title: GM12878, 600U, Cell 51

description:
GM-600U_051.allValidPairs.txt
GM-600U_051.hic
GM-600U_051.mcool
GM-600U_051.clean.smooth.bw
GM-600U_051_20kb_1.3dg.txt
GM-600U_051_20kb_2.3dg.txt
GM-600U_051_20kb_3.3dg.txt
GM-600U_051_20kb_4.3dg.txt
GM-600U_051_20kb_5.3dg.txt
GM-600U_051_10kb_1.3dg.txt
GM-600U_051_10kb_2.3dg.txt
GM-600U_051_10kb_3.3dg.txt
GM-600U_051_10kb_4.3dg.txt
GM-600U_051_10kb_5.3dg.txt
GM-600U_051_5kb_1.3dg.txt
GM-600U_051_5kb_2.3dg.txt
GM-600U_051_5kb_3.3dg.txt
GM-600U_051_5kb_4.3dg.txt
GM-600U_051_5kb_5.3dg.txt
GM-600U_051_20kb_1.clean.3dg.txt
GM-600U_051_20kb_2.clean.3dg.txt
GM-600U_051_20kb_3.clean.3dg.txt
GM-600U_051_20kb_4.clean.3dg.txt
GM-600U_051_20kb_5.clean.3dg.txt
GM-600U_051_10kb_1.clean.3dg.txt
GM-600U_051_10kb_2.clean.3dg.txt
GM-600U_051_10kb_3.clean.3dg.txt
GM-600U_051_10kb_4.clean.3dg.txt
GM-600U_051_10kb_5.clean.3dg.txt
GM-600U_051_5kb_1.clean.3dg.txt
GM-600U_051_5kb_2.clean.3dg.txt
GM-600U_051_5kb_3.clean.3dg.txt
GM-600U_051_5kb_4.clean.3dg.txt
GM-600U_051_5kb_5.clean.3dg.txt


title: cell_123

status: Public on Feb 28 2025

type: SRA

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Chromatin loop calling was performed with SnapHiC and Chromosight package with default parameters.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy and ligation junction signals for each sample. hic and mcool files included contact matrices for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

growth_protocol: GM12878 lymphoblastoid cells were grown in RPMI1640 medium (Gibco, Thermo Fisher Scientific, Cat. # 11875093) media supplemented with 15% FBS and 1% Pen/Strep. GM12878 were cultured at 37° C with 5% CO2 at recommended density.

extract_protocol:
1 million cells were permeabilized with 100 μL Micro-C buffer1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% IGEPAL CA630, 1 x PIC), incubate on ice for 20 min.
Single cells were amplified with the state-of-art transposase-based WGA (Multiplexed End Tagging Amplification), barcoded in 96-well plate, then pooled for library preparation.

tag: tissue

value: blood

tag: cell line

tag: cell type

value: lymphoblastoid


title: GM12878, 600U, Cell 49

description:
GM-600U_049.allValidPairs.txt
GM-600U_049.hic
GM-600U_049.mcool
GM-600U_049.clean.smooth.bw
GM-600U_049_20kb_1.3dg.txt
GM-600U_049_20kb_2.3dg.txt
GM-600U_049_20kb_3.3dg.txt
GM-600U_049_20kb_4.3dg.txt
GM-600U_049_20kb_5.3dg.txt
GM-600U_049_10kb_1.3dg.txt
GM-600U_049_10kb_2.3dg.txt
GM-600U_049_10kb_3.3dg.txt
GM-600U_049_10kb_4.3dg.txt
GM-600U_049_10kb_5.3dg.txt
GM-600U_049_5kb_1.3dg.txt
GM-600U_049_5kb_2.3dg.txt
GM-600U_049_5kb_3.3dg.txt
GM-600U_049_5kb_4.3dg.txt
GM-600U_049_5kb_5.3dg.txt
GM-600U_049_20kb_1.clean.3dg.txt
GM-600U_049_20kb_2.clean.3dg.txt
GM-600U_049_20kb_3.clean.3dg.txt
GM-600U_049_20kb_4.clean.3dg.txt
GM-600U_049_20kb_5.clean.3dg.txt
GM-600U_049_10kb_1.clean.3dg.txt
GM-600U_049_10kb_2.clean.3dg.txt
GM-600U_049_10kb_3.clean.3dg.txt
GM-600U_049_10kb_4.clean.3dg.txt
GM-600U_049_10kb_5.clean.3dg.txt
GM-600U_049_5kb_1.clean.3dg.txt
GM-600U_049_5kb_2.clean.3dg.txt
GM-600U_049_5kb_3.clean.3dg.txt
GM-600U_049_5kb_4.clean.3dg.txt
GM-600U_049_5kb_5.clean.3dg.txt

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy for each sample. hic and mcool files included contact matrices for each sample.
Supplementary files format and content: .3dg files of single-cell 3D genome structures

tag: genotype

value: WT

tag: mnase titration

value: 600U MNase


title: GM12878, 600U, Cell 50

description:
GM-600U_050.allValidPairs.txt
GM-600U_050.hic
GM-600U_050.mcool
GM-600U_050.clean.smooth.bw
GM-600U_050_20kb_2.3dg.txt
GM-600U_050_20kb_3.3dg.txt
GM-600U_050_20kb_4.3dg.txt
GM-600U_050_20kb_5.3dg.txt
GM-600U_050_10kb_2.3dg.txt
GM-600U_050_10kb_3.3dg.txt
GM-600U_050_10kb_4.3dg.txt
GM-600U_050_10kb_5.3dg.txt
GM-600U_050_5kb_2.3dg.txt
GM-600U_050_5kb_3.3dg.txt
GM-600U_050_5kb_4.3dg.txt
GM-600U_050_5kb_5.3dg.txt
GM-600U_050_20kb_2.clean.3dg.txt
GM-600U_050_20kb_3.clean.3dg.txt
GM-600U_050_20kb_4.clean.3dg.txt
GM-600U_050_20kb_5.clean.3dg.txt
GM-600U_050_10kb_2.clean.3dg.txt
GM-600U_050_10kb_3.clean.3dg.txt
GM-600U_050_10kb_4.clean.3dg.txt
GM-600U_050_10kb_5.clean.3dg.txt
GM-600U_050_5kb_2.clean.3dg.txt
GM-600U_050_5kb_3.clean.3dg.txt
GM-600U_050_5kb_4.clean.3dg.txt
GM-600U_050_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAPs HiCAR_Mdx_rep2

city: Durham

first: Yarui

last: Diao

state: NC

address: 303 Research Drive

department: Cell Biology

country: USA

institute: Duke University

description:
FAP_HiCAR_Mdx_rep2
HiCAR for FAPs from Mdx mouse
FAP_HiCAR_accessibleFragment_Mdx.bw
FAP_HiCAR_HiC-Matrix_Mdx.hic

data_processing:
*library strategy: HiCAR
The HiCAR reads were analyzed by jianhong/hicar pipeline (v 2.0.0rc). Briefly, the 5' end adapter ' TGTGCGAACTCAGACC' was trimmed by `cutadapt` (v 4.2) and the reads will be mapped by BWA to mouse genome mm10, filtered by pairtools and used to call interactions by peakachu (v 2.1 ). The raw reads were mapped by BWA (bwa mem v 0.7.17-r1188 with parameter -SP to skip mate rescue and pairing). The enzyme was assigned as 'MseI'. The valid pairs were selected by pairtools (v 0.3.0) if the pair_type is 'UU', 'UR' or 'RU' and parsed with parameter ' --min-mapq 10 --max-molecule-size 2000 --max-inter-align-gap 50 --walks-policy 5 unique --no-flip --drop-seq --drop-sam '. The Aggregate Peak Analysis (APA) was performed by juicer_tools (v 3.0.0 ref).
The tracks and heatmaps of HiCAR signals were plotted by Bioconductor package trackViewer (v 1.33.5), ComplexHeatmap (v 2.2.0) and deepTools (v 3.1.3).
Assembly: mm10
Supplementary files format and content: Big wig files containing binarized chromatin accessibility tracks in bedgraph format.
Supplementary files format and content: hic files with binarized chromatin interaction frequency for each 10kb bin across the genome.

organism: Mus musculus

source_name: Muscle

extract_protocol:
Single cells were collected from mouse muscle by disection and mincing of muscle tissue, digestion using collagenase II and dispase in wash medium, and training using a 20-gauge needle and a 40 micrometer filter. FAPs were then isolated by Sca1+, propidium iodide negative FACS sorted cells.
HiCAR

value: Muscle

value: Fibro-adipogenic progenitors

value: Mdx


title: GM12878, 600U, Cell 52

description:
GM-600U_052.allValidPairs.txt
GM-600U_052.hic
GM-600U_052.mcool
GM-600U_052.clean.smooth.bw
GM-600U_052_20kb_1.3dg.txt
GM-600U_052_20kb_2.3dg.txt
GM-600U_052_20kb_5.3dg.txt
GM-600U_052_10kb_1.3dg.txt
GM-600U_052_10kb_2.3dg.txt
GM-600U_052_10kb_5.3dg.txt
GM-600U_052_5kb_1.3dg.txt
GM-600U_052_5kb_2.3dg.txt
GM-600U_052_5kb_5.3dg.txt
GM-600U_052_20kb_1.clean.3dg.txt
GM-600U_052_20kb_2.clean.3dg.txt
GM-600U_052_20kb_5.clean.3dg.txt
GM-600U_052_10kb_1.clean.3dg.txt
GM-600U_052_10kb_2.clean.3dg.txt
GM-600U_052_10kb_5.clean.3dg.txt
GM-600U_052_5kb_1.clean.3dg.txt
GM-600U_052_5kb_2.clean.3dg.txt
GM-600U_052_5kb_5.clean.3dg.txt


title: cell_118


title: Patient5_Bcell_POST

type: RNA

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

hyb_protocol: For mRNA:Following fragmentation, 5,5ug of ds-cDNA were hybridized for 16hr at 45ºC on GeneChip Clariom S human array cartridge. Array cartridge was washed and stained in the Affymetrix GCS300 System. For miRNA: 130 ng of biotin-labeled RNA were hybridized for 40 hr at 4ºC on GeneChip miR4.0 cartridge. Array cartridge was washed and stained in the Affymetrix GCS300 System.

scan_protocol: Array cartridge was scanned using the GCS300System, 7G with autoloder.

data_processing: Raw expression values were obtained directly from .CEL file and were preocessed using the RMA method in oligo R package to get normalizae expression values.

label: biotin

molecule: total RNA

source_name: B cell

label_protocol: For mRNA samples: Biotinylated ds-cDNA were prepared according to the standard Affymetric, ThermoFisher, protocol from 1ng total RNA, GeneChip Pico Kit manual workflow, user guide. For miRNA samples: biotinylated RNA were prepared according to the standard Affymetrix, ThermoFisher, protocol from 130ng total RNA, GeneChip FlashTag Biotin HSR RNA.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) and serum were collected pre- and post-belimumab treatment (6 months). PBMCs were isolated via Ficoll-Hypaque gradient centrifugation (Vacutainer CPT, BD Biosciences) and B, T and myeloid cell subset were sorted using spectral cytometry. RNA and miRNA were obtained using using the RNeasy Mini Kit following the manufacturer’s instructions, with quality and concentration assessed via Bioanalyzer PicoChip.

tag: group

value: Post-treatment


title: Mouse muscle Sca1+ FAPs HiCAR_Mdx_rep1

description:
FAP_HiCAR_Mdx_rep1
HiCAR for FAPs from Mdx mouse
FAP_HiCAR_accessibleFragment_Mdx.bw
FAP_HiCAR_HiC-Matrix_Mdx.hic


title: cell_117


title: Patient5_Tcell_POST

source_name: T cell


title: Sca1+ FAP_Kdm6b-CutNtag_WT_rep2

description:
Kdm6b cut-and-tag for FAPs from wildtype mouse
FAP_Kdm6b-CutNtag_WT.bw

data_processing:
Cut-and-Tag reads were trimmed using TrimGalore (v 0.6.6) and then aligned to UCSC mm10 reference genome by bowtie2 (v 2.4.4). Low quality reads were removed using samtools (v 1.15.1, with parameter ' -q 20 -F 0x004 -F 0x0008 -f 0x001'). Duplicated reads were marked by picard (v 3.1.0). The genomic coverage was saved in bigwig format and normalized by CPM method by bedTools (v 2.31.1), UCSC Utilities bedclip (v 377) and BedGraphToBigWig (v 445). Binding peaks were called by SEACR (v 1.3) with parameters '0.05 non stringent' with clipped bedGraph files. The differential binding peaks were analyzed by Bioconductor package DiffBind (v 3.4.11) and the peaks were annotated by Bioconductor package ChIPpeakAnno (v 3.28.1). The coverage for selected regions was performed by deepTools (v 3.1.3).
Assembly: mm10
Supplementary files format and content: binarized bigwig file, fragment counts per million.
Library strategy: CUT&TAG

extract_protocol:
Single cells were collected from mouse muscle by disection and mincing of muscle tissue, digestion using collagenase II and dispase in wash medium, and training using a 20-gauge needle and a 40 micrometer filter. FAPs were then isolated by Sca1+, propidium iodide negative FACS sorted cells.
About 10,000 of FAPs (Sca1+) from WT, Mdx, and Utrn-/Mdx mice were collected by FACS. FAPs were bound with concanavalin A beads for immobilization, then incubated with primary antibodies (Kdm6b, H3K27me3, Fosl1) at 4 ℃ overnight and secondary antibody 30 mins at RT. After, cells are immobilized with concanavalin beads, permebilized cells were tagmented with pA-Tn5 with sequencing adapter. This is then followed by DNA purification, and final libraries were amplified by Q5 polymerase (NEB, M0491L) and quantified using a Qubit™ 1X dsDNA HS Assay Kit and a High Sensitivity D1000 Tapestation.

value: Wild type


title: GM12878, 600U, Cell 48

description:
GM-600U_048.allValidPairs.txt
GM-600U_048.hic
GM-600U_048.mcool
GM-600U_048.clean.smooth.bw
GM-600U_048_20kb_1.3dg.txt
GM-600U_048_20kb_2.3dg.txt
GM-600U_048_20kb_3.3dg.txt
GM-600U_048_20kb_4.3dg.txt
GM-600U_048_10kb_1.3dg.txt
GM-600U_048_10kb_2.3dg.txt
GM-600U_048_10kb_3.3dg.txt
GM-600U_048_10kb_4.3dg.txt
GM-600U_048_5kb_1.3dg.txt
GM-600U_048_5kb_2.3dg.txt
GM-600U_048_5kb_3.3dg.txt
GM-600U_048_5kb_4.3dg.txt
GM-600U_048_20kb_1.clean.3dg.txt
GM-600U_048_20kb_2.clean.3dg.txt
GM-600U_048_20kb_3.clean.3dg.txt
GM-600U_048_20kb_4.clean.3dg.txt
GM-600U_048_10kb_1.clean.3dg.txt
GM-600U_048_10kb_2.clean.3dg.txt
GM-600U_048_10kb_3.clean.3dg.txt
GM-600U_048_10kb_4.clean.3dg.txt
GM-600U_048_5kb_1.clean.3dg.txt
GM-600U_048_5kb_2.clean.3dg.txt
GM-600U_048_5kb_3.clean.3dg.txt
GM-600U_048_5kb_4.clean.3dg.txt


title: cell_122


title: Patient4_MyleoidCell_POST

source_name: Myeloid cell


title: Sca1+ FAP_Kdm6b-CutNtag_WT_rep1


title: cell_116


title: GM12878, 600U, Cell 47

description:
GM-600U_047.allValidPairs.txt
GM-600U_047.hic
GM-600U_047.mcool
GM-600U_047.clean.smooth.bw
GM-600U_047_20kb_2.3dg.txt
GM-600U_047_20kb_3.3dg.txt
GM-600U_047_20kb_4.3dg.txt
GM-600U_047_10kb_2.3dg.txt
GM-600U_047_10kb_3.3dg.txt
GM-600U_047_10kb_4.3dg.txt
GM-600U_047_5kb_2.3dg.txt
GM-600U_047_5kb_3.3dg.txt
GM-600U_047_5kb_4.3dg.txt
GM-600U_047_20kb_2.clean.3dg.txt
GM-600U_047_20kb_3.clean.3dg.txt
GM-600U_047_20kb_4.clean.3dg.txt
GM-600U_047_10kb_2.clean.3dg.txt
GM-600U_047_10kb_3.clean.3dg.txt
GM-600U_047_10kb_4.clean.3dg.txt
GM-600U_047_5kb_2.clean.3dg.txt
GM-600U_047_5kb_3.clean.3dg.txt
GM-600U_047_5kb_4.clean.3dg.txt


