title: TM62


title: TM63

status: Public on Jan 31 2018

type: SRA

city: Urbana

first: William

middle: W

last: Metcalf

state: Illinois

address: 601 South Goodwin Avenue

department: Microbiology

country: USA

institute: University of Illinois - Urbana-Champaign

library_source: transcriptomic

data_processing:
Data processed with Casava 1.8.2 via manufacturer's instructions. Furthur processing performed with CLC Genomics Workbench 7.
Fastq files imported and trimmed for quality (Quality: 0.001, Ambiguous: 2, Discard: min 30, max 100) and Illumina adapter sequences removed.
After trimming, remaining reads that mapped to stable RNAs (16s, 23s, 5s rRNA and tRNAs) removed (Similarity: 0.9, Length: 0.85, Mismatch: 2, Insertion: 3, Deletion: 3, Global Alignment and Stand-alone read).
Remaining reads mapped to the genome for RNA-seq analyses (Similarity: 0.9, Length: 0.85, Mismatch: 2, Insertion: 3, Deletion: 3, Maximum number hits for a read: 10).
Mapped reads normalized with default settings, and differently expressed genes identified with the empirical analysis of differential gene expression (EDGE test).
Genome_build: Methanosarcina barkeri Fusaro chromosome (NC_007355) and plasmid (NC_007349)
Supplementary_files_format_and_content: Excel file (.xlsx) containing raw and normalized expression values for each sample, and pairwise comparisons of each genotype against all other genotypes.

molecule: total RNA

organism: Methanosarcina barkeri str. Fusaro

growth_protocol: Grown to mid-exponential phase in High Salt medium with 125 mM methanol

extract_protocol:
2.5 ml culture combined with equivalent volume of TRIzol reagent (Ambion, Carlsbad, CA) and incubated at room temperature for 5 min. RNA isolated with Direct-zol RNA MiniPrep kit from Zymo Research (Irvine, CA). 16S and 23S rRNA was removed via substractive hybridization with biotinylated RNA probes and streptavidin-coated magnetic beads.
Illumina's TruSeq Stranded RNA Sample Prep kit followed. The result was 5' to 3' strand-specific libraries. All libraries pooled and qPCR quantitated. A single lane was used to sequence the pool with 101 cycles on a HiSeq2000. TruSeq SBS sequencing kit version 3 used.

tag: genotype


title: TM68

value: delta-vhx delta-hpt::PmcrB-fC31int-attP


title: HO004

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Initial QC performed using FastQC v 0.11.2
Tophat v 2.0.13 was used to align samples
Cufflinks v 2.2.1 was used to generate abundances and fpkm values with max-bundle-frans <10000000> and masked genes with length <200
Genome_build: hg19
Supplementary_files_format_and_content: matrix of fpkm values per sample

organism: Homo sapiens

source_name: osteosarcoma

extract_protocol:
total RNA was extracted using Thermo Fisher TotalRNA kit
TruSeq RNA v2
average insert size of 200 selected

tag: tissue

value: osteosarcoma

tag: tumor type

value: primary


title: 5h HepG2 SALP-seq

city: NanJing

first: Jian

last: Wu

state: Jiangsu

address: Sipailou 2#, Sipailou 2#

country: China

institute: Southeast University

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents 5h HepG2

library_source: genomic

data_processing:
The raw reads data were separated according to the barcode using a homemade Perl scripts.
All reads were cut to 30 bp and aligned to the human genome (hg19) using Bowtie program (version 1.1.2)
Peak calling was performed with macs2 with the following parameters: -f BEDPE –keep-dup=2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

growth_protocol: HeLa, HepG2 and 293T cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, GIBCO), GM12878 cells were cultured in RPMI 1640, which were all supplemented with 10% fetal bovine serum (FBS, GIBCO) with 100 μg/mL streptomycin and 100 units/mL penicillin at 37°C in 5% CO2.

extract_protocol:
The nuclei of 100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) were extracted.
Nuclei then tagmented by Tn5 transposome with different barcoded Tn5 adaptors.The denatured tagmented gDNA was ligated with variant single strand adaptors. Then elongated, purified with Ampure XP beads and amplified with Illumina compatible primers. The genome DNA of HepG2 were digested with Hind III and sonicated, and genome DNA libraries were constructed with SALP protocol.

tag: cell line

tag: cell type

value: primary epithelial cells

tag: fragment method

value: Tagmentation

tag: cell number


title: TM78


title: Sonicated HepG2 genome DNA

value: Sonication


title: Hind III digested HepG2 genome DNA

value: Enzyme digestion


title: 2_5k HepG2 SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents 2_5k HepG2


title: TM61


title: 10k HepG2 SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents 10k HepG2


title: 5k HepG2 SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents 5k HepG2


title: 50k HepG2 SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents 50k HepG2


title: 293T SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents 293T


title: HepG2 SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents HepG2


title: HeLa SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents HeLa

source_name: HeLa

value: HeLa


title: GM12878 SALP-seq

description:
100,000 GM12878, HeLa, HepG2, and 293T cells, and various numbers of HepG2 cells (50,000, 10,000, 5,000, 2,500, and 500) tagmented chromatin were pooled together.
This sample represents GM12878

value: lymphoblastoid cells


title: HPB-ALL_DMSO

city: Barcelona

first: Christos

last: Gekas

address: Carrer del Doctor Aiguader 88, Lab277

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
Read quality was assessed with FastQC (v0.11.2) and reads were trimmed (first 3 nt removed), converted to Sanger format and filtered for >35 quality score with the FASTX Toolkit
Reads were mapped against the human genome (GRCh38, Ensembl release 77) with TopHat (v2.0.13) using the following parameters: min-anchor-length 8; max splice-mismatches 0; min/max intron length 70/500,000; max-multihits 2; initial read mapping with bowtie-n; max-insertion-length 3; max-deletion-length 3; min/max-coverage-intron 50/20,000.
Transcript annotation and expression calculation (FPKM; fragments per kilobase of transcript per million mapped reads) for each sample was performed with Cufflinks (v2.2.1).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text with Gene Annotations and FPKM values for each sample, obtained using Cufflinks

source_name: HPB-ALL T-ALL cells

extract_protocol:
RNA from 4 T-ALL cell lines (RPMI8402, HPB-ALL, JURKAT, CCRF-CEM) subjected to 3 hrs of DMSO or PKF115-584 (310nM) treatment was collected and purified with the RNEasy Mini kit (QIAgen)
RNA was quantifed by Nanodrop and quality assessed by Agilent Bioanalyzer 2100. 2µg of each RNA sample (RIN 9.3-10.0) was subjected to Solexa stranded mRNA-seq (polyA+) library preparation and sequenced on a Solexa HiSeq 2000 sequencer (Illumina)

value: HPB-ALL

tag: treatment

value: DMSO


title: D5C180

city: Jena

first: Jörg

last: Linde

address: Naumburger Str. 96 a

department: Institute for Bacterial Infections and Zoonoses

country: Germany

institute: Federal Research Institute for Animal Health - Friedrich-Loeffler-Institute

data_processing:
FASTQ files were received from LGC Genomics, Berlin, Germany
Sequenced reads were trimmed for low-quality regions (btrim windowsize 15 average 20
Mapping of read pairs using TopHat (v2.0.6; -G GFF from CADRE; -maxintronlength 10000)
Read counting using htseq-count (-mode union, -s no, -type CDS)
Calculation of RPKM values using raw counts, sum of totally mapped reads and sum of CDS length using CADRE GFF file
Genome_build: Aspergillus fumigatus A1163 (CADRE)
Supplementary_files_format_and_content: counts_RPKM.xls

organism: Aspergillus fumigatus CEA10

source_name: Hyphae/ Blood

growth_protocol: A. fumigatus spores were cultivated in RPMI/ 5% FCS for 14 h, human neutrophils were isolated from fresh blood and mixed 1:1 with hyphae

extract_protocol:
After selected time points, RNA from fungus and neutrophils were isolated with Qaigen Plant Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols; 100 bp paired-end

value: Neutrophils

tag: treatment protocol

value: Fungus and Neutrophils were cultivated separably over selected time points and were united for RNA isolation

tag: cultivation time (minutes)


title: D1C180


title: D4C90


title: D1C90


title: D5C90


title: D6C90


title: D5C30


title: TM67


title: D6C30


title: D6T180

value: Fungus and Neutrophils were cultivated together over selected time points and than RNA was isolated


title: D1C30


title: D2T180


title: D1T180


title: D4T180


title: D5T30


title: D6T30


title: D6C180


title: D1T90


title: D6T90


title: D1T30


title: D4T0


title: D4T90


title: D1T0


title: D5T0


title: H3K27ac_ChIPSeq

city: DURHAM

first: Alejandro

last: Berrio

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

data_processing:
Reads from 9 individuals divided in three pools were combined
ChIP and INPUT reads were aligned to the vole genome (MicOch1.0) using bwa 0.7.12
Non-unique and low quality alignments (Phred =<20) were removed using samtools 0.1.18
We used Model-based Analysis of ChIP-Seq (MACS2 2.0.10) to find peaks with significant enrichment compared to the INPUT control (q value cutoff = 0.05).
Genome_build: Genome_build: MicOch1.0
Supplementary_files_format_and_content: Significant peak regions (q value < 0.05) reported by MACS2 are tabulated in .xls format, visualization of Fold-Enrichment  across the genome in bdg

organism: Microtus ochrogaster

source_name: Ventral Pallidum

extract_protocol:
Theventral pallidum was collected from freshly dissected brains and immediately fixed. Cells and nuclei were lysed on ice. Chromatin was extracted and sheared. Antibody against H3K27ac was used to pull down putative enhancer DNA using magnetic beads
Libraries were prepared for Illumina sequencing using KAPA Library Preparation Kit (cat# KK8230) according to manufacturer's protocol

value: Brain

tag: antibody

value: H3K27ac antibody (Abcam, ab4729)


title: Input_ChIPSeq


title: 20mo male

status: Public on Jan 30 2018

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Old male

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

organism: Mus musculus

source_name: Thymus

growth_protocol: Animals kept in SPF conditions

extract_protocol:
Total RNA was extracted from sorted B cells using Invitrogen RNAaqueous micro kit
RNA libraries were prepared using standard Illumina protocols

treatment_protocol: Thymocytes were stained with CD19-APC, tagged with anti-APC magnetic beads (Miltenyi Biotec) and magnetically enriched. CD19+ were sorted from enriched samples using BD FACS Aria to a minimum purity of 98.5% or better.

