title: ES2_GR

city: Wenzhou

first: Jiaying

last: Tong

address: Chashan Street

institute: Wenzhou Medical University

description:
Library name: sample6
with GR

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human ovarian cancer cells SKOV3

growth_protocol: Cells were incubated at 37 ℃ in 5% CO2 and maintained in 5A medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: ES2 cells (3×10^5 cells per well, placed in 6-well plates) were treated with T-oligo G4+RHPS4 for 7 days. After the treatment, the cells were collected and total RNA was extracted from each group using TRIzol (TaKaRa Company, Japan). Finally, paired-end sequencing was performed on the Illumina HiSeq 4000 platform at LC-BIO Technology Company (Hangzhou, China).

value: Human ovarian cancer cells SKOV3

value: Epithelial cell

value: WT

value: cell line

value: total RNA

value: paired-end


title: 24137X1_GEMM_KN_HED798_FOXA1_rep1

status: Public on Apr 23 2026

type: SRA

city: Salt lake City

first: Headtlove

last: Essel Dadzie

state: UT

address: 2000 circle of Hope

department: Oncological Sciences

country: USA

institute: University of Utah

description: Library name: 24137X1

library_source: genomic

data_processing:
Fastq alignments were pre-processed with the merge_umi_fastq application from the UMIScripts package (https://github.com/HuntsmanCancerInstitute/UMIScripts) to associate the UMI sequence, provided as a third Fastq file, into the read comment.
Reads were aligned using Bowtie2 v2.2.9 to the standard chromosomes of the mouse genome (version mm10) or the human genome (version hg38).
Duplicate alignments based on the UMI code were removed using the bam_umi_dedup application (UMIScripts) allowing for 1 mismatch.
Peaks were called using MACS2 v2.2.7 with a significance of q-value <1e-8 for exogenous experiments and q-value < 0.01 for endogenous experiments.
Coverage tracks were generated with MACS2 as Reads Per Million.
Assembly: hg38 and mm10
Supplementary files format and content: bigwig, BED files (except for Input samples)

molecule: genomic DNA

organism: Mus musculus

source_name: Lung tissue

growth_protocol: 3D organoid lines were cultured in 50% L-WRN conditioned media.

extract_protocol:
For all organoid ChIP-seq experiments, two 24-well plates (approximately 4 – 8 million cells) were collected in Cell Recovery Solution (500 μl per dome). Organoids were submerged in ice for 30 min before centrifugation at 4°C (300G). Cells were washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). After the third wash, organoids were resuspended in 5 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) and rotated at room temperature for 35 min. Formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were washed with cold PBS, then frozen at -80. Cell pellets were thawed on ice for 5 min then lysed in 1 ml of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) for all TF experiments or 400 ul of Chromatrap Hypotonic buffer (catalog #100007) for all histone experiments. Samples were centrifuged at 4°C (1000G) then resuspended in 1ml of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) or 100 μl of Chromatrap Lysis buffer (catalog #100005) for TF and histone ChIPs respectively. All lysis buffers were supplemented with protease inhibitors. Chromatin extract was sonicated with QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 min; amplitude: 70%). After sonication, chromatin extract of histone samples was brought up to a volume of 1 ml with RIPA lysis buffer. Chromatin from all samples was immunoprecipitated with antibodies premixed with Protein A/G Dynabeadsper antibody used. For sorted nuclei from GEMMs,  At 14 weeks post-tumor initiation, KN and KNH tumor-bearing mice were euthanized. The rib cage was dissected to expose the trachea and heart, and lungs were perfused with cold PBS, snap-frozen, and minced on ice. Homogenized tissue was centrifuged (300G, 4°C, 5 min) and crosslinked in 2 mM DSG + 1% formaldehyde. After fixation, nuclei were extracted using TST buffer, dounced, and filtered through 70 μm/35 μm strainers. GFP-positive nuclei were sorted using BD FACSAria (85 μm nozzle) into PBS + 1% BSA + protease inhibitors.For ChIP-seq, nuclei (10M for TF ChIP-seq) were pelleted (500G, 4°C, 10 min), lysed, and sonicated (QSonica Q800R, 30s on/off, 20 min, 70%). Chromatin was immunoprecipitated with antibodies premixed with Protein A/G Dynabeads per antibody used.
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

treatment_protocol: 429A were transiently treated with 2mM 4-OHT (dissolved in 100% Ethanol) or vehicle(100% Ethanol) for 72 (organoid culture) hr to activate CreERT2 nuclear activity and generate isogenic pairs. 1311G#5 were transiently treated with AD5-Cmv-Cre to delete HNF4α in vitro.

tag: tissue

value: Lung tissue

tag: cell line

tag: cell type

tag: genotype

value: KN

tag: treatment

value: Control

tag: chip antibody

value: FOXA1(Abcam ab170933)


title: Patient 79, Timepoint 2

city: New Haven

first: Kevin

middle: C

last: Johnson

state: CT

address: 333 Cedar Street

department: Neurosurgery

institute: Yale University

description:
Library name: SN17-1
ATAC

library_source: genomic single cell

data_processing:
cellranger-arc-2.0.2
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: cellranger-arc-2.0.2 atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi files.

organism: Homo sapiens

source_name: Brain

extract_protocol:
Frozen IDH-mutant glioma samples were processed by a protocol using EZ lysis buffer (Millipore Sigma). Briefly, frozen samples were thawed and mechanically dissociated in Nuclei EZ lysis buffer via dounce homogenization. The solutions were incubated on ice for 5 minutes and mixed 1-2 times during incubation. Single-nuclei suspensions were filtered through a 70 μm strainer and centrifuged at 500g for 5 minutes at 4 C, resuspended in Nuclei EZ Lysis Buffer and incubated on ice for 5 minutes. The solutions were centrifuged at 500g for 5 minutes at 4 C and resuspended three times in 1% BSA/0.2 U/μL RNase Inhibitor/PBS buffer. Final suspension of nuclei was stained by DAPI, filtered through a 40 μm strainer, and counted using a Countess II automated cell counter (Thermo Fisher Scientific). The number of nuclei was then determined for use in 10x Single Cell Multiome ATAC + Gene Expression v1 workflow.
10x Genomics Single Cell Multiome ATAC + Gene Expression  v1 kit were used according to manufacturer's protocol.

value: Brain

value: Glioma

tag: care id

tag: batch


title: ES2_Control

country: China

description:
Library name: sample1
without any drugs

library_source: transcriptomic

molecule: total RNA

source_name: Human ovarian cancer cells ES2

value: Human ovarian cancer cells ES2


title: 24131X2_429A_KN_Hnf4a_rep1

description: Library name: 24131X2

source_name: Lung organoids

value: Lung organoids

value: 3D cell line

value: HNF4α (Perseus Proteomics PP-H1415)


title: 23754X4_1311g#5_KN_input_rep2

description: Library name: 23754X4

value: No Antibody


title: ES2_T

description:
Library name: sample2
with T


title: ES2_TR

description:
Library name: sample5
with TR

value: Human ovarian cancer cells SKOV3


title: 24137X2_GEMM_KN_HED798_Hnf4a_rep1

description: Library name: 24137X2


title: 24515X1_GEMM_KN_HED934_input

description: Library name: 24515X1


title: 25736X1_HCI_IMA03_KN_input_rep1

description:
Library name: 25736X1
ChIP-seq

source_name: Lung

extract_protocol:
For all organoid ChIP-seq experiments, two 24-well plates (approximately 4 – 8 million cells) were collected in Cell Recovery Solution (500 μl per dome). Organoids were submerged in ice for 30 min before centrifugation at 4°C (300G). Cells were washed three times in cold PBS. On the second wash, PBS was supplemented with DNase solution (containing a final concentration of 200U/ml DNase [Worthington], 2.5 mM MgCl2, 500 mM CaCl2). After the third wash, organoids were resuspended in 5 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) and rotated at room temperature for 35 min. Formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were washed with cold PBS, then frozen at -80. Cell pellets were thawed on ice for 5 min then lysed in 1 ml of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) for all TF experiments or 400 ul of Chromatrap Hypotonic buffer (catalog #100007) for all histone experiments. Samples were centrifuged at 4°C (1000G) then resuspended in 1ml of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) or 100 μl of Chromatrap Lysis buffer (catalog #100005) for TF and histone ChIPs respectively. All lysis buffers were supplemented with protease inhibitors. Chromatin extract was sonicated with QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 min; amplitude: 70%). After sonication, chromatin extract of histone samples was brought up to a volume of 1 ml with RIPA lysis buffer. Chromatin from all samples was immunoprecipitated with antibodies premixed with Protein A/G Dynabeadsper antibody used. For sorted nuclei from GEMMs, At 14 weeks post-tumor initiation, KN and KNH tumor-bearing mice were euthanized. The rib cage was dissected to expose the trachea and heart, and lungs were perfused with cold PBS, snap-frozen, and minced on ice. Homogenized tissue was centrifuged (300G, 4°C, 5 min) and crosslinked in 2 mM DSG + 1% formaldehyde. After fixation, nuclei were extracted using TST buffer, dounced, and filtered through 70 μm/35 μm strainers. GFP-positive nuclei were sorted using BD FACSAria (85 μm nozzle) into PBS + 1% BSA + protease inhibitors.For ChIP-seq, nuclei (10M for TF ChIP-seq) were pelleted (500G, 4°C, 10 min), lysed, and sonicated (QSonica Q800R, 30s on/off, 20 min, 70%). Chromatin was immunoprecipitated with antibodies premixed with Protein A/G Dynabeads per antibody used.
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

value: Lung


title: 24131X1_429A_KN_input_rep1

description: Library name: 24131X1


title: Patient 79, Timepoint 1

description:
Library name: SN17-0
ATAC


title: 24515X2_GEMM_KN_HED934_FOXA1_rep2

description: Library name: 24515X2


title: 24131X3_429A_KN_input_rep2

description: Library name: 24131X3


title: Patient 73, Timepoint 2

description:
Library name: SN07-2
ATAC


title: ES2_R

description:
Library name: sample4
with R

value: Epithelial cell

value: WT


title: 23754X3_1311g#5_KN_Hnf4a_rep2

description: Library name: 23754X3


title: 23754X2_1311g#5_KN_Input_rep1

description: Library name: 23754X2


title: ES2_G

description:
Library name: sample3
with G4

value: cell line

value: total RNA


title: 23754X1_1311g#5_KN Hnf4a_rep1

description: Library name: 23754X1


title: Patient 71, Timepoint 2

description:
Library name: SN05-1
ATAC


title: 24131X4_429A_KN_Hnf4a_rep2

description: Library name: 24131X4


title: 21021X2_1311G#5_KNH_FOXA1_rep2

description: Library name: 21021X2


title: 21021X3_1311g#5_KN_input_rep2

description: Library name: 21021X3


title: 21021X4_1311G#5_KNH_input_rep2

description: Library name: 21021X4

value: KNH

value: Cre-virus


title: Patient 71, Timepoint 1

description:
Library name: SN05-0
ATAC


title: Patient 111, Timepoint 3

description:
Library name: SJ20-3
ATAC


title: Patient 111, Timepoint 2

description:
Library name: SJ20-2
ATAC


title: Patient 111, Timepoint 1

description:
Library name: SJ20-1
ATAC


title: Patient 73, Timepoint 1

description:
Library name: SN07-1
ATAC


title: 20899X4_1311G#5_KNH_FOXA1_rep1

description: Library name: 20899X4


title: 21021X1_1311G#5_KN_FOXA1_rep2

description: Library name: 21021X1

value: KN

value: Control


title: 20899X3_1311G#5_KN_FOXA1_rep1

description: Library name: 20899X3

value: FOXA1(Abcam ab170933)


