title: H2AK119ub CUT&RUN mat del mESC day 3 line 1 rep 1

description: male

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and library size using Seqmonk.
FPKM reads were called over defined MACS2 peaks (determined by calling peaks between all H3K27me3 sample libraries and all input (no Ab) libraries) using the features over probes pipeline in Seqmonk
FPKM reads were calculated over genes +/- 10kb using the features over probes pipeline in Seqmonk, then were normalised to the geometric average of FPKM reads over MACS peaks in Microsoft Excel
Differential genome-wide peaks were called using the csaw v1.24.3 package between wt and maternal null samples at each day, as well as between days each for wt and maternal null
Assembly: GRCm38.p6
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_diff_FPKM_over_MACS_peaks.txt: tab-delimited text file containing FPKM reads over defined MACS2 peaks (determined by calling peaks between all H2AK119ub sample libraries and all input (no Ab) libraries)
Supplementary files format and content: benetti_CUT_RUN_diff_FPKM_values_for_probes_over_Hox.txt: tab-delimited text file containing FPKM reads calculated over genes +/- 10kb, and normalised to the geometric average of FPKM reads over MACS peaks (in benetti_H2AK119ub_CUT_RUN_diff_FPKM_over_MACS_peaks.txt). Note that this file is contained in the H3K27me3 CUT&RUN folder.
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_d2_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw at day 2 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_d2.5_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw at day 2.5 of differentiation between wt and maternal null samples
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_d3_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw at day 3 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2_vs_d2.5.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2.5_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2_vs_d2.5.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2.5_vs_d3.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H2AK119ub_CUT_RUN_csaw_peaks_2i_wt_vs_matdel.txt: tab-delimited text file containing differential H2AK119ub CUT&RUN peaks called by csaw ain mESCs grown in 2i + LIF medium between Smchd1 wildtype and maternal null samples.
Library strategy: CUT&RUN

value: H2AK119ub (Cell Signalling Technologies, D27C40)


title: H2AK119ub CUT&RUN mat del mESC day 3 line 2 rep 1

status: Public on Jun 27 2022

type: SRA

city: Parkville

first: Natalia

last: Benetti

state: Victoria

address: 1G Royal Parade

country: Australia

institute: WEHI

description: male

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: primary mouse embryonic stem cell line

growth_protocol: mESCs derived, and cultured as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

extract_protocol:
CUT&RUN was performed as described in Skene and Henikoff eLife 2017;6:e21856 DOI: 10.7554/eLife.21856 DNA was purified by phenol/chloroform/isoamylalcohol extraction followed by glycogen/ethanol precipitation
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: cell line

value: primary mouse embryonic stem cell line

tag: cell type

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors

tag: genotype

value: Smchd1[del/+] (maternally deleted)

tag: time

value: day 3 differentation

tag: antibody


title: H2AK119ub CUT&RUN mat del mESC day 3 line 1 rep

description: male


title: H2AK119ub CUT&RUN mat del mESC day 2.5 line 1 rep 1

description: male

value: day 2.5 differentation


title: H2AK119ub CUT&RUN mat del mESC day 2.5 line 2 rep 2

description: male


title: H2AK119ub CUT&RUN mat del mESC day 2.5 line 2 rep 1

description: male


title: H2AK119ub CUT&RUN mat del mESC day 2 line 2 rep 2

description: male

value: day 2 differentation


title: H2AK119ub CUT&RUN mat del mESC day 2 line 1 rep 2

description: male


title: H2AK119ub CUT&RUN mat del mESC day 2 line 2 rep 1

description: male


title: H2AK119ub CUT&RUN mat del mESC day 2 line 1 rep 1

description: male


title: H2AK119ub CUT&RUN wt mESC day 3 line 1 rep 2

description: male

value: Smchd1[fl/+] (wild-type)


title: H2AK119ub CUT&RUN wt mESC day 3 line 2 rep 1

description: male


title: H2AK119ub CUT&RUN wt mESC day 3 line 2 rep 2

description: male


title: H2AK119ub CUT&RUN wt mESC day 2.5 line 2 rep 1

description: male


title: H2AK119ub CUT&RUN wt mESC day 2.5 line 1 rep 2

description: male


title: H2AK119ub CUT&RUN wt mESC day 2.5 line 2 rep 2

description: male


title: H2AK119ub CUT&RUN wt mESC day 3 line 1 rep 1

description: male


title: H2AK119ub CUT&RUN wt mESC day 2 line 2 rep 1

description: male


title: H2AK119ub CUT&RUN wt mESC day 2.5 line 1 rep 1

description: male


title: H3K27me3 CUT&RUN wt mESC day 2 line 2 rep 2

description: male

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and library size using Seqmonk.
FPKM reads were called over defined MACS2 peaks (determined by calling peaks between all H3K27me3 sample libraries and all input (no Ab) libraries) using the features over probes pipeline in Seqmonk
FPKM reads were calculated over genes +/- 10kb using the features over probes pipeline in Seqmonk, then were normalised to the geometric average of FPKM reads over MACS peaks in Microsoft Excel
Differential genome-wide peaks were called using the csaw v1.24.3 package between wt and maternal null samples at each day, as well as between days each for wt and maternal null
Assembly: GRCm38.p6
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_diff_FPKM_over_MACS_peaks.txt: tab-delimited text file containing FPKM reads over defined MACS2 peaks (determined by calling peaks between all H3K27me3 sample libraries and all input (no Ab) libraries)
Supplementary files format and content: benetti_CUT_RUN_diff_FPKM_values_for_probes_over_Hox.txt: tab-delimited text file containing FPKM reads calculated over genes +/- 10kb, and normalised to the geometric average of FPKM reads over MACS peaks (in benetti_H3K27me3_CUT_RUN_diff_FPKM_over_MACS_peaks.txt)
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_d2_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw at day 2 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_d2.5_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw at day 2.5 of differentiation between wt and maternal null samples
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_d3_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw at day 3 of differentiation between Smchd1 wildtype and maternal null samples
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_matdel_d2_vs_d2.5.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_matdel_d2_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_matdel_d2.5_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 maternal null samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_wt_d2_vs_d2.5.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 2.5 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_wt_d2_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_wt_d2.5_vs_d3.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw in Smchd1 wildtype samples between days 2.5 and 3 of differentiation
Supplementary files format and content: benetti_H3K27me3_CUT_RUN_csaw_peaks_2i_wt_vs_matdel.txt: tab-delimited text file containing differential H3K27me3 CUT&RUN peaks called by csaw ain mESCs grown in 2i + LIF medium between Smchd1 wildtype and maternal null samples.
Library strategy: CUT&RUN

value: H3K27me3 (Cell Signalling Technologies, C36B11)


title: H2AK119ub CUT&RUN mat del mESC day 3 line 2 rep 2

description: male


title: RNAseq mat del mESC day 2.5 diff line 1 rep 3

description: male

library_source: transcriptomic

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Assembly: GRCm38.p6
Supplementary files format and content: benetti_ESC_RNAseq_log2RPKM_Hox.txt: tab-delimited text file containing log2-transformed RPKM counts normalized by sequencing depth for all Hox genes. Transcript isoforms were merged.
Supplementary files format and content: benetti_ESC_RNAseq_log2RPKM_diff_factors.txt is a  tab-delimited text files containing log2-transformed RPKM counts normalized by sequencing depth for all Hox genes: tab-delimited text file containing log2-transformed RPKM counts normalized by sequencing depth for a list of pluripotency and differentiation factors relevant to mESC to NMP differentiation. Transcript isoforms were merged.
Supplementary files format and content: benetti_ESC_RNAseq_raw_counts_all_genes.txt: tab-delimited text file of raw read counts over all genes

molecule: polyA RNA

extract_protocol:
100ng total RNA extracted with Quick-RNA Miniprep Kit (Zymo) then used as library prep input
TruSeq Stranded or non-stranded mRNA kit (Illumina)

treatment_protocol: mESCSs were differentiated into NMPs as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z


title: H2AK119ub CUT&RUN wt mESC day 2 line 1 rep 1

description: male


title: H2AK119ub CUT&RUN wt mESC day 2 line 1 rep 2

description: male


title: RNAseq wt mESC day 2 diff line 1 rep 3

description: male


title: RNAseq mat del mESC DME LIF line 1 rep 3

description: male

value: day 0 differentation


title: Alginate oligosaccharide planktonic replicate 2

status: Public on Jun 25 2022

city: Cambridge

first: Julia

last: Schwartzman

state: MA

address: 15 Vassar St

department: Civil and Environmental Engineering

country: USA

institute: MIT

data_processing:
Paired-end Illumina reads were trimmed using Trimmomatic (v0.30) to remove sequencing adapters and low quality reads (phred >30)(Bolger et al., 2014).
The remaining paired reads were checked for quality using FastQC (version 0.11.9) (Brown et al., 2017) and mapped to the predicted coding regions of the V. splendidus 12B01 genome (assembly ASM15276v1) using Bowtie2 (v 2.3.4.1)(Langmead and Salzberg, 2012), outputting SAM files.
SAM files were sorted by position using SAMTools (V 1.9) (Danecek et al., 2021), and mapping was parsed using HTSeq (Anders et al., 2015) to obtain count tables.
Assembly: Genbank Accession # AAMR00000000.1
Supplementary files format and content: count tables from HTSeq

molecule: total RNA

organism: Vibrio splendidus

growth_protocol: Incubation temperature was 25°C. For experimental measurements, precultures were established in a defined minimal medium (Amarnath K, et al. 2021. bioRxiv. doi:10.1101/2021.06.24.449802). Minimal medium contained 10 mM ammonium as sole source nitrogen and carbon source indicated. Precultures were grown with 10 mM glucose to an optical density of 0.4-0.6, as measured at 600 nm with a 1 cm path cuvette on a Genesys 20 Spectrophotometer (Thermo Scientific, Waltham, MA), rinsed by pelleting cells at 5000 rcf for 1 min in a tabletop microcentrifuge (Eppendorf, Hamburg, Germany), and resuspended in carbon-free defined minimal medium such that the final was 1.0. Experimental cultures were initiated by inoculating cells to an initial OD of 0.01 in 250 mL borosilicate glass Erelenmeyer flasks containing 70 mL of alginate minimal medium. Low viscosity alginate (Sigma-Aldrich A1112, St. Louis, MO) was added as the medium carbon source at 700 mg/L (0.07% w/v). Shaking was established by orbital rotation of flasks at setting 2 on an orbital shaker (Model 3500, VWR, Radnor, PA), which corresponds to ~100 rpm.

