title: NGP_XL177A_H2AK119Ub

description:
Library name: NGP_XL177A_H2AK119Ub
ChIP for H2AK119Ub


title: Mycelia, 2

status: Public on Feb 26 2026

type: SRA

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

state: CA

address: 2125 Delaware Ave. Suite B

country: USA

institute: RealSeq Biosciences

description: Library name: Mycelia_2

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed of adapter sequence using cutadapt version 4.6 [--nextseq-trim=15 -u 1 -a TGGAATTCTCGGGTGCCAAGG -m 15] (31). Reads were then aligned to ncRNA transcripts identified using RFAM, with the addition of the high-confidence set of tRNA isodecoders containing -CCA tails identified using tRNAScan-SE (32),  and then to theC. posadasii strain Silveira (GCA_000170175.2) genome. ShortStack v4.1.0 (33) with the parameters [-pad 3 –mincov 0.5rpm] was used to identify potential novel sRNA transcripts. Reads overlapping with known annotations were summed and the corresponding read counts were used for downstream differential analysis.
Assembly: GCA_000170175.2 (Silveria 2011)
Supplementary files format and content: csv files contain raw read counts for each sample

molecule: total RNA

organism: Coccidioides posadasii

source_name: culture

growth_protocol: C. posadasii (strain Δcts2/Δard1/Δcts3, NR-166; BEI Resources) arthroconidia were harvested from 6-week-old plates as previously described (29). The spores were inoculated at 1 × 106 arthroconidia into a 250 mL baffled Erlenmeyer flask containing 100 mL of 2xGYE at 150 rpm at 30 °C for 48 hours. Conditioned medium was harvested by collecting conditioned media with cells into centrifuge tubes and spun at 12,000 × g for 8 min to pellet the cells. The supernatant was pooled and filtered with a 0.22-µm syringe filter before being stored at −80°C.  To generate samples for the time course, in which arthroconidia transition to mycelia, 1 × 106 of harvested arthroconidia were incubated in 250 mL flat-bottom Erlenmeyer flasks (Corning, Corning, NY, USA) in 100 mL of 2x GYE media at 150 rpm at 30 °C. After 48 hours, the conditioned medium with cells was placed in into centrifuge tubes and spun at 12,000 × g for 8 min to pellet the cells. Half of the filtered fungal cells were kept for RNA isolation, while the condition media was spun down and supernatant was removed for extracellular RNA isolation. The remaining cells were reinoculated in fresh 2X GYE for 48 hours at 150 rpm at 30 °C. At 72 hrs post-media change, the fungal cells were separated from the growth media by filtering with a sterile 40 µm nylon mesh cell strainer.  Half of the filtered fungal cells were kept for RNA isolation, while the condition media was filtered with a 0.22-µm syringe filter before being stored at −80°C for extracellular RNA isolation. The remaining half of the filtered fungal cells were reintroduced again into fresh 2X GYE for 24 hours at 150 rpm at 30 °C.  This sample processing was performed again at 96 hrs for a total of 3 replicates of fungal cell samples and filtered conditioned media. C. posadasii spherules were propagated and harvested from 6-week-old plates as previously described (29). For spherule samples, 50 mL of Converse medium (30) was inoculated to a final concentration of 106 arthroconidia/mL. Cultures are then incubated at 39°C in a 10% CO2 shaking incubator at 150 rpm for ~ 3 days. Spherules are harvested by filtering culture through a nested filter into a 50 mL conical tube and then centrifuged at 9000 x g for 8 mins to pellet. Pellets were washed with 1x PBS twice, pelleted, then snap frozen for storage at -80°C until use.

extract_protocol:
C. posadasii mycelium, arthroconidia, and young (no endosporulation) spherule samples were stored in RNA Shield (Zymo Research) at −80°C until processing using the Quick-RNA™ Fungal
For small RNA-seq, libraries were prepared from total RNA using the RealSeq®-Biofluids library preparation kit (RealSeq Biosciences) according to the manufacturer’s instructions. Libraries for each ecotype, as well as cell-free and exosome samples, were generated separately and then pooled for the analysis. In some cases, triplicate libraries for each sample type and condition were not met, and thus, only duplicates were used in downstream analyses to avoid batch effects in the data. Finally, prepared libraries were pooled and subjected to single-end 75 cycles of sequencing using the F3 50 cycle sequencing kit (Note: reagents for 50 additional cycles above what is represented were included to account for index sequencing needs) on the Singular G4 system according to the manufacturer’s instructions (Singular Genomics).

treatment_protocol: For treatment of RNA with the Ribomarker® platform, 10 uL of RNA sample was incubated in a 15 μl reaction mixture containing 1.5 μl Ribomarker® Buffer 1, 1.5 uL of Ribomarker® Enzyme 1, and 2 uL of RNase-Free H2O at 37 °C for 10 min, followed by 80 °C for 2 min. Then, to this mixture was added 2 uL of Ribomarker® Buffer 2 and 2 uL of Ribomarker® Enzyme 2, which was then incubated at 37 °C for 60 min. Finally, 1 uL of Buffer 3 was added to the reaction and incubated at 37 °C for 60 min. The treated RNA was then isolated using an RNA Clean and Concentrator-5 kit for downstream use in library preparation.

tag: cell type

value: culture

tag: genotype


title: Acute Myeloid Leukemia Patient Blood Sample, PS_78299

city: San Antonio

first: Bowen

last: Yang

state: TEXAS

address: 7703 Floyd Curl Drive, Mail code 7971

institute: University of Texas Health Science Center at San Antonio

description: Library name: AML3_R

data_processing:
ChIP-seq reads were aligned to hg19 using Bowtie2 and peaks were called with MACS2 (default parameters), followed by filtering to retain high-confidence peaks reproducibly detected across replicates. RNA-seq reads were aligned to hg19 using STAR; alternative splicing was quantified using rMATS, and skipped exon (SE) events were summarized using PSI values (significance thresholds: |ΔPSI| > 0.1 and FDR < 0.05). H3K79me2 peaks were assigned to SE events based on genomic overlap with exon bodies and flanking intronic regions for integrated chromatin–splicing analyses.
Assembly: hg19
Supplementary files format and content: Tab-separated value files and matrix files from the output of MISO alternative spilicing tool.

organism: Homo sapiens

source_name: Peripheral Blood

extract_protocol:
ChIP DNA: Primary tissue samples were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. Nuclei were isolated, chromatin was sheared to ~200–500 bp using a Covaris E220, and immunoprecipitation was performed overnight at 4°C with anti-H3K79me2 (Abcam, ab3594). DNA was purified using the MinElute PCR Purification Kit (Qiagen). RNA: Total RNA was extracted using TRIzol (Invitrogen) followed by DNase I treatment. RNA integrity was assessed by Agilent 2100 Bioanalyzer and samples with RIN ≥ 7 were used.
ChIP-Seq Library: ChIP DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) and sequenced on an Illumina NextSeq 3000. RNA-Seq Library: Poly(A)+ RNA was enriched using oligo(dT) magnetic beads. Strand-specific libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on an Illumina NextSeq 3000 (~50M reads per sample).

treatment_protocol: For DOT1L inhibition, Mixed Lineage Leukemia rearrangement samples were treated with EPZ5676 (pinometostat) prior to RNA-seq and H3K79me2 ChIP-seq.

tag: tissue

value: Peripheral Blood

tag: treatment


title: RNA-seq 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep3

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

country: China

institute: Tsinghua University

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep3
RNA-seq sample EMX1_dmso_editing_rep3

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)

molecule: polyA RNA

extract_protocol:
Dynabeads M-280 sheep anti-Rabbit IgG (Invitrogen, 11201D) were diluted 1:10 in 1× PBS (Invitrogen, AM9624), magnetically washed, and incubated with Nesprin1 antibody (abcam, ab192234) at room temperature for 30 minutes. Antibody-coupled beads were washed and resuspended in cell lysis buffer containing 10 mM HEPES (Gibco, 15630106), 2.5 mM MgCl2 (Invitrogen, AM9530G), 10 mM KCl (Sigma, P9333), 1 mM DTT (ThermoFisher, 707265ML), 0.5% Triton X-100 (Sigma, 93443), and 2 U recombinant RNase inhibitor (Takara, 2313A). A population of 500 GFP-positive cells per sample was sorted into 10 µL lysis buffer in 96-well plates, centrifuged at 700 g for 1 minute, and incubated at 4°C with shaking (300 rpm) for 30 minutes. After magnetic separation, the supernatant was transferred to a new plate for RNA-seq workflow, while nuclei were retained for ATAC-side tagmentation workflow in AR-seq. RNA in the supernatant was purified using 2.2× VAHTS RNA Clean Beads (Vazyme, N412-03) and reverse-transcribed using SMART-seq2.
RNA-seq library construction was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501), following the manufacturer's manual. Libraries were generated from SMART-seq2-derived cDNA and sequenced in paired-end mode on short-read sequencing platforms.

tag: cell line

tag: batch


title: RNA-seq 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep1
RNA-seq sample EMX1_pft-a_editing_rep1


title: Healthy Patient Bone Marrow Sample, BM_RIJIV

description: Library name: BM4_R

source_name: Bone Marrow

value: Bone Marrow


title: RNA-seq 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep2
RNA-seq sample EMX1_dmso_editing_rep2


title: NGP_Vehicle_H2AK119Ub

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

description:
Library name: NGP_Vehicle_H2AK119Ub
ChIP for H2AK119Ub

library_source: genomic

data_processing:
Quality control tests for unmapped sequenced were performed using FASTQC software and aligned to the human GRCh38/hg38 genome with bowtie2 (v2.5.3) aligner. PCR duplicates were removed with Picard. Mapped reads were normalized to reads per kilobase per million (RPKM) and tracks for RPKM were created using bamCoverage tool as part of DeepTools (v3.5.3). Peak calling was performed against the input control using MACS2 (v2.2.9) software and the significance cut-offf of FDR ≤0.01.  Quantification of ChIP-seq signal under the curve (AUC) for peak regions was calculated by converting BigWig to bedGraph files using the UCSC utility bigWigToBedGraph (v3.7.7) . These files were then intersected with merged peak regions using bedtools v2.27.1, producing files that included overlapping signal segments for each peak. The intersected files were loaded into python as data frames, and each entry’s contribution to the AUC was calculated by multiplying the length of peak (i.e., end - start) with its associated signal intensity value. These values were then aggregated across all intervals corresponding to the same peak, resulting in peak-wise AUC.  MACS2-detected peaks for which log2(AUC+1) was ≤ 12, irrespective of the sample conditions, or overlapping with the ENCODE black-listed regions for hg38 were filtered. Peaks were annotated with the nearest hg38 gene using the annotatePeak function in ChIPseeker (v1.42.1) in R with promoters identified as within 3kb of the transcription start site. Log2 fold-change in AUC between conditions were determined Motif analysis was performed using HOMER (v5.1) platform with a P value cut-off of ≤0.01 and ChIP-seq binding peaks were visualized using Integrative Genomic Viewer (IGV) v2.9.0.
Heatmaps for global H2AK119Ub ChIP-seq tracks were created using computeMatrix and plotHeatmap tools available in deepTools. For consensus analysis in Figure 5G, rows were rank ordered according to highest to lowest changes in gene transcription with PCGF1 knockout RNA-sequencing in NB-SD. Metaplots on RPKM normalized enrichment were created using plotProfile in deepTools.
Assembly: Hg38
Supplementary files format and content: RPKM normalized bigwig signal files

molecule: genomic DNA

source_name: NGP

growth_protocol: Neuroblastoma cell lines KELLY, NB1, NB-SD, NGP, and SK-N-AS were kindly provided by the Stegmaier laboratory at the Dana-Farber Cancer Institute (DFCI).  KELLY, NB1, and NB-SD were grown in RPMI-1640 (Corning, 10040CV) and NGP and SK-N-AS were grown in Dulbecco's Modified Eagle Medium (DMEM)(Corning, 10013CV) supplemented with 10% FBS (Corning, 35015CV) and 1x penicillin-streptomycin-glutamine (Gibco, 10378016).

