title: Human OFs derived from patient 2(B), co-cultured with TGF-β for 24 hours and without nimodipine pretreatment [B_model]

value: Orbital fibroblasts (OFs)


title: 20190523_KWR020_MSC_+HA-SPI1_rep2

status: Public on Dec 30 2025

type: SRA

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

country: USA

institute: Dana Farber Cancer Institute

description: Library name: Sample 205

library_source: transcriptomic

data_processing:
ATAC-seq, CUT&RUN, and CUT*TAG reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project’s unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
RNAseq reads were aligned to the GRCh38 genome using STAR v2.5.2b, with GTF annotation from GENCODE v46. Gene counts were obtained using --quantMode "GeneCounts". Differential gene analysis was performed using DESeq2 v1.48.1 in R v4.5.1.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN, CUT&TAG, and ATAC-seq bigWig files give the normalized coverage of DNA fragments across the genome in RPM. In CUT&RUN samples of BRG1 profiling in hMSCs comparing truncations of PU.1, samples were normalized over all SMARCA4 peaks using the method described in DESeq2. In hMSCs expressing PU.1 and SMARCD2-SWIFT, IgG RPM was subtracted to obtain a reduced-background bigWig. Peaks were called using MACS3 and IgG peaks were subtracted when applicable. Gene counts are provided for RNA-seq read counts mapped to exons of given genes, produced using STAR geneCounts.

molecule: polyA RNA

organism: Homo sapiens

source_name: hMSC

extract_protocol:
CUT&RUN: Cells were pelleted by centrifugation (300 rcf, 5 minutes, room temperature) and were washed with PBS containing 200mM Glycine. Cells were resuspended with 100ul/sample of Nuclear Extraction Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) for 2 min on ice. Nuclei were pelleted by centrifugation (600 rcf, 3 minutes, 4C), and resuspended in 100ul/sample cold Wash150 Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) and incubated with activated ConA beads at room temperature for 15 minutes. Nuclei-ConA bead complexes were resuspended in 50 ul/sample cold Antibody Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS, 2mM EDTA supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), 0.01% Digitonin, and 0.5 ug primary antibody/sample, and incubated overnight nutating at 4C. Following removal of supernatant, ConA-nuclei complexes were washed twice with Digitonin Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), and 0.01% Digitonin. Samples were then resuspended in 50ul Digitonin Buffer and 2 ul of CUTANA pAG-MNase (Epicypher, Cat#: 15-1116) each and incubated at room temperature for 10 minutes. Samples were washed twice with Digitonin Buffer and resuspended in 50ul Digitonin Buffer and 1ul of 100mM CaCl2 per sample. Following incubation nutating at 4C for 2 hours, samples received 33ul of Stop Buffer containing 340 mM NaCl, 20 mM EDTA, 4 mM EGTA supplemented with fresh 50 ug/mL RNase A, 50 ug/ml Glycogen and incubated at 37C for 1 hour to release MNase digested DNA fragments. Supernatant was collected into fresh tubes and supplemented with 0.8uL 10% SDS and 1uL of 20mg/mL Proteinase K for overnight incubation at 55C. DNA was purified with Ampure XP (Beckman Coulter, Cat#: A63881) beads and 80% EtOH washes. DNA was eluted with 25uL of 0.1X TE buffer and transferred to new tubes. DNA fragments were prepared for next generation sequencing with CUTANA CUT&RUN Library Prep Kit (Epicypher, Cat#: 14-1001) according to manufacturer protocol. ATAC-seq: Nuclei were resuspended in transposition mix (1X TD Buffer, 2.5 ul TDE1 Nextera Tn5 Transposase (Illumina)) and incubated with mild rotation for 30 min at 37°C. Tagmented DNA was purified using MinElute PCR cleanup kit (Qiagen). RNA-seq: 2 X 106 live cells as were washed with PBS and RNA was extracted using QIAshredder and RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. CUT&TAG: Cells were processed for Cut & Tag as previously published and according to manufacturer’s CUTANA protocol (Epicypher) with the use of BioMag Plus Concanavalin A beads (Polysciences), CUTANA pAG-Tn5 (Epicypher), primary antibodies, and Guinea Pig anti-Rabbit IgG (Heavy & Light chain) antibody (Antibodies-Online). Tn5 transposed fragments were amplified between 14-18 cycles using NEB Next HF 2X PCR Master Mix (NEB) and custom primers originally designed for ATAC-seq library amplification to allow for multiplexing of 50+ samples. Amplified DNA was purified using 0.75X AMPpure Beads (Beckman Coulter) to remove primer-dimers.
CUT&RUN: Concanavalin A (ConA) beads (Polysciences, Cat#: 86057-10) were activated with Bead Activation Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were stored on ice until used. 500,000 cells per sample were harvested and resuspended in media at 1 million cells per mL. Cells were lightly crosslinked with 16% paraformaldehyde at a final concentration of 0.1% at room temperature for 2 minutes. Crosslinking was quenched with 2.5M Glycine at a final concentration of 200mM at room temperature for 5 minutes.  Cells were pelleted by centrifugation (300 rcf, 5 minutes, room temperature) and were washed with PBS containing 200mM Glycine. Cells were resuspended with 100ul/sample of Nuclear Extraction Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) for 2 min on ice. Nuclei were pelleted by centrifugation (600 rcf, 3 minutes, 4C), and resuspended in 100ul/sample cold Wash150 Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) and incubated with activated ConA beads at room temperature for 15 minutes. Nuclei-ConA bead complexes were resuspended in 50 ul/sample cold Antibody Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS, 2mM EDTA supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), 0.01% Digitonin, and 0.5 ug primary antibody/sample, and incubated overnight nutating at 4C. Following removal of supernatant, ConA-nuclei complexes were washed twice with Digitonin Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), and 0.01% Digitonin. Samples were then resuspended in 50ul Digitonin Buffer and 2 ul of CUTANA pAG-MNase (Epicypher, Cat#: 15-1116) each and incubated at room temperature for 10 minutes. Samples were washed twice with Digitonin Buffer and resuspended in 50ul Digitonin Buffer and 1ul of 100mM CaCl2 per sample. Following incubation nutating at 4C for 2 hours, samples received 33ul of Stop Buffer containing 340 mM NaCl, 20 mM EDTA, 4 mM EGTA supplemented with fresh 50 ug/mL RNase A, 50 ug/ml Glycogen and incubated at 37C for 1 hour to release MNase digested DNA fragments. Supernatant was collected into fresh tubes and supplemented with 0.8uL 10% SDS and 1uL of 20mg/mL Proteinase K for overnight incubation at 55C. DNA was purified with Ampure XP (Beckman Coulter, Cat#: A63881) beads and 80% EtOH washes. DNA was eluted with 25uL of 0.1X TE buffer and transferred to new tubes. DNA fragments were prepared for next generation sequencing with CUTANA CUT&RUN Library Prep Kit (Epicypher, Cat#: 14-1001) according to manufacturer protocol. CUT&RUN experiments were performed in one replicate but with antibodies for different mSWI/SNF subunits. Overlap between distinct subunit peaks were used for high confidence in results. ATAC-seq: ATAC-seq was performed as previously described with 100,000 cells per sample. Cells were dissociated and counted, as described above, 7-days post transduction with lentivirus. Cells were washed with cold PBS, resuspend in lysis buffer (10mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL) and centrifuged at 500 g for 10 min at 4°C. Nuclei were resuspended in transposition mix (1X TD Buffer, 2.5 ul TDE1 Nextera Tn5 Transposase (Illumina)) and incubated with mild rotation for 30 min at 37°C. Tagmented DNA was purified using MinElute PCR cleanup kit (Qiagen). Samples were amplified using 10 total PCR amplification cycles with custom PCR Primers using NEBNext HF PCR Master Mix (NEB). Samples were purified with 1.2X Agencourt AMPure XP beads (Beckman Coulter) and size distribution was determined using D5000 HS reagents and screentapes (Agilent) on 2200 TapeStation Instrument (Agilent). Samples were pooled in equimolar amounts and sequenced on Illumina Next-seq 500 with NextSeq 500/550 High Output Kit V2 75 cycles (Illumina) using 37bp paired-end sequencing parameters. ATAC-Seq experiments were performed in two replicates. RNA-seq: Cells were dissociated and counted, as described above, 7-days post transduction with lentivirus. 2 X 106 live cells as were washed with PBS and RNA was extracted using QIAshredder and RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. 1 µg of total RNA was used as input for library preparation and processed per the manufacturer’s instructions using NEBNext Poly(A) mRNA magnetic isolation module (NEB) followed by the NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB) with NEBNext Multiplex Oligos for Illumina (NEB). Samples were collected in biological replicate. ERCC synthetic RNA spike-in control (Thermo Fisher Scientific) was added at the beginning of library preparation per manufacturer’s recommendations to normalize samples across conditions. Libraries were quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and size distribution was verified using Tapestation D1000 HS reagents and screentapes (Agilent). Equimolar amounts of libraries were pooled, denatured, and sequenced on Illumina Next-seq 500 with NextSeq 500/550 High Output Kit V2 75 cycles (Illumina) according to standard Illumina protocols with single-end sequencing parameters. RNA-Seq were performed in two biological replicates. CUT&TAG: CUT&TAG was performed following published protocols (Epicypher). Cells were dissociated from culture plates using TrypLE Express (Thermo Fisher Scientific) and washed once with PBS pH 7.4 (Gibco). Cells were counted with Countess II (Invitrogen). 200,000-500,000 live cells were used per epitope as determined by Trypan Blue (Thermo Fisher Scientific) exclusion. Cells were processed for Cut & Tag as previously published and according to manufacturer’s CUTANA protocol (Epicypher) with the use of BioMag Plus Concanavalin A beads (Polysciences), CUTANA pAG-Tn5 (Epicypher), primary antibodies, and Guinea Pig anti-Rabbit IgG (Heavy & Light chain) antibody (Antibodies-Online). Tn5 transposed fragments were amplified between 14-18 cycles using NEB Next HF 2X PCR Master Mix (NEB) and custom primers originally designed for ATAC-seq library amplification to allow for multiplexing of 50+ samples. Amplified DNA was purified using 0.75X AMPpure Beads (Beckman Coulter) to remove primer-dimers. Libraries were quantified and QC’d as above. Samples were sequenced by the Dana Farber Cancer Institute Molecular Biology Core Facility using paired-end read parameters on an Illumina Nextseq 500 (Illumina) using Illumina NextSeq 500/550 High Output Kit V2 75 cycles (Illumina).

