title: T84 IFNLR KO cells at low density, replicate 1

description: sample 16


title: T1 Cas9-0xBS bio rep 1

status: Public on Jun 02 2025

type: SRA

city: St. Louis

first: Richard

middle: Keith

last: Slotkin

state: Missouri

address: 975 N Warson Rd

country: USA

institute: Donald Danforth Plant Science Center

description:
Library name: BSAS_T1_Cas9-0xBS_bio_rep_1
Bisulfite amplicon sequencing (BSAS)

library_source: genomic

data_processing:
Raw reads were trimmed for adapters and mapped to all the amplicons pooled together for sequencing using methylpy (https://github.com/yupenghe/methylpy)
Assembly: Custom genome containing amplicon sequences
Supplementary files format and content: allC tsv files containing methylation results produced from methylpy

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: All Arabidopsis plants were grown at 22°C on Pro-Mix FPX soil in Conviron MTPS-120 growth chambers under the long day (16 hours light / 8 hours dark) in the Plant Growth Facility at the Donald Danforth Plant Science Center.

extract_protocol:
Genomic DNA was extracted using DNA Extraction Buffer followed by isopropanol precipitation.
DNA  was treated with RNAse A, recovered with phenol chloroform isolation then treated with sodium bisulfite using the EZ DNA methylation kit (Zymo Research). PCR-amplified amplicons were gel-purified and pooled in equimolar ratios. The Illumina Nextera DNA Flex kit (https://doi.org/10.1101/779215) was used to prepare the library. Single-end Illumina sequencing of 300 bp with an Illumina MiSeq.

tag: tissue

value: Inflorescence

tag: cell line

value: other

tag: cell type

tag: genotype


title: T84 IFNLR KO cells at high density, replicate 3

city: Gainesville

first: Yagmur

last: Keser

state: Florida

address: 1200 Newell Dr.

department: Molecular Genetics and Microbiology (MGM)

institute: University of Florida

description: sample 15

library_source: transcriptomic

data_processing:
Novogene Illumina PE150 sequencing was used.
Assembly: GRCh38 - hg38
Supplementary files format and content: tap deliminated 'gene_count.txt' file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Wild type (WT) T84 as well as T84 reporter and knock-out (KO) cells were cultured in a 50:50 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM) and F12 supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and 100 μg/mL streptomycin. All cells were cultured on collagen coated surfaces, and were kept in a constant humid atmosphere at 37°C, 5% CO2 and 21% oxygen.

extract_protocol:
RNA was isolated using the RNAeasy RNA extraction kit. ≥ 200 ng of total RNA was used to generate sequencing library.
RNA libraries were prepared for RNA-sequencing by Novogene.

treatment_protocol: For high cell density, 2.2x10^5 cells/cm2 were seeded. One-day post-seeding, medium was exchanged with fresh medium, and two days post-seeding, cells were harvested for sequencing. For low cell density, 2.7x10^4 cells/cm2 were seeded. One-day post-seeding cell were harvested for sequencing.

value: intestinal epithelial cells

value: IFNLR KO

tag: treatment

value: high density


title: Fixation_DSP_HEK293T_Anti-G3BP1_rep2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

country: China

institute: Peking University

description: HEK293T_fixative_editing.tsv.gz;HEK293T_fixative_TPM.tsv.gz

data_processing:
Reads mapping to abundant RNA types were discarded using BWA-MEM (v0.7.17), retaining unmapped reads for further analysis. The processed reads were aligned to the human genome (hg38) via a two-round mapping strategy designed to capture more mismatches for RNA editing candidates, sequentially utilizing HISAT2 (v2.2.1) and BWA-MEM, with GENCODE (v40) as the transcriptome guide. Unique mapped reads with up to 0.04 mismatches per fragment relative to read length were selected using pysam (v0.22.1) (https://github.com/pysam-developers/pysam) for subsequent analysis. PCR duplicates were removed using Picard (v3.1.1) (https://github.com/broadinstitute/picard).
All usable reads spanning exon-exon junctions were segmented using the GATK (v4.5.0.0) SplitNCigarReads command. Base quality scores were recalibrated using two rounds of GATK BaseRecalibrator and ApplyBQSR commands. RNA variants were identified from BAM files of usable reads via the GATK HaplotypeCaller command. RNA single nucleotide variants were selected using the GATK SelectVariants command. Single nucleotide polymorphisms (SNPs) from dbSNP (v151), the 1000 Genomes Project, and the University of Washington Exome Sequencing Project were removed in SNVs. Raw counts were quantified using Subread featureCounts (v2.0.1) and normalized to transcripts per million (TPM) as gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM
Supplementary files format and content: tab-delimited text including RNA editing data

molecule: polyA RNA

source_name: HEK293T cell line

growth_protocol: HeLa and HEK293T cells were cultured in high glucose DMEM supplemented with 10% (v/v) FBS and 1% (v/v) PS.All cells were maintained at 37°C with 5% CO2.

extract_protocol:
For large samples, total RNA was extracted following the standard TRIzol protocol (Invitrogen) for bulk RNA library construction. For small samples, mRNA was isolated with Oligo d(T)25 Magnetic Beads (NEB, S1419S) and directly subjected to Smart-seq2 protocol, as detailed in Plate-based scMAPIT-seq.
RNA-seq library was generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604) or Smart-seq2 protocol.

value: HEK293T cell line

value: WT

tag: fixation

value: DSP

tag: primary antibody

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

tag: secondary antibody

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)

tag: pag-deaminase

tag: inhouseid


title: CHIPseq, WT, rep3

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: Library name: CHIPseq_WT_rep3

library_source: other

data_processing:
For all sequencing data, a sequencing quality profile was generated using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using bwa-mem tools (BWA (Version 0.7.17) and reference genome GCA_000001405.15_GRCh38 (Li, 2013). In parallel reads were aligned to the D.melanogaster genome BDGP6 to quantify spike-in counts. Only uniquely mapping and high-quality reads (> q30) were included in the analyses. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
OK-seq data in untreated RPE1 cells was downloaded from Chen et al. 2019 (datasets GSM3130725 and GSM3130726). Sequences were trimmed using TrimGalore (Version 0.6.5), and aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Replication initiation zones were subsequently defined using the replication fork directionality analysis R toolkit (OKseqHMM; available on https://github.com/CL-CHEN-Lab/OK-Seq), with read coverage threshold 6 for GSM3130725 and 1 for GSM3130726, and smoothing window size 15 kb. Initiation zones present in both datasets were identified using mergePeaks of HOMER tools (Version 4.8.2), with -d given. Origins were defined as the center of initiation zones. For all origins, their nearest TSS was defined using annotatePeaks of HOMER tools, together with the distance between the TSS and the origin. Here, a negative distance represents an origin upstream of the TSS (co-directional transcription relative to replication), while a positive distance represents an origin downstream of a TSS (head-on transcription relative to replication). To allow for clean transcription versus replication analyses, we further selected only origins for which their nearest TSS was not preceded by another gene within 5kb upstream of the TSS. This resulted in a list of 2,040 origins.  A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. These 3,000 actively transcribed genes were used in downstream analyses, unless stated otherwise.
Read-density profiles around origin or TSS/TTS coordinates were defined using the AnnotatePeaks.pl tool of HOMER using normalization to 10M reads (for profiles around origins), or to the number of identified Drosophila spike-in reads (for profiles around TSSs of transcribed genes). Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019). Where indicated, average profiles were trimmean 0.1 (0.05 from top, 0.05 from bottom) to remove extreme values.
Assembly: Hg38
Supplementary files format and content:
TSScoordinates_InclBrUseqInWTmock.txt: tab-delimited text file containing coordinates of 9944 TSSs, including associated BrUseq signal in WT cells
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_WT_mock_rep1.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20KO_mock_rep1.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20-CCNC-dKO_mock_rep1.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
OriginCenter_OKseq_Select5kbUpstreamTSSempty.txt: tab-delimited text file containing coordinates of origins identified as described.
ChIPseqRPB1_ReadDensityAroundOKseqOrigins_200KbWindow_WT_rep*.txt: tab-delimited text file containing read-density/10M reads at the indicated distance from a set of origins

molecule: other

source_name: RPE1 iCas9 p53/puro-dKO WT

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 in DMEM GlutaMAX (Gibco), supplemented with 10% fetal calf serum (Avantor, VWR) and penicillin/streptomycin (Sigma).

extract_protocol:
Attached cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed once with PBS followed by incubation with 1% FA for 20 min at RT. Fixation was stopped by the addition of glycine in PBS to a final concentration of 0.1 M for 3 min at RT. This was followed by washing with cold PBS and collection of the cells in 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), and 20 mM Hepes (pH 7.6) in miliQ. Chromatin was pelleted by centrifugation for 5 min at 400 × g and incubated in 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) in miliQ for 10 min at 4 °C. Chromatin was again pelleted by centrifugation and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6) in miliQ) to a final concentration of 15 × 10^6 cells/mL. Chromatin was sonicated to approximately one nucleosome using the Bioruptor Pico (Diagenode), 15 cycles of 30s ON/30 s OFF in a 4°C water bath. ChIP was performed using 28 μg of chromatin (22 μg for CFAP20/CCNC-KO) + 40 ng of Drosophila spike-in chromatin (32.6 ng for CFAP20/CCNC-KO; Active Motif, 53083) with 3 μl of RNAPII antibody (Active Motif, 61686) and 1 μg spike-in antibody (Active Motif, 61686) by overnight incubation at 4 °C. Protein-chromatin-pull down followed with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D, 10003D). ChIP samples were extensively washed and purified using Qiagen MinElute kit.
Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NextSeq500 or HiSeq X, using paired-end sequencing with 42 or 151 bp from each end.

treatment_protocol: Cells were grown to 80-90% confluency

value: RPE1 iCas9 p53/puro-dKO WT

tag: genome used_to_map_to

value: Hg38 | BDGP6 (spike-in)

value: untreated

tag: pulldown antibody

value: Rabbit anti-RPB1 (Active Motif, 61686) | anti-D.Melanogaster H2Av (Active Motif, 61686)

tag: type of_material

value: ChIP DNA


title: Fixation_DSP_HEK293T_Anti-G3BP1_rep1


title: Fixation_DSP_HEK293T_IgG_rep2

value: rabbit IgG (CST, 2729S)


title: SplenocyteTconv_RRBS_25ng_01

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

description: Splenic Tconv cells from 18-20 week-old healthy mice

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

organism: Mus musculus

extract_protocol:
Genomic DNA was extracted from flow cytometry-sorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. For WGEM-seq libraries, gDNA was first fragmented to a size of 240–290-bp using the Covaris E220 sonicator and then enzymatically converted with TET2 and APOBEC (New England Biolabs) per the manufacturer’s instructions. For WGBS libraries, gDNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Additional restriction enzyme digestion step was included for RRBS and RREM-seq libraries, in which gDNA was fragmented with MspI (New England Biolabs) and then size-selected for 100- to 250-bp fragments using solid-phase reversible immobilization beads (MagBio Genomics). CG-enriched gDNA was then bisulfite converted for RRBS libraries and enzymatically converted for RREMseq libraries. Random priming, adaptor ligation, PCR product clean-up, and final library amplification were performed using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs) for WGEM-seq libraries and the Pico Methyl-Seq Library Prep Kit (Zymo Research) was used for WGBS, RRBS, and RREM-seq libraries. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and four pooled libraries per run were sequenced on an Illumina NextSeq 2000 instrument using the 200 cycles NextSeq 2000 P3 reagent kit (whole-genome libraries) or the 100 cycles NextSeq 2000 P2 reagent kit (reduced representation libraries).
EM-seq (whole-genome and reduced representation) and Bisulfite-seq (whole-genome and reduced representation)


title: SplenocyteTconv_RRBS_25ng_02


title: Fixation_DSP_HEK293T_IgG_rep1


title: T84 IFNLR KO cells at high density, replicate 1

description: sample 13


title: T84 IFNLR KO cells at high density, replicate 2

description: sample 14


title: SplenocyteTconv_WGEM-seq_25ng_02

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Library strategy: WGEM-seq


title: Fixation_input_HEK293T_untreated_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S234

city: Thousand Oaks

first: Abraham

last: Anderson

state: California

address: 1 amgen center drive

institute: Amgen Inc.

