title: Single sgRNA target S11_rep2

description:
Library name: S11_rep2
Alias column: S11_rep2
SIQ outcomes for single-sgRNA sites.xlsx

data_processing:
All sequencing data for single-sgRNA groups were generated in-house, except for samples S12, which were sourced from published paper. In house scripts were developed to extract NGS reads containing target-specific primer sequences. Quality filtering was performed using Trimmomatic (v0.39) with the parameter AVGQUAL:30 to eliminate low-quality reads. In instances where paired reads exhibited significant quality disparities, only the higher-quality end was retained. The processed reads were then analyzed using SIQ (v1.3) through a two-stage workflow: (i) merging overlapping paired-end reads and (ii) aligning the merged consensus sequences to target references for variant detection, utilizing default parameters (Min support: 2; Max base error: 0.08; TINS search distance: 100). While most analyses relied on paired-end data, single-end processing was employed in three specific scenarios: (i) when targets exceeded 300 bp, (ii) in cases of insufficient merge efficiency, or (iii) due to substantial quality discordance between read pairs (Supplementary Table 2).
All sequencing data for dual-sgRNA groups were generated in-house, except for samples D5 and D32, which were sourced from published paper. For data analysis, primer-specific reads were extracted and quality control was performed on the NGS data for each dual-sgRNA site (Supplementary Table 1), following the same workflow applied to single-sgRNA sites. Next, a two-stage alignment approach, adapted from Chakrabarti et al, was implemented. In the initial stage, reads were aligned to the reference genome using BBMap (v39.01). During this phase, reads that aligned as proper pairs were discarded, and only the remaining reads were retained for further analysis using Samtools (v1.6). In the second stage, these remaining reads were aligned to the reference genome using BBMap (v39.01) with a threshold that permitted indels of up to 3000 bp. Finally, unmapped reads and secondary alignments were filtered out utilizing Samtools (v1.6) and Sambamba (v1.0.0). Indels were detected and characterized using R scripts adapted from Chakrabarti et al., with positions and lengths determined through CIGAR string parsing. For each target's two cut sites (3 bp upstream of NGG PAMs), indels overlapping the ±10 bp window surrounding either cut site were analyzed. Reads containing these indels were classified as edited reads and were categorized into three types: type 1, which includes indels spanning the windows of both cut sites; type 2, consisting of indels that overlap the window of only one cut site; and type 3, involving concurrent indels that overlap the windows of both cut sites without spanning. Type 1 is prioritized over the other types. Unedited reads were defined as: (i) quality-trimmed reads before alignment, excluding the remaining reads from the initial alignment, and (ii) reads whose indels fell completely outside both cut site windows. For type 1 analysis, type 1 reads were extracted to SIQ (v1.3) and precisely ligated sequences were utilized as references to explore the accurate ligation (Supplementary Table 2).
Assembly: Target sequences (Supplementary Table 1)
Supplementary files format and content: Table S3. SIQ outcomes for single-sgRNA sites.xlsx is the indel profiles for GSM9129596 to GSM9129681.
Supplementary files format and content: Table S5. SIQ outcomes for dual-sgRNA sites is the indel profiles for GSM9129682 to GSM9129779.
Supplementary files format and content: Table S8. SIQ outcomes for AAV dose groups is the indel profiles for GSM9129780 to GSM9129797.
Supplementary files format and content: Table S9. SIQ outcomes for in vivo perturbation is the indel profiles for GSM9129798 to GSM9129853.

extract_protocol:
MuSCs were isolated by fluorescence-activated cell sorting (FACS) based on established protocols. Briefly, hindlimb muscles from Pax7Cas9 mice were collected and digested with collagenase II (1000 U/ml; Worthington) for 90 minutes at 37°C. The tissue suspension was then washed in washing medium [Ham’s F-10 medium (Sigma-Aldrich), 10% heat-inactivated horse serum (HIHS) (Gibco), penicillin/streptomycin (1×, Gibco)]. MuSCs were further liberated by collagenase II (1000 U/ml) and dispase (11 U/ml) treatment for 40 minutes at 37°C. Mononuclear cells were filtered through a 40 μm cell strainer, and GFP+ MuSCs were sorted using a BD FACSAria Fusion cell sorter (BD Biosciences).
Genomic DNA from MuSCs infected with AAV9-sgRNA or AAV9-dual sgRNA was amplified using the Q5 High-Fidelity 2× Master Mix (NEB). PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and subjected to library preparation with the NEBNext® Ultra™ II DNA Library Preparation Kit (NEB). Barcoded libraries were pooled and sequenced on the Illumina HiSeq 1500 platform.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 19

status: Public on Apr 23 2026

type: SRA

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: TKI_IO_pre_19
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

library_source: transcriptomic

data_processing:
RNA-seq sequencing reads were aligned against human genome assembly hg19 by STAR 2-pass alignment. Gene level raw read count values were computed by using the R package GenomicAlignments over aligned reads with UCSC KnownGene in hg19 as the base gene model. The Union counting mode was used and only mapped paired reads after alignment quality filtering were considered. Finally, gene level FPKM (Fragments Per Kilobase Million) values were computed by the R package DESeq2. Batch corrected FPKM expression matrix was derived by the ComBat function implemented by the R package sva.
Assembly: hg19
Supplementary files format and content: Tab-delimited files including raw count file, FPKM count file, and batch-corrected FPKM count file

molecule: total RNA

organism: Homo sapiens

source_name: primary tumor

extract_protocol:
For snap frozen tissues, 20-30mg frozen tissue was homogenized in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from the aqueous phase using the miRNeasy Micro or Mini Kit (Qiagen catalog # 217084/217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol with 350 µL input. Samples were eluted in 15-16 µL RNase-free water. For FFPE tissues, sections were deparaffinized using the mineral oil method. Briefly, 800µL mineral oil was mixed with the sections and the sample was incubated at 65°C for 10 minutes. Phases were separated by centrifugation in 360µL Buffer PKD and Proteinase K was added for digestion. After a three-step incubation (65°C for 45’, 80°C for 15’, 65°C for 30’) and additional centrifugation, the aqueous phase containing RNA was removed and DNase treated. The RNA was then extracted using the RNeasy FFPE Kit (QIAGEN catalog # 73504) according to the manufacturer’s instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 432ng-1µg of total RNA with DV200 values from 24-83% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR.

tag: tissue

value: primary tumor

tag: histopathology

value: clear cell renal cell carcinoma

tag: first-line treatment

value: Lenvatinib + Pembrolizumab

tag: tumor grade

tag: batch


title: Primary Schlemm's canal cells, siControl, replicate 1

city: Chicago

first: Benjamin

middle: R

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

description: Library name: S68SC-siCtr-1

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: tab-delimited text file with raw counts for each sample, generated with htseq

source_name: Schlemm's canal endothelium

extract_protocol:
Total RNA was isolated using the RNEasy Mini Kit (Qiagen) according to manufacturer's directions
Libraries were generated by the NUSeq core at Northwestern University using the Illumina TruSeq kit

value: Schlemm's canal endothelium

tag: cell line

tag: cell type

value: Primary human endothelial cells

tag: treatment

value: siControl


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 20

description:
Library name: TKI_IO_pre_20
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S9_rep1

city: Hong Kong

first: Yang

last: Fu

address: Prince of Wales Hospital, N.T, H.K, 32 Ngan Shing St, Sha Tin

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: S9_rep1
Alias column: S9_rep1
SIQ outcomes for single-sgRNA sites.xlsx

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: skeletal muscle

value: skeletal muscle

tag: strain

tag: age

value: 6 weeks

tag: sample group

value: Single sgRNA target


title: Primary Schlemm's canal cells, siPROX1, replicate 2

description: Library name: S68SC-siPROX1-2


title: Single sgRNA target S9_rep2

description:
Library name: S9_rep2
Alias column: S9_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S10_rep1

description:
Library name: S10_rep1
Alias column: S10_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 17

description:
Library name: TKI_IO_pre_17
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K4me2_30min(biol rep2)_ChIP-Seq

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description: Library name: H3K4me2_30min_2

data_processing:
Read adapters trimmed with Cutadapt v1.18  --minimum-length 20  --nextseq-trim=20
Alignment to Chicken T2T genome GCA_024206055.2 with BWA-MEM v0.7.16 and -M parameter
Alignment to Chicken T2T genome GCA_024206055.2 with BWA-MEM v0.7.16 and -M parameter
Removal of secondary (0x100), supplementary (0x800), and unmapped (0x4) reads (-F 2304), retention of properly paired reads (-f 3)
BigWig tracks were generated using deepTools v3.5.0 bamCoverage to compute normalised coverage in bins of 1 bp using the BPM (bins per million reads) method.
Assembly: GCA_024206055.2
Supplementary files format and content: bigWig of read coverage

organism: Gallus gallus

source_name: Bursa

growth_protocol: RPMI1640, 10% FBS, 1% Chicken serum. Cells were culutured at 39C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenchng and cell lysis, chromatin was shear using Diagenode Biorupter.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) according to the manufacturer’s protocol. The library size distribution was analysed by Agilent Bioanalyzer with High Sensitivity DNA chip and submitted for Illumina deep sequencing (100 bp pair-end) at the Edinburgh Clinical Research Facility. Sequencing was performed on the NextSeq 2000 platform using the NextSeq 1000/2000 P2 Reagents (100 cycles).

treatment_protocol: Cells were blocked at G2 with 1NMPP1 (G2). After 1NMPP1 washout, cells were collected at 5 min, 7.5 min, 15 min and 30 min.

