title: CEMBA181220_5F_4_CEMBA181220_5F_5_H4_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_H4_ad004

status: Public on Sep 28 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACB

tag: Sex

value: male

tag: age

tag: strain


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title: CEMBA181220_5F_4_CEMBA181220_5F_5_E6_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E9_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E6_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E6_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E5_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E5_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E6_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E5_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E6_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E8_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E6_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E8_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E3_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E12_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E2_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E10_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E10_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E10_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E10_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E11_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D9_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E10_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D9_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D9_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D9_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D9_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E10_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E1_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D9_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D8_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_E10_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D5_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D5_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D5_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D5_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D5_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D5_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D6_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D4_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D7_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D4_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D5_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D4_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D4_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D4_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D4_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D3_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D4_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D11_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D12_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D1_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D1_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D1_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D1_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D1_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C9_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D1_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D10_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C8_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C9_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C8_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C8_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C8_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C8_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C9_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C8_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C9_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C7_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C7_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C7_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_D1_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C9_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C9_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C7_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C7_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C8_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C7_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C7_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C5_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C5_ad004


title: Venus_negative_mouse_#3

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR
Genome wide transcript counting was performed by HTSeq or featureCounts to generate FPKM matrix
Differential expression analysis was performed with DESeq2 package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Raw count value for each sample

molecule: total RNA

source_name: Isolated mouse hepatocytes

growth_protocol: Notch-Venus reporter mice were kept on NASH diet for 16 weeks, and subjected to hepatocyte isolation and FACS based on Venus signals.

extract_protocol:
RNA was extracted using the NucleoSpin RNA (Clontech) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

tag: notch-venus signal

value: Venus-negative

tag: mouse

value: Mouse #3

tag: cell type

value: Isolated mouse hepatocytes


title: Venus_positive_mouse_#1

value: Venus-positive

value: Mouse #1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C5_ad010


title: Venus_positive_mouse_#2

value: Mouse #2


title: Venus_negative_mouse_#2


title: Venus_positive_mouse_#3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad008


title: Tumor_mouse_#2

source_name: Dissected mouse tissue

growth_protocol: L-NICD mice were kept on NASH diet for 16 weeks, and sacrificed for liver tissue harvest to separate surrounding non-tumor livers and tumors.

extract_protocol:
RNA was extracted using Trizol (ThermoFisher) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

tag: tissue

value: Tumor

value: L-NICD Mouse #2


title: Tumor_mouse_#3

value: L-NICD Mouse #3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C5_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C5_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C5_ad008


title: Tumor_mouse_#1

value: L-NICD Mouse #1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C4_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C6_ad010


title: Non-tumor_mouse_#3

value: surrounding non-tumor liver


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C4_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C5_ad001


title: Non-tumor_mouse_#2


title: Venus_negative_mouse_#1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C4_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C4_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C4_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C4_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad012


title: E2APBX1_murine_leukemia_BAHCC1_WT_rep#2

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: BCBP

institute: UNC Lineberger Comprehensive Cancer Center

data_processing:
RNA-seq reads were mapped to onto the reference mouse genome (mm9) using MapSplice and quantified using RSEM.
Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: mm9

source_name: E2a-Pbx1-transformed, Bahcc1-WT murine leukemia cells

growth_protocol: The E2a-Pbx1-transformed murine acute leukemia cell lines are cultured in the Opti-MEM medium supplemented with 15% FBS (Invitrogen, 16000-044), 1% antibiotics, 50 μM β-mercaptoethanol, 10 ng/mL murine SCF (PeproTech, 250-03) and 5 ng/ml murine Flt3 ligand (Sigma, SRP3198)

extract_protocol:
For RNA-seq, total RNAs were extracted using RNeasy Plus kit (Qiagen, 74136) and residual DNAs were removed using Turbo DNA-free kit (Thermo Fisher, AM1907) to ensure the purity of RNA sample.
RNA libraries were made with standard Illumina protocols or prepared by Novogene Inc.

treatment_protocol: For RNA-seq, the freshly growing cells are collected for total RNA extraction.

tag: treatment condition

value: E2a-Pbx1 transgene into Bahcc1 WT cells


title: E2APBX1_murine_leukemia_BAHCC1_BAH_mutant_rep#1

source_name: E2a-Pbx1-transformed, Bahcc1-Y2537A-mutated murine leukemia cells

value: E2a-Pbx1 transgene into Bahcc1 Y2537A knockin cells


title: E2APBX1_murine_leukemia_BAHCC1_WT_rep#1


title: E2APBX1_murine_leukemia_BAHCC1_BAH_mutant_rep#2


title: E2APBX1_murine_leukemia_WT_input

data_processing:
ChIP-seq reads were aligned to mouse genome build mm9 using STAR version 2.7.1a  (mismatches are extended and low quality sequences are trimmed at this step). Non-primary alignment and PCR duplicates were then removed by samtools.  Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools. Genomic binding profiles were generated using the deepTools “bamCompare” functions with options [--operation ratio ---pseudocount 1 -binSize 10 --extendReads 250] and normalized to the matched input.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
Genome_build: mm9

source_name: HSPCs

growth_protocol: The E2A-PBX1-transformed murine acute leukemia cell lines are cultured in the Opti-MEM medium supplemented with 15% of FBS (Invitrogen, 16000-044), 1% antibiotics, 50 μM of β-mercaptoethanol, 10 ng/mL of murine SCF (PeproTech, 250-03) and 5 of ng/ml murine Flt3 ligand (Sigma, SRP3198)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies against H3K27me3.
Libraries were prepared by High-Throughput Sequencing Facility (HTSF) at UNC at Chapel Hill.

treatment_protocol: For ChIP-seq experiments, cells were collected, followed by cell fixation with 1% of formaldehyde, sonication, antibody enrichment, ChIP DNA recovery, library preparation, and subsequent deep sequencing.

value: Mouse hematopoietic stem and progenitor cells (HSPCs)

value: Isolated from WT Bahcc1 mouse and transduced by E2A-Pbx1 retroviruses

tag: chip antbody

value: n/a (input)


title: E2APBX1_murine_leukemia_H3K27me3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C4_ad008

value: ACB

value: male


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad007


title: PD6SE6 = Screen Replicate 3, GFP-negative

city: Clayton

first: Partha

last: Das

state: VIC

address: 15 innovation walk

country: Australia

institute: Monash Biomedicine Discovery Institute, Monash University

description: RE CRISPR-Cas9 pool screen

data_processing:
The obtained deep sequencing data in .FASTQ format was inspected first by FASTQC. Next, reads were trimmed for adaptors using Trimmomatic. The resulting fastq files were used to identiy sgRNAs in the particular cell populations (GFP-low and pre-sort).
Genome_build: mm9

source_name: mouse embryonic stem cell

growth_protocol: Mouse ESCs (mESCs) were cultured in mouse ESC media that contains DMEM, supplemented with 15% fetal calf serum, 0.1mM b-mercaptoethanol, 2mM L-glutamine, 0.1mM NEAA, 1% of nucleoside mix , 1000 U/ml LIF/ESGRO, and 50U/ml Penicillin/Streptomycin. mESCs were cultured at 37ºC, 5% CO2.