title: GM12878, 600U, Cell 46

description:
GM-600U_046.allValidPairs.txt
GM-600U_046.hic
GM-600U_046.mcool
GM-600U_046.clean.smooth.bw
GM-600U_046_20kb_1.3dg.txt
GM-600U_046_20kb_2.3dg.txt
GM-600U_046_20kb_3.3dg.txt
GM-600U_046_20kb_4.3dg.txt
GM-600U_046_20kb_5.3dg.txt
GM-600U_046_10kb_1.3dg.txt
GM-600U_046_10kb_2.3dg.txt
GM-600U_046_10kb_3.3dg.txt
GM-600U_046_10kb_4.3dg.txt
GM-600U_046_10kb_5.3dg.txt
GM-600U_046_5kb_1.3dg.txt
GM-600U_046_5kb_2.3dg.txt
GM-600U_046_5kb_3.3dg.txt
GM-600U_046_5kb_4.3dg.txt
GM-600U_046_5kb_5.3dg.txt
GM-600U_046_20kb_1.clean.3dg.txt
GM-600U_046_20kb_2.clean.3dg.txt
GM-600U_046_20kb_3.clean.3dg.txt
GM-600U_046_20kb_4.clean.3dg.txt
GM-600U_046_20kb_5.clean.3dg.txt
GM-600U_046_10kb_1.clean.3dg.txt
GM-600U_046_10kb_2.clean.3dg.txt
GM-600U_046_10kb_3.clean.3dg.txt
GM-600U_046_10kb_4.clean.3dg.txt
GM-600U_046_10kb_5.clean.3dg.txt
GM-600U_046_5kb_1.clean.3dg.txt
GM-600U_046_5kb_2.clean.3dg.txt
GM-600U_046_5kb_3.clean.3dg.txt
GM-600U_046_5kb_4.clean.3dg.txt
GM-600U_046_5kb_5.clean.3dg.txt


title: cell_115


title: Patient4_Bcell_POST


title: cell_114


title: Patient5_MyleoidCell_POST


title: GM12878, 600U, Cell 45

description:
GM-600U_045.allValidPairs.txt
GM-600U_045.hic
GM-600U_045.mcool
GM-600U_045.clean.smooth.bw
GM-600U_045_20kb_1.3dg.txt
GM-600U_045_20kb_2.3dg.txt
GM-600U_045_20kb_3.3dg.txt
GM-600U_045_20kb_4.3dg.txt
GM-600U_045_20kb_5.3dg.txt
GM-600U_045_10kb_1.3dg.txt
GM-600U_045_10kb_2.3dg.txt
GM-600U_045_10kb_3.3dg.txt
GM-600U_045_10kb_4.3dg.txt
GM-600U_045_10kb_5.3dg.txt
GM-600U_045_5kb_1.3dg.txt
GM-600U_045_5kb_2.3dg.txt
GM-600U_045_5kb_3.3dg.txt
GM-600U_045_5kb_4.3dg.txt
GM-600U_045_5kb_5.3dg.txt
GM-600U_045_20kb_1.clean.3dg.txt
GM-600U_045_20kb_2.clean.3dg.txt
GM-600U_045_20kb_3.clean.3dg.txt
GM-600U_045_20kb_4.clean.3dg.txt
GM-600U_045_20kb_5.clean.3dg.txt
GM-600U_045_10kb_1.clean.3dg.txt
GM-600U_045_10kb_2.clean.3dg.txt
GM-600U_045_10kb_3.clean.3dg.txt
GM-600U_045_10kb_4.clean.3dg.txt
GM-600U_045_10kb_5.clean.3dg.txt
GM-600U_045_5kb_1.clean.3dg.txt
GM-600U_045_5kb_2.clean.3dg.txt
GM-600U_045_5kb_3.clean.3dg.txt
GM-600U_045_5kb_4.clean.3dg.txt
GM-600U_045_5kb_5.clean.3dg.txt


title: Sca1+ FAP_Kdm6b-CutNtag_Utrn-Mdx_rep1

description:
Kdm6b cut-and-tag for FAPs from Utrophin-Dystrophin double KO mouse
FAP_Kdm6b-CutNtag_Utrn-Mdx.bw

value: Utrn-/- , Mdx


title: cell_113


title: Patient4_Tcell_POST


title: GM12878, 600U, Cell 44

description:
GM-600U_044.allValidPairs.txt
GM-600U_044.hic
GM-600U_044.mcool
GM-600U_044.clean.smooth.bw
GM-600U_044_20kb_2.3dg.txt
GM-600U_044_20kb_3.3dg.txt
GM-600U_044_20kb_4.3dg.txt
GM-600U_044_10kb_2.3dg.txt
GM-600U_044_10kb_3.3dg.txt
GM-600U_044_10kb_4.3dg.txt
GM-600U_044_5kb_2.3dg.txt
GM-600U_044_5kb_3.3dg.txt
GM-600U_044_5kb_4.3dg.txt
GM-600U_044_20kb_2.clean.3dg.txt
GM-600U_044_20kb_3.clean.3dg.txt
GM-600U_044_20kb_4.clean.3dg.txt
GM-600U_044_10kb_2.clean.3dg.txt
GM-600U_044_10kb_3.clean.3dg.txt
GM-600U_044_10kb_4.clean.3dg.txt
GM-600U_044_5kb_2.clean.3dg.txt
GM-600U_044_5kb_3.clean.3dg.txt
GM-600U_044_5kb_4.clean.3dg.txt


title: Patient3_MyleoidCell_POST


title: Patient3_Bcell_POST


title: Sca1+ FAP_Kdm6b-CutNtag_Mdx_rep1

description:
Kdm6b cut-and-tag for FAPs from Mdx mouse
FAP_Kdm6b-CutNtag_Mdx.bw


title: GM12878, 600U, Cell 43

description:
GM-600U_043.allValidPairs.txt
GM-600U_043.hic
GM-600U_043.mcool
GM-600U_043.clean.smooth.bw
GM-600U_043_20kb_1.3dg.txt
GM-600U_043_20kb_2.3dg.txt
GM-600U_043_20kb_3.3dg.txt
GM-600U_043_20kb_4.3dg.txt
GM-600U_043_20kb_5.3dg.txt
GM-600U_043_10kb_1.3dg.txt
GM-600U_043_10kb_2.3dg.txt
GM-600U_043_10kb_3.3dg.txt
GM-600U_043_10kb_4.3dg.txt
GM-600U_043_10kb_5.3dg.txt
GM-600U_043_5kb_1.3dg.txt
GM-600U_043_5kb_2.3dg.txt
GM-600U_043_5kb_3.3dg.txt
GM-600U_043_5kb_4.3dg.txt
GM-600U_043_5kb_5.3dg.txt
GM-600U_043_20kb_1.clean.3dg.txt
GM-600U_043_20kb_2.clean.3dg.txt
GM-600U_043_20kb_3.clean.3dg.txt
GM-600U_043_20kb_4.clean.3dg.txt
GM-600U_043_20kb_5.clean.3dg.txt
GM-600U_043_10kb_1.clean.3dg.txt
GM-600U_043_10kb_2.clean.3dg.txt
GM-600U_043_10kb_3.clean.3dg.txt
GM-600U_043_10kb_4.clean.3dg.txt
GM-600U_043_10kb_5.clean.3dg.txt
GM-600U_043_5kb_1.clean.3dg.txt
GM-600U_043_5kb_2.clean.3dg.txt
GM-600U_043_5kb_3.clean.3dg.txt
GM-600U_043_5kb_4.clean.3dg.txt
GM-600U_043_5kb_5.clean.3dg.txt


title: cell_111


title: GM12878, 600U, Cell 42

description:
GM-600U_042.allValidPairs.txt
GM-600U_042.hic
GM-600U_042.mcool
GM-600U_042.clean.smooth.bw
GM-600U_042_20kb_1.3dg.txt
GM-600U_042_20kb_2.3dg.txt
GM-600U_042_20kb_3.3dg.txt
GM-600U_042_20kb_4.3dg.txt
GM-600U_042_20kb_5.3dg.txt
GM-600U_042_10kb_1.3dg.txt
GM-600U_042_10kb_2.3dg.txt
GM-600U_042_10kb_3.3dg.txt
GM-600U_042_10kb_4.3dg.txt
GM-600U_042_10kb_5.3dg.txt
GM-600U_042_5kb_1.3dg.txt
GM-600U_042_5kb_2.3dg.txt
GM-600U_042_5kb_3.3dg.txt
GM-600U_042_5kb_4.3dg.txt
GM-600U_042_5kb_5.3dg.txt
GM-600U_042_20kb_1.clean.3dg.txt
GM-600U_042_20kb_2.clean.3dg.txt
GM-600U_042_20kb_3.clean.3dg.txt
GM-600U_042_20kb_4.clean.3dg.txt
GM-600U_042_20kb_5.clean.3dg.txt
GM-600U_042_10kb_1.clean.3dg.txt
GM-600U_042_10kb_2.clean.3dg.txt
GM-600U_042_10kb_3.clean.3dg.txt
GM-600U_042_10kb_4.clean.3dg.txt
GM-600U_042_10kb_5.clean.3dg.txt
GM-600U_042_5kb_1.clean.3dg.txt
GM-600U_042_5kb_2.clean.3dg.txt
GM-600U_042_5kb_3.clean.3dg.txt
GM-600U_042_5kb_4.clean.3dg.txt
GM-600U_042_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAP_H3K27me3-CutNtag_PdgfraCre-Kdm6bcKO_rep2

description:
H3K27Me3 cut-and-tag for mouse FAPs from PdgfraCre-dependent cKO of Kdm6b
FAP_H3K27me3-CutNtag_PdgfraCre-Kdm6bcKO.bw

tag: treatment

value: Tamoxifen


title: cell_110

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: Patient3_Tcell_POST


title: Patient2_MyleoidCell_POST


title: GM12878, 600U, Cell 41

description:
GM-600U_041.allValidPairs.txt
GM-600U_041.hic
GM-600U_041.mcool
GM-600U_041.clean.smooth.bw
GM-600U_041_20kb_1.3dg.txt
GM-600U_041_20kb_2.3dg.txt
GM-600U_041_20kb_3.3dg.txt
GM-600U_041_10kb_1.3dg.txt
GM-600U_041_10kb_2.3dg.txt
GM-600U_041_10kb_3.3dg.txt
GM-600U_041_5kb_1.3dg.txt
GM-600U_041_5kb_2.3dg.txt
GM-600U_041_5kb_3.3dg.txt
GM-600U_041_20kb_1.clean.3dg.txt
GM-600U_041_20kb_2.clean.3dg.txt
GM-600U_041_20kb_3.clean.3dg.txt
GM-600U_041_10kb_1.clean.3dg.txt
GM-600U_041_10kb_2.clean.3dg.txt
GM-600U_041_10kb_3.clean.3dg.txt
GM-600U_041_5kb_1.clean.3dg.txt
GM-600U_041_5kb_2.clean.3dg.txt
GM-600U_041_5kb_3.clean.3dg.txt


title: Patient2_Bcell_POST


title: cell_109


title: GM12878, 600U, Cell 40

description:
GM-600U_040.allValidPairs.txt
GM-600U_040.hic
GM-600U_040.mcool
GM-600U_040.clean.smooth.bw
GM-600U_040_20kb_1.3dg.txt
GM-600U_040_20kb_2.3dg.txt
GM-600U_040_20kb_3.3dg.txt
GM-600U_040_20kb_4.3dg.txt
GM-600U_040_20kb_5.3dg.txt
GM-600U_040_10kb_1.3dg.txt
GM-600U_040_10kb_2.3dg.txt
GM-600U_040_10kb_3.3dg.txt
GM-600U_040_10kb_4.3dg.txt
GM-600U_040_10kb_5.3dg.txt
GM-600U_040_5kb_1.3dg.txt
GM-600U_040_5kb_2.3dg.txt
GM-600U_040_5kb_3.3dg.txt
GM-600U_040_5kb_4.3dg.txt
GM-600U_040_5kb_5.3dg.txt
GM-600U_040_20kb_1.clean.3dg.txt
GM-600U_040_20kb_2.clean.3dg.txt
GM-600U_040_20kb_3.clean.3dg.txt
GM-600U_040_20kb_4.clean.3dg.txt
GM-600U_040_20kb_5.clean.3dg.txt
GM-600U_040_10kb_1.clean.3dg.txt
GM-600U_040_10kb_2.clean.3dg.txt
GM-600U_040_10kb_3.clean.3dg.txt
GM-600U_040_10kb_4.clean.3dg.txt
GM-600U_040_10kb_5.clean.3dg.txt
GM-600U_040_5kb_1.clean.3dg.txt
GM-600U_040_5kb_2.clean.3dg.txt
GM-600U_040_5kb_3.clean.3dg.txt
GM-600U_040_5kb_4.clean.3dg.txt
GM-600U_040_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAP_H3K27me3-CutNtag_Pdgfra-ckoCntrl_rep2

description:
H3K27Me3 cut-and-tag for cKO cntrl mouse FAPs
FAP_H3K27me3-CutNtag_Pdgfra-ckoCntrl.bw


title: Sca1+ FAP_Kdm6b-CutNtag_Utrn-Mdx_rep2


title: cell_108


title: cell_107


title: GM12878, 600U, Cell 39

description:
GM-600U_039.allValidPairs.txt
GM-600U_039.hic
GM-600U_039.mcool
GM-600U_039.clean.smooth.bw
GM-600U_039_20kb_1.3dg.txt
GM-600U_039_20kb_2.3dg.txt
GM-600U_039_20kb_3.3dg.txt
GM-600U_039_20kb_4.3dg.txt
GM-600U_039_20kb_5.3dg.txt
GM-600U_039_10kb_1.3dg.txt
GM-600U_039_10kb_2.3dg.txt
GM-600U_039_10kb_3.3dg.txt
GM-600U_039_10kb_4.3dg.txt
GM-600U_039_10kb_5.3dg.txt
GM-600U_039_5kb_1.3dg.txt
GM-600U_039_5kb_2.3dg.txt
GM-600U_039_5kb_3.3dg.txt
GM-600U_039_5kb_4.3dg.txt
GM-600U_039_5kb_5.3dg.txt
GM-600U_039_20kb_1.clean.3dg.txt
GM-600U_039_20kb_2.clean.3dg.txt
GM-600U_039_20kb_3.clean.3dg.txt
GM-600U_039_20kb_4.clean.3dg.txt
GM-600U_039_20kb_5.clean.3dg.txt
GM-600U_039_10kb_1.clean.3dg.txt
GM-600U_039_10kb_2.clean.3dg.txt
GM-600U_039_10kb_3.clean.3dg.txt
GM-600U_039_10kb_4.clean.3dg.txt
GM-600U_039_10kb_5.clean.3dg.txt
GM-600U_039_5kb_1.clean.3dg.txt
GM-600U_039_5kb_2.clean.3dg.txt
GM-600U_039_5kb_3.clean.3dg.txt
GM-600U_039_5kb_4.clean.3dg.txt
GM-600U_039_5kb_5.clean.3dg.txt


title: Patient2_Tcell_POST


title: Mouse muscle Sca1+ FAP_H3K27me3-CutNtag_Pdgfra-ckoCntrl_rep1


title: GM12878, 600U, Cell 38

description:
GM-600U_038.allValidPairs.txt
GM-600U_038.hic
GM-600U_038.mcool
GM-600U_038.clean.smooth.bw
GM-600U_038_20kb_1.3dg.txt
GM-600U_038_20kb_2.3dg.txt
GM-600U_038_20kb_3.3dg.txt
GM-600U_038_20kb_5.3dg.txt
GM-600U_038_10kb_1.3dg.txt
GM-600U_038_10kb_2.3dg.txt
GM-600U_038_10kb_3.3dg.txt
GM-600U_038_10kb_5.3dg.txt
GM-600U_038_5kb_1.3dg.txt
GM-600U_038_5kb_2.3dg.txt
GM-600U_038_5kb_3.3dg.txt
GM-600U_038_5kb_5.3dg.txt
GM-600U_038_20kb_1.clean.3dg.txt
GM-600U_038_20kb_2.clean.3dg.txt
GM-600U_038_20kb_3.clean.3dg.txt
GM-600U_038_20kb_5.clean.3dg.txt
GM-600U_038_10kb_1.clean.3dg.txt
GM-600U_038_10kb_2.clean.3dg.txt
GM-600U_038_10kb_3.clean.3dg.txt
GM-600U_038_10kb_5.clean.3dg.txt
GM-600U_038_5kb_1.clean.3dg.txt
GM-600U_038_5kb_2.clean.3dg.txt
GM-600U_038_5kb_3.clean.3dg.txt
GM-600U_038_5kb_5.clean.3dg.txt


title: Patient1_MyleoidCell_POST


title: Mouse muscle Sca1+ FAP_H3K27me3_WT_CutNtag_rep3

description:
H3K27Me3 cut-and-tag for FAPs from WT mouse
FAP_H3K27me3_WT_CutNtag.bw


title: cell_106


title: cell_112


title: GM12878, 600U, Cell 37

description:
GM-600U_037.allValidPairs.txt
GM-600U_037.hic
GM-600U_037.mcool
GM-600U_037.clean.smooth.bw
GM-600U_037_20kb_1.3dg.txt
GM-600U_037_20kb_2.3dg.txt
GM-600U_037_20kb_3.3dg.txt
GM-600U_037_20kb_4.3dg.txt
GM-600U_037_20kb_5.3dg.txt
GM-600U_037_10kb_1.3dg.txt
GM-600U_037_10kb_2.3dg.txt
GM-600U_037_10kb_3.3dg.txt
GM-600U_037_10kb_4.3dg.txt
GM-600U_037_10kb_5.3dg.txt
GM-600U_037_5kb_1.3dg.txt
GM-600U_037_5kb_2.3dg.txt
GM-600U_037_5kb_3.3dg.txt
GM-600U_037_5kb_4.3dg.txt
GM-600U_037_5kb_5.3dg.txt
GM-600U_037_20kb_1.clean.3dg.txt
GM-600U_037_20kb_2.clean.3dg.txt
GM-600U_037_20kb_3.clean.3dg.txt
GM-600U_037_20kb_4.clean.3dg.txt
GM-600U_037_20kb_5.clean.3dg.txt
GM-600U_037_10kb_1.clean.3dg.txt
GM-600U_037_10kb_2.clean.3dg.txt
GM-600U_037_10kb_3.clean.3dg.txt
GM-600U_037_10kb_4.clean.3dg.txt
GM-600U_037_10kb_5.clean.3dg.txt
GM-600U_037_5kb_1.clean.3dg.txt
GM-600U_037_5kb_2.clean.3dg.txt
GM-600U_037_5kb_3.clean.3dg.txt
GM-600U_037_5kb_4.clean.3dg.txt
GM-600U_037_5kb_5.clean.3dg.txt