description: Library name: S234

data_processing:
Transcript level pseudo-alignment and quantification to the Ensembl GRCh37 Release 97 (July 2019) reference was performed using Kallisto (version 0.44). Raw counts or transcripts per million (TPM) were calculated for 180,253 transcripts in the Ensembl reference. 134,160 transcripts were covered by the Tempus|RS panel.
Assembly: Ensembl GRCh37 Release 97 (July 2019)
Supplementary files format and content: tab-delimited text file with columns for ensembl_gene, hgnc_symbol, <sampleID>. TPM values are in the <sampleID> column.

source_name: tumor biopsy

extract_protocol:
Total nucleic acid (TNA) was extracted from tissue specimens using a Chemagic 360 or similar instrumentation, and the recovered TNA was quantified and qualified, and may have been concentrated if necessary. Extracted TNA that was intended for processing by Tempus|RS was treated with Invitrogen TURBO DNase to degrade DNA. The minimum amount of input total RNA required to perform the test was 50 ng. RNA was fragmented using heat and magnesium, with variable parameters, to yield similar sized fragments from RNA inputs with different starting size distributions.
Strand-specific library preparation was performed using the KAPA RNA HyperPrep Kit for Illumina with KAPA single indexed 6 base pair adapters. The libraries were amplified with high fidelity, low-bias PCR using primers complementary to adapter sequences. After library preparation and amplification, targets were captured by hybridization, clean-up of captured targets was performed, and unbound fragments were washed away. Library capture is conducted using the xGen Exome Research Panel v1 probe set, along with the xGen Hybridization and Wash Kit and xGen Universal Blockers. The enriched targets are amplified using the KAPA HiFi HotStart ReadyMix and primers supplied in the KAPA Library amplification kit, followed by a magnetic bead-based clean-up. The amplified target-captured libraries were sequenced with a 2x76 read length to an average of 50 million total reads on an Illumina HiSeq4000 System using patterned flowcells.

value: tumor biopsy

tag: study

tag: atm

tag: kpclsignature

value: KP

value: low


title: T84 IFNL2/3 KO cells at low density, replicate 3

description: sample 12

value: intestinal epithelial cells

value: IFNL2/3 KO

value: low density


title: SplenocyteTreg_RREM-seq_2ng_02

description: Splenic Treg cells from 18-20 week-old healthy mice

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Library strategy: RREM-seq


title: Fixation_input_HEK293T_untreated_rep1

value: HEK293T cell line


title: pre-treatment tumor RNA from individual with NSCLC_S233

description: Library name: S233


title: T84 IFNL2/3 KO cells at low density, replicate 2

description: sample 11


title: pre-treatment tumor RNA from individual with NSCLC_S232

description: Library name: S232

value: KL


title: CHIPseq, WT, rep2

description: Library name: CHIPseq_WT_rep2


title: T84 IFNL2/3 KO cells at low density, replicate 1

description: sample 10


title: pre-treatment tumor RNA from individual with NSCLC_S230

description: Library name: S230

value: KC

value: high


title: T1 Cas9-1xBS bio rep 2

description:
Library name: BSAS_T1_Cas9-1xBS_bio_rep_2
Bisulfite amplicon sequencing (BSAS)

value: Inflorescence

value: other


title: 500cells_HeLa_Anti-G3BP1_rep1

source_name: HeLa cell line

value: HeLa cell line

value: WT

value: 500 cells

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: 500cells_HeLa_IgG_rep1

value: rabbit IgG (CST, 2729S)


title: SplenocyteTreg_RREM-seq_25ng_01


title: T84 IFNL2/3 KO cells at high density, replicate 1

description: sample 7

value: high density


title: T84 IFNL2/3 KO cells at high density, replicate 3

description: sample 9


title: 500cells_HeLa_IgG_rep2


title: SplenocyteTreg_RRBS_25ng_02


title: T84 IFNL2/3 KO cells at high density, replicate 2

description: sample 8


title: 5Kcells_HeLa_Anti-G3BP1_rep2

value: 5000 cells


title: SplenocyteTreg_RREM-seq_25ng_02


title: pre-treatment tumor RNA from individual with NSCLC_S229

description: Library name: S229

value: tumor biopsy

value: KP

value: low


title: SplenocyteTreg_RRBS_25ng_01


title: T84 WT cells at low density, replicate 3

description: sample 6

value: intestinal epithelial cells

value: low density


title: SplenocyteTconv_WGEM-seq_25ng_01


title: 500cells_HeLa_Anti-G3BP1_rep2


title: SplenocyteTreg_RREM-seq_2ng_01


title: 5Kcells_HeLa_Anti-G3BP1_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S226

description: Library name: S226

value: KL


title: SplenocyteTreg_WGEM-seq_25ng_02


title: T84 WT cells at low density, replicate 2

description: sample 5


title: pre-treatment tumor RNA from individual with NSCLC_S231

description: Library name: S231

value: KC

value: high


title: 5Kcells_HeLa_IgG_rep2


title: T84 WT cells at low density, replicate 1

description: sample 4


title: pre-treatment tumor RNA from individual with NSCLC_S225

description: Library name: S225


title: SplenocyteTreg_WGEM-seq_25ng_01


title: PacBioHiFi_HEK293_DSP_IgG

data_processing:
Isoseq (v4.0.0) refine command was employed to remove polyA tails and concatemers from full-length (FL) reads, generating full-length non-chimeric (FLNC) transcripts. FLNC BAM files were converted to FASTQ format using bedtools (v2.31.1) bamtofastq command. Minimap2 (v2.28) was utilized to align FLNC transcripts to the human genome (hg38) guided by GENCODE v40 transcript annotation. IsoQuant (v3.4.1) was then used to assign reads to annotated isoforms based on their intron and exon structures, filter non-uniquely assigned or ambiguous reads, and quantify transcript expression.
Reads uniquely assigned to isoforms were annotated with transcript and gene ENSEMBL IDs in alignment BAM files using the package pysam (v0.22.1) by adding tags in BAM files. BAMtools (v2.5.2) was subsequently used to split the BAM files into single-transcript alignment BAM files. RNA editing detection for each single-transcript alignment BAM file was performed using Reditools2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM in the isoform level
Supplementary files format and content: tab-delimited text including RNA editing data in the isoform level

source_name: HEK293 cell line

growth_protocol: HEK293T cells were cultured in high glucose DMEM supplemented with 10% (v/v) FBS and 1% (v/v) PS.All cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted following the standard TRIzol protocol (Invitrogen).
RNA-seq library was constructed using the Kinnex full-length RNA kit (Pacbio, 103-072-000).

treatment_protocol: Other

value: HEK293 cell line

value: DSP

value: DI


title: T84 WT cells at high density, replicate 3

description: sample 3

value: WT


title: pre-treatment tumor RNA from individual with NSCLC_S224

description: Library name: S224


title: PacBioHiFi_HEK293_DSP_Anti-G3BP1

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: DG


title: 50Kcells_HeLa_Anti-G3BP1_rep1

value: HeLa cell line

value: 50000 cells

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: pre-treatment tumor RNA from individual with NSCLC_S227

description: Library name: S227

value: tumor biopsy


title: T84 WT cells at high density, replicate 1

description: sample 1

value: high density


title: 5Kcells_HeLa_IgG_rep1

value: 5000 cells

value: rabbit IgG (CST, 2729S)


title: pre-treatment tumor RNA from individual with NSCLC_S228

description: Library name: S228

value: low


title: pre-treatment tumor RNA from individual with NSCLC_S223

description: Library name: S223


title: T84 WT cells at high density, replicate 2

description: sample 2

value: intestinal epithelial cells


title: 50Kcells_HeLa_IgG_rep2


title: PacBioHiFi_HEK293_FA_IgG

value: FI


title: 50Kcells_HeLa_Anti-G3BP1_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S220

description: Library name: S220

value: KP


title: pre-treatment tumor RNA from individual with NSCLC_S222

description: Library name: S222

value: KC


title: PacBioHiFi_HEK293_FA_Anti-G3BP1

value: HEK293 cell line

value: FG


title: SecondaryAb_HEK293T_Anti-G3BP1_rep2

description: HEK293T_secondaryAb+-_editing.tsv.gz;HEK293T_fixative_editing.tsv.gz

value: HEK293T cell line

value: WT


title: Whole Blood, H11_177

type: RNA

city: London

first: Paula

last: Longhi

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary, University of London

description: Gene expression data from human whole blood

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: rma

label: biotin

source_name: Whole Blood

label_protocol: Affymetrix protocol

extract_protocol: RNA from whole blood was extracted using the PAXgene blood RNA isolation kit.

