title: MCF10A-CA1_IgG_rep1

status: Public on Aug 09 2021

city: Watervliet

first: Ali

middle: Salman

last: Ropri

state: NY

address: 12 Lakeshore Dr., Apt 1B

department: Biomedical Sciences

institute: SUNY Albany

data_processing:
 Quality of samples for ChIP were assessed using the Bioconductor package FastQC (version 0.11.9)
Data was mapped to the human reference genome (hg38 assembly) using STAR Aligner (version 2.7.0)
PCR duplicated reads were filtered using Sambamba (version 0.7.1)
The MACS2 (version 2.2.7.1) algorithm was used to identify enriched regions (peaks). Default parameters were used except to ensure broad regions were identified; broad peak calling was used with a broad cutoff of 0.1. Reads were normalized to mapped reads.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

source_name: Epithelial Cells

growth_protocol: MCF10A, MCF10A-AT1, DCIS.com, and MCF10A-CA1 cells were grown to a final count of 5 x 10^6. The cells were maintained in a culture of Dulbecco's modified Eagle's medium (DMEM) medium supplemented with 5% horse serum, 20 ng/mL EGF, 0.5 mg/mL hydrocortisone, 100 ng/mL cholera toxin, 10 μg/mL insulin and 1× antibiotic‐antimycotic (Gibco, Grand Island, NY)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
1 to 10 ng of DNA was prepared for sequencing using NEBNext Ultra II DNA Library Prep Kit (E7645S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (E7335S)

value: Breast; Mammary gland

tag: disease state

value: invasive ductal carcinoma

tag: cell type

value: epithelial cells

tag: chip antibody

value: IgG- Cell Signaling(Rabbit (DA1E) mAb IgG XP® Isotype Control #3900

value: Untreated


title: MCF10A-CA1_H3K_rep2

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: tissue

value: H3K27ac (abcam ChIP Grade (ab4729))

tag: treatment


title: P112 HC

status: Public on Sep 13 2021

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (refdata-cellranger-GRCh38-3.0.0)  and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GrCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

molecule: total RNA

source_name: skin biopsy

extract_protocol:
For each described sample, one single 6mm punch biopsy was taken and processed immediately. Each sample was cut into small pieces and digested in the C Tube (Miltenyi Biotec, Bergisch Gladbach, Germany) using the enzyme mix as provided by the Whole Skin Dissociation Kit for human (Miltenyi Biotec) in a total volume of 0,5ml RPMI medium with enzymatic supplements as described in the manufacturer's instructions. The sample was then incubated for a total of one hour in a water bath at 37°C. The sample was then further dissociated using the gentleMACS Dissociator (Miltenyi Biotec) running the program h_skin_01. After termination of the program steps 10-14 were conducted as detailed in the manufacturer's instructions. Finally, the cell pellet was resuspended in PBS with 0,08% BSA reaching a total volume of not more than 100µl. A cell aliquot was stained with trypan blue and cell numbers and percentages of dead cells were assessed by manual counting. Samples with not more than 30% dead cells were then subjected to scRNA-seq processing as detailed below.
5' gene expression sequencing was performed using the Chromium Controller and Single Cell 5' Library  (10x Genomics) according to the manufacturer's protocol. Sequencing was performed using the Illumina NovaSeq 6000 platform and the 150bp paired-end configuration.

tag: lesion type

value: healthy control

tag: diagnosis

tag: chemistry

value: Single Cell 5' PE


title: P116 HC


title: P115 HC


title: MCF10A-CA1_H3K_rep1


title: MCF10A-AT1_IgG_rep2

value: atypical ductal hyperplasia


title: MCF10A-AT1_IgG_rep1


title: MCF10A-AT1_H3K_rep2


title: MCF10A_IgG_rep1

value: normal


title: MCF10A_H3K_rep2


title: MCF10A-AT1_H3K_rep1


title: ChIPseq_H3K9me3_CT_rep1

status: Public on Mar 29 2022

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description:
input: Input_histone_CT_rep1
H3K9me3_CT.bw
H3K9me3_CT_peaks.bed

data_processing:
RNA-seq:   RNA-seq reads were mapped using STAR v2.6.1c with GENCODE v33 gene annotation. Read counts per gene were obtained using the ‘--quantMode’ parameter in STAR. Differentially expression analysis was performed with edgeR v3.30.0. Quasi-likelihood negative binomial generalized log-linear model and t-test relative to a fold change threshold of 1.5 were used to calculate per gene p-values. The obtained p-values were adjusted with Benjamini–Hochberg correction for multiple testing (FDR). FDR threshold of 0.01 was used to define differentially expressed genes.
ChIP-seq:   ChIP-seq reads were mapped using bowtie v2.2.3 with ‘--no-discordant’ and ‘--no-mixed’ options. Uniquely mapped reads with MAPQ>30 were selected using SAMtools v1.5, PCR duplicates were filtered with Picard MarkDuplicates, reads overlapping with the hg19 blacklist regions were discarded. The bigWig files with the ratio of RPKM-normalized ChIP-seq signal to the input in 50 bp bins were generated using deepTools2 with ‘--pseudocount’ set to 0 1 and ‘--smoothLength’ of 3 bins. Peaks were called using MACS2 with broad-cutoff of 0.1 (H3K9me3 and H3K27me3) in broad peak mode, qvalue of 0.05 (H3K27ac and H3K4me3) and p-value of 0.001 (CTCF) in narrow peak mode.
Hi-C:  Hi-C reads were mapped using bowtie v2.2.3 with the ‘--very-sensitive’ mode and the iterative mapping procedure implemented in hiclib package. Non-uniquely mapped reads, reads mapped on the same fragment and possible PCR duplicates were eliminated. Filtered reads pairs were aggregated into into genomic bins of different sizes to obtain Hi-C contact matrices. Contacts matrices were normalized using the ICE balancing implemented in cooler v0.7.9. Chromatin compartments were annotated using PCA implemented in cooltools v0.3.2 call-compartments function for 100 kb resolution contact matrices. TADs were annotated using the Armatus algorithm implemented in lavaburst package for 20 kb resolution contact matrices.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: normalized signal tracks in bigWig format; read counts per gene in TXT format. ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format. Hi-C: contact matrices in MCOOL format; compartment eigenvectors in TXT format; TADs in BED format.

source_name: A549 immortalized cell line

growth_protocol: A549 (K‐RAS G12S) cells were obtained from ATCC (ATCC CCL-185). Cells were cultured in Dulbecco’s modified Eagle’s Medium DMEM (Sigma) supplemented with 10% FBS (Gibco), 1% penicillin/streptomycin (Sigma), maintained at 37°C and 5% CO2.

extract_protocol:
RNA-seq: RNA extraction was performed using RNeasy mini-kit (Qiagen) followed by Turbo DNA-free kit (Ambion).  ChIP-seq: Cells were collected with or without formaline fixation. Chromatin was fragmented by MNase digestion (histone ChIP) or sonication (CTCF ChIP), and immunoprecipitated by different antibodies. DNA was purified using MinElute columns from Qiagen.  Hi-C: Cells were fixed with 2% of formaldehyde, chromatin was digested with DpnII, DNA ends were biotinylated and re-ligated in situ. DNA was purified by reverse-crosslinking, followed by phenol/chloroform extraction, ethanol precipitation and additional purification using AMPure XP magnetic beads. DNA was sheared by sonication, ligation junctions were enriched by Biotin pull-down.
RNA-seq: Libraries were constructed using Truseq stranded total RNA kit (Illumina).  ChIP-seq: Libraries were prepared using the MicroPlex V2 library preparation kit (Diagenode).  Hi-C: Libraries were prepared with standard protocol using TruSeq adapters (Illumina).

treatment_protocol: SETDB1 knockout was performed through CRISPR/Cas9-mediated gene disruption. The sgRNA were synthesized (Sigma) as oligonucleotide DNA sequences and cloned into PX458 plasmid (Addgene, Plasmid #48138). Cloning was performed according to a protocol described by Ran et al. (PMID: 24157548).

tag: antibody

tag: genotype

value: Control (CT)

tag: disease

value: lung adenocarcinoma


title: MCF10A_H3K_rep1


title: HiC_KO_rep1

description:
HiC_KO.mcool
TADs_KO.bed
compartment_signal.bed

value: SETDB1 knockout (KO)


title: RNAseq_CT_rep1

description:
gene_counts.txt
RNAseq_CT.bw


title: LX22 hSCLC PDX2

status: Public on May 01 2021

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

description:
Human_PDX_LX22_RNA_082018
processed data file: hSCLC_PDX_fpkm_whole_genome.txt

data_processing:
Reads were mapped to hg19 assembly using tophat
Transcripts quantification and differential expression was estimated using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: FPKM matrix

source_name: LX22 hSCLC PDX2

growth_protocol: Cells were maintained in RPMI-1640 media (ThermoFisher Scientific, 11875135) supplemented with 5% heat deactivated fetal bovine serum (Sigma Aldrich) without antibiotics at 37 °C in a humidified atmosphere containing 5% CO2 and 95% air.

extract_protocol: RNAs were extracted using the Arcturus PicoPure RNA (Thermofisher Scientific,  KIT0204) isolation Kit as recommended by the manufacturer.

treatment_protocol: No treatment

tag: tissue/cell line

value: JHU-LX22-SCLC PDX

tag: tissue/cell type

value: Small cell lung cancer PDX flank

tag: passage

tag: sirna

value: no treatment


title: H2107 NT rep2

description:
H2107_hSCLC_NT-CTRL_rep2_RNA
processed data file: H2107_ASCL1_ANP_KD_fpkm_whole_genome.txt

extract_protocol:
Cells were harvested in Trizol 72h after treatment. RNAs were extracted using the Arcturus PicoPure RNA (Thermofisher Scientific,  KIT0204) isolation Kit as recommended by the manufacturer.
Libraries were constructed by using the KAPA RNA HyperPrep Kits as per manufacturer’s instructions.

treatment_protocol: Cells( 3x105 cells/ml) were transfected with 25 nM siRNA using the X-Treme siRNA transfection reagent (Sigma-Aldrich 4476093001) in Opti-MEM™ reduced serum medium (ThermoFisher Scientific) as per manufacturer’s recommendations.

