title: Pdgfra.CRE_Piezo1.WT_SED#3

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

value: SED


title: WT_exe#1

status: Public on Jan 13 2026

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description: Library name: WT_exe#1

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

source_name: Muscle

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).

tag: tissue

value: Muscle

tag: cell type

value: Mesenchymal stromal cells

tag: treatment


title: Setd8KO_ATAC_1

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: Sample18

library_source: genomic

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)

molecule: genomic DNA

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

tag: genotype


title: 3A_NTC_BACH2_g8 (Bisulfite-Seq)

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
Library name: P18201_1024
TMS_BACH2_g8_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

organism: Homo sapiens

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).
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.

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).

tag: cell line

value: epithelial-like cell

value: dCas9_DNMT3A, non targeted guide RNA (NTC), day3, run on BACH2 TMS panel


title: Pdgfra.CRE_Piezo1.WT_SED#2

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


title: Ctrl_ATAC_2

description: Library name: Sample17

value: Ctrl


title: Ctrl_ATAC_1

description: Library name: Sample16


title: sham_ileum

city: Seoul

first: Hyeonuk

last: Jeon

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

department: College of Medicine

country: South Korea

institute: Yonsei University

description:
Library name: Sample_2
sham-7-14-IL

library_source: transcriptomic single cell

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

molecule: total RNA

organism: Rattus norvegicus

source_name: Ileum

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: Ileum

tag: Sex

value: male

value: Sprague-Dawley

value: sham


title: GalNAc‐Mdm2ASO_HFHC09

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 7
mdm2ASO_HFHC-09

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: WT_sed#3

description: Library name: WT_sed#3


title: Setd8KO_2

description: Library name: Sample14


title: WT_sed#2

description: Library name: WT_sed#2


title: SunTag_NTC_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1023
TMS_BACH2_g8_Pannel

value: dCas9_SunTag_scFv GCN4_DNMT3A, non targeted guide RNA (NTC), day3, run on BACH2 TMS panel


title: Ctrl_1

description: Library name: Sample10


title: Ctrl_3

description: Library name: Sample12


title: WT_sed#1

description: Library name: WT_sed#1


title: Nes17_ATAC_2

description: Library name: Sample8

value: Retinal progenitor cells


title: GalNAc‐conASO_HFHC-04

description:
Library name: Sample 3
conASO_HFHC-04

value: WT

value: GalNAc‐conASO


title: GalNAc‐conASO_HFHC-02

description:
Library name: Sample 2
conASO_HFHC-02


title: P0 cortical neurons, miR-17-5p-Sponge 3

city: Marseille Cedex 9

first: Fanny

last: Mann

address: 163 Avenue de Luminy

country: France

institute: IBDM

description:
DESeq2_norm_count_table.xlsx
Differential expression analysis,xlsx
spg17_FACS_3

data_processing:
Alignment on mm10 (GRCm38) genome by STAR (2.7.6a) tool
Differential expression analysis by R Deseq2 (v1.30.1) package
Removal of GM and transcripts with Basemean <1000 reads
Assembly: mm10
Supplementary files format and content: Matrix file containing Deseq2 normalized counts
Supplementary files format and content: Matrix file of the differential expression analysis (base mean and log2fold change)

source_name: Brain

extract_protocol:
Total RNA was extracted with the RNeasy Micro kit (Qiagen). 50 ng of total RNA corresponding to ~ 100000 cells from ~10 brains were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Ligation following manufacturer's protocols.

treatment_protocol: Control plasmid or miR-17-5P-Sponge plasmid electroporated in utero at E15.5

value: Brain

value: cortical neurons

tag: strain background

value: Swiss (RjOrl:SWISS).

value: miR-17-5p sponge


title: GalNAc‐conASO_HFHC-01

description:
Library name: Sample 1
conASO_HFHC-01


title: P0 cortical neurons, miR-17-5p-Sponge 2

description:
DESeq2_norm_count_table.xlsx
Differential expression analysis,xlsx
spg17_FACS_2


title: M.SssI_NTC_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1022
TMS_BACH2_g8_Pannel

value: epithelial-like cell

value: dCas9_M.SssI, non targeted guide RNA (NTC), day3, run on BACH2 TMS panel


title: GalNAc‐conASO_HFHC-05

description:
Library name: Sample 4
conASO_HFHC-05


title: P0 cortical neurons, control 3

description:
DESeq2_norm_count_table.xlsx
Differential expression analysis,xlsx
cont_FACS_3

value: control plasmid


title: 3Ak_KRAB_NTC_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1021
TMS_BACH2_g8_Pannel

value: dCas9_DNMT3A_KRAB, non targeted guide RNA (NTC), day3, run on BACH2 TMS panel


title: GalNAc‐Mdm2ASO_HFHC-06

description:
Library name: Sample 5
mdm2ASO_HFHC-06


title: B12, PFF injected_D75

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
Sequencing data in FASTQ format were aligned to the reference genome (refdata-gex-mm10-2020-A) using Space Ranger software (10X Genomics, version 1.3.0).
Assembly: mm10
Supplementary files format and content: tar archive including matrix and imaging files in output of SpaceRanger
Library strategy: Spatial transcriptomics

extract_protocol:
Fresh frozen cryosections (10µm thickness) of sagittal brain hemisections were cut and mounted on 10X Visium spatially bar coded slides. Tissue permeabilization, RNA extraction and second strand synthesis for bar coded cDNA library construction was performed according to the instructions in 10X Genomics Visium Kit PN-1000189
Spatial RNA-seq libraries were prepared according to the manufacturer's guidelines (Visium, 10x Genomics). Resulting libraries were pooled and sequenced on an MGI G400 sequencer, followed by de-multiplexing using the library index sequences.

value: Transgenic M83+/+ mice [B6; C3-Tg(Prnp-SNCA*A53T)83Vle/J]

value: PFF injected_D75


title: Nes17_ATAC_1

description: Library name: Sample7

value: Retina


title: Nes14_ATAC_2

description: Library name: Sample6


title: Nes17_1

description: Library name: Sample3


title: Ctrl_2

description: Library name: Sample11

value: Retinal cells

value: Ctrl


title: B11, PFF injected_D75


title: 3A_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1015
TMS_CXCR4_Pannel

value: dCas9_DNMT3A, CXCR4 targeted guide RNA8 ,day3


title: 3Akr NTC_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1027
TMS_CXCR4_Pannel

value: dCas9_DNMT3A_KRAB, non targeted guide RNA (NTC), day3, run on CXCR4 TMS panel


title: WT_exe#3

description: Library name: WT_exe#3

value: Muscle

value: Mesenchymal stromal cells


title: Nes17_2

description: Library name: Sample4

value: Retinal progenitor cells


title: P0 cortical neurons, miR-17-5p-Sponge 1

description:
DESeq2_norm_count_table.xlsx
Differential expression analysis,xlsx
spg17_FACS_1

value: Brain

value: cortical neurons

value: WT


title: Nes14_ATAC_1

description: Library name: Sample5


title: d3A_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1016
TMS_CXCR4_Pannel

value: epithelial-like cell

value: dCas9_dDNMT3A, CXCR4 targeted guide RNA8 ,day3


title: Nes14_1

description: Library name: Sample1


title: M.SssI_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1013
TMS_CXCR4_Pannel

value: dCas9_M.SssI, CXCR4 targeted guide RNA8 ,day3


title: 3A3A_NTC_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1019
TMS_BACH2_g8_Pannel

value: dCas9_DNMT3A_DNMT3A, non targeted guide RNA (NTC) , day3, run on BACH2 TMS panel


title: P0 cortical neurons, control 2

description:
DESeq2_norm_count_table.xlsx
Differential expression analysis,xlsx
cont_FACS_2

value: Swiss (RjOrl:SWISS).

value: control plasmid


title: B10, PFF injected_D75

value: Transgenic M83+/+ mice [B6; C3-Tg(Prnp-SNCA*A53T)83Vle/J]

value: PFF injected_D75


title: Lipofectamin_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1017
TMS_CXCR4_Pannel

value: Lipofectamin, CXCR4 targeted guide RNA8 ,day3


title: SunTag_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1014
TMS_CXCR4_Pannel

value: dCas9_SunTag_scFv GCN4_DNMT3A, CXCR4 targeted guide RNA8 ,day3


title: 3A3L_NTC_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1020
TMS_BACH2_g8_Pannel

value: dCas9_DNMT3A_DNMT3L, non targeted guide RNA (NTC), day3, run on BACH2 TMS panel


title: Non-transfected_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1018
TMS_CXCR4_Pannel

value: Non-transfected,  CXCR4 targeted guide RNA8 ,day3


title: 3A_KRAB_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1012
TMS_CXCR4_Pannel

value: dCas9_DNMT3A_KRAB, CXCR4 targeted guide RNA8 ,day3


title: P0 cortical neurons, control 1

description:
DESeq2_norm_count_table.xlsx
Differential expression analysis,xlsx
cont_FACS_1


