title: D161_NT

description:
Gene expression data from purified NK cells after 5 day activation with IL-2 (Donor 161).
sample: 161

hyb_protocol: Sample was hybridized to Human Affymetrix Clariom S array using an Affymetrix GeneChip Hybridization Oven 645.

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples.

source_name: Total RNA from purified NK cells after 5 day activation with IL-2

label_protocol: 100ng from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: RNA was extracted following Qiagen protocol (RNeasy Micro Kit).

tag: donor


title: D134_NT

status: Public on Sep 10 2021

type: RNA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description:
Gene expression data from purified NK cells after 5 day activation with IL-2 (Donor 134).
sample: 134

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: condition

value: NT

tag: cell type

value: NK cells


title: D105_NT

description:
Gene expression data from purified NK cells after 5 day activation with IL-2 (Donor 105).
sample: 105


title: D161_KT

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta and IL-2 (Donor 161).
sample: 161

source_name: Total RNA from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta and IL-2

value: KT


title: D134_KT

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta and IL-2 (Donor 134).
sample: 134


title: 139KD1

description: Gene expression data from purified NK cells after 12h activation in plate-coated anti-CD16 (KD1) and 200u/ml IL-2 (Donor 139)

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 2.0 ST array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from purified NK cells after 12h activation in plate-coated anti-CD16 (KD1) and IL-2 (200U/ml)

label_protocol: 100ng from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: RNA was extracted following Quiagen protocol (RNeasy Micro Kit)

tag: individual

value: donor 139

tag: treatment


title: D105_KT

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta and IL-2 (Donor 105).
sample: 105


title: D134_KTU

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta+Urelumab and IL-2 (Donor 134).
sample: 134

source_name: Total RNA from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta+Urelumab and IL-2

value: KTU


title: D161_KTU

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta+Urelumab and IL-2 (Donor 161).
sample: 161


title: 129NT

description: Gene expression data from purified NK cells after 12h treatment with IL-2 (Donor 129)

source_name: Total RNA from purified NK cells after 12h treatment with IL-2 (200U/ml)

value: donor 129


title: D161_KD1

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1) and 200u/ml IL-2 (Donor 161).
sample: 161

source_name: Total RNA from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1) and IL-2


title: 129KD1

description: Gene expression data from purified NK cells after 12h activation in plate-coated anti-CD16 (KD1) and 200u/ml IL-2 (Donor 129)


title: RNA-seq: EBNA2- (P3HR1) EBV infected Ramos B cells replicate 2

status: Public on Sep 23 2021

type: SRA

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19 and hg38) using STAR (version 2.5.2a)(Dobin et. al., 2013).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
The featureCounts function (Rsubread version: 3.5.3) was used to count reads (Liao et al. 2014) and create non-normalized gene counts.
DESeq2 (version 3.5.3) was used to calculate differential gene expression (Love et al. 2014).
Genome_build: hg19; hg38
Supplementary_files_format_and_content: Non-normalized gene counts in a tab separated text file. Columns are 1) gene name; 2) non-normalized read count.
Supplementary_files_format_and_content: Aligned reads in bigWig format
Supplementary_files_format_and_content: Differential genes identified by DESeq2 in a tab separated text file. Columns are 1) gene name; 2) log2FoldChange; 3) raw-pvalue; 4) adjusted p-value.

source_name: Ramos B cells

growth_protocol: Cells were cultured in 10% FBS supplemented RPMI medium 1640 for 2 weeks.

extract_protocol:
Total RNA was extracted using the mirVANA Isolation Kit (Ambion) from Ramos B cells.
RNA was depleted of ribosomal RNA and sequenced at Cincinnati Children’s Hospital Medical Center (CCHMC) DNA Sequencing and Genotyping Core Facility.

treatment_protocol: Cells were infected with EBV with EBNA+ strain (B95.8) and EBNA2- strain (P3HR1), respectively.

value: Ramos B cells

tag: infection

value: EBNA- (P3HR1) Epstein-Barr virus (EBV)


title: D105_KTU

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1)+TGFbeta+Urelumab and IL-2 (Donor 105).
sample: 105


title: 180103_A5B5_C5D5_S2 [VF-020]

status: Public on May 25 2021

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

data_processing:
Demultiplexing, bcl2fastq v2.18.0.12 --no-lane-splitting --barcode-mismatches 1 -l INFO -r 4 -d 4 -p 4 -w 4
Alignment to hg38, STAR v2.5.3a STAR --runMode alignReads --runThreadN 24 --genomeLoad NoSharedMemory --outSAMunmapped None --outSAMattributes Standard  --limitOutSAMoneReadBytes 1000000 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 25 --quantMode GeneCounts --outSAMprimaryFlag AllBestScore
Quality Control filter samples by: minimum technical replicate correlation = 0.98; minimum biological replicate correlation = 0.96; minimum gene count per sample = 5000; minimum mapping rate = 0.75; minimum raw gene read count = 50;
Genome_build: hg38 with gencode v29 primary assembly annotation used for STAR alignment
Supplementary_files_format_and_content: human count matrix (ASCII text) from running STAR alignment with --quantmode GeneCounts parameter for each sample

molecule: polyA RNA

source_name: VF_Collagen_no TGFb1

extract_protocol:
Samples were collected in 350 μL of TRK Lysis Buffer supplied with the E.Z.N.A. Total RNA Kit I (Omega Bio-tek, Norcross, GA) after 48 hours and stored in - 80°C. RNA was then isolated according to the manufacturer’s instructions. Using the GoScript™ Reverse Transcription System (Promega, Madison, WI) according to the manufacturer’s instructions, RNA was converted into cDNA.
Libraries  were prepared using Illumina® TruSeq® DNA Sample Preparation Kits high-throughput protocol.

treatment_protocol:
1DME = Dulbecco’s Modified Eagle Medium (DMEM) (Life Technologies) with 10% fetal bovine serum (Genesee Scientific, San Diego, CA) and 1% penicillin/streptomycin. Media was replaced every 3 days.
2ECM = scaffold derived from porcine extracellular matrices are a naturally derived material produced by decellularization of native tissues and consisting of proteins such as collagen, elastin, laminin, glycosaminoglycans, hyaluronic acid, fibrinogen and vitronectin
3COL = Collagen

value: Vocal Fold fibroblast

tag: media

value: Collagen

value: N


title: 180103_C5__S11 [VF-021]

source_name: DF_porcine extracellular matrices_TGFb1

value: Dermal Fibroblast

value: porcine extracellular matrices

value: Y


title: 171218_A5__S9 [VF-009]

source_name: DF_porcine extracellular matrices_no TGFb1


title: 171218_A3B3_C3D3_S12 [VF-006]

source_name: VF_porcine extracellular matrices_no TGFb1


title: 171218_A4B4__S4 [VF-007]

source_name: VF_porcine extracellular matrices_TGFb1


title: 171218_C2__S18 [VF-013]


title: 171218_C4D4__S8 [VF-015]


title: 180103_A1_A4_S3 [VF-019]

source_name: DF_Dulbecco’s Modified Eagle Medium_no TGFb1

value: Dulbecco’s Modified Eagle Medium


title: 171218_C1D1__S7 [VF-011]

source_name: VF_Dulbecco’s Modified Eagle Medium_no TGFb1


title: 171218_C6D6__S14 [VF-018]


title: 171218_C4__S1 [VF-016]

source_name: DF_Dulbecco’s Modified Eagle Medium_TGFb1


title: 171218_C5__S2 [VF-017]


title: 171218_C3_C6_S13 [VF-014]


title: 171218_A3_A6_S3 [VF-005]

source_name: DF_Collagen_no TGFb1


title: 171218_A5B5_C5D5_S5 [VF-008]


title: 171218_C2D2__S11 [VF-012]

source_name: VF_Dulbecco’s Modified Eagle Medium_TGFb1


title: D134_KD1

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1) and 200u/ml IL-2 (Donor 134).
sample: 134


title: 171218_A2B2__S10 [VF-003]


title: 171218_A2__S6 [VF-004]


title: D105_KD1

description:
Gene expression data from purified NK cells after 5 day activation in plate-coated anti-CD16 (KD1) and 200u/ml IL-2 (Donor 105).
sample: 105


title: 171218_A1B1__S15 [VF-002]


title: SK1 WT / S288c chrIX–chrIII–chrI, cen1∆, cen9∆ Input rep 2

status: Public on May 21 2021

city: New York

first: Andreas

last: Hochwagen

state: New York

address: 100 Washington Square East, 1009 Silver Center

department: Biology

institute: New York University

library_source: genomic

data_processing:
ChIP-seq reads trimmed for low-quality sequence and mapped to a custom hybrid S288C/SK1 genome using bowtie v1.2.0 with parameters -q -m 1 -v 0 -p 8 -S
Peaks called using macs2 v2.1.1 command “callpeak” with parameters --keep-dup="auto" -B --nomodel --extsize 200 --SPMR -g 2.4e7
Normalized signal track produced by comparing ChIP treatment against input control using macs2 v2.1.1 command “bdgcmp” with parameter -m FE
Genome_build: Custom hybrid S288C/SK1 genome built by concatenating recently published S288C and SK1 genome assemblies (Yue et al. Nat. Genet. 2017)
Supplementary_files_format_and_content: bedGraph files: Fold enrichment of ChIP signal track compared to input sample at each base position

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Cell suspension in synchronous meiosis

growth_protocol: Synchronous meiosis cultures were prepared by inoculating BYTA medium at OD600 = 0.3 and growing for 16.5 hours at 30°C. Cells were washed twice with water, resuspended in SPO medium at OD600 = 2.0 and incubated at 30°C.