value: Whole Blood

tag: age

tag: surgery

value: Valve

tag: gender

value: Male


title: PRC2_HEK293T_Anti-CHTOP_rep1

tag: cell line

value: Anti-CHTOP (Invitrogen, PA544307)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: SecondaryAb_HEK293T_IgG_rep1

tag: genotype


title: PRC2_HEK293T_Anti-SUZ12_rep2

tag: treatment

value: Anti-SUZ12 (CST, 3737)


title: Whole Blood, H10_165

tag: tissue


title: NosecondaryAb_HEK293T_IgG_rep2

tag: fixation

tag: primary antibody


title: SecondaryAb_HEK293T_Anti-G3BP1_rep1

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

tag: secondary antibody

tag: pag-deaminase


title: pre-treatment tumor RNA from individual with NSCLC_S215

description: Library name: S215

value: tumor biopsy


title: Whole Blood, H08_112


title: SecondaryAb_HEK293T_IgG_rep2

value: rabbit IgG (CST, 2729S)

tag: inhouseid


title: pre-treatment tumor RNA from individual with NSCLC_S219

description: Library name: S219

value: KL

value: low


title: 50Kcells_HeLa_IgG_rep1

value: HeLa cell line

value: 50000 cells


title: PRC2_HEK293T_Anti-CHTOP_rep2


title: PRC2_HEK293T_IgG_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S218

description: Library name: S218

value: KP


title: Whole Blood, H09_84


title: Whole Blood, H06_184

value: CABG


title: NosecondaryAb_HEK293T_Anti-G3BP1_rep1

value: HEK293T cell line


title: Whole Blood, H05_134


title: PRC2_HEK293T_Anti-EZH2_rep2

value: WT

value: Anti-EZH2 (CST, 5246)


title: PRC2_HEK293T_IgG_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S213

description: Library name: S213


title: pre-treatment tumor RNA from individual with NSCLC_S217

description: Library name: S217

value: high


title: Whole Blood, H07_172

value: Whole Blood

value: Valve

value: Female


title: pre-treatment tumor RNA from individual with NSCLC_S216

description: Library name: S216


title: pre-treatment tumor RNA from individual with NSCLC_S221

description: Library name: S221


title: Whole Blood, H04_171

value: Male


title: NosecondaryAb_HEK293T_IgG_rep1


title: PRC2_HEK293T_Anti-EED_rep2

value: Anti-EED (CST, 85322)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: PRC2_HEK293T_Anti-SUZ12_rep1

value: Anti-SUZ12 (CST, 3737)


title: FA0.5_HeLa_IgG_rep1

description: HeLa_FAconcentration_TPM.tsv.gz;HeLa_FAconcentration_editing.tsv.gz

value: rabbit IgG (CST, 2729S)


title: NosecondaryAb_HEK293T_Anti-G3BP1_rep2

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: pre-treatment tumor RNA from individual with NSCLC_S214

description: Library name: S214

value: tumor biopsy

value: low


title: PRC2_HEK293T_Anti-EZH2_rep1


title: PRC2_HEK293T_Anti-EED_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S210

description: Library name: S210

value: KP


title: FA0.5_HeLa_IgG_rep2

value: HeLa cell line


title: FA0.2_HeLa_IgG_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S209

description: Library name: S209


title: FA0.2_HeLa_IgG_rep1


title: FA0.1_HeLa_IgG_rep1


title: Whole Blood, H01_154


title: pre-treatment tumor RNA from individual with NSCLC_S211

description: Library name: S211

value: KL


title: FA0.5_HeLa_Anti-G3BP1_rep2

value: WT


title: HeLa_siG3BP1_untreated_rep1

description: HeLa_siG3BP1_TPM.tsv.gz;HeLa_siG3BP1_DEGs_DESeq2.tsv.gz


title: pre-treatment tumor RNA from individual with NSCLC_S212

description: Library name: S212


title: HeLa_siNC_untreated_rep1

value: si-NC


title: HeLa_siG3BP1_Anti-G3BP1_rep2

description: HeLa_siG3BP1_TPM.tsv.gz;HeLa_siG3BP1_editing.tsv.gz


title: Whole Blood, G12_164


title: pre-treatment tumor RNA from individual with NSCLC_S206

description: Library name: S206

value: KC

value: high


title: Whole Blood, H02_103

value: Whole Blood

value: Valve


title: pre-treatment tumor RNA from individual with NSCLC_S208

description: Library name: S208


title: HeLa_siNC_untreated_rep2


title: Whole Blood, G11_107

value: Female


title: pre-treatment tumor RNA from individual with NSCLC_S205

description: Library name: S205


title: HeLa_siG3BP1_untreated_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S204

description: Library name: S204


title: HeLa_siG3BP1_IgG_rep2


title: FA0.5_HeLa_Anti-G3BP1_rep1


title: Whole Blood, G10_168


title: HeLa_siG3BP1_Anti-G3BP1_rep1


title: FA0.1_HeLa_Anti-G3BP1_rep2


title: FA0.2_HeLa_Anti-G3BP1_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S202

description: Library name: S202


title: Whole Blood, G08_122

value: CABG

value: Male


title: Whole Blood, G07_90


title: HeLa_siNC_Anti-G3BP1_rep1

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: HeLa_siNC_Anti-G3BP1_rep2


title: Untreated_HeLa_rep2


title: FA0.2_HeLa_Anti-G3BP1_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S207

description: Library name: S207


title: Untreated_HeLa_rep1


title: Whole Blood, G05_146


title: Whole Blood, G09_181


title: Whole Blood, G06_155


title: pre-treatment tumor RNA from individual with NSCLC_S203

description: Library name: S203


title: Whole Blood, H03_143


title: HeLa_siNC_IgG_rep2

value: rabbit IgG (CST, 2729S)


title: HeLa_siNC_IgG_rep1


title: HeLa_siG3BP1_IgG_rep1


title: Whole Blood, G02_139


title: OE-DF2-FLAG_Anti-FLAG_secondaryAb_rep2

value: Anti-FLAG (Sigma, F1804)

value: rabbit anti-mouse (Abcam, catalog no. ab46450)


title: pre-treatment tumor RNA from individual with NSCLC_S199

description: Library name: S199

value: tumor biopsy

value: low


title: Whole Blood, G04_189


title: pre-treatment tumor RNA from individual with NSCLC_S201

description: Library name: S201

value: KP


title: Diff7-Unstim

city: Ridgefield

first: Aleksandra

last: Ivovic

address: 900 Ridgebury Rd

institute: Boehringer Ingelheim

description: Library name: a0e72abc-c72d-4571-8283-2adcf6f599c6

data_processing:
Sequencing reads from bulk RNA-seq experiments were aligned using STAR aligner version 2.5.2b and aligned against human reference genome hs38d1_ensembl86. Transcript abundances were calculated using featureCounts software version 1.5.1.
Assembly: hs38d1_ensembl86
Supplementary files format and content: A comma-separated text file containing sample-level raw count information.

source_name: iPSC

extract_protocol:
MagMax total RNA kit (#AM1830) from Invitrogen
Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First  strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: iPSC

value: IDM 201B7

tag: cell type

value: iPSC-derived macrophage

value: Medium

tag: batch


title: Whole Blood, G03_81


title: OE-DF2-FLAG_Anti-FLAG_secondaryAb_rep1

value: HeLa cell line


title: HEK293T_Anti-PTBP1_rep2

description: HEK293T_diffAb_PTBP1_editing.tsv.gz;HEK293T_diffAb_PTBP1_TPM.tsv.gz

value: HEK293T cell line

value: WT

value: Anti-PTBP1 (Milipore, MABE986)


title: pre-treatment tumor RNA from individual with NSCLC_S198

description: Library name: S198

tag: study

value: KL


title: Diff7-5ng-mL-TNFa

description: Library name: 8f64a9b6-567f-41db-8627-e14e7cf289ba


title: HEK293T_Anti-G3BP1-Abcam_rep2

value: Anti-G3BP1 (Abcam, ab56574)


title: pre-treatment tumor RNA from individual with NSCLC_S196

description: Library name: S196

tag: atm


title: Diff7-0-4ng-mL-IFNy

description: Library name: 0ae0f864-71c1-414f-bb47-a3dd039b2790


title: Diff7-2ng-mL-TGFb

description: Library name: 21a54112-598e-4aac-a24b-1dad7c81abb0


title: OE-DF2-FLAG_IgG_secondaryAb_rep2

value: mouse IgG (Santa Cruz, sc-2025)


title: HEK293T_Anti-PTBP1_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S195

description: Library name: S195

tag: kpclsignature

value: KC


title: HEK293T_Anti-G3BP1-Abcam_rep1


title: HEK293T_mIgG_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S194

description: Library name: S194


title: Diff6-5ng-mL-TNFa

description: Library name: d8778bd7-2371-440c-87bc-86a91d989ea7


title: HEK293T_Anti-G3BP1-Proteintech_rep2

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: pre-treatment tumor RNA from individual with NSCLC_S192

description: Library name: S192

value: tumor biopsy


title: OE-DF2-FLAG_IgG_rep2


title: Diff6-Unstim

description: Library name: 8475233a-7d16-465d-9873-faf4756ed8bd


title: OE-DF2-FLAG_NC_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S193

description: Library name: S193

value: low


title: HEK293T_mIgG_rep1

value: rabbit anti-mouse (Abcam, catalog no. ab46450)


title: Diff6-0-4ng-mL-IFNy

description: Library name: 72a805b5-fde3-463d-b4ce-8e98e2482381

value: iPSC


title: HEK293T_rIgG_rep2

value: rabbit IgG (CST, 2729S)


title: OE-DF2-FLAG_NC_rep1


title: Diff6-5ng-mL-IL1B

description: Library name: aa7bffad-3ea4-4566-a154-ff168028e97c

value: IDM 201B7

value: iPSC-derived macrophage


title: pre-treatment tumor RNA from individual with NSCLC_S189

description: Library name: S189


title: OE-DF2-FLAG_Anti-FLAG_rep2

value: HeLa cell line

value: Anti-FLAG (Sigma, F1804)


title: pre-treatment tumor RNA from individual with NSCLC_S191

description: Library name: S191

value: KP


title: HEK293T_Anti-G3BP1-Proteintech_rep1

value: HEK293T cell line

value: WT


title: FA0.1_HeLa_IgG_rep2


title: OE-DF2-FLAG_IgG_rep1


title: OE-DF2-FLAG_IgG_secondaryAb_rep1


title: Diff7-5ng-mL-IL1B

description: Library name: cf697b46-7e51-4bd2-98ca-70dd8b179af1


title: Diff6-2ng-mL-TGFb

description: Library name: 76cd0e2e-0938-4039-a0ef-b5b79324abd3


title: Diff5-5ng-mL-TNFa

description: Library name: 176b8fde-2d2a-480f-8096-7a98ce908d55


title: HEK293T_rIgG_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S197

description: Library name: S197

value: KL


title: OE-DF2-FLAG_Anti-FLAG_rep1


title: DHL10ZOTA2RNA070122

city: miami

first: Jonathan

middle: H

last: Schatz

address: 1580 NW 10th Ave 1st floor

department: Department of Medicine

institute: university of miami

data_processing:
Picard was used to analyze the reads.
STAR was used to align the reads to Hg38.
Cutadapt was used to process the data.
Assembly: Hg38
Supplementary files format and content: tab delimited text file containing raw counts for each sample

source_name: cell lines

growth_protocol: RPMI1 with 10% FBS  and penicillin/streptomycin

extract_protocol:
Treated cells were spun down and RNA was isolated using Qiagen RNA extraction kit .
Total RNA was prepped with the Nugen Universal Plus mRNA-Seq with NuQuant (M01485 v6) using 500ng via Qubit and 14 cycles PCR. Libraries were sequenced on Illumina Novaseq 6000 and ~35M PE100 reads were generated per sample.

treatment_protocol: zotatifin (12.5 nM for 24 hours) or DMSO

value: cell lines

value: DLBCL

value: ZOTA

value: ZOTATIFIN


title: OE-FLAG_Anti-FLAG_rep2

value: OE-FLAG


title: OE-FLAG_Anti-FLAG_rep1


title: Diff5-5ng-mL-IL1B

description: Library name: e386a759-49a6-4c88-a906-a5ba2fb193bc


title: pre-treatment tumor RNA from individual with NSCLC_S187

description: Library name: S187

value: tumor biopsy

value: low


title: pre-treatment tumor RNA from individual with NSCLC_S186

description: Library name: S186


title: DHL10ZOTA1RNA070122


title: Enzyme36_HEK293T_Anti-G3BP1

description: HEK293T_pAG-deaminases_concentration_editing.tsv.gz;