value: Small cell lung cancer cell line

value: control siRNA-A (Santa Cruz Biotechnology sc-37007)


title: LX44 hSCLC PDX3

description:
Human_PDX_LX44_RNA_082018
processed data file: hSCLC_PDX_fpkm_whole_genome.txt

source_name: LX44 hSCLC PDX3

value: JHU-LX44-SCLC PDX


title: HiC_CT_rep2

description:
HiC_CT.mcool
TADs_CT.bed
compartment_signal.bed


title: H2107 NT rep1

description:
H2107_hSCLC_NT-CTRL_rep1_RNA
processed data file: H2107_ASCL1_ANP_KD_fpkm_whole_genome.txt


title: LX110 hSCLC PDX1

description:
Human_PDX_LX110_RNA_082018
processed data file: hSCLC_PDX_fpkm_whole_genome.txt

source_name: LX110 hSCLC PDX1

value: JHU-LX110-SCLC PDX


title: H2107 ASCL1 KD rep2

description:
H2107_hSCLC_ASCL1-KD_rep2_RNA
processed data file: H2107_ASCL1_ANP_KD_fpkm_whole_genome.txt

source_name: H2107 ASCL1 KD

value: ASCL1 siRNA (ThermoFisher Scientific, 36758255)


title: RNAseq_CT_rep3

description:
gene_counts.txt
RNAseq_CT.bw


title: MCF10A-CA1_IgG_rep2

value: Breast; Mammary gland

value: invasive ductal carcinoma

value: epithelial cells

value: IgG- Cell Signaling(Rabbit (DA1E) mAb IgG XP® Isotype Control #3900

value: Untreated


title: H2107 3TF KD rep1

description:
H2107_hSCLC_ANP-KD_rep1_RNA
processed data file: H2107_ASCL1_ANP_KD_fpkm_whole_genome.txt

source_name: H2107 3TF KD

value: NKX2-1 MISSION® siRNA (Sigma-Aldrich, HS0100189848), PROX1 siRNA (Santa Cruz Biotechnology sc-106451), ASCL1 siRNA (ThermoFisher Scientific, 36758255)


title: H2107 3TF KD rep2

description:
H2107_hSCLC_ANP-KD_rep2_RNA
processed data file: H2107_ASCL1_ANP_KD_fpkm_whole_genome.txt


title: H2107 ASCL1 KD rep1

description:
H2107_hSCLC_ASCL1-KD_rep1_RNA
processed data file: H2107_ASCL1_ANP_KD_fpkm_whole_genome.txt


title: Input_ChIPseq_Recovery_rep2

status: Public on Mar 22 2021

data_processing:
Hi-C:
Alignment: Hi-C reads were mapped using bowtie v2.2.3 with the ‘--very-sensitive’ mode and the iterative mapping procedure implemented in hiclib. Filtering: non-uniquely mapped reads, reads mapped on the same fragment and possible PCR duplicates were eliminated. Binning: filtered reads pairs were aggregated into into genomic bins of different sizes to obtain Hi-C contact matrices. Balancing: contacts matrices were normalized using the iterative correction procedure implemented in cooler v0.7.9.
Compartment annotation. Chromatin compartments were annotated using PCA implemented in cooltools v0.3.2 call-compartments function for 100 kb resolution contact matrices.
Domain detection. TADs were annotated using the insulation score algorithm implemented in cooltools v0.3.2 diamond-insulation function for 20 kb resolution contact matrices. The window size for insulation score calculation was set to 360 kb.
Loop detection. Loops were annotated using CPU version of HiCCUPS (Juicer Tools v1.11.09) for 5, 10 and 25 kb resolution contact matrices with recommended parameters for medium resolution Hi-C maps.

ChIP-seq:
Reads were mapped using bowtie v2.2.3 with the ‘--very-sensitive’ mode. Non-uniquely mapped reads, possible PCR and optical duplicates were filtered out using SAMtools v1.5. The bigWig files with the ratio of RPKM normalized ChIP-seq signal to the input were generated using deepTools2 for each biological replicate. Peaks were called using PePr with a p-value cutoff of 1e-5 and a sliding window size of 100 bp.
Genome_build: hg19

Supplementary_files_format_and_content: Hi-C contact matrices in mcool format for each replicate; eigenvector text files in bedGraph-like format at 100 kb resolutions with a column for the eigenvector for each condition; TADs in BED format for each condition; loops in BEDPE format for each condition; normalized ChIP-seq signal tracks in bigWig format for each replicate; ChIP-seq peaks in BED format for each condition.

growth_protocol: Human HeLa cells were obtained from ATCC. All cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol:
Hi-C: Hi-C libraries were prepared as described previously [PMID: 26518482], with minor modifications. A total of 5-10 million cells were fixed in 1× phosphate buffered solution (PBS) with 2% formaldehyde for 10 minutes with occasional mixing. The reaction was quenched with by addition of 2 M glycine to a final concentration of 125 mM. Cells were pelleted by centrifugation (1,000 g, 10 minutes, 4 °C), resuspended in 50 μl of 1× PBS, snap-frozen in liquid nitrogen and stored at -80 °C. Cells were lysed in 1.5 ml of isotonic buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% (v/v) NP-40 substitute (Fluka), 1% (v/v) Triton-X100 (Sigma), 1× Halt™ Protease Inhibitor Cocktail (Thermo Scientific)) on ice for 15 minutes. Cells were pelleted by centrifugation at 2,500g for 5 minutes, resuspended in 100 μl of 1× DpnII buffer (NEB) and pelleted again. The pellet was resuspended in 200 μl of 0.3% SDS in 1.1× DpnII buffer and incubated at 37 °C for 1 hour. Then 330 μl of 1.1× DpnII buffer and 53 μl of 20% Triton X-100 (Sigma) were added, and the suspension was incubated at 37 °C for 1 hour. Next, 600 U of DpnII enzyme (NEB) were added, and the chromatin was digested overnight (14-16 hours) at 37 °C with shaking (1,400 rpm). In the morning, 200 U of DpnII enzyme were added and the cells were incubated for additional 2 hours. DpnII was then inactivated by incubation at 65 °C for 20 minutes. The nuclei were harvested for 10 minutes at 5,000 g, washed with 100 μl of 1× NEBuffer 2 and resuspended in 125 μl of 1.2× NEBuffer 2. Cohesive DNA ends were biotinylated by adding 25 μl of the biotin fill-in mixture (0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (NEB)). The samples were incubated at 37 °C for 75 minutes with shaking (1,400 rpm). Nuclei were pelleted by centrifugation at 3,000g for 5 minutes, resuspended in 300 μl of 1× T4 DNA ligase buffer (Fermentas) and pelleted again. The pellet was resuspended in 300 μl of 1× T4 DNA ligase buffer, and 75 U of T4 DNA ligase (Fermentas) were added. Chromatin fragments were ligated at 20 °C for 6 hours. The cross-links were reversed by overnight incubation at 65 °C in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation (glycogen (Thermo Scientific) at a concentration of 20 μg/ml was used as co-precipitator). After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl pH 8.0. To remove residual RNA, samples were treated with 50 μg of RNase A (Thermo Scientific) for 45 min at 37 °C. To remove residual salts and DTT, the DNA was additionally purified using Agencourt AMPure XP beads (Beckman Coulter).   ChIP-seq: ChIP-seq was performed with an anti-CTCF antibody (Active Motif, 61311) as described [PMID: 25646466, 26704968].
Hi-C: Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U of T4 DNA polymerase (NEB) in NEBuffer 2 supplied with 0.025 mM dATP and 0.025 mM dGTP at 20 °C for 4 hours. Next, the DNA was purified using Agencourt AMPure XP beads. The DNA was then dissolved in 500 μl of sonication buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.1% SDS) and was sheared to a size of approximately 100-1,000 bp using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified) using AMICON Ultra Centrifugal Filter Units to a total volume of about 50 μl. The DNA ends were repaired by adding 62.5 μl MQ water, 14 μl of 10× T4 DNA ligase reaction buffer (Fermentas), 3.5 μl of 10 mM dNTP mix (Fermentas), 5 μl of 3 U/μl T4 DNA polymerase (NEB), 5 μl of 10 U/μl T4 polynucleotide kinase (NEB), and 1 μl of 5 U/μl Klenow DNA polymerase (NEB) and incubating at 20 °C for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 μl 10× NEBuffer 2, 1.2 μl of 10 mM dATP, 1 μl of MQ water and 3.6 μl of 5 U/μl Klenow (exo-) (NEB). The reactions were carried out for 30 minutes at 37 °C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65 °C for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 200 μl of 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 10 μl of MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads with captured ligation junctions were resuspended in 50 μl of adapter ligation mixture composed of 41.5 μl MQ water, 5 μl 10× T4 DNA ligase reaction buffer (Fermentas), 2.5 μl of Illumina TruSeq adapters and 1 μl of 5 U/μl T4 DNA ligase (Fermentas). Adapter ligation was performed at 22 °C for 2.5 hours, and the beads were sequentially washed twice with 100 μl of TWB (5 mM Tris-HCl (pH 8.0), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl of 1× binding buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 2 M NaCl) and once with 100 μl of CWB (10 mM Tris-HCl (pH 8.0) and 50 mM NaCl) and then resuspended in 20 μl of MQ water. Test PCR reactions containing 4 μl of the streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles needed to generate enough PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98 °C, followed by 6, 9, 12, 15 and 18 cycles of 20 s at 98 °C, 15 s at 65 °C, and 20 s at 72 °C. The PCR reactions were separated on a 2% agarose gel supplied with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 12-15 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified using Agencourt AMPure XP beads.  ChIP-seq: ChIP samples were prepared for next-generation sequencing using a NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs).

treatment_protocol: To obtain transiently permeabilized cells, HeLa cells were incubated with 1% Tween 20 in DPBS for 10 min at room temperature, washed twice with DPBS and transferred to the culture medium. To obtain 1,6-hexanediol treated cells, transiently-permeabilized HeLa cells were incubated with 5% 1,6-hexanediol (Sigma-Aldrich, #240117) in the culture medium at room temperature, washed twice with DPBS and transferred to the culture medium. For recovery experiments, HeLa cells that were treated as described with 1,6-hexanediol were incubated in the culture medium for 1.5 h at 37°C.