extract_protocol:
25 ml of the meiotic culture was harvested and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as described in (Blitzblau and Hochwagen, 2013).
Library preparation was performed using KAPA Hyper Prep Kit, with 3µM adapters. Input was 10ng and 9 PCR cycles were used to amplify the DNA. Amplified ChIP DNA between 300 and 500 bp was quantified using qPCR as well as an agilent 2200 TapeStation System. Fragments were sequenced on an illumine NextSeq 500 instrument using a 150-bp single-end sequencing protocol.

tag: chip antibody

value: input

tag: meiotic time-point

value: 3 hours

tag: strain code

tag: fusion

value: SK1 WT / S288c chrIX-chrIII-chrI, cen1{delta}, cen9{delta}


title: SK1 WT / S288c chrIX–chrIII–chrI, cen1∆, cen3∆ Input

value: SK1 WT / S288c chrIX-chrIII-chrI, cen1{delta}, cen3{delta}


title: SK1 WT / S288c chrIX–chrIII–chrI, cen1∆, cen9∆ Input rep 1


title: SK1 WT / S288c chrIX–chrIII–chrI, cen1∆, cen3∆ ChIP

value: Anti-Red1 (Lot#16440; kind gift of N. Hollingsworth)


title: SK1 WT / S288c chrIX–chrIII–chrI, cen1∆, cen9∆ ChIP rep 2


title: 171218_A6B6__S17 [VF-010]


title: SK1 WT / S288c chrIX–chrIII–chrI, cen1∆, cen9∆ ChIP rep 1


title: SK1 WT / S288c chrIV–chrI, cen4∆ Input

value: SK1 WT / S288c chrIV-chrI, cen4{delta}


title: SK1 WT / S288c chrIV–chrI, cen4∆ ChIP


title: SK1 WT / S288c chrIV–chrI, cen1∆ ChIP rep 2

value: SK1 WT / S288c chrIV-chrI, cen1{delta}


title: SK1 WT / S288c chrIV–chrI, cen1∆ ChIP rep 1


title: 171218_A1_A4_S16 [VF-001]


title: SK1 WT / S288c WT Input rep 1

value: SK1 WT / S288c WT


title: SK1 WT / S288c WT ChIP rep 1


title: 4N_Replicate_3_H3K9me3_ChIP-seq

status: Public on May 06 2021

city: New Haven

first: Jennifer

last: VanOudenhove

state: CT

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

institute: Yale University

description:
4N_R6 [H3K9me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig

data_processing:
Align to genome using bowtie 2.3.1
Generate bam format and normalize with samtools 1.3.1
Sort bam with samtools 1.3.1
Index bam with samtools 1.3.1
Merged bams from alignment for 3 Replicates of 2N and 4N respectively to prepare for ChromImpute
Convert to tagAlign format for size estimation of combined and single replicates
Estimate fragment size using phantompeakqualtools for combined and single replicates
Call peaks with MACS2 2.1.1.20160309 for combined and single replicates
Convert combined bedGraph to binary for ChromImpute 1.0.3
Generate global distance measurements for ChromImpute
Generate features for training
Generate trained predictors
Generate imputed signal track
Convert imputed signals to ChromHMM singal format using DeepTOOLS 2.0
Binarize imputed signals for ChromHMM
Generate Chromatin State Segmentation with ChromHMM 1.12
Generate files for UCSC genome browser based on published Roadmap Epigenome Conventions
Convert segmentation beds to bigBed format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are the imputed bigWigs that are the output imputed signal tracks from ChromImpute, bigBed files are the 25 State chromatin segmentations that come from ChromHMM

growth_protocol: iPScs were maintained in feeder-free conditions and differentiated to the CM lineage by sequential targeting of the WNT pathway as described (Lian, X  et al. 2012).

extract_protocol:
Fixed cells pellets were processed for ChIP as previously described (Cotney and Noonan, 2015).
ChIP-seq libraries were prepared using the SMARTer® ThruPLEX® DNA-seq 48S Kit,  Cat No. R400427, Takara Bio USA.

treatment_protocol: Following differentiation DNA content was determined by FACS sorting.

value: iPSC Derived Cardiomyocytes

tag: dna content

tag: chip antibody vendor

value: Diagenode

tag: antibody catalog number


title: SK1 WT / S288c chrIV–chrI, cen1∆ Input rep 2


title: 4N_Replicate_2_Input_ChIP-seq

description:
4N_R2 [Input]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig

value: none (Input)


title: SK1 WT / S288c WT Input rep 2


title: 4N_Replicate_3_H3K36me3_ChIP-seq

description:
4N_R6 [H3K36me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_3_H3K4me3_ChIP-seq

description:
4N_R6 [H3K4me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_3_H3K4me2_ChIP-seq

description:
4N_R6 [H3K4me2]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig

value: Abcam


title: Jurkat HiChIP

status: Public on May 19 2021

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

data_processing:
Library strategy: HiChIP
HiChIP data were processed and analyzed using MAPS41 v1.9 as implemented within the Arima Genomics bioinformatics pipeline available at https://github.com/ijuric/MAPS
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig coverage tracks

source_name: Jurkat

growth_protocol: Cell lines were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine. CD34+ cells were isolated by positive selection from human umbicilal cord blood and expanded for 3 days in StemSpan SFEM II (StemCell Technologies 09655) supplemented with the following cytokines each at 100 ng/mL: IL6 (Peprotech 200-06), thrombopoietin (Peprotech 300-18), SCF (300-07), and FLT3-ligand (Peprotech 300-19), and 1 uM StemRegenin 1 (Cayman Chemical 10625).

extract_protocol:
for cell lines and CD34+ cells, freshly cultured cells were counted using trypan blue and a cell suspension volume corresponding to 10 million live cells was washed once with PBS (-Ca2+ -Mg2+) and then crosslinked in a volume of 5 mL PBS with 2% formaldehyde for 10 minutes at room temperature, followed by quenching with Stop Solution 1 according to the Arima protocol. For cryopreserved patient samples, one vial of cells was thawed in a 37°C water bath and the entire contents of the vial were immediately transferred to 5 mL PBS where cells were counted before proceeding with crosslinking as above. The total number of cells used per patient sample ranged from 1.6 million to 8 million cells.
All H3K27ac HiChIP experiments were performed using the Arima-HiC+ kit (Arima Genomics A101020) according precisely to the manufacturer’s protocols (Arima-HiC+ Document numbers A160168 v00 (HiChIP) and A160169 v00 (library preparation)),

treatment_protocol: no treatment

value: cell line

value: H3K27ac (Active Motif am91193 lot#22420004)

value: untreated

tag: cell line

value: T-ALL cell line Jurkat


title: 4N_Replicate_3_H3K4me1_ChIP-seq

description:
4N_R6 [H3K4me1]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: SK1 WT / S288c chrIV–chrI, cen1∆ Input rep 1


title: 4N_Replicate_3_Input_ChIP-seq

description:
4N_R6 [Input]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_3_H3K27ac_ChIP-seq

description:
4N_R6 [H3K27ac]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_2_H3K9me3_ChIP-seq

description:
4N_R2 [H3K9me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_2_H3K36me3_ChIP-seq

description:
4N_R2 [H3K36me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_1_Input_ChIP-seq

description:
4N_R1 [Input]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_2_H3K4me2_ChIP-seq

description:
4N_R2 [H3K4me2]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_2_H3K27ac_ChIP-seq

description:
4N_R2 [H3K27ac]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_2_H3K4me1_ChIP-seq

description:
4N_R2 [H3K4me1]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_2_H3K4me3_ChIP-seq

description:
4N_R2 [H3K4me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_3_H3K27me3_ChIP-seq

description:
4N_R6 [H3K27me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: SK1 WT / S288c WT ChIP rep 2


title: 4N_Replicate_1_H3K27me3_ChIP-seq

description:
4N_R1 [H3K27me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_1_H3K9me3_ChIP-seq

description:
4N_R1 [H3K9me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_1_H3K27ac_ChIP-seq

description:
4N_R1 [H3K27ac]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_1_H3K4me3_ChIP-seq

description:
4N_R1 [H3K4me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_1_H3K4me2_ChIP-seq

description:
4N_R1 [H3K4me2]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_H3K27ac_ChIP-seq

description:
2N_R6 [H3K27ac]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_Input_ChIP-seq

description:
2N_R6 [Input]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_H3K36me3_ChIP-seq

description:
2N_R6 [H3K36me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_H3K9me3_ChIP-seq

description:
2N_R6 [H3K9me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_H3K27ac_ChIP-seq

description:
2N_R5 [H3K27ac]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_H3K9me3_ChIP-seq

description:
2N_R5 [H3K9me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_H3K27me3_ChIP-seq

description:
2N_R6 [H3K27me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_Input_ChIP-seq

description:
2N_R5 [Input]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_H3K4me3_ChIP-seq

description:
2N_R6 [H3K4me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_H3K4me3_ChIP-seq

description:
2N_R5 [H3K4me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_1_H3K36me3_ChIP-seq

description:
4N_R1 [H3K36me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_H3K4me2_ChIP-seq

description:
2N_R5 [H3K4me2]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_H3K36me3_ChIP-seq

description:
2N_R5 [H3K36me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_H3K4me1_ChIP-seq

description:
2N_R6 [H3K4me1]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_2_H3K27me3_ChIP-seq

description:
4N_R2 [H3K27me3]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_H3K27me3_ChIP-seq

description:
2N_R5 [H3K27me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_1_H3K36me3_ChIP-seq

description:
2N_R4 [H3K36me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_3_H3K4me2_ChIP-seq

description:
2N_R6 [H3K4me2]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_2_H3K4me1_ChIP-seq

description:
2N_R5 [H3K4me1]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_1_H3K9me3_ChIP-seq

description:
2N_R4 [H3K9me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_1_Input_ChIP-seq

description:
2N_R4 [Input]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_1_H3K27me3_ChIP-seq

description:
2N_R4 [H3K27me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_1_H3K27ac_ChIP-seq

description:
2N_R4 [H3K27ac]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_1_H3K4me3_ChIP-seq