extract_protocol:
A Qiagen RNeasy kit was used to isolate total RNA, following manufacturer’s protocol, except for the following modifications: cells were resuspended in 15 mg/mL lysozyme in TE buffer, and incubated for room temperature for 30 min, prior to addition of buffer RLT. Samples were lysed by mechanical disruption using lysing matrix B (MPBio, Santa Ana, CA). Samples in lysing matrix shaken in a homogenizer (MPBio) for 10X 30 second intervals, taking care to keep samples from heating up. Samples were treated with DNase digestion using a Turbo DNA free DNAse kit (Ambion, Austin, TX), following manufacturer’s instructions. The integrity and purity of total RNA was assessed running a sample on an Agilent 4200 Tapestation in a HS RNA screen tape (Agilent, Santa Clara, CA). Depletion of rRNA was accomplished using the Ribominus Yeast and Bacteria transcriptome isolation kit (Invitrogen, Waltham, MA) and included ethanol precipitation with glycogen to concentrate remaining mRNA.
Ethanol precipitated samples were resuspended in FPF sample buffer from the TruSeq stranded mRNA-Seq kit reagents (Illumina, San Diego, CA). mRNA abundance was quantified using a Quant-iT RNA Assay kit (Invitrogen) on a Tecan Spark plate reader equipped with a monochrometer, following manufacturer’s instructions (Tecan, Männendorf, Switzeland). The quality of the mRNA was further assessed using an Agilent HS tape. We analyzed resulting samples on a Bioanalyzer to confirm mRNA depletion, and concentrated samples using ethanol precipitation with glycogen. Samples were screened for quality by requiring an RNA integrity number (RIN) or more than 8. mRNA remaining from rRNA depletion of 2-10 µg total RNA was used as template to create sequencing libraries. Sequencing libraries were prepared using an Illumina TruSeq Stranded mRNA library preparation kit (Illumina). Libraries were assessed for quality using screen tapes and fluorescence-based plate reader assays prior to pooling.

treatment_protocol: Cultures were grown an indicated stage of self-organization, as defined by microscopy. Cells cultured on oligosaccharides were gown to mid-exponential phase. 30 mL RNA Protect Bacterial Reagent (Qiagen, Hilden, Germany) was added to 15 mL cultures and incubated at 4 °C overnight. Cells were collected by centrifugation at 5000 rcf and 4°C in a Sorvall Legend XIR centrifuge (Thermo Fisher, Waltham, MA), equipped with a Fiberlite F15-6x100g rotor for 30 min. Supernatant was decanted, leaving pelleted cell material which was frozen at -20°C.

tag: strain

tag: carbon source

value: 0.07percent w/v alginate oligosaccharides

tag: growth stage

value: planktonic:exponential growth


title: III_50B_HR80 H3K27me3_ChIP-seq

status: Public on Jun 24 2022

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Histone modification

data_processing:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
ChIP-seq peak identification with SICER 1.1 with the following setting: redundancy threshold (1), window size (200), fragment size (100), effective genome fraction (0.8), gap size (600),  FDR (0.01)
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: etiolated seedling

growth_protocol: Seedlings were grown on Linsmaier and Skoog medium supplemented with 1% sucrose, sample 12 is derived from flowers of soil-grown plants

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: t-dna mutant

tag: antibodies

value: H3K27me3 (Active Motif, 39156)


title: IV_SALK_059379 H2A.Z_ChIP-seq

description: Histone variant

source_name: flowers

value: H2A.Z (Active Motif, 39647)


title: III_Col-0 IgG_ChIP-seq

description: control

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: III_Col-0 H2A.Z_ChIP-seq

description: Histone variant


title: III_Col-0 H3K4me3_ChIP-seq

description: Histone modification

value: H3K4me3 (EMD Millipore, 04-745)


title: III_50B_HR80 H3K4me3_ChIP-seq

description: Histone modification


title: III_Col-0 H3K27me3_ChIP-seq

description: Histone modification


title: III_50B_HR80 H2A.Z_ChIP-seq

description: Histone variant


title: PolII_UD2

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark Street

department: Molecular Biosciences

institute: Northwestern University

data_processing:
[RNA-seq] Reads were aligned using HiSat2. Number of Raw reads at each gene was calculated using htseq-count, and DESeq2 was used for differential expression analysis in R
[ChIP-seq]Reads were aligned using Bowtie2. Peaks were called with MACS2.
Assembly: hg19
Supplementary files format and content: RNA-seq data is in format of table containing counts at each gene and DESeq output information.

organism: Homo sapiens

source_name: human keratinoctyes

growth_protocol: neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium

extract_protocol:
For  RNA-seq, RNA was extracted using Quick-RNA™ MiniPrep (Zymo Research)
For RNA-seq, NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina was used for library construction. For ChIP-seq, NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) was used for library construction. Illumina DNA E7805 kit for inputs < 100ng was used for Nascent RNA-seq

treatment_protocol: To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 10 uM of siRNA for each target were nucleofected (Lonza to keratinocytes)

value: primary human neonatal keratinocytes

tag: treatment

value: None, undifferentiated keratinocytes

tag: chip antibody

value: Rabbit anti-RNAPolymerase II, Cell Signaling, Cat #14958


title: PolII_UD1


title: PolII_TPA_30minB

value: TPA 30min


title: PolII_KL2_1hrB

value: KL 1hr


title: PolII_KL2_1hrA


title: PolII_KL2_3hr_r2

value: KL 3hr


title: PolII_TPA_1hr

value: TPA 1hr


title: PolII_TPA_1hr_r2


title: PolII_KL2_3hr


title: PolII_DMSO_3hr_r2

value: DMSO 3hr


title: PolII_DMSO_3hr


title: PolII_DMSO_1hrB

value: DMSO 1hr


title: PolII_DF2

value: differentiated, 100% confluent, high Calcium


title: ChIP_HEXIM1_UD_r2

value: Rabbit anti-HEXIM1, Abcam, Cat#ab25388


title: PolII_DMSO_1hrA


title: HACDK9_TPA_r2

value: 1hr TPA

value: Mouse anti-HA, ProteinTech, Cat#66006


title: Alginate oligosaccharide planktonic replicate 1

value: 0.07percent w/v alginate oligosaccharides

value: planktonic:exponential growth


title: HACDK9_TPA


title: PolII_DF1


title: HACDK9_KL2_r2

value: 3hr KL


title: PolII_TPA_30minA


title: NascentRNA_3hrKLA

data_processing:
[RNA-seq] Reads were aligned using HiSat2. Number of Raw reads at each gene was calculated using htseq-count, and DESeq2 was used for differential expression analysis in R
[ChIP-seq]Reads were aligned using Bowtie2. Peaks were called with MACS2.
Assembly: hg19
Supplementary files format and content: RNA-seq data is in format of table containing counts at each gene and DESeq output information.
Library strategy: Nascent RNA-seq


title: NascentRNA_3hrKLB


title: NascentRNA_1hrKLA

value: 1hr KL


title: HACDK9_DMSO

value: primary human neonatal keratinocytes

value: 3hr DMSO


title: HACDK9_DMSO_r2


title: NascentRNA_DMSOA


title: NascentRNA_1hrKLB


title: II_SALK_061267 H3K4me3_ChIP-seq

description: Histone modification

value: H3K4me3 (EMD Millipore, 04-745)


title: II_SALK_061267 H2A.Z_ChIP-seq

description: Histone variant

value: H2A.Z (Active Motif, 39647)


title: I_SALK_117411 H3K27me3_ChIP-seq

description: Histone modification

source_name: de-etiolated seedling

value: H3K27me3 (Active Motif, 39156)


title: II_SALK_061267 H3K27me3_ChIP-seq

description: Histone modification


title: II_Col-0 H2A.Z_ChIP-seq

description: Histone variant


title: II_Col-0 IgG_ChIP-seq

description: control

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: I_SALK_117411 H2A.Z_ChIP-seq

description: Histone variant


title: I_SALK_069537 H3K4me3_ChIP-seq

description: Histone modification


title: II_Col-0 H3K27me3_ChIP-seq

description: Histone modification


title: HACDK9_KL2


title: I_SALK_017723 H3K4me3_ChIP-seq

description: Histone modification


title: I_SALK_069537 H3K27me3_ChIP-seq

description: Histone modification


title: II_Col-0 H3K4me3_ChIP-seq

description: Histone modification


title: I_SALK_069537 H2A.Z_ChIP-seq

description: Histone variant


title: I_SAIL_232 H3K27me3_ChIP-seq

description: Histone modification


title: I_SALK_117411 H3K4me3_ChIP-seq

description: Histone modification


title: I_SALK_017723 H2A.Z_ChIP-seq

description: Histone variant


title: I_SALK_059379 H3K27me3_ChIP-seq

description: Histone modification


title: I_SAIL_232 H3K4me3_ChIP-seq

description: Histone modification


title: NascentRNA_DMSOB


title: I_SALK_017723 H3K27me3_ChIP-seq

description: Histone modification


title: I_SALK_059379 H3K4me3_ChIP-seq

description: Histone modification


title: I_Col-0 H3K27me3_ChIP-seq

description: Histone modification


title: I_SAIL_232 H2A.Z_ChIP-seq

description: Histone variant


title: I_Col-0 H2A.Z_ChIP-seq

description: Histone variant


title: I_Col-0 H3K4me3_ChIP-seq

description: Histone modification


title: I_Col-0 IgG_ChIP-seq

description: control


title: MeDIP-Seq MI_72h_rep2

status: Public on Jun 23 2022

city: Shanghai

first: Han

last: Yuru

state: Shanghai

address: 279 Zhouzhu Rd. Pudong New District, Shanghai

country: China

institute: Shanghai University of Medicine and Health Sciences

description:
MI_72h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (62 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.

