title: shMCT-1, anti-IL6R, replicate 2

city: Zhunan

first: Hsin-Ling

last: Hsu

state: Miaoli

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

data_processing:
Data processing steps followed the MoTrPAC Consortium pipeline for RNA-seq
Raw FASTQ files were trimmed using Cutadapt v1.18. Trimmed reads shorter than 20 bp were removed.
Pre-alignment QC metrics were generated using FastQC
Alignment of trimmed reads to the mouse reference genome (mm10) was performed using STAR v2.7.0d
Filtering of low-expressed genes and normalization were performed using RSEM and edgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TMM for each sample

source_name: breast, mammary gland

growth_protocol: 4T1 scramble and shMCT-1 cells were regularly maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 6 µg/ml of puromycin

extract_protocol:
Total mRNA samples were isolated using Rneasy Mini Kit (Qiagen)
RNA-seq libraries were generated using Universal Plus mRNA-Seq Kit (NuGEN/Tecan) according to the manufacturer's instruction

treatment_protocol: Each group was treated with or without 100 ng/ml anti-mouse-IL6R for 48 h

value: breast, mammary gland

value: breast cancer cell line

value: MCT-1 knockdown


title: Rsc8-degron live cells, 180 min auxin, rep 1

status: Public on Mar 21 2024

type: SRA

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

country: USA

institute: NICHD, NIH

library_source: genomic

data_processing:
Paired-end data were aligned to yeast genome using Bowtie 2
bam files were analysed to obtain DNA fragment ends and coverage: "Cuts" and "Occupancy" files.
The 'fcut' ratio for each nucleotide in each chromosome was calculated as the fraction: no. of ends/coverage.
fcut data are provided here as .wig files
Assembly: SacCer3
Library strategy: qDA-seq (Chereji et al. (2019) Genome Research 29, 1985-1995)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Genomic DNA was purified from yeast cells by extracting proteins three times with SDS, washing out the SDS, then removing the cell wall using lytic enzyme. The DNA was purified by chloroform extraction and isopropanol precipitation and a 70% ethanol wash. The DNA was further purified using Beckman-Coulter Ampure beads at a 0.4:1 volume ratio.
Genomic DNA was digested with excess DpnI and sonicated to ~300 bp fragments. Paired-end libraries were prepared using the New England Biolabs kits and protocols.

tag: cell line

tag: cell type

value: strain

tag: genotype

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 rsc8-degron-3HA::LEU2 ho::TIR1-Dam-degron-3HA-KanMX


title: Rsc8-degron live cells, 0 min auxin, rep 1


title: MOLM13 CUT&Tag CEBPA 24h Combination replicate 3

city: Portland

first: William

middle: Montgomery

last: Yashar

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Knight Cancer Institute

institute: OHSU

description: CUT&Tag

data_processing:
Library strategy: CUT&Tag
Libraries were aligned to the human genome (hg38) using Bowtie2 and the following options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Peaks were called using GoPeaks and the following option -mdist 1000
CPM normalized tracks were generated with DeepTools
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential peaks were identified using DESeq2 with default parameters
Genome_build: hg38

organism: Homo sapiens

source_name: MOLM13 cell line

extract_protocol:
Libraries were prepared according to published protocol Kaya-Okur et al 2019
The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) performed the sequencing at 37 BP PE

tag: treatment

value: 1 nM quizartinib + 100 nM GSK2879552

tag: time point

value: 24 hours

tag: antibody

value: CEBPA (#8178, Cell Signaling Technologies)


title: shMCT-1, IgG, replicate 2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

value: IgG


title: shMCT-1, anti-IL6R, replicate 1


title: SR36_RF

city: Madison

first: Jack

last: Shireman

state: WI

address: 600 Highland Ave

institute: UW-Madison

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR36_RF

data_processing:
Alignment with STAR
Quantifiaction and normalization with RSEM
DE analysis with Deseq2
data visualization in R using standard packages
QC with Multi-QC
Assembly: HG38
Supplementary files format and content: .matrix
Supplementary files format and content: .csv

molecule: polyA RNA

source_name: Brain

extract_protocol:
extracted using Quiagen All Prep
Poly A tail RNA Seq library prep
Bulk RNA seq (done by novogene)

treatment_protocol: Stereotatic Radiation

value: Brain

value: Brain Metastases

value: SRS


title: SR35_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR35_PR


title: wild type live cells, 480 min auxin, 240 min SM, rep 2

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-Dam-degron-3HA-KanMX


title: shMCT-1, IgG, replicate 1


title: wild type live cells, 420 min auxin, 180 min SM, rep 2


title: MOLM13 CUT&Tag CEBPA 24h Combination replicate 1

description: CUT&Tag


title: scramble, anti-IL6R, replicate 2

value: negative control


title: SR35_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR35_CR


title: MOLM13 CUT&Tag CEBPA 24h GSK2879552 replicate 2

description: CUT&Tag


title: MOLM13 CUT&Tag IgG with CEBPA 24h DMSO replicate 1

description: CUT&Tag

value: DMSO

value: Normal Rabbit IgG (#2729, Cell Signaling Technologies)


title: wild type live cells, 360 min auxin, 120 min SM, rep 2


title: MOLM13 CUT&Tag CEBPA 24h Combination replicate 2

description: CUT&Tag


title: Rsc8-degron live cells, 240 min auxin, 0 min SM, rep 1


title: SR34_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR34_PR


title: MOLM13 CUT&Tag CEBPA 24h GSK2879552 replicate 1

description: CUT&Tag


title: SR34_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR34_CR


title: scramble, IgG, replicate 1


title: wild type live cells, 300 min auxin, 60 min SM, rep 2


title: MOLM13 CUT&Tag CEBPA 24h Quizartinib replicate 2

description: CUT&Tag

value: 1 nM quizartinib


title: MOLM13 CUT&Tag CEBPA 24h Quizartinib replicate 3

description: CUT&Tag


title: wild type live cells, 270 min auxin, 30 min SM, rep 2


title: scramble, anti-IL6R, replicate 1

value: breast, mammary gland


title: scramble, IgG, replicate 2

value: breast cancer cell line


title: SR32_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR32_CR


title: MOLM13 CUT&Tag CEBPA 24h Quizartinib replicate 1

description: CUT&Tag


title: LepR+ Pressfit Bone [Sample_XY.9274_Press.Fit.Lepr.Pos.2]

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
Detailed pipeline description and parametrization is available at https://gitlab.com/hssgenomics/pipelines/-/tree/master/RNAseq . Briefly, Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to thehuman genome (hg38) and reads in exons were counted against Gencode with STAR2.6 Aligner. Differential gene expression analysis was performed in R using edgeR. Genes with low expression levels (<3 counts per million in at least one group) were filtered from all downstream analyses. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an FDR-corrected pvalue less than 0.05 were considered differentially expressed. Downstream analyses were performed in R using a visualization platform built with Shiny developed by bioinformaticians at the David Z. Rosensweig Genomics Research Center at HSS
Assembly: mm10
Supplementary files format and content: comma separated text files of counts for each sample

source_name: Pressfit

extract_protocol: LEPR+ cells obtained from peri-implant bone or fibrous tissue from mouse undergoing tibia implantation. Single cells were obtained, stained for Flow cytometry antibodies and FACS was conducted to sort the desired cell types. RNA sample were prepared using the RNAeasy Plust Micro Kit Cat no 74034. cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced on NovaSeq 6000 sequencer

value: Pressfit

value: Bone


title: LepR+ Pressfit Bone [Sample_XY.9274_Press.Fit.Lepr.Pos.1]


title: wild type live cells, 0 min auxin, rep 2

value: strain


title: SR30_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR30_CR


title: SR31_CR2

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR31_CR2


title: MOLM13 CUT&Tag CEBPA 24h DMSO replicate 2

description: CUT&Tag


title: LepR+ PMMA Fibrotic [Sample_XY.9274_PMMA.Lepr.Pos.4]

source_name: PMMA

value: PMMA

value: Fibrous


title: SR30_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR30_PR


title: wild type live cells, 180 min auxin, rep 2


title: MOLM13 CUT&Tag CEBPA 24h DMSO replicate 3

description: CUT&Tag

value: 24 hours

value: CEBPA (#8178, Cell Signaling Technologies)


title: MOLM13 CUT&Tag CEBPA 24h DMSO replicate 1

description: CUT&Tag


title: LepR+ PMMA Fibrotic [Sample_XY.9274_PMMA.Lepr.Pos.5]


title: MOLM13 CUT&Tag CEBPA 24h GSK2879552 replicate 3

description: CUT&Tag


title: SR29_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR29_CR

value: Brain


title: wild type live cells, 240 min auxin, 0 min SM, rep 2


title: MOLM13 CUT&Tag H3K9Ac 6h Combination replicate 3

description: CUT&Tag@home

data_processing:
Library strategy: CUT&Tag@home
Libraries were aligned to the human genome (hg38) using Bowtie2 and the following options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Peaks were called using GoPeaks and the following option -mdist 1000
CPM normalized tracks were generated with DeepTools
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential peaks were identified using DESeq2 with default parameters
Genome_build: hg38

extract_protocol:
Libraries were prepared according to published protocol Henikoff et al 2020
The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) performed the sequencing at 37 BP PE

value: 1 nM quizartinib + 100 nM GSK2879552

value: 6 hours

value: H3K9Ac (#C15410004, diagenode)


title: wild type live cells, 480 min auxin, 240 min SM, rep 1

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-Dam-degron-3HA-KanMX


title: wild type live cells, 420 min auxin, 180 min SM, rep 1


title: LepR+ PMMA Fibrotic [Sample_Lin.A_L002]


title: LepR+ Pressfit Bone [Sample_Lin.4_L002]


title: SR28_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR28_PR

value: Brain Metastases

value: SRS


title: wild type live cells, 300 min auxin, 60 min SM, rep 1


title: wild type live cells, 360 min auxin, 120 min SM, rep 1


title: SR29_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR29_PR


title: SR28_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR28_CR


title: SR26_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR26_PR


title: MOLM13 CUT&Tag H3K9Ac 6h Combination replicate 2

description: CUT&Tag@home


title: LepR+ PMMA Fibrotic [Sample_LepR.plus.C_L002]


title: LepR+ Pressfit Bone [Sample_Lin.3_L002]


title: wild type live cells, 270 min auxin, 30 min SM, rep 1


title: MOLM13 CUT&Tag H3K9Ac 6h Combination replicate 1

description: CUT&Tag@home


title: MOLM13 CUT&Tag H3K9Ac 6h GSK2879552 replicate 3

description: CUT&Tag@home


title: LepR+ PMMA Fibrotic [Sample_LepR.plus.B_L002]


title: SR26_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR26_CR


title: LepR+ PMMA Fibrotic [Sample_LepR.plus.A_L002]


title: SR25_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR25_PR


title: wild type live cells, 240 min auxin, 0 min SM, rep 1


title: MOLM13 CUT&Tag H3K9Ac 6h GSK2879552 replicate 1

description: CUT&Tag@home


title: LepR+ PMMA Fibrotic [Sample_D._L002]


title: SR25_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR25_CR


title: wild type live cells, 0 min auxin, rep 1


title: LepR+ Pressfit Bone [Sample_2.plus_L002]


title: wild type live cells, Dam-GFP, 240 min SM, rep 2

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-Dam-degron-GFP-3HA-KanMX


title: MOLM13 CUT&Tag H3K9Ac 6h Quizartinib replicate 1

description: CUT&Tag@home

value: 1 nM quizartinib


title: MOLM13 CUT&Tag H3K9Ac 6h Quizartinib replicate 2

description: CUT&Tag@home


title: wild type live cells, Dam-GFP, 120 min SM, rep 2


title: SR23_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR23_PR


title: Primary myotubes, 48hrs, OSM, rep2

city: Sarıyer

first: Samet

last: Agca

state: İstanbul

address: Rumelifeneri Yolu

department: Graduate School of Sciences and Engineering

country: Turkey

institute: Koc University

data_processing:
The quality check of the raw and  trimmed data was performed with FastQC (v.0.11.9) and MultiQC (v1.12).
Adaptor sequences and poor-quality sequences were removed with trimGalore (v0.6.5).
Trimmed sequences was mapped onto this index using STAR (v2.7.3a) alignReads run mode.
Alignments were quantified using HTSeq-count (v0.11.1) Python package.
Differential gene expression analysis was done with R Studio (v2021.09.2+382) and DESeq2 (v1.34.0) R package.
Assembly: GRCm39 (mm39)
Supplementary files format and content: tab-delimited text files include count values for each sample
Supplementary files format and content: Normalized_gene_counts.xlsx file include normalized gene counts for each sample
Supplementary files format and content: Significant Gene Lists_padj_0.05.xlsx file include significantly differential expressed genes in each condition with respect to control

source_name: primary myotubes

growth_protocol: Mouse primary myoblasts were isolated from limb muscles of pups (2-3 days old) and cultured in Ham’s F-10 nutrient mixture (Invitrogen) with 20% FBS (Invitrogen) supplemented with 2.5 ng/ml basic fibroblast growth factor (bFGF) (Sigma) and penicillin/streptomycin (Invitrogen). Myoblasts were then transferred to DMEM (Sigma 5796) supplemented with 5% horse serum and penicillin/streptomycin (Invitrogen) for differentiation.

