title: Gcn_Arg3

status: Public on Jan 01 2024

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

description:
htseq_Gcn_counts.txt
DEseq_Gcn_counts_normalized.txt

data_processing:
BCL raw data was converted to FASTQ data and demultiplexed by bcl2fastq Conversion Software (Illumina)
After checking the quality of the samples (FastQC, v.0.11.7), the files were mapped to the mouse genome (Genome build GRCm38) downloaded from Ensembl using the STAR aligner (v. 2.7.4a).
The mapped bam files were then quantified on a gene level based on the Ensembl annotations, using the HTseq tool in Python.
Using the DESeq2 package (R 4.0.3, DESeq version 1.30.1), the count data was normalized by the size factor to estimate the effective library size. A filtering step of removing genes with low reads in all conditions was used (total of all Wt or Gcn ko counts < 1) .
The analysis of two different conditions against each other resulted in a list of differentially expressed genes for each comparison. Genes with an adjusted p-value of ≤ 0.05 were then considered to be differentially expressed for downstream analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: 2 tables with raw gene counts for every gene and every sample; 2 tables of normalized gene counts after filtering and DESeq2 normalization

growth_protocol: ES cells were grown on 0.1% gelatin-coated dishes in DMEM high glucose GlutaMAX containing 15% fetal bovine serum, 1% penicillin-streptomycin, β-mercaptoethanol and 10 ng/ml recombinant murine leukemia inhibitory factor. Cells were incubated at 37°C in 5% CO2.

extract_protocol:
RNA isolation was performed using the Direct-zol RNA Miniprep Plus kit from Zymo Research.
mRNA sequencing libraries were prepared with 1 µg of total RNA of each sample using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module.
Paired-end sequencing was performed on Illumina NextSeq 500 (2 × 43 bp reads). The samples were multiplexed and sequenced on one High Output Kit v2.5 to reduce batch effects.

treatment_protocol: ES cells were seeded the day before then starved for 3h using SILAC medium supplemented with penicillin-streptomycin, GlutaMAX, glucose, 5% dialyzed FBS, β-mercaptoethanol, LIF, L-Lys and with or without L-Arg or L-Leu. The same medium containing all amino acids was used for the control treatment (unstarved). 3 replicates were used per condition.

value: embryonic stem cell (ESC)

value: Eif2ak4-/- (GCN2 knock-out)

value: arginine-starved


title: Gcn_Leu3

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: cell line

tag: genotype

tag: treatment

value: leucine-starved


title: Gcn_Unstarved3

value: untreated


title: Gcn_Arg2


title: Gcn_Unstarved2


title: Gcn_Leu1


title: Gcn_Unstarved1


title: Gcn_Arg1


title: Gcn_Leu2


title: Wt_Arg3

description:
htseq_Wt_counts.txt
DEseq_Wt_counts_normalized.txt

value: wild type


title: Wt_Arg2


title: water inoculated spikelet in CDC Falcon 3

status: Public on Jan 24 2024

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

country: Canada

institute: Agriculture and AgriFood Canada

data_processing:
Illumina Casava1.7 software used for basecalling
reads trimmed using trimmomatic v0.36 for adapter sequences and low-quality reads
trimmed reads mapped to T. aestivum and F. graminearum using hisat2
count data generated using featureCounts
Differential expression analysis performed using DESeq2
Assembly: T. aestivum IWGSC release 56 ,F. graminearum PH-1 (ASM24013v3)
Supplementary files format and content: tab delimited count data sheets

organism: Triticum aestivum

source_name: wheat spikelet

growth_protocol: seeds were sown in 4” pots with a mixture of 50% Sunshine #5 soilless mix (Sungro, Horticulture Canada, Seba Beach, AB, Canada) and 50% soil, plus 6 g of Osmocote slow release fertilizer (14-14-14; Everris NA, Dublin Ohio, United States). Wheat plants were grown in controlled-environment cabinets with 16 h of light at 22°C and 8 h of dark at 15°C. Plant-prod 20-20-20 soluble fertilizer (Master Plant Products Brampton Ontario, Canada) was applied in the water at a rate of 0.75 g/L and 2 g of slow release fertilizer (14-14-14) was added 40 days after planting. At the three-leaf stage, the plants were thinned to one plant per pot.

extract_protocol:
RNA extraction was performed from sectioned rachis node and rachilla samples using the Trizol Reagent (Ambion), according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: At 50% of anthers extrusion, single floret inoculation was performed with 10 µL of Fg inoculum at a concentration of 5 x 104 macroconidia /mL,  and water (control) between the lemma and palea at the midpoint of the spike

tag: tissue

value: wheat spikelet

value: CDC Falcon

value: uninfected


title: Wt_Unstarved1


title: Wt_Leu3


title: Wt_Unstarved2


title: Wt_Leu2


title: Wt_Leu1


title: Wt_Unstarved3


title: Wt_Arg1


title: NF9511b NF2 control Rep1

status: Public on May 22 2023

city: San Francisco

first: Harish

last: Vasudevan

state: CA

address: 1450 3rd street

country: USA

institute: UCSF

description: Bulk RNA-seq

data_processing:
Libraries were demultiplexed, quality assessed via FASTQC, and then aligned to the human genome using HISAT2
hg19
See manuscript for TPM matrices as supplementary info

organism: Homo sapiens

extract_protocol:
RNA extraction from bulk tissues or cell lines
Library was performed according to the manufacter’s instructions for Illumina Tru Seq RNA kit.

value: Human pNF cell line


title: NF9511b NF2 control Rep2

description: Bulk RNA-seq


title: Coculture CAF and Organoid_1, scRNAseq

status: Public on May 11 2023

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

description:
SORT-seq
UMC-ST-s036

library_source: transcriptomic single cell

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode, cell barcode, and UMI. Read 2 was assigned 60 base pairs and used to map to the reference transcriptome Homo sapiens (hg38) with BWA-MEM. Data was demultiplexed as described in Grün et al. (2014). Briefly, Mapping and generation of count tables were automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Downstream analysis was performed with Seurat v4.1.1. Dimension reduction was performed with UMAP based on the first 30 principal components. Gene Ontology analysis was done using the package clusterProfiler on differential expression analysis (logFC > 0.5, min.pct = 0.25) of the Seurat clusters. To obtain DEGs that distinguished the organoid clusters, comparisons were made only between the organoid clusters. The same was done for the CAF clusters. Signatures were evaluated with the AddModuleScore function and retrieved from the Hallmark dataset of the molecular signature database. New signatures were generated by performing differential expression analysis on the Seurat clusters (logFC > 0.75, min.pct = 0.5, min.diff.pct = 0.1).
Assembly: hg38
Supplementary files format and content: Tab-separated barcode and read count files

source_name: colorectal liver metastasis

extract_protocol:
On day 8 of the experiment, droplets were scooped out of the well and resuspended in Liberase to dissolve the co-culture matrix. Cell clusters and organoids were digested into single cells through incubation and resuspension with TrypLE. Viable single cells were sorted in 384-well cell capture plates using the BD FACSAria II. Plates were shipped on dry ice to Single Cell Discoveries, where single-cell RNA sequencing was performed according to an adapted version of the SORT-seq protocol
Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit.

value: Colon Cancer Organoids & Cancer-associated Fibroblasts

value: colorectal liver metastasis

tag: strain

value: P19bT, LCAF5


title: CAF mono 2D, scRNAseq

description:
SORT-seq
UMC-ST-s035

value: Cancer-associated Fibroblasts


title: Organoid mono, scRNAseq

description:
SORT-seq
UMC-ST-s032

value: Colon Cancer Organoids


title: Epithelial, KO, Ileum, SPF [ZE31]

status: Public on Mar 29 2023

city: Chicago

first: Joseph

middle: Joy

last: Sifakis

state: IL

address: 900 East 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
RNAseq raw data processed on the GENPIPES framework "stringtie" and "rnaseq" pipeline was used
Reads were trimmed using Timmomatic
Reads were aligned to reference genome using STAR aligner
Alighments were sorted and filtered for duplicates using Picard
Gene-level read counts were calculated from spliced alignments using Htseq count
Assembly: Mus_musculus.GRCm38

source_name: Ileum

extract_protocol:
Qiagen plus RNAeasy mini or micro
Illumina Truseq for tissue or SMARTseq v4 Takara for epithelial cells

value: Ileum

value: Epithelial

value: GATA4 KO


title: Epithelial, KO, Ileum, SPF [ZE30]


title: Epithelial, WT, Ileum, SPF [ZE28]

value: WT


title: CAF mono 3D, scRNAseq

description:
SORT-seq
UMC-ST-s033


title: Epithelial, WT, Ileum, SPF [ZE29]


title: Epithelial, KO, Jejunum, SPF [ZE24]

source_name: Jejunum

value: Jejunum


title: Epithelial, KO, Jejunum, SPF [ZE25]


title: Epithelial, KO, Jejunum, SPF [ZE26]


title: Epithelial, WT, Ileum, SPF [ZE27]


title: Epithelial, WT, Jejunum, SPF [ZE23]


title: Epithelial, WT, Jejunum, SPF [ZE21]


title: Epithelial, WT, Jejunum, SPF [ZE22]


title: Epithelial, KO, Ileum, SPF [ZE20]


title: Epithelial, WT, Ileum, SPF [ZE17]


title: Epithelial, WT, Ileum, SPF [ZE18]


title: Coculture CAF and Organoid_2, scRNAseq

description:
SORT-seq
UMC-ST-s037


title: Epithelial, KO, Ileum, SPF [ZE19]


title: Epithelial, KO, Jejunum, SPF [ZE15]


title: Epithelial, WT, Jejunum, SPF [ZE13]


title: BMMC_lpsMA_rep1

status: Public on Dec 19 2023

type: genomic

city: Blacksburg

first: Blake

middle: Alexander

last: Caldwell

state: VA

address: 149 Life Sciences I Building, 970 Washington Street SW

department: Biological Sciences

institute: Virginia Tech

description: Unsorted monocytes from cultured BMMCs

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.14.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Cultured BMMCs, LPS with MA

label_protocol: Standard Illumina Protocol

growth_protocol: In vitro bone marrow monocyte (BMMC) LPS exhaustion experiments were performed as previously described (Pradhan et al., 2021, Front. Immunol.). Briefly, bone marrow cells were harvested from 6- to 8-week-old C57BL/6 WT female mice, seeded at a density of 3x105 cells/cm2, and cultured in complete RPMI 1640 media (10% fetal bovine serum, 1% penicillin-streptomycin, 1% L-glutamine) supplemented with 10 ng/mL M-CSF (PeproTech). Cells were cultured for 5 days at 37˚C in a humidified 5% CO2 atmosphere under continuous high-dose 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) stimulation with methoxy mycolic acid (MA, 10 µg/mL; Avanti).

extract_protocol: Cultured BMMCs were harvested by manual disruption and processed for genomic DNA using a DNeasy Blood and Tissue Kit (Qiagen).

tag: Sex

value: Female

tag: age

value: LPS-MA

value: Cultured primary bone marrow monocytes


title: BMMC_lpsMA_rep2

description: Unsorted monocytes from cultured BMMCs

treatment_protocol: Cells were cultured for 5 days at 37˚C in a humidified 5% CO2 atmosphere under continuous high-dose 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) stimulation with methoxy mycolic acid (MA, 10 µg/mL; Avanti).


