title: Mouse, P91, WT, male

description: Library name: Cheadle_DV01_4733_M_WT


title: Mouse, P71, WT, female

status: Public on Dec 30 2025

type: SRA

city: Cold Spring Harbor

first: Lucas

last: Cheadle

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Lab

description: Library name: Cheadle_DV01_4806_F_WT

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism: Mus musculus

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.

tag: tissue

value: hippocampus


title: Carrier low 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 215 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.

molecule: total RNA

organism: Homo sapiens

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: 20200727_KEWCR333_CandR_MSC_OTX2_HA

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: Library name: Sample 71

library_source: genomic

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

molecule: genomic DNA

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: chip antibody

value: HA-Tag (CST, 3724)

tag: treatment

value: HA-OTX2 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-B1

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

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

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: Carrier low Phe 3


title: 20200727_KEWCR330_CandR_MSC_REST_HA

description: Library name: Sample 69

value: HA-Tag (CST, 3724, Lot 6)

value: HA-REST transduced


title: Mouse, P71, KO, male

description: Library name: Cheadle_DV01_4808_M_KO


title: Mouse, P79, KO, female

description: Library name: Cheadle_DV02_5175_F_KO


title: 20200727_KEWCR328_CandR_MSC_REST_BRG1

description: Library name: Sample 68


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-A2


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-A14


title: 20180916_KEWCR138_CandR_MSC_BRG1_CS

description: Library name: Sample 67

value: SMARCA4 (CST, 49360, Lot 1)


title: Mouse, P79, WT, male

description: Library name: Cheadle_DV02_5176_M_WT


title: Carrier low Phe 2


title: Noncarrier low Phe 5

value: Noncarrier


title: Noncarrier low Phe 4


title: 20180916_KEWCR135_CandR_FOXA1_HA_500

description: Library name: Sample 66

value: HA-Tag (CST, 3724, Lot 9)

value: HA-FOXA1 transduced


title: Noncarrier low Phe 3


title: Carrier low Phe 1


title: 3 serum samples of pediatric patients younger than 4 years old pre anesthetics expoure pooled replicate 3

city: Milwaukee

first: Xiaowen

last: Bai

state: WI

address: 8701 Watertown Plank Road

department: Department of Cell Biology, Neurobiology & Anatomy

institute: Medical College of Wisconsin

description: Gene expression in serum pre and post anesthesia exposure

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 Whole Human Genome Oligo Microarrays (G4112A) 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: The labeled cRNAs were hybridized onto the LncRNA Array v3.0 (8 x 60K, Arraystar).

data_processing: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

source_name: serum, patients

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: serum

extract_protocol: The total RNA was isolated using the TRIZOL reagent according to the manufacturer's instruction

treatment_protocol: pediatric patients younger than 4 years old  pre and post  longer exposure of general anesthetics (>3hrs) exposure

value: whole blood

tag: sample type

value: pooled samples from both gender

value: < 4 years old


title: 20190516_KEWATAC003_MSC_+HA-GATA3

description: Library name: Sample 75

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: HA-GATA3 transduced


title: 20180916_KEWCR134_CandR_FOXA1_HA_250

description: Library name: Sample 65


title: Carrier low Phe 4

value: iPSC

value: Carrier


title: 3 serum samples of pediatric patients younger than 4 years old pre anesthetics expoure pooled replicate 1


title: 20180916_KEWCR133_CandR_FOXA1_BRG1

description: Library name: Sample 64

value: hMSC


title: 3 serum samples of pediatric patients younger than 4 years old post anesthetics expoure pooled replicate 3


title: VSMC, si_CDCP1_1

city: Shijiazhuang

first: Xin

last: Ji

address: No. 20, South Second Ring East Road

country: China

institute: Hebei Normal University

description:
Library name: Sample 7
vascular smooth muscle cells, si-CDCP1, Ang II treatment

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: gene_fpkm.txt

organism: Rattus

source_name: aorta

growth_protocol: VSMCs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: VSMCs were treated with Ang II after CDCP1 knockdown

value: aorta

tag: cell type

value: vascular smooth muscle cell

tag: genotype

value: CDCP1 knockdown

value: Ang II treatment

tag: batch

value: primary culture


title: H9c2 cells, ET+AA treatment2

city: Omaha

first: Weilun

last: Ai

state: NE

address: 42nd and Emile

institute: University of Nebraska Medical Center

description: Library name: EA2

data_processing:
We used nf-core v3.17.0 (Ewels et al., 2020) pipeline in Nextflow v24.10.2 (Di Tommaso et al., 2017) to perform the RNAseq analysis.
The nf-core pipeline trim the fastq files using cutadapt (Martin & Marcel 2011) and trimgalore to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by FastQC (Andrews 2010). FastQC: a quality control tool for high throughput sequence data; available online at:http://www.bioinformatics.babraham.ac.uk/projects/fastqc) for quality control.
The trimmed fastq files were processed by our newly developed standard pipelines utilizing STAR (Dobin et a., 2011) as the aligner and RSEM (Li & Dewey, 2011) as the tool for annotation and quantification at the gene level.
Assembly: The trimmed fastq files were mapped to rat (Rnor_6.0) reference genome.
Supplementary files format and content: The raw counts were used for differential expressed gene (DEG) analysis by DESeq2 (Love et al., 2014). The text files in the genes folder give normalized expression abundance in TPM and FPKM values for all the available genes.

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
RNA was extracted using TRIzol reagent (Ambion Life Technologies).
500 ng of total RNA from each sample using the NuGEN Universal Plus mRNA-Seq library kit from TECAN following the manufacturers recommended procedure (TECAN, USA Redwood City, CA 94063

value: Heart

value: Cadiomyoblast


title: 3 serum samples of pediatric patients younger than 4 years old post anesthetics expoure pooled replicate 2


title: 20180916_KEWCR131_CandR_SOX2_HA_250

description: Library name: Sample 62

value: HA-SOX2 transduced


title: H9c2 cells, ET+AA treatment1

description: Library name: EA1


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-A13

value: FC

value: M

value: 9 months


title: 3 serum samples of pediatric patients younger than 4 years old post anesthetics expoure pooled replicate 1

value: whole blood

value: pooled samples from both gender


title: VSMC, si_NC_3

description:
Library name: Sample 5
vascular smooth muscle cells, si-NC, Ang II treatment

value: WT


title: VSMC, si_NC_2

description:
Library name: Sample 3
vascular smooth muscle cells, si-NC, Ang II treatment


title: DMSO control 6 h  treated hiPSC-derived cerebral oragnoid replicate 4

description: Gene expression after treatment

source_name: hiPSC-derived cerebral oragnoid

growth_protocol: The hiPSC-derived cerebral organoids were culture at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: hiPSC-derived cerebral organoids were treated with single propofol (10 μg/ml) exposure (against its DMSO control) for 6 h.

value: cerebral oragnoid

tag: tiime

value: Day 60


title: 20180916_KEWCR127_CandR_MYOD1_BRG1

description: Library name: Sample 59

value: hMSC

value: HA-MYOD1 transduced


title: DMSO control 6 h  treated hiPSC-derived cerebral oragnoid replicate 3

description: Gene expression after treatment


title: 20180916_KEWCR123_CandR_ERG_HA_pAG

description: Library name: Sample 58

value: HA-Tag (CST, 3724, Lot 9)

value: HA-ERG transduced


title: DMSO control 6 h  treated hiPSC-derived cerebral oragnoid replicate 1

description: Gene expression after treatment


title: 3 serum samples of pediatric patients younger than 4 years old pre anesthetics expoure pooled replicate 2

value: < 4 years old


title: Heavy polysomes, heat shock, Rep2

city: Lubbock

first: Zemfira

middle: N.

