title: LYZKL2

description: Library name: Sample 4

data_processing:
The Cell Ranger software pipeline (v6.1.2) provided by 10×Genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix, using the reference genome mm10 (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A).
For each cell, we quantified the numbers of genes and UMIs and kept high-quality cells with the detection threshold of 600-4000 genes and 1000-25000 UMIs.
All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read
Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).
Assembly: Mus_musculus_Ensemble_94
Supplementary files format and content: excel with FPKM for every gene (Rows) and every sample (Columns)

growth_protocol: Siglec-F low macrophages were sorted from lung tumors of Tmem173fl/fl→KrasLSL-G12D/+Lkb1fl/fl (WTKL) and Tmem173fl/fl;Lyz2-Cre→KrasLSL-G12D/+Lkb1fl/fl (LYZKL) chimeric mice that were intranasally injected with Ad-Cre (2x106 pfu per mouse).

extract_protocol:
The Cd11b+Ly6G-CD64+Siglec-Flow population was isolated based FACS. The cells were homogenized in 1 ml TRIzol (invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene)
After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). The cDNAs were then amplified by PCR with 12 cycles. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification via PCR (8 cycles). The purified libraries were sequenced on the Illumina NovaSeq 6000 with 28 cycles of read1, 8 cycles of i7 index, and 91 cycles of read2. And finally, 150 bp paired-end reads were generated.

treatment_protocol: 8 weeks after intranasal injection of Ad-Cre

value: lung

value: macrophages


title: siUSP32_2

status: Public on Nov 29 2025

type: SRA

city: Zhengzhou

first: Zehao

last: Hong

state: Henan

address: No. 1 Jianshe East Road

department: Breast surgery

country: China

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: Sample5

library_source: transcriptomic

data_processing:
Using MGISEQ-2000RS sequencing platform.
The sequencing data was filtered with SOAPnuke (v.1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5 ) is more than 20%; (3) Removing reads whose unknown base ('N base') ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Transcripts per million (TPM) were calculated.
Assembly: GCF_00001405.39_GRCh38.p13
Supplementary files format and content: tpms for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: triple negetive breast cancer

extract_protocol:
Lysis of cells with Trizol Reagent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using MGISEQ-2000RS protocols.

tag: tissue

value: triple negetive breast cancer

tag: cell line

tag: cell type

value: triple negetive breast cancer cells


title: siUSP32_1

description: Library name: Sample4


title: Mouse, FLOX_8, HFD 16 weeks

city: Wuhan

first: Xiaoge

last: Zhang

state: Hubei

address: BAYI road

institute: wuhan university

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

organism: Mus musculus

source_name: Pancreatic islet

growth_protocol: Animals were housed in laboratory cages at 22 ± 3 °C unless specifically indicated, with a humidity of 35 ± 5% under a 12-h dark/light cycle (lights on at 7:00 a.m.).

extract_protocol:
Total RNA from tissue was extracted and purified with TRIzol reagent
The sequencing library was performed on DNBSEQ-T7 platform (PE150) using DNBSEQ-T7RS Reagent Kit

treatment_protocol: Endothelial cell specific IRE1α-knockout mice (Ern1EC-KO) mice were produced after Tamoxifen intraperitoneal injection. Ern1fl/fl; VE-cadherin-Cre-ERT2 mice and Ern1fl/fl mice were injected with 2 mg of tamoxifen for 5 consecutive days at the age of 4 weeks. For diet-induced obesity, male Ern1fl/fl mice and their Ern1EC-KO littermates were fed a high-fat diet (HFD, 60% kcal fat; Research Diets) for 16 weeks, starting at 8 weeks of age.

value: Pancreatic islet

tag: genotype

value: Ern1 floxed

tag: treatment

value: 60% fat diet for 16 weeks


title: 90min MNase-seq

city: State College

first: Shane

middle: Douglas

last: Stoeber

state: Pennsylvania

address: 406 South Frear Building

department: BMMB

country: USA

institute: Penn State

description: Library name: 90min MNase-seq

library_source: genomic

data_processing:
20 million reads per sample were generated and aligned to the sacCer3 genome assembly using Bowtie2 with presets “--very-sensitive". Bigwig files were generated using deepTools bamcoverage (version 3.5.6) using a 130-170bp size selection and alignments were trimmed by 15bp on either side using offset 15 -15. Two biological replica were performed at each time point
Assembly: sacCer3
Supplementary files format and content: bigwig and bed

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
For MNase-seq, 1.5 OD660 units of cells were harvested and washed sequentially with 1 mL water and 1 mL 1M sorbitol. The pellet was re-suspended in 0.5mL spheroplasting solution (1 M sorbitol, 0.5 mM 2-mercaptoethanol, 0.18 mg/ml zymolyase) and incubated at room temperature for 7 minutes with gentle inversion. Spheroplasts were collected by centrifugation at 500 x g for 3 min, washed twice with 1 mL of 1 M sorbitol, and resuspended in 200 μL digestion buffer (1 M sorbitol, 50 mM NaCl, 100 mM Tris-Cl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 1 mM 2-mercaptoethanol, 0.5 mM spermidine, 0.075% NP-40). Samples were incubated at 37°C for 8 min with 1U of MNase (Sigma N3755). Reactions were terminated by adding 20 μL quench buffer (250 mM EDTA and 5% SDS). DNA was purified by phenol–chloroform extraction.
MNase and ChIP sequencing libraries were prepared using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina® (Catalog # E7645L) according to the manufacturer’s instructions. The sequencing libraries were sequenced on a NextSeq 2000 machine in 2 x 50 bp paired-end sequencing mode at the Genomics Research Incubator at The Pennsylvania State University.

value: 90min cbf1 induction


title: Patient-derived xenograft, HF2303 Tumor

city: Ann Arbor

first: Wajd

middle: N.

last: Al-Holou

state: MI

address: 1500 E Medical Center Dr

department: Neurosurgery

institute: University of Michigan

description: Library name: 12002-SP-1

library_source: transcriptomic single cell

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files and the Cell Ranger Pipeline (version 8.0.0) was used to align reads and generate count matrices.
Assembly: For patient-derived GBM models (GBM12, GBM38, and HF2303), cells were aligned to a combined human and mouse reference transcriptome GRCh38_and_GRCm39-2024-A with the addition of luciferase sequence and the syngeneic TRP GBM cells were aligned to mouse reference transcriptome GRCm39-2024-A with the addition of luciferase sequence using Cell Ranger (version 8.0.0).
Supplementary files format and content: Tab-separated value files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: Brain tumor

extract_protocol:
Intracranial syngeneic TRP GBM tumors and patient-derived GBM tumors (GBM12, GBM38, and HF2303) were harvested and dissociated using Collagenase Type II (Invitrogen, 17101015) with rotation at 37°C. The cell suspension was passed through a 40um strainer (Fisherbrand, 22363547), centrifuged, and resuspended followed by application of RBC lysis buffer (Biolegend).
Single cell suspensions were subjected to counting on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 1000 cells/µL. Single cell 3’ gene expression libraries were generated using the 10x Genomics Chromium instrument following the manufacturer’s protocol. In brief, suspensions were loaded onto the 10x chip along with reverse transcription (RT) master mix and appropriate gel beads. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed, and the resulting Post GEM-RT product was cleaned up and the cDNA amplified. cDNA was subjected to enzymatic fragmentation and size selection to optimize the cDNA size prior to final library construction following the manufacturer’s protocol (10x Genomics; 3’ v4 (mouse)).  Final library quality was assessed using the LabChip GX (PerkinElmer). Pooled libraries were then subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files and the Cell Ranger Pipeline (10x Genomics) was used to align reads and generate count matrices.

value: Brain tumor

value: IDH WT


title: Patient-derived xenograft, GBM12 Brain

description: Library name: 12000-SP-2

source_name: Brain cortex

value: Brain cortex


title: 60 min MNase-seq

description: Library name: 60 min MNase-seq

value: 60min cbf1 induction


title: Patient-derived xenograft, GBM12 Tumor

description: Library name: 12000-SP-1


title: LYZKL1

first: Zhidong

address: Donghu Road, No. 115, Wuchang District

institute: Wuhan University

description: Library name: Sample 3

source_name: lung

value: 8 weeks after intranasal injection of Ad-Cre

tag: batch


title: siControl_3

description: Library name: Sample3


title: WTKL2

description: Library name: Sample 2


title: 30min MNase-seq

description: Library name: 30min MNase-seq

value: 30min cbf1 induction


title: siControl_2

description: Library name: Sample2


title: Patient-derived xenograft, GBM38 Brain

description: Library name: 11913-SP-2


title: Patient-derived xenograft, GBM38 Tumor

description: Library name: 11913-SP-1


title: siControl_1

description: Library name: Sample1


title: 0min MNase-seq

description: Library name: 0min MNase-seq

value: 0min cbf1 induction


title: RELACS ChIP-Seq, Day7 Neuron,ctrl, H3K4me1, rep3

status: Public on Nov 28 2025

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep3_H3K4me1
RELACS Pellet3

data_processing:
Fastq files were aligned with snakePipes version 3 against the mm10 reference genome, using the DNA-mapping mode and the ChIP-seq mode.
Assembly: mm10
Supplementary files format and content: deepTools bamCompare (v3) was used to generate the subtract bigwig files.

growth_protocol: NPCs were kept in NB 27 medium supplemented with 10 ng/ml EGF and 10 ng/ml FGF.

extract_protocol:
Cells were fixed with 1% PFA for 15 minutes at RT , Nuclei extraction, quantification and ChIP was performed using the published RELACS protocol (Arrigoni et al, 2018) Antibodies: H3K4me1 ( Diagenode; C15410194), H3K4me3 ( Diagenode; C15410003), H3K27me3 ( Diagenode; C15410195), H3K9me3 ( Diagenode; C15410193), , H3K27ac ( Diagenode; C15410196).
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645)

value: Day7 Neurons

value: Tir1+, MSL1-AID

value: control


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, Input, rep3

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep3_Input
RELACS Pellet3


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, Input, rep1

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep1_Input
RELACS Pellet1


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, Input, rep2

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep2_Input
RELACS Pellet2


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, H3K4me1, rep1

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep1_H3K4me1
RELACS Pellet1


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, H3K27ac, rep3

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep3_H3K27ac
RELACS Pellet3


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, H3K27ac, rep1

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep1_H3K27ac
RELACS Pellet1


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, H3K27ac, rep3

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep3_H3K27ac
RELACS Pellet3

value: Auxin treated D0-7


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, H3K27ac, rep2

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep2_H3K27ac
RELACS Pellet2


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, Input, rep3

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep3_Input
RELACS Pellet3


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, H3K4me1, rep3

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep3_H3K4me1
RELACS Pellet3


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, H3K27ac, rep2

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep2_H3K27ac
RELACS Pellet2


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, Input, rep1

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep1_Input
RELACS Pellet1


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, H3K4me1, rep1

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep1_H3K4me1
RELACS Pellet1


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, H3K27ac, rep1

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep1_H3K27ac
RELACS Pellet1


title: RELACS ChIP-Seq, Day7 Neuron, ctrl, H3K4me1, rep2

description:
Library name: Day7_Neu_Diff_M1AID_ctrl_Rep2_H3K4me1
RELACS Pellet2


title: CUTRUN, NPCs, dNM1F, IgG

description: Library name: NPC_dN_M1F_IgG

data_processing:
Fastq files were aligned with snakePipes version 3 against the mm10 reference genome, using the DNA-mapping mode and the ChIP-seq mode.
Assembly: mm10
Supplementary files format and content: deepTools bamCompare (v3) was used to generate the subtract bigwig files.
Library strategy: CUT&Run

source_name: MSL1-F KO

growth_protocol: NPCs were kept in NB 27 medium supplemented with 10 ng/ml EGF and 10 ng/ml FGF. Neuronal differentiation NPCs were plated on poly-d-lysine-coated (0.1 mg/ml, Gibco) tissue culture treated plates (Corning) in N2B27 medium supplemented with 5 ng/ml basic FGF, and differentiated for seven days with medium replacement on days 1, 3 and 5.