description:
2N_R4 [H3K4me3]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: 4N_Replicate_1_H3K4me1_ChIP-seq

description:
4N_R1 [H3K4me1]
processed data file:
4N.bigBed
4N_DNase.pval.signal.bigWig
4N_H2A.Z.pval.signal.bigWig
4N_H3K27ac.pval.signal.bigWig
4N_H3K27me3.pval.signal.bigWig
4N_H3K36me3.pval.signal.bigWig
4N_H3K4me1.pval.signal.bigWig
4N_H3K4me2.pval.signal.bigWig
4N_H3K4me3.pval.signal.bigWig
4N_H3K79me2.pval.signal.bigWig
4N_H3K9ac.pval.signal.bigWig
4N_H3K9me3.pval.signal.bigWig
4N_H4K20me1.pval.signal.bigWig


title: 2N_Replicate_1_H3K4me2_ChIP-seq

description:
2N_R4 [H3K4me2]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig


title: wt_3

status: Public on Apr 30 2021

city: Trondheim

first: Jing

last: Ye

address: Høgskoleringen 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Norwegian University of Science and Technology (NTNU)

data_processing:
Pair-end reads of 100bp were read via the BGISEQ-500 platform. Low quality reads were ltered using the BGI-internal software SOAPnuke (reads with adaptors, reads in which unknown bases are >10 and low-quality reads with threshold 15 were removed.
Genome mapping was done using the HISAT software. Transcripts were then reconstructed using StringTie and compared to reference using Cucompare. The coding potential of StringTie and compared to reference using Cucompare. The coding potential of novel transcripts was predicted using CPC. SNP and INDEL detection was done using GATK. Clean reads were mapped to Mus musculus (house mouse) genome assembly GRCm38 (mm10) from Genome Reference Consortium using Bowtie2 and gene expression levels were calculated using the RSEM software package
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: normalized counts FPKMs in .xlsx format

organism: Mus musculus

growth_protocol: animals housed in an SPF facility (55% humidity, 21°C, 12h/12h light cycle) until an age of 3-6 months; only male animals were used

extract_protocol:
Animals were killed by isoflurane overdose and neck dislocation. No perfusion was performed. The brain was taken out in <120s and immediately frozen in liquid nitrogen until further processing. Brains were cut at 8µm thickness and CA1 isolated using a commercially available laser dissection microscope (MMI instruments, Eching, Germany)
library was constructed by BGI The final library was constructed making a single strand DNA circle. Rolling circle replication created DNA  nanoballs, which yields more fluorescent signal during sequencing. Pair-end reads of 100bp were read via the BGISEQ-500 platform.

treatment_protocol: only "baseline" condition: no intervention, animals taken directly from home cage

tag: strain background

tag: Sex

value: male

tag: genotype

value: wildtype

tag: tissue

value: brain

tag: brain region


title: 2N_Replicate_1_H3K4me1_ChIP-seq

description:
2N_R4 [H3K4me1]
processed data file:
2N.bigBed
2N_DNase.pval.signal.bigWig
2N_H2A.Z.pval.signal.bigWig
2N_H3K27ac.pval.signal.bigWig
2N_H3K27me3.pval.signal.bigWig
2N_H3K36me3.pval.signal.bigWig
2N_H3K4me1.pval.signal.bigWig
2N_H3K4me2.pval.signal.bigWig
2N_H3K4me3.pval.signal.bigWig
2N_H3K79me2.pval.signal.bigWig
2N_H3K9ac.pval.signal.bigWig
2N_H3K9me3.pval.signal.bigWig
2N_H4K20me1.pval.signal.bigWig

tag: cell type


title: N2_3


title: N2_2


title: N1_3


title: N1_2_2


title: N1_2_1


title: N1_1


title: Asyn p300i Rep A input

status: Public on Mar 01 2021

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

data_processing:
Fastq files were first aligned to the Drosophila genome (version DM6) and unaligned reads were mapped to mm10.
All low quality reads were filtered out (Q<20) with the use of samtools
Duplicate reads were removed with the use of picard tools
Additional filtering of reads from chrM and blacklisted regions ws performed with the use of bedtools
Filtered reads from Drosophila were used to normalize each sample and bedgraph and/or BigWig files were generated with the use of bedtools and kentUtils
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files. All files were normalized based on Drosophila spike-in and ratio of Chip/Input was generated with the use of deepTools for each replicate.

source_name: iPSCs

growth_protocol: Mouse FUCCI2a clonal iPSCs were cultured on irradiated feeder cells in KO-DMEM media with FBS, LIF, and 2i (MEK inhibitor & GSK3 inhibitor).

extract_protocol:
5 million cells were cross-linked with 1% formaldehyde, quenched, and snap frozen until ready to proceed. 5 million formaldehyde-fixed Drosophila nuclei were added to each sample prior to sonication for normalization. After fragmentation, inputs were set aside, and remaining chromatin was immunoprecipitated using H3K27ac antibody and stringent washes. After elution, DNA was reverse-crosslinked and then purified using ZYMO kit.
25ng of immunoprecipitated (ChIP) or input (input) material were used for library prep. Libraries were preared using KAPA HyperPrep kit according to manufacturer's instructions.

treatment_protocol: see individual treatment descriptions

value: iPSCs reprogrammed from MEFs

tag: strain

value: R26Fucci2aR (mixed C57BL/6, DBA/2, and CD1 background)

tag: treatment

value: Asynchronous cells were collected after:3hrs p300i treatment (20uM A485)


title: Asyn1h DMSO Rep A input

value: Asynchronous cells were collected after:3hrs DMSO treatment (1:2500) and then 1hr recovery in fresh media


title: N2_1


title: EG1 p300i Rep B input

value: Early G1 cells were collected after:6hr treatment with Nocodazole (200ng/ml) & 3hr simultaneous treatment with p300i (20uM A485), then mitotic shake off. Mitotic cells were released into fresh media for 1hr to enter early G1.


title: Asyn DMSO Rep A input

value: Asynchronous cells were collected after:3hrs DMSO treatment (1:2500)


title: Asyn1h p300i Rep B input

value: Asynchronous cells were collected after:3hrs p300i treatment (20uM A485) and then 1hr recovery in fresh media


title: Asyn DMSO Rep B input


title: Asyn p300i Rep B input


title: EG1 DMSO Rep A input

value: Early G1 cells were collected after:6hr treatment with Nocodazole (200ng/ml) & 3hr simultaneous treatment with DMSO (1:2500), then mitotic shake off. Mitotic cells were released into fresh media for 1hr to enter early G1.


title: N1_2


title: Mit p300i Rep B input

value: Mitotic cells were collected after:6hr treatment with Nocodazole (200ng/ml) then mitotic shake-off. Cells were also treated with p300i (20uM A485) for 3hrs prior to mitotic shake-off.


title: wt_2


title: EG1 p300i Rep A input


title: Asyn1h p300i Rep A input


title: Mit p300i Rep A input


title: Mit DMSO Rep B input

value: Mitotic cells were collected after:6hr treatment with Nocodazole (200ng/ml) then mitotic shake-off. Cells were also treated with DMSO (1:2500) for 3hrs prior to mitotic shake-off.


title: Asyn1h DMSO Rep B input


title: Asyn1h p300i Rep B ChIP

value: H3K27ac (Abcam, ab4729)


title: EG1 DMSO Rep B input


title: Mit DMSO Rep A input


title: Asyn1h p300i Rep A ChIP


title: Asyn1h DMSO Rep B ChIP


title: N1_2_3


title: Asyn p300i Rep B ChIP

description: ASYNpb


title: Asyn p300i Rep A ChIP

description: ASYNpa


title: Asyn DMSO Rep B ChIP

description: ASYNdb


title: Asyn DMSO Rep A ChIP

description: ASYNda


title: EG1 p300i Rep B ChIP


title: Mit DMSO Rep A ChIP

description: MITda


title: wt_1


title: EG1 p300i Rep A ChIP


title: Mit p300i Rep A ChIP

description: MITpa


title: Asyn p300i Rep A

description: ad.hic

data_processing:
Alignment was performed with Bowtie2 (--very-sensitive) option
Matrices with 20kb resolution were build with HiCExplorer (v2.2.1.1) and HiCBuildMatrix
Correction with ICE was completed after filtering of the aligned reads with samtools with the use of hicCorrectMatrix and all time points were normlized with each other with hicNormalize.
Matrices in 20kb resolution were used to identify topologically associated domains (TADs) with hicFindTADs and the use of the following parameters, “--minDepth 120000 --maxDepth 420000 --step 40000 --delta 0.01--thresholfComparisons 0.01 --correctForMultipleTesting FDR”. Boundaries calculated in each replicate were merged and only boundaries with an insulation score <-0.3 were considered as TAD borders
Compartment identification was performed with the use of Cscore algorithm for each replicate and chromosome separately with the use of the following parameter minDis = 1000000. All compartments were assign to active (A) and inactive (B) compartments based on gene density in each 100kb region
Genome_build: mm10
Supplementary_files_format_and_content: Replicates were merged and .h5 files were generated with 20kb resolution. .h5 files were converted to .hic files with juicer-tools (1.19.02 version)

extract_protocol:
2 million cells were cross-linked with 1% formaldehyde, quenched, and snap frozen until ready to proceed. Arima Hi-C kit was then used to digest, fill/mark ends with biotin, and ligate DNA.
Arima Hi-C kit along with KAPA Hyper Prep reagents were used for library construction. Ligated DNA was fragmented using Pico bioruptor and size selected, then biotin enrichment was performed. After End repair and dA-tailing, adapter ligation was performed using SeqCap Adapter Kit A & B indexes.