title: Patient 109, Timepoint 1

description:
Library name: SJ15-1
ATAC

value: Brain

value: Glioma


title: Patient 108, Timepoint 2

description:
Library name: SJ13-2
ATAC


title: Patient 109, Timepoint 2

description:
Library name: SJ15-2
ATAC


title: Patient 108, Timepoint 1

description:
Library name: SJ13-1
ATAC


title: Patient 110, Timepoint 1

description:
Library name: SJ17-1
ATAC


title: Patient 110, Timepoint 2

description:
Library name: SJ17-2
ATAC


title: 23784X2 KNH

description:
Library name: 23784X2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq data from both KN (n=2) and KNH(n=2) tumors were demultiplexed using the 10x cellranger mkfastq version 7.2.0 to create fastq files with the I1 sample index, R1 cell barcode+UMI, and R2 sequence.
Reads were aligned to the mouse genome (mm10 with custom CRE-ERT2 reference)  using cellranger count 7.2.0 with include-introns set to true.
Assembly: mm10
Supplementary files format and content: Filtered gene barcode matrix in H5 format

source_name: lung tumor

extract_protocol:
We performed whole-lung enzymatic digestion to generate single-cell suspensions. GFP(+) live tumor cells from both genotypes were sorted on the same day of library preparation. Cells were resuspended in PBS containing 0.5% BSA. On the day of library prep, cells were thawed, washed in cold PBS, and resuspended in PBS with 0.5% BSA. Dead cells were excluded by DAPI staining, and single, live cells were isolated using a BD FACSAria cell sorter.
Protocols used to generate scRNA-seq data with 10x Genomics Chromium platform can be found at https://support.10xgenomics.com/single-cell-gene-expression. In brief, the Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 3 (PN-1000075) was used to barcode individual cells with 16bp 10X barcodes and to tag cell specific transcript molecules with 10bp Unique Molecular Identifier (UMI) according to the manufacturer’s instructions. The following protocol was performed at the High-Throughput Genomics Shared Resource at Huntsman Cancer Institute, University of Utah. Single cells were suspended in PBS with 0.04% BSA, and the cell suspension was passed through a 40 micron cell strainer. Viability and cell count were assessed on Countess II (Thermo Scientific). Suspensions were equilibrated to targeted cell recovery of 10,000 cells. 10x Gel Beads and reverse transcription reagents were added and cell suspensions were loaded to Chromium Single Cell A (PN-120236) to form Gel Beads-in emulsions (GEMs) - the nano-droplets. Within individual GEMs, cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing, end repair, adaptor ligation and sample indexing were performed in bulk according to the manufacturer’s instructions. The resulting barcoding libraries were qualified on Agilent D1000 ScreenTape on Agilent Technology 2200 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumina Platforms (KK4842). Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2 × 150 PE mode.

treatment_protocol: KN and KNH mice were injected with tamoxifen or corn oil 10 weeks after intubation with Adenoviral mSPC-FlpO, and two weeks later, single cells were collected from lung tumors.

value: lung tumor

value: KrasFSF-G12D, Rosa26(FSF-CreERT2/SUN1), NKx2-1(F/F), Hnf4a(F/F)


title: 23784X1 KN

description:
Library name: 23784X1
10X Genomics

value: KrasFSF-G12D, Rosa26(FSF-CreERT2/SUN1), NKx2-1(F/F), Hnf4a(F/+)


title: 24139X2_KNH_GEMM_rep4

description: Library name: 24139X2_KNH_GEMM_rep4

data_processing:
The mm39  genome and gene annotation files were downloaded from Ensembl release 110  and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3.
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited matrix

source_name: lung

extract_protocol:
RNA was isolated via Trizol-chloroform extraction followed by column-based purification. The aqueous phase was brought to a final concentration of 35% ethanol, and RNA was purified using the PureLink RNA Mini kit according to the manufacturer’s instructions (ThermoFisher Scientific).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA isolation. Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

value: lung

value: Tissue


title: Patient 107, Timepoint 1

description:
Library name: SJ12-1
ATAC


title: Patient 107, Timepoint 2

description:
Library name: SJ12-2
ATAC


title: 24130X2_429A_KNH_rep1

description: Library name: 24130X2_429A_KNH_rep1

value: 3D cell line


title: Patient 105, Timepoint 3

description:
Library name: SJ08-3
ATAC


title: 20899X2_1311G#5_KNH_input_rep1

description: Library name: 20899X2

value: Lung organoids

value: No Antibody


title: Patient 106, Timepoint 2

description:
Library name: SJ10-2
ATAC


title: 24130X3_429A_KN_rep2

description: Library name: 24130X3_429A_KN_rep2

value: Ethanol


title: 23772X6_KNH_GEMM_rep2

description: Library name: 23772X6_KNH_GEMM_rep2


title: Patient 106, Timepoint 1

description:
Library name: SJ10-1
ATAC


title: 24139X1_KNH_GEMM_rep3

description: Library name: 24139X1_KNH_GEMM_rep3


title: 20899X1_1311G#5_KN_input_rep1

description: Library name: 20899X1


title: Patient 105, Timepoint 1

description:
Library name: SJ08-0
ATAC


title: Patient 104, Timepoint 2

description:
Library name: SJ07-2
ATAC


title: 24130X1_429A_KN_rep1

description: Library name: 24130X1_429A_KN_rep1


title: 24130X4_429A_KNH_rep2

description: Library name: 24130X4_429A_KNH_rep2


title: 23772X5_KNH_GEMM_rep1

description: Library name: 23772X5_KNH_GEMM_rep1


title: Patient 104, Timepoint 1

description:
Library name: SJ07-1
ATAC


title: 23772X4_KN_GEMM_rep4

description: Library name: 23772X4_KN_GEMM_rep4


title: Patient 105, Timepoint 2

description:
Library name: SJ08-2
ATAC


title: 23772X3_KN_GEMM_rep3

description: Library name: 23772X3_KN_GEMM_rep3


title: Patient 101, Timepoint 2

description:
Library name: SJ04-2
ATAC


title: Patient 103, Timepoint 2

description:
Library name: SJ06-2
ATAC


title: 23772X1_KN_GEMM_rep1

description: Library name: 23772X1_KN_GEMM_rep1


title: 19825X4_1311G#4_KN_rep2

description: Library name: 19825X4_1311G#5_KN_rep2


title: Patient 100, Timepoint 2

description:
Library name: SJ03-1
ATAC


title: Patient 103, Timepoint 1

description:
Library name: SJ06-1
ATAC


title: 23772X2_KN_GEMM_rep2

description: Library name: 23772X2_KN_GEMM_rep2


title: Patient 100, Timepoint 1

description:
Library name: SJ03-0
ATAC


title: 19825X3_1311G#4_KN_rep1

description: Library name: 19825X3_1311G#5_KN_rep1


title: 19825X1_1311G#4_KNH_rep1

description: Library name: 19825X1_1311G#5_KNH_rep1


title: KVpR kidney tumor cells, CSF1Ri + aPD1 (NR), replicate1

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: PC_NR1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software
Assembly: 10x Genomics refdata-cellranger-mm10-3.0.0
Supplementary files format and content: Tab-delimited values files and matrix files

molecule: polyA RNA

source_name: tumor

extract_protocol:
Tumors were coarsely minced using a scalpel and enzymatically dissociated using either a mouse or human tumor dissociation kit (Miltenyi) for 25mins at 37c using the Octo-dissociator (Miltenyi). Digested cells were neutralized in DMEM + 10% FBS and successively washed in PBS and strained through 100um, 70μm and 45μm cell strainers with an RBC lysis step in between (Ack lysis buffer; Gibco). Single cell suspensions were stained with DAPI (BD Pharmingen) and calcein AM (Invitrogen) and FACS sorted for live single cells. Cells were counted using a hemocytometer and up to 10,000 cells were loaded into the Chromium Controller (10x genomics).  For normal kidney samples, kidney cortexes from tumor-free mice were micro-dissected prior to processing as described for tumors above for one sample (NK1) which did not include many CD45+ cells. For the second normal kidney sample (NK2), CD45+ and CD45- cells were flow sorted and combined at a 4:1 ratio to enrich for CD45+ cells, prior to loading into the chromium controller as described above.
Cells were processed using the Next GEM 5’ mRNA V2 kit (10x genomics) with strict adherence to manufacturer’s protocols. Gene expression libraries were sequenced at a target depth of 200 million reads per sample.

treatment_protocol: Tumor bearing KVpR mice were either untreated or treated with single agents or combinations of the following: Lenvatinib (oral gavage 5-7 days/week; 8mg/kg; Selleckchem/MedChemExpress), aPD1 (intraperitoneal injection twice weekly, clone RMP1-14, 100μg, Bioxcell), or ), BLZ945 (oral gavage 5-7 days/week; CSF1Ri, 200mg/kg, Selleckchem/ MedChemExpress).