extract_protocol:
Cells were fixed with 0.1% PFA for 10 minutes at RT, subsequently CUT&RUN was performed with minor modifications as published (Skene and Henikoff, 2017). Antibodies: H4K16ac (abcam ab109463).
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645)

value: MSL1-F KO

value: NPCs


title: CUTRUN, NPCs, M1F, IgG

description: Library name: NPC_M1F_IgG


title: CUTRUN, NPCs, dNM1F H4K16ac, rep2

description: Library name: NPC_dN_M1F_H4K16ac_Rep2


title: CUTRUN, NPCs, M1F, H4K16ac, rep2

description: Library name: NPC_M1F_H4K16ac_Rep2


title: WTKL1

description: Library name: Sample 1

value: lung

value: macrophages


title: CUTRUN, NPCs, dNM1F, H4K16ac, rep1

description: Library name: NPC_dN_M1F_H4K16ac_Rep1


title: CUTRUN, NPCs, M1F, H4K16ac, rep1

description: Library name: NPC_M1F_H4K16ac_Rep1


title: CUTRUN, Day7 Neuron, ctrl, H4K16ac, rep2

description: Library name: D7_Neu_Diff_M1AID_ctrl_H4K16ac_Rep2


title: CUTRUN, Day7 Neuron, ctrl, IgG

description: Library name: D7_Neu_Diff_M1AID_ctrl_IgG


title: CUTRUN, Day7 Neuron, ctrl, H4K16ac, rep1

description: Library name: D7_Neu_Diff_M1AID_ctrl_H4K16ac_Rep1


title: CUTRUN, Day7 Neuron, Auxin treated Day0-7, IgG

description: Library name: D7_Neu_Diff_M1AID_Aux_IgG

value: Auxin treated Day0-7


title: CUTRUN, Day7 Neuron, Auxin treated Day0-7, H4K16ac, rep2

description: Library name: D7_Neu_Diff_M1AID_Aux_H4K16ac_Rep2


title: CUTRUN, Day7 Neuron, ctrl, IgG

extract_protocol:
Cells were fixed with 0.1% PFA for 10 minutes at RT, subsequently CUT&RUN was performed with minor modifications as published (Skene and Henikoff, 2017). Antibodies: MOF ( abcam; ab200660), FLAG (Sigma; F1804), V5 (Thermo Fisher; MA1-34099), H4K16ac (abcam ab109463), MSL2 (Sigma; HPA003413).
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645)


title: CUTRUN, Day7 Neuron, ctrl, MSL1-V5

description: Library name: D7_Neu_Diff_M1AID_ctrl_V5


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, Input, rep2

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep2_Input
RELACS Pellet2


title: RELACS ChIP-Seq, Day7 Neuron, Auxin treated, H3K4me1, rep2

description:
Library name: Day7_Neu_Diff_M1AID_Aux_D0_7_Rep2_H3K4me1
RELACS Pellet2


title: MicroC, Day7 Neuron, Aux Day0-7, rep2

description: Library name: D7_Neu_Diff_Micro_C_Aux_Rep2

data_processing:
The microC data was processed with the makePairs module implemented in snakePipes (3.1.0) (Bhardwaj et al. 2019) . Briefly, the fastq files were trimmed using fastp (0.23.4) (Chen et al. 2018) and aligned to the mm10 reference genome using BWA (0.7.18) (Li and Durbin 2009). Bamfiles were processed into pairs and subsequently deduplicated using pairtools (1.1.3) (Open2C et al. 2024) and subsequently converted into an mcool format using cooler (0.10.3) (Abdennur and Mirny 2020).
Assembly: mm10
Supplementary files format and content: Downstream analysis was performed using cooltools (version 0.7.1) (Open2C et al. 2024), and pileups were generated using coolpuppy (1.1.0) (Flyamer et al. 2020). Compartment scores were calculated at a 100kb resolution, using the first eigenvector oriented by the genomic GC content. Boundary scores were calculated using the cooler files at a resolution of 15kb, in sliding windows of 45kb. Only strong boundaries present in both samples were retained for calculating pairwise spearman correlations. Loops were called using the cooler files at a resolution at 15kb, using the cooltools.dots functionality with the false discovery rate set at 0.01 and the max_nans_tolerated set to 4. Loops were called separately for the samples, and the union of those was taken for downstream analysis. Loops intersecting with the genes of interest (either MSLc primed genes or genes of the GO-term Nervous System development which demonstrated upregulation throughout Neuronal differentiation (log2fc > 0.5, padj < 0.01; NPC vs Day7 Neurons)) were used to generate the pileup plots. For the control regions, pixels spanning the same average distance as the loop set of interest were randomly sampled from the cooler files.

extract_protocol:
NPCs and Day 7 In-vitro differentiated neurons were harvested, counted and collected in 10%FCS/1XPBS and double crosslinked using formaldehyde (ThermoFisher #28908) and DSG (disuccinimidyl glutarate, 7.7Å) (TCI, D5445), respectively. Following quenching of the fixation reactions and washes in ice-cold 1xPBS, 5M cell aliquots were pelleted and snap-frozen in liquid nitrogen for storage at −80°C. Cell membranes were solubilized to extract intact nuclei by resuspending crosslinked 5M cell pellets in Micro-C Buffer #1 (MB#1; 50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 5 mM MgCl2, 1M CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) at 1M cells per 100 μL for 20 min on ice. Following an MB#1 wash, samples were resuspended in 250 μL MB#1 and 1 μL of 20 U/μL MNase (Worthington Biochem #LS004798). The digestion reaction was thoroughly mixed and incubated at 37°C for 15 min on a thermomixer shaking 850rpm. MNase was inactivated by the addition of 200mM EGTA (4 mM final conc.) and incubating for 10 min at 65˚C. at this stage, a digestion efficiency determination step was performed: aliquots of digested and undigested samples were treated with Proteinase K for 1-2 hours at 65˚C, to reverse crosslink. After purification of the the DNA using ZymoClean DNA purification kit, the fragments size was measured on TapeStation, to ensure primarily (~80%) mononucleosomal fragments (150-200 bp). Digested nuclei were washed twice with ice-cold Micro-C Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2). To generate blunt ends on digested DNA fragments prior to proximity ligation and add biotinylated nucleotides, a series of enzymatic processing steps were performed. First, for addition of 5’-phosphate groups and removal of 3’-phosphate groups, digested samples were incubated with: 10xNEBuffer 2.1 (NEB, #B7202S), 100mM ATP (NEB, #P0756), 100mM DTT and 10U/μL T4 PNK (NEB, #M0201), at 37°C for 15 min with interval mixing. Then 50 U of DNA Polymerase I Klenow Fragment (NEB #M0210) was added to the reaction and incubated at 37°C for 15 min with interval mixing. Next, the following mixture was added to each sample: 10 mM dGTP and dTTP (NEB, #N0446), 1mM Biotin-dATP and Biotin-dCTP (Jena Bioscience, #NU-835-BIO14, #NU-809-BIOX), T4 DNA Ligase Buffer and BSA. The reactin was incubated for 45 min at 25°C with interval mixing and then quenched by 30 mM EDTA heat inactivate for 20 min at 65°C. Finally, the samples were washed once with cold Micro-C Buffer #3 (50 mM Tris-HCl pH 7.5, 10 mM MgCl2). Proximity ligation and Removal of unligated ends was performed by first washing the samples with 1x Ligase buffer, followed by resuspending in ligation reaction mix: 10x NEB Ligase buffer, 200xBSA, and 400U/ μl NEB T4 Ligase (NEB, #M0202L) and slowly rotating at RT for 2-3 h. Then, the chromatin was collected and removal of biotinylated dNTPs from all unligated fragment ends was performed by incubating the samples in 10x NEBuffer#1 (NEB # B7001) and 100U/ μl Exonuclease III (NEB # M0206), for 15 min at 37°C with interval mixing. Reverse crosslinking of the samples was performed by incubating with 20mg/ml Proteinase K, 10% SDS and 100mg/ml RNase A overnight at 65°C. After reverse crosslinking, Dinucleosomal DNA was purified in two steps: first, phenol:chloroform:isoamylic alcohol DNA extraction was performed. Then, the samples were loaded on 2% agarose gel. Band between 250 – 400 bp was cut out of the gel and then purified Zymo Gel Purification kit (Zymo Research #D4008). DNA amounts were Measured using Qubit™ High Sensitivity dsDNA kit. The biotin-bound ligated DNA contact fragments were pulled down using Dynabeads MyOne Streptavidin C1 (Invitrogen #65001) in TBW (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl), and then washed once with 10mM Tris-HCl pH 7.5.
For each micro-C sample, libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645), without size selection and with Pre-PCR wash of the beads with 100 μl 0.1xTE. PCR amplification of libraries was performed with 8 cycles of enrichment. Finally, libraries were purified using 0.9X AmPure XP beads (Beckman Coulter #A63880). Final libraries were quality controlled for size and concentration and sequenced on a NovaSeq Illumina sequencer with 100-bp paired-end reads.

value: Auxin treated during Day0-7 of Neuronal differentiation


title: MicroC, Day7 Neuron, Aux Day0-7, rep1

description: Library name: D7_Neu_Diff_Micro_C_Aux_Rep1


title: MicroC, NPC, ctrl, rep3

description: Library name: NPC_Micro_C_ctrl_Rep3


title: MicroC, Day7 Neuron, ctrl, rep2

description: Library name: D7_Neu_Diff_Micro_C_ctrl_Rep2


title: MicroC, Day7 Neuron, ctrl, rep1

description: Library name: D7_Neu_Diff_Micro_C_ctrl_Rep1


title: MicroC, Day7 Neuron, ctrl, rep3

description: Library name: D7_Neu_Diff_Micro_C_ctrl_Rep3


title: scRNAseq, WT, E9.5 whole embryo, rep3

description: Library name: scRNA_embryo_WT_Rep3

data_processing:
Raw sequencing data were processed by Cell Ranger ARC v2 pipeline, using mm10 as reference genome. Quality control and filtering were performed on RNA and ATAC data separately using Seurat version 5.2.1 (Hao et al.,2021) and Signac version 1.40.0 (Stuart et al., 2021). For RNA sequencing assay, multiple datasets coming from different conditions were analysed together.  Cells with less than 1,000 detected RNA counts and more than 30,000 RNA counts, were discarded. Similarly cells which had less than 2,000 or more than 100,000 ATAC counts were discarded. In addition cells which had more than 5% of counts originating from mitochondrial genes were discarded to retain high-quality cells.  Following filtering, 30,834 good quality cells were retained (WT 17,898, MSL1 KO: 12,936). Both modalities were pre-processed separately, as the FindTopFeatures(), RunTFIDF() and RunSVD() were carried out for the ATAC modality, while SCTransform() and RunPCA() were carried out for the RNA modality. Subsequently both modalities were used in the FindMultiModalNeighbors() function. The FindClusters() function was used for clustering and RunUMAP() was used for dimensional reduction. To assign celltypes, a reference dataset was used, which included age matched whole E9.5 embryos (Amadei et al., 2022). Using FindTransferanchors(), TransferData() and AddMetaData() celltype probabilities were calculated and added to the Seurat object. Due to low celltype probability scores across all cells, embryo 119 was excluded from further analysis. All cells with a maximum probability < 0.5 were discarded as low quality predictions, which resulted in 16984 cells for which a celltype could be assigned with high confidence (WT 10.394, MSL1 KO: 6590). All processed data files submitted to GEO were derived from this final Seurat object containing high-confidence cell type annotations.
Assembly: mm10
Supplementary files format and content: The matrices and other supplementary data are saved as separate modalities in the processed files

molecule: polyA RNA

source_name: whole embryo

growth_protocol: WT and Msl1 KO E9.5 embryos were dissected and incubated in 1 ml Trypsin (pre-warmed to 37°C) for 10 min. Tissues were disrupted further by carefully pipetting up and down 10 times every two minutes. Subsequently, Trypsin was inactivated by the addition of 5 ml 10% FBS/PBS. Single Cell Suspensions were passed through a Cell Strainer (Falcon), which was subsequently washed with 2 ml 10% FBS/PBS to increase cell recovery. After centrifugation (1100 rpm, 5 mins), the supernatant was removed and the pellets were resuspended in 1 ml of room temperature cryopreservation medium (10% DMSO/FBS), cooled down to -70 °C in a Mr.Frosty and stored at -70°C for up to two months.

extract_protocol:
Samples were processed using the Chromium Single Cell Multiome ATAC + Gene expression kit. Nuclei were isolated as described in the manuscript. Integrity and roundness of nuclei was checked by staining 10 μl of nuclei suspension with DAPI. Successively, nuclei were counted using a Trypan Blue assay on the automated cell counter Countess (Thermo Fisher Scientific).
Single-cell encapsulation and library preparation were performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide, CG000338).

