title: tm-2-ToB

city: Ningbo

first: zhang

middle: yu

last: hong

address: No. 818, Fenghua Street

institute: Ningbo University

description:
Library name: R_ToB
One sample from ToBRFV  inoculated tm-2 tomato plants

data_processing:
10x Genomics Cell Ranger (v3.1.0) was used to convert raw BCL files to FASTQ, align reads, and quantify gene expression. Low-quality barcodes and UMIs were filtered before mapping reads to the reference genome. Reads uniquely mapped to transcripts with over 50% exon overlap were kept for UMI counting, with UMI sequences corrected for sequencing errors. Valid cell barcodes were identified using the EmptyDrops method. The final output was cell-by-gene expression matrices generated from UMI counts and cell barcode assignments.
Assembly: Genome assembly SL3.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Solanum lycopersicum

source_name: tomato leaf

extract_protocol:
The leaf strips were subjected to vacuum infiltration for 5 minutes and then incubated in the dark at 27°C with gentle shaking (50 rpm) for 3 hours to facilitate digestion. The resulting suspension was filtered through a 40 μm cell strainer and centrifuged at 100 g for 5 minutes at 4°C to collect the protoplasts. After removing the supernatant enzyme solution, protoplasts were washed twice with W5 solution (154 mM NaCl, 125 mM CaCl2·2H2O, 5 mM glucose, 2 mM MES, 5 mM KCl, pH 5.7).Protoplasts were then resuspended in 0.8 M mannitol solution to minimize cell aggregation. Concentrations were determined using a microscope, and viability was assessed by staining with 0.04% (w/v) trypan blue.
Following the manufacturer’s protocol, protoplast suspensions were immediately loaded into the Chromium Controller Instrument (10× Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-In-Emulsions (GEMs). Single-cell RNA sequencing (scRNA-seq) libraries were prepared from the resulting cDNA using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1, following the vendor’s user guide. Silane magnetic beads were employed to remove residual biochemical reagents and primers from the post-GEM reaction mixture. Full-length barcoded cDNAs were subsequently amplified by PCR to obtain sufficient material for library construction. The finalized libraries were adaptor-ligated for Illumina bridge amplification and quality-controlled using an Agilent 2100 Bioanalyzer. Sequencing was performed on an Illumina NovaSeq 6000 platform (Gene Denovo, Guangzhou, China) to generate paired-end 150 bp reads.

value: tomato leaf

tag: treatment

value: ToBRFV inoculated


title: Human meningioma, FFPE, [MN1-1]

status: Public on Apr 09 2026

type: RNA

city: San Francisco

first: Minh

middle: P

last: Nguyen

state: California

country: USA

institute: University of California, San Francisco

description: Nanostring nCounter

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

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

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

molecule: total RNA

organism: Homo sapiens

source_name: FFPE meningioma

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

tag: tissue

value: FFPE meningioma

tag: disease

value: meningioma

tag: tumor grade

tag: Sex

value: Female

tag: age at surgery

tag: outcome

value: censored


title: Human meningioma, FFPE, [MN2-1]

description: Nanostring nCounter

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

value: Male

value: progression


title: Human meningioma, FFPE, [MN115]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN117]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN4-1]

description: Nanostring nCounter


title: Tm-22-ToB

type: SRA

country: China

description:
Library name: T2_ToB
One sample from ToBRFV  inoculated Tm-22 tomato plants

library_source: transcriptomic single cell

molecule: polyA RNA

tag: genotype


title: Human meningioma, FFPE, [MN114]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN113]

description: Nanostring nCounter


title: V5-tagged PAX3-FOXO1

city: Durham

first: Benjamin

middle: Kakimoto

last: Lau

state: NC

address: 3 Genome Court

institute: Duke University

description: Library name: Sample_6

library_source: genomic

data_processing:
The Fastq files were first mapped to the main reference genome (hg38) using STAR (v.2.7.11a).
The non-primary alignment, PCR duplicates, or blacklist regions were removed from the aligned data by using Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of signals.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: RF4-flag cells with endogenous PAX3-FOXO1 knocked down (shP3F1 RF4-Flag), followed by expression of a V5-tagged PAX3-FOXO1

growth_protocol: A previously generated human rhabdomyosarcoma RF4 cell line, which carries a Flag tag knockin to C-terminus of endogenous PAX3-FOXO1 (termed RH4-Flag), was a kind gift from Dr. Beat Schäfer and cultured in RPMI supplemented with 10% FBS.

extract_protocol:
Briefly, 500,000 of human tumor cells were used in each assay.
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030) followed by the PCR-based amplification using i5/i7 primers.

treatment_protocol: Endogenous PAX3-FOXO1 in the RF4-flag cells was knocked down with an shRNA targeting the PAX3-FOXO1 breakpoint (termed shP3F1 RF4-flag cells), followed by ectopic expression of a V5-tagged PAX3-FOXO1, PAX3-INO80D, PAX3-MAML1 or PAX3-NCOA1. Cells were maintained in RPMI supplemented with 10% FBS.

tag: cell line

tag: cell type

value: human rhabdomyosarcoma cell line

tag: cut&tag antibody

value: V5 tag antibody, Abcam, 9116


title: Tm-22-Mock

description:
Library name: T2_CK
One sample from  the pcb-GUS control inoculated Tm-22 tomato plants

value: pcb-GUS inoculated


title: Human meningioma, FFPE, [MN110]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN112]

description: Nanostring nCounter


title: tm-2-Mock

description:
Library name: R_CK
One sample from  pcb-GUS control inoculated tm-2 tomato plants


title: Human meningioma, FFPE, [MN106]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN111]

description: Nanostring nCounter


title: V5-tagged PAX3-MAML1

description: Library name: Sample_8

source_name: shP3F1 RF4-Flag cells with the expression of a V5-tagged PAX3-MAML1


title: beads PAX3-FOXO1

description: Library name: Sample_10

source_name: shP3F1 RF4-Flag cells with the expression of a V5-tagged PAX3-FOXO1

value: no antibody


title: NCOA1

description: Library name: Sample_4

value: NCOA1 antibody, ABclonal, A9058


title: V5-tagged PAX3-INO80D

description: Library name: Sample_7

source_name: shP3F1 RF4-Flag cells with the expression of a V5-tagged PAX3-INO80D


title: V5-tagged PAX3-NCOA1

description: Library name: Sample_9

source_name: shP3F1 RF4-Flag cells with the expression of a V5-tagged PAX3-NCOA1


title: beads

description: Library name: Sample_5


title: MAML1

description: Library name: Sample_3

value: MAML1 antibody, Cell Signaling Technology, 12166


title: Human meningioma, FFPE, [MN104]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN103]

description: Nanostring nCounter


title: INO80D

description: Library name: Sample_2

value: INO80D antibody, Atlas Antibodies, HPA043976


title: Human meningioma, FFPE, [MN102]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN101]

description: Nanostring nCounter


title: Flag-tagged PAX3-FOXO1

description: Library name: Sample_1

source_name: RF4, with a Flag tag knockin to endogenous PAX3-FOXO1 (RF4-Flag)

value: Flag antibody, Cell Signaling Technology, 8146T


title: Human meningioma, FFPE, [MN100]

description: Nanostring nCounter


title: zebrafish 1k cell, PCR_EM-seq

city: Wuhan City

first: Zhiyuan

last: Hu

address: No. 115 East Lake Road (Donghu Road), Wuchang District

department: Medical Research Institute

institute: Wuhan University

description: Library name: PCR_EM_1kcell

data_processing:
Adapter and quality filtering were performed with Trim Galore (v0.6.10). Parameters were applied specifically for each sample group: Converted HeLa were trimmed with default parameters, while methylc and fish samples were trimmed with -paired --length 35 --clip_R1 10 --clip_R2 15 --three_prime_clip_R 10 --three_prime_clip_R2 10. Trimmed reads were aligned to the human reference genome (GRCh38) or the zebrafish reference genome (GRCz11.114) with spike-in sequences included. Converted DNA libraries were aligned using Bismark (v0.24.2) with default parameters. Zebrafish samples were aligned using Bismark (v0.24.2) with --maxins 1000. PCR duplicates were removed using deduplicated_bismark. Methylation information was extracted from deduplicated BAM files using bismark_methylation_extractor with default settings.
Assembly: GRCh38, GRCz11.114
Supplementary files format and content: Supplementary_files_format_and_content: CpG modification bismark report in the bedGraph format
Library strategy: EM-seq

organism: Danio rerio

source_name: zebrafish embryo

growth_protocol: HeLa cells were cultured in a humidified incubator at 37°C with 5% CO₂. The cells were maintained in the DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin. Cells were seeded at a density of approximately 50,000 cells/cm² in T25 flasks and passaged upon reaching 80-90% confluency. Zebrafish were raised and maintained under standard conditions.

extract_protocol:
HeLa cells were detached, collected, and pelleted by centrifugation at 300 × g for 5 min. Genomic DNA was subsequently extracted using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme) according to the manufacturer’s protocol. Genomic DNA was fragmented to an average size of ~300  bp using a Covaris M220 Focused-ultrasonicator. Embryos of zebrafish were collected at four developmental stages: 64-cell, 128-cell, 1k-cell, and Germ ring. Before DNA extraction, embryos were bleached with bleach solution (0.1 ml 5% NaClO in 170 ml system water) for 5 min and rinsed thoroughly with 1× PBS. Genomic DNA was isolated using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme), according to the manufacturer’s protocol. Genomic DNA from the embryos was fragmented to an average size of around 300 bp using the Bioruptor Pico sonication device (Diagenode). For the 128-cell, 1K-cell, and Germ-ring samples, an optimised sonication program was used, i.e., 15 s ON/30 s OFF, 4 cycles for the 50-μl sample volume. For the 64-cell-stage gDNA, 3 cycles of 15 s ON/30 s OFF were used instead.
End repair and A-tailing were performed for fragmented DNA using the VANTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) with EM-seq adapters (NEB) according to the manufacturer’s protocol. After adapter ligation, unmethylated cytosines in the DNA were enzymatically converted to uracil using the EpiArt DNA Enzymatic Methylation Kit (Vazyme), following the manufacturer’s protocol. For FINE-EM-seq libraries, FINE amplification was applied on converted DNA(including 1 ng, 100 pg, 1 pg HeLa gDNA and 1 ng of each stage's zebrafish gDNA), followed by a 3-cycle PCR to add full-length adapters for Illumina sequencing. For PCR methylation libraries, converted DNA was amplified using 2× Synthesis Mix (ABclonal) or HiFi V3 (Vazyme). PCR thermal cycling consisted of an initial denaturation at 98°C for 45 s; followed by 16 cycles (for 1 ng), 20 cycles (for 100 pg), or 23 cycles (for 10 pg) of 98°C for 15 s, 60°C for 30 s, and 72°C for 20 s; followed by a final extension at 72°C for 1 min and then hold at 12°C. The amplified DNA was purified twice using 0.8× VANTS DNA Clean Beads (Vazyme).