value: CD19+ thymic B cells

tag: age

value: 20 months

tag: strain


title: Young male (1.5mo)

description: Young male

value: 1.5 months


title: 5wo male #2

description: Young male

value: 5 weeks


title: 16mo female

description: Old female

value: 16 months


title: 4wo female #2

description: Young female

value: 4 weeks


title: Old female (10mo)

description: Old female

value: 10 months


title: D5T90


title: 18mo male

description: Old male

value: 18 months


title: D4T30


title: D6T0


title: young female (2mo)

description: Young female

value: 2 months


title: ES_rep1

first: Thomas

last: Graf

address: c/Dr. Aiguader, 88. PRBB Building

department: Gene Regulation, Stem Cells and Cancer

institute: CRG (Center for Genomic Regulation)

data_processing:
Reads were aligned using STAR, default mode for paired-end data
Gene expression was quantified using bedtools multibamcov
Sample scaling and statistical analysis were performed using the R package DESeq2 (1.6.3) (R 3.1.0 and bioconductor 3.0)
Genome_build: GRCm38.78
Supplementary_files_format_and_content: bigWig files used for browser exploration of the data.

source_name: embryo (inner cell mass)

growth_protocol: B and Ba cells were grown in RPMI medium; D2-D8, iPS and ES in N2B27 medium. All cells were grown on feeders (mitomycin-C treated mouse embryonic fibroblasts)

extract_protocol:
Cells were collected, seperated from feeders by pre-plating and RNA was extracted using the miRNeasy mini kit (Qiagen).
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit.

treatment_protocol: C/EBPa was induced with beta-estradiol; OSKM with doxycycline.

value: embryo (inner cell mass)

tag: culture

value: low passage (p<10)


title: D1_ATAC

data_processing:
Reads were mapped to the UCSC mouse genome build (mm10) using Bowtie2 with standard settings.
Reads mapping to multiple locations in the genome were removed using SAMtools.
PCR duplicates were filtered using Picard.
Bam files were parsed to HOMER for downstream analyses and browser visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files used for browser exploration of the data.

source_name: bone marrow

growth_protocol: B and Ba cells were grown in RPMI medium; D2-D8 and ES in N2B27 medium. All cells were grown on feeders (mitomycin-C treated mouse embryonic fibroblasts)

extract_protocol:
Cells were collected, seperated from feeders by pre-plating and genomic DNA was tagmented using the Tn5 transposase.
Libraries were constructed using the Illumina Nextera DNA Library Prep Kit.

value: bone marrow

value: cultured primary cells (short term)


title: iPS_rep1

value: low passage (p<5)


title: iPS_rep2


title: D8_rep2

value: primary cells (short term)


title: ES_rep2


title: 1mo female

description: Young female

value: 1 month


title: D8_rep1


title: 5wo male #1

description: Young male


title: 2 yo male

description: Old male

value: 24 months


title: D6_rep1


title: D4_rep2


title: D2_rep1


title: D2_rep2


title: D4_rep1


title: 4wo female #1

description: Young femlae

value: CD19+ thymic B cells


title: Ba_rep2


title: D8_ATAC

extract_protocol:
Cells were collected, seperated from feeders by pre-plating and genomic DNA was tagmented using the Tn5 transposase.
Libraries were constructed using the Illumina Nextera DNA Library Prep Kit. Tagmented DNA was amplified for 12-14 cycles using primers described in Buenrostro et al. (Nature Methods 2014). Amplified libraries were purified and size-selected (200-800bp) using Ampure XP beads.


title: B_rep2


title: D4C30

value: Neutrophils

value: Fungus and Neutrophils were cultivated separably over selected time points and were united for RNA isolation


title: PSC_ATAC


title: D6_ATAC


title: Ba_rep1


title: B_rep1


title: TM83

value: delta-ech::FRT delta-vht::FRT delta-frh delta-hpt::PmcrB-fC31int-attB


title: D4_ATAC


title: D6_rep2


title: Ba_ATAC


title: D2_ATAC


title: PSC_HiC_rep1

data_processing:
Reads were pre-processed using Trimmomatic with the recommended arguments for paired end reads (ILLUMINACLIP:TruSeq3-PE.fa:2:30:12:1:true LEADING:3 TRAILING:3 MAXINFO:targetLength:0.999 MINLEN:36, where the adapters’ file (TruSeq3-PE.fa) was the one provided with the software
TADbit’s fragment based mapping module (aligning with GEM) with the default parameters was used to align reads.
TADbit’s filtering module was used  to filter out non-informative contacts (self-circle, dangling ends, extra-dangling ends, errors, duplicated and random breaks).
Contact matrices were obtained and poor bins (containing low counts) were filtered out using TADbit’s routines.
A single round of ICE was performed to remove biases and obtain normalized matrices, that were leveled to obtain an average  content of one interaction per cell, also with TADbit
Raw and normalized counts at 50kb resolution are stored as tab-separated files with chromosome as first column, first genomic coordinate of the first bin as second column, first genomic coordinate of the second bin as third column and number of contacts as fourth column.
Genome_build: mm10
Supplementary_files_format_and_content: 50kb contact matrices, both with raw contacts and normalized contacts.

extract_protocol:
Cells were collected and seperated from feeders by pre-plating. Crosslinked nuclei were digested with MboI followed by fill-in with bio-dATP, in-situ ligation and DNA extraction.
DNA was sonicated and libraries were constructed using the the NEBNext DNA Library Prep Kit (New England Biolabs). Libraries were amplified for 8-12 cycles using Illumina TruSeq primers. Amplified libraries were purified and size-selected (>250bp) using Ampure XP beads.


title: PSC_HiC_rep2


title: D8_HiC_rep2


title: D4C180


title: D6_HiC_rep1


title: D4_HiC_rep2


title: D4_HiC_rep1


title: D2_HiC_rep2


title: D2_HiC_rep1


title: Ba_HiC_rep1


title: Ba_HiC_rep2


title: B_HiC_rep2


title: B_HiC_rep1


title: D8_CTCF_ChIPseq

growth_protocol: B and Ba cells were grown in RPMI medium; D2-D8 and iPS cells in N2B27 medium. All cells were grown on feeders (mitomycin-C treated mouse embryonic fibroblasts)

extract_protocol:
Cells were collected and seperated from feeders by pre-plating. Crosslinked and sonicated chromatin was immunoprecipitated with H3K4me2 or CTCF antibodies.
CTCF ChIP-Seq libraries were constructed using the Illumina TruSeq ChIP Library Preparation Kit; H3K4me2 ChIPm-Seq libraries were generated using the  Illumina Nextera DNA Library Prep Kit.

value: CTCF (Millipore/07-729)


title: D2_CTCF_ChIPseq


title: D4_CTCF_ChIPseq


title: D6_CTCF_ChIPseq


title: Ba_4C_rep1

data_processing:
Library strategy: 4C-Seq
The sequence of the reading primer was trimmed from the 5’ of reads using the demultiplex.py script from the R package fourCseq (allowing 4 mismatches). Reads in which this sequence could not be found were discarded.
Reads were mapped using STAR and processed using fourCseq to filter out reads not located at the end of a valid fragment and to count reads per fragment.
Signal tracks were made after smoothing RPKM counts per fragment with a running mean over five fragments.
Genome_build: mm10
Supplementary_files_format_and_content: Aligned sequencing  reads to restriction fragments for each sample

growth_protocol: B and Ba cells were grown in RPMI medium; D2 and ES in N2B27 medium. All cells were grown on feeders (mitomycin-C treated mouse embryonic fibroblasts)

extract_protocol:
Cells were collected and seperated from feeders by pre-plating. Crosslinked nuclei were digested with Csp6I followed by ligation under dilute conditions and DNA extraction.
DNA was digested with DpnII and again ligated under dilute conditions to generate PCR-amplifiable circular DNA. Libraries were constructed using inverse-PCR (30 cycles) with viewpoint-specific primers carrying Illumina sequencing adapters.