value: whole embryo

value: WT


title: scRNAseq, MSL1 KO, E9.5 whole embryo, rep3

description: Library name: scRNA_embryo_M1KO_Rep3

value: MSL1 KO


title: MicroC, NPC, ctrl, rep1

description: Library name: NPC_Micro_C_ctrl_Rep1


title: scRNAseq, WT, E9.5 whole embryo, rep2

description: Library name: scRNA_embryo_WT_Rep2


title: scRNAseq, WT, E9.5 whole embryo, rep1

description: Library name: scRNA_embryo_WT_Rep1


title: scRNAseq, MSL1 KO, E9.5 whole embryo, rep1

description: Library name: scRNA_embryo_M1KO_Rep1


title: scATACseq, MSL1 KO, E9.5 whole embryo, rep3

description: Library name: scATAC_embryo_M1KO_Rep3

library_source: genomic single cell


title: scATACseq, MSL1 KO, E9.5 whole embryo, rep2

description: Library name: scATAC_embryo_M1KO_Rep2


title: scATACseq, WT, E9.5 whole embryo, rep2

description: Library name: scATAC_embryo_WT_Rep2


title: scATACseq, WT, E9.5 whole embryo, rep1

description: Library name: scATAC_embryo_WT_Rep1


title: scATACseq, MSL1 KO, E9.5 whole embryo, rep1

description: Library name: scATAC_embryo_M1KO_Rep1


title: RNASeq,Day14 Neurons, dN-MSL1-F, rep4

description:
Library name: D14_Neu_Diff_dN_M1F_Rep4
stranded mRNA Seq

data_processing:
Fastq files were aligned with snakePipes version 3 against the mm10 reference genome, using the mRNAseq command
Assembly: mm10
Supplementary files format and content: tsv files read counts generated by featureCounts

growth_protocol: NPCs were kept in NB 27 medium supplemented with 10 ng/ml EGF and 10 ng/ml FGF. Neuronal differentiation NPCs were plated on poly-d-lysine-coated (0.1 mg/ml, Gibco) tissue culture treated plates (Corning) in N2B27 medium supplemented with 5 ng/ml basic FGF, and differentiated for seven days with medium replacement on days 1, 3 and 5. On day 7, the medium was replaced with N2B27 medium without FGF-2 and neural cells were matured for further seven days with half of the medium replaced on days 9, 11 and 13. Astrocyte differentiation: NPCs were differentiated into astrocytes as previously described (Conti et al., 2005) with some modifications. In brief, on Day0, NPCs were plated on poly-d-lysine-coated (0.1 mg/ml, Gibco) tissue culture treated plates (Corning) in N2B27 medium supplemented with 1 ng/ml basic FGF and 20 ng/ml BMP4, and differentiated for 3 days with medium replacement every 24h.

extract_protocol:
Cells were lysed in TRIzol and RNA isolated with Quick-RNA Miniprep Kit (Zymo, R1055).
Libraries were prepared using the Stranded mRNA Prep, Ligation kit (Illumina, 20040534).

value: Day14 Neurons


title: CUTRUN, Day7 Neuron, Auxin treated Day0-7, H4K16ac, rep1

description: Library name: D7_Neu_Diff_M1AID_Aux_H4K16ac_Rep1


title: RNASeq,Day14 Neurons, dN-MSL1-F, rep2

description:
Library name: D14_Neu_Diff_dN_M1F_Rep2
stranded mRNA Seq


title: MicroC, Day7 Neuron, Aux Day0-7, rep3

description: Library name: D7_Neu_Diff_Micro_C_Aux_Rep3


title: RNASeq,Day14 Neurons, dN-MSL1-F, rep1

description:
Library name: D14_Neu_Diff_dN_M1F_Rep1
stranded mRNA Seq


title: RNASeq,Day14 Neurons, MSL1-F, rep3

description:
Library name: D14_Neu_Diff_M1F_Rep3
stranded mRNA Seq


title: scRNAseq, MSL1 KO, E9.5 whole embryo, rep2

description: Library name: scRNA_embryo_M1KO_Rep2


title: RNASeq,Day14 Neurons, MSL1-F, rep2

description:
Library name: D14_Neu_Diff_M1F_Rep2
stranded mRNA Seq


title: RNASeq,Day14 Neurons, MSL1-F, rep1

description:
Library name: D14_Neu_Diff_M1F_Rep1
stranded mRNA Seq


title: RNASeq,NPCs, dN-MSL1-F, rep4

description:
Library name: NPC_dN_M1F_E4_Rep4
stranded mRNA Seq


title: RNASeq,NPCs, dN-MSL1-F, rep1

description:
Library name: NPC_dN_M1F_E4_Rep1
stranded mRNA Seq


title: RNASeq,NPCs, MSL1-F, rep3

description:
Library name: NPC_M1F_Rep3
stranded mRNA Seq


title: RNASeq,NPCs, dN-MSL1-F, rep3

description:
Library name: NPC_dN_M1F_E4_Rep3
stranded mRNA Seq


title: scATACseq, WT, E9.5 whole embryo, rep3

description: Library name: scATAC_embryo_WT_Rep3


title: RNASeq,NPCs, MSL1-F, rep4

description:
Library name: NPC_M1F_Rep4
stranded mRNA Seq


title: J18_14d dex -> T_repA

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building, 415 Curie Boulevard

institute: University of Pennsylvania

description:
Library name: J18
Next Generation Sequencing

library_source: other

data_processing:
For ATAC-seq, we processed data by aligning paired-end FASTQ files to the hg19 reference genome using Bowtie2, then filtering for nucleosome-free fragments (insert size < 100 bp) representing accessible chromatin regions. Coverage was calculated from these filtered fragments, normalized to reads per million (RPM) for cross-sample comparison, and exported as bigwig files.
Assembly: hg19
Supplementary files format and content: for single cell sequencing data, the tab-delimited text file includes normalized and log2normalized counts. For bulk RNA-seq, the tab-delimited text file includes log2 counts per million for each sample. For ATAC seq, the bigwig files represent genome-wide chromatin accessibility signal for each sample that can be visualized in genome browsers such as Igv.

molecule: other

growth_protocol: WM989 A6-G3 melanoma cell line, first described in Shaffer et al, 2017, and kindly provided by the lab of Dr. Meenhard Herlyn, were derived by twice single-cell bottlenecking the WM989 melanoma cell line. The identities of WM989 A6-G3 was verified by DNA STR microsatellite fingerprinting at the Wistar Institute.  Cells were grown in Tu2% (80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4mM CaCl2, 50 U ml−1 penicillin and 50 μg ml−1 streptomycin) in humdified atmosphere with 5% CO2 at 37C.

extract_protocol:
For bulk RNA-seq, each biological replicate came from a separate passage and was processed separately. For ATAC-seq, we lysed the cells and set up the transposition reaction with the Tn5 transposase (generously provided by our collaborators in the Kavitha Sarma lab at The Wistar Institute) at 37℃ for 30 minutes. We isolated the transposed and adaptor-ligated genomic DNA from the reaction with the Zymo DNA Clean and Concentrator-5 Kit (Zymo #D4014) and then amplified the libraries using the custom primers described in Supplemental Table 4 (originally designed by the William Greenleaf lab at Stanford University).
Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases. For ATAC-seq, we isolated the transposed and adaptor-ligated genomic DNA from the reaction with the Zymo DNA Clean and Concentrator-5 Kit (Zymo #D4014) and then amplified the libraries using the custom primers (originally designed by the William Greenleaf lab at Stanford University). We sequenced our libraries on a NextSeq2000 with a P3 100-cycle kit (illumina 20040559), with 60 bp paired-end reads at a depth of approximately 25 million reads per sample.

treatment_protocol: Cells in each experiment were treated as described in the title of the sample, abbreviations are defined as follow. For ATAC-seq samples, T: 1nM trametinib, jnk8: 1uM JNK-IN-8, dex: dexamethasone, and repA v repB designating the biological replicate.

value: Human melanoma cells

value: BRAF - V600E


title: J17_14d dex+jnk8 -> T+jnk8_repA

description:
Library name: J17
Next Generation Sequencing


title: J16_3d dmso_repB

description:
Library name: J16
Next Generation Sequencing


title: RNASeq,Day14 Neurons, dN-MSL1-F, rep3

description:
Library name: D14_Neu_Diff_dN_M1F_Rep3
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K9me3, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3_H3K9me3
RELACS Pellet6

value: 24h Auxin treated


title: J14_14d dmso -> T_repB

description:
Library name: J14
Next Generation Sequencing


title: RNASeq, ESCs, MSL1-F KO, rep4

description:
Library name: ESC_M1KO_E4_Rep4
stranded mRNA Seq

value: ESCs

value: MSL1-FLAG KO


title: RNASeq, ESCs, MSL1-F KO, rep3

description:
Library name: ESC_M1KO_E4_Rep3
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K4me3, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3_H3K4me3
RELACS Pellet6

value: Tir1+, MSL1-AID


title: J12_3d dex jnk8_repB

description:
Library name: J12
Next Generation Sequencing


title: RNASeq,Day14 Neurons, MSL1-F, rep4

description:
Library name: D14_Neu_Diff_M1F_Rep4
stranded mRNA Seq


title: J13_3d (-)_repB

description:
Library name: J13
Next Generation Sequencing


title: J11_3d dex_repA

description:
Library name: J11
Next Generation Sequencing


title: RNASeq,NPCs, dN-MSL1-F, rep2

description:
Library name: NPC_dN_M1F_E4_Rep2
stranded mRNA Seq


title: J10_14d dex -> dmso_repB

description:
Library name: J10
Next Generation Sequencing


title: RNASeq, ESCs, MSL1-F KO, rep2

description:
Library name: ESC_M1KO_E4_Rep2
stranded mRNA Seq


title: J9_14d dex+jnk8 -> T+jnk8_repB

description:
Library name: J9
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K27me3, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3_H3K27me3
RELACS Pellet6


title: RNASeq, ESCs, MSL1-F KO, rep1

description:
Library name: ESC_M1KO_E4_Rep1
stranded mRNA Seq


title: J7_14d dex -> T_repB

description:
Library name: J7
Next Generation Sequencing


title: J8_14d dex -> T+jnk8_repB

description:
Library name: J8
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K4me1, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3_H3K4me1
RELACS Pellet6


title: RNASeq,NPCs, MSL1-F, rep2

description:
Library name: NPC_M1F_Rep2
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, Input, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3_Input
RELACS Pellet6


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K27ac, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3_H3K27ac
RELACS Pellet6


title: J6_14d dmso -> T_repA

description:
Library name: J6
Next Generation Sequencing


title: J15_3d dex_repB

description:
Library name: J15
Next Generation Sequencing


title: J5_3d dex jnk8_repA

description:
Library name: J5
Next Generation Sequencing


title: J4_14d dex -> dmso_repA

description:
Library name: J4
Next Generation Sequencing


title: MicroC, NPC, ctrl, rep2

description: Library name: NPC_Micro_C_ctrl_Rep2

value: control


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, Input, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2_Input
RELACS Pellet5


title: J3_3d dmso_repA

description:
Library name: J3
Next Generation Sequencing


title: J2_14d dex -> T+jnk8_repA

description:
Library name: J2
Next Generation Sequencing


title: RNASeq, ESCs, MSL1-F, rep4

description:
Library name: ESC_M1F_Rep4
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K9me3, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2_H3K9me3
RELACS Pellet5


title: RNASeq, ESCs, MSL1-F, rep3

description:
Library name: ESC_M1F_Rep3
stranded mRNA Seq


title: RNASeq, ESCs, MSL1-F, rep2

description:
Library name: ESC_M1F_Rep2
stranded mRNA Seq


title: J1_3d (-)_repA

description:
Library name: J1
Next Generation Sequencing


title: Sample_191_PMA_pretreatyes_pma_T_5224

description:
Library name: JLPR_BurnInSample191
Next Generation Sequencing

data_processing:
For bulk RNA-seq, Log2CPM values were generated from kallisto transcript abundance estimates by importing counts using tximport with transcript-to-gene mapping from Ensembl annotations, followed by filtering to retain genes with >1 CPM in at least 2 samples, TMM normalization using edgeR's calcNormFactors function, and log2 transformation of the normalized counts per million.
Assembly: hg19
Supplementary files format and content: For bulk RNA-seq, the tab-delimited text file includes log2 counts per million for each sample.

extract_protocol:
For bulk RNA-seq, each biological replicate came from a separate passage and was processed separately. We extracted RNA using the Zymo Direct-zol RNA Miniprep Kit (R2053).
Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases. For bulk RNA-seq, we prepared libraries using the Single Cell/Low Input RNA Library Prep Kit for Illumina. We sequenced each sample at a depth of approximately 20 million reads on a NextSeq2000 (60 base pair length) with a P3 100 kit.