extract_protocol:
Cells were harvested 72hrs after differentiation. Total RNA was isolated and DNase-treated using Qiazol reagent (Qiagen) and Direct-zol RNA MiniPrep kit (Zymo Research).
Samples were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Differentiated mouse primary myotubes were treated with OSM, LIF or IL6 for 48 hr (250 ng/ml each)

value: primary myotubes

value: WT

value: OSM


title: Primary myotubes, 48hrs, LIF, rep2

value: LIF


title: MOLM13 CUT&Tag H3K9Ac 6h GSK2879552 replicate 2

description: CUT&Tag@home


title: wild type live cells, Dam-GFP, 0 min SM, rep 2

value: strain


title: wild type live cells, Dam-GFP, 60 min SM, rep 2


title: SR21_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR21_PR


title: MOLM13 CUT&Tag H3K9Ac 6h DMSO replicate 2

description: CUT&Tag@home

value: DMSO


title: MOLM13 CUT&Tag H3K9Ac 6h DMSO replicate 3

description: CUT&Tag@home


title: SR21_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR21_CR


title: MOLM13 CUT&Tag H3K9Ac 6h DMSO replicate 1

description: CUT&Tag@home


title: Primary myotubes, 48hrs, LIF, rep1


title: wild type live cells, Dam-GFP, 240 min SM, rep 1


title: SR20_RF

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR20_RF


title: MOLM13 CUT&Tag H3K9Ac 6h Quizartinib replicate 3

description: CUT&Tag@home


title: LepR+ Pressfit Bone [Sample_LepR.plus.4_L002]

value: Pressfit

value: Bone


title: SR24_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR24_CR

value: Brain


title: Primary myotubes, 48hrs, OSM, rep1


title: Primary myotubes, 48hrs, IL6, rep2


title: MOLM13 CUT&Tag H3K9me1 6h Combination replicate 3

description: CUT&Tag@home

value: 1 nM quizartinib + 100 nM GSK2879552


title: wild type live cells, Dam-GFP, 120 min SM, rep 1


title: SR23_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR23_CR


title: wild type live cells, 180 min auxin, rep 1


title: SR19CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR19CR


title: wild type live cells, Dam-GFP, 30 min SM, rep 2


title: SR18_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR18_PR


title: MOLM13 CUT&Tag H3K9me1 6h Combination replicate 1

description: CUT&Tag@home

value: 6 hours


title: MOLM13 CUT&Tag H3K9me1 6h Combination replicate 2

description: CUT&Tag@home


title: wild type live cells, Dam-GFP, 30 min SM, rep 1


title: SR18_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR18_CR


title: Primary myotubes, 48hrs, Control, rep2

value: Control


title: wild type live cells, Dam-GFP, 0 min SM, rep 1


title: MOLM13 CUT&Tag H3K9me1 6h GSK2879552 replicate 2

description: CUT&Tag@home


title: SR17_RF

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR17_RF


title: Primary myotubes, 48hrs, Control, rep1


title: MOLM13 CUT&Tag H3K9me1 6h GSK2879552 replicate 3

description: CUT&Tag@home


title: SR16_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR16_PR


title: arrested wild type live cells, 420 min alpha-factor, 240 min SM, rep 2

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-Dam-degron-3HA-KanMX


title: MOLM13 CUT&Tag H3K9me1 6h GSK2879552 replicate 1

description: CUT&Tag@home


title: SR16_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR16_CR

value: Brain Metastases


title: arrested wild type live cells, 300 min alpha-factor, 180 min SM, rep 2


title: MOLM13 CUT&Tag H3K9me1 6h Quizartinib replicate 3

description: CUT&Tag@home


title: Primary myotubes, 48hrs, IL6, rep1


title: P0 Six2TGC; Tsc1-2

city: Cincinnati

first: Alison

middle: Jarmas

last: Perl

state: Ohio

address: 3333 Burnet Ave.

institute: CCHMC

data_processing:
BAM files utilized for BAC integration analysis were initially mapped to the mm10 reference genome by bwa (version: 0.7.17-r1188) with parameters “bwa mem -SP5M” and samblaster (v0.1.25) to mark the PCR duplicated reads.
Hi-C library sequencing reads were processed with Juicer (v1.5.7). Only high-quality reads (MAPQ>30 with both ends uniquely mapped and no PCR duplication) were utilized for the analysis.
Assembly: mm10
Supplementary files format and content: .hiC

source_name: Nephron progenitor cells

extract_protocol:
Isolated kidneys were digested with 2.5 mg/ml collagenase D at 37 degrees celsius for 20-25 minutes. NPCs were sorted by FACS (Sony SH800S) on the basis of GFP-positivity.
Libraries were prepared using Arima-HiC Kit, low input protocol (Arima Genomics) and Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences). Libraries were pooled into a single sample and sequenced on an Illumina NovaSeq 6000 using 150bp paired-end sequencing.

value: Nephron progenitor cells

tag: strain

value: Six2TGC; Tsc1

tag: age


title: P0 Six2TGC; Tsc1-1


title: SR15_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR15_PR

value: SRS


title: P0 Six2TGC-3


title: arrested wild type live cells, 210 min alpha-factor, 30 min SM, rep 2


title: SR15_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR15_CR


title: MOLM13 CUT&Tag H3K9me1 6h Quizartinib replicate 1

description: CUT&Tag@home

value: 1 nM quizartinib


title: arrested wild type live cells, 240 min alpha-factor, 60 min SM, rep 2


title: wild type live cells, Dam-GFP, 60 min SM, rep 1

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-Dam-degron-GFP-3HA-KanMX


title: P0 Six2TGC-2


title: arrested wild type live cells, 180 min alpha-factor, 0 min SM, rep 2


title: MOLM13 CUT&Tag H3K9me1 6h Quizartinib replicate 2

description: CUT&Tag@home


title: SR14_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR14_PR


title: SR14_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR14_CR


title: P0 Six2TGC; Tsc1-3


title: MOLM13 CUT&Tag H3K9me1 6h DMSO replicate 3

description: CUT&Tag@home


title: P0 Six2TGC-1


title: arrested wild type live cells, 0 min alpha-factor, rep 2


title: P0 Cited1-3


title: MOLM13 CUT&Tag H3K9me1 6h DMSO replicate 2

description: CUT&Tag@home


title: SR12_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR12_PR


title: P0 Cited1-2


title: SR12_CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR12_CR


title: MOLM13 CUT&Tag H3K9me1 6h DMSO replicate 1

description: CUT&Tag@home


title: arrested wild type live cells, 300 min alpha-factor, 180 min SM, rep 1


title: arrested wild type live cells, 420 min alpha-factor, 240 min SM, rep 1


title: MOLM13 CUT&Tag IgG 6h Combination replicate 3

description: CUT&Tag

value: Normal Rabbit IgG (#2729, Cell Signaling Technologies)


title: arrested wild type live cells, 240 min alpha-factor, 60 min SM, rep 1


title: P0 Cited1-1


title: D7, multiplex

city: Chapel Hill

first: Li

last: Qian

state: North Carolina

address: 111 Mason Farm Road, MBRB

department: Department of Pathology

institute: UNC

description:
10x Genomics
D7_barcodes.tsv.gz
D7_features.tsv.gz
D7_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
After sequencing, bcl2fastq ver 2.20.0 was used to create fastq files.
CellRanger multi was then used to identify cells specific to each condition and create gene expression matrices using the CellPlex CMOs (control #307, Etv2 #308, Sox17-Erg #309)
Data was further processed and analyzed using Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

growth_protocol: EGM2 Media

extract_protocol:
10x Genomics
Cells were detached from cell culture plates with accutase.  Then labeled with CellPlex Oligos (control #307, Etv2 #308, Sox17-Erg #309) following CellPlex standard protocol).  Libraries of cellplex labeled cells were then constructed using standard 10X Genomics 3' Reagent Kit v3.1
scRNAseq with 3' CellPlex

value: heart

value: iEC


title: SR11CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR11CR


title: SR08_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR08_PR


title: arrested wild type live cells, 210 min alpha-factor, 30 min SM, rep 1

value: strain


title: MOLM13 CUT&Tag IgG 6h Combination replicate 2

description: CUT&Tag


title: MOLM13 CUT&Tag IgG 6h Combination replicate 1

description: CUT&Tag


title: SR7PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR7PR


title: D7, gene, expression


title: arrested wild type live cells, 180 min alpha-factor, 0 min SM, rep 1


title: arrested wild type live cells, 0 min alpha-factor, rep 1


title: MOLM13 CUT&Tag IgG 6h GSK2879552 replicate 2

description: CUT&Tag


title: SR7CR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR7CR


title: MOLM13 CUT&Tag IgG 6h GSK2879552 replicate 3

description: CUT&Tag


title: D3, gene, expression

description:
10x Genomics
D3_barcodes.tsv.gz
D3_features.tsv.gz
D3_matrix.mtx.gz


title: se, w4, rep2

description:
Kapa mRNA, Stranded
SE_4W_R3_GAACCGCG-TGACCTTA_S12

data_processing:
Reads were demulitplexed using  bcl2fastq ver 2.20.0
High GC content was trimmed using BBDuk
Transcript expression was quantified using Salmon
DESeq2 was used to compare gene expression between conditions at each timepoint
Assembly: mm10
Supplementary files format and content: csv file of DESeq2 counts of all samples

growth_protocol: EGM2 media

extract_protocol:
Trizol Extraction
Kapa mRNA, Stranded

tag: time

value: Week 4


title: wild type live cells, 240 min SM, rep 2


title: D3, mulitplex


title: MOLM13 CUT&Tag IgG 6h GSK2879552 replicate 1

description: CUT&Tag


title: MOLM13 CUT&Tag IgG 6h Quizartinib replicate 3

description: CUT&Tag


title: SR05_PR

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
SR05_PR


title: NU00913

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
NU00913


title: NU01164

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
NU01164


title: MOLM13 CUT&Tag IgG 6h Quizartinib replicate 2

description: CUT&Tag


title: se, d7, rep2

description:
Kapa mRNA, Stranded
SE_D7_R3_CGCTATGT-TCCGACAC_S18

value: Day 7


title: wild type live cells, 60 min SM, rep 2


title: NU00890

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
NU00890

value: Brain


title: wild type live cells, 30 min SM, rep 2


title: se, w4, rep1

description:
Kapa mRNA, Stranded
SE_4W_R2_TCATCCTT-AGCGAGCT_S11


title: se, d7, rep1

description:
Kapa mRNA, Stranded
SE_D7_R2_GTGAATAT-TCTCATTC_S17


title: MOLM13 CUT&Tag IgG 6h Quizartinib replicate 1

description: CUT&Tag


title: NU00617

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
NU00617


title: wild type live cells, 0 min SM, rep 2


title: MOLM13 CUT&Tag IgG 6h DMSO replicate 3

description: CUT&Tag

value: DMSO


title: se, d3, rep2

description:
Kapa mRNA, Stranded
SE_D3_R3_TCTGTTGG-TCGAATGG_S15

value: Day 3


title: wild type live cells, 240 min SM, rep 1


title: MOLM13 CUT&Tag IgG 6h DMSO replicate 2

description: CUT&Tag

value: 6 hours


title: NU00570

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
NU00570


title: wild type live cells, 120 min SM, rep 1

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-Dam-degron-3HA-KanMX


title: control, w4, rep2

description:
Kapa mRNA, Stranded
PMX_4W_R3_AGGTTATA-CAGTTCCG_S3

value: fibroblast


title: wild type live cells, 120 min SM, rep 2


title: wild type live cells, 30 min SM, rep 1


title: MOLM13 CUT&Tag RBP1 6h Combination replicate 3

description: CUT&Tag

value: 1 nM quizartinib + 100 nM GSK2879552

value: RBP1 (#2629, Cell Signaling Technologies)