value: tumor

tag: mouse genotype

value: Ksp-CreERT2 Vhlf/f p53f/f Rb1f/f

tag: Sex

value: male

value: CSF1Ri + aPD1

tag: treatment time

value: long-term

tag: treatment response_group

value: non-responder

value: I


title: Patient 101, Timepoint 1

description:
Library name: SJ04-1
ATAC

value: Brain

value: Glioma


title: KVpR kidney tumor cells, Lenvatinib + aPD1 (eR), replicate4

description:
Library name: PL_eR4
10x Genomics

value: Lenvatinib + aPD1

value: ~2 weeks

value: responder


title: Patient 100, Timepoint 3

description:
Library name: SJ03-2
ATAC


title: 19825X2_1311G#4_KNH_rep2

description: Library name: 19825X2_1311G#5_KNH_rep2

value: lung

value: KNH


title: Patient 85, Timepoint 2

description:
Library name: NL23-1
ATAC


title: Patient 85, Timepoint 1

description:
Library name: NL23-0
ATAC


title: KVpR kidney tumor cells, Lenvatinib + aPD1 (eR), replicate3

description:
Library name: PL_eR3
10x Genomics


title: Patient 81, Timepoint 1

description:
Library name: NL12-0
ATAC


title: Patient 91, Timepoint 1

description:
Library name: NL26-0
ATAC


title: KVpR kidney tumor cells, Lenvatinib + aPD1 (eR), replicate1

description:
Library name: PL_eR1
10x Genomics

value: O


title: KVpR kidney tumor cells, Lenvatinib + aPD1 (eNR), replicate1

description:
Library name: PL_eNR1
10x Genomics


title: Patient 80, Timepoint 2

description:
Library name: NL11-1
ATAC


title: KVpR kidney tumor cells, Lenvatinib + aPD1 (eR), replicate2

description:
Library name: PL_eR2
10x Genomics


title: Patient 81, Timepoint 2

description:
Library name: NL12-1
ATAC


title: KVpR kidney tumor cells, Lenvatinib (eR), replicate3

description:
Library name: Ln_eR3
10x Genomics

value: Lenvatinib


title: Patient 91, Timepoint 2

description:
Library name: NL26-1
ATAC


title: KVpR kidney tumor cells, Lenvatinib (eR), replicate4

description:
Library name: Ln_eR4
10x Genomics


title: Patient 80, Timepoint 1

description:
Library name: NL11-0
ATAC


title: Patient 61, Timepoint 2

description:
Library name: NL05-2
ATAC


title: KVpR kidney tumor cells, Lenvatinib (eR), replicate1

description:
Library name: Ln_eR1
10x Genomics


title: Patient 60, Timepoint 2

description:
Library name: NL04-1
ATAC


title: Patient 61, Timepoint 1

description:
Library name: NL05-1
ATAC


title: Patient 60, Timepoint 1

description:
Library name: NL04-0
ATAC


title: KVpR kidney tumor cells, Lenvatinib (aNR), replicate6

description:
Library name: Ln_aNR6
10x Genomics

value: acquired non-responder


title: KVpR kidney tumor cells, Lenvatinib (aNR), replicate4

description:
Library name: Ln_aNR4
10x Genomics

value: tumor


title: Patient 59, Timepoint 3

description:
Library name: NL03-3
ATAC


title: Patient 59, Timepoint 2

description:
Library name: NL03-2
ATAC


title: KVpR kidney tumor cells, Lenvatinib (aNR), replicate3

description:
Library name: Ln_aNR3
10x Genomics

value: Ksp-CreERT2 Vhlf/f p53f/f Rb1f/f


title: Patient 57, Timepoint 2

description:
Library name: NL01-2
ATAC


title: KVpR kidney tumor cells, Lenvatinib (aNR), replicate2

description:
Library name: Ln_aNR2
10x Genomics

value: male


title: KVpR kidney tumor cells, aPD (eR), replicate3

description:
Library name: PD_eR3
10x Genomics

value: U


title: Patient 59, Timepoint 1

description:
Library name: NL03-1
ATAC


title: Patient 57, Timepoint 1

description:
Library name: NL01-1
ATAC


title: KVpR kidney tumor cells, Lenvatinib (eR), replicate2

description:
Library name: Ln_eR2
10x Genomics


title: KVpR kidney tumor cells, aPD (eR), replicate2

description:
Library name: PD_eR2
10x Genomics


title: Patient 46, Timepoint 2

description: Library name: N170024

data_processing:
cellranger-6.1.2 using include-introns parameter set to `True` was applied to all samples.
Assembly: GRCh38-2020-A
Supplementary files format and content: A mixture of CellRanger filtered_feature_bc_matrix formats. The formats included either .h5 or tab-separated values files and matrix files.

extract_protocol:
Nuclei isolation from frozen glioma samples was performed by three separate laboratories using two different protocols. Frozen glioma samples from the same patient were processed together.                                                                                Protocol 1: Laboratory 1 and Laboratory 2 processed the cohorts from MDACC and Pitié-Salpêtrière Hospital by the protocol previously described by from Slyper et al (PMID:32405060) . Briefly, frozen samples were thawed and mechanically dissociated in 0.49% CHAPS with salts and Tris (ST) buffer (10mM Tris-HCL pH7.5, 146mM NaCl, 1mM CaCl2, 21mM MgCl2). Single-nuclei suspensions were filtered using a 40 μm strainer, centrifuged at 500g for 5min, and resuspended in ST buffer with 0.01% BSA (Sigma). Final nuclei suspensions were stained by trypan blue and counted using a hemocytometer. The number of nuclei was then determined for use in 10x Genomics Single Cell 3' v3 RNA workflow. Protocol 2: Laboratory 3 processed the cohorts from LIH-NORLUX, Seoul National, and Saint Joseph Hospital by a protocol using EZ lysis buffer (Millipore Sigma). Briefly, frozen samples were thawed and mechanically dissociated in Nuclei EZ lysis buffer via dounce homogenization. The solutions were incubated on ice for 5 minutes and mixed 1-2 times during incubation. Single-nuclei suspensions were filtered through a 70 μm strainer and centrifuged at 500g for 5 minutes at 4 C, resuspended in Nuclei EZ Lysis Buffer and incubated on ice for 5 minutes. The solutions were centrifuged at 500g for 5 minutes at 4 C and resuspended three times in 1% BSA/0.2 U/μL RNase Inhibitor/PBS buffer. Final suspension of nuclei was stained by DAPI, filtered through a 40 μm strainer, and counted using a Countess II automated cell counter (Thermo Fisher Scientific). The number of nuclei was then determined for use in 10x Genomics Single Cell 3' v3 RNA or 10x Single Cell Multiome ATAC + Gene Expression v1 workflows.
10x Genomics Chromium Single Cell 3’ Reagent  v3 kit or 10x Genomics Single Cell Multiome ATAC + Gene Expression  v1 kit were used according to manufacturer's protocol.

tag: extraction protocol_number

value: Protocol 1

tag: care project_id

tag: platform used_to_generate_data

value: 10x 3' Gene Expression

value: laboratory 2


title: Patient 44, Timepoint 2

description: Library name: N141108

value: Brain


title: KVpR kidney tumor cells, aPD (eNR), replicate2

description:
Library name: PD_eNR2
10x Genomics

value: non-responder


title: Patient 46, Timepoint 1

description: Library name: N131243

value: Glioma


title: KVpR kidney tumor cells, aPD (eNR), replicate1

description:
Library name: PD_eNR1
10x Genomics

value: ~2 weeks

value: S


title: KVpR kidney tumor cells, Lenvatinib (aNR), replicate5

description:
Library name: Ln_aNR5
10x Genomics

value: long-term


title: Patient 19, Timepoint 2

description: Library name: P19T2

value: laboratory 3


title: KVpR kidney tumor cells, Lenvatinib (aNR), replicate1

description:
Library name: Ln_aNR1
10x Genomics

value: O


title: KVpR kidney tumor cells, aPD (PR), replicate3

description:
Library name: PD_PR3
10x Genomics

value: partial responder


title: Patient 44, Timepoint 1

description: Library name: N1204557493


title: KVpR kidney tumor cells, aPD (eR), replicate1

description:
Library name: PD_eR1
10x Genomics

value: responder


title: KVpR kidney tumor cells, aPD (PR), replicate2

description:
Library name: PD_PR2
10x Genomics

value: tumor


title: Patient 18, Timepoint 1

description: Library name: P18T1


title: KVpR kidney tumor cells, aPD (eNR), replicate3

description:
Library name: PD_eNR3
10x Genomics

value: Ksp-CreERT2 Vhlf/f p53f/f Rb1f/f


title: Patient 19, Timepoint 1

description: Library name: P19T1


title: KVpR kidney tumor cells, aPD (PR), replicate1

description:
Library name: PD_PR1
10x Genomics

value: male


title: Patient 18, Timepoint 2

description: Library name: P18T2


title: KVpR kidney tumor cells, aPD (aNR), replicate1

description:
Library name: PD_aNR1
10x Genomics

value: acquired non-responder


title: Patient 17, Timepoint 2

description: Library name: P17T2

value: Protocol 1


title: KVpR kidney tumor cells, aPD (NR), replicate2

description:
Library name: PD_NR2
10x Genomics

value: I


title: Patient 17, Timepoint 1

description: Library name: P17T1

value: 10x 3' Gene Expression


title: Patient 16, Timepoint 1

description: Library name: P16T1

value: Brain


title: Patient 16, Timepoint 2

description: Library name: P16T2


title: Patient 15, Timepoint 2

description: Library name: MDA368441

value: laboratory 2


title: KVpR kidney tumor cells, CSF1Ri (eNR), replicate2

description:
Library name: Cs_eNR2
10x Genomics

value: non-responder


title: KVpR kidney tumor cells, CSF1Ri + aPD1 (eNR), replicate1

description:
Library name: PC_eNR1
10x Genomics

value: CSF1Ri + aPD1

value: ~2 weeks


title: KVpR kidney tumor cells, CSF1Ri (eNR), replicate1

description:
Library name: Cs_eNR1
10x Genomics

value: Q


title: Patient 15, Timepoint 1

description: Library name: MDA142726

value: Glioma


title: Patient 14, Timepoint 2

description: Library name: MDA642937


title: Patient 14, Timepoint 1

description: Library name: MDA271111


title: KVpR kidney tumor cells, aPD (NR), replicate1

description:
Library name: PD_NR1
10x Genomics

value: long-term

value: O


title: Patient 13, Timepoint 2

description: Library name: MDA839700


title: KVpR kidney tumor cells, untreated, replicate1

description:
Library name: UT1
10x Genomics

value: Untreated


title: Patient 13, Timepoint 1

description: Library name: MDA114341


title: KVpR kidney tumor cells, untreated, replicate3

description:
Library name: UT3
10x Genomics

value: tumor


title: Muscle, single-nuclei, 7d post-overloading, Batch Exp2, Chip2, R2

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

description:
Library name: Exp2_Plant_7dOVL_2_Chip2_Library_S13
10X Genomics

data_processing:
scRNA-seq and snRNA-seq data were processed using cellranger (v7.1.0) mapped to GRCm39 genome.
Visium spatial data were processed using 10X Genomics Space Ranger (v.2.0.0) mapped to Mm10-2020-A genome.
Human bulk RNA-seq data was processed using the nfcore pipeline: reads were trimmed using Trimgalore (v.0.6.10), and quantified using Salmon (v.1.10.3) with GRCh38 genome.
Assembly: GRCm39 for single-cell and single-nuclei. Mm10-2020-A for spatial transcriptomics. GRCh38 for human bulk RNA-seq.
Supplementary files format and content: CellRanger output files
Supplementary files format and content: tab-delimited text files with raw counts and TPM for each sample: human_gene_raw_counts.tsv, human_gene_tpm.tsv
Supplementary files format and content: Space Ranger output files