tag: antibody

value: Bursa

value: lymphoblast

tag: time


title: Single sgRNA target S11_rep1

description:
Library name: S11_rep1
Alias column: S11_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: Primary Schlemm's canal cells, siControl, replicate 2

description: Library name: S68SC-siCtr-2


title: WT_CDK1as_H3K4me2_7.5min(biol rep2)_ChIP-Seq

description: Library name: H3K4me2_7.5min_2


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 15

description:
Library name: TKI_IO_pre_15
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S8_rep2

description:
Library name: S8_rep2
Alias column: S8_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 14

description:
Library name: TKI_IO_pre_14
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K4me2_7.5min(biol rep1)_ChIP-Seq

description: Library name: H3K4me2_7.5min_1


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 13

description:
Library name: TKI_IO_pre_13
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S7_rep2

description:
Library name: S7_rep2
Alias column: S7_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me2_5min(biol rep1)_ChIP-Seq

description: Library name: H3K4me2_5min_1


title: Single sgRNA target S8_rep1

description:
Library name: S8_rep1
Alias column: S8_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me2_G2(biol rep2)_ChIP-Seq

description: Library name: H3K4me2_G2_2


title: Single sgRNA target S7_rep1

description:
Library name: S7_rep1
Alias column: S7_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CRISPRaSEC_S046_plasmid

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: UCSF Gladstone Institutes

description:
Library name: CRISPRaSEC_S046_plasmid
Sequencing of pooled sgRNA plasmid library.

library_source: other

data_processing:
Demultiplexed FASTQ files were processed to quantify sgRNA read counts per sample by aligning reads to the relevant sgRNA reference library.
For each screen, sgRNA count tables were generated (rows = sgRNAs; columns = samples) and used as input for downstream statistical testing.
Differential sgRNA and gene enrichment between paired conditions (e.g., GFP-positive vs GFP-negative; marker-high vs marker-low) was computed using MAGeCK (RRA).
Statistical outputs include gene-level and sgRNA-level summary tables containing effect direction, p-values, and FDR for each comparison.
Assembly: Not applicable (sgRNA amplicon sequencing; reads aligned to sgRNA reference libraries, not to a genome)
Supplementary files format and content: Processed files include tab-delimited sgRNA count matrices for each screen and corresponding sgRNA library annotation files mapping sgRNA IDs/sequences to target genes.
Supplementary files format and content: MAGeCK output tables are provided at both gene and sgRNA resolution for all genome-wide and secondary CRISPRn/CRISPRa screens, including p-values and FDR as reported by MAGeCK.

molecule: other

organism: synthetic construct

source_name: plasmid library

growth_protocol: Primary human CD4+ T cells were isolated from healthy donor leukopaks by negative selection and cultured in complete RPMI. Cells were activated with anti-CD3/CD28 stimulation prior to pooled screen transduction and infection.

extract_protocol:
After sorting, cell pellets were processed for genomic DNA extraction. Integrated sgRNA cassettes were PCR-amplified from genomic DNA for next-generation sequencing.
sgRNA amplicons were generated by PCR, purified, pooled, and sequenced on Illumina instruments as single-end reads.

treatment_protocol: Activated CD4+ T cells transduced with pooled CRISPR knockout (CRISPRn) or CRISPR activation (CRISPRa) libraries were challenged with replication-competent GFP-reporter HIV. For secondary screens, additional conditions included different HIV inoculum concentrations, VSV-G pseudotyped HIV-GFP, and FACS-based marker assays (e.g., CD4, CXCR4, CD25, CD69). Cells were sorted into the indicated bins (e.g., GFP-positive/GFP-negative or marker-high/marker-low) for sequencing-based quantification of sgRNA representation.

value: plasmid library

value: plasmid DNA library sequencing

value: CRISPRa-secondary


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 11

description:
Library name: TKI_IO_pre_11
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

source_name: metastatic tumor

value: metastatic tumor


title: CRISPRnSEC_S040_plasmid

description:
Library name: CRISPRnSEC_S040_plasmid
Sequencing of pooled sgRNA plasmid library.

value: CRISPRn-secondary


title: 786-O,PDT_3

city: Tianjin

first: jianqiao

last: Li

address: No. 23 Pingjiang Road, Hexi District, Tianjin

country: China

institute: The Second Hospital of Tianjin Medical University

description: Library name: Sample 6

data_processing:
Raw sequencing reads were subjected to quality control to remove adapter sequences, reads containing poly-N, and low-quality reads, and clean reads were obtained for subsequent analysis.
Clean reads were aligned to the human reference genome (GRCh38/hg38).
Gene expression levels were quantified based on the mapped reads, and raw read count values for each gene were generated.
Gene expression values were normalized and presented as TPM and/or FPKM values for each sample.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample.

growth_protocol: 786-O renal cell carcinoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37°C. Cells were maintained under standard cell culture conditions and passaged when they reached approximately 80-90% confluence.

extract_protocol:
Total RNA was isolated from treated 786-O cells using TRIzol reagent following the manufacturer's instructions. RNA quality, concentration, and purity were evaluated before subsequent library preparation and RNA-seq analysis.
RNA-seq library construction was performed by Sangon Biotech (Shanghai, China) according to their standard library preparation protocol. Total RNA samples that passed quality control were used for cDNA library preparation and subsequent high-throughput sequencing.

treatment_protocol: 786-O renal cell carcinoma cells were seeded and cultured to the appropriate confluence before treatment. Cells in the Dark group were incubated with DTP at the indicated concentration and kept in the dark without laser exposure. Cells in the PDT group were incubated with the same concentration of DTP and then irradiated with a 650 nm diode laser at the indicated energy density. Following treatment, cells were further incubated for the indicated time and then harvested for total RNA extraction.

value: Kidney cancer cells

value: PDT


title: Single sgRNA target S6_rep1

description:
Library name: S6_rep1
Alias column: S6_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 9

description:
Library name: TKI_IO_pre_9
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: primary tumor

value: clear cell renal cell carcinoma


title: Single sgRNA target S6_rep2

description:
Library name: S6_rep2
Alias column: S6_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 10

description:
Library name: TKI_IO_pre_10
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Lenvatinib + Pembrolizumab


title: WT_CDK1as_H3K4me2_5min(biol rep2)_ChIP-Seq

description: Library name: H3K4me2_5min_2


title: WT_CDK1as_H3K4me1_30min(biol rep1)_ChIP-Seq

description: Library name: H3K4me1_30min_1


title: 786-O,PDT_1

description: Library name: Sample 4


title: Single sgRNA target S5_rep2

description:
Library name: S5_rep2
Alias column: S5_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 8

description:
Library name: TKI_IO_pre_8
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 12

description:
Library name: TKI_IO_pre_12
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: 786-O,PDT_2

description: Library name: Sample 5


title: WT_CDK1as_H3K4me2_G2(biol rep1)_ChIP-Seq

description: Library name: H3K4me2_G2_1


title: WT_CDK1as_H3K4me1_15min(biol rep2)_ChIP-Seq

description: Library name: H3K4me1_15min_2


title: 786-O,Dark_3

description: Library name: Sample 3

value: Dark


title: Single sgRNA target S5_rep1

description:
Library name: S5_rep1
Alias column: S5_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 7

description:
Library name: TKI_IO_pre_7
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: 105_Dox

type: RNA

city: Kobe

first: Junji

last: Otani

state: Hyogo

address: Kusunoki-cho 7-5-1, Chuo-ku

department: Department of Medicine

country: Japan

institute: Kobe university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: DKO cells cultured with Dox

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: H1299 cells were cultured in RPMI-1640 medium supplemented with 10% FBS in 5% CO2 at 37C.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: 1 ug/ml Dox for 48h


title: WT_CDK1as_H3K4me1_30min(biol rep2)_ChIP-Seq

description: Library name: H3K4me1_30min_2


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 6

description:
Library name: TKI_IO_pre_6
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Axitinib + Pembrolizumab


title: Single sgRNA target S4_rep2

description:
Library name: S4_rep2
Alias column: S4_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle


title: WT_CDK1as_H3K4me1_15min(biol rep1)_ChIP-Seq

description: Library name: H3K4me1_15min_1


title: Single sgRNA target S4_rep1

description:
Library name: S4_rep1
Alias column: S4_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks


title: 786-O,Dark_2

description: Library name: Sample 2


title: 786-O,Dark_1

description: Library name: Sample 1


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 5

description:
Library name: TKI_IO_pre_5
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Axitinib + Avelumab


title: Single sgRNA target S3_rep2

description:
Library name: S3_rep2
Alias column: S3_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: Single sgRNA target


title: WT_CDK1as_H3K4me1_7.5min(biol rep1)_ChIP-Seq

description: Library name: H3K4me1_7.5min_1

value: Bursa

value: lymphoblast


title: WT_CDK1as_H3K4me1_7.5min(biol rep2)_ChIP-Seq

description: Library name: H3K4me1_7.5min_2


title: WT Bmem (4wk)-rep3

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: B3_S7
Column name in raw counts table salmon_gene_counts.txt: B1-S7

data_processing:
RNA-sequencing data was aligned to  mouse (Mus musculus) reference genome (GRCm39) using STAR aligner (version 2.7.10a) with default parameters
Raw FASTQ files were quality-checked using FastQC, and low-quality reads and adapter sequences were trimmed using Trimmomatic.
Normalized gene counts (DeSeq2) were used to determine differentially expressed genes (DESeq2 v.1.26.0)
mm10
Assembly: GRCm38 - mm10
Supplementary files format and content: tab-delimited file includes raw gene counts for each sample

source_name: Spleen

extract_protocol:
Sorted cells were lysed in TRIzol and total RNA isolated using the miRNeasy Micro Kit (#217084, Qiagen), following the manufacturer’s instructions. The isolated RNA was further processed using the Monarch RNA Cleanup kit 10ug (New England BioLabs Inc #T2050L).
Libraries were prepared from 0.5ng of total RNA using the Takara Bio SMART-Seq v4 PLUS Kit (Takara Bio R400753) following the manufacturer’s instructions.

treatment_protocol: Adoptive B cell co-transfer into CD45.1/2 recipient mice 1 day prior to immunization (1:! Mix of CD45.1 WT B cells and CD45.2 DAF KO B cells). Memory B cells isolated from splenic B cell fraction via flow sorting based on surface markers and antigen binding (NP), 4 weeks post-immunization with NP-OVA antigen (i.p.)

value: Spleen

value: Memory B cell

tag: genotype

value: Wildtype

value: NA (flow-sorted)