data_processing:
The reads with low overall quality, containing sequencing primers, and with low end quality were filtered using FASTX (http://hannonlab.cshl.edu/fastx_toolkit/index.html). The reads from each MeDIP sample were mapped to the mouse (mm10) genome using Bowtie2(Langmead and Salzberg, 2012) and default parameters to obtain BAM files. We apply MACS2(Zhang, et al., 2008) to the bam file obtained in the above step to find the peak enrichment region and obtain the enrichment region of the sample peak. Then, annotation of the peaks was performed. The distribution of the peaks on the chromosomes (promoter, 5’UTR, CDS, 3’UTR, Intron and TTR, where promoter is 2000bp upstream of the transcription start site and TTR is 5000bp downstream of the transcription termination site) was obtained according to the information on the location of the peaks. On CpG Island, the CpG shore is located 2000 bp downstream of CpG Island and the CpG shelf is located within 2000 bp to 4000 bp downstream of CpG Island. Differential analysis was performed on the peaks of the control and other MI groups using the R package MEDIPS(Lienhard, et al., 2014) with parameters set to |log2FC| >1 and p-value < 0.05. Differentially methylated regions (DMRs) were annotated using the same procedure as for peak annotation above.
Assembly: mm10
Supplementary files format and content: bed

source_name: myocardial tissue

extract_protocol:
The genomic DNA was sheared to a peak of 250bp fragments using the Covaris S2 ultrasound system.
The end repair and adenylation of the 3' end processes were carried out. After the connector ligation reaction, fragment selection was performed using beads. Then, immunoprecipitation of the methylated DNA was performed and the eluted DNA was amplified by PCR to generate the final sequencing library. The Agilent Bioanalyzer 2100 was used to purify the PCR products and assess the library quality. Finally, the illumina Novoseq 6000 was used to perform paired-end sequencing.
MeDIP-seq

tag: tissue

value: myocardial tissue

value: Cardiomyocytes


title: MeDIP-Seq MI_72h_rep1

description:
MI_72h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (61 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_24h_rep3

description:
MI_24h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (60 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_24h_rep2

description:
MI_24h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (59 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_24h_rep1

description:
MI_24h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (58 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_6h_rep3

description:
MI_6h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (57 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_1h_rep2

description:
MI_1h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (53 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_6h_rep2

description:
MI_6h_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (56 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_10m_rep1

description:
MI_10m_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (50 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq control_rep3

description:
control_rep3
The mice in the control group received the same operation, sutured through the inferior artery, but not ligated

value: control


title: MeDIP-Seq MI_10m_rep3

description:
MI_10m_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (51 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: MeDIP-Seq MI_1h_rep3

description:
MI_1h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (54 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: Control-8-MAP2

city: Stanford

first: Inma

last: Cobos

state: California

address: 300 Pasteur Drive, Lane Building, L235

institute: STANFORD UNIVERSITY MEDICAL SCHOOL

data_processing:
Sequencing data quality check. Performed with Illumina SAV.
Demultiplexing. Performed with Illumina Bcl2fastq2 v 2.19 program.
Alignment and filtering. Performed with Cellranger v3.0.1; cellranger count function, default parameters.
Barcode and UMI counting. Performed with Cellranger v3.0.1; cellranger count function, default parameters.
Assembly: GRCh38 1.2.0 (10x Cellranger)
Supplementary files format and content: Matrices in the Hierarchical Data Format (HDF5 or H5) from Cellranger v3.0.1; cellranger count function, default parameters.

source_name: Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen

extract_protocol:
Fresh-frozen tissue from the prefrontal cortex (Brodmann area 9; BA9) of healthy control donors was thawed on ice, and the cortical ribbon spanning all cortical layers was micro-dissected. Gentle mechanical dissociation without detergents or enzymatic digestion followed by sucrose-iodixanol gradient centrifugation was used to purify cells with relatively well-preserved somas. Immunostaining and fluorescence-activated cell sorting using the pan-neuronal marker MAP2 was used to collect neuronal somas.
RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 or v3 assay.

tag: number of cells sequenced

tag: age

tag: gender

value: M

tag: pmi (hr)

tag: rin

tag: brain weight (gr)

tag: disease

value: Healthy control

tag: ad stage

value: NIH-AA score A0B0C0

tag: other pathology

tag: biomaterial provider

value: NIH NeuroBioBank - Mount Sinai Brain Bank


title: MeDIP-Seq MI_72h_rep3

description:
MI_72h_rep3
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (63 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.

tag: cell type


title: MeDIP-Seq control_rep2

description:
control_rep2
The mice in the control group received the same operation, sutured through the inferior artery, but not ligated


title: MeDIP-Seq MI_6h_rep1

description:
MI_6h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (55 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.


title: Control-4-MAP2

value: Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen

value: F

value: UCLA-Easton Center brain bank; Departments of Neurology and Pathology; UCLA David Geffen School of Medicine


title: Control-3-MAP2

value: NIH-AA score A0B1C0

value: NIH NeuroBioBank - Sepulveda repository


title: Control-7-MAP2


title: MeDIP-Seq control_rep1

description:
control_rep1
The mice in the control group received the same operation, sutured through the inferior artery, but not ligated


title: Control-2-MAP2

value: NIH-AA score A1B1C0


title: control_rep3

status: Public on Jun 22 2022

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

data_processing:
Adapter sequences were trimmed using Cutadapt version 2.4.
For sequence mapping, Human reference genome (Ensembl version GRCh38)  was used.
Sequence mapping and transcript assembling were performed using Hisat2 and StringTie (version 1.3.6). A python script prepDE.py from StringTie was used to extract read count information.
The read counts were imported into edgeR for differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl gene ids and read counts for each sample.

source_name: lung adenocarcinoma cell line

growth_protocol: Lung adenocarcinoma cell line A549 was cultured in RPMI-1640 media supplemented with 10% FBS, 100U/mL penicillin, and 100µg/mL streptomycin. A549 media was also supplemented with additional L-glutamine. Cells were confirmed to be negative for mycoplasma.

extract_protocol:
RNA was isolated using TRIzol.
Libraries were made and RNA-seq profiles were generated by GeneWiz (www.GENEWIZ.com). The NEBNext Ultra II RNA Library Prep kit was used and the libraries were sequenced on HiSeq 4000.

treatment_protocol: A459 cells were infected with lentiviral vectors expressing lncRNA PSLR-1, -2 or empty vector and were harvested 48 hrs later (four replicates of each).

tag: transfection

value: Control RNA transfected

tag: cell line

value: A459 cells


title: control_rep2


title: Control-1-MAP2


title: control_rep4


title: WU13235, snrna, rep2

first: Matthew

middle: C

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description:
10X genomics
AllNuclei_snRNA_metadata.csv
AllNuclei_snRNA_rawCount.tar.gz
AllNuclei_snRNA_ScaledCount.tar.gz
CF_snRNA_metadata.csv
CF_snRNA_rawCount.csv.gz
CF_snRNA_scaled.data.csv.gz
CM_snRNA_metadata.csv
CM_snRNA_rawCount.csv.gz
CM_snRNA_scaled.data.csv.gz
Endothelial_snRNA_metadata.csv
Endothelial_snRNA_rawCount.csv.gz
Endothelial_snRNA_scaled.data.csv.gz
Immune_snRNA_metadata.csv
Immune_snRNA_rawCount.csv.gz
Immune_snRNA_scaled.data.csv.gz

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Raw and scaled count matrices, along with metadadata in csv formats all output from Suerat objects.

molecule: nuclear RNA

source_name: Cardiac

extract_protocol:
Fresh blood samples were kept on ice until isolation was started. In a sterile laminar flow hood, equal parts blood and Dulbecco’s phosphate-buffered saline (PBS) were mixed with 2% fetal bovine serum (FBS; STEMCELL Technologies, Cat. #07905). CCardiac nuclei were isolated by using density gradient centrifugation with Optiprep Density Gradient Medium (Sigma). All nuclei were isolated from the 30% to 40% interface and then diluted into nuclei wash buffer (PBS containing 1.0 % bovine serum albumin [BSA]) (Sigma) with 0.2 U/uL RNase inhibitor (Enzymatics/Qiagen, Y9240L) before being spun down at 1000 x g for 5 minutes. Next, the supernatant was removed, and the nuclei were washed twice with 25 mL of nuclei wash buffer. Nuclei were then resuspended in an appropriate volume of nuclei wash buffer to achieve a concentration appropriate for use with 10X Genomics Single Cell 3’ Reagents. LymphoprepTM solution (STEMCELL Technologies, Cat. #07801) was added to a SepMateTM-15 (IVD) tube (STEMCELL Technologies, Cat. #85415). The blood was carefully layered on top of the LymoprepTM solution and spun at 1200 G for 20 minutes. The plasma layer was pipetted off, aliquotted, and stored at –80°C. The PBMC layer was poured off and washed in 10 mL of Dulbecco’s PBS with 2% FBS and spun at 1000 G for 4 minutes to pellet PBMCs for downstream experiments.
For PBMCS, the single cell 3’ v2 protocol (10x Genomics) was used. For cardiac nuclei, the single cell 3’ v3 protocol (10x Genomics) was used. Library preparaation was performed according to the manufacter’s instructions.

value: Cardiac

tag: diagnosis

value: Donor


title: control_rep1


title: MeDIP-Seq MI_1h_rep1

description:
MI_1h_rep1
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (52 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.

value: myocardial tissue

tag: treatment


title: MeDIP-Seq MI_10m_rep2

description:
MI_10m_rep2
The experiment was divided into 6 groups. Each group contained 3 mice, 5 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group (0 h). The operation group was divided into 10 min, 1 h, 6 h, 24 h and 72 h subgroups after MI. The mice were anaesthetized with sodium pentobarbital (50 mg/kg, intraperitoneally) and placed on the operating table. The mice in the surgery group were intubated, and the left anterior descending coronary artery was ligated to induce MI, separately.