last: Karamysheva

state: TX

department: Cellular Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

description: Sample 23

data_processing:
Read filtering with fastp v0.23.4. Alignment with STAR v2.7.11. Remove duplicates with MarkDuplicates (Picard) v3.1.1. Read counting with FeatureCounts (Subread) v2.0.6.
Assembly: TritrypDB-67. Leishmania major friedlin
Supplementary files format and content: txt file including raw counts for each sample

organism: Leishmania major

source_name: Heavy polysomes

growth_protocol: Leishmania promastigotes were grown at a density of 1×10^5 cells/mL, in 60 mL of M199 culture medium supplemented with 10% Fetal Bovine Serum (FBS) and penicillin/streptomycin mixture (100 units and 100 µg respectively, per mL of media) in a T175 culture flask (Rodriguez-Almonacid, Bustamante and Karamysheva, 2024). Parasites were cultured at 27°C for 48 hours or until they reach the logarithmic phase (~5-7x10^6 cells/mL).

extract_protocol:
RNA isolation was made using Direct-zol TM RNA MiniPrep (Zymo Research, Cat: R2052) following the manufacturer's instructions. The RNA was recovered in 30 µL nuclease-free water and quantified by NanoDrop™ One/OneC.
Paramagnetic beads coupled with oligo d(T)25 were combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 430bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used.

treatment_protocol: After propagation, parasites of treated group were incubated at 37ºC during two hours.

value: Heavy polysomes

value: Friedlin

value: Promastigotes

value: Heat shock


title: H9c2 cells, Control2

description: Library name: C2

value: Heart

value: Cadiomyoblast


title: VSMC, si_CDCP1_3

description:
Library name: Sample 11
vascular smooth muscle cells, si-CDCP1, Ang II treatment

value: aorta

value: vascular smooth muscle cell

value: CDCP1 knockdown

value: Ang II treatment

value: primary culture


title: H9c2 cells, ET+AA treatment3

description: Library name: EA3


title: Tibial osteotomy tissues, TOE_4d_4h

city: Changchun

first: Tiecheng

last: Yu

state: Jilin

address: Xinmin Street No.1

department: Department of Orthopaedics

institute: the First Hospital of Jilin University

description:
Library name: SAMPLE8
10x Genomics

data_processing:
Single-cell RNA-seq data preprocessing: The FASTQ files were processed and aligned to GRCh38 human reference genome using Cell Ranger software (version 9.0.0) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode. The UMI count matrix was then analyzed using Seurat[1] (version 4.0.0) R package. To remove low-quality cells and likely multiplet captures, a set of criteria were conducted: Cells were filtered by (1) gene numbers (gene numbers < 200), (2) UMI (UMI <1000), (3) log10GenesPerUMI (log10GenesPerUMI < 0.7), (4) percentage of mitochondrial RNA UMIs (proportion of UMIs mapped to mitochondrial genes > 10%) and (5) percentage of hemoglobin RNA UMIs (proportion of UMIs mapped to hemoglobin genes > 5%). Subsequently, the DoubletFinder[2] package (version 2.0.3) was used to identify potential doublets. To obtain the normalized gene expression data, library size normalization was processed using the NormalizeData function. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and log-transformed the results. Top 2000 highly variable genes (HVGs) were calculated using the Seurat function FindVariableGenes (mean.function=FastExpMean, dispersion.function= FastLogVMR). Principal-component analysis (PCA) was performed to reduce the dimensionality with RunPCA function. Graph-based clustering was performed to cluster cells according to their gene expression profile with the FindClusters function. Cells were visualized using a 2-dimensional Uniform Manifold Approximation and Projection (UMAP) algorithm with the RunUMAP function. The FindAllMarkers function (test.use = presto) was used to identify marker genes of each cluster. Differentially expressed genes(DEGs) were selected using the function FindMarkers (test.use = presto). P value < 0.05 and |log2foldchange| > 0.58 was set as the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R(version 4.0.3) based on the hypergeometric distribution.
Assembly: GCF_015227675.2_mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: tibial circular osteotomy tissues

extract_protocol:
1. GEM Generation & Barcoding  Prepare Master Mix on ice, containing RT Reagent, Template Switch Oligo, Reducing Agent B, and RT Enzyme C.  Load Master Mix, cell suspension, Gel Beads, and Partitioning Oil into designated wells of Chromium Chip B.  Run the Chromium Controller to generate Gel Beads-in-Emulsion (GEMs).  Transfer GEMs to a tube strip and perform GEM-Reverse Transcription (GEM-RT) incubation (53°C for 45 min, 85°C for 5 min, then hold at 4°C).  2. Post GEM-RT Cleanup & cDNA Amplification  Add Recovery Agent to each sample and remove the lower oil phase.  Prepare Dynabeads Cleanup Mix and incubate with samples to bind cDNA.  Wash beads with 80% ethanol, elute with Elution Solution I, and transfer purified sample.  Amplify cDNA using cDNA Amplification Mix in a thermal cycler (98°C for 3 min; cycled steps: 98°C for 15s, 63°C for 20s, 72°C for 1 min; 72°C for 1 min; hold at 4°C).  Clean up amplified cDNA using SPRIselect beads (0.6X ratio), wash with ethanol, and elute with Buffer EB
3. 3' Gene Expression Library Construction  Fragmentation, End Repair & A-tailing: Incubate purified cDNA with Fragmentation Mix (32°C for 5 min, 65°C for 30 min).  Perform double-sided size selection using SPRIselect beads (0.6X and 0.8X ratios) to purify fragmented DNA.  Adaptor Ligation: Ligate adaptors using Ligation Buffer, DNA Ligase, and Adaptor Oligos (20°C for 15 min).  Clean up ligation product with SPRIselect beads (0.8X ratio).  Sample Index PCR: Amplify libraries using Sample Index PCR Mix and Chromium i7 Sample Indices (98°C for 45s; cycled steps: 98°C for 20s, 54°C for 30s, 72°C for 20s; 72°C for 1 min; hold at 4°C).  Perform a final double-sided size selection with SPRIselect beads (0.6X and 0.8X ratios) and elute the final library in Buffer EB.  4. Post-Library Quality Control  Assess library quality and size distribution using the Agilent 2100 Bioanalyzer.

value: tibial circular osteotomy tissues

value: TO model Rat under rESWT treatment at 4 days post-injury (sample was collected after 4h)


title: 20180916_KEWCR120_CandR_ERG_BRG1_pA

description: Library name: Sample 55

value: hMSC


title: H9c2 cells, Control3

description: Library name: C3


title: 20180916_KEWCR130_CandR_SOX2_BRG1

description: Library name: Sample 61

value: HA-SOX2 transduced


title: 20180916_KEWCR132_CandR_SOX2_HA_500

description: Library name: Sample 63

value: HA-Tag (CST, 3724, Lot 9)


title: Noncarrier low Phe 2

value: iPSC

value: Noncarrier


title: 20180916_KEWCR128_CandR_MYOD1_HA

description: Library name: Sample 60

value: HA-MYOD1 transduced


title: AMB_200205_9mo_2A_3A_1_P1-1-F3-A1

value: FC

value: M

value: 9 months


title: Heavy polysomes, control, Rep3

description: Sample 21

value: Heavy polysomes

value: Friedlin

value: Promastigotes

value: WT

value: Control


title: VSMC, si_NC_1

description:
Library name: Sample 1
vascular smooth muscle cells, si-NC, Ang II treatment

value: aorta

value: vascular smooth muscle cell

value: Ang II treatment

value: primary culture


title: Heavy polysomes, heat shock, Rep3

description: Sample 24

value: Heat shock


title: Heavy polysomes, control, Rep2

description: Sample 20


title: VSMC, si_CDCP1_2

description:
Library name: Sample 9
vascular smooth muscle cells, si-CDCP1, Ang II treatment

value: CDCP1 knockdown


title: H9c2 cells, Control1

description: Library name: C1

value: Heart

value: Cadiomyoblast


title: Tibial osteotomy tissues, TO_4d_24h

description:
Library name: SAMPLE5
10x Genomics

value: tibial circular osteotomy tissues

value: TO model Rat without rESWT treatment at 4 days post-injury (sample was collected after 24h)