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 3

description:
Library name: TKI_IO_pre_3
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Cabozantinib + Nivolumab


title: 105

source_name: DKO cells cultured without Dox


title: WT Bmem (4wk)-rep1

description:
Library name: B1_S5
Column name in raw counts table salmon_gene_counts.txt: B1-S5


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 2

description:
Library name: TKI_IO_pre_2
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 1

description:
Library name: TKI_IO_pre_1
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K4me1_5min(biol rep2)_ChIP-Seq

description: Library name: H3K4me1_5min_2


title: DAF KO Bmem (4wk)-rep3

description:
Library name: A3_S3
Column name in raw counts table salmon_gene_counts.txt: A1_S3

value: DAF/CD55 KO


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 4

description:
Library name: TKI_IO_pre_4
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: primary tumor


title: Single sgRNA target S2_rep1

description:
Library name: S2_rep1
Alias column: S2_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me1_G2(biol rep2)_ChIP-Seq

description: Library name: H3K4me1_G2_2


title: WT_CDK1as_H3K4me1_5min(biol rep1)_ChIP-Seq

description: Library name: H3K4me1_5min_1


title: DAF KO Bmem (4wk)-rep2

description:
Library name: A2_S2
Column name in raw counts table salmon_gene_counts.txt: A1_S2


title: Single sgRNA target S3_rep1

description:
Library name: S3_rep1
Alias column: S3_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S1_rep2

description:
Library name: S1_rep2
Alias column: S1_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: GBe11s25

status: Public on Apr 22 2026

city: Seattle

first: Jay

last: Sarthy

state: WA

address: 1920 Terry Ave

department: Ben Towne Center for Childhood Cancer Research

institute: Seattle Children's Research Institute

description: Library name: Sample 11

data_processing:
ATAC-seq 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. 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 and binding 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.
Assembly: GRCh38
Supplementary files format and content: ATAC-seq bigWig files give the normalized coverage of chromatin accessibility across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).

source_name: WSU-AML

growth_protocol: M-07e cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS, 1X GlutaMAX (Gibco), and 10 ng/mL recombinant human IL-3 (STEMCELL Technologies). Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
1×10⁶ cells per replicate were washed in cold PBS and processed for ATAC-seq using the Active Motif ATAC-seq Kit (Cat. No. 53150) according to the manufacturer's protocol. Briefly, nuclei were isolated, and chromatin was tagmented with the kit-supplied Tn5 transposase. Tagmented DNA was purified and used directly for library amplification.
ATAC-seq libraries were prepared and sequenced in-house using the Active Motif ATAC-seq Kit (Cat. No. 53150). Paired-end sequencing was performed on an Illumina instrument.

treatment_protocol: M-07e cells were treated with 100 nM FHD-286 (SMARCA2/4 ATPase inhibitor) for 24 or 48 hours, or with DMSO vehicle control, as indicated in sample metadata.

value: WSU-AML


title: WT_CDK1as_H3K4me1_G2(biol rep1)_ChIP-Seq

description: Library name: H3K4me1_G2_1


title: Single sgRNA target S2_rep2

description:
Library name: S2_rep2
Alias column: S2_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: human cortical organoid

city: Daejon

first: Eunjoon

last: Kim

address: KAIST, Kuseong-dong, Yuseong-ku

department: Dept of biological sciences

country: South Korea

institute: IBS

description:
Library name: HN00230676
10x genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing reads were processed using Cell Ranger (version 8.0.1). The reference mouse genome index was built using the GRCh38 human reference genome assembly. Single cell RNA-seq data QC and analysis was performed mainly using Seurat (5.2.0).
Assembly: GRCh38 human reference genome assembly
Supplementary files format and content: Tab-seperated values files and matrix files; filtered_feature_bc_matrix

source_name: cortical organoid

extract_protocol:
Organoids were dissociated in Papain-based dissociation media. Dissociated cells were filtered, and washed with HBSS. Cell viability were analyzed using Trypan Blue assay and automated cell counter Countess (Thermo Fisher).
library was performed according to the manufacter's instructions (Chromium Next GEM Single Cell 3p RNA library v3.1, 10x genomics)

value: cortical organoid


title: DAF KO Bmem (4wk)-rep1

description:
Library name: A1_S1
Column name in raw counts table salmon_gene_counts.txt: A1_S1


title: WT Bmem (4wk)-rep2

description:
Library name: B2_S6
Column name in raw counts table salmon_gene_counts.txt: B1-S6


title: FK4

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

hyb_protocol: Configuration A

data_processing:
Data was exported using AtoMx, and imported into an anndata object using squidpy
Matrix value are total counts per cell for each gene

source_name: Fetal Kidney

extract_protocol: FFPE sections were cut at 5 micron thickness and prepared per CosMx protocol.

tag: gestational age


title: GBe11s9

description: Library name: Sample 10


title: FK1


title: GBe11s22

description: Library name: Sample 9

value: DMSO


title: GBe11s18

description: Library name: Sample 6


title: GBe11s17

description: Library name: Sample 5


title: HK2524


title: Single sgRNA target S1_rep1

description:
Library name: S1_rep1
Alias column: S1_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: GBe11s10

description: Library name: Sample 7


title: GBe11s21

description: Library name: Sample 8


title: GBe11s14

description: Library name: Sample 2


title: GBe11s3

description: Library name: Sample 3


title: SKe2s21

description: Library name: Sample 21

data_processing:
RNA-seq reads were trimmed using TrimGalore v0.6.10 (cutadapt v4.9) and ribosomal RNA reads were removed using SortMeRNA v4.3.7 (nf-core/rnaseq v3.21.0). Reads were aligned to the GRCh38/hg38 reference genome using STAR v2.7.10a and quantified at the gene level using Salmon v1.10.3 (star_salmon workflow). Gene-level counts were imported using tximeta v1.20.1/tximport.
Differential expression analysis was performed using DESeq2 v1.40 with median-of-ratios size-factor normalization. Results for each contrast (treatment vs. DMSO) were extracted using Wald statistics with LFC shrinkage via ashr. DEG thresholds: |log2FoldChange| >= 1 and BH-adjusted p-value < 0.05.
Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler v4.8 with genes ranked by DESeq2 Wald statistic. MSigDB Hallmark (H) and C2 curated (Reactome, KEGG, WikiPathways) gene sets were tested (minGSSize = 5, maxGSSize = 500, eps = 0, seed = 2110; BH FDR < 0.25). Re-analysis of published cord blood RNA-seq data (Le et al. 2022; GEO: GSE181726) comparing CBFA2T3-GLIS2 transduced vs. GFP control cells used the same DESeq2 pipeline.
Assembly: GRCh38
Supplementary files format and content: Per-sample STAR ReadsPerGene count tables (unstranded column) generated using STAR v2.7.10a with GENCODE v46 GRCh38 annotations. Rows are gene IDs, values are read counts mapped to exons per gene.

molecule: polyA RNA

growth_protocol: M-07e cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS, 1X GlutaMAX (Gibco), and 10 ng/mL recombinant human IL-3 (STEMCELL Technologies). WSU-AML cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS and 1X GlutaMAX (Gibco). All cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted from drug-treated cells using the RNeasy Mini Kit (Qiagen, Cat. No. 74104) according to the manufacturer's protocol.
RNA-seq libraries were prepared and sequenced by Novogene. Strand-specific polyA-selected libraries were sequenced paired-end on an Illumina NovaSeq X instrument.

treatment_protocol: Cells were treated with FHD-286 (SMARCA2/4 ATPase inhibitor; provided by Foghorn Therapeutics) at 1 nM, 10 nM, or 100 nM; Palbociclib (CDK4/6 inhibitor; MedChem, HY-50767); or FHD-286 and Palbociclib in combination for 48 hours. DMSO vehicle controls were included in parallel for each treatment condition.

value: Palbociclib


title: SKe2s24

description: Library name: Sample 24

value: Palbociclib and FHD-286 Combination


title: SKe2s23

description: Library name: Sample 23


title: SKe2s22

description: Library name: Sample 22


title: GBe11s13

description: Library name: Sample 1


title: SKe2s19

description: Library name: Sample 19


title: SKe2s20

description: Library name: Sample 20


title: SKe2s18

description: Library name: Sample 18


title: SKe2s17

description: Library name: Sample 17


title: SKe2s14

description: Library name: Sample 14


title: GBe11s4

description: Library name: Sample 4


title: SKe2s09

description: Library name: Sample 9


title: SKe2s12

description: Library name: Sample 12


title: SKe2s06

description: Library name: Sample 6


title: SKe2s08

description: Library name: Sample 8


title: SKe2s11

description: Library name: Sample 11


title: SKe2s10

description: Library name: Sample 10


title: SKe2s04

description: Library name: Sample 4


title: SKe2s15

description: Library name: Sample 15


title: SKe2s05

description: Library name: Sample 5


title: SKe2s07

description: Library name: Sample 7


title: SKe2s13

description: Library name: Sample 13


title: SKe2s02

description: Library name: Sample 2


title: SKe2s16

description: Library name: Sample 16


title: SKe2s01

description: Library name: Sample 1


title: SKe2s03

description: Library name: Sample 3


title: CZe2s06_K562_H3K27me3_rep2

description: Library name: Sample 24

data_processing:
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. CUT&Tag 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 and binding 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.
Assembly: GRCh38
Supplementary files format and content: CUT&Tag bigWig files give the normalized coverage of histone modifications and transcription factor binding across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).
Library strategy: CUT&Tag

growth_protocol: M-07e cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS, 1X GlutaMAX (Gibco), and 10 ng/mL recombinant human IL-3 (STEMCELL Technologies). WSU-AML cells were seeded at 1×10⁶ cells/mL in RPMI (Gibco) supplemented with 10% FBS and 1X GlutaMAX (Gibco). K562 cells were seeded at 0.2 ×10⁶ cells/mL and cultured in IMDM (Gibco) supplemented with 10% FBS and 1% Penstrep. All cells were maintained at 37°C with 5% CO₂.