value: zebrafish embryo

tag: input amount


title: Human meningioma, FFPE, [MN96]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN98]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN97]

description: Nanostring nCounter


title: zebrafish 1k cell, FINE-EM-seq

description: Library name: FINE_EM_1kcell


title: zebrafish 64cell, PCR_EM-seq

description: Library name: PCR_EM_64cell


title: zebrafish 128 cell, PCR_EM-seq

description: Library name: PCR_EM_128cell


title: zebrafish 64cell, FINE-EM-seq

description: Library name: FINE_EM_64cell


title: Human meningioma, FFPE, [MN93]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN99]

description: Nanostring nCounter


title: zebrafish 128 cell, FINE-EM-seq

description: Library name: FINE_EM_128cell


title: zebrafish germ ring, PCR_EM-seq

description: Library name: PCR_EM_Germ_ring


title: zebrafish germ ring, FINE-EM-seq, biol rep 2

description: Library name: Germ_ring_2

extract_protocol:
HeLa cells were detached, collected, and pelleted by centrifugation at 300 × g for 5 min. Genomic DNA was subsequently extracted using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme) according to the manufacturer’s protocol. Genomic DNA was fragmented to an average size of ~300  bp using a Covaris M220 Focused-ultrasonicator.  Embryos of zebrafish were collected at four developmental stages: 64-cell, 128-cell, 1k-cell, and Germ ring. Before DNA extraction, embryos were bleached with bleach solution (0.1 ml 5% NaClO in 170 ml system water) for 5 min and rinsed thoroughly with 1× PBS. Genomic DNA was isolated using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme), according to the manufacturer’s protocol. Genomic DNA from the embryos was fragmented to an average size of around 300 bp using the Bioruptor Pico sonication device (Diagenode). For the 128-cell, 1K-cell, and Germ-ring samples, an optimised sonication program was used, i.e., 15 s ON/30 s OFF, 4 cycles for the 50-μl sample volume. For the 64-cell-stage gDNA, 3 cycles of 15 s ON/30 s OFF were used instead.
End repair and A-tailing were performed for fragmented DNA using the VANTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) with EM-seq adapters (NEB) according to the manufacturer’s protocol. After adapter ligation, unmethylated cytosines in the DNA were enzymatically converted to uracil using the EpiArt DNA Enzymatic Methylation Kit (Vazyme), following the manufacturer’s protocol. For FINE-EM-seq libraries, FINE amplification was applied on converted DNA(including 1 ng, 100 pg, 1 pg HeLa gDNA and 1 ng of each stage's zebrafish gDNA), followed by a 3-cycle PCR to add full-length adapters for Illumina sequencing. For PCR methylation libraries, converted DNA was amplified using 2× Synthesis Mix (ABclonal) or HiFi V3 (Vazyme). PCR thermal cycling consisted of an initial denaturation at 98°C for 45 s; followed by 16 cycles (for 1 ng), 20 cycles (for 100 pg), or 23 cycles (for 10 pg) of 98°C for 15 s, 60°C for 30 s, and 72°C for 20 s; followed by a final extension at 72°C for 1 min and then hold at 12°C. The amplified DNA was purified twice using 0.8× VANTS DNA Clean Beads (Vazyme).


title: Human meningioma, FFPE, [MN94]

description: Nanostring nCounter


title: zebrafish germ ring, FINE-EM-seq

description: Library name: FINE_EM_Germ_ring


title: zebrafish 1k cell, FINE-EM-seq, biol rep 2

description: Library name: 1kcell_2


title: Human meningioma, FFPE, [MN92]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN91]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN95]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN86]

description: Nanostring nCounter


title: zebrafish germ ring, FINE-EM-seq, biol rep 1

description: Library name: Germ_ring_1


title: Human meningioma, FFPE, [MN90]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN88]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN85]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN89]

description: Nanostring nCounter


title: zebrafish 64 cell, FINE-EM-seq, biol rep 2

description: Library name: 64cell_2


title: Human meningioma, FFPE, [MN84]

description: Nanostring nCounter


title: zebrafish 128 cell, FINE-EM-seq, biol rep 2

description: Library name: 128cell_2


title: Human meningioma, FFPE, [MN83]

description: Nanostring nCounter


title: zebrafish 1k cell, FINE-EM-seq, biol rep 1

description: Library name: 1kcell_1


title: zebrafish 64cell, FINE-EM-seq, biol rep 1

description: Library name: 64cell_1


title: MM.1S cells LenR biol rep 3

city: Yantai

first: Xinlong

last: Guo

state: Shandong province

address: No. 198, Binhai East Road, Muping District, Yantai City, Shandong Province, China

department: Shandong Laboratory of Yantai Drug Discovery

institute: Bohai Rim Advanced Research Institute for Drug Discovery

description:
Library name: Sample 6
Column name in expressed_genes_FPKM.txt: LenR3

library_source: transcriptomic

data_processing:
Raw FASTQ files were quality checked using FastQC (v0.11.9) Reads were aligned to the hg38 reference genome using hisat2 (v2.2.1) Gene counts were quantified using featureCounts (v2.0.3) Differential expression genes were analyzed using edgeR (v3.40.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample
Supplementary files format and content: xlsx files include FPKM values for each Sample

growth_protocol: MM.1S cells were maintained in RPMI 1640 supplemented containing 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in an incubator containing 5% CO2 at 37 oC with suitable humidity.

extract_protocol:
RNA was harvested by ANOROAD (Beijing, China).
RNA libraries for RNA-seq were prepared using VAHTS  Universal  V6  RNA-seq  Library Prep  Kit  for  Illumina ® (NR604-01/02) following manufacturer's protocols.

treatment_protocol: To establish a lenalidomide-resistant (LenR) MM cell line, MM.1S cells were subjected to continuous treatment with 10 nM lenalidomide, with the dosage increased 10-fold each month over a period of 3 months. Concurrently, another group of MM cells received continuous treatment with dimethyl sulfoxide (DMSO) as solvent control (WT).

value: Tumor cells

value: WT

value: lenalidomide


title: zebrafish 128 cell, FINE-EM-seq, biol rep 1

description: Library name: 128cell_1


title: MM.1S cells LenR biol rep 2

description:
Library name: Sample 5
Column name in expressed_genes_FPKM.txt: LenR2


title: MM.1S cells WT biol rep 3

description:
Library name: Sample 3
Column name in expressed_genes_FPKM.txt: WT3

value: DMSO


title: Human meningioma, FFPE, [MN80]

description: Nanostring nCounter

value: FFPE meningioma

value: meningioma

value: Female


title: Human meningioma, FFPE, [MN79]

description: Nanostring nCounter

value: censored


title: Human meningioma, FFPE, [MN78]

description: Nanostring nCounter

value: Male


title: Human meningioma, FFPE, [MN81]

description: Nanostring nCounter


title: MM.1S cells LenR biol rep 1

description:
Library name: Sample 4
Column name in expressed_genes_FPKM.txt: LenR1


title: Xenopus limb explant, ALI, H3K27ac, rep1

city: Geneva

first: Hanrong

address: B1 0 266.045 (Campus Biotech bâtiment B1)

department: Brain Mind Institute

country: Switzerland

institute: EPFL

description: Library name: 01102024_KH_X-ALI_H3K27ac

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

organism: Xenopus laevis

source_name: limb explants

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

value: limb explants


title: Human meningioma, FFPE, [MN75]

description: Nanostring nCounter


title: MM.1S cells WT biol rep 1

description:
Library name: Sample 1
Column name in expressed_genes_FPKM.txt: WT1


title: MM.1S cells WT biol rep 2

description:
Library name: Sample 2
Column name in expressed_genes_FPKM.txt: WT2


title: Human meningioma, FFPE, [MN76]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN77]

description: Nanostring nCounter


title: IL4_C

city: Boston

first: Susan

last: Patalano

state: MA

address: 100 Morrissey Blvd.

department: Center for Personalized Cancer Therapy

institute: UMASS Boston

description: N1 prostate stromal fibroblasts were treated with IL-4 (20ng/mL) for 24 hours before RNA was collected with Qiagen miRNEasy Kit (Qiagen 217084) and sent out to Arraystar for analysis

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Array V2 and incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: After slide washing, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: N1 postate stromal fibroblasts

label_protocol: Enriched circRNAs were amplified and transcribed into fluorescent cDNA by random priming using an Arraystar Super RNA Labeling Kit according to manufacturer protocol

extract_protocol: RNA extracted via Qiagen MiRNeasy kit by manufacturer's instructions

tag: age

value: aged


title: IL4_B


title: Human meningioma, FFPE, [MN73]

description: Nanostring nCounter


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

description: Library name: 01102024_KH_X-96-well_H3


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

description: Library name: 01102024_KH_X-96-well_H3K27ac


title: Human meningioma, FFPE, [MN71]

description: Nanostring nCounter


title: IL4_A


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

description: Library name: 01102024_KH_X-96-well_H3K27me3


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

description: Library name: 01102024_KH_X-96-well_H3K4me3


title: tumor2

city: Changzhou, Jiangsu

first: yue

last: cao

address: juqian street

department: The Third Afiliated Hospital of

institute: Soochow University

description: Plasma exosomes isolated by ultracentrifugation (100,000g ×2h; TEM verified).   Total RNA extracted with TRIzol (Thermo Fisher, 15596026), followed by RNase R digestion (Epicentre MRR092; 3U/μg RNA, 37°C/15min) for circRNA enrichment.   Labeled with Cy3 using Arraystar Super RNA Labeling Kit (AS-LB-002).   Hybridized to Arraystar Human circRNA Array V2 (Design ID 075731) at 65°C/17h.   Raw data acquired via Agilent G2505C scanner and processed with Feature Extraction v11.0.1.1 (no ch2 sample involved).

