering was performed using FindNeighbors and FindClusters. Marker genes were identified by differential expression analysis across clusters and used for cluster annotation.
Assembly: Rnor_6.0
Supplementary files format and content: Tap-seperated values file and matrix file

organism: Rattus norvegicus

source_name: Common limb

extract_protocol:
Small intenstine tissue from rat was stored in the Tissue Storage Solution (miltenyi biotech, cat no. 130-100-008) at 4°C. Prior to dissociation, tissue was washed with phosphate buffered saline (PBS), and 0.2g of tissue was minced into 1–2 mm pieces.The minced tissue was then transferred into a gentleMACS C tube (miltenyi biotech, cat no. 130-093-237) containing 2.3mL of enzyme mix from the Human Tumor Dissociation Kit (miltenyi biotech, cat no. 130-095-929). Using the gentleMACS Dissociator with Heaters (miltenyi biotech, cat no. 130-096-427), the C tube was mounted upside down and processed with the 37C_h_TDK_1 program.  After termination of the program, the C tube was detached and cell suspension was sequentially passed through 70 and 30-μm strainer to separate cells from debris and undigested tissue chunks. The cell suspension was pelleted by centrifuging at 300g, 4°C, for 5 min. The supernatant was discarded, and pellet was gently resuspended in cold Ca2+ and Mg2+ free 0.04% BSA/PBS. And then, the cell suspension was counted with a LUNA-FX7™ Automated Fluorescence Cell Counter (logos biosystems) using a acridine orange (AO) and propidium iodide (PI) staining (logos biosystems, cat no. F23001).  Dead cells were removed using the Dead Cells Removal Kit (miltenyi Biotech, Cat no 130-090-101). The cell suspension was centrifuged at 300g, 4°C, for 5 min and resuspended in 100ul of Dead Cell Removal MicroBeads. The sample was mixed well and incubated for 15 min at room temperature. The labeled cell suspension was then applied to an MS columns (miltenyi biotech, cat no. 130-042-201), and the flow-through containing unlabeled live cells were collected. The MS column was washed 4 times with 500ul of 1x Binding Buffer, and all unlabeled cells were pooled and pelleted by centrifuging at 300g, 4°C, for 5 min.The resulting pellets were washed 3 times and gently resuspended in cold Ca2+ and Mg2+ free 0.04% BSA/PBS.  Finally, as described above, cell counts and viability were assessed using a LUNA-FX7™ Automated Fluorescence Cell Counter.
According to the 10x Chromium Single Cell 3’ v3.1 protocol (10x Genomics, document no. CG000315) Single Cell RNA-seq libraries were prepared using the 10x Chromium controller and Next Gem Single cell 3’ Reagent v3.1 kits (10x genomics, PN-1000123). Briefly, the cell suspension (target recovery 10,000 cells) was mixed with reverse transcription master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell G Chip (10x genomics, PN-1000120) to generate single-cell Gel Bead-in-emulsion (GEM). Poly-adenylated mRNA from single cells were uniquely barcoded and reverse-transcribed within GEM. After barcoded full-length cDNA was generated from mRNA through GEM-RT incubation, the barcoded cDNA molecules were amplified with PCR. For 3’ Gene Expression Library construction, the enriched cDNA was sequentially subjected to the enzymatic fragmentation, end-repair, A-tailing, adaptor ligation and index PCR. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). The library was sequenced using HiSeq platform (Illumina), and 150 bp paired-end reads were generated.

value: Common limb

tag: Sex

value: male

value: Sprague-Dawley

value: RYGB


title: RNA_WT_CpGA6h_01

value: Control


title: HumanBrain-Tumor-Astrocytoma

description: Xenium data from CTRL2

value: 61 years


title: SunTag NTC_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1029
TMS_CXCR4_Pannel

value: dCas9_SunTag_scFv GCN4_DNMT3A, non targeted guide RNA (NTC), day3, run on CXCR4 TMS panel


title: Pdgfra.CRE_Piezo1.WT_AEXd1#3

description: Library name: Pdgfra.CRE_Piezo1.WT_AEXd1#2

value: Muscle

value: Mesenchymal stromal cells


title: sham_jejunum

description:
Library name: Sample_1
sham-7-14-Jeju

source_name: Jejunum

value: Jejunum

value: sham


title: 3A3L NTC_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1026
TMS_CXCR4_Pannel

value: dCas9_DNMT3A_DNMT3L, non targeted guide RNA (NTC), day3, run on CXCR4 TMS panel


title: GalNAc‐Mdm2ASO_HFHC-10

description:
Library name: Sample 8
mdm2ASO_HFHC-10

data_processing:
Raw reads were mapped against the GRCm39 mouse genome assembly using STAR aligner (v2.7.10b) with the default options.
The number of reads mapped to each of genes was counted by using featureCounts of subread package (v 2.0.3). Parameters: -s 0 -p --countReadPairs -t exon -g gene_id
Assembly: GRCm39
Supplementary files format and content: csv file containing TMM values for each sample

source_name: Liver

extract_protocol:
RNA was extracted using the RNeasy mini kit (catalog #74104, Qiagen).
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library/Illumina platforms following manufacturer's protocols.

value: Liver

value: MDM2 knockdown

tag: diet

value: HFHC


title: Setd8KO_3

description: Library name: Sample15

value: Retina

value: Retinal cells


title: RYGB_AL

description:
Library name: Sample_3
RYGB-5-9-AL

source_name: Alimentary limb

value: Alimentary limb


title: WT_exe#2

description: Library name: WT_exe#2

source_name: Muscle


title: 3A3A NTC_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1025
TMS_CXCR4_Pannel

value: epithelial-like cell

value: dCas9_DNMT3A_DNMT3A, non targeted guide RNA (NTC), day3, run on CXCR4 TMS panel


title: 3A_NTC_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1030
TMS_CXCR4_Pannel

value: dCas9_DNMT3A, non targeted guide RNA (NTC), day3, run on CXCR4 TMS panel


title: Setd8KO_1

description: Library name: Sample13


title: GalNAc‐Mdm2ASO_HFHC-07

description:
Library name: Sample 6
mdm2ASO_HFHC-07