title: Human main RNA-seq matched CUT&RUN time-course sample D7_1

city: Boston

first: Nilay

last: Sethi

state: Massachusetts

address: 450 Brookline Avenue, D742

department: MCO

institute: Dana-Farber cancer institute

description:
Library name: rnaseq_D7_1
Main RNA-seq sample corresponding to the CUT&RUN SOX9 degradation/recovery time-course; day 7; source directory rnaseq; paired FASTQ files rnaseq/D7_1_1.fq.gz and rnaseq/D7_1_2.fq.gz.

data_processing:
Sequencing reads were demultiplexed and delivered as compressed FASTQ files.
Read quality was assessed and adapter/low-quality sequence was removed as needed.
Human ATAC-seq, CUT&RUN, and RNA-seq reads were aligned to the hg38 reference genome.
Assay-specific downstream analyses were performed to generate accessibility, occupancy, peak, and expression outputs.
Assembly: hg38
Supplementary files format and content: Tar.gz archive containing processed data files for this study, including per-sample processed outputs generated from ATAC-seq, CUT&RUN, and RNA-seq datasets.

source_name: colon

growth_protocol: HT29-dTAG and LS180 human colon cancer cells were maintained under standard cell-culture conditions at 37 C in a humidified incubator with 5% CO2.

extract_protocol:
For ATAC-seq, nuclei were prepared and transposed using standard assay workflows. For CUT&RUN, chromatin-protein complexes were captured and digested using standard CUT&RUN procedures. For RNA-seq, total RNA was isolated using standard RNA extraction methods.
Sequencing libraries were prepared using standard Illumina-compatible ATAC-seq, CUT&RUN, and RNA-seq library construction workflows.

treatment_protocol: For the main time-course datasets, cells were treated with DMSO or SOX9-degradation/recovery conditions and harvested at the indicated time points (DMSO, D2, D4, D5, D7, D10, and D13). Additional samples include ARID1A/ARID1B perturbation and SOX9-variant conditions as noted in the sample descriptions.

value: colon

value: epithelial cell

value: SOX9 degradation/recovery time course

value: main RNA-seq dataset matched to the SOX9 degradation and recovery CUT&RUN sample series; day 7

value: rnaseq


title: Human main RNA-seq matched CUT&RUN time-course sample D4_1

status: Public on Jun 16 2026

type: SRA

country: USA

description:
Library name: rnaseq_D4_1
Main RNA-seq sample corresponding to the CUT&RUN SOX9 degradation/recovery time-course; day 4; source directory rnaseq; paired FASTQ files rnaseq/D4_1_1.fq.gz and rnaseq/D4_1_2.fq.gz.

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: main RNA-seq dataset matched to the SOX9 degradation and recovery CUT&RUN sample series; day 4

tag: batch


title: HTO counts of multiplex sSL0256 containing tissue & timepoint(s) CTX (L); P4

city: Klosterneuburg

first: Gaia

last: Novarino

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (ISTA)

description:
Library name: sSL0256_HTO
Samples #23/452, #23/728, #23/529, #23/88, #23/1504, #22/2922, #23/452, #23/728, #23/529, #23/88, #23/1504, #22/2922 with genotypes Bckdk-/-, Bckdk-/-, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/-, Bckdk-/-, Bckdk-/-, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/- and sex f, m, f, m, f, m, f, m, f, m, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds

library_source: other

data_processing:
Pre-processing was done per 10X lane (i.e., per multiplexing group of 4-6 samples). Peaks for the snATAC-seq modality were called for each run separately using MACS2 (v2.2.7.1) within Signac. A set of consensus peaks for the snATAC-seq analysis was created according to Signac. CMO demultiplexing information was taken from Cellranger output and added as metadata. Doublets were identified using scDblFinder6 (v1.14.0), separately for snRNA-seq and snATAC-seq modality. snRNA-seq parameters for the scDblFinder function were dims = 50, cluster = TRUE, knownUse = “discard”. snATAC-seq features were first aggregated (aggregateFeatures function, k = 500) and parameters for scDblFinder were dims = 50, aggegateFeatures = TRUE. Cells identified as doublets based on CMO data were included as known doublets (knownDoublets parameter). Quality control metrics such as the percentage of mitochondrial reads, nucleosome signal, and transcription start site (TSS) enrichment were calculated per run. After removing known and estimated doublets outlier thresholds for snRNA-seq read counts (nCount_RNA) or snATAC-seq read counts (nCount_ATAC) were derived using the isOutlier function from the scuttle package7 (v1.10.2) with parameters nmads = 3, type = “both”, log = TRUE. Nuclei falling outside these thresholds or with more than 5% of mitochondrial reads were removed. Complete datasets for each time point/tissue were created by integrating individual Seurat objects representing separate 10X lanes (i.e., multiplexing groups). snRNA-seq data were normalized using SCTransform8,9 from Seurat with parameter vst.flavor = “v2”. Integration of normalized snRNA-seq data was performed according to Seurat using the reciprocal PCA method with the following non-default parameters: SelectIntegrationFeatures(nfeatures = 2500), FindIntegrationAnchors(reduction = “rpca”), IntegrateData(dims = 1:50). Integration of snATAC-seq data was performed at the level of the LSI embedding using IntegrateEmbeddings(dims.to.integrate = 1:50) function with the integration anchors derived from snRNA-seq data. Identification of cell types was performed using the combination of both modalities, snRNA-seq and snATAC-seq. A PCA embedding was derived for the integrated snRNA-seq data, weighted nearest neighbor (WNN) graph was calculated using the FindMultimodalNeighbors function with the integrated LSI and integrated PCA reductions as input and dims_atac = 2:50, dims_rna = 1:50. The resulting WNN graph was used for UMAP visualization of the dataset and identification of clusters
Samples used for multi-omics analyses were de-multiplexed, and the raw sequencing data was converted to FASTQ format using bcl2fastq (v2.20.0.422). Joint processing of the gene expression and ATAC modalities was performed using the cellranger-arc software (v2.0.0). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). To capture CMO reads, the gene expression modality was separately processed using the cellranger count pipeline (v7.0.0 and v7.1.0), aligning it against the mm10 reference genome (refdata-gex-mm10-2020-A, obtained from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz). Each nucleus was assigned to the sample of origin as part of further demultiplexing, for which a Gaussian mixture model was fitted to the CMO count distributions. The probability that a given CMO read count was derived from background or positive signal was then inferred (as described in2).
Assembly: mm10
Supplementary files format and content: Cellranger output files (GEX): filtered feature matrix (h5 format); QC categories (csv)
Supplementary files format and content: Cellranger output files (ATAC): filtered feature matrix (h5 format); atac fragments (tsv & index); atac peak annotation (tsv & bed)
Supplementary files format and content: Downstream pipeline: integrated seurat object (RDS); pipeline input sample table (xlsx)

molecule: protein

organism: Mus musculus

source_name: Cortex

extract_protocol:
Single nuclei were extracted using the 10X Genomics nuclei isolation kit (Chromium Nuclei Isolation Kit CG000505, Rev A). Samples were pooled after barcoding with cholesterol-modified oligos (CMOs) and a CMO Co-Anchor. Afterwards, single nuclei of pooled samples were encapsulated in Gel-Beads-in  emulsions (GEMs) on a 10X Chromium Controller using Chromium Next GEM Chip J Single Cell kit (PN-1000230), Chromium Next GEM Single Cell Multiome GEM Kit A (PN-1000232), Chromium Next GEM Single Cell Multiome Gel Bead Kit A (PN-1000231) as instructed by the manufacturer.
The library was prepared according to the 10X protocol using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev F. The hasthag oligo (HTO) libraries were prepared alongside cDNA amplification. Here, an ADT additive primer was added to the reaction. During cDNA cleanup, supernatant was saved to purify Hash-DNA. HTO libraries were generated using unique combinations of i5 and i7 indices.

value: Cortex

value: mixed

value: mixed samples (multiplex)


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K9me3_1

description:
Library name: histone_mark_cutrun_DMSO_H3K9me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K9me3_1_1.fq.gz and histone_mark_cutrun/DMSO_H3K9me3_1_2.fq.gz.