title: D2_4C_rep2


title: PSC_4C_rep2


title: Bcell_4C_rep1


title: D8_HiC_rep1


title: D2_4C_rep1


title: Bcell_4C_rep2


title: Ba_4C_rep2


title: P30_230_tech_rep1_wt

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

data_processing:
alignment was done with GSNAP-gmap-2015-06-23
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
Genome_build: mm9
Supplementary_files_format_and_content: complete_GEO_rnaseq.xlsx: normalized read counts for genes.
Supplementary_files_format_and_content: TableS1.xlsx: Complete lists of genes and transcripts of the 13 developmental clusters.
Supplementary_files_format_and_content: TableS2.xlsx: GO enrichments of the 13 developmental clusters. Bonferroni-corrected pvalues are represented in Zscore values.
Supplementary_files_format_and_content: TableS3.xlsx: Lists of markers of cell types and cell subtypes.
Supplementary_files_format_and_content: TableS4.xlsx: Developmental profiles of markers.
Supplementary_files_format_and_content: TableS5.xlsx: Validation of astrocytes drivers.
Supplementary_files_format_and_content: TableS6.xlsx: Validation of ependymal drivers.
Supplementary_files_format_and_content: TableS7.xlsx: Validation of interneurons drivers.
Supplementary_files_format_and_content: TableS8.xlsx: Validation of macrophages drivers.
Supplementary_files_format_and_content: TableS9.xlsx: Validation of oligodendrocytes drivers.
Supplementary_files_format_and_content: TableS10.xlsx: Validation of pyramidal neurons drivers.

source_name: whole hippocampus

extract_protocol:
Total RNA was Trizol extracted. RNA was treated with DNase (Qiagen, 79254) and purified on the RNeasy MinElute Cleanup Kit (Qiagen, 74204). 2000 ng of total RNA were treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Illumina MRZH11124). Depleted RNA was precipitated 1 h at -80°C in three volumes of ethanol plus 1 µg of glycogen. RNA was then washed and resuspended in 36 µl of RNase free water. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution and the RNA was fragmented by incubation at 95°C for 3 minutes. For reverse transcription, cDNA first strand synthesis was performed with random examer primers. cDNA second strand synthesis was performed with dUNTPs, to ensure strand specificity.
The RNA-seq library was synthetized with KAPA Hyper prep kit (KK8504), a treatment with USER enzyme (NEB, M5505L) was added to digest the unspecific strand. The libraries were pooled (4/lane) and sequenced on the illumina HiSeq, which yielded approximately 40 million single-end reads per sample.

value: brain

tag: tissue compartment

value: hippocampus

value: wild type


title: P30_230_tech_rep3_wt


title: P30_1_223_wt


title: D6_HiC_rep2


title: P30_355_wt


title: P30_2_226_wt


title: P30_230_tech_rep2_wt


title: P15_5_wt


title: Bcell_ATAC


title: PSC_4C_rep1


title: P7_1_wt


title: P1_3_wt_2


title: P7_h4_wt


title: P15_6_wt


title: P1_4_wt


title: ef_WT_178_E7

source_name: whole embryonic forebrain

value: forebrain


title: P15_8_wt


title: P7_h1_wt


title: P1_3_wt_1


title: ef_178E10_wt


title: P1_7_wt


title: ef_179E1_wt


title: P30_2_234_wt


title: M2 INPUT

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

data_processing:
Sequenced reads quality was assessed using fastQC
Sequenced reads were aligned to the human genome (GRCh37/hg19) by using Bowtie2 version 2.2.3
In order to find the regions of ChIP-seq enrichment over background, we used different peak caller. For MYC ChIP-seq we used MACS2 (p-value 1x10-6), while for histone modifications we used SICER V1.1 (window size = 200; gap size = 200; FDR 0.01).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The bed files contains the genomic regions of the peaks identified after peak calling

growth_protocol: hTERT-immortalized human mammary epithelial cells (IMECs) and IMEC-MYC were cultured at 37°C and 5% CO2 in 1:1 DMEM/F-12 medium (gibco #11320-074) supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), bovine pituitary extract (BPE) (Clonetics, MEGM SingleQuots #CC-4136) and hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136). Spheres were cultured as follow: single cells were plated in ultralow attachment plates (Corning) at a density of 2x104 viable cells/ml in DMEM/F-12 medium supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136), B-27 Supplement (gibco # 17504044), 20 ng/ml human FGF-basic (PeproTech #100-18B) and 5 μg/ml heparin (Sigma-Aldrich #H3149). Formed mammospheres were collected after 6 days.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched by glycine at a final concentration of 0.125 M, for 5 min at room temperature. Cells were lysed in lysis buffer (50 mM Tris-HCl pH 8, 0.1 % SDS, 10 mM EDTA pH 8, 1 mM PMSF, protease inhibitor cocktail) and chromatin was sonicated to an average size of 0.1-0.5 kb, using a Branson D250 sonifier (4 cycles of 30 seconds, 20% amplitude).
Five nanograms of immunoprecipitaded and purified DNA were used to generate ChIP-seq libraries. Briefly, end repair of DNA fragments was achieved by sequential 15 min incubations at 12°C and 25°C with T4 PNK (10U/μl), T4 POL (3U/μl) and 0.1 mM dNTPs. A-base addition was performed by incubating end-repaired DNA fragments with Klenow (3’ → 5’ exo, 5U/μl) and 167 μM dATP for 30 min at 30°C. Adaptor ligation was achieved by using the NEB Quick ligation kit (M2200L) and perfoming an incubation of 15 min at 25°C. Processed DNA fragments were finally amplified with a thermal cycler for 14 cicles, by using the Agilent PfuUltra II Fusion HS DNA Pol kit (600674). All DNA purification steps between the different enzymatic reactions were performed by using Agencourt AMPure XP SPRI beads (Beckman, A63882). The obtained libraries were subjected to quality control on Agilent Bioanalyzer (Agilent Technologies, G2943CA).

treatment_protocol: IMECs and IMEC-MYC were maintained in DMEM/F-12 medium (gibco #11320-074) supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), bovine pituitary extract (BPE) (Clonetics, MEGM SingleQuots #CC-4136) and hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136). Spheres were cultured in DMEM/F-12 medium supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136), B-27 Supplement (gibco # 17504044), 20 ng/ml human FGF-basic (PeproTech #100-18B) and 5 μg/ml heparin (Sigma-Aldrich #H3149).

value: non-transformed human mammary epithelial cells

tag: gender

value: female

tag: cell fraction

tag: chip antibody

value: none (genomic DNA)


title: IMEC MYC H3K27ac

source_name: hTERT-immortalized human mammary epithelial cells

tag: tissue

value: IMEC MYC

value: anti-acethyl histone H3 Lys27 4729 Abcam


title: M2 H3K27ac


title: M2 H3K4me3

value: anti-trimethyl histone H3 Lys4 07-473 Millipore


title: M2 H3K4me1

value: anti-monomethyl histone H3 Lys4 8895 Abcam


title: IMEC MYC H3K4me3


title: IMEC MYC INPUT


title: P30_64_wt

tag: genotype


title: IMEC WT MYC

value: IMEC WT

value: anti-MYC sc-764 Santa Cruz Biotechnology


title: IMEC WT H3K27ac


title: IMEC WT H3K4me1


title: IMEC WT H3K4me3


title: Liver_131

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4.
Reads were mapped using TopHat2.
Counting of reads per gene was done using featureCounts
Counts were normalized to RPM and RPKM values as described in Mortazavi et al. (2008) taken gene lengths into account given by  featureCounts
Genome_build: mm10, RefSeq annotation from 2014-06-08
Supplementary_files_format_and_content: xls file containing read counts per gene, rpms and rpkms

source_name: liver

extract_protocol:
Total RNA was extracted using the prepGold total RNA kit.
Around 1 μg of total RNA was used for library preparation using Illumina TruSeq RNA sample prep kit v2 following the manufacturer's description.

value: Cd1 nu/nu

value: liver


title: Liver_112


title: Liver_132


title: Liver_130


title: IMEC WT INPUT


title: Liver_126

value: PBS


title: Liver_128


title: Liver_129


title: Liver_127


title: Liver_124


title: PSC_H3K4me2_ChIPm

value: bone marrow

value: low passage (p<5)

value: H3K4me2 (Abcam/ab32356)


title: M2 MYC


title: Liver_125


title: IMEC MYC MYC


title: IMEC MYC H3K4me1


title: D6_H3K4me2_ChIPm

value: primary cells (short term)


title: D4_H3K4me2_ChIPm


title: B_H3K4me2_ChIPm


title: Ba_H3K4me2_ChIPm


title: D2_H3K4me2_ChIPm


title: PLAC8-EGFP1

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: trophoblast cells over expressed with PLAC8

data_processing:
After removing bacodes, adapters and low-quality reads, clean reads were mapped to the human genome (hg19 version) with Tophat (Langmead et al., Genome Biology,  Biology, 2009, 10, R25) allowing 2 mismatches.Gene expression level was calculated as reads per kilobases per million reads (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: The expression level (RPKM and reads count) and GO/KEGG annotation of genes in each sample.

source_name: HTR8-Svneo cell line

growth_protocol: HTR8/Svneo cells were  cultured in the normal CO2 incubator for 48 h with the RPMI 1640 medium (contain 10% FBS).

extract_protocol:
RNA was harvested using Trizol reagent and extracted with chloroform. RNA concentration and quality were tested by Agilent 2100.  0.2 ug of total RNA was utilized for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard dUTP strand-specific RNA-seq library  protocols

treatment_protocol: No special treatment.