title: B6, PFF injected_D45

value: PFF injected_D45


title: Nes14_2

description: Library name: Sample2

value: Retina

value: Retinal progenitor cells


title: Paternal-PN

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

country: China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

data_processing:
Raw reads were first processed by fastp(version 0.20.1) to filter out low quality reads and remove sequencing adapters. Then, clean reads were aligned to the mm10 genome using hisat2 (version 2.2.1) with the parameters -X 2000 --very-sensitive --no-spliced-alignment. All unmapped reads, non-uniquely mapped reads, mitochondrial reads and PCR duplicates were removed. Peak calling was performed using MACS2(version 2.2.6),and blacklisted regions were excluded. The BED interval of the fragment is obtained by adjusting the BAM alignment interval of the sequenced read-pair using sinto (version 0.8.0). Quality metrics including mapping rate, unique fragments, fraction reads in peak, reads in mitochondrial genome and reads in sexual chromosome were generated by custom python scripts. Pesudobulk samples of each development stages or cell types were obtained by merging the bam files of the group. Peak calling was performed using MACS2 (version 2.2.6),and blacklisted regions were excluded. For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads (RPKM) with 100 bp bin size to generate signal tracks using bamCoverage in deeptools (version 3.5.4). A count matrix over the union of peaks was generated by counting the number of reads from individual cells that overlap the union peaks using coverageBed from the bedtools(version 2.26.0). To analyzing repetitive elements, featureCounts (version 2.0.1) were used to quantify aligned reads on repetitive loci (RepeatMasker defined track was download as GTF format files from UCSC Table Browser), and the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads (RPKM).
Assembly: mm10
Supplementary files format and content: CellRanger format files: barcodes.tsv.gz,genes.tsv.gz,matrix.mtx.gz
Supplementary files format and content: Fragments file: fragment_file.tsv.gz;fragment_file.tsv.gz.tbi

source_name: pre-implantation embryos

growth_protocol: mESCs were cultured with feeders in mESC medium containing 83% high-glucose DMEM (Hyclone), 15% fetal bovine serum (FBS, Gibco), Glutamax (Gibco, 100 ×), NEAA (non-essential amino acids, Gibco, 100 ×), β-mercaptoethanol (Sigma-Aldrich), 3 μM CHIR99021 (Stemgent), 1 μM PD0325901 (Stemgent), and 1000 U/mL leukemia inhibitory factor (LIF) (Millipore).

extract_protocol:
The ULI-scATAC-seq libraries of mESCs, oocytes, and early mouse embryos were prepared by modifying a previously described plate-based scATAC-seq. Briefly, the tagmentation mix (33 mM Tris-acetate, pH 7.8, 66 mM potassium acetate, 10 mM magnesium acetate, 16% dimethylformamide, 0.01% digitonin and 25% of Tn5 from the TruePrep kit from Vazyme, TD501-02) was prepared as microdroplets in a 60-mm culture dish and overlaid with mineral oil to prevent evaporation. Samples of cells or nuclei were transferred into a microdroplet with the aid of a micromanipulator. The tagmentation reaction was carried out in an incubator at 37 ℃ for 30 min, and the samples were then transferred into a fresh microdroplet for another 30 min of incubation. Typically, about 20 cells/nuclei reacted in a 0.1 μL microdroplets but the volume could be scaled up flexibly as needed. The reaction was stopped by adding equal volume of tagmentation stop buffer (10 mM Tris-HCl, pH 8.0, 20 mM EDTA, pH 8.0) and left on ice for 10 min. Single cell/nucleus was picked using a hand-held pipette and transferred into a PCR tube containing 2 μL 2 × lysis buffer (100 mM Tris-HCl, pH 8.0, 100 mM NaCl, 40 μg/mL Proteinase K, 0.4% SDS), 1.2 μL H2O (Takara, 9012), 0.8 μL of 10 μM Nextera Index Primer Mix (0.4 μL each), and incubated at 65 ℃ for 15 min to release Tn5. 4 μL of 10% Tween-20 was added to quench SDS.
The above mixture was combined with 10 μL PCR mix (NEB, M0541L) and 2 μL H2O for library fragment amplification (PCR conditions: 72 °C for 5 min; 98 °C for 5 min; then 18 cycles of (98 °C for 10 s, 63 °C for 30 s, and 72 °C for 20 s); followed by 4 °C hold). Subsequently, purification (VAHTS DNA Clean Beads, N411-02) and qubit quantification (Vazyme Biotech, EQ111-01) were carried out. The libraries were mixed and subjected to sequencing using Illumina HiSeq X platform (Annoroad Gene Technology Corporation).

value: pre-implantation embryos

value: PPN


title: NIH/3T3, GFP control, biological replicate#3

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: 3T3_ctrl_3

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.

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

value: GFP-control expression


title: B8, PFF injected_D45

value: Brain


title: 3A3L_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1011
TMS_CXCR4_Pannel

value: epithelial-like cell

value: dCas9_DNMT3A_DNMT3L, CXCR4 targeted guide RNA8 ,day3


title: NIH/3T3, GFP control, biological replicate#2

description: Library name: 3T3_ctrl_2


title: maternal-PN

value: MPN


title: PN

value: PN


title: 3A3A_CXCR4 (Bisulfite-Seq)

description:
Library name: P18201_1010
TMS_CXCR4_Pannel

value: dCas9_DNMT3A_DNMT3A, CXCR4 targeted guide RNA8 ,day3


title: B7, PFF injected_D45

value: Transgenic M83+/+ mice [B6; C3-Tg(Prnp-SNCA*A53T)83Vle/J]


title: NIH/3T3, GFP control, biological replicate#1

description: Library name: 3T3_ctrl_1


title: NIH/3T3, EML4-ALK expression, biological replicate#3

description: Library name: 3T3_EML4-ALK_3

value: EML4-ALK expression


title: B3, PBS injected_D75

value: PBS injected_D75


title: Non-transfected_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1009
TMS_BACH2_g8_Pannel

value: Non-transfected,  BACH2 targeted guide RNA8 ,day3


title: NIH/3T3, EML4-ALK expression, biological replicate#2

description: Library name: 3T3_EML4-ALK_2


title: B4, PBS injected_D75


title: Lipofectamin_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1008
TMS_BACH2_g8_Pannel

value: Lipofectamin, BACH2 targeted guide RNA8 ,day3


title: lateral septum,rep 2

city: ChongQing

first: Mingrui

last: Xu

address: Xinqiao

institute: Second Affiliated Hospital of Army Medical University

data_processing:
Raw sequencing reads were filtered and demultiplexed using PISA (https://github.com/shiquan/PISA). Reads were aligned to the GRCm38 mouse genome using STAR (v2.7.4a) and sorted by Sambamba (v0.7.0)
Cell clustering was performed using the Seurat (v4.1.0) R toolkit (https://github.com/satijalab/seurat). Qualified cells were filtered according to number of detected genes (between 500 and 6 500) and percentage of mitochondrial genes (< 0.1%). Genes expressed in < 3 cells were removed. The filtered dataset was log-normalized and scaled, and principal component analysis (PCA) was conducted. The first 18 PCs were used for graph-based clustering in Seurat using the Louvain algorithm. Non-neuronal clusters were identified by expression of Pdgfra, Oligo1, Mki67, Slc1a3, Mal, C1qa, Foxj1, and Cldn5 (Supplementary Fig. 1). A cluster with high mitochondrial gene expression and low detected genes was removed (data not shown). Neuronal cells were then clustered and processed as described above. Analysis of differentially expressed genes (DEGs) in all neuronal clusters was performed using the FindAllMarkers function in Seurat. Fold-changes and p-values of gene expression between SST+ and Calb1+ clusters were calculated using the FindMarkers function with the MAST algorithm
Assembly: GRCm38
Supplementary files format and content: fq.gz files are DNBSEQ-G400 platform raw data, others are processed data

extract_protocol:
The lateral septum tissue of male C57BL/6 mice at 2-month old were taken for single cell RNA-seq
Briefly, the single-nucleus suspensions were converted to barcoded libraries using droplet generation, emulsion breakage, bead collection, reverse transcription, cDNA amplification, and purification. Indexed sequencing libraries were constructed according to the manufacturer’s protocols. Sequencing library quality was evaluated using a QubitTM ssDNA Assay Kit (#Q10212; Thermo Fisher Scientific, USA). Libraries were sequenced using an ultra-high-throughput DIPSEQ T1 sequencer with the following strategy: 30 bp for read 1, inclusive of 10 bp cell barcode 1, 10 bp cell barcode 2, and 10 bp unique molecular identifier (UMI), 100 bp of transcript sequence for read 2, and 10 bp for sample index.


title: MII-oocyte

source_name: oocytes

value: oocytes

value: MII


title: lateral septum,rep 3


title: NIH/3T3, CBX3::ALK expression, biological replicate#3

description: Library name: 3T3_CBX3-ALK_3

value: CBX3::ALK expression


title: d3A_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1007
TMS_BACH2_g8_Pannel

value: dCas9_dDNMT3A, BACH2 targeted guide RNA8 ,day3


title: 3A_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1006
TMS_BACH2_g8_Pannel

value: dCas9_DNMT3A, BACH2 targeted guide RNA8 ,day3


title: MI-oocyte

value: MI


title: NIH/3T3, EML4-ALK expression, biological replicate#1

description: Library name: 3T3_EML4-ALK_1


title: NIH/3T3, CBX3::ALK expression, biological replicate#2

description: Library name: 3T3_CBX3-ALK_2


title: BS-Nano - mESC treated with DNMTi rep3

city: Cambridge

first: Bongmin

last: Bae

address: 16 Divinity Ave

institute: Harvard University

description: Library name: BS-Nano_DNMTi_3

library_source: other

data_processing:
Fastq files were mapped to Cast SNP masked and CT converted mouse GRCm39 genome using minimap2. Reads were split according to SNPs to phase reads originated from maternal vs paternal allele. For each allele, CpG methylation percentage was calculated.
Assembly: GRCm39
Supplementary files format and content: CpG methylation percentage

molecule: other

source_name: F1.2-3 mESC

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.