title: Mitotic_1h_ATAC_ReplicateB

description: FUCCI2 iPSCs were treated with Nocodazole (200ng/ml) for 6 hours followed by mitotic shake-off, and then release into fresh medium for 1 hour

data_processing:
Cutadapt was used to trim adaptors
Alignment was performed with Bowtie2 (--very-sensitive -X 2000) option
Filtering deduplication and tn5 insertion position correction at each read end by shifting +4 / -5 bp from the positive and negative strand  was performed with the use of picard tools, samtools and bedtools
Samples were normalized based on # of aligned reads
Peak calling was performed with MACS2 (v2.1.1)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: atac.bed file containing the coordinates of all the peaks that were called after merging all time points

source_name: Induced Pluripotent Stem cells

growth_protocol: Mouse FUCCI2 clonal iPSCs were cultured on irradiated feeder cells in KO-DMEM media with FBS, LIF, and 2i (MEK inhibitor & GSK3 inhibitor).

extract_protocol:
50,000 cells were lysed and then centrifuged to obtain nuclei.
Libraries were prepared by Nextera DNA library preparation kit: transposition reaction with Tn5, DNA isolation, and then library amplification

treatment_protocol: FUCCI2 iPSCs were treated with Nocodazole (200ng/ml) for 6 hours followed by mitotic shake-off, and then release into fresh medium for 1, and 3 hours while Asynchronous cells remained untreated

value: Induced Pluripotent Stem cells

tag: agent

value: Nocodazole


title: Mitotic_0h_ATAC_ReplicateB

description: FUCCI2 iPSCs were treated with Nocodazole (200ng/ml) for 6 hours followed by mitotic shake-


title: Asyn1h DMSO Rep B


title: EG1 DMSO Rep B ChIP

tag: chip antibody


title: Asyn p300i Rep B

description: ap.hic


title: Asyn1h DMSO Rep A ChIP


title: EG1 DMSO Rep A ChIP


title: Asyn DMSO Rep A

description: ad.hic


title: Mitotic_3h_ATAC_ReplicateB

description: FUCCI2 iPSCs were treated with Nocodazole (200ng/ml) for 6 hours followed by mitotic shake-off, and then release into fresh medium for 3 hours


title: Asynchronous_ATAC_ReplicateA

description: FUCCI2 iPSCs were untreated


title: Asynchronous_ATAC_ReplicateB

description: FUCCI2 iPSCs were untreated


title: EG1 DMSO Rep A


title: Mitotic_1h_ATAC_ReplicateA


title: Mit p300i Rep B


title: Asyn1h p300i Rep A


title: Mitotic_0h_ATAC_ReplicateA


title: Asyn1h p300i Rep B


title: Mit DMSO Rep A


title: EG1 p300i Rep B


title: Mit DMSO Rep B ChIP

description: MITdb


title: Mit p300i Rep A


title: Asyn1h DMSO Rep A


title: Mit DMSO Rep B


title: Asyn1h p300i Rep C

data_processing:
Library strategy: PRO-seq
Cutadapt was used to trim adaptors and shorten reads to 24 bp
Alignment was performed with Bowtie2 (--very-sensitive) option
Filtering and isolation of uniquely mapped reads was performed with picard tools and samtools
All samples were normalized to reads mapped to Drosophia genomic DNA and number of nuclei
Analysis was focused in protein coding genes after discarding the first and last 500bp [TSS + 500bp, TES -500bp] in order to avoid getting signal from the promoter and transcription end site
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Average signal of PROseq data is presented in BigWig files of the normalized read counts by timepoint and treatment. *_m.bw = minus strand; *_p.bw = plus strand

extract_protocol:
2 million cells were lysed, washed, and fractionated by centrifugation to obtain nuclei. Nuclei were stored in glycerol freezing buffer until library preparation.
PRO-seq libraries were prepared using biotin-NTP-supplemented run-ons from 0.2-0.5 x 10^6 permeabilized cells with Drosophila nuclei spike-in. NRO-RNA was purified using Norgen RNA isolation columns (Norgen Biotek cat. # 17200), followed by base hydrolysis on ice for 10min.  After the first binding and 3’-ligation, the NRO-RNA was bound to beads and all subsequent reactions (decapping, end repair, 5’-ligation, reverse transcription) were performed as in (Mahat et al., 2016), except that the reactions were done on the beads in 20μl. All biochemical steps after the 3’-ligation were performed with rotation except for reverse transcription. After reverse transcription, cDNA was eluted twice with 25μl ddH2O by heating for 1min at 80˚C, returning tubes to magnet, and collecting supernatant.


title: Asyn1h p300i Rep A


title: Asyn1h p300i Rep B


title: Asyn p300i Rep C

description: ASYNpc


title: Asyn p300i Rep B

description: ASYNpb


title: EG1 p300i Rep C


title: Asyn DMSO Rep C

description: ASYNdc


title: Mit p300i Rep B ChIP

description: MITpb


title: Asyn DMSO Rep B

description: ap.hic


title: EG1 DMSO Rep C


title: EG1 DMSO Rep B


title: Asyn DMSO Rep B

description: ASYNdb


title: EG1 p300i Rep B


title: Asyn DMSO Rep A

description: ASYNda


title: EG1 DMSO Rep B


title: EG1 p300i Rep A


title: Mitotic_3h_ATAC_ReplicateA


title: Mit p300i Rep B

description: MITpb


title: EG1 DMSO Rep A


title: Mit p300i Rep A

description: MITpa


title: Mit DMSO Rep A

description: MITda


title: Mit DMSO Rep B

description: MITdb


title: Asyn p300i Rep A

description: ASYNpa


title: 4Cseq_of_TGFB2_ESC_rep2

description:
4Cseq of TGFB2 ESC replicate 2
av_Asynchronous.bedGraph

data_processing:
All sequenced reads were demultiplexed with the use of fastx-toolkit while VP primer was trimmed with the use of fastq_trimmer
Bowtie 2 with very-sensitive option was used for aligning the trimmed reads (size > 40bp) to the mouse genome (mm10)
Samtools was used to filter for high quality uniquely mapped reads
Smoothening of the 4C signal was performed by calculating the number of raw reads within the 10kb binned genome with a sliding window of 500bp followed by sequencing depth normalization of the cis interaction identified around the viewpoint (+/- 1MB)
R and DESeq were used to depict the differential enrichment between the sliding windows and bins with an enrichment of > 3 CPM, pvalue <0.05 and fold > 2 between any two time points were scored as differential interacting regions. Bedtools were used to filter and merge significant interacting bins per time point
Genome_build: mm10
Supplementary_files_format_and_content: bedGrah of the average signal from both replicates in each time point for all genes

source_name: ESC

growth_protocol: Two independent, male iPSC clones (described above) were used as biological replicates for all analyses in this study. iPSCs were cultured at 37°C on irradiated feeder cells in FBS/LIF+2i conditions. Specifically, KO-DMEM media (Invitrogen) supplemented with 15% heat-inactivated fetal bovine serum, GlutaMAX, penicillin-streptomycin, non-essential amino acids, beta-mercaptoethanol, and 1000 U/ml LIF, plus 2i (1uM MEK inhibitor (Stemgent 04-0006) and 3uM GSK3 inhibitor (Stemgent 04-0004-10)) was used.

extract_protocol:
2 million cells were crosslinked in 1% formaldehyde at RT for 10 min and quenched with 125 mM glycine for 5 min. The cell pellets were washed twice in PBS and resuspended in 300μl lysis buffer (10mM Tris-HCl (pH 8.0), 10mM NaCl, 0.2% Igepal CA630 (Sigma I8896)), then incubated on ice for 20 min. Following centrifugation at 2500xg for 5 min at 4°C, the pellet was resuspended in 50uL of 0.5% SDS and incubated for 10 min at 65°C. SDS was quenched with 145uL water and 25uL of 10% TritonX-100 for 15 mins at 37°C. 25ul of CutSmart buffer (NEB B7204S) was added with 10ul DpnII enzyme (NEB R0543M) and the samples were incubated overnight at 37°C with 700rpm rotation. After confirming the digestion efficiency, the enzyme was inactivated by incubating at 65ºC for 20 mins. The samples were then diluted with 669μl Milli-Q water, 120μl T4 ligation buffer (NEB B0202), 60μl 10mM ATP (NEB P0756S), 120μl 10% Triton X-100, 6μl 20mg/ml BSA and 5μl 400U/μl T4 DNA Ligase (NEB M0202) for 3h on a rotor at RT. The samples were then treated with proteinase K and reverse crosslinked overnight.
Following RNAse treatment, phenol/chloroform extraction and DNA precipitation, the pellets were dissolved in 100μl of 10mM Tris pH 8. The second digestion was performed by adding 20μl 10x buffer B (Fermentas), 10μl Csp6I (Fermentas, ER0211), 80μl milli-Q water, and incubating overnight at 37°C with 700rpm rotation. After confirming the second digestion efficiency, the enzyme was again inactivated. Another ligation was performed by adding 300μl T4 ligation buffer, 150μl 10mM ATP, 5μl T4 DNA Ligase, and Milli-Q water to 3mL and incubating overnight at 16°C. The DNA was purified by phenol/chloroform extraction and ethanol precipitation, resulting in the 4C-template.
4C-seq

treatment_protocol: To arrest cells in mitosis, 80-90% confluent mouse iPSCs were passaged 1:3 on gelatinized plates the day before synchronization. Nocodazole (200ng/ml) (Sigma, M1404) was added to the medium for 6hr prior to collection by mitotic shake-off. 1/3 of cells were processed immediately (for mitotic time point), while the remaining cells were washed 2x with PBS and released into pre-warmed (37°C) media and plated on gelatin. Cells were then collected at 1hr and 3hrs after release. Aliquots from each time point were used for estimation of synchronization and release efficiency by FACS (BD FACS Canto II analyzer and BD FACS Diva v8.0.3 software) after ethanol fixation and staining with 300nM DAPI (Biolegend, 422801).