extract_protocol:
Genomic DNA was isolated using Qiagen Blood/Tissue DNeasy kit
PCR amplification was performed using Nextera primers (Illumina) to make the libraries for deep sequencing

treatment_protocol: mESCs were harvested, washed with 1X PBS- twice at 4C, followed by genomic DNA isolation

tag: cell line

value: Oct4-GFP reporter+Cas9

tag: genotype

value: Wild-type

value: mouse embryonic stem cell


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad004


title: Interphase_F1.1

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Paired-eend reads were align to Mouse (mm10) and S.pombe (ASM294v2.20) refernece genome with bwa;
Aligned reads were analysis use hicexplorer, and generated 40K bin size matrix;
Genome_build: Mouse (mm10) + S.pombe (ASM294v2.20)
Supplementary_files_format_and_content: h5 format Hi-C matrix were generated by hicCorrectMatrix

source_name: interphase cells

growth_protocol: F1.1 cells were synchronised for mitotic Hi-C by a thymidine block. Cells were arrested for 18 hours by the addition of 2mM thymidine and collected by mitotic shake off 5 and then 8 hours after release. Cells were fixed in 1% PFA and collected as for ChIP

extract_protocol:
Hi-C experiment were conducted using HindIII (Naumova et al. 2013).
Hi-C libraries prepared as previously described (Naumova et al. 2013).

value: mouse mammary tumour


title: PD5SE5 = Screen Replicate 3, Pre-Sort

description: RE CRISPR-Cas9 pool screen


title: PD4SE4 = Screen Replicate 2, GFP-negative

description: RE CRISPR-Cas9 pool screen


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad012


title: PD3SE3 = Screen Replicate 2, Pre-Sort

description: RE CRISPR-Cas9 pool screen


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C3_ad008


title: PD1SE1 = Screen Replicate 1, Pre-Sort

description: RE CRISPR-Cas9 pool screen


title: PD2SE2 = Screen Replicate 1, GFP-negative

description: RE CRISPR-Cas9 pool screen


title: Non-tumor_mouse_#1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad001


title: WT_oct4_96hr_ATACseq

description: ATAC-seq

data_processing:
The obtained deep sequencing data in .FASTQ format was inspected first by FASTQC. Next, reads were trimmed for adapters using Trimmomatic (Bolger et al. 2014). The resulting fastq files were aligned with Bowtie2 (Langmead and Salzberg 2012) with the following options  --local -X 2000. Peaks were called with MACS2 (Zhang et al. 2008) with the following options callpeak --gsize mm --nomodel --shift -100 --extsize 200 --call-summit.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

extract_protocol:
DNA was purified using Qiagen MinElute PCR purification kit, and eluted in nuclease-free water
PCR amplification was performed using Nextera primers (Illumina) to make the libraries for deep sequencing

treatment_protocol: mESCs were harvested, washed with 1X PBS- twice at 4C, followed by lysis, and transposition with Tn5


title: WT_J1_ATACseq

description: raw data not available for this sample


title: Mitotic_F1.1

source_name: mitotic cells


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad006


title: WT_oct4_8hr_ATACseq

description: ATAC-seq


title: WT_oct4_24hr_ATACseq

description: ATAC-seq


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad012


title: Mef treated with DOX, UNC & C3 replicate 2

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

data_processing:
RNA-seq raw sequencing data were aligned to mouse genome version mm10 with the tophat algorithm (version 2.1.0) and the use of «--b2-very-sensitive» parameter.
Samtools (version 1.8) was used for data filtering and file format conversion.
Aligned reads were assigned into exons with the use of HT-seq count (version 0.5.4p3) algorithm and the following parameters «-m intersection -nonempty».
Differentially expressed genes were identified with the use of DESeq R package (R.3.4.4)
Genome_build: mm10
Supplementary_files_format_and_content: RawCounts.csv : Tab-delimited text file with raw counts per gene

source_name: Mef cells treated with DOX, L-ascorbic acid, CHIR99021 and iALK5 and UNC

growth_protocol: MEF cultures were established by trypsin digestion of midgestation (embryonic day (E) 13.5–E15.5) embryos and maintained in DMEM supplemented with 10% FBS, L-glutamine, penicillin/streptomycin, nonessential amino acids and β-mercaptoethanol. Reprogrammable MEFs were heterozygous Rosa26-rtTA and for Oct4-GFP and either heterozygous for a DOX-inducible OKSM allele (Stadtfeld et al., 2010b) or homozygous for an inducible OKS allele.

extract_protocol:
Total RNA was extracted from cells with the RNeasy Plus Kit (Qiagen).
Total RNA with RIN values > 8 were subjected to Automated TruSeq stranded total RNA with RiboZero Gold library preparation (Illumina).

treatment_protocol: Reprogramming was carried out as previously described (Vidal et al., 2014). Briefly, 250 cells/cm2 were seeded on a layer of irradiated feeder cells in ESC medium in the presence of 1 ug/ml Dox and, if applicable, L-ascorbic acid (50 μg/ml), CHIR99021 (3 μM) and TGF-b RI Kinase Inhibitor II (250 nM) (“3c”). If applicable, UNC0638 (1 μM) was added. Media was changed every other day. Colonies were scored visually either after alkaline phosphatase staining or using the Oct4-GFP reporter allele.

value: Mouse Embryonic Fibroblasts undergoing reprogramming

tag: treatment

value: DOX + UNC + C3


title: Mef treated with DOX, UNC & C3 replicate 3


title: Mef treated with DOX, UNC & C3 replicate 1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad007


title: Mef treated with DOX & C3 replicate 3

source_name: Mef cells treated with DOX, L-ascorbic acid, CHIR99021 and iALK5

value: DOX + C3


title: Mef treated with DOX & C3 replicate 2


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad006


title: Mef treated with DOX & C3 replicate 1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C2_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad002


title: Mef treated with DOX & UNC replicate 3

source_name: Mef cells treated with DOX and UNC

value: DOX + UNC


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad004


title: Mef treated with DOX & UNC replicate 2


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C12_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad012


title: WT_oct4_0hr_ATACseq

description: ATAC-seq


title: Mef treated with DOX & UNC replicate 1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad010


title: Mef treated with DOX replicate 3

source_name: Mef cells treated with DOX

value: DOX


title: Mef treated with DOX replicate 2


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 90 hours

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: HEK293-PFL-TFEB cells induce TFEB expression after 90 hours of tetracycline removal

data_processing:
Reads were aligned and assigned to Human Gencode  release 19 transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: Human Gencode  release 19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and  RPKM values for each Sample

organism: Homo sapiens

source_name: human embryonic kidney cells (HEK293)

growth_protocol: The cells were grown for 90 hours at 37°C in 5% CO2

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (500 ng) from each sample was prepared using TruSeq RNA sample prep reagents (Illumina, San Diego, CA, USA) according to manufacturer's instructions
The amplified fragmented cDNA of ∼200 bp in size were sequenced in paired-end mode using the HiSeq 1000 (Illumina) with a read length of 2×100 bp

treatment_protocol: The cells grown in tetracycline (100ng/ml) were plated in 16 colture plates (one for each time point).Tetracycline was removed at time 0h to induce TFEB expression and samples were collected every 6h up to 90h for a total of 16 time points.