extract_protocol:
Cells were harvested, washed in cold PBS, and resuspended in nuclear extraction buffer. Intact nuclei were incubated with primary antibodies targeting mSWI/SNF complex subunits (SMARCC1, SMARCB1, SMARCA4) or histone modifications (H3K4me1, H3K4me3, H3K27ac), or IgG isotype control, followed by secondary antibody and protein A/G-Tn5 (pAG-Tn5) transposase fusion incubation. DNA was simultaneously fragmented and tagged by MgCl₂-activated Tn5 transposition at 37°C. Released tagged fragments were purified for library preparation.
CUT&Tag libraries were prepared in-house using the CUT&Tag protocol (Kaya-Okur et al., 2019). Libraries were sequenced by Novogene on an Illumina instrument.

treatment_protocol: Cells were maintained under standard culture conditions without drug treatment prior to harvesting for chromatin profiling.

tag: chip antibody

value: H3K27me3 (Cell Signaling Technology, 9733S)


title: CZe2s03_K562_H3K4me3_rep1

description: Library name: Sample 21

value: H3K4me3 (Active Motif, 39159)


title: GBe3s40_WSU_IgG

description: Library name: Sample 20

value: IgG (Abcam, AB172730)


title: GBe3s39_WSU_IgG

description: Library name: Sample 19


title: CZe2s05_K562_H3K27me3_rep1

description: Library name: Sample 23


title: GBe3s33_WSU_SMARCB1

description: Library name: Sample 15

value: SMARCB1 (Cell Signaling Technology, 91735S)


title: GBe3s34_WSU_SMARCB1

description: Library name: Sample 16


title: GBe3s18_M07e_BRG1

description: Library name: Sample 8

value: SMARCA4 (Abcam, ab110641)


title: CZe2s04_K562_H3K4me3_rep2

description: Library name: Sample 22


title: GBe3s38_WSU_BRG1

description: Library name: Sample 18


title: GBe3s26_WSU_SMARCC1

description: Library name: Sample 12

value: SMARCC1 (Cell Signaling Technology, 11956S)


title: GBe3s19_M07e_IgG

description: Library name: Sample 9


title: GBe3s17_M07e_BRG1

description: Library name: Sample 7


title: GBe3s31_WSU_H3K4me1

description: Library name: Sample 13

value: H3K4me1 (Abcam, ab8895)


title: GBe3s32_WSU_H3K4me1

description: Library name: Sample 14


title: GBe3s13_M07e_SMARCB1

description: Library name: Sample 5


title: GBe3s12_M07e_H3K4me1

description: Library name: Sample 4


title: GBe3s37_WSU_BRG1

description: Library name: Sample 17


title: GBe3s14_M07e_SMARCB1

description: Library name: Sample 6


title: GBe3s11_M07e_H3K4me1

description: Library name: Sample 3


title: GBe3s20_M07e_IgG

description: Library name: Sample 10


title: GBe3s25_WSU_SMARCC1

description: Library name: Sample 11


title: GBe3s6_M07e_SMARCC1

description: Library name: Sample 2


title: GBe3s5_M07e_SMARCC1

description: Library name: Sample 1


title: JFS2858_K562_SMARCA4_rep2

description: Library name: Sample 19

data_processing:
CUT&RUN 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 and binding 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.
Assembly: GRCh38
Supplementary files format and content: CUT&RUN bigWig files give the normalized coverage of protein-DNA interactions across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).
Library strategy: CUT&RUN

growth_protocol: M-07e cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS, 1X GlutaMAX (Gibco), and 10 ng/mL recombinant human IL-3 (STEMCELL Technologies). WSU-AML cells were seeded at 1×10⁶ cells/mL and cultured in RPMI (Gibco) supplemented with 10% FBS and 1X GlutaMAX (Gibco). K562 cells were seeded at 0.2 ×10⁶ cells/mL and cultured in IMDM (Gibco) supplemented with 10% FBS and 1% Penstrep. All cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were harvested, washed in cold PBS, and nuclei were isolated according to the AutoCUT&RUN protocol (Janssens et al., 2018; Epigenetics Chromatin 11:74). Nuclei were incubated overnight at 4°C with primary antibodies targeting mSWI/SNF complex subunits (SMARCC1, SMARCB1, SMARCA4), the CBFA2T3::GLIS2 fusion protein components (CBFA2T3, GLIS2), or histone modifications (H3K27me3, H3K4me1, H3K4me3, H3K27ac), or IgG isotype control. Following primary antibody incubation, nuclei were incubated with protein A-MNase fusion (pA-MNase). Chromatin cleavage was initiated by addition of CaCl₂ at 0°C. Released DNA fragments were purified for library preparation.
CUT&RUN libraries were prepared at the Fred Hutchinson Cancer Center Genomics Core using the AutoCUT&RUN protocol. Paired-end 150 bp sequencing was performed on an Illumina instrument.


title: JFS2757_K562_SMARCA4_rep1

description: Library name: Sample 17


title: JFS2857_K562_SMARCC1_rep1

description: Library name: Sample 18


title: HepG2, diast, Rep1

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description:
Library name: sample7
Column name in HepG2_diast_Counts: HepG2_WlWkHsHK (Rep1)

data_processing:
Differential expression analysis for RNA-seq data was performed using the following bioinformatics pipeline. Reads were trimmed and quality-filtered using fastp (v0.24.0). The trimmed reads were aligned to the human genome (hg38) using the ENCODE genome index ENCFF285DRD and the STAR aligner (v2.5.1b). Subsequently, gene-level quantification was conducted using RSEM (v1.2.31) with the ENCODE genome index ENCFF598IDH to generate a gene-level count matrix. Ribosomal RNA (rRNA) sequences were filtered out based on annotations from the human genome hg38 GTF reference file.
Assembly: hg38
Supplementary files format and content: processed files include gene-level quantification for each replicate
Supplementary files format and content: annotation of column names in counts file to associate column names with replicate number and condition

growth_protocol: Human liver cancer cell line HepG2 was cultured in DMEM-high glucose (Thermo Fisher) with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) from HepG2.
RNA-seq library is prepared using KAPA RNA HyperPrep kit (Roche): we used 2ug total RNA and each library was assigned unique i5 and i7 primers to aid in demultiplexing post-sequencing. The library was PCR amplified with the following program (98°C for 45s; 98°C for 15s, 60°C for 30s, 7°2C for 30s and repeat for 11 cycles); 72°C for 1min). PCR reactions from each sample were combined and purified using 0.8X KAPA HyperPure Beads (Roche). Sample concentration post-purification was measured using Qubit™ dsDNA Quantification Assay Kits (Invitrogen).

treatment_protocol: HepG2 were treated with the following microbial metabolites collected from in vitro microbial community treated with solvent control, antimicrobial cyclic peptide (wLwKhShK), control diast cyclic peptide (WlWkHsHK). Metabolite treatment was carried out by the addition of a 1:32 ratio of metabolite to cell culture media and incubated with cells for 48 hours.


title: HepG2, diast, Rep2

description:
Library name: sample8
Column name in HepG2_diast_Counts: HepG2_WlWkHsHK (Rep2)


title: HepG2, wLwKhShK, Rep2

description:
Library name: sample6
Column name in HepG2_wLwKhShK_Counts: HepG2_wLwKhShK (Rep2)


title: HepG2, media, Rep2

description:
Library name: sample2
Column name in HepG2_Media_Counts: HepG2_GAM (Rep2)


title: HepG2, media, Rep1

description:
Library name: sample1
Column name in HepG2_Media_Counts: HepG2_GAM (Rep1)


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_1h_+_aux_5h_HeLa rep2

city: Vienna

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: Library name: 340694

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.4
bowtie2 mapping against hg19 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with HOMER for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan)

extract_protocol:
Cells were cross-linked in falcon tube. The DNA was fragmented, biotynilated at both ends, and ligated at newly blunted ends together. Biotinylated DNA was captured and prepared for paired-end Illumina sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_1h_+_aux_5h_HeLa rep4

description: Library name: 343309


title: HepG2, wLwKhShK, Rep1

description:
Library name: sample5
Column name in HepG2_wLwKhShK_Counts: HepG2_wLwKhShK (Rep1)


title: BJ/HRAS-ER H2B-GFP, IP phosphoRPA32, Rep 4 Day 2

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

country: Italy

institute: University of Udine

description: Library name: 33_repB

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.5.1 with default configuration
Duplicate reads were flagged using samtools but no duplicates were removed
peaks were called using MACS2 version 2.2.9.1
Assembly: GRCh38
Supplementary files format and content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 6 --normalizeUsing RPKM

source_name: BJ-hTERT

growth_protocol: BJ/hTERT fibroblasts were grown in Earle’s salts Minimal Essential medium (MEM) (Euroclone), supplemented with Non-Essential Amino Acids (NEAA) (Euroclone). All culture media were enriched with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin (Euroclone) and 100 μg/mL streptomycin (Euroclone). Regular testing for Mycoplasma contamination was performed on all cell lines