library_source: genomic

molecule: genomic DNA

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; DMSO control; CUT&RUN target H3K9me3


title: HTO counts of multiplex sSL0236 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0236_HTO
Samples GN3F/22/1974, GN3F/22/2030, GN3F/22/2656, GN3F/22/2652, GN3F/22/2099, GN3F/22/2102, GN3F/22/1974, GN3F/22/2030, GN3F/22/2656, GN3F/22/2652, GN3F/22/2099, GN3F/22/2102 with genotypes Ash1l+/-, Ash1l+/-, Kdm6b+/-, Kdm6b+/-, Usp7+/-, Usp7+/-, Ash1l+/-, Ash1l+/-, Kdm6b+/-, Kdm6b+/-, Usp7+/-, Usp7+/- and sex m, f, f, m, m, f, m, f, f, m, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K4me3_2

description:
Library name: histone_mark_cutrun_DMSO_H3K4me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K4me3_2_1.fq.gz and histone_mark_cutrun/DMSO_H3K4me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; DMSO control; CUT&RUN target H3K4me3


title: HTO counts of multiplex sSL0240 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0240_HTO
Samples 325073, 324883, GN3F/22/2027, GN3F/22/2607, #GN22/3F/2682, #GN22/3F/2687, 325073, 324883, GN3F/22/2027, GN3F/22/2607, #GN22/3F/2682, #GN22/3F/2687 with genotypes C57BL6/J, C57BL6/J, Ash1l+/-, Ash1l+/-, Kmt5b+/-, Kmt5b+/-, C57BL6/J, C57BL6/J, Ash1l+/-, Ash1l+/-, Kmt5b+/-, Kmt5b+/- and sex f, m, m, f, m, f, f, m, m, f, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K4me1_2

description:
Library name: histone_mark_cutrun_DMSO_H3K4me1_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K4me1_2_1.fq.gz and histone_mark_cutrun/DMSO_H3K4me1_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; DMSO control; CUT&RUN target H3K4me1


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K27me3_2

description:
Library name: histone_mark_cutrun_DMSO_H3K27me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K27me3_2_1.fq.gz and histone_mark_cutrun/DMSO_H3K27me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; DMSO control; CUT&RUN target H3K27me3


title: HCT116 mAID2-RAD21 sorbitol 6h replicate 2 RNA-seq

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

description:
Library name: HCT116-mAID2-RAD21-sorbitol-6h-2
RNA-seq of HCT116 mAID2-RAD21 cells treated with sorbitol for 6h, replicate 2

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Strand-specific bigWig files containing normalized RNA-seq signal tracks for each replicate and timepoint. This includes merged untreated and sorbitol replicate bigWig files. Files are provided separately for forward and reverse strands.

molecule: other

growth_protocol: HCT116-RAD21-mAID2 cells were cultured in standard conditions (37 °C, 5% CO₂) in McCoy's 5A medium supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cells were regularly monitored for mycoplasma contamination and maintained at 30–80% confluence prior to experimental treatments.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
mRNA or total RNA input was subjected to library preparation compatible with strand-specific sequencing. Libraries were constructed using manufacturer protocols, indexed, pooled, and sequenced.

treatment_protocol: HCT116-RAD21-mAID2 cells were serum-starved for 1 h and treated with 1 µM 5-phenyl-indole-3-acetic acid (5-Ph-IAA; BioAcademia #30-003) for 6 h to deplete RAD21, adapted from Yesbolatova et al. For RNA-seq, cells received one of three conditions in serum-free media: control (no treatment) for 6 h, 0.2 M sorbitol for 6 h, or 0.2 M sorbitol with 1 µM 5-Ph-IAA for 6 h. Cells were harvested immediately and processed for downstream library preparation.

value: 0.2M sorbitol for 6h


title: GEX counts of multiplex sSL0242 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0242_GEX
sSL0242_GEX_filtered_feature_bc_matrix.h5
sSL0242_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds

library_source: transcriptomic single cell

molecule: nuclear RNA


title: Human main RNA-seq matched CUT&RUN time-course sample D7_2

description:
Library name: rnaseq_D7_2
Main RNA-seq sample corresponding to the CUT&RUN SOX9 degradation/recovery time-course; day 7; source directory rnaseq; paired FASTQ files rnaseq/D7_2_1.fq.gz and rnaseq/D7_2_2.fq.gz.


title: Human main RNA-seq matched CUT&RUN time-course sample DMSO_2

description:
Library name: rnaseq_DMSO_2
Main RNA-seq sample corresponding to the CUT&RUN SOX9 degradation/recovery time-course; DMSO control; source directory rnaseq; paired FASTQ files rnaseq/DMSO_2_1.fq.gz and rnaseq/DMSO_2_2.fq.gz.

value: main RNA-seq dataset matched to the SOX9 degradation and recovery CUT&RUN sample series; DMSO control


title: ATAC counts of multiplex sSL0243 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0243_ATAC
sSL0243_ATAC_filtered_feature_bc_matrix.h5
sSL0243_ATAC_fragments.tsv.gz
sSL0243_ATAC_fragments.tsv.gz.tbi
sSL0243_ATAC_peak_annotation.tsv
sSL0243_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds

library_source: genomic single cell


title: HTO counts of multiplex sSL0243 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0243_HTO
Samples GN23/252, GN23/447, GN23/86, GN23/5663, GN3F/22/188, GN3F/22/2823, GN23/252, GN23/447, GN23/86, GN23/5663, GN3F/22/188, GN3F/22/2823 with genotypes Bckdk-/-, Bckdk-/-, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/-, Bckdk-/-, Bckdk-/-, Hnrnpu+/-, Hnrnpu+/-, Trip12+/-, Trip12+/- and sex f, m, f, m, f, m, f, m, f, m, f, m from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0256 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0256_GEX
sSL0256_GEX_filtered_feature_bc_matrix.h5
sSL0256_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0256 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0256_ATAC
sSL0256_ATAC_filtered_feature_bc_matrix.h5
sSL0256_ATAC_fragments.tsv.gz
sSL0256_ATAC_fragments.tsv.gz.tbi
sSL0256_ATAC_peak_annotation.tsv
sSL0256_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0237 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0237_HTO
Samples 324893, 324891, GN3F/22/2660, GN3F/22/2839, GN3F/22/2153, GN3F/22/3095, 324893, 324891, GN3F/22/2660, GN3F/22/2839, GN3F/22/2153, GN3F/22/3095 with genotypes C57BL6/J, C57BL6/J, Kdm6b+/-, Kdm6b+/-, Usp7+/-, Usp7+/-, C57BL6/J, C57BL6/J, Kdm6b+/-, Kdm6b+/-, Usp7+/-, Usp7+/- and sex f, m, f, m, m, f, f, m, f, m, m, f from tissue CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L), CTX (L) at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cx_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K27Ac_2

description:
Library name: histone_mark_cutrun_DMSO_H3K27Ac_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K27Ac_2_1.fq.gz and histone_mark_cutrun/DMSO_H3K27Ac_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; DMSO control; CUT&RUN target H3K27Ac


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K4me3_1

description:
Library name: histone_mark_cutrun_DMSO_H3K4me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K4me3_1_1.fq.gz and histone_mark_cutrun/DMSO_H3K4me3_1_2.fq.gz.