treatment_protocol: Cells in each experiment were treated as described in the title of the sample, abbreviations are defined as follow. For bulk RNA-seq samples, cells were either pre-treated or not pre-treated with the compound noted immediately after the sample name, T: 1nM trametinib, 8: 1uM JNK-IN-8.


title: RNASeq, ESCs, MSL1-F, rep1

description:
Library name: ESC_M1F_Rep1
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K4me3, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2_H3K4me3
RELACS Pellet5


title: Sample_192_PMA_pretreatyes_pma_T_5224

description:
Library name: JLPR_BurnInSample192
Next Generation Sequencing


title: Sample_190_PMA_pretreatyes_pma_T_5224

description:
Library name: JLPR_BurnInSample190
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K4me1, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2_H3K4me1
RELACS Pellet5


title: RNASeq Timecourse, Day14, MSL1-F KO, Rep3

description:
Library name: Timecourse_D14_Neu_Diff_M1KO_Rep3
stranded mRNA Seq

value: MSL1-F KO


title: RNASeq,NPCs, MSL1-F, rep1

description:
Library name: NPC_M1F_Rep1
stranded mRNA Seq

value: NPCs


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K27me3, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2_H3K27me3
RELACS Pellet5


title: Sample_189_PMA_pretreatyes_T_5224_4

description:
Library name: JLPR_BurnInSample189
Next Generation Sequencing


title: RNASeq Timecourse, Day14, MSL1-F KO, Rep2

description:
Library name: Timecourse_D14_Neu_Diff_M1KO_Rep2
stranded mRNA Seq


title: Sample_187_PMA_pretreatyes_T_5224_4

description:
Library name: JLPR_BurnInSample187
Next Generation Sequencing


title: Sample_188_PMA_pretreatyes_T_5224_4

description:
Library name: JLPR_BurnInSample188
Next Generation Sequencing


title: Sample_186_PMA_pretreatyes_pma_T_8

description:
Library name: JLPR_BurnInSample186
Next Generation Sequencing


title: Sample_185_PMA_pretreatyes_pma_T_8

description:
Library name: JLPR_BurnInSample185
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, Input, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1_Input
RELACS Pellet4


title: RNASeq Timecourse, Day14, MSL1-F KO, Rep1

description:
Library name: Timecourse_D14_Neu_Diff_M1KO_Rep1
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K27ac, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2_H3K27ac
RELACS Pellet5


title: RNASeq Timecourse, Day10, MSL1-F KO, Rep3

description:
Library name: Timecourse_D10_Neu_Diff_M1KO_Rep3
stranded mRNA Seq

value: Day10 Neurons


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K9me3, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1_H3K9me3
RELACS Pellet4


title: Sample_181_PMA_pretreatyes_T_8_4

description:
Library name: JLPR_BurnInSample181
Next Generation Sequencing


title: RNASeq Timecourse, Day10, MSL1-F KO, Rep2

description:
Library name: Timecourse_D10_Neu_Diff_M1KO_Rep2
stranded mRNA Seq


title: Sample_184_PMA_pretreatyes_pma_T_8

description:
Library name: JLPR_BurnInSample184
Next Generation Sequencing


title: Sample_182_PMA_pretreatyes_T_8_4

description:
Library name: JLPR_BurnInSample182
Next Generation Sequencing


title: RNASeq Timecourse, Day10, MSL1-F KO, Rep1

description:
Library name: Timecourse_D10_Neu_Diff_M1KO_Rep1
stranded mRNA Seq


title: Sample_183_PMA_pretreatyes_T_8_4

description:
Library name: JLPR_BurnInSample183
Next Generation Sequencing


title: Sample_180_PMA_pretreatno_pma_T_5224

description:
Library name: JLPR_BurnInSample180
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K4me3, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1_H3K4me3
RELACS Pellet4


title: Sample_179_PMA_pretreatno_pma_T_5224

description:
Library name: JLPR_BurnInSample179
Next Generation Sequencing


title: RNASeq Timecourse, Day7, MSL1-F KO, Rep3

description:
Library name: Timecourse_D7_Neu_Diff_M1KO_Rep3
stranded mRNA Seq

value: Day7 Neurons


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K4me1, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1_H3K4me1
RELACS Pellet4


title: Sample_177_PMA_pretreatno_T_5224_4

description:
Library name: JLPR_BurnInSample177
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K27me3, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1_H3K27me3
RELACS Pellet4


title: Sample_178_PMA_pretreatno_pma_T_5224

description:
Library name: JLPR_BurnInSample178
Next Generation Sequencing


title: Sample_176_PMA_pretreatno_T_5224_4

description:
Library name: JLPR_BurnInSample176
Next Generation Sequencing


title: RNASeq Timecourse, Day7, MSL1-F KO, Rep2

description:
Library name: Timecourse_D7_Neu_Diff_M1KO_Rep2
stranded mRNA Seq


title: Sample_175_PMA_pretreatno_T_5224_4

description:
Library name: JLPR_BurnInSample175
Next Generation Sequencing


title: Sample_174_PMA_pretreatno_pma_T_8

description:
Library name: JLPR_BurnInSample174
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, 24h Auxin treated, H3K27ac, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1_H3K27ac
RELACS Pellet4


title: Sample_173_PMA_pretreatno_pma_T_8

description:
Library name: JLPR_BurnInSample173
Next Generation Sequencing


title: RNASeq Timecourse, Day7, MSL1-F KO, Rep1

description:
Library name: Timecourse_D7_Neu_Diff_M1KO_Rep1
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, ctrl, Input, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3_Input
RELACS Pellet3


title: Sample_169_PMA_pretreatno_T_8_4

description:
Library name: JLPR_BurnInSample169
Next Generation Sequencing


title: RNASeq Timecourse, Day3, MSL1-F KO, Rep2

description:
Library name: Timecourse_D3_Neu_Diff_M1KO_Rep2
stranded mRNA Seq

value: Day3 Neurons


title: RNASeq Timecourse, Day3, MSL1-F KO, Rep3

description:
Library name: Timecourse_D3_Neu_Diff_M1KO_Rep3
stranded mRNA Seq


title: RNASeq Timecourse, Day3, MSL1-F KO, Rep1

description:
Library name: Timecourse_D3_Neu_Diff_M1KO_Rep1
stranded mRNA Seq


title: Sample_170_PMA_pretreatno_T_8_4

description:
Library name: JLPR_BurnInSample170
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K4me3, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3_H3K4me3
RELACS Pellet3


title: RNASeq Timecourse, Day0, MSL1-F KO, Rep4

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep4
stranded mRNA Seq


title: Sample_166_PMA_pretreatyes_pre_pma_T

description:
Library name: JLPR_BurnInSample166
Next Generation Sequencing


title: Sample_167_PMA_pretreatyes_pre_pma_T

description:
Library name: JLPR_BurnInSample167
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K4me1, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3_H3K4me1
RELACS Pellet3


title: Sample_168_PMA_pretreatyes_pre_pma_T

description:
Library name: JLPR_BurnInSample168
Next Generation Sequencing


title: Sample_165_PMA_pretreatyes_pre_T_4

description:
Library name: JLPR_BurnInSample165
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K27me3, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3_H3K27me3
RELACS Pellet3


title: RNASeq Timecourse, Day0, MSL1-F KO, Rep2

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep2
stranded mRNA Seq


title: Sample_161_PMA_pretreatyes_pre_pma

description:
Library name: JLPR_BurnInSample161
Next Generation Sequencing


title: RNASeq Timecourse, Day0, MSL1-F KO, Rep1

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep1
stranded mRNA Seq


title: Sample_160_PMA_pretreatyes_pre_pma

description:
Library name: JLPR_BurnInSample160
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K27ac, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3_H3K27ac
RELACS Pellet3


title: Sample_172_PMA_pretreatno_pma_T_8

description:
Library name: JLPR_BurnInSample172
Next Generation Sequencing


title: Sample_162_PMA_pretreatyes_pre_pma

description:
Library name: JLPR_BurnInSample162
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, Input, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2_Input
RELACS Pellet2


title: Sample_159_PMA_pretreatyes_pre_DMSO_4

description:
Library name: JLPR_BurnInSample159
Next Generation Sequencing


title: RNASeq Timecourse, Day14, MSL1-F, Rep3

description:
Library name: Timecourse_D14_Neu_Diff_M1F_Rep3
stranded mRNA Seq


title: Sample_171_PMA_pretreatno_T_8_4

description:
Library name: JLPR_BurnInSample171
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K9me3, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3_H3K9me3
RELACS Pellet3


title: RELACS ChIP-Seq, NPC, ctrl, H3K9me3, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2_H3K9me3
RELACS Pellet2


title: RELACS ChIP-Seq, NPC, ctrl, H3K4me3, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2_H3K4me3
RELACS Pellet2


title: Sample_158_PMA_pretreatyes_pre_DMSO_4

description:
Library name: JLPR_BurnInSample158
Next Generation Sequencing


title: Sample_157_PMA_pretreatyes_pre_DMSO_4

description:
Library name: JLPR_BurnInSample157
Next Generation Sequencing


title: RNASeq Timecourse, Day14, MSL1-F, Rep2

description:
Library name: Timecourse_D14_Neu_Diff_M1F_Rep2
stranded mRNA Seq


title: Sample_155_PMA_pretreatno_pma_T

description:
Library name: JLPR_BurnInSample155
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K4me1, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2_H3K4me1
RELACS Pellet2


title: Sample_163_PMA_pretreatyes_pre_T_4

description:
Library name: JLPR_BurnInSample163
Next Generation Sequencing


title: Sample_164_PMA_pretreatyes_pre_T_4

description:
Library name: JLPR_BurnInSample164
Next Generation Sequencing


title: Sample_156_PMA_pretreatno_pma_T

description:
Library name: JLPR_BurnInSample156
Next Generation Sequencing


title: RNASeq Timecourse, Day0, MSL1-F KO, Rep3

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep3
stranded mRNA Seq


title: Sample_154_PMA_pretreatno_pma_T

description:
Library name: JLPR_BurnInSample154
Next Generation Sequencing


title: Sample_152_PMA_pretreatno_T_4

description:
Library name: JLPR_BurnInSample152
Next Generation Sequencing


title: RNASeq Timecourse, Day10, MSL1-F, Rep3

description:
Library name: Timecourse_D10_Neu_Diff_M1F_Rep3
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, ctrl, H3K27me3, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2_H3K27me3
RELACS Pellet2


title: RNASeq Timecourse, Day14, MSL1-F, Rep1

description:
Library name: Timecourse_D14_Neu_Diff_M1F_Rep1
stranded mRNA Seq


title: Sample_151_PMA_pretreatno_T_4

description:
Library name: JLPR_BurnInSample151
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K27ac, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2_H3K27ac
RELACS Pellet2


title: RNASeq Timecourse, Day10, MSL1-F, Rep2

description:
Library name: Timecourse_D10_Neu_Diff_M1F_Rep2
stranded mRNA Seq


title: Sample_153_PMA_pretreatno_T_4

description:
Library name: JLPR_BurnInSample153
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, Input, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1_Input
RELACS Pellet1


title: Sample_150_PMA_pretreatno_pma

description:
Library name: JLPR_BurnInSample150
Next Generation Sequencing


title: Sample_148_PMA_pretreatno_pma

description:
Library name: JLPR_BurnInSample148
Next Generation Sequencing


title: RNASeq Timecourse, Day10, MSL1-F, Rep1

description:
Library name: Timecourse_D10_Neu_Diff_M1F_Rep1
stranded mRNA Seq


title: Sample_145_PMA_pretreatno_DMSO_4

description:
Library name: JLPR_BurnInSample145
Next Generation Sequencing


title: RNASeq Timecourse, Day7, MSL1-F, Rep3

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep3
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, ctrl, H3K9me3, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1_H3K9me3
RELACS Pellet1


title: Sample_147_PMA_pretreatno_DMSO_4

description:
Library name: JLPR_BurnInSample147
Next Generation Sequencing


title: Sample_144_AICAR_pretreatyes_aicar_T_5224

description:
Library name: JLPR_BurnInSample144
Next Generation Sequencing


title: RNASeq Timecourse, Day7, MSL1-F, Rep2

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep2
stranded mRNA Seq


title: Sample_143_AICAR_pretreatyes_aicar_T_5224

description:
Library name: JLPR_BurnInSample143
Next Generation Sequencing


title: Sample_141_AICAR_pretreatyes_T_5224_3

description:
Library name: JLPR_BurnInSample141
Next Generation Sequencing


title: Sample_142_AICAR_pretreatyes_aicar_T_5224

description:
Library name: JLPR_BurnInSample142
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K4me1, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1_H3K4me1
RELACS Pellet1