extract_protocol:
Cells were resuspended in 300 μL cell lysis buffer (0.1 M Tris pH 8, 0.2 M NaCl, 5 mM EDTA, 0.1% SDS, and 10 units/mL Proteinase K) and incubated at 50 °C 1h to overnight. gDNA was precipitated with 600 μL of 100% isopropanol and incubated at -20 °C for 2 hours before centrifuging at 12,000 xg for 15 minutes. The supernatant was carefully discarded, and the remaining pellet was washed with 500 μL of 70% ethanol. Samples were again centrifuged at 12,000 xg for 15 minutes, supernatant was discarded, and the pellet was resuspended in 50 μL of water.
Bisulfite treatment was performed using EpiTect Fast DNA Bisulfite kit (Qiagen 59824) following manufacturer’s instruction. Bisulfite converted DNA was eluted in 15 μL of water. Target fragment was PCR amplified using EpiMark Hot Start Taq (NEB). 1.5 μL of eluted DNA was used for each reaction. PCR was performed at 95 °C 30 sec / 45X 95 °C 30 sec 45 °C 30 sec 68 °C 30 sec / 68 °C 5 min using bisulfite conversion-aware primers. PCR product was gel purified and pooled for sequencing at Plasmidsaurus using Premium PCR sequencing service.

value: F1.2-3 mESC


title: GV-oocyte

value: GV


title: SunTag_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1005
TMS_BACH2_g8_Pannel

value: epithelial-like cell

value: dCas9_SunTag_scFv GCN4_DNMT3A, BACH2 targeted guide RNA8 ,day3


title: Pool_Bulge_2

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: NR9

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: in vitro slicing assay

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).

tag: pirna target_pool

value: Bulge

value: in vitro slicing assay

tag: mapped to


title: mESC

source_name: mESCs

value: mESCs

value: ESC


title: lateral septum,rep 1

value: Brain


title: BS-Nano - mESC treated with DNMTi rep1

description: Library name: BS-Nano_DNMTi_1


title: BS-Nano - mESC treated with DNMTi rep2

description: Library name: BS-Nano_DNMTi_2


title: M.SssI_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1004
TMS_BACH2_g8_Pannel

value: dCas9_M.SssI, BACH2 targeted guide RNA8 ,day3


title: 3A_KRAB_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1003
TMS_BACH2_g8_Pannel

value: dCas9_DNMT3A_KRAB, BACH2 targeted guide RNA8 ,day3


title: NIH/3T3, CBX3::ALK expression, biological replicate#1

description: Library name: 3T3_CBX3-ALK_1


title: Pool_Bulge_1

description: Library name: NR8


title: BS-Nano - mESC treated with DMSO rep3

description: Library name: BS-Nano_DMSO_3

value: DMSO


title: Blastocyst

value: pre-implantation embryos

value: Blastocyst


title: 8-cell stage


title: Pool_Perfect_2

description: Library name: NR7

value: Perfect


title: BS-Nano - mESC treated with DMSO rep2

description: Library name: BS-Nano_DMSO_2


title: 207339140089_R02C01

status: Public on Jan 12 2026

type: genomic

city: Chicago

first: Drew

last: Duckett

state: IL

address: 541 N Fairbanks Ct, 8th Floor

department: Pathology

institute: Northwestern Medicine

description: SAMPLE 185

hyb_protocol: MethylationEPIC beadarrays were performed according to the Infinium HD Methylation Assay Protocol, as previously described with minor changes. Eight µl of restored FFPE bs-DNA was used for each sample and 28 µl of hybridization volume was used when loading the microarray.

scan_protocol: Samples were scanned using Illumina's iScan according to manufacturer's recommendations for infinuim arrays

data_processing:
Bioconductor (Version 3.17) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
matrix processed value definition: Average Beta

label: biotin/DNP

source_name: Brain Tumor

label_protocol: Bisulfite conversion: Samples ranging from 50 ng to 500 ng of FFPE DNA was pipetted into strip tubes and processed using the EZ-96 DNA Methylation kit (Zymo Research Corp., CA, USA) following the manufacturer's recommendations for Infinium assays.

extract_protocol: Samples included in the study were all formalin-fixed for 8 hours followed by paraffin-embedding (FFPE) and stored at room temperature. All samples were extracted using either Covaris (FFPE DNA Kit, Covaris, Inc., MA, USA) or Purigen Biosystems (FFPE DNA Kit, Purigen Biosystems, CA, USA) following the manufacturer’s instructions.

tag: tissue type

value: FFPE

value: meningioma

tag: who grade

tag: choudhury class

value: Immune Enriched

tag: kmeans cluster

value: F


title: 207339140089_R03C01

description: SAMPLE 186

value: Merlin Intact


title: 4-cell stage


title: Math1 Neurons, Precrossing

city: Toledo

first: Bhakti

middle: Ajit

last: Khot

state: Ohio

address: 3050 W Towerview Blvd, Wolfe Hall Room 3238

department: Dept of Molecular, Cellular & Developmental Biology

institute: University of Toledo

description: Library name: Pre_miRNA

data_processing:
Illumina bcl2fastq 2.20 software.
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software
Raw sequence reads were quality and adapter trimmed using Trimmomatic (v0.30)
The trimmed reads with a length of 18 to 32 bp were retained. These trimmed reads were compared to, and annotated with small RNA database (miRbase 22).
Assembly: Gallus_gallus.GRCg6a.106.gff3
Supplementary files format and content: Processed excel file contains list of miRNAs with mature and precursor sequence, Chromosome location, Raw read counts

organism: Gallus gallus

source_name: Embryonic spinal cord

extract_protocol:
RNA was isolated using Pure Link RNA Mini and mirVana miRNA isolation kit
RNA quality was tested and RNA library preparation by performed using NEB Small RNA library Prep Kit according to manufacturers instructions by Azenta

value: Embryonic spinal cord

value: Commissural Neurons

value: Wild Type


title: 2-cell stage


title: Pool_Perfect_1

description: Library name: NR6

value: in vitro slicing assay


title: 207339140050_R06C01

description: SAMPLE 182


title: Morula

value: Morula


title: 3A3A_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1001
TMS_BACH2_g8_Pannel

value: epithelial-like cell

value: dCas9_DNMT3A_DNMT3A, BACH2 targeted guide RNA8 ,day3


title: 207339140065_R08C01

description: SAMPLE 184


title: 207339130057_R07C01

description: SAMPLE 179

value: Hypermitotic


title: BS-Nano - mESC treated with DMSO rep1

description: Library name: BS-Nano_DMSO_1

value: F1.2-3 mESC

value: DMSO


title: 207339140050_R02C01

description: SAMPLE 181

value: M


title: 3A3L_BACH2_g8 (Bisulfite-Seq)

description:
Library name: P18201_1002
TMS_BACH2_g8_Pannel

value: dCas9_DNMT3A_DNMT3L, BACH2 targeted guide RNA8 ,day3


title: 207339130056_R01C01

description: SAMPLE 178

value: FFPE


title: 207339140065_R06C01

description: SAMPLE 183

value: meningioma


title: 207339130047_R08C01

description: SAMPLE 176


title: 207339130094_R07C01

description: SAMPLE 180


title: 207339130047_R02C01

description: SAMPLE 174


title: 207339130032_R05C01

description: SAMPLE 171


title: 207339130042_R05C01

description: SAMPLE 173

value: Immune Enriched


title: 207339130032_R06C01

description: SAMPLE 172

value: F


title: 207339130014_R04C01

description: SAMPLE 168


title: 207339130053_R01C01

description: SAMPLE 177

value: Merlin Intact


title: 207339130047_R07C01

description: SAMPLE 175


title: 207339130014_R08C01

description: SAMPLE 169


title: 207339130007_R05C01

description: SAMPLE 167


title: 207339130007_R04C01

description: SAMPLE 166


title: 207339130007_R01C01

description: SAMPLE 164


title: 207339130018_R06C01

description: SAMPLE 170


title: 207257770140_R03C01

description: SAMPLE 158


title: 207335100104_R02C01

description: SAMPLE 163


title: 207257770092_R08C01

description: SAMPLE 153


title: 207257770092_R06C01

description: SAMPLE 152


title: 207257770091_R03C01

description: SAMPLE 149


title: 207257770126_R04C01

description: SAMPLE 156


title: 207255330145_R03C01

description: SAMPLE 146


title: 207335100072_R02C01

description: SAMPLE 161


title: 207335100040_R07C01

description: SAMPLE 160


title: 207255330120_R06C01

description: SAMPLE 145


title: 207255330096_R04C01

description: SAMPLE 140


title: 207255330120_R01C01

description: SAMPLE 143


title: 207335100093_R01C01

description: SAMPLE 162


title: 207257770091_R01C01

description: SAMPLE 148


title: 207255330056_R07C01

description: SAMPLE 136


title: 207257770092_R02C01

description: SAMPLE 150


title: 207257770092_R03C01

description: SAMPLE 151


title: 207257770016_R08C01

description: SAMPLE 147


title: 207335100027_R03C01

description: SAMPLE 159


title: 207255330107_R03C01

description: SAMPLE 141


title: 207255330095_R03C01

description: SAMPLE 139


title: 206993480042_R05C01

description: SAMPLE 131


title: 207255330095_R02C01

description: SAMPLE 138


title: 207255330056_R02C01

description: SAMPLE 135


title: 207257770108_R02C01

description: SAMPLE 154


title: 207257770129_R08C01

description: SAMPLE 157


title: 207339130007_R03C01

description: SAMPLE 165


title: 207257770109_R05C01

description: SAMPLE 155


title: 206993480026_R01C01

description: SAMPLE 127


title: 207255330055_R08C01

description: SAMPLE 134


title: 208762960035_R01C01

hyb_protocol: Methylation EPICv2 beadarrays were performed according to the Infinium HD Methylation Assay Protocol, as previously described with minor changes. Eight µl of restored FFPE bs-DNA was used for each sample and 28 µl of hybridization volume was used when loading the microarray.