title: Noncarrier low Phe 1

value: iPSC

value: Noncarrier


title: Heavy polysomes, heat shock, Rep1

description: Sample 22

value: Heavy polysomes


title: Tibial osteotomy tissues, TOE_4d_24h

description:
Library name: SAMPLE9
10x Genomics

value: TO model Rat under rESWT treatment at 4 days post-injury (sample was collected after 24h)


title: 10 μg/ml propofol 6 h treated hiPSC-derived cerebral oragnoid replicate 4

description: Gene expression after treatment

value: cerebral oragnoid

value: Day 60


title: 20180916_KEWCR117_CandR_FOS_HA

description: Library name: Sample 53

value: hMSC

value: HA-Tag (CST, 3724, Lot 9)

value: HA-FOS transduced


title: 20180916_KEWCR121_CandR_ERG_HA_pA

description: Library name: Sample 56

value: HA-ERG transduced


title: Tibial osteotomy tissues, TOE_2d_24h

description:
Library name: SAMPLE7
10x Genomics

value: TO model Rat under rESWT treatment at 2 days post-injury (sample was collected after 24h)


title: 10 μg/ml propofol 6 h treated hiPSC-derived cerebral oragnoid replicate 3

description: Gene expression after treatment


title: DMSO control 6 h  treated hiPSC-derived cerebral oragnoid replicate 2

description: Gene expression after treatment


title: 20180916_KEWCR122_CandR_ERG_BRG1_pAG

description: Library name: Sample 57


title: Tibial osteotomy tissues, TOE_2d_4h

description:
Library name: SAMPLE6
10x Genomics

value: TO model Rat under rESWT treatment at 2 days post-injury (sample was collected after 4h)


title: 20180916_KEWCR118_CandR_MSC_BRG1

description: Library name: Sample 54


title: 10 μg/ml propofol 6 h treated hiPSC-derived cerebral oragnoid replicate 2

description: Gene expression after treatment


title: Light polysomes, heat shock, Rep3

description: Sample 18

source_name: Light polysomes

value: Light polysomes

value: Friedlin

value: Promastigotes

value: WT

value: Heat shock


title: Light polysomes, heat shock, Rep2

description: Sample 17


title: P43_RNA-Seq_1

city: Novosibirsk

first: Nikita

last: Torgunakov

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics

description:
Library name: P43_RNA-Seq_1
Raw data are not provided due to patient privacy concerns.

data_processing:
Transcriptome analysis. RNA-seq reads were aligned to the human reference genome (GRCh37/hg19) using STAR (v2.5.2b).Coverage files in BigWig format were generated using bamCoverage (v 3.5.5)
Assembly: hg19
Supplementary files format and content: *.bw files in BigWig format containing sequencing coverage data.

source_name: blood

extract_protocol:
Transcriptome analysis. For transcriptome analysis, total RNA was extracted from the two independent clones of patient iPS cells.
Transcriptome analysis. Stranded oligo-dT-based RNA-sequencing.

treatment_protocol: Transcriptome analysis. Reprogramming of patient blood cells into induced pluripotent stem (iPS) cells was performed by episomal vectors cocktail contained: reprogramming vectors expressed OCT4 (addgene #41813), MYC and LIN28 (addgene #41855), p53 carboxy-terminal dominant-negative fragment (addgene #41856), SOX2 and KLF4 (addgene #41814), EBNA1 (addgene # 41857).

value: blood

value: iPSC


title: Tibial osteotomy tissues, TO_2d_24h

description:
Library name: SAMPLE3
10x Genomics

value: tibial circular osteotomy tissues

value: TO model Rat without rESWT treatment at 2 days post-injury (sample was collected after 24h)


title: Tibial osteotomy tissues, TO_2d_4h

description:
Library name: SAMPLE2
10x Genomics

value: TO model Rat without rESWT treatment at 2 days post-injury (sample was collected after 4h)


title: Heavy polysomes, control, Rep1

description: Sample 19

value: Heavy polysomes

value: Control


title: P43_Hi-C

description:
Library name: P43_Hi-C
Raw data are not provided due to patient privacy concerns.

data_processing:
3C experiment. The “fastq” files with sequences were preprocessed with cutadapt ver-4.6. Next, the juicer ver-1.5.6 was used to make the files with aligned read pairs.
Assembly: hg19
Supplementary files format and content: *_mnd_cut.txt.gz files containing valid Hi-C pairs (described as "Long format" in Juicer documentation here: https://github.com/aidenlab/juicer/wiki/Pre#long-format), modified to remove fields <cigar1> <sequence1> <cigar2> <sequence2> <readname1> <readname2> due to patient privacy concerns. Fields <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> remain.

extract_protocol:
3C experiment. The 3C part was performed on the peripheral blood mononuclear cells (PBMC) according to DNase I protocol10. In brief, 2.5 million cells were fixed using 1% formaldehyde, lysed, and then subjected to digestion with DNase I (Thermo Fisher Scientific, USA). The digested DNA ends were labeled with biotin-15-dCTP (Biosan, Russia) and ligated overnight using T4 DNA ligase (Thermo Fisher Scientific, USA). To reverse the formaldehyde crosslinks, the samples were incubated with Proteinase K (NEB, UK) at 65°C overnight, followed by ethanol precipitation. Unligated biotin-labeled ends were removed through treatment with T4 polymerase (NEB, UK).
3C experiment. The KAPA HyperPlus kit (Roche) was used for NGS library preparation. Biotin-filled DNA fragments were pulled down using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific, USA), and the libraries were subsequently amplified.

value: Lymphocytes


title: 20180916_KEWCR114_CandR_OCT4_BRG1

description: Library name: Sample 50

value: hMSC

value: HA-POU5F1 transduced


title: Tibial osteotomy tissues, TO_2d_0h

description:
Library name: SAMPLE1
10x Genomics

value: TO model Rat without rESWT treatment at 2 days post-injury  (sample was collected after 0h)


title: 20180916_KEWCR113_CandR_Nanog_HA

description: Library name: Sample 49

value: HA-Tag (CST, 3724, Lot 9)

value: HA-NANOG transduced


title: Tibial osteotomy tissues, TO_4d_4h

description:
Library name: SAMPLE4
10x Genomics

value: TO model Rat without rESWT treatment at 4 days post-injury (sample was collected after 4h)


title: Light polysomes, heat shock, Rep1

description: Sample 16

value: Light polysomes

value: Friedlin

value: Promastigotes


title: Light polysomes, control, Rep2

description: Sample 14

value: WT


title: Light polysomes, control, Rep3

description: Sample 15


title: HepG2, pGRHL2, rep4

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

data_processing:
RNAseq reads were mapped on human genome (hg38) using Hisat2 v.2.2.1
Read counting was performed using the count function of the HTSeq tool (version 0.9.1)using the following parameters: mode = UNION, Stranded = No, Minimum alignment quality = 10, Feature types = Exon, ID attributes = Gene ID (Anders et al. 2015)
Normalization of gene expression data and differential expression analyses were performed in R (R_Core_Team 2023) using the DESeq2 (version 1.40.2) package (Love et al. 2014)
Pre-filtering was applied to remove genes with low counts, i.e. genes with cumulated reads in all samples below 10
Normalized gene expression data were obtained by dividing Rlog normalized gene expression data obtained from DESeq2 by transcript lengths. Transcript lengths had previously been calculated by averaging the lengths of all transcripts associated to a given gene symbol in Ensembl (GRCm39 or GRCh.38.p13) (Cunningham et al. 2022).
Assembly: Hg38
Supplementary files format and content: Matrix tab-delimited file includes raw counts for all samples ("FPKM_RNASeq_HepG2_overexpression_Grhl2_GeneID.txt")

growth_protocol: William E complemented with 10% fetal bovine serum, 2 mM Glutamine, 1x penicillin/streptomycin, 20mU/ml bovin insulin, 50 nM dexamethasone. Cells were cultured at 37°C at 5%CO2 on gelatin coated dish.