title: Sca1+ FAP_Kdm6b-CutNtag_Mdx_rep2


title: Patient1_Bcell_POST


title: Mouse muscle Sca1+ FAP_H3K27me3_WT_CutNtag_rep2


title: GM12878, 600U, Cell 36

description:
GM-600U_036.allValidPairs.txt
GM-600U_036.hic
GM-600U_036.mcool
GM-600U_036.clean.smooth.bw
GM-600U_036_20kb_1.3dg.txt
GM-600U_036_20kb_2.3dg.txt
GM-600U_036_20kb_3.3dg.txt
GM-600U_036_20kb_4.3dg.txt
GM-600U_036_20kb_5.3dg.txt
GM-600U_036_10kb_1.3dg.txt
GM-600U_036_10kb_2.3dg.txt
GM-600U_036_10kb_3.3dg.txt
GM-600U_036_10kb_4.3dg.txt
GM-600U_036_10kb_5.3dg.txt
GM-600U_036_5kb_1.3dg.txt
GM-600U_036_5kb_2.3dg.txt
GM-600U_036_5kb_3.3dg.txt
GM-600U_036_5kb_4.3dg.txt
GM-600U_036_5kb_5.3dg.txt
GM-600U_036_20kb_1.clean.3dg.txt
GM-600U_036_20kb_2.clean.3dg.txt
GM-600U_036_20kb_3.clean.3dg.txt
GM-600U_036_20kb_4.clean.3dg.txt
GM-600U_036_20kb_5.clean.3dg.txt
GM-600U_036_10kb_1.clean.3dg.txt
GM-600U_036_10kb_2.clean.3dg.txt
GM-600U_036_10kb_3.clean.3dg.txt
GM-600U_036_10kb_4.clean.3dg.txt
GM-600U_036_10kb_5.clean.3dg.txt
GM-600U_036_5kb_1.clean.3dg.txt
GM-600U_036_5kb_2.clean.3dg.txt
GM-600U_036_5kb_3.clean.3dg.txt
GM-600U_036_5kb_4.clean.3dg.txt
GM-600U_036_5kb_5.clean.3dg.txt


title: cell_105


title: Patient1_Tcell_POST


title: Mouse muscle Sca1+ FAP_H3K27me3_WT_CutNtag_rep1


title: Mouse muscle Sca1+ FAP_H3K27me3-CutNtag_PdgfraCre-Kdm6bcKO_rep1


title: GM12878, 600U, Cell 35

description:
GM-600U_035.allValidPairs.txt
GM-600U_035.hic
GM-600U_035.mcool
GM-600U_035.clean.smooth.bw
GM-600U_035_20kb_1.3dg.txt
GM-600U_035_20kb_2.3dg.txt
GM-600U_035_20kb_3.3dg.txt
GM-600U_035_20kb_4.3dg.txt
GM-600U_035_20kb_5.3dg.txt
GM-600U_035_10kb_1.3dg.txt
GM-600U_035_10kb_2.3dg.txt
GM-600U_035_10kb_3.3dg.txt
GM-600U_035_10kb_4.3dg.txt
GM-600U_035_10kb_5.3dg.txt
GM-600U_035_5kb_1.3dg.txt
GM-600U_035_5kb_2.3dg.txt
GM-600U_035_5kb_3.3dg.txt
GM-600U_035_5kb_4.3dg.txt
GM-600U_035_5kb_5.3dg.txt
GM-600U_035_20kb_1.clean.3dg.txt
GM-600U_035_20kb_2.clean.3dg.txt
GM-600U_035_20kb_3.clean.3dg.txt
GM-600U_035_20kb_4.clean.3dg.txt
GM-600U_035_20kb_5.clean.3dg.txt
GM-600U_035_10kb_1.clean.3dg.txt
GM-600U_035_10kb_2.clean.3dg.txt
GM-600U_035_10kb_3.clean.3dg.txt
GM-600U_035_10kb_4.clean.3dg.txt
GM-600U_035_10kb_5.clean.3dg.txt
GM-600U_035_5kb_1.clean.3dg.txt
GM-600U_035_5kb_2.clean.3dg.txt
GM-600U_035_5kb_3.clean.3dg.txt
GM-600U_035_5kb_4.clean.3dg.txt
GM-600U_035_5kb_5.clean.3dg.txt


title: cell_104


title: Mouse muscle Sca1+ FAP_H3K27me3_Utrn-Mdx_CutNtag_rep2

description:
H3K27Me3 cut-and-tag for FAPs from Utrophin-Dystrophin double KO mouse
FAP_H3K27me3_Utrn-Mdx_CutNtag.bw


title: Patient10_MyleoidCell_PRE

value: Pre-treatment


title: cell_103


title: Patient10_Bcell_PRE


title: GM12878, 600U, Cell 33

description:
GM-600U_033.allValidPairs.txt
GM-600U_033.hic
GM-600U_033.mcool
GM-600U_033.clean.smooth.bw
GM-600U_033_20kb_1.3dg.txt
GM-600U_033_20kb_2.3dg.txt
GM-600U_033_20kb_3.3dg.txt
GM-600U_033_20kb_4.3dg.txt
GM-600U_033_20kb_5.3dg.txt
GM-600U_033_10kb_1.3dg.txt
GM-600U_033_10kb_2.3dg.txt
GM-600U_033_10kb_3.3dg.txt
GM-600U_033_10kb_4.3dg.txt
GM-600U_033_10kb_5.3dg.txt
GM-600U_033_5kb_1.3dg.txt
GM-600U_033_5kb_2.3dg.txt
GM-600U_033_5kb_3.3dg.txt
GM-600U_033_5kb_4.3dg.txt
GM-600U_033_5kb_5.3dg.txt
GM-600U_033_20kb_1.clean.3dg.txt
GM-600U_033_20kb_2.clean.3dg.txt
GM-600U_033_20kb_3.clean.3dg.txt
GM-600U_033_20kb_4.clean.3dg.txt
GM-600U_033_20kb_5.clean.3dg.txt
GM-600U_033_10kb_1.clean.3dg.txt
GM-600U_033_10kb_2.clean.3dg.txt
GM-600U_033_10kb_3.clean.3dg.txt
GM-600U_033_10kb_4.clean.3dg.txt
GM-600U_033_10kb_5.clean.3dg.txt
GM-600U_033_5kb_1.clean.3dg.txt
GM-600U_033_5kb_2.clean.3dg.txt
GM-600U_033_5kb_3.clean.3dg.txt
GM-600U_033_5kb_4.clean.3dg.txt
GM-600U_033_5kb_5.clean.3dg.txt


title: GM12878, 600U, Cell 34

description:
GM-600U_034.allValidPairs.txt
GM-600U_034.hic
GM-600U_034.mcool
GM-600U_034.clean.smooth.bw
GM-600U_034_20kb_1.3dg.txt
GM-600U_034_20kb_2.3dg.txt
GM-600U_034_20kb_3.3dg.txt
GM-600U_034_20kb_4.3dg.txt
GM-600U_034_20kb_5.3dg.txt
GM-600U_034_10kb_1.3dg.txt
GM-600U_034_10kb_2.3dg.txt
GM-600U_034_10kb_3.3dg.txt
GM-600U_034_10kb_4.3dg.txt
GM-600U_034_10kb_5.3dg.txt
GM-600U_034_5kb_1.3dg.txt
GM-600U_034_5kb_2.3dg.txt
GM-600U_034_5kb_3.3dg.txt
GM-600U_034_5kb_4.3dg.txt
GM-600U_034_5kb_5.3dg.txt
GM-600U_034_20kb_1.clean.3dg.txt
GM-600U_034_20kb_2.clean.3dg.txt
GM-600U_034_20kb_3.clean.3dg.txt
GM-600U_034_20kb_4.clean.3dg.txt
GM-600U_034_20kb_5.clean.3dg.txt
GM-600U_034_10kb_1.clean.3dg.txt
GM-600U_034_10kb_2.clean.3dg.txt
GM-600U_034_10kb_3.clean.3dg.txt
GM-600U_034_10kb_4.clean.3dg.txt
GM-600U_034_10kb_5.clean.3dg.txt
GM-600U_034_5kb_1.clean.3dg.txt
GM-600U_034_5kb_2.clean.3dg.txt
GM-600U_034_5kb_3.clean.3dg.txt
GM-600U_034_5kb_4.clean.3dg.txt
GM-600U_034_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAP_H3K27me3_Utrn-Mdx_CutNtag_rep1


title: cell_101


title: Mouse muscle Sca1+ FAP_H3K27me3_Mdx_CutNtag_rep3

description:
H3K27Me3 cut-and-tag for FAPs from Mdx mouse
FAP_H3K27me3_Mdx_CutNtag.bw


title: GM12878, 600U, Cell 32

description:
GM-600U_032.allValidPairs.txt
GM-600U_032.hic
GM-600U_032.mcool
GM-600U_032.clean.smooth.bw
GM-600U_032_20kb_1.3dg.txt
GM-600U_032_20kb_2.3dg.txt
GM-600U_032_20kb_3.3dg.txt
GM-600U_032_20kb_4.3dg.txt
GM-600U_032_20kb_5.3dg.txt
GM-600U_032_10kb_1.3dg.txt
GM-600U_032_10kb_2.3dg.txt
GM-600U_032_10kb_3.3dg.txt
GM-600U_032_10kb_4.3dg.txt
GM-600U_032_10kb_5.3dg.txt
GM-600U_032_5kb_1.3dg.txt
GM-600U_032_5kb_2.3dg.txt
GM-600U_032_5kb_3.3dg.txt
GM-600U_032_5kb_4.3dg.txt
GM-600U_032_5kb_5.3dg.txt
GM-600U_032_20kb_1.clean.3dg.txt
GM-600U_032_20kb_2.clean.3dg.txt
GM-600U_032_20kb_3.clean.3dg.txt
GM-600U_032_20kb_4.clean.3dg.txt
GM-600U_032_20kb_5.clean.3dg.txt
GM-600U_032_10kb_1.clean.3dg.txt
GM-600U_032_10kb_2.clean.3dg.txt
GM-600U_032_10kb_3.clean.3dg.txt
GM-600U_032_10kb_4.clean.3dg.txt
GM-600U_032_10kb_5.clean.3dg.txt
GM-600U_032_5kb_1.clean.3dg.txt
GM-600U_032_5kb_2.clean.3dg.txt
GM-600U_032_5kb_3.clean.3dg.txt
GM-600U_032_5kb_4.clean.3dg.txt
GM-600U_032_5kb_5.clean.3dg.txt


title: Patient9_MyleoidCell_PRE


title: Mouse muscle Sca1+ FAP_H3K27me3_Mdx_CutNtag_rep2


title: GM12878, 600U, Cell 31

description:
GM-600U_031.allValidPairs.txt
GM-600U_031.hic
GM-600U_031.mcool
GM-600U_031.clean.smooth.bw
GM-600U_031_20kb_1.3dg.txt
GM-600U_031_20kb_2.3dg.txt
GM-600U_031_20kb_3.3dg.txt
GM-600U_031_20kb_4.3dg.txt
GM-600U_031_20kb_5.3dg.txt
GM-600U_031_10kb_1.3dg.txt
GM-600U_031_10kb_2.3dg.txt
GM-600U_031_10kb_3.3dg.txt
GM-600U_031_10kb_4.3dg.txt
GM-600U_031_10kb_5.3dg.txt
GM-600U_031_5kb_1.3dg.txt
GM-600U_031_5kb_2.3dg.txt
GM-600U_031_5kb_3.3dg.txt
GM-600U_031_5kb_4.3dg.txt
GM-600U_031_5kb_5.3dg.txt
GM-600U_031_20kb_1.clean.3dg.txt
GM-600U_031_20kb_2.clean.3dg.txt
GM-600U_031_20kb_3.clean.3dg.txt
GM-600U_031_20kb_4.clean.3dg.txt
GM-600U_031_20kb_5.clean.3dg.txt
GM-600U_031_10kb_1.clean.3dg.txt
GM-600U_031_10kb_2.clean.3dg.txt
GM-600U_031_10kb_3.clean.3dg.txt
GM-600U_031_10kb_4.clean.3dg.txt
GM-600U_031_10kb_5.clean.3dg.txt
GM-600U_031_5kb_1.clean.3dg.txt
GM-600U_031_5kb_2.clean.3dg.txt
GM-600U_031_5kb_3.clean.3dg.txt
GM-600U_031_5kb_4.clean.3dg.txt
GM-600U_031_5kb_5.clean.3dg.txt


title: cell_100


title: Patient9_Bcell_PRE


title: Mouse muscle Sca1+ FAP_H3K27me3_Mdx_CutNtag_rep1


title: cell_099


title: cell_098


title: Patient9_Tcell_PRE


title: Mouse muscle Sca1+ FAP_Fosl1-CutNtag_WT_rep2

description:
Fosl1 cut-and-tag for FAPs from wildtype mouse
FAP_Fosl1-CutnTag_WT.bw


title: GM12878, 600U, Cell 30

description:
GM-600U_030.allValidPairs.txt
GM-600U_030.hic
GM-600U_030.mcool
GM-600U_030.clean.smooth.bw
GM-600U_030_20kb_1.3dg.txt
GM-600U_030_20kb_2.3dg.txt
GM-600U_030_20kb_3.3dg.txt
GM-600U_030_20kb_4.3dg.txt
GM-600U_030_20kb_5.3dg.txt
GM-600U_030_10kb_1.3dg.txt
GM-600U_030_10kb_2.3dg.txt
GM-600U_030_10kb_3.3dg.txt
GM-600U_030_10kb_4.3dg.txt
GM-600U_030_10kb_5.3dg.txt
GM-600U_030_5kb_1.3dg.txt
GM-600U_030_5kb_2.3dg.txt
GM-600U_030_5kb_3.3dg.txt
GM-600U_030_5kb_4.3dg.txt
GM-600U_030_5kb_5.3dg.txt
GM-600U_030_20kb_1.clean.3dg.txt
GM-600U_030_20kb_2.clean.3dg.txt
GM-600U_030_20kb_3.clean.3dg.txt
GM-600U_030_20kb_4.clean.3dg.txt
GM-600U_030_20kb_5.clean.3dg.txt
GM-600U_030_10kb_1.clean.3dg.txt
GM-600U_030_10kb_2.clean.3dg.txt
GM-600U_030_10kb_3.clean.3dg.txt
GM-600U_030_10kb_4.clean.3dg.txt
GM-600U_030_10kb_5.clean.3dg.txt
GM-600U_030_5kb_1.clean.3dg.txt
GM-600U_030_5kb_2.clean.3dg.txt
GM-600U_030_5kb_3.clean.3dg.txt
GM-600U_030_5kb_4.clean.3dg.txt
GM-600U_030_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAP_Fosl1-CutNtag_Utrn-Mdx_rep2

description:
Fosl1 cut-and-tag for FAPs from Utrophin-Dystrophin double KO mouse
FAP_Fosl1-CutNtag_Utrn-Mdx.bw


title: Patient8_Bcell_PRE


title: GM12878, 600U, Cell 28

description:
GM-600U_028.allValidPairs.txt
GM-600U_028.hic
GM-600U_028.mcool
GM-600U_028.clean.smooth.bw
GM-600U_028_20kb_1.3dg.txt
GM-600U_028_20kb_2.3dg.txt
GM-600U_028_20kb_3.3dg.txt
GM-600U_028_20kb_4.3dg.txt
GM-600U_028_20kb_5.3dg.txt
GM-600U_028_10kb_1.3dg.txt
GM-600U_028_10kb_2.3dg.txt
GM-600U_028_10kb_3.3dg.txt
GM-600U_028_10kb_4.3dg.txt
GM-600U_028_10kb_5.3dg.txt
GM-600U_028_5kb_1.3dg.txt
GM-600U_028_5kb_2.3dg.txt
GM-600U_028_5kb_3.3dg.txt
GM-600U_028_5kb_4.3dg.txt
GM-600U_028_5kb_5.3dg.txt
GM-600U_028_20kb_1.clean.3dg.txt
GM-600U_028_20kb_2.clean.3dg.txt
GM-600U_028_20kb_3.clean.3dg.txt
GM-600U_028_20kb_4.clean.3dg.txt
GM-600U_028_20kb_5.clean.3dg.txt
GM-600U_028_10kb_1.clean.3dg.txt
GM-600U_028_10kb_2.clean.3dg.txt
GM-600U_028_10kb_3.clean.3dg.txt
GM-600U_028_10kb_4.clean.3dg.txt
GM-600U_028_10kb_5.clean.3dg.txt
GM-600U_028_5kb_1.clean.3dg.txt
GM-600U_028_5kb_2.clean.3dg.txt
GM-600U_028_5kb_3.clean.3dg.txt
GM-600U_028_5kb_4.clean.3dg.txt
GM-600U_028_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAP_Fosl1-CutNtag_WT_rep1