title: 207255330115_R01C01

description: SAMPLE 142


title: 207255330094_R01C01

description: SAMPLE 137


title: 206993480040_R04C01

description: SAMPLE 130


title: 208762960034_R07C01


title: 206993480007_R01C01

description: SAMPLE 125


title: 208762960034_R06C01


title: 207255330055_R05C01

description: SAMPLE 133


title: 206993480026_R07C01

description: SAMPLE 129


title: 207255330120_R02C01

description: SAMPLE 144


title: 206993480026_R02C01

description: SAMPLE 128


title: 206972290022_R05C01

description: SAMPLE 123


title: 206993480042_R06C01

description: SAMPLE 132


title: 208168230071_R02C01


title: 206972290133_R01C01

description: SAMPLE 124


title: 206972290022_R04C01

description: SAMPLE 122


title: 206972290001_R03C01

description: SAMPLE 121


title: 208166650084_R07C01


title: 208166650084_R03C01


title: 206949980035_R02C01

description: SAMPLE 118


title: 206966340003_R06C01

description: SAMPLE 119


title: 206993480007_R04C01

description: SAMPLE 126


title: 208762960035_R03C01


title: 208166650125_R06C01


title: 208762960034_R08C01


title: 208025840095_R07C01


title: 206915420047_R04C01

description: SAMPLE 114


title: 208762960035_R02C01


title: 208034710010_R01C01


title: 208034710031_R01C01


title: 208168230070_R01C01


title: 206909170093_R05C01

description: SAMPLE 112


title: 206966340113_R01C01

description: SAMPLE 120


title: 206915410081_R05C01

description: SAMPLE 113


title: 206909170093_R03C01

description: SAMPLE 111


title: 208025840072_R02C01


title: 207882990042_R05C01


title: 206917400007_R04C01

description: SAMPLE 116


title: 208025840072_R01C01


title: 208166650020_R04C01


title: 206915420047_R07C01

description: SAMPLE 115


title: 208025840074_R06C01


title: 206772660152_R01C01

description: SAMPLE 107


title: 207690200148_R02C01


title: 208034710010_R06C01


title: 207827480069_R04C01


title: 207690200124_R04C01


title: 206917400012_R05C01

description: SAMPLE 117


title: 206772660105_R03C01

description: SAMPLE 106


title: 207882990042_R08C01


title: 207882990004_R02C01


title: 206909170026_R05C01

description: SAMPLE 110


title: 207882990004_R03C01


title: 206648960146_R01C01

description: SAMPLE 97


title: 207690200045_R03C01


title: 207687880095_R04C01


title: 207687880095_R01C01


title: 206772660105_R02C01

description: SAMPLE 105


title: 206839580143_R01C01

description: SAMPLE 109


title: 206772660104_R04C01

description: SAMPLE 103


title: 206648960113_R02C01

description: SAMPLE 95


title: 206839580129_R07C01

description: SAMPLE 108


title: 206772660104_R08C01

description: SAMPLE 104


title: 206522580083_R06C01

description: SAMPLE 93


title: 207690200141_R03C01


title: 207690200026_R02C01


title: 206648960168_R08C01

description: SAMPLE 100


title: 207500650103_R06C01


title: PAO1ΔphaF_pEV replicate C

first: Simon

last: Dove

state: Massachusetts

address: Boston Childrens Hospital, 300 Longwood Avenue EN761.1

department: Infectious Diseases

institute: Boston Children's Hospital

description: Library name: Sample 9C

data_processing:
fastq records trimming (cutadapt 2.10)
bigwig file generation (deepTools version 3.5.1)
Assembly: Pseudomonas aeruginosa PAO1: NC_002516.2
Supplementary files format and content: Bigwig format

organism: Pseudomonas aeruginosa

source_name: PAO1 with phaF deletion

growth_protocol: Bacterial strains were grown with aeration at 37˚C , shaking at 200 rpm, in LB medium

extract_protocol:
TRI Reagent was used for RNA extraction
Final libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015)

treatment_protocol: Cells were harvested by centrifugation, washed with PBS, UV crosslinked and pellets stored at -80˚C.

tag: strain

value: PAO1 with phaF deletion

value: PAO1 with phaF deletion (pEV)

value: Growth:OD ≈ 2.0 in LB


title: 207690200013_R01C01


title: 206648960178_R02C01

description: SAMPLE 102


title: 206522580056_R01C01

description: SAMPLE 90


title: 206522580061_R06C01

description: SAMPLE 91


title: PAO1ΔphaF_pEV replicate A

description: Library name: Sample 9A


title: 206522580083_R07C01

description: SAMPLE 94


title: 206648960146_R03C01

description: SAMPLE 98


title: PAO1_pEV replicate C

description: Library name: Sample 8C

value: WT (pEV)


title: 206648960118_R03C01

description: SAMPLE 96


title: 207690200124_R05C01


title: 206648960178_R01C01

description: SAMPLE 101


title: 207690200021_R06C01


title: PAO1-PhaF-V_Tot replicate C

description: Library name: Sample 7C

value: phaF-VSVG


title: 206522570159_R04C01

description: SAMPLE 86


title: 206648960153_R08C01

description: SAMPLE 99


title: 206522580039_R02C01

description: SAMPLE 87


title: PAO1ΔphaF_pEV replicate B

description: Library name: Sample 9B


title: 207687880089_R05C01


title: 206439840001_R08C01

description: SAMPLE 83


title: PAO1_pEV replicate B

description: Library name: Sample 8B


title: 206522580061_R08C01

description: SAMPLE 92


title: 206439840003_R02C01

description: SAMPLE 84


title: 206522580045_R04C01

description: SAMPLE 89


title: artery, control group, 30 days after surgery4, bio rep 4

city: Beijing

first: Fei

address: Room 421, Building 5

institute: Beihang University

description: Library name: L30_4

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
Assembly: The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Supplementary files format and content: To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.    RSEM was used to quantify gene abundances.    Essentially, differential expression analysis was performed using the DESeq2 or DEGseq.    DEGs with log2FC1 and FDR< 0.05(DESeq2) or FDR < 0.001(DEGseq) were considered to be significantly different expressed genes.

organism: Oryctolagus cuniculus

source_name: artery

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer's instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).Only high-quality RNA sample [OD260/280=1.8~2.2,OD260/230>2.0,RQN>6.5,28S:18S21.0, >1ug OR OD260/280-1.8-2.2, RIN>6.5,>10ng ]was used to construct sequencing library.
The sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeqReagent Kit.