extract_protocol:
RNA were purified using Nucleospin RNA kit from Macherey Nagel according to the manufacturer's instructions and processed for analysis using RNAseq.
RNA seq librairies were prepared using Optimal Dual-mode mRNA Library Prep Kit following manufacturer's protocols
RNA seq, paired-end, 150bp

treatment_protocol: Human HepG2 cells were transfected with a plasmid coding for GRHL2 fused to a flag tag or a pcDNA vector. RNA were harvested 48h later.

value: Human hepatocarcinoma cell line

tag: plasmid


title: P43_RNA-Seq_2

description:
Library name: P43_RNA-Seq_2
Raw data are not provided due to patient privacy concerns.

value: blood

value: iPSC


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E15.5 - 6

city: Piscataway

first: Brian

last: Daniels

state: NJ

address: 604 Allison Road

department: Cell Biology and Neuroscience

institute: Rutgers, The State University of New Jersey

description: Library name: 8712-4

data_processing:
RNA-seq: Raw data quality was evaluated by FastQC.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
the gene hit counts table was used for downstream differential expression analysis via DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCm38
Supplementary files format and content: RNA-seq: tab-delimited text file includes unique gene hit counts for each sample

source_name: Fetal brain

extract_protocol:
Total RNA from brain samples was harvested using Qiagen RNeasyMicro kit following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Pregnant hSTAT2 mice were subcutaneously injected with either PBS or maDakar (Zika virus) on either embryonic day (E) 12.5 or E16.5. Brains of the offspring were harvested on E15.5, E18.5, or 3-weeks post birth.

value: Fetal brain

value: PBS


title: 10 μg/ml propofol 6 h treated hiPSC-derived cerebral oragnoid replicate 1

description: Gene expression after treatment

value: cerebral oragnoid

value: Day 60


title: 20180916_KEWCR112_CandR_Nanog_BRG1

description: Library name: Sample 48

value: hMSC


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E15.5 - 5

description: Library name: 8712-2


title: Light polysomes, control, Rep1

description: Sample 13

value: Control


title: HepG2, pGRHL2, rep3


title: Monosomes, heat shock, Rep3

description: Sample 12

source_name: Monosomes

value: Monosomes

value: Heat shock


title: 20180916_KEWCR116_CandR_FOS_BRG1

description: Library name: Sample 52

value: HA-FOS transduced


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E15.5 - 4

description: Library name: 8115-3


title: 20180916_KEWCR110_CandR_STAT3_BRG1

description: Library name: Sample 46

value: HA-STAT3 transduced


title: HepG2, pcDNA3, rep3


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E15.5 - 3

description: Library name: 8115-2


title: 20180916_KEWCR115_CandR_OCT4_HA

description: Library name: Sample 51

value: HA-Tag (CST, 3724, Lot 9)

value: HA-POU5F1 transduced


title: Monosomes, heat shock, Rep2

description: Sample 11

value: Friedlin

value: Promastigotes


title: 20180916_KEWCR109_CandR_IRF4_HA

description: Library name: Sample 45

value: HA-IRF4 transduced


title: HepG2, pGRHL2, rep2

value: Human hepatocarcinoma cell line


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E15.5 - 2

description: Library name: 8111-5


title: Monosomes, heat shock, Rep1

description: Sample 10

value: WT


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E15.5 - 1

description: Library name: 8111-2

value: Fetal brain


title: 20180916_KEWCR108_CandR_IRF4_BRG1

description: Library name: Sample 44


title: HepG2, pcDNA3, rep2


title: Monosomes, control, Rep3

description: Sample 9


title: HepG2, pGRHL2, rep1


title: HepG2, pcDNA3, rep1


title: Monosomes, control, Rep1

description: Sample 7


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E15.5 - 5

description: Library name: 8106-3

value: ZIKV-maDakar


title: HepG2, pcDNA3, rep4


title: Monosomes, control, Rep2

description: Sample 8


title: 20180916_KEWCR111_CandR_STAT3_HA

description: Library name: Sample 47


title: HepG2_DI_n4

data_processing:
RNAseq reads were mapped on human genome (hg38) using Hisat2 v.2.2.1
Read counting was performed using the count function of the HTSeq tool (version 0.9.1)using the following parameters: mode = UNION, Stranded = No, Minimum alignment quality = 10, Feature types = Exon, ID attributes = Gene ID (Anders et al. 2015)
Normalization of gene expression data and differential expression analyses were performed in R (R_Core_Team 2023) using the DESeq2 (version 1.40.2) package (Love et al. 2014)
Pre-filtering was applied to remove genes with low counts, i.e. genes with cumulated reads in all samples below 10
Normalized gene expression data were obtained by dividing Rlog normalized gene expression data obtained from DESeq2 by transcript lengths. Transcript lengths had previously been calculated by averaging the lengths of all transcripts associated to a given gene symbol in Ensembl (GRCm39 or GRCh.38.p13) (Cunningham et al. 2022).
Assembly: Hg38
Supplementary files format and content: Matrix tab-delimited file includes raw counts for all samples ("RNASeq_HepG2_Ezhionly_FPKM_hgnc_gene_ID.csv")

treatment_protocol: Human HepG2 cells were treated with vehicle (0,2% DMSO) or Ezh1/2 inhibitors (UNC1999 and Valmetostat Tosylate used both at 1µM) for 4 days.

value: Ezh1/2 inhibitors


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E15.5 - 4

description: Library name: 7875-4


title: 20190607_KEWCR102_CandR_FOXA1_BRG1

description: Library name: Sample 40

value: SMARCA4 (CST, 2729, Lot 8)

value: HA-FOXA1 transduced


title: HepG2_vehicle_n4

value: Vehicle


title: Input, heat shock, Rep2

description: Sample 5

source_name: Input

value: Input


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E15.5 - 3

description: Library name: 7875-1


title: Input, heat shock, Rep3

description: Sample 6

value: Heat shock


title: 20190607_KEWCR092_CandR_ERG_HA

description: Library name: Sample 39

value: hMSC

value: HA-ERG transduced


title: HepG2_DI_n3


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E15.5 - 2

description: Library name: 7848-5


title: Input, heat shock, Rep1

description: Sample 4


title: 20190607_KEWCR091_CandR_ERG_BRG1

description: Library name: Sample 38


title: 20180916_KEWCR107_CandR_SPI1_HA

description: Library name: Sample 43

value: HA-Tag (CST, 3724, Lot 9)

value: HA-SPI1 transduced


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E15.5 - 6

description: Library name: 8106-6


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E15.5 - 1

description: Library name: 7848-2


title: Input, control, Rep3

description: Sample 3

value: Friedlin

value: Control


title: 20190607_KEWCR089_CandR_ERG_HA

description: Library name: Sample 37


title: 20180916_KEWCR106_CandR_SPI1_BRG1

description: Library name: Sample 42


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E18.5 - 6

description: Library name: 6244-5

value: PBS


title: Input, control, Rep1

description: Sample 1

value: Promastigotes


title: 20190607_KEWCR103_CandR_FOXA1_HA

description: Library name: Sample 41


title: 20190607_KEWCR088_CandR_ERG_BRG1

description: Library name: Sample 36


title: Input, control, Rep2

description: Sample 2

value: WT


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E18.5 - 5

description: Library name: 6244-1

value: Fetal brain


title: HepG2_DI_n1

value: Human hepatocarcinoma cell line


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E18.5 - 4

description: Library name: 6110-6


title: HepG2_DI_n2

value: Ezh1/2 inhibitors


title: HepG2_vehicle_n1


title: 20190607_KEWCR086_CandR_Nanog_HA

description: Library name: Sample 35

value: HA-NANOG transduced


title: CNBMP

city: Jejusi

first: Hyesung

last: Kim

address: Aran 13 gil, 15

department: Convergence Biomedical Science

country: South Korea

institute: Jeju National University College of medicine

description: Library name: CNBMP

data_processing:
Single-cell RNA sequencing data were processed and analyzed using Python (v3.11.0) and the Scanpy toolkit (v1.10.3). Raw sequencing reads were aligned and quantified using Cell Ranger (10x Genomics) to generate gene-barcode count matrices, which were imported into Python as AnnData objects for downstream analysis. Cells with low gene counts or high mitochondrial content were filtered out. The data were normalized, log-transformed, and highly variable genes were identified for dimensionality reduction. Principal component analysis (PCA) was used to reduce dimensionality, and neighborhood graphs were computed to enable clustering with the Leiden algorithm and visualization with UMAP.
Assembly: GRCh38
Supplementary files format and content: .h5

source_name: Large intestine

extract_protocol:
Organoid samples were dissociated using TrypLE (Thermo Fisher, Cat. No. 12605010) at 37°C for the following duration: 15 min for Inc IM and Com ; 20 min for An  and Com IM; and 25 min for LI and  SI.
Single Cell RNA-seq libraries were prepared using the 10x Chromium iX and GEM-X Single Cell 3' Kit v4 (10x genomics, PN-1000691). Briefly, the cell suspension (target recovery 10,000 cells) was mixed with reverse transcription master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a GEM-X Single Cell 3' Chip Kit v4 (10x genomics, PN-1000690) to generate single-cell Gel Bead-in-emulsion (GEM).