extract_protocol:
ChIP sequencing and CUT&RUN sequencing
Histone ChIP-sequencing was performed as previously described17,24. 2 x 107 cells per sample were crosslinked in 1% formaldehyde for 10 minutes and quenched in 0.20M glycine for 5 minutes. Cells were lysed using an SDS buffer (100 mM NaCl, 50 mM Tris-Cl (pH 8.0), 5 mM EDTA (pH 8.0), 0.2% NaN3, 10% SDS) with 1X HALT protease inhibitor (Thermo cat#78429) and incubated at room temperature with gentle inversion for 2 minutes. Following centrifugation at 15,000 rpm nuclei were resuspended in IP buffer (two parts SDS buffer to one part triton dilution buffer (100 mM Tris-Cl (pH 8.0), 100 mM NaCl, 5 mM EDTA (pH 8.0) 0.2% NaN3, 5.0% Triton X-100)), and sheared for 15 minutes on a Covaris E220 ultrasonicator (5% duty cycle, peak power 140 W, cycles per burst 200) at 4 °C. Immunoprecipitation was performed with prepared antibody protein A magnetic beads conjugated overnight at 4°C with rotation. 10µg of antibody H2AK119ub (Cell Signaling Technology, 8240S) and 2 µL of the spike-in drosophila antibody (Active Motif, 61686) for normalization were added to each sample and rotated at 4°C overnight. The next day, chromatin were sequentially washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl), twice with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl), twice with LiCl wash buffer (0.25 M LiCl, 1% IGPAL-CH 630, 1% deoxycholic acid, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA), once with ice cold Tris-EDTA (TE), and then eluted in fresh elution buffer. IP samples were decrosslinked with 2.5 M NaCl, proteinase K, and RNAse A and then incubated at 65°C for 18 hours. DNA for all samples was isolated by incubating with AMPure beads (Beckman Coulter, A63880) for 20 minutes at room temperature, washing twice with 80% ethanol, and eluting in 1x TE. CUT&RUN sequencing was performed with the EpiCypher CUTANA ChIC/CUT&RUN (v5.0 #14-1048)  Kit according to manufacturer instructions. Briefly, ~1 x 10^6 cells were adsorbed to activated ConA beads and washed. 0.5 µg of the following antibodies were incubated into specified reaction tubes at 4°C overnight: RING1B (CST #5694), PCGF1 (Invitrogen #49390), PCGF1 (Abcam #259943), EZH2 (CST #5246), and isotype control supplemented with 0.01%  digitonin. The next morning cells were washed with cell permeabilization buffer and manufacturer recommended volume of pAG-MNase and calcium chloride added to each reaction. Chromatin was digested for 2 hours at 4°C before quenching. DNA was purified with AMPure XP beads prior to library preparation using the CUTANA CUT&RUN library Prep Kit (14-1001) according to manufacturer instructions.

value: NGP

value: Neuroblastoma

value: Vehicle


title: Arthrocelia, 1

description: Library name: Arthrocelia_1


title: Healthy Patient Bone Marrow Sample, BM_20070422

description: Library name: BM2_R


title: H520 cells,DDX17 shRNA,H3K4me3

city: hefei

first: xiaozheng

last: wei

address: tanghelu

institute: Anhui Medical University

description:
Library name: H520_H3K4me3_shDDX17
In H520 cells, knockdown of DDX17 was performed and H3K4me3 antibodies were used for sequencing.

data_processing:
Use FastQC software to perform quality assessment of CUT&Tag sequencing data, identify and remove low-quality sequences.
Use Bowtie2 software to accurately align the quality-controlled sequences with the reference genome.
Use the Macs3 software to perform Peak Calling on the comparison results, identifying the gene promoter regions associated with specific DNA-binding proteins.
Normalize the peak sets obtained from Peak Calling using DeepTools software.
Use IGV software to generate visual charts that intuitively display the peak position of the combination.
Assembly: hg19
Supplementary files format and content: bigWig,fastq

source_name: lung

growth_protocol: H1299,A549,H520 cells were cultured in DMEM medium (Vivocell) with 10% FBS. They were all cultured at 37 °C with 5% CO2.

extract_protocol:
After the cells are digested, add serum-containing culture medium to stop digestion, and perform cell counting. For each sample, take 1-1.5x10^6 cells and centrifuge at 110xg for 5 minutes, discard the culture medium, wash once with 1xPBS, and then resuspend. According to the kit instructions, use lectin-coated magnetic beads to capture the cells, permeabilize the cells, and then add secondary antibodies corresponding to the primary antibodies (without HRP). Use Mg2* to activate Protein A/G-Tn5 transposase to cut the target fragment, terminate the reaction with proteinase K, and add adapters for amplification at both ends before purification and sequencing. Based on the analysis of the sequencing results, decide on the subsequent experiments.
Using the Novogene library amplification kit, first prepare the components required for library amplification in a sterilized PCR tube: the components and their corresponding volumes are: 15 μl of resuspended DNA Extract Beads Pro, 25 μl of 2×CAM, 5 μl of N5XX, 5 μl of N7XX, totaling 50 μl. Then, gently pipette the mixed components to ensure they are well combined, and perform the reaction in the PCR machine according to the following program: 72°C for 3 minutes; 95°C for 3 minutes; then 98°C for 10 seconds, followed by 60°C for 5 seconds for 9 to 20 cycles; then 72°C for 1 minute, and hold at 4°C.

treatment_protocol: CUT&Tag of IgG and ZNF200 in H1299 cells, CUT&Tag of IgG and ZNF200 after stable transfection of DDX17-HA in H1299 cells, and after knocking down ZNF200 in H1299,H520 and A549 cells stably transfected with DDX17-HA, as well as CUT&Tag of HA, and also knocking down ZNF200 and DDX17 in H520 and A549 cell lines compared to the control group for H3K4me3 CUT&Tag.

value: lung

value: Non-Small Cell Lung Cancer

value: WT

value: DDX17 shRNA


title: Healthy Patient Bone Marrow Sample, BM_ND16600

description: Library name: BM3_R


title: Arthroconidia, 2

description: Library name: Arthroconidia_2


title: Arthroconidia, 3

description: Library name: Arthroconidia_3


title: RNA-seq 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep1
RNA-seq sample EMX1_dmso_editing_rep1


title: H520 cells,NonT shRNA,,H3K4me3

description:
Library name: H520_H3K4me3_SHC
In H520 cells, the infection control group virus SHC was incubated with H3K4me3 antibodies for sequencing.

value: NonT shRNA


title: A549 cells,DDX17 shRNA,H3K4me3

description:
Library name: A549_H3K4me3_shDDX17
In A549 cells, knockdown of DDX17 was performed and H3K4me3 antibodies were used for sequencing.


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, FMTC

description: Library name: MLLr24_C_T

data_processing:
ChIP-seq reads were aligned to hg19 using Bowtie2 and peaks were called with MACS2 (default parameters), followed by filtering to retain high-confidence peaks reproducibly detected across replicates. RNA-seq reads were aligned to hg19 using STAR; alternative splicing was quantified using rMATS, and skipped exon (SE) events were summarized using PSI values (significance thresholds: |ΔPSI| > 0.1 and FDR < 0.05). H3K79me2 peaks were assigned to SE events based on genomic overlap with exon bodies and flanking intronic regions for integrated chromatin–splicing analyses.
Assembly: hg19
Supplementary files format and content: Tab-separated value files and matrix files

value: EPZ-5676 Treatment


title: RNA-seq 20210218_hek293t_be_ZSWIM3_rep1

description:
Library name: 20210218_hek293t_be_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC6

description: Library name: MLLr22_C_T


title: Arthroconidia, 1

description: Library name: Arthroconidia_1


title: RNA-seq 20210218_hek293t_be_ZSWIM3_rep2

description:
Library name: 20210218_hek293t_be_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: H520 cells,ZNF200 shRNA,H3K4me3

description:
Library name: H520_H3K4me3_shZNF200
In H520 cells, knockdown of ZNF200 was performed and H3K4me3 antibodies were used for sequencing.

value: ZNF200 shRNA


title: HGSOC_rep1

type: RNA

city: Prague

first: Michal

last: Hensler

state: Prague 7

address: Jankovcova 1518/2

country: Czech Republic

institute: Sotio Biotech a.s.

hyb_protocol: A total of 380 genes were included in the analysis. Hybridization steps were performed within the Xenium Catalyst program (10xGenomics).

scan_protocol: Scan protocol were performed within the Xenium Catalyst program (10xGenomics).

data_processing: Primary data analysis was performed within the Xenium Catalyst program (10xGenomics).

source_name: Primary ovarian cancer

extract_protocol: tissue preparation protocol: All steps for sample preparation were performed within the Xenium Catalyst program (10xGenomics).

value: Primary ovarian cancer

tag: tissue preservation method

value: FFPE

value: untreated


title: NSCLC_rep2

source_name: Primary lung cancer

value: Primary lung cancer


title: Healthy Patient Bone Marrow Sample, BM_200804711

description: Library name: BM1_R


title: H520 cells,DDX17-OE,ZNF200 shRNA,HA

description:
Library name: H520_DDX17_HA_shZNF200
In H520 cells, overexpress DDX17, knock down ZNF200, and incubate with HA antibody for sequencing.

value: DDX17-OE,ZNF200 shRNA


title: A549 cells,ZNF200 shRNA,H3K4me3

description:
Library name: A549_H3K4me3_shZNF200
In A549 cells, knockdown of ZNF200 was performed and H3K4me3 antibodies were used for sequencing.


title: HGSOC_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS2

description: Library name: MLLr23_C_T

value: Peripheral Blood


title: A549 cells,NonT shRNA,H3K4me3

description:
Library name: A549_H3K4me3_SHC
In A549 cells, the infection control group virus SHC was incubated with H3K4me3 antibodies for sequencing.


title: RNA-seq 20210218_hek293t_be_TYR_rep6

description:
Library name: 20210218_hek293t_be_TYR_rep6
RNA-seq sample TYR_rep6


title: H520 cells,DDX17-OE,NonT shRNA,,HA

description:
Library name: H520_DDX17_HA_SHC
In H520 cells, overexpress DDX17, infect with the control group SHC virus, and incubate with HA antibodies for sequencing.

value: DDX17-OE,NonT shRNA


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC11

description: Library name: MLLr21_C_T


title: NSCLC_rep1


title: RNA-seq 20210218_hek293t_be_TYR_rep3

description:
Library name: 20210218_hek293t_be_TYR_rep3
RNA-seq sample TYR_rep3


title: C27_31900

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

hyb_protocol: The slide was assayed with the Xenium Prime 5K Human Pan Tissue and Pathways panel. Probe hybridization, ligation, amplification, and autofluorescence quenching were performed following 10X Genomics protocols without modifications.

scan_protocol: Slide scanning was performed with Xenium Analyzer v4.0.1.2 at the University of Rochester’s Genomics Research Center. Cell segmentation was performed using the Xenium In Situ Multimodal Cell Segmentation workflow (10X Genomics; CG000750).

data_processing: Segmented cells were filtered for quality, clustered, and scored for human specificity based upon a custom metric dependent on the average specificity of human vs. mouse probes per gene. Remaining mouse cells were filtered following this step based on transcriptional comparisons to mouse and human scRNA-seq.

label: Xenium probe set

organism:
Homo sapiens
Mus musculus

source_name: Homo sapiens Mus musculus Chimera

label_protocol:
Xenium probe set
Xenium probe set

extract_protocol: tissue preparation protocol: Ten micron thick PFA fixed frozen Sagittal brain sections of perinatally transplanted 16-19 wk human glial chimeric mice ((WA09: n=4, C27: n=2) were placed in the sample area of a Xenium slide.

value: Brain

value: Other


title: RNA-seq 20210218_hek293t_be_TYR_rep5

description:
Library name: 20210218_hek293t_be_TYR_rep5
RNA-seq sample TYR_rep5


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC9

description: Library name: MLLr20_C_T


title: RNA-seq 20210218_hek293t_be_TYR_rep2

description:
Library name: 20210218_hek293t_be_TYR_rep2
RNA-seq sample TYR_rep2


title: WA09_GFP_44480

value: GFP


title: A549 cells,DDX17-OE,ZNF200 shRNA,HA

description:
Library name: A549_DDX17_HA_shZNF200
In A549 cells, overexpress DDX17, knock down ZNF200, and incubate with HA antibody for sequencing.