value: HeLa

value: 1,6-hexanediol + recovery


title: CTCF_ChIPseq_Recovery_rep2


title: Input_ChIPseq_Recovery_rep1


title: MCF10A_IgG_rep2

value: normal


title: HiC_Recovery_T_rep1

extract_protocol:
5-10 million cells were fixed in 1× phosphate buffered solution (PBS) with 2% formaldehyde for 10 minutes with occasional mixing. The reaction was quenched with by addition of 2 M glycine to a final concentration of 125 mM. Cells were pelleted by centrifugation (1,000 g, 10 minutes, 4 °C), resuspended in 50 μl of 1× PBS, snap-frozen in liquid nitrogen and stored at -80 °C. Cells were lysed in 1.5 ml of isotonic buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% (v/v) NP-40 substitute (Fluka), 1% (v/v) Triton-X100 (Sigma), 1× Halt™ Protease Inhibitor Cocktail (Thermo Scientific)) on ice for 15 minutes. Cells were pelleted by centrifugation at 2,500g for 5 minutes, resuspended in 100 μl of 1× DpnII buffer (NEB) and pelleted again. The pellet was resuspended in 200 μl of 0.3% SDS in 1.1× DpnII buffer and incubated at 37 °C for 1 hour. Then 330 μl of 1.1× DpnII buffer and 53 μl of 20% Triton X-100 (Sigma) were added, and the suspension was incubated at 37 °C for 1 hour. Next, 600 U of DpnII enzyme (NEB) were added, and the chromatin was digested overnight (14-16 hours) at 37 °C with shaking (1,400 rpm). In the morning, 200 U of DpnII enzyme were added and the cells were incubated for additional 2 hours. DpnII was then inactivated by incubation at 65 °C for 20 minutes. The nuclei were harvested for 10 minutes at 5,000 g, washed with 100 μl of 1× NEBuffer 2 and resuspended in 125 μl of 1.2× NEBuffer 2. Cohesive DNA ends were biotinylated by adding 25 μl of the biotin fill-in mixture (0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (NEB)). The samples were incubated at 37 °C for 75 minutes with shaking (1,400 rpm). Nuclei were pelleted by centrifugation at 3,000g for 5 minutes, resuspended in 300 μl of 1× T4 DNA ligase buffer (Fermentas) and pelleted again. The pellet was resuspended in 300 μl of 1× T4 DNA ligase buffer, and 75 U of T4 DNA ligase (Fermentas) were added. Chromatin fragments were ligated at 20 °C for 6 hours. The cross-links were reversed by overnight incubation at 65 °C in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation (glycogen (Thermo Scientific) at a concentration of 20 μg/ml was used as co-precipitator). After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl pH 8.0. To remove residual RNA, samples were treated with 50 μg of RNase A (Thermo Scientific) for 45 min at 37 °C. To remove residual salts and DTT, the DNA was additionally purified using Agencourt AMPure XP beads (Beckman Coulter).
Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U of T4 DNA polymerase (NEB) in NEBuffer 2 supplied with 0.025 mM dATP and 0.025 mM dGTP at 20 °C for 4 hours. Next, the DNA was purified using Agencourt AMPure XP beads. The DNA was then dissolved in 500 μl of sonication buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.1% SDS) and was sheared to a size of approximately 100-1,000 bp using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified) using AMICON Ultra Centrifugal Filter Units to a total volume of about 50 μl. The DNA ends were repaired by adding 62.5 μl MQ water, 14 μl of 10× T4 DNA ligase reaction buffer (Fermentas), 3.5 μl of 10 mM dNTP mix (Fermentas), 5 μl of 3 U/μl T4 DNA polymerase (NEB), 5 μl of 10 U/μl T4 polynucleotide kinase (NEB), and 1 μl of 5 U/μl Klenow DNA polymerase (NEB) and incubating at 20 °C for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 μl 10× NEBuffer 2, 1.2 μl of 10 mM dATP, 1 μl of MQ water and 3.6 μl of 5 U/μl Klenow (exo-) (NEB). The reactions were carried out for 30 minutes at 37 °C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65 °C for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 200 μl of 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 10 μl of MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads with captured ligation junctions were resuspended in 50 μl of adapter ligation mixture composed of 41.5 μl MQ water, 5 μl 10× T4 DNA ligase reaction buffer (Fermentas), 2.5 μl of Illumina TruSeq adapters and 1 μl of 5 U/μl T4 DNA ligase (Fermentas). Adapter ligation was performed at 22 °C for 2.5 hours, and the beads were sequentially washed twice with 100 μl of TWB (5 mM Tris-HCl (pH 8.0), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl of 1× binding buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 2 M NaCl) and once with 100 μl of CWB (10 mM Tris-HCl (pH 8.0) and 50 mM NaCl) and then resuspended in 20 μl of MQ water. Test PCR reactions containing 4 μl of the streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles needed to generate enough PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98 °C, followed by 6, 9, 12, 15 and 18 cycles of 20 s at 98 °C, 15 s at 65 °C, and 20 s at 72 °C. The PCR reactions were separated on a 2% agarose gel supplied with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 12-15 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified using Agencourt AMPure XP beads.

treatment_protocol: To obtain transiently permeabilized cells, HeLa cells were incubated with 1% Tween 20 in DPBS for 10 min at room temperature, washed twice with DPBS and transferred to the culture medium. To obtain HEX-treated cells, transiently-permeabilized HeLa cells were incubated with 5% 1,6-hexanediol (Sigma-Aldrich, #240117) in the culture medium at room temperature, washed twice with DPBS and transferred to the culture medium. For recovery experiments, HeLa cells that were treated as described with Tween-20 and HEX were incubated in the culture medium for 1.5 h at 37°C.

value: Tween-20 + recovery


title: CTCF_ChIPseq_Recovery_rep1


title: HiC_Recovery_T_rep2


title: Input_ChIPseq_Hex5_rep2

extract_protocol:
ChIP-seq was performed with an anti-CTCF antibody (Active Motif, 61311) as described [PMID: 25646466, 26704968] for two biological replicates.
ChIP samples were prepared for next-generation sequencing using a NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs).


title: LX48 hSCLC PDX4

description:
Human_PDX_LX48_RNA_082018
processed data file: hSCLC_PDX_fpkm_whole_genome.txt

source_name: LX48 hSCLC PDX4

value: JHU-LX48-SCLC PDX

value: Small cell lung cancer PDX flank


title: HiC_Tween_rep2


title: CTCF_ChIPseq_Hex5_rep2

value: CTCF


title: HiC_Tween_rep1


title: Input_ChIPseq_Control_rep2


title: Input_ChIPseq_Control_rep1


title: CTCF_ChIPseq_Control_rep2


title: CTCF_ChIPseq_Hex5_rep1


title: CTCF_ChIPseq_Control_rep1


title: Input_ChIPseq_Hex5_rep1


title: HiC_Hex5_rep2


title: HiC_Recovery_rep1


title: HiC_Hex5_rep1


title: HiC_Recovery_rep2


title: HiC_Control_rep1


title: HiC_Control_rep2


title: NEI001-K88N-Patient-D200-3

status: Public on Feb 17 2021

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description:
CRX disease modeling in retinal organoid (K88N mutation)
K88N_raw_counts.txt
K88N_norm_counts_5CPM.txt

data_processing:
Fastq files were generated from reads passing chastity filter.
Transcript-level quantification was performed with kallisto v0.45.0 against Ensembl release 94
Transcript counts were summarized to the gene level using tximport using the lengthscaledTPM option (raw_counts.txt files)
Genes with <5cpm were removed and remaining genes were TMM-normalized and converted to counts per million (CPM) (norm_counts_5CPM.txt files)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: raw count txt file, abundance measurements txt file

molecule: polyA RNA

source_name: Retinal Organoid

growth_protocol: Retinal organoids were derived using a combination of 2D and 3D culture. Embryoid bodies were formed from iPSCs by EDTA treatment, cultured for 7 days in neural induction medium followed by plating on Matrigel. Between 3-4 weeks neural retina domains were dissected from adherent cultures forming organoids, which were subsequently maintained as floating cultures in ultra-low attachment 96-well plate format until collection.

extract_protocol:
Organoids were snap frozen on dry ice at the indicated day of differentiation. Frozen samples were thawed on ice and RNA extracted using Qiagen Rneasy Mini Kit according to the manufacturer's manual. RNA quality was determined using Agilent Bioanalyzer, all samples had RIN >7.
RNA was isolated from 3 frozen organoids per sample using QIAGEN RNeasy Kit according to manufacturer’s manual. RNA quality was assessed using Bioanalyzer (Agilent Technologies). Samples with RIN >7 were subsequently used for library generation using TruSeq Library Prepartation Kit (Illumina Inc.).

treatment_protocol: All samples were cultured in identical conditions.

tag: age


title: NEI001-K88N-Patient-D200-2


title: NEI001-K88N-Patient-D200-1


title: NEI001-K88N-Control-D200-3

description:
Control retinal organoid
K88N_raw_counts.txt
K88N_norm_counts_5CPM.txt

value: WT


title: NEI001-K88N-Control-D200-2


title: NEI001-K88N-Control-D200-1


title: NEI001-K88N-Patient-D120-3


title: NEI001-K88N-Patient-D120-2


title: NEI002-I138fs-Patient-D150-3

description:
CRX disease modeling in retinal organoid (I138fs mutation)
I138fs_raw_counts.txt
I138fs_norm_counts_5CPM.txt


title: NEI001-K88N-Patient-D120-1


title: NEI002-I138fs-Patient-D150-1


title: NEI002-I138fs-Patient-D150-2


title: NEI001-K88N-Control-D120-3


title: NEI002-I138fs-Patient-D90-3


title: NEI002-I138fs-Patient-D90-2


title: NEI002-I138fs-Patient-D90-1


title: NEI002-I138fs-Patient-D200-4


title: NEI002-I138fs-Patient-D200-2


title: NEI002-I138fs-Patient-D200-1


title: NEI002-I138fs-Patient-D125-1


title: NEI002-I138fs-Patient-D200-3


title: NEI002-I138fs-Control-D150-2


title: NEI002-I138fs-Control-D150-3

description:
Control retinal organoid
I138fs_raw_counts.txt
I138fs_norm_counts_5CPM.txt


title: NEI002-I138fs-Patient-D125-3


title: NEI002-I138fs-Control-D150-1


title: NEI002-I138fs-Control-D90-2


title: NEI002-I138fs-Control-D90-3


title: NEI002-I138fs-Control-D90-1


title: NEI002-I138fs-Control-D200-3


title: NEI002-I138fs-Control-D200-2


title: NEI002-I138fs-Control-D200-1


title: NEI002-I138fs-Control-D200-4


title: NEI002-I138fs-Control-D125-2


title: NEI002-I138fs-Control-D125-3


title: NEI001-K88N-Control-D120-2


title: NEI002-I138fs-Control-D125-1


title: NEI001-K88N-Control-D120-1


title: NEI002-I138fs-Patient-D125-2


title: MCF10A_WT_p53_2

status: Public on Jan 26 2021

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

data_processing:
Alignment was done using Bowtie, allowing only unique reads to be considered.
For detecting regions of local read enrichment (peaks), MACS algorithm was applied with default parameters for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak file that were generated by MACS

growth_protocol: Cells were cultured in DMEM/ Ham's F-12 (Biological Industries) supplemented with 100 ng/ml cholera toxin (Sigma), 20 ng/ml epidermal growth factor (EGF)(corning), 0.01 mg/ml insulin(Sigma), 500 ng/ml hydrocortisone (Sigma), 1% penicillin- streptomycin (Gibco), 5% horse serum (Biological Industries) and kept at 37℃ in a 5% CO2 incubator (Thermo Scientific). Parental and transformed cells were subjected to no more than five passages in culture when used in experiments.

extract_protocol:
Cells were cross-linked for 10 min at 37°C in 1% formaldehyde followed by quenching with 125 mM glycine for 10 min. Fixed cells were lysed with SDS Lysis Buffer (1% SDS, 50mM Tris pH 8.1, 10mM EDTA) supplemented with protease inhibitor and sonicated for 560 seconds (ME220 sonicator, Covaris). Cleared chromatin was diluted 1:10 with dilution Buffer (16.7mM Tris-HCl 8.1; 1.2mM EDTA; 167mM NaCl; 1.1% Triton) and incubated over night with 5 ug α-p53 (DO-1, Santa-Cruz) bound to magnetic beads (Dynabeads Protein G). Chromatin was washed with low salt buffer (20mM Tris-HCl 8.1; 2mM EDTA; 150mM NaCl; 1% triton; 0.1% SDS), high salt buffer (20mM Tris-HCl 8.1; 2mM EDTA; 500mM NaCl; 1% triton; 0.1% SDS), LiCl buffer (10mM Tris-HCl 8.1; 1mM EDTA; 1% NP-40; 250mM LiCl) at 4°C, and twice with TE (10mM Tris-HCl 8.1; 1mM EDTA) at room temp. Complexes were eluted with Elution buffer (10mM Tris-HCl 8.1; 1mM EDTA; 200mM NaCl; 1% SDS). Crosslinks were reversed with 1 mg/mL Proteinase K overnight at 65°C.
Purified DNA was used to prepare sequencing libraries using NEBNext UltraII DNA Library Prep Kit (New England Biolabs). Library concentration was measured by DNA High Sensitivity Kit (Invitrogen) on a Qubit fluorometer (Invitrogen). Library quality and fragment sizes were assessed on a Bioanalyzer (Agilent).