value: Large intestine

value: organoid


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E18.5 - 3

description: Library name: 6110-3


title: CN

description: Library name: CN


title: HepG2, H3K27ac

data_processing:
ChIP-seq reads were aligned to Hg38 using Chromap version 0,1,3-R256 and the following parameters: remove PCR duplicates; error threshold = 8; min-num-seeds = 2; max seed frequency = 500-1,000; max-num-best-mappings = 1; max-insert-size = 1,000; MAPQ threshold = 10; min-read-length = 30; bc-error-threshold = 1; bc-probability-threshold = 0.90.
Signal tracks were obtained using the bamCoverage function of the DeepTools version 3.5.1 (Ramírez et al. 2016) with the following parameters: -bs 25 --normalizeUsing CPM -e 200.
Assembly: Hg38
Supplementary files format and content: Signal tracks were obtained using the bamCoverage function of the DeepTools version 3.5.1 (Ramírez et al. 2016) with the following parameters: -bs 25 --normalizeUsing CPM -e 200.

growth_protocol: William E complemented with 10% fetal bovine serum, 2 mM Glutamine, 1x penicillin/streptomycin, 20mU/ml bovin insulin, 50 nM dexamethasone. Cells were cultured at 37°C at 5%CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor sonicator (Diagenode)
ChIP seq librairies were prepared by BGI platform using in-house BGI library kit

value: H3K27ac (Active Motif #39685)


title: 20190510_KEWCR080_CandR_FOS_HA

description: Library name: Sample 33

value: HA-FOS transduced


title: SIBMP

description: Library name: SIBMP

source_name: Small intestine

value: Small intestine


title: 20190510_KEWCR079_CandR_FOS_BRG1

description: Library name: Sample 32

value: hMSC


title: HepG2_vehicle_n3

value: Vehicle


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E18.5 - 4

description: Library name: 5763-5

value: ZIKV-maDakar


title: HepG2, H3K27m3


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E18.5 - 3

description: Library name: 5763-3


title: 20190510_KEWCR077_CandR_JUN_HA

description: Library name: Sample 31

value: HA-Tag (CST, 3724, Lot 9)

value: HA-JUN transduced


title: HepG2_vehicle_n2


title: HepG2, Input


title: ComBMP

description: Library name: ComBMP

source_name: Stomach

value: Stomach


title: SI

description: Library name: SI


title: 20190510_KEWCR076_CandR_JUN_BRG1

description: Library name: Sample 30


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E18.5 - 2

description: Library name: 5711-5

value: PBS


title: HepG2, pGRHL2, Flag, rep4

data_processing:
ChIP-seq reads were aligned to Hg38 using Chromap version 0,1,3-R256 and the following parameters: remove PCR duplicates; error threshold = 8; min-num-seeds = 2; max seed frequency = 500-1,000; max-num-best-mappings = 1; max-insert-size = 1,000; MAPQ threshold = 10; min-read-length = 30; bc-error-threshold = 1; bc-probability-threshold = 0.90.
Signal tracks were obtained using the bamCoverage function of the DeepTools version 3.5.1 (Ramírez et al. 2016) with the following parameters: -bs 25 --normalizeUsing CPM -e 200.
Assembly: Hg38
Supplementary files format and content: Bam files were generated using the bamCoverage function of the DeepTools version 3.5.1 (Ramírez et al. 2016) with the following parameters: -bs 25 --normalizeUsing CPM -e 200".

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and nuclear lysis, chromatin was sonicated using a Bioruptor sonicator (Diagenode) and used for ChIP assay followed by high-throughput sequencing.
ChIP seq librairies were prepared by BGI platform using in-house BGI library kit

treatment_protocol: Plasmids were transfected in HepG2 cells using JetPrime according to the manufacturer's instruction. Transfected cells were cultured 48h at 37°c at 5% CO2


title: hSTAT2 mouse, Fetal brain, PBS, E12.5 injection, E18.5 - 1

description: Library name: 5711-1


title: HepG2, pGRHL2, Flag, rep3


title: ComGF

description: Library name: ComGF


title: 20190607_KEWCR085_CandR_Nanog_BRG1

description: Library name: Sample 34


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E18.5 - 2

description: Library name: 5649-6


title: IncomBMP

description: Library name: IncomBMP


title: 20190510_KEWCR074_CandR_OCT4_HA

description: Library name: Sample 29

value: HA-POU5F1 transduced


title: IncomGF

description: Library name: IncomGF


title: 20190510_KEWCR071_CandR_STAT3_HA

description: Library name: Sample 27

value: HA-STAT3 transduced


title: hSTAT2 mouse, Fetal brain, ZIKV, E12.5 injection, E18.5 - 1

description: Library name: 5649-1

value: Fetal brain


title: HepG2, pGRHL2, Flag, rep2

value: Human hepatocarcinoma cell line


title: HepG2, pGRHL2, Flag, rep1


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 8

description: Library name: 6113-5

source_name: Weanling brain

value: Weanling brain


title: HepG2, pcDNA3, Flag, rep4


title: 20190510_KEWCR073_CandR_OCT4_BRG1

description: Library name: Sample 28


title: 20190510_KEWCR070_CandR_STAT3_BRG1

description: Library name: Sample 26


title: naBMP

description: Library name: naBMP


title: naGF

description: Library name: naGF


title: 20190510_KEWCR068_CandR_IRF4_HA

description: Library name: Sample 25

value: HA-IRF4 transduced


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 7

description: Library name: 6113-1


title: HepG2, pcDNA3, Flag, rep3


title: hSTAT2 mouse, Weanling brain, PBS, E12.5 injection, 3W - 6

description: Library name: 5631-5


title: LI_ATAC

description: Library name: LI_ATAC

library_source: other

data_processing:
Peaks were called in the aligned sequence data using a model-based analysis of ATAC-seq (MACS2 version 2.1.1.20160309).(9) The algorithm empirically models the length of ATAC-Seq fragments from the sequence data, considering local genomic biases in a distribution of mapped reads. The following parameters were used: macs2 callpeak -t ATAC-seq.bam -g hs --bdg --nolambda --keep-dup all --broad. Among the called peaks, the peaks overlapping with ENCODE blacklisted regions were removed. ChIPseeker (version 1.22.1) (10), a bioconductor package within R (version 4.2.2) to facilitate batch annotation of enriched peaks, was used to identify nearby genes and transcripts from the peaks obtained from MACS2.
Assembly: GRCh38
Supplementary files format and content: mapping.bowtie2.stats.txt,peak_annotation.stats.txt,raw_throughput.txt,trim_throughput.txt

molecule: other

extract_protocol:
Organoid samples were dissociated using TrypLE (Thermo Fisher, Cat. No. 12605010) at 37°C for the following duration: 15 min for Inc IM and Com ; 20 min for An  and Com IM; and 25 min for LI and  SI.
Before starting analysis, Trim Galore (version 0.6.10) was used to remove adapter sequences and trim bases with base quality lower than three from both ends of the reads. Also using sliding window trim method, bases that does not qualify for window size=4, and mean quality=15 are filtered. Afterwards, reads less than 36 bp in length are excluded to produce high quality data.