molecule: nuclear RNA

source_name: plantaris muscle

extract_protocol:
scRNA-seq: Plantaris muscles were manually minced and dissociated in digestion media containing Dulbecco's Modified Eagle's medium (DMEM), liberase (0.1 mg/g muscle weight) (Roche, #5401020001; 5 mg/ml), and dispase 0.3% (Sigma-Aldrich, #D4693-1G) at 37°C for 1.5 h in a shaker incubator. The muscle homogenate was filtered, pelleted, and frozen in freezing media containing FBS (Gibco, # 26-170-043) with 10% DMSO (Sigma, C6164-50ML) for storage at -80 °C. For FACS-sorting, cells were thawed in a water bath and resuspended in PBS with 1% goat serum (FACS buffer). PE-Cy7-conjugated anti-CD45 (1/200, Biolegend, 103114) and anti-Sca-1 (1/200, Biolegend, 108114) were used for lineage-negative selection, and BV605-conjugated anti-CD31 (1/200, Biolegend, 102418) was used for positive staining of ECs. Cells were pelleted and then incubated with the corresponding Cell Multiplexing Oligos (CMOs)(10x Genomics) for 5 min at RT. Cells were then washed, pelleted, and resuspended in 0.05% UltraPure BSA (ThermoFisher, #AM2616) diluted in calcium- and magnesium-free PBS. Cells from all conditions were pooled together, sorted using a FACS Aria II (BD) sorte,r and collected in 0.05 % UltraPure BSA. ECs were selected based on CD31+ staining, while from the CD31- fraction, Sca1-/ CD45- cells were selected (Lin-) to enrich for MuSCs and SCs. Cell concentration was determined using an automatic cell counter (BioRad T20 Cell Counter) and the concentration was adjusted if needed to meet the optimal range for loading on the 10X Chromium chip. The nuclei were loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v3.1 (dual index) following the manufacturer’s protocol. Following library construction, libraries were sequenced on the Illumina NextSeq system.
snRNA-seq: Plantaris muscles were isolated from mice immediately following euthanasia and snap-frozen in liquid nitrogen for storage at -80 °C. The Chromium Nuclei Isolation Kit was used following the manufacturer’s protocol with slight optimizations that were found to be most effective for skeletal muscle tissue. In brief, two plantaris muscles were mechanically disrupted with a pestle in Lysis Buffer. Tissue homogenate was then transferred to a Nuclei Isolation Column and centrifuged (16,000 g for 20 seconds at 4°C). The column was then discarded, and flowthrough transferred to a 1.5 ml LoBind Eppendorf. Nuclei suspension was centrifuged at 700 g for 5 minutes at 4°C before adding Debris Removal Buffer and 700 g for 10 minutes at 4 ºC after incubation. Nuclei were then resuspended in Wash Buffer followed by a final centrifugation step (700 g for 5 minutes at 4°C). Then, nuclei were resuspended in 70 μl when using two plantaris muscles as starting material. Nuclei concentration was determined using an automatic cell counter (BioRad T20 Cell Counter) and the concentration was adjusted if needed to meet the optimal range for loading on the 10X Chromium chip. DAPI was added to a small aliquot of the nuclei that were quality-controlled with a fluorescent microscope to ensure that they were intact, had rounded borders, the majority occurring as singlets, and that there was no residual debris. The nuclei were loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v3 following the manufacturer’s protocol. We aimed to load ~15,000 nuclei for each run.
Spatial transcriptomics: sagittal cryo-sections of the plantaris muscle were directly collected onto a Visium slide (10x Genomics PN-1000193), ensuring each section was within the 8x8 µm fiducial frame. The Visium slide was fixed in 100% methanol at -20°C for 30 minutes, followed by Hematoxylin staining for 6 minutes (Sigma-Aldrich MH16-500ML) and Eosin staining for 1 minute (Sigma-Aldrich HT110216-500ML). The slide was then mounted with 30% glycerol and a cover slip. For each section, a white-field H&E image with a fiducial frame was captured using a Leica SP8 system.
human bulk RNA-seq: Human muscle biopsies from 3 patients with disrupted innervation and 3 patients subjected to pre- and post-exercise training were analyzed by bulk RNA-seq
scRNA-seq: Library was performed according to the manufacturer's instructions (Single Cell 3’ Reagent Kit v3.1 (dual index), 10X Genomics).
snRNA-seq: Library was performed according to the manufacturer's instructions (Single Cell 3’ Reagent Kit v3, 10X Genomics).
Spatial transcriptomics: Library was performed accordiing to the manufacturer's instructions (Visium Spatial Gene Expression Slides and Reagent kit, PN-1000193, 10X Genomics).
human bulk RNA-seq: Library was performed according to the manufacturer's instructions (SMART-Seq® mRNA LP)

value: plantaris muscle

value: 7d post-overloading


title: Muscle, single-nuclei, basal, Batch Exp2, Chip2

description:
Library name: Exp2_Plant_Basal_Chip2_Library_S7
10X Genomics

value: basal


title: Muscle, single-nuclei, basal, Batch Exp2, Chip1

description:
Library name: Exp2_Plant_Basal_Chip1_Library_S1
10X Genomics


title: KVpR normal kidney cells, untreated, replicate2

description:
Library name: NK2
10x Genomics

source_name: normal kidney cortex, immune cell enrichment

value: Ksp-CreERT2 Vhlf/f p53f/f Rb1f/f

value: male

value: S


title: Muscle, single-nuclei, 7d post-overloading, Batch Exp2, Chip1, R2

description:
Library name: Exp2_Plant_7dOVL_2_Chip1_Library_S6
10X Genomics


title: KVpR kidney tumor cells, CSF1Ri (NR), replicate1

description:
Library name: Cs_NR1
10x Genomics


title: Muscle, single-nuclei, 7d post-overloading, Batch Exp2, Chip1, R1

description:
Library name: Exp2_Plant_7dOVL_1_Chip1_Library_S5
10X Genomics


title: Patient 12, Timepoint 2

description: Library name: MDA1228524

value: Brain

value: Protocol 1

value: 10x 3' Gene Expression


title: Patient 12, Timepoint 1

description: Library name: MDA96996

value: laboratory 2


title: KVpR kidney tumor cells, untreated, replicate2

description:
Library name: UT2
10x Genomics

value: I


title: Patient 11, Timepoint 2

description: Library name: MDA477951


title: KVpR kidney tumor cells, untreated, replicate4

description:
Library name: UT4
10x Genomics


title: Muscle, single-nuclei, 7d post-denervation, Batch Exp2, Chip2

description:
Library name: Exp2_Plant_7dDenS2_Chip2_Library_S9
10X Genomics

value: 7d post-denervation


title: Muscle, single-nuclei, 7d post-denervation, Batch Exp2, Chip1

description:
Library name: Exp2_Plant_7dDenS2_Chip1_Library_S3
10X Genomics


title: KVpR normal kidney cells, untreated, replicate1

description:
Library name: NK1
10x Genomics

source_name: normal kidney cortex

value: normal kidney cortex


title: Muscle, single-nuclei, 7d post-overloading, Batch Exp2, Chip2, R1

description:
Library name: Exp2_Plant_7dOVL_1_Chip2_Library_S12
10X Genomics


title: Ck0315_10

city: Charlottesville

first: Hao

last: Jiang

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University fo Virginia

description: Sample 16

data_processing:
For RNA-seq, all the reads were mapped to the USCS mouse reference genome (GRCm39/mm39) with GENCODE version M33 using STAR (v2.7.9a).
Low quality mapped reads (MQ<30) were removed from the analysis.
Read count tables were generated using rsem (v.1.3.0).
Deferential Expression (DE) analyses were performed using NOISeq (v2.46.0).
All of the downstream statistical analyses and generating plots were performed in R (v4.3.1).
Assembly: mm39
Supplementary files format and content: Count tables (read counts for genomic features)

source_name: Bone marrow

growth_protocol: c-Kit+ cells were isolated from mouse bone marrows. After overnight prestimulation, cells were transduced with retrovirus for 2 days. Then the cells were plated in methylcellulose medium for Colony Forming Cell (CFC) assays. Cells for RNA-seq were collected at certain points during CFC.

extract_protocol:
For samples 1-16, total RNAs were isolated using RNeasy Plus Mini Kit (Qiagen). 300 ng of total RNA was used for the construction of RNA-seq library. The quality of total RNA was detected using Qubit RNA IQ Assay Kits. Poly(A) mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB#E7490).
The RNA-seq libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7760S) following manufacture's protocol. The library concentrations were meansured using Qubit 4 fluorometer. The fragment distributions of the libraries were detected using Agile 2100 Bioanalyzer.

treatment_protocol: For samples 1-3, cells were pre-stimulated with culture medium 1. For samples 4-6, cells were pre-stimulated with culture medium 2. For samples 7-16, cells were pre-stimulated with culture medium 2. For samples 1 and 4, cells were transduced with retrovirus containing mock empty vector. For samples 2 and 5, cells were transduced with retrovirus containing (1-590)ASXL1-WT. For samples 3 and 6, cells were transduced with retrovirus containing (1-590)ASXL1-10RA mutant. For samples 7 and 12, cells were transduced with retrovirus containing empty vectors. For samples 8 and 13, cells were transduced with retrovirus containing (1-1067)ASXL1-WT. For samples 9 and 14, cells were transduced with retrovirus containing (1-1067)ASXL1-36EA mutant. For samples 10 and 15, cells were transduced with retrovirus containing (1-1067)ASXL1-36EQ mutant. For samples 11 and 16, cells were transduced with retrovirus containing (1-1067)ASXL1-34DN mutant. For samples 1-3 and 4-6, cells were all collected after 1st round of CFC. For samples 7-11, cells were collected after retroviral infection but before 1st round plating for CFC. For samples 12-16, cells were collected after 2nd round of CFC.