value: artery

value: HASMC

value: common carotid artery

value: tissue

value: transplatation


title: vein, control, unoperated2,bio rep 2

description: Library name: V3

source_name: vein

value: vein

value: external jugular vein


title: 206439840001_R01C01

description: SAMPLE 81

value: FFPE


title: PAO1_pEV replicate A

description: Library name: Sample 8A


title: 206430120150_R01C01

description: SAMPLE 79

value: meningioma


title: artery, experimental group, 14 days after surgery4,bio rep 4

description: Library name: R14_4


title: 206430120150_R04C01

description: SAMPLE 80

value: Immune Enriched


title: 206467000126_R01C01

description: SAMPLE 85

value: M


title: PAO1-PhaF-V_Tot replicate B

description: Library name: Sample 7B


title: vein, control, unoperated1, bio rep 1

description: Library name: V2


title: 207687880090_R02C01


title: vein, control, unoperated4,bio rep 4

description: Library name: V1


title: artery, control group, 30 days after surgery3,bio rep 3

description: Library name: L30_3


title: PAO1-PhaF-V_Tot replicate A

description: Library name: Sample 7A


title: vein, control, unoperated3,bio rep 3

description: Library name: V4


title: 206430120128_R01C01

description: SAMPLE 78

value: F


title: artery, control group, 30 days after surgery2,bio rep 2

description: Library name: L30_2


title: 206522580044_R07C01

description: SAMPLE 88

value: Hypermitotic


title: 206430120091_R04C01

description: SAMPLE 77


title: artery, control group, 30 days after surgery1,bio rep 1

description: Library name: L30_1


title: 206430120076_R04C01

description: SAMPLE 74


title: artery, experimental group, 30 days after surgery4,bio rep 4

description: Library name: R30_4


title: 206439840001_R03C01

description: SAMPLE 82


title: 206430120074_R05C01

description: SAMPLE 73


title: 206430120091_R02C01

description: SAMPLE 76


title: artery, control group, 14 days after surgery2,bio rep 2

description: Library name: L14_2


title: artery, control group, 14 days after surgery1, bio rep 1

description: Library name: L14_1


title: 206144420134_R02C01

description: SAMPLE 64


title: artery, control group, 14 days after surgery4,bio rep 4

description: Library name: L14_4


title: 206430120011_R04C01

description: SAMPLE 70

value: Merlin Intact


title: 206144420134_R03C01

description: SAMPLE 65


title: artery, experimental group,14 days after surgery2,bio rep 2

description: Library name: R14_2


title: 206430120051_R07C01

description: SAMPLE 72


title: 206430120089_R01C01

description: SAMPLE 75


title: 206430120033_R01C01

description: SAMPLE 71


title: 206144420134_R06C01

description: SAMPLE 66


title: 206144420135_R02C01

description: SAMPLE 68


title: 206144080088_R02C01

description: SAMPLE 62


title: MP13, LB, biol rep 2

city: Edmonton

first: Kat

last: Pick

address: 116 St & 85 Ave NW

country: Canada

institute: University of Alberta

description: Library name: MP13_LB2

data_processing:
Demultiplexing, quality control, and adapter trimming was performed by SeqCenter using bcl-convert (v4.1.5)
Reads were trimmed with fastp (v0.23.4) (parameters: --cut_front --cut_tail, --length_required 75, --overrepresentation_analysis)
Trimmed reads were mapped to the reference genome with botwie2 (v2.5.3), then converted from .sam to .bam using samtools sort (v1.19.2)
Raw counts were generated with featureCounts (v2.0.6) (parameters: -p, -s 2)
Lowly expressed genes were filtered out using edgeR (v3.40.2) filterByExpr command
After filtering lowly expressed genes, library sizes were calculated and samples were normalized using edgeR (v3.40.2) calcNormFactors command (with default TMM normalization)
Counts per million (cpm) values were calculated using edgeR (v3.40.2) cpm command
Assembly: NCBI genome assembly ASM3426537v1
Supplementary files format and content: tab delimited text file containing raw counts for all Samples (from featureCounts)
Supplementary files format and content: csv file containing normalized cpm values for expressed genes for all Samples (from edgeR)

organism: Escherichia coli MP1

extract_protocol:
Total RNA extraction was performed with the Biosearch MasterPure Complete DNA and RNA Purification Kit, following the manufacturers protocol with the following modifications: cells were washed twice in PBS prior to lysis, and the DNAse treatment step was performed twice.
Library preparation was performed by SeqCenter. RNA samples were DNAse treated (Invitrogen RNAse free DNAse), then libraries were prepared using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: Overnight cultures grown in LB were sub-cultured into either LB or simulated intestinal fluid and grown until mid-log phase (OD600 ~0.4)

value: WT

value: LB

tag: biological replicate


title: MP13, simulated intestinal fluid, biol rep 2

description: Library name: MP13_SIF2

value: simulated intestinal fluid


title: artery, control group, 14 days after surgery3,bio rep 3

description: Library name: L14_3

value: artery


title: MP13, LB, biol rep 1

description: Library name: MP13_LB1


title: 206119350094_R04C01

description: SAMPLE 60


title: 206119350029_R04C01

description: SAMPLE 58


title: KP7, simulated intestinal fluid, biol rep 1

description: Library name: KP7_SIF1


title: artery, experimental group, 14 days after surgery3, bio rep 3

description: Library name: R14_3

value: HASMC


title: artery, experimental group, 30 days after surgery1,bio rep 1

description: Library name: R30_1

value: common carotid artery


title: 206116800045_R07C01

description: SAMPLE 56


title: KP7, LB, biol rep 1

description: Library name: KP7_LB1


title: MP13, simulated intestinal fluid, biol rep 1

description: Library name: MP13_SIF1


title: 206430120001_R02C01

description: SAMPLE 69


title: 206144420073_R04C01

description: SAMPLE 63


title: 206144420134_R07C01

description: SAMPLE 67


title: KP7, simulated intestinal fluid, biol rep 2

description: Library name: KP7_SIF2


title: 206119350094_R03C01

description: SAMPLE 59


title: artery, experimental group, 14 days after surgery，bio rep 1

description: Library name: R14_1

value: tissue


title: KP7, LB, biol rep 2

description: Library name: KP7_LB2


title: 206116800124_R04C01

description: SAMPLE 57


title: 206144080057_R02C01

description: SAMPLE 61


title: wounding 120 min systemic leaf, small RNA

city: Taipei 106319

first: Shih-Tong

last: Jeng

state: Taipei

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

institute: National Taiwan University

description:
Library name: WT+2S_sRNA
column name in sRNA_processed.tsv: "WT+2S", "TP2M_WT+2S"

data_processing:
Sequences were trimmed for TruSeq universal and indexed adapter, and low-quality sequences were removed (QV<20) with CLC Genomics Workbench v9.5.
Assembled transcript read counts were extracted and normalized with RPKM using CLC Genomics Workbench. Trimmed sRNA read counts were calculated and normalized with TP2M.
Trimmed transcriptome sequences were subject to de novo assembly using Trinity v2.0.6 and contig clustering using CD-HIT v4.6. Assembled contig sequences were blasted with the NCBI database using NCBI BLAST+ v2.2.28 (BlastN) and FastAnnotator (BlastX).
Trimmed sRNA sequences were annotated using SHRiMP v2.2.3 against miRbase (Release 21).
Assembly: de novo assembly, FASTA available on series record: Contig_cluster.fa.gz
Supplementary files format and content: tab-delimited format files including raw and RPKM-normalized read counts of RNA-seq for each sample
Supplementary files format and content: tab-delimited format file including raw and TP2M-normalized read counts of sRNA-seq

organism: Ipomoea batatas

source_name: leaf

growth_protocol: Sweet potato plants (Ipomoea batatas cv. Tainung 57) were grown in a controlled environment (16 hr light per 8 hr dark at 25°C; light 20 μmol photons m-2sec-1).

extract_protocol:
Total RNAs from sweet potato leaves were extracted using Trizol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using the Ovation RNA-Seq Systems 1-16 for Model Organisms (Arabidopsis) (NuGEN) following the manufacturer's instructions. Subsequently, Arabidopsis InDA-C primers were employed to remove cytoplasmic and mitochondrial rRNA. Small RNA libraries for sRNA-seq were prepared using TruSeqSmall RNA Library Prep Kit (Illumina) following the manufacturer's instructions.

value: leaf

value: cv. Tainung 57

value: wounding


title: wounding 120 min systemic leaf, transcriptome

description: Library name: WT+2S_transcriptome


title: non-wounding systemic leaf, small RNA

description:
Library name: WT-1S_sRNA
column name in sRNA_processed.tsv: "WT-1S", "TP2M_WT-1S"

value: non-wounding


title: 206116800014_R06C01

description: SAMPLE 55

value: FFPE

value: meningioma


title: M_IP Tau_IP

city: Atlanta

first: Anu

last: Korukonda

state: Georgia

address: 615 Michael St

institute: Emory University

description:
Library name: A26
M_IP Tau_Immunoprecipitated fraction

data_processing:
Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X plus (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20M in each direction). Fastq files were assessed for quality using FastQC and Nextera adaptor trimming was performed using trimGalore. Reads were mapped to the mouse genome GRCm38 (mm10) and human tau using STAR alignment and raw counts were obtained using the featureCounts package in R Bioconductor.
Assembly: mm10
Supplementary files format and content: .txt file with raw counts for all samples

source_name: brainstem tissue

extract_protocol:
RNA was extracted using Zymo RNA Clean & Concentrator-5 kit.
Library construction was performed with SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA). Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA).

treatment_protocol: 2-3 month old TH-Cre;Slc6a2-eGFP/Rpl10a received stereotaxic infusions of P364S mutant human tau or EYFP into the mouse locus coeruleus.

value: brainstem tissue

value: female

tag: sample type

value: Immunoprecipitate (IP)

value: Tau


title: non-wounding systemic leaf, transcriptome

description: Library name: WT-1S_transcriptome

tag: tissue


title: 206116800014_R05C01

description: SAMPLE 54

value: Immune Enriched

value: F


title: 206116800007_R08C01

description: SAMPLE 53


title: 206116800004_R06C01

description: SAMPLE 49

value: Merlin Intact


title: 206116800007_R02C01

description: SAMPLE 51

value: M


title: 206116800007_R01C01

description: SAMPLE 50


title: artery, experimental group,30 days after surgery3,bio rep 3

description: Library name: R30_3

value: artery

value: HASMC

tag: cell type

value: transplatation


title: L_P Tau_Pre-IP

description:
Library name: A18
L_P Tau_Total homogenate

value: male

value: Total brainstem (Pre-IP)

tag: treatment


title: M_P Tau_Pre-IP

description:
Library name: A19
M_P Tau_Total homogenate

tag: genotype


title: 206116800007_R05C01

description: SAMPLE 52


title: H_IP EYFP_IP

description:
Library name: A10
H_IP EYFP_Immunoprecipitated fraction

value: EYFP


title: L_IP Tau_IP

description:
Library name: A25
L_IP Tau_Immunoprecipitated fraction


title: 206116800004_R04C01

description: SAMPLE 48

value: Hypermitotic


title: 206116800004_R01C01

description: SAMPLE 47

value: FFPE


title: 206116790138_R03C01

description: SAMPLE 43

value: meningioma


title: K_P EYFP_Pre-IP

description:
Library name: A17
K_P EYFP_Total homogenate

value: brainstem tissue


title: 206116790137_R07C01

description: SAMPLE 41


title: B_P Tau Pre-IP

description:
Library name: A2
B_P Tau_Total homogenate


title: 206116790138_R07C01

description: SAMPLE 45


title: 206116790103_R04C01

description: SAMPLE 39


title: C_IP_Tau_IP

description:
Library name: A9
C_IP_Tau_Immunoprecipitated fraction

value: female


title: artery, experimental group,30 days after surgery2,bio rep 2

description: Library name: R30_2

tag: cell line

value: common carotid artery

value: tissue


title: I_IP EYFP_IP

description:
Library name: A11
I_IP EYFP_Immunoprecipitated fraction

tag: Sex

value: Immunoprecipitate (IP)