title: control, w4, rep1

description:
Kapa mRNA, Stranded
PMX_4W_R2_CTGCTTCC-GATAGATC_S2


title: MOLM13 CUT&Tag RBP1 6h Combination replicate 2

description: CUT&Tag


title: SJ049_VEN

city: Memphis

first: Jun

last: Yang

state: TN

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

description: 10x Genomics

data_processing:
Sequencing data were run on Cell Ranger multi version 7.0.0 to generate feature barcode matrices and information for clustering and gene expression.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
PDX cells from individual treated and untreated mice were fixed separately using the 10X Genomics CG000478 Demonstrated Protocol Cell & Nuclei Fixation Chromium Fixed RNA Profiling Rev B. After fixation, individual samples were counted and target genes were barcoded with unique sample barcodes during probe hybridization. Uniquely barcoded samples were counted using Trypan Blue stain and then pooled in equal numbers following 10X Genomics CG000565 Chromium Fixed RNA Profiling Multiplexed Samples Pooling Workbook Rev B. Pooled cells were washed and 8000 cells were targeted from each sample to be partitioned into GEMS on Chip Q using the 10X Genomics Chromium Chromium Fixed RNA Profiling kit. Partitioned cells underwent barcoding, reverse transcription, cDNA amplification and sample index ligation following the 10X Genomics CG000527 Chromium Fixed RNA Profiling Mouse/Human Chimera Isolation kit (Stemcell Technologies, 19849)
Libraries were prepared following 10x Single Cell Gene Expression Flex Fixed RNA Profiling (FRP) protocol and sequenced on Illumina NovaSeq 6000 149 system  (Illumina).
The Single Cell Gene Expression Flex Fixed RNA Profiling (FRP)

value: spleen

value: human leukemia PDX cells

value: venetoclax


title: SJ049_COM

description: 10x Genomics

value: L-asparaginase + venetoclax


title: control, d7, rep2

description:
Kapa mRNA, Stranded
PMX_D7_R3_TATCGCAC-CTTAGTGT_S9

value: heart


title: MOLM13 ChIP-seq STAT5 24h Combination replicate 2

description: ChIP-seq

data_processing:
Libraries were aligned to the human genome (hg38) using Bowtie2 and the following options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Peaks were called using GoPeaks and the following option -mdist 1000
CPM normalized tracks were generated with DeepTools
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential peaks were identified using DESeq2 with default parameters
Genome_build: hg38

extract_protocol:
Libraries were prepared using the SimpleChIP plus Enzymatic Chromatin IP Kit (Cell Signaling Technology)
Genewiz performed the sequencing using a HiSeqX at 150 BP PE

value: 24 hours

value: STAT5 (#94205S, Cell Signaling Technology)


title: wild type live cells, 0 min SM, rep 1

value: strain


title: MOLM13 CUT&Tag RBP1 6h Combination replicate 1

description: CUT&Tag


title: NU00612

description:
both peripheral and center samples included  if available CR= center PR = Peripheral FR= undetermined
NU00612

value: Brain Metastases

value: SRS


title: se, d3, rep1

description:
Kapa mRNA, Stranded
SE_D3_R2_GGTCACGA-GTATTATG_S14

value: iEC


title: control, d7, rep1

description:
Kapa mRNA, Stranded
PMX_D7_R2_ACAGGCGC-CTCTGCCT_S8

value: Day 7


title: SJ049_CTRL

description: 10x Genomics

value: control


title: control, d3, rep2

description:
Kapa mRNA, Stranded
PMX_D3_R3_CTCACCAA-CTAGGCAA_S6

value: Day 3


title: LPS Replicate 4

city: Mainz

first: Wolfram

last: Ruf

address: Langenbeckstrasse 1

country: Germany

institute: CTH Mainz

data_processing:
Reads were mapped to GRCh38 hg38 with star on the fly
Assembly: GRCh38 - hg38
Supplementary files format and content: Tab delimited text file

source_name: MM1 cells

growth_protocol: MM1 cells were cultured in RPMI, 10% FCS, at 37°C with 5% CO2.

extract_protocol:
Trizol protocol
Illumina TruSeq stranded mRNA library prep kit

treatment_protocol: stimulation for 1 hour

value: MM1 cells

value: LPS


title: control, d3, rep1

description:
Kapa mRNA, Stranded
PMX_D3_R2_AACTGTAG-ACGCCGCA_S5

value: fibroblast


title: MOLM13 CUT&Tag RBP1 6h GSK2879552 replicate 3

description: CUT&Tag

value: 6 hours

value: RBP1 (#2629, Cell Signaling Technologies)


title: HL7G and NAPc2 Replicate 4

value: HL7G and NAPc2


title: MOLM13 ChIP-seq STAT5 24h GSK2879552 replicate 2

description: ChIP-seq


title: MOLM13 CUT&Tag RBP1 6h GSK2879552 replicate 1

description: CUT&Tag


title: MOLM13 CUT&Tag B173 DMSO replicate 1

description: CUT&Tag

value: DMSO

value: Normal Rabbit IgG (#2729, Cell Signaling Technologies)


title: MOLM13 ChIP-seq STAT5 24h GSK2879552 replicate 1

description: ChIP-seq

value: 24 hours


title: wild type live cells, 60 min SM, rep 1

value: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-Dam-degron-3HA-KanMX


title: Unstimm Replicate 4

value: Unstimm


title: MOLM13 CUT&Tag RBP1 6h Quizartinib replicate 3

description: CUT&Tag

value: 1 nM quizartinib


title: batch2_H3K36me3_Fus_P423L_rep1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameters ‘-q 20 --paired’.
Trimmed reads were uniquely mapped to the mouse reference genome (mm9) using Bowtie2 (Langdon, 2015) (version 2.4.2).
Peaks were identified using MACS2 (Zhang et al., 2008) (version 2.2.7.1) with the parameters ‘–nomodel -f BAMPE -g mm’. For H3K27me3 and H3K36me3 modifications, parameter ‘--broad’ was added.
Genome coverage bigwig files were generated by BEDtools (Quinlan, 2014) (version 3.5.0) genomecov and bedGraphToBigWig (version 4) (https://www.encodeproject.org/software/bedgraphtobigwig/) with the parameter ‘-scale 10,000,000/mapped_reads_number’.
Assembly: mm9
Supplementary files format and content: BigWig files
Library strategy: CUT&Tag

extract_protocol:
105 cells were collected in NE buffer (20 mM HEPES pH 7.5, 0.5 mM spermidine, 10 mM KCl, 0.1% TritonX-100, 10% Glycerol, and 1 mM PMSF) and kept on ice for 10 min.
10 µl ConA beads which were pre-washed by binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) were added to each sample and incubated at room temperature for 10 min. After being washed with washing buffer (20 mM HEPES pH 7.5, 0.5 mM spermidine, 150 mM NaCl, and 0.1% BSA) once, beads were incubated with blocking buffer (20 mM HEPES pH 7.5, 0.5 mM spermidine, 150 mM NaCl, 0.1% BSA, and 2 mM EDTA) at room temperature for 5 min. Samples were incubated with diluted primary antibodies (1:100 dilution in washing buffer) at room temperature for 2 h. After washing with washing buffer once, secondary antibodies were added at a 1:100 dilution and incubated at room temperature for 30 min. PA-Tn5 transposons were then added and incubated at room temperature for 30 min. Beads were washed with washing buffer twice and incubated with 10 mM MgCl2 in washing buffer at 37 °C for 1h. The 30 μl tagmentation reaction was stopped by adding 2.25 μl 0.5 M EDTA, 2.75 μl 10% SDS, and 0.5 μl 20 mg/ml Proteinase K and incubated at 55 °C for 30 min, and then 70 °C for 20 min. DNA was purified by 0.9X of VAHTS DNA clean beads (VAHTS, Cat. #N411-03).

value: Embryonic stem cells

value: Fus P423L


title: IgG Replicate 4

value: IgG


title: SJ049_ASP

description: 10x Genomics

value: spleen

value: human leukemia PDX cells

value: L-asparaginase


title: MOLM13 ChIP-seq STAT5 24h Quizartinib replicate 2

description: ChIP-seq

value: STAT5 (#94205S, Cell Signaling Technology)


title: HL5B Replicate 4

value: MM1 cells


title: batch2_H3K36me3_WT_rep2

value: WT


title: MOLM13 CUT&Tag RBP1 6h Quizartinib replicate 2

description: CUT&Tag

value: 6 hours

value: RBP1 (#2629, Cell Signaling Technologies)


title: NAPc2 Replicate 4


title: batch2_H3K36me3_WT_rep1


title: MOLM13 ChIP-seq STAT5 24h Combination replicate 1

description: ChIP-seq

value: 1 nM quizartinib + 100 nM GSK2879552


title: MOLM13 CUT&Tag RBP1 6h Quizartinib replicate 1

description: CUT&Tag


title: MOLM13 CUT&Tag RBP1 6h DMSO replicate 3

description: CUT&Tag

value: DMSO


title: MOLM13 ChIP-seq STAT5 24h DMSO replicate 1

description: ChIP-seq

value: 24 hours


title: HL7G Replicate 4


title: MOLM13 ChIP-seq IgG 24h Combination replicate 2

description: ChIP-seq

value: Normal Rabbit IgG (#2729, Cell Signaling Technologies)


title: MOLM13 CUT&Tag RBP1 6h DMSO replicate 1

description: CUT&Tag


title: HL5B and NAPc2 Replicate 4

value: HL5B and NAPc2


title: batch2_Fus_WT_rep2


title: MOLM13 CUT&Tag RBP1 6h DMSO replicate 2

description: CUT&Tag


title: MOLM13 ChIP-seq IgG 24h Combination replicate 1

description: ChIP-seq


title: batch2_H3K36me3_Fus_P423L_rep2


title: batch2_Fus_Fus_P423L_rep1


title: LPS Replicate 3

value: LPS


title: batch2_Fus_WT_rep1

value: Embryonic stem cells


title: MOLM13 CUT&Tag H3K4me3 6h Combination replicate 3

description: CUT&Tag

value: H3K4me3 (#9751, Cell Signaling Technologies)


title: HL7G and NAPc2 Replicate 3

value: HL7G and NAPc2


title: batch1_H3K36me3_WT_rep2


title: MOLM13 ChIP-seq STAT5 24h Quizartinib replicate 1

description: ChIP-seq

value: 1 nM quizartinib


title: MOLM13 ChIP-seq IgG 24h GSK2879552 replicate 1

description: ChIP-seq


title: MOLM13 CUT&Tag H3K4me3 6h Combination replicate 1

description: CUT&Tag


title: MOLM13 CUT&Tag H3K4me3 6h Combination replicate 2

description: CUT&Tag


title: MOLM13 ChIP-seq IgG 24h GSK2879552 replicate 2

description: ChIP-seq


title: batch1_H3K36me3_WT_rep1


title: MOLM13 ChIP-seq STAT5 24h DMSO replicate 2

description: ChIP-seq


title: batch1_H3K36me3_Setd2_KO2_rep2

value: Setd2 KO


title: Unstimm Replicate 3

value: Unstimm


title: MOLM13 CUT&Tag H3K4me3 6h GSK2879552 replicate 3

description: CUT&Tag


title: IgG Replicate 3

value: IgG


title: MOLM13 ChIP-seq IgG 24h Quizartinib replicate 2

description: ChIP-seq


title: MOLM13 ChIP-seq IgG 24h Quizartinib replicate 1

description: ChIP-seq


title: HL5B Replicate 3

value: MM1 cells


title: MOLM13 CUT&Tag H3K4me3 6h GSK2879552 replicate 2

description: CUT&Tag


title: MOLM13 CUT&Tag RBP1 6h GSK2879552 replicate 2

description: CUT&Tag


title: MOLM13 CUT&Tag H3K4me3 6h GSK2879552 replicate 1

description: CUT&Tag


title: NAPc2 Replicate 3


title: MOLM13 ChIP-seq IgG 24h DMSO replicate 1

description: ChIP-seq


title: batch1_H3K36me3_Setd2_KO1_rep2


title: HL7G Replicate 3


title: batch1_H3K36me3_Setd2_KO2_rep1


title: MOLM13 CUT&Tag H3K4me3 6h Quizartinib replicate 3

description: CUT&Tag


title: HL5B and NAPc2 Replicate 3


title: MOLM13 ChIP-seq RUNX1 24h Combination replicate 2

description: ChIP-seq

value: RUNX1 (ab23980, Abcam)