extract_protocol:
Chromatin was extracted from BJ/hTERT, BJ/hTERT/HRASG12V-ER, BJ-hTERT/HRASG12V-ER/HDAC4-FLAG, BJ-hTERT/HRASG12V-ER/RPA70-GFP and BJ-hTERT/HRASG12V-ER/H2B-GFP cells and immunoprecipitated with 3 μg of BRCA1, 6 μg of IgG, and 3μg of RNA Pol II Ser5, 3μg RPA32 or phosphoRPA32, 2 μg  γH2AX antibodies. For each ChIP, approximately 3x106 BJ cells were used. Cells were treated as indicated and DNA-protein complexes were crosslinked with 1% formaldehyde (Sigma-Aldrich) for 15 minutes at room temperature. Following quenching with PBS/glycine (125 mM) and two PBS washes, the cells were harvested, centrifuged, and then lysed on ice for 10 minutes using Swelling buffer (20 mM Tris-HCl pH 8, 85 mM KCl, 0.5% NP-40) containing freshly added PIC and PMSF. The samples were centrifuged and the resulting pellets were resuspended in Nuclei lysis buffer (10 mM Tris-HCl pH 7.5, 1% NP-40, 0.5% Na deoxycholate, 0.1% SDS) and incubated on ice for 10 minutes. Following this, the samples were sonicated at 4°C using a Bioruptor Plus (Diagenode) with 30-second pulses for 30 minutes, yielding genomic DNA fragments with an average size of approximately 300 bp. After centrifugation, the supernatants were precleared with magnetic Dynabeads protein A or G (Thermo Fisher Scientific). 1/100 of the samples were taken as input and the remainder was immunoprecipitated overnight at 4°C on a rotating system with the previously mentioned antibodies in the presence of 8 µl of magnetic Dynabeads protein G (Thermo Fisher Scientific) in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 16.7 mM Tris-HCl pH 8, 167 mM NaCl) and Nuclei lysis buffer in a 1:1 ratio. Immunoprecipitated complexes were washed three times with Low Salt Immune Complex Wash Buffer (0.1% SDS, 1% Triton X-100, 20 mM Tris-HCl pH 8, 150 mM NaCl), twice with High Salt Immune Complex Wash Buffer (0.1% SDS, 1% Triton X-100, 20 mM Tris-HCl pH 8, 2 mM EDTA, 500 mM NaCl) and once with LiCl Immune Complex Wash Buffer (250 mM LiCl, 1% NP-40, 0.2% Na-deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8) at 4°C with rotation. A final wash with TE (10 mM Tris-HCl pH 8, 1 mM EDTA) was performed. 100 µl of TE/RNase A (0.2 mg/ml, Ambion) were added to immunocomplexes and inputs, and samples were incubated for 30 minutes at 37°C. Input and beads were resuspended in a 1:1 mixture of TES (50 mM Tris-HCl pH 8, 10 mM EDTA, 2% SDS) and Reverse Crosslinking buffer (250 mM Tris-HCl pH 7.5, 62.5 mM EDTA, 1.25 M NaCl) with 0.27 mg/ml Proteinase K (ITW Reagents). Crosslinking was reversed using the following protocol in a thermocycler: 5 hours at 37°C, 10 hours at 68°C and 1 hour at 10°C. Genomic DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research), eluted in 30 µl water and chromatin was quantified using a Qubit Fluorometer. For DRIP-seq (IP with S9.6), cells were treated as indicated, and DNA-protein complexes were crosslinked with 1% formaldehyde (Sigma-Aldrich) for 10 minutes at room temperature. After quenching with PBS/glycine (125 mM) for 5 minutes at room temperature and two washes in PBS, cells were collected, centrifuged and then lysed for 10 minutes on ice with SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0) supplemented with PIC and PMSF. Cells were sonicated at 4°C using Bioruptor Plus (Diagenode) with 30-second pulses for 30 minutes, resulting in an average fragment size of ~300 bp for genomic DNA. Samples were centrifuged and the supernatants were diluted with binding buffer solution (10 mM NaPO4, 140 mM NaCl, 0.05% Triton X-100) before preclearing with magnetic Dynabeads protein A or G (Thermo Fisher Scientific) for at least 1 hour at 4°C with rotation. Supernatants were collected using a magnetic bead system. 1/50 of the sample was taken as input, which was split equally for genomic DNA extraction and RNA extraction using Tri-Reagent (Sigma-Aldrich, Germany). The remaining samples were immunoprecipitated overnight at 4°C on a rotating wheel with 6 µg of S9.6 antibody, 6 µg of IgG, and 8 µl of magnetic Dynabeads protein G (Thermo Fisher Scientific). Immunoprecipitated complexes were washed three times with binding buffer and then inputs and beads were resuspended in 100 µl TES (50 mM Tris-HCl pH 8, 10 mM EDTA, 2% SDS) and Reverse Crosslinking salt mixture (250 mM Tris-HCl pH 7.5, 62.5 mM EDTA, 1.25 M NaCl, 0.27 mg/ml Proteinase K (ITW Reagents)). After incubation in a thermocycler (5 hours at 37°C, 10 hours at 68°C, 1 hour at 10°C), nucleic acids were purified with ChIP DNA Clean & Concentrator kit (Zymo Research), eluted in 30 µl water and quantified using a Qubit Fluorometer. dsRNA were removed prior to library preparation by treating samples with 10u RNAseIII (Ambion).
DNA SMART ChIP-Seq Kit (Takara) was used for library generation of samples subjected to Illumina sequencing. To generate ChIP-seq libraries with the DNA SMART ChIP-Seq Kit, a priming site was added to the 3’ end of the DNA template using the Terminal Deoxynucleotidyl Transferase. This was followed by annealing of a Poly(dA) Primer, which anneals to the T-tail. This primer was then used by the SMARTScribe RT to copy the DNA strand. Sequencing libraries were then generated by PCR-mediated addition of Illumina adapters. DNA nanoball (DNB) technology was applied for library preparation of samples subjected to BGI-seq 500 sequencing following manifacturer (Roche)

treatment_protocol: 4-OHT (Merck, Germany) was used to induce HRAS expression (HRAS G12V is Era fused) at 1µM; were indicated 4-OHT was used for 2 days (proliferative phase) or 8 days to reach senescence

value: BJ-hTERT

value: fibroblasts

value: diploid

value: 4-OHT 1mM


title: BJ/HRAS-ER RPA70-GFP, IP phosphoRPA32, Rep 4 Day 2

description: Library name: 32_repB


title: BJ/HRAS-ER RPA70-GFP, IP phosphoRPA32, Rep 3 Day 2

description: Library name: 23_repA


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_1h_+_aux_5h_HeLa rep1

description: Library name: 340693


title: HepG2, metabolites, Rep2

description:
Library name: sample4
Column name in HepG2_Metabolites_Counts: HepG2_HC1 (Rep2)


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_1h_+_aux_5h_HeLa rep3

description: Library name: 343308


title: Control vector Rep-3

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description:
Library name: sample3
Biological replicate No.3

data_processing:
RNAseq reads were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 (https://zenodo.org/record/5109461#.Ya2yLFPMJhE) developed at the LUMC. FastQC was used for checking raw read QC.
Adapter clipping was performed using Cutadapt (v2.10) with the default settings.
RNAseq reads’ alignment was performed using STAR (v2.7.5a) with human reference genome GRCh38.
The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=reverse”. The gene annotation used for quantification was Ensembl version 114.
Assembly: GRCh38
Supplementary files format and content: TSV, raw gene count with Ensembl v114

growth_protocol: MDA-MB-231 cells were purchased from American Type Culture Collection (ATCC) and cultured in Dulbecco’s modified Eagle medium (DMEM; Thermo Fisher Scientific; 41965062) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific; 16000044) and 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific; 15140163).

extract_protocol:
RNA was extracted by a NucleoSpin RNA kit (Macherey Nagel; Cat. Nr.: 740955) according to the manufacturer's instructions.
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI) in Poland using the DNBSEQ platform.

treatment_protocol: Cells were transduced with lentiviral expressing constructs overnight. After two days culture, 10 µg/mL blasticidin was added to the medium for selecting stable cells. After another 3 days culture, cells were ready for RNA isolation.

value: human breast cancer cell line

value: Transduced with empty expressing construct


title: Control vector Rep-1

description:
Library name: sample1
Biological replicate No.1


title: HepG2, metabolites, Rep1

description:
Library name: sample3
Column name in HepG2_Metabolites_Counts: HepG2_HC1 (Rep1)


title: Gingival tissue from patient P010

first: Tianfan

last: Cheng

address: 34 Hospital Road, Sai Ying Pun

department: Faculty of Dentistry

institute: The University of Hong Kong

description: Library name: lib2_P010-PT

data_processing:
Raw data were preprocessed with Cell Ranger v5.0.1 analysis pipeline (Zheng et al. 2017) (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) for demultiplexing, barcode processing, genome alignment (GRCh38 v2020-A) and single-cell 3’ gene counting (UMI counts). The sequencing was achieved with >340 million reads per sample.
Assembly: GRCh38 v2020-A
Supplementary files format and content: raw read counts in gene-barcode matrix

source_name: Gingiva

extract_protocol:
Single cell suspensions were generated using the Tumor Dissociation Kit, human (Miltenyi Biotec) on a gentleMACS™ Dissociator (Miltenyi Biotec). For PT, the ‘h_skin_01’ program was selected and performed at 37℃, 45min, while for other tissues, the ‘h_tumor_01’ was selected with the same temperature and time settings. A total of three samples for GT, PT and ST (one sample/tissue) from different patients was included in the study. The single-cell suspensions were filtered through the Falcon® 40 µm Cell Strainer (Corning, USA), counted and examined for viability (>80%) using a hemocytometer.
Single cells were encapsulated into GEMs (Gel Bead in Emulsion) on a Chromium™ Controller using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10× Genomics, USA), with following cell lysis and reverse transcription to 10×-barcoded cDNA inside. After post-GEM-RT cleanup, cDNAs were purified using SPRIselect Bead-Based Reagent (Beckman Coulter, USA) and amplified on an Applied Biosystems SimpliAmp Thermal Cycler (Thermo Fisher, USA). The products were further fragmented, end-repaired, A-tailed, ligated with adapters, amplified with sample index PCR and SPRIselect-purified. The final libraries, containing barcode, UMI and cDNA, were sequenced on the DNBSEQ-G400 (BGI, China).