tag: type

value: ESC

tag: gene


title: 4Cseq_of_SOX2_ESC_rep2

description:
4Cseq of SOX2 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_SMC3_ESC_rep2

description:
4Cseq of SMC3 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_NEUROD1_ESC_rep2

description:
4Cseq of NEUROD1 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_MYCN_ESC_rep2

description:
4Cseq of MYCN ESC replicate 2
av_Asynchronous.bedGraph

value: MYCN


title: 4Cseq_of_EIF1A_ESC_rep2

description:
4Cseq of EIF1A ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_TGFB2_ESC_rep1

description:
4Cseq of TGFB2 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_CAMK2N1_ESC_rep2

description:
4Cseq of CAMK2N1 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_F3_ESC_rep2

description:
4Cseq of F3 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_BHLHE40_ESC_rep2

description:
4Cseq of BHLHE40 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_SOX2_ESC_rep1

description:
4Cseq of SOX2 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_PFKFB3_ESC_rep1

description:
4Cseq of PFKFB3 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_F3_ESC_rep1

description:
4Cseq of F3 ESC replicate 1
av_Asynchronous.bedGraph


title: EG1 p300i Rep A


title: 4Cseq_of_NEUROD1_ESC_rep1

description:
4Cseq of NEUROD1 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_EIF1A_ESC_rep1

description:
4Cseq of EIF1A ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_GATA6_ESC_rep1

description:
4Cseq of GATA6 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_MYCN_ESC_rep1

description:
4Cseq of MYCN ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_BHLHE40_ESC_rep1

description:
4Cseq of BHLHE40 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_PFKFB3_Mit_0.5Hours_rep2

description:
4Cseq of PFKFB3 Mit 0.5Hours replicate 2
av_mit30min.bedGraph

value: ESC exiting mitosis ( 30 minutes)

tag: timepoint (h)


title: 4Cseq_of_SOX2_Mit_0.5Hours_rep2

description:
4Cseq of SOX2 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_PFKFB3_ESC_rep2

description:
4Cseq of PFKFB3 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_GATA6_ESC_rep2

description:
4Cseq of GATA6 ESC replicate 2
av_Asynchronous.bedGraph


title: 4Cseq_of_BHLHE40_Mit_0.5Hours_rep2

description:
4Cseq of BHLHE40 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_NEUROD1_Mit_0.5Hours_rep2

description:
4Cseq of NEUROD1 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_SMC3_Mit_0.5Hours_rep2

description:
4Cseq of SMC3 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_TGFB2_Mit_0.5Hours_rep2

description:
4Cseq of TGFB2 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_MYCN_Mit_0.5Hours_rep2

description:
4Cseq of MYCN Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_CAMK2N1_ESC_rep1

description:
4Cseq of CAMK2N1 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_SOX2_Mit_0.5Hours_rep1

description:
4Cseq of SOX2 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_MYCN_Mit_0.5Hours_rep1

description:
4Cseq of MYCN Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_EIF1A_Mit_0.5Hours_rep2

description:
4Cseq of EIF1A Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_NEUROD1_Mit_0.5Hours_rep1

description:
4Cseq of NEUROD1 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_F3_Mit_0.5Hours_rep1

description:
4Cseq of F3 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_GATA6_Mit_0.5Hours_rep1

description:
4Cseq of GATA6 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_F3_Mit_0.5Hours_rep2

description:
4Cseq of F3 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_0.5Hours_rep1

description:
4Cseq of CAMK2N1 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_PFKFB3_Mit_0.5Hours_rep1

description:
4Cseq of PFKFB3 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_0.5Hours_rep2

description:
4Cseq of CAMK2N1 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_SMC3_Mit_0.5Hours_rep1

description:
4Cseq of SMC3 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_BHLHE40_Mit_0.5Hours_rep1

description:
4Cseq of BHLHE40 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_SMC3_Mit_3Hours_rep2

description:
4Cseq of SMC3 Mit 3Hours replicate 2
av_mit3h.bedGraph

value: ESC exiting mitosis ( 3 hours)


title: 4Cseq_of_SOX2_Mit_3Hours_rep2

description:
4Cseq of SOX2 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_PFKFB3_Mit_3Hours_rep2

description:
4Cseq of PFKFB3 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_NEUROD1_Mit_3Hours_rep2

description:
4Cseq of NEUROD1 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_MYCN_Mit_3Hours_rep2

description:
4Cseq of MYCN Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_EIF1A_Mit_0.5Hours_rep1

description:
4Cseq of EIF1A Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: 4Cseq_of_GATA6_Mit_3Hours_rep2

description:
4Cseq of GATA6 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_F3_Mit_3Hours_rep2

description:
4Cseq of F3 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_BHLHE40_Mit_3Hours_rep2

description:
4Cseq of BHLHE40 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_TGFB2_Mit_3Hours_rep1

description:
4Cseq of TGFB2 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_SMC3_ESC_rep1

description:
4Cseq of SMC3 ESC replicate 1
av_Asynchronous.bedGraph


title: 4Cseq_of_GATA6_Mit_0.5Hours_rep2

description:
4Cseq of GATA6 Mit 0.5Hours replicate 2
av_mit30min.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_3Hours_rep2

description:
4Cseq of CAMK2N1 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_SMC3_Mit_3Hours_rep1

description:
4Cseq of SMC3 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_SOX2_Mit_3Hours_rep1

description:
4Cseq of SOX2 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_MYCN_Mit_3Hours_rep1

description:
4Cseq of MYCN Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_GATA6_Mit_3Hours_rep1

description:
4Cseq of GATA6 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_PFKFB3_Mit_3Hours_rep1

description:
4Cseq of PFKFB3 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_TGFB2_Mit_3Hours_rep2

description:
4Cseq of TGFB2 Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_F3_Mit_3Hours_rep1

description:
4Cseq of F3 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_SMC3_Mit_1Hour_rep2

description:
4Cseq of SMC3 Mit 1Hour replicate 2
av_mit1h.bedGraph

value: ESC exiting mitosis ( 1 hours)


title: 4Cseq_of_SOX2_Mit_1Hour_rep2

description:
4Cseq of SOX2 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_MYCN_Mit_1Hour_rep2

description:
4Cseq of MYCN Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_NEUROD1_Mit_3Hours_rep1

description:
4Cseq of NEUROD1 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_BHLHE40_Mit_3Hours_rep1

description:
4Cseq of BHLHE40 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_3Hours_rep1

description:
4Cseq of CAMK2N1 Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_F3_Mit_1Hour_rep2

description:
4Cseq of F3 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_EIF1A_Mit_3Hours_rep2

description:
4Cseq of EIF1A Mit 3Hours replicate 2
av_mit3h.bedGraph


title: 4Cseq_of_EIF1A_Mit_3Hours_rep1

description:
4Cseq of EIF1A Mit 3Hours replicate 1
av_mit3h.bedGraph


title: 4Cseq_of_TGFB2_Mit_1Hour_rep2

description:
4Cseq of TGFB2 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_NEUROD1_Mit_1Hour_rep2

description:
4Cseq of NEUROD1 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_1Hour_rep2

description:
4Cseq of CAMK2N1 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_GATA6_Mit_1Hour_rep2

description:
4Cseq of GATA6 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_PFKFB3_Mit_1Hour_rep2

description:
4Cseq of PFKFB3 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_BHLHE40_Mit_1Hour_rep2

description:
4Cseq of BHLHE40 Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_SOX2_Mit_1Hour_rep1

description:
4Cseq of SOX2 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_TGFB2_Mit_1Hour_rep1

description:
4Cseq of TGFB2 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_PFKFB3_Mit_1Hour_rep1

description:
4Cseq of PFKFB3 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_NEUROD1_Mit_1Hour_rep1

description:
4Cseq of NEUROD1 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_MYCN_Mit_1Hour_rep1

description:
4Cseq of MYCN Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_EIF1A_Mit_1Hour_rep2

description:
4Cseq of EIF1A Mit 1Hour replicate 2
av_mit1h.bedGraph


title: 4Cseq_of_EIF1A_Mit_1Hour_rep1

description:
4Cseq of EIF1A Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_F3_Mit_1Hour_rep1

description:
4Cseq of F3 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_GATA6_Mit_1Hour_rep1

description:
4Cseq of GATA6 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_BHLHE40_Mit_1Hour_rep1

description:
4Cseq of BHLHE40 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_1Hour_rep1

description:
4Cseq of CAMK2N1 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_TGFB2_Mit_0Hours_rep2

description:
4Cseq of TGFB2 Mit 0Hours replicate 2
av_mit0h.bedGraph

value: ESC exiting mitosis ( 0 hours)


title: 4Cseq_of_SMC3_Mit_0Hours_rep2

description:
4Cseq of SMC3 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_SOX2_Mit_0Hours_rep2

description:
4Cseq of SOX2 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_GATA6_Mit_0Hours_rep2

description:
4Cseq of GATA6 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_PFKFB3_Mit_0Hours_rep2

description:
4Cseq of PFKFB3 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_NEUROD1_Mit_0Hours_rep2

description:
4Cseq of NEUROD1 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_F3_Mit_0Hours_rep2

description:
4Cseq of F3 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_EIF1A_Mit_0Hours_rep2

description:
4Cseq of EIF1A Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_0Hours_rep2

description:
4Cseq of CAMK2N1 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_SOX2_Mit_0Hours_rep1

description:
4Cseq of SOX2 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_MYCN_Mit_0Hours_rep2

description:
4Cseq of MYCN Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_SMC3_Mit_0Hours_rep1

description:
4Cseq of SMC3 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_TGFB2_Mit_0Hours_rep1

description:
4Cseq of TGFB2 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_SMC3_Mit_1Hour_rep1

description:
4Cseq of SMC3 Mit 1Hour replicate 1
av_mit1h.bedGraph


title: 4Cseq_of_NEUROD1_Mit_0Hours_rep1

description:
4Cseq of NEUROD1 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_BHLHE40_Mit_0Hours_rep2

description:
4Cseq of BHLHE40 Mit 0Hours replicate 2
av_mit0h.bedGraph


title: 4Cseq_of_MYCN_Mit_0Hours_rep1

description:
4Cseq of MYCN Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_F3_Mit_0Hours_rep1

description:
4Cseq of F3 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_GATA6_Mit_0Hours_rep1

description:
4Cseq of GATA6 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_CAMK2N1_Mit_0Hours_rep1

description:
4Cseq of CAMK2N1 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_EIF1A_Mit_0Hours_rep1

description:
4Cseq of EIF1A Mit 0Hours replicate 1
av_mit0h.bedGraph


title: RNA-seq of MIT ESC replicate 2

description: Mitotic RNA-seq replicate 2

data_processing:
Tophat2 with v2very-sensitive option was used for alligning the paired end reads in mm10
Samtools was used to sort and filter unmapped reads
Htseq-count was used to assing reads to genes
Genome_build: mm10
Supplementary_files_format_and_content: RPKM of protein coding and lncRNA genes

extract_protocol:
Total RNA from 300,000 asynchronous cells per replicate was prepared with TRIZOL (Life technologies #15596018) following manufacturer’s instructions.
Libraries were generated by the Weill Cornell Genomics core facility using the Illumina TruSeq stranded mRNA library preparation kit (#20020594) and sequenced on an Illumina HiSeq4000 platform on SE50 mode.