hyb_protocol: Hybridization solution: 25 μL (Agilent GE Hybridization Kit); Hybridization: Arraystar V2 array, 65°C/17h in Agilent Oven G2545A (rotation 10 rpm); Wash: Gene Expression Wash Buffers 1 & 2 (Agilent)

scan_protocol: Scanner: Agilent G2505C; Settings: 535 nm excitation, 550-600 nm emission, 3 μm resolution, 100% PMT gain; Software: Agilent Feature Extraction v11.0.1.1 (grid: 075731_D_F_20211028)

data_processing: 1. Background correction: normexp (offset=50); 2. Normalization: quantile (limma v3.54.0); 3. Probe filtering: remove control probes; 4. circRNA annotation: Arraystar circRNA database (GRCh38/hg38)

source_name: Plasma exosome

label_protocol: Arraystar Super RNA Labeling Kit (AS-LB-002): 2 μg RNase R-treated RNA labeled with Cy3-dUTP via random priming, 37°C/2h

extract_protocol: Plasma exosomes: sequential centrifugation (500g/5min → 2,000g/10min → 10,000g/10min → 0.22-μm filtration → 100,000g ×2h); Total RNA: TRIzol extraction (Thermo Fisher, 15596026); circRNA enrichment: RNase R digestion (Epicentre MRR092, 3U/μg RNA, 37°C/15min)

tag: tag

value: diagnosis:diffuse large B-cell lymphoma

value: treatment status:treatment-naive


title: Normal3

value: healthy


title: Vehicle_C

description: N1 prostate stromal fibroblasts were mock treated with Vehcle for 24 hours before RNA was collected with Qiagen miRNEasy Kit (Qiagen 217084) and sent out to Arraystar for analysis

value: Vehicle


title: Normal2


title: tumor3


title: Human meningioma, FFPE, [MN69]

description: Nanostring nCounter


title: Xenopus limb explant, ALI, H3, rep3

description: Library name: 01102024_KH_X-ALI_H3


title: Xenopus limb explant, ALI, H3K4me3, rep3

description: Library name: 01102024_KH_X-ALI_H3K4me3


title: Human meningioma, FFPE, [MN67]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN68]

description: Nanostring nCounter


title: IL13_C

description: N1 prostate stromal fibroblasts were treated with IL-13 (20ng/mL) for 24 hours before RNA was collected with Qiagen miRNEasy Kit (Qiagen 217084) and sent out to Arraystar for analysis


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

description: Library name: 15082024_KH_X-96-well_H3


title: Xenopus limb explant, ALI, H3K27me3, rep3

description: Library name: 01102024_KH_X-ALI_H3K27me3


title: smc3-K113Q with smc1-T1117I

city: berkeley

first: lorenzo

last: costantino

state: california

address: berker hall

department: MCB

institute: University of California, Berkeley

description: Library name: K113Q TI

data_processing:
1. Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley 2. allValidPairs files were generated by HiC-Pro package (>2.10 version) 3. mcool files were converted from allValidPairs by Cooler package 4. hic file were converted from allValidPairs by Juicer tools Genome_build: sacCer3 Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with mutiple resolutions
Assembly: sacCer3
Supplementary files format and content: Micro-C XL data are provided in .hic and .mcool format

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown to early-log phase (OD600 0.1-0.2) at the temperature indicated (23°C or 30°C) overnight and arrested in G1 using the pheromone alpha-factor at a concentration of 10-8M. Cells were released from G1 by washing with YPD containing auxin (if indicated) and 0.15 mg/mL pronase E three times, and once with YPD. After the last wash, cells were resuspended in YPD medium containing 15 µg/mL nocodazole and auxin if indicated. Cultures were then once again incubated at 23°C/30°C for 3h. For the time course, cells were released from alpha-factor into fresh media and collected every 15min with no other drugs.

extract_protocol:
Micro-C products were extracted as the following steps: 1) Digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP by DNA Polymerase I, Large (Klenow) Fragment ; 3) Proximal ligation by T4 DNA ligase and remove unligated ends by Exonuclease III; 4) Purify ligated dinucleosomal DNA by the standard Phenol:Chloroform:Isoamyl Alcohol (25:24:1) and ethanol precipitation procedure. Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with the individual enzymes purchased from Lucigen or the NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme or NEB Q5 enzyme with the lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 on the Illumina HiSeq 4000 sequencer.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with the individual enzymes purchased from Lucigen or the NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme or NEB Q5 enzyme with the lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 on the Illumina HiSeq 4000 sequencer.

treatment_protocol: If indicated, auxin was added to a final concentration of 500 µM to deplete AID-tagged proteins after a 2.5 hours arrest. We used the Micro-C protocol reported in (Hsieht et al., 2016, Nature Methods) with some minor modifications. Yeast cultures in the indicated conditions were immediately crosslinked with 3% formaldehyde for 15 minutes at 30°C, then quenched with 125 mM glycine at room temperature for 5 minutes. Washed yeast cells were then spheroplasted with 250 ug/mL Zymolyase in the Buffer Z at 30°C. Washed spheroplasts were resuspended in the 3mM DSG crosslinking solution and incubated at 30°C for 40 minutes. Crosslinking reaction was quenched with 125 mM glycine at room temperature for 5 minutes. Crosslinked cells can be stored at -80 ̊C for few months or proceed to chromatin fragmentation immediately.

tag: strain

tag: genetic background

value: yeast cells

value: smc3-K113Q smc1-T1117I-LEU2:leu2-3,112 smc1delta::HPH LacO-NAT::lys4 GFPLacI-HIS3:his3-11,15 trp1-1 ura3-52 bar1 GAL+


title: Human meningioma, FFPE, [MN66]

description: Nanostring nCounter


title: IL13_B


title: smc1-D1164E eco1∆

description: Library name: DE eco1∆

value: eco1delta::G418 smc1-D1164E-LEU2:leu2-3,112 smc1delta::HPH trp1-1 LacO-NAT::lys4 GFPLacI-HIS3:his3-11,15 ura3-52 GAL+ bar1


title: ECO1-AID

description: Library name: ECO1-AID

value: ECO1-3V5-AID2-G418 TIR1-CaTRP1 LacO(DK)-NAT::lys4 leu2-3,112 GAL+ GFPLacI-HIS3:his3-11,15 bar1 ura3-52


title: tumor1


title: smc1-D1164E

description: Library name: DE

value: smc1-D1164E-LEU2:leu2-3,112 trp1-1 smc1delta::HPH LacO(DK)-NAT::lys4 bar1 GFPLacI-HIS3:his3-11,15 ura3-52 GAL+


title: Vehicle_B


title: Vehicle_A


title: Normal1


title: smc1-T1117I

description: Library name: TI

value: smc1-T1117I-LEU2:leu2-3,112 smc1delta::HPH LacO-NAT::lys4 GFPLacI-HIS3:his3-11,15 trp1-1 ura3-52 bar1 GAL+


title: IL13_A


title: Human meningioma, FFPE, [MN65]

description: Nanostring nCounter

value: FFPE meningioma


title: wpl1∆

description: Library name: wpl1∆

value: ECO1-3V5-AID2-G418 TIR1-CaTRP1 LacO-NAT::lys4 leu2-3,112 GAL+ pHIS3-GFPLacI-HIS3:his3-11,15 bar1 ura3-52


title: ECO1-AID wpl1∆

description: Library name: ECO1-AID wpl1∆

value: ECO1-3V5-AID2-G418 rad61delta::HPH TIR1-CaTRP1 LacO(DK)-NAT::lys4 pHIS3-GFPLacI-HIS3:his3-11,15 bar1 leu2-3,112 ura3-52 GAL+


title: smc3-K113Q

description: Library name: K113Q

value: SMC3-K113Q-LEU2:leu2-3,112 smc3-N607-3V5-AID TIR1-CaTRP1 LacO-NAT::lys4 GFPLacI-HIS3:his3-11,15 ura3-52 bar1 GAL+


title: Human meningioma, FFPE, [MN64]

description: Nanostring nCounter

value: meningioma

value: Female

value: censored


title: smc3-K112R

description: Library name: K112R

value: smc3-K112R TIR1-CgTRP1 LacO-NAT::lys4 GFPLacI-HIS3:his3-11,15 leu2-3,112 ura3-52 bar1 GAL+


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

description: Library name: 13082024_KH_X-96-well_H3

value: limb explants


title: WT biological rep2

description: Library name: WT2

value: TIR1-CgTRP1 LacO-NAT::lys4 GFPLacI-HIS3:his3-11,15 leu2-3,112 ura3-52 bar1 GAL+


title: WT biological rep1

description: Library name: WT1


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

description: Library name: 15082024_KH_X-96-well_H3K27me3


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

description: Library name: 15082024_KH_X-96-well_H3K4me3


title: Xenopus limb explant, ALI, H3K4me3, rep2

description: Library name: 15082024_KH_X-ALI_H3K4me3


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

description: Library name: 13082024_KH_X-96-well_H3K4me3


title: smc3-K113R

description: Library name: K113R

value: smc3-K113R-URA3::ura3-52 SMC3-3V5-AID608 TIR1- CaTRP1::trp1-1 LacO-NAT::lys4 pHIS3-GFP-LacI-HIS3:his3- 11,15 ura3-52 bar1


title: Human meningioma, FFPE, [MN60]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN61]

description: Nanostring nCounter

value: Male


title: Xenopus limb explant, ALI, H3K27me3, rep2

description: Library name: 15082024_KH_X-ALI_H3K27me3


title: Human meningioma, FFPE, [MN63]

description: Nanostring nCounter


title: WT biological rep3

description: Library name: WT3

value: yeast cells


title: flox_lox-51

city: Shanghai

first: Jieyu

state: Shanghai

address: 138 Yixueyuan Rd,

institute: fudan university

description:
Library name: Sample 5
FLOX-3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hista2
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cufflinks
Assembly: mm10
Supplementary files format and content: Matrix table with FPKM for every gene and every sample

organism: Mus musculus

source_name: heart

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild-type (WT) and LTBP4 cardiomyocyte-specific knockout (LTBP4-CKO) mice aged 10-12 weeks underwent transaortic constriction (TAC) surgery. During the procedure, the transverse aorta was isolated and constricted using a 27-gauge needle and 7-0 silk suture, followed by layered closure of the chest wall.