value: Gingiva


title: circRNA overexpression Rep-2

description:
Library name: sample5
Biological replicate No.2

value: Transduced with expressing construct for circTGFBR2(3-6)


title: circRNA overexpression Rep-1

description:
Library name: sample4
Biological replicate No.1


title: BJ/HRAS-ER/HRAS-ER not induced, IP S9.6, Rep B

description: Library name: BJ17_repB

value: Untreated


title: BJ/HRAS-ER/HDAC4, IP RNA PolII Ser5, Rep B

description: Library name: BJ23_repB


title: BJ/HRAS-ER not induced H2B-GFP, IP phosphoRPA32, Rep 4 Day 2

description: Library name: 31_repB


title: Control vector Rep-2

description:
Library name: sample2
Biological replicate No.2


title: circRNA overexpression Rep-3

description:
Library name: sample6
Biological replicate No.3


title: BJ/HRAS-ER/HDAC4, IP BRCA1, Rep B

description: Library name: BJ34_repB


title: Socket tissue from tooth 11 from patient P011

description: Library name: lib3_P011-37ST


title: BJ/HRAS-ER not induced H2B-GFP, IP phosphoRPA32, Rep 3 Day 2

description: Library name: 13_repA


title: BJ/HRAS-ER H2B-GFP, IP phosphoRPA32, Rep 3 Day 2

description: Library name: 15_repA


title: BJ/HRAS-ER, Input, Rep A + B

description:
Library name: BJ55
pulled input of Rep A and B

value: input


title: BJ/HRAS-ER/HDAC4, IP S9.6, Rep B

description: Library name: BJ26_repB


title: BJ/HRAS-ER/HRAS-ER not induced, IP BRCA1, Rep B

description: Library name: BJ16_repB


title: Granulation tissue from tooth 46 from patient P020

description: Library name: lib1_P020-GT


title: BJ/HRAS-ER/HRAS-ER not induced, IP RNA PolII Ser5, Rep B

description: Library name: BJ14_repB


title: BJ/HRAS-ER not induced, IP S9.6, Rep B

description: Library name: BJ8_repB


title: BJ/HRAS-ER/HDAC4, IP BRCA1, Rep A

description: Library name: BJ34_repA


title: BJ/HRAS-ER/HDAC4, IP S9.6, Rep A

description: Library name: BJ26_repA


title: BJ/HRAS-ER not induced, IP RNA PolII Ser5, Rep B

description: Library name: BJ5_repB


title: BJ/HRAS-ER/HRAS-ER not induced, IP S9.6, Rep A

description: Library name: BJ17_repA


title: BJ/HRAS-ER/HDAC4, IP RNA PolII Ser5, Rep A

description: Library name: BJ23_repA


title: BJ/HRAS-ER/HRAS-ER not induced, IP BRCA1, Rep A

description: Library name: BJ16_repA


title: BJ/HRAS-ER/HRAS-ER not induced, IP RNA PolII Ser5, Rep A

description: Library name: BJ14_repA


title: BJ/HRAS-ER not induced, IP BRCA1, Rep A

description: Library name: BJ7_repA


title: BJ/HRAS-ER not induced, IP S9.6, Rep A

description: Library name: BJ8_repA


title: BJ/HRAS-ER not induced, IP BRCA1, Rep B

description: Library name: BJ7_repB


title: BJ/HRAS-ER not induced, IP RNA PolII Ser5, Rep A

description: Library name: BJ5_repA


title: 23_DQ_AF_9-3-20_(Clariom_S_Mouse)

first: Emanuel

middle: José

last: Novais

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

description: Gene expression data from 17-weeks annulus fibrosis DQ SM/J mouse

hyb_protocol: Gene chips (Mouse Clariom S) were hybridized with fragmented and biotin-labeled cDNA. Arrays were washed and stained with GeneChip hybridization wash & stain kit.

scan_protocol: Scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Chp files were generated by sst-rma normalization from Affymetrix cel file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 software. The SST-RMA algorithm was used for data normalization.

label: biotin

label_protocol: Fragmented biotin labeled cDNA was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: NP and AF tissue were dissected from tail discs from SM/J mice (n=4-6 per group).

extract_protocol: Pooled tissue from single animal served as an individual sample. Samples were homogenized and total RNA was extracted using RNeasy® Mini kit (Qiagen).

value: Annulus Fibrosus

value: SM/J

value: DQ


title: 12627839_surgery (IO360 9.15.2023)

city: Oklahoma City

first: Suresh

last: Niture

state: OK

address: 800 NE 10th St, Department Of Radiation Oncology

institute: Department of Radiation Oncology, Stephenson Cancer Center, Oklahoma Unive

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 20

hyb_protocol: Panel standard is a DNA oligo blend containing all BC360 and IO 360 probe target sequences, that is run on each cartridge within the experiment for normalization of non-PAM50 genes; while reference sample is an RNA oligo blend containing PAM50 probe target sequences for PAM50 genes.

scan_protocol: nCounter MAX/FLEX prep station and scanner nCounter technology provides a robust method for multiplexing up to 800 gene expression targets using direct detection technology. The simple, efficient workflow requires just 15 minutes hands-on time for most panels using an automated benchtop processing system and produces highly reproducible data, requiring no amplification or technical replicates in less than 24 hours. This workflow rapidly accelerates biomarker validation and biomarker development, providing gene expression data you can count on.

data_processing:
Housekeeper Normalization for non-TIS and non-PAM50 Genes
Genes are normalized using a ratio of the expression value to the geometric mean of all housekeeping genes on the panel.
Housekeeper Normalization for TIS Genes
Genes in the TIS signature are normalized using a ratio of the expression value to the geometric mean of the housekeeper genes used only for the TIS signature.
Housekeeper Normalization for PAM50 Genes
Genes in the PAM50 signature are normalized using a ratio of the expression value to the geometric mean of the housekeeper genes used only for the PAM50 signature.
Panel Standard Normalization for non-PAM50 Genes
Genes not in the PAM50 signature are additionally normalized using a ratio of the housekeeper-normalized data and a panel standard run on the same cartridge as the observed data. In the absence of a panel standard column, values from panel standard run on the same codeset lot as the observed data may be substituted. If a cartridge is missing a panel standard run, the average of all panel standards present is substituted for that cartridge.
Reference Sample Normalization for PAM50 genes
Genes in the PAM50 signature are additionally normalized using a ratio of the housekeeper-normalized data and a reference sample run on the same codeset lot from a NanoString archive is used.
Final Adjustments
The housekeeper-normalized and panel standard-normalized data is Log(2) transformed. A constant of 8 is added to TIS so that it is on the same scale as investigational use only (IUO) TIS, making scores comparable across research use only (RUO) and IUO assays. Other non-TIS signatures are also adjusted with constants to express values in a similar range.
Differential Expression Analysis
Grouping Variable
Differential expression is fit on a per gene or per signature basis using a linear model for analyses without a blocking factor. The statistical model uses the expression value or signature score as the dependent variable and fits a grouping variable as a fixed effect to test for differences in the levels of that grouping variable.
Expression(gene or signature)= μ+Group+ε
P-values are adjusted within each analysis, gene or signature, and on the grouping variable level difference t-test using the Benjamini and Yekutieli False Discovery Rate (FDR) adjustment to account for correlations amongst the tests. All models are fit using the limma package in R.

label: Photocleavable oligonucleotide

source_name: primary breast cancer

label_protocol: The nanoString (nCounter Run) technology was used, and two approaches were applied for tumor analysis: 1) The nCounter® Breast Cancer 360™ panel and 2) PanCancer IO 360 panel.  Breast Cancer 360™ data analysis report provides a unique 360° view of gene expression for the breast tumor microenvironment and immune response, and PanCancer IO 360 panel provides a unique 360 ° view of gene expression for the tumor, microenvironment, and immune response. 19 BC samples passed all QCs, which include 5 Pre-RT (biopsy), and 14 post-RT (surgery). Three samples failed housekeeping geomean QC and were excluded from the analysis. Two-panel standards were used for normalization.  In IO 360 panel, 20 samples passed all QCs. 2 samples failed housekeeping geomean QC and were excluded from the analysis. One panel standard was used for normalization.

growth_protocol: Breast Cancer Patients were recruited at Myco College of Medicine, Jacksonville, FL. The study was conducted through a protocol approved by the Myco College of Medicine Institutional Review Board (IRB)

extract_protocol: Paraffin-embedded tissue biopsy samples from 20 BC patients (5 biopsy and  15 post RT surgical) were used to extract total RNA. We used whole sections of biopsy and surgical tissue for RNA extraction. RNA samples were isolated using the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The quality and concentration of RNA were estimated using the NanoDrop ND-1000 spectrophotometer. Further analysis of RNA integrity was performed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer.

treatment_protocol: n this cohort study, we isolated 20 tumor tissues from 20 breast cancer patients, of which 5 tumors were collected during diagnosis and biopsy.  These patients were treated with standard radiation therapy (RT), and treatment included a total of 30 Gy radiation in three weeks.

tag: tissues

value: primary breast cancer

tag: race

value: Not Hispanic or Latino

tag: histology

value: Grade I

tag: Sex

value: Female

tag: Stage


title: 17_Veh_AF_9-3-20_(Clariom_S_Mouse)

description: Gene expression data from 17-weeks annulus fibrosis Veh SM/J mouse

tag: tissue

value: Veh


title: 18_Veh_AF_9-3-20_(Clariom_S_Mouse)


title: 7814749_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 19


title: 20_DQ_AF_9-3-20_(Clariom_S_Mouse)


title: 21_DQ_AF_9-3-20_(Clariom_S_Mouse)


title: 11_DQ_NP_7-21-20_(Clariom_S_Mouse)

description: Gene expression data from 17-weeks nucleus pulpous DQ SM/J mouse

value: Nucleus Pulposus


title: 22_DQ_AF_9-3-20_(Clariom_S_Mouse)


title: 12_DQ_NP_7-21-20_(Clariom_S_Mouse)


title: 13_Veh_AF_9-3-20_(Clariom_S_Mouse)


title: 19_DQ_AF_9-3-20_(Clariom_S_Mouse)


title: 15_Veh_AF_9-3-20_(Clariom_S_Mouse)


title: 24_DQ_AF_9-3-20_(Clariom_S_Mouse)


title: 10_DQ_NP_7-21-20_(Clariom_S_Mouse)


title: 16_Veh_AF_9-3-20_(Clariom_S_Mouse)


title: 14_Veh_AF_9-3-20_(Clariom_S_Mouse)