tag: cells


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad007


title: Mef treated with DOX replicate 1


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 72 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 72 hours of tetracycline removal


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C11_ad001


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 66 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 66 hours of tetracycline removal


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 84 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 84 hours of tetracycline removal


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 60 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 60 hours of tetracycline removal


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C10_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C10_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C10_ad007


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 54 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 54 hours of tetracycline removal


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C10_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C10_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C10_ad002


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 48 hours

description: HEK293-PFL-TFEB cells induce TFEB expression  after 48 hours of tetracycline removal


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 30 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 30 hours of tetracycline removal


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 36 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 36 hours of tetracycline removal


title: CEMBA181220_5F_4_CEMBA181220_5F_5_C10_ad001


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 42 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 42 hours of tetracycline removal


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 24 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 24 hours of tetracycline removal


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad012


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 18 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 18 hours of tetracycline removal


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 78 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 78 hours of tetracycline removal


title: OCI3_sh988_rep3

description: processed data file: RNA_seq_O3_BAHCC1_shEV_vs_KD

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

growth_protocol: Jurkat, RS4;11 and OCI-AML3 cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit.
RNA libraries were made with standard Illumina protocols or prepared by Novogene Inc.

treatment_protocol: For BAHCC1 knockdown (KD) experiments, Jurkat, RS4;11 and OCI-AML3 cells were infected with lentivirus encoding empty vector control (shEV) or sh-BAHCC1, followed by drug selection to generate stable cell lines. For compound treatment experiments, Jurkat cells were treated with 5 µM of DMSO or UNC1999 for five days and collected. For BAHCC1 gene-editing experiments, CRISPR/cas9-based genomic editing tools were used to site-specifically mutate BAHCC1 within the BAHCC1 BAH domain (Y2533A or W2554G). For RNA-seq experiments, cells were grown in regular medium and collected.


title: OCI3_sh988_rep2


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 12 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 12 hours of tetracycline removal


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad006


title: OCI3_sh988_rep1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad008


title: OCI3_shEV_rep3

value: shEV


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad012


title: HEK293-PFL-TFEB cells grown in absence of Tetracycline for 6 hours

description: HEK293-PFL-TFEB cells induce TFEB expression after 6 hours of tetracycline removal


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B9_ad002


title: OCI3_shEV_rep2


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad010


title: OCI3_shEV_rep1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad006


title: HEK293-PFL-TFEB cells overexpressing TFEB grown in absence of Tetracycline for 18 hours (INPUT)

description: DNA INPUT from HEK293-PFL-TFEB cells induce TFEB expression after 18 hours of tetracycline removal

data_processing:
ChIP-seq reads were aligned with Bowtie v.2.2.9 to the hg19 genome assembly with --very-sensitive parameter enabled
Duplicated reads were removed using SAMTOOLS (RMDUP)
peaks were called using MACS version 2 with parameters --nomodel --extsize 200 -p 5e-2
TFEB binding regions were considered as the ones present in at least two out of six samples
Genome_build: Hg19
Supplementary_files_format_and_content: wig files were generated using UCSC tools

extract_protocol:
Lysates were clarified from sonicated nuclei and TFEB-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: HEK293 stable clone expressing a  TFEB_TET-OFF system (HEK293-PFL-TFEB )

tag: chip antibody


title: HEK293-PFL-TFEB cells overexpressing TFEB were grown in absence of Tetracycline for 90 hours (replicate 1)

description: HEK293-PFL-TFEB cells induce TFEB expression after 90 hours of tetracycline removal

value: Monoclonal ANTI-FLAG M2 antibody produced in mouse F1804


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad004


title: Jurkat_luc_Y2533A_rep2

description: processed data file: RNA-seq_Jurkat_BAHCC1_WT_vs_Mut

value: Jurkat cells


title: HEK293-PFL-TFEB cells overexpressing TFEB were grown in absence of Tetracycline for 36 hours (replicate 2)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad002


title: Jurkat_luc_Y2533A_rep1


title: Jurkat_luc_WT_rep3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad007


title: HEK293-PFL-TFEB cells grown in presence of Tetracycline (CTRL)

description: Synthetic construct stably expressing TFEB in HEK293 cells (HEK293-PFL-TFEB) was grown in tretracycline


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad010


title: Jurkat_luc_WT_rep2


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad006


title: HEK293-PFL-TFEB cells overexpressing TFEB were grown in absence of Tetracycline for 18 hours (replicate 2)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad002


title: HEK293-PFL-TFEB cells overexpressing TFEB were grown in absence of Tetracycline for 18 hours (replicate 1)


title: Jurkat_luc_WT_rep1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad004


title: HEK293-PFL-TFEB cells overexpressing TFEB were grown in absence of Tetracycline for 90 hours (replicate 2)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad012


title: Jurkat_W2554G_rep2


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad010


title: Jurkat_W2554G_rep3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B8_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad004


title: Jurkat_W2554G_rep1


title: HEK293-PFL-TFEB cells overexpressing TFEB were grown in absence of Tetracycline for 36 hours (replicate 1)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B6_ad002


title: Jurkat_WT_rep2

value: WT


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad012


title: Jurkat_WT_rep3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad007


title: Jurkat_sh993_rep3

description: processed data file: RNA-seq_Jurkat_BAHCC1_shEV_vs_KD


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad004


title: S243_S4c [F-0243-5-1]

city: Wakefield

first: Dmitry

last: Shvartsman

state: MA

address: 11 Audbubon Rd

department: Research Development

institute: Cellaria Inc

data_processing:
Sequence libraries were sequenced on Illumina NextSeq with sequence reads returned as fastq formatted files
Sequence reads were mapped on the human genome using RSEM software
Genome_build: GRCh38 release 87
Supplementary_files_format_and_content: tab separated ascii files; expected counts, TPM, FPKM

source_name: HUES8_stage 4 directed differentiation

growth_protocol: HUES8 cells were grown and differentiatied as described in Pagliuca FW, Millman JR, Gürtler M, Segel M, Van Dervort A, Ryu JH, Peterson QP, Greiner D, Melton DA. Generation of functional human pancreatic β cells in vitro. Cell. 2014 Oct 9;159(2):428-39. doi: 10.1016/j.cell.2014.09.040. .

extract_protocol:
Whole cell cluster samples were snap-frozen in RNAlater reagent and RNA was extracted with Quagen midiRNA kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

tag: cell line source

tag: cell type source

value: embryonic stem cells

value: directed differention of beta cells

tag: time point

value: stage 4 directed differentiation


title: S243_S3c [F-0243-4-1]

source_name: HUES8_stage 3 directed differentiation

value: stage 3 directed differentiation


title: med31_2

type: RNA

city: Ruston

first: Jamie

middle: J

last: Newman

state: Louisiana

address: 1 Adams Blvd, CTH 215, Biological Sciences

department: Biological Sciences

institute: Louisiana Tech University

description: gene expression data 72 hours after knockdown induction

hyb_protocol: Following fragmentation, 5.2 ug of labeled ss-DNA was hybridized for 16 hr at 4℃ to GeneChip HTA 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: Arrays were normalized with the SST-RMA algorithm in Affymetrix Expression Console v1.4.1.46.   Signal intensities were generated in Affymetrix Transcriptome Analysis Console Software v4.0 using default analysis settings.