title: RNASeq Timecourse, Day7, MSL1-F, Rep1

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep1
stranded mRNA Seq


title: Sample_137_AICAR_pretreatyes_aicar_T_8

description:
Library name: JLPR_BurnInSample137
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K27me3, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1_H3K27me3
RELACS Pellet1


title: Sample_139_AICAR_pretreatyes_T_5224_3

description:
Library name: JLPR_BurnInSample139
Next Generation Sequencing


title: RNASeq Timecourse, Day3, MSL1-F, Rep3

description:
Library name: Timecourse_D3_Neu_Diff_M1F_Rep3
stranded mRNA Seq


title: Sample_149_PMA_pretreatno_pma

description:
Library name: JLPR_BurnInSample149
Next Generation Sequencing


title: Sample_136_AICAR_pretreatyes_aicar_T_8

description:
Library name: JLPR_BurnInSample136
Next Generation Sequencing


title: Sample_135_AICAR_pretreatyes_T_8_3

description:
Library name: JLPR_BurnInSample135
Next Generation Sequencing


title: Sample_140_AICAR_pretreatyes_T_5224_3

description:
Library name: JLPR_BurnInSample140
Next Generation Sequencing


title: RNASeq Timecourse, Day0, MSL1-F, Rep4

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep4
stranded mRNA Seq


title: RNASeq Timecourse, Day3, MSL1-F, Rep1

description:
Library name: Timecourse_D3_Neu_Diff_M1F_Rep1
stranded mRNA Seq


title: RNASeq Timecourse, Day7, MSL1-F, Rep4

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep4
stranded mRNA Seq


title: RELACS ChIP-Seq, NPC, ctrl, H3K4me3, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1_H3K4me3
RELACS Pellet1


title: Sample_146_PMA_pretreatno_DMSO_4

description:
Library name: JLPR_BurnInSample146
Next Generation Sequencing


title: Sample_138_AICAR_pretreatyes_aicar_T_8

description:
Library name: JLPR_BurnInSample138
Next Generation Sequencing


title: Sample_134_AICAR_pretreatyes_T_8_3

description:
Library name: JLPR_BurnInSample134
Next Generation Sequencing


title: Sample_133_AICAR_pretreatyes_T_8_3

description:
Library name: JLPR_BurnInSample133
Next Generation Sequencing


title: RNASeq Timecourse, Day0, MSL1-F, Rep3

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep3
stranded mRNA Seq


title: Sample_132_AICAR_pretreatno_aicar_T_5224

description:
Library name: JLPR_BurnInSample132
Next Generation Sequencing


title: RNASeq Timecourse, Day0, MSL1-F, Rep2

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep2
stranded mRNA Seq


title: Sample_131_AICAR_pretreatno_aicar_T_5224

description:
Library name: JLPR_BurnInSample131
Next Generation Sequencing


title: RNASeq Timecourse, Day0, MSL1-F, Rep1

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep1
stranded mRNA Seq


title: RNASeq Timecourse, Day3, MSL1-F, Rep4

description:
Library name: Timecourse_D3_Neu_Diff_M1F_Rep4
stranded mRNA Seq


title: Sample_129_AICAR_pretreatno_T_5224_3

description:
Library name: JLPR_BurnInSample129
Next Generation Sequencing


title: RNASeq, Day14 Neurons, increased (2x Density), MSL1-F KO, Rep2

description:
Library name: D14_Neu_Diff_M1KO_2x_Density_Rep2
stranded mRNA Seq

value: 2x Seeding Density


title: Sample_130_AICAR_pretreatno_aicar_T_5224

description:
Library name: JLPR_BurnInSample130
Next Generation Sequencing


title: RNASeq, Day14 Neurons, increased (2x Density), MSL1-F KO, Rep1

description:
Library name: D14_Neu_Diff_M1KO_2x_Density_Rep1
stranded mRNA Seq


title: RNASeq, Day14 Neurons, increased (2x Density), MSL1-F KO, Rep3

description:
Library name: D14_Neu_Diff_M1KO_2x_Density_Rep3
stranded mRNA Seq


title: Sample_128_AICAR_pretreatno_T_5224_3

description:
Library name: JLPR_BurnInSample128
Next Generation Sequencing


title: RNASeq, Day14 Neurons, increased (2x Density), MSL1-F, Rep3

description:
Library name: D14_Neu_Diff_M1F_2x_Density_Rep3
stranded mRNA Seq


title: Sample_126_AICAR_pretreatno_aicar_T_8

description:
Library name: JLPR_BurnInSample126
Next Generation Sequencing


title: RNASeq, Day14 Neurons, normal (1x Density), MSL1-F KO, Rep1

description:
Library name: D14_Neu_Diff_M1KO_1x_Density_Rep1
stranded mRNA Seq

value: 1x Seeding Density


title: RNASeq, Day14 Neurons, normal (1x Density), MSL1-F KO, Rep3

description:
Library name: D14_Neu_Diff_M1KO_1x_Density_Rep3
stranded mRNA Seq


title: Sample_124_AICAR_pretreatno_aicar_T_8

description:
Library name: JLPR_BurnInSample124
Next Generation Sequencing


title: Sample_127_AICAR_pretreatno_T_5224_3

description:
Library name: JLPR_BurnInSample127
Next Generation Sequencing


title: Sample_125_AICAR_pretreatno_aicar_T_8

description:
Library name: JLPR_BurnInSample125
Next Generation Sequencing


title: RNASeq, Day14 Neurons, increased (2x Density), MSL1-F, Rep2

description:
Library name: D14_Neu_Diff_M1F_2x_Density_Rep2
stranded mRNA Seq


title: Sample_122_AICAR_pretreatno_T_8_3

description:
Library name: JLPR_BurnInSample122
Next Generation Sequencing


title: RNASeq, Day14 Neurons, normal (1x Density), MSL1-F KO, Rep2

description:
Library name: D14_Neu_Diff_M1KO_1x_Density_Rep2
stranded mRNA Seq


title: Sample_119_AICAR_pretreatyes_pre_aicar_T

description:
Library name: JLPR_BurnInSample119
Next Generation Sequencing


title: Sample_123_AICAR_pretreatno_T_8_3

description:
Library name: JLPR_BurnInSample123
Next Generation Sequencing


title: RNASeq, Day14 Neurons, normal (1x Density), MSL1-F, Rep1

description:
Library name: D14_Neu_Diff_M1F_1x_Density_Rep1
stranded mRNA Seq


title: RNASeq, Day14 Neurons, increased (2x Density), MSL1-F, Rep1

description:
Library name: D14_Neu_Diff_M1F_2x_Density_Rep1
stranded mRNA Seq


title: RNASeq, Day14 Neurons, normal (1x Density), MSL1-F, Rep2

description:
Library name: D14_Neu_Diff_M1F_1x_Density_Rep2
stranded mRNA Seq


title: Sample_118_AICAR_pretreatyes_pre_aicar_T

description:
Library name: JLPR_BurnInSample118
Next Generation Sequencing


title: RNASeq, Day3 Astrocytes, Auxin treated Day0-3, Rep4

description:
Library name: D3_Astro_diff_M1AID_Auxin_D0_to_D3_Rep4
stranded mRNA Seq

value: Day3 Astrocytes

value: Auxin treated during Day0-3 of Astrocyte differentiation


title: Sample_117_AICAR_pretreatyes_pre_T_3

description:
Library name: JLPR_BurnInSample117
Next Generation Sequencing


title: RELACS ChIP-Seq, NPC, ctrl, H3K27ac, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1_H3K27ac
RELACS Pellet1


title: Sample_116_AICAR_pretreatyes_pre_T_3

description:
Library name: JLPR_BurnInSample116
Next Generation Sequencing


title: RNASeq, Day3 Astrocytes, Auxin treated Day0-3, Rep2

description:
Library name: D3_Astro_diff_M1AID_Auxin_D0_to_D3_Rep2
stranded mRNA Seq


title: RNASeq, Day3 Astrocytes, Auxin treated Day0-3, Rep3

description:
Library name: D3_Astro_diff_M1AID_Auxin_D0_to_D3_Rep3
stranded mRNA Seq


title: RNASeq, Day3 Astrocytes, Auxin treated Day0-3, Rep1

description:
Library name: D3_Astro_diff_M1AID_Auxin_D0_to_D3_Rep1
stranded mRNA Seq


title: RNASeq Timecourse, Day3, MSL1-F, Rep2

description:
Library name: Timecourse_D3_Neu_Diff_M1F_Rep2
stranded mRNA Seq


title: RNASeq, Day3 Astrocytes, control, Rep4

description:
Library name: D3_Astro_diff_M1AID_ctrl_Rep4
stranded mRNA Seq


title: Sample_115_AICAR_pretreatyes_pre_T_3

description:
Library name: JLPR_BurnInSample115
Next Generation Sequencing


title: RNASeq, Day14 Neurons, normal (1x Density), MSL1-F, Rep3

description:
Library name: D14_Neu_Diff_M1F_1x_Density_Rep3
stranded mRNA Seq

value: Day14 Neurons


title: Sample_120_AICAR_pretreatyes_pre_aicar_T

description:
Library name: JLPR_BurnInSample120
Next Generation Sequencing

value: Human melanoma cells


title: Sample_121_AICAR_pretreatno_T_8_3

description:
Library name: JLPR_BurnInSample121
Next Generation Sequencing

value: BRAF - V600E


title: RNASeq, Day3 Astrocytes, control, Rep3

description:
Library name: D3_Astro_diff_M1AID_ctrl_Rep3
stranded mRNA Seq


title: Sample_111_AICAR_pretreatyes_pre_DMSO_3

description:
Library name: JLPR_BurnInSample111
Next Generation Sequencing


title: Sample_109_AICAR_pretreatyes_pre_DMSO_3

description:
Library name: JLPR_BurnInSample109
Next Generation Sequencing


title: RNASeq, Day3 Astrocytes, control, Rep1

description:
Library name: D3_Astro_diff_M1AID_ctrl_Rep1
stranded mRNA Seq


title: Sample_108_AICAR_pretreatno_aicar_T

description:
Library name: JLPR_BurnInSample108
Next Generation Sequencing


title: RNASeq, Day3 Astrocytes, control, Rep2

description:
Library name: D3_Astro_diff_M1AID_ctrl_Rep2
stranded mRNA Seq


title: Sample_110_AICAR_pretreatyes_pre_DMSO_3

description:
Library name: JLPR_BurnInSample110
Next Generation Sequencing


title: RNASeq, NPCs, Auxin treated 24 hours, rep4

description:
Library name: NPC_M1AID_Auxin_24h_Rep4
stranded mRNA Seq

value: 24h Auxin treated


title: RNASeq, NPCs, Auxin treated 24 hours, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1
stranded mRNA Seq


title: Sample_113_AICAR_pretreatyes_pre_aicar

description:
Library name: JLPR_BurnInSample113
Next Generation Sequencing


title: Sample_106_AICAR_pretreatno_aicar_T

description:
Library name: JLPR_BurnInSample106
Next Generation Sequencing


title: RNASeq, NPCs, Auxin treated 24 hours, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2
stranded mRNA Seq


title: Sample_114_AICAR_pretreatyes_pre_aicar

description:
Library name: JLPR_BurnInSample114
Next Generation Sequencing


title: Sample_104_AICAR_pretreatno_T_3

description:
Library name: JLPR_BurnInSample104
Next Generation Sequencing


title: Sample_105_AICAR_pretreatno_T_3

description:
Library name: JLPR_BurnInSample105
Next Generation Sequencing


title: Sample_103_AICAR_pretreatno_T_3

description:
Library name: JLPR_BurnInSample103
Next Generation Sequencing


title: RNASeq, NPCs, control, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2
stranded mRNA Seq


title: RNASeq, NPCs, control, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1
stranded mRNA Seq


title: RNASeq, NPCs, control, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3
stranded mRNA Seq