value: Bone marrow

value: Purified c-Kit+ cells

value: hematopoietic stem and progenitor cells (HSPCs)

tag: condition

value: cells collected after 2nd round  of CFC assay


title: Patient 11, Timepoint 1

description: Library name: MDA76060

value: Glioma


title: Patient 10, Timepoint 2

description: Library name: MDA1180425


title: Ck0315_9

description: Sample 15


title: Muscle, single-nuclei, 3d post-denervation, Batch Exp2, Chip2

description:
Library name: Exp2_Plant_3dDen_Chip2_Library_S8
10X Genomics

value: plantaris muscle

value: 3d post-denervation


title: Muscle, single-nuclei, 3d post-overloading, Batch Exp2, Chip2, R1

description:
Library name: Exp2_Plant_3dOVL_1_Chip2_Library_S10
10X Genomics

value: 3d post-overloading


title: Muscle, single-nuclei, 3d post-denervation, Batch Exp2, Chip1

description:
Library name: Exp2_Plant_3dDen_Chip1_Library_S2
10X Genomics


title: Ck0315_8

description: Sample 14


title: Patient 111, Timepoint 3

description: Library name: SJ20-3

value: Protocol 2

value: 10x Multiome ATAC + Gene Expression

value: laboratory 1


title: Muscle, single-nuclei, 3d post-overloading, Batch Exp1, R1

description:
Library name: Exp1_Plant_3dOVL_S4
10X Genomics


title: Ck0315_7

description: Sample 13


title: Muscle, single-nuclei, 3d post-overloading, Batch Exp2, Chip1

description:
Library name: Exp2_Plant_3dOVL_2_Chip1_Library_S4
10X Genomics


title: Muscle, single-nuclei, 3d post-overloading, Batch Exp2, Chip2, R2

description:
Library name: Exp2_Plant_3dOVL_2_Chip2_Library_S11
10X Genomics


title: Muscle, single-nuclei, 7d post-overloading, Batch Exp1, R1

description:
Library name: Exp1_Plant_7dOVL_1_S5
10X Genomics

value: 7d post-overloading


title: Muscle, single-nuclei, 3d post-denervation, Batch Exp1, R2

description:
Library name: Exp1_Plant_3dDen_2_S3
10X Genomics


title: Ck0315_6

description: Sample 12

value: mock


title: Patient 10, Timepoint 1

description: Library name: MDA1111150

value: Brain

value: Protocol 1

value: 10x 3' Gene Expression

value: laboratory 2


title: Muscle, single-nuclei, 7d post-overloading, Batch Exp1, R2

description:
Library name: Exp1_Plant_7dOVL_2_S6
10X Genomics


title: Patient 111, Timepoint 2

description: Library name: SJ20-2


title: Patient 111, Timepoint 1

description: Library name: SJ20-1


title: Muscle, single-nuclei, basal, Batch Exp1, R1

description:
Library name: Exp1_Plant_Basal_S1
10X Genomics

value: basal


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A2, R3  (GEX)

description:
Library name: SAMPLE_A2_REP3 (GEX)
10X Genomics


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A2, R2  (GEX)

description:
Library name: SAMPLE_A2_REP2 (GEX)
10X Genomics


title: Patient 110, Timepoint 2

description: Library name: SJ17-2


title: Ck0315_3

description: Sample 9

value: Bone marrow

value: Purified c-Kit+ cells

value: cells collected after retroviral infection but before plating for CFC assay


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A2, R2 (CMO)

description:
Library name: SAMPLE_A2_REP2 (CMO)
10X Genomics


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A2, R1  (GEX)

description:
Library name: SAMPLE_A2_REP1 (GEX)
10X Genomics


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A2, R3 (CMO)

description:
Library name: SAMPLE_A2_REP3 (CMO)
10X Genomics


title: Ck0315_5

description: Sample 11

value: hematopoietic stem and progenitor cells (HSPCs)


title: Muscle, single-nuclei, 3d post-denervation, Batch Exp1, R1

description:
Library name: Exp1_Plant_3dDen_1_S2
10X Genomics

value: plantaris muscle


title: Ck0315_2

description: Sample 8


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A, R2  (GEX)

description:
Library name: SAMPLE_A_REP2 (GEX)
10X Genomics

value: A


title: Ck0315_1

description: Sample 7


title: Ck0315_4

description: Sample 10


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A2, R1 (CMO)

description:
Library name: SAMPLE_A2_REP1 (CMO)
10X Genomics


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A, R2 (CMO)

description:
Library name: SAMPLE_A_REP2 (CMO)
10X Genomics


title: Patient 109, Timepoint 1

description: Library name: SJ15-1

value: Glioma


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A, R1 (GEX)

description:
Library name: SAMPLE_A_REP1 (GEX)
10X Genomics


title: Patient 110, Timepoint 1

description: Library name: SJ17-1

value: Protocol 2


title: GBO60, control

description: Library name: GBO60_ctl

data_processing:
cellranger-9.0.1 using include-introns parameter set to `True`.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Organoids were dissociated into single cells by using human tumor dissociation kit (Miltenyi Biotec, 130-095-929). Due to low cell numbers detected for these models, all dissociated cells were submitted for 10x single cell RNA-sequencing.
The two different experimental conditions per glioma organoids (10Gy irradiation and control), were profiled by 10x single-cell RNA sequencing 3' v4 (polA).

treatment_protocol: Organoids were either treated with a single 10Gy dose of irradiation on day 0 or no treatment control and were allowed to recover for 7 days.

value: Grade 3

tag: disease timepoint

value: Initial

value: IDH-mutant, astrocytoma

value: Control


title: GBO60 10Gy irradiation

description: Library name: GBO60_10Gy

tag: tissue

value: Brain

value: Irradiation


title: Ck0201_9

description: Sample 6

tag: cell line

value: condition 2

value: prestimulating culture mdium2:50 ng/ml CSF, 50 ng/ml Flt-3, 50 ng/ml TPO


title: Ck0201_8

description: Sample 5

tag: cell type


title: Patient 108, Timepoint 1

description: Library name: SJ13-1

value: 10x Multiome ATAC + Gene Expression

value: laboratory 1


title: Muscle, single-cell, basal, 3d, and 7d post-overloading and post-denervation, Batch A, R1 (CMO)

description:
Library name: SAMPLE_A_REP1 (CMO)
10X Genomics


title: Patient 108, Timepoint 2

description: Library name: SJ13-2


title: Ck0201_7

description: Sample 4

value: Bone marrow

value: Purified c-Kit+ cells

tag: genotype

value: mock


title: GBO57, 10Gy irradiation

description: Library name: GBO57_10Gy

value: Grade 4

value: Recurrent

tag: treatment


title: Patient 107, Timepoint 2

description: Library name: SJ12-2

value: Glioma


title: GBO74, control

description: Library name: GB074_ctl

value: Grade 2


title: THP-1, BODIPY low, biol rep 2

city: Nanjing

first: Xinmei

last: Huang

address: No.321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

description: Library name: Sample 6

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapter trimming and quality filtering were performed with Cutadapt.
Reads were mapped to the SAM CRISPRa gRNA reference library using  count_spacers.python.
Differential gRNA enrichment analysis between BODIPY^high and BODIPY^low populations was performed using MAGeCK.
Assembly: Not applicable (gRNA sequences mapped to synthetic CRISPR library, not genome)
Supplementary files format and content: Processed data files include gRNA counts for each sample.
Supplementary files format and content: Files are provided in Excel (.xlsx) format.
Library strategy: CRISPR Screen

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Genomic DNA was extracted from sorted BODIPY^high and BODIPY^low THP-1 cell populations using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. DNA was quantified using a Qubit fluorometer.
Amplification of integrated gRNA sequences from genomic DNA was performed using nested PCR with primers specific to the SAM CRISPRa library backbone. PCR products were purified and sequenced on an Illumina platform using paired-end 150 bp reads.

treatment_protocol: THP-1 cells were transduced with the SAM CRISPR activation pooled library along with MS2-p65-HSF1 constructs. After blasticidin selection, cells were treated with oxidized low-density lipoprotein (oxLDL, 100 μg/mL) for 24 hours to induce foam cell formation, followed by a 48-hour cholesterol efflux period.

value: Macrophages

value: BODIPY low

value: CRISPRa screen and FACS sorting


title: Patient 109, Timepoint 2

description: Library name: SJ15-2

value: Protocol 2


title: Patient 107, Timepoint 1

description: Library name: SJ12-1

value: Brain


title: THP-1, BODIPY high,  biol rep 2

description: Library name: Sample 4

value: BODIPY high


title: Patient 106, Timepoint 2

description: Library name: SJ10-2


title: Ck0201_2

description: Sample 2

value: hematopoietic stem and progenitor cells (HSPCs)

value: condition 1

value: prestimulating culture medium1:50 ng/ml CSF, 50 ng/ml Flt-3, 50 ng/ml TPO, 10 ng/ml IL-3, 10 ng/ml IL-7


title: GBO57, control

description: Library name: GBO57_ctl

value: IDH-mutant, astrocytoma

value: Control


title: Ck0201_3

description: Sample 3

value: Bone marrow

value: Purified c-Kit+ cells

value: prestimulating culture medium1:50 ng/ml CSF, 50 ng/ml Flt-3, 50 ng/ml TPO, 10 ng/ml IL-3, 10 ng/ml IL-8


title: THP-1, Input, biol rep 2

description: Library name: Sample 2


title: GBO74, 10Gy irradiation

description: Library name: GB074_10Gy

value: Initial

value: Irradiation


title: Ck0201_1

description: Sample 1

value: mock

value: prestimulating culture medium1:50 ng/ml CSF, 50 ng/ml Flt-3, 50 ng/ml TPO, 10 ng/ml IL-3, 10 ng/ml IL-6


title: Patient 106, Timepoint 1

description: Library name: SJ10-1

value: Glioma

value: 10x Multiome ATAC + Gene Expression

value: laboratory 1


title: THP-1, BODIPY low, biol rep 1

description: Library name: Sample 5

value: Macrophages

value: BODIPY low

value: CRISPRa screen and FACS sorting


title: THP-1, Input, biol rep 1

description: Library name: Sample 1


title: RS2h

city: Shanghai

first: Huateng

last: Cao

address: 320 Yue Yang Road

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Using Seurat Seurat v4.0.4, the "*_all.markers.csv" files showing all cluster markers, were generated from SD6h, RS2h or combined data, the "combined_markersi2.csv" file is the DEG result of i2 cluster in combined data.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain (POA)

extract_protocol:
Act-seq
10X Genomics

tag: strain

tag: age

value: Brain (POA)

value: pooled male and female


title: THP-1, BODIPY high,  biol rep 1

description: Library name: Sample 3

value: BODIPY high


title: N9_8_SCT_T

city: Oxford

first: Bethan

last: Psaila

state: Oxfordshire

address: John Radcliffe Hospital MRC Weatherall Institute – Molecular Medicine

department: MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: Sample 5
scRNA-seq of d18 bone marrow organoid, engrafted with mutCALR CAR T cells (healthy donor)

data_processing:
scRNA-seq raw data was processed first using the CellRanger pipeline (10x Genomics, v.7.0.0), post-processed using CellBender (v.0.3.0), Souporcell (v.3.0.0) and analysed with Seurat (v.5.2.1).
Assembly: GRCh38-2020-A
Supplementary files format and content: Subset and processed R object

source_name: hiPSC-derived bone marrow organoid engrafted with mutCALR CAR T cells (healthy donor)

growth_protocol: Human bone marrow organoids were generated from the SCT wild-type iPSC line as previously described in Khan et al 2023. Primary mutCALR+ MPN cells or CAR T cells (healthy donor) were thawed and rested overnight prior to engraftment.