treatment_protocol: The p53 samples were treated with nutlin before the fixation.

value: mammary gland; breast

value: epithelial

tag: genotype/variation

value: Parental

value: α-p53 (DO-1, Santa-Cruz)


title: MCF10A_WT_input_p53_1

tag: cell type


title: VR0131

status: Public on Jan 14 2021

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data for the sense strand were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Genome_build: Human sequenced genome GRCh38 v91
Supplementary_files_format_and_content: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.

source_name: Blood

extract_protocol:
A blood sample was collected in PAXgene Blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) before the administration of the anti-TNF agent (week 0) and after 2 weeks of treatment (week 2). Total whole blood RNA was extracted using PAXgene Blood RNA kits (PreAnalitiX) according to the manufacturer’s instructions. RNA concentrations were measured using the Quawell Q5000 Spectrophotometer (Quawell Technology Inc, San Jose, CA, USA). RNA integrity was verified using the Agilent RNA 6000 Nano Kit in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Extracted RNA was stored at −80 °C until further processing. All RNA samples fulfilled the following criteria: RNA integrity ˃7.
200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Blood

tag: primary response

value: Non-responder

tag: weeks fron start of treatment

tag: anti-tnf

value: Infliximab

tag: disease state

value: pediatric inflammatory bowel disease


title: MCF10A_WT_p53_1

tag: cell line

tag: tissue

tag: chip antibody


title: RS0041

value: Adalimumab


title: PM0051


title: RM0161


title: MCF10A_WT_input_p53_2


title: VR0161

value: Responder


title: RM0171


title: VV0011


title: GM0031


title: PAZ0161


title: JC0121


title: REH_XRP44X

status: Public on Oct 30 2020

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: Cell line experiment in REH comparing two drugs targeting ETS-factors at 72 h. XRP44X (1 microM) sample.

data_processing:
Data was aligned with Cell Ranger 3.1.0 to combined human (hg19) and mouse (mm10) genome as reference from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 3.1.0 following alignment.
The mouse cells were left out by filtering cells which cellranger characterized as mouse or doublet cells or had more than 500 counts assigned to mouse genes.
The mouse genes were filtered out from the count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: barcode annotation: 10x Cell Ranger filtered barcode list; feature annotation: 10x Cell Ranger feature list; count matrix: 10x Cell Ranger filtered UMI count matrix

source_name: REH pre-B-ALL cell line

growth_protocol: The E/R+ REH cell line (ACC-22, DSMZ, Germany) was maintained in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM  L-glutamine (Gibco, Thermo Fisher), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich).

extract_protocol:
Viability was checked using Trypan blue with Cellometer Mini Automated Cell Counter (Nexcelom Bioscience) and Dead Cell Removal Kit (#130-090-101, MACS miltenyi Biotech) was used. Viable cells were eluted by rinsing twice with 1 ml binding buffer. Subsequently 0.42-0.5 million cells were methanol fixated according to 10X Genomics Methanol Fixation of Cells for Single Cell RNA Sequencing protocol User guide CG000136 Rev E, using a mix of two RNAse inhibitors (RNase Inhibitor, Thermo Fisher, Carlsbad, CA, USA and RNasin® Plus RNase Inhibitor, Promega, Madison, WI, USA). Samples were stored < 6 weeks before proceeding with Chromium run.
Cells were thawn following the MetOH fixation protocol and processed for loading following the Chromium Single Cell 3´Reagent Kits v3 User guide CG000183  Rev C. REH cells were prepared into pools together with mouse cells (not this study) and human cell singlets separated in data analysis step. Loading concentration of 2100-2200 cells/uL was used. Using 10X GemCode Technology, the poly-A transcripts are barcoded with an Illumina R1 sequence, a 16 bp 10X barcode and a 10 bp Unique Molecular Identifier (UMI). 13 cycles of PCR were used to amplify the cDNA.

treatment_protocol: REH cells were seeded into 6-well plates (0.6 milion/ml concentration) and treated with XRP44X (Sigma-Aldrich) (1 µM), TK216 (MedChemExpress, NJ USA)  (800 nM) or DMSO for 72 h

tag: time

tag: construct

tag: treatment


title: REH_VNC

description: Cell line experiment in REH comparing two drugs targeting ETS-factors at 72 h.Vincristine (1nM) sample.

value: Vincristine


title: REH_DEX

description: Cell line experiment in REH comparing two drugs targeting ETS-factors at 72 h.Dexamethasone (10nM) sample.

value: Dexamethasone


title: TKO6.8.11_Mb_1

status: Public on Sep 16 2020

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

country: Japan

institute: The National Institutes of Natural Sciences NINS

data_processing:
The RNA-seq libraries were each sequenced (101 cycles) using the Illumina HiSeq platforms.
Raw sequence reads were aligned to the reference mouse genomes (GRCm38/mm10) by TopHat2.
Genome-wide expression levels were measured as a unit of fragments per kilobase of exon per million fragments mapped (FPKM) using Cufflinks and the numbers of reads were counted per gene per sample using htseq-count within HTSeq.
Differentially expressed genes (DEGs) were identified by DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Mus musculus

source_name: Midbrain tissue

extract_protocol:
Total RNA was extracted using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively.
Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) and the KAPA HTP Library Preparation Kits (KAPA Biosystems) according to the manufacturer’s instructions. The RNA-seq libraries were each sequenced (101 cycles) using the Illumina HiSeq platforms.

tag: strain

tag: genotype

tag: developmental stage

value: Midbrain


title: TKO6.8.11_Fb_1

source_name: Forebrain tissue

value: Forebrain


title: TKO6.8.11_Mb_3


title: TKO6.8.11_Fb_4


title: TKO6.8.11_Mb_2


title: TKO6.8.11_Fb_3


title: TKO6.8.11_Fb_2


title: D0051


title: DKO6.8_Mb_2

value: Cdh6.8_Double_knockout_cranial defect


title: TKO6.8.11_Mb_4


title: DKO6.8_Fb_3


title: DKO8.11_Mb_3


title: DKO6.8_Fb_1


title: DKO8.11_Mb_2


title: DKO8.11_Mb_1


title: DKO6.8_Mb_1


title: DKO8.11_Fb_3


title: RM0101


title: DKO6.8_Fb_2


title: WT_Mb_5

value: Wild-type


title: DKO8.11_Fb_1


title: WT_Mb_4


title: WT_Mb_2


title: WT_Mb_3


title: DKO8.11_Fb_2


title: WT_Mb_6


title: WT_Mb_1


title: WT_Fb_5


title: WT_Fb_6


title: DKO6.8_Mb_3


title: WT_Fb_3


title: WT_Fb_2


title: WT_Fb_1


title: WT_Fb_4


title: Tumor_Patient6

status: Public on Jul 29 2020

type: genomic

city: Baltimore

first: Thomas

last: Pisanic

address: Shaffer Hall 200D, 3400 N Charles St

department: Institute for NanoBioTechnology

institute: Johns Hopkins University

description:
Sentrix Position: R01C01
Bisulfite-treated Genomic DNA
203841900047_R01C01

hyb_protocol: After restoration using Infinium DNA restoration kit (WG-321-1002), the bisulfite-treated (BST) DNA was analyzed using Illumina's Infinium Human MethylationEPIC BeadChip Kit (WG-317-1002) by following the manufacturer's manual.

scan_protocol: Polymer-coated chips were image-processed in Illumina’s iScan scanner.

data_processing: R Version 3.6.1, minfi R package version 1.30.0

label: Cy5 and Cy3

source_name: Laser Capture Microdissected High Grade Serous Carcinoma Tumor, Patient 4

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using QIAamp DNA FFPE tissue kit. 50 ng of DNA from each sample underwent bisulfite conversion using EZ DNA Methylation Kit (Zymo, D5001) according to the manufacturer’s protocol and then processed/restored according to the Illumina Infinium FFPE DNA Restoration Kit.

treatment_protocol: Samples were microdissected from FFPE tissue slide using laser microdissection

tag: uniqueid

tag: histology

value: Concomitant High Grade Serous Carcinoma Tumor

tag: tissue type

value: FFPE tissue

tag: patient age

tag: race

value: W

tag: gender

value: Female

tag: patient id

tag: p53 pattern

tag: tp53 mutation

tag: germline mutations

tag: concurrent hgsoc

value: Yes

tag: other tumors

value: No

tag: batch id

value: b


title: AdjacentNormal_Patient3

description:
Sentrix Position: R04C01
Bisulfite-treated Genomic DNA
203723050102_R04C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 3

value: APST

value: c


title: AdjacentNormal_Patient12

description:
Sentrix Position: R07C01
Bisulfite-treated Genomic DNA
203841900047_R07C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 12

value: BRCA2 mutation (+)  Mutation status N/A

value: Breast cancer; hogekin lymphoma


title: AdjacentNormal_Patient11

description:
Sentrix Position: R04C01
Bisulfite-treated Genomic DNA
203841900046_R04C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 11


title: p53Signature_Patient11

description:
Sentrix Position: R05C01
Bisulfite-treated Genomic DNA
203841900046_R05C01

value: P53 Signature Lesion

value: Missense


title: STIC_Patient12

description:
Sentrix Position: R08C01
Bisulfite-treated Genomic DNA
203841900047_R08C01

source_name: Laser Capture Microdissected STIC, Patient 12

value: Serous Tubal Intraepithelial Carcinoma (STIC)

value: Nonsense


title: AdjacentNormal_Patient13

description:
Sentrix Position: R07C01
Bisulfite-treated Genomic DNA
203841900046_R07C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 13


title: AdjacentNormal_Patient4

description:
Sentrix Position: R08C01
Bisulfite-treated Genomic DNA
203723050102_R08C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 4

value: Uterine endometrioid carcinoma


title: DormantSTIC_Patient13

description:
Sentrix Position: R08C01
Bisulfite-treated Genomic DNA
203841900046_R08C01

source_name: Laser Capture Microdissected Dormant STIC (STIL), Patient 13

value: Dormant Serous Tubal Intraepithelial Carcinoma


title: Tumor_Patient8

description:
Sentrix Position: R04C01
Bisulfite-treated Genomic DNA
203841900047_R04C01

source_name: Laser Capture Microdissected High Grade Serous Carcinoma Tumor, Patient 8

value: Concomitant High Grade Serous Carcinoma Tumor

value: BRCA2 mutation (+)  c.1189_1190ins


title: 50446_ LCM_50ng

description:
Sentrix Position: R02C01
Bisulfite-treated Genomic DNA
for protocol validation only
203282450180_R02C01

source_name: Laser Capture Microdissected Cancer Sample, 50ng

value: FFPE tissue

value: v


title: STIC_Patient4

description:
Sentrix Position: R07C01
Bisulfite-treated Genomic DNA
203723050102_R07C01