tag: cell line

value: hMSC

tag: treatment

value: HA-SPI1 transduced


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-P4

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

tag: brain region

value: FC

tag: gender

value: M

tag: age

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-3-J16-A18


title: Human OFs derived from patient 3(C),without nimodipine pretreatment or TGF-β, served as the control group [C_blank]

city: Guangzhou

first: Qian

last: Chen

state: Guangdong Province

address: No. 54 Xianlie South Rd

department: Zhongshan Ophthalmic Center

country: China

institute: Zhongshan Ophthalmic Center

description:
counts_anno
model-vs-blank-all.gene

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: Orbital fibroblasts (OFs)

growth_protocol: Human orbital fibroblasts (OFs) were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
The total RNA was isolated from cultured cells using a RNeasy Mini Kit (QIAGEN, Valencia, CA)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Fibrotic phenotype switching of human orbital fibroblasts was induced by co-cultured with TGF-β for 24 hours, with or without nimodipine pretreatment

tag: cell type

tag: genotype

value: WT


title: Human OFs derived from patient 1(A) co-cultured with TGF-β for 24 hours and without nimodipine pretreatment [A_model]

description:
counts_anno
model-vs-blank-all.gene
model-vs-blank-diff-q-val-0.05-FC-2.gene


title: 20190523_KWR019_MSC_+HA-SPI1_rep1

description: Library name: Sample 204


title: Intestinal-organoids, J2STAT1-KO line, 5 day differentiated, media treated, 24h

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description: Library name: J2STAT1KO_media_INT_24h

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Raw count and Differentially expressed gene list

growth_protocol: HIOs were grown as multilobular 3-dimensional (3D) HIOs in Matrigel and maintained in L-WRN complete media. For HuNoV infection, the 3D HIOs were dissociated by trypsinization and pipetting and seeded onto collagen IV coated 96-well plates using a 1:1 ratio of IntestiCult™ Organoid Growth Medium Human Basal Medium (StemCell Technologies, 100-0190) and Organoid Supplement (StemCell Technologies, 100-0191) (referred to as OGM proliferation medium) supplemented with 10 µM ROCK inhibitor Y-27632 for 24 hours. The HIEs were then differentiated for 5 days using a 1:1 ratio of Intesticult™ OGM Human Basal Medium and complete medium without growth factors (CMGF (-) medium, advanced DMEM/F12 prepared with 1X GlutaMAX and 10 mM HEPES) with media changes every two days prior to inoculation with HuNoV.

extract_protocol:
Total cellular RNAs were extracted from intestinal organoids (HIOs) using RNeasy Mini Kit (Qiagen) according to the manufacture's instructions.
Libraries were amplified for 13 PCR cycles in 50 μl reactions containing 150 pmol of P1.1 (5'-AAT GAT ACG GCG ACC ACC GAGA) and P3 (5’-CAA GCA GAA GAC GGC ATA CGA GA) primers and Kapa HiFi Hot Start Library Amplification kit (Cat# KK2612, Roche Sequencing and Life Science). A set of 96 unique dual-index barcodes (Illumina TruSeq UD Indexes, # 20022370) were used for sample barcoding. Libraries were purified with Agencourt AMPure XP beads (Beckman Coulter, Cat # A63882) after each enzymatic reaction and PCR amplification, and were quantified using the Fragment Analyzer (Agilent Technologies, Inc.) electrophoresis system.

treatment_protocol: Five-day differentiated HIE monolayers were washed once with CMGF (−) medium and inoculated with gamma irradiated (g) GII.3 HuNoV, live GII.3 HuNoV or media in OGM differentiation medium containing 500 μM bile acid glycochenodeoxycholic acid (GCDCA) for 1–2 h at 37°C. The inoculum was removed, and monolayers were washed twice with CMGF (−) medium to remove unbound virus. OGM differentiation medium (100 μL containing 500 μM GCDCA) was then added, and the cultures were incubated at 37°C for 24hours.

tag: culture status

value: differentiated

value: media

tag: media

value: Intesticult™ OGM, 500 µM GCDCA

tag: time

value: 24 hour


title: 20190523_KWR018_MSC_WT_rep2

description: Library name: Sample 203


title: 20251029_AMT065_hMSC_V5-SPI1-L84P_ARID1A

description: Library name: Sample 201

data_processing:
ATAC-seq, CUT&RUN, and CUT*TAG reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project’s unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
RNAseq reads were aligned to the GRCh38 genome using STAR v2.5.2b, with GTF annotation from GENCODE v46. Gene counts were obtained using --quantMode "GeneCounts". Differential gene analysis was performed using DESeq2 v1.48.1 in R v4.5.1.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN, CUT&TAG, and ATAC-seq bigWig files give the normalized coverage of DNA fragments across the genome in RPM. In CUT&RUN samples of BRG1 profiling in hMSCs comparing truncations of PU.1, samples were normalized over all SMARCA4 peaks using the method described in DESeq2. In hMSCs expressing PU.1 and SMARCD2-SWIFT, IgG RPM was subtracted to obtain a reduced-background bigWig. Peaks were called using MACS3 and IgG peaks were subtracted when applicable. Gene counts are provided for RNA-seq read counts mapped to exons of given genes, produced using STAR geneCounts.
Library strategy: CUT&RUN

tag: chip antibody

value: ARID1A (CST, 12354S)

value: V5-SPI1-L84P transduced


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-P3


title: Intestinal-organoids, J2 line, 5 day differentiated, media treated, 24h

description: Library name: J2_media_INT_24h


title: Human OFs derived from patient 2(B),without nimodipine pretreatment or TGF-β, served as the control group [B_blank]

description:
counts_anno
model-vs-blank-all.gene


title: Intestinal-organoids, J2STAT1-KO line, 5 day differentiated, GII.3 treated, 24h

description: Library name: J2STAT1KO_GII3_INT_24h


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-P15


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-O4


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-P16


title: 20190523_KWR017_MSC_WT_rep1

description: Library name: Sample 202


title: 786-O, Input

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

description: Library name: s786OIN

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
Assembly: hg19
Supplementary files format and content: BigWig and peak text files (BED) were generated

source_name: cell line

growth_protocol: Human renal cell carcinoma cell lines were were acquired from commercially-avaiable sources. They were maintained in a humidified incubator at 37°C with 5% CO2. Cells were cultured in standard growth medium (RPMI-1640 or DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin) and passaged upon reaching 80-90% confluency. For sample collection, cells were grown under standard culture conditions without treatment.

extract_protocol:
Cell pellets were harvested during exponential growth phase, washed with phosphate-buffered saline, and snap-frozen for subsequent DNA/RNA extraction and sequencing.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

tag: tissue

value: cell line

value: human kidney cell line

tag: antibody


title: A498, ATAC-seq

description: Library name: AT498


title: 20251029_AMT062_hMSC_V5-SPI1-L73A_ARID1A

description: Library name: Sample 200

value: V5-SPI1-L73A transduced


title: Intestinal-organoids, J2 line, 5 day differentiated, GII.3 treated, 24h

description: Library name: J2_GII3_INT_24h


title: A498, Input

description: Library name: A498IN


title: Intestinal-organoids, J2STAT1-KO line, 5 day differentiated, gGII.3 treated, 24h

description: Library name: J2STAT1KO_gGII3_INT_24h


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-O3


title: 20251029_AMT061_hMSC_V5-SPI1-F70A_ARID1A

description: Library name: Sample 199

value: V5-SPI1-F70A transduced


title: UMRC6, Input

description: Library name: RC6IN


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-O16


title: CTL2

city: Changchun

first: Shu

last: Zheng

state: 吉林Jilin

address: Xinmin Road

institute: Jilin University

description: Library name: CTL2

library_source: transcriptomic single cell

data_processing:
(1) Alignment: We aligned Illumina-generated FASTQ files to the human reference genome (GRCh38) using the STAR algorithm.
(2) Data Aggregation: To account for sequencing depth differences across libraries, we aggregated and down-sampled the data using Cell Ranger Aggregate. This step resulted in gene-barcode matrices for each sample.
(3) Quality Control and Downstream Analysis: We performed quality control and downstream analysis of single-cell RNA-seq data using Seurat.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: placenta

extract_protocol:
After collecting placental tissues, they were immediately processed into single-cell suspensions. The process involved washing, cutting, digesting, filtering, lysing red blood cells, removing dead cells, staining, and finally suspending the cells in a solution. The single-cell suspension was loaded onto the Chromium Controller to generate single-cell gel beads, followed by single-cell RNA sequencing using the Illumina Novaseq6000 sequencer.
The single-cell suspension was loaded onto the Chromium Controller according to the manufacturer's instructions (10X Genomics) to generate single-cell gel beads. After the generation of single-cell gel beads, single-cell RNA-seq libraries were constructed using the single-cell 3' library and gel bead kit V3.1 on an Illumina Novaseq6000 sequencer, employing a paired-end strategy with 150 bp read lengths, to generate sequencing data of at least 150 gigabases per sample.

value: placenta

tag: subject status

value: normotensive control


title: 20251029_AMT060_hMSC_V5-SPI1-WT_ARID1A

description: Library name: Sample 198

value: hMSC

value: V5-SPI1 transduced


title: 769P, Input

description: Library name: P769IN


title: 20251029_AMT059_hMSC_EV_ARID1A

description: Library name: Sample 197


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-O15

value: FC

value: M


title: Intestinal-organoids, J2 line,  5 day differentiated, gGII.3 treated, 24h

description: Library name: J2_gGII3_INT_24h


title: PE002

description: Library name: PE002

value: preeclamptic case


title: UMRC6, H3K27ac ChIP-Seq

description: Library name: K27RC6IP

value: H3K27ac anitbody, Diagenode C15410196


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-N3

value: 9 months


title: 20251029_AMT048_hMSC_EV_IgG

description: Library name: Sample 195

value: IgG (Epicypher, 13-0042)


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-N4


title: 20251029_AMT049_hMSC_V5-SPI1-WT_IgG

description: Library name: Sample 196


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-N16


title: Intestinal-organoids, J4 line, 5 day differentiated, gGII.3 treated, 24h

description: Library name: J4_gGII3_INT_24h

value: differentiated

value: Intesticult™ OGM, 500 µM GCDCA

value: 24 hour


title: 769P, H3K27ac ChIP-Seq

description: Library name: K27769IP

value: cell line


title: pe_9

description:
Library name: PE_9
PE

data_processing:
Total RNA integrity was verified using the Agilent Bioanalyzer 2100 system (RIN ≥7 required for library construction).
Strand-specific libraries were generated via poly-A selection, cDNA synthesis with dUTP-based strand marking, adapter ligation, and size selection (250–300 bp insert size).
Final libraries were quantified with Qubit fluorometry and Bioanalyzer size profiling, then normalized for pooling.
Pooled libraries were sequenced on the Illumina NovaSeq 6000 platform using paired-end 150 bp reads, yielding ~40 million reads per sample.
Raw sequencing data were processed through Illumina DRAGEN Bio-IT Platform for base calling and FASTQ file generation.
Assembly: hg38
Supplementary files format and content: tab-delimited files include FPKM values for each sample