title: GM12878, 600U, Cell 29

description:
GM-600U_029.allValidPairs.txt
GM-600U_029.hic
GM-600U_029.mcool
GM-600U_029.clean.smooth.bw
GM-600U_029_20kb_1.3dg.txt
GM-600U_029_20kb_2.3dg.txt
GM-600U_029_20kb_3.3dg.txt
GM-600U_029_20kb_4.3dg.txt
GM-600U_029_20kb_5.3dg.txt
GM-600U_029_10kb_1.3dg.txt
GM-600U_029_10kb_2.3dg.txt
GM-600U_029_10kb_3.3dg.txt
GM-600U_029_10kb_4.3dg.txt
GM-600U_029_10kb_5.3dg.txt
GM-600U_029_5kb_1.3dg.txt
GM-600U_029_5kb_2.3dg.txt
GM-600U_029_5kb_3.3dg.txt
GM-600U_029_5kb_4.3dg.txt
GM-600U_029_5kb_5.3dg.txt
GM-600U_029_20kb_1.clean.3dg.txt
GM-600U_029_20kb_2.clean.3dg.txt
GM-600U_029_20kb_3.clean.3dg.txt
GM-600U_029_20kb_4.clean.3dg.txt
GM-600U_029_20kb_5.clean.3dg.txt
GM-600U_029_10kb_1.clean.3dg.txt
GM-600U_029_10kb_2.clean.3dg.txt
GM-600U_029_10kb_3.clean.3dg.txt
GM-600U_029_10kb_4.clean.3dg.txt
GM-600U_029_10kb_5.clean.3dg.txt
GM-600U_029_5kb_1.clean.3dg.txt
GM-600U_029_5kb_2.clean.3dg.txt
GM-600U_029_5kb_3.clean.3dg.txt
GM-600U_029_5kb_4.clean.3dg.txt
GM-600U_029_5kb_5.clean.3dg.txt


title: Patient8_MyleoidCell_PRE


title: cell_096

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: cell_097


title: Patient10_Tcell_PRE


title: cell_102


title: GM12878, 600U, Cell 27

description:
GM-600U_027.allValidPairs.txt
GM-600U_027.hic
GM-600U_027.mcool
GM-600U_027.clean.smooth.bw
GM-600U_027_20kb_1.3dg.txt
GM-600U_027_20kb_2.3dg.txt
GM-600U_027_20kb_3.3dg.txt
GM-600U_027_20kb_4.3dg.txt
GM-600U_027_20kb_5.3dg.txt
GM-600U_027_10kb_1.3dg.txt
GM-600U_027_10kb_2.3dg.txt
GM-600U_027_10kb_3.3dg.txt
GM-600U_027_10kb_4.3dg.txt
GM-600U_027_10kb_5.3dg.txt
GM-600U_027_5kb_1.3dg.txt
GM-600U_027_5kb_2.3dg.txt
GM-600U_027_5kb_3.3dg.txt
GM-600U_027_5kb_4.3dg.txt
GM-600U_027_5kb_5.3dg.txt
GM-600U_027_20kb_1.clean.3dg.txt
GM-600U_027_20kb_2.clean.3dg.txt
GM-600U_027_20kb_3.clean.3dg.txt
GM-600U_027_20kb_4.clean.3dg.txt
GM-600U_027_20kb_5.clean.3dg.txt
GM-600U_027_10kb_1.clean.3dg.txt
GM-600U_027_10kb_2.clean.3dg.txt
GM-600U_027_10kb_3.clean.3dg.txt
GM-600U_027_10kb_4.clean.3dg.txt
GM-600U_027_10kb_5.clean.3dg.txt
GM-600U_027_5kb_1.clean.3dg.txt
GM-600U_027_5kb_2.clean.3dg.txt
GM-600U_027_5kb_3.clean.3dg.txt
GM-600U_027_5kb_4.clean.3dg.txt
GM-600U_027_5kb_5.clean.3dg.txt


title: Mouse muscle Sca1+ FAP_Fosl1-CutNtag_Mdx_rep2

description:
Fosl1 cut-and-tag for FAPs from Mdx mouse
FAP_Fosl1-CutNtag_Mdx.bw


title: cell_094


title: GM12878, 600U, Cell 26

description:
GM-600U_026.allValidPairs.txt
GM-600U_026.hic
GM-600U_026.mcool
GM-600U_026.clean.smooth.bw
GM-600U_026_20kb_1.3dg.txt
GM-600U_026_20kb_2.3dg.txt
GM-600U_026_20kb_3.3dg.txt
GM-600U_026_20kb_4.3dg.txt
GM-600U_026_20kb_5.3dg.txt
GM-600U_026_10kb_1.3dg.txt
GM-600U_026_10kb_2.3dg.txt
GM-600U_026_10kb_3.3dg.txt
GM-600U_026_10kb_4.3dg.txt
GM-600U_026_10kb_5.3dg.txt
GM-600U_026_5kb_1.3dg.txt
GM-600U_026_5kb_2.3dg.txt
GM-600U_026_5kb_3.3dg.txt
GM-600U_026_5kb_4.3dg.txt
GM-600U_026_5kb_5.3dg.txt
GM-600U_026_20kb_1.clean.3dg.txt
GM-600U_026_20kb_2.clean.3dg.txt
GM-600U_026_20kb_3.clean.3dg.txt
GM-600U_026_20kb_4.clean.3dg.txt
GM-600U_026_20kb_5.clean.3dg.txt
GM-600U_026_10kb_1.clean.3dg.txt
GM-600U_026_10kb_2.clean.3dg.txt
GM-600U_026_10kb_3.clean.3dg.txt
GM-600U_026_10kb_4.clean.3dg.txt
GM-600U_026_10kb_5.clean.3dg.txt
GM-600U_026_5kb_1.clean.3dg.txt
GM-600U_026_5kb_2.clean.3dg.txt
GM-600U_026_5kb_3.clean.3dg.txt
GM-600U_026_5kb_4.clean.3dg.txt
GM-600U_026_5kb_5.clean.3dg.txt


title: Patient8_Tcell_PRE


title: Patient7_MyleoidCell_PRE


title: Mouse muscle Sca1+ FAP_Fosl1-CutNtag_Utrn-Mdx_rep1


title: GM12878, 600U, Cell 25

description:
GM-600U_025.allValidPairs.txt
GM-600U_025.hic
GM-600U_025.mcool
GM-600U_025.clean.smooth.bw
GM-600U_025_20kb_1.3dg.txt
GM-600U_025_20kb_2.3dg.txt
GM-600U_025_20kb_5.3dg.txt
GM-600U_025_10kb_1.3dg.txt
GM-600U_025_10kb_2.3dg.txt
GM-600U_025_10kb_5.3dg.txt
GM-600U_025_5kb_1.3dg.txt
GM-600U_025_5kb_2.3dg.txt
GM-600U_025_5kb_5.3dg.txt
GM-600U_025_20kb_1.clean.3dg.txt
GM-600U_025_20kb_2.clean.3dg.txt
GM-600U_025_20kb_5.clean.3dg.txt
GM-600U_025_10kb_1.clean.3dg.txt
GM-600U_025_10kb_2.clean.3dg.txt
GM-600U_025_10kb_5.clean.3dg.txt
GM-600U_025_5kb_1.clean.3dg.txt
GM-600U_025_5kb_2.clean.3dg.txt
GM-600U_025_5kb_5.clean.3dg.txt


title: Patient7_Bcell_PRE


title: Patient7_Tcell_PRE


title: GM12878, 600U, Cell 24

description:
GM-600U_024.allValidPairs.txt
GM-600U_024.hic
GM-600U_024.mcool
GM-600U_024.clean.smooth.bw
GM-600U_024_20kb_1.3dg.txt
GM-600U_024_20kb_2.3dg.txt
GM-600U_024_20kb_3.3dg.txt
GM-600U_024_20kb_4.3dg.txt
GM-600U_024_20kb_5.3dg.txt
GM-600U_024_10kb_1.3dg.txt
GM-600U_024_10kb_2.3dg.txt
GM-600U_024_10kb_3.3dg.txt
GM-600U_024_10kb_4.3dg.txt
GM-600U_024_10kb_5.3dg.txt
GM-600U_024_5kb_1.3dg.txt
GM-600U_024_5kb_2.3dg.txt
GM-600U_024_5kb_3.3dg.txt
GM-600U_024_5kb_4.3dg.txt
GM-600U_024_5kb_5.3dg.txt
GM-600U_024_20kb_1.clean.3dg.txt
GM-600U_024_20kb_2.clean.3dg.txt
GM-600U_024_20kb_3.clean.3dg.txt
GM-600U_024_20kb_4.clean.3dg.txt
GM-600U_024_20kb_5.clean.3dg.txt
GM-600U_024_10kb_1.clean.3dg.txt
GM-600U_024_10kb_2.clean.3dg.txt
GM-600U_024_10kb_3.clean.3dg.txt
GM-600U_024_10kb_4.clean.3dg.txt
GM-600U_024_10kb_5.clean.3dg.txt
GM-600U_024_5kb_1.clean.3dg.txt
GM-600U_024_5kb_2.clean.3dg.txt
GM-600U_024_5kb_3.clean.3dg.txt
GM-600U_024_5kb_4.clean.3dg.txt
GM-600U_024_5kb_5.clean.3dg.txt


title: scRNAseq_wildtype_muscle_rep2

description: scRNAseq for wildtype mouse muscle

library_source: transcriptomic single cell

data_processing:
CellRanger (version 6.0.1) was used for creating the gene count matrix.
Harmony was used for batch correction, while seurat (version 4.0.0) was used for clustering and plotting the UMAP, using default parameters. Cell type annotation was guided by the localization of marker-gene expression to specific clusters
Assembly: mm10
Supplementary files format and content: RDS file of seurat object with all cells.

molecule: polyA RNA

extract_protocol:
Single cells were collected from mouse muscle by disection and mincing of muscle tissue, digestion using collagenase II and dispase in wash medium, and training using a 20-gauge needle and a 40 micrometer filter. For samples with immune depletion, cd45 antibody was used to remove immune cells by FACS.
16000 cells were counted using a hemocytometer and loaded onto a 10x Genomics Chromium chip per manufacturer's recommendations. Reverse transcription and library preparation was performed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Gemomis, CG000204) according to manufacturer’s protocols. After a cleanup with SPRIselect Reagent Kit (Beckman, C10640), final libraries were quantified using a Qubit™ 1X dsDNA HS Assay Kit (Invitrogen, Q33231) and fragment size distribution was verified using a High Sensitivity D1000 Tapestation (Agilent, 5067-5582).

value: Wildtype


title: Mouse muscle Sca1+ FAP_Fosl1-CutNtag_Mdx_rep1


title: cell_093


title: cell_092


title: GM12878, 600U, Cell 23

description:
GM-600U_023.allValidPairs.txt
GM-600U_023.hic
GM-600U_023.mcool
GM-600U_023.clean.smooth.bw
GM-600U_023_20kb_1.3dg.txt
GM-600U_023_20kb_2.3dg.txt
GM-600U_023_20kb_3.3dg.txt
GM-600U_023_20kb_4.3dg.txt
GM-600U_023_20kb_5.3dg.txt
GM-600U_023_10kb_1.3dg.txt
GM-600U_023_10kb_2.3dg.txt
GM-600U_023_10kb_3.3dg.txt
GM-600U_023_10kb_4.3dg.txt
GM-600U_023_10kb_5.3dg.txt
GM-600U_023_5kb_1.3dg.txt
GM-600U_023_5kb_2.3dg.txt
GM-600U_023_5kb_3.3dg.txt
GM-600U_023_5kb_4.3dg.txt
GM-600U_023_5kb_5.3dg.txt
GM-600U_023_20kb_1.clean.3dg.txt
GM-600U_023_20kb_2.clean.3dg.txt
GM-600U_023_20kb_3.clean.3dg.txt
GM-600U_023_20kb_4.clean.3dg.txt
GM-600U_023_20kb_5.clean.3dg.txt
GM-600U_023_10kb_1.clean.3dg.txt
GM-600U_023_10kb_2.clean.3dg.txt
GM-600U_023_10kb_3.clean.3dg.txt
GM-600U_023_10kb_4.clean.3dg.txt
GM-600U_023_10kb_5.clean.3dg.txt
GM-600U_023_5kb_1.clean.3dg.txt
GM-600U_023_5kb_2.clean.3dg.txt
GM-600U_023_5kb_3.clean.3dg.txt
GM-600U_023_5kb_4.clean.3dg.txt
GM-600U_023_5kb_5.clean.3dg.txt


title: scRNAseq_wildtype_immune_depleted_muscle_rep3

description: scRNAseq for wildtype mouse muscle, with immune cells depleted.


title: Patient6_MyleoidCell_PRE


title: cell_091


title: scRNAseq_Utrn-Mdx_muscle_rep1

description: scRNAseq for Utrn-Mdx double KO mouse muscle


title: Patient6_Bcell_PRE


title: GM12878, 600U, Cell 22

description:
GM-600U_022.allValidPairs.txt
GM-600U_022.hic
GM-600U_022.mcool
GM-600U_022.clean.smooth.bw
GM-600U_022_20kb_1.3dg.txt
GM-600U_022_20kb_2.3dg.txt
GM-600U_022_20kb_3.3dg.txt
GM-600U_022_20kb_4.3dg.txt
GM-600U_022_20kb_5.3dg.txt
GM-600U_022_10kb_1.3dg.txt
GM-600U_022_10kb_2.3dg.txt
GM-600U_022_10kb_3.3dg.txt
GM-600U_022_10kb_4.3dg.txt
GM-600U_022_10kb_5.3dg.txt
GM-600U_022_5kb_1.3dg.txt
GM-600U_022_5kb_2.3dg.txt
GM-600U_022_5kb_3.3dg.txt
GM-600U_022_5kb_4.3dg.txt
GM-600U_022_5kb_5.3dg.txt
GM-600U_022_20kb_1.clean.3dg.txt
GM-600U_022_20kb_2.clean.3dg.txt
GM-600U_022_20kb_3.clean.3dg.txt
GM-600U_022_20kb_4.clean.3dg.txt
GM-600U_022_20kb_5.clean.3dg.txt
GM-600U_022_10kb_1.clean.3dg.txt
GM-600U_022_10kb_2.clean.3dg.txt
GM-600U_022_10kb_3.clean.3dg.txt
GM-600U_022_10kb_4.clean.3dg.txt
GM-600U_022_10kb_5.clean.3dg.txt
GM-600U_022_5kb_1.clean.3dg.txt
GM-600U_022_5kb_2.clean.3dg.txt
GM-600U_022_5kb_3.clean.3dg.txt
GM-600U_022_5kb_4.clean.3dg.txt
GM-600U_022_5kb_5.clean.3dg.txt


title: cell_089


title: GM12878, 600U, Cell 21

description:
GM-600U_021.allValidPairs.txt
GM-600U_021.hic
GM-600U_021.mcool
GM-600U_021.clean.smooth.bw
GM-600U_021_20kb_1.3dg.txt
GM-600U_021_20kb_2.3dg.txt
GM-600U_021_20kb_3.3dg.txt
GM-600U_021_20kb_4.3dg.txt
GM-600U_021_20kb_5.3dg.txt
GM-600U_021_10kb_1.3dg.txt
GM-600U_021_10kb_2.3dg.txt
GM-600U_021_10kb_3.3dg.txt
GM-600U_021_10kb_4.3dg.txt
GM-600U_021_10kb_5.3dg.txt
GM-600U_021_5kb_1.3dg.txt
GM-600U_021_5kb_2.3dg.txt
GM-600U_021_5kb_3.3dg.txt
GM-600U_021_5kb_4.3dg.txt
GM-600U_021_5kb_5.3dg.txt
GM-600U_021_20kb_1.clean.3dg.txt
GM-600U_021_20kb_2.clean.3dg.txt
GM-600U_021_20kb_3.clean.3dg.txt
GM-600U_021_20kb_4.clean.3dg.txt
GM-600U_021_20kb_5.clean.3dg.txt
GM-600U_021_10kb_1.clean.3dg.txt
GM-600U_021_10kb_2.clean.3dg.txt
GM-600U_021_10kb_3.clean.3dg.txt
GM-600U_021_10kb_4.clean.3dg.txt
GM-600U_021_10kb_5.clean.3dg.txt
GM-600U_021_5kb_1.clean.3dg.txt
GM-600U_021_5kb_2.clean.3dg.txt
GM-600U_021_5kb_3.clean.3dg.txt
GM-600U_021_5kb_4.clean.3dg.txt
GM-600U_021_5kb_5.clean.3dg.txt


title: scRNAseq_Utrn-Mdx_Immune-delpleted_muscle_rep3

description: scRNAseq for Utrn-Mdx double KO mouse muscle, with immune cells depleted