value: heart

value: WT

value: TAC


title: smc3-K112Q

description: Library name: K112Q

value: smc3-K112Q TIR1-CgTRP1 LacO-NAT::lys4 GFPLacI-HIS3:his3-11,15 leu2-3,112 ura3-52 bar1 GAL+


title: LTBP4-4

description:
Library name: Sample 6
LTBP4-CKO3


title: Human meningioma, FFPE, [MN62]

description: Nanostring nCounter

value: FFPE meningioma


title: Xenopus limb explant, ALI, H3, rep2

description: Library name: 15082024_KH_X-ALI_H3


title: Female HFD paw epidermis replicate 3

city: chicago

first: Daniela

middle: Maria

last: MEnichella

state: illinois

address: 303 E Superior

department: Neurology

institute: Northwestern University

description:
Library name: Female_HFD_3
Female C57BL/6J, 16-18 weeks, HFD, replicate 3

data_processing:
FASTQ files were generated using cellranger mkfastq.
Reads were aligned to the mouse reference genome (mm10-2020-A) using Cell Ranger 7.2.0 (cellranger count).
Quality control in Seurat v5.0.0: cells with <200 or >6,000 detected features excluded; cells with >5% mitochondrial reads excluded.
Normalization: Log-normalization with scale factor 10,000 (Seurat NormalizeData).
Clustering: PCA + UMAP (dims 1:30); SNN graph-based clustering (Seurat FindClusters). Male/female datasets integrated using Seurat IntegrateData (CCA).
Assembly: GRCm38 (mm10-2020-A)
Supplementary files format and content: Cell Ranger filtered feature-barcode matrix: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz (per sample, compressed as .tar.gz)

source_name: paw epidermis

growth_protocol: C57BL/6J mice (6-8 weeks old) were fed regular diet (RD, 11% fat) or high-fat diet (HFD, 42% fat, EnvigoTD88137) for 10 weeks.

extract_protocol:
Glabrous hind paw skin was harvested and incubated in Dispase (2.3 mg/ml, Sigma-Aldrich D4693) overnight at 4°C. The epidermis was gently peeled off from the dermis and incubated in TrypLE Express (Gibco 12604-013) for 10 min at 37°C. Single cells were collected in RPMI 1640 and centrifuged at 300g for 5 min at 4°C.
Single-cell suspensions were loaded onto the 10x Genomics Chromium controller using the Chromium Single Cell 3' Gene Expression kit (v3.1 chemistry), targeting 5,000-8,000 cells per sample.

treatment_protocol: No pharmacological treatment.

value: paw epidermis

value: epidermal cells

value: wild-type

value: High-Fat Diet (HFD, 42% fat, EnvigoTD88137)


title: Female HFD paw epidermis replicate 2

description:
Library name: Female_HFD_2
Female C57BL/6J, 16-18 weeks, HFD, replicate 2


title: Human meningioma, FFPE, [MN59]

description: Nanostring nCounter

value: meningioma

value: Female


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

description: Library name: 13082024_KH_X-96-well_H3K27me3


title: Female HFD paw epidermis replicate 1

description:
Library name: Female_HFD_1
Female C57BL/6J, 16-18 weeks, HFD, replicate 1


title: Human meningioma, FFPE, [MN58]

description: Nanostring nCounter

value: censored


title: Xenopus limb explant, ALI, H3, rep1

description: Library name: 13082024_KH_X-ALI_H3

value: limb explants


title: Male HFD paw epidermis replicate 3

description:
Library name: Male_HFD_3
Male C57BL/6J, 16-18 weeks, HFD, replicate 3


title: Male HFD paw epidermis replicate 1

description:
Library name: Male_HFD_1
Male C57BL/6J, 16-18 weeks, HFD, replicate 1


title: Human meningioma, FFPE, [MN57]

description: Nanostring nCounter


title: Female RD paw epidermis replicate 2

description:
Library name: Female_RD_2
Female C57BL/6J, 16-18 weeks, RD, replicate 2

value: Regular Diet (RD, 11% fat)


title: Xenopus limb explant, ALI, H3K4me3, rep1

description: Library name: 13082024_KH_X-ALI_H3K4me3


title: Human meningioma, FFPE, [MN56]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN55]

description: Nanostring nCounter


title: Male RD paw epidermis replicate 3

description:
Library name: Male_RD_3
Male C57BL/6J, 16-18 weeks, RD, replicate 3


title: Female RD paw epidermis replicate 3

description:
Library name: Female_RD_3
Female C57BL/6J, 16-18 weeks, RD, replicate 3


title: Female RD paw epidermis replicate 1

description:
Library name: Female_RD_1
Female C57BL/6J, 16-18 weeks, RD, replicate 1


title: NELFA CUT and RUN on RG purified from GW17/20 cerebral cortex – dbGap_Library_ID: GW1720_RG_NELFA

first: Mitchel

last: Cole

state: CA

address: 35 Medical Center Way

department: Neurological Surgery

institute: UCSF

description: Library name: GW1720_RG_NELFA

data_processing:
Adapter trimming was performed on raw FASTQ files prior to alignment with trim galore (v0.6.10) using default parameters.
Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1)  and parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Reads were coordinate sorted and filtered for quality score > 30  with samtools sort and view respectively. For GOCaRT/CnR PCR duplicates were removed with picard tools markDupliates.
For LaminB1/SON, filtered bam files were downsampled to match IgG read depth. For visualization and further analysis, downsampled bam files of LaminB1/SON were converted to log2-normalized bigwig files using the deepTools   Cut&RUN bigwigs were generated from bam files with bamCoverage and RPGC normalization. RNA bigwigs were generated from bam files with bamCoverage and BPM normalization.
LADs were called using a two-state Hidden Markov Model (pomegranate v1.1.2) on the median of two biological replicate IgG-normalized BigWig files with a 30 kb bin size. SPADs were called using SEACR (v1.3) in non-stringent mode (top 25% of regions by AUC) on 10 kb-binned average scores derived from bedtools map, retaining only regions present in both replicates. H3K4me3 and H3K27me3 peaks were called with MACs2 (V2.12) using two replicates of samples and control IgG  and options --broad -q 0.05. Regions overlapping ENCODE blacklisted regions were discarded.
Assembly: hg38
Supplementary files format and content: bigwig files - LMNB1 or SON log 2 enrichment over IgG controls; Histone enrichment normalized by regions per genomic context (deeptools).
Supplementary files format and content: Bed files - lamina associated domains
Library strategy: CUT&RUN

source_name: cerebral cortex

growth_protocol: Human brain tissue samples (GW16-GW20) were collected from de-identified donors with previous patient consent in strict observance of legal and institutional ethical regulations. All protocols were approved by the Human Gamete, Embryo and Stem Cell Research Committee (GESCRC) and Institutional Review Board (IRB) at the University of California, San Francisco (UCSF). Primary human brain tissue was collected in artificial cerebrospinal fluid (ACSF) containing 125 mM NaCl, 2.5 mM KCl, 1 mM MgCl2, 1 mM CaCl2 and 1.25 mM NaH2PO4 under a stereotaxic dissection microscope (Leica).

extract_protocol:
Snap-frozen cortical tissue was cut into small pieces and transferred to a pre-chilled 7-mL Dounce Tissue Grinder (Wheaton) containing 5 mL nuclei extraction buffer (NEB: 10 mM HEPES pH 7.4, 25 mM KCl, 5 mM MgCl2, 0.25 M sucrose, 0.1% Triton X-100, 1x Halt protease inhibitor cocktail (Thermo Fisher)). RiboLock (Thermo Fisher) was added to all the buffers to preserve RNA integrity. While still on ice, the tissue was dissociated with 5-6 strokes with loose pestle A followed by 8-10 strokes with tight pestle B, until no tissue pieces were visible. The sample was incubated on ice for 5 min after which it was transferred to a pre-chilled 15-ml conical tube. The sample was centrifuged at 500 g for 10 min at 4 °C. The supernatant was removed, and the nuclear pellet was resuspended in 10 mL NEB without Triton X-100. The homogenate was passed through a 40 μm strainer into a 50 mL conical tube. Formaldehyde was added to a final concentration of 0.1% and the sample was incubated for 2 min at room temperature with rotation. Glycine was added to a final concentration of 75 mM to quench the reaction. BSA was added to a final concentration of 1% and the sample was centrifuged at 500 g for 10 min at 4 °C. The supernatant was discarded, and the nuclear pellet was resuspended in 1 mL staining buffer (PBS containing 1% BSA). The nuclei were filtered through a 40 µm strainer into a 1.5 mL low-bind microcentrifuge tube and counted under the microscope. The nuclei were pelleted at 500 g for 10 min at 4 °C and resuspended in 100-150 μL of staining buffer. Antibody staining was carried out for 1 hour at 4 °C with rotation with the following antibodies: PAX6-Alexa Fluor 488 (BD Biosciences, 1:20 dilution), EOMES-PE-Cy7 (Invitrogen, 1:20 dilution), and SATB2-Alexa Fluor 647 (Abcam, 1:100 dilution). After staining, 900 μL of staining buffer was added and the samples were centrifuged at 500 g for 10 min at 4 °C. The nuclear pellet was resuspended in 1 mL of staining buffer and centrifuged at 500 g for 10 min at 4 °C. Nuclei were resuspended in 1-2 mL of staining buffer (depending upon the starting material and yield) and filtered into a 70 µm mesh FACS tube (BD). DAPI was added at 1 μg/ml just before FANS. AbC™ Total Compensation capture beads (Thermo Fisher) were used for generating single color compensation controls. FANS was conducted on BD FACS Aria II Cytometer using a 70 μm nozzle. Sorted nuclei were collected in 5 mL tubes containing 300-500 μL of collection buffer (PBS containing 5% BSA and RNasin Plus RNase inhibitor (Promega)). Sorted nuclei were collected by centrifuging at 500 g for 10 min at 4 °C and processed for downstream analyses (RNA-seq, Fab blocking and GO-CaRT/CUT&RUN).
Sequencing libraries for GO-CaRT/CUT&RUN were generated using KAPA HyperPrep Kit (KAPA, KK8504) following the manufacturer’s instructions. The libraries were amplified for 12–14 PCR cycles. DNA fragments were quantified by Tapestation D1000 (Agilent) and Qubit high sensitivity dsDNA (Invitrogen) assays, pooled, and sequenced by 150-bp paired-end sequencing on NovaSeq X Plus systems (Illumina).