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples from PE high-risk and control groups were collected in EDTA anticoagulant tubes, immediately mixed with TRIzol Reagent by vigorous vortexing to ensure complete cell lysis and RNA stabilization. Transcriptome profiling was performed using the Illumina NovaSeq 6000 platform with paired-end 150 bp sequencing, generating ~40 million reads per sample to achieve high coverage depth.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit folowing manufacturer's protocols.

value: Peripheral blood

value: PE high-risk


title: A498, H3K27ac ChIP-Seq

description: Library name: K27498IP

value: human kidney cell line


title: PE003

description: Library name: PE003

value: placenta


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-N15


title: pe_8

description:
Library name: PE_8
PE


title: UMRC6, HIF2a ChIP-Seq

description: Library name: HIFRC6IP

value: HIF2α antibody, abcam, ab199


title: 20251029_AMT078_U20S_HA-SMARCD2_HA_CSTMouse

description: Library name: Sample 194

source_name: U-2 OS

value: U-2 OS

value: HA-Tag (CST, 2367S)

value: HA-SMARCD2 transduced


title: 20251029_AMT077_U20S_HA-SMARCD1_HA_CSTMouse

description: Library name: Sample 193

value: HA-SMARCD1 transduced


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-M4

value: FC

value: M


title: pe_7

description:
Library name: PE_7
PE


title: 20251029_AMT076_U20S_EV_HA_CSTMouse

description: Library name: Sample 192


title: 786-O, HIF2a ChIP-Seq

description: Library name: HIF786O


title: 786-O, H3K27ac ChIP-Seq

description: Library name: s786O27AC

value: H3K27ac anitbody, Diagenode C15410196


title: pe_6

description:
Library name: PE_6
PE


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-M3

value: 9 months


title: pe_10

description:
Library name: PE_10
PE


title: 769P, HIF2a ChIP-Seq

description: Library name: HIF769IP


title: pe_5

description:
Library name: PE_5
PE


title: pe_4

description:
Library name: PE_4
PE


title: Human OFs derived from patient 1(A) without nimodipine pretreatment or TGF-β, served as the control group [A_blank]

description:
counts_anno
model-vs-blank-all.gene

value: Orbital fibroblasts (OFs)

value: WT


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-M15


title: A498, HIF2a ChIP-Seq

description: Library name: HIF498IP


title: 20251029_AMT069_U20S_EV_SMARCA4

description: Library name: Sample 189

value: SMARCA4 (CST, 49360S)


title: pe_3

description:
Library name: PE_3
PE


title: UMRC6, ATAC-seq

description: Library name: ATUMRC6

value: cell line


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-L4


title: pe_2

description:
Library name: PE_2
PE

value: Peripheral blood


title: 20250806_AMT006_U20S_ATAC_SMARCD2-SWIFT_rep2

description: Library name: Sample 188

value: SMARCD2-SWIFT transduced


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-L16


title: 20250806_AMT002_U20S_ATAC_EV_rep2

description: Library name: Sample 186


title: pe_1

description:
Library name: PE_1
PE

value: PE high-risk


title: 769P, ATAC-seq

description: Library name: AT769P

value: human kidney cell line


title: 20250806_AMT001_U20S_ATAC_EV_rep1

description: Library name: Sample 185


title: 20251029_AMT071_U20S_HA-SMARCD2_SMARCA4

description: Library name: Sample 191


title: HepG2 cells as controls [C3.IP]

city: Nanjing

first: Han

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

description:
Library name: C3.IP
HepG2 cells as controls,3

data_processing:
Paired-end reads were obtained from the Illumina HiSeq 4000 sequencer and subjected to quality control using a Q30 threshold. Following the trimming of 3' adaptors and the removal of low-quality reads using Cutadapt software (v1.9.3), the reads were aligned to the reference genome (UCSC HG19) utilizing Hisat2 software (v2.0.4). Methylated sites on RNAs, referred to as peaks, were identified using MACS software. Differentially methylated sites on RNAs were detected with diffReps. The identified peaks were subsequently mapped to the transcriptome using custom scripts.
Assembly: UCSC HG19
Supplementary files format and content: CSV file
Library strategy: MeRIP-Seq

extract_protocol:
In summary, 5 µg of fragmented mRNAs were retained as an input control for RNA sequencing, while 500 µg of fragmented mRNAs were incubated with 5 µg of anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer (comprising 150 mM NaCl, 0.1% NP-40, 10 mM Tris–HCl, pH 7.4) for 2 hours at 4°C. Subsequently, the mixture underwent immunoprecipitation through incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. The mRNAs bound to the beads were eluted using N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and extracted with Trizol reagent (Thermo Fisher) according to the manufacturer's instructions.
The purified mRNAs were employed for RNA sequencing library preparation using the NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample (without immunoprecipitation) and the m6A immunoprecipitated sample underwent 150 bp paired-end sequencing on an Illumina HiSeq sequencer.

value: hepatic cells


title: control_10

description:
Library name: CTL_10
control

value: control


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-M16


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-L15


title: 20251029_AMT070_U20S_HA-SMARCD1_SMARCA4

description: Library name: Sample 190

value: U-2 OS


title: HepG2 cells as controls [C3.Input]

description:
Library name: C3.Input
HepG2 cells as controls,3


title: 20230717_MAATAC14_MOLM13_shSMARCD2_V5-SMARCD2-R290W_rep2

description: Library name: Sample 172

value: shSMARCD2 and V5-SMARCD2-R290W transduction


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-K4


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-K3


title: 20230717_MAATAC13_MOLM13_shSMARCD2_V5-SMARCD2_rep2

description: Library name: Sample 171

value: shSMARCD2 and V5-SMARCD2 transduction


title: control_9

description:
Library name: CTL_9
control


title: control_8

description:
Library name: CTL_8
control


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-L3

value: FC


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-K16

value: M


title: 786-O, ATAC-seq

description: Library name: AT7860


title: HepG2 cells as controls [C2.Input]

description:
Library name: C2.Input
HepG2 cells as controls,2


title: 20250806_AMT005_U20S_ATAC_SMARCD2-SWIFT_rep1

description: Library name: Sample 187


title: 20230717_MAATAC12_MOLM13_shSMARCD2_V5-SMARCD2-R290W_rep1

description: Library name: Sample 170


title: control_7

description:
Library name: CTL_7
control


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-K15


title: 20230717_MAATAC11_MOLM13_shSMARCD2_V5-SMARCD2_rep1

description: Library name: Sample 169


title: HepG2 cells as controls [C1.Input]

description:
Library name: C1.Input
HepG2 cells as controls,1


title: control_6

description:
Library name: CTL_6
control


title: 20230717_MAATAC10_MOLM13_shSMARCD2_EV

description: Library name: Sample 168


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-J4


title: control_5

description:
Library name: CTL_5
control


title: HepG2 cells as controls [C2.IP]

description:
Library name: C2.IP
HepG2 cells as controls,2


title: 20230717_MAATAC07_MOLM13_shSCR_EV

description: Library name: Sample 167

value: shScramble


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-J3

value: 9 months


title: control_4

description:
Library name: CTL_4
control


title: control_3

description:
Library name: CTL_3
control


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-J16


title: HepG2 cells co-cultivated with H.pylori [T2.IP]

description:
Library name: T2.IP
HepG2 cells co-cultivated with H.pylori,2


title: 20230515_MAATAC06_MOLM13_shSMARCD2_V5-SMARCD2-R290W

description: Library name: Sample 166


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-J15


title: HepG2 cells co-cultivated with H.pylori [T2.Input]

description:
Library name: T2.Input
HepG2 cells co-cultivated with H.pylori,2


title: 20230515_MAATAC05_MOLM13_shSMARCD2_V5-SMARCD2

description: Library name: Sample 165


title: HepG2 cells as controls [C1.IP]

description:
Library name: C1.IP
HepG2 cells as controls,1


title: control_1

description:
Library name: CTL_1
control


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-I4


title: control_2

description:
Library name: CTL_2
control


title: HepG2 cells co-cultivated with H.pylori [T3.Input]

description:
Library name: T3.Input
HepG2 cells co-cultivated with H.pylori,3


title: 20230515_MAATAC04_MOLM13_shSMARCD2_EV

description: Library name: Sample 164


title: HepG2 cells co-cultivated with H.pylori [T1.IP]

description:
Library name: T1.IP
HepG2 cells co-cultivated with H.pylori,1


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-I3


title: HepG2 cells co-cultivated with H.pylori [T1.Input]

description:
Library name: T1.Input
HepG2 cells co-cultivated with H.pylori,1


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-I16


title: 20230515_MAATAC01_MOLM13_shSCR_EV

description: Library name: Sample 163


title: Pure, CD4 T cells

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

data_processing:
Fastq file were aligned using STAR (2.7.1a) on UCSC hg38 genome
Bam file where counted using featureCounts (v2.0.0) with options -p -s 2 -T 15 -t exon -g gene_name
Gene counts were normalized using standard DESeq2 procedure
Assembly: hg38
Supplementary files format and content: tab delimited count matrix

source_name: FACS sorted from blood samples

extract_protocol:
For all samples, DNA/RNA was extracted using the ALLPrep tissue kit (Qiagen, Venlo, The Netherlands) following the manufacturer’s instructions.
Magnetic mRNA Isolation Kit from NEB : NEBNext Ultra II Directional RNA
NovaSeq 2*100 bases

value: FACS sorted from blood samples

tag: sample id_orig

tag: sample id

tag: molecule type

value: RNA part of double extraction (RNA/DNA)


title: pcDLBCL-LT 4 – Tanscriptome

city: Vienna

first: Johannes

last: Griss

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

description: 10x Genomics, 5’ Version 2, Whole Transcriptome

data_processing:
Preprocessing of the scRNA-seq data was performed using Cell Ranger version 7.0.1 (10x Genomics). Raw sequencing files were demultiplexed using the Cell Ranger command “mkfastq.” Each sample was aligned to the human reference genome assembly “refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0” using the Cell Ranger command “count”.  BCR sequences were processed using CellRanger’s “vdj” command.
Assembly: GRCh38-2020-A
Supplementary files format and content: mtx (count matrix in sparse matrix format)
Supplementary files format and content: barcodes.tsv (barcode ids)
Supplementary files format and content: features.tsv (gene ids)
Supplementary files format and content: BCR_all_contig_annotations.csv (BCR contig data)