title: batch1_H3K36me3_Setd2_KO1_rep1


title: LPS Replicate 2


title: batch1_H3K36me3_Fus_KO2_rep2

value: Fus KO


title: MOLM13 ChIP-seq IgG 24h DMSO replicate 2

description: ChIP-seq


title: MOLM13 ChIP-seq RUNX1 24h Combination replicate 1

description: ChIP-seq


title: MOLM13 ChIP-seq RUNX1 24h GSK2879552 replicate 2

description: ChIP-seq


title: batch1_H3K36me3_Fus_KO2_rep1


title: HL7G and NAPc2 Replicate 2


title: MOLM13 ChIP-seq RUNX1 24h GSK2879552 replicate 1

description: ChIP-seq


title: Unstimm Replicate 2


title: MOLM13 CUT&Tag H3K4me3 6h DMSO replicate 2

description: CUT&Tag

value: 6 hours


title: MOLM13 CUT&Tag H3K4me3 6h DMSO replicate 3

description: CUT&Tag


title: batch1_H3K36me3_Fus_KO1_rep1


title: IgG Replicate 2


title: MOLM13 ChIP-seq RUNX1 24h Quizartinib replicate 2

description: ChIP-seq


title: batch1_H3K27me3_WT_rep2

value: WT


title: HL5B Replicate 2


title: MOLM13 ChIP-seq RUNX1 24h Quizartinib replicate 1

description: ChIP-seq


title: MOLM13 CUT&Tag H3K4me3 6h DMSO replicate 1

description: CUT&Tag

value: DMSO


title: MOLM13 CUT&Tag H3K4me1 6h Combination replicate 3

description: CUT&Tag

value: 1 nM quizartinib + 100 nM GSK2879552

value: H3K4me1 (#5326, Cell Signaling Technologies)


title: batch1_H3K27me3_WT_rep1


title: MOLM13 CUT&Tag H3K4me1 6h Combination replicate 2

description: CUT&Tag


title: batch1_H3K27me3_Setd2_KO2_rep2


title: MOLM13 ChIP-seq RUNX1 24h DMSO replicate 2

description: ChIP-seq

value: 24 hours


title: MOLM13 ChIP-seq RUNX1 24h DMSO replicate 1

description: ChIP-seq


title: MOLM13 CUT&Tag H3K4me1 6h Combination replicate 1

description: CUT&Tag


title: HL5B and NAPc2 Replicate 2

value: HL5B and NAPc2


title: MOLM13 CUT&Tag H3K4me3 6h Quizartinib replicate 1

description: CUT&Tag


title: batch2_Fus_Fus_P423L_rep2

value: Embryonic stem cells

value: Fus P423L


title: HL7G Replicate 2


title: batch1_H3K36me3_Fus_KO1_rep2


title: batch1_H3K27me3_Setd2_KO2_rep1


title: MOLM13 CUT&Tag H3K4me3 6h Quizartinib replicate 2

description: CUT&Tag

value: H3K4me3 (#9751, Cell Signaling Technologies)


title: LPS Replicate 1

value: LPS


title: batch1_H3K27me3_Setd2_KO1_rep2

value: Setd2 KO


title: MOLM13 ChIP-seq LSD1 24h Combination replicate 1

description: ChIP-seq

value: LSD1 (ab17721, Abcam)


title: MOLM13 ChIP-seq LSD1 24h GSK2879552 replicate 2

description: ChIP-seq


title: MOLM13 CUT&Tag H3K4me1 6h GSK2879552 replicate 2

description: CUT&Tag


title: MOLM13 CUT&Tag H3K4me1 6h GSK2879552 replicate 3

description: CUT&Tag


title: batch1_H3K27me3_Fus_KO2_rep2


title: HL7G and NAPc2 Replicate 1

value: HL7G and NAPc2


title: MOLM13 ChIP-seq LSD1 24h GSK2879552 replicate 1

description: ChIP-seq


title: Unstimm Replicate 1

value: MM1 cells

value: Unstimm


title: batch1_H3K27me3_Setd2_KO1_rep1


title: MOLM13 CUT&Tag H3K4me1 6h Quizartinib replicate 2

description: CUT&Tag

value: 1 nM quizartinib


title: NAPc2 Replicate 2


title: IgG Replicate 1

value: IgG


title: MOLM13 CUT&Tag H3K4me1 6h GSK2879552 replicate 1

description: CUT&Tag

value: 6 hours


title: MOLM13 CUT&Tag H3K4me1 6h Quizartinib replicate 3

description: CUT&Tag


title: batch1_H3K27me3_Fus_KO1_rep2

value: Fus KO


title: batch1_H3K27me3_Fus_KO2_rep1


title: MOLM13 ChIP-seq LSD1 24h Quizartinib replicate 2

description: ChIP-seq


title: MOLM13 ChIP-seq LSD1 24h Combination replicate 2

description: ChIP-seq

value: 1 nM quizartinib + 100 nM GSK2879552


title: MOLM13 CUT&Tag H3K4me1 6h Quizartinib replicate 1

description: CUT&Tag

value: H3K4me1 (#5326, Cell Signaling Technologies)


title: HL5B Replicate 1


title: batch1_H3K27me3_Fus_KO1_rep1


title: NAPc2 Replicate 1


title: MOLM13 ChIP-seq LSD1 24h DMSO replicate 2

description: ChIP-seq

value: DMSO

value: 24 hours


title: batch1_Fus_WT_rep2

value: Embryonic stem cells

value: WT


title: MOLM13 ChIP-seq LSD1 24h Quizartinib replicate 1

description: ChIP-seq


title: HL7G Replicate 1


title: MOLM13 CUT&Tag H3K4me1 6h DMSO replicate 2

description: CUT&Tag


title: batch1_Fus_WT_rep1


title: MOLM13 ChIP-seq LSD1 24h DMSO replicate 1

description: ChIP-seq


title: batch1_Fus_Setd2_KO2_rep2


title: HL5B and NAPc2 Replicate 1

value: HL5B and NAPc2


title: MOLM13 CUT&Tag H3K4me1 6h DMSO replicate 1

description: CUT&Tag


title: MOLM13 ChIP-seq MYC 24h Combination replicate 1

description: ChIP-seq

value: MYC (#13987, Cell Signaling Technologies)


title: batch1_Fus_Setd2_KO2_rep1

value: Setd2 KO


title: SJ204_ASP_scMultiome (ATAC-Seq)

description:
PDX2_ASP
10x Genomics

data_processing:
Sequencing data were run on Cell Ranger version 3.1.0 to generate feature barcode matrices and information for clustering and gene expression.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cryopreserved primary patient samples were thawed quickly at 37 °C water bath, followed by dead cell removal (Miltenyi Biotec,130-090-101). Then the live cells (cell viability > 90%) were collected and subjected to lysis, library construction. For PDX cells, following RBC lysis (QIAGEN, 158904), human leukemia cells were enriched by EasySep Mouse/Human Chimera Isolation kit (Stemcell Technologies, 19849)
Libraries were prepared following  10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol and sequenced on Illumina NovaSeq 6000 149 system  (Illumina).
scMultiome

value: spleen

value: human leukemia cells


title: MOLM13 CUT&Tag H3K27Ac 6h Combination replicate 2

description: CUT&Tag

value: H3K27Ac (ab4729, Abcam)


title: MOLM13 CUT&Tag H3K27Ac 6h Combination replicate 3

description: CUT&Tag


title: SJ049_ASP_scMultiome (ATAC-Seq)

description:
PDX1_ASP
10x Genomics


title: MOLM13 ChIP-seq MYC 24h GSK2879552 replicate 1

description: ChIP-seq


title: batch1_Fus_Setd2_KO1_rep1


title: batch1_Fus_Fus_KO2_rep2


title: MOLM13 CUT&Tag H3K27Ac 6h GSK2879552 replicate 3

description: CUT&Tag


title: MOLM13 ChIP-seq MYC 24h Quizartinib replicate 2

description: ChIP-seq


title: MOLM13 ChIP-seq MYC 24h Quizartinib replicate 1

description: ChIP-seq


title: MOLM13 CUT&Tag H3K27Ac 6h Combination replicate 1

description: CUT&Tag


title: SJ156_scMultiome (ATAC-Seq)

description:
Patient 4
10x Genomics

source_name: Peripheral blood

value: Peripheral blood

value: Peripheral blood leukocytes


title: batch1_Fus_Fus_KO2_rep1


title: SJ049_CTRL_scMultiome (ATAC-Seq)

description:
PDX1_CTRL
10x Genomics


title: SJ149_scMultiome (ATAC-Seq)

description:
Patient 3
10x Genomics


title: MOLM13 CUT&Tag H3K4me1 6h DMSO replicate 3

description: CUT&Tag


title: MOLM13 CUT&Tag H3K27Ac 6h GSK2879552 replicate 1

description: CUT&Tag


title: MOLM13 ChIP-seq MYC 24h DMSO replicate 2

description: ChIP-seq


title: MOLM13 CUT&Tag H3K27Ac 6h GSK2879552 replicate 2

description: CUT&Tag


title: batch1_Fus_Fus_KO1_rep2


title: MOLM13 ChIP-seq MYC 24h Combination replicate 2

description: ChIP-seq


title: SJ009_scMultiome (ATAC-Seq)

description:
Patient 2
10x Genomics


title: batch1_Fus_Fus_KO1_rep1


title: SJ204_CTRL_scMultiome (ATAC-Seq)

description:
PDX2_CTRL
10x Genomics


title: batch1_Fus_Setd2_KO1_rep2


title: MOLM13 ChIP-seq MYC 24h DMSO replicate 1

description: ChIP-seq


title: MOLM13 CUT&Tag H3K27Ac 6h Quizartinib replicate 3

description: CUT&Tag

value: 1 nM quizartinib


title: MOLM13 ChIP-seq MYC 24h GSK2879552 replicate 2

description: ChIP-seq


title: MOLM13 CUT&Tag H3K27Ac 6h Quizartinib replicate 2

description: CUT&Tag

value: 6 hours


title: batch2_rip_seq_Smyd5_KO_Input_rep2

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameters ‘-q 20 --paired’.
Trimmed reads were uniquely mapped to the mouse reference genome (mm9) using Bowtie2 (Langdon, 2015) (version 2.4.2).
PCR duplicates were removed using MarkDuplicates tool of Picard (version 2.23.3) (https://broadinstitute.github.io/picard/) with the parameter ‘--REMOVE DUPLICATES = true’.
Peaks were identified using MACS2 (Zhang et al., 2008) (version 2.2.7.1) with the parameters ‘–nomodel -f BAMPE -g mm’.
Genome coverage bigwig files were generated by deepTools (Ramirez et al., 2014) (version 3.5.0) bamCoverage with the parameter ‘--scaleFactor 1,000,000/(the number of reads mapped to hg19 genome)’.
Assembly: mm9
Supplementary files format and content: BigWig files

extract_protocol:
Cells were collected and washed with cold PBS once. Hela cells were spiked in as the internal control for normalization. 1 ml cold polysome lysis buffer (50 mM KCl, 25 mM Tris pH 7.4, 5 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 100 U/ml RNAase inhibitor, and 1× protease inhibitor cocktail) was added and incubated on ice for 10 min. Samples were cleaned by centrifugation at 14,000 rpm 4 °C for 10 min. 10% of the lysate was saved as the input sample. Others were incubated with Anti-DYKDDDDK G1 Affinity Resin beads (GenScript, Cat. #L00432) which were washed with NT2 buffer (50 mM Tris pH 7.4, 150 mM NaCl, 1 mM MgCl2, and 0.05% NP-40) at 4 °C for 4h. Beads were washed with NT2 buffer 5 times to remove unbound material. RNA was purified by Trizol reagent (Sangon Biotech, Cat. #B610409)
library preparation was done by RNA-seq library prep kit (VAHTS, Cat. #NR604)

value: Smyd5 KO


title: FKl/l-2-3 [V24]

city: Houston

first: Susan

last: Hamilton

state: TX

address: One Baylor Plaza

department: Integrative Physiology

institute: Baylor College of Medicine

data_processing:
Raw sequence data (.bcl files) generated from Illumina platform were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Reads from the fastq files were quality checked and filtered using FastQC and trimmed with Trim-Galore.
Quality filtered reads were mapped to the mm10 genome assembly using STAR and quantified using RSEM.
Assembly: mm10
Supplementary files format and content: Both Excel and csv (comma-separated files) giving Gene ID, log fold-change, p-values, adjusted p-values, and Gene Name.
Supplementary files format and content: Excel file giving the altered cardiotoxicity functions, the associated genes, p-values and adjusted p-values (computed using Ingenuity Pathway Analysis; IPA).