value: cerebral cortex


title: Human meningioma, FFPE, [MN54]

description: Nanostring nCounter


title: Male HFD paw epidermis replicate 2

description:
Library name: Male_HFD_2
Male C57BL/6J, 16-18 weeks, HFD, replicate 2


title: Rt1A

city: tongliao

first: zhao

last: jaiwei

address: No. 996 West Xilamulun Street, Keerqin District, Tongliao City, Inner Mongolia Autonomous Region

department: inner mongolia university for nationalities

data_processing:
The first strand cDNA is then amplified by PCR to form the second strand cDNA.
After the double strand DNA is amplified by secondary PCR, it can be used for SMRBell library construction and sequencing.
Assembly: Genome assembly
Supplementary files format and content: The Excel file includes the FPKM value for each Sample

organism: Cenchrus spinifex

source_name: Mixed thorn buds, roots, stems, and leaves of the small flowered

extract_protocol:
Take out samples of the thorn buds, roots, stems, and leaves of the small flowered Tribulus terrestris stored in a -80 ° C refrigerator at various stages, and place them in a mortar. Inject liquid nitrogen for finegrinding. Utilizing TaKaRa MiniBEST Plant RNA Extraction Kit。 Extract total RNA from Tribulus terrestris using a reagent kit and follow the experimental procedure instructions.
cDNA library


title: Male RD paw epidermis replicate 2

description:
Library name: Male_RD_2
Male C57BL/6J, 16-18 weeks, RD, replicate 2


title: NELFE CUT and RUN on RG purified from GW17/20 cerebral cortex – dbGap_Library_ID: GW1720_RG_NELFE

description: Library name: GW1720_RG_NELFE


title: Male RD paw epidermis replicate 1

description:
Library name: Male_RD_1
Male C57BL/6J, 16-18 weeks, RD, replicate 1


title: Mouse embryo at E18.75 profiled with sci-ATAC-seq3

city: Hanover

first: Chengxiang

last: Qiu

state: NH

address: Vail 604, 74 College St

department: Department of Molecular and Systems Biology

institute: Dartmouth College

description: Library name: E18.75

library_source: genomic single cell

data_processing:
BCL files were converted to FASTQ format using bcl2fastq/v2.20, and each read was assigned a four-component cell barcode (row and column addresses for tagmentation and PCR from the P5 and P7 ends, respectively). Barcodes were error-corrected to the nearest known sequence within an edit distance of 2, and reads with uncorrectable barcodes were discarded. Reads were trimmed with Trimmomatic/v0.36 and mapped to the mm10 reference genome using Bowtie2 with "-X 2000 -3 1" options. Low-quality and non-uniquely mapped reads (MAPQ < 10) were removed with Samtools, and BAM files were sorted, merged across lanes with Sambamba, and indexed. PCR duplicates were identified per cell by unique fragment endpoints, and peaks were called per sample using MACS2, then merged into a master peak set of 376K peaks. Cells were distinguished from background by fitting a mixture of two negative binomials to unique read counts, with a global minimum threshold of 500 unique reads per cell. Sparse matrices of unique reads within the master peak set were generated for each sample for downstream analysis.
Assembly: mm10
Supplementary files format and content: The peak-by-cell matrix (sparse matrix; MTX), cell and peak metadata (TXT), and fragment files (TXT).

source_name: Whole mouse embryo

extract_protocol:
Snap-frozen tissues were pulverized, processed for nuclei fixation, and banked for future use. On the day of the experiment, frozen fixed nuclei were thawed, repermeabilized in Omni lysis buffer, and diluted in ATAC-RSB (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂) with 0.1% Tween-20. A mixture of GM12878 human and CH12-LX mouse cells were included as an internal barnyard control. Nuclei were pelleted, resuspended in tagmentation master mix (Nextera TD buffer, 1X DPBS, 0.01% Digitonin, 0.1% Tween-20) at 50,000 nuclei per well with 2.5 μl Nextera v2 enzyme, and incubated at 55°C for 30 minutes. The reaction was stopped with 40 mM EDTA and 1 mM Spermidine at 37°C for 15 minutes, after which tagmented nuclei were pooled, pelleted, washed, and resuspended in ATAC-RSB with 0.1% Tween-20.
For three-level indexing at 384 × 384 × 384 resolution, tagmented nuclei were phosphorylated (1X PNK buffer, 1 mM rATP, T4 PNK) at 37°C for 30 minutes across four 96-well LoBind plates. Sequential ligation of N5 and N7 oligos (384 distinct barcodes each) was performed using T7 DNA ligase at 25°C for 1 hour per round, with stop solution added between steps. Pooled nuclei were then distributed across four 96-well plates at 1,000–4,000 nuclei per well, and cross-links were reversed with Proteinase K and 1% SDS at 65°C for 16 hours. Libraries were amplified using Nextera PCR Mastermix and indexed P5/P7 oligos, purified with Zymo Clean & Concentrate-5 and 1X AMPure beads, and quantified on an Agilent 4200 Tapestation. Final libraries were pooled at 2 nM and sequenced on an Illumina NextSeq 550 followed by deep sequencing on a NovaSeq 6000 (read 1 and 2: 51 cycles each; index 1 and 2: 10+15 dark+10 cycles).

value: Whole mouse embryo


title: RNA Pol II (total) CUT and RUN on RG purified from GW17/20 cerebral cortex – dbGap_Library_ID: GW1720_RG_Pol II CTD

description: Library name: GW1720_RG_Pol II CTD


title: Mouse embryo at E18.5 profiled with sci-ATAC-seq3

description: Library name: E18.5


title: Mouse embryo at P0 profiled with sci-ATAC-seq3

description: Library name: P0


title: Human meningioma, FFPE, [MN52]

description: Nanostring nCounter

source_name: FFPE meningioma


title: Mouse embryo at E18.0 profiled with sci-ATAC-seq3

description: Library name: E18.0


title: Human meningioma, FFPE, [MN53]

description: Nanostring nCounter


title: Mouse embryo at E18.25 profiled with sci-ATAC-seq3

description: Library name: E18.25


title: Mouse embryo at E17.5 profiled with sci-ATAC-seq3

description: Library name: E17.5


title: RNA Pol II Ser5P CUT and RUN on EN purified from GW17 cerebral cortex – dbGap_Library_ID: GW17_140_EN_Pol II Ser5P

description: Library name: GW17_EN_Pol II Ser5P


title: Human meningioma, FFPE, [MN51]

description: Nanostring nCounter


title: Mouse embryo at E17.25 profiled with sci-ATAC-seq3

description: Library name: E17.25


title: RNA Pol II Ser5P CUT and RUN on RG purified from GW17/20 cerebral cortex – dbGap_Library_ID: GW1720_RG_Pol II Ser5P

description: Library name: GW1720_RG_Pol II Ser5P


title: RNA Pol II Ser2P CUT and RUN on RG purified from GW17/20 cerebral cortex – dbGap_Library_ID: GW1720_RG_Pol II Ser2P

description: Library name: GW1720_RG_Pol II Ser2P


title: Mouse embryo at E16.5 profiled with sci-ATAC-seq3

description: Library name: E16.5


title: Mouse embryo at E16.75 profiled with sci-ATAC-seq3

description: Library name: E16.75


title: Human meningioma, FFPE, [MN49]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN50]

description: Nanostring nCounter

value: progression


title: RNA Pol II Ser5P CUT and RUN on RG purified from GW17 cerebral cortex – dbGap_Library_ID: GW17_140_RG_Pol II Ser5P

description: Library name: GW17_RG_Pol II Ser5P


title: RNA Pol II Ser2P CUT and RUN on EN purified from GW17 cerebral cortex – dbGap_Library_ID: GW17_140_EN_Pol II Ser2P

description: Library name: GW17_EN_Pol II Ser2P


title: Mouse embryo at E16.25 profiled with sci-ATAC-seq3

description: Library name: E16.25


title: Mouse embryo at E15.5 profiled with sci-ATAC-seq3

description: Library name: E15.5


title: Mouse embryo at E16.0 profiled with sci-ATAC-seq3

description: Library name: E16.0


title: RNA Pol II Ser2P CUT and RUN on RG purified from GW17 cerebral cortex – dbGap_Library_ID: GW17_140_RG_Pol II Ser2P

description: Library name: GW17_RG_Pol II Ser2P


title: Mouse embryo at E15.75 profiled with sci-ATAC-seq3

description: Library name: E15.75


title: Mouse embryo at E17.0 profiled with sci-ATAC-seq3

description: Library name: E17.0


title: Human meningioma, FFPE, [MN47]

description: Nanostring nCounter


title: Mouse embryo at E15.25 profiled with sci-ATAC-seq3

description: Library name: E15.25


title: Mouse embryo at E15.0 profiled with sci-ATAC-seq3

description: Library name: E15.0


title: H3K4me3 CUT and RUN on EN purified from GW16 cerebral cortex (rep3) – dbGap_Library_ID: GW16_EN_H3K4me3

description: Library name: GW16-EN-H3K4me3-rep3


title: Human meningioma, FFPE, [MN46]

description: Nanostring nCounter


title: Mouse embryo at E14.75 profiled with sci-ATAC-seq3

description: Library name: E14.75


title: Human meningioma, FFPE, [MN48]

description: Nanostring nCounter


title: Mouse embryo at E14.25 profiled with sci-ATAC-seq3

description: Library name: E14.25


title: Mouse embryo at E14.375 profiled with sci-ATAC-seq3

description: Library name: E14.375


title: Human meningioma, FFPE, [MN45]

description: Nanostring nCounter


title: Mouse embryo at E13.75 profiled with sci-ATAC-seq3

description: Library name: E13.75


title: H3K4me3 CUT and RUN on EN purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_2_EN_H3K4me3

description: Library name: GW17-EN-H3K4me3-rep1


title: Mouse embryo at E14.0 profiled with sci-ATAC-seq3

description: Library name: E14.0


title: Mouse embryo at E13.5 profiled with sci-ATAC-seq3

description: Library name: E13.5


title: Human meningioma, FFPE, [MN44]

description: Nanostring nCounter

value: Male


title: Human meningioma, FFPE, [MN43]

description: Nanostring nCounter


title: Mouse embryo at E13.0 profiled with sci-ATAC-seq3

description: Library name: E13.0


title: H3K4me3 CUT and RUN on RG purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_RG_H3K4me3