title: Epithelial, KO, Ileum, SPF [ZE32]


title: Epithelial, WT, Ileum, SPF [ZE08]


title: Epithelial, WT, Ileum, SPF [ZE07]


title: Tissue, WT, Jejunum, GF [GF.17.1]

value: Whole Tissue


title: Epithelial, KO, Jejunum, SPF [ZE06]


title: Epithelial, WT, Jejunum, SPF [ZE01]


title: Tissue, WT, Jejunum, GF [GF.16.1]


title: Epithelial, WT, Jejunum, SPF [ZE03]


title: BMMC_lpsMA_rep3

description: Unsorted monocytes from cultured BMMCs


title: Epithelial, KO, Jejunum, SPF [ZE04]


title: Epithelial, KO, Ileum, SPF [ZE12]


title: Epithelial, WT, Ileum, SPF [ZE09]


title: Epithelial, KO, Ileum, SPF [ZE10]


title: Tissue, KO, Jejunum, GF [GF.16]


title: Epithelial, KO, Jejunum, SPF [ZE16]


title: Epithelial, WT, Jejunum, SPF [ZE14]


title: Epithelial, WT, Jejunum, SPF [ZE02]


title: Sample 13 Control

status: Public on Feb 29 2024

first: Christopher

last: Pascoe

state: MB

address: 602-715 McDermot Avenue, Children's Hospital Research Institute of Manitoba

department: Physiology & Pathophysiology

institute: University of Manitoba

data_processing:
Raw reads were quality and adapter trimmed using cutadapt and then aligned to the Hg38 reference genome using STAR
Gene count matrix generated using FeatureCounts
Assembly: Hg38
Supplementary files format and content: csv file with raw counts for each sample

source_name: Lung

extract_protocol:
RNA extracted from lung tissue stored in RNAlater using Ambion PureLink RNA Mini Kit
Illumina's TruSeq mRNA Stranded kit

treatment_protocol: E-cigarette habits were collected by questionnaire

value: Lung

value: Control


title: Tissue, KO, Jejunum, GF [GF.15]


title: BMMC_lpsMA_rep4

description: Unsorted monocytes from cultured BMMCs


title: Epithelial, KO, Ileum, SPF [ZE11]


title: Epithelial, KO, Jejunum, SPF [ZE05]


title: Tissue, WT, Jejunum, GF [GF.12.1]


title: Tissue, KO, Jejunum, GF [GF.13]


title: Tissue, WT, Jejunum, GF [GF.15.1]


title: Tissue, KO, Jejunum, GF [GF.12]


title: Tissue, KO, Jejunum, GF [GF.14]


title: Tissue, WT, Jejunum, GF [GF.13.1]


title: Tissue, WT, Jejunum, GF [GF.14.1]


title: Tissue, KO, Jejunum, GF [GF.17]


title: Tissue, WT, Jejunum, GF [GF.11.1]


title: Tissue, KO, Jejunum, GF [GF.11]


title: Tissue, KO, Ileum, SPF [9.1I]


title: Tissue, KO, Jejunum, SPF [11.1J]


title: Tissue, KO, Ileum, SPF [7.1I]


title: Tissue, KO, Ileum, SPF [11.1I]


title: Tissue, WT, Ileum, SPF [11I]


title: Tissue, KO, Ileum, SPF [10.1I]


title: Tissue, WT, Ileum, SPF [10I]


title: Tissue, KO, Ileum, SPF [8.1I]


title: Tissue, KO, Jejunum, GF [GF.10]


title: Tissue, KO, Jejunum, SPF [7.1J]


title: Tissue, KO, Jejunum, SPF [8.1J]


title: Tissue, WT, Jejunum, SPF [11J]


title: Tissue, WT, Jejunum, SPF [10J]


title: Tissue, WT, Jejunum, SPF [9J]


title: Tissue, KO, Jejunum, SPF [9.1J]


title: Tissue, KO, Ileum, SPF [3.1I]


title: Tissue, KO, Jejunum, SPF [10.1J]


title: Tissue, WT, Ileum, SPF [7I]


title: Tissue, WT, Ileum, SPF [1I]


title: Tissue, WT, Ileum, SPF [9I]


title: Tissue, KO, Ileum, SPF [1.1I]


title: Tissue, KO, Jejunum, SPF [3.1J]


title: Tissue, WT, Ileum, SPF [3I]


title: Tissue, WT, Jejunum, SPF [7J]


title: Tissue, WT, Jejunum, SPF [8J]


title: Tissue, WT, Ileum, SPF [8I]


title: Tissue, WT, Ileum, SPF [2I]


title: Tissue, WT, Jejunum, GF [GF.10.1]


title: Tissue, KO, Jejunum, SPF [1.1J]


title: Tissue, KO, Jejunum, SPF [2.1J]


title: Tissue, KO, Ileum, SPF [2.1I]


title: Tissue, WT, Jejunum, SPF [2J]


title: Tissue, WT, Jejunum, SPF [3J]


title: VUILD85-MF

status: Public on Mar 20 2023

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

data_processing:
Reads with a read quality <3 were filtered and CellRanger Count v3.02 (10x Genomics) was used to align reads to the GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Tab-separated values file containing cell barcodes
Supplementary files format and content: Aggregated_expression.tar: Tar archive containing TSV files of aggregated expression for each cell population.
Supplementary files format and content: *_Seurat.rds: RDS files of Seurat objects for each major cell lineage.
Supplementary files format and content: limix_res_*.tar: Tar archives containing txt files of limix eQTL summary stats.
Supplementary files format and content: mashr_applied_*.tar: Tar archives containing TSV files of mashr eQTL summary stats.

extract_protocol:
Tissue samples were digested in either collagenase I/dispase II (1 μg/ml) or Miltenyi Multi-Tissue Dissociation Kit using a gentleMACS Octo Dissociator (Miltenyi Inc.). Tissue lysates were serially filtered through sterile gauze, 100- and 40-μm sterile filters (Fischer). The resulting suspensions then underwent cell sorting using serial columns (Miltenyi Microbeads, CD235a and CD45) or fluorescence-activated cell-sorting (FACS) at VUMC or FACSat the Translational Genomics Research Institute (TGen). CD45− and C45+ populations were mixed 2:1 in samples processed at VUMC and used to generate the scRNA-seq libraries. At TGen, calcein acetoxymethyl was used to stain live cells, and 10,000 to 15,000 live cells were sorted directly into the 10x reaction buffer and transferred to the 10x 5′ chip A (10x Genomics).
scRNA-seq libraries were generated using the 10x Chromium platform 3′ v2 or 5′ library preparation kits (10x Genomics) according to the manufacturer’s recommendations and targeting 5000 to 10,000 cells per sample.

tag: disease state/diagnosis

value: CWP

value: M

tag: tobacco status_(ever-smoker)

value: N

tag: self-reported ethnicity

value: Caucasian

tag: tissue type


title: VUHD111


title: VUHD103


title: Tissue, WT, Jejunum, SPF [1J]


title: VUHD117


title: 20221004_hpap_7_Pool_Well1_RNA, RNA derived cDNA

status: Public on Jan 03 2023

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

data_processing:
Raw BCL files were converted to fastq files using either cellranger mkfastq (for RNA) or bcl2fastq (for ADT/HTO)
For RNA, fastq files were aligned to hg38, counted, and filtered for QC using cellranger count.
For ADT/HTO, fastq files were aligned to ADT or HTO catalog references. Alignments were barcode corrected and counted as part of the kallisto bustools pipeline (KITE; see https://github.com/betts-lab/scc-proc for snakemake pipeline).
Assembly: hg38
Supplementary files format and content: RNA: tar.gz archive of cellranger output (matrix.tsv.gz, features.tsv.gz, barcodes.tsv.gz). ADT/HTO: tar.gz archive of kallisto bustools output (output.genes.txt, output.mtx, output.barcodes.txt)
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: polyA RNA

source_name: mononuclear cells

extract_protocol:
Pooled samples were placed through the 3' scRNAseq v3.1 pipeline (10X Genomics) to generate single cell partitions sharing cDNA, antibody derived tag, and hashing antibody barcodes. Each well of a 10X chip was superloaded with ~1.75X manufacturer's recommended maximum cell count. cDNA extract protocol followed manufacturer's instructions. To extract antibody derived tag and hashing tag sequences, the supernatant from cDNA Cleanup - SPRIselect (Step 2.3d in Protocol CG000315 Rev C, or equivalent step) was saved for further processing following the standard CITEseq protocol (https://cite-seq.com/protocols/).
Dual indexed cDNA libraries were generated following manufacturer's instructions (10X Genomics Protocol CG000315 Rev C, or equivalent for high-throughput protocols). Dual indexed antibody derived tag and hashing tag libraries were generated following standard CITEseq protocol (https://cite-seq.com/protocols/) using primers recommended from Biolegend. Antibody derived tag and hashing tag sequences were enriched in the initial cDNA amplification step of the 3' scRNAseq v3.1 protocol via addition of additive primers (https://cite-seq.com/protocols/).

treatment_protocol: All samples were thawed from -150℃ cryopreservation. Individual tubes were gently shaken in a 37℃ water bath until the frozen cells were partially thawed. Cells were then quickly resuspended in at least 14 mL cold R10 + DNAse (RPMI-1640 supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin/streptomycin in the presence of 10 U/mL DNAse I) and spun down at 500 xg to pellet. The cell pellet was resuspended in R10 + DNase I and counted. Cells were then rested at 2E6 cells/mL in R10 + DNAse I for 2 hours. After resting, cells were washed in cold Cell Staining Buffer (Biolegend) 2 times, filtered through a 70 um filter, and counted. 5E5 cells from each sample were incubated with Human TruStain FcX (Biolegend) at 4℃ for 10 min at the manufacturer's recommended concentration of 10E6 cells/mL. Then, each individual sample was incubated with a unique TotalSeq-A compatible Hashing Antibody (Biolegend) at 0.5 ug antibody at 11.8E6 cells/mL. Then, samples were incubated with the TotalSeq-A Universal cocktail (Biolegend #399907) according to manufacturer's instructions. Samples were washed 3X with Cell Staining Buffer and counted. Cells from each sample were then pooled, concentrated to 2000 cells/uL, and filtered through a 40 um FlowMi filter (Bel-Art).

value: mononuclear cells

tag: individuals and tissues (mixed samples)

value: HPAP-024_Head, HPAP-024_MES, HPAP-024_Spleen, HPAP-026_Head, HPAP-026_MES, HPAP-026_Spleen, HPAP-098_Head, HPAP-098_Spleen

tag: run number


title: VUHD106

value: Former Smoker


title: VUILD86-MF

value: European


title: 20221004_hpap_7_Pool_Well2_RNA, RNA derived cDNA


title: 20221004_hpap_7_Pool_Well4_RNA, RNA derived cDNA


title: 20221012_hpap_6_Pool_Well8_RNA, RNA derived cDNA

value: HPAP-016_Tail, HPAP-016_MES, HPAP-016_Spleen, HPAP-020_Head, HPAP-020_SMA, HPAP-020_Spleen, HPAP-099_Head, HPAP-099_Spleen


title: 20221004_hpap_7_Pool_Well8_RNA, RNA derived cDNA


title: VUILD86-LF


title: 20221004_hpap_7_Pool_Well3_RNA, RNA derived cDNA


title: 20221004_hpap_7_Pool_Well7_RNA, RNA derived cDNA


title: 20221012_hpap_6_Pool_Well7_RNA, RNA derived cDNA


title: VUHD098


title: VUHD092


title: VUILD85-LF


title: VUHD094


title: VUHD105

value: Unknown


title: 20221012_hpap_6_Pool_Well6_RNA, RNA derived cDNA


title: 20221004_hpap_7_Pool_Well5_RNA, RNA derived cDNA


title: 20221004_hpap_7_Pool_Well6_RNA, RNA derived cDNA


title: 20221012_hpap_6_Pool_Well4_RNA, RNA derived cDNA


title: 20221012_hpap_6_Pool_Well5_RNA, RNA derived cDNA


title: VUHD108


title: 20221012_hpap_6_Pool_Well3_RNA, RNA derived cDNA


title: 20221012_hpap_6_Pool_Well2_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well7_RNA, RNA derived cDNA

value: HPAP-102_Head, HPAP-102_MES, HPAP-102_Spleen, HPAP-107_Head, HPAP-107_MES, HPAP-110_Spleen, HPAP-110_Head, HPAP-110_Spleen


title: 20221012_hpap_6_Pool_Well1_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well8_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well5_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well6_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well3_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well1_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well2_RNA, RNA derived cDNA