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K27Ac_1

description:
Library name: histone_mark_cutrun_DMSO_H3K27Ac_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K27Ac_1_1.fq.gz and histone_mark_cutrun/DMSO_H3K27Ac_1_2.fq.gz.


title: GEX counts of multiplex sSL0232 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0232_GEX
sSL0232_GEX_filtered_feature_bc_matrix.h5
sSL0232_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds

source_name: Forebrain

value: Forebrain


title: ATAC counts of multiplex sSL0237 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0237_ATAC
sSL0237_ATAC_filtered_feature_bc_matrix.h5
sSL0237_ATAC_fragments.tsv.gz
sSL0237_ATAC_fragments.tsv.gz.tbi
sSL0237_ATAC_peak_annotation.tsv
sSL0237_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K9me3_1

description:
Library name: histone_mark_cutrun_D7_H3K9me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K9me3_1_1.fq.gz and histone_mark_cutrun/D7_H3K9me3_1_2.fq.gz.

value: colon

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 7; CUT&RUN target H3K9me3


title: HTO counts of multiplex sSL0232 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0232_HTO
Samples #LSMO251, #LSMO257, #LSMO93, #LS97, #LSMO413, #LSMO415, #LSMO251, #LSMO257, #LSMO93, #LS97, #LSMO413, #LSMO415 with genotypes Ash1l+/-, Ash1l+/-, Cul3+/-, Cul3+/-, Kmt5b+/-, Kmt5b+/-, Ash1l+/-, Ash1l+/-, Cul3+/-, Cul3+/-, Kmt5b+/-, Kmt5b+/- and sex f, m, f, f, f, m, f, m, f, f, f, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K9me3_2

description:
Library name: histone_mark_cutrun_D7_H3K9me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K9me3_2_1.fq.gz and histone_mark_cutrun/D7_H3K9me3_2_2.fq.gz.

value: epithelial cell


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K4me3_2

description:
Library name: histone_mark_cutrun_D7_H3K4me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K4me3_2_1.fq.gz and histone_mark_cutrun/D7_H3K4me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 7; CUT&RUN target H3K4me3


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K4me1_1

description:
Library name: histone_mark_cutrun_DMSO_H3K4me1_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K4me1_1_1.fq.gz and histone_mark_cutrun/DMSO_H3K4me1_1_2.fq.gz.


title: ATAC counts of multiplex sSL0231 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0231_ATAC
sSL0231_ATAC_filtered_feature_bc_matrix.h5
sSL0231_ATAC_fragments.tsv.gz
sSL0231_ATAC_fragments.tsv.gz.tbi
sSL0231_ATAC_peak_annotation.tsv
sSL0231_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K4me3_1

description:
Library name: histone_mark_cutrun_D7_H3K4me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K4me3_1_1.fq.gz and histone_mark_cutrun/D7_H3K4me3_1_2.fq.gz.


title: HTO counts of multiplex sSL0231 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0231_HTO
Samples #LSMO365, #LSMO370, #LSMO71, #LSMO72, #LSMO276, #LSMO279, #LSMO365, #LSMO370, #LSMO71, #LSMO72, #LSMO276, #LSMO279 with genotypes Bckdk-/-, Bckdk-/-, Cul3+/-, Cul3+/-, Kdm6b+/-, Kdm6b+/-, Bckdk-/-, Bckdk-/-, Cul3+/-, Cul3+/-, Kdm6b+/-, Kdm6b+/- and sex f, m, m, f, f, m, f, m, m, f, f, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K4me1_1

description:
Library name: histone_mark_cutrun_D7_H3K4me1_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K4me1_1_1.fq.gz and histone_mark_cutrun/D7_H3K4me1_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 7; CUT&RUN target H3K4me1


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K4me1_2

description:
Library name: histone_mark_cutrun_D7_H3K4me1_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K4me1_2_1.fq.gz and histone_mark_cutrun/D7_H3K4me1_2_2.fq.gz.


title: GEX counts of multiplex sSL0234 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0234_GEX
sSL0234_GEX_filtered_feature_bc_matrix.h5
sSL0234_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0231 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0231_GEX
sSL0231_GEX_filtered_feature_bc_matrix.h5
sSL0231_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K27me3_2

description:
Library name: histone_mark_cutrun_D7_H3K27me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K27me3_2_1.fq.gz and histone_mark_cutrun/D7_H3K27me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 7; CUT&RUN target H3K27me3


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K27me3_1

description:
Library name: histone_mark_cutrun_D7_H3K27me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K27me3_1_1.fq.gz and histone_mark_cutrun/D7_H3K27me3_1_2.fq.gz.


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K27Ac_2

description:
Library name: histone_mark_cutrun_D7_H3K27Ac_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K27Ac_2_1.fq.gz and histone_mark_cutrun/D7_H3K27Ac_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 7; CUT&RUN target H3K27Ac


title: Human histone-mark CUT&RUN multi-time-point sample D7_H3K27Ac_1

description:
Library name: histone_mark_cutrun_D7_H3K27Ac_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 7; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D7_H3K27Ac_1_1.fq.gz and histone_mark_cutrun/D7_H3K27Ac_1_2.fq.gz.


title: ATAC counts of multiplex sSL0230 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0230_ATAC
sSL0230_ATAC_filtered_feature_bc_matrix.h5
sSL0230_ATAC_fragments.tsv.gz
sSL0230_ATAC_fragments.tsv.gz.tbi
sSL0230_ATAC_peak_annotation.tsv
sSL0230_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds

value: mixed


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K9me3_2

description:
Library name: histone_mark_cutrun_D5_H3K9me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K9me3_2_1.fq.gz and histone_mark_cutrun/D5_H3K9me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 5; CUT&RUN target H3K9me3


title: GEX counts of multiplex sSL0230 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0230_GEX
sSL0230_GEX_filtered_feature_bc_matrix.h5
sSL0230_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds

value: mixed samples (multiplex)


title: HTO counts of multiplex sSL0230 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0230_HTO
Samples #LSMO227, #LSMO228, #LSMO216, #LSMO217, #LSMO331, #LSMO335, #LSMO227, #LSMO228, #LSMO216, #LSMO217, #LSMO331, #LSMO335 with genotypes Ash1l+/-, Ash1l+/-, Trip12+/-, Trip12+/-, Kmt5b+/-, Kmt5b+/-, Ash1l+/-, Ash1l+/-, Trip12+/-, Trip12+/-, Kmt5b+/-, Kmt5b+/- and sex m, f, f, m, m, f, m, f, f, m, m, f from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K9me3_1

description:
Library name: histone_mark_cutrun_D5_H3K9me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K9me3_1_1.fq.gz and histone_mark_cutrun/D5_H3K9me3_1_2.fq.gz.


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K4me3_1

description:
Library name: histone_mark_cutrun_D5_H3K4me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K4me3_1_1.fq.gz and histone_mark_cutrun/D5_H3K4me3_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 5; CUT&RUN target H3K4me3


title: HTO counts of multiplex sSL0219 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0219_HTO
Samples #LSMO206, #LSMO207, #LSMO128, #LSMO129, #LSMO54, #LSMO55, #LSMO206, #LSMO207, #LSMO128, #LSMO129, #LSMO54, #LSMO55 with genotypes Ash1l+/-, Ash1l+/-, Wac+/-, Wac+/-, Setd5+/-, Setd5+/-, Ash1l+/-, Ash1l+/-, Wac+/-, Wac+/-, Setd5+/-, Setd5+/- and sex f, m, m, f, f, m, f, m, m, f, f, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K4me3_2

description:
Library name: histone_mark_cutrun_D5_H3K4me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K4me3_2_1.fq.gz and histone_mark_cutrun/D5_H3K4me3_2_2.fq.gz.


title: ATAC counts of multiplex sSL0219 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0219_ATAC
sSL0219_ATAC_filtered_feature_bc_matrix.h5
sSL0219_ATAC_fragments.tsv.gz
sSL0219_ATAC_fragments.tsv.gz.tbi
sSL0219_ATAC_peak_annotation.tsv
sSL0219_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0219 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0219_GEX
sSL0219_GEX_filtered_feature_bc_matrix.h5
sSL0219_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K4me1_2

description:
Library name: histone_mark_cutrun_D5_H3K4me1_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K4me1_2_1.fq.gz and histone_mark_cutrun/D5_H3K4me1_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 5; CUT&RUN target H3K4me1


title: HTO counts of multiplex sSL0257 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0257_HTO
Samples #LSMO188, #LSMO189, #LSMO295, #LSMO303, #LSMO450, #LSMO448, #LSMO188, #LSMO189, #LSMO295, #LSMO303, #LSMO450, #LSMO448 with genotypes Wac+/-, Wac+/-, Kdm6b+/-, Kdm6b+/-, Kmt5b+/-, Kmt5b+/-, Wac+/-, Wac+/-, Kdm6b+/-, Kdm6b+/-, Kmt5b+/-, Kmt5b+/- and sex f, m, f, m, f, m, f, m, f, m, f, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K4me1_1

description:
Library name: histone_mark_cutrun_D5_H3K4me1_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K4me1_1_1.fq.gz and histone_mark_cutrun/D5_H3K4me1_1_2.fq.gz.