source_name: Skin

extract_protocol:
Punch-biopsies or gastroscopic biopsies from lesional skin / mucosa of lymphoma patients were minced and treated with 500 U/ml collagenase IV (Worthington Biochemical) and 50 U/ml DNAse I (Sigma-Aldrich) in RPMI Medium 1640 (Gibco), and incubated at 37°C for 30 min. Then samples were sieved using a 70 µm cell strainers. Single-cell suspensions were subjected to scRNA-seq processing (10x Genomics, Pleasanton, Calif).
Single cell suspensions were subjected to scRNA-seq using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v2 (10X Genomics, Pleasanton, CA), according to the manufacturer’s protocol. B-cell receptor (BCR) sequences were enriched from the cDNA using the respective reagents, and following the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin


title: HepG2 cells co-cultivated with H.pylori [T3.IP]

description:
Library name: T3.IP
HepG2 cells co-cultivated with H.pylori,3

tag: cell line

value: WT

tag: treatment


title: Pure, Cancer Basal

source_name: cell line MiaPaCa2

value: cell line MiaPaCa2


title: 20230427_MACR072_MOLM13_shSMARCD2_V5-SMARCD2-R290W_Igg

description: Library name: Sample 162

value: IgG (Epicypher, 13-0042)


title: 20230427_MACR071_MOLM13_shSMARCD2_V5-SMARCD2_Igg

description: Library name: Sample 161


title: Pure, Fibroblast

source_name: Mix of 2 primary cell lines

value: Mix of 2 primary cell lines


title: pcFCL 5 – Tanscriptome


title: 20230427_MACR070_MOLM13_shSMARCD2_EV_Igg

description: Library name: Sample 160


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-I15

tag: strain

tag: brain region


title: Pure, CD8 T Cells


title: pcMZL 9 – Tanscriptome


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-H4

tag: gender

tag: age


title: 20230427_MACR067_MOLM13_shSCR_EV_Igg

description: Library name: Sample 159


title: Pure, B cells


title: HREC cells, All rep 6

city: Baulkham Hills

first: Fergus

middle: Campbell

last: McLellan

state: NSW

address: 13 Delaigh Avenue

department: School of Vision Science

country: Australia

institute: University of New South Wales

description: Azenta GENEWIZ

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
Trimmed reads were mapped to reference genome GRCH38 using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using feature Counts from the subread package v.1.5.2.
Assembly: HRCh38
Supplementary files format and content: Text document files including raw counts for each sample

source_name: Primary

growth_protocol: Primary Human Retinal Endothelial Cells (Cell Systems [#ACBRI 181]) grown in Endothelial Basal Media-2  BulletKit Media (Lonza #CC-3162) coated in 0.2% gelatin from porcine skin (Sigma-Aldrich, #G1890) for 30 minutes

extract_protocol:
Total RNA was extracted using E.Z.N.A.Total RNA Kit I (Omega Bio-Tech, Norcross, GA, USA)
RNA libraries for RNA-seq were prepared using the NEBNExt Ultra RNA Library Prep Kit for Illumina using the manufacturer's instructions.

treatment_protocol: Cells were treated for 24 hours with 10ng/ml of respective treatment, the All group combined all 6 treatments at a total volume of 10ng/ml

value: Primary

tag: cell type

value: Retinal Microvascular Endothelial Cells

value: All Treatments


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-H16


title: Pure, Cancer Classical

source_name: cell line CAPAN1

value: cell line CAPAN1


title: HREC cells, All rep 4

description: Azenta GENEWIZ


title: HREC cells, All rep 5

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-G4


title: Pure,Macrophages


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-H15


title: 20230427_MACR065_MOLM13_shSMARCD2_V5-SMARCD2_H3K27ac

description: Library name: Sample 157


title: 20230427_MACR066_MOLM13_shSMARCD2_V5-SMARCD2-R290W_H3K27ac

description: Library name: Sample 158

value: shSMARCD2 and V5-SMARCD2-R290W transduction


title: HREC cells, All rep 3

description: Azenta GENEWIZ


title: Pure, Endothelial cells

source_name: HMEC-1 cell line

value: HMEC-1 cell line


title: 20230427_MACR064_MOLM13_shSMARCD2_EV_H3K27ac

description: Library name: Sample 156


title: HREC cells, All rep 2

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-G3

value: FC


title: 20230427_MACR061_MOLM13_shSCR_EV_H3K27ac

description: Library name: Sample 155


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-G16

value: M


title: In vitro mixture, 9 cell-types, mix30

source_name: In vitro mixture

value: In vitro mixture


title: HREC cells, All rep 1

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-H3

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-G15


title: In vitro mixture, 9 cell-types, mix29


title: 20230427_MACR059_MOLM13_shSMARCD2_V5-SMARCD2_V5

description: Library name: Sample 153

value: shSMARCD2 and V5-SMARCD2 transduction


title: HREC cells, VEGF rep 6

description: Azenta GENEWIZ

value: Vascular Endothelial Growth Factor A


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-F4


title: 20230427_MACR058_MOLM13_shSMARCD2_EV_V5

description: Library name: Sample 152


title: In vitro mixture, 9 cell-types, mix28

value: RNA part of double extraction (RNA/DNA)


title: HREC cells, VEGF rep 5

description: Azenta GENEWIZ


title: 20230427_MACR055_MOLM13_shSCR_EV_V5

description: Library name: Sample 151

value: shScramble


title: In vitro mixture, 9 cell-types, mix27


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-F16


title: HREC cells, VEGF rep 4

description: Azenta GENEWIZ


title: HREC cells, VEGF rep 3

description: Azenta GENEWIZ


title: 20230427_MACR053_MOLM13_shSMARCD2_V5-SMARCD2_SPI1

description: Library name: Sample 149


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-F15


title: 20230427_MACR054_MOLM13_shSMARCD2_V5-SMARCD2-R290W_SPI1

description: Library name: Sample 150


title: In vitro mixture, 9 cell-types, mix26


title: Pure, Neutrophils

value: FACS sorted from blood samples


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-E4


title: In vitro mixture, 9 cell-types, mix24


title: 20230427_MACR052_MOLM13_shSMARCD2_EV_SPI1

description: Library name: Sample 148


title: HREC cells, VEGF rep 1

description: Azenta GENEWIZ


title: HREC cells, VEGF rep 2

description: Azenta GENEWIZ


title: 20230427_MACR049_MOLM13_shSCR_EV_SPI1

description: Library name: Sample 147


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-E3


title: In vitro mixture, 9 cell-types, mix25


title: 20230427_MACR060_MOLM13_shSMARCD2_V5-SMARCD2-R290W_V5

description: Library name: Sample 154


title: HREC cells, IL6 rep 6

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-E16


title: In vitro mixture, 9 cell-types, mix22


title: HREC cells, IL6 rep 5

description: Azenta GENEWIZ


title: 20230427_MACR048_MOLM13_shSMARCD2_V5-SMARCD2-R290W_SMARCA4

description: Library name: Sample 146

value: SMARCA4 (CST, 49360, Lot 3)


title: In vitro mixture, 9 cell-types, mix23


title: 20230427_MACR047_MOLM13_shSMARCD2_V5-SMARCD2_SMARCA4

description: Library name: Sample 145


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-E15


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-F3


title: HREC cells, IL6 rep 4

description: Azenta GENEWIZ


title: 20230427_MACR046_MOLM13_shSMARCD2_EV_SMARCA4

description: Library name: Sample 144


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-D4


title: HREC cells, IL6 rep 3

description: Azenta GENEWIZ


title: HREC cells, IL6 rep 2

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-D3


title: In vitro mixture, 9 cell-types, mix19


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-D15


title: HREC cells, IL6 rep 1

description: Azenta GENEWIZ


title: 20230427_MACR042_MOLM13_shSMARCD2_V5-SMARCD2-R290W_ARID1A

description: Library name: Sample 142

value: ARID1A (CST, 12354, Lot 4)