value: Large intestine

value: organoid


title: 20190510_KEWCR067_CandR_IRF4_BRG1

description: Library name: Sample 24

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


title: HepG2, pcDNA3, Flag, rep1


title: hSTAT2 mouse, Weanling brain, PBS, E12.5 injection, 3W - 5

description: Library name: 5631-2


title: 20190410_KEWCR065_CandR_RUNX1_HA

description: Library name: Sample 23

value: HA-RUNX1 transduced


title: SI_ATAC

description: Library name: SI_ATAC

value: Small intestine


title: ComGF_ATAC

description: Library name: ComGF_ATAC


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 6

description: Library name: 5450-4


title: NME1.3 (231-H1.3)

city: Hong Kong

first: Vasu

last: Saini

address: Clearwater Bay

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
Raw reads obtained from DNBSEQ-G400 were trimmed using cutadapt to remove adapter sequences, primers, poly-A tails, and other types of unwanted sequences.
The trimmed reads were then be mapped to the genome (UCSC hg38) using STAR with default parameters.
Reads were quantified and differentially expressed genes (DEGs) were identified using DEBrowser (v1.19.1) as a graphical interface to DESeq2 with significance considered at q-value ≤ 0.05 and absolute fold change ≥ 1.2.
List of DEGs were used to generate heatmaps and venn diagram by using DEBrowser [Kucukural et al., 2019] and VennDiagram package in R [Chen et al., 2011].
Genome_build: UCSC hg38
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts for every gene of every sample
Supplementary_files_format_and_content: xlsx file containing processed gene counts of every sample

source_name: Breast cancer cell line

growth_protocol: MCF-7 cells were grown in DMEM conditioned medium

extract_protocol:
Cells were lysed in TRIzol. Whole RNA was isolated with Macherey-Nagel minikit according to the manufacturer's instructions. RNA quality was verified with Agilent 5400 fragment analyzer prior to library preparation.
SMART-Seq2 library construction was performed according to manufacturer's protocol.

treatment_protocol: MCF-7 cells were treated with PBS (control) or exosomes isolated from MDA-MB-231 cells or MDA-MB-231/H1 cells for 24 h

value: Breast cancer cell line

value: wild type

value: MDA-MB-231/Nm23-H1 exosomes


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 5

description: Library name: 5450-1

value: ZIKV-maDakar


title: 20190410_KEWCR056_CandR_ERG_HA

description: Library name: Sample 21

source_name: hMSC

value: hMSC

value: HA-Tag (CST, 3724, Lot 9)

value: HA-ERG transduced


title: IncomGF_ATAC

description: Library name: IncomGF_ATAC

value: Stomach


title: NME1.2 (231-H1.2)


title: naGF_ATAC

description: Library name: naGF_ATAC


title: 20190410_KEWCR055_CandR_ERG_BRG1

description: Library name: Sample 20


title: NME1.1 (231-H1.1)


title: hSTAT2 mouse, Weanling brain, PBS, E12.5 injection, 3W - 4

description: Library name: 5433-4

value: PBS


title: hSTAT2 mouse, Weanling brain, PBS, E12.5 injection, 3W - 3

description: Library name: 5433-3


title: X231.3

value: MDA-MB-231 exosomes


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 4

description: Library name: 5346-5


title: X231.2


title: 20190410_KEWCR053_CandR_SOX2_HA

description: Library name: Sample 19

value: HA-SOX2 transduced


title: CCA1-ox_Roots_Rep_2

city: Cerdanyola del Vallès

first: LU

last: XIONG

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: CRAG

description: Library name: OX_Rt_2

data_processing:
Raw data (raw reads) in FASTQ format were first processed using in-house perl scripts. Clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality.
Assembly: Arabidopsis Tair 10 genome assembly
Supplementary files format and content: txt  file with FPKM reads for each sample

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Total RNA was isolated using a RNeasy Plant Mini Kit including on-column DNase digestion with the RNase-Free DNase Set (Qiagen).
Sequencing libraries were generated using the Novogene NGS Stranded RNA Library Prep Set (PT044).

value: Root


title: 20190410_KEWCR052_CandR_SOX2_BRG1

description: Library name: Sample 18

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).


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 3

description: Library name: 5346-2

value: Weanling brain


title: 20190410_KEWCR050_CandR_Nanog_HA

description: Library name: Sample 17

value: HA-NANOG transduced


title: CCA1-ox_Roots_Rep_1

description: Library name: OX_Rt_1


title: HepG2, pcDNA3, Flag, rep2

value: Human hepatocarcinoma cell line


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 2

description: Library name: 5341-5


title: WT_Roots_Rep_3

description: Library name: WT_Rt_3

value: WT


title: 20190410_KEWCR064_CandR_RUNX1_BRG1

description: Library name: Sample 22

value: HA-RUNX1 transduced


title: hSTAT2 mouse, Weanling brain, ZIKV, E12.5 injection, 3W - 1

description: Library name: 5341-1


title: X231.1

value: Breast cancer cell line


title: PBS.3

value: wild type


title: 20190410_KEWCR047_CandR_JUN_HA

description: Library name: Sample 15

value: HA-JUN transduced


title: hSTAT2 mouse, Weanling brain, PBS, E12.5 injection, 3W - 2

description: Library name: 4769-4


title: 20190410_KEWCR046_CandR_JUN_BRG1

description: Library name: Sample 14


title: 20190410_KEWCR049_CandR_Nanog_BRG1

description: Library name: Sample 16


title: PBS.2


title: PBS.1


title: 20190410_KEWCR044_CandR_GATA3_HA

description: Library name: Sample 13

value: HA-GATA3 transduced


title: CCA1-ox_Shoots_Rep_3

description: Library name: OX_Sh_3

source_name: Shoot

value: Shoot


title: CCA1-ox_Roots_Rep_3

description: Library name: OX_Rt_3


title: T47D breast cancer cells, NT, rep3

city: Jerusalem

first: Rami

last: Aqeilan

address: Hadassah medical school

department: Immunology and Cancer Research

country: Israel

institute: Hebrew University

description:
Library name: T47D_rep3
sBLISS

data_processing:
sBLISS fastq files are initially de-multiplexed using sample barcodes. Quality control is performed with trim galore to eliminate residual adapters, trim reads to a base quality of at least 20, and filter out short reads smaller than 20 bp. Initial and final sample qualities are assessed with fastqc. Quality-processed fastq files are aligned to the GRCh38 assembly with hisat2, then sorted and indexed using samtools. The resulting bam files are de-duplicated with umi-tools, utilizing genomic coordinates and Unique Molecular Identifiers (UMI). Custom Python and R scripts are employed to identify read start positions and convert bam files to bigwig format and BED files for downstream analysis. An additional custom R script is used to discard a blacklist of positions, primarily within centromeres.
BED format Breakome data was associated with genes  using Bedtools V2.26.0. Breaks are counted per gene based on overlapping annotations, GRCh38 gene annotations were downloaded from GENCODE
Assembly: GRCh38
Supplementary files format and content: xlsx file contains raw (non-normalized) break counts per gene per sample