title: 20220801_hpap_4_Pool_Well6_RNA, RNA derived cDNA

value: HPAP-012_Head, HPAP-012_MES, HPAP-012_Spleen, HPAP-023_Head, HPAP-023_Spleen, HPAP-114_Tail, HPAP-114_MES, HPAP-114_Spleen


title: 20220801_hpap_4_Pool_Well2_RNA, RNA derived cDNA


title: 20220801_hpap_4_Pool_Well7_RNA, RNA derived cDNA


title: 20220801_hpap_4_Pool_Well4_RNA, RNA derived cDNA


title: 20220801_hpap_4_Pool_Well5_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run2_Well9_RNA, RNA derived cDNA

value: HPAP-043_Head, HPAP-043_Spleen, HPAP-095_Head, HPAP-095_Spleen


title: 20220801_hpap_4_Pool_Well1_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run2_Well12_RNA, RNA derived cDNA


title: 20220801_hpap_4_Pool_Well3_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run2_Well16_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run2_Well11_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run2_Well14_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run2_Well10_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run2_Well13_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run1_Well8_RNA, RNA derived cDNA

value: HPAP-048_Head, HPAP-048_MES, HPAP-048_Spleen, HPAP-095_SMA


title: 20220531_hpap_2_Pool_Run1_Well6_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run1_Well1_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run1_Well5_RNA, RNA derived cDNA


title: 20220531_hpap_2_Pool_Run1_Well2_RNA, RNA derived cDNA


title: 20220923_hpap_5_Pool_Well4_RNA, RNA derived cDNA


title: 20220119_hpap_1_Pool_A3_RNA, RNA derived cDNA

value: HPAP-021_Head, HPAP-023_Head, HPAP-027_Head, HPAP-095_Head


title: 20220119_hpap_1_Pool_A2_RNA, RNA derived cDNA


title: 20220801_hpap_4_Pool_Well8_RNA, RNA derived cDNA


title: 20220119_hpap_1_Pool_A4_RNA, RNA derived cDNA


title: MNGC246: Pten/Hif1a(i)pe-/-

status: Public on Jun 07 2022

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

data_processing:
Alignment, barcode and UMI filtering and counting were performed using Cell Ranger 3.0.1 count and mouse reference 3.0.0 (mm10 and Ensembl release 93).
cs* files : FACS sorted cells from a PTEN(i)pe-/- mouse, 3-, 6-, 9- and 15-month after gene inactivation were aggregated using Cell Ranger 3.0.1 aggr, cells from clusters 10, 12 and 20 from graph-based clustering were selected and among these cells only cells with at least 100 genes and less than 5,000 genes and with less than 20% mitochondrial reads were retained using Seurat 3.2.0 (files *monthsAGI_barcodes.tsv.gz provide the barcodes corresponding to each time point).
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: Prostate

extract_protocol:
Mice prostates were mechanically and enzymatically dissociated. Single living cells were obtained by FACS sorting.
Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples were processed on the Chromium Controller from 10X Genomics (Leiden, The Netherlands). Ten thousand cells were loaded per well. Single cell 3’ mRNA seq library were generated according to Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry [Longitudinal study of luminal cells] / v3 Chemistry [Pten(i)pe-/-, PtenL2/L2 and Pten/Hif1a(i)pe-/-] ) from 10X Genomics (ref CG00052 Rev E [Longitudinal study of luminal cells] / CG000183 Rev A [Pten(i)pe-/-, PtenL2/L2 and Pten/Hif1a(i)pe-/-]). Briefly, Gel Beads-in-Emulsion (GEMs) were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip. Following full length cDNA synthesis and barcoding from poly-adenylated mRNA, GEM were broken and pooled before cDNA amplification by PCR. After enzymatic fragmentation and size selection, sequencing library were constructed by adding Illumina (Paris, France) P5 and P7 primers as well as sample index via end repair, A tailing, adaptor ligation and PCR. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).

value: Prostate

tag: condition

value: 3 months after genes inactivation

tag: cells

value: DAPI- FACS-sorted cells


title: MNGC245: PtenL2/L2

value: 3 months after tamoxifen administration


title: MNGC244: Pten(i)pe-/-

value: 3 months after gene inactivation


title: MNGC172: Longitudinal study of luminal cells

value: 3-, 6-, 9-, and 15-month after gene inactivation


title: Spider late germ-disc 2, snRNA-seq

status: Public on May 04 2022

city: Takatsuki

first: Yasuko

last: Akiyama-Oda

state: Osaka

address: Murasaki-cho 1-1

country: Japan

institute: JT Biohistory Research Hall

description: BD Rhapsody

data_processing:
We used BD Rhapsody WTA analysis pipeline on the Seven Bridges Genomics cloud platform.
After quality filter of read pairs, the cell barcode and the unique molecular index (UMI) were identified from R1 reads, and R2 reads were aligned to the STAR index created form the Paratsteatoda genome reference using STAR-2.5.2b.
Following a UMI error correction step, a cell/gene count matrix, the final output of the pipeline,  was obtained.
Using the Seurat package (v.4.0.3), the count matrix was filtered by the number of unique genes and/or the total number of RNA molecules.
Differentially expressed genes (DEGs) between two ectodermal clusters were removed from the count matrix.
The count matrix was log-normalized.
Assembly: GCF_000365465.2_Ptep_2.0 and GCF_000365465.3_Ptep_3.0
Supplementary files format and content: Comma-separated text files that include the count matrix of the pipeline output.
Supplementary files format and content: Tab-separated text files that include the filtered count matrix.
Supplementary files format and content: Tab-separated text files that include the filtered count matrix after removal of DEGs.
Supplementary files format and content: Tab-separated text files that include the log-normalized count matrix.

organism: Parasteatoda tepidariorum

source_name: 20 whole embryos

growth_protocol: Embryos were incubated at 25 ˚C until they reached the appropriate stages.

extract_protocol:
The spider embryos were dechorionated with 100% commercial bleach, rinsed with distilled water, and transferred into CGBS-CMF (55 mM NaCl, 40 mM KCl, 10 mM Tricine, pH6.95)-0.01% (for cell) or 0.5% (for nucleus) BSA solution, where vitelline membrane was manually removed with forceps. For preparation of dissociated cells, the devitellinized sample was filtered through 40-mm cell strainer (pluriStrainer-Mini) and collected in a 1.5-mL DNA LoBind Tube (Eppendorf). For preparation of nuclei, the devitellinized sample was centrifuged in a 1.5-mL tube (Eppendorf) and suspended in 400 mL homogenization buffer (250 mM Sucrose, 10 mM Tris (pH 8.0), 25 mM KCl, 5 mM MgCl2, 0.1% Triton-X100, 0.1 mM DTT, 100 u/mL RNase Inhibitor (SUPERaseIn RNase Inhibitor: Invitrogen, AM2694), Protease Inhibitor at 1:100 dilution (Nacalai tesque, 25955-11)), where the sample was homogenized with a loose plastic pestle (fisher scientific) by 40 strokes. The sample was then centrifuged and suspended with CGBS-CMF-0.5% BSA-100 u/mL RNase Inhibitor solution, followed by filteration through the 40-mm cell strainer. The centrifugation and resuspension steps were repeated twice. Adding 4 volumes of CellCover (Anacyte Laboratories), the cell and nucleus samples were stored at 4 ˚C until use.
The stored cells or nuclei were centrifuged and resuspended with the CGBS-CMF-based solution, and they were individualized using BD Rhapsody microwell-based platform, followed by library construction according to the manufacture’s instructions. Construction of the single-nucleus RNA-seq library was performed with some modifications; RNase Inhibitor was added to the Sample buffer, and Proteinase K was added to the Lysis buffer, and the lysis step was prolonged from 2 minutes to 5 minutes.
Single-cell and single-nucleus RNA-seq

value: 20 whole embryos

value: all extracted nuclei

value: WT

tag: Stage

value: late stage 5


title: NC-3

status: Public on Dec 13 2021

city: Shanghai

first: Yuan-Yuan

last: Luo

address: Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China

country: China

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat(version:2.0.9).
Bowtie were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the RPKM value of each gene was calculated.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample ...

source_name: liver cancer

growth_protocol: Huh7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.All cells were cultured in a 5% CO2 humidified atmosphere at 37˚C.

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hsa_circ_0098181 overexpressing and control plasmid were transfected into Huh7 cells with Lipofectamine 2000. After 48 hours transfection, total RNA was extracted for further RNA sequencing.


title: Liver, R&Z_WT_CD_170d_1

status: Public on Dec 10 2021

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

data_processing:
Basecalling by Illumina's standard pipeline
QC step, sickle reads with quality > Q20
QC step, trim_galore removing Illumina adaptors
Mapping step: STAR 2.5.0a extra paramaters outSAMmultNmax 1 --quantMode GeneCounts --outSAMunmapped Within
Quanitification step: featureCounts 1.5.0-p3 using NCBI mm10 gtf (mm10.ncbiRefSeq.gtf.gz)
Genome_build: mm10 (NCBI)
Supplementary_files_format_and_content:  Gene Name,Chromosome,Start,End,Strand,Length,Counts

source_name: Liver

extract_protocol:
RNA was extracted from liver tissue using Quiagen Rneasy mini kit
SMARTSEQ2 protocol

value: adult liver

value: Wild-type

tag: chronic damage

value: Yes

tag: time point

value: 170 days


title: Liver, R&Z_WT_CD_4d_2

tag: genotype

value: 4 days


title: Liver, R&Z_WT_CD_4d_1


title: Liver, R&Z_WT_3M_3

value: No

value: 3 months


title: Liver, R&Z_WT_CD_50d_1

value: 50 days


title: Liver, R&Z_WT_CD_170d_2


title: Liver, R&Z_KO_CD_170d_1

value: Rnf43 and Znrf3 mutant


title: Liver, R&Z_KO_CD_170d_2


title: Liver, R&Z_WT_7M_1

value: 7 months


title: Liver, R&Z_KO_CD_4d_2


title: Liver, R&Z_KO_CD_4d_1


title: Liver, R&Z_KO_CD_50d_1


title: Liver, R&Z_KO_CD_50d_2


title: Liver, R&Z_WT_3M_2


title: Liver, R&Z_KO_7M_2


title: Liver, R&Z_WT_PHx_21d_3

description:
countsFile.csv.gz
S29

data_processing:
Basecalling by Illumina's standard pipeline
QC step, sickle reads with quality > Q20
QC step, trim_galore removing Illumina adaptors
Mapping step: STAR 2.5.0a extra paramaters outSAMmultNmax 1 --quantMode GeneCounts --outSAMunmapped Within
Quanitification step: featureCounts 1.5.0-p1 using NCBI mm10 gtf
Genome_build: mm10 (NCBI)
Supplementary_files_format_and_content: FeatureCounts output: Gene Name, Gene Length, Read Count

tag: partial hepatectomy

value: 21 days


title: Liver, R&Z_KO_7M_1

tag: tissue


title: Liver, R&Z_WT_PHx_21d_2

description:
countsFile.csv.gz
S28

tag: strain


title: Liver, R&Z_WT_PHx_7d_3

description:
countsFile.csv.gz
S23

value: 7 days


title: Liver, R&Z_WT_PHx_21d_1

description:
countsFile.csv.gz
S27


title: Liver, R&Z_WT_PHx_7d_2

description:
countsFile.csv.gz
S22


title: Ovarian cancer tumor, patient 6, C2D8

status: Public on Jun 20 2022

first: Daniela

middle: Elena

last: Matei

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
1. filter probes failing in 1+ sample. 2. Filter detection P-value < 0.01 (quality). 3. Remove probes with SNPs at CpG site. 4. Exclude cross reactive probes. 5.BIMQ normalization 6.COMBAT batch effect correction;
Wilcoxon Rank test with BH p-value adjustment

label: Cy3, Cy5

source_name: tumor biopsy sample

extract_protocol: DNA was extracted from tumor biopsies using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia CA) according to the manufacturer instructions.