title: In vitro mixture, 9 cell-types, mix17


title: 20230427_MACR041_MOLM13_shSMARCD2_V5-SMARCD2_ARID1A

description: Library name: Sample 141


title: HREC cells, Thrombin rep 6

description: Azenta GENEWIZ

value: Primary

value: Thrombin


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-D16


title: 20230427_MACR040_MOLM13_shSMARCD2_EV_ARID1A

description: Library name: Sample 140


title: HREC cells, Thrombin rep 4

description: Azenta GENEWIZ

value: Retinal Microvascular Endothelial Cells


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-C3


title: 20230309_MA010_RNA_MOLM13_shSCR_EV_rep2

description: Library name: Sample 138


title: HREC cells, Thrombin rep 5

description: Azenta GENEWIZ


title: In vitro mixture, 9 cell-types, mix16


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-C16


title: In vitro mixture, 9 cell-types, mix14


title: In vitro mixture, 9 cell-types, mix21


title: 20230427_MACR037_MOLM13_shSCR_EV_ARID1A

description: Library name: Sample 139


title: In vitro mixture, 9 cell-types, mix20


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-C15


title: HREC cells, Thrombin rep 3

description: Azenta GENEWIZ


title: 20230309_MA009_RNA_MOLM13_shSMARCD2_V5-SMARCD2-R290W_rep2

description: Library name: Sample 137


title: In vitro mixture, 9 cell-types, mix13


title: 20230427_MACR043_MOLM13_shSCR_EV_SMARCA4

description: Library name: Sample 143


title: HREC cells, Thrombin rep 2

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-B4


title: In vitro mixture, 9 cell-types, mix12


title: 20230309_MA008_RNA_MOLM13_shSMARCD2_V5-SMARCD2_rep2

description: Library name: Sample 136


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-C4


title: In vitro mixture, 9 cell-types, mix18


title: In vitro mixture, 9 cell-types, mix15


title: HREC cells, Thrombin rep 1

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-B3


title: 20230309_MA007_RNA_MOLM13_shSMARCD2_EV_rep2

description: Library name: Sample 135


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-B16


title: 20230309_MA004_RNA_MOLM13_shSCR_EV_rep1

description: Library name: Sample 134


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-B15


title: In vitro mixture, 9 cell-types, mix9


title: 20230309_MA003_RNA_MOLM13_shSMARCD2_V5-SMARCD2-R290W_rep1

description: Library name: Sample 133


title: HREC cells, TNFa rep 4

description: Azenta GENEWIZ

value: Tumour Necrosis Factor Alpha


title: HREC cells, TNFa rep 5

description: Azenta GENEWIZ


title: In vitro mixture, 9 cell-types, mix8


title: HREC cells, TNFa rep 3

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-A3


title: 20230309_MA001_RNA_MOLM13_shSMARCD2_EV_rep1

description: Library name: Sample 131


title: In vitro mixture, 9 cell-types, mix7


title: HREC cells, TNFa rep 2

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-A16


title: In vitro mixture, 9 cell-types, mix6


title: 20210914_DSGCT033_hTERTMSC_D2R290W_SPI1_BRG1

description: Library name: Sample 130

data_processing:
ATAC-seq, CUT&RUN, and CUT*TAG reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project’s unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
RNAseq reads were aligned to the GRCh38 genome using STAR v2.5.2b, with GTF annotation from GENCODE v46. Gene counts were obtained using --quantMode "GeneCounts". Differential gene analysis was performed using DESeq2 v1.48.1 in R v4.5.1.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN, CUT&TAG, and ATAC-seq bigWig files give the normalized coverage of DNA fragments across the genome in RPM. In CUT&RUN samples of BRG1 profiling in hMSCs comparing truncations of PU.1, samples were normalized over all SMARCA4 peaks using the method described in DESeq2. In hMSCs expressing PU.1 and SMARCD2-SWIFT, IgG RPM was subtracted to obtain a reduced-background bigWig. Peaks were called using MACS3 and IgG peaks were subtracted when applicable. Gene counts are provided for RNA-seq read counts mapped to exons of given genes, produced using STAR geneCounts.
Library strategy: CUT&TAG

value: hMSC

value: SMARCA4 (CST, D1Q7F, Lot 3)

value: HA-SPI1 and V5-SMARCD2-R290W transduced


title: 20210914_DSGCT032_hTERTMSC_D2R290W_SPI1_V5

description: Library name: Sample 129

value: V5 (CST, D3H8Q, Lot 6)


title: HREC cells, TNFa rep 1

description: Azenta GENEWIZ


title: In vitro mixture, 9 cell-types, mix5

value: In vitro mixture


title: In vitro mixture, 9 cell-types, mix11


title: HREC cells, TNFa rep 6

description: Azenta GENEWIZ


title: HREC cells, TGFB2 rep 6

description: Azenta GENEWIZ

value: Transforming Growth Factor Beta 2


title: In vitro mixture, 9 cell-types, mix4


title: In vitro mixture, 9 cell-types, mix10


title: 20210914_DSGCT031_hTERTMSC_D2R290W_SPI1_HA

description: Library name: Sample 128

value: HA-Tag (CST, C29F4, Lot 10)


title: HREC cells, TGFB2 rep 5

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-P2

value: FC

value: M

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-A4


title: In vitro mixture, 9 cell-types, mix3

value: RNA part of double extraction (RNA/DNA)


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-P14


title: 20210914_DSGCT026_hTERTMSC_D2_SPI1_V5

description: Library name: Sample 126

value: HA-SPI1 and V5-SMARCD2 transduced


title: 20230309_MA002_RNA_MOLM13_shSMARCD2_V5-SMARCD2_rep1

description: Library name: Sample 132

value: shSMARCD2 and V5-SMARCD2 transduction


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-P13


title: HREC cells, TGFB2 rep 4

description: Azenta GENEWIZ

value: Primary


title: In vitro mixture, 9 cell-types, mix2


title: 20210914_DSGCT027_hTERTMSC_D2_SPI1_BRG1

description: Library name: Sample 127


title: HREC cells, TGFB2 rep 3

description: Azenta GENEWIZ


title: In vitro mixture, 9 cell-types, mix1


title: HREC cells, TGFB2 rep 2

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-O2


title: HREC cells, TGFB2 rep 1

description: Azenta GENEWIZ


title: 20210914_DSGCT024_hTERTMSC_D2_E_BRG1

description: Library name: Sample 124

value: V5-SMARCD2 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-O14


title: GDM-AGA-27

city: Linyi City

first: Peng

last: xi

state: Shandong Province

address: Jiefang Road, Linyi City

department: Neonatology

institute: Linyi People's Hospital

data_processing:
The filtering criteria are as follows:  (1) Remove reads with adapters;  (2) When the N content in any sequencing read exceeds 10% of the base number of that read, remove the paired reads;  (3) When the low-quality (Q<=20) base number contained in any sequencing read exceeds 50% of the base number of that read, remove this. Paid reads.  Data quality control fastp 0.23.2.  Comparing genomes hisat2 2.2.1.  Gene quantitative featureCounts 2.0.3.  Variable shear rMATS 4.1.2.
Assembly: Ensembl/Homo_sapiens.GRCh38.109
Supplementary files format and content: Ctrl-AGA_vs_GDM-AGA.all.annot.xlsx file includes counts and FPKM values.

growth_protocol: Store at 80 ℃.

extract_protocol:
Extract total RNA from placental tissue using TRIzol reagent. Specifically: 1. Take the tissue from a -80 ℃ freezer, add a small amount of liquid nitrogen, grind it, take about 100 mg of the sample and place it in a 2 mL centrifuge tube. Add 1 mL of TRIzol reagent and lyse at room temperature for 10 minutes;  2. Add 0.2mL of chloroform to the lysis solution, cover the centrifuge tube tightly, vigorously shake the centrifuge tube for 15 seconds, let it stand at room temperature for 2-3 minutes, and centrifuge at 4 ℃ and 12000 rpm for 15 minutes. After centrifugation, the mixture can be divided into three layers, and RNA exists in the upper aqueous layer;  3. Carefully aspirate the upper aqueous phase into a new centrifuge tube, add 0.5mL of isopropanol, invert and mix well. Place on ice for 10 minutes, then centrifuge at 4 ℃ and 12000 rpm for 10 minutes. After centrifugation, RNA gel like precipitates can be seen attached to the side and bottom of the centrifuge tube. Discard the supernatant;  4. Wash the inner side of the tube wall thoroughly with 75% ethanol prepared by adding 1mL of DEPC water, and suspend and precipitate. Centrifuge at 4 ℃ and 12000 rpm for 3 minutes, discard the supernatant; Repeat twice;  5. Let the sample dry at room temperature for 2-3 minutes, add DEPC water to dissolve RNA, take a small amount of RNA solution for detection, and store the rest at -80 ℃.
Using the NEBNext Ultra RNA Library Prep Kit for library construction, mRNA with polyA tails was first enriched using Oligo (dT) magnetic beads. The mRNA was randomly broken into small fragments using divalent cations in the fragmentation buffer. Short fragments of RNA were used as templates to synthesize the first and second strands of cDNA. Double stranded cDNA was purified using purified magnetic beads, followed by end repair, adding an A tail at the 3 'end, and connecting sequencing adapters. After connection, DNA magnetic bead purification and fragment selection were performed. Finally, PCR enrichment was performed to obtain the final cDNA library.

treatment_protocol: Quickly freeze in liquid nitrogen within 10 minutes, then transfer to -80 after staying overnight.

value: placenta

tag: disease state

value: Gestational diabetes


title: 20210914_DSGCT022_hTERTMSC_D2_E_HA

description: Library name: Sample 122

value: hMSC


title: GDM-AGA-19


title: GDM-AGA-17


title: HREC cells, TGFb1 rep 5

description: Azenta GENEWIZ

value: Retinal Microvascular Endothelial Cells

value: Transforming Growth Factor Beta 1


title: HREC cells, TGFb1 rep 4

description: Azenta GENEWIZ


title: 20210914_DSGCT001_hTERTMSC_E_E_HA

description: Library name: Sample 119


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-P1


title: 20210217_KEWCR410_CandR_MSC_SPI1_ETSonly_HA

description: Library name: Sample 118

value: SPI1-dDBD transduced


title: GDM-AGA-6


title: HREC cells, TGFb1 rep 1

description: Azenta GENEWIZ


title: 20210914_DSGCT025_hTERTMSC_D2_SPI1_HA

description: Library name: Sample 125


title: AMB_200205_9mo_2A_3A_1_P1-2-F8-A15


title: HREC cells, Control rep 6

description: Azenta GENEWIZ

value: No Treatment


title: GDM-AGA-8


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-N14


title: Ctrl-AGA-14

value: Control


title: 20210914_DSGCT002_hTERTMSC_E_E_V5

description: Library name: Sample 120

value: V5 (CST, D3H8Q, Lot 6)


title: HREC cells, Control rep 5

description: Azenta GENEWIZ


title: 20210217_KEWCR395_CandR_MSC_SPI1deltaETS_HA

description: Library name: Sample 116

value: SPI1-dTAD transduced


title: HREC cells, TGFb1 rep 6

description: Azenta GENEWIZ


title: 20210914_DSGCT023_hTERTMSC_D2_E_V5

description: Library name: Sample 123


title: GDM-AGA-22


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-O13

value: FC

value: M


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-O1

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-M14


title: 20210914_DSGCT003_hTERTMSC_E_E_BRG1

description: Library name: Sample 121

value: SMARCA4 (CST, D1Q7F, Lot 3)