extract_protocol:
sBLISS was conducted as previously described (M Bouwman, B. A. et al. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc doi:10.1038/s41596-020-0397-2., Hidmi, O., Oster, S., Shatleh, D., Monin, J. & Aqeilan, R. I. Protocol for mapping physiological DSBs using in-suspension break labeling in situ and sequencing. STAR Protoc 5, (2024).). In summary, 106 cells were fixed in 2% paraformaldehyde in 10% FCS/PBS for 10 minutes at room temperature. The fixation was quenched with 125 mM glycine for 5 minutes at room temperature, followed by another 5 minutes on ice and two washes in ice-cold PBS. Cells were lysed for 60 minutes on ice, and their nuclei were permeabilized for 60 minutes at 37°C. Next, nuclei were rinsed twice with CutSmart Buffer containing 0.1% Triton X-100 (CS/TX100), and double-strand break (DSB) ends were blunted in situ using NEB’s Quick Blunting Kit for 60 minutes at room temperature. The blunted nuclei were then washed twice with 1x CS/TX100 before in situ ligation of the sBLISS adapters to the DSB ends. Adaptor ligation was carried out with T4 DNA Ligase for 20-24 hours at 16°C, with BSA and ATP added. Following ligation, the nuclei underwent two washes with 1x CS/TX100, and genomic DNA was extracted using Proteinase K at 55°C for 14-18 hours. Proteinase K was then heat-inactivated for 10 minutes at 95°C, followed by extraction using Phenol:Chloroform:Isoamyl Alcohol, Chloroform, and ethanol precipitation.
Preparation of sBLISS libraries: The purified DNA was sonicated in 100 μL of ultra-pure water using Covaris M220 for 60 seconds. Sonicated samples were concentrated with AMPure XP beads (Beckman Coulter), and fragment sizes were evaluated using a BioAnalyzer 2100 (Agilent Technologies), targeting a range of 300 bp to 800 bp with a peak around 400-600 bp. The sonicated DNA was then in vitro transcribed using the MEGAscript T7 Kit for 14 hours at 37°C. After RNA purification and ligation of the 3’-Illumina adaptors, the RNA underwent reverse transcription. The final library indexing and amplification step was performed with NEBNext® Ultra™ II Q5® Master Mix.


title: hSTAT2 mouse, Fetal brain, ZIKV, E16.5 injection, E18.5 - 6

description: Library name: ZIKV-2582-2

value: Fetal brain

value: ZIKV-maDakar


title: hSTAT2 mouse, Weanling brain, PBS, E12.5 injection, 3W - 1

description: Library name: 4769-1


title: CCA1-ox_Shoots_Rep_2

description: Library name: OX_Sh_2


title: T47D breast cancer cells, NT, rep2

description:
Library name: T47D_rep2
sBLISS


title: 20190410_KEWCR039_CandR_OCT4_BRG1

description: Library name: Sample 11

value: hMSC

value: HA-POU5F1 transduced


title: 20190410_KEWCR043_CandR_GATA3_BRG1

description: Library name: Sample 12


title: CCA1-ox_Shoots_Rep_1

description: Library name: OX_Sh_1


title: T47D breast cancer cells, NT, rep1

description:
Library name: T47D_rep1
sBLISS


title: WT_Shoots_Rep_3

description: Library name: WT_Sh_3


title: hSTAT2 mouse, Fetal brain, ZIKV, E16.5 injection, E18.5 - 4

description: Library name: ZIKV-2560-2


title: 20190410_KEWCR037_CandR_SPI1_HA

description: Library name: Sample 10

value: HA-Tag (CST, 3724, Lot 9)

value: HA-SPI1 transduced


title: hSTAT2 mouse, Fetal brain, ZIKV, E16.5 injection, E18.5 - 5

description: Library name: ZIKV-2582-1


title: WT_Roots_Rep_2

description: Library name: WT_Rt_2

value: Root


title: MDAMB468 breast cancer cells, NT, rep3

description:
Library name: MDAMB468_rep3
sBLISS


title: WT_Shoots_Rep_2

description: Library name: WT_Sh_2


title: MDAMB468 breast cancer cells, NT, rep2

description:
Library name: MDAMB468_rep2
sBLISS


title: 20190410_KEWCR036_CandR_SPI1_BRG1

description: Library name: Sample 9


title: hSTAT2 mouse, Fetal brain, ZIKV, E16.5 injection, E18.5 - 3

description: Library name: ZIKV-2560-1


title: hSTAT2 mouse, Fetal brain, ZIKV, E16.5 injection, E18.5 - 2

description: Library name: ZIKV-2526-4


title: WT_Roots_Rep_1

description: Library name: WT_Rt_1


title: WT_Shoots_Rep_1

description: Library name: WT_Sh_1


title: MDAMB468 breast cancer cells, NT, rep1

description:
Library name: MDAMB468_rep1
sBLISS


title: 20190410_KEWCR031_CandR_SPI1_HA

description: Library name: Sample 7


title: hSTAT2 mouse, Fetal brain, PBS, E16.5 injection, E18.5 - 6

description: Library name: PBS-3287-6

value: PBS


title: genomic_DNAmethylation_CLG-5

type: genomic

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

description: Genomic DNA from CLG-5

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to the standard Illumina protocol

scan_protocol: HiScan2000 according to the standard Illumina settings

data_processing: minfi preprocessRaw function, betas extracted

label: Cy3 and Cy5

source_name: placenta (chorionic villi)

label_protocol: Standard Illumina protocol

extract_protocol: Qiagen Dneasy blood & tissue kit

value: placenta (chorionic villi)

tag: source

value: Genomic DNA from CLG-5

tag: status

value: CIUE low grade

tag: Sex

value: Female

value: NO

value: Y


title: MDAMB436 breast cancer cells, NT, rep2

description:
Library name: MDAMB436_rep2
sBLISS


title: 20190410_KEWCR033_CandR_MSC_BRG1

description: Library name: Sample 8


title: 20190410_KEWCR030_CandR_SPI1_BRG1

description: Library name: Sample 6


title: genomic_DNAmethylation_SPLA-12_v

description: Genomic DNA from SPLA-12_v

tag: tissue

value: Genomic DNA from SPLA-12_v

value: Non-CIUE

value: N


title: hSTAT2 mouse, Fetal brain, PBS, E16.5 injection, E18.5 - 5

description: Library name: PBS-3287-5

value: Fetal brain


title: 20190410_KEWCR028_CandR_GATA3_HA

description: Library name: Sample 5

tag: cell line

value: HA-GATA3 transduced


title: MDAMB436 breast cancer cells, NT, rep1

description:
Library name: MDAMB436_rep1
sBLISS


title: genomic_DNAmethylation_NP-9_v

description: Genomic DNA from NP-9_v

value: Genomic DNA from NP-9_v


title: genomic_DNAmethylation_NP-8

description: Genomic DNA from NP-8

value: Genomic DNA from NP-8

value: Male


title: hSTAT2 mouse, Fetal brain, PBS, E16.5 injection, E18.5 - 3

description: Library name: PBS-2646-2


title: genomic_DNAmethylation_SPLA-11_v

description: Genomic DNA from SPLA-11_v

value: Genomic DNA from SPLA-11_v


title: 20190410_KEWCR027_CandR_GATA3_BRG1

description: Library name: Sample 4

value: hMSC

tag: chip antibody


title: hSTAT2 mouse, Fetal brain, PBS, E16.5 injection, E18.5 - 4

description: Library name: PBS-2646-6

tag: treatment

value: PBS


title: MCF10a non-malignant cells, NT, rep1

description:
Library name: MCF10a_rep1
sBLISS


title: genomic_DNAmethylation_CLG-7_v

description: Genomic DNA from CLG-7_v

value: placenta (chorionic villi)

value: Genomic DNA from CLG-7_v

value: YES


title: hSTAT2 mouse, Fetal brain, PBS, E16.5 injection, E18.5 - 2

description: Library name: PBS-2453-4


title: genomic_DNAmethylation_CHG-13_v

description: Genomic DNA from CHG-13_v

value: Genomic DNA from CHG-13_v

value: CIUE high grade

value: Female


title: MCF7 breast cancer cells, NT, rep4

description:
Library name: MCF7_rep4
sBLISS


title: 20190410_KEWCR021_CandR_HOXA9_BRG1

description: Library name: Sample 2

value: HA-HOXA9 transduced


title: hSTAT2 mouse, Fetal brain, ZIKV, E16.5 injection, E18.5 - 1

description: Library name: ZIKV-2526-1

value: ZIKV-maDakar


title: 20190213_KEW001_CandR_MSC_BRG1

description: Library name: Sample 1

value: SMARCA4 (Abcam, 110641)


title: hSTAT2 mouse, Fetal brain, PBS, E16.5 injection, E18.5 - 1

description: Library name: PBS-2453-1

value: Fetal brain


title: genomic_DNAmethylation_CHG-14_v

description: Genomic DNA from CHG-14_v

value: Genomic DNA from CHG-14_v

value: NO

value: Y


title: MDAMB436 breast cancer cells, NT, rep3

description:
Library name: MDAMB436_rep3
sBLISS


title: ST-HSC, scRNA-seq

city: Stanford

first: Irving

last: Weissman

address: 265 Campus Dr.