source_name: Laser Capture Microdissected STIC, Patient 4

value: W

value: Female


title: Adjacent_NormalPatient7

description:
Sentrix Position: R02C01
Bisulfite-treated Genomic DNA
203723050102_R02C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 7

value: No


title: 50446_ LCM_10ng

description:
Sentrix Position: R03C01
Bisulfite-treated Genomic DNA
for protocol validation only
203282450180_R03C01

source_name: Laser Capture Microdissected Cancer Sample, 10ng


title: AdjacentNormal_Patient8

description:
Sentrix Position: R06C01
Bisulfite-treated Genomic DNA
203723050102_R06C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 8

value: Yes


title: AdjacentNormal_Patient6

description:
Sentrix Position: R06C01
Bisulfite-treated Genomic DNA
203723050101_R06C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 6

value: c


title: STIC_Patient13

description:
Sentrix Position: R06C01
Bisulfite-treated Genomic DNA
203841900046_R06C01

source_name: Laser Capture Microdissected STIC, Patient 13

value: b


title: AdjacentNormal_Patient9

description:
Sentrix Position: R05C01
Bisulfite-treated Genomic DNA
203841900047_R05C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 9

value: Uterine serous carcinoma


title: STIC_Patient2

description:
Sentrix Position: R07C01
Bisulfite-treated Genomic DNA
203723050101_R07C01

source_name: Laser Capture Microdissected STIC, Patient 2

value: MMMT


title: Betty.HLE

status: Public on Jul 20 2020

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

data_processing:
Library strategy: WGS
All gibbon genomic shot-gun data were aligned to the gibbon genome reference (Nleu3.0) using BWA
MELT v2.1.3 was used to predict de novo LAVA insertions and deletions (indels) from each of the 23 whole genome shot-gun alignments
We characterized all LAVA inserts based on information such as genomic location, length, and insertion position relative to closest gene [intergenic, exonic, intronic, promoter (<3Kb upstream of gene) or terminator (<3Kb downstream of gene)]
The initial set of LAVA predictions was next filtered to remove: 1) low quality inserts, as assessed by MELT, 2) single copy inserts in the population, 3) inserts shorter than 290bp (the minimum length required to discriminate a composite LAVA from its non-SVA subunits), and 4) inserts found on unplaced Nleu3.0 contigs.
We generated binary LAVA genotype profiles for all gibbon individuals (heterozygous or homozygous LAVA insertion=1, homozygous absence of LAVA= 0)
Genome_build: Nleu3.0
Supplementary_files_format_and_content: an excel spreadsheet containing position, genomic and genotype information for all LAVA insertions across 23 gibbons

organism: Hoolock leuconedys

source_name: blood

extract_protocol:
Total gDNA was extracted from blood of gibbons and randomly sheared
sheared gDNA was used to generate illumina libraries using the NEBNext Ultra II library contruction kit (NEB)

tag: tissue

value: blood


title: Drew.HLE


title: 50446_ LCM_500ng

description:
Sentrix Position: R01C01
Bisulfite-treated Genomic DNA
for protocol validation only
203282450180_R01C01

source_name: Laser Capture Microdissected Cancer Sample, 500ng


title: Maung.HLE


title: STIC_Patient9

description:
Sentrix Position: R06C01
Bisulfite-treated Genomic DNA
203841900047_R06C01

source_name: Laser Capture Microdissected STIC, Patient 9

value: Serous Tubal Intraepithelial Carcinoma (STIC)

value: Missense


title: Auts2KO_4_RNASeq

status: Public on Jun 17 2020

data_processing:
The RNA-seq libraries were each sequenced (101 cycles) using the Illumina HiSeq platforms.
Raw sequence reads were aligned to the reference mouse genomes (GRCm38/mm10) by HISAT2.
Genome-wide expression levels were measured as a unit of transcripts per kilobase million (TPM) using StringTie and the numbers of reads were counted per gene per sample using htseq-count within HTSeq.
Differentially expressed genes (DEGs) were identified by DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Hippocampal tissues

extract_protocol:
Total RNA was extracted from hippocampal tissues of 4 control and 4 KO mice at P14 using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively.
Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) and the KAPA HTP Library Preparation Kits (KAPA Biosystems) according to the manufacturer’s instructions. The RNA-seq libraries were each sequenced (101 cycles) using the Illumina HiSeq platforms.

tag: strain

value: hippocampus

tag: age


title: Auts2KO_3_RNASeq

tag: genotype


title: Auts2KO_2_RNASeq


title: Auts2KO_1_RNASeq


title: Control_4_RNASeq


title: C4T_50ng

description:
Sentrix Position: R06C01
Bisulfite-treated Genomic DNA
for protocol validation only
203282450180_R06C01

tag: uniqueid


title: Control_2_RNASeq


title: Control_3_RNASeq


title: Control_1_RNASeq


title: STIC_Patient7

description:
Sentrix Position: R01C01
Bisulfite-treated Genomic DNA
203723050102_R01C01

source_name: Laser Capture Microdissected STIC, Patient 7

tag: histology


title: STIC_Patient6

description:
Sentrix Position: R05C01
Bisulfite-treated Genomic DNA
203723050101_R05C01

source_name: Laser Capture Microdissected STIC, Patient 6

tag: tissue type


title: STIC_Patient3

description:
Sentrix Position: R03C01
Bisulfite-treated Genomic DNA
203723050102_R03C01

source_name: Laser Capture Microdissected STIC, Patient 3

tag: patient age

value: Nonsense

value: APST


title: CA1a_Inp_H_r2_R1

status: Public on Jun 01 2020

city: TALLAHASSEE

first: LAUREN

last: COLE

state: Florida

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY

description: Heavy MNase digest

data_processing:
Basecalls performed with CAVASA version v1.8.4
Sequencing data aligned to the HG19 genome using bowtie2 version 2.2.2, --wrapper basic -0 --end-to-end -p 23 --no-mixed --no-discordant -I 0 -X 500 -q -x  -S
Using samtools via the R package gyro (https://github.com/dvera/gyro), raw files converted from sam to bam files, minQual=10
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated using bedtools via the R package travis (https://github.com/dvera/travis) and mat10 files were created using the package genmat (https://github.com/dvera/genmat). Nucleosome distributions were calculated by fragments per million for each bp in the 2kb surrounding each TSS.

source_name: Human breast epithelial cells, virally transformed

growth_protocol: MCF-10A and MCF-10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% Horse Serum, 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human EGF, 500 ng/mL Hydrocortisone and 100 ng/mL Cholera Toxin.

extract_protocol:
Nuclei were isolated in nucleus isolation buffer containing: 10 mM HEPES at pH 7.8, 2 mM MgOAc2, 0.3 M sucrose, 1 mM CaCl2, and 1% Nonidet P-40.  The nuclei were then pelleted by centrifugation at 1000g for 5 min at 4°C.
Using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), DNA sequencing libraries were prepared for the mononucleosomal-sized and sub-nucleosomal-sized fragments for each sample.  DNA was end-prepped using NEB Prep enzyme mix, end-repair reaction buffer (10X), and 30 ng of DNA for each samples, then held at 30 degrees Celsius for 30 minutes and then at 65 degrees Celsius for 30 minutes.  Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes. The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted ligated products. The universal and indexed sequences were added by PCR using 23 ul of adaptor-ligated DNA fragments, NEBNext High Fidelity 2X PCR Master Mix, index primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina, and Universal PCR Primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina. Then PCR was done for 8 cycles (not including the initial denaturation and final extension).  The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted products.  The libraries were quality-checked using Agilent 2100 Bioanalyzer High-Sensitivity. Across the libraries, the samples ranged between 200-400bp and there were no adapter or primer dimers.

treatment_protocol: For EMT induction, MCF-10A cells were treated with 5 ng/ml TGF-β1 (Redsystems) for 8 days. MCF-10A cells were transduced with the lentviral vector pLVTHM shH2A.Z as previously described (Domaschenz, 2017). GFP-positive cells were sorted 2 days post-transduction and further cultured for 8 days before being processed.

value: Human breast epithelial cells

tag: cell type

tag: treatment


title: CA1a_Inp_L_r2_R1

description: Light MNase digest


title: CA1a_H2AZ_L_r2_R1

description: Light MNase digest


title: CA1a_Inp_L_r1_R1

description: Light MNase digest


title: CA1a_H2AZ_H_r2_R1

description: Heavy MNase digest


title: CA1a_H2AZ_H_r1_R1

description: Heavy MNase digest


title: MT_RNAPII

status: Public on Sep 01 2019

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

data_processing:
Quality of sequencing was assed with FastQC v0.11.4 & adapters were removed by the sequencing facility.
Human hg19 and mouse mm10 from Illumina igenomes UCSC collection were used as reference genomes. Chip-seq data were aligned with Bowtie v1.0.0 allowing 3 mismatches and keeping uniquely aligned reads.
Sam ouputs were converted to Bam with Samtools v1.0.6 and sorted with Picard tools v1.88
Data were further processed with Pasha to obtain wiggle files that were converted to bigwigs.
Some chip-seq tracks were further spike-in normalized using drosophila dna.
Genome_build: Hg19, mm10 and dm3
Supplementary_files_format_and_content: bigwig

source_name: Myotube

growth_protocol: E14Tga2 (ATCC, CRL-1821) ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent).  For embryoid body differentiation, 600K mESCs were plated in suspension plates with medium containing DMEM (Life Technologies), 20% FBS, 1% NEAA, 1% Pen/Strep, 2 mM L-Glutamine, 100 mM Ascorbic acid (Sigma).  After 5 days, EB colonies were collected for downstream applications. Human myoblasts are seeded on gelatinized plates and grown in Ham’s F-10 media (Gibco/Thermo Fisher) supplemented with 15% fetal bovine serum (Atlanta Biologicals), 1mM sodium pyruvate (Sigma), 100ug/ml penicillin/streptomycin (Gibco/Thermo Fisher), 2.5ng/ml basic human fibroblast growth factor (Promega), 1X GlutaMax (Thermo Fisher) and 1uM Dexamethasone.  Once 90% confluent the myoblasts are differentiated to myotubes by changing the media to DMEM (Gibco/Thermo Fisher) supplemented with 2% Horse Serum (Hyclone) and 100ug/ml penicillin/streptomycin (Gibco/Thermo Fisher).  Differentiation proceeds for 6 days and the efficiency can be monitored with microscopy as myotubes are easily visually detected.

extract_protocol:
For ChIP-seq, nuclei was isolated from cells fixed with 1% Formaldehyde. Next, chromatin was fragmented into ~250bp.  Chromatin immunoprecipitation was performed with the indicated antibodies. For RNA-seq, total RNA was isolated with RNAeasy (Qiagen) and reverse transcribed using Superscript III and random hexamers (Life Technologies) to synthesize the 1st strand. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I (NEB, M0209L) and the E. coli ligase (Enzymatics, L6090L).
For ChIP-seq and RNA-seq, libraries were prepared by standard protocol. First, fragments are repaired to generate  blunt 5' P ends  using 'EndIT DNA End Repair kit' (Epicentre). Second, 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB). Third,  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Lastly, libraries were size selected using 'Ampure beads' (Beckman Coulter), then amplified, quantified and pooled.