value: lung


title: WA09_40012


title: RNA-seq 20210218_hek293t_be_TYR_rep4

description:
Library name: 20210218_hek293t_be_TYR_rep4
RNA-seq sample TYR_rep4


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC3

description: Library name: MLLr17_C_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC10

description: Library name: MLLr16_C_T


title: H1299 cells,DDX17-OE,ZNF200 shRNA,HA

description:
Library name: H1299_DDX17_HA_shZNF200
In H1299 cells, overexpress DDX17, knock down ZNF200, and incubate with HA antibody for sequencing.

value: Non-Small Cell Lung Cancer


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC4

description: Library name: MLLr14_C_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC7

description: Library name: MLLr19_C_T


title: H1299 cells,DDX17-OE,HA

description:
Library name: H1299_DDX17_HA
In H1299 cells, overexpress DDX17 and incubate with HA antibodies for sequencing.

value: WT


title: H1299 cells,DDX17-OE,NonT shRNA,,HA

description:
Library name: H1299_DDX17_HA_SHC
In H1299 cells, overexpress DDX17, infect with the control group SHC virus, and incubate with HA antibodies for sequencing.


title: H1299 cells,DDX17-OE,IgG

description:
Library name: H1299_DDX17_IgG
In H1299 cells, overexpress DDX17 and incubate with IgG antibodies for sequencing.


title: RNA-seq 20210218_hek293t_be_TYR_rep1

description:
Library name: 20210218_hek293t_be_TYR_rep1
RNA-seq sample TYR_rep1


title: A549 cells,DDX17-OE,NonT shRNA,,HA

description:
Library name: A549_DDX17_HA_SHC
In A549 cells, overexpress DDX17, infect with the control group SHC virus, and incubate with HA antibodies for sequencing.


title: RNA-seq 20210218_hek293t_be_EMX1_rep4

description:
Library name: 20210218_hek293t_be_EMX1_rep4
RNA-seq sample EMX1_rep4


title: RNA-seq 20210218_hek293t_be_EMX1_rep6

description:
Library name: 20210218_hek293t_be_EMX1_rep6
RNA-seq sample EMX1_rep6


title: RNA-seq 20210218_hek293t_be_EMX1_rep5

description:
Library name: 20210218_hek293t_be_EMX1_rep5
RNA-seq sample EMX1_rep5


title: H1299 cells,ZNF200

description:
Library name: H1299_ZNF200
In H1299 cells, incubate ZNF200 antibodies for sequencing.


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC2

description: Library name: MLLr15_C_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC12

description: Library name: MLLr18_C_T


title: WA09_GFP_44471


title: WA09_39982


title: CUT&Tag nih3t3_zswim3_h3k9me3_rep2

description:
Library name: nih3t3_zswim3_h3k9me3_rep2
CUT&Tag sample nih3t3_zswim3_h3k9me3_rep2

data_processing:
Read adaptors were trimmed using cutadapt (version 3.4). Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For coverage bigwig, deepTools bamCoverage was used on aligned BAM files with parameter "--normalizeUsing RPKM --binSize 1" to generate genome coverage bigWig files. For peak calling used in normalization and visualization, MACS2 callpeak used "--nolambda -f BAMPE -g [hs/mm per cell line] --bdg -q 0.05" for H3K27ac.
For peak calling used in normalization and visualization, MACS2 callpeak used "--nolambda -f BAMPE -g [hs/mm per cell line] --bdg -q 0.05" for H3K27ac and CTCF. For H3K27me3 peak calling, "--broad --broad-cutoff 0.1" was added after the H3K27ac parameters. For H3K9me3 peak calling, "--broad --broad-cutoff 0.05" was added after the H3K27ac parameters.
Assembly: hg38/mm10
Supplementary files format and content: coverage bigWig
Supplementary files format and content: MACS2 peaks
Library strategy: CUT&Tag

organism: Mus musculus

extract_protocol:
CUT&Tag libraries were generated using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) following the manufacturer's instructions with minor adjustments. Harvested cells were washed once with 500 μL Wash Buffer and resuspended in 100 μL Wash Buffer. Ten microliters of Concanavalin A beads were added and incubated at room temperature for 10 minutes with intermittent gentle inversion. Bead-bound cells were resuspended in 50 μL pre-chilled Antibody Buffer containing primary antibody against CTCF (Active Motif, 61932), H3K27ac (Abcam, ab4729), H3K9me3 (Active Motif, 39161), or H3K27me3 (Cell Signaling, C36B11), and incubated overnight at 2-8°C.
On day 2, beads were washed and resuspended in 50 μL Dig-wash Buffer supplemented with 0.01 mg/mL secondary antibody (Novoprotein, N269), incubated at room temperature for 30-60 minutes on a tube rotator, and washed three times with 200 μL Dig-wash Buffer. Beads were resuspended in 100 μL Dig-300 Buffer containing 2 μL pA/G-Tnp transposome and incubated for 1 hour at room temperature with gentle rotation. After three washes with 200 μL Dig-300 Buffer, beads were resuspended in 50 μL tagmentation buffer (5× TTBL diluted in Dig-300 Buffer). Tagmentation was performed at 37°C for 60 minutes in a thermocycler with heated lid disabled. To stop reaction and extract DNA, 5 μL Proteinase K, 100 μL Buffer L/B, and 20 μL DNA Extract Beads were added, and DNA was eluted in 20 μL nuclease-free water. Purified DNA was amplified using CUT&Tag Amplification Mix (CAM) and indexed primers (12-14 cycles for ~10,000 cells), then final PCR products were purified using VAHTS DNA Clean Beads (Vazyme, N411). Sequencing libraries were generated on the Illumina NovaSeq 6000 platform.


title: H1299 cells,IgG

description:
Library name: H1299_IgG
In H1299 cells, incubate IgG antibodies for sequencing.


title: CUT&Tag nih3t3_zswim3_h3k27me3_rep2

description:
Library name: nih3t3_zswim3_h3k27me3_rep2
CUT&Tag sample nih3t3_zswim3_h3k27me3_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC5

description: Library name: MLLr13_C_T


title: CUT&Tag nih3t3_zswim3_h3k9me3_rep1

description:
Library name: nih3t3_zswim3_h3k9me3_rep1
CUT&Tag sample nih3t3_zswim3_h3k9me3_rep1


title: RNA-seq 20210218_hek293t_be_EMX1_rep3

description:
Library name: 20210218_hek293t_be_EMX1_rep3
RNA-seq sample EMX1_rep3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC8

description: Library name: MLLr12_C_T


title: H520 cells,DDX17-KD,H3K4me3

description:
Library name: H520_H3K4me3_shDDX17
In H520 cells, knockdown of DDX17 was performed and H3K4me3 antibodies were used for sequencing.

data_processing:
Use FastQC software to perform quality assessment of sequencing data, identify and remove low-quality sequences.
Use Bowtie2 software to accurately align the quality-controlled sequences with the reference genome.Use samtools to remove mitochondrial genes.
Use the Macs3 software to perform Peak Calling on the comparison results, identifying the gene promoter regions associated with specific DNA-binding proteins.
Normalize the peak sets obtained from Peak Calling using DeepTools software.
Use IGV software to generate visual charts that intuitively display the peak position of the combination.
Assembly: hg19
Supplementary files format and content: bigWig,fastq

growth_protocol: A549,H520 cells were cultured in DMEM medium (Vivocell) with 10% FBS. They were all cultured at 37 °C with 5% CO2.

treatment_protocol: Knockdown of ZNF200 and DDX17 in H520 and A549 cell lines, followed by ATAC-seq using an H3K4me3 antibody compared to the control group.


title: CUT&Tag nih3t3_zswim3_h3k27me3_rep1

description:
Library name: nih3t3_zswim3_h3k27me3_rep1
CUT&Tag sample nih3t3_zswim3_h3k27me3_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TC1

description: Library name: MLLr11_C_T


title: RNA-seq 20210218_hek293t_be_ZSWIM3_rep3

description:
Library name: 20210218_hek293t_be_ZSWIM3_rep3
RNA-seq sample ZSWIM3_rep3


title: RNA-seq 20210218_hek293t_be_EMX1_rep2

description:
Library name: 20210218_hek293t_be_EMX1_rep2
RNA-seq sample EMX1_rep2


title: RNA-seq 20210218_hek293t_be_EMX1_rep1

description:
Library name: 20210218_hek293t_be_EMX1_rep1
RNA-seq sample EMX1_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS9

description: Library name: MLLr9_C_T


title: H520 cells,ZNF200-KD,H3K4me3

description:
Library name: H520_H3K4me3_shZNF200
In H520 cells, knockdown of ZNF200 was performed and H3K4me3 antibodies were used for sequencing.


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS10

description: Library name: MLLr10_C_T


title: RNA-seq 20201212_hek293t_cas9_ZSWIM3-L_rep3

description:
Library name: 20201212_hek293t_cas9_ZSWIM3-L_rep3
RNA-seq sample ZSWIM3-L_rep3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS8

description: Library name: MLLr8_C_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS7

description: Library name: MLLr7_C_T


title: CUT&Tag nih3t3_wt_h3k9me3_rep2

description:
Library name: nih3t3_wt_h3k9me3_rep2
CUT&Tag sample nih3t3_wt_h3k9me3_rep2


title: CUT&Tag nih3t3_zswim3_h3k27ac_rep2

description:
Library name: nih3t3_zswim3_h3k27ac_rep2
CUT&Tag sample nih3t3_zswim3_h3k27ac_rep2


title: RNA-seq 20201212_hek293t_cas9_ZSWIM3-L_rep2

description:
Library name: 20201212_hek293t_cas9_ZSWIM3-L_rep2
RNA-seq sample ZSWIM3-L_rep2


title: A549 cells,ZNF200-KD,H3K4me3

description:
Library name: A549_H3K4me3_shZNF200
In A549 cells, knockdown of ZNF200 was performed and H3K4me3 antibodies were used for sequencing.


title: CUT&Tag nih3t3_zswim3_h3k27ac_rep1

description:
Library name: nih3t3_zswim3_h3k27ac_rep1
CUT&Tag sample nih3t3_zswim3_h3k27ac_rep1


title: CUT&Tag nih3t3_wt_h3k9me3_rep1

description:
Library name: nih3t3_wt_h3k9me3_rep1
CUT&Tag sample nih3t3_wt_h3k9me3_rep1


title: RNA-seq 20201212_hek293t_cas9_ZSWIM3-L_rep1

description:
Library name: 20201212_hek293t_cas9_ZSWIM3-L_rep1
RNA-seq sample ZSWIM3-L_rep1


title: A549 cells,SHC,H3K4me3

description:
Library name: A549_H3K4me3_SHC
In A549 cells, the infection control group virus SHC was incubated with H3K4me3 antibodies for sequencing.

value: SHC


title: H520 cells,SHC,H3K4me3

description:
Library name: H520_H3K4me3_SHC
In H520 cells, the infection control group virus SHC was incubated with H3K4me3 antibodies for sequencing.


title: RNA-seq 20201212_hek293t_cas9_ZIM3-L_rep2

description:
Library name: 20201212_hek293t_cas9_ZIM3-L_rep2
RNA-seq sample ZIM3-L_rep2


title: RNA-seq 20201212_hek293t_cas9_ZIM3-L_rep3

description:
Library name: 20201212_hek293t_cas9_ZIM3-L_rep3
RNA-seq sample ZIM3-L_rep3


title: A549 cells,DDX17-KD,H3K4me3

description:
Library name: A549_H3K4me3_shDDX17
In A549 cells, knockdown of DDX17 was performed and H3K4me3 antibodies were used for sequencing.


title: NGP_XL177A_Rep3

description: Library name: NGP_XL177A_Rep3

data_processing:
Quality control tests for unmapped sequenced were performed using FASTQC (v.0.12.0) software and aligned to the human GRCh38/hg38 genome with STAR (v2.7.11) genome aligner. Gene level counts were summarized using featureCounts in the Subread package (v.2.23.3) in R. Gene counts were normalized and dfferential gene expression analysis performed using DESeq2 package (v1.49.3). Gene expression was estimated on the basis of Log2(TPM+1) scores for normalized reads. Expressed genes are defined by a log2(TPM+1) of ≥1 for at least one sample. Cut-offs for alterations in gene expression were determined by a log2 fold-change of greater or less than 1.0 and an adjusted P. value of ≤ 0.10.
Assembly: Hg38
Supplementary files format and content: Summarized counts for all samples and log2 fold-change in gene expression as compared to its control group.