department: Stem Cell Institute

institute: Stanford University

description: 10x genomics

data_processing:
The data processing was done using the Cell Ranger V7.2
Assembly: mm10
Supplementary files format and content: Tab-separated valued files and matrix files

source_name: Bone marrow

extract_protocol:
Hematopoietic stem cells were isolated from wild-type mouse bone marrow
Sequence library was prepared through 10X Genomic 3' v2

value: Bone marrow

tag: strain

value: HSCs

value: WT

tag: group

value: ST-HSC


title: MCF7 breast cancer cells, NT, rep2

description:
Library name: MCF7_rep2
sBLISS


title: genomic_DNAmethylation_SPLN-18_v

description: Genomic DNA from SPLN-18_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-18_v

value: Non-CIUE

value: Male

value: N


title: MCF7 breast cancer cells, NT, rep1

description:
Library name: MCF7_rep1
sBLISS


title: LT-HSC, scRNA-seq

description: 10x genomics

value: LT-HSC


title: genomic_DNAmethylation_CLG-9_v

description: Genomic DNA from CLG-9_v

value: Genomic DNA from CLG-9_v

value: CIUE low grade

value: YES


title: Cobetia marina sp MM1IDA2H-1 growth at 41°C Replicate 3

city: Valparaíso

first: M.

middle: Alejandro

last: Dinamarca

state: Valparaíso

address: Gran Bretaña 1093

department: Centro de Micro-Bioinnovaci{on

country: Chile

institute: Universidad de Valparaíso

data_processing:
Quality control and adapter trimming was performed with bcl-convert (v. 4.2.4; default parameters). Read mapping was performed with HISAT2 (v. 2.2.0; default parameters + ‘--very-sensitive’). Read quantification was performed using Subread`s  featureCounts (v. 2.0.6; default parameters + ‘-Q 20’)  functionality. Read counts were normalized usingedgeR’s (v. 4.0.2) Trimmed Mean of M values (TMM) algorithm, using default parameters. Subsequent values were then converted to counts per million (CPM). Differential expression analysis was performed using edgeR’s (v. 1.14.5) glmQLFTest, with default parameters. The file “All Quantified Genes.tsv” contains the results of the glmQLFTest for all genes in addition to the normalized counts per million. The differentially expressed gene’s normalized counts per million were then used to create a heatmap. The PCA is based on the global expression of all genes. Finally, pathway analysis was performed using limma’s (v. 3.44.3) “kegga” functionality, using default parameters. The genes that were considered Up/Down in this analysis were at Benjamini-Hochberg adjusted p-value < . 05.
Assembly: ASM172048v1r
Supplementary files format and content: The processed file iare in "tsv" format and contain The file “All Quantified Genes.tsv” contains the results of the glmQLFTest for all genes in addition to the normalized counts per million

organism: Cobetia marina

source_name: Bacterial cell

extract_protocol:
For Total RNA extraction, cells were harvested by centrifugation and RNA was extracted using EZNA Total RNA Kit I according to manufacturer´s instructions
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices

value: Bacterial cell


title: genomic_DNAmethylation_CHG-18_v

description: Genomic DNA from CHG-18_v

value: Genomic DNA from CHG-18_v

value: CIUE high grade

value: Female


title: PBMCs, Day 0, ATAC individual 45

city: Olsztyn

first: Maciej

last: Rybiński

state: Warmian-Masurian Voivodeship

address: Trylińskiego 18

institute: Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences.

description: Library name: Ind45d0

data_processing:
ATAC-seq: Paired-end reads were aligned using the STAR aligner. ENCODE-identified blacklisted regions and reads with mapping quality score < 2 were filtered out. Duplicates were identified and marked with samtools markdup. Peak calling done with MACS3 (version 3.0.1) utilizing callpeak function with the parameters --f BAMPE --verbose 3 --shift 0 -g hs -q 0.01 -B. Consensus peak summits matrix generated with DiffBind utilizing dba.count function with summits parameter set to 75.
Assembly: GRCh38.p14
Supplementary files format and content: Cohort_Consensus.csv - Matrix of raw values corresponding to each specific peak summit (rows) across all samples (columns) generated by DiffBind.

source_name: peripheral blood

extract_protocol:
ATAC-seq: nuclei were isolated from 100,000 PBMCs by incubation in 50 µl lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20; 0.1% IGEPAL CA-630; 0.01% digitonin). After 3 minutes on ice, 1 ml wash buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20) was added. Nuclei were pelleted and subjected to transposition using a Tn5 transposase reaction mix (Illumina), supplemented with 0.01% digitonin and 0.1% Tween-20. The transposition reaction was carried out at 37 °C for 30 minutes in a thermomixer. Transposed DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research), followed by PCR amplification, purification, and size selection with SPRISelect beads (Beckman Coulter). Library quality was assessed using an Agilent TapeStation. Indexed libraries were quantified, pooled, and prepared for sequencing.
ATAC-seq  libraries were sequenced paired-end on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).

treatment_protocol: Peripheral blood samples were obtained from 38 healthy adults enrolled in the VitDPAS trial (ClinicalTrials.gov Identifier: NCT06104111). The study protocol was approved by the Ethics Committee of the Olsztyn Chamber of Doctors (#31/2023/VIII).

value: peripheral blood

value: PBMC

value: monocytes, T and B cells

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: MCF10a non-malignant cells, NT, rep2

description:
Library name: MCF10a_rep2
sBLISS


title: 20190410_KEWCR022_CandR_HOXA9_HA

city: Boston

first: Cigall

last: Kadoch

address: 440 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: Sample 3

value: hMSC

value: HA-Tag (CST, 3724, Lot 9)

value: HA-HOXA9 transduced


title: PBMCs, Day 1, ATAC individual 44

description: Library name: Ind44d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: PBMCs, Day 0, ATAC individual 44

description: Library name: Ind44d0


title: HMLE non-malignant cells, NT, rep3

description:
Library name: HMLE_rep3
sBLISS

source_name: HMLE

value: HMLE


title: HMLE non-malignant cells, NT, rep4

description:
Library name: HMLE_rep4
sBLISS


title: Cobetia marina sp MM1IDA2H-1 growth at 41°C Replicate 2


title: genomic_DNAmethylation_SPLA-13_v

description: Genomic DNA from SPLA-13_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLA-13_v

value: Non-CIUE

value: Male

value: NO

value: Y

value: partial T1 due to t(1;10)


title: Cobetia marina sp MM1IDA2H-1 growth at 41°C Replicate 1

value: Bacterial cell


title: PBMCs, Day 1, ATAC individual 43

description: Library name: Ind43d1

value: peripheral blood


title: HMLE non-malignant cells, NT, rep2

description:
Library name: HMLE_rep2
sBLISS


title: Cobetia marina sp MM1IDA2H-1 growth at 38°C Replicate 3


title: genomic_DNAmethylation_CHG-4_v

description: Genomic DNA from CHG-4_v

value: Genomic DNA from CHG-4_v

value: CIUE high grade

value: Female

value: YES

value: N


title: genomic_DNAmethylation_SPLN-9_v

description: Genomic DNA from SPLN-9_v

value: Genomic DNA from SPLN-9_v


title: HMLE non-malignant cells, NT, rep1

description:
Library name: HMLE_rep1
sBLISS


title: Cobetia marina sp MM1IDA2H-1 growth at 38°C Replicate 2


title: MCF7 breast cancer cells, NT, rep3

description:
Library name: MCF7_rep3
sBLISS


title: DKAT breast cancer cells, NT, rep3

description:
Library name: DKAT_rep3
sBLISS

source_name: DKAT

value: DKAT