description: Library name: GW17-RG-H3K4me3-rep2


title: H3K4me3 CUT and RUN on RG purified from GW16 cerebral cortex (rep3) – dbGap_Library_ID: GW16_RG_H3K4me3

description: Library name: GW16-RG-H3K4me3-rep3


title: Mouse embryo at E12.75 profiled with sci-ATAC-seq3

description: Library name: E12.75


title: Human meningioma, FFPE, [MN41]

description: Nanostring nCounter


title: H3K27me3 CUT and RUN on EN purified from GW16 cerebral cortex (rep3) – dbGap_Library_ID: GW16_EN_H3K27me3

description: Library name: GW16-EN-H3K27me3-rep3


title: H3K4me3 CUT and RUN on RG purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_2_RG_H3K4me3

description: Library name: GW17-RG-H3K4me3-rep1


title: H3K27me3 CUT and RUN on EN purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_EN_H3K27me3

description: Library name: GW17-EN-H3K27me3-rep2


title: Mouse embryo at E12.5 profiled with sci-ATAC-seq3

description: Library name: E12.5


title: Mouse embryo at E13.25 profiled with sci-ATAC-seq3

description: Library name: E13.25


title: Mouse embryo at E12.0 profiled with sci-ATAC-seq3

description: Library name: E12.0


title: Human meningioma, FFPE, [MN39]

description: Nanostring nCounter


title: Mouse embryo at E12.25 profiled with sci-ATAC-seq3

description: Library name: E12.25


title: Mouse embryo at E11.5 profiled with sci-ATAC-seq3

description: Library name: E11.5


title: Mouse embryo at E11.25 profiled with sci-ATAC-seq3

description: Library name: E11.25


title: Human meningioma, FFPE, [MN40]

description: Nanostring nCounter


title: Mouse embryo at E10.75 profiled with sci-ATAC-seq3

description: Library name: E10.75


title: Human meningioma, FFPE, [MN37]

description: Nanostring nCounter


title: H3K4me3 CUT and RUN on EN purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_EN_H3K4me3

description: Library name: GW17-EN-H3K4me3-rep2


title: Mouse embryo at E11.0 profiled with sci-ATAC-seq3

description: Library name: E11.0


title: Mouse embryo at E11.75 profiled with sci-ATAC-seq3

description: Library name: E11.75


title: H3K27me3 CUT and RUN on RG purified from GW16 cerebral cortex (rep3) – dbGap_Library_ID: GW16_RG_H3K27me3

description: Library name: GW16-RG-H3K27me3-rep3


title: Human meningioma, FFPE, [MN36]

description: Nanostring nCounter


title: H3K27me3 CUT and RUN on EN purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_2_EN_H3K27me3

description: Library name: GW17-EN-H3K27me3-rep1


title: Human meningioma, FFPE, [MN42]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN70]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN33]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN35]

description: Nanostring nCounter


title: H3K27me3 CUT and RUN on RG purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_RG_H3K27me3

description: Library name: GW17-RG-H3K27me3-rep2


title: Mouse embryo at E10.0 profiled with sci-ATAC-seq3

description: Library name: E10.0


title: Mouse embryo at E10.25 profiled with sci-ATAC-seq3

description: Library name: E10.25


title: Mouse embryo at E10.5 profiled with sci-ATAC-seq3

description: Library name: E10.5


title: Human meningioma, FFPE, [MN82]

description: Nanostring nCounter


title: H3K27me3 CUT and RUN on RG purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_2_RG_H3K27me3

description: Library name: GW17-RG-H3K27me3-rep1


title: RGCs, P84, 2 weeks post ONC, Sample 4

city: Farmington

first: Jacob

last: Brady

state: Connecticut

address: 263 Farmington Avenue

department: Neuroscience

institute: UConn School of Medicine

description:
Library name: Injured_Sample4
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using CellRanger v7.0.1
Assembly: Mouse mm39
Supplementary files format and content: Tab-separated values and matrix files

source_name: Retina

extract_protocol:
Uninjured and injured (2 weeks post-ONC) RGCs from 12-week old mice of both sexes were Thy1-immunopanned from single cell retinal suspension (10 retinas per batch), after immunopanning depletion of macrophages. Cells were resuspended in DPBS with 0.04% BSA.
Cell count and viability were determined using trypan blue on a Countess FL II, and 6,000 cells per batch were loaded for capture onto the Chromium System using the v3 single cell reagent kit (10X Genomics). Following capture and lysis, cDNA was synthesized and amplified (12 cycles) as per manufacturer's protocol (10X Genomics). The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on Novaseq 6000 with 150 cycle sequencing.

value: Retina

value: Retinal Ganglion Cells

value: 2 weeks after optic nerve crush


title: RGCs, P84, Sample 6

description:
Library name: Uninjured_Sample6
10X Genomics


title: RGCs, P84, Sample 4

description:
Library name: Uninjured_Sample4
10X Genomics


title: H3K9me2 CUT and RUN on EN purified from GW20 cerebral cortex – dbGap_Library_ID: GW20_EN_H3K9me2

description: Library name: GW20-EN-H3K9me2


title: RGCs, P84, 2 weeks post ONC, Sample 1

description:
Library name: Injured_Sample1
10X Genomics


title: RGCs, P84, Sample 3

description:
Library name: Uninjured_Sample3
10X Genomics


title: RGCs, P84, 2 weeks post ONC, Sample 2

description:
Library name: Injured_Sample2
10X Genomics


title: H3K9me2 CUT and RUN on IPC purified from GW20 cerebral cortex – dbGap_Library_ID: GW20_IPC_H3K9me2

description: Library name: GW20-IPC-H3K9me2


title: H3K9me2 CUT and RUN on RG purified from GW20 cerebral cortex – dbGap_Library_ID: GW20_RG_H3K9me2

description: Library name: GW20-RG-H3K9me2


title: RGCs, P84, Sample 5

description:
Library name: Uninjured_Sample5
10X Genomics


title: Human meningioma, FFPE, [MN32]

description: Nanostring nCounter

value: FFPE meningioma


title: RGCs, P84, Sample 2

description:
Library name: Uninjured_Sample2
10X Genomics


title: RGCs, P84, Sample 1

description:
Library name: Uninjured_Sample1
10X Genomics


title: Human meningioma, FFPE, [MN29]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN34]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN30]

description: Nanostring nCounter


title: LaminB1 GO-CaRT on IPC purified from GW20 cerebral cortex (rep2) – dbGap_Library_ID: GW20_141_IPC_LMNB

description: Library name: GW20-IPC-LMNB1-rep2

data_processing:
Adapter trimming was performed on raw FASTQ files prior to alignment with trim galore (v0.6.10) using default parameters.
Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1)  and parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Reads were coordinate sorted and filtered for quality score > 30  with samtools sort and view respectively. For GOCaRT/CnR PCR duplicates were removed with picard tools markDupliates.
For LaminB1/SON, filtered bam files were downsampled to match IgG read depth. For visualization and further analysis, downsampled bam files of LaminB1/SON were converted to log2-normalized bigwig files using the deepTools   Cut&RUN bigwigs were generated from bam files with bamCoverage and RPGC normalization. RNA bigwigs were generated from bam files with bamCoverage and BPM normalization.
LADs were called using a two-state Hidden Markov Model (pomegranate v1.1.2) on the median of two biological replicate IgG-normalized BigWig files with a 30 kb bin size. SPADs were called using SEACR (v1.3) in non-stringent mode (top 25% of regions by AUC) on 10 kb-binned average scores derived from bedtools map, retaining only regions present in both replicates. H3K4me3 and H3K27me3 peaks were called with MACs2 (V2.12) using two replicates of samples and control IgG  and options --broad -q 0.05. Regions overlapping ENCODE blacklisted regions were discarded.
Assembly: hg38
Supplementary files format and content: bigwig files - LMNB1 or SON log 2 enrichment over IgG controls; Histone enrichment normalized by regions per genomic context (deeptools).
Supplementary files format and content: Bed files - lamina associated domains


title: LaminB1 GO-CaRT on EN purified from GW20 cerebral cortex (rep1) – dbGap_Library_ID: GW20_EN_LMNB

description: Library name: GW20-EN-LMNB1-rep1


title: RGCs, P84, 2 weeks post ONC, Sample 3

description:
Library name: Injured_Sample3
10X Genomics


title: Mouse 455, WT, DMSO

city: Iowa City

first: Jared

middle: M.

last: McLendon

state: Iowa

address: 180 South Grand Ave, CPB 554

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

description: Library name: 174-03_S131

data_processing:
Kallisto index using default settings
kallisto quant using default settings, 100 bootstraps, across 16 threads
Sleuth version 0.3.0 aggregating abundance on Ensemble fenes, with two step likelihood Ration Test and Wald test.
Assembly: ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary files format and content: Kallisto/sleuth count matrix. Aggregated on ensembl gene ID, metric is "scaled reads per base"

source_name: Heart, ventricle

extract_protocol:
miRNeasy RNA Isolation Kit (Qiagen, Ref# 217084)
Illumina paired end, polyA  library prep.