growth_protocol: Summarized log2(TPM+1) for all samples and log2 fold-change in gene expression as compared to its control group.

extract_protocol:
RNA was extracted from either cell lines with the indicated treatments or chunks of NB-SD xenograft tumors treated with vehicle or 75 mg/kg XL177A twice daily with the RNeasy Mini Kit (Qiagen) and oncolumn DNA digestion according to the manufacturer protocol.
Non-directional eukaryotic mRNA library preparation from total RNA was performed by Novogene and sequenced on an Illumina Novaseq X Plus platform.

value: NGP

value: Neuroblastoma


title: CUT&Tag nih3t3_wt_h3k27me3_rep2

description:
Library name: nih3t3_wt_h3k27me3_rep2
CUT&Tag sample nih3t3_wt_h3k27me3_rep2


title: RNA-seq 20201212_hek293t_cas9_ZIM3-L_rep1

description:
Library name: 20201212_hek293t_cas9_ZIM3-L_rep1
RNA-seq sample ZIM3-L_rep1


title: CUT&Tag nih3t3_wt_h3k27me3_rep1

description:
Library name: nih3t3_wt_h3k27me3_rep1
CUT&Tag sample nih3t3_wt_h3k27me3_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS5

description: Library name: MLLr5_C_T

value: EPZ-5676 Treatment


title: NGP_XL177A_Rep2

description: Library name: NGP_XL177A_Rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS4

description: Library name: MLLr4_C_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS3

description: Library name: MLLr3_C_T


title: RNA-seq 20201212_hek293t_cas9_SMPDL3B-L_rep2

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-L_rep2
RNA-seq sample SMPDL3B-L_rep2


title: CUT&Tag nih3t3_wt_h3k27ac_rep1

description:
Library name: nih3t3_wt_h3k27ac_rep1
CUT&Tag sample nih3t3_wt_h3k27ac_rep1


title: NGP_Veh_Rep3

description: Library name: NGP_Veh_Rep3

value: Control


title: CUT&Tag nih3t3_wt_h3k27ac_rep2

description:
Library name: nih3t3_wt_h3k27ac_rep2
CUT&Tag sample nih3t3_wt_h3k27ac_rep2


title: NGP_Veh_Rep1

description: Library name: NGP_Veh_Rep1


title: RNA-seq 20201212_hek293t_cas9_SMPDL3B-H_rep3

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-H_rep3
RNA-seq sample SMPDL3B-H_rep3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, FMC

description: Library name: MLLr24_C


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS1

description: Library name: MLLr1_C_T


title: CUT&Tag nih3t3_emx1_h3k9me3_rep2

description:
Library name: nih3t3_emx1_h3k9me3_rep2
CUT&Tag sample nih3t3_emx1_h3k9me3_rep2


title: CUT&Tag nih3t3_emx1_h3k9me3_rep1

description:
Library name: nih3t3_emx1_h3k9me3_rep1
CUT&Tag sample nih3t3_emx1_h3k9me3_rep1


title: NGP_Veh_Rep2

description: Library name: NGP_Veh_Rep2


title: RNA-seq 20201212_hek293t_cas9_SMPDL3B-H_rep2

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-H_rep2
RNA-seq sample SMPDL3B-H_rep2


title: CUT&Tag nih3t3_emx1_h3k27me3_rep2

description:
Library name: nih3t3_emx1_h3k27me3_rep2
CUT&Tag sample nih3t3_emx1_h3k27me3_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS1

description: Library name: MLLr23_C


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS2

description: Library name: MLLr2_C_T


title: RNA-seq 20201212_hek293t_cas9_SMPDL3B-L_rep3

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-L_rep3
RNA-seq sample SMPDL3B-L_rep3


title: RNA-seq 20201212_hek293t_cas9_SMPDL3B-L_rep1

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-L_rep1
RNA-seq sample SMPDL3B-L_rep1


title: CUT&Tag nih3t3_emx1_h3k27me3_rep1

description:
Library name: nih3t3_emx1_h3k27me3_rep1
CUT&Tag sample nih3t3_emx1_h3k27me3_rep1


title: RNA-seq 20201212_hek293t_cas9_SMPDL3B-H_rep1

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-H_rep1
RNA-seq sample SMPDL3B-H_rep1


title: NBSD_XL177A_Rep2

description: Library name: NBSD_XL177A_Rep2

source_name: NBSD

value: NBSD


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS7

description: Library name: MLLr22_C


title: NBSD_XL177A_Rep3

description: Library name: NBSD_XL177A_Rep3


title: CUT&Tag nih3t3_emx1_h3k27ac_rep2

description:
Library name: nih3t3_emx1_h3k27ac_rep2
CUT&Tag sample nih3t3_emx1_h3k27ac_rep2


title: RNA-seq 20201212_hek293t_cas9_MPP4-L_rep3

description:
Library name: 20201212_hek293t_cas9_MPP4-L_rep3
RNA-seq sample MPP4-L_rep3


title: NBSD_XL177A_Rep1

description: Library name: NBSD_XL177A_Rep1


title: RNA-seq 20201212_hek293t_cas9_MPP4-L_rep2

description:
Library name: 20201212_hek293t_cas9_MPP4-L_rep2
RNA-seq sample MPP4-L_rep2


title: NBSD_Veh_Rep3

description: Library name: NBSD_Veh_Rep3


title: CUT&Tag nih3t3_emx1_h3k27ac_rep1

description:
Library name: nih3t3_emx1_h3k27ac_rep1
CUT&Tag sample nih3t3_emx1_h3k27ac_rep1


title: CUT&Tag mesc_tcf19_ctcf_rep2

description:
Library name: mesc_tcf19_ctcf_rep2
CUT&Tag sample mesc_tcf19_ctcf_rep2

source_name: mESC

value: mESC


title: RNA-seq 20201212_hek293t_cas9_IKZF5-L_rep3

description:
Library name: 20201212_hek293t_cas9_IKZF5-L_rep3
RNA-seq sample IKZF5-L_rep3


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS8

description: Library name: MLLr19_C


title: KELLY_XL177A_Rep3

description: Library name: KELLY_XL177A_Rep3

source_name: KELLY

value: KELLY


title: CUT&Tag mesc_tcf19_ctcf_rep1

description:
Library name: mesc_tcf19_ctcf_rep1
CUT&Tag sample mesc_tcf19_ctcf_rep1


title: RNA-seq 20201212_hek293t_cas9_MPP4-L_rep1

description:
Library name: 20201212_hek293t_cas9_MPP4-L_rep1
RNA-seq sample MPP4-L_rep1


title: RNA-seq 20201212_hek293t_cas9_IKZF5-L_rep1

description:
Library name: 20201212_hek293t_cas9_IKZF5-L_rep1
RNA-seq sample IKZF5-L_rep1


title: NBSD_Veh_Rep1

description: Library name: NBSD_Veh_Rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS13

description: Library name: MLLr18_C


title: NBSD_Veh_Rep2

description: Library name: NBSD_Veh_Rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, TCS6

description: Library name: MLLr6_C_T


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS10

description: Library name: MLLr20_C


title: CUT&Tag mesc_pou5f1_ctcf_rep2

description:
Library name: mesc_pou5f1_ctcf_rep2
CUT&Tag sample mesc_pou5f1_ctcf_rep2


title: CUT&Tag mesc_nanogse_ctcf_rep2

description:
Library name: mesc_nanogse_ctcf_rep2
CUT&Tag sample mesc_nanogse_ctcf_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS11

description: Library name: MLLr16_C


title: KELLY_Xl177A_Rep1

description: Library name: KELLY_Xl177A_Rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, C2

description: Library name: MLLr17_C


title: CUT&Tag mesc_pou5f1_ctcf_rep1

description:
Library name: mesc_pou5f1_ctcf_rep1
CUT&Tag sample mesc_pou5f1_ctcf_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS12

description: Library name: MLLr21_C


title: CUT&Tag mesc_nanogse_ctcf_rep1

description:
Library name: mesc_nanogse_ctcf_rep1
CUT&Tag sample mesc_nanogse_ctcf_rep1


title: RNA-seq 20201212_hek293t_cas9_IKZF5-L_rep2

description:
Library name: 20201212_hek293t_cas9_IKZF5-L_rep2
RNA-seq sample IKZF5-L_rep2


title: RNA-seq 20201212_hek293t_cas9_GALE-L_rep3

description:
Library name: 20201212_hek293t_cas9_GALE-L_rep3
RNA-seq sample GALE-L_rep3


title: KELLY_XL177A_Rep2

description: Library name: KELLY_XL177A_Rep2


title: RNA-seq 20201212_hek293t_cas9_GALE-L_rep2

description:
Library name: 20201212_hek293t_cas9_GALE-L_rep2
RNA-seq sample GALE-L_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS6

description: Library name: MLLr14_C


title: KELLY_Veh_Rep3

description: Library name: KELLY_Veh_Rep3


title: NGP_XL177A_Rep1

description: Library name: NGP_XL177A_Rep1


title: KELLY_Veh_Rep2

description: Library name: KELLY_Veh_Rep2


title: RNA-seq 20201212_hek293t_cas9_GALE-L_rep1

description:
Library name: 20201212_hek293t_cas9_GALE-L_rep1
RNA-seq sample GALE-L_rep1


title: CUT&Tag mesc_nanog_ctcf_rep2

description:
Library name: mesc_nanog_ctcf_rep2
CUT&Tag sample mesc_nanog_ctcf_rep2


title: RNA-seq 20201212_hek293t_cas9_GALE-H_rep3

description:
Library name: 20201212_hek293t_cas9_GALE-H_rep3
RNA-seq sample GALE-H_rep3


title: CUT&Tag mesc_nanog_ctcf_rep1

description:
Library name: mesc_nanog_ctcf_rep1
CUT&Tag sample mesc_nanog_ctcf_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS5

description: Library name: MLLr13_C


title: RNA-seq 20201212_hek293t_cas9_GALE-H_rep2

description:
Library name: 20201212_hek293t_cas9_GALE-H_rep2
RNA-seq sample GALE-H_rep2


title: KELLY_Veh_Rep1

description: Library name: KELLY_Veh_Rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS9

description: Library name: MLLr12_C


title: CUT&Tag mesc_emx1_ctcf_rep2

description:
Library name: mesc_emx1_ctcf_rep2
CUT&Tag sample mesc_emx1_ctcf_rep2


title: RNA-seq 20201212_hek293t_cas9_GALE-H_rep1

description:
Library name: 20201212_hek293t_cas9_GALE-H_rep1
RNA-seq sample GALE-H_rep1


title: NBSD_Vehicle_Input

description:
Library name: NBSD_Vehicle_Input
Input sample

value: Vehicle


title: CUT&Tag mesc_emx1_ctcf_rep1

description:
Library name: mesc_emx1_ctcf_rep1
CUT&Tag sample mesc_emx1_ctcf_rep1


title: NBSD_XL177A_H2AK119Ub

description:
Library name: NBSD_XL177A_H2AK119Ub
ChIp for H2AK119Ub

value: 1 µM XL177A


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS4

description: Library name: MLLr11_C

value: Peripheral Blood


title: mESC PEM-seq Tcf19 locus

description:
Library name: mesc_tcf19
PEM-seq library for editing outcome quantification at Tcf19.