source_name: whole heart

extract_protocol:
Isolated hearts were homogenized in TRIzol reagent (Life Technologies) and cleared by centrifugation. For phase separation, 0.2ml chloroform per 1ml of TRIzol used for the initial homogenization was added in each tube. The tubes were capped securely, shaken by hand for around 15 seconds and centrifuged for 15 mins at 12,000xg and 4°C. The aqueous phase containing RNA was carefully transferred into a new tube. To precipitate RNA, 0.5ml isopropanol per 1 ml of TRIzol used for initial homogenization was added in each tube. The samples were incubated at room temperature for 10 minutes and centrifuged for 10 minutes at 12,000xgand 4°C. The total RNA forms a white gel-like pellet at the bottom of tube. As a wash, 1ml 75% ethanol per 1ml of TRIzol used forinitial homogenization was added after discarding the supernatant. The samples were vortexed and centrifuged for 5 minutes at 7,500xg and4°C. The washing step was repeated twice with 75% ethanol. The final pellet was briefly dried via air exposure, resuspended in 20-50ul RNase-free water and/or incubated in 55-60°C for 10 minutes.
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

value: whole heart

value: FKl/l

tag: batch


title: SJ204_ASP_scMultiome (GEX)

description:
PDX2_ASP
10x Genomics


title: FKl/l-2-2 [V23]


title: batch2_rip_seq_Smyd5_KO_Input_rep1


title: SJ004_scMultiome (ATAC-Seq)

description:
Patient 1
10x Genomics


title: FKl/l MHC+-1-3 [V22]

value: FKl/l MHC+


title: SJ204_CTRL_scMultiome (GEX)

description:
PDX2_CTRL
10x Genomics


title: MOLM13 CUT&Tag H3K27Ac 6h DMSO replicate 3

description: CUT&Tag

value: DMSO


title: batch2_rip_seq_Smyd5_KO_IP_rep2

value: Embryonic stem cells


title: MOLM13 CUT&Tag H3K27Ac 6h Quizartinib replicate 1

description: CUT&Tag


title: FKl/l MHC+-1-2 [V21]


title: MHC CRE Only-1-3 [V20]

value: MHC CRE Only


title: batch2_rip_seq_Smyd5_KO_IP_rep1


title: SJ049_ASP_scMultiome (GEX)

description:
PDX1_ASP
10x Genomics


title: MOLM13 CUT&Tag H3K27Ac 6h DMSO replicate 2

description: CUT&Tag


title: SJ049_CTRL_scMultiome (GEX)

description:
PDX1_CTRL
10x Genomics


title: MOLM13 CUT&Tag H3K27Ac 2h Combination replicate 3

description: CUT&Tag

value: 1 nM quizartinib + 100 nM GSK2879552

value: 2 hours


title: FKl/l MHC+-2-2 [V18]


title: FKl/l MHC+-2-3 [V19]


title: batch2_rip_seq_Fus_P423L_Input_rep1

value: Fus P423L


title: batch2_rip_seq_Fus_P423L_IP_rep2


title: MHC CRE Only-1-2 [V17]


title: SJ149_scMultiome (GEX)

description:
Patient 3
10x Genomics


title: batch2_rip_seq_Fus_P423L_Input_rep2


title: SJ156_scMultiome (GEX)

description:
Patient 4
10x Genomics


title: batch2_rip_seq_Fus_P423L_IP_rep1


title: MOLM13 CUT&Tag H3K27Ac 2h Combination replicate 1

description: CUT&Tag


title: MOLM13 CUT&Tag H3K27Ac 2h Combination replicate 2

description: CUT&Tag


title: MOLM13 CUT&Tag H3K27Ac 2h GSK2879552 replicate 3

description: CUT&Tag


title: SJ009_scMultiome (GEX)

description:
Patient 2
10x Genomics


title: FKl/l MCK+-1-3 [V16]

value: FKl/l MCK+


title: MOLM13 CUT&Tag H3K27Ac 2h GSK2879552 replicate 2

description: CUT&Tag


title: 1323 MYCN rep3

city: Los Angeles

first: Miller

last: Huang

state: CA

address: 4650 Sunset Blvd, #57

department: Pediatrics

institute: Children's Hospital Los Angeles

data_processing:
Sequence reads were mapped to the full hg19 transcriptome and gene counts were generated using STAR 2.4.2a
Expression values (TPM,FPKM,expected counts) were calculated using RSEM 1.3.1
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM, FPKM, and expected counts for each gene

source_name: Neuroblastoma

extract_protocol:
RNA was extracted using a Qiagen DNA/RNA kit
Completed by Novogene

value: Neuroblastoma

value: trunk neural crest

value: MYCN

value: doxycycline


title: batch2_rip_seq_WT_Input_rep1

value: WT


title: MOLM13 CUT&Tag H3K27Ac 6h DMSO replicate 1

description: CUT&Tag

value: 6 hours

value: H3K27Ac (ab4729, Abcam)


title: FKl/l-1-3 [V14]

value: whole heart


title: MOLM13 CUT&Tag H3K27Ac 2h GSK2879552 replicate 1

description: CUT&Tag


title: MOLM13 CUT&Tag H3K27Ac 2h Quizartinib replicate 3

description: CUT&Tag

value: 1 nM quizartinib


title: 1323 MYCN rep1


title: batch2_rip_seq_WT_IP_rep2


title: batch2_rip_seq_WT_IP_rep1


title: FKl/l MHC+-2-1 [V12]

value: FKl/l MHC+


title: WTC11, ALK/MYCN, rep3

value: ALK/MYCN


title: MOLM13 CUT&Tag H3K27Ac 2h Quizartinib replicate 2

description: CUT&Tag


title: batch1_rip_seq_Fus_KO2_Input_rep2

value: Embryonic stem cells

value: Fus KO


title: FKl/l MHC+-1-1 [V11]


title: batch1_rip_seq_Fus_KO2_Input_rep1


title: WTC11, ALK/MYCN, rep2


title: MOLM13 CUT&Tag H3K27Ac 2h Quizartinib replicate 1

description: CUT&Tag


title: SJ004_scMultiome (GEX)

description:
Patient 1
10x Genomics

value: Peripheral blood

value: Peripheral blood leukocytes


title: FKl/l MCK+-2-3 [V15]


title: batch2_rip_seq_WT_Input_rep2


title: batch1_rip_seq_Fus_KO2_IP_rep2


title: WTC11, ALK/MYCN, rep1


title: MOLM13 CUT&Tag H3K27Ac 2h DMSO replicate 3

description: CUT&Tag

value: DMSO

value: 2 hours


title: WTC11, MYCN, rep3

value: Neuroblastoma


title: MOLM13 CUT&Tag H3K27Ac 2h DMSO replicate 2

description: CUT&Tag


title: MHC CRE Only-2-3 [V9]

value: MHC CRE Only


title: MOLM13 CUT&Tag H3K27Ac 2h DMSO replicate 1

description: CUT&Tag


title: WTC11, MYCN, rep2

value: trunk neural crest

value: MYCN


title: batch1_rip_seq_Fus_KO1_Input_rep1


title: 1323 MYCN rep2

value: doxycycline


title: WTC11, MYCN, rep1


title: batch1_rip_seq_Fus_KO1_Input_rep2


title: MHC CRE Only-1-1 [V10]


title: FKl/l MCK+-1-1 [V7]

value: FKl/l MCK+


title: MHC CRE Only-2-2 [V6]


title: Primary AML Sample 2603 scATAC-seq 24h Combination

description: single cell ATAC-seq

data_processing:
Sequencing from scRNAseq libraries was aligned using Cell Ranger
Bigwigs were generated using ArchR
Peaks were called using MACS2

extract_protocol:
10X scATAC-seq libraries were prepared using the Chromium Single Cell ATAC Library and Gel Bead kit v1.1 (10x Genomics, 1000176) according to the manufacturers instructions
The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) performed the sequencing at 50 BP PE

value: primary AML blasts

value: 500 nM quizartinib + 500 nM GSK2879552

value: 24 hours


title: Early Day1 Wild-type(N2) feed with E. coli OP50

city: Ashburn

first: Shihong

middle: Max

last: Gao

address: 19700 Helix Dr

institute: Janelia Research Campus

description: 10x Genomics

data_processing:
We used Cell ranger (6.0, 10x Genomics) to align Raw base call (BCL) sequence files or FASTQ files to the C. elegans genome (WS282, Wormbase), and generated feature-barcode matrices. Doublets were removed based on the recommended ratio provided by the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 user guide (CG000204 Rev D), with a score calculated by Doubletfinder (Github/chris-mcginnis-ucsf). The feature-barcode matrices for each sample were constructed into a Seurat (R package, 4.0.5) object for downstream analysis. Cells were filtered by requiring a minimum of 100 genes to be expressed, and genes were filtered by being expressed in at least 3 cells. Integration of samples was performed with Seurat canonical correlation analysis (CCA) method to remove the batch effects. We tested CCA, reciprocal principal component analysis (PCA) and Harmony (0.1) for integration and chose the method with the best performance. The top 2,000 variable features were used for integration anchor identification. UMAP and tSNE dimension reduction were performed with the first 50 dimensions from PCA. Clustering was performed at multiple Leiden resolutions.
Assembly: WS282
Supplementary files format and content: Tab-separated values files and matrix files