title: 09_DQ_NP_7-21-20_(Clariom_S_Mouse)


title: 12600485_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 18

value: Grade II


title: 08_DQ_NP_7-21-20_(Clariom_S_Mouse)


title: 12367726_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 15

value: Grade III


title: 12701592_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 16


title: 6758297_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 17

value: Ductal


title: 7779018_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 12


title: 7680218_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 11

value: Hispanic or Latino


title: 7953417_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 14


title: 12589546_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 9


title: 12295292_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 13


title: 12703144_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 10


title: 06_Veh_NP_7-21-20_(Clariom_S_Mouse)

description: Gene expression data from 17-weeks nucleus pulpous Veh SM/J mouse


title: 12357728_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 7


title: 7951254_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 8


title: 04_Veh_NP_7-21-20_(Clariom_S_Mouse)


title: 07_DQ_NP_7-21-20_(Clariom_S_Mouse)


title: 03_Veh_NP_7-21-20_(Clariom_S_Mouse)


title: 12627839_biopsy (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 5


title: 6589688_surgery (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 6


title: 12589546_biopsy (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 4


title: 05_Veh_NP_7-21-20_(Clariom_S_Mouse)


title: UNCseq1758 ROI3 ARID1A Negitive_Mutated

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description: Library name: UNCseq1757 ROI3 ARID1A Neg

data_processing:
The .dcc files generated by the NanoString GeoMx Digital Spatial Profiler represent ROI digital counts derived from spatially resolved transcriptomic profiling.
The Hs_R_NGS_WTA_v1.0.pkc file is the probe annotation (PKC) file for the GeoMx Human RNA Whole Transcriptome Atlas (NGS-based) panel, used to map probe-level counts in .dcc files to gene targets and associated control probes during downstream processing.
Assembly: FASTQ files process into DCC files by geomxngspipline build 2.3.3.10
Supplementary files format and content: Nanostring genome assembly
Supplementary files format and content: DCC file format
Library strategy: Spatial Transcriptomics

source_name: Endometrium

growth_protocol: No growth protocol

extract_protocol:
Nanostring antigen retrieval protocol
Nanostring library construction protocol

treatment_protocol: No treatment protocol

value: Endometrium

value: ARID1A Mutated

tag: batch

value: total RNA


title: 4569357_biopsy (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 3


title: UNCseq1757 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1757 ROI2 ARID1A Neg


title: 10_SMJ 4W 91 AF_(Clariom_S_Mouse)

description: Gene expression data from 4-weeks annulus fibrosis SM/J mouse

source_name: 10_SMJ 4W 91 AF


title: 16_SMJ 4W 94 NP_(Clariom_S_Mouse)

description: Gene expression data from 4-weeks nucleus pulpous SM/J mouse

source_name: 16_SMJ 4W 94 NP


title: 14_SMJ 4W 91 NP_(Clariom_S_Mouse)

source_name: 14_SMJ 4W 91 NP


title: 6589688_biopsy (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 2


title: UNCseq1757 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1757 ROI3 ARID1A Pos


title: 13_SMJ 4W 90 NP_(Clariom_S_Mouse)

source_name: 13_SMJ 4W 90 NP


title: 12_SMJ 4W 94 AF_(Clariom_S_Mouse)

source_name: 12_SMJ 4W 94 AF


title: 01_Veh_NP_7-21-20_(Clariom_S_Mouse)


title: 9_SMJ 4W 90 AF_(Clariom_S_Mouse)

source_name: 9_SMJ 4W 90 AF


title: Summer 18

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

description: Library name: S_18

data_processing:
Reads were filtered and trimmed to remove adapter-derived or low-quality bases using trim_galore tool v0.6.10 with parameter –stringency=6 and FASTQC v0.12.1 was used to verify quality of the outputs.
Illumina reads were aligned to the Microtus_ochrogaster reference genome (MicOch1) with Hisat2.
Read counts were generated for each annotated gene using HTSeq-Count. Read normalization, variance estimation and pair-wise differential expression analysis with multiple testing corrections were conducted using the R Bioconductor DESeq2 package and RPKM (Reads Per Kilobase of exon per Megabase of library size) were computed during this process.
Gene set enrichment analyses were performed with R package “clusterProfiler” v4.10.1 using mm10 annotation database (org.Mm.eg.db)
Violin plots, histograms, volcano plots and were generated using R package “ggplot2” v3.5.1. Heatmaps were obtained using R package “plotheatmap”. Statistical tests were realized with R or Graphpad PRISM 5.
Assembly: MicOch1
Supplementary files format and content: tabular file with RPKM expression

organism: Microtus ochrogaster

source_name: Testis

extract_protocol:
Total mRNA was isolated from frozen tissues using miRNeasy mini-Kit (Qiagen, France), with DNAse treatment. The quality and quantity of total RNAs were determined using 4150 TapeStation and RNA ScreenTapes (Agilent Technologies).
cDNA libraries were prepared using KAPA mRNA HyperPrep Kit (Roche Diagnostics). This kit captures messenger RNA using magnetic oligo-dT beads and it fragments the material using heat and magnesium. Then first strand cDNA was synthetized using random priming and Illumina adapters were added by ligation. Library preparation was performed according to supplier recommendations and as previously described (Khaled et al. 2021), using 1 µg of total RNA input to ensure high diversity.

value: Testis

value: WT

value: Summer


title: UNCseq1757 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1757 ROI2 ARID1A Pos


title: 7814749_biopsy (IO360 9.15.2023)

description:
Total tumor RNA
IO360 9.15.2023
SAMPLE 1


title: 11_SMJ 4W 93 AF_(Clariom_S_Mouse)

source_name: 11_SMJ 4W 93 AF

value: Annulus Fibrosus

value: SM/J


title: 15_SMJ 4W 93 NP_(Clariom_S_Mouse)

source_name: 15_SMJ 4W 93 NP


title: Summer 16

description: Library name: S_16


title: UNCseq1757 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1757 ROI1 ARID1A Neg


title: Summer 17

description: Library name: S_17


title: UNCseq1757 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1757 ROI1 ARID1A Pos


title: Summer 15

description: Library name: S_15


title: Summer 13

description: Library name: S_13


title: Summer 11

description: Library name: S_11


title: Summer 12

description: Library name: S_12


title: UNCseq1804 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1804 ROI3 ARID1A Neg


title: UNCseq1804 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1804 ROI1 ARID1A Neg


title: Summer 14

description: Library name: S_14


title: UNCseq1804 ROI4 ARID1A Negitive_Mutated

description: Library name: UNCseq1804 ROI4 ARID1A Neg


title: Summer 10

description: Library name: S_10


title: UNCseq0585 ROI6 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI6 ARID1A Neg


title: UNCseq1804 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1804 ROI2 ARID1A Neg


title: Summer 9

description: Library name: S_9


title: Summer 8

description: Library name: S_8


title: UNCseq0585 ROI5 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI5 ARID1A Neg


title: UNCseq0585 ROI4 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI4 ARID1A Neg


title: Summer 5

description: Library name: S_5


title: UNCseq1084 ROI5 ARID1A Negitive_Mutated

description: Library name: UNCseq1084 ROI5 ARID1A Neg


title: UNCseq0886 ROI6 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI6 ARID1A Pos


title: UNCseq0585 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI3 ARID1A Neg


title: Summer 7

description: Library name: S_7


title: UNCseq0886 ROI5 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI5 ARID1A Pos


title: Summer 2

description: Library name: S_2


title: Summer 3

description: Library name: S_3


title: Summer 6

description: Library name: S_6


title: UNCseq0585 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI1 ARID1A Neg


title: Summer 1

description: Library name: S_1


title: UNCseq0886 ROI4 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI4 ARID1A Pos


title: UNCseq0886 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI3 ARID1A Pos


title: UNCseq0886 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI2 ARID1A Pos


title: UNCseq0886 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq0886 ROI1 ARID1A Pos


title: UNCseq2451 ROI6 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI6 ARID1A Neg

value: ARID1A Wild-Type


title: Summer 4

description: Library name: S_4


title: Winter - 11

description: Library name: W-_11

value: Winter


title: UNCseq2451 ROI5 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI5 ARID1A Neg


title: Winter - 7

description: Library name: W-_7


title: Winter - 10

description: Library name: W-_10


title: Winter - 8

description: Library name: W-_8


title: UNCseq2451 ROI4 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI4 ARID1A Neg


title: Winter - 6

description: Library name: W-_6


title: Winter - 9

description: Library name: W-_9


title: UNCseq0585 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq0585 ROI2 ARID1A Neg


title: Winter - 4

description: Library name: W-_4


title: Winter - 3

description: Library name: W-_3


title: UNCseq2451 ROI1 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI1 ARID1A Neg


title: Winter - 2

description: Library name: W-_2


title: UNCseq1480 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1480 ROI2 ARID1A Neg


title: UNCseq1480 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1480 ROI3 ARID1A Neg


title: Winter - 1

description: Library name: W-_1


title: UNCseq2451 ROI2 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI2 ARID1A Neg


title: Winter + 5

description: Library name: W+_5


title: UNCseq1480 ROI1  ARID1A Negitive_Mutated

description: Library name: UNCseq1480 ROI1  ARID1A Neg


title: 02_Veh_NP_7-21-20_(Clariom_S_Mouse)

description: Gene expression data from 17-weeks nucleus pulpous Veh SM/J mouse


title: Winter - 5

description: Library name: W-_5


title: UNCseq2451 ROI3 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2451 ROI3 ARID1A Neg


title: Tonsil, 5 DPI, replicate D

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Library name: sample093

data_processing:
Raw FASTQ files were aligned to the combined AGM (ChlSab1, Ensembl v112) and NiV Bangladesh (GCA_003147825.1) genomes using STAR v2.7.11b.
samtools BAM; contains read alignments
PCR duplicates were removed with samtools v1.20
Count matrices were generated with featureCounts (Rsubread v2.20.0)
Assembly: ChlSab1 (Ensembl v112) and NiV Bangladesh (NCBI GCA_003147825.1)
Supplementary files format and content: TSV; contains featureCounts raw counts

organism: Chlorocebus aethiops

source_name: Tonsil

extract_protocol:
Approximately 100 mg of each sample was stored in 1 mL RNAlater (Qiagen) for 7 days for stabilization. RNAlater was removed, and tissues were homogenized in 600 μL RLT buffer (Qiagen) in a 2 mL cryovial using a TissueLyser (Qiagen) and ceramic beads. RNA was isolated using the RNeasy MiniKit (Qiagen), according to the vendor's instructions. Residual genomic DNA was digested and RNA cleaned via the Zymo Clean and Concentrator-5 kit according to the manufacturer's instructions.
Libraries were constructed by poly-A selection and sequenced via Illumina NextSeq 550 to a target depth of 50 million reads.