data_processing:
Raw FASTQ data were processed using the PEM-Q pipeline. A slight modification (https://github.com/lilab-thu/GenomeEditingChromatinPurtabations2025) was introduced to accommodate barcode length in this dataset. Reference genome used in processing was mm10.
Editing-event tables were generated per target locus for downstream quantification of deletions, insertions, and translocation-related events.
Assembly: mm10
Supplementary files format and content: PEM-Q pipeline output

source_name: embryo

extract_protocol:
PEM-seq was performed following the published protocol with minor modifications. Two million GFP-positive viable cells were isolated by FACS, and genomic DNA was extracted using standard procedures. Purified genomic DNA was used as input for downstream shearing and primer-extension workflow.
Purified DNA was sheared to a peak size of 300-700 bp using an M220 focused ultrasonicator (Covaris). For primer extension, biotinylated primers were subjected to repeated cycles of annealing and denaturation with 20 µg of fragmented genomic DNA, followed by primer extension using Bst Polymerase 3.0 (M0374S, NEB). Excess biotinylated primers were removed using VAHTS DNA Clean Beads (1.2:1 bead-to-sample ratio). The purified DNA was denatured at 95°C for 5 minutes and immediately chilled on ice for 5 minutes. Biotinylated extension products were captured with Dynabeads MyOne Streptavidin C1 and washed with B&W buffer and nuclease-free water according to the manufacturer's instructions. For bridge-adapter ligation, beads were resuspended in a ligation mixture containing 15% PEG8000, T4 DNA ligase (EL0011, Thermo Scientific), and annealed bridge adapters, and incubated overnight at room temperature. Bead-bound ligation products were washed and subjected to on-beads nested PCR using I5 nested primers, I7 index primers, and Taq polymerase (TransGen Biotech) for 16 cycles. PCR products were purified using VAHTS DNA Clean Beads and subsequently amplified with FastPfu (TransGen Biotech) to incorporate Illumina P5 and P7 adapters. Final PEM-seq libraries were sequenced on a DNBSEQ-T7 platform.

value: embryo

value: embryonic stem cell

value: wild type

value: CRISPR-Cas9 editing


title: NBSD_XL177A_Input

description:
Library name: NBSD_XL177A_Input
Input sample


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS10

description: Library name: MLLr10_C


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS9

description: Library name: MLLr9_C


title: NBSD_Vehicle_H2AK119Ub

description:
Library name: NBSD_Vehicle_H2AK119Ub
ChIp for H2AK119Ub


title: RNA-seq 20201212_hek293t_cas9_FKBP2-L_rep2

description:
Library name: 20201212_hek293t_cas9_FKBP2-L_rep2
RNA-seq sample FKBP2-L_rep2


title: mESC PEM-seq NanogSE locus

description:
Library name: mesc_nanogse
PEM-seq library for editing outcome quantification at NanogSE.


title: RNA-seq 20201212_hek293t_cas9_FKBP2-L_rep3

description:
Library name: 20201212_hek293t_cas9_FKBP2-L_rep3
RNA-seq sample FKBP2-L_rep3


title: mESC PEM-seq Pou5f1 locus

description:
Library name: mesc_pou5f1
PEM-seq library for editing outcome quantification at Pou5f1.


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS8

description: Library name: MLLr8_C


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS7

description: Library name: MLLr7_C


title: RNA-seq 20201212_hek293t_cas9_FKBP2-L_rep1

description:
Library name: 20201212_hek293t_cas9_FKBP2-L_rep1
RNA-seq sample FKBP2-L_rep1


title: ATAC-seq 20251117_nih3t3_rnp_ZSWIM3_6h_rep2

description:
Library name: 20251117_nih3t3_rnp_ZSWIM3_6h_rep2
ATAC-seq sample ZSWIM3_6h_rep2

data_processing:
ATAC-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For uploaded processed bigWig files, bamCoverage was used with -p 8 --normalizeUsing RPKM --binSize 100.
Assembly: mm10/hg38
Supplementary files format and content: ATAC-seq coverage bigWig

extract_protocol:
Cells were collected and washed with ice-cold PBS. Cell pellets were resuspended in ATAC-seq RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 10 minutes. ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL-630 or digitonin) was then added for washing. Nuclei were pelleted in a pre-chilled centrifuge. Nuclei were incubated with Tn5 transposase and tagmentation buffer at 37°C for 30 minutes. Stop buffer and Proteinase K were added, and samples were incubated at 55°C for 30 minutes to terminate tagmentation and remove proteins.
PCR was performed to amplify the ATAC library for 5 cycles using KAPA HiFi PCR kit. To determine additional amplification cycles for each sample, qPCR was performed, and the additional cycle number was determined as the cycle reaching one-third of maximal abundance in the qPCR amplification curve. All samples were then amplified for another N+3 cycles, followed by final extension. Libraries were purified with DNA clean beads and sequenced as paired-end libraries on Illumina platforms.


title: C27_33475

value: Brain

value: Other


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, BS3

description: Library name: MLLr15_C


title: CITE-seq, K7 PDX, ADT

city: New York

first: Sophie

last: Hanina

address: 630 West 168th Street

institute: Columbia University

description: Library name: SH-2852_12_2 adt

library_source: other

data_processing:
CellRanger count pipeline
Assembly: GRCh38
Supplementary files format and content: CellRanger output files
Library strategy: CITE-seq

molecule: protein

source_name: Kidney PDX

extract_protocol:
The single-cell RNA-Seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets.
Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Around 10,000 cells were targeted for each sample. Samples were sometimes multiplexed together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO)  and specific extracellular protein epitope characterized (using Antibody Derived Tag - ADT)

value: Kidney PDX

tag: disease state

value: ccRCC

tag: library type

value: ADT

tag: adt

value: Total seq A-5006 anti-human CD70, Total seq A-5007 anti-human CAIX, TotalSeq™-A0050 anti-human CD19


title: ATAC-seq 20251117_nih3t3_rnp_ZSWIM3_6h_rep1

description:
Library name: 20251117_nih3t3_rnp_ZSWIM3_6h_rep1
ATAC-seq sample ZSWIM3_6h_rep1


title: RNA-seq 20201212_hek293t_cas9_FKBP2-H_rep2

description:
Library name: 20201212_hek293t_cas9_FKBP2-H_rep2
RNA-seq sample FKBP2-H_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS6

description: Library name: MLLr6_C


title: CITE-seq, K7 PDX, GEX

description: Library name: SH-2852_12_2 rna

value: mRNA


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS5

description: Library name: MLLr5_C


title: ATAC-seq 20251117_nih3t3_rnp_ZSWIM3_12h_rep2

description:
Library name: 20251117_nih3t3_rnp_ZSWIM3_12h_rep2
ATAC-seq sample ZSWIM3_12h_rep2


title: CITE-seq, K7 PDX, HTO

description: Library name: SH-2852_12_2 hto

value: HTO

tag: hto

value: TotalSeq™-A0251 anti-human Hashtag 1


title: CITE-seq, K5 PDX, HTO

description: Library name: SH-2852_11_1 hto


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS3

description: Library name: MLLr3_C


title: RNA-seq 20201212_hek293t_cas9_EMX1_rep3

description:
Library name: 20201212_hek293t_cas9_EMX1_rep3
RNA-seq sample EMX1_rep3


title: RNA-seq 20201212_hek293t_cas9_FKBP2-H_rep3

description:
Library name: 20201212_hek293t_cas9_FKBP2-H_rep3
RNA-seq sample FKBP2-H_rep3


title: ATAC-seq 20251117_nih3t3_rnp_EMX1_6h_rep2

description:
Library name: 20251117_nih3t3_rnp_EMX1_6h_rep2
ATAC-seq sample EMX1_6h_rep2


title: CITE-seq, K5 PDX, ADT

description: Library name: SH-2852_11_1 adt


title: CITE-seq, K5 PDX, GEX

description: Library name: SH-2852_11_1 rna


title: ATAC-seq 20251117_nih3t3_rnp_EMX1_6h_rep1

description:
Library name: 20251117_nih3t3_rnp_EMX1_6h_rep1
ATAC-seq sample EMX1_6h_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS4

description: Library name: MLLr4_C


title: RNA-seq 20201212_hek293t_cas9_EMX1_rep1

description:
Library name: 20201212_hek293t_cas9_EMX1_rep1
RNA-seq sample EMX1_rep1


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS1

description: Library name: MLLr1_C


title: RNA-seq 20201212_hek293t_cas9_EMX1-H_rep3

description:
Library name: 20201212_hek293t_cas9_EMX1-H_rep3
RNA-seq sample EMX1-H_rep3


title: RNA-seq 20201212_hek293t_cas9_EMX1_rep2

description:
Library name: 20201212_hek293t_cas9_EMX1_rep2
RNA-seq sample EMX1_rep2


title: ATAC-seq 20251117_nih3t3_rnp_EMX1_12h_rep2

description:
Library name: 20251117_nih3t3_rnp_EMX1_12h_rep2
ATAC-seq sample EMX1_12h_rep2


title: Acute Myeloid Leukemia Patient Blood Sample, PS743835

description: Library name: AML4_C


title: Multiome, Patient 8, RCC, ATAC

description: Library name: SH-2865_8 ATAC

library_source: genomic single cell

data_processing:
FASTQ files from the 10x Multiome were aligned to GRCh38 (CellRanger human reference genome GRCh38-2020-A-2.0.0) using CellRanger Arc 2.0.2 with default parameters. After alignment, ambient RNA reads were removed in all samples using SoupX(23) v.1.6.2 with default parameters
Assembly: GRCh38
Supplementary files format and content: CellRange Arc fragments output
Supplementary files format and content: R object of Soupx result

source_name: Kidney

extract_protocol:
Single Cell Multiome ATAC + Gene Expression was performed with 10X genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and demonstrated protocol - Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing.
Cells were lysed for 4min and resuspended in Diluted Nuclei Buffer (10x Genomics, PN- 2000207). Lysis efficiency and nuclei concentration was evaluated on Countess II automatic cell counter by trypan blue staining.  Nuclei were loaded in the transposition reaction, targeting recovery of 10,000 nuclei after encapsulation. After transposition reaction nuclei were encapsulated and barcoded.

value: Kidney

value: Renal Cell Carcinoma

tag: donor

value: patient 6

value: ATAC


title: RNA-seq 20201212_hek293t_cas9_EMX1-H_rep2

description:
Library name: 20201212_hek293t_cas9_EMX1-H_rep2
RNA-seq sample EMX1-H_rep2


title: ATAC-seq 20250831_nih3t3_cas12a_NDUFS3-2_rep2

description:
Library name: 20250831_nih3t3_cas12a_NDUFS3-2_rep2
ATAC-seq sample NDUFS3-2_rep2


title: Mixed Lineage Leukemia Rearrangement Patient Blood Sample, CS2

description: Library name: MLLr2_C

value: Peripheral Blood


title: Acute Myeloid Leukemia Patient Blood Sample, PS78299

description: Library name: AML3_C


title: ATAC-seq 20251117_nih3t3_rnp_EMX1_12h_rep1

description:
Library name: 20251117_nih3t3_rnp_EMX1_12h_rep1
ATAC-seq sample EMX1_12h_rep1


title: Multiome, Patient 7, RCC, ATAC

description: Library name: SH-2865_7 ATAC

value: patient 5


title: RNA-seq 20201212_hek293t_cas9_FKBP2-H_rep1

description:
Library name: 20201212_hek293t_cas9_FKBP2-H_rep1
RNA-seq sample FKBP2-H_rep1


title: RNA-seq 20201212_hek293t_cas9_EMX1-H_rep1

description:
Library name: 20201212_hek293t_cas9_EMX1-H_rep1
RNA-seq sample EMX1-H_rep1


title: Multiome, Patient 8, RCC, GEX

description: Library name: SH-2865_8 RNA

library_source: transcriptomic single cell

molecule: nuclear RNA


title: Multiome, Patient 7, RCC, GEX

description: Library name: SH-2865_7 RNA


title: ATAC-seq 20251117_nih3t3_rnp_ZSWIM3_12h_rep1

description:
Library name: 20251117_nih3t3_rnp_ZSWIM3_12h_rep1
ATAC-seq sample ZSWIM3_12h_rep1


title: ATAC-seq 20250831_nih3t3_cas12a_NDUFS3-2_rep1

description:
Library name: 20250831_nih3t3_cas12a_NDUFS3-2_rep1
ATAC-seq sample NDUFS3-2_rep1


title: Multiome, Patient 6, RCC, ATAC

description: Library name: SH-2865_6 ATAC

value: patient 4


title: ATAC-seq 20250831_nih3t3_cas12a_NDUFS3-1_rep2

description:
Library name: 20250831_nih3t3_cas12a_NDUFS3-1_rep2
ATAC-seq sample NDUFS3-1_rep2


title: RNA-seq 20201212_hek293t_cas9_CIB4-L_rep3

description:
Library name: 20201212_hek293t_cas9_CIB4-L_rep3
RNA-seq sample CIB4-L_rep3


title: Healthy Patient Bone Marrow Sample, BMRIJIV

description: Library name: BM4_C

value: Bone Marrow


title: RNA-seq 20201212_hek293t_cas9_CIB4-L_rep2

description:
Library name: 20201212_hek293t_cas9_CIB4-L_rep2
RNA-seq sample CIB4-L_rep2