tag: sample type

value: Treated

tag: resistance

value: Responder


title: Liver, R&Z_WT_PHx_7d_1

description:
countsFile.csv.gz
S21


title: Ovarian cancer tumor, patient 14, C2D8

value: Non-Responder


title: Liver, R&Z_KO_PHx_7d_3

description:
countsFile.csv.gz
S26


title: Liver, R&Z_KO_PHx_7d_1

description:
countsFile.csv.gz
S24


title: Liver, R&Z_KO_PHx_21d_2

description:
countsFile.csv.gz
S31


title: Liver, R&Z_KO_PHx_21d_3

description:
countsFile.csv.gz
S32


title: Liver, R&Z_WT_7M_2

description:
countsFile.csv.gz
S9


title: Liver, R&Z_WT_7M_3

description:
countsFile.csv.gz
S10


title: Liver, R&Z_WT_7M_4

description:
countsFile.csv.gz
S11


title: Liver, R&Z_KO_7M_5

description:
countsFile.csv.gz
S14


title: Ovarian cancer tumor, patient 31, C2D8


title: Ovarian cancer tumor, patient 6, C1D1

value: Baseline (control)


title: Ovarian cancer tumor, patient 5, C1D1


title: Ovarian cancer tumor, patient 3, C1D1


title: Liver, R&Z_KO_7M_4

description:
countsFile.csv.gz
S13


title: Ovarian cancer tumor, patient 16, C2D8


title: Ovarian cancer tumor, patient 1, C1D1


title: Ovarian cancer tumor, patient 14, C1D1


title: Ovarian cancer tumor, patient 2, C1D1


title: Ovarian cancer tumor, patient 5, C2D8


title: Liver, R&Z_KO_7M_3

description:
countsFile.csv.gz
S12


title: Liver, R&Z_WT_1M_1

description:
countsFile.csv.gz
S1

value: 1 month


title: Ovarian cancer tumor, patient 33, C2D8


title: Liver, R&Z_WT_1M_2

description:
countsFile.csv.gz
S2

value: adult liver


title: Ovarian cancer tumor, patient 31, C1D1


title: Ovarian cancer tumor, patient 2, C2D8


title: Ovarian cancer tumor, patient 4, C2D8


title: Liver, R&Z_KO_1M_4

description:
countsFile.csv.gz
S8


title: Liver, R&Z_WT_1M_3

description:
countsFile.csv.gz
S3

value: Wild-type


title: Liver, R&Z_WT_1M_4

description:
countsFile.csv.gz
S4


title: Liver, R&Z_KO_1M_3

description:
countsFile.csv.gz
S7


title: Liver, R&Z_KO_1M_1

description:
countsFile.csv.gz
S5


title: Ovarian cancer tumor, patient 9, C1D1


title: Liver, R&Z_KO_1M_2

description:
countsFile.csv.gz
S6


title: Liver, R&Z_WT_3M_4

description:
countsFile.csv.gz
S16


title: Liver, R&Z_WT_3M_3

description:
countsFile.csv.gz
S15


title: Ovarian cancer tumor, patient 4, C1D1


title: Ovarian cancer tumor, patient 9, C2D8


title: L4_1_TiF-P46

status: Public on Sep 27 2021

city: Xianyang

first: Young

last: Tang

state: Shaanxi

address: #22 Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
Sequencing adapters and reads with low quality were trimmed using Cutadapt before mapping. The quality of reads after filtering was examined using fastQC.
For mapping, bovine genomic sequence and RefSeq gene coordinate (ARS-UCD1.2/bosTau9) were downloaded from the UCSC genome browser. All filtered reads were aligned to bovine reference genome by RNA STAR (Galaxy Version 2.7.8a) with default parameters.
The number of reads per gene was counted by featureCounts (Galaxy Version 2.0.1). Differentially expressed genes between different samples were identified using default parameters in DESeq2 (Galaxy Version 2.11.40.6+galaxy1), which generated a principal component analysis plot and the heatmap of the sample-to-sample distance matrix.
The most differentially expressed genes (adjusted p-value < 0.05) were extracted from DESeq2 results with an absolute fold change > 5. The normalized counts for those dif-ferentially expressed genes and the Z-score of the counts were calculated on the galaxy platform and exhibited as heatmaps by Heatmap2 (Galaxy Version 3.0.1).
Genome_build: ARS-UCD1.2/bosTau9
Supplementary_files_format_and_content: Tabular files include Log(FC) values for every gene and normalized counts for all samples.
Supplementary_files_format_and_content: Tabular file for heatmap2 including normalized gene counts for all samples with absolute expression fold change > 5 compared with bMSCs

organism: Bos taurus

source_name: biPSCs

growth_protocol: bMSCs were maintained with ATCC low serum MSC medium; biPSCs were maintained in either KT medium or TiF medium.

extract_protocol:
Total RNA was isolated from bovine cells with different treatments using RNeasy Mini kit (Qiagen). The quality of total RNA was examined by Nanodrop, Agarose Gel Electrophoresis and the Aglient 2100 bioanalyzer. rRNA was then removed by using Ribo-Zero-rRNA Removal kit (Epicentre, Madison, WI, USA).
First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. Finally, sequencing libraries were quantified by using Agilent 2100 bioanalyzer and then fed into Illumina sequencers.

treatment_protocol: Cells were grown in their respective media until 80% confluence before RNA extraction

tag: cell type

value: biPSCs

value: holstein

tag: treatment

value: reprogrammed and maintained in TiF medium


title: Liver, R&Z_WT_3M_5

description:
countsFile.csv.gz
S17

value: No


title: Ovarian cancer tumor, patient 33, C1D1


title: bMSC3

source_name: mesenchymal stem cells

value: mesenchymal stem cells

value: untreated


title: bMSC2


title: Ovarian cancer tumor, patient 1, C2D8


title: Liver, R&Z_KO_PHx_7d_2

description:
countsFile.csv.gz
S25

value: Rnf43 and Znrf3 mutant

value: Yes


title: bMSC1


title: Gem72-treated PTENpe-/- #3

status: Public on Aug 04 2021

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10

extract_protocol: RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Number RS-122-2101). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Prostate

tag: tumor stage

value: Prostatic intraepithelial neoplasia

value: Pten(i)pe-/- (Prostatic luminal cell-specific Pten gene invalidation)


title: Vehicle-treated (1 week)

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.7.7 and Cell Ranger 3.0.1 mkfastq.
Alignment, barcode and UMI filtering and counting were performed using Cell Ranger 3.0.1 count and mouse reference 3.0.0 (mm10 and Ensembl release 93).
Genome_build: mm10
Supplementary_files_format_and_content: Filtered (contains only detected cellular barcodes) feature-barcode matrix (each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)) in Market Exchange Format (MEX) and gzipped.
Supplementary_files_format_and_content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

extract_protocol:
Mice prostates were mechanically and enzymatically dissociated. Single living cells were obtained by FACS sorting.
Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisted of  > 95% viable cells were processed on the Chromium Controller from 10X Genomics (Leiden, The Netherlands). Ten thousand cells were loaded per well to yield approximately 5 to 6,000 captured cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs). Single cell 3’ mRNA seq library were generated according to Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) from 10X Genomics (ref CG00052 Rev E). Briefly, GEMs were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip A. Following full length cDNA synthesis and barcoding from poly-adenylated mRNA, GEM were broken and pooled before cDNA amplification by PCR using 10 cycles. After enzymatic fragmentation and size selection, sequencing library were constructed by adding Illumina (Paris, France) P5 and P7 primers as well as sample index via end repair, A tailing, adaptor ligation and PCR with 12 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).

value: Vehicle-treated (1 week)


title: Gemini-72-treated (1 week)

value: Gemini-72-treated (1 week)


title: Gem72-treated PTENpe-/- #1


title: L4_6_TiF-P53


title: vehicle-treated PTENpe-/- #3

value: vehicle-treated


title: vehicle-treated PTENpe-/- #2


title: vehicle-treated PTENpe-/- #1


title: wild type #2

value: normal prostate

value: PtenL2/L2 (Pten floxed mice; control)

value: control


title: Liver, R&Z_KO_3M_1

description:
countsFile.csv.gz
S18

value: adult liver

value: 3 months


title: Liver, R&Z_KO_PHx_21d_1

description:
countsFile.csv.gz
S30

value: 21 days


title: SEM_RNAP2S5p_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_Pol2S5_SE_DMSO_1_0119)

status: Public on Jun 10 2021

city: Grand Rapids

first: Derek

middle: H

last: Janssens

state: MI

address: 333 Bostwick Ave. NE

department: Epigenetics

institute: Van Andel Institute

description: Automated CUT&Tag for RNAP2S5p in the SEM KMT2Ar cell line grown with DMSO for 72hrs

library_source: genomic

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19_fragments.bed.gz).  3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: CUT&TAG

extract_protocol:
AutoCUTnTag_protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: cut&tag antibody

value: RNAPIISer5P Cell Signaling Technologies cat# 13523

value: SEM KMT2A-AF4 B-ALL cell line with DMSO for 72hrs


title: SEM_RNAP2S5p_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_Pol2S5_SE_DMSO_2_0119)


title: SEM_Menin_AutoCUTnTag_Rep2_(20210126_DJ_Hs_Men2_SE_DMSO_0112)

description: Automated CUT&RUN for Menin in the SEM KMT2Ar cell line

extract_protocol:
AutoCUTnRUN_protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: Menin Bethyl cat# A300-105A

value: SEM KMT2A-AF4 B-ALL cell line


title: SEM_RNAP2S5p_AutoCUTnTag_(20200313_DJ_Hs_PolS5p_SE_0310)

description: Automated CUT&Tag for RNAP2S5p in the SEM KMT2Ar cell line


title: Ovarian cancer tumor, patient 16, C1D1

value: Baseline (control)

value: Non-Responder


title: SEM_IgG_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_IgG_SE_DMSO_2_0119)

description: Automated CUT&Tag for IgG control in the SEM KMT2Ar cell line grown with DMSO for 72hrs

value: IgG Abcam cat# ab46540


title: SEM_H3K4me3_VTP50469_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K4me3_SE_VTP_1_0119)

description: Automated CUT&Tag for H3K4me3 in the SEM KMT2Ar cell line treated with 30 uM VTP50469 for 72hrs

value: H3K4me3 Active Motif cat# 39159

value: SEM KMT2A-AF4 B-ALL cell line with 30 uM VTP50469 for 72hrs


title: SEM_IgG_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_IgG_SE_DMSO_1_0119)


title: SEM_H3K4me3_EPZ5676_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K4me3_SE_EPZ_1_0119)

description: Automated CUT&Tag for H3K4me3 in the SEM KMT2Ar cell line treated with 30 uM EPZ-5676 for 72hrs

value: SEM KMT2A-AF4 B-ALL cell line with 30 uM EPZ-5676 for 72hrs


title: Gem72-treated PTENpe-/- #2

value: Prostate

value: Prostatic intraepithelial neoplasia

value: Pten(i)pe-/- (Prostatic luminal cell-specific Pten gene invalidation)


title: Ovarian cancer tumor, patient 3, C2D8

value: Treated


title: SEM_Menin_AutoCUTnTag_Rep1_(20210126_DJ_Hs_Men1_SE_DMSO_0112)


title: SEM_H3K4me3_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K4me3_SE_DMSO_2_0119)

description: Automated CUT&Tag for H3K4me3 in the SEM KMT2Ar cell line grown with DMSO for 72hrs


title: wild type #1

value: normal prostate

value: PtenL2/L2 (Pten floxed mice; control)

value: control


title: SEM_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_SEM_2_0125)

description: Automated CUT&Tag for H4K16ac in the SEM KMT2Ar cell line

value: H4K16ac Abcam cat# ab109463


title: SEM_H3K27ac_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K27ac_SE_DMSO_2_0119)

description: Automated CUT&Tag for H3K27ac in the SEM KMT2Ar cell line grown with DMSO for 72hrs