value: Wild type

value: Myotube

tag: chip antibody

value: RNAPII, Santa Cruz, #sc-899


title: MT_LEDGF

value: LEDGF, Proteintech, #25504-1-AP


title: MB_RNAPII

source_name: Myoblast

value: Myoblast


title: MT_HDGF2

value: HDGF2, Proteintech, #15134-1-AP


title: MB_LEDGF


title: MB_SPT16

value: SPT16, Cell Signaling, #12191


title: MT_H3K36me3

value: H3K36me3, Abcam, #ab9050


title: MB_H3K36me2

value: H3K36me2, Cell Signaling, #2901


title: MB_H3K36me3


title: MB_HDGF2


title: MT_H3K36me2


title: MT_H3K27me3

value: H3K27me3, Cell Signaling, #9733


title: AdjacentNormal_Patient2

description:
Sentrix Position: R08C01
Bisulfite-treated Genomic DNA
203723050101_R08C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 2

value: FFPE tissue

tag: race

value: W

tag: gender

value: Female

tag: patient id

tag: p53 pattern

value: No

value: MMMT

value: c


title: MB_H3K27me3


title: AdjacentNormal_Patient1

description:
Sentrix Position: R04C01
Bisulfite-treated Genomic DNA
203723050101_R04C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 1

tag: tp53 mutation

tag: germline mutations

value: BRCA2 mutation (+)  c.26del (p.Pro9fs)

tag: concurrent hgsoc

tag: other tumors


title: STIC_Patient8

description:
Sentrix Position: R05C01
Bisulfite-treated Genomic DNA
203723050102_R05C01

source_name: Laser Capture Microdissected STIC, Patient 8

value: Serous Tubal Intraepithelial Carcinoma (STIC)

value: Nonsense

value: BRCA2 mutation (+)  c.1189_1190ins

value: Yes

tag: batch id


title: A_Inp_L_r2_R1

description: Light MNase digest

source_name: Human breast epithelial cells, immortalized

tag: tissue

value: Human breast epithelial cells


title: A_H2AZ_H_r2_R1

description: Heavy MNase digest


title: A_H2AZ_L_r2_R1

description: Light MNase digest


title: A_H2AZ_H_r1_R1

description: Heavy MNase digest


title: A_Inp_L_r1_R1

description: Light MNase digest


title: A_Inp_H_r1_R1

description: Heavy MNase digest


title: A_Inp_H_r2_R1

description: Heavy MNase digest


title: A_H2AZ_L_r1_R1

description: Light MNase digest


title: H3K36me3_2

tag: genotype

value: Wild type

value: 293-TRex cell line


title: H3K27me3_2


title: Flag-HDGF2

value: FLAG, Sigma, #A2220


title: SPT16

value: SPT16, Cell Signaling, #12191


title: H3K36me2

value: H3K36me2, Cell Signaling, #2901


title: Flag-LEDGF


title: C4T_10ng

description:
Sentrix Position: R07C01
Bisulfite-treated Genomic DNA
for protocol validation only
203282450180_R07C01

source_name: Laser Capture Microdissected Cancer Sample, 10ng

tag: uniqueid

tag: histology

value: FFPE tissue

value: v


title: Control-Input_ChIP-seq

status: Public on Feb 08 2019

city: Houston

first: Kunal

last: Rai

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -n 1 -m 1 --best --strata. These criteria preserved only the best reads that uniquely mapped to the genome with 1 or fewer mismatches. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare Control and UBR7-shRNA ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 0.1.19
Genome_build: hg19
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-7 to identify H2BK120ub enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Scaled bigWig files were then converted to bedGraph files using the bigWigToBedGraph tool.

source_name: MCF10A Cell Line

growth_protocol: MCF10A cells were maintained in DMEM / Ham’s F12 supplemented with 5% horse serum (Gibco), EGF, insulin, hydrocortisone, cholera toxin (Sigma) and 1% antibiotic-antimycotic.

extract_protocol:
Histone-DNA complexes were isolated using antibodies described from Control and UBR7-shRNA sonicated nuclei.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

treatment_protocol: shRNA plasmids for UBR7 with pLKO.1-puro backbone (Sigma Aldrich) were screened for efficient knock-down.Two out seven shRNAs were selected for subsequent experiments. Four micrograms of shRNA and packaging vectors were transfected as described previously (ref). Cells were selected using puromycin (10 μg / ml) (Sigma) for 3days.

tag: cell line

value: Human mammary epithelial cell line

tag: chip-antibody

value: none (input)


title: C4T_500ng

description:
Sentrix Position: R05C01
Bisulfite-treated Genomic DNA
for protocol validation only
203282450180_R05C01

tag: tissue type

tag: patient age

value: Female


title: Pol II

tag: chip antibody

value: RNAPII, Santa Cruz, #sc-899


title: ChIP_gH2AX_exp1_MCF10A

status: Public on Nov 28 2018

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

institute: University of Naples "FEDERICO II"

description: Normal growing MCF10A cells

data_processing:
Alignments were performed with BWA  to hg18 or mm9 using default parameters.
The 8-oxodG peaks were identified from uniquely mapped reads without duplicates using MACS and the p-value cutoff used for peak detection was 1e-5. The gH2AX peaks were identified from uniquely mapped reads without duplicates using SICER and FDR 0.01 was used as cutoff.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: SAMtools and BEDtools were used for filtering steps and file formats conversion.

source_name: normal breast cells

growth_protocol: MCF10A cells were cultured in 1:1 mixture DMEM-F12 supplemented with 5% horse serum, 10 µg/ml insulin, 0,5 µg/ml hydrocortisone, 100 ng/ml cholera enterotoxin, and 20 ng/ml epidermal growth factor, and incubated at 37°C in humidified atmosphere with 5% CO2. Mouse embryonic fibroblasts MEF (3T9-MycER) were grown in DMEM medium supplemented with 10% serum, penicillin/streptomycin and 2 mM L-Gln.

extract_protocol:
Genomic DNA from MCF10A cells or from growing MEFs was extracted by using Dneasy Blood&Tissue kit. Genomic DNA were sonicated and immunoprecipitated with antibodies anti 8-oxodG O/N. Eluted DNA was processed for library preparation. For ChIp_Seq anti gH2AX, lysates were clarified from sonicasted nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions

tag: cell type

value: normal breast cells

value: gH2AX (ab81299, Abcam)


title: ChIP_gH2AX_exp2_MCF10A

description: Normal growing MCF10A cells


title: Control-H3K9me3_ChIP-seq

value: H3K9me3 Abcam ab8898


title: FS2

status: Public on Dec 20 2018

city: Utrecht

first: Frans

last: Schutgens

address: Uppsalalaan 8

institute: Hubrecht Institute / UMC Utrecht

description: Kidney organoids 70 105 126

data_processing:
Paired-end reads from Illumina sequencing were aligned to the human transcriptome with BWA. Reads per gene were normalized to the number of total reads for that sample. Per gene, Z-scores were calculated and these were depicted in a heatmap
Genome_build: hg10
Supplementary_files_format_and_content: coutt files contain normalised abundance counts

source_name: Human kidney organoids

growth_protocol: From cortical kidney tissue, tubular fragments were isolated by collagenase digestion (C9407, Sigma) for 45 minutes at 1 mg/ml. Fragments were seeded in growth factor-reduced Matrigel (Corning) or Basement Membrane Extract (BME - R&D Systems) and cultured in medium (ADMEM / F12 supplemented with 1% penicillin / streptomycin, HEPES, Glutamax, N-acetylcysteine (1 mM, Sigma) and 1.5% B27 supplement (Gibco)), supplemented with 10% Rspo1-conditioned medium or 1% Rspo3-conditioned medium, the latter produced via the r-PEX protein expression platform (U-Protein Express), EGF (50 ng/ml, Peprotech), FGF-10 (100 ng/ml, Preprotech), Rho-kinase inhibitor Y-27632 (10 µM, Abmole) A8301 (5 µM, Tocris Bioscience), primocine (0.1 mg/ml, Invivogen).

extract_protocol:
Passage 3 or 4 organoid samples (n = 3; 200 ul of BME per sample) and matched cortical kidney tissue samples (n = 3) were harvested with TRIzol reagent (Life Technologies) and RNA was isolated according to manufacturer’s instructions. RNA samples were processed into cDNA libraries based on the CEL-seq2 technique as described previously.
Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75 bp read length the Illumina NextSeq. Tissue samples and organoids were processed and sequenced in parallel.

value: wild-type

value: Cultured kidney organoids


title: FS1

description: Kidney tissue 70 105 126

source_name: Human kidney tissue

value: Cortical kidney tissue


title: Participant 14

status: Public on Aug 31 2018

type: RNA

city: Washington

first: Matthew

last: Edwardson

state: DC

address: 4000 Reservoir Rd NW, Building D, Room 207

department: Neurology

institute: Georgetown University

description: SAMPLE 14

data_processing:
miRNA expression values were normalized with log transformation followed by quantile normalization
normalized file reports normalized signal (against housekeeping genes)
Fold change file reports good vs. poor recovery ratios

label: FAM

source_name: Plasma

label_protocol: RT performed using 33ng total RNA  with Applied Biosystems Megaplex RT Primers, Human Pool A and B v3.0, followed by 12 cycles preamplification.  cDNAs loaded onto Taqman Array Human MicroRNA A+B Cards, v3.0, Applied Biosystems.  qRT-PCR performed on 7900HT rtPCR System (Applied Biosystems)

extract_protocol: Total RNA extracted from 200uL plasma using Qiagen miRNeasy Serum/Plasma Kit

tag: recovery

value: Good

value: plasma

tag: delta-arat

tag: days post-stroke

tag: age

tag: gender

value: F

tag: ischemic or hemorrhagic stroke

value: Hemorrhagic


title: Participant 21

description: SAMPLE 21

value: Ischemic


title: Participant 23

description: SAMPLE 23

value: M


title: Participant 11

description: SAMPLE 11


title: Participant 15

description: SAMPLE 15


title: Participant 25

description: SAMPLE 25

value: Poor


title: Participant 12

description: SAMPLE 12


title: Participant 20

description: SAMPLE 20


title: Participant 19

description: SAMPLE 19


title: Participant 13

description: SAMPLE 13


title: Participant 17

description: SAMPLE 17


title: Participant 16

description: SAMPLE 16


title: Participant 24

description: SAMPLE 24


title: Participant 26

description: SAMPLE 26


title: Participant 18

description: SAMPLE 18


title: Participant 27

description: SAMPLE 27


title: Participant 22

description: SAMPLE 22


title: Participant 10

description: SAMPLE 10


title: Participant 8

description: SAMPLE 8


title: Participant 6

description: SAMPLE 6


title: Participant 7

description: SAMPLE 7


title: Participant 5

description: SAMPLE 5


title: CA1a_H2AZ_L_r1_R1

description: Light MNase digest

value: Human breast epithelial cells

tag: treatment


title: Participant 4

description: SAMPLE 4

tag: tissue


title: Participant 9

description: SAMPLE 9


title: AdjacentNormal_Patient5

description:
Sentrix Position: R02C01
Bisulfite-treated Genomic DNA
203723050101_R02C01