extract_protocol:
Organoids were dissociated with collagenase D and live cells were FACS-isolated and re-counted for chip loading.
Libraries for samples 1-5 were prepared using the Chromium Single Cell 5’ High Throughput kit v2, Dual Index (PN-1000263).

value: Bone marrow haematopoietic and stromal cells


title: Patient 105, Timepoint 3

description: Library name: SJ08-3

value: Brain

value: Protocol 2

tag: batch


title: Patient 105, Timepoint 2

description: Library name: SJ08-2


title: Patient 104, Timepoint 2

description: Library name: SJ07-2


title: N9_5_SCT_236_T

description:
Library name: Sample 4
scRNA-seq of d18 bone marrow organoid, engrafted with CD34+ mutCALR+ MPN cells and mutCALR CAR T cells (healthy donor)

source_name: hiPSC-derived bone marrow organoid engrafted with CD34+ cells from mutCALR+ MPN patient and mutCALR CAR T cells (healthy donor)


title: SD6h

description: 10x Genomics


title: N9_1_SCT

description:
Library name: Sample 1
scRNA-seq of d18 bone marrow organoid, untreated

source_name: hiPSC-derived bone marrow organoid

value: hiPSC-derived bone marrow organoid


title: Nbn-KO_rep1

city: Hong Kong

first: Yang

last: Fu

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

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: Nbn-KO_rep1
SgCtrl vs. sgNbn spreadsheet: Alias column: Nbn_rep1
SIQ outcomes for in vivo perturbation.xlsx

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

source_name: skeletal muscle

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

value: skeletal muscle

value: 6 weeks

tag: sample group

value: Nbn-KO


title: Patient 105, Timepoint 1

description: Library name: SJ08-0


title: Nbn-KO_rep2

description:
Library name: Nbn-KO_rep2
SgCtrl vs. sgNbn spreadsheet: Alias column: Nbn_rep2
SIQ outcomes for in vivo perturbation.xlsx


title: Patient 104, Timepoint 1

description: Library name: SJ07-1


title: N9_3_SCT_GAL1

description:
Library name: Sample 2
scRNA-seq of d18 bone marrow organoid, untreated and control CAR T cells

source_name: hiPSC-derived bone marrow organoid, control CAR T cells


title: Neurospora crassa, KTC, rep3

city: Beijing

first: Shuting

last: Ye

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

description:
Library name: Sample18
WTK3

data_processing:
Basecalling was performed using a software developed for DNBSEQ-T7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al.,  Genome Research, 1997.
Assembly: GCA_000182925.2
Supplementary files format and content: FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: Transcriptomic profiling of the WT, get-3ko and get-4ko strains, with or without Ketoconazole treatment, were analyzed by high-throughput RNA sequencing (RNA-seq). Ketoconazole (Sigma) was added, with final concentration of 2 μg/mL.

value: mycelia

value: WT

value: Ketoconazole


title: Neurospora crassa, KTC, rep1

description:
Library name: Sample16
WTK1


title: Neurospora crassa, KTC, rep2

description:
Library name: Sample17
WTK2


title: Neurospora crassa, Control, rep1

description:
Library name: Sample13
WTC1

value: No treatment


title: Neurospora crassa, Control, rep3

description:
Library name: Sample15
WTC3


title: Neurospora crassa, Control, rep2

description:
Library name: Sample14
WTC2


title: Nbn-KO_rep3

description:
Library name: Nbn-KO_rep3
SgCtrl vs. sgNbn spreadsheet: Alias column: Nbn_rep3
SIQ outcomes for in vivo perturbation.xlsx


title: Nbn-KO_rep5

description:
Library name: Nbn-KO_rep5
SgCtrl vs. sgNbn spreadsheet: Alias column: Nbn_rep5
SIQ outcomes for in vivo perturbation.xlsx


title: Patient 103, Timepoint 1

description: Library name: SJ06-1

source_name: Brain

value: Glioma

value: 10x Multiome ATAC + Gene Expression

value: laboratory 1


title: Neurospora crassa get-4  mutant, KTC, rep1

description:
Library name: Sample10
get4K1

value: get-4 knockout


title: Nbn-KO_rep6

description:
Library name: Nbn-KO_rep6
SgCtrl vs. sgNbn spreadsheet: Alias column: Nbn_rep6
SIQ outcomes for in vivo perturbation.xlsx


title: Patient 103, Timepoint 2

description: Library name: SJ06-2


title: Neurospora crassa get-4  mutant, KTC, rep2

description:
Library name: Sample11
get4K2


title: Patient 101, Timepoint 2

description: Library name: SJ04-2


title: Nbn-KO_rep4

description:
Library name: Nbn-KO_rep4
SgCtrl vs. sgNbn spreadsheet: Alias column: Nbn_rep4
SIQ outcomes for in vivo perturbation.xlsx


title: Neurospora crassa get-4  mutant, KTC, rep3

description:
Library name: Sample12
get4K3


title: Neurospora crassa get-4  mutant, Control, rep2

description:
Library name: Sample8
get4C2


title: Ctrl-for-Nbn_rep1

description:
Library name: Ctrl-for-Nbn_rep1
SgCtrl vs. sgNbn spreadsheet: Alias column: Ctrl_rep1
SIQ outcomes for in vivo perturbation.xlsx

value: Ctrl-for-Nbn


title: Ctrl-for-Nbn_rep2

description:
Library name: Ctrl-for-Nbn_rep2
SgCtrl vs. sgNbn spreadsheet: Alias column: Ctrl_rep2
SIQ outcomes for in vivo perturbation.xlsx


title: Neurospora crassa get-3  mutant, KTC, rep2

description:
Library name: Sample5
get3K2

value: get-3 knockout


title: Neurospora crassa get-3  mutant, KTC, rep3

description:
Library name: Sample6
get3K3


title: Neurospora crassa get-4  mutant, Control, rep3

description:
Library name: Sample9
get4C3


title: Ctrl-for-Nbn_rep3

description:
Library name: Ctrl-for-Nbn_rep3
SgCtrl vs. sgNbn spreadsheet: Alias column: Ctrl_rep3
SIQ outcomes for in vivo perturbation.xlsx


title: Neurospora crassa get-3  mutant, Control, rep2

description:
Library name: Sample2
get3C2


title: Patient 100, Timepoint 2

description: Library name: SJ03-1


title: Patient 100, Timepoint 3

description: Library name: SJ03-2


title: Ctrl-for-Nbn_rep4

description:
Library name: Ctrl-for-Nbn_rep4
SgCtrl vs. sgNbn spreadsheet: Alias column: Ctrl_rep4
SIQ outcomes for in vivo perturbation.xlsx


title: Neurospora crassa get-4  mutant, Control, rep1

description:
Library name: Sample7
get4C1


title: Neurospora crassa get-3  mutant, KTC, rep1

description:
Library name: Sample4
get3K1


title: Patient 100, Timepoint 1

description: Library name: SJ03-0


title: Neurospora crassa get-3  mutant, Control, rep1

description:
Library name: Sample1
get3C1


title: Kidney, normal 3, glomerulus region 6

city: Calgary

first: Justin

last: Chun

state: Alberta

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

description:
Library name: Normal-Normal3-Glom-086-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

data_processing:
FASTQ files were processed into gene count data for each sample using the GeoMx NGS Pipeline. Read depth was performed with total transcripts identified across nuclei, corresponding to an average of transcripts per nucleus.
Assembly: GRCh38
Supplementary files format and content: Processed data files are supplied as RDS objects aggregating all samples pre and post data processing.
Library strategy: Spatial Transcriptomics

source_name: Kidney cortex

extract_protocol:
5 um sectioned tissue samples from 2 FFPE transplant control pre-implantation biopsies and 3 DKD (class III) biopsies were prepared on slides.
Nanostring GeoMx Human Whole Transcriptome Atlas probes were hybridized to the tissue overnight. The fluorescent conjugated morphology markers used were CD10, PanCK, and SYTO 13 nucleic acid stain. Regions of interest were selected on the GeoMx Digital Spatial Profiler. RNA-ID and UMI-containing oligonucleotide tags were UV-cleaved from the WTA panel within the chosen ROIs and collected in a 96-well collection plate. Illumina i5 and i7 dual indexing primers were added to the oligonucleotide tags during PCR to index each ara of illumination uniquely.

value: Kidney cortex

tag: disease state

value: Non-diseased control

tag: group

value: Normal

tag: region

value: Glom


title: N9_4_SCT_236

description:
Library name: Sample 3
scRNA-seq of d18 bone marrow organoid, engrafted with CD34+ mutCALR+ MPN cells

source_name: hiPSC-derived bone marrow organoid engrafted with CD34+ cells from mutCALR+ MPN patient

value: Bone marrow haematopoietic and stromal cells


title: Patient 101, Timepoint 1

description: Library name: SJ04-1

value: Brain

tag: extraction protocol_number

value: Protocol 2


title: Kidney, normal 3, glomerulus region 5

description:
Library name: Normal-Normal3-Glom-085-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal 3, glomurulus region 4

description:
Library name: Normal-Normal3-Glom-084-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Neurospora crassa get-3  mutant, Control, rep3

description:
Library name: Sample3
get3C3

value: mycelia


title: Patient 99, Timepoint 3

description: Library name: SJ02-3

tag: care project_id

value: 10x 3' Gene Expression


title: Ctrl-for-Nbn_rep5

description:
Library name: Ctrl-for-Nbn_rep5
SgCtrl vs. sgNbn spreadsheet: Alias column: Ctrl_rep5
SIQ outcomes for in vivo perturbation.xlsx

value: skeletal muscle

value: 6 weeks


title: Patient 99, Timepoint 2

description: Library name: SJ02-2

value: Glioma

tag: platform used_to_generate_data


title: Ctrl-for-Nbn_rep6

description:
Library name: Ctrl-for-Nbn_rep6
SgCtrl vs. sgNbn spreadsheet: Alias column: Ctrl_rep6
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 3, glomerulus region 9

description:
Library name: DKD-DKD3-Glom-083-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: DKD class III

value: DKD


title: Ku80-KO_rep2

description:
Library name: Ku80-KO_rep2
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep2
SIQ outcomes for in vivo perturbation.xlsx


title: Ku80-KO_rep1

description:
Library name: Ku80-KO_rep1
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep1
SIQ outcomes for in vivo perturbation.xlsx


title: Patient 81, Timepoint 2

description: Library name: NL12-1

value: 10x Multiome ATAC + Gene Expression

value: laboratory 1


title: Kidney, DKD replicate 1, blood vessel region 3

description:
Library name: DKD-DKD1-BV-076-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: BV