value: H3K27ac Millipore cat# MABE647

value: SEM KMT2A-AF4 B-ALL cell line with DMSO for 72hrs


title: SEM_ENL_AutoCUTnTag_Rep2_(20201110_DJ_Hs_ENL_SE_1104)

description: Automated CUT&Tag for ENL in the SEM KMT2Ar cell line

value: MLLT3/ENL Cell Signaling Technologies cat# 14893S

value: SEM KMT2A-AF4 B-ALL cell line


title: SEM_H3K4me3_VTP50469_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K4me3_SE_VTP_2_0119)


title: SEM_H3K27ac_EPZ5676_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K27ac_SE_EPZ_2_0119)

description: Automated CUT&Tag for H3K27ac in the SEM KMT2Ar cell line treated with 30 uM EPZ-5676 for 72hrs


title: SEM_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_SEM_1_0125)


title: SEM_H3K4me3_EPZ5676_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K4me3_SE_EPZ_2_0119)


title: SEM_H3K4me3_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K4me3_SE_DMSO_1_0119)


title: SEM_Dot1L_AutoCUTnTag_Rep2_(20201110_DJ_Hs_Dot1L_SE_1104)

description: Automated CUT&Tag for Dot1L in the SEM KMT2Ar cell line

value: Dot1L Cell Signaling Technologies cat# 90878S


title: RS411_RNAP2S5p_DMSO_AutoCUTnTag_Rep1_(20210129_DJ_Hs_Pol2S5_RS_DMSO_1_0125)

description: Automated CUT&Tag for RNAP2S5p in the RS4;11 KMT2Ar cell line grown with DMSO for 72hrs

value: RNAPIISer5P Cell Signaling Technologies cat# 13523

value: RS4;11 KMT2A-AF4 B-ALL cell line with DMSO for 72hrs


title: SEM_H3K27ac_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K27ac_SE_DMSO_1_0119)


title: RS411_Menin_AutoCUTnTag_Rep1_(20210126_DJ_Hs_Men1_RS_DMSO_0112)

description: Automated CUT&RUN for Menin in the RS4;11 KMT2Ar cell line

value: Menin Bethyl cat# A300-105A

value: RS4;11 KMT2A-AF4 B-ALL cell line


title: RS411_Menin_AutoCUTnTag_Rep2_(20210126_DJ_Hs_Men2_RS_DMSO_0112)


title: RS411_IgG_DMSO_AutoCUTnTag_Rep2_(20210129_DJ_Hs_IgG_RS_DMSO_2_0125)

description: Automated CUT&Tag for IgG control in the RS4;11 KMT2Ar cell line grown with DMSO for 72hrs

value: IgG Abcam cat# ab46540


title: RS411_IgG_DMSO_AutoCUTnTag_Rep1_(20210129_DJ_Hs_IgG_RS_DMSO_1_0125)


title: SEM_H3K27ac_EPZ5676_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K27ac_SE_EPZ_1_0119)

value: SEM KMT2A-AF4 B-ALL cell line with 30 uM EPZ-5676 for 72hrs


title: RS411_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_RS411_2_0125)

description: Automated CUT&Tag for H4K16ac in the RS4;11 KMT2Ar cell line


title: RS411_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_RS411_1_0125)


title: RS411_H3K27ac_EPZ5676_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_RS_EPZ_2_0125)

description: Automated CUT&Tag for H3K27ac in the RS4;11 KMT2Ar cell line treated with 30 uM EPZ-5676 for 72hrs

value: RS4;11 KMT2A-AF4 B-ALL cell line with 30 uM EPZ-5676 for 72hrs


title: RS411_RNAP2S5p_AutoCUTnTag_(20200313_DJ_Hs_PolS5p_RS_0310)

description: Automated CUT&Tag for RNAP2S5p in the RS4;11 KMT2Ar cell line


title: RS411_H3K27ac_EPZ5676_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_RS_EPZ_1_0125)


title: RS411_H3K4me3_VTP50469_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K4me3_RS_VTP_2_0125)

description: Automated CUT&Tag for H3K4me3 in the RS4;11 KMT2Ar cell line treated with 30 uM VTP50469 for 72hrs

value: H3K4me3 Active Motif cat# 39159

value: RS4;11 KMT2A-AF4 B-ALL cell line with 30 uM VTP50469 for 72hrs


title: RS411_H3K4me3_DMSO_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K4me3_RS_DMSO_1_0125)

description: Automated CUT&Tag for H3K4me3 in the RS4;11 KMT2Ar cell line grown with DMSO for 72hrs


title: MPAL2_RNAP2S5p_AutoCUTnTag_Rep1_(20200324_DJ_Hs_P2S5_A5_0323)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the MPAL-2 patient sample

value: sorted CD45+ cells from the MPAL-2 KMT2A-AF4 patient sample


title: RS411_RNAP2S5p_DMSO_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Pol2S5_RS_DMSO_2_0125)


title: RS411_H3K4me3_DMSO_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K4me3_RS_DMSO_2_0125)


title: RS411_Dot1L_AutoCUTnTag_Rep2_(20201110_DJ_Hs_Dot1L_RS_1104)

description: Automated CUT&Tag for Dot1L in the RS4;11 KMT2Ar cell line


title: MPAL2_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_A5_2_0125)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the MPAL-2 patient sample


title: RS411_ENL_AutoCUTnTag_Rep2_(20201110_DJ_Hs_ENL_RS_1104)

description: Automated CUT&Tag for ENL in the RS4;11 KMT2Ar cell line


title: MPAL2_H3K27ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_A5_2_0125)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the MPAL-2 patient sample


title: RS411_H3K4me3_VTP50469_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K4me3_RS_VTP_1_0125)


title: MPAL2_RNAP2S5p_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Pol2S5_A5_2_0125)


title: RS411_H3K27ac_DMSO_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_RS_DMSO_1_0125)

description: Automated CUT&Tag for H3K27ac in the RS4;11 KMT2Ar cell line grown with DMSO for 72hrs


title: RS411_H3K27ac_DMSO_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_RS_DMSO_2_0125)


title: MPAL2_ENL_AutoCUTnTag_Rep2_(20210129_DJ_Hs_ENL_A5_2_0125)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL2_H3K27ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_A5_1_0125)


title: MPAL1_RNAP2S5p_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Pol2S5_TB11_2_0125)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the MPAL-1 patient sample

value: sorted CD45+ cells from the MPAL-1 KMT2A-AF9 patient sample


title: MPAL2_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_A5_1_0125)

value: H4K16ac Abcam cat# ab109463


title: MPAL2_Dot1L_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Dot1L_A5_2_0125)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL1_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_TB11_2_0125)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the MPAL-1 patient sample


title: MPAL1_RNAP2S5p_AutoCUTnTag_Rep1_(20200324_DJ_Hs_P2S5_TB11_0323)


title: MPAL1_H3K27ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_TB11_1_0125)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the MPAL-1 patient sample

value: H3K27ac Millipore cat# MABE647


title: RS411_H3K4me3_EPZ5676_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K4me3_RS_EPZ_2_0125)

description: Automated CUT&Tag for H3K4me3 in the RS4;11 KMT2Ar cell line treated with 30 uM EPZ-5676 for 72hrs


title: MPAL1_H3K27ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_TB11_2_0125)


title: MPAL1_ENL_AutoCUTnTag_Rep2_(20210129_DJ_Hs_ENL_TB11_2_0125)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the MPAL-1 patient sample


title: RS411_H3K4me3_EPZ5676_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K4me3_RS_EPZ_1_0125)


title: MPAL1_Dot1L_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Dot1L_TB11_2_0125)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the MPAL-1 patient sample


title: ML2_KMT2A_N1_AutoCUTnRUN_(200331_JS_HsEc_031020_JFS1299)

description: Automated CUT&RUN for the KMT2A N-terminal in the ML-2 KMT2Ar cell line

source_name: CUT&RUN

tag: cut&run antibody

value: KMT2A-N1 Millipore cat# 05-764

value: ML-2 KMT2A-AF6 AML cell line


title: ML2_KMT2A_C2_AutoCUTnRUN_(200331_JS_HsEc_031020_JFS1302)

description: Automated CUT&RUN for the KMT2A C-terminal region in the ML-2 KMT2Ar cell line

value: KMT2A-C2 Millipore cat# 05-765


title: ML2_IgG_AutoCUTnRUN_(200331_JS_HsEc_031020_JFS1305)

description: Automated CUT&RUN for IgG control in the ML-2 KMT2Ar cell line


title: ML2_H3K27ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_ML2_2_0125)

description: Automated CUT&Tag for H3K27ac in the ML-2 KMT2Ar cell line


title: ML2_KMT2A_C1_AutoCUTnRUN_(200331_JS_HsEc_031020_JFS1301)

value: KMT2A-C1 Santa Cruz cat# sc-374392


title: ML2_H3K27ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_ML2_1_0125)


title: KOPN8_RNAP2S5p_AutoCUTnTag_(20200313_DJ_Hs_PolS5p_KO_0310)

description: Automated CUT&Tag for RNAP2S5p in the KOPN-8 KMT2Ar cell line

value: RNAPIISer5P Cell Signaling Technologies cat# 13523

value: KOPN-8 KMT2A-ENL B-ALL cell line


title: KOPN8_RNAP2S5p_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_Pol2S5_KO_DMSO_1_0119)

description: Automated CUT&Tag for RNAP2S5p in the KOPN-8 KMT2Ar cell line grown with DMSO for 72hrs

value: KOPN-8 KMT2A-ENL B-ALL cell line with DMSO for 72hrs


title: KOPN8_Menin_AutoCUTnTag_Rep2_(20210127_DJ_Hs_Men2_KO_DMSO_0112)

description: Automated CUT&RUN for Menin in the KOPN-8 KMT2Ar cell line

value: Menin Bethyl cat# A300-105A


title: KOPN8_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_KOPN8_2_0125)

description: Automated CUT&Tag for H4K16ac in the KOPN-8 KMT2Ar cell line


title: MPAL1_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_TB11_1_0125)


title: KOPN8_RNAP2S5p_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_Pol2S5_KO_DMSO_2_0119)


title: KOPN8_Menin_AutoCUTnTag_Rep1_(20210127_DJ_Hs_Men1_KO_DMSO_0112)


title: KOPN8_IgG_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_IgG_KO_DMSO_1_0119)

description: Automated CUT&Tag for IgG control in the KOPN-8 KMT2Ar cell line grown with DMSO for 72hrs

value: IgG Abcam cat# ab46540


title: KOPN8_IgG_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_IgG_KO_DMSO_2_0119)


title: KOPN8_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_KOPN8_1_0125)


title: KOPN8_H3K4me3_EPZ5676_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K4me3_KO_EPZ_2_0119)

description: Automated CUT&Tag for H3K4me3 in the KOPN-8 KMT2Ar cell line treated with 30 uM EPZ-5676 for 72hrs

value: KOPN-8 KMT2A-ENL B-ALL cell line with 30 uM EPZ-5676 for 72hrs


title: KOPN8_H3K4me3_VTP50469_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K4me3_KO_VTP_1_0119)

description: Automated CUT&Tag for H3K4me3 in the KOPN-8 KMT2Ar cell line treated with 30 uM VTP50469 for 72hrs

value: KOPN-8 KMT2A-ENL B-ALL cell line with 30 uM VTP50469 for 72hrs


title: KOPN8_H3K4me3_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K4me3_KO_DMSO_1_0119)

description: Automated CUT&Tag for H3K4me3 in the KOPN-8 KMT2Ar cell line grown with DMSO for 72hrs

value: H3K4me3 Active Motif cat# 39159


title: KOPN8_H3K4me3_EPZ5676_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K4me3_KO_EPZ_1_0119)


title: KOPN8_H3K4me3_VTP50469_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K4me3_KO_VTP_2_0119)


title: KOPN8_H3K27ac_EPZ5676_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K27ac_KO_EPZ_2_0119)

description: Automated CUT&Tag for H3K27ac in the KOPN-8 KMT2Ar cell line treated with 30 uM EPZ-5676 for 72hrs