title: RNAseq, Day 14 Neurons,Auxin treated Day0-14, rep4

description:
Library name: D14_Neu_Diff_M1F_Auxin_Rep4
stranded mRNA Seq

value: Auxin treated during Day0-14 of Neuronal differentiation


title: Sample_101_AICAR_pretreatno_aicar

description:
Library name: JLPR_BurnInSample101
Next Generation Sequencing


title: Sample_102_AICAR_pretreatno_aicar

description:
Library name: JLPR_BurnInSample102
Next Generation Sequencing


title: RNAseq, Day 14 Neurons,Auxin treated Day0-14, rep3

description:
Library name: D14_Neu_Diff_M1F_Auxin_Rep3
stranded mRNA Seq


title: Sample_100_AICAR_pretreatno_aicar

description:
Library name: JLPR_BurnInSample100
Next Generation Sequencing


title: RNAseq, Day 14 Neurons,Auxin treated Day0-14, rep2

description:
Library name: D14_Neu_Diff_M1F_Auxin_Rep2
stranded mRNA Seq


title: Sample_99_AICAR_pretreatno_DMSO_3

description:
Library name: JLPR_BurnInSample99
Next Generation Sequencing


title: RNASeq, NPCs, Auxin treated 24 hours, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3
stranded mRNA Seq


title: Sample_107_AICAR_pretreatno_aicar_T

description:
Library name: JLPR_BurnInSample107
Next Generation Sequencing


title: Sample_112_AICAR_pretreatyes_pre_aicar

description:
Library name: JLPR_BurnInSample112
Next Generation Sequencing


title: RNASeq, NPCs, control, rep4

description:
Library name: NPC_M1AID_ctrl_Rep4
stranded mRNA Seq


title: Sample_98_AICAR_pretreatno_DMSO_3

description:
Library name: JLPR_BurnInSample98
Next Generation Sequencing


title: Sample_96_compound C_pretreatyes_compC_T_5224

description:
Library name: JLPR_BurnInSample96
Next Generation Sequencing


title: RNAseq, Day 14 Neurons,ctrl, rep4

description:
Library name: D14_Neu_Diff_M1F_no_Auxin_Rep4
stranded mRNA Seq


title: RNAseq, Day 14 Neurons,ctrl, rep2

description:
Library name: D14_Neu_Diff_M1F_no_Auxin_Rep2
stranded mRNA Seq


title: Sample_95_compound C_pretreatyes_compC_T_5224

description:
Library name: JLPR_BurnInSample95
Next Generation Sequencing


title: Sample_97_AICAR_pretreatno_DMSO_3

description:
Library name: JLPR_BurnInSample97
Next Generation Sequencing


title: Sample_94_compound C_pretreatyes_compC_T_5224

description:
Library name: JLPR_BurnInSample94
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-14, rep4

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D14_Rep4
stranded mRNA Seq


title: RNAseq, Day 14 Neurons,ctrl, rep1

description:
Library name: D14_Neu_Diff_M1F_no_Auxin_Rep1
stranded mRNA Seq


title: RNAseq, Day 14 Neurons,ctrl, rep3

description:
Library name: D14_Neu_Diff_M1F_no_Auxin_Rep3
stranded mRNA Seq


title: Sample_93_compound C_pretreatyes_T_5224_2

description:
Library name: JLPR_BurnInSample93
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-14, rep2

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D14_Rep2
stranded mRNA Seq


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-14, rep1

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D14_Rep1
stranded mRNA Seq


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-14, rep3

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D14_Rep3
stranded mRNA Seq


title: Sample_90_compound C_pretreatyes_compC_T_8

description:
Library name: JLPR_BurnInSample90
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, Auxin treated Day 7-14, rep4

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D7_to_D14_Rep4
stranded mRNA Seq

value: Auxin treated during Day7-14 of Neuronal differentiation


title: Sample_88_compound C_pretreatyes_compC_T_8

description:
Library name: JLPR_BurnInSample88
Next Generation Sequencing


title: Sample_89_compound C_pretreatyes_compC_T_8

description:
Library name: JLPR_BurnInSample89
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, Auxin treated Day 7-14, rep2

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D7_to_D14_Rep2
stranded mRNA Seq

value: Tir1+, MSL1-AID


title: Sample_91_compound C_pretreatyes_T_5224_2

description:
Library name: JLPR_BurnInSample91
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, Auxin treated Day 7-14, rep1

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D7_to_D14_Rep1
stranded mRNA Seq


title: Sample_87_compound C_pretreatyes_T_8_2

description:
Library name: JLPR_BurnInSample87
Next Generation Sequencing


title: RNAseq, Day 14 Neurons,Auxin treated Day0-14, rep1

description:
Library name: D14_Neu_Diff_M1F_Auxin_Rep1
stranded mRNA Seq


title: Sample_86_compound C_pretreatyes_T_8_2

description:
Library name: JLPR_BurnInSample86
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-7, rep4

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D7_Rep4
stranded mRNA Seq

value: Auxin treated during Day0-7 of Neuronal differentiation


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-7, rep3

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D7_Rep3
stranded mRNA Seq


title: Sample_85_compound C_pretreatyes_T_8_2

description:
Library name: JLPR_BurnInSample85
Next Generation Sequencing


title: Sample_83_compound C_pretreatno_compC_T_5224

description:
Library name: JLPR_BurnInSample83
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-7, rep1

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D7_Rep1
stranded mRNA Seq


title: RNAseq, Day 14 Neurons, Auxin treated Day 0-7, rep2

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D0_to_D7_Rep2
stranded mRNA Seq


title: Sample_82_compound C_pretreatno_compC_T_5224

description:
Library name: JLPR_BurnInSample82
Next Generation Sequencing


title: Sample_84_compound C_pretreatno_compC_T_5224

description:
Library name: JLPR_BurnInSample84
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, control, rep4

description:
Library name: D14_Neu_Diff_M1AID_ctrl_Rep4
stranded mRNA Seq

value: control


title: Sample_81_compound C_pretreatno_T_5224_2

description:
Library name: JLPR_BurnInSample81
Next Generation Sequencing


title: RNAseq, Day 14 Neurons, control, rep2

description:
Library name: D14_Neu_Diff_M1AID_ctrl_Rep2
stranded mRNA Seq


title: RNAseq, Day 14 Neurons, control, rep3

description:
Library name: D14_Neu_Diff_M1AID_ctrl_Rep3
stranded mRNA Seq


title: Sample_77_compound C_pretreatno_compC_T_8

description:
Library name: JLPR_BurnInSample77
Next Generation Sequencing


title: CUTRUN, NPC, M1F KO, IgG

description: Library name: NPC_M1KO_IgG

value: MSL1-F KO

value: NPCs

value: MSL1-FLAG KO


title: Sample_92_compound C_pretreatyes_T_5224_2

description:
Library name: JLPR_BurnInSample92
Next Generation Sequencing


title: Sample_80_compound C_pretreatno_T_5224_2

description:
Library name: JLPR_BurnInSample80
Next Generation Sequencing


title: CUTRUN, NPC, M1F KO,MSL1-FLAG, rep2

description: Library name: NPC_M1KO_FLAG_Rep2


title: RNAseq, Day 14 Neurons, control, rep1

description:
Library name: D14_Neu_Diff_M1AID_ctrl_Rep1
stranded mRNA Seq


title: RNAseq, Day 14 Neurons, Auxin treated Day 7-14, rep3

description:
Library name: D14_Neu_Diff_M1AID_Auxin_D7_to_D14_Rep3
stranded mRNA Seq


title: Sample_76_compound C_pretreatno_compC_T_8

description:
Library name: JLPR_BurnInSample76
Next Generation Sequencing


title: CUTRUN, NPC, M1F KO,MSL1-FLAG, rep1

description: Library name: NPC_M1KO_FLAG_Rep1


title: CUTRUN, NPC, M1F, IgG

description: Library name: NPC_M1F_IgG


title: Sample_74_compound C_pretreatno_T_8_2

description:
Library name: JLPR_BurnInSample74
Next Generation Sequencing


title: Sample_79_compound C_pretreatno_T_5224_2

description:
Library name: JLPR_BurnInSample79
Next Generation Sequencing


title: Sample_75_compound C_pretreatno_T_8_2

description:
Library name: JLPR_BurnInSample75
Next Generation Sequencing


title: CUTRUN, NPC, M1F, MSL1-FLAG, rep2

description: Library name: NPC_M1F_FLAG_Rep2


title: Sample_73_compound C_pretreatno_T_8_2

description:
Library name: JLPR_BurnInSample73
Next Generation Sequencing


title: Sample_72_compound C_pretreatyes_pre_compC_T

description:
Library name: JLPR_BurnInSample72
Next Generation Sequencing


title: CUTRUN, NPC, 24h Auxin treated, IgG

description: Library name: NPC_M1AID_24h_IgG


title: CUTRUN, NPC, M1F, MSL1-FLAG, rep1

description: Library name: NPC_M1F_FLAG_Rep1


title: Sample_71_compound C_pretreatyes_pre_compC_T

description:
Library name: JLPR_BurnInSample71
Next Generation Sequencing


title: CUTRUN, NPC, 24h Auxin treated, H4K16ac, rep2

description: Library name: NPC_M1AID_24hAux_H4K16ac_Rep2


title: CUTRUN, NPC, 24h Auxin treated, H4K16ac, rep1

description: Library name: NPC_M1AID_24hAux_H4K16ac_Rep1


title: Sample_70_compound C_pretreatyes_pre_compC_T

description:
Library name: JLPR_BurnInSample70
Next Generation Sequencing


title: Sample_69_compound C_pretreatyes_pre_T_2

description:
Library name: JLPR_BurnInSample69
Next Generation Sequencing


title: Sample_68_compound C_pretreatyes_pre_T_2

description:
Library name: JLPR_BurnInSample68
Next Generation Sequencing


title: CUTRUN, NPC, 24h Auxin treated, MOF, rep2

description: Library name: NPC_M1AID_24hAux_MOF_Rep2


title: Sample_78_compound C_pretreatno_compC_T_8

description:
Library name: JLPR_BurnInSample78
Next Generation Sequencing


title: Sample_67_compound C_pretreatyes_pre_T_2

description:
Library name: JLPR_BurnInSample67
Next Generation Sequencing


title: Sample_66_compound C_pretreatyes_pre_compC

description:
Library name: JLPR_BurnInSample66
Next Generation Sequencing


title: Sample_65_compound C_pretreatyes_pre_compC

description:
Library name: JLPR_BurnInSample65
Next Generation Sequencing


title: CUTRUN, NPC, 24h Auxin treated, MSL1-V5, rep2

description: Library name: NPC_M1AID_24hAux_V5_Rep2


title: Sample_64_compound C_pretreatyes_pre_compC

description:
Library name: JLPR_BurnInSample64
Next Generation Sequencing


title: CUTRUN, NPC, 24h Auxin treated, MSL2, rep1

description: Library name: NPC_M1AID_24hAux_MSL2_Rep1


title: CUTRUN, NPC, 24h Auxin treated, MSL1-V5, rep1

description: Library name: NPC_M1AID_24hAux_V5_Rep1


title: CUTRUN, NPC, ctrl, H4K16ac, rep2

description: Library name: NPC_M1AID_ctrl_H4K16ac_Rep2


title: Sample_63_compound C_pretreatyes_pre_DMSO_2

description:
Library name: JLPR_BurnInSample63
Next Generation Sequencing


title: Sample_61_compound C_pretreatyes_pre_DMSO_2

description:
Library name: JLPR_BurnInSample61
Next Generation Sequencing


title: CUTRUN, NPC, ctrl, IgG

description: Library name: NPC_M1AID_ctrl_IgG


title: Sample_60_compound C_pretreatno_compC_T

description:
Library name: JLPR_BurnInSample60
Next Generation Sequencing


title: CUTRUN, NPC, ctrl, H4K16ac, rep1

description: Library name: NPC_M1AID_ctrl_H4K16ac_Rep1


title: CUTRUN, NPC, ctrl, MOF, rep2

description: Library name: NPC_M1AID_ctrl_MOF_Rep2


title: Sample_59_compound C_pretreatno_compC_T

description:
Library name: JLPR_BurnInSample59
Next Generation Sequencing


title: CUTRUN, NPC, ctrl, MOF, rep1

description: Library name: NPC_M1AID_ctrl_MOF_Rep1


title: Sample_58_compound C_pretreatno_compC_T

description:
Library name: JLPR_BurnInSample58
Next Generation Sequencing


title: Sample_57_compound C_pretreatno_T_2

description:
Library name: JLPR_BurnInSample57
Next Generation Sequencing


title: CUTRUN, NPC, ctrl, MSL2, rep2

description: Library name: NPC_M1AID_ctrl_MSL2_Rep2


title: CUTRUN, NPC, 24h Auxin treated, MOF, rep1

description: Library name: NPC_M1AID_24hAux_MOF_Rep1


title: Sample_56_compound C_pretreatno_T_2

description:
Library name: JLPR_BurnInSample56
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-AID Auxin treated Day0-7, rep2