value: Tonsil

tag: timepoint

value: 5 DPI


title: Tonsil, 5 DPI, replicate C

description: Library name: sample092


title: UNCseq1357 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1357 ROI2 ARID1A Neg


title: UNCseq1357 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1357 ROI1 ARID1A Neg


title: Winter + 2

description: Library name: W+_2


title: Winter + 3

description: Library name: W+_3


title: UNCseq1357 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1357 ROI3 ARID1A Pos


title: UNCseq1357 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1357 ROI3 ARID1A Neg


title: UNCseq1480 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1480 ROI2 ARID1A Pos


title: UNCseq1480 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1480 ROI3 ARID1A Pos


title: UNCseq1480 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1480 ROI1 ARID1A Pos


title: Winter + 1

description: Library name: W+_1


title: Tonsil, 5 DPI, replicate A

description: Library name: sample090


title: UNCseq1357 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1357 ROI2 ARID1A Pos


title: Tonsil, 4 DPI, replicate D

description: Library name: sample089

value: 4 DPI


title: UNCseq0451 ROI6 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI6 ARID1A Neg


title: Winter + 4

description: Library name: W+_4


title: UNCseq1357 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1357 ROI1 ARID1A Pos


title: Tonsil, 5 DPI, replicate B

description: Library name: sample091


title: Tonsil, 4 DPI, replicate C

description: Library name: sample088


title: Patient15,PBMC,LACB1(RNA-seq)

city: jinan

first: yuanyuan

last: Zhang

address: jinan

institute: Shandong Second Medical University

description: Library name: LACB

data_processing:
RNA-seq:Raw reads were subjected to quality control using FastQC.Clean reads were aligned to the human reference genome using HISAT2.Gene expression levels were quantified using featureCounts.Differential expression analysis was performed using DESeq2.
ChIP-seq:Raw reads were quality-checked using FastQC.Reads were aligned to the human genome using Bowtie2.Peak calling was performed using MACS2.Peaks were annotated using HOMER.
Assembly: hg38 and mm10
Supplementary files format and content: fastq,bdg

source_name: peripheral blood

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from healthy donors and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37°C in a 5% CO₂ incubator.

extract_protocol:
RNA-seq:Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA quality and integrity were assessed using an Agilent 2100 Bioanalyzer. ChIP-seq:Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was isolated, lysed, and sonicated to generate DNA fragments of 200–500 bp.
RNA-seq:RNA-seq libraries were prepared using a poly(A) selection method with the Illumina TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions. ChIP-seq:Immunoprecipitated DNA was collected using magnetic beads and used for library construction with the NEBNext Ultra II DNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with lactate (LAC, 10 mM) for 8 hours. Control cells were treated with PBS.

value: peripheral blood

tag: cell line

value: primary cells

tag: cell type

value: peripheral blood mononuclear cells


title: UNCseq0451 ROI4 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI4 ARID1A Neg


title: UNCseq0451 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI3 ARID1A Neg


title: Patient15,PBMC,LACC1(RNA-seq)

description: Library name: LACC


title: UNCseq0451 ROI5 RID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI5 RID1A Neg


title: Tonsil, 4 DPI, replicate B

description: Library name: sample087


title: Patient15,PBMC,LACA1(RNA-seq)

description: Library name: LACA


title: Tonsil, 4 DPI, replicate A

description: Library name: sample086


title: UNCseq0451 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI1 ARID1A Neg


title: UNCseq0451 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq0451 ROI2 ARID1A Neg


title: UNCseq1531 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq1531 ROI2 ARID1A Neg


title: UNCseq1531 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq1531 ROI1 ARID1A Neg


title: Tonsil, 3 DPI, replicate D

description: Library name: sample085

value: 3 DPI


title: Patient15,PBMC,conA1(RNA-seq)

description: Library name: CONA


title: UNCseq1531 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq1531 ROI2 ARID1A Pos

value: Endometrium


title: UNCseq1531 ROI3 ARID1A Positive_Mutated

description: Library name: UNCseq1531 ROI3 ARID1A Pos

value: ARID1A Mutated


title: UNCseq1531 ROI1 ARID1A Positive_Mutated

description: Library name: UNCseq1531 ROI1 ARID1A Pos

value: total RNA


title: Patient15,PBMC,conB1(RNA-seq)

description: Library name: CONB


title: Patient15,PBMC,conC1(RNA-seq)

description: Library name: CONC


title: Tonsil, 3 DPI, replicate C

description: Library name: sample084


title: UNCseq2155 ROI3 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2155 ROI3 ARID1A Neg


title: GBe8s13_cordBlood-CG_k4me3-2

description: Library name: Sample 10

data_processing:
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. The data was then 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 and binding 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.
Assembly: GRCh38
Supplementary files format and content: CUT&Tag bigWig files give the normalized coverage of histone modifications and transcription factor binding across the genome (deepTools bamCoverage --binSize 40 --normalizeUsing CPM --exactScaling).
Library strategy: CUT&Tag

source_name: Blood

growth_protocol: Human umbilical cord blood CD34+ HSCs were isolated, sorted, and cultured as described in Le et al. (2022; J Clin Invest 132:e157101). Briefly, fresh CB was processed with red blood cell lysis, CD34+ enriched by CliniMACS, and HSCs sorted as DAPI⁻CD34+Lin⁻CD38⁻CD90loCD45RA⁻EPCR+ by FACS on a BD FACSAria II. Cells were cultured in endothelial co-culture conditions.

extract_protocol:
Transduced cord blood cells were harvested, washed, and processed for CUT&Tag as described for cell lines. Nuclei were incubated with antibodies targeting SMARCA4 (BRG1), H3K27ac, H3K4me3, or IgG control, followed by secondary antibody and pA-Tn5 incubation. Tagmentation was activated by MgCl₂ at 37°C and resulting DNA fragments were purified.
CUT&Tag libraries were prepared in-house using the CUT&Tag protocol (Kaya-Okur et al., 2019) and sequenced in-house at the Seattle Children's Research Institute Genomics Core. Paired-end sequencing was performed on an Illumina instrument.

treatment_protocol: CD34+ cord blood HSCs were transduced overnight with concentrated lentivirus encoding CBFA2T3::GLIS2 or GFP control as described in Le et al. (2022). Fresh media was added the following morning. Biological replicate experiments were completed for CBFA2T3::GLIS2 and single experiments for GFP control as indicated.

value: Blood

value: CD34+ Cord Blood Cells

value: H3K4me3 (Active Motif, 39159)

tag: treatment

value: CBFA2T3::GLIS2 transduced


title: UNCseq2155 ROI1 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2155 ROI1 ARID1A Neg


title: UNCseq2155 ROI3 ARID1A Positive_Wild-Type

description: Library name: UNCseq2155 ROI3 ARID1A Pos


title: UNCseq2155 ROI2 ARID1A Positive_Wild-Type

description: Library name: UNCseq2155 ROI2 ARID1A Pos


title: Tonsil, 3 DPI, replicate A

description: Library name: sample082


title: UNCseq2155 ROI2 ARID1A Negitive_Wild-Type

description: Library name: UNCseq2155 ROI2 ARID1A Neg


title: GBe8s12_cordBlood-CG_k4me3-1

description: Library name: Sample 9


title: UNCseq2155 ROI1 ARID1A Positive_Wild-Type

description: Library name: UNCseq2155 ROI1 ARID1A Pos


title: Tonsil, baseline, replicate E

description: Library name: sample080

value: Baseline


title: Tonsil, baseline, replicate F

description: Library name: sample081


title: UNCseq2171 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq2171 ROI3 ARID1A Neg


title: UNCseq1531 ROI3 ARID1A Negitive_Mutated

description: Library name: UNCseq1531 ROI3 ARID1A Neg


title: UNCseq2171 ROI1 ARID1A Negitive_Mutated

description: Library name: UNCseq2171 ROI1 ARID1A Neg


title: UNCseq2171 ROI2 ARID1A Negitive_Mutated

description: Library name: UNCseq2171 ROI2 ARID1A Neg


title: GBe8s9_cordBlood-CG_k27ac-2

description: Library name: Sample 7

value: H3K27ac (EMD Millipore, MABE647)


title: GBe7s11_cordBlood-CG_IgG-1

description: Library name: Sample 8

value: IgG (Abcam, AB172730)


title: Tonsil, baseline, replicate D

description: Library name: sample079

value: Tonsil


title: GBe8s8_cordBlood-CG_k27ac-1

description: Library name: Sample 6


title: UNCseq2171 ROI2 ARID1A Positive_Mutated

description: Library name: UNCseq2171 ROI2 ARID1A Pos


title: GBe8s6_cordBlood-CG_BRG1-1

description: Library name: Sample 4

value: SMARCA4 (Abcam, ab110641)


title: Tonsil, baseline, replicate C

description: Library name: sample078


title: GBe8s7_cordBlood-CG_BRG1-2

description: Library name: Sample 5


title: UNCseq1550 ROI6 ARID1A Positive_Mutated

description: Library name: UNCseq1550 ROI6 ARID1A Pos


title: Tonsil, baseline, replicate B

description: Library name: sample077


title: Lung, 5 DPI, replicate C

description: Library name: sample074

source_name: Lung

value: Lung

value: 5 DPI