title: Acute Myeloid Leukemia Patient Blood Sample, PS754422

description: Library name: AML1_C


title: Multiome, Patient 6, RCC, GEX

description: Library name: SH-2865_6 RNA


title: ATAC-seq 20250831_nih3t3_cas12a_EMX1-4_rep2

description:
Library name: 20250831_nih3t3_cas12a_EMX1-4_rep2
ATAC-seq sample EMX1-4_rep2


title: ATAC-seq 20250831_nih3t3_cas12a_NDUFS3-1_rep1

description:
Library name: 20250831_nih3t3_cas12a_NDUFS3-1_rep1
ATAC-seq sample NDUFS3-1_rep1


title: ATAC-seq 20250831_nih3t3_cas12a_EMX1-4_rep1

description:
Library name: 20250831_nih3t3_cas12a_EMX1-4_rep1
ATAC-seq sample EMX1-4_rep1


title: Multiome, Patient 5, RCC, ATAC

description: Library name: SH-2687_5 ATAC

value: patient 3


title: Healthy Patient Bone Marrow Sample, BMND16600

description: Library name: BM3_C


title: RNA-seq 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep3

description:
Library name: 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep3
RNA-seq sample ZSWIM3_editing_72h_rep3


title: RNA-seq 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep1

description:
Library name: 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep1
RNA-seq sample ZSWIM3_editing_72h_rep1


title: Acute Myeloid Leukemia Patient Blood Sample, PS88351

description: Library name: AML2_C


title: RNA-seq 20201212_hek293t_cas9_CIB4-L_rep1

description:
Library name: 20201212_hek293t_cas9_CIB4-L_rep1
RNA-seq sample CIB4-L_rep1


title: Healthy Patient Bone Marrow Sample, BM20070422

description: Library name: BM2_C


title: RNA-seq 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep2

description:
Library name: 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep2
RNA-seq sample ZSWIM3_editing_72h_rep2


title: ATAC-seq 20250831_nih3t3_cas12a_EMX1-2_rep2

description:
Library name: 20250831_nih3t3_cas12a_EMX1-2_rep2
ATAC-seq sample EMX1-2_rep2


title: RNA-seq 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep3

description:
Library name: 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep3
RNA-seq sample ZSWIM3_editing_48h_rep3


title: Multiome, Patient 4, RCC, ATAC

description: Library name: SH-2687_4 ATAC

value: patient 2


title: RNA-seq 20250731_nih3t3_rnp_ZSWIM3_rep2

description:
Library name: 20250731_nih3t3_rnp_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: ATAC-seq 20250831_nih3t3_cas12a_EMX1-2_rep1

description:
Library name: 20250831_nih3t3_cas12a_EMX1-2_rep1
ATAC-seq sample EMX1-2_rep1


title: Healthy Patient Bone Marrow Sample, BM200804711

description: Library name: BM1_C


title: Multiome, Patient 4, RCC, GEX

description: Library name: SH-2687_4 RNA


title: TryptophanControl-3

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

description: Library name: Sample 57

data_processing:
FastQC 0.11.9 was used to evaluate quality of seqenced reads.
Gene abundance estimates were obtained for each sample using kallisto (version 0.50.1).
Transcript estimates are read into gene counts using tximport (version 1.32.0), then counts are normalized using DESeq2 (version 1.44.0).
Counts tables were generated for each amino acid. Leucine, isoleucine, and valine share the BCAA samples as their controls. All other amino acids have their own unique controls.
Assembly: GRCh38 (Release 45)
Supplementary files format and content: csv files include DESeq2 normalized counts for each sample

source_name: Jurkat

extract_protocol:
RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1μg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jurkat

value: Tryptophan control

tag: time-point

value: Day 3


title: Multiome, Patient 3, RCC, GEX

description: Library name: SH-2687_3 RNA

value: patient 1


title: TryptophanControl-4

description: Library name: Sample 58


title: TryptophanControl-5

description: Library name: Sample 59


title: Multiome, Patient 5, RCC, GEX

description: Library name: SH-2687_5 RNA

value: mRNA


title: RNA-seq 20250731_nih3t3_rnp_ZSWIM3_rep1

description:
Library name: 20250731_nih3t3_rnp_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: Multiome, Patient 3, RCC, ATAC

description: Library name: SH-2687_3 ATAC


title: shCSE1L_2_day7_3

city: Toronto

first: Veronique

last: Voisin

state: ON

address: 101 College St, room 8-353

country: Canada

institute: University Health Network

description: Library name: S1469D73

data_processing:
Samples were then submitted to Novagene (Novogene Corporation Inc., Sacramento, CA)  for high-throughput sequencing on the Illumina NovaSeqXPlus plaform  using 2 x 150 bp paired-ended sequencing to obtain ~50 M reads per sample.
Raw data were aligned using HISAT2 against GRCh38 by Novogene using default parameter.
Read counts were generated using Feature Counts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text data frame that includes raw gene count value for each sample
Supplementary files format and content: BAM files from the alignment using HISAT2

source_name: cell line

growth_protocol: TEX cells were cultured in IMDM medium supplemented with 20% fetal bovine serum (FBS), 2 mM l-glutamine (Thermo Fisher Scientific, Cat# 25030081), 2 ng/ml human recombinant interleukin-3 (IL-3, R&D Systems, Cat# 203-IL) and 20 ng/ml human recombinant stem cell factor (SCF, R&D Systems, Cat# 255-SC).

extract_protocol:
Total RNA was isolated from both control and CSE1L knockdown TEX cells using the RNeasy Plus Mini Kit (QIAGEN, Cat# 74134), following the manufacturer’s protocol. RNA concentration and purity were assessed using a NanoDrop spectrophotometer.
Next-generation sequencing libraries were made using AbClonal mRNA-seq Lib Prep Kit for  Illumina.

treatment_protocol: TEX cells were transduced with lentiviral particles expressing either control shRNA or shRNAs targeting CSE1L. Transduced cells were selected with puromycin (2 µg/ml). Total RNA was isolated from cells after 3 and 7 days of puromycin selection.

tag: day

value: TEX

value: Leukemic cells  (cell line)


title: RNA-seq 20250731_nih3t3_rnp_EMX1_rep2

description:
Library name: 20250731_nih3t3_rnp_EMX1_rep2
RNA-seq sample EMX1_rep2


title: RNA-seq 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep1

description:
Library name: 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep1
RNA-seq sample ZSWIM3_editing_48h_rep1


title: TryptophanControl-2

description: Library name: Sample 56


title: RNA-seq 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep2

description:
Library name: 20201124_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep2
RNA-seq sample ZSWIM3_editing_48h_rep2


title: RNA-seq 20201124_hek293t_cas9_timeseries_TYR_editing_72h_rep3

description:
Library name: 20201124_hek293t_cas9_timeseries_TYR_editing_72h_rep3
RNA-seq sample TYR_editing_72h_rep3


title: shCSE1L_2_day7_2

description: Library name: S1469D72


title: TryptophanControl-1

description: Library name: Sample 55


title: shCSE1L_2_day7_1

description: Library name: S1469D71


title: shCSE1L_1_day7_3

description: Library name: S1150D73


title: RNA-seq 20250731_nih3t3_cas12a_ZSWIM3-2_rep1

description:
Library name: 20250731_nih3t3_cas12a_ZSWIM3-2_rep1
RNA-seq sample ZSWIM3-2_rep1


title: RNA-seq 20201124_hek293t_cas9_timeseries_TYR_editing_48h_rep3

description:
Library name: 20201124_hek293t_cas9_timeseries_TYR_editing_48h_rep3
RNA-seq sample TYR_editing_48h_rep3


title: PhenylalanineControl-4

description: Library name: Sample 53

value: Phenylalanine control


title: RNA-seq 20250731_nih3t3_cas12a_ZSWIM3-2_rep2

description:
Library name: 20250731_nih3t3_cas12a_ZSWIM3-2_rep2
RNA-seq sample ZSWIM3-2_rep2


title: shCSE1L_1_day7_1

description: Library name: S1150D71


title: RNA-seq 20201124_hek293t_cas9_timeseries_TYR_editing_72h_rep1

description:
Library name: 20201124_hek293t_cas9_timeseries_TYR_editing_72h_rep1
RNA-seq sample TYR_editing_72h_rep1


title: PhenylalanineControl-5

description: Library name: Sample 54


title: PhenylalanineControl-3

description: Library name: Sample 52


title: PhenylalanineControl-1

description: Library name: Sample 50


title: PhenylalanineControl-2

description: Library name: Sample 51


title: RNA-seq 20250731_nih3t3_cas12a_ZSWIM3-1_rep1

description:
Library name: 20250731_nih3t3_cas12a_ZSWIM3-1_rep1
RNA-seq sample ZSWIM3-1_rep1


title: RNA-seq 20201124_hek293t_cas9_timeseries_EMX1_editing_72h_rep3

description:
Library name: 20201124_hek293t_cas9_timeseries_EMX1_editing_72h_rep3
RNA-seq sample EMX1_editing_72h_rep3


title: GFP-KD_day7_3

description: Library name: GFPD73

value: CONTROL (GFP-KD)


title: RNA-seq 20201124_hek293t_cas9_timeseries_TYR_editing_48h_rep1

description:
Library name: 20201124_hek293t_cas9_timeseries_TYR_editing_48h_rep1
RNA-seq sample TYR_editing_48h_rep1


title: MethionineControl-5

description: Library name: Sample 49

value: Methionine control


title: RNA-seq 20250731_nih3t3_cas12a_EMX1-2_rep1

description:
Library name: 20250731_nih3t3_cas12a_EMX1-2_rep1
RNA-seq sample EMX1-2_rep1


title: GFP-KD_day7_2

description: Library name: GFPD72


title: RNA-seq 20250731_nih3t3_rnp_EMX1_rep1

description:
Library name: 20250731_nih3t3_rnp_EMX1_rep1
RNA-seq sample EMX1_rep1


title: RNA-seq 20201124_hek293t_cas9_timeseries_TYR_editing_72h_rep2

description:
Library name: 20201124_hek293t_cas9_timeseries_TYR_editing_72h_rep2
RNA-seq sample TYR_editing_72h_rep2


title: RNA-seq 20250731_nih3t3_cas12a_EMX1-2_rep2

description:
Library name: 20250731_nih3t3_cas12a_EMX1-2_rep2
RNA-seq sample EMX1-2_rep2


title: RNA-seq 20201124_hek293t_cas9_timeseries_EMX1_editing_72h_rep2

description:
Library name: 20201124_hek293t_cas9_timeseries_EMX1_editing_72h_rep2
RNA-seq sample EMX1_editing_72h_rep2


title: shCSE1L_1_day7_2

description: Library name: S1150D72


title: GFP-KD_day7_1

description: Library name: GFPD71


title: RNA-seq 20201124_hek293t_cas9_timeseries_TYR_editing_48h_rep2

description:
Library name: 20201124_hek293t_cas9_timeseries_TYR_editing_48h_rep2
RNA-seq sample TYR_editing_48h_rep2


title: RNA-seq 20250731_nih3t3_cas12a_ZSWIM3-1_rep2

description:
Library name: 20250731_nih3t3_cas12a_ZSWIM3-1_rep2
RNA-seq sample ZSWIM3-1_rep2


title: RNA-seq 20250731_nih3t3_cas12a_EMX1-1_rep2

description:
Library name: 20250731_nih3t3_cas12a_EMX1-1_rep2
RNA-seq sample EMX1-1_rep2


title: MethionineControl-4

description: Library name: Sample 48


title: RNA-seq 20201124_hek293t_cas9_timeseries_EMX1_editing_72h_rep1

description:
Library name: 20201124_hek293t_cas9_timeseries_EMX1_editing_72h_rep1
RNA-seq sample EMX1_editing_72h_rep1


title: shCSE1L_2_day1_2

description: Library name: S1469D32


title: shCSE1L_2_day1_1

description: Library name: S1469D31


title: MethionineControl-3

description: Library name: Sample 47


title: MethionineControl-2

description: Library name: Sample 46


title: RNA-seq 20250731_nih3t3_cas12a_EMX1-1_rep1

description:
Library name: 20250731_nih3t3_cas12a_EMX1-1_rep1
RNA-seq sample EMX1-1_rep1