tag: cell phase

value: Mitotic


title: 4Cseq_of_PFKFB3_Mit_0Hours_rep1

description:
4Cseq of PFKFB3 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: 4Cseq_of_BHLHE40_Mit_0Hours_rep1

description:
4Cseq of BHLHE40 Mit 0Hours replicate 1
av_mit0h.bedGraph


title: RNA-seq of EG1 ESC replicate 1

description: EG1 RNA-seq replicate 1


title: RNA-seq of LG1 ESC replicate 1

description: LG1 RNA-seq replicate 1


title: RNA-seq of Asynchronous ESC replicate 2

description: ESC RNA-seq replicate 2

value: Asynchronous


title: RNA-seq of Asynchronous ESC replicate 1

description: ESC RNA-seq replicate 1


title: RNA-seq of EG1 ESC replicate 2

description: EG2 RNA-seq replicate 2


title: Mitotic_3h_ProSeq_ReplicateA

description: FUCCI2 iPSCs were treated with Nocodazole (200ng/ml) for 6 hours followed by mitotic shake-off, and then release into fresh medium for 3 hours

data_processing:
Library strategy: PRO-seq
Cutadapt was used to trim adaptors and shorten reads to 24 bp
Alignment was performed with Bowtie2 (--very-sensitive) option
Filtering and isolation of uniquely mapped reads was performed with picard tools and samtools
All samples were normalized to reads mapped to Drosophia genomic DNA and number of nuclei
Analysis was focused in protein coding genes after discarding the first and last 500bp [TSS + 500bp, TES -500bp] in order to avoid getting signal from the promoter and transcription end site
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv file of average normalized pro-seq signal of protein coding genes after removal of the first and last 500bp

extract_protocol: 2 million cells were lysed, washed, and fractionated by centrifugation to obtain nuclei. Nuclei were stored in glycerol freezing buffer until library preparation.


title: RNA-seq of MIT ESC replicate 1

description: Mitotic RNA-seq replicate 1


title: Mitotic_1h_ProSeq_ReplicateA

description: FUCCI2 iPSCs were treated with Nocodazole (200ng/ml) for 6 hours followed by mitotic shake-off, and then release into fresh medium for 1 hour


title: Mitotic_3h_ProSeq_ReplicateB


title: FUCCI2 iPSCs, Mitotic_1h_HiC_ReplicateB

description:
HiC_Mit1h_B
HiC in cells 1h after mitotic exit

data_processing:
Alignment was performed with Bowtie2 (--very-sensitive) option
Matrices with 20kb resolution were build with HiCExplorer (v2.2.1.1) and HiCBuildMatrix
Correction with ICE was completed after filtering of the aligned reads with samtools with the use of hicCorrectMatrix and all time points were normlized with each other with hicNormalize.
Matrices in 20kb resolution were used to identify topologically associated domains (TADs) with hicFindTADs and the use of the following parameters, “--minDepth 120000 --maxDepth 420000 --step   40000 --delta   0.01--thresholfComparisons   0.01 --correctForMultipleTesting  FDR”. Boundaries  calculated  in  each  replicate  were  merged  and  only  boundaries  with  an  insulation score <-0.3 were considered as TAD borders
Cis-chromatin interactions were calculated for each replicate with the use of FitHiC (v2.0.6) with the use of the following parameters “-r  20000 -L  40000 -U 10000000”. Only loops that were common in both replicates with a q-value < 0.01 and more than 5 contacts were   scored as valid loops
Compartment identification was   performed   with   the   use   of   Cscore   algorithm    for   each   replicate   and chromosome  separately  with  the  use  of  the  following  parameter  minDis  =  1000000.  All compartments were assign to active (A) and inactive (B) compartments based on gene density in  each  100kb  region  and  compartments  were  classified  into  4  categories  based  on  their eigenvalue.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Normalized and corrected h5 matrices of HiC reads (interactions) per replicate generated from HiCExplorer

extract_protocol:
2M cells were cross-linked with 1% formaldehyde, lysed to obtain nuclei, and then digested with MboI. Digested chromatin was biotin-labeled, ligated, reverse-crosslinked, and ethanol-precipitated to purify DNA.
DNA was sonicated and SPRI selected for 300-500bp. Streptavidin beads were used for biotin pulldown. Ligation with SeqCap Adapter Kit A indexes was done and then library amplification was performed directly off of streptavidin beads using KAPA HiFi HotStart ReadyMix.

value: Nocodazole, mitotic shake-off, release into fresh medium

tag: time

value: 1h after mitotic exit


title: FUCCI2 iPSCs, Mitotic_1h_HiC_ReplicateA

description:
HiC_Mit1h_A
HiC in cells 1h after mitotic exit


title: FUCCI2 iPSCs, Mitotic_3h_HiC_ReplicateB

description:
HiC_Mit3h_B
HiC in cells 3h after mitotic exit

value: 3h after mitotic exit


title: FUCCI2 iPSCs, Mitotic_0h_HiC_ReplicateB

description:
HiC_Mit0h_B
HiC in mitotic cells


title: FUCCI2 iPSCs, Mitotic_0h_HiC_ReplicateA

description:
HiC_Mit0h_A
HiC in mitotic cells


title: FUCCI2 iPSCs, Mitotic_3h_HiC_ReplicateA

description:
HiC_Mit3h_A
HiC in cells 3h after mitotic exit


title: Mitotic_0h_ProSeq_ReplicateB

description: FUCCI2 iPSCs were treated with Nocodazole (200ng/ml) for 6 hours followed by mitotic shake-


title: FUCCI2 iPSCs, Asynchronous_HiC_ReplicateB

description:
HiC_Asyn_B
HiC in Asynchronous cells

value: untreated


title: Mitotic_1h_ProSeq_ReplicateB


title: pooled sample used for control

status: Public on Feb 26 2021

description: ChIP libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s recommendations. 1ng of ChIP-DNA was used to prepare each library. ChIP input libraries were prepared by pooling equal amounts of purified sonicated and non-IPed DNA from each sample. 1ng of the pooled ChIP-input DNA was used for library preparation. Libraries were quantified and sizing was determined using the High Sensitivity DNA Assay reagents and chip in the Agilent 2100 Bioanalyzer System and the Qubit 1X dsDNA HS Assay Kit respectively. Individual libraries were then pooled and sequenced 75bp paired end on the NextSeq 550 using the NextSeq 500/550 High Output Kit v2.5.

data_processing:
ChIP-seq datasets were processed and analyzed using an in-house automated pipeline (https://github.com/MarioPujato/NextGenAligner); the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19/GRCh37) using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS)(Zhang et al., 2008) with the control/input aligned reads as background (callpeak -g hs -q 0.01 –broad -c input/control).
ENCODE blacklist regions (Amemiya et al., 2019) were removed using the hg19-blacklist.v2.bed.gz file available at https://github.com/Boyle-Lab/Blacklist/tree/master/lists.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called by MACS2 in broadPeak format
Supplementary_files_format_and_content: Aligned reads in bigWig format

growth_protocol: Generation of A549-ACE2 cells was performed as previously described (Blanco-Melo et al., 2020; Daniloski et al., 2020). Briefly, A549 cells were transduced with lentiviral vector pHR-PGK expressing human ACE2 coding sequence. A549 cells were then transduced with the lentivirus in the presence of polybrene (8 μg/ml). Cells were used for downstream assays after 48h post transduction.

extract_protocol: 24 hours post infection, media was removed from the well, and replaced with Fixation buffer (PBS, 2% FBS, 1% Methanol-Free Formaldehye). Cells were fixed at room temperature for 10 min. 2M Glycine was then added to a final concentration of 0.125M, and cells were incubated at room temperature for 5min to quench the reaction. Supernatants were removed from wells, and each well was washed 3 times with cold PBS. Cells were then lysed in the well using 250ul of SDS Lysis Buffer [100mM NaCl, 50mM Tris pH8.0, 5mM EDTA, 0.02% NaN3, 0.5% SDS + 1X Halt Protease and Phosphatase Inhibitor (Thermo Scientific)] and cell lysates were collected in a 1.5ml tube and snap frozen at -80oC. On the day of sonication, lysates were thawed, and diluted with 125ul of Triton Dilution Buffer [100mM Tris pH8.5, 100mM NaCl, 5mM EDTA, 0.02% NaN3, 5% TritonX-100 + 1X Halt Protease and Phosphatase Inhibitor]. Lysates were then sonicated for 5 - 30 sec ON/ 30 sec OFF cycles twice using the Bioruptor Pico. Each sonicated lysate was then pre-cleared using 10ul of Rabbit-IgG Dynabeads for 1 hour, rotating at 4oC. 1ug of anti-H3K27ac antibody was then added to 300ul of pre-cleared lysate. Immunoprecipitation (IP) was performed with overnight rotation at 4oC. To recover IP-complexes, 10ul of Dynabeads M-280 Sheep anti-Rabbit IgG were added to each reaction and tubes were rotated for 2 hours at 4oC. Bead-chromatin complexes were then washed 6 times on a magnet using ice cold RIPA wash buffer [50mM Hepes-KOH pH7.6, 100mM LiCl, 1mM EDTA, 1% NP-40, 0.5% Na-Deoxycholate]. Washed beads were then incubated in 125ul Elution buffer [1% SDS, 0.1M NaHCO3] at 65oC overnight for elution and de-crosslinking. ChIP DNA was then purified using the MinElute PCR purification kit (Qiagen) and quantified using the Qubit 1X dsDNA HS Assay Kit.