title: GM12878, 600U, Cell 20

description:
GM-600U_020.allValidPairs.txt
GM-600U_020.hic
GM-600U_020.mcool
GM-600U_020.clean.smooth.bw
GM-600U_020_20kb_1.3dg.txt
GM-600U_020_20kb_2.3dg.txt
GM-600U_020_20kb_3.3dg.txt
GM-600U_020_20kb_4.3dg.txt
GM-600U_020_20kb_5.3dg.txt
GM-600U_020_10kb_1.3dg.txt
GM-600U_020_10kb_2.3dg.txt
GM-600U_020_10kb_3.3dg.txt
GM-600U_020_10kb_4.3dg.txt
GM-600U_020_10kb_5.3dg.txt
GM-600U_020_5kb_1.3dg.txt
GM-600U_020_5kb_2.3dg.txt
GM-600U_020_5kb_3.3dg.txt
GM-600U_020_5kb_4.3dg.txt
GM-600U_020_5kb_5.3dg.txt
GM-600U_020_20kb_1.clean.3dg.txt
GM-600U_020_20kb_2.clean.3dg.txt
GM-600U_020_20kb_3.clean.3dg.txt
GM-600U_020_20kb_4.clean.3dg.txt
GM-600U_020_20kb_5.clean.3dg.txt
GM-600U_020_10kb_1.clean.3dg.txt
GM-600U_020_10kb_2.clean.3dg.txt
GM-600U_020_10kb_3.clean.3dg.txt
GM-600U_020_10kb_4.clean.3dg.txt
GM-600U_020_10kb_5.clean.3dg.txt
GM-600U_020_5kb_1.clean.3dg.txt
GM-600U_020_5kb_2.clean.3dg.txt
GM-600U_020_5kb_3.clean.3dg.txt
GM-600U_020_5kb_4.clean.3dg.txt
GM-600U_020_5kb_5.clean.3dg.txt


title: scRNAseq_Utrn-Mdx_Immune-delpleted_muscle_rep2


title: Patient5_MyleoidCell_PRE


title: cell_090


title: Patient6_Tcell_PRE


title: cell_095


title: Patient5_Bcell_PRE


title: GM12878, 600U, Cell 18

description:
GM-600U_018.allValidPairs.txt
GM-600U_018.hic
GM-600U_018.mcool
GM-600U_018.clean.smooth.bw
GM-600U_018_20kb_1.3dg.txt
GM-600U_018_20kb_2.3dg.txt
GM-600U_018_20kb_3.3dg.txt
GM-600U_018_20kb_4.3dg.txt
GM-600U_018_20kb_5.3dg.txt
GM-600U_018_10kb_1.3dg.txt
GM-600U_018_10kb_2.3dg.txt
GM-600U_018_10kb_3.3dg.txt
GM-600U_018_10kb_4.3dg.txt
GM-600U_018_10kb_5.3dg.txt
GM-600U_018_5kb_1.3dg.txt
GM-600U_018_5kb_2.3dg.txt
GM-600U_018_5kb_3.3dg.txt
GM-600U_018_5kb_4.3dg.txt
GM-600U_018_5kb_5.3dg.txt
GM-600U_018_20kb_1.clean.3dg.txt
GM-600U_018_20kb_2.clean.3dg.txt
GM-600U_018_20kb_3.clean.3dg.txt
GM-600U_018_20kb_4.clean.3dg.txt
GM-600U_018_20kb_5.clean.3dg.txt
GM-600U_018_10kb_1.clean.3dg.txt
GM-600U_018_10kb_2.clean.3dg.txt
GM-600U_018_10kb_3.clean.3dg.txt
GM-600U_018_10kb_4.clean.3dg.txt
GM-600U_018_10kb_5.clean.3dg.txt
GM-600U_018_5kb_1.clean.3dg.txt
GM-600U_018_5kb_2.clean.3dg.txt
GM-600U_018_5kb_3.clean.3dg.txt
GM-600U_018_5kb_4.clean.3dg.txt
GM-600U_018_5kb_5.clean.3dg.txt


title: GM12878, 600U, Cell 19

description:
GM-600U_019.allValidPairs.txt
GM-600U_019.hic
GM-600U_019.mcool
GM-600U_019.clean.smooth.bw
GM-600U_019_20kb_1.3dg.txt
GM-600U_019_20kb_2.3dg.txt
GM-600U_019_20kb_3.3dg.txt
GM-600U_019_20kb_4.3dg.txt
GM-600U_019_20kb_5.3dg.txt
GM-600U_019_10kb_1.3dg.txt
GM-600U_019_10kb_2.3dg.txt
GM-600U_019_10kb_3.3dg.txt
GM-600U_019_10kb_4.3dg.txt
GM-600U_019_10kb_5.3dg.txt
GM-600U_019_5kb_1.3dg.txt
GM-600U_019_5kb_2.3dg.txt
GM-600U_019_5kb_3.3dg.txt
GM-600U_019_5kb_4.3dg.txt
GM-600U_019_5kb_5.3dg.txt
GM-600U_019_20kb_1.clean.3dg.txt
GM-600U_019_20kb_2.clean.3dg.txt
GM-600U_019_20kb_3.clean.3dg.txt
GM-600U_019_20kb_4.clean.3dg.txt
GM-600U_019_20kb_5.clean.3dg.txt
GM-600U_019_10kb_1.clean.3dg.txt
GM-600U_019_10kb_2.clean.3dg.txt
GM-600U_019_10kb_3.clean.3dg.txt
GM-600U_019_10kb_4.clean.3dg.txt
GM-600U_019_10kb_5.clean.3dg.txt
GM-600U_019_5kb_1.clean.3dg.txt
GM-600U_019_5kb_2.clean.3dg.txt
GM-600U_019_5kb_3.clean.3dg.txt
GM-600U_019_5kb_4.clean.3dg.txt
GM-600U_019_5kb_5.clean.3dg.txt


title: cell_086


title: cell_088


title: Patient5_Tcell_PRE


title: GM12878, 600U, Cell 17

description:
GM-600U_017.allValidPairs.txt
GM-600U_017.hic
GM-600U_017.mcool
GM-600U_017.clean.smooth.bw
GM-600U_017_20kb_1.3dg.txt
GM-600U_017_20kb_2.3dg.txt
GM-600U_017_20kb_3.3dg.txt
GM-600U_017_20kb_4.3dg.txt
GM-600U_017_20kb_5.3dg.txt
GM-600U_017_10kb_1.3dg.txt
GM-600U_017_10kb_2.3dg.txt
GM-600U_017_10kb_3.3dg.txt
GM-600U_017_10kb_4.3dg.txt
GM-600U_017_10kb_5.3dg.txt
GM-600U_017_5kb_1.3dg.txt
GM-600U_017_5kb_2.3dg.txt
GM-600U_017_5kb_3.3dg.txt
GM-600U_017_5kb_4.3dg.txt
GM-600U_017_5kb_5.3dg.txt
GM-600U_017_20kb_1.clean.3dg.txt
GM-600U_017_20kb_2.clean.3dg.txt
GM-600U_017_20kb_3.clean.3dg.txt
GM-600U_017_20kb_4.clean.3dg.txt
GM-600U_017_20kb_5.clean.3dg.txt
GM-600U_017_10kb_1.clean.3dg.txt
GM-600U_017_10kb_2.clean.3dg.txt
GM-600U_017_10kb_3.clean.3dg.txt
GM-600U_017_10kb_4.clean.3dg.txt
GM-600U_017_10kb_5.clean.3dg.txt
GM-600U_017_5kb_1.clean.3dg.txt
GM-600U_017_5kb_2.clean.3dg.txt
GM-600U_017_5kb_3.clean.3dg.txt
GM-600U_017_5kb_4.clean.3dg.txt
GM-600U_017_5kb_5.clean.3dg.txt


title: Patient4_MyleoidCell_PRE


title: GM12878, 600U, Cell 16

description:
GM-600U_016.allValidPairs.txt
GM-600U_016.hic
GM-600U_016.mcool
GM-600U_016.clean.smooth.bw
GM-600U_016_20kb_1.3dg.txt
GM-600U_016_20kb_2.3dg.txt
GM-600U_016_20kb_3.3dg.txt
GM-600U_016_20kb_4.3dg.txt
GM-600U_016_20kb_5.3dg.txt
GM-600U_016_10kb_1.3dg.txt
GM-600U_016_10kb_2.3dg.txt
GM-600U_016_10kb_3.3dg.txt
GM-600U_016_10kb_4.3dg.txt
GM-600U_016_10kb_5.3dg.txt
GM-600U_016_5kb_1.3dg.txt
GM-600U_016_5kb_2.3dg.txt
GM-600U_016_5kb_3.3dg.txt
GM-600U_016_5kb_4.3dg.txt
GM-600U_016_5kb_5.3dg.txt
GM-600U_016_20kb_1.clean.3dg.txt
GM-600U_016_20kb_2.clean.3dg.txt
GM-600U_016_20kb_3.clean.3dg.txt
GM-600U_016_20kb_4.clean.3dg.txt
GM-600U_016_20kb_5.clean.3dg.txt
GM-600U_016_10kb_1.clean.3dg.txt
GM-600U_016_10kb_2.clean.3dg.txt
GM-600U_016_10kb_3.clean.3dg.txt
GM-600U_016_10kb_4.clean.3dg.txt
GM-600U_016_10kb_5.clean.3dg.txt
GM-600U_016_5kb_1.clean.3dg.txt
GM-600U_016_5kb_2.clean.3dg.txt
GM-600U_016_5kb_3.clean.3dg.txt
GM-600U_016_5kb_4.clean.3dg.txt
GM-600U_016_5kb_5.clean.3dg.txt


title: scRNAseq_Mdx_muscle_ImmuneDepleted_rep3

description: scRNAseq for Mdx mouse muscle, with immune cells depleted


title: scRNAseq_Mdx_muscle_rep2

description: scRNAseq for Mdx mouse muscle, no cell depletion.


title: FAP_WT_RNA_rep2

description:
FAP_WT_RNA_rep2
Bulk RNAseq for FAPs from wildtype mouse

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.7) and mapped with STAR (v 2.7.10a, with parameters "--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend" and supplying the UCSC mm10 annotation) to mouse genome (mm10). The mapped reads were counted using salmon (v 1.4.0). Bioconductor package DESeq2 (v 1.34.0) was employed to analyze differential expressions (DE) with genotype information. Gene Ontology enrichment tests were performed to analyze enriched biological processes by clusterProfiler (v 4.2.2). The volcano plots were created by EnhancedVolcano (v 1.12.0). TPM values were quantified from Salmon (v 1.4.0) quantification and summarized via tximport (v 1.22.0).
Assembly: mm10
Supplementary files format and content: bigwig, binarized transcript counts per million.

extract_protocol:
Single cells were collected from mouse muscle by disection and mincing of muscle tissue, digestion using collagenase II and dispase in wash medium, and training using a 20-gauge needle and a 40 micrometer filter. FAPs were then isolated by Sca1+, propidium iodide negative FACS sorted cells.
Smart-seq3 library preparation protocol; RNA-seq, with Tn5 fragmentation


title: cell_084

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: Patient4_Bcell_PRE


title: Patient4_Tcell_PRE


title: GM12878, 600U, Cell 15

description:
GM-600U_015.allValidPairs.txt
GM-600U_015.hic
GM-600U_015.mcool
GM-600U_015.clean.smooth.bw
GM-600U_015_20kb_1.3dg.txt
GM-600U_015_20kb_2.3dg.txt
GM-600U_015_20kb_3.3dg.txt
GM-600U_015_20kb_4.3dg.txt
GM-600U_015_20kb_5.3dg.txt
GM-600U_015_10kb_1.3dg.txt
GM-600U_015_10kb_2.3dg.txt
GM-600U_015_10kb_3.3dg.txt
GM-600U_015_10kb_4.3dg.txt
GM-600U_015_10kb_5.3dg.txt
GM-600U_015_5kb_1.3dg.txt
GM-600U_015_5kb_2.3dg.txt
GM-600U_015_5kb_3.3dg.txt
GM-600U_015_5kb_4.3dg.txt
GM-600U_015_5kb_5.3dg.txt
GM-600U_015_20kb_1.clean.3dg.txt
GM-600U_015_20kb_2.clean.3dg.txt
GM-600U_015_20kb_3.clean.3dg.txt
GM-600U_015_20kb_4.clean.3dg.txt
GM-600U_015_20kb_5.clean.3dg.txt
GM-600U_015_10kb_1.clean.3dg.txt
GM-600U_015_10kb_2.clean.3dg.txt
GM-600U_015_10kb_3.clean.3dg.txt
GM-600U_015_10kb_4.clean.3dg.txt
GM-600U_015_10kb_5.clean.3dg.txt
GM-600U_015_5kb_1.clean.3dg.txt
GM-600U_015_5kb_2.clean.3dg.txt
GM-600U_015_5kb_3.clean.3dg.txt
GM-600U_015_5kb_4.clean.3dg.txt
GM-600U_015_5kb_5.clean.3dg.txt


title: FAP_WT_RNA_rep1

description:
FAP_WT_RNA_rep1
Bulk RNAseq for FAPs from wildtype mouse


title: cell_083


title: Patient3_MyleoidCell_PRE


title: cell_087


title: Patient3_Bcell_PRE


title: cell_082


title: GM12878, 600U, Cell 13

description:
GM-600U_013.allValidPairs.txt
GM-600U_013.hic
GM-600U_013.mcool
GM-600U_013.clean.smooth.bw
GM-600U_013_20kb_1.3dg.txt
GM-600U_013_20kb_2.3dg.txt
GM-600U_013_20kb_3.3dg.txt
GM-600U_013_20kb_4.3dg.txt
GM-600U_013_20kb_5.3dg.txt
GM-600U_013_10kb_1.3dg.txt
GM-600U_013_10kb_2.3dg.txt
GM-600U_013_10kb_3.3dg.txt
GM-600U_013_10kb_4.3dg.txt
GM-600U_013_10kb_5.3dg.txt
GM-600U_013_5kb_1.3dg.txt
GM-600U_013_5kb_2.3dg.txt
GM-600U_013_5kb_3.3dg.txt
GM-600U_013_5kb_4.3dg.txt
GM-600U_013_5kb_5.3dg.txt
GM-600U_013_20kb_1.clean.3dg.txt
GM-600U_013_20kb_2.clean.3dg.txt
GM-600U_013_20kb_3.clean.3dg.txt
GM-600U_013_20kb_4.clean.3dg.txt
GM-600U_013_20kb_5.clean.3dg.txt
GM-600U_013_10kb_1.clean.3dg.txt
GM-600U_013_10kb_2.clean.3dg.txt
GM-600U_013_10kb_3.clean.3dg.txt
GM-600U_013_10kb_4.clean.3dg.txt
GM-600U_013_10kb_5.clean.3dg.txt
GM-600U_013_5kb_1.clean.3dg.txt
GM-600U_013_5kb_2.clean.3dg.txt
GM-600U_013_5kb_3.clean.3dg.txt
GM-600U_013_5kb_4.clean.3dg.txt
GM-600U_013_5kb_5.clean.3dg.txt


title: scRNAseq_Mdx_muscle_rep4


title: FAP_Utrn-Mdx_RNA_rep1

description:
FAP_Utrn-Mdx_RNA_rep1
Bulk RNAseq for FAPs from Utrophin and Mdx double KO mouse


title: FAP_Utrn-Mdx_RNA_rep2

description:
FAP_Utrn-Mdx_RNA_rep2
Bulk RNAseq for FAPs from Utrophin and Mdx double KO mouse


title: cell_080


title: cell_081


title: GM12878, 600U, Cell 12

description:
GM-600U_012.allValidPairs.txt
GM-600U_012.hic
GM-600U_012.mcool
GM-600U_012.clean.smooth.bw
GM-600U_012_20kb_1.3dg.txt
GM-600U_012_20kb_2.3dg.txt
GM-600U_012_20kb_3.3dg.txt
GM-600U_012_20kb_4.3dg.txt
GM-600U_012_20kb_5.3dg.txt
GM-600U_012_10kb_1.3dg.txt
GM-600U_012_10kb_2.3dg.txt
GM-600U_012_10kb_3.3dg.txt
GM-600U_012_10kb_4.3dg.txt
GM-600U_012_10kb_5.3dg.txt
GM-600U_012_5kb_1.3dg.txt
GM-600U_012_5kb_2.3dg.txt
GM-600U_012_5kb_3.3dg.txt
GM-600U_012_5kb_4.3dg.txt
GM-600U_012_5kb_5.3dg.txt
GM-600U_012_20kb_1.clean.3dg.txt
GM-600U_012_20kb_2.clean.3dg.txt
GM-600U_012_20kb_3.clean.3dg.txt
GM-600U_012_20kb_4.clean.3dg.txt
GM-600U_012_20kb_5.clean.3dg.txt
GM-600U_012_10kb_1.clean.3dg.txt
GM-600U_012_10kb_2.clean.3dg.txt
GM-600U_012_10kb_3.clean.3dg.txt
GM-600U_012_10kb_4.clean.3dg.txt
GM-600U_012_10kb_5.clean.3dg.txt
GM-600U_012_5kb_1.clean.3dg.txt
GM-600U_012_5kb_2.clean.3dg.txt
GM-600U_012_5kb_3.clean.3dg.txt
GM-600U_012_5kb_4.clean.3dg.txt
GM-600U_012_5kb_5.clean.3dg.txt