tag: condition

value: overexpression of PLAC8

tag: passages

tag: group

value: experiment


title: CON-EGFP2

description: trophoblast cells over expressed with control plasmid

value: overexpression of EGFP

value: control


title: CON-EGFP1


title: RELA ChIP-seq M tri-DAP dup1

city: Singapore

first: Lisa

last: Borghini

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Infectious Diseases

country: Singapore

institute: GIS

description: processed data file: MtriDAP_peaks.bed

data_processing:
mapping of the reads to hg19 with BWA
Filtering with samtools 1.2 (samtools view -bh -F 1804 -q 20)
Peak calling with Dfilter 1.5 (run_dfilter15.sh -f=bam -ks=20 -bs=50 -lpval=2 -nonzero -refine -wig) and IDR method: For each RELA ChIP-seq replicate, 3 calls were carried out against different controls as following: (a) against no treatment control RELA ChIP-seq, (b) against input DNA and (c) against both no treatment control RELA ChIP-seq and Input DNA merged together. The first 100,000 most confident peaks were extracted from each call. Irreproducibility Discovery Rate (IDR) analysis was performed first between calls (a) and (b) for each replicate (IDR analyses 1 and 2 beside for replicates 1 and 2 respectively), then between calls (c) of each duplicates (IDR analysis 3 beside). This strategy allows discovery of both reproducible peaks against the 2 controls within each replicates, and in between the 2 duplicates. The peaks with IDR<=0.05 were considered reproducible. The number of reproducible peaks in IDR analysis 1 and 2 was lower than in IDR analysis 3, so the reproducible peaks identified in IDR analysis 3 were considered the final peaks for a condition. Coordinates of the final peaks were extracted from the IDR analysis output by taking the overlap of the coordinates from the 2 duplicates with Bedops –intersect command.
Black listed regions were removed found in wgEncodeDacMapabilityConsensusExcludable.bed (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/) were removed from the final list of peaks using bedtools intersect command. Any peaks falling in chromosome Y was also filtered out as the cell line studied is derived from a female.
Genome_build: hg19
Supplementary_files_format_and_content: For each duplicates, a WIG file generated from the peak call (C) is given.  For each condition, the final reproducible peaks are given in a bed file.

source_name: RELA ChIP-seq M tri-DAP

growth_protocol: Detroit 562 cells were purchased from ATCC and cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum performance (Gibco), 100U/ml penicillin, 100ug/ml streptomycin (Gibco) and 1mM sodium pyruvate (Gibco).

extract_protocol:
After treatment, cells were crosslinked with 0.75% formaldehyde for 8 minutes and cross-linking was quenched with 180mM Glycine for 10 minutes at room temperature. Cells were then lysed with cell lysis buffer (0.25% Triton X-100, 10mM EDTA, 0.1M NaCl in 10mM Tris-HCl pH8) for 20 minutes at 4°C. Nuclei were collected by centrifugation at 4,000rpm for 10 minutes at 4°C and lysed in nuclei lysis buffer (1% NP-40, 0.5% NaDOC, 0.1% SDS in PBS) for 20 minutes at 4°C. Chromatin shearing was performed using a sonicator (Bioruptor, Diagenode) on high setting for 45 cycles of 30 seconds ON/45 seconds OFF, leading to a fragment range of 100-250bp.
ChIP-seq libraries were built following the library-on-beads protocol from Wallerman et al. (Wallerman et al. 2015). Chromatin was incubated with anti-RELA antibody (NFKB p65 (c20): sc-372) bound to protein G magnetic beads (Dyanabeads protein G, Thermo Fisher scientific) prepared by mixing 4ug of antibody with 40uL of beads in PBS+0.5%BSA for 4 to 6 hours at room temperature. Immunoprecipitation was performed by rotation at 4°C overnight. After immunoprecipitation, samples were washed twice with nuclei lysis buffer, twice with nuclei lysis buffer complemented with 350mM NaCl, twice with LiCl/NP-40 buffer (0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% NaDOC in 10mM Tris-HCl pH8) and once with PBS. Libraries on beads were then built using NEBnext DNA library prep kit (New England Biolabs) according to the manufacturer’s instructions. Due to the nature of the samples, minor adjustments were done: two washes with PBS were performed in between each step of the preparation and elution of the DNA from the beads was done after adaptor ligation. ChIP samples were eluted in Elution buffer (10mM EDTA, 1% SDS in 50mM Tris-HCl pH7.5) for 4 hours at 65°C and purified with Agencourt AMPure XP beads (Beckman Coulter). PCR reaction was performed using Phusion High-Fidelity PCR Master Mix (Thermo scientific) and custom primers for multiplexing. The following program was applied: 3 minutes at 98°C; 17x(30 seconds at 98°C, 30 seconds at 65°C, 30 seconds at 72°C); 5 minutes at 72°C. Samples were loaded on a DNA1000 bioanalyzer chip (Agilent) to check the size of the libraries as well as the concentration. As a control, 2-5% of input DNA was reverse cross-linked at 65°C for minimum 6 hours and libraries were prepared using the same library preparation kit.  Samples were sequenced on an Illumina HiSeq Rapid 2x76bp.

treatment_protocol: Detroit 562 cells were treated with LPS at 1μg/mL for 80 minutes, TNFα at 10ng/mL for 50 minutes, Pam2CSK4 at 1μg/mL for 60 minutes, Poly I:C at 10μg/mL for 90 minutes or M tri-DAP at 15 μg/mL for 90 minutes.  For each experiment, a “no treatment” control consisting of a change of culture medium was processed along with the treated samples.

tag: cell type

value: Detroit 562 cells

value: M tri-DAP

tag: batches


title: RELA ChIP-seq Poly I:C dup2

description: processed data file: PolyIC_peaks.bed

source_name: RELA ChIP-seq Poly I:C

tag: treatment

value: Poly I:C


title: RELA ChIP-seq Poly I:C dup1

description: processed data file: PolyIC_peaks.bed


title: RELA ChIP-seq M tri-DAP dup2

description: processed data file: MtriDAP_peaks.bed


title: Liver_123


title: RELA ChIP-seq Pam2CSK4 dup2

description: processed data file: Pam2CSK4_peaks.bed

source_name: RELA ChIP-seq Pam2CSK4


title: RELA ChIP-seq TNFa dup1

description: processed data file: TNFa_peaks.bed

source_name: RELA ChIP-seq TNFa

value: TNFa


title: D8_H3K4me2_ChIPm


title: RELA ChIP-seq Pam2CSK4 dup1

description: processed data file: Pam2CSK4_peaks.bed


title: RELA ChIP-seq LPS dup2

description: processed data file: LPS_peaks.bed

source_name: RELA ChIP-seq LPS

value: LPS


title: RELA ChIP-seq LPS dup1

description: processed data file: LPS_peaks.bed


title: RELA ChIP-seq No Treatment Batch 4

source_name: RELA ChIP-seq No Treatment

value: no treatment


title: RELA ChIP-seq No Treatment Batch 3


title: RELA ChIP-seq No Treatment Batch 5


title: RELA ChIP-seq No Treatment Batch 1


title: RELA ChIP-seq No Treatment Batch 8


title: PLAC8-EGFP2


title: Input DNA

source_name: Input DNA

value: no batch


title: RELA ChIP-seq No Treatment Batch 2


title: Old human rep 3

description: replicate 3

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

growth_protocol: Human patients undergoing corrective heart surgery

treatment_protocol: Thymocytes were stained with CD19-APC, tagged with anti-APC magnetic beads (Miltenyi Biotec) and magnetically enriched. CD19+ were sorted from enriched samples using BD FACS Aria to a minimum purity of at least 98.5% or better.

value: CD19+ thymic B cells

value: 61 years


title: Old human rep 1

description: replicate 1

value: 42 years


title: RELA ChIP-seq No Treatment Batch 7


title: Young human rep 3

description: replicate 3

value: 4 years


title: Old human rep 2

description: replicate 2

value: 57 years


title: Young human rep 2

description: replicate 2

value: 5 months


title: No treatment RNA-seq Batch3

data_processing:
mapping of the reads to hg19 with TopHat
Differential gene expression analysis with CuffDiff, using the Ensemble gtf file GRCh37.73 and running the treated condition against the non-treated condition (for the same batch) bam file (cuffdiff-2.2.0 -u -o xxx GRCh37.73_+chrm.gtf no_treatment.bam treatment.bam)
Calculate the average Log2 (Fold change) for each condition: mean of the Log2 (Fold change) of both duplicates for each condition
Genome_build: hg19
Supplementary_files_format_and_content: For each replicate, the 'gene_exp.diff' output file from cuffdiff against non-treated sample is given

source_name: No treatment RNA-seq

extract_protocol:
Total RNAs were extracted using the RNeasy Plus Universal kit (Qiagen) and loaded on a NanoRNA Bioanalyzer chip (Agilent) for qualification and quantification.
Libraries for RNA-seq were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s instructions.  Samples were sequenced on an Illumina NextSeq-High 1x76bp

treatment_protocol: Detroit 562 cells were treated with LPS at 1μg/mL for 100 minutes, TNFα at 10ng/mL for 70 minutes, Pam2CSK4 at 1μg/mL for 80 minutes, Poly I:C at 10μg/mL for 110 minutes or M tri-DAP at 20 μg/mL for 110 minutes.   For each experiment, a “no treatment” control consisting of a change of culture medium was processed along with the treated samples.