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)

value: 36 μg/ml rAPOBEC1-pAG-hADAR2


title: Diff5-2ng-mL-TGFb

description: Library name: f07b59a3-b57b-489a-9d1d-9605c46ba56b

value: iPSC

value: IDM 201B7

value: iPSC-derived macrophage


title: pre-treatment tumor RNA from individual with NSCLC_S185

description: Library name: S185

value: KC

value: high


title: Enzyme36_HEK293T_IgG

value: HEK293T cell line

value: WT

value: rabbit IgG (CST, 2729S)


title: Diff5-0-4ng-mL-IFNy

description: Library name: 9deb72e6-74b3-4895-a824-10f076fcf218


title: DHL10ZOTA3RNA070122

value: cell lines

value: DLBCL


title: pre-treatment tumor RNA from individual with NSCLC_S200

description: Library name: S200

value: KL


title: pre-treatment tumor RNA from individual with NSCLC_S188

description: Library name: S188


title: DHL10DMSO1RNA070122

value: DMSO

value: control DMSO


title: Enzyme30_HEK293T_Anti-G3BP1

value: 30 μg/ml rAPOBEC1-pAG-hADAR2


title: pre-treatment tumor RNA from individual with NSCLC_S190

description: Library name: S190

value: tumor biopsy

value: low


title: Diff4-Unstim

description: Library name: 27e8395c-09c2-4050-a08a-0152c06f2f49

value: Medium


title: Diff4-5ng-mL-IL1B

description: Library name: 72cf4fb8-2416-490e-9057-fe7cd6ae7539

value: iPSC


title: pre-treatment tumor RNA from individual with NSCLC_S183

description: Library name: S183

value: KP


title: Enzyme24_HEK293T_IgG

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)

value: 24 μg/ml rAPOBEC1-pAG-hADAR2


title: DHL10DMSO2RNA070122


title: pre-treatment tumor RNA from individual with NSCLC_S182

description: Library name: S182

value: high


title: Diff4-5ng-mL-TNFa

description: Library name: 6deeb210-590f-42bd-80c7-3562067af837

value: IDM 201B7

value: iPSC-derived macrophage


title: Enzyme24_HEK293T_Anti-G3BP1

value: HEK293T cell line

value: WT

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: Diff5-Unstim

description: Library name: 6ec247d0-d89d-4768-9aa9-24ac7d24aba6


title: Diff3-Unstim

description: Library name: d5b03858-bcfd-454e-854d-c347364533d3


title: pre-treatment tumor RNA from individual with NSCLC_S179

description: Library name: S179

value: KC


title: pre-treatment tumor RNA from individual with NSCLC_S178

description: Library name: S178


title: Diff4-0-4ng-mL-IFNy

description: Library name: a9121f7f-6a1d-4336-8a02-f7486ff042d0


title: Enzyme30_HEK293T_IgG

value: rabbit IgG (CST, 2729S)


title: DHL10DMSO3RNA070122

value: cell lines

value: DLBCL

value: DMSO

value: control DMSO


title: Enzyme18_HEK293T_IgG

value: 18 μg/ml rAPOBEC1-pAG-hADAR2


title: A2 Lung

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 28+50-base paired-end mode.
Raw sequencing data for the sample was converted to a matrix of expression using Space Ranger version: 1.3.0 (10X Genomics).
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
The gene expressions of human FFPE slide were detected by Visium CytAssist and 10x Visium Spatial Gene Expression Reagent Kits for FFPE.
RNA libraries were prepared by using 10x Visium spatial protocols.

value: Lung


title: pre-treatment tumor RNA from individual with NSCLC_S184

description: Library name: S184

value: tumor biopsy


title: HCC1954, RIT treated, Rep10

city: Los Angeles

first: Claire

last: Storey

state: CA

address: 10833 Le Conte Ave

institute: UCLA

data_processing:
Bbsplit was used to separate mouse and human reads. Alignment of reads was done via the STAR algorithm as previously described (23104886).
Ambiguous reads were discarded and FastQC analysis was utilized to confirm sequence quality. Low read count filtering was used to remove transcriptomic features for which fewer than 4 samples had at least 5 read counts of a gene.
Assembly: Hg38 and Mm19
Supplementary files format and content: CSV file containing raw human read counts
Supplementary files format and content: CSV file containing raw human murine counts

source_name: XENOGRAFT

growth_protocol: U118MG (glioblastoma), HCC1954 (breast cancer), were purchased from ATCC. HuO9 (osteosarcoma) was purchased from the Japanese Cancer Research Resources Bank (Tokyo, Japan). All cell lines were cultured according to the manufacturer’s instructions and frequently tested for Mycoplasma.

extract_protocol:
Tumor tissue was preserved in RNAlater stabilization solution before isolation with the Qiagen Rneasy kit (Catalog #74004)
RNA quality control was assayed via TapeStation (Agilent) and stranded mRNA library preparation performed in accordance with Illumina protocols.

treatment_protocol: Animals received either 20-50MBq Lutetium-177 labeled DUNP19 or PBS intravenously.

value: XENOGRAFT

value: Breast Cancer

value: 20MBq DUNP19-177Lu, 53 day


title: Enzyme18_HEK293T_Anti-G3BP1

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: pre-treatment tumor RNA from individual with NSCLC_S180

description: Library name: S180

value: low


title: pre-treatment tumor RNA from individual with NSCLC_S181

description: Library name: S181

value: KP


title: D2 Lung


title: Enzyme42_HEK293T_Anti-G3BP1

value: HEK293T cell line

value: WT

value: 42 μg/ml rAPOBEC1-pAG-hADAR2


title: HCC1954, RIT treated, Rep9


title: Diff3-5ng-mL-TNFa

description: Library name: 6b4938ab-74bc-4136-b7c0-a301b4f38eb5

value: iPSC

value: IDM 201B7

value: iPSC-derived macrophage


title: Enzyme12_HEK293T_IgG

value: rabbit IgG (CST, 2729S)

value: 12 μg/ml rAPOBEC1-pAG-hADAR2


title: pre-treatment tumor RNA from individual with NSCLC_S177

description: Library name: S177

value: KL


title: pre-treatment tumor RNA from individual with NSCLC_S175

description: Library name: S175


title: pre-treatment tumor RNA from individual with NSCLC_S176

description: Library name: S176


title: Enzyme6_HEK293T_IgG

value: 6 μg/ml rAPOBEC1-pAG-hADAR2


title: Enzyme6_HEK293T_Anti-G3BP1

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: Diff3-2ng-mL-TGFb

description: Library name: 6c393b59-b89e-48a6-8dc7-1e3a57c5481e


title: Diff3-5ng-mL-IL1B

description: Library name: bc791176-be42-4926-ba0d-8f2d33185df5


title: pre-treatment tumor RNA from individual with NSCLC_S174

description: Library name: S174

value: tumor biopsy


title: Enzyme12_HEK293T_Anti-G3BP1


title: HCC1954, RIT treated, Rep6

value: XENOGRAFT

value: Breast Cancer


title: Diff2-Unstim

description: Library name: 29064eda-af4b-4ea8-b70f-4907b877575d

value: Medium


title: HCC1954, RIT treated, Rep5

value: 20MBq DUNP19-177Lu, 50 day


title: pre-treatment tumor RNA from individual with NSCLC_S173

description: Library name: S173

value: KP

value: low


title: HCC1954, RIT treated, Rep7

value: 20MBq DUNP19-177Lu, 53 day


title: Diff2-5ng-mL-TNFa

description: Library name: f3a1d7f7-96ee-48cb-8664-d93a02245427


title: Diff2-5ng-mL-IL1B

description: Library name: f889e437-722e-4d51-92e6-f2c0ee56e5b2


title: HCC1954, RIT treated, Rep8


title: HCC1954, RIT treated, Rep4

value: 20MBq DUNP19-177Lu, 34 day


title: Diff3-0-4ng-mL-IFNy

description: Library name: 3757e307-3bf5-4567-ba7c-5d43629c1495

value: iPSC


title: HCC1954, RIT treated, Rep3


title: pre-treatment tumor RNA from individual with NSCLC_S172

description: Library name: S172

value: KC


title: FA0.5_S_HEK293T_IgG_rep2

description: HEK293T_FAconcentration_pAG-deaminases_TPM.tsv.gz;HEK293T_FAconcentration_pAG-deaminases_editing.tsv.gz

value: HEK293T cell line

value: WT

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)

value: rAPOBEC1-pAG; hADAR2-pAG


title: FA0.5_S_HEK293T_IgG_rep1

value: rabbit IgG (CST, 2729S)


title: pre-treatment tumor RNA from individual with NSCLC_S171

description: Library name: S171


title: FA0.5_S_HEK293T_Anti-G3BP1_rep1

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: Diff2-2ng-mL-TGFb

description: Library name: 78c98529-cb83-4939-9671-30a21201b13f

value: IDM 201B7

value: iPSC-derived macrophage


title: HCC1954, RIT treated, Rep2

value: XENOGRAFT

value: Breast Cancer


title: pre-treatment tumor RNA from individual with NSCLC_S170

description: Library name: S170

value: tumor biopsy

value: KL


title: FA0.5_S_HEK293T_Anti-G3BP1_rep2


title: FA0.1_HeLa_Anti-G3BP1_rep1

description: HeLa_FAconcentration_TPM.tsv.gz;HeLa_FAconcentration_editing.tsv.gz

value: HeLa cell line


title: Diff2-0-4ng-mL-IFNy

description: Library name: d5b35764-5316-4d11-b02e-c81dfd83be5f


title: Diff4-2ng-mL-TGFb

description: Library name: 89132dfe-f2ae-40c8-9006-d0f3b02cdf39


title: HCC1954, PBS treated, Rep8

value: PBS, 34 day


title: FA0.5_AC_HEK293T_IgG_rep1


title: HCC1954, RIT treated, Rep1

value: 20MBq DUNP19-177Lu, 53 day


title: FA0.5_AC_HEK293T_Anti-G3BP1_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S169

description: Library name: S169

value: low


title: Pooled monocultures of WT iNs, WT iAs, and WT iMGLs

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description:
Library name: AL121
10X Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were mapped using the 10xGenomics Cellranger (v7.0.0) pipeline and a GRCh38 index and resulted in an average of >4K mapped and filtered reads per cell. Mappings and counts were analyzed using the Seurat package (v5.0.3) in R (v4.4.1) using RStudio (v1.4.1103). Briefly, imported Cellranger data were filtered to remove cells with <1000 or > 5000 mapped genes and with > 15% mapping to mitochondrial genes, and to remove suspected doublets. After filtering, normalized and scaled data were clustered using the 2000 most highly variable features. Uniform Manifold Approximation and Projection (UMAP) was run on the first 20 principal components.
Assembly: Human hg38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: iNs, iAs, iMGLs

extract_protocol:
Cells were dissociated with a 1:1 mixture of warm trypsin-EDTA:cold StemPro Accutase Cell Dissociation Reagent for 10min at 37°C. Trypsin was quenched with Trypsin Neutralization Solution (ScienCell, Cat# 0113-2) prior to collection of cell suspension. Cell suspensions were centrifuged for 5 min at 300 x g and resuspended in 1 mL of BrainPhys media. The cell pellet was triturated gently with a p1000 tip and passed through a 40µM Flowmi Cell Strainer (Millipore, BAH136800040-50) to remove debris. Cell suspensions were centrifuged at 200 rcf for 5min and resuspended in 0.04% BSA in PBS. Washes were repeated two more times. At the end of the final wash, cell suspension was passed through another 40µM Flowmi Cell Strainer and counted.
Each triple-culture was loaded onto an individual 10X Chromium Chip well (~64,000 cells per well) and resulting emulsions were used to generate scRNAseq libraries using the Chromium Next GEM Single Cell 3’ v3.1 chemistry. This loading results in a higher percentage of doublets (which are filtered downstream), ultimately yielding ~20,000 recovered singlet cells per 10x well. Libraries were multiplexed and sequenced on a NovaSeq to an average depth of >20K reads per cell based on estimated yields.