title: KOPN8_H3K27ac_DMSO_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K27ac_KO_DMSO_1_0119)

description: Automated CUT&Tag for H3K27ac in the KOPN-8 KMT2Ar cell line grown with DMSO for 72hrs


title: KOPN8_ENL_AutoCUTnTag_Rep2_(20201110_DJ_Hs_ENL_2_KO_1104)

description: Automated CUT&Tag for ENL in the KOPN-8 KMT2Ar cell line

value: MLLT3/ENL Cell Signaling Technologies cat# 14893S


title: KOPN8_ENL_AutoCUTnTag_Rep1_(20201110_DJ_Hs_ENL_KO_1104)


title: ML2_KMT2A_N2_AutoCUTnRUN_(200331_JS_HsEc_031020_JFS1300)

description: Automated CUT&RUN for the KMT2A N-terminal region in the ML-2 KMT2Ar cell line

value: KMT2A-N2 Cell Signaling Technologies cat# 14689S


title: KOPN8_H3K27ac_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K27ac_KO_DMSO_2_0119)


title: KOPN8_H3K27ac_EPZ5676_AutoCUTnTag_Rep1_(20210120_DJ_Hs_K27ac_KO_EPZ_1_0119)


title: KOPN8_Dot1L_AutoCUTnTag_Rep2_(20201110_DJ_Hs_Dot1L_2_KO_1104)

description: Automated CUT&Tag for Dot1L in the KOPN-8 KMT2Ar cell line

value: Dot1L Cell Signaling Technologies cat# 90878S


title: KOPN8_Dot1L_AutoCUTnTag_Rep1_(20201110_DJ_Hs_Dot1L_KO_1104)


title: K562_KMT2A_N1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N1_K5_1208)

description: Automated CUT&RUN for the KMT2A N-terminal region in the K562 myelogenous leukemia cell line

value: K562 CML cell line


title: K562_IgG_AutoCUTnRUN_(20201218_DJ_Hs_IgG_K5_1208)

description: Automated CUT&RUN for IgG control in the K562 myelogenous leukemia cell line


title: CD34_RNAP2S5p_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_Pol2s5_2_0101)

description: Automated CUT&Tag for RNAP2S5p in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: sorted CD34+ HSPCs from donor sample


title: K562_KMT2A_C2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C2_K5_1208)

description: Automated CUT&RUN for the KMT2A C-terminal region in the K562 myelogenous leukemia cell line


title: KOPN8_H3K4me3_DMSO_AutoCUTnTag_Rep2_(20210120_DJ_Hs_K4me3_KO_DMSO_2_0119)


title: K562_KMT2A_C1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C1_K5_1208)


title: CD34_KMT2A_N1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N1_CD34_1208)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: KMT2A-N1 Millipore cat# 05-764


title: CD34_RNAP2S5p_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_Pol2s5_1_0101)


title: CD34_KMT2A_N2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N2_CD34_1208)


title: CD34_KMT2A_C1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C1_CD34_1208)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD34+ hematopoietic stem/progenitor cells from donor sample


title: K562_KMT2A_N2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N2_K5_1208)


title: CD34_KMT2A_C2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C2_CD34_1208)


title: CD34_IgG_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_IgG_2_0101)

description: Automated CUT&Tag for IgG control in sorted CD34+ hematopoietic stem/progenitor cells from donor sample


title: CD34_IgG_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_IgG_1_0101)


title: CD34_IgG_AutoCUTnRUN_(20201218_DJ_Hs_IgG_CD34_1208)

description: Automated CUT&RUN for IgG control in sorted CD34+ hematopoietic stem/progenitor cells from donor sample


title: CD34_H3K4me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_K4m3_1_0101)

description: Automated CUT&Tag for H3K4me3 in sorted CD34+ hematopoietic stem/progenitor cells from donor sample


title: CD34_H3K4me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_K4m3_2_0101)


title: CD34_H3K4me1_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_K4m1_1_0101)

description: Automated CUT&Tag for H3K4me1 in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: H3K4me1 Thermo cat# 710795


title: CD34_H4K16ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_K16ac_1_0101)

description: Automated CUT&Tag for H4K16ac in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: H4K16ac Abcam cat# ab109463


title: CD34_H3K36me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_K36m3_1_0101)

description: Automated CUT&Tag for H3K36me3 in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: H3K36me3 Epicypher cat# 13-0031


title: CD34_H3K9me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_K9m3_1_0101)

description: Automated CUT&Tag for H3K9me3 in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: H3K9me3 Abcam cat# ab8898


title: CD34_H3K27me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_K27m_1_0101)

description: Automated CUT&Tag for H3K27me3 in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: H3K27me3 Cell Signaling Technologies cat# 9733S


title: CD34_H3K27me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_K27m_2_0101)


title: CD34_H3K27ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_K27ac_1_0101)

description: Automated CUT&Tag for H3K27ac in sorted CD34+ hematopoietic stem/progenitor cells from donor sample

value: H3K27ac Millipore cat# MABE647


title: CD34_H3K27ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_K27ac_2_0101)


title: CD34_H4K16ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_K16ac_2_0101)


title: CD34_ENL_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_ENL_2_0101)

description: Automated CUT&Tag for ENL in sorted CD34+ hematopoietic stem/progenitor cells from donor sample


title: CD34_ENL_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_ENL_1_0101)


title: CD34_H3K9me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_K9m3_2_0101)


title: CD34_Dot1L_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_Dot1L_2_0101)

description: Automated CUT&Tag for Dot1L in sorted CD34+ hematopoietic stem/progenitor cells from donor sample


title: CD34_Dot1L_AutoCUTnTag_Rep1_(20210108_DJ_Hs_CD34_Dot1L_1_0101)


title: AML5_RNAP2S5p_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_Pol2s5_2_0101)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the AML-5 patient sample

value: RNAPIISer5P Cell Signaling Technologies cat# 13523

value: sorted CD45+ cells from the AML-5 KMT2A-AF10 patient sample


title: CD34_H3K4me1_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_K4m1_2_0101)


title: AML5_RNAP2S5p_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_Pol2s5_1_0101)


title: AML5_KMT2A_N2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N2_A109C_1208)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the AML-5 patient sample


title: AML5_KMT2A_N1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N1_A109C_1208)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the AML-5 patient sample


title: CD34_H3K36me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_CD34_K36m3_2_0101)


title: AML5_KMT2A_C1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C1_A109C_1208)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the AML-5 patient sample

value: KMT2A-C1 Santa Cruz cat# sc-374392


title: AML5_IgG_AutoCUTnRUN_(20201218_DJ_Hs_IgG_A109C_1208)

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the AML-5 patient sample

value: IgG Abcam cat# ab46540


title: AML5_H3K9me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_K9m3_2_0101)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the AML-5 patient sample


title: AML5_H4K16ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_K16ac_1_0101)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the AML-5 patient sample


title: AML5_IgG_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_IgG_2_0101)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the AML-5 patient sample


title: AML5_H4K16ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_K16ac_2_0101)


title: AML5_H3K9me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_K9m3_1_0101)


title: AML5_H3K4me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_K4m3_2_0101)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the AML-5 patient sample

value: H3K4me3 Active Motif cat# 39159


title: AML5_H3K4me1_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_K4m1_1_0101)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the AML-5 patient sample


title: AML5_H3K4me1_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_K4m1_2_0101)


title: AML5_H3K36me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_K36m3_2_0101)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the AML-5 patient sample


title: AML5_H3K27me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_K27m_2_0101)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the AML-5 patient sample


title: AML5_H3K36me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_K36m3_1_0101)


title: AML5_H3K27me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_K27m_1_0101)


title: AML5_H3K27ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_K27ac_2_0101)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the AML-5 patient sample


title: AML5_KMT2A_C2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C2_A109C_1208)

value: KMT2A-C2 Millipore cat# 05-765


title: AML4_RNAP2S5p_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_Pol2s5_2_0101)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the AML-4 patient sample

value: sorted CD45+ cells from the AML-4 KMT2A-AF10 patient sample


title: AML5_ENL_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_ENL_2_0101)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the AML-5 patient sample

value: MLLT3/ENL Cell Signaling Technologies cat# 14893S


title: AML5_Dot1L_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_Dot1L_1_0101)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the AML-5 patient sample

value: Dot1L Cell Signaling Technologies cat# 90878S


title: AML5_ENL_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_ENL_1_0101)


title: AML5_IgG_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_IgG_1_0101)


title: AML4_RNAP2S5p_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_Pol2s5_1_0101)


title: AML4_KMT2A_N1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N1_A384C_1208)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the AML-4 patient sample


title: AML5_H3K27ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_K27ac_1_0101)


title: AML5_H3K4me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A109_K4m3_1_0101)


title: AML4_KMT2A_C2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C2_A384C_1208)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the AML-4 patient sample


title: AML4_KMT2A_C1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C1_A384C_1208)


title: AML4_IgG_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_IgG_2_0101)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the AML-4 patient sample


title: AML4_KMT2A_N2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N2_A384C_1208)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the AML-4 patient sample

value: KMT2A-N2 Cell Signaling Technologies cat# 14689S


title: AML4_IgG_AutoCUTnRUN_(20201218_DJ_Hs_IgG_A384C_1208)

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the AML-4 patient sample


title: AML4_H4K16ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_K16ac_1_0101)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the AML-4 patient sample


title: AML4_H4K16ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_K16ac_2_0101)


title: AML4_H3K9me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_K9m3_1_0101)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the AML-4 patient sample


title: AML4_H3K4me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_K4m3_2_0101)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the AML-4 patient sample


title: AML5_Dot1L_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A109_Dot1L_2_0101)


title: AML4_H3K4me1_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_K4m1_1_0101)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the AML-4 patient sample


title: AML4_H3K36me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_K36m3_2_0101)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the AML-4 patient sample


title: AML4_H3K4me1_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_K4m1_2_0101)


title: AML4_H3K27me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_K27m_2_0101)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the AML-4 patient sample


title: AML4_H3K27me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_K27m_1_0101)


title: AML4_H3K27ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_K27ac_2_0101)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the AML-4 patient sample


title: AML4_H3K36me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_K36m3_1_0101)


title: AML4_H3K9me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_K9m3_2_0101)


title: AML4_H3K27ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_K27ac_1_0101)


title: AML4_H3K4me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_K4m3_1_0101)


title: AML4_Dot1L_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_Dot1L_2_0101)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the AML-4 patient sample


title: AML3_RNAP2S5p_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_Pol2s5_1_0101)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the AML-3 patient sample

value: sorted CD45+ cells from the AML-3 KMT2A-AF9 patient sample


title: AML4_ENL_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_ENL_1_0101)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the AML-4 patient sample


title: AML3_RNAP2S5p_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_Pol2s5_2_0101)


title: AML4_ENL_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A384_ENL_2_0101)


title: AML3_IgG_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_IgG_1_0101)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the AML-3 patient sample


title: AML4_IgG_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_IgG_1_0101)


title: AML3_KMT2A_C1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C1_A107C_1208)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the AML-3 patient sample


title: AML3_IgG_AutoCUTnRUN_(20201218_DJ_Hs_IgG_A107C_1208)