value: Cardiomyocytes


title: WU198RV, snrna, rep2


title: WU198LV, snrna, rep1


title: WU13235, snrna, rep1


title: Control-5-MAP2


title: WU198RV, snrna, rep1


title: WU198LV, snrna, rep2


title: P86, snrna, rep1

value: HCM


title: P86, snrna, rep2


title: P75, snrna, rep2

value: DCM


title: P75, snrna, rep1


title: P64, snrna, rep1

value: HLH Variant s/p Glenn


title: P64, snrna, rep2


title: P40, snrna, rep1

value: HLHS s/p Fontan


title: P36, snrna, rep1


title: P28, snrna, rep2

value: TOF


title: P28, snrna, rep1


title: P26, snrna, rep2


title: Control-6-MAP2

value: Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen

value: M

value: Healthy control

value: NIH NeuroBioBank - Mount Sinai Brain Bank


title: P8, snrna, rep2

value: HLHS


title: P26, snrna, rep1


title: P8, snrna, rep1


title: UK1, snrna, rep2


title: UK1, snrna, rep3


title: UK1, snrna, rep1


title: UK2, snrna, rep3


title: UK2, snrna, rep2


title: P33, snrna, rep2


title: UK2, snrna, rep1


title: P33, snrna, rep1


title: P37, pbmc, scrna

description:
10X genomics
PBMCs_sRNA_metadata.csv
PBMCs_sRNA_rawCount.csv.gz
PBMCs_sRNA_scaled.data.csv.gz

source_name: PBMC

value: PBMC

value: Complex SV s/p repair


title: P40, snrna, rep2


title: Donor1, pbmc, scrna

value: donor

value: adult


title: P41, pbmc, scrna

value: DCM s/p VAD


title: P40, pbmc, scrna


title: P36, snrna, rep2

value: Cardiac


title: P36, pbmc, scrna


title: P32, pbmc, scrna

value: DCM/LVNC


title: P3, pbmc, scrna


title: P4, pbmc, scrna

value: Supracardiac TAPVR


title: P25, pbmc, scrna


title: P2, pbmc, scrna


title: P26, pbmc, scrna


title: P28, pbmc, scrna


title: P1, pbmc, scrna

value: PAVC


title: P28, CM, atac

data_processing:
Reads were mapped to the mouse genome human genome (hg19) or mouse genome (mm9) using Bowtie2 with default paired-end settings. Next, all non-nuclear reads, and improperly paired reads were discarded. Duplicated reads were next removed with picard MarkDuplicates (http://broadinstitute.github.io/picard). Peak calling was carried out with MACS2 (callpeak  --nomodel –broad). Blacklisted regions removed along with peaks of low sequencing quality (require > q30). Reads were counted for each condition from the comprehensive peak file using bedtools (multicov module)
Assembly: hg19
Supplementary files format and content: bigWig output from Homer.

extract_protocol:
Nuclear isolation, library preparation, and quality control were performed according to Hill et. al. (2021) for PCM1 isolation and ATAC-seq. Briefly, fresh cardiac tissue was harvested on ice and immediately homogenized with a Biogen Series PRO200 (PRO Scientific) prior to dounce homogenization. Nuclei were isolated via density gradient centrifugation with optiprep density gradient medium (Sigma). All nuclei isolated from 30-40% interface were pre-cleared with Protein-G Dynabeads (Life technologies). Next, nuclei were immunoprecipitated with an anti-PCM1 (Sigma, HPA023370) antibody and Protein-G Dynabeads to enrich for cardiomyocyte nuclei. CD14+ cells were isolated by using the CD14 MicroBeads (Miltenyi Biotec, 130-050-201) as per the manufacturer’s instructions. Briefly, PBMCs were washed twice with Dulbecco’s PBS containing 2% FBS (STEMCELL technologies, #07905) before being bound to CD14 MicroBeads and isolated with MS columns (Miltenyi Biotec, 130-042-201). Cells were subjected to two rounds of purification before ATAC-seq. NK cells were isolated from CD14+ cell–depleted PBMC pools by taking the flow through from the CD14+ MACS enrichment. After flowing through the MACS MS columns, NK cells were isolated by using the human NK cell isolation kit (Miltenyi Biotec, 130-092-657) according to the manufacturer’s instructions, allowing for the isolation of both cell types simultaneously from the same patient sample. After the purification of NK cells and CD14+ monocytes from density gradient–purified PBMCs, we performed ATAC-seq by using the Omni-ATAC protocol with roughly 50,000 cells as input.
OMNI-ATAC protocol with 50,000 cells or cardiomyocyte nuclei as input.

value: Cardiomyocytes


title: P75, CM, atac

value: DCM


title: 13-198, CM, atac

value: Donor


title: P22, CM, atac

value: AS s/p repair


title: P20, CM, atac

value: TOF


title: P45, Nkcell, atac

value: NK


title: P5, CM, atac


title: P45, CD14, atac


title: P10, CM, atac


title: P8, CM, atac


title: P43, NKcell, atac

value: Shone's Variant s/p repair


title: P43, CD14, atac


title: P42, CD14, atac

value: PAPVR


title: P42, NKcell, atac

value: PBMC


title: P36, CD14, atac


title: P40, CD14, atac

value: HLHS s/p Fontan


title: P39, CD14, atac


title: P35, CD14, atac

value: ASD/PAPVR


title: P34, CD14, atac

value: AS, coarct s/p repair


title: P26, CM, atac


title: P27, CD14, atac

value: PM VSD


title: mTAIL-seq_shRnf219-1

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

description: processed data file: SHC_vs_shRnf219.xls

data_processing:
We used STAR to align read1 to the reference genome (mm10) to get the detail alignment. Then, paired reads were mapped using STAR to allow soft-clipping to the alignments. We filter the read2 by removing read without the tag (GTCAG) on positions 15–25 nt from the 5’-end. Those consecutive poly(A) on filtered read2 not entirely aligned to the genome were considered as putative poly(A) tags. Using reference genome annotation (GENCODE vM23), we assigned these putative poly(A) tags by considering read1 alignment overlapped with annotated genes. Then we could calculate the poly(A) length for each poly(A) tag and assign these poly(A) length to each gene
Assembly: UCSC mm10 (GRCm38)
Supplementary files format and content: Excel shows the median poly(A) tail length of each gene.
Library strategy: mTAIL-Seq

extract_protocol:
Extract total RNA by TRIzol
mTAIL-seq library was constructed as previously described_x000D_(Lim, J., Lee, M., Son, A., et al. (2016). mTAIL-seq reveals dynamic poly(A)_x000D_tail regulation in oocyte-to-embryo development. Genes Dev. 30,_x000D_1671–1682.) with an additional gel purification after 5' _x000D_adapter ligation.

treatment_protocol: Non-targeting shRNA or Rnf219 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, ES cells were selected with 2 ug/ml of puromycin for additional 48 hours and then were grown one passage off feeders for 30 min before harvesting

tag: strain

value: C57BL/6 (female) x 129/S (male)

value: mES

tag: shRNA

value: Rnf219 shRNA


title: jmj24_LD_H3K4me3_repeat2

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq version 2.16.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
The SICER was used to identify ChIP-enriched peaks between wild type and mutant.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness).

extract_protocol:
Chromatin isolated from 11-day-old seedlings in LD were subjected to sonication and immunoprecipitation with the anti-H3K4me3 antibody.
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp pair-end sequencing)

tag: growth conditions

value: long day (16 h light, 8 h dark)

tag: genotype

tag: chip antibody

value: Millipore, 07-473


title: jmj24_LD_H3K4me3_repeat1


title: mTAIL-seq_SHC-1

value: Non-targeting


title: atx4/5_LD_H3K4me3_repeat2


title: gDNA_WB_DBA_12

status: Public on Jun 21 2022

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: Healthy whole blood sample, DBA

hyb_protocol: Bisulphite converted DNA (EZ DNA Methylation Kit, Zymo Research, CA, USA) was amplified, fragmented and hybridised to Illumina Infinium MouseMethylation BeadChip using standard Illumina protocol

scan_protocol: The array samples were scanned with the iScan System

data_processing:
The three different datasets (B6 training, B6 validation and DBA) were processed separately. The raw data from IDAT files was read and processed in R with the ENmix package, and the betas were normalized using the ENmixD method (ENmix background correction and RELIC dye-bias normalization). Probes with detection p-values > 0.01 or more than 10% of NA values were filtered out. One sample with more than 10% missing values was not considered for further analysis. Furthermore, CpGs on X and Y chromosomes were not considered for epigenetic clocks. Probe-type bias adjustment was performed with the Regression on Correlated Probes method
Normalized beta values (ENmixD normalization) with probe-type bias adjustment (Regression on Correlated Probes method)

label: Cy5 and Cy3

source_name: Whole blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was isolated from whole blood samples (taken by submandibular bleeding or post mortem from vena cava or heart) using the QIAamp® DNA Mini and Blood Mini kit (Qiagen GmbH, Hilden, Germany), according to manufacturer's instructions

tag: age (weeks)

tag: Sex

value: male

tag: sample type

value: Whole blood

tag: condition

value: healthy

tag: dataset

value: DBA


title: mTAIL-seq_SHC-2


title: gDNA_WB_DBA_10

description: Healthy whole blood sample, DBA

value: female


title: mTAIL-seq_shRnf219-2


title: gDNA_WB_DBA_11

description: Healthy whole blood sample, DBA


title: gDNA_WB_DBA_7

description: Healthy whole blood sample, DBA


title: gDNA_WB_DBA_6

description: Healthy whole blood sample, DBA


title: gDNA_WB_DBA_9

description: Healthy whole blood sample, DBA


title: gDNA_WB_DBA_4

description: Healthy whole blood sample, DBA


title: gDNA_WB_DBA_5

description: Healthy whole blood sample, DBA


title: P39, NKcell, atac

tag: tissue

value: NK

value: TOF

tag: age


title: P40, NKcell, atac

value: PBMC

tag: cell type

value: HLHS s/p Fontan


title: gDNA_WB_DBA_3

description: Healthy whole blood sample, DBA


title: gDNA_WB_DBA_1

description: Healthy whole blood sample, DBA


title: gDNA_WB_DBA_2

description: Healthy whole blood sample, DBA


title: gDNA_WB_B6_V9

description: Healthy whole blood sample, validation set

value: B6 validation


title: gDNA_WB_B6_V10


title: P33, CD14, atac


title: atx4/5_LD_H3K4me3_repeat1


title: gDNA_WB_B6_V12


title: gDNA_WB_B6_V7


title: gDNA_WB_B6_V3


title: gDNA_WB_B6_V4


title: gDNA_WB_B6_V6


title: gDNA_WB_B6_V1


title: gDNA_WB_B6_T11

description: Healthy whole blood sample, training set

value: B6 training


title: gDNA_WB_B6_T10


title: gDNA_WB_DBA_8

description: Healthy whole blood sample, DBA


title: gDNA_WB_B6_T7


title: gDNA_WB_B6_T8


title: gDNA_WB_B6_T9


title: gDNA_WB_B6_T4


title: gDNA_WB_B6_T6


title: gDNA_WB_B6_V5


title: gDNA_WB_B6_T12


title: gDNA_WB_B6_T3


title: gDNA_WB_B6_T2


title: gDNA_WB_B6_T1


title: SB70_Placebo

status: Public on Jun 18 2022

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

description: Centrifuged bone needle biopsy; centrifuged bone was digested twice with liberase according to manufacturer protocol (30 minutes, 37 degrees C); remaining bone was homogenized for osteocyte enriched RNA