title: FAP_Mdx_RNA_rep2

description:
FAP_Mdx_RNA_rep2
Bulk RNAseq for FAPs from Mdx mouse


title: Patient3_Tcell_PRE


title: cell_085


title: FAP_Mdx_RNA_rep1

description:
FAP_Mdx_RNA_rep1
Bulk RNAseq for FAPs from Mdx mouse


title: GM12878, 600U, Cell 11

description:
GM-600U_011.allValidPairs.txt
GM-600U_011.hic
GM-600U_011.mcool
GM-600U_011.clean.smooth.bw
GM-600U_011_20kb_1.3dg.txt
GM-600U_011_20kb_2.3dg.txt
GM-600U_011_20kb_3.3dg.txt
GM-600U_011_20kb_4.3dg.txt
GM-600U_011_20kb_5.3dg.txt
GM-600U_011_10kb_1.3dg.txt
GM-600U_011_10kb_2.3dg.txt
GM-600U_011_10kb_3.3dg.txt
GM-600U_011_10kb_4.3dg.txt
GM-600U_011_10kb_5.3dg.txt
GM-600U_011_5kb_1.3dg.txt
GM-600U_011_5kb_2.3dg.txt
GM-600U_011_5kb_3.3dg.txt
GM-600U_011_5kb_4.3dg.txt
GM-600U_011_5kb_5.3dg.txt
GM-600U_011_20kb_1.clean.3dg.txt
GM-600U_011_20kb_2.clean.3dg.txt
GM-600U_011_20kb_3.clean.3dg.txt
GM-600U_011_20kb_4.clean.3dg.txt
GM-600U_011_20kb_5.clean.3dg.txt
GM-600U_011_10kb_1.clean.3dg.txt
GM-600U_011_10kb_2.clean.3dg.txt
GM-600U_011_10kb_3.clean.3dg.txt
GM-600U_011_10kb_4.clean.3dg.txt
GM-600U_011_10kb_5.clean.3dg.txt
GM-600U_011_5kb_1.clean.3dg.txt
GM-600U_011_5kb_2.clean.3dg.txt
GM-600U_011_5kb_3.clean.3dg.txt
GM-600U_011_5kb_4.clean.3dg.txt
GM-600U_011_5kb_5.clean.3dg.txt


title: cell_079


title: Kdm6b FAP WT RNA rep2

description:
Mdx_Kdm6b_WT_rep2
Matched control for Kdm6b conditional KO in FAPs


title: GM12878, 600U, Cell 10

description:
GM-600U_010.allValidPairs.txt
GM-600U_010.hic
GM-600U_010.mcool
GM-600U_010.clean.smooth.bw
GM-600U_010_20kb_1.3dg.txt
GM-600U_010_20kb_2.3dg.txt
GM-600U_010_20kb_3.3dg.txt
GM-600U_010_20kb_4.3dg.txt
GM-600U_010_20kb_5.3dg.txt
GM-600U_010_10kb_1.3dg.txt
GM-600U_010_10kb_2.3dg.txt
GM-600U_010_10kb_3.3dg.txt
GM-600U_010_10kb_4.3dg.txt
GM-600U_010_10kb_5.3dg.txt
GM-600U_010_5kb_1.3dg.txt
GM-600U_010_5kb_2.3dg.txt
GM-600U_010_5kb_3.3dg.txt
GM-600U_010_5kb_4.3dg.txt
GM-600U_010_5kb_5.3dg.txt
GM-600U_010_20kb_1.clean.3dg.txt
GM-600U_010_20kb_2.clean.3dg.txt
GM-600U_010_20kb_3.clean.3dg.txt
GM-600U_010_20kb_4.clean.3dg.txt
GM-600U_010_20kb_5.clean.3dg.txt
GM-600U_010_10kb_1.clean.3dg.txt
GM-600U_010_10kb_2.clean.3dg.txt
GM-600U_010_10kb_3.clean.3dg.txt
GM-600U_010_10kb_4.clean.3dg.txt
GM-600U_010_10kb_5.clean.3dg.txt
GM-600U_010_5kb_1.clean.3dg.txt
GM-600U_010_5kb_2.clean.3dg.txt
GM-600U_010_5kb_3.clean.3dg.txt
GM-600U_010_5kb_4.clean.3dg.txt
GM-600U_010_5kb_5.clean.3dg.txt


title: Patient2_Bcell_PRE


title: cell_078


title: GM12878, 600U, Cell 9

description:
GM-600U_009.allValidPairs.txt
GM-600U_009.hic
GM-600U_009.mcool
GM-600U_009.clean.smooth.bw
GM-600U_009_20kb_1.3dg.txt
GM-600U_009_20kb_3.3dg.txt
GM-600U_009_20kb_5.3dg.txt
GM-600U_009_10kb_1.3dg.txt
GM-600U_009_10kb_3.3dg.txt
GM-600U_009_10kb_5.3dg.txt
GM-600U_009_5kb_1.3dg.txt
GM-600U_009_5kb_3.3dg.txt
GM-600U_009_5kb_5.3dg.txt
GM-600U_009_20kb_1.clean.3dg.txt
GM-600U_009_20kb_3.clean.3dg.txt
GM-600U_009_20kb_5.clean.3dg.txt
GM-600U_009_10kb_1.clean.3dg.txt
GM-600U_009_10kb_3.clean.3dg.txt
GM-600U_009_10kb_5.clean.3dg.txt
GM-600U_009_5kb_1.clean.3dg.txt
GM-600U_009_5kb_3.clean.3dg.txt
GM-600U_009_5kb_5.clean.3dg.txt


title: Kdm6b FAP WT RNA rep1

description:
Mdx_Kdm6b_WT_rep1
Matched control for Kdm6b conditional KO in FAPs


title: cell_077


title: GM12878, 600U, Cell 14

description:
GM-600U_014.allValidPairs.txt
GM-600U_014.hic
GM-600U_014.mcool
GM-600U_014.clean.smooth.bw
GM-600U_014_20kb_1.3dg.txt
GM-600U_014_20kb_4.3dg.txt
GM-600U_014_20kb_5.3dg.txt
GM-600U_014_10kb_1.3dg.txt
GM-600U_014_10kb_4.3dg.txt
GM-600U_014_10kb_5.3dg.txt
GM-600U_014_5kb_1.3dg.txt
GM-600U_014_5kb_4.3dg.txt
GM-600U_014_5kb_5.3dg.txt
GM-600U_014_20kb_1.clean.3dg.txt
GM-600U_014_20kb_4.clean.3dg.txt
GM-600U_014_20kb_5.clean.3dg.txt
GM-600U_014_10kb_1.clean.3dg.txt
GM-600U_014_10kb_4.clean.3dg.txt
GM-600U_014_10kb_5.clean.3dg.txt
GM-600U_014_5kb_1.clean.3dg.txt
GM-600U_014_5kb_4.clean.3dg.txt
GM-600U_014_5kb_5.clean.3dg.txt


title: Patient2_Tcell_PRE


title: GM12878, 600U, Cell 8

description:
GM-600U_008.allValidPairs.txt
GM-600U_008.hic
GM-600U_008.mcool
GM-600U_008.clean.smooth.bw
GM-600U_008_20kb_2.3dg.txt
GM-600U_008_20kb_3.3dg.txt
GM-600U_008_20kb_4.3dg.txt
GM-600U_008_20kb_5.3dg.txt
GM-600U_008_10kb_2.3dg.txt
GM-600U_008_10kb_3.3dg.txt
GM-600U_008_10kb_4.3dg.txt
GM-600U_008_10kb_5.3dg.txt
GM-600U_008_5kb_2.3dg.txt
GM-600U_008_5kb_3.3dg.txt
GM-600U_008_5kb_4.3dg.txt
GM-600U_008_5kb_5.3dg.txt
GM-600U_008_20kb_2.clean.3dg.txt
GM-600U_008_20kb_3.clean.3dg.txt
GM-600U_008_20kb_4.clean.3dg.txt
GM-600U_008_20kb_5.clean.3dg.txt
GM-600U_008_10kb_2.clean.3dg.txt
GM-600U_008_10kb_3.clean.3dg.txt
GM-600U_008_10kb_4.clean.3dg.txt
GM-600U_008_10kb_5.clean.3dg.txt
GM-600U_008_5kb_2.clean.3dg.txt
GM-600U_008_5kb_3.clean.3dg.txt
GM-600U_008_5kb_4.clean.3dg.txt
GM-600U_008_5kb_5.clean.3dg.txt


title: Patient1_MyleoidCell_PRE


title: Kdm6b FAP-cKO2 RNA

description:
Mdx_PdgfraCre_Kdm6b_cKO replicate 2
Kdm6b conditional KO in FAPs

value: Pdgfra-Cre, Kdm6b-/-


title: Patient1_Bcell_PRE


title: GM12878, 600U, Cell 7

description:
GM-600U_007.allValidPairs.txt
GM-600U_007.hic
GM-600U_007.mcool
GM-600U_007.clean.smooth.bw
GM-600U_007_20kb_1.3dg.txt
GM-600U_007_20kb_2.3dg.txt
GM-600U_007_20kb_3.3dg.txt
GM-600U_007_20kb_4.3dg.txt
GM-600U_007_20kb_5.3dg.txt
GM-600U_007_10kb_1.3dg.txt
GM-600U_007_10kb_2.3dg.txt
GM-600U_007_10kb_3.3dg.txt
GM-600U_007_10kb_4.3dg.txt
GM-600U_007_10kb_5.3dg.txt
GM-600U_007_5kb_1.3dg.txt
GM-600U_007_5kb_2.3dg.txt
GM-600U_007_5kb_3.3dg.txt
GM-600U_007_5kb_4.3dg.txt
GM-600U_007_5kb_5.3dg.txt
GM-600U_007_20kb_1.clean.3dg.txt
GM-600U_007_20kb_2.clean.3dg.txt
GM-600U_007_20kb_3.clean.3dg.txt
GM-600U_007_20kb_4.clean.3dg.txt
GM-600U_007_20kb_5.clean.3dg.txt
GM-600U_007_10kb_1.clean.3dg.txt
GM-600U_007_10kb_2.clean.3dg.txt
GM-600U_007_10kb_3.clean.3dg.txt
GM-600U_007_10kb_4.clean.3dg.txt
GM-600U_007_10kb_5.clean.3dg.txt
GM-600U_007_5kb_1.clean.3dg.txt
GM-600U_007_5kb_2.clean.3dg.txt
GM-600U_007_5kb_3.clean.3dg.txt
GM-600U_007_5kb_4.clean.3dg.txt
GM-600U_007_5kb_5.clean.3dg.txt


title: GM12878, 600U, Cell 6

description:
GM-600U_006.allValidPairs.txt
GM-600U_006.hic
GM-600U_006.mcool
GM-600U_006.clean.smooth.bw
GM-600U_006_20kb_1.3dg.txt
GM-600U_006_20kb_2.3dg.txt
GM-600U_006_20kb_3.3dg.txt
GM-600U_006_20kb_4.3dg.txt
GM-600U_006_20kb_5.3dg.txt
GM-600U_006_10kb_1.3dg.txt
GM-600U_006_10kb_2.3dg.txt
GM-600U_006_10kb_3.3dg.txt
GM-600U_006_10kb_4.3dg.txt
GM-600U_006_10kb_5.3dg.txt
GM-600U_006_5kb_1.3dg.txt
GM-600U_006_5kb_2.3dg.txt
GM-600U_006_5kb_3.3dg.txt
GM-600U_006_5kb_4.3dg.txt
GM-600U_006_5kb_5.3dg.txt
GM-600U_006_20kb_1.clean.3dg.txt
GM-600U_006_20kb_2.clean.3dg.txt
GM-600U_006_20kb_3.clean.3dg.txt
GM-600U_006_20kb_4.clean.3dg.txt
GM-600U_006_20kb_5.clean.3dg.txt
GM-600U_006_10kb_1.clean.3dg.txt
GM-600U_006_10kb_2.clean.3dg.txt
GM-600U_006_10kb_3.clean.3dg.txt
GM-600U_006_10kb_4.clean.3dg.txt
GM-600U_006_10kb_5.clean.3dg.txt
GM-600U_006_5kb_1.clean.3dg.txt
GM-600U_006_5kb_2.clean.3dg.txt
GM-600U_006_5kb_3.clean.3dg.txt
GM-600U_006_5kb_4.clean.3dg.txt
GM-600U_006_5kb_5.clean.3dg.txt


title: Kdm6b FAP-cKO1 RNA

description:
Mdx_PdgfraCre_Kdm6b_cKO replicate 1
Kdm6b conditional KO in FAPs


title: cell_076

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: GM12878, 600U, Cell 5

description:
GM-600U_005.allValidPairs.txt
GM-600U_005.hic
GM-600U_005.mcool
GM-600U_005.clean.smooth.bw
GM-600U_005_20kb_1.3dg.txt
GM-600U_005_20kb_2.3dg.txt
GM-600U_005_20kb_3.3dg.txt
GM-600U_005_20kb_4.3dg.txt
GM-600U_005_10kb_1.3dg.txt
GM-600U_005_10kb_2.3dg.txt
GM-600U_005_10kb_3.3dg.txt
GM-600U_005_10kb_4.3dg.txt
GM-600U_005_5kb_1.3dg.txt
GM-600U_005_5kb_2.3dg.txt
GM-600U_005_5kb_3.3dg.txt
GM-600U_005_5kb_4.3dg.txt
GM-600U_005_20kb_1.clean.3dg.txt
GM-600U_005_20kb_2.clean.3dg.txt
GM-600U_005_20kb_3.clean.3dg.txt
GM-600U_005_20kb_4.clean.3dg.txt
GM-600U_005_10kb_1.clean.3dg.txt
GM-600U_005_10kb_2.clean.3dg.txt
GM-600U_005_10kb_3.clean.3dg.txt
GM-600U_005_10kb_4.clean.3dg.txt
GM-600U_005_5kb_1.clean.3dg.txt
GM-600U_005_5kb_2.clean.3dg.txt
GM-600U_005_5kb_3.clean.3dg.txt
GM-600U_005_5kb_4.clean.3dg.txt


title: cell_075


title: sd+ males 2

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

description:
Hand dissection
Day6
mRNA
Biological replicate 2
Processed data file: Scalloped_raw_gene_counts.txt
Processed data file: Scalloped_TPM.tsv

data_processing:
Cleaning (fastq-mcf).
Mapping to D. melanogaster genome r_6.03 using STAR/2.5.1 (default parameters).
Quantification of gene expression measures with STAR/2.5.1 (option --quantMode GeneCounts) using D. melanogaster gene annotation release 6.03 from FlyBase.
Genome_build: Drosophila melanogaster FlyBase release 6
Supplementary_files_format_and_content: Scalloped_raw_gene_counts.tsv: Tab-delimited text file; table of counts (from STAR/2.5.1).
Supplementary_files_format_and_content: Scalloped_RPM.tsv: Tab-delimited text file; table of normalized counts (RPM).

organism: Drosophila melanogaster

source_name: eye imaginal disc, sd+ males

growth_protocol: Animals were raised at 25C on standard media.

extract_protocol:
RNA was extracted using the RNeasy mini spin kit (Qiagen) and stored at -80°C.
Purification of poly-A containing mRNA is performed by using poly-T oligo-attached magnetic beads. The mRNA is then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Subsequently, a second cDNA strand is synthesized using DNA Polymerase I and RNase H. Then, a single 'A' base and the adapter are added to the cDNA fragments. Finally, the products are purified and enriched with PCR to create the final cDNA library.
Illumina TruSeq Stranded mRNA library prep.

treatment_protocol: Dissection tools and surfaces were treated with RNaseZap (Sigma). Imaginal discs were dissected from 45 larvae per sample and transferred into RNase-free 1xPBS on ice.