treatment_protocol: The day before infection, 200k A549-ACE2 cells were plated in a 12 well dishes. Cells were either mock-infected (PBS only) or infected with SARS-CoV-2 virus at MOI 0.5.

tag: cell

tag: infection

value: Pool

tag: antibody


title: Mitotic_0h_ProSeq_ReplicateA


title: FUCCI2 iPSCs, Asynchronous_HiC_ReplicateA

description:
HiC_Asyn_A
HiC in Asynchronous cells


title: SARS-CoV-2-infected sample at time = 24 hours; replicate 3

value: Infected

value: Abcam ab4729


title: SARS-CoV-2-infected sample at time = 24 hours; replicate 2


title: RNA-seq of LG1 ESC replicate 2

description: LG2 RNA-seq replicate 2


title: SARS-CoV-2-infected sample at time = 24 hours; replicate 1


title: SARS-CoV-2-infected sample at time = 8 hours; replicate 3


title: SARS-CoV-2-infected sample at time = 8 hours; replicate 1


title: Asynchronous_ProSeq_ReplicateA

description: FUCCI2 iPSCs were untreated

value: Induced Pluripotent Stem cells


title: uninfected sample at time = 0 hours; replicate 3

value: Uninfected


title: uninfected sample at time = 0 hours; replicate 2


title: SARS-CoV-2-infected sample at time = 8 hours; replicate 2


title: MPC_18

status: Public on Jan 31 2021

description: gene expression profile

data_processing:
Alignment was performed with STAR 2.5.0a
DeSeq2 was used to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing the FPKM table counts

source_name: Micropapillary High Grade T1 Urothelial Bladder Cancer

extract_protocol:
AllPrep FFPE Kit (Qiagen, Germantown, Maryland, USA)
TruSeq Stranded RNA Access Library Prep Kit

tag: micropapillarity

tag: gender (female = 0)


title: uninfected sample at time = 0 hours; replicate 1


title: Asynchronous_ProSeq_ReplicateB

description: FUCCI2 iPSCs were untreated


title: MPC_15

description: gene expression profile


title: MPC_13

description: gene expression profile


title: MPC_17

description: gene expression profile


title: MPC_9

description: gene expression profile


title: MPC_8

description: gene expression profile


title: MPC_7

description: gene expression profile


title: MPC_5

description: gene expression profile


title: MPC_12

description: gene expression profile


title: MPC_6

description: gene expression profile


title: MPC_1

description: gene expression profile


title: vh184

description: gene expression profile


title: vh180

description: gene expression profile


title: vh176

description: gene expression profile


title: vh171

description: gene expression profile


title: vh165

description: gene expression profile


title: vh163

description: gene expression profile


title: vh159

description: gene expression profile


title: vh153

description: gene expression profile


title: vh151

description: gene expression profile


title: vh162

description: gene expression profile


title: vh150

description: gene expression profile


title: vh146

description: gene expression profile


title: MPC_3

description: gene expression profile


title: MPC_4

description: gene expression profile


title: vh140

description: gene expression profile


title: vh145

description: gene expression profile


title: vh134

description: gene expression profile


title: vh135

description: gene expression profile


title: vh125

description: gene expression profile


title: vh127

description: gene expression profile


title: vh144

description: gene expression profile


title: vh118

description: gene expression profile


title: vh123

description: gene expression profile


title: MPC_11

description: gene expression profile


title: vh117

description: gene expression profile


title: vh126

description: gene expression profile


title: vh113

description: gene expression profile


title: vh121

description: gene expression profile


title: vh128

description: gene expression profile


title: MPC_16

description: gene expression profile


title: vh116

description: gene expression profile


title: vh103

description: gene expression profile


title: vh101

description: gene expression profile


title: vh102

description: gene expression profile


title: vh100

description: gene expression profile


title: vh91

description: gene expression profile


title: vh78

description: gene expression profile


title: vh79

description: gene expression profile


title: vh105

description: gene expression profile


title: vh112

description: gene expression profile


title: 4Cseq_of_TGFB2_Mit_0.5Hours_rep1

description:
4Cseq of TGFB2 Mit 0.5Hours replicate 1
av_mit30min.bedGraph


title: vh93

description: gene expression profile


title: vh68

description: gene expression profile


title: vh66

description: gene expression profile


title: vh62

description: gene expression profile


title: vh61

description: gene expression profile


title: vh49

description: gene expression profile


title: vh56

description: gene expression profile


title: vh52

description: gene expression profile


title: vh46

description: gene expression profile


title: vh45

description: gene expression profile


title: vh42

description: gene expression profile


title: vh34

description: gene expression profile


title: vh32

description: gene expression profile


title: vh81

description: gene expression profile


title: vh55

description: gene expression profile


title: vh31

description: gene expression profile


title: vh29

description: gene expression profile


title: vh73

description: gene expression profile


title: vh97

description: gene expression profile


title: vh7

description: gene expression profile


title: vh59

description: gene expression profile


title: vh96

description: gene expression profile


title: vh24

description: gene expression profile


title: vh21

description: gene expression profile


title: vh15

description: gene expression profile


title: vh16

description: gene expression profile


title: vh14

description: gene expression profile


title: vh3

description: gene expression profile


title: vh12

description: gene expression profile


title: vh2

description: gene expression profile


title: vh1

description: gene expression profile


title: vh5

description: gene expression profile


title: vh30

description: gene expression profile


title: HEK293T_H3S28ph_dMSK1_non-targeting_gRNAs_pooled

status: Public on Jan 08 2021

city: Houston

first: Isaac

middle: B

last: Hilton

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

data_processing:
Illumina HiSeq Basecalling software used for basecalling for RNA-seq
Reads were aligned to the hg38 genome using HISAT2 version 2.1.0. Transcript abundance was calculated using the function featureCounts from Subread version 2.0.1.
Illumina HiSeq3000 for basecalling for ChIP-seq
Reads were aligned to the hg38 genome using Bowtie2 version 2.3.4.2. Peaks were called with MACS2 version 2.1.2.1
Genome_build: hg38
Supplementary_files_format_and_content: text file with feature counts or bdg files

extract_protocol:
DNA was fragmented with a bioruptor and chromatin was isolated with indicated antibody.
ChIP libraries were prepared using the KAPA Hyper Prep Kit (Roche) following the manufacturer’s protocol.  Briefly, 3 ng of fragmented DNA were used to repair the ends before ligation to a diluted NEXTflex DNA adapter (PerkinElmer).  The adaptor-ligated DNA was then enriched using 10 cycles of PCR (1 cycle at 98°C for 45 sec; 10 cycles at 98°C for 15 sec, 60°C for 30 sec, 72°C for 30 sec; and 1 cycle at 72°C for 1 min).  DNA was purified using AMPure XP beads (Beckman Coulter) after adaptor ligation and PCR enrichment, and the libraries were run on a 2200 TapeStation (Agilent Technologies) for quality control.  A KAPA Library Quantification Kit (KAPA Biosystems) was utilized to quantify the libraries for pooling, and a final concentration of 1.5 nM was loaded onto an Illumina cBOT for cluster generation before sequencing on an Illumina HiSeq3000 for sequencing using a Single Read 50 bp run.

tag: cell line

value: embroyonic kidney cells


title: HEK293T_H3S28ph_dMSK1_OCT4_gRNAs_re4

description:
S28Ph2_S75_L008
processed data file: S28ph_OCT4_targeted_pooled.bdg.txt

value: H3S28ph (abcam, ab32388)


title: HEK293T_H3S28ph_dMSK1_non-targeting_gRNAs_re1

description:
S28Ph3_S9_L001
processed data file: S28ph_non_targeting_pooled.bdg.txt


title: HEK293T_H3S28ph_dMSK1_OCT4_gRNAs_re3

description:
S28Ph1_S74_L008
processed data file: S28ph_OCT4_targeted_pooled.bdg.txt


title: HEK293T_H3S28ph_dMSK1_non-targeting_gRNAs_re4

description:
S28Ph4_S77_L008
processed data file: S28ph_non_targeting_pooled.bdg.txt


title: HEK293T_H3S28ph_dMSK1_non-targeting_gRNAs_re2

description:
S28Ph4_S10_L001
processed data file: S28ph_non_targeting_pooled.bdg.txt


title: HEK293T_H3S28ph_dMSK1_non-targeting_gRNAs_re3

description:
S28Ph3_S76_L008
processed data file: S28ph_non_targeting_pooled.bdg.txt


title: HEK293T_H3S28ph_dMSK1_OCT4_gRNAs_re2

description:
S28Ph2_S8_L001
processed data file: S28ph_OCT4_targeted_pooled.bdg.txt


title: HEK293T_FLAG_dCas9_dMSK1_non-targeting_gRNAs_re2

value: FLAG (Sigma-Aldrich, F1804)


title: HEK293T_H3S28ph_dMSK1_OCT4_gRNAs_pooled


title: HEK293T_H3S28ph_dMSK1_OCT4_gRNAs_re1

description:
S28Ph1_S7_L001
processed data file: S28ph_OCT4_targeted_pooled.bdg.txt


title: vh19

description: gene expression profile


title: A375_dCas9-dMSK1-PLX-4720-treatment-_re3

description:
amplified DNA
gRNA_counts.txt

data_processing:
RNA-seq:
Illumina HiSeq Basecalling software used for basecalling.
Reads were de-multiplexed and then aligned to the hg38 genome using HISAT2 version 2.1.0. Transcript abundance was calculated using the function featureCounts from Subread version 2.0.1.
CRISPRa screen:
Illumina MiSeq Basecalling software used for basecalling.
MAGECK-VISPR version 0.5.4 (quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR) using Robust Rank Aggregation (RRA) default parameters. Guide counts were determined based on perfectly matched sequencing reads only.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: featureCounts.txt: Tab-delimited text file with feature counts.
Supplementary_files_format_and_content: gRNA counts.txt: Tab-delimited text file with gRNA counts.