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Assembly: h19
Supplementary files format and content: tab-delimited text files include RPKM and count values for each Sample

source_name: Centrifuged bone needle biopsy, digested 2X

extract_protocol:
Bone needle biopsy was centrifuged to remove loosely adherent marrow, and homogenized in QIAZol Reagent. Alternatively, a fraction of centrifuge bone was serially digested with liberase (2 digestions, 30 minutes, 37degreesC), washed and homogenized in QIAZol reagent. RNA was extracted from non-digested and digested samples, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared according to the manufacturer’s instructions for the NuGen Ovation RNA-Seq version 2 and Encore NGS Library Systems (San Carlos, CA).

value: Bone biopsy

value: 25-37 years

tag: subject status

value: pre-menopausal young women

value: Placebo


title: SB71_Placebo


title: SB62_Placebo


title: SB53_Placebo


title: SB50_Placebo


title: SB45_Placebo


title: gDNA_WB_B6_V2


title: SB43_Placebo


title: SB39_Placebo


title: SB32_Placebo


title: gDNA_WB_B6_T5


title: CutAndTag.AC7.ARID2.WT

status: Public on Jun 16 2022

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: hg19
Supplementary files format and content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes.
Library strategy: Cut&Tag

source_name: cancer cell line

growth_protocol: AC7 cells were grown in DMEM (Gibco, 11960-44), supplemented with 15% FBS, 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122). BT549 cells were grown in RPMI (Gibco, 21870-076), supplemented with 10% FBS, 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
ChIP-seq protocol: Cells were trypsonized, washed with room temperature PBS twice to remove trypsin, and divided into 40 million-cell aliquots.  Cells were fixed using 1% formaldehyde (Sigma Aldrich) for 10 min at 37 °C with constant stirring to keep cells in solution, and finally quenched with 125 mM glycine for 5 min at 37 °C. Quenched cells were washed with cold PBS, and stored in 10-million aliquots at −80 °C until they were used. 10 millions cells were used per epitope in subsequent chromatin immunoprecipitations. Following nuclei extraction, chromatin was sonicated using a Covaris E220 Focused-Ultrasonicator system. Sonicated chromatin was cleared by centrifugation for 10 min at 10,000 r.p.m. (15,000 g). Soluble fractions were incubated with the indicated antibodies (see antibody list) overnight at 4°C, and captured using Protein G Dynabeads (Thermo Fisher). All ChIP-seq samples received 20 ng of spike-in Drosophila chromatin (Active Motif), and 2 µg spike-in antibody (Active Motif) for normalization post sequencing. Antibody-chromatin complexes were captured with Protein G Dynabeads (Thermo Fisher), washed extensivley, eluted, and treated with RNAse A (Roche) for 30 min at 37 °C and Proteinase K (Life Technologies) for 3 h at 65 °C. ChIP DNA samples were extracted using SPRI beads (Beckman Coulter Agencourt AMP Xpure), washed with 80% Ethanol, and eluted using 0.1X TE. ChIP DNA samples were stored at -20C before library prep were initiated. All ChIP seq libraries were processed with Illumina’s NEBNext Ultra II DNA library Prep Kit (Followed standard protocols). All ChIP seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing.
ATAC-seq protocol: ATAC-seq protocol was adapted from following protocol [cit] with slight modifications covered below. 50,000 - 100,000 cells were trypsonized, and washed with cold PBS to remove trypsin. When appropriate, lysing steps were carried out in 10X bulk. Cell pellets were resuspended in 50μl cold ATAC-seq resuspension buffer (RSB) containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2, supplemented with fresh NP40 (final 0.1% v/v), Tween-20 (final 0.1% v/v), Digitonin (final 0.01% v/v). Resuspended cells were incubated in lysis buffer for 3-5 min on ice. Lysis step was quenched with 1 mL of RSB supplemented with Tween-20 (final 0.1% v/v) and pelleted at 500 g for 10 min at 4°C. Cell pellets were resuspended in 50μl transposition reaction mix containing 25 μl 2X TD buffer, 2.5 μl transposase, 16.5 μl 1X PBS, 0.5 μl 1% digitonin (final 0.01% v/v), 0.5 μl 10% Tween-20 (final 0.1% v/v), and 5 μl water nuclease-free water. Transposition reaction was assembled, mixed, and incubated at 37°C for 30 min with constant shaking of 1,000 RPM on a thermomixer. To purify the tagmented DNA, Qiagen MinElute Reaction Cleanup Kit was used. Standard protocol (Buenrostro et al., 2015) [cit] with 10-12 cycles of amplification was used to amplify tagmented library. ATAC-seq libraries were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing.
RNA-seq protocol: 1,000,000 cells were trypsonized, and washed with cold PBS to remove trypsin. RNA was purified using the Qiagen RNeasy kit, and further processed in the Illumina TruSeq Stranded mRNA library prep kit with appropriate RNA spike-in to mitigate experimental errors. All RNA-seq samples were analyzed by Tapestation to assess quality, and a Qubit Fluorometer to measure concentration. All ChIP seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing. For fresh frozen primary samples, 15-25 mg fresh frozen tissue samples were harvested on ice, and washed with cold PBS. Samples were immediately resuspended in cold Qiagen proprietary RLT buffer. The tissue was initially grinded with in a 1.5mL eppendorf tube with a small pestle, and further homogenized using a QiaShredder.  Remaining protocol was followed as done with RNA-seq for the cell cultures.
Cut&Tag protocol: CUT&Tag was carried out according to Epicypher’s protocol in 8-strip PCR tube with slight modifications. Concanavalin A coated magnetic beads were activated with Bead Activation Buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were kept at room temperature until used. 100,000 cells were trypsonized, washed with cold PBS to remove trypsin. Cells were lysed sing cold Nuclear Extraction Buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor (Roche). Nuclei samples were incubated with activated Concanavalin A beads at room temperature for  10 min. The nuclei-Concanavalin A bead complex was resuspended in Antibody 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), 0.01% Digitonin, and 500 ng of primary antibody. Following overnight incubation at 4°C, primary antibody was removed, and beads were washed once with Digitonin 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. Secondary antibody were added, and incubated with nuclei-Concanavalin A bead complex for 1 hr at room temperature. Nuclei-Concanavalin A bead complex were washed with Digitonin 150 Buffer twice before resuspensinon in 50uL cold Digitonin300 Buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. 2.0 µL CUTANA pAG-Tn5 (Epicypher) was added to each sample, and in incubated on a nutator for 1 hr at room temperature. Following incubation, beads were washed with cold Digitonin300 Buffer. Targeted chromatin tagmentation and library amplification were carried out exactly according to Epicypher’s protocol.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). BT549 cells were lentivirally infected with either Empty vector, GFP, or full length SMARCE1 for 24h and then selected with blasticidin for 5-7 days. Cells were harvested 7 days post-infection. For compound treatments, cells were seeded in 6 well-plate or 10cm dishes depending on the experimental setup. Cells were treated at indicated concentrations over 5-7 days with DMSO controls. Media containing fresh compounds was added on day 3. Cells were harvested for genomics experiments using standard protocol.

tag: cell line

value: wild type

tag: antibody

value: Rabbit anti-ARID2; PA5_35857; ab2553167

tag: ngs approach

value: CutAndTag


title: SB18_Placebo

tag: treatment


title: SB10_Placebo


title: CutAndTag.AC7.ARID2.SMARCE1_KO

value: SMARCE1 null


title: PolyA-seq_MYC.L1RP_4

first: Roberto

last: Chiarle

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

data_processing:
Sequences in library were similarly processed as previously described(Mara Compagno et al., Nature 2017). Briefly, reads for each experimental condition were demultiplexed by designed barcodes plus followed portion of primer if barcode length less than 8 bp. For PolyA-seq, reads were further filtered by the presence of primer (7 Poly(A) was imposed to primer directly) plus additional 8 Poly(A), then the barcode and primer portion of the remained sequences were masked for alignment analysis. Next, the processed sequences were aligned to human genome (GRCh38/hg38) using BLAT, and finally aligned sequences were further cleaned by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random ligation with HaeIII restriction sites). L1 insertion junction position was determined based on the genomic position of the 5’ end of the aligned read.
Assembly: hg38
Supplementary files format and content: bed file for L1 insertion junction