title: GEX counts of multiplex sSL0257 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0257_GEX
sSL0257_GEX_filtered_feature_bc_matrix.h5
sSL0257_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K27me3_1

description:
Library name: histone_mark_cutrun_D5_H3K27me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K27me3_1_1.fq.gz and histone_mark_cutrun/D5_H3K27me3_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 5; CUT&RUN target H3K27me3


title: ATAC counts of multiplex sSL0257 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0257_ATAC
sSL0257_ATAC_filtered_feature_bc_matrix.h5
sSL0257_ATAC_fragments.tsv.gz
sSL0257_ATAC_fragments.tsv.gz.tbi
sSL0257_ATAC_peak_annotation.tsv
sSL0257_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K27me3_2

description:
Library name: histone_mark_cutrun_D5_H3K27me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K27me3_2_1.fq.gz and histone_mark_cutrun/D5_H3K27me3_2_2.fq.gz.


title: ATAC counts of multiplex sSL0221 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0221_ATAC
sSL0221_ATAC_filtered_feature_bc_matrix.h5
sSL0221_ATAC_fragments.tsv.gz
sSL0221_ATAC_fragments.tsv.gz.tbi
sSL0221_ATAC_peak_annotation.tsv
sSL0221_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K27Ac_2

description:
Library name: histone_mark_cutrun_D5_H3K27Ac_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K27Ac_2_1.fq.gz and histone_mark_cutrun/D5_H3K27Ac_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 5; CUT&RUN target H3K27Ac


title: GEX counts of multiplex sSL0221 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0221_GEX
sSL0221_GEX_filtered_feature_bc_matrix.h5
sSL0221_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0232 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0232_ATAC
sSL0232_ATAC_filtered_feature_bc_matrix.h5
sSL0232_ATAC_fragments.tsv.gz
sSL0232_ATAC_fragments.tsv.gz.tbi
sSL0232_ATAC_peak_annotation.tsv
sSL0232_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0221 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0221_HTO
Samples #LSMO243, #LSMO316, #LSMO260, #LSMO264, #LSMO383, #LSMO390, #LSMO243, #LSMO316, #LSMO260, #LSMO264, #LSMO383, #LSMO390 with genotypes Setd5+/-, Setd5+/-, Usp7+/-, Usp7+/-, Hnrnpu+/-, Hnrnpu+/-, Setd5+/-, Setd5+/-, Usp7+/-, Usp7+/-, Hnrnpu+/-, Hnrnpu+/- and sex f, m, m, f, f, m, f, m, m, f, f, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D5_H3K27Ac_1

description:
Library name: histone_mark_cutrun_D5_H3K27Ac_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 5; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D5_H3K27Ac_1_1.fq.gz and histone_mark_cutrun/D5_H3K27Ac_1_2.fq.gz.


title: Human histone-mark CUT&RUN multi-time-point sample D4_IgG_2

description:
Library name: histone_mark_cutrun_D4_IgG_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target IgG control; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_IgG_2_1.fq.gz and histone_mark_cutrun/D4_IgG_2_2.fq.gz.

value: IgG control

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 4; CUT&RUN target IgG control


title: HTO counts of multiplex sSL0216 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0216_HTO
Samples #LSMO195, #LSMO196, #LSMO64, #LSMO66, #LSMO163, #LSMO164, #LSMO195, #LSMO196, #LSMO64, #LSMO66, #LSMO163, #LSMO164 with genotypes Bckdk-/-, Bckdk-/-, Usp7+/-, Usp7+/-, Trip12+/-, Trip12+/-, Bckdk-/-, Bckdk-/-, Usp7+/-, Usp7+/-, Trip12+/-, Trip12+/- and sex m, f, f, m, f, f, m, f, f, m, f, f from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds

value: Forebrain


title: Human histone-mark CUT&RUN multi-time-point sample D4_IgG_1

description:
Library name: histone_mark_cutrun_D4_IgG_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target IgG control; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_IgG_1_1.fq.gz and histone_mark_cutrun/D4_IgG_1_2.fq.gz.

value: colon


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K9me3_2

description:
Library name: histone_mark_cutrun_D4_H3K9me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K9me3_2_1.fq.gz and histone_mark_cutrun/D4_H3K9me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 4; CUT&RUN target H3K9me3


title: ATAC counts of multiplex sSL0216 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0216_ATAC
sSL0216_ATAC_filtered_feature_bc_matrix.h5
sSL0216_ATAC_fragments.tsv.gz
sSL0216_ATAC_fragments.tsv.gz.tbi
sSL0216_ATAC_peak_annotation.tsv
sSL0216_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: GEX counts of multiplex sSL0216 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0216_GEX
sSL0216_GEX_filtered_feature_bc_matrix.h5
sSL0216_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K4me3_2

description:
Library name: histone_mark_cutrun_D4_H3K4me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K4me3_2_1.fq.gz and histone_mark_cutrun/D4_H3K4me3_2_2.fq.gz.

value: epithelial cell

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 4; CUT&RUN target H3K4me3


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K9me3_1

description:
Library name: histone_mark_cutrun_D4_H3K9me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K9me3_1_1.fq.gz and histone_mark_cutrun/D4_H3K9me3_1_2.fq.gz.


title: GEX counts of multiplex sSL0217 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0217_GEX
sSL0217_GEX_filtered_feature_bc_matrix.h5
sSL0217_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0217 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0217_ATAC
sSL0217_ATAC_filtered_feature_bc_matrix.h5
sSL0217_ATAC_fragments.tsv.gz
sSL0217_ATAC_fragments.tsv.gz.tbi
sSL0217_ATAC_peak_annotation.tsv
sSL0217_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K4me3_1

description:
Library name: histone_mark_cutrun_D4_H3K4me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K4me3_1_1.fq.gz and histone_mark_cutrun/D4_H3K4me3_1_2.fq.gz.


title: 514-N-ctrl-sol

status: Public on Jun 17 2026

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description:
Library name: 514-N-ctrl-sol
2x150 Paired-End

data_processing:
Sequencing was performed on the Illumina NovaSeq platform using a 2x150 Paired-End configuration
Raw sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The reads were then mapped to the reference genome (mm10) using the STAR aligner v.2.5.2b.
Assembly: mm10
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: TPM_values.csv

molecule: total RNA

source_name: Muscle

growth_protocol: Mice were housed at 23˚C or 30˚C in ventilated cages under a 12 h – 12 h light/dark cycle. Mice were fed a standard diet (Lab Diet 5008) with free access to food and water unless specified.

extract_protocol:
Total RNA were extracted using Rneasy kit (QIAGEN)
ERCC RNA Spike-In Mix (ThermoFisher) was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The next steps included performing rRNA depletion using QIAGEN FastSelect rRNA HMR Kit (Qiagen). RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina according to manufacturer’s instructions.

value: Muscle

value: wild type


title: HTO counts of multiplex sSL0234 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0234_HTO
Samples #LSMO358, #LSMO360, #LSMO442, #LSMO444, #LSMO112, #LSMO358, #LSMO360, #LSMO442, #LSMO444, #LSMO112 with genotypes C57BL6/J, C57BL6/J, Hnrnpu+/-, Hnrnpu+/-, Ptchd1 -/y, C57BL6/J, C57BL6/J, Hnrnpu+/-, Hnrnpu+/-, Ptchd1 -/y and sex f, m, f, m, m, f, m, f, m, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: OCI-AML-3 sgControl Cells, Replicate 2

city: Chicago

first: Feng

last: Yue

address: 420 E. Superior St.

institute: Northwestern University

description: Library name: OCI-AML-3-sgControl-Rep2

data_processing:
RNA-Seq raw pair-end FASTQ files underwent quality control using fastp (version 0.23.4) with default settings to remove low-quality reads and trim adapters.
Cleaned RNA-Seq data were aligned to the reference genome hg38 using STAR (version 2.7.11b) with default parameters. Gene expression quantification was determined with featureCounts from the subread package (version 2.0.6), considering only the properly mapped pair-end read counts
Assembly: hg38
Supplementary files format and content: tab-delimited file including raw reads

growth_protocol: U937 cells and MOLM-13 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS). THP-1 cells were maintained in RPMI-1640 supplemented with 10% FBS and 50nM BME. OCI-AML-3 cells were cultured in MEM α supplemented with 20% FBS. All cell cultures were supplemented with 1X Antibiotic-Antimycotic and were grown in 37°C with 5% CO2.