treatment_protocol: Intraperitoneal injection of DMSO or MRL5

value: Heart, ventricle

value: WT/WT

value: M

value: DMSO

tag: time

value: 4 Hours


title: Mouse 373, WT, DMSO

description: Library name: 148-12_S0

tag: treatment


title: Mouse 370, GX, MRL5

description: Library name: 148-11_S0

tag: tissue

value: GX/GX


title: LaminB1 GO-CaRT on EN purified from GW20 cerebral cortex (rep2) – dbGap_Library_ID: GW20_141_EN_LMNB

description: Library name: GW20-EN-LMNB1-rep2


title: Human meningioma, FFPE, [MN28]

description: Nanostring nCounter

tag: disease

value: meningioma

value: Female

value: censored


title: LaminB1 GO-CaRT on IPC purified from GW20 cerebral cortex (rep1) – dbGap_Library_ID: GW20_IPC_LMNB

description: Library name: GW20-IPC-LMNB1-rep1

value: cerebral cortex


title: Human meningioma, FFPE, [MN31]

description: Nanostring nCounter

tag: tumor grade


title: Mouse 452, WT, DMSO

description: Library name: 174-02_S130

tag: Sex


title: Mouse 444, GX, MRL5

description: Library name: 174-01_S129


title: Mouse 380, WT, MRL5

description: Library name: 148-14_S0


title: LaminB1 GO-CaRT on RG purified from GW20 cerebral cortex (rep2) – dbGap_Library_ID: GW20_141_RG_LMNB

description: Library name: GW20-RG-LMNB1-rep2


title: Human meningioma, FFPE, [MN27]

description: Nanostring nCounter

tag: age at surgery


title: Mouse 357, GX, MRL5

description: Library name: 148-07_S86


title: Mouse 360, GX, MRL5

description: Library name: 148-09_S88


title: LaminB1 GO-CaRT on RG purified from GW20 cerebral cortex (rep1) – dbGap_Library_ID: GW20_RG_LMNB

description: Library name: GW20-RG-LMNB1-rep1


title: Mouse 355, GX, MRL5

description: Library name: 148-05_S83


title: SON GO-CaRT on EN purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_3_EN_SON

description: Library name: GW17-EN-SON-rep2


title: Human meningioma, FFPE, [MN25]

description: Nanostring nCounter

tag: outcome


title: Human meningioma, FFPE, [MN22]

description: Nanostring nCounter


title: Mouse 358, GX, DMSO

description: Library name: 148-08_S87

tag: genotype


title: SON GO-CaRT on EN purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_EN_SON

description: Library name: GW17-EN-SON-rep1


title: Mouse 354, GX, DMSO

description: Library name: 148-04_S82


title: SON GO-CaRT on IPC purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_IPC_SON

description: Library name: GW17-IPC-SON-rep2


title: Human meningioma, FFPE, [MN21]

description: Nanostring nCounter


title: SON GO-CaRT on IPC purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_IPC_SON

description: Library name: GW17-IPC-SON-rep1


title: Mouse 361, GX, DMSO

description: Library name: 148-10_S0


title: Human meningioma, FFPE, [MN23]

description: Nanostring nCounter


title: 53BP1_KO_JH4RSSbait_2

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

description:
Library name: Sample 11
JH4-RSS bait\, 53BP1 knockout\, Emu-Bcl2\, RAG1 deficient

data_processing:
Standard basecalling formats for Novaseq reads
Novaseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was extracted overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using VDJ-HTGTS-Seq (Hu et al., 2016)

treatment_protocol: v-Abl transformed pro-B cell lines were cultured in R15 medium and stimulated with 3 uM STI-571 treated for 4 days.

tag: cell line

value: v-Abl transformed pro-B cell line

value: RAG1 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: Human meningioma, FFPE, [MN24]

description: Nanostring nCounter

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

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


title: WT_JH4RSSbait_2

description:
Library name: Sample 10
JH4-RSS bait\, Emu-Bcl2\, RAG1 deficient

value: Emu-Bcl2\, RAG1 deficient


title: Mouse 349, WT, MRL5

description: Library name: 148-02_S81


title: JH1O_53BP1_DNA-PKcs_DKO_JH1bait_3

description:
Library name: Sample 9
JH1 bait\, 53BP1 and DNA-PKcs knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 and DNA-PKcs knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: HCT116_5FU_1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA37705

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in a 100+100 base paired-end mode.
The DNBSEQ-G400 control software operated base calling analysis software and delivered raw sequencing data.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: The human CRC cell lines HCT116, SW480, DLD-1 were maintained using Low-Glucose DMEM (Sigma-Aldrich) supplemented with 10% FBS (Thermo Fisher Scientific) at 37°C 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
According to the manufacturer's instructions, library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA). Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

treatment_protocol: CRC cell lines were seeded at a density of 2 × 10⁵ cells/well in 6-well plates. Cells with cell viability >90% and 60-80% confluency were used.

tag: cell type

value: colorectal cancer cell


title: Human meningioma, FFPE, [MN19]

first: Minh

description: Nanostring nCounter

value: FFPE meningioma


title: Mouse 356, GX, DMSO

description: Library name: 148-06_S85

value: Heart, ventricle


title: SON GO-CaRT on RG purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_RG_SON

description: Library name: GW17-RG-SON-rep1


title: SON GO-CaRT on RG purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_RG_SON

description: Library name: GW17-RG-SON-rep2


title: HCT116_WT_3

description: Library name: GA37704

value: negative control


title: HCT116_WT_1

description: Library name: GA37702


title: Human meningioma, FFPE, [MN18]

description: Nanostring nCounter


title: JH1O_53BP1_DNA-PKcs_DKO_JH1bait_2

description:
Library name: Sample 8
JH1 bait\, 53BP1 and DNA-PKcs knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: LaminB1 GO-CaRT on EN purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_EN_LMNB

description: Library name: GW17-EN-LMNB1-rep2


title: LaminB1 GO-CaRT on EN purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_EN_LMNB

description: Library name: GW17-EN-LMNB1-rep1


title: JH1O_53BP1_RNF168_DKO_JH1bait_3

description:
Library name: Sample 6
JH1 bait\, 53BP1 and RNF168 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 and RNF168 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_RNF168_DKO_JH1bait_1

description:
Library name: Sample 4
JH1 bait\, 53BP1 and RNF168 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_DNA-PKcs_DKO_JH1bait_1

description:
Library name: Sample 7
JH1 bait\, 53BP1 and DNA-PKcs knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_RNF168_DKO_JH1bait_2

description:
Library name: Sample 5
JH1 bait\, 53BP1 and RNF168 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: DLD1_OX_3

description: Library name: GA39799


title: Human meningioma, FFPE, [MN17]

description: Nanostring nCounter


title: HCT116_WT_2

description: Library name: GA37703


title: Human meningioma, FFPE, [MN16]

description: Nanostring nCounter

value: Male


title: DLD1_5FU_3

description: Library name: GA39796


title: Human meningioma, FFPE, [MN20]

description: Nanostring nCounter

value: progression


title: LaminB1 GO-CaRT on IPC purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_IPC_LMNB

description: Library name: GW17-IPC-LMNB1-rep2


title: Human meningioma, FFPE, [MN15]

description: Nanostring nCounter


title: DLD1_OX_2

description: Library name: GA39798


title: JH1O_RNF168_KO_JH1bait_3

description:
Library name: Sample 3
JH1 bait\, RNF168 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RNF168 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: LaminB1 GO-CaRT on RG purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_RG_LMNB

description: Library name: GW17-RG-LMNB1-rep1


title: Human meningioma, FFPE, [MN12]

description: Nanostring nCounter

value: meningioma


title: DLD1_WT_3

description: Library name: GA39793


title: JH1O_RNF168_KO_JH1bait_2

description:
Library name: Sample 2
JH1 bait\, RNF168 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: DLD1_OX_1

description: Library name: GA39797


title: KO mouse placenta, male fetus-1, RNA-seq-E17.5

city: Toronto

first: Sascha

last: Drewlo

address: 2075 Bayview Ave.

country: Canada

institute: Sunnybrook Research Institute

description: Library name: KO-27M-R2

data_processing:
Data analysis was performed using Illumina BaseSpace platform integrated with DRAGEN RNA pipeline
Assembly: GRCm39
Supplementary files format and content: .csv file includes TPM for each sample

source_name: Whole Placenta tissue (E17.5)

extract_protocol:
RNA was extracted with QIAzol lysis reagent, DNase treated and purified with Rneasy Mini kit. 250ng per sample was used for library prep.
Libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocol.

value: Whole Placenta tissue (E17.5)

value: FNDC5 Knockout


title: LaminB1 GO-CaRT on IPC purified from GW17 cerebral cortex (rep1) – dbGap_Library_ID: GW17_IPC_LMNB

city: San Francisco

description: Library name: GW17-IPC-LMNB1-rep1

value: cerebral cortex


title: LaminB1 GO-CaRT on RG purified from GW17 cerebral cortex (rep2) – dbGap_Library_ID: GW17_140_RG_LMNB

description: Library name: GW17-RG-LMNB1-rep2


title: Human meningioma, FFPE, [MN9]

institute: University of California, San Francisco

description: Nanostring nCounter

value: Female

value: censored


title: Human meningioma, FFPE, [MN13]

description: Nanostring nCounter


title: DLD1_5FU_2

description: Library name: GA39795


title: JH1O_RNF168_KO_JH1bait_1

description:
Library name: Sample 1
JH1 bait\, RNF168 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: KO mouse placenta, male fetus-3, RNA-seq-E17.5

description: Library name: KO-26M-R2


title: Human meningioma, FFPE, [MN11]

description: Nanostring nCounter


title: NELFE CUT&RUN on WTC11 iPSC-derived NPCs (20 days of differentiation)

description: Library name: NPC_NELFE

data_processing:
Adapter trimming was performed on raw FASTQ files prior to alignment with trim galore (v0.6.10) using default parameters.
Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1)  and parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 for GO-CaRT/C&R. Trimmed reads were aligned with STAR and parameter --outFilterMatchNmin 50 (v2.7.11b) for RNA
Reads were coordinate sorted and filtered for quality score > 30  with samtools sort and view respectively. For GOCaRT/CnR PCR duplicates were removed with picard tools markDupliates. For RNA reads were separated into forward strand reads and reverse strand reads with samtools view --samFlagExclude 16 or --samFlagInclude 16 resepctively
For LaminB1, filtered bam files were downsampled to match IgG read depth. For visualization and further analysis, downsampled bam files of LaminB1 were converted to log2-normalized bigwig files using the deepTools   Cut&RUN bigwigs were generated from bam files with bamCoverage and RPGC normalization. RNA bigwigs were generated from bam files with bamCoverage and BPM normalization.
Lamina associated domains were called using a two-state Hidden Markov Model (pomegranate v1.1.2) on the median of two biological replicate IgG-normalized BigWig files with a 30 kb bin size. Regions overlapping ENCODE blacklisted regions were discarded.
Assembly: hg38
Supplementary files format and content: bigwig files - LMNB1 log 2 enrichment over IgG controls; Histone enrichment normalized by regions per genomic context (deeptools). RNA shows bins per million enrichment by strand.
Supplementary files format and content: Bed files - lamina associated domains
Library strategy: CUT&RUN

source_name: iPSC-derived NPCs

growth_protocol: Human iPSC line WTC11 was maintained in StemFlex medium (Gibco) on plates coated with Matrigel (Corning) and passaged as clumps with ReLeSR (StemCell Technologies).