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), penicillin-streptomycin (100 units per ml) and L-glutamine (2 mM). Cells were cultured at 37 °C with 5% CO2

extract_protocol:
Genomic DNA was extracted using rapid lysis buffer containing 20 μg/ml Proteinase K and incubation at 56 °C overnight, followed by standard isopropanol extraction, wash in 70% ethanol and resuspension in TE buffer.
50 μg genomic DNA was digested overnight with HaeIII enzyme (recognizes and cuts at 5’-GG/CC-3’), followed by 3’A addition by Klenow polymerase (3′–5′ exo-; New England Biolabs) and adaptor ligation (composed of an upper linker and a lower 3′-modified linker) by T4 DNA Ligase (Promega). To reduce sequencing background, ligation reactions were digested with Xba I to remove the exogenous LINE-1 sequence from plasmid (first blocking). In the first round of PCR, DNA was amplified using Biotin-LEAP, together with adaptor specific reverse primer (AP1) and Phusion polymerase (Thermo Fisher Scientific). 20 PCR cycles were performed in the following conditions: 98 °C for 20 s, 56 °C for 30 s, and 72 °C for 1 min. Multiple reactions were performed in generating large-scale libraries. Biotinylated PCR products were captured by Dynabeads MyOne StreptavidinC1 kit (Invitrogen) for 2-3 hours at room temperature with rotation, followed by 2 h digestion with Xba I (second blocking). PCR products were then eluted in 95% formamide/10 mM EDTA and purified by PCR extraction kit (Qiagen). The second round emulsion-PCR (EM-PCR) was performed in an oil-surfactant mixture by nested forward primer (SV40-polyA-F) and nested adaptor specific reverse primer (AP2) using the following conditions: 20 cycles of 94 °C for 30 s, 57 °C for 30 s, and 72 °C for 1 min. The PCR products was then extracted three times with diethyl ether and DNA was re-purified by PCR extraction kit (Qiagen). The third round of PCR was performed with barcoded forward and reverse primer (10-12 cycles of 98 °C for 20 s, 60 °C for 30 s, and 72 °C for 1 min). PCR products were size fractionated for DNA fragments between 300 bp and 1000 bp on a 1% agarose gel and purified by Gel extraction kit (Qiagen).
PolyA-seq

treatment_protocol: Cells were transfected with L1 reporters and CRIPSR/cas9 editing is introduced 5 days post-transfection

tag: crispr tech

value: Canonical CRISPR/Cas9

tag: target

value: MYC

tag: seq type

value: PolyA L1 insertion


title: Sample 1

status: Public on Jun 17 2022

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: Fresh-frozen post mortem orbitofrontal cortex tissues of Brodmann area 11 (BA 11) from two neurotypical individuals obtained from the NSW Brain Tissue Resource Centre in Sydney, Australia were used for single-nuclei RNA-sequencing.

data_processing:
Sequence reads were demultiplexed using the sample index, aligned to a pre-mRNA reference and UMI were counted after demultiplexing of nuclei barcodes using Cell Ranger v3.1.0.
The pre-mRNA reference is based on transcriptome GRCh38_ensrel93.
Assembly: GRCh38
Supplementary files format and content: tsv/mtx files with filtered gene counts per sample (10x Cellranger output)

source_name: postmortem tissue from orbitofrontal cortex

extract_protocol:
Nuclei were isolated from frozen, dissected brain samples (50 - 60 mg) by dounce-homogenisation in nuclei extraction buffer. Homogenate was layered onto a sucrose cushion and ultra-centrifuged. Nuclei pellet was resuspended in resuspension buffer, filtered through a cell strainer cap, stained with DAPI and counted using a hemocytometer.
Single nuclei RNA-seq libraries were prepared following the user guide of 10X Genomics (Chromium Single Cell 3’ Reagents kit v3) with a target recovery of 10,000 nuclei per sample.
Libraries were assessed using a High Sensitivity DNA Analysis Kit for the 2100 Bioanalyzer (Agilent), were then pooled equimolarily and treated with Illumina Free Adapter Blocking Reagent before sequencing on the NovaSeq 6000 System (Illumina).

value: Male

tag: pmi

tag: rin

tag: ethnicity

value: European


title: PolyA-seq_U2OS_MYC.L1-RTm_3

description: Please note that the bed file for this sample contains no insertion junctions, as expected.


title: PolyA-seq_MYC.L1RP_2


title: sample.ginkgo.28034347.experiment.ginkgo.39011

city: Austin

first: Joshua

last: Urrutia

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/Bacillus0x20subtilis0x201680x20Marburg/1

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: cell culture

extract_protocol:
Total RNA was extracted using Magjet RNA extraction kit (Thermo) according to manufacturer's instructions.
RNA quality was assessed using Tapestation (Agilent). KAPA RNA Hyperprep kit (Roche) was used for ribosomal RNA depletion and Illumina compatible library preparation.

tag: temperature

value: 30.0 celsius

tag: timepoint

value: 23.0 hour


title: PolyA-seq_U2OS_MYC.L1-ORFeus_5

tag: condition


title: PolyA-seq_U2OS_MYC.L1-RTm_5


title: PolyA-seq_U2OS_MYC.L1-RTm_1


title: SB22_Placebo

tag: tissue


title: PolyA-seq_HeLa_MYC.L1-RTm_6

source_name: Hela

value: Hela


title: PolyA-seq_U2OS_MYC.L1-ORFeus_3


title: PolyA-seq_U2OS_MYC.L1-ORFeus_1


title: Sample 2

tag: age

tag: Sex

value: Female


title: SB54_Placebo

value: Bone biopsy

tag: subject status


title: PolyA-seq_U2OS_MYC.L1-ORFeus_2

tag: cell line


title: PolyA-seq_MYC.L1RP_3


title: PolyA-seq_U2OS_MYC.L1-RTm_4


title: PolyA-seq_U2OS_MYC.L1-RTm_2


title: SB35_Placebo

value: 25-37 years


title: PolyA-seq_HeLa_MYC.L1-RTm_5


title: SB30_Placebo

value: pre-menopausal young women


title: PolyA-seq_MYC.L1RP_1


title: PolyA-seq_HeLa_MYC.L1-RTm_3


title: PolyA-seq_U2OS_MYC.L1-ORFeus_4


title: PolyA-seq_HeLa_MYC.L1-RTm_2


title: PolyA-seq_HeLa_MYC.L1-ORFeus_1


title: PolyA-seq_HeLa_MYC.L1-ORFeus_5


title: SOX9OE, H3K4me1 CUT&Tag, rep2

status: Public on Jun 15 2022

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

data_processing:
All reads were mapped to the hg19/GRCh37 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Assembly: hg19/GRCh37
Supplementary files format and content: tracks in BigWig file format
Library strategy: CUT&Tag

source_name: Umbilical vein endothelial cells

growth_protocol: HUVECs were cultivated in Medium 200 (Thermo Fisher Scientific) supplemented with 2% low serum growth supplement and 1% Penicillin Streptomycin.

extract_protocol:
CUT&RUN, CUT&Tag, ATAC-seq
NEBnext DNA Ultra ii (New England Biolabs)

value: HUVEC

tag: transduced with

value: SOX9 expression plasmid

tag: cut&run/tag antibody

value: H3K4me1 (C15410037, Diagenode)


title: PolyA-seq_HeLa_MYC.L1-ORFeus_3


title: SOX9OE_ATAC_48h

data_processing:
All reads were mapped to the hg19/GRCh37 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE  -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Assembly: hg19/GRCh37
Supplementary files format and content: tracks in BigWig file format

growth_protocol: HUVECs were cultivated in Medium 200 (Thermo Fisher Scientific) supplemented with 2% low serum growth supplement  and 1% Penicillin Streptomycin.

extract_protocol: NEBnext DNA Ultra ii (New England Biolabs)


title: SOX9OE, H3S28P CUT&Tag, rep2

value: H3S28P (ab5169, Abcam)


title: PolyA-seq_HeLa_MYC.L1-ORFeus_2


title: PolyA-seq_HeLa_MYC.L1-RTm_1


title: Empty, H3K27ac CUT&Tag, rep2

value: Empty vector

value: H3K27ac (ab4729, Abcam)


title: Empty, H3S28P CUT&Tag, rep2


title: PolyA-seq_HeLa_MYC.L1-ORFeus_4

value: Canonical CRISPR/Cas9

value: MYC


title: SOX9OE, H3K27ac CUT&Tag, rep2


title: SOX9OE_ATAC_24h


title: SOX9OE, H3K27me3 CUT&Tag, rep2


title: Ini-seq2_15_minutes_control

first: Guillaume

last: Guilbaud

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: Medical Research Council - LMB

data_processing:
Reads were map with Bowtie2 against hg38. Only reads mapped at a unique genomic position were kept. PCR duplicates were removed
Ini-seq 2 origins and efficency were called with a custum peak caller (https://github.com/Sale-lab)
Assembly: hg38
Supplementary files format and content: Ini-seq 2 15 minutes: Origins position and effiency score (Z-score)

source_name: Bladder carcinoma

extract_protocol:
Ini-seq2 Heavy-Light and Light-Light fraction were isolated by isopycnic centrifugation, desolted and precipitated.  SNS-seq samples were processed as descirbed in Akerman et al. Nature Communications volume 11, Article number: 4826 (2020).
Libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S)

tag: cell type

value: Bladder carcinoma

tag: fraction

value: Heavy-Light and Light-light


title: SOX9OE_ATAC_96h_(rep2)


title: PolyA-seq_HeLa_MYC.L1-RTm_4

tag: crispr tech

tag: target

value: PolyA L1 insertion


title: control ChIP-seq input - 5

status: Public on Jun 11 2022

first: Aiwei

last: Wu

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Reads were aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Assembly: Hg38
Supplementary files format and content: BigWig files contains normalized read count (CPM, in 50-bp bins).

source_name: K562 cell line

growth_protocol: Human cells K562 were cultured in 90% DMEM + 10% FBS+ 2% Penicillin/Streptomycin + 2 mM L-Glutamine.

extract_protocol:
For immunoprecipitation, on day 1 antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat. no. 10002D) by incubating at 4 °C for 3 hours. Afterwards, the bead-antibody complexes were washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4 °C overnight. On day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH 7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10 µg/ml RNase A for both elution and RNA digestion, and incubated at 55 °C for 1 hour. Then Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the temperature was increased to 65 °C for crosslink reversal. After incubation for 4 to 6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).
ChIP-seq libraries: The libraries were constructed with 2–10 ng immunoprecipitated DNA. After end-repair, A-tailing, and barcode ligation, barcoded DNA was amplified by 16-cycle PCR.  Libraries were sequenced on Illumina HiSeq X Ten.

treatment_protocol: For double fixation with EGS (Thermo, cat. no. 21565) and formaldehyde, cells were fixed initially with 1.5 mM EGS at room temperature for 30 min, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For double fixation with DMA (Thermo, cat. no. 20660) and formaldehyde, cells were fixed initially with 25 mM DMA at room temperature for 1 hour, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For sonication, fixed cells were washed twice with PBS and resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH 7.4) supplemented with Protease Inhibitor Cocktail (Millipore, cat. no. 535140) at a concentration of 40 million cells/ml; genomic DNA was disrupted to a size range of 100 to 500 bp.