value: iNs, iAs, iMGLs

value: Monocultures


title: pre-treatment tumor RNA from individual with NSCLC_S168

description: Library name: S168

value: KC

value: high


title: HCC1954, PBS treated, Rep7

value: PBS, 21 day


title: pre-treatment tumor RNA from individual with NSCLC_S167

description: Library name: S167


title: HCC1954, PBS treated, Rep6

value: PBS, 14 day


title: fAD iNs cultures with WT iAs and WT iMGLs

description:
Library name: AL119
10X Genomics

value: fAD iNs


title: FA0.5_AC_HEK293T_Anti-G3BP1_rep1

value: HEK293T cell line

value: WT

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: pre-treatment tumor RNA from individual with NSCLC_S166

description: Library name: S166

value: tumor biopsy

value: KP


title: FA0.5_AC_HEK293T_IgG_rep2

value: rabbit IgG (CST, 2729S)


title: Enzyme42_HEK293T_IgG

description: HEK293T_pAG-deaminases_concentration_editing.tsv.gz;

value: 42 μg/ml rAPOBEC1-pAG-hADAR2


title: FA0.5_AN_HEK293T_IgG_rep2


title: D1 Lung

value: Lung


title: WT iNs cultures with WT iAs and WT iMGLs

description:
Library name: AL117
10X Genomics

value: WT iNs


title: HeLa_10xGenomics_IgG

description: scMAPIT-seq

data_processing:
The raw reads were aligned to the human genome (hg38) using STARsolo (v2.7.11b). Cells with fewer than 2,000 genes, fewer than 10,000 UMIs, more than 20% mitochondrial gene expression, and fewer than 5% or more than 30% ribosomal protein gene expression were excluded from further analyses using package Scanpy (v1.10.1).
Function CellCycleScoring in Seurat was used to identify cell cycle phases (G1, S, and G2/M) using the expression profiles of cells restricted to following cell cycle marker genes from function cc.genes in Seurat. Based on UMAP visualization, every cell cycle phase was split into ‘early’ and ‘late’ substages, with both substages containing approximately the same number of cells. Reads corresponding to these selected cells were extracted using the package pysam (v0.22.1) from the aligned BAM files. And UMI-tools (v1.1.4) was used for deduplication based on the mapping coordinate and the UMI attached to each read. BAMtools (v2.5.2) was then used to split the BAM files into single-cell alignment BAM files base on the “CB” tag. RNA editing detection for each single-cell alignment BAM file was performed using Reditools2.
Assembly: GRCh38
Supplementary files format and content: AnnData files with RNA expression and editing data

growth_protocol: HeLa cells were cultured in high glucose DMEM supplemented with 10% (v/v) FBS and 1% (v/v) PS.All cells were maintained at 37°C with 5% CO2.

extract_protocol: 10x Genomics v3.1 libraries were prepared according to the manufacturer’s instructions.

value: HeLa cell line

value: I


title: FA0.5_AN_HEK293T_IgG_rep1


title: FA0.2_AN_HEK293T_IgG_rep2


title: HCC1954, PBS treated, Rep5

value: XENOGRAFT

value: Breast Cancer

value: PBS, 34 day


title: HCC1954, PBS treated, Rep4


title: pre-treatment tumor RNA from individual with NSCLC_S164

description: Library name: S164

value: KL

value: high


title: pre-treatment tumor RNA from individual with NSCLC_S163

description: Library name: S163

value: low


title: HeLa_10xGenomics_Anti-G3BP1

description: scMAPIT-seq

value: WT

value: G


title: pre-treatment tumor RNA from individual with NSCLC_S165

description: Library name: S165


title: FA0.2_AN_HEK293T_IgG_rep1

value: HEK293T cell line

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: HCC1954, PBS treated, Rep3

value: PBS, 14 day


title: pre-treatment tumor RNA from individual with NSCLC_S162

description: Library name: S162

value: tumor biopsy

value: KP


title: 3099_Cacna1H_neurons_in_mPFC_female_Pro_Input_Rep2

first: Kun

last: Li

address: HaiDian

institute: Tsinghua University

description: Library name: Sample37

data_processing:
Sequencing reads were aligned to the UCSC mm10 reference genome with STAR (version 2.3.0e_r291). Aligned reads were quantified by the ‘htseq-count’ module of ‘HTSeq’ framework (version 0.6.0). Differential gene expression analysis was performed by using DESeq2 (version 1.34.0). Genes were identified as differentially expressed with a false discovery rate (FDR) adjusted p value < 0.05 and log2Fold Change > 1.2 or < -1.2.
Assembly: mm10
Supplementary files format and content: text file includes raw counts

source_name: mPFC

extract_protocol:
The mPFC cortices were dissected in dissection buffer (1X HBSS, 2.5 mM HEPES-KOH 35 mM Glucose, 4 mM NaHCO3, RNase-free water, freshly added 100 μg/mL cycloheximide) using a brain matrix. The tissues were immediately homogenized in an ice-cold homogenization buffer (150 mM KCl, 10 mM HEPES pH 7.4, 5 mM MgCl2, 0.5 mM dithiothreitol (Sigma-Aldrich, D9779), 100 μg/mL cycloheximide (Inalco, 1758-9310), 20 U/μL SUPERase-In RNase Inhibitor (Ambion, AM2696), 40 U/μL RNasin Ribonuclease Inhibitor (Promega, N2515), and EDTA-free protease inhibitors) in the cold room using a motor-driven Teflon glass homogenizer. Polyribosomes were immunoprecipitated by monoclonal anti-EGFP antibodies (MSKCC Antibody & Bioresource Core Facility. a mixture of clones 19C8 and 19F7) that have been conjugated to Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific, 65601), which were pre-incubated with Recombinant Protein L (Pierce, 29997) for 16 hours at 4°C on an end-over-end rotator. The RNeasy Plus Micro Kit (QIAGEN, 74034) was used to extract and purify RNAs from ribosomes according to the manufacturer's instructions. The RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
cDNA was synthesized and further amplified using the Oviation RNA-seq System V2 Kit (NuGEN,7102-32). cDNA fragments of 200 bp were end-repaired and ligated with adapters for NextSeq 500 technology using NEBNext Ultra™ II DNA Library Prep Kit (New England Biolabs, E7645L) and NEBNext® Multiplex Oligos (New England Biolabs, E7500S) for Illumina. The cDNA libraries were sequenced on the NextSeq 500 System (Ilumina Inc., San Diego, CA, USA). The quality of libraries was evaluated by using Bioanalyzer High Sensitivity DNA Analysis (Agilent, 5067-4626) on the Aglient 2200 TapeStation system.

value: mPFC

value: Cacna1h+ cell


title: 3101_Cacna1H_neurons_in_mPFC_female_Pro_IP_Rep2

description: Library name: Sample38


title: FA0.1_AN_HEK293T_IgG_rep2

value: rabbit IgG (CST, 2729S)


title: 3100_Cacna1H_neurons_in_mPFC_female_Pro_IP_Rep1

description: Library name: Sample36


title: HCC1954, PBS treated, Rep1

value: PBS, 50 day


title: FA0.1_AN_HEK293T_IgG_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S161

description: Library name: S161


title: 3098_Cacna1H_neurons_in_mPFC_female_Pro_Input_Rep1

description: Library name: Sample35


title: HCC1954, PBS treated, Rep2

value: XENOGRAFT


title: HuO9, RIT treated, Rep16

value: Osteosarcoma


title: 3081_Cacna1H_neurons_in_mPFC_female_Es_IP10

description: Library name: Sample34


title: FA0.5_AN_HEK293T_Anti-G3BP1_rep2

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: pre-treatment tumor RNA from individual with NSCLC_S160

description: Library name: S160


title: HuO9, RIT treated, Rep15


title: FA0.5_AN_HEK293T_Anti-G3BP1_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S159

description: Library name: S159

value: KL


title: 3080_Cacna1H_neurons_in_mPFC_female_Es_Input10

description: Library name: Sample33


title: FA0.2_AN_HEK293T_Anti-G3BP1_rep2


title: HuO9, RIT treated, Rep14


title: 3095_Cacna1H_neurons_in_mPFC_female_Es_IP9

description: Library name: Sample32


title: pre-treatment tumor RNA from individual with NSCLC_S158

description: Library name: S158

value: KC

value: high


title: pre-treatment tumor RNA from individual with NSCLC_S157

description: Library name: S157


title: FA0.2_AN_HEK293T_Anti-G3BP1_rep1

value: WT


title: HuO9, RIT treated, Rep13


title: HuO9, RIT treated, Rep12


title: 3094_Cacna1H_neurons_in_mPFC_female_Es_Input9

description: Library name: Sample31


title: pre-treatment tumor RNA from individual with NSCLC_S155

description: Library name: S155


title: pre-treatment tumor RNA from individual with NSCLC_S156

description: Library name: S156

value: low


title: FA0.1_AN_HEK293T_Anti-G3BP1_rep2

value: HEK293T cell line


title: HuO9, RIT treated, Rep10


title: HuO9, RIT treated, Rep11


title: Untreated_HEK293T_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S154

description: Library name: S154


title: 3107_Cacna1H_neurons_in_mPFC_female_Met_IP16

description: Library name: Sample30


title: HuO9, RIT treated, Rep9


title: FA0.1_AN_HEK293T_Anti-G3BP1_rep1

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: pre-treatment tumor RNA from individual with NSCLC_S153

description: Library name: S153


title: Untreated_HEK293T_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S152

description: Library name: S152


title: LI_8h_3

city: detroit

first: Shailendra

last: Giri

state: MI

address: 2799 W grand boul

department: Neurology Research

institute: henry ford hospital

description: Library name: LI_8h_3

data_processing:
Paired-end sequencing (150 bp) was performed with an Illumina NovaSeq 6000 via NOVOGENE INC. We performed QC with FastQC and aligned 150 bp paired_x0002_end reads to GRCm38-mm10, with approximately 80% uniquely mapped reads in mixed glial samples via the STAR aligner. The STAR aligner was subsequently utilized for count calling for each sample. For differential expression analysis, we employed the limma-Voom package in R, with a padj cutoff of 0.0005 and a log-fold change (logFC) threshold of 1.5 in mixed glial samples were set. The threshold for filtering out genes with low expression was set to 0.1 counts per million (CPM) in atleast 80% of the samples. For count normalization, we used the trimmed mean of M values (TMM) method. Finally, R was used to generate the plots for visualization.
Assembly: MM10
Supplementary files format and content: tab delimited