title: Female_Knockout

city: Houston

first: Mingfu

last: Wu

address: 4349 Martin Luther King Boulevard

department: Department of Pharmacological and Pharmaceutical Sciences

institute: University of Houston

description:
Library name: Sample 4
10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger software v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
The tissues were homogenized, and the nuclei were extracted using 10X Genomics Chromium nuclei isolation kit following manufacturer protocol (10X Genomics, Pleasanton, CA).
The nuclei suspension was used as input for automated microfluidic single nuclei capture and barcoding using the 10X Genomics Chromium IX platform. snRNA-seq libraries were generated using Chromium Next GEM Single Cell 5′ Gene Expression v2 kit (10X Genomics) according to the manufacturer's protocol. Single-nuclei gel beads in emulsion (GEMs) were generated and single nuclei were uniquely barcoded. cDNA was recovered and selected for using DynaBead MyOne Silane Beads (Thermo Fisher Scientific) and SPRIselect beads (Beckman Coulter). The constructed library underwent quality control assessment using a High-sensitivity d1000 DNA screentape (Agilent) and then quantified with a Qubit Fluorometer (Thermo Fisher Scientific) and with a Kapa Library Quantification Kit (Kapa Biosystems) by using the AriaMX instrument (Agilent).

value: Heart

tag: gender

value: Female


title: 205854140146_R06C01

description: SAMPLE 37

value: Immune Enriched

value: F


title: 205854140143_R03C01

description: SAMPLE 35

value: M


title: I_P EYFP_Pre-IP

description:
Library name: A5
I_P EYFP_Total homogenate


title: 206116790143_R01C01

description: SAMPLE 46


title: C_P Tau_Pre-IP

description:
Library name: A3
C_P Tau_Total homogenate

value: Tau


title: K_IP EYFP_IP

description:
Library name: A24
K_IP EYFP_Immunoprecipitated fraction


title: 206116790137_R08C01

description: SAMPLE 42


title: 206116790138_R04C01

description: SAMPLE 44

value: Merlin Intact


title: Male_Control

description:
Library name: Sample 1
10X Genomics

value: Male

value: Control


title: B_IP Tau_IP

description:
Library name: A8
B_IP Tau_Immunoprecipitated fraction

value: male


title: 205854140146_R05C01

description: SAMPLE 36

value: FFPE

value: Hypermitotic


title: 205854130089_R01C01

description: SAMPLE 30

value: meningioma


title: H_P EYFP_Pre-IP

description:
Library name: A4
H_P EYFP_Total homogenate

value: brainstem tissue

value: female

value: Total brainstem (Pre-IP)

value: EYFP


title: 206116790095_R02C01

description: SAMPLE 38


title: Male_Knockout

description:
Library name: Sample 2
10X Genomics

value: Heart


title: 205854140125_R05C01

description: SAMPLE 34


title: 99557_Intact_XYSry

city: Los Angeles

first: Karen

last: Reue

state: CA

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

description: Library name: X99557

data_processing:
RNA-seq alignment was performed with STAR (2.7.10a) to GRCm39.106 genome build and read counts generated with quantMode in STAR.
Differential gene expression analysis was performed with DESeq2 (1.36.0).
Assembly: GRCm39.106
Supplementary files format and content: FCG_Liver_counts.csv raw counts generated from STAR

extract_protocol:
Liver was snap frozen, then RNA was isolated from homogenized liver with trizol based on manufacturer's instructions.
Total RNAseq libraries were generated with KAPA mRNA HyperPrep kit based on manufacturer's instructions.

treatment_protocol: At 75 days of age, gonadectomy (GDX) was performed on a cohort of mice to remove acute gonadal effects. At 15-17 weeks of age, all mice (GDX and intact gonads) were fed a high-fat diet (60% calories from fat, Bioserv F3282). Mice with intact gonads were fed a HFD for 11 weeks and GDX mice were fed a HFD for 15 weeks.

value: Liver

value: XY-;SryTg

value: HFD and Intact gonads


title: 98893_Intact_XXSry

description: Library name: X98893

value: XX;SryTg


title: 205854130047_R05C01

description: SAMPLE 29

value: F


title: 205854140009_R04C01

description: SAMPLE 33

value: Immune Enriched


title: 97856_Intact_XX

description: Library name: X97856

value: XX


title: 93558_Intact_XX

description: Library name: X93558


title: 205854120102_R05C01

description: SAMPLE 27


title: Female_Control

description:
Library name: Sample 3
10X Genomics

value: Female

value: Control


title: 89895_Intact_XY

description: Library name: X89895

value: XY-


title: 95271_Intact_XXSry

description: Library name: X95271


title: 89033_Intact_XYSry

description: Library name: X89033


title: 206116790103_R07C01

description: SAMPLE 40

value: FFPE

value: Merlin Intact


title: 88616_GDX_XY

description: Library name: X88616

value: HFD and Gonadectomy


title: 205854120102_R04C01

description: SAMPLE 26

value: meningioma


title: 205848680008_R03C01

description: SAMPLE 23


title: 99639_GDX_XY

description: Library name: X99639


title: 205854130089_R07C01

description: SAMPLE 31


title: 205854140009_R01C01

description: SAMPLE 32


title: 205854130047_R01C01

description: SAMPLE 28


title: 205848670089_R06C01

description: SAMPLE 18

value: Hypermitotic

value: M


title: 205848680008_R01C01

description: SAMPLE 21


title: 205848670149_R02C01

description: SAMPLE 19


title: 93559_GDX_XXSry

description: Library name: X93559


title: 81790_Intact_XX

description: Library name: X81790


title: 205848670089_R04C01

description: SAMPLE 17


title: 71064_GDX_XXSry

description: Library name: X71064


title: 799_Intact_XY

description: Library name: X799


title: 87592_GDX_XX

description: Library name: X87592


title: 76370_Intact_XYSry

description: Library name: X76370


title: 70608_GDX_XX

description: Library name: X70608


title: 205848680153_R03C01

description: SAMPLE 25


title: 205841340119_R08C01

description: SAMPLE 16


title: 69572_Intact_XX

description: Library name: X69572


title: 76112_GDX_XY

description: Library name: X76112


title: 72268_GDX_XY

description: Library name: X72268


title: 69848_GDX_XYSry

description: Library name: X69848


title: 70314_Intact_XYSry

description: Library name: X70314


title: 205841320142_R03C01

description: SAMPLE 15


title: 69358_GDX_XXSry

description: Library name: X69358


title: 205841320122_R04C01

description: SAMPLE 12


title: 205841320122_R06C01

description: SAMPLE 14


title: 53085_Intact_XY

description: Library name: X53085


title: 205841320122_R03C01

description: SAMPLE 11


title: 59091_GDX_XYSry

description: Library name: X59091


title: 205848680008_R02C01

description: SAMPLE 22


title: 205841320122_R05C01

description: SAMPLE 13


title: 66804_Intact_XX

description: Library name: X66804


title: 205841320078_R03C01

description: SAMPLE 7


title: 205848680023_R06C01

description: SAMPLE 24


title: 69065_Intact_XY

description: Library name: X69065


title: 205841320074_R03C01

description: SAMPLE 6


title: 205841320078_R04C01

description: SAMPLE 8


title: 37517_GDX_XXSry

description: Library name: X37517


title: 49580_Intact_XX

description: Library name: X49580


title: 63079_GDX_XY

description: Library name: X63079


title: 48525_Intact_XY

description: Library name: X48525


title: 37366_Intact_XXSry

description: Library name: X37366


title: 205841320078_R06C01

description: SAMPLE 9


title: 30544_GDX_XYSry

description: Library name: X30544


title: dTAG_6h, IgG , replica 1

city: Memphis

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

description:
Library name: diffdTAG_6h_IgG
CUT&RUN

data_processing:
Followed the nf-core/cutandrun Nextflow pipeline (revision 3.2.2) using default/standard processing steps for CUT&RUN data, including read QC, trimming, alignment, filtering, and peak calling.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Run

growth_protocol: Differentiation condition: IMDM containing 2% FBS, 3% human AB serum, 3 U/mL EPO, 10 μg/mL insulin, 3 U/mL heperin, 1mg/mL human holo-transferrin, 50 ng/mL hSCF and 1 μg/mL doxycline.

extract_protocol:
Differentiated HUDEP2 cells expressing FKBP12F36V-GATA1 were subjected to induced degradation of GATA1 for 0.5, 3, and 6 hours, resulting in the purification of CUT&RUN DNA. The CUT&RUN process was performed using the CUTANA™ ChIC/CUT&RUN Kit (REF#14-1048).
CUT&RUN libraries were constructed according to the CUTANA™ CUT&RUN Library Prep Kit (REF#14-1001 and 14-1002) protocol.