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-N2


title: HREC cells, TGFb1 rep 3

description: Azenta GENEWIZ


title: Ctrl-AGA-13


title: HREC cells, TGFb1 rep 2

description: Azenta GENEWIZ


title: GDM-AGA-11


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-N13


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-M13


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-N1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-M2


title: 20210217_KEWCR392_CandR_MSC_SPI1WT_HA

description: Library name: Sample 114

value: SPI1 transduced


title: 20210217_KEWCR409_CandR_MSC_SPI1_ETSonly_BRG1

description: Library name: Sample 117


title: GDM-AGA-5


title: 20210217_KEWCR394_CandR_MSC_SPI1deltaETS_BRG1

description: Library name: Sample 115


title: Ctrl-AGA-9


title: 20210217_KEWCR390_CandR_MSC_SPI1WT_BRG1

description: Library name: Sample 113


title: Ctrl-AGA-12


title: HREC cells, Control rep 4

description: Azenta GENEWIZ

value: Primary


title: Ctrl-AGA-8


title: HREC cells, Control rep 3

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-M1


title: HREC cells, Control rep 2

description: Azenta GENEWIZ


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-L14


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-L2


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-L13


title: 20240626_MACR251_BIN67_BRG1K785R_SPI1_SMARCC1

description: Library name: Sample 110

value: SMARCC1 (CST, 11956S, Lot 2)

value: SPI1 and SMARCA4-K785R transduced


title: Ctrl-AGA-3

value: placenta


title: 20210217_KEWCR386_CandR_MSC_empty_BRG1

description: Library name: Sample 111

value: hMSC


title: 20210217_KEWCR388_CandR_MSC_empty_HA

description: Library name: Sample 112


title: HREC cells, Control rep 1

description: Azenta GENEWIZ

value: Retinal Microvascular Endothelial Cells


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-L1


title: 20240626_MACR245_BIN67_BRG1WT_SPI1_SMARCC1

description: Library name: Sample 109

value: SPI1 and SMARCA4 transduced


title: Ctrl-AGA-7


title: Ctrl-AGA-2


title: pcFCL 3 – Transcriptome

data_processing:
Preprocessing of the scRNA-seq data was performed using Cell Ranger version 7.0.1 (10x Genomics). Raw sequencing files were demultiplexed using the Cell Ranger command “mkfastq.” Each sample was aligned to the human reference genome assembly “refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0” using the Cell Ranger command “count”.   BCR sequences were processed using CellRanger’s “vdj” command.
Assembly: GRCh38-2020-A
Supplementary files format and content: mtx (count matrix in sparse matrix format)
Supplementary files format and content: barcodes.tsv (barcode ids)
Supplementary files format and content: features.tsv (gene ids)
Supplementary files format and content: BCR_all_contig_annotations.csv (BCR contig data)

value: Skin


title: pcFCL 2 – Transcriptome


title: ARPE-19 cells, adTAZ 4

first: Chen

last: min

state: Guangdong

address: No.7 Jinsui Road, Tianhe District

institute: Zhongshan Ophthalmic Center, Sun Yat-sen  University, China

data_processing:
The RNA sequencing reads were first trimmed to remove poly-A and unqualified reads were eliminated using Cutadapt.
The remaining reads were then aligned to the Homo sapiens reference genome GRCh38 using HISAT2 (v2.1.0).
The reads were pooled at the gene level using HTSeq (v0.9.1).
Gene expression values were calculated from fragments per kilobases per million fragments (FPKM) values, which were obtained by adding a pseudo count of 1 and log2 transforming the results.
Assembly: http://asia.ensembl.org/Homo_sapiens/Info/Index
Supplementary files format and content: tab-delimited txt file includes raw counts for each group.
Supplementary files format and content: tab-delimited txt files include RPKM values for each group.

growth_protocol: ARPE-19 cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serumand 1% penicillin/streptomycin in humidified atomospher with 5% CO2 at 37℃.

extract_protocol:
The collected cells were lysed withTrizol Reagent (Invitrogen Life Technologies) according to the manufacturer's protocol.
The cDNA libraries were constructed and sequenced using an Illumina NovaSeq 6000 platform (Illumina) Shanghai Personal Biotechnology Cp. Ltd.

treatment_protocol: ARPE-19 cells were treated with adenovirus (1×1010 viral particles) expressing JAM-C, TAZ or control in a 10-cm dish. After transfection for 48 hours, the cells were washed twice with cold PBS and the cellular precipitate was collected.

value: retinal pigment epithelial cells

tag: genotype

value: TAZ overexpression

value: Adeviral transfection


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-K2


title: 20240626_MACR239_BIN67_EV_SPI1_SMARCC1

description: Library name: Sample 108


title: pcFCL 4 – Transcriptome


title: MALT 4 – Transcriptome


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-K14


title: 20240626_MACR233_BIN67_BRG1K785R_SMARCC1

description: Library name: Sample 107

value: SMARCA4-K785R transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-K13

value: FC


title: MALT 3 – Transcriptome


title: ARPE-19 cells, adTAZ 3


title: ARPE-19 cells, adTAZ 2


title: 20240626_MACR227_BIN67_BRG1WT_SMARCC1

description: Library name: Sample 106

value: SMARCA4 transduced


title: MALT 2 – Transcriptome


title: MALT 1 – Transcriptome


title: ARPE-19 cells, adTAZ 1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-K1

value: M

value: 9 months


title: 20240626_MACR221_BIN67_EV_SMARCC1

description: Library name: Sample 105


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-J2


title: rB-LP 2 – Transcriptome


title: 20240626_MACR254_BIN67_BRG1K785R_SPI1_SPI1

description: Library name: Sample 104


title: ARPE-19 cells, adJAM-C 3

value: JAM-C overexpression


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-J14


title: 20240626_MACR248_BIN67_BRG1WT_SPI1_SPI1

description: Library name: Sample 103


title: rB-LP 1 – Transcriptome


title: ARPE-19 cells, adJAM-C 2


title: pcMZL 8 – Tanscriptome


title: ARPE-19 cells, adJAM-C 1


title: 20240626_MACR242_BIN67_EV_SPI1_SPI1

description: Library name: Sample 102

value: SPI1 transduced


title: ARPE-19 cells, adGFP 3

value: control


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-J13


title: pcDLBCL-LT 3 – Transcriptome


title: 20240626_MACR236_BIN67_BRG1K785R_SPI1

description: Library name: Sample 101


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-J1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-I2


title: 20240626_MACR230_BIN67_BRG1WT_SPI1

description: Library name: Sample 100


title: ARPE-19 cells, adGFP 2


title: pcDLBCL-LT 2 – Transcriptome


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-I13


title: 20240626_MACR224_BIN67_EV_SPI1

description: Library name: Sample 99


title: ARPE-19 cells, adGFP 1


title: pcFCL 1 – Transcriptome


title: Vash-1, Highlight&Cold stress, 24h, rep2

city: Gifu

first: Kazuki

last: Sugekawa

state: Gifu

country: Japan

institute: Gifu University

description: Library name: Vash-1_HLC_2

data_processing:
Obtained reads (CAGE tags) were mapped to the Arabidopsis genome sequence (Araport11) with 2% mismatch allowance by STAR (https://github.com/alexdobin/STAR, version 2.7.9a)
Data for the two conditions (with and without stress treatment) with three biological replicates were combined to prepare 50.5 M, 53.8 M, 64.4 M, and 53.4 M effective TSS tags for Altenb-2, Kly-1, Shigu-2, and Vash-1, respectively.
They were then subjected to cluster analysis to determine the cluster area, peak positions, and tag counts of the TSS clusters for each accession using TSS clustering tools (https://github.com/yyyamamoto/TSS-analysis).
Clusters with small TSS tags of less than 5 were removed.
Assembly: Araport11
Supplementary files format and content: tab-delimited text file includes cluster data for each accession. ACL: Altenb-2 clusters, KCL: Kly-1 clusters, SCL: Shigu-2 clusters, VCL: Vash-1 clusters.

organism: Arabidopsis thaliana

source_name: Aerial parts

growth_protocol: Four accessions of Arabidopsis thaliana, Altenb-2, Kly-1, Shigu-2, and Vash-1, whose genome sequences were determined, were used for this study. Seeds were surface sterilized, vernalized at 4 ℃ for 2-4 days in the dark and grown at 22 ℃ under continuous light (40 μE・m-2・s-1) for 2 weeks.

extract_protocol:
Total RNA was extracted using Sepasol-RNA I Super G (Nacalai Tesque) following the manufacturer's protocol. Then diluted RNA was subjected to Phenol/Chloroform precipitation, LiCl precipitation, and isopropanol precipitation.The concentrations of the extracted RNA samples were measured with a spectrophotometer (BioSpectrometer Basic; Eppendorf), and 10 ng of total RNA was used to CAGE-seq.
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

treatment_protocol: The seedlings were then treated with high light and cold stress conditions with a light intensity of 140 μE・m-2・s-1 at 4 ℃ for 24 hours.

value: Aerial parts

value: WT

value: Highligh and Cold stress


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-I1


title: Vash-1, Highlight&Cold stress, 24h, rep3

description: Library name: Vash-1_HLC_3


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-I14


title: 20240626_MACR238_BIN67_EV_SPI1_IgG

description: Library name: Sample 96

value: IgG (Epicypher, 13-0042)


title: Vash-1, Highlight&Cold stress, 24h, rep1

description: Library name: Vash-1_HLC_1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-H2


title: pcMZL 7 – Transcriptome


title: pcMZL 6 – Transcriptome


title: 20240626_MACR232_BIN67_BRG1K785R_IgG

description: Library name: Sample 95


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-H13


title: pcMZL 5 – Transcriptome


title: 20240626_MACR226_BIN67_BRG1WT_IgG

description: Library name: Sample 94


title: Vash-1, control, rep2

description: Library name: Vash-1_2

value: Control


title: pcMZL 4 – Transcriptome

value: Skin


title: 20240626_MACR220_BIN67_EV_IgG

description: Library name: Sample 93


title: pcDLBCL-LT 1 – Transcriptome


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-H1


title: Vash-1, control, rep1

description: Library name: Vash-1_1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-G2


title: 20240626_MACR250_BIN67_BRG1K785R_SPI1_IgG

description: Library name: Sample 98

value: SPI1 and SMARCA4-K785R transduced


title: 20201027_KEWCT016_BIN67_GATA3_SMARCC1

description: Library name: Sample 92

value: SMARCC1 (CST, 11956, Lot 4)

value: HA-GATA3 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-G14


title: pcMZL 2 – Transcriptome


title: Shigu-2, Highlight&Cold stress, 24h, rep3

description: Library name: Shigu-2_HLC_3


title: 20201027_KEWCT011_BIN67_SMARCC1

description: Library name: Sample 91


title: Shigu-2, Highlight&Cold stress, 24h, rep2

description: Library name: Shigu-2_HLC_2


title: 20240626_MACR244_BIN67_BRG1WT_SPI1_IgG

description: Library name: Sample 97

value: SPI1 and SMARCA4 transduced


title: Shigu-2, Highlight&Cold stress, 24h, rep1

description: Library name: Shigu-2_HLC_1


title: 20201111_KEWCT029_BIN67_HA-GATA3_HA

description: Library name: Sample 90

value: HA-Tag (CST, 3724)


title: rB-LP 5 – Transcriptome


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-H14

value: FC


title: pcMZL 1 – Transcriptome


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-G1

value: M


title: Vash-1, control, rep3

description: Library name: Vash-1_3


title: Shigu-2, control, rep3

description: Library name: Shigu-2_3


title: rB-LP 4 – Transcriptome


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-F2

value: 9 months


title: 20201014_KEWATAC036_MSC_+HA-REST

description: Library name: Sample 88

data_processing:
ATAC-seq, CUT&RUN, and CUT*TAG reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project’s unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
RNAseq reads were aligned to the GRCh38 genome using STAR v2.5.2b, with GTF annotation from GENCODE v46. Gene counts were obtained using --quantMode "GeneCounts". Differential gene analysis was performed using DESeq2 v1.48.1 in R v4.5.1.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN, CUT&TAG, and ATAC-seq bigWig files give the normalized coverage of DNA fragments across the genome in RPM. In CUT&RUN samples of BRG1 profiling in hMSCs comparing truncations of PU.1, samples were normalized over all SMARCA4 peaks using the method described in DESeq2. In hMSCs expressing PU.1 and SMARCD2-SWIFT, IgG RPM was subtracted to obtain a reduced-background bigWig. Peaks were called using MACS3 and IgG peaks were subtracted when applicable. Gene counts are provided for RNA-seq read counts mapped to exons of given genes, produced using STAR geneCounts.