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
Worms were washed three times with PBS and collected in a 1.5 mL tube. We then added 100 μl of homogenization buffer {10.1126/science.abk2432} and grind the worms with a pestle motor for 30 seconds on ice. To minimize nuclei adhesion on the surface, all the pestles, tubes and filters were pre-coated with a homogenization buffer or 1x PBS. 900 μl of homogenization buffer was added to wash the pestle, and the total 1mL homogenized sample was transferred into a 1mL Dounce tissue grinder (Wheaton 357538). The grinder was autoclaved overnight in a 220℃ oven to deactivate ribonuclease. After placing the grinder on ice, 20 strokes were applied using a loose pestle, followed by another 20 strokes using a tight pestle, while avoiding generating foams. The 1000μl samples were filtered through a cell strainer (35 μm) and then through a Flowmi cell strainer (BelArt, H13680-0040) into a new 1.5 mL tube. The tubes were centrifuged for 10 minutes at 1000 g at 4°C, and the supernatant was removed while not disturbing the pellet, which was hardly visible. The pellet was resuspended with 500 μl 1x PBS with 0.5% BSA and RNAase inhibitor and filtered with a Flowmi cell strainer (BelArt, H13680-0040) again into a 5 mL flow cytometer tube. A total of 20 μl was transferred into another flow cytometer tube and diluted with 180 μl 1x PBS with 0.5% BSA and RNAase inhibitor as an unstained control. Hoechst (Invitrogen 33342) was used to stain the nuclei in 1:1000 working concentration. We coated the 1.5 mL sorting collection tube with 1x PBS with 0.5% BSA and RNAase inhibitor and ~300,000 nuclei were sorted with Hoechst 33342 positive gating, which indicates DNA content, and forward scatter area (FSC-A) gating, representing the particle size above threshold. The intestinal nuclei, which are polypoid (32N), usually form an obvious cluster separating from the other 2N somatic nuclei, and these were also included in our collection. The collection tube was centrifuged at 800g for 8 minutes at 4℃ and the sheath buffer supernatant was carefully removed before resuspending the sorted nuclei with 40-50 μl 1x PBS with 0.5% BSA and RNAase inhibitor. The concentration and morphology of the nuclei were checked under a microscope to ensure high-quality nuclei isolation. If the results were desirable, we proceeded to generate gel emulsion with 10X Chromium Controller.  For sorting the nuclei, we used either DB LSR II or Sony MA800 sorter. To obtain the best nuclei morphology and the least RNA degradation, it is recommended to minimize the sorting time. Two researchers could simultaneously set up the sorter and perform nuclei processing.
Library preparation was carried out using the published 10X Chromium Single Cell 3’ v2/v3 Solution protocol (Single/dual index). The resulting libraries were sequenced on the NextSeq550 or NovaSeq6000 platforms, with a depth ranging from 6,306 to 29,862 reads/cell, with the recommended cycle numbers: 26 cycles for Read 1, 8 cycles for i7 index, and 98 cycles for Read 2.

value: whole body

value: day1(48h after L1)


title: batch1_rip_seq_Fus_KO1_IP_rep2

value: Embryonic stem cells


title: KO_Panc1_DMSO

first: PRIYA

last: MONDAL

address: 37 Convent Dr.

institute: NCI

data_processing:
The sgRNA read count and hits calling were analyzed by the MAGeCK v0.5.7 algorithm.
Assembly: hg38
Supplementary files format and content: Text file of sgRNA score in RRA
Library strategy: CRISPR

source_name: Epithelioid Carcinoma

extract_protocol:
Genomic DNA was extracted using the QIAmp DNA blood Cell Maxi Kit (Qiagen) according to the manufacturer’s protocol.
The sgRNA sequences were amplified using Taq polymerase (Takara Bio, Inc.) and adapted for sequencing.
The desired DNA product was purified with 6% TBE gel (Invitrogen) and subjected to massive parallel amplicon sequencing carried out by an Illumina sequencer (NextSeq550 run with a 75Hi kit; 75bp single-end, one 8bp index).

value: Epithelioid Carcinoma

value: Pancreatic Cancer

value: WT


title: batch1_rip_seq_Fus_KO1_IP_rep1

value: Fus KO


title: KO_Panc1_ABX_Rep2


title: Primary AML Sample 2603 scATAC-seq 24h DMSO

description: single cell ATAC-seq

value: DMSO


title: MHC CRE Only-2-1 [V5]

value: whole heart


title: FKl/l-1-2 [V4]

value: FKl/l


title: Primary AML Sample 2645 scATAC-seq 24h Combination

description: single cell ATAC-seq


title: KO_Panc1_ABX_Rep1


title: FKl/l-1-1 [V3]


title: batch1_rip_seq_Fus_KO2_IP_rep1


title: batch1_rip_seq_Setd2_KO2_Input_rep2

value: Setd KO


title: KD_Panc1_DMSO


title: Primary AML Sample 2645 scATAC-seq 24h DMSO

description: single cell ATAC-seq


title: batch1_rip_seq_Setd2_KO2_Input_rep1


title: FKl/l MCK+-2-2 [V2]


title: FKl/l MCK+-1-2 [V8]


title: Primary AML Sample 2684 scATAC-seq 24h Combination

description: single cell ATAC-seq


title: KD_Panc1_ABX_Rep2


title: batch1_rip_seq_Setd2_KO2_IP_rep2


title: Primary AML Sample 2684 scATAC-seq 24h DMSO

description: single cell ATAC-seq


title: FKl/l MCK+-2-1 [V1]


title: batch1_rip_seq_Setd2_KO2_IP_rep1


title: KD_Panc1_ABX_Rep1


title: Primary AML Sample 2714 24h Combination replicate 3

description: RNA-seq

data_processing:
Raw reads were trimmed with Trimmomatic and aligned with STAR
Differential expression analysis was performed using DESeq2
Genome_build: hg38

extract_protocol:
Total RNA was isolated using a RNeasy Plus Mini Kit (Qiagen)
The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) performed the sequencing at 100 BP single end


title: S2

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

description: No mechanical or physical stimulation

data_processing:
Fastq files were analyzed with RSEM v. 1.3.1 in order to obtain normalized counts of expressed genes in TPM. RSEM has been launched using STAR aligner 2.7.1a
Reads were aligned against the human GRCh38 / hg38 genome (Ensembl_database)
RSEM was launched with the following parameters –paired-end --strandedness reverse --calc-ci --ci-memory 12288 --estimate-rspd --append-names –star
Assembly: human GRCh38 / hg38 annotated with Homo_sapiens.GRCh38.100.gtf (Ensembl_database)
Supplementary files format and content: data.matrix.TPM.xlsx = File containing the normalized counts expressed in TPM in all samples.

source_name: Cell seeded on PLA scaffolds

growth_protocol: Human telomerase reverse transcriptase (hTERT)-immortalized bone marrow-derived mesenchymal stem cells (BM-MSCs) of clonal line Y201 were seeded using 0.5% collagen into 3D'printed PLA scaffolds.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and purified using Qiagen RNeasy Mini Kit, following manufacturers' instructions.
Libraries were prepared using 300 ng of total RNA per sample using the Illumina TM Stranded Total RNA Prep,Ligation with Ribo-Zero™ Plus Kit

treatment_protocol: The 3D bone tissue-like models (PLA scaffolds seeded with BM-MSCs) were cultured for 21 days in culture medium for 21 days under 3 culture conditions: static culture; direct perfusion, in which samples were placed in the bioreactor under unidirectional, direct perfusion at 0.3 mL/min; and direct perfusion with PEMF stimulation, in which samples were placed in the bioreactor under unidirectional, direct perfusion at 0.3 mL/min accompanied by PEMF stimulation with 1.5 mT and 75 Hz for 4 h per day (a cumulative dose of around 75 h over a period of 21 days). Samples were evaluated in duplicates (n = 2).

value: BM-MSCs

value: Static Culture

value: Human trabecular bone


title: FKl/l-2-1 [V13]


title: Primary AML Sample 2714 24h Combination replicate 2

description: RNA-seq

value: primary AML blasts


title: batch1_rip_seq_Setd2_KO1_Input_rep2


title: SPF_1X_PBS [ATAC_3_GGACTCCT]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
Paired-end ATAC-Seq reads were first assessed using FASTQC. Reads were trimmed using cutadapt to remove adapters and low quality reads below 30. Pair-end reads were then aligned against the GRCm39/mm10 mouse genome assembly with Bowtie (v2.3.0)84 in local mode, sensitive settings, and a maximum fragment size of 2000. Duplicated reads were marked using Picard (v.2.5.0). Alignments were filtered with SAMtools (v1.3) to exclude reads with mapping quality <30, not properly paired, duplicated, aligned to mitochondrial genome, and/or aligned to ENCODE blacklist regions. Alignments with an insertion size of >100bp were removed to enrich for nucleosome-free reads. ATAC-Seq peaks were called for each replicate using MACS2, using --format BAMPE and --keep-dup all. IDR (v2.0.2) was used to determine consistency of peak detection between individual replicates and peaks with a threshold below 0.10 were merged between replicates for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: gzipped tagAlign file from Picard Suite that include the reads information.

source_name: sorted astrocytes

growth_protocol: Adult male and female mice, and postnatal pups were used on a C57Bl/6J background (#000664, The Jackson Laboratory); NOD/ShiLtJ (#001976, The Jackson Laboratory) mice were obtained from the Jackson Laboratory. B6.Cg-Tg(Gfap-cre)73.12Mvs/J mice65 (The Jackson Laboratory, #012886) mice were crossed with B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J mice66 (The Jackson Laboratory, #007909) to generate Gfap(Cre/+);TdTomato(f/+) (TdTomatoGfap) mice. Postnatal pups were used from the NF-kB reporter strain FVB.Cg-Tg(HIV-EGFP,luc)8Tsb/J67 (The Jackson Laboratory, #027529) at P0-P3. Mice were kept in a pathogen-free facility at the Hale Building for Transformative Medicine at Brigham and Women’s Hospital in accordance with the IACUC guidelines. 10–12-week-old mice were used for stereotactic injection and EAE induction. Pups were sacrificed between P0-P3 for harvesting and culturing astrocytes. All procedures were reviewed and approved under the IACUC guidelines at Brigham and Women’s Hospital.

extract_protocol: After isolation of nuclei, transposition was performed using the kit (Illumina, #FC-121-1030). DNA was then amplified using NEBNext High Fidelity 2X PCR Master Mix (New England Biolabs, #M0541S) for 5 cycles. DNA quantity was then measured using a Viia 7 Real-Time PCR System (Thermo Fisher Scientific) and the number of cycles required to achieve 1/3 of maximal SYBR Green fluorescence was determined and libraries were amplified accordingly. TruSeq adaptors (universal: Ad1_noMX and barcoded: Ad2.1-Ad2.24) were used according to the Buenrostro protocol. Libraries were purified using MiniElute PCR Purification Kit (Qiagen, #28006) followed by double sided Agencourt AMPure XP bead purification (Beckman Coulter, #A63881) to remove primer dimers and large DNA fragments. Libraries were analyzed on a 2100 Bioanalyzer (Agilent Technologies) and High Sensitivity DNA Kit (Agilent Technologies, #5067-4626). Libraries were sequenced by Genewiz on an Illumina HiSeq 4000 by 2x75 bp paired end sequencing.

treatment_protocol: C57Bl/6J mice at age 10-12 weeks were anesthetized using 1-3% isoflurane mixed with oxygen. Heads were shaved and cleaned using 70% ethanol and Betadine (Thermo Fisher, #19-027132) followed by a medial incision of the skin to expose the skull. Mice were injected with 100 ng/mL IL-1β (R&D Systems, #401-ML-005, 100 µg/mL stock in PBS) and 50 ng/mL TNF-α (R&D Systems, #410-MT-010, 100 µg/mL stock in PBS) diluted in PBS or PBS. At day7, mice were re-injected (2X) or injected (1X) with 100 ng/mL IL-1β and 50 ng/mL TNF-α or PBS for 18-24 hours and astrocytes were sorted for further analysis. For EAE experiments, mice were injected with 100 ng/mL IL-1β and 50 ng/mL TNF-α or PBS for 18-24 hours and astrocytes were sorted for further analysis. The lateral ventricles were targeted bilaterally using the coordinates: +/- 1.0 (lateral), -0.44 (posterior), -2.2 (ventral) relative to Bregma. Mice were injected by two 5µL injections using a 25 µL Hamilton syringe (Sigma-Aldrich, #20787) on a stereotaxic alignment system (Kopf, #1900) and the incision was sutured.