source_name: Laser Capture Microdissected Adjacent Normal Fallopian Tube Epithelia, Patient 5

value: FFPE tissue

value: unknown

tag: race

value: W

tag: patient id

tag: p53 pattern

tag: tp53 mutation

tag: germline mutations

tag: concurrent hgsoc

value: No

tag: other tumors

tag: batch id

value: c


title: Participant 3

description: SAMPLE 3


title: STIC_Patient5

description:
Sentrix Position: R01C01
Bisulfite-treated Genomic DNA
203723050101_R01C01

source_name: Laser Capture Microdissected STIC, Patient 5

tag: uniqueid

tag: histology

value: Serous Tubal Intraepithelial Carcinoma (STIC)

tag: tissue type

tag: patient age

value: Female


title: Participant 1

description: SAMPLE 1

tag: recovery

tag: delta-arat

tag: days post-stroke

tag: age


title: Participant 2

description: SAMPLE 2

tag: tissue

tag: gender

tag: ischemic or hemorrhagic stroke


title: CA1a_Inp_H_r1_R1

description: Heavy MNase digest

tag: cell type

tag: treatment


title: SON TSA-Seq Condition 2 (TSA+Sucrose) Replicate

status: Public on Apr 25 2018

city: Urbana

first: Andrew

middle: S

last: Belmont

state: IL

address: 601 S Goodwin Ave, CLSL B509

institute: University of Illinois at Urbana-Champaign

description:
Sample 10
processed data file: SON_TSA-Seq_Score_Condition2.Replicate.bw

data_processing:
Library strategy: TSA-Seq
The raw .bcl files were converted into demultiplexed compressed fastq files using the bcl2fastq v1.8.2 and later v2.17.1.14 conversion software (Illumina).
Raw sequencing reads were first mapped to the human genome (UCSC hg19) using Bowtie 2 version 2.0.2 with default parameters. Chromosome Y was excluded in the reference genome to reduce mapping bias since the K562 cell line was derived from a female.
PCR duplicates reads were removed using samtools version 0.1.19 with default parameters.
We normalized and processed the TSA-Seq data using a sliding window approach as follows. The normalized SON-TSA score was calculated as the log 2 ratio of  (TSA-Seq pulldown reads in a 20 kb window divided by total mapped reads for this pulldown sample) / (input reads in the same 20 kb window divided by total mapped reads for this input). This approach can be interpreted as the fold change between the pulldown sample and the input corrected by the total number of mapped reads in each sample. The window slides on the genome with a step size of 100 bp.
We partitioned the genome into non-overlapping 20 kb bins, averaging the TSA-Seq score over the 100 bp intervals within this bin for the new TSA-Seq 20 kb score.  The values for these 20 kb bins were then smoothed by convolution using a Hanning window of length 21 (21 x 20 kb or 420 kb).  This new smoothed TSA-Seq score with 20 kb sampling was used for SON TSA-Seq decile calculations and comparisons with other genome features
Genome_build: hg19
Supplementary_files_format_and_content: normalized TSA signals were in bigWig format, and the 10 deciles are in BED format. Other data files from analyzing public datasets are in bigWig or bigBed formats.

source_name: bone marrow

growth_protocol: K562 Cells were grown according to the ENCODE protocol, in RPMI with 10% FBS (Sigma-Aldrich) and Antibiotic-antimycotic (GIBCO) at density of 0.4 x 10^6-0.75 x 10^6 /ml

extract_protocol:
Cell lysis and protease digestion were done at 55°C with constant mixing in 10mM Tris, 10mM EDTA, 0.5% SDS and 500µg/ml proteinase K (NEB) for 8-12 hrs (10^7 cells/ml).  NaCl was added for a final 0.2 M concentration and the lysate incubated 20-24 hrs at 65°C with constant mixing to reverse formaldehyde crosslinking.  DNA was extracted 2x using an equal volume of phenol (Fisher)/chloroform/isoamyl alcohol (25:24:1) and 1x with an equal volume of chloroform/isoamyl alcohol (24:1).  Tubes were kept at 55°C for 1h with the cap off to evaporate phenol residues, and then treated with 25 µg/ml RNaseA (Qiagen) at 37o C for 1hr and extracted again.  DNA was then precipitated with 1/10 volume of 3M Na Acetate, pH 5.2, and 2 volumes of 100% EtOH at -20 oC for 20 min – 2 hrs.
For each of the TSA-Seq experiment staining conditions, input and Streptavidin pull-down DNA were used to make sequencing libraries, using the Kapa Hyper Prep Kit (Kapa Biosystems).  DNA was blunt-ended, 3’-end A-tailed, and ligated to indexed adaptors with 6nt barcodes. PCR amplification selectively enriched for those fragments with adapters on both ends. Amplification was carried out for 8-15 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA).  An Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) was used to determine library fragment sizes.  Library fragment concentrations were measured by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.

treatment_protocol: TSA labeling was done in independent cell batches.  For each batch, cells were divided equally and stained according to four labeling protocols: “Condition 1”, “Condition 2”, “Condition 3”, and “No 1o control”.  Identical staining conditions were used except that 50% sucrose was included in the TSA staining buffer for the “Condition 2” protocol, 0.75mM DTT in addition to 50% sucrose was added in the TSA staining buffer for the “Condition 3” protocol, and the anti-SON primary antibody was omitted for the “No 1o control” protocol.  Cells were fixed by adding 10 ml of 8% paraformaldehyde (Sigma-Aldrich) freshly prepared in CMF-PBS (calcium, magnesium-free phosphate buffered saline) to 40 ml of cells in culture media, incubating for 20 min at room temperature (RT), and quenching aldehydes by addition of 5.6 ml of 1.25 M glycine (Fisher Scientific) and incubation for 5 min at RT.  All incubation steps used a rotating platform to mix the cell suspension.  Cells were then pelleted by centrifugation and resuspended in CMF-PBS buffer with 0.5% Triton-X100 (Sigma-Aldrich) for 30 min at RT.  All centrifugations were for 5 min at 100-200g.  Cells were centrifuged at RT and resuspended in 1.5% H2O2 (Fisher Scientific) in CMF-PBS for 1h at RT to quench endogenous peroxidases, followed by 3 washes at RT in PBST (0.1%Triton-X100/CMF-PBS) by repeated centrifugation and cell pellet resuspension.  Cells were resuspended in IgG Blocking Buffer (5% Normal Goat Serum (Sigma-Aldrich) in PBST) at a concentration of 10^7 cells/ml for 1 hr, followed by centrifugation and resuspension in primary antibody solution (Rabbit-anti-SON primary antibodies (Ab1, Atlas antibodies cat # HPA023535) diluted 1:1000 or 1:2000 in IgG Blocking buffer, or rabbit polyclonal-anti-SON primary antibodies (Ab2) diluted 1:2000 in IgG Blocking buffer, or mouse-anti-phosphorylated SC35 primary antibodies (Sigma-Aldrich cat # S4045) diluted 1:500 in IgG Blocking buffer, or mouse monoclonal anti-lamin A/C primary antibody (Clone 5G4) diluted 1:1000 in IgG Blocking buffer, or mouse monoclonal anti-lamin B primary antibodies (Clone 2D8) diluted 1:1000 in IgG Blocking buffer) at 10^7 cells/ml, or mouse monoclonal anti-RNA polymerase II primary antibodies (clone 4H8) (Millipore cat # 05-623) at 0.5 x 107 cells/ml and incubated 20-24 hrs at 4°C (See METHODS for more information about anti-lamin antibodies). For the no primary control, cells were incubated in IgG Blocking buffer only.  Cells were then washed 3x with PBST, resuspended in IgG Blocking buffer with secondary antibodies at 10^7 cells/ml, and incubated 20-24 hrs at 4°C.  Secondary antibodies (Jackson, ImmunoResearch) used were HRP conjugated, goat-anti-rabbit secondary antibody diluted 1:1000 or HRP conjugated goat-anti-mouse secondary antibody diluted 1:200 or 1:1000. Cells then were washed 3x in PBST and resuspended in reaction buffer A (CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Condition 2, or CMF-PBS with 50% sucrose and 1.5mM DTT for Condition 3) at 2 x 10^7 cells/ml.  Equal volumes of buffer B (8mM tyramide-biotin stock solution diluted 1:5000 with 0.003% H2O2 in CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Conditions 2 and 3) were then added.  Cells were incubated for 10 min and then washed 3x in PBST at RT.  Validation of TSA labeling is done by biotin immunostaining.

tag: cell line

tag: disease

value: chronic myelogenous leukemia (CML)

tag: tsa-seq target

value: SON

tag: primary antibody

value: anti-SON primary antibody (Atlas antibodies, catalog# HPA023535)


title: Lamin B TSA-Seq Condition 2 (TSA+Sucrose)

description:
Sample 18
processed data file: LaminB_TSA-Seq_Score_Condition2.bw

value: Lamin B

value: anti-lamin B monoclonal primary antibodies (Clone 2D8)


title: Lamin A/C TSA-Seq Condition 2 (TSA+Sucrose)

description:
Sample 16
processed data file: LaminAC_TSA-Seq_Score_Condition2.bw

value: Lamin A/C

value: anti-lamin A/C monoclonal primary antibody (Clone 5G4)


title: SON TSA-Seq Condition 3 (TSA+Sucrose+DTT)

description:
Sample 12
processed data file: SON_TSA-Seq_Score_Condition3.bw
processed data file: Speckle_distance_Condition3.bw


title: SON TSA-Seq Condition 1 (TSA only)

description:
Sample 3
processed data file: SON_TSA-Seq_Score_Condition1.bw
processed data file: Speckle_distance_Condition1.bw


title: SON TSA-Seq Condition 2 (TSA+Sucrose)

description:
Sample 6
processed data file: SON_TSA-Seq_Score_Condition2.bw
processed data file: hg19F_Sucrose_v_input_10_deciles_WithColor.bed
processed data file: Speckle_distance_Condition2.bw


title: No Primary Control_for_SON TSA-Seq

description:
Sample 1
processed data file: NoPrimaryCtrl_for_SON_TSA-Seq.bw

value: none (No Primary Control)


title: SON TSA-Seq Condition 1 (TSA only) Second pull down

description:
Sample 4
processed data file: SON_TSA-Seq_Score_Condition1_Replicate_2nd_pulldown.bw


title: MCF10A_H3K27me3_ChIP

status: Public on Feb 01 2018

city: Cambridge

first: Dexter

middle: X

last: Jin

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: Chromatin IP against H3K27me3

data_processing:
ChIP-Seq reads were aligned to the human genome (hg38) using Bowtie2 (version 2.3.1).
ChIP-Seq peaks were called using MACS2 (version 2.1.1) with input DNA from matching cells as a control. narrowPeak settings were used for H3K27me3, broadPeak settings were used for H3K4me3 and H3K79me2.
Genome_build: hg38
Supplementary_files_format_and_content: Peak files are provided as .BED files

source_name: Chromatin IP against H3K27me3

growth_protocol: All cells were grown in MEGM supplemented with cholera toxin (100 ng/ml)

extract_protocol:
Nuclei were sonicated to retrieve lysates and protein-DNA complexes were isolated with antibody.
To make libraries, TruSeq protocol was followed

tag: chip antibody

value: H3K27me3 (Abcam, Ab6002)


title: MCF10A_H3K79me2_ChIP

description: Chromatin IP against H3K79me2

source_name: Chromatin IP against H3K79me2


title: SON TSA-Seq Condition 1 (TSA only) Replicate

description:
Sample 8
processed data file: SON_TSA-Seq_Score_Condition1_Replicate.bw


title: MCF10A_H3K4me3_ChIP

description: Chromatin IP against H3K4me3

source_name: Chromatin IP against H3K4me3

value: H3K4me3 (Millipore, #07-473)


title: indivi_72h_rep2

status: Public on Jun 01 2018

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: RNAseq on whole gastruloid collected 72h AA