label: biotin

source_name: med31, Human Bone Marrow Derived MSCs

label_protocol: Biotinylated sense-strand DNA was prepared according to the standard Affymetrix protocol from 250 ng of total RNA (GeneChip WT PLUS Reagent Kit, 2015, rev 3, Affymetrix).

growth_protocol: Human MSCs were cultured under standard culture conditions for 24 hours before being transfected with siRNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells remained under standard culture conditions following siRNA-mediated knockdown for 72 hours before RNA was collected

value: Bone Marrow Derived MSCs

value: MED31 Knockdown


title: Jurkat_sh993_rep2


title: med31_3


title: Jurkat_sh993_rep1


title: med31_1


title: siRNA Control_3

source_name: siRNA Control, Human Bone Marrow Derived MSCs

value: control


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad008

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: ACB

tag: Sex

value: male


title: S243_S2c [F-0243-3-1]

source_name: HUES8_stage 2 directed differentiation

value: stage 2 directed differentiation


title: siRNA Control_2


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B4_ad001

tag: age

tag: strain


title: S243_S1c [F-0243-2-1]

source_name: HUES8_stage 1 directed differentiation

value: stage 1 directed differentiation


title: Jurkat_sh988_rep3


title: Jurkat_WT_rep1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B4_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B4_ad012


title: S243_S0c [F-0243-1-1]

source_name: HUES8_stage 0 directed differentiation

value: stage 0 directed differentiation


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B4_ad004


title: S239_S5c [F-0239-6-1]

source_name: HUES8_stage 5 directed differentiation

value: stage 5 directed differentiation


title: Jurkat_sh988_rep1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B4_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B4_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B5_ad002


title: S239_S4c [F-0239-5-1]


title: Jurkat_shEV_rep3

value: shEV


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad012


title: siRNA Control_1


title: Jurkat_shEV_rep2


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad007


title: S239_S3c [F-0239-4-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad006


title: Jurkat_shEV_rep1


title: Jurkat_sh988_rep2


title: S239_S1c [F-0239-2-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B3_ad002


title: Jurkat_BAHCC1_BAH_mutant_cell_H3K27me3_ChIP

data_processing:
ChIP-seq reads were aligned to human genome build GRCh37/hg19 using STAR version 2.7.1a  (mismatches are extended and low quality sequences are trimmed at this step). Non-primary alignment and PCR duplicates were then removed by samtools.  Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools. Genomic binding profiles were generated using the deepTools “bamCompare” functions with options [--operation ratio ---pseudocount 1 -binSize 10 --extendReads 250] and normalized to the matched input.
Profiles of ChIP-seq read densities were displayed with the Integrative Genomics Viewer (IGV, Broad Institute).
Genome_build: hg19

source_name: Jurkat cells

growth_protocol: HEK293 cells were grown in the DMEM base medium plus 10% of FBS and 1% of antibiotics. Jurkat cells were grown in the RPMI1640 base medium plus 10% of FBS and 1% of antibiotics.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes isolated with specific antibodies against Flag tag (M2; Sigma cat # F1804), anti-acetyl-Histone H3 (H3Ac; Millipore cat# 06-599) or H3K27me3 (Abcam cat # ab6002).
Libraries were prepared by High-Throughput Sequencing Facility (HTSF) at UNC at Chapel Hill.

treatment_protocol: For ChIP-seq experiments, cells were grown in regular medium and collected, followed by cell fixation with 1% of formaldehyde, sonication, antibody enrichment, ChIP DNA recovery, library preparation, and subsequent deep sequencing.

value: Flag-tagged BAHCC1 with a homozygous W2554G mutation


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B4_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B2_ad002


title: S238_S5c [F-0238-6-1]


title: S239_S0c [F-0239-1-1]


title: Jurkat_BAHCC1_BAH_mutant_cell_INPUT_for_H3K27me3

value: Jurkat cells

value: n/a (input)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B12_ad008


title: S238_S4c [F-0238-5-1]

value: embryonic stem cells


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B12_ad007


title: Jurkat_BAHCC1_WT_cell_H3K27me3_ChIP

value: Flag-tagged wildtype BAHCC1


title: S238_S3c [F-0238-4-1]

value: directed differention of beta cells


title: S239_S2c [F-0239-3-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B12_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B12_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B12_ad006


title: HEK293_H3K27me3

source_name: HEK293 cells

value: HEK293 cells

value: parental WT

value: H3K27me3 (abcam, ab6002)


title: S238_S2c [F-0238-3-1]


title: HEK293_input


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B12_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B11_ad007


title: Jurkat_WT_input_for_GSM2279072_H3K27me3

growth_protocol: Jurkat cells were grown in the RPMI1640 base medium plus 10% of FBS and 1% of antibiotics.

value: parental Jurkat cells


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B12_ad012

value: ACB


title: Jurkat_BAHCC1_W2554G_cell_H3Ac_ChIP

value: Anti-acetyl-Histone H3 Antibody (Millipore 06-599)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B11_ad006

value: male


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B11_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B11_ad008


title: S238_S0c [F-0238-1-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B11_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad012


title: S237_S5c [F-0237-6-1]


title: Jurkat_BAHCC1_WT_cell_INPUT_for_H3K27me3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad010


title: Jurkat_BAHCC1_W2554G_cell_input_for_H3Ac

value: Flag-tagged BAHCC1 with a homozygous  W2554G mutation


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B11_ad002


title: Jurkat_BAHCC1_WT_cell_H3Ac_ChIP


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad006


title: S237_S3c [F-0237-4-1]

value: stage 3 directed differentiation


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad004


title: Jurkat_BAHCC1_WT_cell_input_for_H3Ac


title: S238_S1c [F-0238-2-1]

value: stage 1 directed differentiation


title: Jurkat_Flag_BAHCC1_Y2533A_Flag_ChIP

value: Flag-tagged BAHCC1 with a homozygous Y2533A mutation

value: Mouse anti-Flag tag (M2) (Sigma F1804)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad002


title: S237_S1c [F-0237-2-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B1_ad012


title: Jurkat_Flag_BAHCC1_Y2533A_cell_input

value: Jurkat cells


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B10_ad001


title: S237_S4c [F-0237-5-1]

value: stage 4 directed differentiation


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B1_ad007


title: Jurkat_non_Flag_parental_Flag_ChIP

value: parental, non-tagged


title: S237_S0c [F-0237-1-1]

value: embryonic stem cells

value: stage 0 directed differentiation


title: S230_S5c [F-0230-6-1]

value: directed differention of beta cells

value: stage 5 directed differentiation


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B1_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B1_ad004


title: Jurkat_non_Flag_parental_cell_input

value: n/a (input)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad012


title: S230_S4c [F-0230-5-1]


title: Jurkat_Flag_BAHCC1_WT_rep#2_Flag_ChIP

value: Flag-tagged wildtype BAHCC1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B1_ad002

value: ACB


title: S230_S3c [F-0230-4-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad001


title: S237_S2c [F-0237-3-1]

value: stage 2 directed differentiation


title: Jurkat_Flag_BAHCC1_WT_rep#2_input_for_Flag


title: Jurkat_Flag_BAHCC1_WT_rep#1_Flag_ChIP


title: S230_S1c [F-0230-2-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B7_ad012