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the AML-3 patient sample


title: AML3_KMT2A_C2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_C2_A107C_1208)


title: AML3_H4K16ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_K16ac_1_0101)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the AML-3 patient sample


title: AML3_H4K16ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_K16ac_2_0101)


title: AML3_KMT2A_N1_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N1_A107C_1208)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the AML-3 patient sample

value: KMT2A-N1 Millipore cat# 05-764


title: AML3_KMT2A_N2_AutoCUTnRUN_(20201218_DJ_Hs_MLL_N2_A107C_1208)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the AML-3 patient sample


title: AML3_H3K9me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_K9m3_1_0101)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the AML-3 patient sample


title: AML4_Dot1L_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A384_Dot1L_1_0101)


title: AML3_H3K9me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_K9m3_2_0101)


title: AML3_H3K4me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_K4m3_1_0101)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the AML-3 patient sample


title: AML3_IgG_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_IgG_2_0101)


title: AML3_H3K4me1_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_K4m1_2_0101)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the AML-3 patient sample

value: H3K4me1 Thermo cat# 710795


title: AML3_H3K4me1_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_K4m1_1_0101)


title: AML3_H3K36me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_K36m3_2_0101)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the AML-3 patient sample

value: H3K36me3 Epicypher cat# 13-0031


title: AML3_H3K36me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_K36m3_1_0101)


title: AML3_H3K27me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_K27m_2_0101)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the AML-3 patient sample


title: AML3_H3K27me3_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_K27m_1_0101)


title: AML3_H3K27ac_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_K27ac_2_0101)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the AML-3 patient sample


title: AML3_ENL_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_ENL_1_0101)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the AML-3 patient sample


title: AML3_Dot1L_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_Dot1L_2_0101)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the AML-3 patient sample


title: AML3_ENL_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_ENL_2_0101)


title: AML2_RNAP2S5p_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Pol2S5_A6_2_0125)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the AML-2 patient sample

value: sorted CD45+ cells from the AML-2 KMT2A-ENL patient sample


title: AML3_Dot1L_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_Dot1L_1_0101)


title: AML2_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_A6_2_0125)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the AML-2 patient sample

value: H4K16ac Abcam cat# ab109463


title: AML2_RNAP2S5p_AutoCUTnTag_Rep1_(20200324_DJ_Hs_P2S5_A6_0323)


title: AML1_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_A4_2_0125)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the AML-1 patient sample

value: sorted CD45+ cells from the AML-1 KMT2A-Sept6 patient sample


title: AML1_RNAP2S5p_AutoCUTnTag_Rep1_(20200324_DJ_Hs_P2S5_A4_0323)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the AML-1 patient sample

value: RNAPIISer5P Cell Signaling Technologies cat# 13523


title: AML2_H3K27ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_A6_2_0125)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the AML-2 patient sample

value: H3K27ac Millipore cat# MABE647


title: AML2_H3K27ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_A6_1_0125)


title: AML2_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_A6_1_0125)


title: AML1_RNAP2S5p_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Pol2S5_A4_2_0125)


title: AML3_H3K4me3_AutoCUTnTag_Rep2_(20210108_DJ_Hs_A107_K4m3_2_0101)


title: AML1_H3K27ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_A4_2_0125)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the AML-1 patient sample


title: AML1_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_A4_1_0125)


title: AML1_ENL_AutoCUTnTag_Rep2_(20210129_DJ_Hs_ENL_A4_2_0125)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the AML-1 patient sample


title: AML2_ENL_AutoCUTnTag_Rep2_(20210129_DJ_Hs_ENL_A6_2_0125)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the AML-2 patient sample


title: AML2_Dot1L_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Dot1L_A6_2_0125)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the AML-2 patient sample


title: AML1_Dot1L_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Dot1L_A4_2_0125)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the AML-1 patient sample


title: AML1_H3K27ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_A4_1_0125)


title: ALL1_RNAP2S5p_AutoCUTnTag_Rep1_(20200324_DJ_Hs_P2S5_TB13_0323)

description: Automated CUT&Tag for RNAP2S5p in sorted CD45+ cells from the ALL-1 patient sample

value: sorted CD45+ cells from the ALL-1 KMT2A-AF4 patient sample


title: ALL1_H4K16ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K16ac_TB13_1_0125)

description: Automated CUT&Tag for H4K16ac in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_H3K27ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K27ac_TB13_2_0125)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_H4K16ac_AutoCUTnTag_Rep2_(20210129_DJ_Hs_K16ac_TB13_2_0125)


title: ALL1_H3K27ac_AutoCUTnTag_Rep1_(20210129_DJ_Hs_K27ac_TB13_1_0125)


title: ALL1_RNAP2S5p_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Pol2S5_TB13_2_0125)


title: ALL1_ENL_AutoCUTnTag_Rep2_(20210129_DJ_Hs_ENL_TB13_2_0125)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the ALL-1 patient sample


title: AML3_H3K27ac_AutoCUTnTag_Rep1_(20210108_DJ_Hs_A107_K27ac_1_0101)

description: Automated CUT&Tag for H3K27ac in sorted CD45+ cells from the AML-3 patient sample


title: H3K4me3_scCUTnTag_(20200723_DJ_Hs_K4m3_scCnT)

description: Single cell CUT&Tag on the iCell8 for H3K4me3 in KMT2Ar samples; Fastq Sequence Identifier: SampleID_HistoneMark_Relicate#_Cell#

data_processing:
Genome_build: UCSC hg19
A. iCell8 system: 1. We used a custom python script to demultiplex and annotate fastq reads in the following format: Antibody_CellType_Rep_Cell#, e.g K27me3_K562_r1_54. 2. we used Bowtie2 2.3.4.3 with options --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700 to map the paired-end 25bp reads to HG19 of Homo sapiens genomic sequence obtained from UCSC. 3. We extracted properly paired reads from Homo sapiens alignments to generate a fragment bed files <chr> <start> <stop> <barcode> <duplicateCount>. Custom software to analyse these files is available from https://github.com/Henikoff/scCUT-Tag. B. 10X system: Cell Ranger ATAC v1.1 from 10X company with default parameters was used to do the demultiplexing, alignment to HG19 and read quantification.

source_name: CUT&Tag

extract_protocol:
iCell8_scCnT_protocol.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: sorted CD45+ cells from patient sample or KMT2Ar cell lines


title: ALL1_Dot1L_AutoCUTnTag_Rep2_(20210129_DJ_Hs_Dot1L_TB13_2_0125)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the ALL-1 patient sample


title: H3K36me3_scCUTnTag_(20200723_DJ_Hs_K36m3_scCnT)

description: Single cell CUT&Tag on the iCell8 for H3K36me3 in KMT2Ar samples; Fastq Sequence Identifier: SampleID_HistoneMark_Relicate#_Cell#


title: H3K27me3_scCUTnTag_(20200723_DJ_Hs_K27m3_scCnT)

description: Single cell CUT&Tag on the iCell8 for H3K27me3 in KMT2Ar samples; Fastq Sequence Identifier: SampleID_HistoneMark_Relicate#_Cell#

value: H3K27me3 Cell Signaling Technologies cat# 9733S


title: SEM_KMT2A_N2_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1293)

description: Automated CUT&RUN for the KMT2A N-terminal region in the SEM KMT2Ar cell line

extract_protocol:
AutoCUTnRUN_Protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: SEM KMT2A-AF4 B-ALL cell line


title: SEM_KMT2A_N1_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1292)

description: Automated CUT&RUN for the KMT2A N-terminal in the SEM KMT2Ar cell line


title: SEM_KMT2A_C1_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1294)

description: Automated CUT&RUN for the KMT2A C-terminal region in the SEM KMT2Ar cell line

value: KMT2A-C1 Santa Cruz cat# sc-374392


title: SEM_H3K4me3_CUTnTag_(20200504_SH_Hs_SEM_H3K4me3_0502)

description: Manual CUT&Tag for H3K4me3 in the SEM KMT2Ar cell line

extract_protocol:
CnTathome_Protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: H3K4me3 Active Motif cat# 39159


title: SEM_H3K9me3_CUTnTag_(20200423_SH_Hs_SEM_K9me3_0419)

description: Manual CUT&Tag for H3K9me3 in the SEM KMT2Ar cell line

value: H3K9me3 Abcam cat# ab8898


title: SEM_IgG_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1298)

description: Automated CUT&RUN for IgG control in the SEM KMT2Ar cell line

value: IgG Abcam cat# ab46540


title: SEM_H3K36me3_CUTnTag_Rep2_(20200423_SH_Hs_SEM_H3K36me3T_0419)

description: Manual CUT&Tag for H3K36me3 in the SEM KMT2Ar cell line


title: SEM_H3K4me1_CUTnTag_(20200423_SH_Hs_SEM_K4me1T_0418)

description: Manual CUT&Tag for H3K4me1 in the SEM KMT2Ar cell line


title: SEM_H3K27me3_CUTnTag_(20200423_SH_Hs_SEM_K27me3_0416)

description: Manual CUT&Tag for H3K27me3 in the SEM KMT2Ar cell line


title: SEM_H3K36me3_CUTnTag_Rep1_(20200423_SH_Hs_SEM_H3K36me3E_0419)


title: SEM_Dot1L_CUTnTag_(20200504_SH_Hs_SEM_Dot1_D4O_0502)

description: Manual CUT&Tag for Dot1L in the SEM KMT2Ar cell line

value: Dot1L Cell Signaling Technologies cat# 90878S


title: SEM_ENL_CUTnTag_(20200504_SH_Hs_SEM_MLL_ENL_0502)

description: Manual CUT&Tag for ENL in the SEM KMT2Ar cell line

value: MLLT3/ENL Cell Signaling Technologies cat# 14893S


title: SEM_ELL_CUTnTag_(20200504_SH_Hs_SEM_ELL_0502)

description: Manual CUT&Tag for ELL in the SEM KMT2Ar cell line

value: ELL Cell Signaling Technologies cat# 14468S


title: RS411_KMT2A_N1_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1306)

description: Automated CUT&RUN for the KMT2A N-terminal in the RS4;11 KMT2Ar cell line

value: KMT2A-N1 Millipore cat# 05-764

value: RS4;11 KMT2A-AF4 B-ALL cell line


title: RS411_IgG_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1312)

description: Automated CUT&RUN for IgG control in the RS4;11 KMT2Ar cell line


title: RS411_KMT2A_C1_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1308)

description: Automated CUT&RUN for the KMT2A C-terminal region in the RS4;11 KMT2Ar cell line


title: RS411_H3K4me3_CUTnTag_(20200423_SH_Hs_R5411_K4me3_0416)

description: Manual CUT&Tag for H3K4me3 in the RS4;11 KMT2Ar cell line


title: RS411_H3K9me3_CUTnTag_(20200423_SH_Hs_R5411_K9me3_0419)

description: Manual CUT&Tag for H3K9me3 in the RS4;11 KMT2Ar cell line


title: RS411_KMT2A_C2_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1309)

value: KMT2A-C2 Millipore cat# 05-765


title: RS411_H3K4me1_CUTnTag_(20200423_SH_Hs_R5411_K4me1E_0418)

description: Manual CUT&Tag for H3K4me1 in the RS4;11 KMT2Ar cell line

value: H3K4me1 Thermo cat# 710795


title: RS411_H3K36me3_CUTnTag_Rep2_(20200423_SH_Hs_R5411_H3K36me3T_0419)

description: Manual CUT&Tag for H3K36me3 in the RS4;11 KMT2Ar cell line

value: H3K36me3 Epicypher cat# 13-0031


title: RS411_H3K36me3_CUTnTag_Rep1_(20200423_SH_Hs_R5411_H3K36me3E_0419)


title: RS411_H3K27me3_CUTnTag_(20200423_SH_Hs_R5411_K27me3_0416)

description: Manual CUT&Tag for H3K27me3 in the RS4;11 KMT2Ar cell line


title: RS411_ENL_CUTnTag_(20200504_SH_Hs_RS411_MLL_ENL_0502)

description: Manual CUT&Tag for ENL in the RS4;11 KMT2Ar cell line


title: RS411_ELL_CUTnTag_(20200504_SH_Hs_RS411_ELL_0502)

description: Manual CUT&Tag for ELL in the RS4;11 KMT2Ar cell line


title: RS411_Dot1L_CUTnTag_(20200504_SH_Hs_RS411_Dot1_D4O_0502)

description: Manual CUT&Tag for Dot1L in the RS4;11 KMT2Ar cell line


title: MPAL2_KMT2A_N1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1353)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the MPAL-2 patient sample

value: sorted CD45+ cells from the MPAL-2 KMT2A-AF4 patient sample


title: MPAL2_KMT2A_N2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1354)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the MPAL-2 patient sample

value: KMT2A-N2 Cell Signaling Technologies cat# 14689S


title: SEM_KMT2A_C2_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1295)

description: Automated CUT&RUN for the KMT2A C-terminal region in the SEM KMT2Ar cell line


title: MPAL2_KMT2A_C2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1356)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL2_KMT2A_C1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1355)


title: MPAL2_IgG_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1352)