value: No treatment

tag: batch


title: Young human rep 1

description: replicate 1

value: 3 months


title: No treatment RNA-seq Batch4


title: RELA ChIP-seq TNFa dup2

description: processed data file: TNFa_peaks.bed


title: RELA ChIP-seq No Treatment Batch 6


title: No treatment RNA-seq Batch1


title: No treatment RNA-seq Batch2


title: M tri-DAP RNA-seq rep2

source_name: M tri-DAP RNA-seq


title: Poly I:C RNA-seq rep2

source_name: Poly I:C RNA-seq


title: M tri-DAP RNA-seq rep1


title: LS2 rep2

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

description: low starch S2 period replicate2

data_processing:
Clean reads were acquired from initial pair-end reads after trimming low quality (Q < 20) and adaptor sequences by SeqPrep version 1.1
Clean reads from high starch and low starch samples were pooled together to perform the de novo transcriptome assembly using Trinity program (version 2.3.2) with the default K-mer parameter and minimum K-mers coverage of ten, and only transcripts whose length is no less than 200 bp were remained for continue analysis.
Unigenes were annotated by searching against the protein databases including NCBI nr protein database (NCBI non-redundant database), Swiss-Prot database, Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and Cluster of Orthologous Group (COG) database using BLASTX program with the expectation value less than 10-5.
Differentially expressed genes were identified with the edgeR package. Classic model of edgeR was used for the differential expression analysis with false discovery rate (FDR) of 0.05 and two-fold change of Fragments Per Kilobase of gene per Millon mapped reads (FPKM) as significant cutoffs.
Functional enrichment analysis was performed using GOstats. With the hypergeometric test p-value less than 0.001 and gene number more than 50, we got the Gene Ontology enrichment terms. For KEGG enrichment pathways, we used p-value less than 0.01 and gene number more than 5 as threshold.
Supplementary_files_format_and_content: txt file of FPKM value for each sample

organism: Ipomoea batatas

source_name: 65-day-old roots

growth_protocol: Roots of both cultivars were transferred to pots (one per pot) with 18 replicates each in greenhouse under natural light conditions.

extract_protocol:
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
Libraries were constructed through using TruSeq Stranded mRNA in accordance with the standard Illumina instruction.

value: roots

tag: cultivar


title: Poly I:C RNA-seq rep1


title: LS3 rep2

description: low starch S3 period replicate2

source_name: 100-day-old roots

tag: age


title: LS2 rep1

description: low starch S2 period replicate1


title: LS3 rep3

description: low starch S3 period replicate3


title: LS3 rep1

description: low starch S3 period replicate1


title: LS1 rep3

description: low starch S1 period replicate3

source_name: 30-day-old roots


title: LS1 rep2

description: low starch S1 period replicate2


title: Pam2CSK4 RNA-seq rep2

source_name: Pam2CSK4 RNA-seq


title: LS1 rep1

description: low starch S1 period replicate1


title: TNFa RNA-seq rep2

source_name: TNFa RNA-seq


title: LS2 rep3

description: low starch S2 period replicate3


title: LPS RNA-seq rep2

source_name: LPS RNA-seq


title: HS3 rep1

description: high starch S3 period replicate1

value: Chuanshu 218


title: TNFa RNA-seq rep1

value: Detroit 562 cells


title: Pam2CSK4 RNA-seq rep1


title: HS3 rep2

description: high starch S3 period replicate2


title: HS2 rep3

description: high starch S2 period replicate3


title: LPS RNA-seq rep1


title: HS2 rep1

description: high starch S2 period replicate1


title: HS2 rep2

description: high starch S2 period replicate2


title: HS1 rep2

description: high starch S1 period replicate2


title: HS1 rep3

description: high starch S1 period replicate3


title: HS1 rep1

description: high starch S1 period replicate1


title: HUDEP2 (ΔGγ) WT ZBTB7A ChIP-seq Input

status: Public on Jan 29 2018

city: Sydney

first: Merlin

last: Crossley

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

description:
hg38_modified_chr11_genome.fa
hg38refGene_modified_chr11.txt
hg38_modified_chr11.genome

data_processing:
Quality filtering and adapter trimming using Trimmomatic v0.3.2
Reads were aligned to human genome GRCh38 (hg38) using Bowtie v2.2.9 set to --very-sensitive. For the ZBTB7A ChIP-seq in HUDEP2 cells reads were aligned to a modified version of GRCh38 (provided) which had a 4928bp deletion and a point mutation on chr11 between HBG1 and HBE. All downstream analysis for this dataset was done using the modified genome and an associated gene annotation file (provided).
Read coverage tracks were generated using BEDTools genomecov, extending reads based on predicted fragment size and normalising all samples to have the equivalent of 1 million mapped reads. For the BCL11A HUDEP-2 and ZBTB7A K562 ChIP-seq datasets, tracks were generated from all primary mapped alignments to better visualise the read coverage over the γ-globin locus. This was primarily due to the HBG1/HBG2 duplication where reads would align equally to both genes but Bowtie would distribute reads evenly and give a mapping quality score of 1. Tracks for the ZBTB7A ChIP-seq in HUDEP-2(DGg) cells were generated from all unique alignments (mapping quality (MAPQ) > 10).
Peak calling for all datasets was done using the spp package on unique alignments (mapping quality (MAPQ) > 10) after removing duplicates with Picard MarkDuplicates (http://broadinstitute.github.io/picard/).
Where replicates were available, a set of consistent peaks (IDR=0.05) were identified using IDR2 (https://github.com/nboley/idr).
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph (.bdg) files were generated using BEDTools genomecov as mentioned for each sample. BED/regionPeak files contain peaks which were generated from spp or after IDR analysis (optimal peak list was used) as mentioned for each different ChIP-seq. fasta file (gh38_modified_chr11_genome.fa) contains a modified hg38 genome that has a 4928bp deletion on chr11 as mentioned to use for alignment for the HUDEP-2 (ΔGγ) cells. The GenePred Table format file (hg38refGene_modified_chr11.txt) contains modified gene annotations for chr11 to account for the 4928bp deletion and was used for downstream analysis for ChIP-seq in HUDEP-2 (ΔGγ) cells. .genome file is a file that allows the custom genome to be loaded on IGV to be able to view tracks from the HUDEP-2 (ΔGγ) cells ChIP-seq.

source_name: HUDEP2 (ΔGγ) WT ZBTB7A ChIP-seq Input

growth_protocol: HUDEP-2 cells were grown in StemSpan SFEM supplemented with SCF (50 ng/mL), EPO (3 IU/mL), dexamethasone (10‑6M) and doxycycline (1 µg/mL). Media was made up fresh every time before use and supplemented with 1 × penicillin, streptomycin and L-glutamine. Cells were maintained at a concentration of 5x105 cells/mL. K562 cells were maintained in RPMI1640 supplemented with 10% fetal calf serum and 1 × penicillin, streptomycin and L-glutamine.

extract_protocol:
ChIP experiments were performed as previously described (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using highthroughput  sequencing to discover protein-DNA interactions. Methods. Jul 2009;48(3):240-248). Briefly, approximately 5x107-1x108 cells were used for each IP. Cells were crosslinked with 1 % formaldehyde for 10-15 min at RT and the reaction was quenched with glycine at a final concentration of 125 mM. Crosslinked cells were then lysed and sonicated to obtain ~200–300 bp fragments of chromatin. Crosslinked DNA was pulled down at 4 °C overnight using antibody against V5-tag (R960CUS, Life Technologies), ZBTB7A (Santa Cruz Biotechnology Inc, sc-33683 x and eBioscience, 14-3309-82) or control anti-goat IgG (sc-2028). Chromatin was then reverse crosslinked and eluted at 65°C overnight and DNA was purified.If ChIP material was subjected to sequencing, DNA was purified using a Qiagen MinElute Reaction Clean-up kit.
Standard Illumina TruSeq

tag: cell line

tag: antibody


title: HUDEP2 (ΔGγ)195C>G ZBTB7A ChIP-seq

source_name: HUDEP2 (ΔGγ)195C>G ZBTB7A ChIP-seq

value: ZBTB7A (Santa Cruz Biotechnology Inc, sc-33683 x and eBioscience, 14-3309-82)


title: HUDEP2 (ΔGγ) WT ZBTB7A ChIP-seq

source_name: HUDEP2 (ΔGγ) WT ZBTB7A ChIP-seq


title: HUDEP2 BCL11A-ER-V5 ChIP-seq Input 2

source_name: HUDEP2 BCL11A-ER-V5 ChIP-seq Input 2

value: Induction of the BCL11A-ER-V5 system was achieved with the addition of 4-hydroxytamoxifen (dissolved in 100% ethanol) at a final concentration of 10-7 M (0.1 nmol). Cells were harvested after 24 hours of induction for downstream experimentation.


title: SHEP21_24HR_POL2_NOSPIKE

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Chromatin IP against RNA Pol II in SHEP-21N,20hr after tet treatment

data_processing:
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

growth_protocol: SK-N-AS, SH-SY5Y, NGP, BE(2)-C, and KELLY cells were kindly provided by Dr. Kimberly Stegmaier (Dana Farber Cancer Institute) and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS. SHEP-21N cells were kindly provided by Dr. William Weiss (University of California, San Francisco) and cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech). Tet-Off MYCN shutdown was performed by addition of doxycycline (0.2μg/mL) to growth media