extract_protocol:
One million cells were stabilized in RNAprotect (Qiagen, 76526) and were stored in -80C prior to extraction. Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, 75134) and the RNA integrity was evaluated using RNA ScreenTape Analysis (Agilent, 5067-5576).
Library preparation was then performed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina, in conjunction with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs #E7490) following manufacturer’s protocol.

value: AML


title: Donor1, T651M Group, 48 Hour Timepoint

city: Bethesda

first: Skyler

middle: Alexander

last: Kuhn

state: Maryland

address: 9000 Rockville Pike, BG 29B RM 1NN20

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
Library name: Donor1_TM_T48_S26
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor1_TM_T48_S26

data_processing:
Sequencing adapters and low-quality bases were trimmed using Cutadapt v1.18.
Trimmed reads were aligned to the GENCODE (9) GRCh38.p13 primary human reference genome with STAR v2.7.6a in two-pass basic mode.
PCR duplicates were marked using Picard’s MarkDuplicate utility.
Gene expression levels were quantified with RSEM v1.3.3 using v41 of GENCODE's comprehensive annotation.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample.

source_name: blood

growth_protocol: Human monocyte-derived dendritic cells (MDDCs) were generated from cryopreserved human monocytes obtained from 5 donors. After thawing, monocytes were washed with PBS and cultured at 1 x 10^6 cells/mL in DC medium consisting of RPMI + Glutamax, 5% FBS, 15 mM HEPES, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 ug/mL streptomycin, supplemented with IL-4 (20 ng/mL) and GM-CSF (20 ng/mL). Cells were cultured for 5 days with replacement of half of the medium and addition of fresh cytokines every other day. Nonadherent dendritic cells were harvested by centrifugation and resuspended in DC medium. Resulting cells were >95% CD11c+/CD209+ by flow cytometry. For RNA-seq experiments, MDDCs were plated at 1 x 10^6 cells/well in 12-well plates.

extract_protocol:
Cells were harvested by centrifugation and lysed in 1 mL TRIzol reagent per sample, then stored at -80 C until extraction. For RNA isolation, samples were mixed with 200 uL 1-bromo-3-chloropropane and centrifuged at 4 C for 15 minutes at 16,000 x g. The aqueous phase was collected and passed through a QIAshredder column at 21,000 x g for 2 minutes. RNA was purified using the Qiagen AllPrep DNA/RNA system with an additional on-column DNase I treatment. RNA quality was assessed using the Agilent 2100 Bioanalyzer RNA 6000 Pico kit and quantified using the Quant-iT RiboGreen RNA assay.
Sequencing libraries were prepared from 200 ng total RNA using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer’s protocol. Libraries were quality checked by Agilent Bioanalyzer, quantified by KAPA SYBR FAST qPCR, pooled, and sequenced as paired-end reads on Illumina platforms, with final sequencing performed on a NovaSeq 6000 (2 x 100 bp).

treatment_protocol: Human MDDCs were mock-infected or infected with Powassan virus (POWV) at an MOI of 0.1 in a small volume for 1 hour at 37 C and 5% CO2 with occasional gentle rocking. In experiments involving inhibitor treatment, MDDCs were pretreated with ruxolitinib (10 ug/mL) for 1 hour prior to infection and maintained in the culture for the duration of the experiment.

value: blood

value: monocyte-derived dendritic cells

tag: time

value: Hour 48


title: MOLM13 sgSUV39H1 SKO Cells, Replicate 1

description: Library name: MOLM13-SKO-Rep1


title: ATAC counts of multiplex sSL0234 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0234_ATAC
sSL0234_ATAC_filtered_feature_bc_matrix.h5
sSL0234_ATAC_fragments.tsv.gz
sSL0234_ATAC_fragments.tsv.gz.tbi
sSL0234_ATAC_peak_annotation.tsv
sSL0234_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds

value: mixed

value: mixed samples (multiplex)


title: HTO counts of multiplex sSL0220 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0220_HTO
Samples #LSMO232, #LSMO233, #LSMO339, #LSMO341, #LSMO154, #LSMO155, #LSMO232, #LSMO233, #LSMO339, #LSMO341, #LSMO154, #LSMO155 with genotypes C57BL6/J, C57BL6/J, Bckdk-/-, Bckdk-/-, Usp7+/-, Usp7+/-, C57BL6/J, C57BL6/J, Bckdk-/-, Bckdk-/-, Usp7+/-, Usp7+/- and sex m, f, f, m, m, f, m, f, f, m, m, f from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0217 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0217_HTO
Samples #LSMO50, #LSMO51, #LSMO3, #LSMO6, #LSMO134, #LSMO382, #LSMO50, #LSMO51, #LSMO3, #LSMO6, #LSMO134, #LSMO382 with genotypes C57BL6/J, C57BL6/J, Wac+/-, Wac+/-, Hnrnpu+/-, Hnrnpu+/-, C57BL6/J, C57BL6/J, Wac+/-, Wac+/-, Hnrnpu+/-, Hnrnpu+/- and sex m, f, m, f, f, m, m, f, m, f, f, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K4me1_1

description:
Library name: histone_mark_cutrun_D4_H3K4me1_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K4me1_1_1.fq.gz and histone_mark_cutrun/D4_H3K4me1_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 4; CUT&RUN target H3K4me1


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K4me1_2

description:
Library name: histone_mark_cutrun_D4_H3K4me1_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K4me1_2_1.fq.gz and histone_mark_cutrun/D4_H3K4me1_2_2.fq.gz.


title: ATAC counts of multiplex sSL0238 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0238_ATAC
sSL0238_ATAC_filtered_feature_bc_matrix.h5
sSL0238_ATAC_fragments.tsv.gz
sSL0238_ATAC_fragments.tsv.gz.tbi
sSL0238_ATAC_peak_annotation.tsv
sSL0238_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds

value: Cortex


title: GEX counts of multiplex sSL0220 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0220_GEX
sSL0220_GEX_filtered_feature_bc_matrix.h5
sSL0220_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K27Ac_2

description:
Library name: histone_mark_cutrun_D4_H3K27Ac_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K27Ac_2_1.fq.gz and histone_mark_cutrun/D4_H3K27Ac_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 4; CUT&RUN target H3K27Ac


title: GEX counts of multiplex sSL0233 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0233_GEX
sSL0233_GEX_filtered_feature_bc_matrix.h5
sSL0233_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K27me3_2

description:
Library name: histone_mark_cutrun_D4_H3K27me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K27me3_2_1.fq.gz and histone_mark_cutrun/D4_H3K27me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 4; CUT&RUN target H3K27me3


title: ATAC counts of multiplex sSL0220 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0220_ATAC
sSL0220_ATAC_filtered_feature_bc_matrix.h5
sSL0220_ATAC_fragments.tsv.gz
sSL0220_ATAC_fragments.tsv.gz.tbi
sSL0220_ATAC_peak_annotation.tsv
sSL0220_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds

value: Forebrain


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K27Ac_1

description:
Library name: histone_mark_cutrun_D4_H3K27Ac_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K27Ac_1_1.fq.gz and histone_mark_cutrun/D4_H3K27Ac_1_2.fq.gz.

value: colon


title: ATAC counts of multiplex sSL0233 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0233_ATAC
sSL0233_ATAC_filtered_feature_bc_matrix.h5
sSL0233_ATAC_fragments.tsv.gz
sSL0233_ATAC_fragments.tsv.gz.tbi
sSL0233_ATAC_peak_annotation.tsv
sSL0233_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: HTO counts of multiplex sSL0233 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0233_HTO
Samples #LS98, #LSMO397, #LSMO419, #LSMO420, #LSMO84, #LS98, #LSMO397, #LSMO419, #LSMO420, #LSMO84 with genotypes Cul3+/-, Cul3+/-, Trip12+/-, Trip12+/-, Ptchd1 -/y, Cul3+/-, Cul3+/-, Trip12+/-, Trip12+/-, Ptchd1 -/y and sex m, f, f, m, m, m, f, f, m, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D4_H3K27me3_1

description:
Library name: histone_mark_cutrun_D4_H3K27me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 4; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D4_H3K27me3_1_1.fq.gz and histone_mark_cutrun/D4_H3K27me3_1_2.fq.gz.