value: male


title: S230_S0c [F-0230-1-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad004


title: Jurkat_Flag_BAHCC1_WT_rep#1_input_for_Flag


title: S229_S5c [F-0229-6-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad008


title: S229_S4c [F-0229-5-1]


title: Ishikawa_CDYL_sh2

city: Shanghai

first: Xiaowei

last: Zhou

email: 453311049@qq.com, zpxiaxy@shsmu.edu.cn

address: 197 Ruijin 2nd Road

country: China

institute: School of Medicine, Shanghai Jiao Tong University

data_processing:
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina.The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep ) and Sickle (https://github.com/najoshi/sickle ) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using TopHat (http://tophat.cbcb.umd.edu/,  version2.0.0) software.Then the region of gene were expanded following depths of sites and the operon was obtained. In addition, the whole genome was split into multiple 15kbp windows that share 5kbp. New transcribed regions were defined as more than 2 consecutive windows without overlapped region of gene, where at least 2 reads mapped per window in the same orientation.To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample.

extract_protocol:
Total RNA were extracted from the negative control and CDYL-knockdown Ishikawa cells using the TRIzol® Reagent according the manufacturer’s instructions (Thermo Fisher Scientific), and genomic DNA were removed using DNase I (TaKara).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ishikawa cells were transfected with short hairpin RNA (shRNA) against human CDYL or the negative control shRNA.

value: Ishikawa

value: endometrial epithelial cell

value: CDYL gene silencing


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B1_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A8_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A8_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A8_ad006


title: Ishikawa_CDYL_sh1


title: Ishikawa_control2

value: control


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A8_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A8_ad002


title: S229_S2c [F-0229-3-1]


title: Ishikawa_control1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A9_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A8_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A7_ad012


title: S229_S1c [F-0229-2-1]

value: stage 1 directed differentiation


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A7_ad001


title: HC, day 3, rep3

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

institute: University of Birmingham

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E15D3

data_processing:
base calling : base calling was done using RTA for illumina, quality controls were performed using the spike in PhiX at the MGX facility, Montpellier, France
QC and alignment : FastQ files were trimmed and low quality score reads removed. The remaining reads were aligned to the human genome hg38 using bowtie2 (--end-to-end --sensitive -N 0)
peak calling : Peaks were called using a combination of two peak calling programs, MACS2 and SICER. Peaks were first called using MACS2 (default parameters plus --bw 500 -p 1e-5 -s 60 -m 10 30 --gsize 2.7e9), followed by peak calling by SICER (parameters: redundancy threshold = 1, window size (bp) = 200, fragment size = 150 effective genome fraction = 0.85,  gap size (bp) = 600, FDR = 1e-3). MACS2 peaks that intersect SICER peaks from each sample were merged using bedtools intersect
quantification : Quantification of the SNS-seq signal on DNA replication origins was done using the R-package DiffBind (dba.sCore: TMM_minus_background), using all human origin coordinates
Differential gene expression : DGE was performed by MGX, using Deseq2 with default parameters and gencode v25 genes as annotation file
pipelines : can be found at https://github.com/iakerman/SNS-seq upon publication of the manuscript
Genome_build: hg38
Supplementary_files_format_and_content: .xlx, .txt and .bed

source_name: Human cord blood

growth_protocol: Tissue culture cells were grown as indicated in the manuscript

extract_protocol:
RNA was extracted using TriPure, following manufacturer's instructions
Truseq mRNA stranded sample preparation kit (for RNA) and TruSeq ChIP Library Preparation Kit
Stranded mRNA for RNA samples, and ChIP-seq for SNS-seq samples

treatment_protocol: some samples were treated with erythropoietinin (EPO). Please see manuscript for details.

tag: agent

value: eryhtropoietinin, 3 days

value: 3 days


title: S227_S5c [F-0227-6-1]


title: HC, day 0, rep3

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E15D0

value: no treatment with eryhtropoietinin


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A7_ad010

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A8_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A7_ad006


title: S229_S3c [F-0229-4-1]

value: embryonic stem cells

value: stage 3 directed differentiation


title: HC, day 3, rep2

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E14D6


title: S227_S4c [F-0227-5-1]

value: directed differention of beta cells

value: stage 4 directed differentiation


title: HC, day 0, rep2

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E14D3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A7_ad002


title: S227_S2c [F-0227-3-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A7_ad008


title: HC, day 6, rep2

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E14D0

value: eryhtropoietinin, 6 days

value: 6 days


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad001

value: ACB


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad010


title: HC, day 6, rep1 part2

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E13D6


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A7_ad007


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad007


title: SKOV-3_RAME_2

city: SUWON

first: Ki Hong

last: Nam

state: GYEONGGI-DO

address: 2066 Seobu-ro

country: South Korea

institute: Sungkyunkwan University

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2
The alignment file was used for assembling transcripts, estimating their abundance, and detecting the differential expression of genes.
Analysis of the relationship between differentially expressed genes was performed with the Excel-based Differentially Expressed Gene Analysis (ExDEGA) software by eBiogen (ebiogen.com). Differentially expressed genes with fold changes > 2 and P-values < 0.05 were further identified by GO analysis using the Enrichr tool.
Genome_build: hg19

molecule: polyA RNA

growth_protocol: SKOV-3, a human ovarian cancer cell line, was maintained in McCoy’s 5A medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S).

extract_protocol:
The total RNA of SKOV-3 cells was isolated using Trizol reagent.
For the RNAs of DMSO- and RAME-treated SKOV-3 cells, a library was constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen Inc., Vienna, Austria) according to the manufacturer’s instructions. In brief, 500 ng of total RNA was prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA; reverse transcription was then performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library was purified from the PCR components.

treatment_protocol: RAME (40uM) was treated for 24 hr.

tag: cell type

value: Ovarian cancer cell line

value: Rosmarinic acid methyl ester


title: SKOV-3_RAME_1


title: S227_S1c [F-0227-2-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad008

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

value: male


title: HC, day 3, rep1

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E13D3


title: SKOV-3_Control_2

value: DMSO


title: HC, day 6, rep1 part1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A5_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A6_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A5_ad010


title: HC, day 0, rep1 part2

description:
Pseudo_Counts_RLE_RNA-Seq_Kasaai.txt
E13D0


title: S227_S3c [F-0227-4-1]


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A5_ad006


title: SKOV-3_Control_1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A5_ad001


title: HC, day 0, rep1 part1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A5_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A4_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A4_ad007


title: HMEC Control

description:
hmec.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt

data_processing:
Library strategy: SNS-seq
base calling : base calling was done using RTA for illumina, quality controls were performed using the spike in PhiX at the MGX facility, Montpellier, France
QC and alignment : FastQ files were trimmed and low quality score reads removed. The remaining reads were aligned to the human genome hg38 using bowtie2 (--end-to-end --sensitive -N 0)
peak calling : Peaks were called using a combination of two peak calling programs, MACS2 and SICER. Peaks were first called using MACS2 (default parameters plus --bw 500 -p 1e-5 -s 60 -m 10 30 --gsize 2.7e9), followed by peak calling by SICER (parameters: redundancy threshold = 1, window size (bp) = 200, fragment size = 150 effective genome fraction = 0.85,  gap size (bp) = 600, FDR = 1e-3). MACS2 peaks that intersect SICER peaks from each sample were merged using bedtools intersect
quantification : Quantification of the SNS-seq signal on DNA replication origins was done using the R-package DiffBind (dba.sCore: TMM_minus_background), using all human origin coordinates
Differential gene expression : DGE was performed by MGX, using Deseq2 with default parameters and gencode v25 genes as annotation file
pipelines : can be found at https://github.com/iakerman/SNS-seq upon publication of the manuscript
Genome_build: hg38
Supplementary_files_format_and_content: .xlx, .txt and .bed

source_name: Human mammary gland

value: no treatment


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A4_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A4_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A4_ad006