title: Kidney, DKD replicate 1, blood vessel region 1

description:
Library name: DKD-DKD1-BV-074-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Kidney cortex


title: Ku80-KO_rep4

description:
Library name: Ku80-KO_rep4
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep4
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 2, blood vessel region 1

description:
Library name: DKD-DKD2-PT-077-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: PT


title: Patient 91, Timepoint 1

description: Library name: NL26-0


title: Ku80-KO_rep5

description:
Library name: Ku80-KO_rep5
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep5
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 3, interstitium region 1

description:
Library name: DKD-DKD3-IT-080-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: IT


title: Kidney, DKD replicate 1, blood vessel region 2

description:
Library name: DKD-DKD1-BV-075-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 99, Timepoint 1

description: Library name: SJ02-1


title: Kidney, normal 1, blood vessel region 1

description:
Library name: Normal-Normal1-BV-071-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Non-diseased control

value: Normal


title: Kidney, normal 1, blood vessel region 2

description:
Library name: Normal-Normal1-BV-072-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ku80-KO_rep3

description:
Library name: Ku80-KO_rep3
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep3
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 3, glomerulus region 8

description:
Library name: DKD-DKD3-Glom-082-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Glom


title: Patient 91, Timepoint 2

description: Library name: NL26-1

value: Brain

value: Protocol 2


title: Kidney, normal 1, blood vessel region 3

description:
Library name: Normal-Normal1-BV-073-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 1, distal tubule region 3

description:
Library name: DKD-DKD1-DT-070-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: DT


title: Ku80-KO_rep7

description:
Library name: Ku80-KO_rep7
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep7
SIQ outcomes for in vivo perturbation.xlsx

value: skeletal muscle


title: Kidney, DKD replicate 1, distal tubule region 2

description:
Library name: DKD-DKD1-DT-069-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 3, blood vessel region 2

description:
Library name: DKD-DKD3-PT-079-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ku80-KO_rep6

description:
Library name: Ku80-KO_rep6
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep6
SIQ outcomes for in vivo perturbation.xlsx

value: 6 weeks


title: Patient 85, Timepoint 1

description: Library name: NL23-0

value: Glioma


title: Patient 81, Timepoint 1

description: Library name: NL12-0


title: Kidney, DKD replicate 1, distal tubule region 1

description:
Library name: DKD-DKD1-DT-068-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: DKD class III


title: Kidney, normal 3, distal tubule region 3

description:
Library name: Normal-Normal3-DT-067-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 3, glomerulus region 7

description:
Library name: DKD-DKD3-Glom-081-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: DKD


title: Patient 80, Timepoint 2

description: Library name: NL11-1

value: 10x Multiome ATAC + Gene Expression


title: Ku80-KO_rep8

description:
Library name: Ku80-KO_rep8
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ku80_rep8
SIQ outcomes for in vivo perturbation.xlsx


title: Patient 85, Timepoint 2

description: Library name: NL23-1

value: laboratory 1


title: Kidney, normal 3, distal tubule region 1

description:
Library name: Normal-Normal3-DT-065-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal 3, distal tubule region 2

description:
Library name: Normal-Normal3-DT-066-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 80, Timepoint 1

description: Library name: NL11-0


title: Kidney, normal 1, distal tubule region 3

description:
Library name: Normal-Normal1-DT-064-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ctrl-for-Ku80_rep2

description:
Library name: Ctrl-for-Ku80_rep2
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep2
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, normal 1, distal tubule region 2

description:
Library name: Normal-Normal1-DT-063-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 79, Timepoint 2

description: Library name: SN17-1


title: Kidney, DKD replicate 1, proximal tubule region 10

description:
Library name: DKD-DKD1-PT-060-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 1, proximal tubule region 8

description:
Library name: DKD-DKD1-PT-058-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ctrl-for-Ku80_rep3

description:
Library name: Ctrl-for-Ku80_rep3
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep3
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, normal 1, distal tubule region 1

description:
Library name: Normal-Normal1-DT-062-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ctrl-for-Ku80_rep5

description:
Library name: Ctrl-for-Ku80_rep5
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep5
SIQ outcomes for in vivo perturbation.xlsx


title: Ctrl-for-Ku80_rep6

description:
Library name: Ctrl-for-Ku80_rep6
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep6
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 1, proximal tubule region 11

description:
Library name: DKD-DKD1-PT-061-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 1, proximal tubule region 9

description:
Library name: DKD-DKD1-PT-059-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 73, Timepoint 1

description: Library name: SN07-1


title: Patient 73, Timepoint 2

description: Library name: SN07-2


title: Kidney, DKD replicate 2, interstitium region 3

description:
Library name: DKD-DKD2-IT-056-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ctrl-for-Ku80_rep4

description:
Library name: Ctrl-for-Ku80_rep4
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep4
SIQ outcomes for in vivo perturbation.xlsx


title: Patient 71, Timepoint 2

description: Library name: SN05-1


title: Kidney, DKD replicate 2, interstitium region 2

description:
Library name: DKD-DKD2-IT-055-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ctrl-for-Ku80_rep1

description:
Library name: Ctrl-for-Ku80_rep1
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep1
SIQ outcomes for in vivo perturbation.xlsx


title: Patient 79, Timepoint 1

description: Library name: SN17-0


title: Ctrl-for-Ku80_rep7

description:
Library name: Ctrl-for-Ku80_rep7
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep7
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 2, proximal tubule region 11, healthy

description:
Library name: DKD-DKD2-PT-053-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

tag: marker

value: Healthy


title: Kidney, DKD replicate 1, proximal tubule region 7

description:
Library name: DKD-DKD1-PT-057-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Kidney cortex


title: Patient 71, Timepoint 1

description: Library name: SN05-0


title: Kidney, DKD replicate 2, proximal tubule region 10, healthy

description:
Library name: DKD-DKD2-PT-052-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: PT


title: Ctrl-for-Ku80_rep8

description:
Library name: Ctrl-for-Ku80_rep8
SgCtrl vs. sgKu80 spreadsheet: Alias column: Ctrl_rep8
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 2, proximal tubule region 9, healthy

description:
Library name: DKD-DKD2-PT-051-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 2, interstitium region 1

description:
Library name: DKD-DKD2-IT-054-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: IT


title: Kidney, DKD replicate 2, proximal tubule region 7, injured

description:
Library name: DKD-DKD2-PT-049-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 2, proximal tubule region 8, injured

description:
Library name: DKD-DKD2-PT-050-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ctrl-for-Polq_rep5

description:
Library name: Ctrl-for-Polq_rep5
SgCtrl vs. sgPolq spreadsheet: Alias column: Ctrl_rep5
SIQ outcomes for in vivo perturbation.xlsx

value: Ctrl-for-Polq


title: Patient 61, Timepoint 1

description: Library name: NL05-1


title: Ctrl-for-Polq_rep3

description:
Library name: Ctrl-for-Polq_rep3
SgCtrl vs. sgPolq spreadsheet: Alias column: Ctrl_rep3
SIQ outcomes for in vivo perturbation.xlsx


title: Ctrl-for-Polq_rep4

description:
Library name: Ctrl-for-Polq_rep4
SgCtrl vs. sgPolq spreadsheet: Alias column: Ctrl_rep4
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 2, proximal tubule region 6, semi-injured

description:
Library name: DKD-DKD2-PT-048-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 2, proximal tubule region 3, healthy

description:
Library name: DKD-DKD2-PT-045-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 2, glomerulus region 3

description:
Library name: DKD-DKD2-Glom-042-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 2, proximal tubule region 1, healthy

description:
Library name: DKD-DKD2-PT-043-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 60, Timepoint 2

description: Library name: NL04-1


title: Patient 61, Timepoint 2

description: Library name: NL05-2


title: Kidney, DKD replicate 2, proximal tubule region 5, semi-injured

description:
Library name: DKD-DKD2-PT-047-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 59, Timepoint 3

description: Library name: NL03-3


title: Patient 59, Timepoint 2

description: Library name: NL03-2


title: Kidney, DKD replicate 2, glomerulus region 2

description:
Library name: DKD-DKD2-Glom-041-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 2, glomerulus region 1

description:
Library name: DKD-DKD2-Glom-040-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 2, proximal tubule region 2, semi-injured

description:
Library name: DKD-DKD2-PT-044-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 60, Timepoint 1

description: Library name: NL04-0


title: Ctrl-for-Polq_rep2

description:
Library name: Ctrl-for-Polq_rep2
SgCtrl vs. sgPolq spreadsheet: Alias column: Ctrl_rep2
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, normal 2, proximal tubule region 1, healthy

description:
Library name: Normal-Normal2-PT-037-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Non-diseased control

value: Normal


title: Ctrl-for-Polq_rep1

description:
Library name: Ctrl-for-Polq_rep1
SgCtrl vs. sgPolq spreadsheet: Alias column: Ctrl_rep1
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, normal 2, proximal tubule region 3, healthy

description:
Library name: Normal-Normal2-PT-039-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal 2, proximal tubule region 2, healthy

description:
Library name: Normal-Normal2-PT-038-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Polq-KO_rep5

description:
Library name: Polq-KO_rep5
SgCtrl vs. sgPolq spreadsheet: Alias column: Polq_rep5
SIQ outcomes for in vivo perturbation.xlsx

value: Polq-KO


title: Kidney, DKD replicate 2, proximal tubule region 4, healthy

description:
Library name: DKD-DKD2-PT-046-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 59, Timepoint 1

description: Library name: NL03-1

value: Brain

value: Protocol 2


title: Patient 57, Timepoint 2

description: Library name: NL01-2


title: Kidney, normal 2, glomerulus region 3

description:
Library name: Normal-Normal2-Glom-036-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Glom


title: Kidney, DKD replicate 3, blood vessel region 1

description:
Library name: DKD-DKD3-PT-078-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Patient 57, Timepoint 1

description: Library name: NL01-1


title: Polq-KO_rep3

description:
Library name: Polq-KO_rep3
SgCtrl vs. sgPolq spreadsheet: Alias column: Polq_rep3
SIQ outcomes for in vivo perturbation.xlsx

value: skeletal muscle

value: 6 weeks


title: Kidney, normal 2, glomerulus region 1

description:
Library name: Normal-Normal2-Glom-034-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal 2, glomerulus region 2

description:
Library name: Normal-Normal2-Glom-035-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Polq-KO_rep1

description:
Library name: Polq-KO_rep1
SgCtrl vs. sgPolq spreadsheet: Alias column: Polq_rep1
SIQ outcomes for in vivo perturbation.xlsx


title: Polq-KO_rep4

description:
Library name: Polq-KO_rep4
SgCtrl vs. sgPolq spreadsheet: Alias column: Polq_rep4
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, normal 3, glomerulus region 2

description:
Library name: Normal-Normal3-Glom-029-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal 3, proximal tubule region 2, healthy

description:
Library name: Normal-Normal3-PT-032-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: DIPGXIII, H3K4me3, untreated, rep2

city: Houston

first: Rebecca

middle: Lauren

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Library name: CUT_RUN_H3K4me3_DIPGXIII_untreated_REP2

data_processing:
Reads were processed with trimgalore.
Reads were aligned to the genome with bowtie2.
Peaks were called with MACS2.
Differential peak analysis was done with diffbind.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Library strategy: CUT&Run

source_name: cell line

growth_protocol: SU-DIPGXIII cells were passaged weekly with TrypLE Express Enzyme dissociation reagent and grown as neurospheres at 37C and 5% CO2 in glioma stem cell media glioma stem cell media consisting of 1:1 DMEM/F12 and Neurobasal A, 20 µg/mL human EGF, 20 µg/mL FGF-154, B27 without vitamin A, heparin sulfate, sodium pyruvate, HEPES buffer, GlutaMAX, and Antibiotic-Antimycotic at 1X each.