tag: genotype

value: wild type

tag: antibody

value: input

tag: fixation

value: EGS + FA


title: SOX9OE_ATAC_72h


title: Empty, H3K4me1 CUT&Tag, rep2


title: Empty, ATAC, rep2

data_processing:
All reads were mapped to the hg19/GRCh37 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Assembly: hg19/GRCh37
Supplementary files format and content: tracks in BigWig file format


title: Empty, SOX9 CUT&RUN, rep2

data_processing:
All reads were mapped to the hg19/GRCh37 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Assembly: hg19/GRCh37
Supplementary files format and content: tracks in BigWig file format
Library strategy: CUT&RUN

value: SOX9 (AB5535, Millipore)


title: control DOT1L ChIP-seq


title: RNA.02_shCBX2_RNA_U937

city: Rotterdam

first: Ning Qing

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description: RNA-seq in U937 (with shCBX2)

data_processing:
ATAC-seq data were were mapped against mm10 reference genome using BWA-MEM. The mapped reads with mapping quality score <15, as well as optical PCR duplicates, were discarded using SAMtools. The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools; For generating bigWig files of RNA-seq, we mapped FASTQ file using BWA-MEM against hg19, and bigWig files were generated using bam2bw script.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

growth_protocol: U937, were cultured in RPMI 1640 (Euroclone, Italy) supplemented with 10% heat-inactivated FBS (Sigma-Aldrich, Italy), 2 mM L-glutamine (Euroclone) and antibiotics (100 U/mL penicillin, 100 μg/mL streptomycin and 250 ng/mL amphotericin-B). HeLa-S3 cells were grown in DMEM (Euroclone) supplemented with 10% FBS, 100 U/mL penicillin/streptomycin (Euroclone), and 2 mM glutamine (Euroclone).

extract_protocol:
ATAC-seq libraries were prepared following a published protocol (Liu et al. 2017). 100 k U937 cells are harvested. Nuclei were isolated, permeabilized, and tagmented using in-house produced Tn5 transposase; RNA was isolated using a standard Trizol extraction protocols and the result total RNA was treated with DNase I.
For ATAC-seq, the resulted DNA fragments underwent two sequential 9-cycle PCR amplification and the fragments < 700 bp were purified using SPRI beads (Liu et al., 2017); RNA-seq libraries were generated using a standard ribo-zero in coupling with random primering strategy.

treatment_protocol: U937 were diluted to 200000 cells/ml; To generate stable CBX2 knockdown cells, lentiviral shRNAs targeting BRD9 (TRCN0000020324) and scrambled control 339 (TRC000035) plasmids were purchased from Sigma MISSION human shRNA library (Sigma-Aldrich), and the knockdown was performed using a standard lentiviral transduction protocol.

value: Acute myeloid leukemia cell

tag: genetic modification


title: RNA.01_Scramble_RNA_U937

description: RNA-seq in U937 (with Non-targeting control)

value: Non-targeting control


title: Empty, H3K27me3 CUT&Tag, rep2

value: HUVEC


title: ATAC.03_shCBX2-rep1_ATAC_U937

description: ATAC-seq in U937 (with shCBX2)


title: C6_F_iN

status: Public on Jun 10 2022

first: Rachita

last: Yadav

address: 185 Cambridge street

department: Neurology

institute: MGH

description:
C6_F_iN
ATAC
paired-end
Illumina NovaSeq 6000
C6_F_iN

data_processing:
STAR alignemnt and htseq quantification
DESEq2 based differentrial expressed genes
mSIGBD based functional class enrichment
R package "umi4cPackage" to generate 4C peaks, followed by DESeq2 based analysis for differential 4C pattern within peak regions
Standard ENCODE ATACSeq  processing approach to call ATAC peaks
Assembly: GRCh37.75
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample
Supplementary files format and content: tab-delimited text files include differentially expressed genes values for each comparison
Supplementary files format and content: tab-delimited text files include GO annotation for MEF2C and Proximal Boundary deletions
Supplementary files format and content: tab-delimited text files include differential MEf2C exon statistics
Supplementary files format and content: tab-delimited text files include differentially 4C statistics
Supplementary files format and content: tab-delimited ATAC peaks in narrowPeak format
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

extract_protocol:
TRIzol Reagent
TruSeq® Stranded mRNA Library Kit

value: Induced Neurons

value: WT

tag: treatment

value: Cell line


title: C6_E_iN

description:
C6_E_iN
ATAC
paired-end
Illumina NovaSeq 6000
C6_E_iN


title: C6_F

description:
C6_F
ATAC
paired-end
Illumina NovaSeq 6000
C6_F

value: Neural stem cells


title: C6_D_iN

description:
C6_D_iN
ATAC
paired-end
Illumina NovaSeq 6000
C6_D_iN


title: C6_E

description:
C6_E
ATAC
paired-end
Illumina NovaSeq 6000
C6_E


title: C6_B_iN

description:
C6_B_iN
ATAC
paired-end
Illumina NovaSeq 6000
C6_B_iN


title: ATAC.01_Scramble-rep1_ATAC_U937

description: ATAC-seq in U937 (with Non-targeting control)


title: C6_C

description:
C6_C
ATAC
paired-end
Illumina NovaSeq 6000
C6_C


title: C6_B

description:
C6_B
ATAC
paired-end
Illumina NovaSeq 6000
C6_B


title: C6_A_iN

description:
C6_A_iN
ATAC
paired-end
Illumina NovaSeq 6000
C6_A_iN


title: ATAC.04_shCBX2-rep2_ATAC_U937

description: ATAC-seq in U937 (with shCBX2)


title: C6_D

description:
C6_D
ATAC
paired-end
Illumina NovaSeq 6000
C6_D


title: SOX9OE, SOX9 CUT&RUN, rep2

value: SOX9 expression plasmid


title: MEF2C_VP2_iN_proxLOOP_HET_HH_A

description:
MEF2C_VP2_iN_proxLOOP_HET_HH_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_proxLOOP_HET_HH_A


title: C6_A

description:
C6_A
ATAC
paired-end
Illumina NovaSeq 6000
C6_A


title: 4-iN_proxTAD_HET_A4_B_VP2

description:
4-iN_proxTAD_HET_A4_B_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
4-iN_proxTAD_HET_A4_B_VP2


title: MEF2C_VP2_iN_proxTAD_WT_H5_A

description:
MEF2C_VP2_iN_proxTAD_WT_H5_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_proxTAD_WT_H5_A


title: MEF2C_VP2_iN_proxLOOP_HET_BB_C_VP2

description:
MEF2C_VP2_iN_proxLOOP_HET_BB_C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_proxLOOP_HET_BB_C_VP2


title: MEF2C_VP2_iN_MEF2C_HET_R_A_VP2

description:
MEF2C_VP2_iN_MEF2C_HET_R_A_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_MEF2C_HET_R_A_VP2


title: 14-iN_proxLoop_WT_C5_VP2

description:
14-iN_proxLoop_WT_C5_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
14-iN_proxLoop_WT_C5_VP2


title: MEF2C_VP2_iN_MEF2C_HET_R_A

description:
MEF2C_VP2_iN_MEF2C_HET_R_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_MEF2C_HET_R_A


title: MEF2C_VP2_iN_MEF2C_HET_R_B_VP2

description:
MEF2C_VP2_iN_MEF2C_HET_R_B_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_MEF2C_HET_R_B_VP2


title: MEF2C_VP2_iN_proxTAD_HET_A4_B

description:
MEF2C_VP2_iN_proxTAD_HET_A4_B
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_proxTAD_HET_A4_B


title: MEF2C_VP2_iN_MEF2C_HET_K_B_VP2

description:
MEF2C_VP2_iN_MEF2C_HET_K_B_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_MEF2C_HET_K_B_VP2


title: MEF2C_VP2_iN_MEF2C_HET_K_A

description:
MEF2C_VP2_iN_MEF2C_HET_K_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_MEF2C_HET_K_A


title: 6-iN_LRG_HET_BA_MEF2C_VP2

description:
6-iN_LRG_HET_BA_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
6-iN_LRG_HET_BA_MEF2C_VP2


title: 4-iN_Insul_HET_H1B_MEF2C_VP2

description:
4-iN_Insul_HET_H1B_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
4-iN_Insul_HET_H1B_MEF2C_VP2


title: 11-iN_LRG_WT_E_MEF2C_VP2

description:
11-iN_LRG_WT_E_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
11-iN_LRG_WT_E_MEF2C_VP2


title: 15-iN_Insul_HET_H1C_MEF2C_VP2

description:
15-iN_Insul_HET_H1C_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
15-iN_Insul_HET_H1C_MEF2C_VP2


title: 2-iN_insul_HET_G11_VP2

description:
2-iN_insul_HET_G11_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
2-iN_insul_HET_G11_VP2


title: 20-iN_LRG_WT_AA_MEF2C_VP2

description:
20-iN_LRG_WT_AA_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
20-iN_LRG_WT_AA_MEF2C_VP2


title: gDNA_WB_B6_V8

description: Healthy whole blood sample, validation set

tag: age (weeks)

value: female

tag: strain

tag: sample type

value: Whole blood

tag: condition

value: healthy

tag: dataset

value: B6 validation


title: 16-iN_proxLoop_HET_HH_A_VP2

description:
16-iN_proxLoop_HET_HH_A_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
16-iN_proxLoop_HET_HH_A_VP2

tag: cell line


title: C6_C_iN

description:
C6_C_iN
ATAC
paired-end
Illumina NovaSeq 6000
C6_C_iN


title: MEF2C_VP2_iN_insul_HET_G11

description:
MEF2C_VP2_iN_insul_HET_G11
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_insul_HET_G11


title: 1-iN_Insul_HET_H1A_MEF2C_VP2

description:
1-iN_Insul_HET_H1A_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
1-iN_Insul_HET_H1A_MEF2C_VP2


title: MEF2C_VP2_iN_insul_WT_H1

description:
MEF2C_VP2_iN_insul_WT_H1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_insul_WT_H1


title: MEF2C_VP2_NSC_ProxTAD_B9_A_HET

description:
MEF2C_VP2_NSC_ProxTAD_B9_A_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_ProxTAD_B9_A_HET