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the MPAL-2 patient sample


title: RS411_KMT2A_N2_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1307)

description: Automated CUT&RUN for the KMT2A N-terminal region in the RS4;11 KMT2Ar cell line


title: MPAL1_KMT2A_C2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1372)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the MPAL-1 patient sample

value: sorted CD45+ cells from the MPAL-1 KMT2A-AF9 patient sample


title: MPAL1_KMT2A_C1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1371)


title: MPAL1_KMT2A_N2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1370)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the MPAL-1 patient sample


title: MPAL1_IgG_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1368)

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the MPAL-1 patient sample


title: MPAL1_KMT2A_N1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1369)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the MPAL-1 patient sample


title: ML2_H3K9me3_CUTnTag_(20200423_SH_Hs_ML_2_K9me3_0419)

description: Manual CUT&Tag for H3K9me3 in the ML-2 KMT2Ar cell line

value: ML-2 KMT2A-AF6 AML cell line


title: ML2_H3K4me3_CUTnTag_(20200423_SH_Hs_ML_2_K4me3_0416)

description: Manual CUT&Tag for H3K4me3 in the ML-2 KMT2Ar cell line


title: ML2_H3K4me1_CUTnTag_(20200423_SH_Hs_ML_2_K4me1E_0418)

description: Manual CUT&Tag for H3K4me1 in the ML-2 KMT2Ar cell line


title: ML2_H3K36me3_CUTnTag_Rep1_(20200423_SH_Hs_ML_2_H3K36me3E_0419)

description: Manual CUT&Tag for H3K36me3 in the ML-2 KMT2Ar cell line


title: KOPN8_KMT2A_N1_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1313)

description: Automated CUT&RUN for the KMT2A N-terminal in the KOPN-8 KMT2Ar cell line

value: KOPN-8 KMT2A-ENL B-ALL cell line


title: KOPN8_KMT2A_C2_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1316)

description: Automated CUT&RUN for the KMT2A C-terminal region in the KOPN-8 KMT2Ar cell line


title: ML2_H3K27me3_CUTnTag_(20200423_SH_Hs_ML_2_K27me3_0416)

description: Manual CUT&Tag for H3K27me3 in the ML-2 KMT2Ar cell line

value: H3K27me3 Cell Signaling Technologies cat# 9733S


title: KOPN8_IgG_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1319)

description: Automated CUT&RUN for IgG control in the KOPN-8 KMT2Ar cell line


title: KOPN8_KMT2A_C1_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1315)

value: KMT2A-C1 Santa Cruz cat# sc-374392


title: KOPN8_H3K36me3_CUTnTag_Rep1_(20200423_SH_Hs_KOPN8_H3K36me3E_0419)

description: Manual CUT&Tag for H3K36me3 in the KOPN-8 KMT2Ar cell line


title: KOPN8_H3K4me1_CUTnTag_(20200423_SH_Hs_KOPN8_K4me1E_0418)

description: Manual CUT&Tag for H3K4me1 in the KOPN-8 KMT2Ar cell line


title: KOPN8_H3K9me3_CUTnTag_(20200423_SH_Hs_KOPN8_K9me3_0419)

description: Manual CUT&Tag for H3K9me3 in the KOPN-8 KMT2Ar cell line

value: H3K9me3 Abcam cat# ab8898


title: KOPN8_H3K36me3_CUTnTag_Rep2_(20200423_SH_Hs_KOPN8_H3K36me3T_0419)


title: KOPN8_H3K27me3_CUTnTag_(20200423_SH_Hs_KOPN8_K27me3_0416)

description: Manual CUT&Tag for H3K27me3 in the KOPN-8 KMT2Ar cell line


title: K562_H3K9me3_CUTnTag_(20200423_SH_Hs_K562_K9me3_0419)

description: Manual CUT&Tag for H3K9me3 in K562 cells

value: K562 human immortalized myelogenous leukemia cell line


title: K562_H3K4me3_CUTnTag_(20200511_SH_Hs_K5x_H3K4me3_0505)

description: Manual CUT&Tag for H3K4me3 in K562 cells

value: H3K4me3 Active Motif cat# 39159


title: K562_H3K4me1_CUTnTag_(20200511_SH_Hs_K5x_H3K4me1_0505)

description: Manual CUT&Tag for H3K4me1 in K562 cells


title: K562_H3K36me3_CUTnTag_(20200423_SH_Hs_K562_K36me3T_0419)

description: Manual CUT&Tag for H3K36me3 in K562 cells


title: K562_ENL_CUTnTag_Rep2_(20200511_SH_Hs_K5n_MLLENL_0505)

description: Manual CUT&Tag for ENL in K562 cells

value: MLLT3/ENL Cell Signaling Technologies cat# 14893S


title: K562_H3K27me3_CUTnTag_(20200423_SH_Hs_K562_K27me3_0416)

description: Manual CUT&Tag for H3K27me3 in K562 cells


title: K562_ENL_CUTnTag_Rep1_(20200511_SH_Hs_K5x_MLLENL_0505)

description: Manual CUT&Tag for ENL in K562 cells


title: K562_Dot1L_CUTnTag_Rep1_(20200511_SH_Hs_K5x_Dot1L_0505)

description: Manual CUT&Tag for Dot1L in K562 cells

value: Dot1L Cell Signaling Technologies cat# 90878S


title: ML2_H3K36me3_CUTnTag_Rep2_(20200423_SH_Hs_ML_2_H3K36me3T_0419)


title: AML2_KMT2A_N1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1361)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the AML-2 patient sample

value: KMT2A-N1 Millipore cat# 05-764

value: sorted CD45+ cells from the AML-2 KMT2A-ENL patient sample


title: K562_ELL_CUTnTag_Rep2_(20200511_SH_Hs_K5n_ELL_0505)

description: Manual CUT&Tag for ELL in K562 cells

value: ELL Cell Signaling Technologies cat# 14468S


title: K562_ELL_CUTnTag_Rep1_(20200511_SH_Hs_K5x_ELL_0505)

description: Manual CUT&Tag for ELL in K562 cells


title: KOPN8_KMT2A_N2_AutoCUTnRUN_(20200331_JS_HsEc_031020_JFS1314)

description: Automated CUT&RUN for the KMT2A N-terminal region in the KOPN-8 KMT2Ar cell line


title: AML1_KMT2A_N1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1345)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the AML-1 patient sample

value: sorted CD45+ cells from the AML-1 KMT2A-Sept6 patient sample


title: AML2_IgG_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1360)

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the AML-2 patient sample

value: IgG Abcam cat# ab46540


title: AML2_KMT2A_N2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1362)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the AML-2 patient sample


title: H1_KMT2A_N1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1339)

description: Automated CUT&RUN for the KMT2A N-terminal region in H1 hESCs

value: H1 human embryonic stem cells


title: AML1_KMT2A_C2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1348)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the AML-1 patient sample

value: KMT2A-C2 Millipore cat# 05-765


title: K562_Dot1L_CUTnTag_Rep2_(20200511_SH_Hs_K5n_Dot1L_0505)

description: Manual CUT&Tag for Dot1L in K562 cells


title: AML1_KMT2A_N2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1346)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the AML-1 patient sample

value: KMT2A-N2 Cell Signaling Technologies cat# 14689S


title: ALL1_KMT2A_C1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1379)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the ALL-1 patient sample

value: sorted CD45+ cells from the ALL-1 KMT2A-AF4 B-ALL patient sample


title: AML1_IgG_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1344)

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the AML-1 patient sample


title: AML1_KMT2A_C1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1347)


title: ALL1_KMT2A_N2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1378)

description: Automated CUT&RUN for the KMT2A N-terminal region in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_KMT2A_N1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1377)

description: Automated CUT&RUN for the KMT2A N-terminal in sorted CD45+ cells from the ALL-1 patient sample


title: SEM_H3K9me3_AutoCUTnTag_(20200313_DJ_Hs_K9m3_SE_0310)

description: Automated CUT&Tag for H3K9me3 in the SEM KMT2Ar cell line

extract_protocol:
AutoCUT&Tag_Protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: SEM KMT2A-AF4 B-ALL cell line


title: KOPN8_H3K4me3_CUTnTag_(20200423_SH_Hs_KOPN8_K4me3_0416)

description: Manual CUT&Tag for H3K4me3 in the KOPN-8 KMT2Ar cell line

value: KOPN-8 KMT2A-ENL B-ALL cell line


title: SEM_H3K4me3_AutoCUTnTag_(20200313_DJ_Hs_K4m3_SE_0310)

description: Automated CUT&Tag for H3K4me3 in the SEM KMT2Ar cell line


title: SEM_IgG_AutoCUTnTag_(20200313_DJ_Hs_IgG_SE_0310)

description: Automated CUT&Tag for IgG control in the SEM KMT2Ar cell line


title: SEM_H3K4me1_AutoCUTnTag_(20200313_DJ_Hs_K4m1_SE_0310)

description: Automated CUT&Tag for H3K4me1 in the SEM KMT2Ar cell line

value: H3K4me1 Thermo cat# 710795


title: SEM_H3K27me3_AutoCUTnTag_(20200313_DJ_Hs_K27m_SE_0310)

description: Automated CUT&Tag for H3K27me3 in the SEM KMT2Ar cell line

value: H3K27me3 Cell Signaling Technologies cat# 9733S


title: AML2_KMT2A_C2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1364)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the AML-2 patient sample


title: RS411_IgG_AutoCUTnTag_(20200313_DJ_Hs_IgG_RS_0310)

description: Automated CUT&Tag for IgG control in the RS4;11 KMT2Ar cell line

value: RS4;11 KMT2A-AF4 B-ALL cell line


title: AML2_KMT2A_C1_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1363)

value: KMT2A-C1 Santa Cruz cat# sc-374392


title: RS411_H3K9me3_AutoCUTnTag_(20200313_DJ_Hs_K9m3_RS_0310)

description: Automated CUT&Tag for H3K9me3 in the RS4;11 KMT2Ar cell line

value: H3K9me3 Abcam cat# ab8898


title: RS411_H3K4me1_AutoCUTnTag_(20200313_DJ_Hs_K4m1_RS_0310)

description: Automated CUT&Tag for H3K4me1 in the RS4;11 KMT2Ar cell line


title: RS411_H3K4me3_AutoCUTnTag_(20200313_DJ_Hs_K4m3_RS_0310)

description: Automated CUT&Tag for H3K4me3 in the RS4;11 KMT2Ar cell line

value: H3K4me3 Active Motif cat# 39159


title: RS411_H3K36me3_AutoCUTnTag_(20200313_DJ_Hs_K36m3_RS_0310)

description: Automated CUT&Tag for H3K36me3 in the RS4;11 KMT2Ar cell line

value: H3K36me3 Epicypher cat# 13-0031


title: MPAL2_IgG_AutoCUTnTag_Rep2_(20200528_DJ_Hs_IgG_A5_0520)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the MPAL-2 patient sample

value: sorted CD45+ cells from the MPAL-2 KMT2A-AF4 patient sample


title: ALL1_KMT2A_C2_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1380)

description: Automated CUT&RUN for the KMT2A C-terminal region in sorted CD45+ cells from the ALL-1 patient sample


title: RS411_H3K27me3_AutoCUTnTag_(20200313_DJ_Hs_K27m_RS_0310)

description: Automated CUT&Tag for H3K27me3 in the RS4;11 KMT2Ar cell line


title: MPAL2_H3K4me1_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m1_A5_0520)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL2_IgG_AutoCUTnTag_Rep1_(20200324_DJ_Hs_IgG_A5_0323)


title: MPAL2_H3K9me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K9m3_A5_0520)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL2_H3K4me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m3_A5_0323)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL2_H3K36me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K36m_A5_0323)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the MPAL-2 patient sample