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A4_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A4_ad008


title: RS4_sh988_rep2

description: processed data file: RNA_seq_RS4_BAHCC1_shEV_vs_KD

value: RS4;11 cells


title: HMEC SNS-seq replicate 1

description:
hmec.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
HMEC_1


title: HMEC SNS-seq replicate 2

description:
hmec.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
HMEC_2


title: WT33_P4CNCC_INPUT_matchedToCTCFRAD21_ChIPseq_replicate1

city: Stanford

first: Hannah

middle: Katherine

last: Long

address: Lokey Stem Cell Research Building

department: Chemical and Systems Biology

institute: Stanford University

description: Input

data_processing:
ChIP sequencing reads were trimmed using skewer and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
ATAC sequencing reads were trimmed to remove Nextera adapter sequences using cutadapt and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
RNA sequencing reads were trimmed using cutadapt and aligned to human gene models (hg38) using HISAT2. Read counts per gene were quantified using featureCounts, gene expression was normalized to fragments per million and plotted in R.
Capture-C analysis was performed using bespoke analysis scripts outlined here: http://userweb.molbiol.ox.ac.uk/public/telenius/captureManual/oligofile.html. For comparison across samples, Capture-C profiles were plotted as the number of unique interactions per restriction fragment normalized to 10,000 interactions in cis.
10X Linked-Read sequencing data was analyzed using Long Ranger (longranger-2.2.2) and visualized using the 10X loupe genome browser.
Genome_build: hg19 and hg38

source_name: cranial neural crest cells

growth_protocol: H9 human embryonic stem cells (hESCs) were obtained from ATCC and cultured in mTeSR (Stem Cell Technologies) and grown on Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning). hESCs were fed every day and passaged every 5-6 days using ReLeSR (Stem Cell Technologies).

extract_protocol:
5-15 million cells were cross-linked per ChIP experiment in 2mL PBS per 6-well with 1% methanol-free formaldehyde for 5-10 min and quenched with a final concentration of 0.125M glycine for 5 min with nutation. Cross-linked cells were washed with PBS, scraped and pelleted by centrifugation, flash-frozen in liquid nitrogen and stored at -80°C. Samples were defrosted on ice and resuspended in 5mL LB1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, with 1X cOmplete Protease Inhibitor Cocktail and optionally 1mM PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, and resuspended in 5mL LB2 (10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, with 1X cOmplete Protease Inhibitor Cocktail and optionally 1mM PMSF) and rotated vertically for 10 min at 4°C. Samples were centrifuged for 5 min at 1350 x g at 4°C, and resuspended in 1mL LB3 per 10 million cells (maximum concentration of cells for Covaris sonication), or 1 mL per ChIP. Samples were sonicated in 1mL AFA tubes for 5 min on E220 evolution Covaris with settings Peak power = 140, Duty Factor = 10, Cycles per burst = 200 to achieve chromatin sized approximately 500-2000bp. Following sonication, samples were re-combined (if aliquoted for sonication), Triton X-100 was added to the fragmented chromatin to a final concentration of 1%, and the chromatin divided for input (1-2%) and ChIP samples. 5μg anti-histone antibody or 5-9μg anti-transcription factor antibody was added per ChIP sample, and incubated overnight at 4°C.  Protein G Dynabeads (ThermoFisher) were first blocked with Block solution (0.5% BSA (w/v) in 1X PBS) and then added to cleared chromatin to bind antibody-bound chromatin for a 4-6 hour incubation. Chromatin-bound Dynabeads were washed at least 6 times with chilled RIPA wash buffer (50 mM Hepes-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate), followed by a wash with chilled TE + 50 mM NaCl. Chromatin was eluted for 15-30 min in Elution Buffer (50 mM Tris, 10 mM EDTA, 1% SDS) at 65°C with frequent vortexing. The ChIP and input samples were then incubated at 65°C overnight to reverse cross-links (12-16 hours). Samples were diluted and sequentially digested with RNase A (0.2 mg/mL) for 2 hours at 37°C followed by Proteinase K (0.2 mg/mL) for 2 hours at 55°C for 2-4 hours to digest protein. ChIP and input samples were purified by phenol-chloroform-isoamylalcohol extraction and precipitation with final concentration 70% ethanol, 0.3M NaOAc pH 5.2 and 1.5μL glycogen.
For library preparation, samples were quantified by Qubit dsDNA HS assay kit, and 10-30ng of ChIP DNA was used for library preparation with end repair, A-tailing, and adaptor ligation (NEB). Following USER enzyme treatment, samples were purified using Nucleospin Gel and PCR Cleanup (Takara) and separated by gel electrophoresis and size-selected for 220-500 bp by gel extraction. Libraries were then amplified to add indices using NEBNext HiFi 2X PCR mix and NEBNext Multiplex Oligos for Illumina kit (NEB, E7335S) with 9-15 cycles (as determined by qPCR). ChIP libraries were purified by two rounds of XP SPRI bead clean-up to deplete adaptors. Library concentration and quality was assessed by Bioanalyzer (to determine size) and KAPA qPCR was used to pool multiple libraries. Samples were sequenced using NextSeq or HiSeq 4000 platform (2x 75bp).

value: H9 embryonic stem cell-derived neural crest (passage 4)

value: wildtype

tag: cell line of origin

value: H9 ESCs (WA09)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad001

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56


title: RS4_sh988_rep1


title: H9_P4CNCC_INPUT_matchedToCTCFRAD21_ChIPseq_replicate1

description: Input


title: HC day3 SNS-seq replicate3

description:
hematopoietic_cells.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt

value: eryhtropoietinin

value: 3 days


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad007


title: RS4_shEV_rep2

value: shEV


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad006


title: H9_P4CNCC_CTCF_ChIPseq_replicate2

value: CTCF (Cell Signaling, 2899S)


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad004


title: HC day0 SNS-seq replicate3


title: H9_P4CNCC_INPUT_matchedToCTCF_ChIPseq_replicate2

description: Input


title: RS4_shEV_rep1


title: HMEC SNS-seq replicate 3

description:
hmec.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
HMEC_3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad008


title: HC day6 SNS-seq replicate2

description:
hematopoietic_cells.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
E14_d6