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

value: neuroblastoma cell line

tag: growth condition

value: 10% Tet-Free FBS, RPMI

tag: treated with

value: 0.2 ug/mL DOX for 2HR

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody catalog #

tag: input

tag: barcode

value: TGACCACT


title: HS3 rep3

description: high starch S3 period replicate3

tag: tissue


title: HUDEP2 BCL11A-ER-V5 ChIP-seq Rep 2

source_name: HUDEP2 BCL11A-ER-V5 ChIP-seq Rep 2

value: V5-tag (R960CUS, Life Technologies)


title: SHEP21_2HR_POL2_NOSPIKE

description: Chromatin IP against RNA Pol II in SHEP-21N, 24hr after tet treatment

treatment_protocol: Tet-Off MYCN shutdown was performed by addition of doxycycline (0.2μg/mL) to growth media

value: 0.2 ug/mL DOX for 24HR

tag: chip antibody

value: TTAGGCAT


title: HUDEP2 BCL11A-ER-V5 ChIP-seq Rep 1

source_name: HUDEP2 BCL11A-ER-V5 ChIP-seq Rep 1


title: GROseq_spt5l_rep2

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: GROseq in spt5l (rep2)

data_processing:
Library strategy: GRO-Seq
GRO-seq: Qseq files from the sequencer were demultiplexed and converted to fastq format with a customized script for downstream analysis. For GRO-seq data, paired-end reads were first trimmed for Illumina adaptors and primers using Cutadapt (v 1.9.1). After trimming, reads less than 10bp long were removed with a customized Perl script. Paired-end reads were then separately aligned to the reference TAIR10 genome using Bowtie (v1.1.0) by allowing only unique hit (-m 1) and up to 3 mismatches (-v 3). Pair reads aligned to positions within 2000bp to each other were considered as correct read pairs using, and reads aligned to Watson or Crick strands were separated by a customized Perl script.
ChIP-seq: Reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie 1.0.0, allowing only uniquely mapping reads with less than two mismatches, and duplicated reads were combined into one read. NRPE1 ChIP-seq peaks were called using MACS2 (v 2.1.1.) with default parameters. ChIP-seq metaplots were plotted using NGSplot (v 2.41.4).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files

organism: Arabidopsis thaliana

source_name: floral tissue, spt5l-1

growth_protocol: All plants were grown on soil under long day conditions (16 hours light, 8 hours dark). Inflorescence tissues were collected and used for the GRO-seq procedure.

extract_protocol:
GRO-seq: Approximately 10 grams of inflorescence and meristem tissue was collected from plants and immediate placed in ice cold grinding buffer (300 mM sucrose, 20 mM Tris, pH 8.0, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, 35% glycerol). Nuclei were isolated as described previously. Briefly, samples were ground with an OMNI International General Laboratory Homogenizer at 4°C until well homogenized, filtered through a 250µm nylon mesh, 100µm nylon mesh, miracloth, and finally a 40µm cell strainer before being split into 50ml conical tubes. Samples were spun for 10 minutes at 5250g, the supernatant was discarded, and the pellets were pooled and resuspended in 25ml of grinding buffer using a dounce homogenizer. The wash step was repeated at least once more and nuclei were resuspended in 1ml of freezing buffer (50 mM Tris, pH 8.0, 5 mM MgCl2, 20% glycerol, 5 mM β-mercaptoethanol). Approximately 5x10e6 nuclei in 200 µl of freezing buffer were run-on in 3x GRO-reaction buffer 16 with. Reactions were stopped after 5 minutes to minimize run on length (~5-15 nts) while still incorporating brUTP by addition of 750 µl Trizol LS and RNA purified according to the manual. Without fragmentation or Terminator treatment, nascent RNA was enriched twice for BrU by αBrdU (Santa Cruz Biotechnology sc-32323AC) and immunoprecipitated as described in Hetzel et al. 2016.
ChIP-seq: Chromatin immunoprecipitation was performed from 2 grams of formaldehyde crosslinked flower tissue as previously described, except that half of the input was immunoprecipitated with 3 µg of affinity purified anti-NRPE1 antibody (Covance) that recognizes the peptide N-CDKKNSETESDAAAWG- C49, and the other half was immunoprecipitated with pre-immune serum as control.
GRO-seq: Sequencing libraries were prepared from precipitated RNA using TruSeq Small RNA Library Prep kit following manufacturer instructions (Illumina). For GROseq in Col-0, nrpd1, nrpe1 and nrpd1/e1 double mutants, 14 cycles of PCR were used to amplify the libraries and the products ranging from 100 to 500bp were size selected by agarose gel. The libraries were sequenced on Illumina HiSeq 2000 platform by paired-end 100bp sequencing. For GROseq in spt5l, 14 cycles of PCR were used to amplify the libraries and the products were size selected by double SPRI bead purification (ratio of Ampure beads to library: 0.5:1 to 1.1:1).
ChIP-seq: DNA libraries for Illumina sequencing were generated using the Ovation Ultralow V2 system (Nugen).

tag: ecotype/background

value: Columbia

tag: genotype/variation

value: floral


title: HUDEP2 BCL11A-ER-V5 ChIP-seq Input 1

source_name: HUDEP2 BCL11A-ER-V5 ChIP-seq Input 1


title: SHEP21_0HR_POL2_NOSPIKE_R2

description: Chromatin IP against RNA Pol II in SHEP-21N, 0hr after tet treatment

tag: cell type

value: 0.2 ug/mL DOX for 0HR

value: TACAGGAT


title: GROseq_spt5l_rep1

description: GROseq in spt5l (rep1)


title: BE2C_shT_6HR_rep2

description: RNA-seq of BE(2)-C cells with a tetracycline inducible TWIST1 shRNA at 3 ,6, 12, 24, and 48 hours after induction with 0.5ug/ml doxycycline

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: BE2C_TWIST_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript; BE2C_TWIST_all_fpkm_exprs_norm.txt:  Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

molecule: polyA RNA

source_name: Neuroblastoma

growth_protocol: BE(2)-C cells cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS. BE(2)-C engineered cells expressing inducible shTWIST1 cultured in DMEM supplemented with Tetracycline-Free FBS (Clontech).

extract_protocol:
Prior to RNA isolation, cell numbers were determined and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.
Total RNA was subject to polyA selection and adapter ligation in preparation for next-generation sequencing (Illumina stranded mRNA library prep)

treatment_protocol: BE(2)-C cells were treated with 1μM JQ1 (DMSO stock solution) at the indicated timepoints.  Tet-on shTWIST1 expression was performed by addition of doxycycline (0.5μg/mL) to growth media.

value: BE(2)-C with tetracycline inducible shTWIST1

tag: bar code

value: AGTTCC


title: BE2C_shT_6HR_rep3

value: ATGTCA


title: BE2C_shT_nodox_rep1

description: RNA-seq of BE(2)-C cells with a tetracycline inducible TWIST1 shRNA with no doxycycline treatment

value: CGATGT


title: BE2C_shT_48HR_rep2

value: TAGCTT


title: BE2C_shT_nodox_rep2

value: TGACCA


title: BE2C_shT_48HR_rep1

value: GATCAG


title: BE2C_shT_48HR_rep3

value: GGCTAC


title: HUDEP2 (ΔGγ)195C>G ZBTB7A ChIP-seq Input


title: BE2C_shT_3HR_rep1

value: GCCAAT


title: BE2C_shT_3HR_rep2

value: CAGATC


title: BE2C_shT_24HR_rep2

value: TTAGGC


title: BE2C_shT_24HR_rep3

value: ACTTGA


title: BE2C_shT_24HR_rep1

value: ATCACG


title: BE2C_shT_nodox_rep3

value: ACAGTG


title: BE2C_shT_12HR_rep1

value: CCGTCC


title: BE2C_shT_12HR_rep3

value: GTGAAA


title: BE2C_shT_12HR_rep2

value: GTCCGC


title: BE2C_JQ1_8HR_2

description: RNA-seq of BE(2)-C cells at 4,8, and 24 hours after 1uM JQ1 treatment


title: BE2C_JQ1_8HR_3


title: BE2C_JQ1_8HR_1

value: AGTCAA


title: BE2C_JQ1_4HR_3

value: CTTGTA


title: BE2C_shT_6HR_rep1

value: BE(2)-C with tetracycline inducible shTWIST1


title: BE2C_DMSO_B1

description: RNA-seq of BE(2)-C cells treated with DMSO

value: CGATGT


title: BE2C_JQ1_24HR_2


title: BE2C_DMSO_B3


title: BE2C_JQ1_24HR_1


title: SHEP_6HR_MYCN

description: Chromatin IP against MYCN in SHEP on cells with tetracycline inducible MYCN at 0,2,6 hours upon treatment with 0.2ug/ml doxycycline

growth_protocol: SHEP_tet-on MYCN cells were cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech).