value: sorted astrocytes

tag: Sex

value: female

value: 10 weeks

value: Germ Free Mice that are injected with PBS 3 times


title: batch1_rip_seq_Setd2_KO1_Input_rep1

value: Embryonic stem cells


title: SPF_1X_PBS [ATAC_3_AGGCAGAA]


title: Primary AML Sample 2714 24h Combination replicate 1

description: RNA-seq

value: 500 nM quizartinib + 500 nM GSK2879552

value: 24 hours


title: S1

description: No mechanical or physical stimulation


title: SPF_1X_PBS [ATAC_3_TCCTGAGC]


title: Primary AML Sample 2714 24h GSK2879552 replicate 3

description: RNA-seq


title: D2

description: Direct Perfusion of 0.3 ml/min

value: Direct Perfusion


title: SPF_1X_PBS [ATAC_3_CGTACTAG]


title: batch1_rip_seq_Setd2_KO1_IP_rep2


title: D1

description: Direct Perfusion of 0.3 ml/min


title: P2

description: Direct Perfusion of 0.3 ml/min + PEMF stimulation (1.5 mT, 75Hz)

value: Direct Perfusion + PEMF stimulation


title: SPF_1X_Cytokine [ATAC_3_CGAGGCTG]

value: Germ Free Mice that are injected with TNFalpha stimulation 3 times


title: batch1_rip_seq_Setd2_KO1_IP_rep1


title: Primary AML Sample 2714 24h GSK2879552 replicate 1

description: RNA-seq


title: SPF_1X_PBS [ATAC_3_TAAGGCGA]


title: P1


title: Primary AML Sample 2714 24h GSK2879552 replicate 2

description: RNA-seq


title: batch1_rip_seq_WT_Input_rep1

value: WT


title: SPF_1X_Cytokine [ATAC_3_GCTACGCT]


title: batch1_rip_seq_WT_Input_rep2


title: Primary AML Sample 2714 24h Quizartinib replicate 3

description: RNA-seq

value: 500 nM quizartinib


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 5

city: Berlin

first: Alina

middle: Katharina

last: Loriani Fard

address: Robert-von-Ostertag Straße 15

department: Department of Veterinary Medicine

institute: Freie Universität Berlin

description: re-analysis of GSM8141848

data_processing:
The FASTQ sequencing files were preprocessed (adapter trimmed, filtered) using Cutadapt and  aligned to the NCBI Reference Sequence (RefSeq) assembly for the dog (Canis lupus familiaris) CanFam3.1 with the STAR aligner. Read counts per gene were generated with two rounds of featureCounts to mitigate the effect of too short 3' UTR annotations. Reads that remained unassigned in the first round were subjected to the second round of featureCounts on an adjusted annotation with a 3' extension by 2 kilobases. Differential gene expression analysis for the comparison apocrine gland anal sac adenocarcinoma (AGASAC) versus hepatoid gland adenoma (HGA) was performed with R using DESeq2. Significance thresholds were drawn at a log2(fold change) of ≤ -1 or ≥ 1 and an adjusted p-value of ≤ 0.05.
Assembly: CanFam3.1 (NCBI RefSeq assembly: GCF_000002285.3)
Supplementary files format and content: tab-delimited text file includes normalized counts and differential expression data for each sample

organism: Canis lupus familiaris

source_name: FFPE

extract_protocol:
Total RNA was extracted utilizing the PureLink FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc.). After DNase I treatment 375 ng total RNA was used for library construction.
QuantSeq 3' mRNA-Seq FWD Library Preparation Kit (Lexogen) was used according to the manufacturer's guidelines (user guide 015UG009V0251) at Lexogen Services (Lexogen GmbH, Vienna) using the low-quality RNA protocol.

value: FFPE

tag: breed

value: Jack Russell Terrier

tag: age (years)

value: male


title: SPF_1X_Cytokine [ATAC_3_CAGAGAGG]


title: batch1_rip_seq_WT_IP_rep2


title: Primary AML Sample 2714 24h Quizartinib replicate 2

description: RNA-seq


title: Primary AML Sample 2714 24h Quizartinib replicate 1

description: RNA-seq


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 4

description: re-analysis of GSM8141847

value: Bullterrier


title: batch1_rip_seq_WT_IP_rep1


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 3

description: re-analysis of GSM8141846

value: Pug


title: Primary AML Sample 2714 24h DMSO replicate 3

description: RNA-seq

value: primary AML blasts

value: DMSO


title: E12_5KO1-E12_5KO1_FKDL210005941-1a-AK2918

city: Tianjin

first: Linlin

last: Liu

address: Weijin Road 97

institute: Nankai university

data_processing:
trim-galore to get clean raw reads
FastQC to evaluate the quality of the clean data
Hisat2(version, 2-2.1.0,parameters:-p 20 -x mm10 -1 fq1 -2 fq2 -S  sample.sam  ) to align genome
Using samtools to convert sam files to bam files
featurecounts to get raw counts
Genome_build: mm10
Supplementary_files_format_and_content: raw counts txt

source_name: primodial germ cells_KO

extract_protocol:
Using MACS to get primodial germ cells, and we seprated 1,000 cells to  do Smart-seq2 with slight modification, and made a library.
We use Tn5  transposase to get our library.

tag: strain background

tag: genotype/variation

value: Rif1-knock out

value: derived from E12.5 primodial germ cells


title: SPF_1X_Cytokine [ATAC_3_CTCTCTAC]

value: sorted astrocytes

value: female

value: 10 weeks


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 2

description: re-analysis of GSM8141845

value: Beagle


title: SPF_1X_Cytokine [ATAC_3_TAGGCATG]


title: E12_5WT1-E12_5WT1_FKDL210005939-1a-AK2427

source_name: primodial germ cells_WT

value: wild type


title: Primary AML Sample 2714 24h DMSO replicate 1

first: William

last: Yashar

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

description: RNA-seq

value: 24 hours


title: SPF 2X CYTOKINE_3 [RNA-Seq]

description: Normal Mice that are injected with TNFalpha stimulation 2 times

data_processing:
The raw sequences are aligned to the GRCm38 reference genome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: gzipped kallisto quantification output.

extract_protocol:
N/A
Sorted cells were lysed and RNA isolated using the Qiagen RNeasy Micro kit (Qiagen, #74004) with on-column DNase I digestion (Qiagen, #79254). RNA was suspended in 10 µL of nuclease free water at 0.5-1 ng/µL and sequenced using SMARTSeq279 at the Broad Institute Technology Labs and the Broad Genomics Platform. Processed RNA-seq data was filtered by removing genes with low read counts. Read counts were normalized using TMM normalization and CPM (counts per million) were calculated to create a matrix of normalized expression values. The fastq files of each RNA-seq data sample were aligned to the Mus musculus GRCm38 transcriptome using Kallisto (v0.46.1), and the same software was used to quantify the alignment results. Differential expression analysis was conducted using DESeq2, and the log2 fold change was adjusted using apeGLM for downstream analysis. Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).


title: SPF 2X CYTOKINE_2 [RNA-Seq]


title: E12_5WT2-E12_5WT2_FKDL210005940-1a-AK2917


title: Primary AML Sample 2645 24h Combination replicate 3

description: RNA-seq

value: 500 nM quizartinib + 500 nM GSK2879552


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, reanalysis, lymphocyte enriched, FFPE, 1

description: re-analysis of GSM8141844

value: Rottweiler

value: male neutered


title: SPF 2X PBS_3 [RNA-Seq]

description: Normal Mice that are injected with PBS stimulation 2 times


title: SPF 2X CYTOKINE_1 [RNA-Seq]


title: E12_5KO2-E12_5KO2_FKDL210005942-1a-AK2147


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 3

description: re-analysis of GSM8141830

value: FFPE

value: Terrier

value: n/s


title: batch2_polya_seq_Fus_P423L_rep1

data_processing:
CCS reads were generated from subreads by ccs (version 6.2.0) (https://github.com/nlhepler/pbccs) with the parameters ‘--skip-polish --min-passes 1 --min-rq 0.9’.
To clean CCS reads, we matched barcode sequence (and TSO sequence) in CCS reads and the reverse complementary of CCS reads. The 5′ adapters were trimmed and CCS reads were oriented from 5′ to 3′. Then 3′ adapters were also matched and trimmed.
3′ adapters were also matched and trimmed. Multiple samples in one library will be extracted separately using demux tool of Demultiple (version 1.2.1) (https://github.com/jfjlaros/demultiplex)with parameters ‘-m 1 -d’.
Duplicate CCS reads were removed according to 12 random nucleotides at 3′ of CCS reads.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for each gene

extract_protocol:
RNA was purified by Trizol reagent (Sangon Biotech, Cat. #B610409)
Binding oligo: /Index//iSp18/ACTCTGCGTTGATACCACTGCT/iBiodT/CCG/iSpC3/CGGAAGCAGTGGTATCAACGCAGAGTNNNNNNNNNNNN/Reverse complementary sequence of index//ideoxyU/TTTTTTTT/3InvdT/ was synthesized for the enrichment and ligation of poly(A) mRNA. /Index/ was designed as the 8 base pairs of sample index. /iSp18/ was synthesized as an internal 18-atom hexaethyleneglycol spacer. /iBiodT/ was biotin labeled dT. /iSpC3/ was a C3 Spacer designed to increase oligos’ self-anneal. NNNNNNNNNNNN was 12 N as the UMI (unique molecular identifiers) for each sequencing read. /ideoxyU/ was used for USER enzyme digestion to remove the following oligo dT before sequencing. /3InvdT/ was 3’ inverted dT which blocked the reverse transcription from undigested oligo. Low salt buffer (0.15 M NaCl, 20 mM Tris pH 7.5, and 1 mM EDTA) was prewarmed at 70 °C. Binding oligos were dissolved in Low salt buffer to make a final concentration of 8 μM. 10 μl of binding oligo was added to 20 μl Streptavidin Magnetic Beads (Thermo, Cat. #65001) which were washed with Washing/binding buffer (0.5 M NaCl, 20 mM Tris- pH 7.5, and 1 mM EDTA) twice. Samples were incubated at room temperature for 30 min with occasional agitation by hands. Beads were then washed with Washing/binding buffer twice. 5 μg total RNA, which was extracted by Trizol reagent (Sangon Biotech, Cat. #B610409) following the manufacturer’s instructions, was dissolved in 50 μl of Washing/binding buffer, denatured at 65 °C for 5 min, and quickly chilled on ice for 2 min, before being incubated with 20 μl of beads. Samples were incubated at room temperature for 30 min and then washed with Washing/binding buffer twice. 0.8 μl 10 mM ATP, 4 μl T4 RNA ligase Reaction buffer (NEB, Cat. # B0216S), 8 μl 50% PEG8000, 1 μl T4 RNA ligase 2 (NEB, Cat. # M0239), 2 μl RNase inhibitor (NEB, Cat. # M0314S), and 4.2 μl H2O were added and incubated at room temperature for 2 h. Beads were washed with Washing/binding buffer twice， followed by 1X CutSmart buffer (NEB, Cat. # B7204) once. 49 μl 1X CutSmart buffer and 1 μl USER enzyme (NEB, Cat. # M5507) were mixed with the beads and incubated at 37 °C for 30 min. After being washed with pre-warmed 70 °C Low-salt buffer at room temperature for 2 min, beads were washed with H2O once. RT reaction was conducted by adding 4 μl 5X SuperScript IV RT Reaction Buffer (Thermo, Cat. #18091200), 1 μl 10 mM DTT, 1 μl 10 mM dNTP, 1 μl RNase inhibitor, 1 μl TSO oligo AAGCAGTGGTATCAACGCAGAGTACATrGrGrG. 3 μl 50% PEG8000, 1 μl SuperScript IV Reverse Transcriptase (Thermo, Cat. #18091200), and 8 μl H2O and incubating at 50 °C for 30 min. Beads were then washed with Low salt buffer and subsequent H2O once. Pre-PCR was conducted by using 25 μl NEBNext® High-Fidelity 2X PCR Master Mix (NEB, Cat. #M0541S), 1 μl 20 μM PCR oligo AAGCAGTGGTATCAACGCAGAGT, and 24 μl H2O at 98 °C for 3 min; 10 cycles of 98 °C for 10 s, 60 °C for 15 s, and 72 °C for 3 min; 72 °C for 5 min. Samples were purified by 0.9X of VAHTS DNA clean beads to 20 μl. The purified sample was used to construct the sequencing library for Sequel II Systems (PacBio) using SMRTbell Express Template Prep Kit 2.0 kit (PacBio) under the manufacturer’s instructions.