description:
Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Rep2
ATAC-Seq

data_processing:
Fastq files were aligned with snakePipes version 3 against the mm10 reference genome, using the DNA-mapping mode and the ATAC-seq mode. To generate the union peak files the TOBIAS package was used (Bentsen et al., 2020).
Assembly: mm10
Supplementary files format and content: peaks were generated using MACS2

value: Day7 Neurons

value: Day0-Day7 Auxin treated


title: CUTRUN, NPC, ctrl, MSL1-V5, rep2

description: Library name: NPC_M1AID_ctrl_V5_Rep2


title: Sample_54_compound C_pretreatno_compC

description:
Library name: JLPR_BurnInSample54
Next Generation Sequencing


title: Sample_55_compound C_pretreatno_T_2

description:
Library name: JLPR_BurnInSample55
Next Generation Sequencing


title: CUTRUN, NPC, 24h Auxin treated, MSL2, rep2

description: Library name: NPC_M1AID_24hAux_MSL2_Rep2


title: Sample_53_compound C_pretreatno_compC

description:
Library name: JLPR_BurnInSample53
Next Generation Sequencing


title: CUTRUN, NPC, ctrl, MSL1-V5, rep1

description: Library name: NPC_M1AID_ctrl_V5_Rep1


title: Sample_62_compound C_pretreatyes_pre_DMSO_2

description:
Library name: JLPR_BurnInSample62
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-AID ctrl, rep4

description:
Library name: D7_Neu_Diff_M1AID_ctrl_Rep4
ATAC-Seq


title: Sample_52_compound C_pretreatno_compC

description:
Library name: JLPR_BurnInSample52
Next Generation Sequencing


title: Sample_51_compound C_pretreatno_DMSO_2

description:
Library name: JLPR_BurnInSample51
Next Generation Sequencing


title: Sample_50_compound C_pretreatno_DMSO_2

description:
Library name: JLPR_BurnInSample50
Next Generation Sequencing


title: Sample_49_compound C_pretreatno_DMSO_2

description:
Library name: JLPR_BurnInSample49
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-AID ctrl, rep2

description:
Library name: D7_Neu_Diff_M1AID_ctrl_Rep2
ATAC-Seq


title: ATAC, Day7 Neuron, MSL1-AID ctrl, rep1

description:
Library name: D7_Neu_Diff_M1AID_ctrl_Rep1
ATAC-Seq


title: ATAC, Day14 Neuron, MSL1-F KO, rep3

description:
Library name: Timecourse_D14_Neu_Diff_M1KO_Rep3
ATAC-Seq


title: Sample_47_dexamethasone_pretreatyes_Dex_T_5224

description:
Library name: JLPR_BurnInSample47
Next Generation Sequencing


title: Sample_46_dexamethasone_pretreatyes_Dex_T_5224

description:
Library name: JLPR_BurnInSample46
Next Generation Sequencing


title: ATAC, Day14 Neuron, MSL1-F KO, rep2

description:
Library name: Timecourse_D14_Neu_Diff_M1KO_Rep2
ATAC-Seq


title: Sample_45_dexamethasone_pretreatyes_T_5224_1

description:
Library name: JLPR_BurnInSample45
Next Generation Sequencing


title: ATAC, Day14 Neuron, MSL1-F KO, rep1

description:
Library name: Timecourse_D14_Neu_Diff_M1KO_Rep1
ATAC-Seq


title: CUTRUN, NPC, ctrl, MSL2, rep1

description: Library name: NPC_M1AID_ctrl_MSL2_Rep1


title: Sample_44_dexamethasone_pretreatyes_T_5224_1

description:
Library name: JLPR_BurnInSample44
Next Generation Sequencing


title: ATAC, Day14 Neuron, MSL1-F, rep4

description:
Library name: Timecourse_D14_Neu_Diff_M1F_Rep4
ATAC-Seq


title: ATAC, Day14 Neuron, MSL1-F, rep2

description:
Library name: Timecourse_D14_Neu_Diff_M1F_Rep2
ATAC-Seq


title: ATAC, Day14 Neuron, MSL1-F, rep3

description:
Library name: Timecourse_D14_Neu_Diff_M1F_Rep3
ATAC-Seq


title: Sample_42_dexamethasone_pretreatyes_Dex_T_8

description:
Library name: JLPR_BurnInSample42
Next Generation Sequencing


title: Sample_40_dexamethasone_pretreatyes_Dex_T_8

description:
Library name: JLPR_BurnInSample40
Next Generation Sequencing


title: ATAC, Day14 Neuron, MSL1-F, rep1

description:
Library name: Timecourse_D14_Neu_Diff_M1F_Rep1
ATAC-Seq


title: ATAC, Day7 Neuron, MSL1-AID Auxin treated Day0-7, rep1

description:
Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Rep1
ATAC-Seq


title: Sample_43_dexamethasone_pretreatyes_T_5224_1

description:
Library name: JLPR_BurnInSample43
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-AID ctrl, rep3

description:
Library name: D7_Neu_Diff_M1AID_ctrl_Rep3
ATAC-Seq


title: ATAC, Day7 Neuron, MSL1-F KO, rep4

description:
Library name: Timecourse_D7_Neu_Diff_M1KO_Rep4
ATAC-Seq


title: Sample_41_dexamethasone_pretreatyes_Dex_T_8

description:
Library name: JLPR_BurnInSample41
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-F KO, rep3

description:
Library name: Timecourse_D7_Neu_Diff_M1KO_Rep3
ATAC-Seq


title: Sample_37_dexamethasone_pretreatyes_T_8_1

description:
Library name: JLPR_BurnInSample37
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-F KO, rep1

description:
Library name: Timecourse_D7_Neu_Diff_M1KO_Rep1
ATAC-Seq


title: Sample_36_dexamethasone_pretreatno_Dex_T_5224

description:
Library name: JLPR_BurnInSample36
Next Generation Sequencing


title: Sample_48_dexamethasone_pretreatyes_Dex_T_5224

description:
Library name: JLPR_BurnInSample48
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-F, rep4

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep4
ATAC-Seq


title: ATAC, Day14 Neuron, MSL1-F KO, rep4

description:
Library name: Timecourse_D14_Neu_Diff_M1KO_Rep4
ATAC-Seq


title: Sample_35_dexamethasone_pretreatno_Dex_T_5224

description:
Library name: JLPR_BurnInSample35
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-F, rep3

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep3
ATAC-Seq


title: Sample_34_dexamethasone_pretreatno_Dex_T_5224

description:
Library name: JLPR_BurnInSample34
Next Generation Sequencing


title: Sample_38_dexamethasone_pretreatyes_T_8_1

description:
Library name: JLPR_BurnInSample38
Next Generation Sequencing


title: Sample_32_dexamethasone_pretreatno_T_5224_1

description:
Library name: JLPR_BurnInSample32
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-F, rep1

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep1
ATAC-Seq


title: Sample_33_dexamethasone_pretreatno_T_5224_1

description:
Library name: JLPR_BurnInSample33
Next Generation Sequencing


title: ATAC, NPC, MSL1-F KO, rep4

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep4
ATAC-Seq


title: Sample_31_dexamethasone_pretreatno_T_5224_1

description:
Library name: JLPR_BurnInSample31
Next Generation Sequencing


title: Sample_39_dexamethasone_pretreatyes_T_8_1

description:
Library name: JLPR_BurnInSample39
Next Generation Sequencing


title: ATAC, NPC, MSL1-F KO, rep3

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep3
ATAC-Seq


title: ATAC, NPC, MSL1-F KO, rep1

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep1
ATAC-Seq


title: ATAC, NPC, MSL1-F KO, rep2

description:
Library name: Timecourse_D0_Neu_Diff_M1KO_Rep2
ATAC-Seq


title: Sample_28_dexamethasone_pretreatno_Dex_T_8

description:
Library name: JLPR_BurnInSample28
Next Generation Sequencing


title: ATAC, NPC, MSL1-F, rep4

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep4
ATAC-Seq


title: Sample_30_dexamethasone_pretreatno_Dex_T_8

description:
Library name: JLPR_BurnInSample30
Next Generation Sequencing


title: Sample_29_dexamethasone_pretreatno_Dex_T_8

description:
Library name: JLPR_BurnInSample29
Next Generation Sequencing


title: ATAC, Day7 Neuron, MSL1-F KO, rep2

description:
Library name: Timecourse_D7_Neu_Diff_M1KO_Rep2
ATAC-Seq


title: ATAC, NPC, MSL1-F, rep3

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep3
ATAC-Seq


title: Sample_27_dexamethasone_pretreatno_T_8_1

description:
Library name: JLPR_BurnInSample27
Next Generation Sequencing


title: Sample_24_dexamethasone_pretreatyes_pre_Dex_T

description:
Library name: JLPR_BurnInSample24
Next Generation Sequencing


title: Sample_26_dexamethasone_pretreatno_T_8_1

description:
Library name: JLPR_BurnInSample26
Next Generation Sequencing


title: ATAC, NPC, MSL1-AID Auxin treated 24 hours, rep3

description:
Library name: NPC_M1AID_Auxin_24h_Rep3
ATAC-Seq


title: Sample_25_dexamethasone_pretreatno_T_8_1

description:
Library name: JLPR_BurnInSample25
Next Generation Sequencing


title: ATAC, NPC, MSL1-F, rep2

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep2
ATAC-Seq


title: ATAC, Day7 Neuron, MSL1-F, rep2

description:
Library name: Timecourse_D7_Neu_Diff_M1F_Rep2
ATAC-Seq


title: Sample_23_dexamethasone_pretreatyes_pre_Dex_T

description:
Library name: JLPR_BurnInSample23
Next Generation Sequencing


title: ATAC, NPC, MSL1-AID Auxin treated 24 hours, rep2

description:
Library name: NPC_M1AID_Auxin_24h_Rep2
ATAC-Seq


title: ATAC, NPC, MSL1-F, rep1

description:
Library name: Timecourse_D0_Neu_Diff_M1F_Rep1
ATAC-Seq


title: ATAC, NPC, MSL1-AID Auxin treated 24 hours, rep1

description:
Library name: NPC_M1AID_Auxin_24h_Rep1
ATAC-Seq


title: Sample_20_dexamethasone_pretreatyes_pre_T_1

description:
Library name: JLPR_BurnInSample20
Next Generation Sequencing


title: Sample_22_dexamethasone_pretreatyes_pre_Dex_T

description:
Library name: JLPR_BurnInSample22
Next Generation Sequencing


title: ATAC, NPC, MSL1-AID ctrl, rep3

description:
Library name: NPC_M1AID_ctrl_Rep3
ATAC-Seq


title: Sample_21_dexamethasone_pretreatyes_pre_T_1

description:
Library name: JLPR_BurnInSample21
Next Generation Sequencing


title: ATAC, NPC, MSL1-AID ctrl, rep1

description:
Library name: NPC_M1AID_ctrl_Rep1
ATAC-Seq


title: Sample_18_dexamethasone_pretreatyes_pre_Dex

description:
Library name: JLPR_BurnInSample18
Next Generation Sequencing


title: Sample_19_dexamethasone_pretreatyes_pre_T_1

description:
Library name: JLPR_BurnInSample19
Next Generation Sequencing


title: ATAC, NPC, MSL1-AID ctrl, rep2

description:
Library name: NPC_M1AID_ctrl_Rep2
ATAC-Seq


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Wwc1 Viewpoint1, rep2

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Wwc1_VP1_Rep2

data_processing:
UMI-4C data were analyzed using the UMI4Cats package (Ramos-Rodríguez, Subirana-Granés, and Pasquali 2021). In brief, the viewpoints per sample were demultiplexed using the 'demultiplexFastq' function and count tables were generated using the 'contactsUMI4C' function, both implemented in UMI4Cats. Only reads containing a proper barcode, PAD-sequence and a restriction cut site were retained and aligned to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: UMI-normalized trends were extracted and converted into bedgraph files for visualization. For this purpose, the median of the normalized values between replicates were used to construct subtract bedgraph files, respectively.
Library strategy: 4C-seq