source_name: Brain

extract_protocol:
Qiagen RNeasy Mini Kit
Poly-A libraries Bulk RNA-seq

treatment_protocol: Stimulated with LI for 8 h in serum-free DMEM

value: Brain

tag: strain

tag: celltype

value: mixed glia from pups


title: HuO9, RIT treated, Rep7


title: pre-treatment tumor RNA from individual with NSCLC_S151

description: Library name: S151

value: tumor biopsy


title: 3105_Cacna1H_neurons_in_mPFC_female_Di_IP_Rep2

description: Library name: Sample26

value: mPFC


title: HuO9, RIT treated, Rep8


title: 3088_Cacna1H_neurons_in_mPFC_female_Met_input12

description: Library name: Sample27

value: Cacna1h+ cell


title: HuO9, RIT treated, Rep6


title: LI_8h_2

description: Library name: LI_8h_2


title: 3104_Cacna1H_neurons_in_mPFC_female_Di_IP_Rep1

description: Library name: Sample24


title: pre-treatment tumor RNA from individual with NSCLC_S150

description: Library name: S150


title: 3106_Cacna1H_neurons_in_mPFC_female_Met_input16

description: Library name: Sample29


title: 3103_Cacna1H_neurons_in_mPFC_female_Di_input_Rep2

description: Library name: Sample25


title: 3089_Cacna1H_neurons_in_mPFC_female_Met_IP12

description: Library name: Sample28


title: pre-treatment tumor RNA from individual with NSCLC_S149

description: Library name: S149

value: KP


title: LI_8h_1

description: Library name: LI_8h_1


title: Un_2

description: Library name: Un_2

value: untreated


title: pre-treatment tumor RNA from individual with NSCLC_S148

description: Library name: S148


title: Un_3

description: Library name: Un_3


title: 3102_Cacna1H_neurons_in_mPFC_female_Di_input_Rep1

description: Library name: Sample23


title: Un_1

description: Library name: Un_1


title: HuO9, RIT treated, Rep4

value: XENOGRAFT


title: HuO9, RIT treated, Rep2

value: Osteosarcoma


title: 3109_Cacna1H_neurons_in_mPFC_male_input_Rep2

description: Library name: Sample21


title: pre-treatment tumor RNA from individual with NSCLC_S147

description: Library name: S147


title: HuO9, RIT treated, Rep1


title: CropSeq Colitis 1, GEX

city: Hamburg

first: Malte

last: Hellmig

state: Hamburg

address: Martinistraße 52

department: III. Department of Medicine

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: 20_14_Colitis
10X Genomics scRNA-seq using Chromium Single Cell 3' v3

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 7.0.0, 10x Genomics, Pleasanton, CA).
Assembly: mm10
Supplementary files format and content: Cellranger output: Tab seperated values files and Matrix table with raw gene counts

source_name: intestine

extract_protocol:
For isolation of intestinal lymphocytes, the small intestine was obtained and cut into 1 cm pieces. We separated lamina propria lymphocytes (LPLs) from intraepithelial lymphocytes (IELs) by incubation with 2 mM DTT at 37°C for 30 min and subsequent filtering through a 100 µm cell strainer (Falcon). The IELs in the supernatant were discarded. The remaining parts were transferred into 50 ml tubes (Falcon, Thermo Fischer), containing DPBS, calcium, magnesium (Gibco), washed by rigorous shaking and repeatedly filtered through a 100 µm cell strainer. Further, the pieces were digested with collagenase D (Roche) and DNAse (Roche) at 37°C for 45 min while rotating in a MACS-Mix tube rotator (Miltenyi Biotec). Subsequently, the small intestines were minced in a MACS cell separator (C-tubes, program “intestine 01”) and filtered through a 70 µm cell strainer (Falcon) until the tissue turns white. The cell strainer was washed with RPMI-medium. Lastly, gradient centrifugation with 37% Percoll (GE Healthcare) was performed. Cells were sorted by Fluorescence-activated cell sorting (FACS) for CD4+ T cells, GFP signal and eBFP2 signal.
All steps were performed according to standard protocol of the Chromium Single Cell 3' v3 kit

value: intestine

value: T cells

value: experimental colitis


title: HuO9, RIT treated, Rep5


title: 3108_Cacna1H_neurons_in_mPFC_male_input_Rep1

description: Library name: Sample19


title: 3110_Cacna1H_neurons_in_mPFC_male_IP_Rep1

description: Library name: Sample20


title: HuO9, PBS treated, Rep6

value: PBS, harvested in RNAlater


title: spleen GD2TIF cells, 2 mon post transfer, TCR

first: Guangyue

last: Zhang

address: Haidian  District

description: Library name: GD2TIF_TCR

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 (Ref ) to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a (Ref)  to map reads to the reference genome GRCm38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Ref ) software, and used to generate expression matrix files for subsequent analysis.
Assembly: mm 10
Supplementary files format and content: Tab separated values files and matrix files
Library strategy: TCR-Seq

source_name: Spleen

extract_protocol:
Retro-virus targeting genes Bcor and Zc3h12a, and delivery GD2 CAR(14g2a) was spun infected into activated Cas9 transgenic T cells, and these T cells were transferred into immunocompetent C57BL/6 mice (1×10^6 per mouse) and distributed. 2 months after, 1×10^6 Splenic GD2TIF cells were sorted by an S3e sorter for library construction and scRNA-seq, TCR-seq.
Single-cell suspensions (2×10^5 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron).

value: Spleen


title: pre-treatment tumor RNA from individual with NSCLC_S144

description: Library name: S144

value: KL

value: low


title: pre-treatment tumor RNA from individual with NSCLC_S145

description: Library name: S145


title: spleen GD2TIF cells, 2 mon post transfer, scRNA

description: Library name: GD2TIF_scRNA

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 (Ref ) to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a (Ref)  to map reads to the reference genome GRCm38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Ref ) software, and used to generate expression matrix files for subsequent analysis.
Assembly: mm 10
Supplementary files format and content: Tab separated values files and matrix files


title: 3096_Cacna1H_neurons_in_mPFC_male_input18

description: Library name: Sample17


title: HuO9, PBS treated, Rep4


title: HuO9, RIT treated, Rep3


title: HuO9, PBS treated, Rep5


title: pre-treatment tumor RNA from individual with NSCLC_S143

description: Library name: S143

value: KC

value: high


title: pre-treatment tumor RNA from individual with NSCLC_S142

description: Library name: S142


title: pre-treatment tumor RNA from individual with NSCLC_S141

description: Library name: S141


title: HuO9, PBS treated, Rep3

value: PBS, harvested in OCT


title: 3091_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_Input_Rep2

description: Library name: Sample15

value: total cell

value: WT


title: 3092_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_IP_Rep1

description: Library name: Sample14

value: mPFC


title: 3093_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_IP_Rep2

description: Library name: Sample16


title: pre-treatment tumor RNA from individual with NSCLC_S146

description: Library name: S146

value: tumor biopsy


title: 3111_Cacna1H_neurons_in_mPFC_male_IP_Rep2

description: Library name: Sample22

value: Cacna1h+ cell


title: HuO9, PBS treated, Rep1

value: XENOGRAFT


title: U118MG, PBS treated, Rep8

value: Glioblastoma

value: PBS, 68 day


title: pre-treatment tumor RNA from individual with NSCLC_S139

description: Library name: S139

value: KP


title: 3090_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_Input_Rep1

description: Library name: Sample13


title: 3097_Cacna1H_neurons_in_mPFC_male_IP18

description: Library name: Sample18


title: 3084_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_Input_Rep3

description: Library name: Sample11


title: pre-treatment tumor RNA from individual with NSCLC_S138

description: Library name: S138


title: U118MG, PBS treated, Rep7

value: PBS, 88 day


title: pre-treatment tumor RNA from individual with NSCLC_S136

description: Library name: S136


title: U118MG, PBS treated, Rep5


title: 3087_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_IP_Rep3

description: Library name: Sample12


title: U118MG, PBS treated, Rep6

value: PBS, 77 day


title: 3083_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_Input_Rep2

description: Library name: Sample9


title: HuO9, PBS treated, Rep2

value: Osteosarcoma


title: pre-treatment tumor RNA from individual with NSCLC_S140

description: Library name: S140


title: pre-treatment tumor RNA from individual with NSCLC_S134

description: Library name: S134


title: 3082_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_Input_Rep1

description: Library name: Sample7


title: U118MG, PBS treated, Rep4

value: PBS, 74 day


title: pre-treatment tumor RNA from individual with NSCLC_S132

description: Library name: S132

value: low


title: U118MG, PBS treated, Rep2


title: 3076_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_male_Input_Rep3

description: Library name: Sample5


title: pre-treatment tumor RNA from individual with NSCLC_S133

description: Library name: S133

value: KL


title: pre-treatment tumor RNA from individual with NSCLC_S131

description: Library name: S131


title: 3078_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_male_IP_Rep2

description: Library name: Sample4


title: mESCs, siControl, Micro-C, rep 2

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina - Chapel Hill

description:
Library name: mESCs, siControl, Micro-C, rep 2
Micro-C sample

data_processing:
Initial processing of Micro-C sequencing was performed with the Juicer software package v1.5.6.
DNA loops were called using the significant interaction peak caller (SIP) using Knight-Ruiz balanced Micro-C matrices
Assembly: Mus musculus (mm10)
Supplementary files format and content: Loops called in bedpe format
Library strategy: MNase-Seq

source_name: V6.5, mESC

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Kagey et al. 2010).

extract_protocol:
The Micro-C library was prepared using the Dovetail® Micro-C Kit according to the manufacturer’s protocol. Briefly, the chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde in the nucleus. The cross-linked chromatin was then digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed with SDS to extract the chromatin fragments and the chromatin fragments were bound to Chromatin Capture Beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends. After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified.
Sequencing libraries were prepared using the Dovetail  Micro-C kit with Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification.

treatment_protocol: 5 x 105 cells wildtype mESCs were plated per well in 6-well plates. 50nM siGLO transfection control reagent (siControl) was transfected per well using DharmaFECT1 (Dharmacon, T-2001) following manufacturer’s instructions. 48 hours after transfection, cells were collected, counted, and 1 million cells were pelleted before freezing for Micro-C library preparation and nuclear fractionation.

value: V6.5, mESC

value: control siRNA (siGLO)


title: U118MG, RIT treated, Rep16


title: pre-treatment tumor RNA from individual with NSCLC_S130

description: Library name: S130


title: pre-treatment tumor RNA from individual with NSCLC_S137

description: Library name: S137

value: high


title: mESCs, siControl, Micro-C, rep 1

description:
Library name: mESCs, siControl, Micro-C, rep 1
Micro-C samples


title: pre-treatment tumor RNA from individual with NSCLC_S135

description: Library name: S135


title: 3086_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_female_IP_Rep2

description: Library name: Sample10

value: total cell

value: WT


title: U118MG, PBS treated, Rep3

value: PBS, 91 day


title: 3075_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_male_Input_Rep2

description: Library name: Sample3

value: mPFC


title: 3079_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_male_IP_Rep3

description: Library name: Sample6


title: U118MG, RIT treated, Rep15

value: XENOGRAFT


title: mESCs, CTCF, rep 4

description:
Library name: CTCF, rep 4
mESCs_CTCF.bw

data_processing:
Alignment: reads were either aligned to a combined mm10+hg38  genome with bowtie (v1.3.1) (parameters -v 2 -p 24 -S -m 1 -best -strata) or to both mm10 and hg38 separately with bowtie2 (v2.4.5)
PCR Duplicate Removal: duplicates were removed with samtools v1.17 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v2.12) with parameters -f BED -g mm -q 0.01
Spike-in Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = (5/(# human reads / # mouse reads))*100
Coverage File Generation: bigwig files were generated using bedtools (v2.25.0) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normaliztion Factor) followed by ucsctools (v320) bedGraphToBigWig
Assembly: Mus musculus (mm10) and Homo sapiens (hg38) as well as a custom built bowtie index of Mus musculus (mm10) plus Homo sapiens (hg38)
Supplementary files format and content: For each ChIP sample, a BigWig coverage track of merged replicates is provided for viewing in a genome browser.