tag: strain/background

value: Canton S

tag: genotype/variation

value: yw sd47M eyFLP/Y; FRT42D sd+w+y+ UbiGFP/+

tag: developmental stage

value: third instar wandering larvae

tag: Sex

value: male

value: eye imaginal discs


title: Patient1_Tcell_PRE


title: Patient2_MyleoidCell_PRE


title: sd+ males 1

description:
Hand dissection
Day6
mRNA
Biological replicate 1
Processed data file: Scalloped_raw_gene_counts.txt
Processed data file: Scalloped_TPM.tsv


title: cell_073

value: blood

value: lymphoblastoid


title: cell_074


title: GM12878, 600U, Cell 4

description:
GM-600U_004.allValidPairs.txt
GM-600U_004.hic
GM-600U_004.mcool
GM-600U_004.clean.smooth.bw
GM-600U_004_20kb_1.3dg.txt
GM-600U_004_20kb_2.3dg.txt
GM-600U_004_20kb_3.3dg.txt
GM-600U_004_20kb_4.3dg.txt
GM-600U_004_20kb_5.3dg.txt
GM-600U_004_10kb_1.3dg.txt
GM-600U_004_10kb_2.3dg.txt
GM-600U_004_10kb_3.3dg.txt
GM-600U_004_10kb_4.3dg.txt
GM-600U_004_10kb_5.3dg.txt
GM-600U_004_5kb_1.3dg.txt
GM-600U_004_5kb_2.3dg.txt
GM-600U_004_5kb_3.3dg.txt
GM-600U_004_5kb_4.3dg.txt
GM-600U_004_5kb_5.3dg.txt
GM-600U_004_20kb_1.clean.3dg.txt
GM-600U_004_20kb_2.clean.3dg.txt
GM-600U_004_20kb_3.clean.3dg.txt
GM-600U_004_20kb_4.clean.3dg.txt
GM-600U_004_20kb_5.clean.3dg.txt
GM-600U_004_10kb_1.clean.3dg.txt
GM-600U_004_10kb_2.clean.3dg.txt
GM-600U_004_10kb_3.clean.3dg.txt
GM-600U_004_10kb_4.clean.3dg.txt
GM-600U_004_10kb_5.clean.3dg.txt
GM-600U_004_5kb_1.clean.3dg.txt
GM-600U_004_5kb_2.clean.3dg.txt
GM-600U_004_5kb_3.clean.3dg.txt
GM-600U_004_5kb_4.clean.3dg.txt
GM-600U_004_5kb_5.clean.3dg.txt

value: WT

value: 600U MNase


title: cell_072


title: GM12878, 600U, Cell 3

description:
GM-600U_003.allValidPairs.txt
GM-600U_003.hic
GM-600U_003.mcool
GM-600U_003.clean.smooth.bw
GM-600U_003_20kb_1.3dg.txt
GM-600U_003_20kb_3.3dg.txt
GM-600U_003_20kb_4.3dg.txt
GM-600U_003_20kb_5.3dg.txt
GM-600U_003_10kb_1.3dg.txt
GM-600U_003_10kb_3.3dg.txt
GM-600U_003_10kb_4.3dg.txt
GM-600U_003_10kb_5.3dg.txt
GM-600U_003_5kb_1.3dg.txt
GM-600U_003_5kb_3.3dg.txt
GM-600U_003_5kb_4.3dg.txt
GM-600U_003_5kb_5.3dg.txt
GM-600U_003_20kb_1.clean.3dg.txt
GM-600U_003_20kb_3.clean.3dg.txt
GM-600U_003_20kb_4.clean.3dg.txt
GM-600U_003_20kb_5.clean.3dg.txt
GM-600U_003_10kb_1.clean.3dg.txt
GM-600U_003_10kb_3.clean.3dg.txt
GM-600U_003_10kb_4.clean.3dg.txt
GM-600U_003_10kb_5.clean.3dg.txt
GM-600U_003_5kb_1.clean.3dg.txt
GM-600U_003_5kb_3.clean.3dg.txt
GM-600U_003_5kb_4.clean.3dg.txt
GM-600U_003_5kb_5.clean.3dg.txt


title: wt/GFP 2

source_name: eye imaginal disc, wt/GFP

value: yw sd47M eyFLP/yw; FRT42D sd+w+y+ UbiGFP/FRT42D


title: cell_071


title: 2PMW_3

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

data_processing:
The quality of samples was assessed using FAST QC (0.11.5- Java-1.8.0_74) (Andrews, 2019). Adapters were removed from samples using Trimmomatic (version 0.39) (Bolger et al., 2014).
Reads were aligned to the british oak genome (https://www.oakgenome.fr/) using Hisat2 (version 2.2.1) (Kim et al., 2019), using default parameters.
Samtools (version 1.12) (Danecek et al., 2021) was used to sort and index Sam files into Bam format. Read counts were generated using HTSeq (version 0.13.5) (Putri et al., 2022) using default thresholds
Assembly: Oak genome assembly PM1N
Supplementary files format and content: For each sample, the rawcount file is provided, generated with htseq-count (Anders et al., 2015).

organism: Quercus robur

source_name: leaves

growth_protocol: Acorns of Quercus robur were sourced from the tree seed company Forestart (https://www.forestart.co.uk) and were germinated according to existing protocols (Sanchez-Lucas et al, 2023). After 72h, germinated acorns were transferred into individual root trainers (Maxi Rootrainers, Haxnicks, RT230101) containing 400 mL of Scott’s Levington M3 Advance Pot & Bedding soil. Germinated acorns were then grown in a glasshouse compartment at 16/8h light day/night (~200 μmol photons m-2s-1), 20℃/18℃ cycle, 42% HR and irrigated to field capacity throughout the experiment.

extract_protocol:
Samples  were collected at 0, 1, and 2dpi, by snap-freezing mock and infected leaves in liquid nitrogen, and stored  at -80°C until processing. Material was collected from 4 biological replicates (plants) per group giving a total of 80 samples for each omics analysis. Total RNA was extracted using the Mini-Plant RNA extraction kit following manufacturer instructions with modifications for leaf tissue. Briefly, a 1:1 combination of PL1 and PL2 was applied during the lysis step. Centrifuge times were duplicated during the extraction and two additional washing steps were incorporated. RNA quality was tested with nanodrop and gel electrophoresis.
Library preparation and sequencing was conducted by Novogene using NovaSeq 6000 PE150. Around 40 million paired reads were generated per sample.

treatment_protocol: Three elicitors were used: Salicylic acid (SA), Jasmonic acid (JA) and β-aminobutyric acid (BABA). Treatments were performed on 3-month-old seedlings. BABA was soil-drenched to a final soil concentration of 5mM as previously described (Sanchez-Lucas et al 2023). SA and JA were sprayed at concentrations of 5mM and 500μM, respectively. Water was used as a control in both soil drench and spray treatments, along with being applied to each elicitor to equalise the amount of water in the soil or on the leaves. All spraying solutions contained 0.002% ethanol and 0.05% Silwet to allow full leaf coverage. Plants were inoculated with PM causal agent, Erysiphe alphitoides, 7 days post elicitor treatment, by spraying leaves with 1.5x106 spores/mL. Mock-inoculated plants were treated with water. All inoculations contained 0.05% of Silwet to allow full leaf coverage. Post-inoculation, all plants were grown under high humidity by covering the plants with plastic bags.

value: leaves

tag: ecotype

value: Forestart

tag: time

value: 2 days post inoculation

value: 3 months

value: Water

tag: infection

value: E. alphitoides


title: 2PMW_2


title: 2PMW_4


title: wt/GFP 1


title: 2PMW_1


title: GM12878, 600U, Cell 1

description:
GM-600U_001.allValidPairs.txt
GM-600U_001.hic
GM-600U_001.mcool
GM-600U_001.clean.smooth.bw
GM-600U_001_20kb_1.3dg.txt
GM-600U_001_20kb_2.3dg.txt
GM-600U_001_20kb_3.3dg.txt
GM-600U_001_20kb_4.3dg.txt
GM-600U_001_20kb_5.3dg.txt
GM-600U_001_10kb_1.3dg.txt
GM-600U_001_10kb_2.3dg.txt
GM-600U_001_10kb_3.3dg.txt
GM-600U_001_10kb_4.3dg.txt
GM-600U_001_10kb_5.3dg.txt
GM-600U_001_5kb_1.3dg.txt
GM-600U_001_5kb_2.3dg.txt
GM-600U_001_5kb_3.3dg.txt
GM-600U_001_5kb_4.3dg.txt
GM-600U_001_5kb_5.3dg.txt
GM-600U_001_20kb_1.clean.3dg.txt
GM-600U_001_20kb_2.clean.3dg.txt
GM-600U_001_20kb_3.clean.3dg.txt
GM-600U_001_20kb_4.clean.3dg.txt
GM-600U_001_20kb_5.clean.3dg.txt
GM-600U_001_10kb_1.clean.3dg.txt
GM-600U_001_10kb_2.clean.3dg.txt
GM-600U_001_10kb_3.clean.3dg.txt
GM-600U_001_10kb_4.clean.3dg.txt
GM-600U_001_10kb_5.clean.3dg.txt
GM-600U_001_5kb_1.clean.3dg.txt
GM-600U_001_5kb_2.clean.3dg.txt
GM-600U_001_5kb_3.clean.3dg.txt
GM-600U_001_5kb_4.clean.3dg.txt
GM-600U_001_5kb_5.clean.3dg.txt


title: cell_070


title: cell_069


title: 2PMS_4

value: SA


title: sd47M/GFP 2

source_name: eye imaginal disc, sd47M/GFP

value: Canton S

value: yw sd47M eyFLP/Y; FRT42D sd+w+y+ UbiGFP/FRT42D


title: sd47M/GFP 1

value: third instar wandering larvae


title: wt/cl 2

source_name: eye imaginal disc, wt/cl

value: w+ cl FRT19A /yw sd47M FRT19A; sd+w+y+/eyFLP


title: cell_068


title: 2PMS_2


title: sd+ females

description:
Hand dissection
Day6
mRNA
Processed data file: Scalloped_raw_gene_counts.txt
Processed data file: Scalloped_TPM.tsv

source_name: eye imaginal disc, sd+ females

value: yw sd47M eyFLP/yw; FRT42D sd+w+y+ UbiGFP/+

value: female

value: eye imaginal discs


title: 2PMS_1


title: cell_067

value: blood

value: lymphoblastoid


title: cell_066


title: GM12878, 600U, Cell 2

description:
GM-600U_002.allValidPairs.txt
GM-600U_002.hic
GM-600U_002.mcool
GM-600U_002.clean.smooth.bw
GM-600U_002_20kb_1.3dg.txt
GM-600U_002_20kb_2.3dg.txt
GM-600U_002_20kb_3.3dg.txt
GM-600U_002_20kb_4.3dg.txt
GM-600U_002_20kb_5.3dg.txt
GM-600U_002_10kb_1.3dg.txt
GM-600U_002_10kb_2.3dg.txt
GM-600U_002_10kb_3.3dg.txt
GM-600U_002_10kb_4.3dg.txt
GM-600U_002_10kb_5.3dg.txt
GM-600U_002_5kb_1.3dg.txt
GM-600U_002_5kb_2.3dg.txt
GM-600U_002_5kb_3.3dg.txt
GM-600U_002_5kb_4.3dg.txt
GM-600U_002_5kb_5.3dg.txt
GM-600U_002_20kb_1.clean.3dg.txt
GM-600U_002_20kb_2.clean.3dg.txt
GM-600U_002_20kb_3.clean.3dg.txt
GM-600U_002_20kb_4.clean.3dg.txt
GM-600U_002_20kb_5.clean.3dg.txt
GM-600U_002_10kb_1.clean.3dg.txt
GM-600U_002_10kb_2.clean.3dg.txt
GM-600U_002_10kb_3.clean.3dg.txt
GM-600U_002_10kb_4.clean.3dg.txt
GM-600U_002_10kb_5.clean.3dg.txt
GM-600U_002_5kb_1.clean.3dg.txt
GM-600U_002_5kb_2.clean.3dg.txt
GM-600U_002_5kb_3.clean.3dg.txt
GM-600U_002_5kb_4.clean.3dg.txt
GM-600U_002_5kb_5.clean.3dg.txt

value: WT

value: 600U MNase


title: 2PMJ_3

value: leaves

value: Forestart

value: JA


title: GM12878, 1000U, Cell 96

value: 1000U MNase


title: cell_065


title: wt/cl 1


title: GM12878, 1000U, Cell 95


title: cell_064


title: sd47M/cl 1

source_name: eye imaginal disc, sd47M/cl

value: w+ cl FRT19A /yw sd47M FRT19A; +/eyFLP


title: sd47M/cl 2


title: 2PMJ_2

value: 2 days post inoculation

value: 3 months

value: E. alphitoides


title: GM12878, 1000U, Cell 93


title: wt FRT42D 2

source_name: eye imaginal disc, wt FRT42D

value: Canton S

value: yw eyFLP; FRT42D/FRT42D tub-Gal80; +/tub-Gal4, UAS-GFP

value: third instar wandering larvae


title: 2PMJ_1


title: cell_063


title: GM12878, 1000U, Cell 94


title: 2PMS_3

value: SA


title: cell_062


title: wt FRT42D 1

value: eye imaginal discs


title: 2PMB_4

value: BABA


title: cell_061

value: blood

value: lymphoblastoid


title: wt FRT19A 2

source_name: eye imaginal disc, wt FRT19A

value: FRT19A/tub-Gal80 FRT19A; eyFLP Act 5C<y+<Gal4, UAS-GFP/+


title: GM12878, 1000U, Cell 90

value: WT


title: wt FRT19A 1


title: 2PMB_2

value: leaves

value: Forestart


title: GM12878, 1000U, Cell 89

value: 1000U MNase


title: sd47M 2

source_name: eye imaginal disc, sd47M

value: sd47M FRT19A/tub-Gal80 FRT19A; eyFLP Act 5C<y+<Gal4, UAS-GFP/+


title: cell_060


title: sd47M 1


title: 2MW_3

value: 2 days post inoculation

value: Water

value: mock


title: GM12878, 1000U, Cell 88


title: yki3SA, sd47M 2

source_name: eye imaginal disc, yki3SA, sd47M

value: Canton S

value: sd47M FRT19A/tub-Gal80 FRT19A; eyFLP Act 5C<y+<Gal4, UAS-GFP/+; UAS-yki3SA/+