extract_protocol:
Genomic DNA was extracted using the Qiagen Quick-gDNA midi kit (Qiagen, #13343) following manufacturer's instructions.
To amplify the gRNAs, we used 8 μg of genomic DNA as a template across eight 100-μL PCR reactions using Q5 hot start polymerase (NEB, #M0493L). We carried out amplification according to the manufacturer's instructions, using 25 cycles at an annealing temperature of 60 ° C with indexed primers. We purified the amplified libraries with QIAquick Gel Extraction Kit (Qiagen, # 28706). Each sample was quantified after purification with the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher, Q32854). Samples were pooled and sequenced using the MiSeq platform (Illumina).

value: skin cells

value: PLX-4720 treated

tag: genotype


title: MPC_2

description: gene expression profile


title: HEK293T_FLAG_dCas9_dMSK1_OCT4_gRNAs_re1

tag: cell type


title: A375_dCas9-dMSK1-PLX-4720-treatment-_re4

description:
amplified DNA
gRNA_counts.txt


title: HEK293T_FLAG_dCas9_dMSK1_non-targeting_gRNAs_re1


title: A375_dCas9-dMSK1-no-treatment-_re2

description:
amplified DNA
gRNA_counts.txt

value: DMSO treated


title: HEK293T_dCas9_dMSK1_non-targeting_gRNAs_re1

description:
dMSK1_3_S38_L005
processed data file: featureCounts_targeted_vs_nontargeted.txt

extract_protocol:
RNA was isolated from transfected cells using the RNeasy Plus mini kit (Qiagen, #74136) following manufacturer’s instructions
RNA-seq library construction using the TruSeq Stranded Total RNA Gold (Illumina, RS-122-2303). The qualities of RNA-seq libraries were verified using the Tape Station D1000 assay (Tape Station 2200, Agilent Technologies) and the quantities of RNA-seq libraries were checked again using real time PCR (QuantStudio 6 Flex Real time PCR System, Applied Biosystem). Libraries were normalized and pooled and then 75-bp paired-end reads were sequenced on the Hiseq 3000 platform (Illumina)


title: A375_dCas9-dMSK1-PLX-4720-treatment-_re2

description:
amplified DNA
gRNA_counts.txt


title: vh122

description: gene expression profile


title: A375_dCas9-dMSK1-PLX-4720-treatment-_re1

description:
amplified DNA
gRNA_counts.txt


title: A375_dCas9-dMSK1-no-treatment-_re1

description:
amplified DNA
gRNA_counts.txt


title: HEK293T_dCas9_dMSK1_non-targeting_gRNAs_re2

description:
dMSK1_4_S39_L005
processed data file: featureCounts_targeted_vs_nontargeted.txt


title: HEK293T_dCas9_dMSK1_OCT4_gRNAs_re2

description:
dMSK1_2_S36_L005
processed data file: featureCounts_targeted_vs_nontargeted.txt


title: HEK293T_dCas9_dMSK1_OCT4_gRNAs_re1

description:
dMSK1_1_S34_L005
processed data file: featureCounts_targeted_vs_nontargeted.txt


title: A375_dCas9-dMSK1-no-treatment-_re3

description:
amplified DNA
gRNA_counts.txt


title: HEK293T_ko2_re2

description: featureCounts.txt

extract_protocol:
RNA was isolated from transfected cells using the RNeasy Plus mini kit (Qiagen, #74136) following manufacturer’s instructions.
RNA-seq library construction using the TruSeq Stranded Total RNA Gold (Illumina, RS-122-2303). The qualities of RNA-seq libraries were verified using the Tape Station D1000 assay (Tape Station 2200, Agilent Technologies) and the quantities of RNA-seq libraries were checked again using real time PCR (QuantStudio 6 Flex Real time PCR System, Applied Biosystem). Libraries were normalized and pooled and then 75-bp paired-end reads were sequenced on the Hiseq 3000 platform (Illumina).

value: embryonic kidney cells


title: HEK293T_ko2_re1

description: featureCounts.txt


title: HEK293T_ko1_re2

description: featureCounts.txt


title: HEK293T_ko1_re1

description: featureCounts.txt


title: HEK293T_WT_re1

description: featureCounts.txt

value: wild type


title: HEK293T_WT_re2

description: featureCounts.txt


title: Single U2OS cell P9_355

status: Public on Dec 11 2020

city: Solna

first: Emma

last: Lundberg

address: Science for Life Laboratory, Tomtebodavägen 23A

country: Sweden

institute: KTH Royal Institute of Technology

data_processing:
Alignment and quantification were performed with RSEM (version 1.3.2-0) using STAR (version 2.7.0f-0.
Genome_build: GRCh38.98
Supplementary_files_format_and_content: Comma-delimited files with TPM or counts for all samples or for all ERCC spike-in sequences.
Supplementary_files_format_and_content: fucci_coords.csv: Comma-delimited file includes FACS intensities and postprocessing from those intensities.

source_name: Single U2OS human cell

growth_protocol: U-2 OS FUCCI cells were kindly provided by Dr. Miyawaki. These cells are endogenously tagged with two fluorescent proteins fused to cell cycle regulators to allow cell cycle monitoring; CDT1 (mKO2-hCdt1+) accumulates in G1 phase, while Geminin (mAG-hGem+) accumulates in S and G2 phases. Cells expressing FUCCI probes are divided into red mKO2(+)mAG(-), yellow mKO2(+)mAG(+), and green mKO2(-)mAG(+) emitting populations. The cells were cultivated in Petri dishes at 37 °C in a 5.0 % CO2 humidified environment in McCoy’s 5A (modified) medium GlutaMAX supplement, (ThermoFisher, 36600021, MA, USA) supplemented with 10% fetal bovine serum (FBS, VWR, Radnor, PA, USA) without antibiotics. The cells were maintained sub-confluent and harvested by trypsinization at log-phase growth (60% confluency) for subsequent analysis.

extract_protocol:
We used the polyA-RNA extraction method from the SMART-Seq2 protocol by Picelli, et al. Nature Methods 2013.
We used the cDNA library preparation method from the SMART-Seq2 protocol by Picelli, et al. Nature Methods 2013, along with ERCC spike-in sequences.

tag: cell cycle phase


title: Single U2OS cell P8_357


title: Single U2OS cell P7_357


title: Single U2OS cell P8_355


title: Single U2OS cell P8_356


title: Single U2OS cell P6_357


title: Single U2OS cell P9_357


title: Single U2OS cell P6_355


title: Single U2OS cell P9_356


title: Single U2OS cell P7_355


title: Single U2OS cell P4_357


title: Single U2OS cell P5_357


title: Single U2OS cell P4_356


title: Single U2OS cell P5_355


title: Single U2OS cell P6_356


title: Single U2OS cell P7_356


title: Single U2OS cell P3_356


title: HEK293T_FLAG_dCas9_dMSK1_OCT4_gRNAs_re2

tag: treatment


title: Single U2OS cell P5_356


title: Single U2OS cell P4_355


title: Single U2OS cell P3_357


title: Single U2OS cell P2_356


title: SEAX_miR124_1

status: Public on Dec 31 2020

description: Gene expression data from SEAX cell line

hyb_protocol: Sample was hybridized to Affymetrix Human PrimeView array according to manual GeneChip 3’ IVT Pico Reagent kit (P/N 703308 Rev. 1) and using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from SEAX cell line

label_protocol: 10ng of total RNA from each sample was processed and labelled according to manual GeneChip 3’ IVT Pico Reagent kit (P/N 703308 Rev. 1)

extract_protocol: RNA was extracted following Quiagen protocol

tag: condition


title: SEAX_miR124_2


title: SEAX_Control_2

value: Control


title: Single U2OS cell P3_355


title: SEAX_Control_1


title: Single U2OS cell P2_357


title: Single U2OS cell P21_355


title: Single U2OS cell P23_356

value: NotAssigned


title: Single U2OS cell P20_357


title: Single U2OS cell P1_356


title: Single U2OS cell P2_355


title: Single U2OS cell P19_356


title: Single U2OS cell P24_357


title: Single U2OS cell P19_355


title: Single U2OS cell P23_355


title: Single U2OS cell P1_357


title: Single U2OS cell P23_357


title: Single U2OS cell P24_356


title: Single U2OS cell P24_355


title: Single U2OS cell P22_357


title: Single U2OS cell P22_355


title: Single U2OS cell P22_356


title: Single U2OS cell P17_357


title: Single U2OS cell P18_357


title: Single U2OS cell P18_356


title: Single U2OS cell P20_355


title: Single U2OS cell P18_355


title: Single U2OS cell P16_357


title: Single U2OS cell P16_356


title: Single U2OS cell P1_355


title: Single U2OS cell P17_355


title: Single U2OS cell P16_355


title: Single U2OS cell P21_356


title: Single U2OS cell P20_356


title: Single U2OS cell P19_357


title: Single U2OS cell P21_357


title: Single U2OS cell P15_357