extract_protocol:
UMI-4C was performed according to the protocol by Schwartzman et al. with small modifications (Schwartzman et al., 2016). In brief, Day 7 In-vitro differentiated neurons were harvested and collected in 10%FCS/1xPBS and crosslinked for 10 min using 2% formaldehyde. Crosslinked cell pellets were snap-frozen and stored at −80°C until further processing. Frozen pellets were resuspended in 250 µL prediluted DpnII buffer and 7.5 µL preheated 10% SDS and incubated on a thermomixer for 1 h at 37°C, shaking at 900 RPM. After adding 75 µL 10% Triton X-100, the solution was incubated again (1 h, 37°C, 900 RPM). The chromatin was digested using 300 U DpnII (NEB, R0543L) in three stages (100 U for 2 h, 100 U overnight, 100 U for 2 h) at 37°C and 900 RPM. The samples were incubated at 65°C for 20 min to inactivate the restriction enzyme and put on ice. Next, the chromatin was ligated by adding 2000 U of T4 DNA ligase (NEB, M0202M) and 10× T4 DNA ligase buffer to a total volume of 650 µL, and the solution was incubated overnight at 16°C with 300 RPM shaking. Ligated chromatin was de-crosslinked by incubation with 4 µL Proteinase K (20 mg/mL, Qiagen, Cat. 19131) overnight at 65°C and 300 RPM. A 3C template was then purified using 1× Ampure XP beads (Beckman Coulter, A63881). Up to 4 µg 3C template per sample were sheared using microTUBE snap-cap tubes (Covaris, 520045) in a Covaris E220 sonicator to an average fragment length of 300 bp.
UMI-4C sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645). For each sample, library prep was performed in up to four parallel reactions with a maximum input of 1000 ng per reaction, including a size selection targeting fragments with a length of 300–400 bp (unless the input was <100 ng) and 4–8 cycles of PCR enrichment depending on the input. Next, a series of nested PCR reactions were performed to enrich for fragments captured in the region of the viewpoints of interest. Both rounds of PCR contained 2 µL 10 mM Illumina enrichment primer 2 (CAAGCAGAAGACGGCATACGA) and either a viewpoint-specific “upstream” (reaction 1, 2 µL 10 mM, see Supp. Table 2) or “downstream” (reaction 2, 2 µL 10 mM, see Supp. Table 2) primer. For each sample, we performed up to eight nested PCR reactions in parallel with an input of 100–200 ng per reaction using the KAPA2G Robust ready mix (Sigma-Aldrich, KK5702) in a volume of 50 µL. PCR program: 3 min at 95°C, 20 cycles (18 cycles for reaction 2) of 15 sec at 95°C, 15 sec at 55°C, 60 sec at 72°C, and final elongation of 5 min at 72°C. Between PCR reactions, the product was cleaned up using 1× AmpureXP beads and eluted in 21 µL. The final PCR product was cleaned up using 0.7× AmpureXP beads and eluted in 25 µL. Reactions per sample were pooled, and library concentration was quantified via qPCR using the KAPA SYBR FAST qPCR master mix (Sigma-Aldrich, KK4602). Final libraries were quality controlled for size and concentration and sequenced on a NovaSeq Illumina sequencer with 100-bp paired-end reads.


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Wwc1 Viewpoint2, rep2

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Wwc1_VP2_Rep2


title: Sample_15_dexamethasone_pretreatyes_pre_DMSO_1

description:
Library name: JLPR_BurnInSample15
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Wwc1 Viewpoint2, rep1

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Wwc1_VP2_Rep1


title: Sample_14_dexamethasone_pretreatyes_pre_DMSO_1

description:
Library name: JLPR_BurnInSample14
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Cxcr4 Viewpoint, rep2

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Cxcr4_Rep2


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Mavs Viewpoint, rep2

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Mavs_Rep2


title: Sample_16_dexamethasone_pretreatyes_pre_Dex

description:
Library name: JLPR_BurnInSample16
Next Generation Sequencing


title: Sample_17_dexamethasone_pretreatyes_pre_Dex

description:
Library name: JLPR_BurnInSample17
Next Generation Sequencing


title: Sample_13_dexamethasone_pretreatyes_pre_DMSO_1

description:
Library name: JLPR_BurnInSample13
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Wwc1 Viewpoint1, rep1

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Wwc1_VP1_Rep1


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Cxcr4 Viewpoint, rep1

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Cxcr4_Rep1


title: Sample_12_dexamethasone_pretreatno_Dex_T

description:
Library name: JLPR_BurnInSample12
Next Generation Sequencing


title: Sample_10_dexamethasone_pretreatno_Dex_T

description:
Library name: JLPR_BurnInSample10
Next Generation Sequencing


title: Sample_11_dexamethasone_pretreatno_Dex_T

description:
Library name: JLPR_BurnInSample11
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, Auxin treated Day0-Day7, Mavs Viewpoint, rep1

description: Library name: D7_Neu_Diff_M1AID_Auxin_D0_to_D7_Mavs_Rep1


title: UMI-4C-Seq, Day7 Neurons, ctrl, Wwc1 Viewpoint1, rep2

description: Library name: D7_Neu_Diff_M1AID_ctrl_Wwc1_VP1_Rep2


title: eWAT ADAR1 -/-, Ifih1 -/-,high fat diet, rep 3

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
Fastq files were aligned to mouse mm10  reference genome using STAR alignment(v2.5.0a) .
Based on GTF annotation files from GENCODE GRCm38 M16, quantification of gene expression was determined using fragments counting mode by FeatureCounts.
Gene expression was normalized to RPKM (Reads Per Kilobase Million).
Assembly: mm10
Supplementary files format and content: txt
Supplementary files format and content: tab-delimited text files include log2(RPKM+1) values for each Sample.

source_name: eWAT

extract_protocol:
Total RNA was extracted from adipose tissues with miRNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: eWAT


title: Sample_6_dexamethasone_pretreatno_Dex

description:
Library name: JLPR_BurnInSample6
Next Generation Sequencing


title: Sample_9_dexamethasone_pretreatno_T_1

description:
Library name: JLPR_BurnInSample9
Next Generation Sequencing


title: Sample_8_dexamethasone_pretreatno_T_1

description:
Library name: JLPR_BurnInSample8
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, ctrl, Cxcr4 Viewpoint, rep2

description: Library name: D7_Neu_Diff_M1AID_ctrl_Cxcr4_Rep2


title: eWAT ADAR1 -/-, Ifih1 -/-,high fat diet, rep 1


title: Sample_3_dexamethasone_pretreatno_DMSO_1

description:
Library name: JLPR_BurnInSample3
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, ctrl, Wwc1 Viewpoint2, rep2

description: Library name: D7_Neu_Diff_M1AID_ctrl_Wwc1_VP2_Rep2


title: Sample_4_dexamethasone_pretreatno_Dex

description:
Library name: JLPR_BurnInSample4
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, ctrl, Wwc1 Viewpoint2, rep1

description: Library name: D7_Neu_Diff_M1AID_ctrl_Wwc1_VP2_Rep1


title: Sample_2_dexamethasone_pretreatno_DMSO_1

description:
Library name: JLPR_BurnInSample2
Next Generation Sequencing


title: Sample_1_dexamethasone_pretreatno_DMSO_1

description:
Library name: JLPR_BurnInSample1
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, ctrl, Mavs Viewpoint, rep1

description: Library name: D7_Neu_Diff_M1AID_ctrl_Mavs_Rep1


title: eWAT ADAR1 flox/flox, Ifih1 -/-, high fat diet, rep 2


title: Tlo+JNKIN8 --> Thi_10xfatemap

description:
Library name: 10xfatemap_S6
Next Generation Sequencing

data_processing:
For scRNA-seq, data from 6 samples was processed using kallisto bustools for transcript quantification, followed by empty droplet removal using DropletUtils. Individual Seurat objects were created for each sample with quality control filtering (removing cells with <1600 or >7200 genes, <2000 or >36000 UMIs, and >20% mitochondrial reads), then merged and normalized using Seurat's log-normalization method. Batch effects between samples were corrected using Harmony integration, and the final normalized expression matrix was exported as logNormalizedCounts.txt and normalizedCounts.txt, representing log-transformed and non-log-transformed normalized gene expression values per cell, respectively.
Assembly: hg19
Supplementary files format and content: for single cell sequencing data, the tab-delimited text file includes normalized and log2normalized counts.

extract_protocol:
For scRNA-seq, we used the 10X Genomics scRNA-seq kit v3 (PN-1000121, PN-1000128, PN-1000213) to sequence barcoded cells. We resuspended the cells (targeting ~10,000 cells for recovery per sample) in PBS and followed the protocol for the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 as per manufacturer directions (10X Genomics).
For scRNA-seq, we used the 10X Genomics scRNA-seq kit v3 (PN-1000121, PN-1000128, PN-1000213) to sequence barcoded cells. We resuspended the cells (targeting ~10,000 cells for recovery per sample) in PBS and followed the protocol for the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 as per manufacturer directions (10X Genomics). In brief, we generated gel beads-in-emulsion (GEMs) using the 10X Chromium system and subsequently extracted and amplified (11 cycles) barcoded cDNA as per post-GEM RT-cleanup instructions. We then used a fraction of this amplified cDNA (25%) and proceeded with fragmentation, end-repair, poly A-tailing, adapter ligation, and 10X sample indexing per the manufacturer's protocol. We quantified libraries using the High Sensitivity dsDNA kit (Thermo Fisher Q32854) on Qubit 2.0 Fluorometer (Thermo Fisher Q32866) and Bioanalyzer 2100 (Agilent G2939BA) analysis prior to sequencing on a NextSeq 2000 machine (Illumina) with a P3 100 kit using 28 cycles for read 1, 91 cycles for read 2, and 8 cycles for i7 index.

treatment_protocol: Cells in each experiment were treated as described in the title of the sample, abbreviations are defined as follow. For scRNAseq samples: Thi: 5nM trametinib, Tlo: 1nM trametinib, JNKIN8: 1uM JNK-IN-8


title: Tlo+JNKIN8_10xfatemap

description:
Library name: 10xfatemap_S5
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, ctrl, Wwc1 Viewpoint1, rep1

description: Library name: D7_Neu_Diff_M1AID_ctrl_Wwc1_VP1_Rep1


title: eWAT ADAR1 flox/flox, Ifih1 -/-, high fat diet, rep 1


title: Thi+JNKIN8_10xfatemap

description:
Library name: 10xfatemap_S4
Next Generation Sequencing


title: UMI-4C-Seq, Day7 Neurons, ctrl, Cxcr4 Viewpoint, rep1

description: Library name: D7_Neu_Diff_M1AID_ctrl_Cxcr4_Rep1


title: iWAT ADAR1 -/-, Ifih1 -/-,high fat diet, rep 3

source_name: iWAT

value: iWAT


title: Tlo_10xfatemap

description:
Library name: 10xfatemap_S2
Next Generation Sequencing


title: Thi_10xfatemap

description:
Library name: 10xfatemap_S1
Next Generation Sequencing


title: Tlo --> Thi_10xfatemap

description:
Library name: 10xfatemap_S3
Next Generation Sequencing


title: Sample_7_dexamethasone_pretreatno_T_1

description:
Library name: JLPR_BurnInSample7
Next Generation Sequencing


title: EpA

city: Guangzhou

first: yang

last: zhou

address: South Shatai Road, Baiyun District

institute: Southern Medical University

description: Library name: sample2

data_processing:
Raw FASTQ sequencing data underwent quality control processing using Trim Galore to ensure optimal sequence integrity. The resulting high-quality sequences were aligned to the GRCm38 mouse reference genome using Bowtie2. To enhance data quality, mitochondrial reads and low-quality alignments were filtered out using SAMtools, while PCR duplicates were eliminated using Sambamba. ENCODE blacklist regions were subsequently removed using BEDtools to minimize potential artifacts. Read coordinates were adjusted using alignmentSieve, followed by sorting and indexing with SAMtools to generate BAM files. Finally, peak calling was performed using MACS3 to identify regions of significant enrichment.
Assembly: GRCm38
Supplementary files format and content: DMSO.bw and Epa.bw

source_name: splenocytes

extract_protocol:
cold lysis buffer was used to get crude nuclei.
40,000 nuclei are subjected to a transposase reaction using Tn5 enzyme (Illumina). The transposed DNA fragments are recovered using the MinElute PCR Purification Kit (Qiagen).PCR amplification is carried out using 1X NEBNext High - Fidelity PCR Master Mix (New England Biolabs, MA). The amplified products are recovered using the MinElute PCR Purification Kit (Qiagen).

value: splenocytes

tag: strain

value: T cell

value: EpA


title: UMI-4C-Seq, Day7 Neurons, ctrl, Mavs Viewpoint, rep2

description: Library name: D7_Neu_Diff_M1AID_ctrl_Mavs_Rep2


title: Sample_5_dexamethasone_pretreatno_Dex

description:
Library name: JLPR_BurnInSample5
Next Generation Sequencing

value: Human melanoma cells

value: BRAF - V600E


title: eWAT ADAR1 -/-, Ifih1 -/-,high fat diet, rep 2