title: HCT116 mAID2-RAD21 + auxin 6h replicate 2 RNA-seq

description:
Library name: HCT116-mAID2-RAD21-auxin-6h-2
RNA-seq of HCT116 mAID2-RAD21 cells treated with auxin for 6h (RAD21 depleted), replicate 2

value: 1uM 5-Ph-IAA for 6h (RAD21 depletion)


title: GEX counts of multiplex sSL0241 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0241_GEX
sSL0241_GEX_filtered_feature_bc_matrix.h5
sSL0241_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K9me3_2

description:
Library name: histone_mark_cutrun_D2_H3K9me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K9me3_2_1.fq.gz and histone_mark_cutrun/D2_H3K9me3_2_2.fq.gz.

value: epithelial cell

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 2; CUT&RUN target H3K9me3


title: GEX counts of multiplex sSL0235 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0235_GEX
sSL0235_GEX_filtered_feature_bc_matrix.h5
sSL0235_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K9me3_1

description:
Library name: histone_mark_cutrun_D2_H3K9me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K9me3_1_1.fq.gz and histone_mark_cutrun/D2_H3K9me3_1_2.fq.gz.


title: HCT116 mAID2-RAD21 serum starvation replicate 2 RNA-seq

description:
Library name: HCT116-mAID2-RAD21-serum-starve-2
RNA-seq of HCT116 mAID2-RAD21 cells after serum starvation (untreated control), replicate 2

value: serum starvation (untreated control)


title: HTO counts of multiplex sSL0235 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0235_HTO
Samples #LSMO290, #LSMO294, #LSMO317, #LSMO375, #LSMO177, #LSMO290, #LSMO294, #LSMO317, #LSMO375, #LSMO177 with genotypes Kdm6b+/-, Kdm6b+/-, Setd5+/-, Setd5+/-, Ptchd1 -/y, Kdm6b+/-, Kdm6b+/-, Setd5+/-, Setd5+/-, Ptchd1 -/y and sex f, f, f, m, m, f, f, f, m, m from tissue Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain, Forebrain at timepoints e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5, e14.5
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K4me3_1

description:
Library name: histone_mark_cutrun_D2_H3K4me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K4me3_1_1.fq.gz and histone_mark_cutrun/D2_H3K4me3_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 2; CUT&RUN target H3K4me3


title: HTO counts of multiplex sSL0223 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0223_HTO
Samples 324883, GN22/5232, GN22/4298, GN22/4097, GN3F/22/2099, GN3F/22/2752, 324883, GN22/5232, GN22/4298, GN22/4097, GN3F/22/2099, GN3F/22/2752 with genotypes C57BL6/J, Ptchd1 -/y, Cul3+/-, Setd5+/-, Usp7+/-, Trip12+/-, C57BL6/J, Ptchd1 -/y, Cul3+/-, Setd5+/-, Usp7+/-, Trip12+/- and sex m, m, m, m, m, m, m, m, m, m, m, m from tissue Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cb_p4_diet_seurat_RNA_assay.rds

source_name: Cerebellum

value: Cerebellum


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K4me1_2

description:
Library name: histone_mark_cutrun_D2_H3K4me1_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K4me1_2_1.fq.gz and histone_mark_cutrun/D2_H3K4me1_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 2; CUT&RUN target H3K4me1


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K4me1_1

description:
Library name: histone_mark_cutrun_D2_H3K4me1_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K4me1_1_1.fq.gz and histone_mark_cutrun/D2_H3K4me1_1_2.fq.gz.


title: ATAC counts of multiplex sSL0235 containing tissue & timepoint(s) Forebrain; e14.5

description:
Library name: sSL0235_ATAC
sSL0235_ATAC_filtered_feature_bc_matrix.h5
sSL0235_ATAC_fragments.tsv.gz
sSL0235_ATAC_fragments.tsv.gz.tbi
sSL0235_ATAC_peak_annotation.tsv
sSL0235_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K27me3_2

description:
Library name: histone_mark_cutrun_D2_H3K27me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K27me3_2_1.fq.gz and histone_mark_cutrun/D2_H3K27me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 2; CUT&RUN target H3K27me3


title: GEX counts of multiplex sSL0223 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0223_GEX
sSL0223_GEX_filtered_feature_bc_matrix.h5
sSL0223_GEX_QC_categories.csv
cb_p4_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0223 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0223_ATAC
sSL0223_ATAC_filtered_feature_bc_matrix.h5
sSL0223_ATAC_fragments.tsv.gz
sSL0223_ATAC_fragments.tsv.gz.tbi
sSL0223_ATAC_peak_annotation.tsv
sSL0223_ATAC_peaks.bed
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K27me3_1

description:
Library name: histone_mark_cutrun_D2_H3K27me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K27me3_1_1.fq.gz and histone_mark_cutrun/D2_H3K27me3_1_2.fq.gz.


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K4me3_2

description:
Library name: histone_mark_cutrun_D2_H3K4me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K4me3_2_1.fq.gz and histone_mark_cutrun/D2_H3K4me3_2_2.fq.gz.


title: ATAC counts of multiplex sSL0224 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0224_ATAC
sSL0224_ATAC_filtered_feature_bc_matrix.h5
sSL0224_ATAC_fragments.tsv.gz
sSL0224_ATAC_fragments.tsv.gz.tbi
sSL0224_ATAC_peak_annotation.tsv
sSL0224_ATAC_peaks.bed
cb_p4_diet_seurat_RNA_assay.rds


title: Human main RNA-seq matched CUT&RUN time-course sample D2_2

description:
Library name: rnaseq_D2_2
Main RNA-seq sample corresponding to the CUT&RUN SOX9 degradation/recovery time-course; day 2; source directory rnaseq; paired FASTQ files rnaseq/D2_2_1.fq.gz and rnaseq/D2_2_2.fq.gz.

value: SOX9 degradation/recovery time course

value: main RNA-seq dataset matched to the SOX9 degradation and recovery CUT&RUN sample series; day 2

value: rnaseq


title: Donor3, MOCK Group, 48 Hour Timepoint

description:
Library name: Donor3_mock_T48_S18
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor3_mock_T48_S18

value: blood

value: monocyte-derived dendritic cells

value: MOCK

value: Hour 48


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K27Ac_2

description:
Library name: histone_mark_cutrun_D2_H3K27Ac_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K27Ac_2_1.fq.gz and histone_mark_cutrun/D2_H3K27Ac_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 2; CUT&RUN target H3K27Ac


title: HTO counts of multiplex sSL0224 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0224_HTO
Samples GN22/5558, GN3F/22/1974, GN22/5361, GN3F/22/2830, GN3F/22/2153, GN22/5663, GN22/5558, GN3F/22/1974, GN22/5361, GN3F/22/2830, GN3F/22/2153, GN22/5663 with genotypes Ptchd1 -/y, Ash1l+/-, Cul3+/-, Wac+/-, Usp7+/-, Hnrnpu+/-, Ptchd1 -/y, Ash1l+/-, Cul3+/-, Wac+/-, Usp7+/-, Hnrnpu+/- and sex m, m, m, m, m, m, m, m, m, m, m, m from tissue Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cb_p4_diet_seurat_RNA_assay.rds

value: mixed

value: mixed samples (multiplex)


title: GEX counts of multiplex sSL0224 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0224_GEX
sSL0224_GEX_filtered_feature_bc_matrix.h5
sSL0224_GEX_QC_categories.csv
cb_p4_diet_seurat_RNA_assay.rds


title: Human main RNA-seq matched CUT&RUN time-course sample D10_2

description:
Library name: rnaseq_D10_2
Main RNA-seq sample corresponding to the CUT&RUN SOX9 degradation/recovery time-course; day 10; source directory rnaseq; paired FASTQ files rnaseq/D10_2_1.fq.gz and rnaseq/D10_2_2.fq.gz.