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A3_ad012


title: HC day3 SNS-seq replicate2

description:
hematopoietic_cells.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
E14_d3


title: HC day6 SNS-seq replicate3


title: Batch2_shT_c

city: London

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

data_processing:
Illumina’ s bcl2fastq Conversion Software v2.19 was used to demultiplex data and generate fastq files
TrimGalore v0.4.12 was used to remove sequencing adapters
TopHat2.1.0 was used to align reads to the human genome UCSC build hg38 with default parameters. Gencode v30 gene annotation were also provided as a reference transcriptome.
HTSeq-count v 0.11.0 was used to obtain read counts per gene with --mode intersection-nonempty and -s reverse parameters
Gene counts were imported into R and used for the differential expression analysis with DESeq2_1.22.1
Genome_build: hg38
Supplementary_files_format_and_content: genes_dea_HFFs.xlsx contains the result of the differential gene expression analysis from DESeq2 for relevant comparisons in HFF samples. gene_tpms_HFFs.tsv contains TPMs for all HFF samples. TEcount_dea_HFFs.xlsx contains the results of differential expression analysis for repeat families derived using TEcounts and DESeq2 for shMPP8 compared to shControl in HFF samples. by_locus_dea_HFFs.xlsx contains the results of differential expression analysis for repeat loci from DESeq2 for shMPP8 compared to shControl in HFF samples. gene_dea_HeLa.xlsx contains the result of the differential gene expression analysis from DESeq2 for shMPP8 compared to shControl in HeLa samples. gene_tpms_HeLa.tsv contains TPMs for all HeLa samples.

source_name: HFF

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific) supplemented with 100U/ml penicillin/streptomycin (Gibco, Thermo Fisher Scientific) and 10% heat-inactivated fetal calf serum (FCS), and grown at 10% CO2 at 37°C. Human primary foreskin fibroblasts (HFFs) were cultured as above but at 5% C02 and split every 3 days 1:3 and not kept longer than 2 weeks before going back to early-passage cells.

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (Qiagen) and treated with DNase (Ambion AM1907). The RNA was quality checked on a 4200 Tapestation using the RNA ScreenTape assay (Agilent Technologies, Wokingham, UK) and the RNA concentration measured using a Qubit RNA Broad Range kit (Life Technologies, Paisley, UK).
Total RNA samples were then processed using KAPA’s stranded RNA HyperPrep RiboErase kit using an input of 500ng per sample. Samples were sequenced on a NextSeq 500 instrument (Illumina Cambridge, Chesterford, UK) after pooling libraries in equimolar quantities, using a 2x 151bp paired-end run resulting in over 15 million reads per sample.
Stranded total RNA-sequencing

treatment_protocol: VSV-G-pseudotyped lentiviral vectors were produced by co-transfecting 293T cells in 10cm plates with 1.5µg of the shRNA plasmid, 1µg p8.91 and 1µg pMDG2 encoding VSV-G. Media was changed one day post transfection and supernatant harvested 48h post-transfection and concentrated via ultracentrifugation (20,000rpm for 2h at 4°C).

value: pHR-SIREN shRNA lentiviral vector expressing a shTASOR hairpin known as 'shTASOR' (see Tunbak et al., 2020 for shRNA sequences)

tag: time-point

value: Day 6 post-tranduction (puromycin selection)

tag: full name

value: Experiment 3:shTASOR


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad007

value: ACB


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad006


title: HC day0 SNS-seq replicate2

description:
hematopoietic_cells.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
E14_d0


title: Batch2_shT_b

value: Experiment 2:shTASOR


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad010


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad001


title: CEMBA181220_5F_4_CEMBA181220_5F_5_B11_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad010


title: HC day0 SNS-seq replicate1

description:
hematopoietic_cells.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
E13_d0


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad007


title: Batch2_shT_a

value: Experiment 1:shTASOR


title: Batch2_shP_a

value: pHR-SIREN shRNA lentiviral vector expressing a shPPHLN1 hairpin known as 'shPPHLN1' (see Tunbak et al., 2020 for shRNA sequences)

value: Experiment 1:shPPHLN1


title: Batch2_shP_c

value: Experiment 3:shPPHLN1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad008

value: male


title: HC day3 Control


title: HC day6 SNS-seq replicate1

description:
hematopoietic_cells.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
E13_d6

value: 6 days


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad012


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad008


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A2_ad004


title: HC day3 SNS-seq replicate1

description:
hematopoietic_cells.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
E13_d3


title: Batch2_shM_c

description: genes_dea_HFFs.xlsx,gene_tpms_HFFs.tsv,TEcount_dea_HFFs.xlsx,by_locus_dea_HFFs.xlsx

value: pHR-SIREN shRNA lentiviral vector expressing a shMPP8 hairpin known as 'shMPP8' (see Tunbak et al., 2020 for shRNA sequences)

value: Experiment 3:shMPP8


title: HC day6 Control

value: eryhtropoietinin


title: Batch2_shP_b

value: Experiment 2:shPPHLN1


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad001


title: Batch2_shM_b

value: Experiment 2:shMPP8


title: HC day0 Control

value: no treatment


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad002


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A10_ad006


title: Batch2_shM_a

value: Experiment 1:shMPP8


title: ImM3 RNAse-lambdaExo Control

description:
Imm3_wnt.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A10_ad008


title: Batch2_shControl_c

value: pHR-SIREN shRNA lentiviral vector expressing a control scrambled hairpin known as 'shControl' (see Tunbak et al., 2020 for shRNA sequences)

value: Day 6 post-tranduction (puromycin selection)

value: Experiment 3:shControl


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad006

value: ACB


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A10_ad007


title: ImM3 SNS-seq replicate 3-part2

description:
Imm3_wnt.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Wnt_3


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A10_ad004


title: CEMBA181220_5F_4_CEMBA181220_5F_5_A12_ad004


title: Batch2_shControl_b

value: Experiment 2:shControl


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad012


title: Batch2_shControl_a

value: Experiment 1:shControl


title: Batch1_shM_c

value: Experiment 6:shMPP8


title: ImM2 RNAse-lambdaExo Control

description:
Imm2_ras.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt


title: ImM3 SNS-seq replicate 1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad010


title: ImM3 SNS-seq replicate 2

description:
Imm3_wnt.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Wnt_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad001


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad007


title: ImM3 SNS-seq replicate 3


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad004


title: ImM2 SNS-seq replicate 3

description:
Imm2_ras.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Ras_3


title: Batch1_shM_a

value: Experiment 4:shMPP8


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E9_ad002

value: male


title: ImM2 SNS-seq replicate 2

description:
Imm2_ras.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Ras_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E8_ad010


title: Batch1_shEmp_c

value: pLKO.1 shRNA lentiviral vector control (sigma) expressing no hairpin (empty) known as 'shEmpty'

value: Experiment 6:shEmpty


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E8_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E8_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E8_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E8_ad002


title: Batch1_shEmp_b

value: Experiment 5:shEmpty


title: Batch1_shM_b

value: pHR-SIREN shRNA lentiviral vector expressing a shMPP8 hairpin known as 'shMPP8' (see Tunbak et al., 2020 for shRNA sequences)

value: Experiment 5:shMPP8


title: Batch1_shEmp_a

value: Experiment 4:shEmpty


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E8_ad008


title: ImM2 SNS-seq replicate 1

description:
Imm2_ras.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Ras_1

value: no treatment


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E7_ad007


title: hESC replicate 2

description:
esc.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
hESC2

source_name: Human embryonic cell line hESC H9


title: hESC Control


title: hESC replicate 1

description:
esc.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
hESC1


title: Batch1_shControl_a

value: Experiment 4:shControl


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E7_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E6_ad012