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10). using TopHat release 2.0.9 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and BedTools (Quinlan, 2014) to extract the unique read coverage along the genome. For visualisation and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the RNAseq read coverage, divided by the number of millions of mapped reads in each sample.

source_name: single gastruloid

growth_protocol: mESCs were cultured on gelatinised tissue-culture flasks in a humidified incubator (5% CO2, 37°C). mESCs were cultured in GMEM supplemented with 10% foetal bovine serum (FBS), non-essential amino acids (NEAA), sodium pyruvate, GlutaMax, beta-mercaptoethanol and LIF (ESL).

extract_protocol:
For RNAseq of individual gastruloids, 10 from each stage (24h, 72h and 120h AA) were individually collected and transferred to 1.5ml Eppendorf tube. After centrifugation, gastruloids were washed once with cold PBS, re-suspended in lysis buffer, and RNA extracted immediately using the RNAeasy micro kit (Qiagen) with on column DNAase digestion. RNA was quantified with the Qubit HS RNA quantification kit (Thermo fisher) and the integrity assessed with bioanalyser.
For each of the replicates of the 24h AA gastruloids, a total of 0.65ng RNA were used for the library preparation while 8ng total RNA from 72h and 120h AA were used for the RNA sequencing. Libraries were prepared using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: mESCs were harvested from tissue-culture flasks, centrifuged and washed twice with warm PBS (containing Ca2+ and Mg2+). After the final wash, cells were re-suspended in a volume (~3-4ml) of fresh, warm N2B27 (NDiff) and the cell concentration determined. The number of cells required to form gastruloids with a diameter at 48h of ~150µm (~300 cells) was determined and seeded in each well of a round-bottomed, low-adherence 96-well plate as 40µl droplets of N2B27. A 24h pulse of 150µl 3µM Chi was added at 48h after aggregation (AA). Medium (150µl) was replaced with the same volume of fresh N2B27 daily.

tag: strain

value: Whole gastruloid

tag: genotype


title: indivi_72h_rep8


title: indivi_72h_rep7


title: indivi_72h_rep1


title: indivi_72h_rep9


title: indivi_72h_rep3


title: indivi_72h_rep5


title: MCF10A_input_DNA

description: Input DNA

source_name: Input DNA


title: MCF10A.H3K9ac.rep2

status: Public on Dec 15 2017

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2.
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6; Scores represent the ChIP-seq tag numbers.

source_name: MCF10A cells, H3K9ac ChIP

growth_protocol: Cells were plated and expanded on 150mm plates until a minimum of 3.5 x 10^5 cells per plate were reached. The media conditions and split ratio for each cell line is depicted in the Excel sheet entitled “Cell line conditions”. Media is replaced every other day, until the desired confluency is reached.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells are harvested from the 150mm plates under sterile conditions into a 50ml conical tube. Aliquots of 100-200ul of this stock are then counted using the Biorad Cell Counter. Counts are repeated three times and the number of cells per ml are then determined. For growth curves, the schema in the Powerpoint entitled “Growthcurveprotocol” is followed. Briefly, 500-5000 cells (for each cell line) were plated onto each well of a 96-well plate on day 0. For each cell line, a total of 7 replicate plates were seeded. The media was changed every other day (days 1, 3, 5, 7, 9, 11, and 13). One plate from each cell line was subjected to MTT proliferation assay every other day (days 1, 3, 5, 7, 9, 11, and 13).

value: Breast cancer cell line

value: Control


title: MCF10A.H3K9ac.rep1


title: indivi_72h_rep6


title: MCF10A.Input.rep2

source_name: MCF10A cells, input


title: indivi_72h_rep4


title: indivi_72h_rep10


title: MCF10AT1 Input

status: Public on May 23 2017

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description: ChIP DNA

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim 10bp from 5'end. (FASTQ Trimmer 1.0.0)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
The reads were aligned to hg38 canonical with STAR (–alignIntronMax 1; v2.4)
Peak calls with MACS2 on individual biological replicates to establish 0.05 IDR cutoff for peak call on pooled samples.
bdgcmp -m FE on MACS2 input and treatment .bdg files; convert to bigwig.
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak - MACS2 narrowPeak calls on pooled biological replicates at pval 1e-5 and then 0.05 IDR filtered
Supplementary_files_format_and_content: .bigwig - FE enrichment over input tracks

source_name: mammary gland/breast epithelial cell

growth_protocol: MCF10A and MCF10AT1 cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF10CA1a cells were grown in DMEM: F12 (Hyclone-SH30271) + 5% (v/v) horse serum (Gibco #16050) +Pen/Strep (Life Technologies)and Glutamine (Life Technologies)  .

extract_protocol:
DNA was extracted in cell lysis buffer (5mM PIPES pH8, 85mM KCL, 1% IGEPAL, protease inhbitors) on ice for 15 minutes, dounce homogenized 20x, and nuclear lysis buffer (50mM Tris-Cl pH8.1, 10mM EDTA, 1%SDS,  protease inhibitors) on ice for 30 minutes, and sonicated 12-14 minutes (140W, 10DF, 200c/b).  Samples were diluted  in RIPA and IP was carried out overnight at 4oC using the recommended antibody concentrations on 150ug of chromatin. Magnetic protein A/G beads were washed and added for an additional 4 hours. Beads were collected and washed 2x with RIPA minus protease inhibitors, and once with a second IP wash buffer (100mM Tris pH9, 500mM LiCl, 1% IGEPAL, 1% deoxycholic acid). Next the DNA was eluted using 50mM NaHCO3, 1%SDS 2 times 30 minutes on a shaker. Formaldehyde crosslinks were reversed using elution buffer plus .6M NaCl overnight at 67oC.
ChIPseq libraries were prepared for sequencing using standard Illumina protocols using the TruSeq ChIP kit (Illumina #IP-202-1012)
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1x106 cells per 100 mm dish and grown to 80-90% confluence. Cells were washed twice with phosphate buffered saline (PBS), fixed with 1% methanol free formaldehyde, glycine neutralized on ice for 5 minutes, and pellets were stored at -80C.

value: breast

value: basal, pre-metastatic

tag: neoplasia type

value: hyperplastic

tag: atcc id


title: MCF10CA1a Input

description: ChIP DNA

value: basal, metastatic

value: tumorigenic


title: MCF10CA1a CTCF ChIPseq Rep1

description:
ChIP DNA
MCF10CA1_CTCF_pooled_FE.bw
MCF10CA1_CTCF_pooled_peaks_passIDR.05.narrowPeak


title: MCF10A Input

description: ChIP DNA

value: basal epithelial, non-tumorigenic

value: fibrocystic disease

value: ATCC CRL-10317


title: MCF10CA1a CTCF ChIPseq Rep2


title: MCF10AT1 CTCF ChIPseq Rep1

description:
ChIP DNA
MCF10AT1_CTCF_pooled_FE.bw
MCF10AT1_CTCF_pooled_peaks_passIDR.05.narrowPeak


title: MCF10AT1 CTCF ChIPseq Rep2


title: MCF10A CTCF ChIPseq Rep1

description:
ChIP DNA
MCF10A_CTCF_pooled_FE.bw
MCF10A_CTCF_pooled_peaks_passIDR.05.narrowPeak


title: MCF10A CTCF ChIPseq Rep2


title: MCF10A.Input.rep1


title: Sox10 rep1 input

status: Public on Apr 01 2012

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing: Basecalling was performed using the standard Illumina Pipeline.  Reads were mapped to the Rattus norvegicus genome (Rn4) using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) to produce SAM files for further analysis. Peak finding was performed using the R package MOSAiCS (31) controlling the false discovery rate at 0.05. MOSAiCS implements a model-based approach where the background distribution for unbound regions take into account systematic biases such as mappability and GC content and the peak regions are described with a two component Negative Binomial mixture model. MOSAiCS is available at www.bioconductor.org/packages/2.8/bioc/vignettes/mosaics/inst/doc/mosaics-example.pdf.

organism: Rattus norvegicus

source_name: sciatic nerve at P15

extract_protocol: ChIP samples ranging in total quantity from 1.3ng (Egr2) - 6.8ng (Sox10), along with 10ng of input controls, were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation.   All libraries were generated using reagents from either the Illumina Paired End Sample Preparation Kit (Illumina Inc., San Diego, CA, USA) or the NEBNext® DNA Sample Prep Reagent Set 1 (New England Biolabs, Ipswitch, MA, USA) and the Illumina protocol "Preparing Samples for ChIP Sequencing of DNA" (Illumina part # 11257047 RevA) as per the manufacturer's instructions but with the following modification: products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen, Carlsbad, California, USA) targeting either 275bp fragments (Egr2) or 200-400bp fragments (Sox10, Sox10 input).  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent Technologies, Santa Clara, CA, USA) and QuantIT PicoGreen dsDNA Kit (Invitrogen, Carlsbad, California, USA), respectively, and libraries were standardized to 10 micromolar.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  A single read, 36 bp run was performed, using standard 36 bp SBS kits (v4) and either SCS 2.6 or 2.8 software on an Illumina Genome Analyzer IIx.

treatment_protocol: ChIP assays were performed on pooled sciatic nerves from Sprague-Dawley rat pups at postnatal day 15 as previously described (Jang et al., 2006) except that for the EGR2 ChIP, immunoprecipitation was carried out using Dynabeads® Protein AG Mix (Invitrogen) in lysis buffer containing 1% TritonX-100 instead of 0.3% TritonX-100. Herring sperm DNA was omitted from the blocking procedure. The antibodies used in this study include SOX10 (Santa Cruz Biotechnology, sc-17342x), and EGR2 (Abcam).

value: Schwann cells

value: Spague-Dawley


title: STIC_Patient1

description:
Sentrix Position: R03C01
Bisulfite-treated Genomic DNA
203723050101_R03C01

source_name: Laser Capture Microdissected STIC, Patient 1

tag: uniqueid

tag: histology

value: Serous Tubal Intraepithelial Carcinoma (STIC)

tag: tissue type

value: FFPE tissue

tag: patient age

tag: race

value: W

value: Female

tag: patient id

tag: p53 pattern

value: Nonsense

tag: tp53 mutation

tag: germline mutations

value: BRCA2 mutation (+)  c.26del (p.Pro9fs)

tag: concurrent hgsoc

value: No

tag: other tumors

tag: batch id

value: c