title: RNA-seq 20201124_hek293t_cas9_timeseries_EMX1_editing_48h_rep3

description:
Library name: 20201124_hek293t_cas9_timeseries_EMX1_editing_48h_rep3
RNA-seq sample EMX1_editing_48h_rep3


title: RNA-seq 20201124_hek293t_cas9_timeseries_EMX1_editing_48h_rep2

description:
Library name: 20201124_hek293t_cas9_timeseries_EMX1_editing_48h_rep2
RNA-seq sample EMX1_editing_48h_rep2


title: RNA-seq 20201124_hek293t_cas9_timeseries_EMX1_editing_48h_rep1

description:
Library name: 20201124_hek293t_cas9_timeseries_EMX1_editing_48h_rep1
RNA-seq sample EMX1_editing_48h_rep1


title: Dataset 5: Timecourse fast-growing DCIS rat mammary gland day 42 #1

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description:
Library name: 4R_Tumor
10X Genomics

data_processing:
The sequenced reads were aligned to either the rat reference genome Rn6. Demultiplexing, barcode calling, gene counting, and group aggregation were subsequently performed. These procedures were all carried out using the 10X Genomics Cell Ranger 7.0.1 and Cell Ranger Aggr. v7.0.1 on 10X Cloud (https://cloud.10xgenomics.com/)
For preprocessing and quality-control, the filtered count matrix files were processed in R using Seurat package. Stringent filtering parameters were set to filter out low-quality reads and dead cells (2000 <nCount < 60000 & percent mt < 20 & percent ribo RPS/RPL < 40). Doublets were identified and removed using DoubletFinder.
The data were normalized using SCTransform and integrated using SCTIntegration prior to decomposing into 30-dimension PCA, clustering and dimensional reduction by UMAP. Subclusters of immune, epithelial, stroma and subsequent T cells, myeloid, and fibroblast clusters were further subsetted and reclustered at same dimension but higher resolution.
DEGs of each seurat cluster at each step were computed using Seurat FindMarkers function. Cell identities were identified and annotated using up to a combination of three methods (1) DEGs of lineage markers, (2) gene modules from previous studies, (3) reference cell atlas such as Celltypist, ProjecTIL.
Downstream analyses relevant to the study include Milo neighborhood analysis, Trajectory analysis Monocle3, FCoEx, single-cell GSEA (Escape), ProjecTIL, CellChat, Gini index quantification, etc.
Assembly: rn6 (Dataset 5)
Supplementary files format and content: barcodes.tsv.gz (barcodes), features.tsv.gz (gene IDs), matrix.mtx.gz (gene expression count matrix), filtered_feature_bc_matrix.h5 (combined features, barcodes, matrix)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Mammary carcinoma

extract_protocol:
For dataset 5, the entired tumor tissues were digested briefly with TryLE Express Enzyme (7 min) and submited for scRNAseq library construction targeting 10000 cells/sample.
For dataset 5, cell and library construction were performed via the 10X Chromium NEXT GEM Single Cell 5' HT Reagent Kit v2 (Dual Index) protocol.

value: Mammary carcinoma

value: Mixed breast cancer and immune cells

value: Sprague Dawley K15 Female

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: Dataset 5: Timecourse fast-growing DCIS rat mammary gland day 56 #1

description:
Library name: 5R_Tumor
10X Genomics

treatment_protocol: For dataset 5, the entired tumor tissues were digested briefly with TryLE Express Enzyme (7 min) and submited for scRNAseq library construction targeting 10000 cells/sample.


title: shCSE1L_1_day1_2

description: Library name: S1150D32


title: shCSE1L_2_day1_3

description: Library name: S1469D33


title: RNA-seq 20200928_hek293t_cas9_wt_rep3

description:
Library name: 20200928_hek293t_cas9_wt_rep3
RNA-seq sample wt_rep3


title: MethionineControl-1

description: Library name: Sample 45


title: shCSE1L_1_day1_3

description: Library name: S1150D33


title: Dataset 5: Timecourse fast-growing DCIS rat mammary gland day 70 #2

description:
Library name: 6L_Tumor
10X Genomics


title: HistidineControl-5

description: Library name: Sample 44

value: Histidine Control


title: HistidineControl-3

description: Library name: Sample 42


title: Dataset 5: Timecourse fast-growing DCIS rat mammary gland day 70 #3

description:
Library name: 6R_Tumor
10X Genomics


title: Dataset 5: Timecourse fast-growing DCIS rat mammary gland day 70 #1

description:
Library name: 3N_Tumor
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_wt_rep1

description:
Library name: 20200928_hek293t_cas9_wt_rep1
RNA-seq sample wt_rep1


title: GFP-KD_day1_3

description: Library name: GFPD33


title: HistidineControl-2

description: Library name: Sample 41


title: Dataset 5: Timecourse fast-growing DCIS rat mammary gland day 84 #1

description:
Library name: 5N_Tumor
10X Genomics


title: HistidineControl-4

description: Library name: Sample 43


title: HistidineControl-1

description: Library name: Sample 40


title: RNA-seq 20200928_hek293t_cas9_wt_rep2

description:
Library name: 20200928_hek293t_cas9_wt_rep2
RNA-seq sample wt_rep2


title: RNA-seq 20200928_hek293t_cas9_empty_vector_rep3

description:
Library name: 20200928_hek293t_cas9_empty_vector_rep3
RNA-seq sample empty_vector_rep3


title: RNA-seq 20200928_hek293t_cas9_empty_vector_rep2

description:
Library name: 20200928_hek293t_cas9_empty_vector_rep2
RNA-seq sample empty_vector_rep2


title: GFP-KD_day1_1

description: Library name: GFPD31


title: Dataset 5: Timecourse microlesions rat mammary gland day 42 #2

description:
Library name: 4R_MG
10X Genomics

source_name: Mammary microlesions

value: Mammary microlesions


title: Dataset 5: Timecourse microlesions rat mammary gland day 42 #1

description:
Library name: 4N_MG
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_empty_vector_rep1

description:
Library name: 20200928_hek293t_cas9_empty_vector_rep1
RNA-seq sample empty_vector_rep1


title: Dataset 5: Timecourse microlesions rat mammary gland day 48 #2

description:
Library name: 4L_MG
10X Genomics


title: GFP-KD_day1_2

description: Library name: GFPD32


title: RNA-seq 20200928_hek293t_cas9_cas9_only_vector_rep3

description:
Library name: 20200928_hek293t_cas9_cas9_only_vector_rep3
RNA-seq sample cas9_only_vector_rep3


title: BCAAControl-5

description: Library name: Sample 39

value: BCAA control


title: [P. putida KT2440] [33 mM NaF] [replicate 1]

city: Kongens Lyngby

first: Oscar

last: Puiggene

address: Kemitorvet 220

department: DTU Biosustain

country: Denmark

institute: Novo Nordisk Foundation Center for Biosustainability

description: Library name: WTF-1A

data_processing:
(Performed by BGI)
By using the internal software SOAPnuke to filter reads removed the reads mapped to rRNAs and get rawdata, they  filtered the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.
By using HISAT2, they mapped the clean reads to the reference genome "NC_002947.4" and by using Bowtie2
the gene expression level for each sample was calculated with RSEM
(Performed by the authors) RNA-Seq data were analyzed using DESeq2 package
Assembly: NC_002947.4
Supplementary files format and content: tab-delimited files include FPKM values for each Sample

organism: Pseudomonas putida

growth_protocol: LB with or without the supplementation of noted concentrations of NaF

extract_protocol:
(Performed by BGI) undisclosed details
(Performed by BGI) Total RNA: (1) mRNA fragmentation, (2) Oligo dT based mRNA enrichment, (3) Random N6 primer Reverse transcription, (4) Bubble adapter ligation, (5) PCR, (6) Heat separation, (7) single-strand circularization, (8) DNB-Seq

treatment_protocol: Noted concentrations of NaF

value: Wild-type

value: 33 mM NaF


title: [P. putida KT2440] [33 mM NaF] [replicate 2]

description: Library name: WTF-2A


title: BCAAControl-3

description: Library name: Sample 37

value: Jurkat

value: Day 3


title: Dataset 5: Timecourse microlesions rat mammary gland day 48 #1

description:
Library name: 3R_MG
10X Genomics


title: BCAAControl-4

description: Library name: Sample 38


title: RNA-seq 20200928_hek293t_cas9_cas9_only_vector_rep1

description:
Library name: 20200928_hek293t_cas9_cas9_only_vector_rep1
RNA-seq sample cas9_only_vector_rep1

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)


title: Dataset 5: Timecourse microlesions rat mammary gland day 56 #2

description:
Library name: 6N_MG
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_cas9_only_vector_rep2

description:
Library name: 20200928_hek293t_cas9_cas9_only_vector_rep2
RNA-seq sample cas9_only_vector_rep2


title: Dataset 5: Timecourse microlesions rat mammary gland day 56 #1

description:
Library name: 5R_MG
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_ZSWIM3_rep3

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_rep3
RNA-seq sample ZSWIM3_rep3


title: BCAAControl-1

description: Library name: Sample 36


title: [P. putida KT2440] [0 mM NaF] [replicate 1]

description: Library name: WT-1A

value: 0 mM NaF


title: 25Valine-5

description: Library name: Sample 35

value: 25% Valine


title: 25Valine-4

description: Library name: Sample 34


title: [P. putida KT2440 ∆crcB ∆PP_3125] [3.5 mM NaF] [replicate 2]

description: Library name: ddF-2A

value: deleted crcB and PP_3125

value: 3.5 NaF


title: 25Valine-3

description: Library name: Sample 33


title: [P. putida KT2440] [0 mM NaF] [replicate 2]

description: Library name: WT-2A


title: Dataset 5: Timecourse microlesions rat mammary gland day 70 #3

description:
Library name: 6R_MG
10X Genomics


title: [P. putida KT2440 ∆crcB ∆PP_3125] [3.5 mM NaF] [replicate 1]

description: Library name: ddF-1A


title: shCSE1L_1_day1_1

description: Library name: S1150D31

value: TEX

value: Leukemic cells  (cell line)


title: RNA-seq 20200928_hek293t_cas9_ZSWIM3_rep1

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: 25Valine-2

description: Library name: Sample 32


title: RNA-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep3

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep3
RNA-seq sample ZSWIM3_dead_sgrna_rep3


title: 25Valine-1

description: Library name: Sample 31


title: RNA-seq 20200928_hek293t_cas9_ZSWIM3_rep2

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: [P. putida KT2440 ∆crcB ∆PP_3125] [0 mM NaF] [replicate 1]

description: Library name: dd-1A


title: Dataset 5: Timecourse microlesions rat mammary gland day 84 #2

description:
Library name: 5N_MG
10X Genomics


title: 25Tryptophan-5

description: Library name: Sample 30

value: 25% Tryptophan


title: [P. putida KT2440 ∆crcB] [0.2 mM NaF] [replicate 2]

description: Library name: dCF-2A

value: deleted crcB

value: 0.2 NaF


title: 25Tryptophan-4

description: Library name: Sample 29


title: 25Tryptophan-3

description: Library name: Sample 28


title: Dataset 5: Timecourse microlesions rat mammary gland day 70 #2

description:
Library name: 6L_MG
10X Genomics

value: Mixed breast cancer and immune cells

value: Sprague Dawley K15 Female

value: N-Nitroso-N-Methylurea(NMU, 50mg/kg, twice, dissolved in pH6 ddH2O)


title: [P. putida KT2440 ∆crcB] [0 mM NaF] [replicate 2]

description: Library name: dC-2A


title: Dataset 5: Timecourse microlesions rat mammary gland day 103 #2

description:
Library name: 5L_MG
10X Genomics

value: Mammary microlesions


title: RNA-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep1

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep1
RNA-seq sample ZSWIM3_dead_sgrna_rep1


title: [P. putida KT2440 ∆crcB] [0.2 mM NaF] [replicate 1]

description: Library name: dCF-1A


title: Dataset 5: Timecourse microlesions rat mammary gland day 84 #1

description:
Library name: 3L_MG
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_TYR_rep3

description:
Library name: 20200928_hek293t_cas9_TYR_rep3
RNA-seq sample TYR_rep3


title: [P. putida KT2440 ∆crcB ∆PP_3125] [0 mM NaF] [replicate 2]