treatment_protocol: Tet-On MYCN induction was performed by addition of doxycycline (0.2μg/mL) to growth media

value: SHEP with tetracycline inducible MYCN

tag: treatment

value: 0.2ug/ml doxycycline

tag: growth protocol

value: 10% Tet-Free FBS, RPMI

value: TGGTTGTT

value: MYCN

value: abcam

tag: chip antibody cat. #


title: BE2C_DMSO_B2

tag: cell line

value: TGACCA


title: SHEP_0HR_INPUT

description: Input control for SHEP on cells with tetracycline inducible MYCN at 0,2,6 hours upon treatment with 0.2ug/ml doxycycline

value: TGTACCTT


title: SHEP_2HR_INPUT

value: TTCTGTGT


title: SHEP_2HR_MYCN

value: CTTGTACT


title: SHEP_6HR_H3K27AC

description: Chromatin IP against H3K27ac in SHEP on cells with tetracycline inducible MYCN at 0,2,6 hours upon treatment with 0.2ug/ml doxycycline

value: TCCGTCTT


title: SHEP_2HR_H3K27AC

value: TAAGCGTT


title: SHEP21_2HR_INPUT

description: Spike in normalized input for SHEP21-N, 2hr after doxycycline treatment

data_processing:
Sequenced reads were aligned to a custom reference bowtie2 index combinging the HG19 and MM9 genome builds
ChIP_RX scaling factors were determined as in Orlando et al., 2014, "Quantitative ChIP-Seq normalization reveals global modulation of the epigenome", PMID 25437568
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19:mm9
Supplementary_files_format_and_content: Processed ChIP-Rx datasets are provided in a cell count normalized scaled bedgraph format. File HG19_SHEP21_SCALE.txt contains ChIP-Rx scale factors for each dataset

growth_protocol: SHEP-21N cells were kindly provided by Dr. William Weiss (University of California, San Francisco) and cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech). Tet-Off MYCN shutdown was performed by addition of doxycycline (0.2μg/mL) to growth media

extract_protocol:
ChIP-Rx was performed as described previously substituting mouse embryonic stem cells in place of Drosophila S2 cells (Orlando et al., 2014). Mouse embryonic stem (ES) cells were grown to 75% confluence and cross-linked with 1% formaldehyde followed by quenching (125 mM glycine) as described in the previous section. Cells were washed in cold PBS and harvested by cell scraper in cold PBS with protease inhibitors (Roche). Cells were centrifuged at 1650 x g for 5 minutes and flash frozen and stored at -80°C 10E06 cells per pellet. Fixed mouse ES cell pellets were resuspended in a cytosolic lysis buffer and then spiked directly into the cytosolic lysate of fixed neuroblastoma cells at a ratio of 5% of the total number of cells. The lysate (neuroblastoma cells spiked with mouse ES cells) was then carried through the ChIP protocol.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

value: 0.2 ug/mL DOX for 2HR

value: TGACCACT

tag: antibody

tag: antibody maker

tag: antibody catalog number


title: SHEP_0HR_MYCN

value: GGCTACAG

tag: chip antibody vendor


title: BE2C_shT_3HR_rep3

value: BE(2)-C with tetracycline inducible shTWIST1

value: CTTGTA


title: BE2C_JQ1_24HR_3

value: GTGAAA


title: SHEP_0HR_H3K27AC

value: SHEP with tetracycline inducible MYCN

value: 0.2ug/ml doxycycline

value: TCTCGGTT


title: SHEP21_2HR_CTCF

description: Spike in normalized ChIP-Seq for CTCF in SHEP21-N, 2hr after doxycycline treatment

value: 0.2 ug/mL DOX for 24HR

value: 10% Tet-Free FBS, RPMI

value: TAGCTTGT

value: CTCF

value: EMD Millipore


title: SHEP21_2HR_H3K4ME3

description: Spike in normalized ChIP-Seq for H3K4me3 in SHEP21-N, 2hr after doxycycline treatment

value: CAGATCTG


title: SHEP21_24HR_H3K4ME3

description: Spike in normalized ChIP-Seq for H3K4me3 in SHEP21-N, 24hr after doxycycline treatment

value: ACTTGATG


title: SHEP21_24HR_CTCF

description: Spike in normalized ChIP-Seq for CTCF in SHEP21-N, 24hr after doxycycline treatment


title: BE2C_JQ1_4HR_2

value: CAGATC


title: SHEP21_0HR_H3K4ME3

description: Spike in normalized ChIP-Seq for H3K4me3 in SHEP21-N, 0hr after doxycycline treatment

value: GCCAATGT


title: SHEP21_0HR_CTCF

description: Spike in normalized ChIP-Seq for CTCF in SHEP21-N, 0hr after doxycycline treatment

value: GATCAGCG


title: SHEP21_0HR_INPUT

description: Spike in normalized input for SHEP21-N, 0hr after doxycycline treatment

value: TTAGGCAT


title: SHEP_6HR_INPUT

value: TCTGCTGT


title: SHEP21_6HR_RNA-seq_rep2

description: RNA-seq of SHEP-21N, 6hr, rep2

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: SHEP21_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript. Please note that the rep0, rep1, rep2 in the *txt files corresponds to rep1, rep2 and rep3 in the sample title, respectively.; SHEP21_all_fpkm_exprs_norm.txt:  Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript. Please note that the rep0, rep1, rep2 in the *txt files corresponds to rep1, rep2 and rep3 in the sample title, respectively.

growth_protocol: SHEP-21N cells were cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech).

treatment_protocol: TET-off MYCN shutdown was performed by addition of doxycycline (0.2 micrograms/mL) to the growth media for the inidicated timepoints.

value: neuroblastoma cell line

tag: treated with

value: doxycycline (0.2 ug/ml) for 6hrs

value: GTCCGC


title: SHEP21_8HR_RNA-seq_rep1

description: RNA-seq of SHEP-21N, 8hr, rep1

value: doxycycline (0.2 ug/ml) for 8hrs

value: CGATGT


title: SHEP21_6HR_RNA-seq_rep3

description: RNA-seq of SHEP-21N, 6hr, rep3

value: GTGAAA


title: SHEP21_4HR_RNA-seq_rep2

description: RNA-seq of SHEP-21N, 4hr, rep2

value: doxycycline (0.2 ug/ml) for 4hrs

value: AGTTCC


title: SHEP21_4HR_RNA-seq_rep3

description: RNA-seq of SHEP-21N, 4hr, rep3

value: ATGTCA


title: SHEP21_6HR_RNA-seq_rep1

description: RNA-seq of SHEP-21N, 6hr, rep1

value: CCGTCC


title: SHEP21_8HR_RNA-seq_rep3

description: RNA-seq of SHEP-21N, 8hr, rep3

value: ACAGTG


title: SHEP21_8HR_RNA-seq_rep2

description: RNA-seq of SHEP-21N, 8hr, rep2

value: TGACCA


title: SHEP21_4HR_RNA-seq_rep1

description: RNA-seq of SHEP-21N, 4hr, rep1

value: AGTCAA


title: SHEP21_2HR_RNA-seq_rep2

description: RNA-seq of SHEP-21N, 2hr, rep2

value: doxycycline (0.2 ug/ml) for 2hrs

value: CAGATC


title: SHEP21_2HR_RNA-seq_rep3

description: RNA-seq of SHEP-21N, 2hr, rep3

value: CTTGTA


title: SHEP21_24HR_RNA-seq_rep2

description: RNA-seq of SHEP-21N, 24hr, rep2

value: doxycycline (0.2 ug/ml) for 24hrs


title: SHEP21_24HR_RNA-seq_rep1

description: RNA-seq of SHEP-21N, 24hr, rep1

value: neuroblastoma cell line


title: SHEP21_16HR_RNA-seq_rep3

description: RNA-seq of SHEP-21N, 16hr, rep3

value: doxycycline (0.2 ug/ml) for 16hrs


title: SHEP21_2HR_RNA-seq_rep1

description: RNA-seq of SHEP-21N, 2hr, rep1

value: GCCAAT


title: SHEP21_24HR_RNA-seq_rep3

description: RNA-seq of SHEP-21N, 24hr, rep3


title: SHEP21_24HR_INPUT

description: Spike in normalized input for SHEP21-N, 24hr after doxycycline treatment

tag: input

value: 0.2 ug/mL DOX for 24HR

value: 10% Tet-Free FBS, RPMI

value: ACAGTGGT


title: SHEP21_0HR_RNA-seq_rep3

description: RNA-seq of SHEP-21N, 0hr, rep3

value: doxycycline (0.2 ug/ml) for 0h


title: NGP_ATAC

description: ATAC-seq of NGP

data_processing:
library strategy: ATAC-seq
Paired end reads were aligned to HG19 referenece genome using bowtie2 with the following parameters: --end-to-end --sensitive --no-unal --no-discordant --mm
Aligned bams were filtered and sorted using samtools by removing chrM, filtering against the ENCODE blacklist, and removing discordant reads.
Peaks were called using MACS1.4 with  p-val =1e-9
Genome_build: hg19
Supplementary_files_format_and_content: Processed ATAC data files are in wiggle format

growth_protocol: SK-N-AS, SH-SY5Y, NGP, BE(2)-C, and KELLY cells were kindly provided by Dr. Kimberly Stegmaier (Dana Farber Cancer Institute) and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS. SHEP-21N cells were kindly provided by Dr. William Weiss (University of California, San Francisco) and cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech).

extract_protocol:
A total of 50,000 cells were lysed, subject to transposition reaction using transposase enzyme (Illumina Nextera DNA preparation kit, cat#: FC-121-1030), and purified using Qiagen MinElute PCR purification kit.
Library amplification was performed using custom Nextera primers and the number of total cycles determined by running a SYBR-dye based qPCR reaction and calucalting the cycle number that corresponds to ¼ the maximum. Amplified libraries were purified using a Qiagen PCR purification kit.