value: erythroid progenitor cell line

value: differentiation, 100 nM dTAG-13

tag: batch


title: 205735150009_R04C01

description: SAMPLE 2


title: 29264_GDX_XX

description: Library name: X29264

value: Liver


title: dTAG_3h, GATA1 , replica 1

description:
Library name: diffdTAG_3h_GATA1_1
CUT&RUN


title: 205841320098_R08C01

description: SAMPLE 10


title: 19562_GDX_XY

description: Library name: X19562


title: dTAG_0.5h, GATA1 , replica 2

description:
Library name: diffdTAG_0.5h_GATA1_2
CUT&RUN


title: 18333_Intact_XXSry

description: Library name: X18333

value: HFD and Intact gonads


title: dTAG_3h, IgG , replica 1

description:
Library name: diffdTAG_3h_IgG
CUT&RUN


title: 14614_Intact_XXSry

description: Library name: X14614

value: XX;SryTg


title: 205841320066_R06C01

description: SAMPLE 5


title: dTAG_6h, GATA1 , replica 2

description:
Library name: diffdTAG_6h_GATA1_2
CUT&RUN


title: DMSO_6h, GATA1 , replica 2

description:
Library name: diffDMSO_6h_GATA1_2
CUT&RUN

value: differentiation, DMSO


title: 205841310053_R03C01

description: SAMPLE 4


title: 28605_GDX_XYSry

description: Library name: X28605

value: XY-;SryTg


title: 205735140150_R04C01

description: SAMPLE 1


title: 205848680007_R02C01

description: SAMPLE 20

value: F


title: 36870_Intact_XY

description: Library name: X36870


title: DMSO_6h, GATA1 , replica 1

description:
Library name: diffDMSO_6h_GATA1_1
CUT&RUN


title: 11587_Intact_XXSry

description: Library name: X11587


title: 24126_GDX_XX

description: Library name: X24126

value: XX


title: 205735150116_R07C01

description: SAMPLE 3

value: Immune Enriched


title: DMSO_3h, GATA1 , replica 1

description:
Library name: diffDMSO_3h_GATA1_1
CUT&RUN


title: dTAG_3h, GATA1 , replica 2

description:
Library name: diffdTAG_3h_GATA1_2
CUT&RUN


title: 21022_GDX_XYSry

description: Library name: X21022


title: Control Ly6Ghi CD101+ rep 3

city: Birmingham

first: Paran

last: Goel

state: Alabama

address: Department of Hematology and O, 701 20th Street South

institute: University of Alabama, Birming

description: Library name: control_C_3

data_processing:
Raw ATAC-seq data were processed using the nf-core/atacseq pipeline (v 2.1.2)(PMID: 32055031), which follows best practices for chromatin accessibility data analysis. The pipeline performs adaptor trimming (Trim Galore!), read alignment to the mm10 genome (Bowtie2), duplicate marking (picard), and duplicate removal (SAMtools) before generating normalised bigWig files scaled to 1 million mapped reads (BEDTools, bedGraphToBigWig).
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Bone Marrow

extract_protocol:
tdTOM+ neutrophil subpopulations (50000) were sorted from AML (Meis1-HoxA9 overexpression) mice and controls nad were washed once with cold phosphate-buffered saline (PBS) and resuspended with 50 µl cold ATAC-Resuspension Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM Mg2Cl, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, and protease inhibitor). After incubation on ice for 3 minutes, the cell nuclei were collected by centrifugation at 500 g for 5 mins at 4°C.
Tn5 transposition of nuclei pellets was carried out at 37°C for 30 min using the DNA Sample Preparation Kit from TruePrep Index Kit V2 for Illumina (Vazyme, TD501). The transposed DNA was purified using DNA purification columns (Zymo Research, D4003) and subjected to PCR amplification for library generation. ATAC-seq libraries were sequenced on the Illumina HiSeq 4000 platform for paired-end 150 cycles.

value: Bone Marrow

value: Neutrophil

value: paired-end


title: Control Ly6Ghi CD101- rep 3

description: Library name: control_B_3


title: 20024_Intact_XYSry

description: Library name: X20024


title: dTAG_6h, GATA1 , replica 1

description:
Library name: diffdTAG_6h_GATA1_1
CUT&RUN


title: DMSO_0.5h, GATA1 , replica 2

description:
Library name: diffDMSO_0.5h_GATA1_2
CUT&RUN


title: dTAG_0.5h, GATA1 , replica 1

description:
Library name: diffdTAG_0.5h_GATA1_1
CUT&RUN


title: Control Ly6Glo CD101- rep 3

description: Library name: control_A_3


title: vASC_SFRP4ko+Capan-1_GFP_2

city: New York

first: Lingyi

last: Cai

state: New York

address: 2960 Broadway

institute: Columbia University

description: Library name: S8

data_processing:
For each sample, we performed gene expression quantification using RSEM (RNA-seq by Expectation Maximization) v1.3.1 with STAR (Spliced Transcripts Alignment to a Reference) v2.7.1a as the aligner (31,32). Paired-end sequencing reads in raw FASTQ format were processed with the “rsem-calculate-expression” function.
We used the DESeq2 (1.30.1) method to identify differentially expressed genes (DEGs). Genes with fewer than ten raw counts across all samples were excluded from the analysis. To create the DESeq2 object, we used the “DESeqDataSetFromMatrix” function, specifying the design to indicate the various experimental conditions. DEGs were estimated using the “lfcShrink” function with a “normal” estimator. We performed Gene Set Enrichment Analysis (GSEA) using the fgsea (v 1.16.0) R package with 50 broad hallmark gene sets and thousands of Gene Ontology (GO) sets. For comparison, we selected DEGs (adj p values < 0.05) and ranked them by fold change. From the ranked list, we chose the top 100 genes for further over-representation analysis. GO term over-representation analysis was conducted using the “enrichGO” function from the clusterProfiler (v3.18.1) package using the org.Hs.eg.db (v3.12.0) annotation database. In independent analyses, Qiagen Ingenuity Pathway Analysis (IPA) software was used to identify condition-dependent changes in signaling networks.
Assembly: GRCh38
Supplementary files format and content: Analyzed data are presented as TPM count in Microsoft Excel format (xlsx).

source_name: Metastatic PDAC

growth_protocol: Cells were grown in DMEM with high glucose (Cytiva, #SH30243.01) supplemented with 20% FBS (Sigma, #F0926) and 1X Antibiotic/Antimycotic solution (Hyclone, #SV30079.01) and maintained at 37C with 5% CO2.

extract_protocol:
After 7-days growth media was aspirated and cells were washed with PBS. Trypsin (0.25%) was used to seperate cells into single cell suspension. Cells were then sorted based on RFP+ or GFP+ expression using FACS. RNA from cells was isolated using the RNeasy Plus Mini Kit (Qiagen, #74104).
RNA samples were submitted to Cancer Genomics Center at The University of Texas Health Science Center at Houston (CPRIT RP240610). For DNA depletion, the RNA samples were treated with DNase using RNeasy Mini Kit (#74104, Qiagen, Germany) and RNase-free DNase Set (#79254, Qiagen, Germany). The treated RNA samples were eluted in 10ul nuclease-free water. Total RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA with DV200 greater than 66% was used for library preparation. Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 (#634418, Takara Bio, Japan) and Unique Dual Index Kit (#634752, Takara Bio, Japan) following the manufacturer’s instructions. The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The libraries were pooled evenly and went for the paired-end 75-cycle sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

treatment_protocol: For coculture experiments, vASC, vASC_LINC, vASC_SFRP4 and Capan-1 cells were plated at 300K:300K cells per well in 6-well plates in replicates and cultured for 7-days. Media was replensihed every 48-hours.

value: Metastatic PDAC

value: pancreatic ductal adenocarcinoma


title: Control Ly6Ghi CD101- rep 2

description: Library name: control_B_2


title: 16037_GDX_XXSry

description: Library name: X16037

source_name: Liver

value: HFD and Gonadectomy


title: CTCF-overexpressed AC16, replicate 3, CTCF ChIP

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description:
Library name: CTCF-OE AC16, replicate 3
Wildtype AC16, CTCF ChIP

data_processing:
Bowtie v.2 was used for alginment, with Human / GRCh38 reference genome. For the processed data, Macs v.2 was used for peak calling
Assembly: GRCh38
Supplementary files format and content: The narrow peak files (chromosome, start, and end coordinates) for each sample are in excel format.

growth_protocol: AC16 cells were cultured in DMEM/F-12 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin (Sigma-Aldrich) at 37 °C in a humidified incubator with 5% CO₂

extract_protocol:
Three days after tranfection, cells were fixed with 1% formaldehyde for 10 min at room temperature and quenching with 125 mM glycine for 5 minutes. Cells were lysed, and chromatin was sonicated for 60 min using the Pixul platform (Active Motif), under the following parameters: Pulse (N):50, PRF (kHz): 1.00, Process Time: 60 minutes, Burst Rate (Hz): 20. Chromatin was incubated overnight at 4 °C with Protein G/A Dynabeads (Invitrogen, #10003D) pre-bound to 1.5 µg of anti-CTCF antibody (Active Motifs, #91285). Bead-bound complexes were extensively washed and resuspended in TT buffer (10 mM Tris-HCl, pH 8.0, 0.05% Tween-20). On-bead library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645L).
Libraries were barcoded using NEXTFLEX Unique Dual Index Barcodes, PCR-amplified for 14 cycles, with Solexa 1GA/1GB primers, and size-selected (200–500 bp) prior to sequencing on an Illumina NovaSeq SP100 platform

treatment_protocol: The control group were transfected with empty plasmid using Lipofectamine 2000; the CTCF-overexpressed (CTCF-OE) group were transfected with pcDNA-CTCF (800ng) plasmid.