value: hMSC

value: HA-REST transduced


title: Shigu-2, control, rep2

description: Library name: Shigu-2_2


title: 20201014_KEWATAC035_MSC_+HA-OTX2

description: Library name: Sample 87

value: HA-OTX2 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-F14

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: Shigu-2, control, rep1

description: Library name: Shigu-2_1

value: Aerial parts


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-F13


title: pcMZL 3 – Transcriptome


title: K562 cells,shPHF8-2

city: jinan

first: Huimin

last: Feng

address: 107 Wenhua Xi Road

institute: Shandong University

data_processing:
Sequencing library was determined by Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kit, Quality control analysis on an Agilent 2100 Bioanalyzer.
Image processing and base recognition were performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
Using Hisat2 software (v2.0.4) to aligned to the reference genome.
Transcript abundance estimation was performed using the StringTie software (v1.2.3).
Assembly: HG19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone Marrow

growth_protocol: The CML cell line K562 was maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol: RNA was harvasted using   1-2ug of total RNA was used for the construction of sequencing libraries

treatment_protocol: We added 10ul shNC/shPHF8-1 lentiviral in 105 K562 cells in the presence of 5ug/ml polybrene and used puromycin to select cells at 2ug/ml after 72 hours.

value: Bone Marrow

value: Chronic Myelogenous Leukemia cells

value: PHF8 knockdown

value: Lentiviral transduction with shPHF8


title: 20201014_KEWATAC034_MSC_+HA-PAX3

description: Library name: Sample 86

value: HA-PAX3 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-G13


title: Kly-1, Highlight&Cold stress, 24h, rep3

description: Library name: Kly-1_HLC_3

value: WT

value: Highligh and Cold stress


title: K562 cells,shPHF8-1


title: Kly-1, Highlight&Cold stress, 24h, rep2

description: Library name: Kly-1_HLC_2


title: 20191009_KEWATAC018_MSC_+HA-POU5F1

description: Library name: Sample 85

value: HA-POU5F1 transduced


title: 20210303_KEWCT058_BIN67_empty_HA

description: Library name: Sample 89


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-E2


title: K562 cells,shControl1

value: Lentiviral transduction with shControl


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-F1


title: K562 cells,shControl2


title: 20190822_KEWATAC015_MSC_+HA-FOXA1

description: Library name: Sample 83

value: HA-FOXA1 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-E14

value: FC


title: 20191009_KEWATAC017_MSC_+HA-MYOD1

description: Library name: Sample 84

value: HA-MYOD1 transduced


title: Kly-1, Highlight&Cold stress, 24h, rep1

description: Library name: Kly-1_HLC_1


title: Kly-1, control, rep3

description: Library name: Kly-1_3

value: Control


title: Kly-1, control, rep2

description: Library name: Kly-1_2


title: rB-LP 3 – Transcriptome

value: Skin


title: 20190822_KEWATAC014_MSC_+HA-SOX2

description: Library name: Sample 82

value: hMSC

value: HA-SOX2 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-E13

value: M

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-E1


title: 20190821_KEWATAC010_MSC_+HA-FOS

description: Library name: Sample 81

value: HA-FOS transduced


title: Altenb-2, Highlight&Cold stress, 24h, rep3

description: Library name: Altenb-2_HLC_3

value: Aerial parts


title: Kly-1, control, rep1

description: Library name: Kly-1_1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-D2


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-D14


title: Altenb-2, Highlight&Cold stress, 24h, rep2

description: Library name: Altenb-2_HLC_2


title: 20190530_KEWATAC008_MSC_+HA-HOXA9

description: Library name: Sample 79

value: HA-HOXA9 transduced


title: Altenb-2, Highlight&Cold stress, 24h, rep1

description: Library name: Altenb-2_HLC_1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-D13


title: 20190530_KEWATAC006_MSC_+HA-NANOG

description: Library name: Sample 78

value: HA-NANOG transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-D1


title: Altenb-2, control, rep3

description: Library name: Altenb-2_3

value: WT


title: 20190516_KEWATAC004_MSC_+HA-JUN

description: Library name: Sample 76

value: HA-JUN transduced


title: Altenb-2, control, rep1

description: Library name: Altenb-2_1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-C2


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-C14


title: Carrier high Phe 5

type: RNA

city: Krakow

first: Miroslaw

last: Bik-Multanowski

address: ul. Wielicka 265

department: Dept. of Medical Genetics

country: Poland

institute: Jagiellonian University

description: Gene expression after treatment with Phe concentration of 600 umol/l

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint Human Gene Exprerssion 60Kv3 for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. GeneSpring software was used for further data analysis.

source_name: phenylketonuria (PKU) patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Universal RNA Purification Kit (Eurx, Poland) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: iPSC

tag: carriership of rs113883650

value: Carrier


title: 20190821_KEWATAC009_MSC_+HA-SPI1

description: Library name: Sample 80

source_name: hMSC

value: HA-SPI1 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-C13

value: FC


title: Carrier high Phe 4


title: Carrier high Phe 2


title: pre.integration

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

description: Library name: pre integration

data_processing:
Reads were trimmed to remove adapter sequences and filtered for quality (Q > 30). UMIs were used to account for possible PCR duplicates. Reads containing the unique identifier were isolated for further analysis CACAGTGGTAGTACT.
Assembly: N/A
Supplementary files format and content: Tab-delimited text file containing processed read counts and RIC scores for each nonamer sequence.

organism: synthetic construct

source_name: synthetic construct

extract_protocol: Plasmid DNA was extracted using a Qiagen plasmid purification kit, according to the manufacturer's instructions. Sequencing libraries were prepared for Illumina next-generation sequencing and sequenced on the Illumina MiSeq platform using the MiSeq Reagent Kit v3 (Illumina), following the manufacturer's protocol.