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E6_ad010


title: Batch1_shControl_b

value: pHR-SIREN shRNA lentiviral vector expressing a control scrambled hairpin known as 'shControl' (see Tunbak et al., 2020 for shRNA sequences)

value: Experiment 5:shControl


title: ImM1 RNAse-lambdaExo Control

description:
Imm1_127.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E7_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E6_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E6_ad008


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E7_ad008


title: ImM1 SNS-seq replicate 3

description:
Imm1_127.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Immortal_3


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E6_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E6_ad004


title: H9_Day11CNCC_CaptureC_SOX9promoter

data_processing:
Library strategy: Capture-C
ChIP sequencing reads were trimmed using skewer and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
ATAC sequencing reads were trimmed to remove Nextera adapter sequences using cutadapt and aligned to the human genome (hg19) using bowtie2. For normalization, bedgraph files were generated from aligned bam files using bedtools genomecov with -scale option to normalize to 1 million reads. For visualization, bigwig files were generated using bedgraphToBigWig.
RNA sequencing reads were trimmed using cutadapt and aligned to human gene models (hg38) using HISAT2. Read counts per gene were quantified using featureCounts, gene expression was normalized to fragments per million and plotted in R.
Capture-C analysis was performed using bespoke analysis scripts outlined here: http://userweb.molbiol.ox.ac.uk/public/telenius/captureManual/oligofile.html. For comparison across samples, Capture-C profiles were plotted as the number of unique interactions per restriction fragment normalized to 10,000 interactions in cis.
10X Linked-Read sequencing data was analyzed using Long Ranger (longranger-2.2.2) and visualized using the 10X loupe genome browser.
Genome_build: hg19 and hg38

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Prescott, 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting (Day 0). Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, neural crest emerged from neuroectodermal spheres attached to the petri dish, and after 11 days, neural crest cells were collected. First, attached neuroectodermal spheres were aspirated off and then the remaining neural crest cells were collected.

extract_protocol:
Capture-C was performed as previously described (Davies et al., 2015). Briefly, cells were crosslinked for 10 min in 2% formaldehyde in PBS, quenched with 125mM glycine for 5 min, scraped, collected and pelleted by centrifugation (500 rcf, 5 min, 4°C). Cells were washed with 5mL cold PBS, pelleted and resuspended in 5mL cold lysis buffer (10mM Tris pH8, 10mM NaCl, 0.2% Ipegal CA-630 in water with cOmplete Protease Inhibitor Cocktail) for 20 min. Cells were pelleted, washed with 5mL cold PBS, pelleted, resuspended in 1mL cold PBS, flash frozen in liquid nitrogen and stored at -80°C.
For 3C library preparation, samples were defrosted on ice, pelleted and resuspended in 1xDpnII digestion buffer before extended digestion with DpnII overnight with addition of extra enzyme. DpnII was then heat inactivated at 65°C and samples were ligated with T4 Ligase for ~22 hours. DNA was extracted by sequential Proteinase K and RNase digestion followed by phenol-chloroform isoamylalcohol extraction and precipitation with ethanol and sodium acetate. Efficiency of digestion and ligation was assessed by gel electrophoresis and digestion efficiency was further assessed by qPCR. For addition of Illumina sequencing adaptors, samples were sheared by Covaris sonication and purified by XP SPRI bead clean-up. Sequencing adaptors were annealed using NEB Ultra II kit. Libraries were PCR amplified using Herculase II polymerase (Agilent) in duplicate to add indexing primers and purified by XP SPRI bead clean-up. Samples were pooled and quantified using Qubit dsDNA BR assay kit.    Biotinylated oligos for capture were designed using the Capsequm online tool (http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) and ordered from IDT. 1-2μg indexed 3C library was mixed with 5μg COT DNA, 1nmol TS-HE Universal Oligo and 1nmol of TS-HE Index Oligo (Nimblegen SeqCap EZ HE-oligo and Accessory kit) and dried by vacuum centrifugation at 55°C until completely dry. The 3C library plus blocking oligos were then carefully resuspended in 7.5μL 2X hybridization buffer and 3μL Hybridization buffer A and denatured at 95°C for 10min. The 3C library was then transferred into a preheated PCR tube at 47°C containing 4.5μL of pooled Biotinylated oligonucleotide capture probes at 2.9μM. After a brief mix and centrifugation, the 3C library oligo mix was incubated at 47°C for 18-20 hrs. Following this incubation, the 3C library was washed and recovered by streptavidin bead (M-270 Dynabeads, Invitrogen) pull down using the Nimblegen SeqCap EZ Hybridization and wash kit. Following the recovery of the captured material, the captured DNA was amplified on the streptavidin beads using KAPA HiFi HotStart ReadyMix and POST-LM PCR oligo 1&2 and purified by XP SPRI bead clean-up. For improved capture efficiency, a second round of capture was performed on the total amplified DNA from the first capture. Following the second round of capture, the library was quantified using KAPA library quantification kit using the average size calculated from Bioanalyzer. Libraries were then sequenced on Illumina HiSeq-4000 (2x 150bp).

value: H9 embryonic stem cell-derived neural crest (Day 11)

value: wildtype

value: H9 ESCs (WA09)

value: SOX9 promoter


title: H9_P4CNCC_CaptureC_SOX9promoter

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Prescott, 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting (Day 0). Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8 days, neural crest emerged from neuroectodermal spheres attached to the petri dish, and after 11 days, neural crest cells were passaged onto fibronectin-coated 6-well plates using accutase and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini). After 2-3 days, neural crest cells were split 1:3 and the following day cells were fed with neural crest long-term media. Long term media: neural crest maintenance media + 50pg/ml BMP2 (PeproTech, 120-02) + 3uM CHIR-99021 (Selleck Chemicals, S2924) (BCh media). cNCCs were then passaged twice to passage 4.

value: H9 embryonic stem cell-derived neural crest (passage 4)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E4_ad001

value: ACB


title: ImM1 SNS-seq replicate 2

description:
Imm1_127.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Immortal_2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E4_ad007

value: male


title: H9_Day4NEC_CaptureC_SOX9promoter

source_name: neurectodermal spheres

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Prescott, 2015). Briefly, hESCs were grown for 5-6 days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting (Day 0). Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 4 days, neurectodermal spheres were collected.

value: H9 embryonic stem cell-derived neurectodermal spheres (Day 4)


title: ImM1 SNS-seq replicate 1 part3

description:
Imm1_127.bed
Peak_counts_V1_TMMminusFULL_akerman_kasaai.txt
Immortal_1


title: Batch1_shControl_c

value: Day 6 post-tranduction (puromycin selection)

value: Experiment 6:shControl


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E7_ad010


title: ImM1 SNS-seq replicate 1 part2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E4_ad002


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E4_ad006


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E4_ad008


title: H9_ESC_CaptureC_SOX9promoter

source_name: human embryonic stem cells

value: H9 human embryonic stem cells


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E3_ad007


title: CEMBA181218_5F_1_CEMBA181218_5F_2_E3_ad002