title: cell_057


title: 2PMB_1

value: 3 months

value: E. alphitoides


title: GM12878, 1000U, Cell 91


title: 2MW_2


title: yki3SA, sd47M 1

value: third instar wandering larvae

value: eye imaginal discs


title: GM12878, 1000U, Cell 87

value: blood


title: GM12878, 1000U, Cell 92

value: lymphoblastoid


title: 2MW_1


title: GM12878, 1000U, Cell 86


title: cell_055


title: cell_056


title: GM12878, 1000U, Cell 84


title: yki3SA

source_name: eye imaginal disc, yki3SA

value: yw eyFLP; FRT42D/FRT42D tub-Gal80; UAS-yki3SA / tub-Gal4, UAS-GFP


title: GM12878, 1000U, Cell 83

source_name: blood

value: WT


title: 2MS_4

value: leaves

value: SA


title: 2PMB_3

value: Forestart

value: BABA


title: Patient10_MyleoidCell_POST_miRNA

value: Post-treatment


title: cell_054


title: cell_058


title: Patient10_Bcell_POST_miRNA


title: cell_059


title: 2MS_3

value: 2 days post inoculation


title: cell_053


title: GM12878, 1000U, Cell 82

value: 1000U MNase


title: 2MS_2

value: mock


title: 2MS_1


title: Patient9_MyleoidCell_POST_miRNA


title: cell_051


title: 2MJ_5

value: JA


title: GM12878, 1000U, Cell 80


title: cell_050


title: GM12878, 1000U, Cell 85


title: cell_052


title: GM12878, 1000U, Cell 79


title: GM12878, 1000U, Cell 81


title: 2MJ_3

value: 3 months


title: cell_049


title: GM12878, 1000U, Cell 78


title: Patient8_MyleoidCell_POST_miRNA


title: 2MJ_4


title: cell_048


title: 2MJ_2


title: GM12878, 1000U, Cell 77


title: cell_047


title: Patient8_Bcell_POST_miRNA


title: 2MJ_1


title: Patient8_Tcell_POST_miRNA


title: cell_046


title: Patient10_Tcell_POST_miRNA


title: 2MB_4


title: GM12878, 1000U, Cell 76


title: Patient9_Bcell_POST_miRNA


title: Patient7_MyleoidCell_POST_miRNA


title: cell_045


title: Patient9_Tcell_POST_miRNA


title: Patient7_Bcell_POST_miRNA


title: GM12878, 1000U, Cell 74


title: 2MB_2


title: GM12878, 1000U, Cell 73


title: cell_044


title: Patient7_Tcell_POST_miRNA


title: 2MB_1


title: cell_043


title: GM12878, 1000U, Cell 71


title: cell_042


title: GM12878, 1000U, Cell 72


title: cell_041


title: Patient6_Bcell_POST_miRNA


title: GM12878, 1000U, Cell 75


title: cell_040


title: 1PMW_3

value: 1 days post inoculation

value: Water

value: E. alphitoides


title: 1PMW_2


title: GM12878, 1000U, Cell 69

value: blood


title: GM12878, 1000U, Cell 68

value: lymphoblastoid


title: GM12878, 1000U, Cell 70


title: 2MB_3


title: Patient5_MyleoidCell_POST_miRNA


title: 1PMW_1


title: Patient6_MyleoidCell_POST_miRNA


title: cell_038


title: Patient5_Tcell_POST_miRNA


title: 1PMS_3


title: Patient5_Bcell_POST_miRNA


title: 1PMW_4


title: 1PMS_2


title: cell_036


title: GM12878, 1000U, Cell 66


title: cell_037


title: Patient6_Tcell_POST_miRNA


title: 1PMS_1


title: Patient4_Bcell_POST_miRNA


title: Patient4_MyleoidCell_POST_miRNA


title: cell_035


title: cell_039


title: GM12878, 1000U, Cell 64


title: Patient4_Tcell_POST_miRNA


title: GM12878, 1000U, Cell 65


title: 1PMJ_4


title: GM12878, 1000U, Cell 63


title: GM12878, 1000U, Cell 67


title: cell_033


title: cell_034


title: Patient3_MyleoidCell_POST_miRNA


title: GM12878, 1000U, Cell 62


title: 1PMJ_2


title: Patient3_Bcell_POST_miRNA


title: cell_032


title: GM12878, 1000U, Cell 61


title: 1PMJ_1


title: GM12878, 1000U, Cell 60


title: Patient3_Tcell_POST_miRNA


title: cell_031


title: 1PMB_4


title: cell_030


title: Patient2_Bcell_POST_miRNA


title: GM12878, 1000U, Cell 59


title: 1PMB_3


title: cell_029


title: 1PMJ_3


title: GM12878, 1000U, Cell 58


title: Patient2_Tcell_POST_miRNA


title: 1PMB_1


title: GM12878, 1000U, Cell 57


title: Patient1_MyleoidCell_POST_miRNA


title: 1MW_4


title: Patient1_Bcell_POST_miRNA


title: GM12878, 1000U, Cell 56


title: cell_026


title: Patient1_Tcell_POST_miRNA


title: cell_027


title: GM12878, 1000U, Cell 55


title: 1MW_2


title: cell_024


title: Patient2_MyleoidCell_POST_miRNA


title: 1MW_3


title: GM12878, 1000U, Cell 54


title: Patient10_MyleoidCell_PRE_miRNA

value: Pre-treatment


title: GM12878, 1000U, Cell 53

value: WT


title: 1PMB_2

value: leaves


title: Patient10_Bcell_PRE_miRNA


title: cell_025


title: 1MS_4

value: SA


title: cell_023


title: GM12878, 1000U, Cell 52


title: 1MS_3

value: Forestart


title: cell_022


title: Patient10_Tcell_PRE_miRNA


title: cell_028


title: GM12878, 1000U, Cell 51


title: Patient9_MyleoidCell_PRE_miRNA


title: cell_021


title: GM12878, 1000U, Cell 50


title: Patient9_Bcell_PRE_miRNA


title: 1MS_2


title: GM12878, 1000U, Cell 49


title: cell_020


title: 1MW_1


title: 1MS_1


title: Patient9_Tcell_PRE_miRNA


title: cell_019


title: Patient8_MyleoidCell_PRE_miRNA


title: 1MJ_4


title: 1MJ_3


title: GM12878, 1000U, Cell 48


title: cell_018


title: GM12878, 1000U, Cell 47


title: cell_017


title: Patient8_Bcell_PRE_miRNA


title: 1MJ_2


title: Patient8_Tcell_PRE_miRNA


title: cell_016


title: 1MJ_1


title: Patient7_MyleoidCell_PRE_miRNA


title: GM12878, 1000U, Cell 46


title: cell_015


title: GM12878, 1000U, Cell 44


title: Patient7_Bcell_PRE_miRNA


title: 1MB_4

value: BABA


title: GM12878, 1000U, Cell 43


title: cell_014


title: 1MB_3


title: GM12878, 1000U, Cell 45


title: Patient7_Tcell_PRE_miRNA


title: cell_013


title: GM12878, 1000U, Cell 42


title: Patient6_MyleoidCell_PRE_miRNA


title: 1MB_2


title: GM12878, 1000U, Cell 41


title: Patient6_Bcell_PRE_miRNA


title: cell_012


title: cell_011


title: 0MW_3

value: 0 days post inoculation


title: GM12878, 1000U, Cell 40


title: Patient6_Tcell_PRE_miRNA


title: Patient5_MyleoidCell_PRE_miRNA


title: GM12878, 1000U, Cell 39


title: cell_010


title: 0MW_2


title: 0MW_1


title: Patient5_Bcell_PRE_miRNA


title: cell_008


title: cell_009


title: GM12878, 1000U, Cell 37


title: 0MS_4


title: Patient5_Tcell_PRE_miRNA


title: cell_007


title: cell_006


title: Patient4_MyleoidCell_PRE_miRNA


title: 0MS_3


title: 0MS_2


title: GM12878, 1000U, Cell 36


title: Patient4_Bcell_PRE_miRNA


title: 1MB_1


title: GM12878, 1000U, Cell 35


title: cell_005


title: GM12878, 1000U, Cell 34


title: Patient4_Tcell_PRE_miRNA


title: GM12878, 1000U, Cell 38


title: GM12878, 1000U, Cell 33


title: 0MJ_4


title: cell_003


title: 0MJ_3


title: Patient3_MyleoidCell_PRE_miRNA


title: Patient3_Bcell_PRE_miRNA


title: cell_004


title: GM12878, 1000U, Cell 31


title: GM12878, 1000U, Cell 32


title: Patient3_Tcell_PRE_miRNA


title: cell_002


title: Patient2_MyleoidCell_PRE_miRNA


title: GM12878, 1000U, Cell 30


title: cell_001


title: 0MB_4


title: Patient2_Bcell_PRE_miRNA


title: 0MB_3


title: 0MJ_1


title: GM12878, 1000U, Cell 28


title: Patient2_Tcell_PRE_miRNA


title: 0MB_2


title: Patient1_MyleoidCell_PRE_miRNA


title: GM12878, 1000U, Cell 27


title: 0MS_1


title: Patient1_Bcell_PRE_miRNA


title: 0MJ_2


title: 0MB_1


title: M16_TAM_EX

type: genomic

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

hyb_protocol: DNA was amplified, fragmented and hybridized to the Infinium Mouse Methylation BeadChip using the standard protocol. Since conversion was a variable in the study, conversion conditions for each sample are available in their associated metadata.

scan_protocol: Arrays were imaged using the Illumina iScan with recommended Illumina settings

data_processing:
methylprep package v 1.7.1
Average Beta

source_name: Gastrocnemius

label_protocol: standard protocol

growth_protocol: Sedentary or voluntary unweighted wheel running for ~20 months.

extract_protocol: Qiagen blood and tissue genomic DNA kit

treatment_protocol: Vehicle or Tamoxifen injections which results in satellite cells being replete and depleted, respectively, prior to the onset of the growth protocol

value: Gastrocnemius

value: Skeletal Muscle

value: TAM

value: EX


title: GM12878, 1000U, Cell 25

value: 1000U MNase


title: GM12878, 1000U, Cell 24


title: Patient1_Tcell_PRE_miRNA


title: M14_TAM_SED

value: SED


title: GM12878, 1000U, Cell 29


title: M11_VEH_EX

value: VEH


title: Day7(#15)_PHx+Gln

city: Tainan

first: Chih Chieh

last: Yen

address: No. 138, ShengLi Rd., North Dist.

department: Department of Oncology

country: Taiwan

institute: National Cheng Kung University Hospital

description: Gene expression after PHx + 2%gln

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Mouse Gene Exp v2 Array Kit (Agilent Technologies, USA) at 65°C for 17 h. After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

scan_protocol: Scanned images are analyzed by Feature extraction10.7.3.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Liver, PHx, 2%Gln, D7, replicate 1

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: Eight-week-old male specific pathogen-free C57BL/6 mice were treated, manipulated, and maintained with either partial hepatectomy or sham surgery. Murine liver specimens were collected according to experimental protocols at specific time points after CO2 euthanasia

extract_protocol: Liver samples were prepared for mRNA expression microarray from day 1 to day 6 post-PHx in fresh frozen condition. Briefly, microarray analyses were performed using the SurePrint G3 GeneChip Mouse Gene Express V2 Array Kit (Agilent, Santa Clara, CA, US; Agilent-074809) according to the manufacturer’s protocols

treatment_protocol: 70% partial hepatectomy (PHx) or sham surgery in the absence of hepatic resection via midline laparotomy was performed in micw. L-glutamic acid 5-amide (Gln) was obtained from MilliporeSigma, MA, US, and mice were fed 0.6% Gln versus PBS in the drinking water starting at 7 days prior to PHx and another 6 days after Phx. Mice were randomized into four groups: 1) sham with Gln supplementation (sham + Gln), 2) sham without Gln supplementation (sham – Gln), 3) PHx with Gln supplementation (PHx + Gln), and 4) PHx without Gln supplementation (PHx – Gln). Remnant livers were collected for further analyses and weighed daily from days 1 to 6 post-PHx.

value: liver

tag: gender

value: male

tag: age


title: Day4(#16)_Sham+Gln

description: Gene expression after Sham + 2%gln

source_name: Liver, Sham, 2%Gln, D4, replicate 1


title: Day6(#20)_PHx+Gln

description: Gene expression after PHx + 2%gln

source_name: Liver, PHx, 2%Gln, D6, replicate 1


title: E coli, sulfur-free, rep2

city: Wuhan

first: Yu-Zhang

last: Wang

address: Mt Luojia

institute: Wuhan University

data_processing:
The Illumina platform converts the sequencing image signals into textual signals through CASAVA base calling and stores them in fastq format as raw data.
Remove adapter sequences from the reads; trims the 5' end bases that are not A, G, C, or T; clips off the ends of low-quality reads (with sequencing quality scores below Q20); discards reads with an N content reaching 10%; and jettisons short segments shorter than 25bp after adapter removal and quality trimming.
Align the high-quality reads from each sample to the reference genome using Bowtie2.
Using the BLAST method, randomly select 10,000 raw reads from each sample and align them with the Rfam database (http://rfam.xfam.org/). Based on the annotation results, calculate the percentage of rRNA in each sample to assess the rRNA contamination rate.
Assembly: Genome assemblyASM584v2, GCF_000005845.2
Supplementary files format and content: Excel file includes Gene expression matrix (TPM) for each Sample

organism: Escherichia coli

extract_protocol:
Total RNA was extracted from the tissue using CTAB method and genomic DNA was removed. Only high-quality RNA sample was used to construct sequencing library.
RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using of total RNA.

tag: strain

value: sulfur-free


title: GM12878, 1000U, Cell 22

tag: tissue

value: blood

value: lymphoblastoid


title: M9_VEH_SED


title: GM12878, 1000U, Cell 26

tag: cell line

value: WT


title: E coli, sulfur-free, rep1


title: E coli, sulfur-free, rep3


title: M34_TAM_EX

tag: cell type


title: Day5(#10)_PHx+Gln

description: Gene expression after PHx + 2%gln

source_name: Liver, PHx, 2%Gln, D5, replicate 1


title: M30_TAM_EX

tag: genotype


title: Day4(#1)_PHx+Gln

description: Gene expression after PHx + 2%gln

source_name: Liver, PHx, 2%Gln, D4, replicate 1


title: GM12878, 1000U, Cell 20

tag: mnase titration


title: Day3(#13)_PHx+Gln

description: Gene expression after PHx + 2%gln

source_name: Liver, PHx, 2%Gln, D3, replicate 1


title: E coli, control, rep3

value: control


title: M27_TAM_EX


title: E coli, control, rep2


title: GM12878, 1000U, Cell 19


title: Day4(#40)_Sham-Gln

description: Gene expression after Sham + placebo

source_name: Liver, Sham, placebo, D4, replicate 1


title: E coli, control, rep1


title: GM12878, 1000U, Cell 23


title: M8_TAM_EX


title: GM12878, 1000U, Cell 18


title: GM12878, 1000U, Cell 21


title: Day2(#2)_PHx+Gln

description: Gene expression after PHx + 2%gln

source_name: Liver, PHx, 2%Gln, D2, replicate 1


title: Mtb, Deferoxamine treated, rep 3

city: New Delhi

first: Ranjan

middle: Kumar

last: Nanda

address: International Centre for Genetic Engineering and Technology, New Delhi-110067, India

department: Translational Health Group

country: India

institute: International Centre for Genetic Engineering and Technology (ICGEB), New Delhi component

data_processing:
Adapter Contamination was removed using bbduk.sh (from BBmap toolkit v39.06) with options (ktrim=l k=23 mink=11 hdist=1 tpe tbo).
Hisat2 (v2.2.1) was used for the alignment of reads to the Mtb genome (Refseq Accession: NC_000962.3) which was subsequently sorted using Samtools (v1.13).
The sorted alignment files in BAM format were used as input for counting reads using featureCounts (v2.0.3).
Assembly: NC_000962.3
Supplementary files format and content: "raw_counts.tsv" file is in TSV format and contains raw read counts of all libraries.

organism: Mycobacterium tuberculosis

source_name: Bacteria

growth_protocol: Middlebrook 7H9 supplemented with OADC enrichment.

extract_protocol:
DFO (0.1 mg/ml) and control were harvested at day 5 post-addition of Deferoxamine by centrifuging the Mtb cultures at 3,500 g for 10 minutes at room temperature. The cell pellet was washed with Tris-EDTA to remove extra media and the pellet was suspended in Trizol reagent (1 ml). The samples were subjected to bead beating (4 cycles, 45 sec each) after adding zirconia beads (~200 μl, 0.1 mm) at 6.5 m/s speed with incubation of 30 sec on ice after each cycle. Chloroform (0.2 ml) was added to the samples and after briefly shaking the tubes, the samples were incubated on ice (for 5 min) and centrifuged at 13,400 g, 4ºC for 20 min. Upper aqueous layer was transferred to a fresh tube and RNA was precipitated by adding isopropyl alcohol (0.5 ml). The samples were then incubated at -80ºC for 20 min and subsequently centrifuged for 10 min at 13,400 g and 4ºC. The purified RNA pellet was washed with 75% ethanol and resuspended in nuclease-free water.
NEBNext Ultra RNA library prep kit

treatment_protocol: Deferoxamine was added at the concentration of 0.1 mg/mL in log-phase Mtb cultures.

value: Bacteria

value: Wildtype

value: Deferoxamine treated


title: GM12878, 1000U, Cell 17


title: Mtb, Deferoxamine treated, rep 2


title: Day6(#36)_PHx-Gln

description: Gene expression after PHx + placebo

source_name: Liver, PHx, placebo, D6, replicate 1


title: GM12878, 1000U, Cell 16


title: M26_VEH_EX

value: Gastrocnemius


title: M19_VEH_EX

value: Skeletal Muscle


title: Mtb, Deferoxamine treated, rep 1


title: Day7(#37)_PHx-Gln

description: Gene expression after PHx + placebo

source_name: Liver, PHx, placebo, D7, replicate 1


title: Day5(#38)_PHx-Gln

description: Gene expression after PHx + placebo

source_name: Liver, PHx, placebo, D5, replicate 1


title: GM12878, 1000U, Cell 15


title: Day1(#18)_PHx+Gln

description: Gene expression after PHx + 2%gln

source_name: Liver, PHx, 2%Gln, D1, replicate 1


title: Mtb, control, rep 2

value: Control


title: Day3(#26)_PHx-Gln

description: Gene expression after PHx + placebo

source_name: Liver, PHx, placebo, D3, replicate 1


title: GM12878, 1000U, Cell 13


title: Day2(#23)_PHx-Gln

description: Gene expression after PHx + placebo

source_name: Liver, PHx, placebo, D2, replicate 1


title: Day4(#34)_PHx-Gln

description: Gene expression after PHx + placebo

source_name: Liver, PHx, placebo, D4, replicate 1


title: M7_VEH_EX

source_name: Gastrocnemius

value: EX


title: M4_TAM_EX

value: TAM


title: Day1(#22)_PHx-Gln

description: Gene expression after PHx + placebo

source_name: Liver, PHx, placebo, D1, replicate 1


title: wildtype/isogenic/MAPT V337M 6d kctd20 +glut 2

city: Los Angeles

first: Joshua

last: Berlind

address: 1425 San Pablo St

institute: University of Southern California

description:
Library name: 4B
10X Genomics
4A4Bbarcodes.tsv.gz
4A4Bmatrix.mtx.gz
4A4Bfeatures.tsv.gz

data_processing:
Data alignment and QC was conducted through the University of Southern California Center for Advanced Research Computing (CARC) using the Cell Ranger count Feature Barcode Analysis pipeline (10X Genomics) for concurrent UMI identification, reference genome (human hg38 genome) alignment, and HTO assignment. Samples were demultiplexed using the HTODemux pipeline in R version 4.0.158. Data was further processed using Seurat v4.0 to remove cells with < 200 detectable genes and > 50% mitochondrial rate118,119. We retrieved roughly 39,000 high quality cells with a depth of 20,000-25,000 reads/cell.
cell hash sequences for demultiplexing- glutamate: CAGGTTGTTGTCATT; glutamate + kctd20 aso: TATTTCCACCCGGTC
Assembly: hg38
Supplementary files format and content: tab separated values files and matrix files

source_name: neural

extract_protocol:
Organoids were dissociated for single-cell RNA sequencing as described with minor modifications117. In brief, organoids were incubated in Papain (Worthington LK003176) with DNase1 (Worthington LK003170) reconstituted per manufacturer instructions for 60 minutes at 37⁰C with gentle shaking at 27 rpm with regular pipetting. Single-cell suspension was added to Earle’s Balanced Salt Solution (EBSS) with Ovomucoid Inhibitor (Worthington LK003182) and DNase1, pelleted, resuspended in ice-cold Neurobasal-A (Invitrogen) with 0.2% bovine serum albumin (BSA), and filtered through 40 µM Flowmi tips (Sigma BAH136800040-50EA). Cell count and viability was determined by Trypan Blue staining using a hemocytometer. Cells were labeled with hashtag-oligonucleotide (HTO) antibodies (Biolegend TotalSeq-B, 405287, 405289, 405291) and libraries were prepared following manufacturer protocols (10X Genomics, CG000206 Rev D).
Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (with Feature Barcoding for Cell Surface Protein); PN-1000128, PN-1000079, PN-1000127, PN-1000213

value: neural

value: organoid

value: neurons, glia

value: mixed

value: 6d glutamate + kctd20 aso


title: wildtype/isogenic/MAPT V337M 6d glut 2

description:
Library name: 3B
10X Genomics
3A3Bbarcodes.tsv.gz
3A3Bmatrix.mtx.gz
3A3Bfeatures.tsv.gz

value: 6d glutamate


title: GM12878, 1000U, Cell 11

source_name: blood

value: blood

value: lymphoblastoid

value: 1000U MNase


title: GM12878, 1000U, Cell 12

value: WT


title: M22_TAM_SED

value: SED


title: GM12878, 1000U, Cell 14


title: GM12878, 1000U, Cell 10