description: Library name: dd-2A


title: Dataset 5: Timecourse microlesions rat mammary gland day 70 #1

description:
Library name: 3N_MG
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_TYR_rep2

description:
Library name: 20200928_hek293t_cas9_TYR_rep2
RNA-seq sample TYR_rep2


title: [P. putida KT2440 ∆crcB] [0 mM NaF] [replicate 1]

description: Library name: dC-1A


title: 25Tryptophan-2

description: Library name: Sample 27


title: 25Tryptophan-1

description: Library name: Sample 26


title: [P. putida KT2440 ∆PP_3125] [30 mM NaF] [replicate 2]

description: Library name: d3F-2A

value: deleted PP_3125

value: 30 mM NaF


title: RNA-seq 20200928_hek293t_cas9_TYR_rep1

description:
Library name: 20200928_hek293t_cas9_TYR_rep1
RNA-seq sample TYR_rep1


title: Bronchoalveolar lavage (BAL) organoids, replicate 2

city: New Haven

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10th Amistad Street

department: Department of Anesthesiology

institute: Yale University

description:
Library name: BAL_3D_2
10X Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v8.0.1 (10x Genomics). Reads were aligned to the Rattus norvegicus reference transcriptome (Rnor_6.0, Ensembl release 95) with intronic reads included. Gene-barcode matrices were generated using the cellranger_count pipeline with default parameters. Further processing, including quality control, normalization, clustering, and downstream analysis, was performed in R using Seurat as described in the manuscript.
Assembly: Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6)
Supplementary files format and content: R objects (.Robj)

source_name: Pulmonary organoids (100% BAL)

growth_protocol: Primary rat lung-derived cells (from pulmonary dissociation and bronchoalveolar lavage) were maintained in organoid culture (in transwells) with a DMEM F12 supplemented with growth factors (Fgf10, Egf), small molecule inhibitors of TGFβ and GSK3 signaling, and antibiotics. Cultures were incubated at 37°C in a humidified atmosphere with 5% CO₂ for 10 days. Organoid cultures were seeded using three defined input ratios of primary cell suspensions: 100% pulmonary dissociation (PD_3D), 100% bronchoalveolar lavaage (BAL_3D), and a 50:50 mix (Mixed_3D).

extract_protocol:
Single-cell suspensions were prepared from dissociated organoids, bronchoalveolar lavage (BAL), and pulmonary dissociation (PD) samples using customized enzymatic or mechanical protocols, followed by filtration to achieve a single-cell suspension. Cells were resuspended in 0.1% BSA in PBS at 1 million cells/mL and processed for single-cell RNA-seq using the Chromium Next GEM Single Cell 3’ v3.1 platform (10x Genomics, Pleasanton, CA), following the manufacturer’s protocol. Cell lysis and mRNA capture occurred within Gel Beads-in-emulsion (GEMs) using barcoded oligo(dT) primers. See manuscript for more detail.
Libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, Pleasanton, CA), following the manufacturer’s protocol. Barcoded cDNA was amplified by PCR, purified with SPRIselect beads, and prepared for sequencing on an Illumina platform. See manuscript for more detail.

value: Pulmonary organoids (100% BAL)

value: WT


title: Bronchoalveolar lavage (BAL) organoids, replicate 3

description:
Library name: BAL_3D_3
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep3

description:
Library name: 20200928_hek293t_cas9_TYR_dead_sgrna_rep3
RNA-seq sample TYR_dead_sgrna_rep3


title: 25Phenylalanine-4

description: Library name: Sample 24

value: Jurkat

value: 25% Phenylalanine

value: Day 3


title: [P. putida KT2440 ∆PP_3125] [30 mM NaF] [replicate 1]

description: Library name: d3F-1A


title: RNA-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep2

description:
Library name: 20200928_hek293t_cas9_TYR_dead_sgrna_rep2
RNA-seq sample TYR_dead_sgrna_rep2


title: RNA-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep1

description:
Library name: 20200928_hek293t_cas9_TYR_dead_sgrna_rep1
RNA-seq sample TYR_dead_sgrna_rep1


title: RNA-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep2

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep2
RNA-seq sample ZSWIM3_dead_sgrna_rep2


title: PD-BAL (50/50, Mixed) organoids, replicate 3

description:
Library name: Mixed_3D_3
10X Genomics

source_name: Pulmonary organoids (50% PD, 50% BAL)

value: Pulmonary organoids (50% PD, 50% BAL)


title: [P. putida KT2440 ∆PP_3125] [0 mM NaF] [replicate 2]

description: Library name: d3-2A

value: 0 mM NaF


title: RNA-seq 20200928_hek293t_cas9_EMX1_rep3

description:
Library name: 20200928_hek293t_cas9_EMX1_rep3
RNA-seq sample EMX1_rep3


title: 25Phenylalanine-3

description: Library name: Sample 23


title: Dataset 5: Timecourse microlesions rat mammary gland day 103 #1

description:
Library name: 1N_MG
10X Genomics


title: RNA-seq 20200928_hek293t_cas9_EMX1_rep2

description:
Library name: 20200928_hek293t_cas9_EMX1_rep2
RNA-seq sample EMX1_rep2


title: WT hi MOI 24h 3

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description: Library name: WT_MOI_hi_24h_3_S66

data_processing:
Transcript abundances were quantified based on the annotated C. posadasii Silveira genome, BioProject PRJNA664774. Relative abundances (reported as TPM values) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.2. Further analysis was restricted to transcripts with estimated counts ≥ 10 in at least nine samples.
Differentially expressed genes were identified by comparing replicates for contrasts of interest using the glmQLFit, glmQLFTest, and topTags functions in edgeR version 4.0.16. Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 2X (absolute log2 fold change ≥ 1) for a given contrast.
Assembly: PRJNA664774
Supplementary files format and content: The results of the edgeR analysis are in processed data file S1_Table_JSAS03.txt, an Excel-compatible tab-delimited text conforming to JavatreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the C. posadassii Silveira systematic gene name from the PRJNA664774 reference genome. The NAME column gives short names taken from Table S1 of Mandel et al [cite: PMID35385558]. The next columns give edgeR BH-adjusted p-values for differential expression in each of the 7 contrasts. The next 6 columns give systematic names and annotations for related genomes as mapped by INPARANOID in Mandel et al [cite: PMID35385558]: previous C. posadasii Silveira annotation (CpV2 and Cp_anno), C. immitis RS  (CiRS and CiRS_anno) and H. ohiense G217B (HcG217B and HcG217B_anno). The next 24 columns give integer-rounded KALLISTO estimated counts for each transcript in each sample. The counts are followed by a GWEIGHT place-holder column for JavaTreeView compatibility. The final 7 columns give the edgeR fit log2 ratios for each contrast. The estimated counts in this file are sufficient to recapitulate the edgeR analysis.

source_name: fungal cell

growth_protocol: BMDM were seeded one day prior to the infection in 6-well plates.  On day of infection, WT and ryp1Δ arthroconidia were added to the wells at an MOI of 0.1 or 1 and the plates were spun at 550 g for 5 min to bring the arthroconidia proximal to the BMDM. At 1 h, the media was removed and replaced with fresh BMM, except for the Coccidioides alone wells.  At each timepoint, cells were washed twice with PBS, then QIAzol was added to each of 2 wells and and incubated for 5 min at room temperature. The contents of 2 wells were then combined for each sample, with three samples per condition and per timepoint.  Each sample underwent bead beating for 2 min to improve yield of fungal RNA. At this point samples were removed from the BSL3.

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep Plus isolation kit (Zymo).
Libraries were made with the NEBNext polyA mRNA magnetic isolation module and NEBNext Ultra II Directional RNA Library Prep kit with dual-indexed multiplexing barcodes as instructed.  Libraries were pooled and sequencing was performed by the Chan-Zuckerberg BioHub-San Francisco on one lane of Novaseq S4.

tag: infection

value: hi MOI

tag: time

tag: replicate

value: fungal cell


title: Bronchoalveolar lavage (BAL) organoids, replicate 1

description:
Library name: BAL_3D_1
10X Genomics


title: 25Phenylalanine-5

description: Library name: Sample 25


title: RNA-seq 20200928_hek293t_cas9_EMX1_rep1

description:
Library name: 20200928_hek293t_cas9_EMX1_rep1
RNA-seq sample EMX1_rep1

extract_protocol:
Dynabeads M-280 sheep anti-Rabbit IgG (Invitrogen, 11201D) were diluted 1:10 in 1× PBS (Invitrogen, AM9624), magnetically washed, and incubated with Nesprin1 antibody (abcam, ab192234) at room temperature for 30 minutes. Antibody-coupled beads were washed and resuspended in cell lysis buffer containing 10 mM HEPES (Gibco, 15630106), 2.5 mM MgCl2 (Invitrogen, AM9530G), 10 mM KCl (Sigma, P9333), 1 mM DTT (ThermoFisher, 707265ML), 0.5% Triton X-100 (Sigma, 93443), and 2 U recombinant RNase inhibitor (Takara, 2313A). A population of 500 GFP-positive cells per sample was sorted into 10 µL lysis buffer in 96-well plates, centrifuged at 700 g for 1 minute, and incubated at 4°C with shaking (300 rpm) for 30 minutes. After magnetic separation, the supernatant was transferred to a new plate for RNA-seq workflow, while nuclei were retained for ATAC-side tagmentation workflow in AR-seq. RNA in the supernatant was purified using 2.2× VAHTS RNA Clean Beads (Vazyme, N412-03) and reverse-transcribed using SMART-seq2.
RNA-seq library construction was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501), following the manufacturer's manual. Libraries were generated from SMART-seq2-derived cDNA and sequenced in paired-end mode on short-read sequencing platforms.


title: [P. putida KT2440 ∆PP_3125] [0 mM NaF] [replicate 1]

description: Library name: d3-1A


title: WT hi MOI 24h 2

description: Library name: WT_MOI_hi_24h_2_S65

tag: cell type


title: 25Phenylalanine-2

description: Library name: Sample 22


title: PD-BAL (50/50, Mixed) organoids, replicate 1

description:
Library name: Mixed_3D_1
10X Genomics

tag: genotype


title: PD-BAL (50/50, Mixed) organoids, replicate 2

description:
Library name: Mixed_3D_2
10X Genomics

tag: tissue


title: 25Phenylalanine-1

description: Library name: Sample 21

tag: treatment


title: WT hi MOI 24h 1

description: Library name: WT_MOI_hi_24h_1_S64


title: Pulmonary dissociation (PD) organoids, replicate 2

description:
Library name: PD_3D_2
10X Genomics

source_name: Pulmonary organoids (100% PD)

value: Pulmonary organoids (100% PD)


title: RNA-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep3

description:
Library name: 20200928_hek293t_cas9_EMX1_dead_sgrna_rep3
RNA-seq sample EMX1_dead_sgrna_rep3

tag: cell line


title: 25Methionine-4

description: Library name: Sample 19

value: 25% Methionine


title: Pulmonary dissociation (PD) organoids, replicate 1

description:
Library name: PD_3D_1
10X Genomics


title: 25Methionine-3

description: Library name: Sample 18


title: RNA-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep1

description:
Library name: 20200928_hek293t_cas9_EMX1_dead_sgrna_rep1
RNA-seq sample EMX1_dead_sgrna_rep1

tag: batch


title: Bronchoalveolar lavage, replicate 3

description:
Library name: BAL_3
10X Genomics

source_name: Bronchoalveolar lavage (primary immune and epithelium)


title: 25Methionine-2

description: Library name: Sample 17


title: WT lo MOI 48h 3

description: Library name: WT_MOI_lo_48h_3_S72

value: lo MOI


title: ryp1 hi MOI 24h 1

description: Library name: Ryp1_MOI_hi_24h_1_S67


title: Bronchoalveolar lavage, replicate 2

description:
Library name: BAL_2
10X Genomics

value: Bronchoalveolar lavage (primary immune and epithelium)


title: 25Methionine-1

description: Library name: Sample 16


title: ryp1 hi MOI 24h 2

description: Library name: Ryp1_MOI_hi_24h_2_S68


title: 25Leucine-5

description: Library name: Sample 15

value: 25% Leucine


title: WT lo MOI 24h 3

description: Library name: WT_MOI_lo_24h_3_S60