value: Embryonic stem cells

value: Fus P423L


title: SPF 2X PBS_2 [RNA-Seq]


title: Primary AML Sample 2645 24h Combination replicate 1

description: RNA-seq

value: primary AML blasts


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 2

description: re-analysis of GSM8141829

value: Goldendoodle

value: male


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 4

description: re-analysis of GSM8141831

value: Boxer


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 1

description: re-analysis of GSM8141828

value: French Bulldog


title: SPF 2X PBS_1 [RNA-Seq]

value: sorted astrocytes

value: female

value: 10 weeks


title: Primary AML Sample 2645 24h GSK2879552 replicate 3

description: RNA-seq

value: 24 hours


title: Primary AML Sample 2714 24h DMSO replicate 2

description: RNA-seq

value: DMSO


title: batch2_polya_seq_WT_rep2

value: WT


title: Canine cutaneous histiocytoma group 1 according to Cockerell & Slauson 1979, reanalysis, FFPE, 5

description: re-analysis of GSM8141832


title: batch2_polya_seq_Fus_P421A_rep1

value: Fus P421A


title: Primary AML Sample 2645 24h GSK2879552 replicate 1

description: RNA-seq


title: Primary AML Sample 2645 24h GSK2879552 replicate 2

description: RNA-seq


title: Primary AML Sample 2645 24h Quizartinib replicate 3

description: RNA-seq

value: 500 nM quizartinib


title: batch2_polya_seq_WT_rep1


title: batch2_polya_seq_Fus_P423L_rep2


title: SPF 1X PBS_3 [RNA-Seq]

description: Normal Mice that are injected with PBS stimulation 1 time


title: batch1_polya_seq_Fus_KO2_rep2

value: Fus KO


title: SPF 1X CYTOKINE_1 [RNA-Seq]

description: Normal Mice that are injected with TNFalpha stimulation 1 time


title: Primary AML Sample 2645 24h Combination replicate 2

description: RNA-seq

value: 500 nM quizartinib + 500 nM GSK2879552


title: SPF 1X PBS_2 [RNA-Seq]


title: Primary AML Sample 2645 24h Quizartinib replicate 1

description: RNA-seq


title: batch1_polya_seq_Fus_KO2_rep1

value: Embryonic stem cells


title: batch1_polya_seq_Fus_KO1_rep2


title: SPF 1X PBS_1 [RNA-Seq]


title: Primary AML Sample 2645 24h Quizartinib replicate 2

description: RNA-seq


title: Primary AML Sample 2645 24h DMSO replicate 3

description: RNA-seq


title: batch2_polya_seq_Fus_P421A_rep2


title: batch1_polya_seq_Fus_KO1_rep1


title: SPF_2X_PBS [ATAC_2_GGACTCCT]

value: Normal Mice that are injected with PBS 2 times


title: SPF 1X CYTOKINE_3 [RNA-Seq]


title: Primary AML Sample 2645 24h DMSO replicate 1

description: RNA-seq

value: primary AML blasts


title: SPF 1X CYTOKINE_2 [RNA-Seq]


title: batch1_polya_seq_Setd2_KO2_rep2

value: Setd2 KO


title: SPF_2X_PBS [ATAC_2_TCCTGAGC]


title: batch1_polya_seq_Setd2_KO2_rep1


title: Primary AML Sample 2624 24h Combination replicate 3

description: RNA-seq


title: SPF_2X_PBS [ATAC_2_AGGCAGAA]


title: batch1_polya_seq_Setd2_KO1_rep2


title: SPF_2X_PBS [ATAC_2_CGTACTAG]


title: Primary AML Sample 2624 24h Combination replicate 1

description: RNA-seq


title: Primary AML Sample 2624 24h GSK2879552 replicate 3

description: RNA-seq


title: batch1_polya_seq_WT_rep2


title: SPF_2X_PBS [ATAC_2_TAAGGCGA]


title: SPF_2X_Cytokine [ATAC_2_CGAGGCTG]

value: Normal Mice that are injected with TNFalpha stimulation 2 times


title: batch1_polya_seq_WT_rep1


title: Primary AML Sample 2624 24h GSK2879552 replicate 2

description: RNA-seq


title: MOLM13 ATAC-seq 24h Combination replicate 3

description: ATAC-seq

data_processing:
Libraries were aligned to the human genome (hg38) using BWA-MEM and sorted using SAMtools
Duplicates were marked with Sambamba, duplicates and mitochondrial reads were removed
CPM normalized tracks were generated with DeepTools
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential accessibility was assessed with DESeq2
Genome_build: hg38

source_name: MOLM13 cell line

extract_protocol:
Libraries were prepared according to published protocol Buenrostro et al 2015
BGI performed the library preparation and sequencing at 100 BP SE

value: 1 nM quizartinib + 100 nM GSK2879552


title: Primary AML Sample 2624 24h GSK2879552 replicate 1

description: RNA-seq


title: Primary AML Sample 2645 24h DMSO replicate 2

description: RNA-seq


title: SPF_2X_Cytokine [ATAC_2_CTCTCTAC]


title: SPF_2X_Cytokine [ATAC_2_CAGAGAGG]


title: SPF_2X_Cytokine [ATAC_2_GCTACGCT]


title: MOLM13 ATAC-seq 24h Combination replicate 2

description: ATAC-seq


title: SPF_2X_Cytokine [ATAC_2_TAGGCATG]


title: Primary AML Sample 2624 24h Quizartinib replicate 3

description: RNA-seq


title: MOLM13 ATAC-seq 24h Combination replicate 1

description: ATAC-seq


title: Primary AML Sample 2624 24h Quizartinib replicate 1

description: RNA-seq


title: Primary AML Sample 2624 24h Quizartinib replicate 2

description: RNA-seq


title: MLVQ52

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description: LSD1skm-/- rep4

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Assembly: mm10

source_name: Total muscles were dissected and RNA was extracted using trizol.

extract_protocol: P2834 : RNA-Seq libraries were generated according to manufacturer's instructions from 400 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

value: Skeletal muscle

value: 9 weeks


title: Primary AML Sample 2624 24h Combination replicate 2

city: Portland

description: RNA-seq


title: MOLM13 ATAC-seq 24h GSK2879552 replicate 3

description: ATAC-seq


title: Primary AML Sample 2624 24h DMSO replicate 3

description: RNA-seq


title: batch1_polya_seq_Setd2_KO1_rep1


title: MLVQ51

description: LSD1skm-/- rep3


title: MLVQ50

description: LSD1skm-/- rep2


title: MOLM13 ATAC-seq 24h GSK2879552 replicate 1

description: ATAC-seq


title: Primary AML Sample 2624 24h DMSO replicate 2

description: RNA-seq


title: MOLM13 ATAC-seq 24h Quizartinib replicate 3

description: ATAC-seq

value: 1 nM quizartinib


title: Primary AML Sample 2624 24h DMSO replicate 1

description: RNA-seq


title: MOLM13 ATAC-seq 24h Quizartinib replicate 2

description: ATAC-seq


title: MLVQ49

description: LSD1skm-/- rep1


title: MOLM13 ATAC-seq 24h Quizartinib replicate 1

description: ATAC-seq


title: Primary AML Sample 2077 24h Combination replicate 3

description: RNA-seq


title: MLVQ48

description: Control rep4


title: MLVQ47

description: Control rep3


title: MOLM13 ATAC-seq 24h DMSO replicate 3

description: ATAC-seq


title: MLVQ46

description: Control rep2


title: Primary AML Sample 2077 24h Combination replicate 1

description: RNA-seq


title: Primary AML Sample 2077 24h Combination replicate 2

description: RNA-seq


title: MOLM13 ATAC-seq 24h DMSO replicate 2

description: ATAC-seq


title: MOLM13 ATAC-seq 24h GSK2879552 replicate 2

description: ATAC-seq


title: Primary AML Sample 2077 24h GSK2879552 replicate 3

description: RNA-seq


title: MLVQ45

description: Control rep1


title: Primary AML Sample 2077 24h GSK2879552 replicate 1

description: RNA-seq


title: Primary AML Sample 2077 24h GSK2879552 replicate 2

description: RNA-seq


title: MLVQ28

description: H3K9me2 24h starved

source_name: Chromatin extrated after immunoprecipitation with various antibodies.

extract_protocol:
P2731
P2727 AND 2731: ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 2-20 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.  , P2731 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 1-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: 10 weeks


title: MOLM13 RNA-seq 24h Combination replicate 2

description: RNA-seq

extract_protocol:
Total RNA was isolated using a RNeasy Plus Mini Kit (Qiagen)
BGI performed the library preparation and sequencing at 50 base pair single end

value: 24 hours


title: Primary AML Sample 2077 24h Quizartinib replicate 3

description: RNA-seq


title: MLVQ21

description: Input 24h starved

extract_protocol:
P2727
P2727 AND 2731: ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 2-20 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.  , P2731 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 1-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.


title: ACLYKD 2

description: ACLYKD Astrocytes

data_processing:
The raw sequences are aligned to the GRCm38 reference genome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: tar gzipped kallisto quantification output.

source_name: ACLYKD Astrocytes

growth_protocol: Mice. C57BL/6J mice (The Jackson Laboratory, 000664) were used as a genetic background for all in vivo experiments. Mice were housed in a conventional, pathogen-free facility at the Hale Building for Transformative Medicine under a standard 12h light/dark cycle at 20–23°C and 50% humidity with access to water and food ad libitum, in accordance with guidelines for care and experimentation defined by the Institutional Animal Care and Use Committee (IACUC). Transgenic mouse genotypes were confirmed by PCR (Transnetyx). When Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice (The Jackson Laboratory, #031008 and #007909) were used, 200mg/kg Tamoxifen (Sigma-Aldrich, T5648) diluted in corn oil (Sigma-Aldrich, C8267) was administered intraperitoneally 2-4 weeks before starting the experiment and TdTomato induction was confirmed by flow cytometry at the time of measurement.

extract_protocol:
Sorted cells were lysed and RNA isolated using the Qiagen RNeasy Micro kit (Qiagen, #74004) with on-column DNase I digestion (Qiagen, #79254). RNA was suspended in 10 µL of nuclease free water at 0.5-1 ng/µL and sequenced using SMARTSeq279 at the Broad Institute Technology Labs and the Broad Genomics Platform. Processed RNA-seq data was filtered by removing genes with low read counts. Read counts were normalized using TMM normalization and CPM (counts per million) were calculated to create a matrix of normalized expression values. The fastq files of each RNA-seq data sample were aligned to the Mus musculus GRCm38 transcriptome using Kallisto (v0.46.1), and the same software was used to quantify the alignment results. Differential expression analysis was conducted using DESeq2, and the log2 fold change was adjusted using apeGLM for downstream analysis.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

value: Female


title: MOLM13 RNA-seq 24h Combination replicate 3

description: RNA-seq


title: p300KD 3

description: p300KD Astrocytes

source_name: p300KD Astrocytes

value: Astrocytes


title: ACLYKD 1

description: ACLYKD Astrocytes


title: Primary AML Sample 2077 24h Quizartinib replicate 2

description: RNA-seq


title: MOLM13 RNA-seq 24h Combination replicate 1

description: RNA-seq


title: MOLM13 RNA-seq 24h GSK2879552 replicate 3

description: RNA-seq


title: MLVQ15

description: LSD1 24h starved


title: Primary AML Sample 2077 24h Quizartinib replicate 1

description: RNA-seq


title: MLVQ6

description: Input fed


title: MOLM13 RNA-seq 24h GSK2879552 replicate 2

description: RNA-seq


title: Primary AML Sample 2077 24h DMSO replicate 3

description: RNA-seq

value: DMSO


title: MOLM13 RNA-seq 24h GSK2879552 replicate 1

description: RNA-seq


title: Primary AML Sample 2077 24h DMSO replicate 2

description: RNA-seq


title: Scramble 3

description: Control Astrocytes

source_name: Control Astrocytes


title: MLVQ5

description: H3K9me2 fed


title: MLVQ27

description: H3K9me1 24h starved


title: MOLM13 RNA-seq 24h Quizartinib replicate 3

description: RNA-seq


title: MLVQ4

description: H3K9me1 fed


title: Scramble 2

description: Control Astrocytes


title: Scramble 1

description: Control Astrocytes


title: MLVQ2

description: LSD1 fed


title: Primary AML Sample 2555 24h Combination replicate 3

description: RNA-seq


title: Primary AML Sample 2077 24h DMSO replicate 1

description: RNA-seq


title: MLVQ1

description: GR fed


title: MOLM13 ATAC-seq 24h DMSO replicate 1

description: ATAC-seq