value: synthetic construct

value: nonamer library plasmid


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-C1


title: Noncarrier high Phe 1

value: Noncarrier


title: Noncarrier high Phe 3


title: 20200727_KEWCR336_CandR_MSC_PAX3_HA

description: Library name: Sample 73

data_processing:
ATAC-seq, CUT&RUN, and CUT*TAG reads were first trimmed using fastp v0.24.0, aligned with Bowtie2 v2.2.9 to the GRCh38 reference genome, and filtered using SAMtools v0.1.19 to remove duplicates and for quality (-F 256 -f 2 -q 30). Reads mapping to regions defined in the ENCODE project’s unified GRCh38 blacklist  bed file were removed using bedtools v2.30.0[14]. ATAC-seq data was processed by merging technical replicates using SAMtools merge. Peaks were called using MACS3 (-f BAMPE -g hs -q 0.001 --nomodel --extsize 200 –broad).
Differential accessibility was determined by calculating reads-per-million values across a merged set of peaks for a given comparison set, and using an RPM fold-change cutoff of 1.5. Differential accessibility was then visualized with venn diagrams generated using eulerr. Site centers with flanking windows of 200bp (total window size of 400bp) were identified across given FASTA sequence sites. Motif enrichment across these sets of sites was determined using HOMER findMotifsGenome.pl against genone-background (-size 400) unless otherwise noted. Barplots were generated to visualize HOMER motif results using ggplot2. Heatmaps and deepTools computeMatrix as used to generate metaplots over indicated peaks. deepTools bamCoverage (--binSize ""40"" --normalizeUsing ""CPM"" --exactScaling) was used to generate bigwig inputs for heatmaps. Stacked bar charts generated with ggplot in R to highlight distance to TSS highlighting the proportion of promotor, promoter proximal and distal enhancer regions, determined using bedtools and the GENCODE v46 annotations.
RNAseq reads were aligned to the GRCh38 genome using STAR v2.5.2b, with GTF annotation from GENCODE v46. Gene counts were obtained using --quantMode "GeneCounts". Differential gene analysis was performed using DESeq2 v1.48.1 in R v4.5.1.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN, CUT&TAG, and ATAC-seq bigWig files give the normalized coverage of DNA fragments across the genome in RPM. In CUT&RUN samples of BRG1 profiling in hMSCs comparing truncations of PU.1, samples were normalized over all SMARCA4 peaks using the method described in DESeq2. In hMSCs expressing PU.1 and SMARCD2-SWIFT, IgG RPM was subtracted to obtain a reduced-background bigWig. Peaks were called using MACS3 and IgG peaks were subtracted when applicable. Gene counts are provided for RNA-seq read counts mapped to exons of given genes, produced using STAR geneCounts.
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN: Cells were pelleted by centrifugation (300 rcf, 5 minutes, room temperature) and were washed with PBS containing 200mM Glycine. Cells were resuspended with 100ul/sample of Nuclear Extraction Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) for 2 min on ice. Nuclei were pelleted by centrifugation (600 rcf, 3 minutes, 4C), and resuspended in 100ul/sample cold Wash150 Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) and incubated with activated ConA beads at room temperature for 15 minutes. Nuclei-ConA bead complexes were resuspended in 50 ul/sample cold Antibody Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS, 2mM EDTA supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), 0.01% Digitonin, and 0.5 ug primary antibody/sample, and incubated overnight nutating at 4C. Following removal of supernatant, ConA-nuclei complexes were washed twice with Digitonin Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), and 0.01% Digitonin. Samples were then resuspended in 50ul Digitonin Buffer and 2 ul of CUTANA pAG-MNase (Epicypher, Cat#: 15-1116) each and incubated at room temperature for 10 minutes. Samples were washed twice with Digitonin Buffer and resuspended in 50ul Digitonin Buffer and 1ul of 100mM CaCl2 per sample. Following incubation nutating at 4C for 2 hours, samples received 33ul of Stop Buffer containing 340 mM NaCl, 20 mM EDTA, 4 mM EGTA supplemented with fresh 50 ug/mL RNase A, 50 ug/ml Glycogen and incubated at 37C for 1 hour to release MNase digested DNA fragments. Supernatant was collected into fresh tubes and supplemented with 0.8uL 10% SDS and 1uL of 20mg/mL Proteinase K for overnight incubation at 55C. DNA was purified with Ampure XP (Beckman Coulter, Cat#: A63881) beads and 80% EtOH washes. DNA was eluted with 25uL of 0.1X TE buffer and transferred to new tubes. DNA fragments were prepared for next generation sequencing with CUTANA CUT&RUN Library Prep Kit (Epicypher, Cat#: 14-1001) according to manufacturer protocol. ATAC-seq: Nuclei were resuspended in transposition mix (1X TD Buffer, 2.5 ul TDE1 Nextera Tn5 Transposase (Illumina)) and incubated with mild rotation for 30 min at 37°C. Tagmented DNA was purified using MinElute PCR cleanup kit (Qiagen). RNA-seq: 2 X 106 live cells as were washed with PBS and RNA was extracted using QIAshredder and RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. CUT&TAG: Cells were processed for Cut & Tag as previously published and according to manufacturer’s CUTANA protocol (Epicypher) with the use of BioMag Plus Concanavalin A beads (Polysciences), CUTANA pAG-Tn5 (Epicypher), primary antibodies, and Guinea Pig anti-Rabbit IgG (Heavy & Light chain) antibody (Antibodies-Online). Tn5 transposed fragments were amplified between 14-18 cycles using NEB Next HF 2X PCR Master Mix (NEB) and custom primers originally designed for ATAC-seq library amplification to allow for multiplexing of 50+ samples. Amplified DNA was purified using 0.75X AMPpure Beads (Beckman Coulter) to remove primer-dimers.
CUT&RUN: Concanavalin A (ConA) beads (Polysciences, Cat#: 86057-10) were activated with Bead Activation Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were stored on ice until used. 500,000 cells per sample were harvested and resuspended in media at 1 million cells per mL. Cells were lightly crosslinked with 16% paraformaldehyde at a final concentration of 0.1% at room temperature for 2 minutes. Crosslinking was quenched with 2.5M Glycine at a final concentration of 200mM at room temperature for 5 minutes.  Cells were pelleted by centrifugation (300 rcf, 5 minutes, room temperature) and were washed with PBS containing 200mM Glycine. Cells were resuspended with 100ul/sample of Nuclear Extraction Buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) for 2 min on ice. Nuclei were pelleted by centrifugation (600 rcf, 3 minutes, 4C), and resuspended in 100ul/sample cold Wash150 Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine and 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001) and incubated with activated ConA beads at room temperature for 15 minutes. Nuclei-ConA bead complexes were resuspended in 50 ul/sample cold Antibody Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS, 2mM EDTA supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), 0.01% Digitonin, and 0.5 ug primary antibody/sample, and incubated overnight nutating at 4C. Following removal of supernatant, ConA-nuclei complexes were washed twice with Digitonin Buffer containing 20 mM HEPES pH 7.9, 150 mM NaCl, 1% Triton X-100, 0.05% SDS supplemented with fresh 0.5 mM Spermidine, 1X protease inhibitor (Sigma Aldrich, Cat# 11836170001), and 0.01% Digitonin. Samples were then resuspended in 50ul Digitonin Buffer and 2 ul of CUTANA pAG-MNase (Epicypher, Cat#: 15-1116) each and incubated at room temperature for 10 minutes. Samples were washed twice with Digitonin Buffer and resuspended in 50ul Digitonin Buffer and 1ul of 100mM CaCl2 per sample. Following incubation nutating at 4C for 2 hours, samples received 33ul of Stop Buffer containing 340 mM NaCl, 20 mM EDTA, 4 mM EGTA supplemented with fresh 50 ug/mL RNase A, 50 ug/ml Glycogen and incubated at 37C for 1 hour to release MNase digested DNA fragments. Supernatant was collected into fresh tubes and supplemented with 0.8uL 10% SDS and 1uL of 20mg/mL Proteinase K for overnight incubation at 55C. DNA was purified with Ampure XP (Beckman Coulter, Cat#: A63881) beads and 80% EtOH washes. DNA was eluted with 25uL of 0.1X TE buffer and transferred to new tubes. DNA fragments were prepared for next generation sequencing with CUTANA CUT&RUN Library Prep Kit (Epicypher, Cat#: 14-1001) according to manufacturer protocol. CUT&RUN experiments were performed in one replicate but with antibodies for different mSWI/SNF subunits. Overlap between distinct subunit peaks were used for high confidence in results. ATAC-seq: ATAC-seq was performed as previously described with 100,000 cells per sample. Cells were dissociated and counted, as described above, 7-days post transduction with lentivirus. Cells were washed with cold PBS, resuspend in lysis buffer (10mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL) and centrifuged at 500 g for 10 min at 4°C. Nuclei were resuspended in transposition mix (1X TD Buffer, 2.5 ul TDE1 Nextera Tn5 Transposase (Illumina)) and incubated with mild rotation for 30 min at 37°C. Tagmented DNA was purified using MinElute PCR cleanup kit (Qiagen). Samples were amplified using 10 total PCR amplification cycles with custom PCR Primers using NEBNext HF PCR Master Mix (NEB). Samples were purified with 1.2X Agencourt AMPure XP beads (Beckman Coulter) and size distribution was determined using D5000 HS reagents and screentapes (Agilent) on 2200 TapeStation Instrument (Agilent). Samples were pooled in equimolar amounts and sequenced on Illumina Next-seq 500 with NextSeq 500/550 High Output Kit V2 75 cycles (Illumina) using 37bp paired-end sequencing parameters. ATAC-Seq experiments were performed in two replicates. RNA-seq: Cells were dissociated and counted, as described above, 7-days post transduction with lentivirus. 2 X 106 live cells as were washed with PBS and RNA was extracted using QIAshredder and RNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. 1 µg of total RNA was used as input for library preparation and processed per the manufacturer’s instructions using NEBNext Poly(A) mRNA magnetic isolation module (NEB) followed by the NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB) with NEBNext Multiplex Oligos for Illumina (NEB). Samples were collected in biological replicate. ERCC synthetic RNA spike-in control (Thermo Fisher Scientific) was added at the beginning of library preparation per manufacturer’s recommendations to normalize samples across conditions. Libraries were quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and size distribution was verified using Tapestation D1000 HS reagents and screentapes (Agilent). Equimolar amounts of libraries were pooled, denatured, and sequenced on Illumina Next-seq 500 with NextSeq 500/550 High Output Kit V2 75 cycles (Illumina) according to standard Illumina protocols with single-end sequencing parameters. RNA-Seq were performed in two biological replicates. CUT&TAG: CUT&TAG was performed following published protocols (Epicypher). Cells were dissociated from culture plates using TrypLE Express (Thermo Fisher Scientific) and washed once with PBS pH 7.4 (Gibco). Cells were counted with Countess II (Invitrogen). 200,000-500,000 live cells were used per epitope as determined by Trypan Blue (Thermo Fisher Scientific) exclusion. Cells were processed for Cut & Tag as previously published and according to manufacturer’s CUTANA protocol (Epicypher) with the use of BioMag Plus Concanavalin A beads (Polysciences), CUTANA pAG-Tn5 (Epicypher), primary antibodies, and Guinea Pig anti-Rabbit IgG (Heavy & Light chain) antibody (Antibodies-Online). Tn5 transposed fragments were amplified between 14-18 cycles using NEB Next HF 2X PCR Master Mix (NEB) and custom primers originally designed for ATAC-seq library amplification to allow for multiplexing of 50+ samples. Amplified DNA was purified using 0.75X AMPpure Beads (Beckman Coulter) to remove primer-dimers. Libraries were quantified and QC’d as above. Samples were sequenced by the Dana Farber Cancer Institute Molecular Biology Core Facility using paired-end read parameters on an Illumina Nextseq 500 (Illumina) using Illumina NextSeq 500/550 High Output Kit V2 75 cycles (Illumina).

value: hMSC

tag: chip antibody

value: HA-Tag (CST, 3724)

value: HA-PAX3 transduced


title: Carrier high Phe 3

tag: tissue


title: Carrier high Phe 1


title: Noncarrier high Phe 4


title: Noncarrier high Phe 2


title: 20200727_KEWCR334_CandR_MSC_PAX3_BRG1

description: Library name: Sample 72

value: SMARCA4 (Abcam, ab110641)


title: Altenb-2, control, rep2

description: Library name: Altenb-2_2

value: Control


title: 20190530_KEWATAC005_MSC_+HA-RUNX1

description: Library name: Sample 77

value: HA-RUNX1 transduced


title: Mouse, P91, WT, female

city: Cold Spring Harbor

first: Lucas

last: Cheadle

address: 1 Bungtown Road

institute: Cold Spring Harbor Lab

description: Library name: Cheadle_DV01_4731_F_WT

data_processing:
Raw FASTQ files were processed using Cell Ranger (v9.0.1, 10x Genomics).
Reads were aligned to the mouse reference genome refdata-gex-GRCm39-2024-A with intronic reads included to accommodate nuclear transcripts.
Ambient RNA contamination was removed using CellBender (v0.3), and denoised count matrices were generated.
Assembly: GRCm39-2024-A
Supplementary files format and content: AllCells_Annotation.tsv.gz cell annotation
Supplementary files format and content: AllCells_gene_counts.mtx.gz gene expression matrix

source_name: hippocampus

extract_protocol:
Nuclei were isolated from dissected mouse hippocampi. Tissue was homogenized and lysed using a detergent-based nuclear isolation buffer, followed by filtration and centrifugation to obtain intact nuclei. Nuclei were resuspended in PBS containing 0.04% BSA prior to library preparation.
Single-nucleus RNA-seq libraries were prepared using the 10x Genomics Chromium X platform with the GEM-X Universal Gene Expression v4 kit, following the manufacturer's instructions. Approximately 20,000 nuclei were targeted per sample. Libraries were quality-checked using an Agilent TapeStation and quantified by qPCR prior to sequencing.

value: hippocampus


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-B2

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: M

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-B14


title: Mouse, P109, KO, male

description: Library name: Cheadle_DV01_4687_M_KO


title: 20190516_KEWATAC001_MSC_Empty

first: Cigall

institute: Dana Farber Cancer Institute

description: Library name: Sample 74


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-B13

first: Joseph

institute: HHMI-Salk-Institute


title: 20200727_KEWCR331_CandR_MSC_OTX2_BRG1

description: Library name: Sample 70

value: HA-OTX2 transduced