title: MEF2C_VP2_iN_distLOOP_HET_C6

description:
MEF2C_VP2_iN_distLOOP_HET_C6
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_distLOOP_HET_C6


title: MEF2C_VP2_iN_distLOOP_HET_C12_VP2

description:
MEF2C_VP2_iN_distLOOP_HET_C12_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_distLOOP_HET_C12_VP2


title: 6-iN_distLoop_HET_A7_MEF2C_VP2

description:
6-iN_distLoop_HET_A7_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
6-iN_distLoop_HET_A7_MEF2C_VP2


title: MEF2C_VP2_iN_distLOOP_WT_C10

description:
MEF2C_VP2_iN_distLOOP_WT_C10
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_distLOOP_WT_C10


title: 9-NSC_ProxLoop_HET_BBA_MEF2C_VP2

description:
9-NSC_ProxLoop_HET_BBA_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
9-NSC_ProxLoop_HET_BBA_MEF2C_VP2


title: MEF2C_VP2_NSC_proxTAD_E6_HET

description:
MEF2C_VP2_NSC_proxTAD_E6_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_proxTAD_E6_HET


title: 18-NSC_ProxLoop_HET_BBA2_MEF2C_VP2

description:
18-NSC_ProxLoop_HET_BBA2_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
18-NSC_ProxLoop_HET_BBA2_MEF2C_VP2


title: 2-NSC_ProxLoop_HET_HHA_MEF2C_VP2

description:
2-NSC_ProxLoop_HET_HHA_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
2-NSC_ProxLoop_HET_HHA_MEF2C_VP2


title: MEF2C_VP2_NSC_MEF2C_HET_R_A_VP2

description:
MEF2C_VP2_NSC_MEF2C_HET_R_A_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_MEF2C_HET_R_A_VP2


title: ATAC.02_Scramble-rep2_ATAC_U937

description: ATAC-seq in U937 (with Non-targeting control)


title: MEF2C_VP2_NSC_proxTAD_H5_A_WT

description:
MEF2C_VP2_NSC_proxTAD_H5_A_WT
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_proxTAD_H5_A_WT


title: MEF2C_VP2_NSC_proxTAD_A4_A_HET

description:
MEF2C_VP2_NSC_proxTAD_A4_A_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_proxTAD_A4_A_HET


title: 3-iN_LRG_HET_JA_MEF2C_VP2

description:
3-iN_LRG_HET_JA_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
3-iN_LRG_HET_JA_MEF2C_VP2


title: 10-NSC_ProxLoop_HET_BBB_MEF2C_VP2

description:
10-NSC_ProxLoop_HET_BBB_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
10-NSC_ProxLoop_HET_BBB_MEF2C_VP2


title: MEF2C_VP2_NSC_MEF2C_HET_K_B_VP2

description:
MEF2C_VP2_NSC_MEF2C_HET_K_B_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_MEF2C_HET_K_B_VP2


title: 14-NSC_LRG_HET_C9C_MEF2C_VP2

description:
14-NSC_LRG_HET_C9C_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
14-NSC_LRG_HET_C9C_MEF2C_VP2


title: 13-NSC_LRG_HET_C9B_MEF2C_VP2

description:
13-NSC_LRG_HET_C9B_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
13-NSC_LRG_HET_C9B_MEF2C_VP2


title: MEF2C_VP2_NSC_distLOOP_HET_C12

description:
MEF2C_VP2_NSC_distLOOP_HET_C12
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_distLOOP_HET_C12


title: MEF2C_VP2_NSC_MEF2C_HET_K_A_VP2

description:
MEF2C_VP2_NSC_MEF2C_HET_K_A_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_MEF2C_HET_K_A_VP2


title: MEF2C_VP2_NSC_insul_HET_C3

description:
MEF2C_VP2_NSC_insul_HET_C3
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_insul_HET_C3


title: MEF2C_VP2_NSC_insul_WT_F11

description:
MEF2C_VP2_NSC_insul_WT_F11
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_insul_WT_F11


title: MEF2C_VP2_NSC_ProxTAD_D1_A_WT

description:
MEF2C_VP2_NSC_ProxTAD_D1_A_WT
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_ProxTAD_D1_A_WT


title: MEF2C_VP2_NSC_insul_HET_C6

description:
MEF2C_VP2_NSC_insul_HET_C6
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_insul_HET_C6


title: MEF2C_VP2_NSC_Insul_A1_HET

description:
MEF2C_VP2_NSC_Insul_A1_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_Insul_A1_HET


title: MEF2C_VP2_NSC_Insul_A3_WT

description:
MEF2C_VP2_NSC_Insul_A3_WT
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_Insul_A3_WT


title: MEF2C_VP2_NSC_distLOOP_WT_B1

description:
MEF2C_VP2_NSC_distLOOP_WT_B1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_distLOOP_WT_B1


title: MEF2C_VP2_NSC_distLOOP_WT_A3

description:
MEF2C_VP2_NSC_distLOOP_WT_A3
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_distLOOP_WT_A3


title: MEF2C_VP2_iN_MEF2C_HET_K_B

description:
MEF2C_VP2_iN_MEF2C_HET_K_B
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_MEF2C_HET_K_B


title: 22-NSC_LRG_HET_C9E_MEF2C_VP2

description:
22-NSC_LRG_HET_C9E_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
22-NSC_LRG_HET_C9E_MEF2C_VP2


title: MEF2C_VP1_iN_proxTAD_HOM_A8_C

description:
MEF2C_VP1_iN_proxTAD_HOM_A8_C
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_proxTAD_HOM_A8_C


title: 21-iN_proxTAD_WT_D1_MEF2C_VP1

description:
21-iN_proxTAD_WT_D1_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
21-iN_proxTAD_WT_D1_MEF2C_VP1


title: MEF2C_VP1_iN_proxLOOP_HOM_GG_A

description:
MEF2C_VP1_iN_proxLOOP_HOM_GG_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_proxLOOP_HOM_GG_A


title: MEF2C_VP1_iN_proxTAD_HOM_C2_A

description:
MEF2C_VP1_iN_proxTAD_HOM_C2_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_proxTAD_HOM_C2_A


title: MEF2C_VP1_iN_proxTAD_WT_H5_A

description:
MEF2C_VP1_iN_proxTAD_WT_H5_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_proxTAD_WT_H5_A


title: 13-iN_proxTAD_HOM_C2_A_VP1

description:
13-iN_proxTAD_HOM_C2_A_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
13-iN_proxTAD_HOM_C2_A_VP1


title: MEF2C_VP1_iN_proxLOOP_HOM_AA_C_VP1

description:
MEF2C_VP1_iN_proxLOOP_HOM_AA_C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_proxLOOP_HOM_AA_C_VP1


title: MEF2C_VP1_iN_proxLOOP_WT_C5

description:
MEF2C_VP1_iN_proxLOOP_WT_C5
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_proxLOOP_WT_C5


title: 6-iN_proxLoop_HOM_AA_A_VP1

description:
6-iN_proxLoop_HOM_AA_A_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
6-iN_proxLoop_HOM_AA_A_VP1


title: MEF2C_VP1_iN_MEF2C_HOM_H_C_VP1

description:
MEF2C_VP1_iN_MEF2C_HOM_H_C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_MEF2C_HOM_H_C_VP1


title: MEF2C_VP1_iN_MEF2C_HOM_X_A_VP1

description:
MEF2C_VP1_iN_MEF2C_HOM_X_A_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_MEF2C_HOM_X_A_VP1


title: MEF2C_VP1_iN_MEF2C_HOM_H_A

description:
MEF2C_VP1_iN_MEF2C_HOM_H_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_MEF2C_HOM_H_A


title: MEF2C_VP2_NSC_distLOOP_HET_B6

description:
MEF2C_VP2_NSC_distLOOP_HET_B6
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_distLOOP_HET_B6


title: MEF2C_VP1_iN_proxLOOP_HOM_AA_A

description:
MEF2C_VP1_iN_proxLOOP_HOM_AA_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_proxLOOP_HOM_AA_A


title: MEF2C_VP1_iN_MEF2C_HOM_H_C

description:
MEF2C_VP1_iN_MEF2C_HOM_H_C
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_MEF2C_HOM_H_C


title: MEF2C_VP1_iN_insul_WT_H1

description:
MEF2C_VP1_iN_insul_WT_H1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_insul_WT_H1


title: MEF2C_VP1_iN_A3_3M

description:
MEF2C_VP1_iN_A3_3M
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_A3_3M


title: 11-iN_LRG_WT_E_MEF2C_VP1

description:
11-iN_LRG_WT_E_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
11-iN_LRG_WT_E_MEF2C_VP1


title: 27-iN_LRGdistLoop_WT_AB_MEF2C_VP1

description:
27-iN_LRGdistLoop_WT_AB_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
27-iN_LRGdistLoop_WT_AB_MEF2C_VP1


title: MEF2C_VP1_iN_distLOOP_WT_C10

description:
MEF2C_VP1_iN_distLOOP_WT_C10
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_distLOOP_WT_C10


title: 20-iN_LRG_WT_AA_MEF2C_VP1

description:
20-iN_LRG_WT_AA_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
20-iN_LRG_WT_AA_MEF2C_VP1


title: MEF2C_VP1_iN_G2_500k

description:
MEF2C_VP1_iN_G2_500k
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_G2_500k


title: MEF2C_VP1_iN_A4_1M

description:
MEF2C_VP1_iN_A4_1M
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_A4_1M


title: MEF2C_VP1_NSC_ProxTAD_C2_A_HOMDEL

description:
MEF2C_VP1_NSC_ProxTAD_C2_A_HOMDEL
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_ProxTAD_C2_A_HOMDEL


title: MEF2C_VP1_NSC_ProxTAD_D1_A_WT

description:
MEF2C_VP1_NSC_ProxTAD_D1_A_WT
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_ProxTAD_D1_A_WT


title: 20-iN_distLoop_WT_A4_MEF2C_VP1

description:
20-iN_distLoop_WT_A4_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
20-iN_distLoop_WT_A4_MEF2C_VP1


title: MEF2C_VP1_NSC_ProxTAD_B9_A_HET

description:
MEF2C_VP1_NSC_ProxTAD_B9_A_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_ProxTAD_B9_A_HET