value: colon

value: epithelial cell

value: main RNA-seq dataset matched to the SOX9 degradation and recovery CUT&RUN sample series; day 10


title: ATAC counts of multiplex sSL0236 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0236_ATAC
sSL0236_ATAC_filtered_feature_bc_matrix.h5
sSL0236_ATAC_fragments.tsv.gz
sSL0236_ATAC_fragments.tsv.gz.tbi
sSL0236_ATAC_peak_annotation.tsv
sSL0236_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds

value: Cortex


title: HTO counts of multiplex sSL0226 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0226_HTO
Samples GN3F/22/2027, GN3F/22/2839, GN22/4907, GN3F/22/3099, #GN3F/22/2823, #GN22/3F/2777, GN3F/22/2027, GN3F/22/2839, GN22/4907, GN3F/22/3099, #GN3F/22/2823, #GN22/3F/2777 with genotypes Ash1l+/-, Kdm6b+/-, Setd5+/-, Usp7+/-, Trip12+/-, Kmt5b+/-, Ash1l+/-, Kdm6b+/-, Setd5+/-, Usp7+/-, Trip12+/-, Kmt5b+/- and sex m, m, m, m, m, m, m, m, m, m, m, m from tissue Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cb_p4_diet_seurat_RNA_assay.rds

value: Cerebellum


title: ATAC counts of multiplex sSL0226 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0226_ATAC
sSL0226_ATAC_filtered_feature_bc_matrix.h5
sSL0226_ATAC_fragments.tsv.gz
sSL0226_ATAC_fragments.tsv.gz.tbi
sSL0226_ATAC_peak_annotation.tsv
sSL0226_ATAC_peaks.bed
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K4me3_2

description:
Library name: histone_mark_cutrun_D13_H3K4me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K4me3_2_1.fq.gz and histone_mark_cutrun/D13_H3K4me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 13; CUT&RUN target H3K4me3


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K9me3_1

description:
Library name: histone_mark_cutrun_D13_H3K9me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K9me3_1_1.fq.gz and histone_mark_cutrun/D13_H3K9me3_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 13; CUT&RUN target H3K9me3


title: GEX counts of multiplex sSL0226 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0226_GEX
sSL0226_GEX_filtered_feature_bc_matrix.h5
sSL0226_GEX_QC_categories.csv
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K4me1_2

description:
Library name: histone_mark_cutrun_D13_H3K4me1_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K4me1_2_1.fq.gz and histone_mark_cutrun/D13_H3K4me1_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 13; CUT&RUN target H3K4me1


title: HTO counts of multiplex sSL0222 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0222_HTO
Samples 324891, GN22/4701, GN22/3951, GN3F/22/2158, GN22/5251, GN3F/22/2474, 324891, GN22/4701, GN22/3951, GN3F/22/2158, GN22/5251, GN3F/22/2474 with genotypes C57BL6/J, Ptchd1 -/y, Cul3+/-, Wac+/-, Hnrnpu+/-, Kmt5b+/-, C57BL6/J, Ptchd1 -/y, Cul3+/-, Wac+/-, Hnrnpu+/-, Kmt5b+/- and sex m, m, m, m, m, m, m, m, m, m, m, m from tissue Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K4me3_1

description:
Library name: histone_mark_cutrun_D13_H3K4me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K4me3_1_1.fq.gz and histone_mark_cutrun/D13_H3K4me3_1_2.fq.gz.


title: GEX counts of multiplex sSL0222 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0222_GEX
sSL0222_GEX_filtered_feature_bc_matrix.h5
sSL0222_GEX_QC_categories.csv
cb_p4_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0222 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0222_ATAC
sSL0222_ATAC_filtered_feature_bc_matrix.h5
sSL0222_ATAC_fragments.tsv.gz
sSL0222_ATAC_fragments.tsv.gz.tbi
sSL0222_ATAC_peak_annotation.tsv
sSL0222_ATAC_peaks.bed
cb_p4_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0225 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0225_ATAC
sSL0225_ATAC_filtered_feature_bc_matrix.h5
sSL0225_ATAC_fragments.tsv.gz
sSL0225_ATAC_fragments.tsv.gz.tbi
sSL0225_ATAC_peak_annotation.tsv
sSL0225_ATAC_peaks.bed
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K27me3_2

description:
Library name: histone_mark_cutrun_D13_H3K27me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K27me3_2_1.fq.gz and histone_mark_cutrun/D13_H3K27me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 13; CUT&RUN target H3K27me3


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K27me3_1

description:
Library name: histone_mark_cutrun_D13_H3K27me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K27me3_1_1.fq.gz and histone_mark_cutrun/D13_H3K27me3_1_2.fq.gz.


title: HTO counts of multiplex sSL0225 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0225_HTO
Samples 327556, GN3F/22/2852, GN3F/22/2652, GN22/4188, GN23/88, #GN22/3F/2682, 327556, GN3F/22/2852, GN3F/22/2652, GN22/4188, GN23/88, #GN22/3F/2682 with genotypes C57BL6/J, Wac+/-, Kdm6b+/-, Setd5+/-, Hnrnpu+/-, Kmt5b+/-, C57BL6/J, Wac+/-, Kdm6b+/-, Setd5+/-, Hnrnpu+/-, Kmt5b+/- and sex m, m, m, m, m, m, m, m, m, m, m, m from tissue Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K27Ac_2

description:
Library name: histone_mark_cutrun_D13_H3K27Ac_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K27Ac_2_1.fq.gz and histone_mark_cutrun/D13_H3K27Ac_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 13; CUT&RUN target H3K27Ac


title: GEX counts of multiplex sSL0258 containing tissue & timepoint(s) Forebrain; e14.5|Cerebellum; P4

description:
Library name: sSL0258_GEX
sSL0258_GEX_filtered_feature_bc_matrix.h5
sSL0258_GEX_QC_categories.csv
cx_e14_diet_seurat_RNA_assay.rds
cb_p4_diet_seurat_RNA_assay.rds

source_name: Forebrain & Cerebellum

value: Forebrain & Cerebellum


title: HTO counts of multiplex sSL0258 containing tissue & timepoint(s) Forebrain; e14.5|Cerebellum; P4

description:
Library name: sSL0258_HTO
Samples #LSMO402, #LSMO274, #LSMO73, #23/728, #LSMO402, #LSMO274, #LSMO73, #23/728, #LSMO402, #LSMO274, #LSMO73, #23/728, #LSMO402, #LSMO274, #LSMO73, #23/728 with genotypes Trip12+/-, Kdm6b+/-, Cul3+/-, Bckdk-/-, Trip12+/-, Kdm6b+/-, Cul3+/-, Bckdk-/-, Trip12+/-, Kdm6b+/-, Cul3+/-, Bckdk-/-, Trip12+/-, Kdm6b+/-, Cul3+/-, Bckdk-/- and sex m, m, m, m, m, m, m, m, m, m, m, m, m, m, m, m from tissue Forebrain, Forebrain, Forebrain, Cerebellum, Forebrain, Forebrain, Forebrain, Cerebellum, Forebrain, Forebrain, Forebrain, Cerebellum, Forebrain, Forebrain, Forebrain, Cerebellum at timepoints e14.5, e14.5, e14.5, P4, e14.5, e14.5, e14.5, P4, e14.5, e14.5, e14.5, P4, e14.5, e14.5, e14.5, P4
cx_e14_diet_seurat_RNA_assay.rds
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K27Ac_1

description:
Library name: histone_mark_cutrun_D13_H3K27Ac_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K27Ac_1_1.fq.gz and histone_mark_cutrun/D13_H3K27Ac_1_2.fq.gz.