extract_protocol:
Neurospheres were dissociated to single cells with TrypLE Express Enzyme, washed with 1X HBSS, counted, and prepared for CUT&RUN with 500,000 cells/sample. CUT&RUN-enriched DNA was prepared using the Cell Signaling Technologies CUT&RUN Kit (catalog# 86652) following the manufacturer's protocol using the following antibodies: pS2-Pol2 (Anti-RNA polymerase II subunit B1 phospho CTD Ser-2, clone 3E10; MilliporeSigma), H3K4me3 (Anti-Histone H3 tri methyl K4; Abcam, ab8580), H3K4me3Q5dop (Anti-H3K4me3Q5dopaminyl; MilliporeSigma, ABE2590), and IgG (Anti-IgG Rabbit; DIAgenode, cat# C15410206). Yeast spike-in DNA (S. cerevisiae; Cell Signaling Technology) was added at 0.5% to each reaction following chromatin digestion.
Sequencing libraries were prepared from 3 ng of enriched DNA using the SMARTer ThruPLEX Plasma-seq kit (Takara Bio, cat# R400681) with dual indexes (Takara Bio, cat# DX34752) according to the manufacturer's protocol. Adapter-ligated libraries were amplified for 11 PCR cycles, purified using AMPure XP beads (Beckman Coulter), and evaluated for fragment size distribution on an Agilent 2100 Bioanalyzer. Library molar concentrations were determined by quantitiative PCR with the KAPA Library Quantification Kit (Roche) before pooling for sequencing on an Illumina NovaSeq 6000 to generate 150-bp paired-end reads.

treatment_protocol: SU-DIPGXIII cells were untreated and samples were collected in biological duplicates.

value: cell line

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: untreated


title: Kidney, DKD replicate 3, proximal tubule region 6, semi-injured

description:
Library name: DKD-DKD3-PT-026-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: DKD class III

value: DKD


title: DIPGXIII, H3K4me3Q5dopaminyl, untreated, rep2

description: Library name: CUT_RUN_H3K4me3Q5dopaminyl_DIPGXIII_untreated_REP2


title: Kidney, normal 3, glomerulus region 3

description:
Library name: Normal-Normal3-Glom-030-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Kidney cortex

value: Healthy


title: Kidney, normal 3, proximal tubule region 1, healthy

description:
Library name: Normal-Normal3-PT-031-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: PT


title: Ctrl-for-Lig4_rep9

description:
Library name: Ctrl-for-Lig4_rep9
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep9
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, normal 3, proximal tubule region 3, healthy

description:
Library name: Normal-Normal3-PT-033-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Non-diseased control


title: Kidney, normal 3, glomerulus region 1

description:
Library name: Normal-Normal3-Glom-028-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Normal


title: DIPGXIII, H3K4me3Q5dopaminyl, untreated, rep1

description: Library name: CUT_RUN_H3K4me3Q5dopaminyl_DIPGXIII_untreated_REP1


title: Kidney, DKD replicate 3, proximal tubule region 4, injured

description:
Library name: DKD-DKD3-PT-024-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: DIPGXIII, pS2-Pol2, untreated, rep2

description: Library name: CUT_RUN_pS2-Pol2_DIPGXIII_untreated_REP2


title: DIPGXIII, H3K4me3, untreated, rep1

description: Library name: CUT_RUN_H3K4me3_DIPGXIII_untreated_REP1


title: Kidney, DKD replicate 3, proximal tubule region 7, healthy

description:
Library name: DKD-DKD3-PT-027-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Polq-KO_rep2

description:
Library name: Polq-KO_rep2
SgCtrl vs. sgPolq spreadsheet: Alias column: Polq_rep2
SIQ outcomes for in vivo perturbation.xlsx

value: Polq-KO


title: Ctrl-for-Lig4_rep8

description:
Library name: Ctrl-for-Lig4_rep8
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep8
SIQ outcomes for in vivo perturbation.xlsx


title: Ctrl-for-Lig4_rep6

description:
Library name: Ctrl-for-Lig4_rep6
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep6
SIQ outcomes for in vivo perturbation.xlsx


title: Ctrl-for-Lig4_rep7

description:
Library name: Ctrl-for-Lig4_rep7
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep7
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 3, proximal tubule region 3, injured

description:
Library name: DKD-DKD3-PT-023-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 3, proximal tubule region 5, healthy

description:
Library name: DKD-DKD3-PT-025-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 3, proximal tubule region 2, injured

description:
Library name: DKD-DKD3-PT-022-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: DIPGXIII, pS2-Pol2, untreated, rep1

description: Library name: CUT_RUN_pS2-Pol2_DIPGXIII_untreated_REP1


title: HepG2 cells carrying a SAMD4B Dox-on expression cassette cultured with Dox for 48h

city: Kobe

first: Junji

last: Otani

state: Hyogo

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

department: Department of Medicine

country: Japan

institute: Kobe university

description:
Library name: Hep-4Bon-plus
Hep-4Bon-plus-LHB0378_L6

data_processing:
Raw reads were quality-checked and adapter and low-quality bases were removed with Trimmomatic.
Transcript-level quantification was performed with Salmon.
Transcript-level abundances from Salmon were imported and summarized to gene-level using tximport.
Assembly: GRCh38.p13 homo sapiens
Supplementary files format and content: A csv file including TPM values for each sample

growth_protocol: were cultured in EMEM supplemented with 10% FBS and 1× MEM non-essential amino acids solution.

extract_protocol:
Total RNA was extracted using RNeasy Plus mini kit (QIAGEN) and purified according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared by GENEWIZ from Azenta life sciences.

treatment_protocol: 1 ug/ml Dox for 48h

value: Liver cancer

value: 1 ug/ml Dox for 48h to induce SAMD4B expression


title: Ctrl-for-Lig4_rep5

description:
Library name: Ctrl-for-Lig4_rep5
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep5
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 3, proximal tubule region 1, healthy

description:
Library name: DKD-DKD3-PT-021-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 3, glomerulus region 4

description:
Library name: DKD-DKD3-Glom-019-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Glom


title: HepG2 cells carrying a SAMD4B Dox-on expression cassette cultured without Dox

description:
Library name: Hep-4Bon-minus
Hep-4Bon-minus-LHB0377_L6


title: Kidney, DKD replicate 3, glomerulus region 3

description:
Library name: DKD-DKD3-Glom-018-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 3, glomerulus region 5

description:
Library name: DKD-DKD3-Glom-020-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 3, glomerulus region 2

description:
Library name: DKD-DKD3-Glom-017-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: DIPGXIII, zotiraciclib+sertraline, rep3

description:
Library name: RNAseq_DIPGXIII_ZTR+sert_REP3
zotiraciclib+sertraline_rep3

data_processing:
Reads were aligned to the genome with STAR.
DESeq2 was used to identify differentially expressed genes.
Assembly: hg38
Supplementary files format and content: count tables for each RNA-seq dataset

growth_protocol: Tumor samples were isolated from xenograft NSG mice bearing SU-DIPGXIIIP*+ZsGreen/luciferase tumors. SU-DIPGXIII cells were passaged weekly with TrypLE Express Enzyme dissociation reagent and grown as neurospheres at 37C and 5% CO2 in glioma stem cell media glioma stem cell media consisting of 1:1 DMEM/F12 and Neurobasal A, 20 µg/mL human EGF, 20 µg/mL FGF-154, B27 without vitamin A, heparin sulfate, sodium pyruvate, HEPES buffer, GlutaMAX, and Antibiotic-Antimycotic at 1X each.

extract_protocol:
Tumor samples were isolated by dissociating whole brains, depleting mouse cells, and using the human cell fraction for bulk RNA-seq. Neurospheres were dissociated to single cells with TrypLE Express Enzyme, washed with 1X HBSS, counted, and prepared for CUT&RUN with 250,000 cells/sample. RNA was extracted with Trizol and used to generate cDNA from mRNA.
Sequencing libraries were prepared from cDNA following Illumina protocols.

treatment_protocol: Mice bearing SU-DIPGXIIIP*+ZsGreen/luciferase tumors were treated for 3 weeks with vehicle or 15 mg/kg zotiraciclib 3 times per weekSU-DIPGXIII cells were treated for 24 hours with DMSO, 20 nM zotiraciclib, 6 nM AZD4573, 5 𝛍M sertraline, 20 nM zotiraciclib + 5 𝛍M sertraline, or 6 nM AZD4573 + 5 𝛍M sertraline in biological triplicates.

value: zotiraciclib+sertraline

tag: time

value: 24 hours


title: Kidney, DKD replicate 1, proximal tubule region 6, injured

description:
Library name: DKD-DKD1-PT-015-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

tag: tissue


title: Ctrl-for-Lig4_rep2

description:
Library name: Ctrl-for-Lig4_rep2
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep2
SIQ outcomes for in vivo perturbation.xlsx

value: skeletal muscle

value: 6 weeks


title: Ctrl-for-Lig4_rep1

description:
Library name: Ctrl-for-Lig4_rep1
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep1
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, DKD replicate 1, proximal tubule region 5, injured

description:
Library name: DKD-DKD1-PT-014-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: DIPGXIII, zotiraciclib+sertraline, rep1

description:
Library name: RNAseq_DIPGXIII_ZTR+sert_REP1
zotiraciclib+sertraline_rep1

value: cell line

tag: cell line

value: SU-DIPGXIII

value: patient-derived tumor cell line


title: Kidney, DKD replicate 3, glomerulus region 1

description:
Library name: DKD-DKD3-Glom-016-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: DKD class III

value: DKD


title: Ctrl-for-Lig4_rep4

description:
Library name: Ctrl-for-Lig4_rep4
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep4
SIQ outcomes for in vivo perturbation.xlsx