source_name: v6.5 mESC

extract_protocol:
mESCs were crosslinked in 1% formaldehyde for 5 minutes before quenching with 2.5M glycine. After chromatin extraction, 5% of HEK293T chromatin was added to the mESC samples to be later used as a spike-in normalization. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before washing and resuspension in Shearing Buffer. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1000 base pairs were generated.
Sequencing libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems).

treatment_protocol: mESCs were untreatd or either treated with BRG1 targeting small molecule drugs (ACBI1 (1µM), BRM014 (10µ), or PFI-3 (30µM)) or DMSO.

tag: chip antibody

value: CTCF (Active Motif, 61311)

value: v6.5 mESC


title: pre-treatment tumor RNA from individual with NSCLC_S128

description: Library name: S128

data_processing:
Transcript level pseudo-alignment and quantification to the Ensembl GRCh37 Release 97 (July 2019) reference was performed using Kallisto (version 0.44). Raw counts or transcripts per million (TPM) were calculated for 180,253 transcripts in the Ensembl reference. 134,160 transcripts were covered by the Tempus|RS panel.
Assembly: Ensembl GRCh37 Release 97 (July 2019)
Supplementary files format and content: tab-delimited text file with columns for ensembl_gene, hgnc_symbol, <sampleID>. TPM values are in the <sampleID> column.

value: tumor biopsy


title: 3074_retroAAV2_EGFP_L10a_AHN_projecting_neurons_in_mPFC_male_Input_Rep1

description: Library name: Sample1


title: U118MG, RIT treated, Rep14

tag: cell line

value: Glioblastoma


title: mESCs, CTCF, rep 5

description:
Library name: CTCF, rep 5
mESCs_CTCF.bw


title: U118MG, RIT treated, Rep12

tag: genotype


title: mESCs, CTCF, rep 2

description:
Library name: CTCF, rep 2
mESCs_CTCF.bw

tag: treatment


title: pre-treatment tumor RNA from individual with NSCLC_S127

description: Library name: S127

tag: tissue

value: KP


title: mESCs, CTCF, rep 3

description:
Library name: CTCF, rep 3
mESCs_CTCF.bw


title: pre-treatment tumor RNA from individual with NSCLC_S126

description: Library name: S126


title: pre-treatment tumor RNA from individual with NSCLC_S125

description: Library name: S125


title: U118MG, RIT treated, Rep13


title: mESCs, RAD21, rep 4

description:
Library name: RAD21, rep 4
mESCs_RAD21.bw

value: RAD21 (abcam, ab992)


title: mESCs, CTCF, rep 1

description:
Library name: CTCF, rep 1
mESCs_CTCF.bw


title: pre-treatment tumor RNA from individual with NSCLC_S123

description: Library name: S123


title: U118MG, RIT treated, Rep9


title: mESCs, RAD21, rep 5

description:
Library name: RAD21, rep 5
mESCs_RAD21.bw


title: pre-treatment tumor RNA from individual with NSCLC_S124

description: Library name: S124


title: U118MG, RIT treated, Rep8


title: U118MG, PBS treated, Rep1

value: PBS, 68 day


title: U118MG, RIT treated, Rep10


title: mESCs, RAD21, rep 3

description:
Library name: RAD21, rep 3
mESCs_RAD21.bw


title: pre-treatment tumor RNA from individual with NSCLC_S121

description: Library name: S121

value: low


title: U118MG, RIT treated, Rep6


title: U118MG, RIT treated, Rep11


title: U118MG, RIT treated, Rep7


title: U118MG, RIT treated, Rep5


title: U118MG, RIT treated, Rep4


title: mESCs, RAD21, rep 1

description:
Library name: RAD21, rep 1
mESCs_RAD21.bw


title: pre-treatment tumor RNA from individual with NSCLC_S118

description: Library name: S118

value: KL


title: FCL091_WGS

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description:
Library name: FCL091_WGS
Unfractionated spleen cells from mice after leukemia development

data_processing:
WGS data were mapped to mm10 mouse genome reference. Tumor/pseudo-control matched variant calling was performed, with the normal sample from a different mouse used as pseudo-control. An ensemble strategy with optimized filtering (SNVs/Indels called by at least 2 callers) was employed to identify potential somatic coding mutations (SNVs/indels) using multiple callers, including Mutect2 (v4.1.2.0), SomaticSniper (v1.0.5.0), VarScan2 (v2.4.3), MuSE (v1.0rc), and Strelka2 (v2.9.10). To exclude mouse germline SNPs, variants observed in either mouse dbsnp142 from NCBI or mouse EVA SNP databases from the European Variation Archive (EVA) at the European Bioinformatics Institute (EBI) were excluded. Variant annotation was performed using Annovar17.
ATAC-seq data were mapped to hg38 human genome reference with BWA mem (0.7.17-r1188), then converted to BAM format and deduplicated with fq2bam (v3.0.0.6). Uniquely mapped properly paired reads were extracted with samtools (v1.2) and fragments were extracted with bedtools (v2.24.0).
Single-cell RNA-seq data were aligned and quantified using the Cell Ranger (v7.0.1) pipeline (http://www.10xgenomics.com) against the human genome GRCh38 (refdata-gex-GRCh38-2020-A).
Assembly: For WGS: mm10.  For ATAC-seq/scRNAseq: hg38
Supplementary files format and content: Tsv for WGS. BigWig for ATAC-seq. Tsv.gz and Mtx.gz for scRNAseq

source_name: spleen

growth_protocol: For conditional knock in mouse cells transplanted into CD45.1 recipients, FACS was used to isolate CD45.2+ spleen cells after staining with CD45.2-FITC antibody.  For conditional knock in mice with spontaneous leukemia, unfractionated spleen cells were used. Spleen from an independent mouse with the same parents was used as a control. [WGS] 0.5-1 million MSKG5191 (NUP98::NSD1) PDX cells were transplanted via tail vein injection into NSG mice.  Spleens were harvested and human leukemic cells were isolated using the human/mouse chimera kit (StemCell Technologies).  Two spleens per sample were combined for scRNAseq, and spleen from three mice were processed as independent replicates for ATAC-seq.

extract_protocol:
DNA for WGS was isolated using the Qiagen AllPrep kit.  For ATAC-seq, 50,000 human leukemic cells were isolated from the spleens of PDX-bearing mice treated for 5 days and washed once in cold PBS before proceeding with cell lysis, nuclei extraction, tagmentation and library preparation as described in PMID 24097267.  Lysis and transposition were adjusted according to the Omni-ATAC protocol (PMID 28846090).  For scRNAseq, leukemic cells were human leukemic cells were isolated from the spleens of PDX-bearing mice treated for 4 weeks, washed three times in PBS + 0.04% BSA, and counted.  The volume of cells to load to have a desired recovery target of 8,000-10,000 cells was calculated and cells were loaded on Chromium Next GEM Chip K (10X Genomics).  Samples were processed using the 10X Genomics 5' kit (v2).
Mouse genomic libraries were generated using the SureSelectXT kit specific for the Illumina HiSeq instrument (G9611B, Agilent Technologies).  ATAC-seq libraries were prepared as described in PMID 24097267 with double-sided bead purification.  Single cell RNA-seq libraries were prepared using Chromium Next GEM Single Cell 5' Reagent Kits v2 (10X Genomics) according to manufacturer's protocols.

treatment_protocol: After the percentage of human leukemia cells in the peripheral blood reached ~30%, treatment was started.  Mice were treated for 5-days (ATAC-seq) or 4 weeks (scRNAseq) with vehicle, 3 mg/kg PF9363 (QD, IP), 75 mg/kg SNDX-5613 (BID, PO), or combination.

value: spleen

value: leukemia

value: no treatment


title: U118MG, RIT treated, Rep3


title: FCL016_WGS

description:
Library name: FCL016_WGS
Unfractionated spleen cells from mice after leukemia development


title: pre-treatment tumor RNA from individual with NSCLC_S120

description: Library name: S120

value: high


title: mESCs, RAD21, rep 2

description:
Library name: RAD21, rep 2
mESCs_RAD21.bw


title: pre-treatment tumor RNA from individual with NSCLC_S119

description: Library name: S119

value: KC


title: U118MG, RIT treated, Rep2


title: pre-treatment tumor RNA from individual with NSCLC_S115

description: Library name: S115


title: U118MG, RIT treated, Rep1


title: pre-treatment tumor RNA from individual with NSCLC_S122

description: Library name: S122


title: FCL087_WGS

description:
Library name: FCL087_WGS
Unfractionated spleen cells from mice (control)


title: FCL030_WGS

description:
Library name: FCL030_WGS
Unfractionated spleen cells from mice (control)


title: pre-treatment tumor RNA from individual with NSCLC_S117

description: Library name: S117


title: FCL085_WGS

description:
Library name: FCL085_WGS
Unfractionated spleen cells from mice (control)


title: 60_H82_NOTCH1_STING_KO_dox

city: Bethesda

first: Nitin

last: Roper

state: MD

address: 37 Convent Drive

department: Developmental Therapeutics Branch

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on NovaSeq 6000 SP.
Samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome and the annotated transcripts using STAR.
Gene expression quantification analysis was performed using STAR/RSEM tools.
RSEM generated read counts for each gene between samples were normalized using TMM method implemented in edgeR and then transformed to RPKM.
Assembly: hg19 and mm10
Supplementary files format and content: csv files contains RSEM RPKM (log2+1) values for each sample

extract_protocol:
RNA was extracted using an AllPrep DNA/RNA extraction kit according to the manufacturer’s protocol (Qiagen #80204).
RNA libraries for bulk RNA-seq were prepared using Illumina Stranded mRNA Prep

value: small cell lung cancer


title: NM50_tertiary_21_WGS

description:
Library name: NM50_tertiary_21_WGS
Spleen cells from tertiary recipient of Nup98::Kdm5a;Vav-Cre HSPCs (after leukemia development)


title: 58_H82_NOTCH1_STING_KO_dox


title: pre-treatment tumor RNA from individual with NSCLC_S116

description: Library name: S116

extract_protocol:
Total nucleic acid (TNA) was extracted from tissue specimens using a Chemagic 360 or similar instrumentation, and the recovered TNA was quantified and qualified, and may have been concentrated if necessary. Extracted TNA that was intended for processing by Tempus|RS was treated with Invitrogen TURBO DNase to degrade DNA. The minimum amount of input total RNA required to perform the test was 50 ng. RNA was fragmented using heat and magnesium, with variable parameters, to yield similar sized fragments from RNA inputs with different starting size distributions.
Strand-specific library preparation was performed using the KAPA RNA HyperPrep Kit for Illumina with KAPA single indexed 6 base pair adapters. The libraries were amplified with high fidelity, low-bias PCR using primers complementary to adapter sequences. After library preparation and amplification, targets were captured by hybridization, clean-up of captured targets was performed, and unbound fragments were washed away. Library capture is conducted using the xGen Exome Research Panel v1 probe set, along with the xGen Hybridization and Wash Kit and xGen Universal Blockers. The enriched targets are amplified using the KAPA HiFi HotStart ReadyMix and primers supplied in the KAPA Library amplification kit, followed by a magnetic bead-based clean-up. The amplified target-captured libraries were sequenced with a 2x76 read length to an average of 50 million total reads on an Illumina HiSeq4000 System using patterned flowcells.