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K9me3_2

description:
Library name: histone_mark_cutrun_D10_H3K9me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K9me3_2_1.fq.gz and histone_mark_cutrun/D10_H3K9me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 10; CUT&RUN target H3K9me3


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K9me3_1

description:
Library name: histone_mark_cutrun_D10_H3K9me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K9me3_1_1.fq.gz and histone_mark_cutrun/D10_H3K9me3_1_2.fq.gz.


title: ATAC counts of multiplex sSL0258 containing tissue & timepoint(s) Forebrain; e14.5|Cerebellum; P4

description:
Library name: sSL0258_ATAC
sSL0258_ATAC_filtered_feature_bc_matrix.h5
sSL0258_ATAC_fragments.tsv.gz
sSL0258_ATAC_fragments.tsv.gz.tbi
sSL0258_ATAC_peak_annotation.tsv
sSL0258_ATAC_peaks.bed
cx_e14_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0251 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0251_ATAC
sSL0251_ATAC_filtered_feature_bc_matrix.h5
sSL0251_ATAC_fragments.tsv.gz
sSL0251_ATAC_fragments.tsv.gz.tbi
sSL0251_ATAC_peak_annotation.tsv
sSL0251_ATAC_peaks.bed
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K4me1_2

description:
Library name: histone_mark_cutrun_D10_H3K4me1_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K4me1_2_1.fq.gz and histone_mark_cutrun/D10_H3K4me1_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 10; CUT&RUN target H3K4me1


title: HTO counts of multiplex sSL0251 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0251_HTO
Samples GN3F/22/2605, GN23/444, GN23/447, GN3F/22/2965, GN3F/22/2922, GN3F/22/2605, GN23/444, GN23/447, GN3F/22/2965, GN3F/22/2922 with genotypes Ash1l+/-, Bckdk-/-, Bckdk-/-, Kdm6b+/-, Trip12+/-, Ash1l+/-, Bckdk-/-, Bckdk-/-, Kdm6b+/-, Trip12+/- and sex m, m, m, m, m, m, m, m, m, m from tissue Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum, Cerebellum at timepoints P4, P4, P4, P4, P4, P4, P4, P4, P4, P4
cb_p4_diet_seurat_RNA_assay.rds


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K4me1_1

description:
Library name: histone_mark_cutrun_D10_H3K4me1_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K4me1_1_1.fq.gz and histone_mark_cutrun/D10_H3K4me1_1_2.fq.gz.


title: Con_no SFN4

city: Baltimore

first: Akira

last: Sawa

address: 600 N Wolfe St Meyer 3-166

institute: Johns Hopkins University

description:
Library name: 143-2
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

data_processing:
FastQC was used to check the quality of reads. Reads were aligned to the mouse genome (mm10) using STAR with the following optional parameters: --runThreadN 8 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts. Count from ReadsPerGene table generated from STAR was used for further analysis
Assembly: mm10
Supplementary files format and content: csv file includes raw count of each sample

source_name: cerebral cortex

extract_protocol:
RNA was extracted from isolated astrocytes by using the picopure RNA isolation kit (Applied Biosystems).
Samples were checked for quality/quantity on Fragment Analyzer and Qubit prior to library prep (RQN > 7; 100-400 ng per sample). NEBNext Poly(A) Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat# E7775) were used to generate libraries.Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

treatment_protocol: Cortical astrocytes were acutely isolated from adult cortices by MACS cell separation. Briefly, cortical tissue samples were obtained from adult mice following saline perfusion and cortical dissection, homogenized using a papain dissociation kit (Miltenyi Biotec #130-107-677), incubated with Fc blocking antibody and magnetic anti-ACSA-2 microbeads (Miltenyi Biotec #130-097-679), bound to MACS LS columns (Miltenyi Biotec #130-042-201) placed on a magnetic stand, washed 3 times with 0.5% BSA buffer to remove unbound cells, and eluted for downstream application.

value: cerebral cortex

tag: Sex

value: male

tag: age

value: Con

tag: diet

value: no SFN

tag: celltype

value: astrocyte


title: cKO_no SFN7

description:
Library name: 141-4
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: cKO


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K27me3_2

description:
Library name: histone_mark_cutrun_D10_H3K27me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K27me3_2_1.fq.gz and histone_mark_cutrun/D10_H3K27me3_2_2.fq.gz.

value: colon

value: epithelial cell

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 10; CUT&RUN target H3K27me3


title: GEX counts of multiplex sSL0251 containing tissue & timepoint(s) Cerebellum; P4

description:
Library name: sSL0251_GEX
sSL0251_GEX_filtered_feature_bc_matrix.h5
sSL0251_GEX_QC_categories.csv
cb_p4_diet_seurat_RNA_assay.rds

value: Cerebellum

value: mixed

value: mixed samples (multiplex)


title: Con_no SFN3

description:
Library name: 143-9
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K4me3_1

description:
Library name: histone_mark_cutrun_D10_H3K4me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K4me3_1_1.fq.gz and histone_mark_cutrun/D10_H3K4me3_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 10; CUT&RUN target H3K4me3


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K27me3_1

description:
Library name: histone_mark_cutrun_D10_H3K27me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K27me3_1_1.fq.gz and histone_mark_cutrun/D10_H3K27me3_1_2.fq.gz.


title: cKO_SFN7

description:
Library name: 143-5
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: SFN


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K27Ac_2

description:
Library name: histone_mark_cutrun_D10_H3K27Ac_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K27Ac_2_1.fq.gz and histone_mark_cutrun/D10_H3K27Ac_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 10; CUT&RUN target H3K27Ac


title: cKO_no SFN6

description:
Library name: 146-1
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K27Ac_1

description:
Library name: histone_mark_cutrun_D10_H3K27Ac_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K27Ac_1_1.fq.gz and histone_mark_cutrun/D10_H3K27Ac_1_2.fq.gz.


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_SMB1_T2

description:
Library name: cutrun2_dT29_SMB1_T2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target SMARCB1/SMB1; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_SMB1_T2_1.fq.gz and cutrun2/dT29_SMB1_T2_2.fq.gz.

value: SMARCB1 perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; T condition/time point; CUT&RUN target SMARCB1/SMB1


title: cKO_SFN6

description:
Library name: Astro5
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: cerebral cortex


title: Con_SFN5

description:
Library name: 147-1
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: male


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_SMB1_R2

description:
Library name: cutrun2_dT29_SMB1_R2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target SMARCB1/SMB1; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_SMB1_R2_1.fq.gz and cutrun2/dT29_SMB1_R2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target SMARCB1/SMB1


title: cKO_SFN5

description:
Library name: Astro4
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Con_SFN4

description:
Library name: 147-3
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: Con


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_SMB1_R1

description:
Library name: cutrun2_dT29_SMB1_R1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target SMARCB1/SMB1; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_SMB1_R1_1.fq.gz and cutrun2/dT29_SMB1_R1_2.fq.gz.


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_SMB1_DM2

description:
Library name: cutrun2_dT29_SMB1_DM2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target SMARCB1/SMB1; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_SMB1_DM2_1.fq.gz and cutrun2/dT29_SMB1_DM2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; DM/DMSO condition; CUT&RUN target SMARCB1/SMB1


title: cKO_SFN4

description:
Library name: Astro1
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: cKO

value: astrocyte


title: Con_SFN3

description:
Library name: 145-1
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_SMB1_DM1

description:
Library name: cutrun2_dT29_SMB1_DM1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target SMARCB1/SMB1; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_SMB1_DM1_1.fq.gz and cutrun2/dT29_SMB1_DM1_2.fq.gz.

value: colon

value: epithelial cell


title: cKO_no SFN5

description:
Library name: 141-2
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: no SFN


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_PBR1_T2

description:
Library name: cutrun2_dT29_PBR1_T2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target PBRM1/PBR1; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_PBR1_T2_1.fq.gz and cutrun2/dT29_PBR1_T2_2.fq.gz.

value: PBRM1 perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; T condition/time point; CUT&RUN target PBRM1/PBR1


title: Con_SFN2

description:
Library name: 145-2
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_PBR1_T1

description:
Library name: cutrun2_dT29_PBR1_T1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target PBRM1/PBR1; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_PBR1_T1_1.fq.gz and cutrun2/dT29_PBR1_T1_2.fq.gz.


title: Con_no SFN1

description:
Library name: 143-1
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_PBR1_DM2

description:
Library name: cutrun2_dT29_PBR1_DM2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target PBRM1/PBR1; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_PBR1_DM2_1.fq.gz and cutrun2/dT29_PBR1_DM2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; DM/DMSO condition; CUT&RUN target PBRM1/PBR1


title: cKO_SFN3

description:
Library name: 147-2
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: SFN


title: cKO_no SFN4

description:
Library name: Astro6
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: cKO_SFN2

description:
Library name: 143-6
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_IgG_T1

description:
Library name: cutrun2_dT29_IgG_T1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target IgG control; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_IgG_T1_1.fq.gz and cutrun2/dT29_IgG_T1_2.fq.gz.

value: IgG control

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; T condition/time point; CUT&RUN target IgG control


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_IgG_R2

description:
Library name: cutrun2_dT29_IgG_R2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target IgG control; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_IgG_R2_1.fq.gz and cutrun2/dT29_IgG_R2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target IgG control