value: Heart

value: human cardiomyocyte

value: CTCF-OE

value: pcDNA-CTCF


title: vASC_SFRP4ko+Capan-1_RFP_2

description: Library name: S7

source_name: adipose stromal vascular fraction

value: adipose stromal vascular fraction

value: vASC

value: adipose stromal cells


title: 13306_GDX_XYSry

description: Library name: X13306

value: Liver

value: XY-;SryTg


title: vASC_SFRP4ko+Capan-1_GFP_1

description: Library name: S6


title: dTAG_0.5h, IgG , replica 1

description:
Library name: diffdTAG_0.5h_IgG
CUT&RUN

value: erythroid progenitor cell line

value: differentiation, 100 nM dTAG-13


title: CTCF-overexpressed AC16, replicate 1, CTCF ChIP

description:
Library name: CTCF-OE AC16, replicate 1
Wildtype AC16, CTCF ChIP


title: 11059_GDX_XX

description: Library name: X11059

value: XX


title: Control Ly6Ghi CD101+ rep 2

description: Library name: control_C_2

value: Bone Marrow

value: Neutrophil


title: Control Ly6Ghi CD101- rep 1

description: Library name: control_B_1

value: paired-end


title: DMSO_6h, IgG , replica 1

description:
Library name: diffDMSO_6h_IgG
CUT&RUN

value: differentiation, DMSO


title: Control Ly6Ghi CD101+ rep 1

description: Library name: control_C_1


title: DMSO_3h, GATA1 , replica 2

description:
Library name: diffDMSO_3h_GATA1_2
CUT&RUN


title: 00575_GDX_XXSry

description: Library name: X00575

value: XX;SryTg

value: HFD and Gonadectomy


title: vASC+Capan-1_RFP_3

description: Library name: S1


title: DMSO_0.5h, IgG , replica 1

description:
Library name: diffDMSO_0.5h_IgG
CUT&RUN


title: Wildtype AC16, replicate 1, CTCF ChIP

description:
Library name: Wildtype AC16, replicate 1
Wildtype AC16, CTCF ChIP

value: Heart

value: human cardiomyocyte

value: Wildtype

value: Empty plasmid


title: Control Ly6Glo CD101- rep 1

description: Library name: control_A_1


title: Capan-1_2

description: Library name: J50

value: Metastatic PDAC

value: pancreatic ductal adenocarcinoma


title: vASC+Capan-1_GFP_3

description: Library name: S2


title: 10606_Intact_XYSry

description: Library name: X10606

value: Liver

value: HFD and Intact gonads


title: vASC+Capan-1_GFP_2

description: Library name: J44


title: vASC+Capan-1_GFP_1

description: Library name: J43


title: DMSO_0.5h, GATA1 , replica 1

description:
Library name: diffDMSO_0.5h_GATA1_1
CUT&RUN

value: erythroid progenitor cell line


title: CTCF-overexpressed AC16, replicate 2, CTCF ChIP

description:
Library name: CTCF-OE AC16, replicate 2
Wildtype AC16, CTCF ChIP

value: CTCF-OE

value: pcDNA-CTCF


title: vASC_SFRP4ko+Capan-1_RFP_1

description: Library name: S5

value: adipose stromal vascular fraction

value: vASC

value: adipose stromal cells


title: 12100_GDX_XX

description: Library name: X12100

value: XX


title: vASC_LINCko+Capan-1_GFP_1

description: Library name: S4


title: vASC_LINCko+Capan-1_RFP_1

description: Library name: S3


title: vASC+Capan-1_RFP_2

description: Library name: J38


title: Huh7_2

city: Woolloongabba

first: Qi

last: Ruan

state: QLD

address: 37 Kent Street

department: Frazer Institute

country: Australia

institute: The University of Queensland

description: Library name: Sample 5

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq 2.20.0.422 pipeline.
The cleaned sequence reads were then aligned against the Homo sapiens genome (Build version HG38).
The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences.
Counts are summarised at gene level using the featureCounts v1.5.3
Assembly: hg38
Supplementary files format and content: tab-delimited text file of the raw count matrix for each sample

source_name: human primary hepatic stellate cell

growth_protocol: Primary HSCs were maintained in DMEM with 2% FBS and antibiotics at humitified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA from primary HSCs was extracted and purified using RNeasy Plus Mini Kit (Qiagen, USA). Individual libraries were quantified by qPCR.
and all libraries were normalized to 2nM and pooled. Libraries were clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents.

treatment_protocol: Primary HSCs were incubated in conditioned medium (CM) collected from Huh7 cells for 24 hours. CM from Huh7 cells in 1% FBS for 18 hours was collected as control and CM from Huh7 cells treated with 10uM cisplatin for 6 hours then replaced with 1% FBS for 18 hours was collected as cisplatin pretreated.

value: human primary hepatic stellate cell

value: untreated


title: DMSO_3h, IgG , replica 1

description:
Library name: diffDMSO_3h_IgG
CUT&RUN

value: differentiation, DMSO


title: Huh7_1

description: Library name: Sample 4


title: vASC_LINC_2

description: Library name: J34


title: Wildtype AC16, replicate 3, CTCF ChIP

description:
Library name: Wildtype AC16, replicate 3
Wildtype AC16, CTCF ChIP

value: Heart

value: human cardiomyocyte


title: vASC_LINC_1

description: Library name: J33


title: R7D5_snATAC-seq

city: Hangzhou

first: Saiyong

last: Zhu

state: Zhejiang

address: 866 Yuhangtang Rd.

department: Life Sciences Institute

institute: Zhejiang University

description:
Library name: Sample 3
10x Genomics

library_source: genomic single cell

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics Cell Ranger ATAC v2.1.0 pipeline
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv

source_name: MEL1 hESC line

growth_protocol: ePPs were cultured on feeder in EF6I medium: DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF, 10 μM 616452, and 1 μM I-BET151 (APExBIO).  R6 medium: DMEM containing 1:50 B27, 0.05% BSA (Yeasen), 10 μM zinc sulfate (Vetec), 10 μg/ml heparin (Sigma), 10 μM 616452 (TargetMol), 1 μM T3 (Sigma), 0.2 μM LDN-193189 (Tocris), 0.2 μM Compound E (MedChem Express), 0.5 mM vitamin C, and 10 μM forskolin (TargetMol). R7 medium: DMEM containing 1:50 B27, 0.05% BSA, 10 μM zinc sulfate, 10 μg/ml heparin, 10 μM 616452, 1 μM T3, 1 mM N-acetyl cysteine (Sigma), 1 μM Trolox (Sigma), and 0.5 mM vitamin C.

extract_protocol:
DNA extraction were performed by LC-Bio Technology.
Libraries were constructed at LC-Bio Technology.

value: MEL1 hESC line

value: ePP-derived islets


title: vASC_1

description: Library name: J31


title: vASC_SFRP4_2

description: Library name: J36


title: Capan-1_1

description: Library name: J49

value: Metastatic PDAC

value: pancreatic ductal adenocarcinoma


title: AML Ly6Ghi CD101+ rep 2

description: Library name: AML_C_2

value: Bone Marrow

value: Neutrophil

value: paired-end


title: AML Ly6Ghi CD101+ rep 3

description: Library name: AML_C_3


title: AML Ly6Glo CD101- rep 4

description: Library name: AML_A_4


title: Huh7_3

description: Library name: Sample 6


title: AML Ly6Ghi CD101+ rep 4

description: Library name: AML_C_4


title: vASC_2

description: Library name: J32


title: AML Ly6Ghi CD101- rep 4

description: Library name: AML_B_4


title: Wildtype AC16, replicate 2, CTCF ChIP

description:
Library name: Wildtype AC16, replicate 2
Wildtype AC16, CTCF ChIP

value: Wildtype

value: Empty plasmid


title: C16_WT_scRNA-seq

description:
Library name: Sample 4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
RNA extraction and sequencing were performed by LC-Bio Technology.
Libraries were constructed at LC-Bio Technology.


title: Cis_2

description: Library name: Sample 2

value: cisplatin-pretreated


title: CHLA90_DMSO_REP3

city: London

first: Sally

middle: Linda

last: George

address: 26 Oakleaf Avenue

country: United Kingdom

institute: The Institute of Cancer Research

description: Library name: GEO5504A23

data_processing:
nf-core/atacseq release 3.0
Assembly: GRCh38, Ensembl release 95
Supplementary files format and content: bigWig files generated by nfcore pipeline
Supplementary files format and content: broadPeak files

growth_protocol: DMEM Glutamax 10% FBS

extract_protocol: OMNI-ATAC protocol

treatment_protocol: 72 hours treatement with either DMSO (vehicle) or 10uM retinoic acid

value: Neuroblastoma

value: ATRX IFF

value: Vehicle DMSO


title: C16_KO_scRNA-seq

description:
Library name: Sample 5
10x Genomics


title: AML Ly6Glo CD101- rep 3

description: Library name: AML_A_3


title: R7D5_scRNA-seq

description:
Library name: Sample 3
10x Genomics


title: EP_scRNA-seq

description:
Library name: Sample 2
10x Genomics

value: ePP-derived endocrine precursors


title: AML Ly6Glo CD101- rep 2

description: Library name: AML_A_2


title: AML Ly6Ghi CD101+ rep 1

description: Library name: AML_C_1


title: Control Ly6Glo CD101- rep 2

description: Library name: control_A_2


title: SKNMM_DMSO_REP3

description: Library name: GEO5504A21

source_name: SKNMM

value: SKNMM


title: vASC_SFRP4_1

description: Library name: J35

value: adipose stromal vascular fraction

value: adipose stromal cells