extract_protocol:
NPCs were harvested using Accutase. The cell pellet was resuspended in 1 mL ice cold PBS (Gibco). The cells were centrifuged at 500g for 3 min at 4 °C and the cell pellet was resuspended in 1 ml of nuclei isolation buffer (NIB: 10 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.1% NP40, 0.5 mM spermidine and 1× Halt protease inhibitor cocktail) and incubated for 10 min on ice. Nuclear pellet was collected by centrifuging at 600g for 3 min at 4°C and again resuspended in 1 ml of NIB to wash. Nuclei were fixed in 0.1% formaldehyde for 2 minutes and washed in NIB. Fixed nuclei were bound to concanavalin A beads and ~100,000 nuclei were subjected to GO-CaRT/CUT&RUN.
Sequencing libraries for GO-CaRT/CUT&RUN were generated using KAPA HyperPrep Kit (KAPA, KK8504) following the manufacturer’s instructions. The libraries were amplified for 12–14 PCR cycles. DNA fragments were quantified by Tapestation D1000 (Agilent) and Qubit high sensitivity dsDNA (Invitrogen) assays, pooled, and sequenced by 150-bp paired-end sequencing on NovaSeq X Plus systems (Illumina).

treatment_protocol: On day 10, iPSC-derived NPCs were passaged using Accutase and plated onto Matrigel-coated 6-well plates in NPC maturation medium supplemented with 10 µM ROCKi. On days 11-12, cells were fed with NPC maturation medium. On day 13, the media was removed and fresh media containing EZH2 inhibitor Tazemetostat (EPZ-6438, Selleckchem, 1 μM) or DMSO was added to the cells. Cells were fed fresh media containing the inhibitor (or DMSO) every day for one week at which point they were harvested for downstream experimental analyses.

value: iPSC-derived NPCs


title: DLD1_5FU_1

description: Library name: GA39794


title: KO mouse placenta, female fetus-3, RNA-seq-E17.5

description: Library name: KO-35F-R4


title: DLD1_WT_1

description: Library name: GA39791


title: KO mouse placenta, female fetus-2, RNA-seq-E17.5 (Incorrectly labelled as WT in the fastq file and library name)

description: Library name: WT-28F-L2


title: DLD1_WT_2

description: Library name: GA39792


title: Human meningioma, FFPE, [MN10]

description: Nanostring nCounter


title: KO mouse placenta, male fetus-2, RNA-seq-E17.5

description: Library name: KO-28M-R1


title: IgG control CUT&RUN on WTC11 iPSC-derived NPCs (20 days of differentiation)

description: Library name: NPC_IgG


title: WT mouse placenta, male fetus-3, RNA-seq-E17.5

description: Library name: WT-42M-L1

value: WT


title: Human meningioma, FFPE, [MN7]

description: Nanostring nCounter


title: RNA-seq on WTC11-iPSC-derived NPCs treated with 1uM EPZ-6438 (EZH2i) for one week rep2

description: Library name: WTCNPC_EPZ1uM_RNA_Rep2

data_processing:
Adapter trimming was performed on raw FASTQ files prior to alignment with trim galore (v0.6.10) using default parameters.
Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1)  and parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 for GO-CaRT/C&R. Trimmed reads were aligned with STAR and parameter --outFilterMatchNmin 50 (v2.7.11b) for RNA
Reads were coordinate sorted and filtered for quality score > 30  with samtools sort and view respectively. For GOCaRT/CnR PCR duplicates were removed with picard tools markDupliates. For RNA reads were separated into forward strand reads and reverse strand reads with samtools view --samFlagExclude 16 or --samFlagInclude 16 resepctively
For LaminB1, filtered bam files were downsampled to match IgG read depth. For visualization and further analysis, downsampled bam files of LaminB1 were converted to log2-normalized bigwig files using the deepTools   Cut&RUN bigwigs were generated from bam files with bamCoverage and RPGC normalization. RNA bigwigs were generated from bam files with bamCoverage and BPM normalization.
Lamina associated domains were called using a two-state Hidden Markov Model (pomegranate v1.1.2) on the median of two biological replicate IgG-normalized BigWig files with a 30 kb bin size. Regions overlapping ENCODE blacklisted regions were discarded.
Assembly: hg38
Supplementary files format and content: bigwig files - LMNB1 log 2 enrichment over IgG controls; Histone enrichment normalized by regions per genomic context (deeptools). RNA shows bins per million enrichment by strand.
Supplementary files format and content: Bed files - lamina associated domains


title: Total Pol II (C-terminal domain antibody) CUT&RUN on WTC11 iPSC-derived NPCs (20 days of differentiation)

description: Library name: NPC_Pol2CTD


title: Human meningioma, FFPE, [MN5]

description: Nanostring nCounter


title: Human meningioma, FFPE, [MN14]

description: Nanostring nCounter


title: WT mouse placenta, male fetus-1, RNA-seq-E17.5

description: Library name: WT-40M-L1


title: Ser5P-phosphorylated Pol II CUT&RUN on WTC11 iPSC-derived NPCs (20 days of differentiation)

description: Library name: NPC_Pol2S5P


title: Human meningioma, FFPE, [MN8]

description: Nanostring nCounter


title: WT mouse placenta, female fetus-3, RNA-seq-E17.5

description: Library name: WT-42F-L3


title: NELFA CUT&RUN on WTC11 iPSC-derived NPCs (20 days of differentiation)

description: Library name: NPC_NELFA


title: RNA-seq on WTC11-iPSC-derived NPCs treated with DMSO for one week rep2

description: Library name: WTCNPC_DMSO_RNA_Rep2


title: WT mouse placenta, male fetus-2, RNA-seq-E17.5

description: Library name: WT-50M-R1


title: SW480_OX_3

description: Library name: GA37719

value: colorectal cancer cell


title: SW480_5FU_3

description: Library name: GA37716


title: WT mouse placenta, female fetus-2, RNA-seq-E17.5

description: Library name: WT-50F-R2


title: SW480_OX_2

description: Library name: GA37718


title: Human meningioma, FFPE, [MN1]

description: Nanostring nCounter

value: FFPE meningioma


title: IgG control for  WTC11-iPSC-derived NPCs treated with 1uM EPZ-6438 (EZH2i) for one week

description: Library name: WTCNPC_EPZ1uM_IgG


title: Ser2P-phosphorylated Pol II CUT&RUN on WTC11 iPSC-derived NPCs (20 days of differentiation)

description: Library name: NPC_Pol2S2P


title: WT mouse placenta, female fetus-1, RNA-seq-E17.5

description: Library name: WT-40F-R1


title: SW480_WT_2

description: Library name: GA37712


title: SW480_OX_1

description: Library name: GA37717


title: KO mouse placenta, female fetus-1, RNA-seq-E17.5

description: Library name: KO-27F-L1


title: Human meningioma, FFPE, [MN6]

description: Nanostring nCounter


title: Sample 9 single cell for microglia sequenced with novaseq

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
Library name: samp9_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus

data_processing:
FASTQ files were processed with Cell Ranger v6.1.2, with the refdata-gex-mm10-2020-A Cell Ranger reference (10x Genomics) and with the expected number of cells set based on estimated loading
The downsampleReads command in DropletUtils v1.14.2 was used to downsample all samples to the same number of reads per cell, then the emptyDropsCellRanger command was used to remove empty droplets.
This count matrix was then loaded in R v4.0.3. A Seurat v4.0.0 object was created, cells with less than 200 genes were removed, and the data was LogNormalized with NormalizeData
Variable genes were extracted with FindVariableFeatures, data was scaled with ScaleData, and PCA was run with RunPCA with npcs=60. Dimensionality reduction was performed on the count data with scGBM v0.1.0, using the gbm.sc command with M=25 and subset=50,000, using just the variable genes
Clusters were calculated with the FindNeighbors and FindClusters commands using dims=1:25 and the scGBM reduction
Assembly: mm10
Supplementary files format and content: h5ad containing clustered object

source_name: Hippocampus

extract_protocol:
For single nuclei data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Nuclei were filtered, washed, and purified through sequential centrifugation steps. The final nuclei suspension was resuspended in RNase inhibitor-containing buffer, filtered, and counted prior to loading for single-nucleus RNA-seq. For single cell data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Cell suspensions were filtered, subjected to debris removal, and microglia were enriched using CD11b magnetic bead-based isolation. Purified cells were resuspended in RNase inhibitor-containing buffer and assessed for viability prior to scRNA-seq.
Single-nucleus and single-cell RNA-seq libraries were generated using the Chromium™ Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) following the manufacturer’s instructions, targeting recovery of up to 10,000 nuclei per sample. For single nucleus data, twenty-four libraries were pooled and sequenced on one NextSeq 500 flow cell and four NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1. For single cell data, twenty-four libraries from different animals were pooled based on molar concentrations and sequenced on one NextSeq 500 flow cell and two NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1.

value: Hippocampus

value: Microglia


title: Human meningioma, FFPE, [MN4]

last: Nguyen

description: Nanostring nCounter


title: SW480_5FU_2

description: Library name: GA37715


title: Human meningioma, FFPE, [MN3]

description: Nanostring nCounter


title: SW480_5FU_1

description: Library name: GA37714


title: KC1

first: Juanjuan

last: Shi

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

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

description: Library name: KC1

data_processing:
scRNAseq reads were trimmed by fastp to remove adaptor sequences. The trimmed reads were aligned to mm10 CellRanger v3.0.0. Seraut package was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
Assembly: mm10
Supplementary files format and content: txt

source_name: pancreas

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution until processing. The tissue samples were processed as described below. Briefly, samples were first washed with PBS, minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase I  and  for 45 min at 37°C, with agitation . After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells.  After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA).

value: pancreas

value: primary cells


title: KC2

description: Library name: KC2


title: Sample 6 single cell for microglia sequenced with novaseq

description:
Library name: samp6_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: RNA-seq on WTC11-iPSC-derived NPCs treated with 1uM EPZ-6438 (EZH2i) for one week rep1

description: Library name: WTCNPC_EPZ1uM_RNA_Rep1


title: Human meningioma, FFPE, [MN2]

description: Nanostring nCounter


title: RNA-seq on WTC11-iPSC-derived NPCs treated with DMSO for one week rep1

description: Library name: WTCNPC_DMSO_RNA_Rep1


title: SW480_WT_3

description: Library name: GA37713

value: negative control