title: pre-treatment tumor RNA from individual with NSCLC_S113

description: Library name: S113


title: pre-treatment tumor RNA from individual with NSCLC_S112

description: Library name: S112


title: pre-treatment tumor RNA from individual with NSCLC_S114

description: Library name: S114


title: pre-treatment tumor RNA from individual with NSCLC_S111

description: Library name: S111


title: 56_H82_NOTCH1_STING_KO_no_dox


title: pre-treatment tumor RNA from individual with NSCLC_S110

description: Library name: S110


title: 55_H82_NOTCH1_STING_KO_no_dox


title: NM50_primary_9_WGS

description:
Library name: NM50_primary_9_WGS
Spleen cells from primary recipient of Nup98::Kdm5a;Vav-Cre HSPCs (no disease, used as control)


title: NM50_secondary_76_WGS

description:
Library name: NM50_secondary_76_WGS
Spleen cells from secondary recipient of Nup98::Kdm5a;Vav-Cre HSPCs (after leukemia development)


title: NM50_secondary_79_WGS

description:
Library name: NM50_secondary_79_WGS
Spleen cells from secondary recipient of Nup98::Kdm5a;Vav-Cre HSPCs (after leukemia development)


title: NM50_primary_7_WGS

description:
Library name: NM50_primary_7_WGS
Spleen cells from primary recipient of Nup98::Kdm5a;Vav-Cre HSPCs (no disease, used as control)


title: 54_H69_NOTCH1_dox


title: pre-treatment tumor RNA from individual with NSCLC_S108

description: Library name: S108


title: 53_H69_NOTCH1_dox


title: 51_H69_NOTCH1_no_dox


title: pre-treatment tumor RNA from individual with NSCLC_S106

description: Library name: S106


title: pre-treatment tumor RNA from individual with NSCLC_S105

description: Library name: S105


title: NM50_primary_5_WGS

description:
Library name: NM50_primary_5_WGS
Spleen cells from primary recipient of Nup98::Kdm5a;Vav-Cre HSPCs (after leukemia development)


title: 50_H69_NOTCH1_no_dox


title: 52_H69_NOTCH1_dox


title: pre-treatment tumor RNA from individual with NSCLC_S104

description: Library name: S104


title: Mouse_Brain_H3K27me3_2

city: Toronto

first: Amin

last: Nooranikhojasteh

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description:
Library name: Mouse_Brain_H3K27me3_Rep2
Fresh brain tissue

data_processing:
Adapters and low-quality bases were trimmed using Trim Galore! (v0.6.10) with --paired --quality 20 --length 20
Reads were aligned to the reference genome using Bowtie2 (v2.4.1) with --very-sensitive --local -X 2000 --no-unal -x <genome_index>
BAM files were processed using Samtools (v1.11), with view -q 10 | sort | index for filtering, sorting, and indexing.
Duplicate reads were marked using Picard (v3.1.1) with MarkDuplicates.
Peaks were called using MACS2 (v2.2.9.1) with -f BAMPE -q 0.05 and genome sizes set to 2.7e9 (mm10); the --broad option was used for H3K27me3 samples to identify broad peaks. For SEACR (v1.3) peaks were called in stringent mode with a false discovery rate threshold of 0.01, following BAM-to-bedGraph conversion using bedtools genomecov. For GoPeaks (v1.1), Peaks were identified using  with --mdist 1000 for regular histone marks and --mdist 3000 --broad for H3K27me3, with an FDR cutoff of 0.01, generating BED files for each genome alignment. For LanceOtron  (v1.2.7), Peaks were called from bigWig files generated with bamCoverage (deepTools), with output saved in BED format; bigWig files were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: bigwig, bed, narrowPeak, broadPeak
Library strategy: CUT&Run

extract_protocol:
The CUT&RUN procedure was performed following the standard protocol described by Meers et al. (1). Fresh brain tissue was homogenized, and nuclei were isolated using a lysis buffer optimized for brain tissue, followed by incubation with Concanavalin A-coated magnetic beads. The isolated nuclei were then incubated overnight at 4°C with the respective antibodies targeting the histone marks H3K4me3, H3K27ac, H3K27me3 and IgG. Antibody concentrations were optimized according to the manufacturer’s recommendations. Following antibody binding, the nuclei were treated with Protein A/GMNase fusion protein to cleave the chromatin at the antibody-bound sites. After MNase activation, the DNA fragments were released and collected for downstream sequencing.
CUT&RUN libraries were prepared from the released DNA fragments using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs). The libraries were sequenced using Illumina NovaSeq 6000 with paired-end 50 base pair (50-PE) reads at a sequencing depth of approximately 40 million reads per sample.

value: Brain

tag: antibody


title: Mouse_Brain_H3K27me3_1

description:
Library name: Mouse_Brain_H3K27me3_Rep1
Fresh brain tissue


title: FCL009_WGS

description:
Library name: FCL009_WGS
Unfractionated spleen cells from mice after leukemia development


title: 57_H82_NOTCH1_STING_KO_no_dox


title: pre-treatment tumor RNA from individual with NSCLC_S109

description: Library name: S109


title: 49_H69_NOTCH1_no_dox


title: Mouse_Brain_H3K27ac_2

description:
Library name: Mouse_Brain_H3K27ac_Rep2
Fresh brain tissue


title: Mouse_Brain_H3K4me3_2

description:
Library name: Mouse_Brain_H3K4me3_Rep2
Fresh brain tissue


title: NM50_primary_6_WGS

description:
Library name: NM50_primary_6_WGS
Spleen cells from primary recipient of Nup98::Kdm5a;Vav-Cre HSPCs (after leukemia development)


title: Mouse_Brain_H3K4me3_1

description:
Library name: Mouse_Brain_H3K4me3_Rep1
Fresh brain tissue


title: 46_H69_parental

value: parental


title: 59_H82_NOTCH1_STING_KO_dox


title: pre-treatment tumor RNA from individual with NSCLC_S100

description: Library name: S100


title: Mouse_Brain_H3K27ac_1

description:
Library name: Mouse_Brain_H3K27ac_Rep1
Fresh brain tissue


title: pre-treatment tumor RNA from individual with NSCLC_S103

description: Library name: S103


title: 48_H69_parental


title: pre-treatment tumor RNA from individual with NSCLC_S101

description: Library name: S101


title: pre-treatment tumor RNA from individual with NSCLC_S102

description: Library name: S102


title: pre-treatment tumor RNA from individual with NSCLC_S099

description: Library name: S099


title: pre-treatment tumor RNA from individual with NSCLC_S107

description: Library name: S107


title: pre-treatment tumor RNA from individual with NSCLC_S098

description: Library name: S098


title: Sting_scBCR

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description: 10×Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits v3.1 (1000020). B Cell V(D)J enrichment was performed in these samples according to the 10×Genomics Chromium™ single-cell V(D)J enrichment kit

data_processing:
The count models in Cell Ranger (v 7.2.0) were used to align the raw sequencing reads to the mm10 reference genome, generating a counts table for the transcriptomic data. Additionally, the VDJ model in Cell Ranger was employed to detect the BCR clonotype using single-cell barcodes, utilizing the GRCm38 version of the reference genome files
To filter out low-quality single-cell data, the Seurat (v 4.4.0) pipeline was employed along with miQC (v 1.10.0) spline models. In the Ad5XBB.1.5+RBDXBB.1.5-HR group, 544 of 16,284 cells, in the WT group, 446 of 18,646 cells, and in the Sting-/- Ad5XBB.1.5+RBDXBB.1.5-HR group, 487 of 16,286 cells were removed.
Assembly: refdata-gex-GRCh38-2020-Arefdata-gex-mm10-2020-A
Supplementary files format and content: MTX
Supplementary files format and content: RDS

source_name: lung

extract_protocol:
Single-cell RNA sequencing (scRNA-seq) was performed on female C57BL/6 mice treated with PBS, as well as on Ad5XBB.1.5+RBDXBB.1.5-HR groups, including Sting-/- mice that also received Ad5XBB.1.5+RBDXBB.1.5-HR immunization as previously described. Forty-eight hours after the final vaccination, the mice were euthanized, and lung tissues were collected. The lungs were minced with scissors and treated with a tissue dissociation solution to generate a single-cell suspension. After treatment with a red blood cell lysis reagent, the suspension was filtered through 40-µm strainers and resuspended in PBS.
Single-cell suspensions from four mice per group were pooled and loaded onto a 10x Chromium Single Cell and VDJ library construction system (10x Genomics, 5’scRNA+BCR). The concentration of single-cell suspensions was adjusted to 500–1200 cells/µl. Between 10,000 and 18,000 cells were loaded, with subsequent steps performed following the standard protocols provided by the manufacturer.
10X 5' scRNA+TCR

value: lung

tag: group

value: Sting

tag: library type

value: TCR


title: 45_CORL88_STING_KO_TAS1440


title: PBS_scBCR

value: PBS


title: pre-treatment tumor RNA from individual with NSCLC_S096

description: Library name: S096

source_name: tumor biopsy

value: tumor biopsy

value: KP


title: 42_CORL88_STING_KO_DMSO


title: 47_H69_parental


title: Wildtype_scBCR

value: Wildtype


title: pre-treatment tumor RNA from individual with NSCLC_S097

description: Library name: S097


title: ESC_ChIP-INPUT_WT_rep1

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description: Library name: ESC_ChIP-INPUT_WT_rep1

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 34 for R1 and 34 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)) on gelatin-coated plates.

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Chromatin was isolated and used for ChIP according to standard procedures.
ChIP-seq. Libraries were constructed according to the Illumina Nextera protocol.

value: Embryonic stem cells

value: Input


title: Wildtype_scRNA


title: ESC_ChIP-H3K27ac_WT_rep1

description: Library name: ESC_ChIP-H3K27ac_WT_rep1

value: Active Motif 39133


title: 40_CORL88_STING_KO_DMSO


title: 41_CORL88_STING_KO_DMSO


title: 44_CORL88_STING_KO_TAS1440


title: pre-treatment tumor RNA from individual with NSCLC_S094

first: Abraham

last: Anderson

address: 1 amgen center drive

description: Library name: S094

value: low


title: pre-treatment tumor RNA from individual with NSCLC_S095

description: Library name: S095


title: PBS_scRNA