value: NGP

value: Neuroblastoma

tag: growth condition

value: 10% FBS, DMEM

tag: barcode

value: TTCTGCCT


title: SHEP21_0HR_RNA-seq_rep2

description: RNA-seq of SHEP-21N, 0hr, rep2

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: SHEP21_all_fpkm_exprs_raw.txt: Tab-delimited text file matix containing raw FPKM values for each transcript. Please note that the rep0, rep1, rep2 in the *txt files corresponds to rep1, rep2 and rep3 in the sample title, respectively.; SHEP21_all_fpkm_exprs_norm.txt:  Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript. Please note that the rep0, rep1, rep2 in the *txt files corresponds to rep1, rep2 and rep3 in the sample title, respectively.. Please note that the rep0, rep1, rep2 in the *txt files corresponds to rep1, rep2 and rep3 in the sample title, respectively.

value: TGACCA


title: MM1S_ATAC

description: ATAC-seq of MM1.S

source_name: Multiple Myeloma

value: Multiple Myeloma

value: 10% FBS, RPMI

value: CGAGGCTG


title: SHEP21_16HR_RNA-seq_rep1

description: RNA-seq of SHEP-21N, 16hr, rep1


title: SHEP21_16HR_RNA-seq_rep2

description: RNA-seq of SHEP-21N, 16hr, rep2

value: CAGATC


title: SHEP21_ATAC

description: ATAC-seq of SHEP-21N, 0hr

value: CCTCTCTG


title: KELLY_ATAC

description: ATAC-seq of KELLY

value: KELLY

value: CATGCCTA


title: SHEP21_2HR_INPUT_NOSPIKE_rep2

description: Input for SHEP21-N, 2hr (replicate 2)

value: neuroblastoma cell line

value: 0.2 ug/mL DOX for 2HR

tag: chip antibody

value: ATCACGTT


title: BE2C_ATAC

description: ATAC-seq of BE(2)-C

value: TCGCCTTA


title: SHEP21_2HR_TWIST

description: Chromatin IP against TWIST in SHEP-21N, 2hr

value: 10% Tet-Free FBS, RPMI

value: TWIST

value: abcam

value: CGATGTTT


title: SHEP21_2HR_MYCN

description: chromatin IP against MYCN in SHEP-21N, 2hr

value: MYCN

value: GCCAAT


title: SHEP21_2HR_INPUT_NOSPIKE

description: Input for SHEP21-N, 2hr

value: CGATGT


title: SHEP21_24HR_MYCN_NOSPIKE

description: Chromatin IP against MYCN in SHEP-21N, 24hr

value: 0.2 ug/mL DOX for 24HR

value: GCCAATGT


title: SHEP21_2HR_H3K27AC_NOSPIKE

description: Chromatin IP against H3K27ac in SHEP-21N, 2hr

value: ACAGTG


title: SHEP21_24HR_INPUT_NOSPIKE_rep2

description: Input for SHEP21-N, 24hr (replicate 2)


title: SHEP21_0HR_TWIST

description: Chromatin IP against TWIST1 in SHEP-21N, 0hr

value: TTCAGCTC


title: SHEP21_24HR_B_TWIST

description: Chromatin IP against TWIST1 in SHEP-21N, 24hr


title: SHEP21_0HR_MYCN_NOSPIKE

description: Chromatin IP against MYCN in SHEP-21N, 0hr

value: TCCTCAAT


title: SHEP21_24HR_H3K27AC_NOSPIKE

description: Chromatin IP against H3K27ac in SHEP-21N, 24hr


title: NGP_MYCN

description: Chromatin IP against MYCN in NGP

value: NGP

value: 10% FBS, DMEM

value: TAGTCTTG


title: KELLY_INPUT

description: Input for KELLY

value: KELLY

value: neuroblastoma cell line

value: TTAGGC


title: SHEP21_0HR_H3K27AC_NOSPIKE

description: Chromatin IP against H3K27ac in SHEP-21N, 0hr

value: 10% Tet-Free FBS, RPMI

value: TGACCA


title: KELLY_MYCN

description: Chromatin IP against MYCN in KELLY

value: abcam

value: TTCCATTG


title: KELLY_H3K27AC

description: Chromatin IP against H3K27ac in KELLY

value: CAGATC


title: NGP_H3K27AC

description: Chromatin IP against H3K27ac in NGP

value: GCCAAT


title: NGP_INPUT

description: Input for NGP

value: CGATGT


title: SHEP21_0HR_INPUT_NOSPIKE

description: Input for SHEP21-N, 0hr

value: ATCACG


title: BE2C_TWIST

description: Chromatin IP against TWIST in BE(2)-C

value: TWIST

value: TAACGCTG


title: SHEP21_0HR_POL2_CHIPRX

description: Spike in normalized chromatin IP against RNA Pol 2 in SHEP-21N, 0hr

value: Santa Cruz


title: SHEP21_2HR_INPUT_CHIPRX

description: Spike in normalized input for SHEP21-N, 2hr

value: 0.2 ug/mL DOX for 2HR

value: ACAGTG


title: SHEP21_24HR_POL2_CHIPRX

description: Spike in normalized chromatin IP against RNA Pol 2 in SHEP-21N, 24hr

value: 0.2 ug/mL DOX for 24HR


title: SHEP21_24HR_MYCN_CHIPRX

description: Spike in normalized chromatin IP against MYCN in SHEP-21N, 24hr

value: MYCN


title: SHEP21_2HR_POL2_CHIPRX

description: Spike in normalized chromatin IP against RNA Pol 2 in SHEP-21N, 2hr

value: neuroblastoma cell line


title: SHEP21_0HR_INPUT_CHIPRX

description: Spike in normalized input for SHEP21-N, 0hr

value: AACACG


title: SHEP21_0HR_MYCN_CHIPRX

description: Spike in normalized chromatin IP against MYCN in SHEP-21N, 0hr

value: 10% Tet-Free FBS, RPMI


title: SHEP21_24HR_INPUT_CHIPRX

description: Spike in normalized input for SHEP21-N, 24hr

value: TTAGGC


title: SHEP21_24HR_INPUT_NOSPIKE

description: Input for SHEP21-N, 24hr


title: THMYCN_139423_H3K27Ac

description: Chromatin IP against H3K27ac in tumors from Th-MYCN mice

data_processing:
Sequenced reads were aligned to MM9 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: mm9
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

source_name: Th-MYCN mouse

growth_protocol: All experimental protocols were monitored and approved by The Institute of Cancer Research Animal Welfare and Ethical Review Body, in compliance with guidelines specified by the UK Home Office Animals (Scientific Procedures) Act 1986 and the United Kingdom National Cancer Research Institute guidelines for the welfare of animals in cancer research (Workman et al., 2010). Th-MYCN mice were genotyped to detect the presence of human MYCN transgene 27. Palpable intra-abdominal tumors or ganglia from Th-MYCN mice at 12-14 days of age were dissected and harvested for ChIP and immunohistochemistry.

extract_protocol:
For ChIP, tumors and ganglia were immediately flash frozen in liquid nitrogen and stored at -80°C. For immunohistochemistry, tumor and ganglia tissue were immediately fixed in 4% paraformaldehyde before being processed.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

tag: tissue

value: THMYCN tumor

tag: strain

value: Th-MYCN

value: TGCGATCT

value: abcam


title: THMYCN_139076_input

description: Chromatin whole cell extract input control in tumors from Th-MYCN mice

value: TTCTGTGT


title: THMYCN_139076_MYCN

description: Chromatin IP against MYCN in tumors from Th-MYCN mice

value: TTGGAGGT


title: THMYCN2_input

value: TCAGGAGG


title: THMYCN2_MYCN

value: TCCAGTCG


title: THMYCN1_input

value: TGAACTGG


title: THMYCN1_H3K27Ac

value: GGCACAAC


title: CG_H3K27Ac

description: Chromatin IP against H3K27ac in celiac ganglia from Th-MYCN mice

value: celiac ganglia

value: CTTGTACT


title: SCG_input

description: Chromatin whole cell extract input control in superior cervical ganglia from Th-MYCN mice

value: superior cervical ganglia

value: TGGTTGTT


title: CG_input

description: Chromatin whole cell extract input control in celiac ganglia from Th-MYCN mice

value: GGCTACAG


title: SHEP21_24HR_H3K27AC_CHIPRX

description: Spike in normalized chromatin IP against H3K27ac in SHEP-21N, 24hr

tag: cell type

value: neuroblastoma cell line

value: 0.2 ug/mL DOX for 24HR

value: 10% Tet-Free FBS, RPMI

value: GCCAAT


title: SHEP21_2HR_MYCN_CHIPRX

description: Spike in normalized chromatin IP against MYCN in SHEP-21N, 2hr

value: 0.2 ug/mL DOX for 2HR

value: MYCN


title: SHEP21_2HR_H3K27AC_CHIPRX

description: Spike in normalized chromatin IP against H3K27ac in SHEP-21N, 2hr

value: CGATGT

value: abcam


title: SHEP21_0HR_H3K27AC_CHIPRX

description: Spike in normalized chromatin IP against H3K27ac in SHEP-21N, 0hr

value: TGACCA


title: THMYCN_139423_input

value: THMYCN tumor

value: Th-MYCN

value: GGTTGGAC


title: Big94

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Tophat5 (version 2.0.4) was used for alignment with the following parameters: --bowtie1, --max-multihits  5, --genome-read-mismatches  1 --segment-mismatches  1 --segment-length 20 --splice-mismatches 0.
Gene expression levels were quantified with cufflinks (version 2.0.2) with the following parameters: -N, -u
Further, gene expression values were normalized for library size with cuffnorm following parameters:  -o  -L --library-norm-method classic-fpkm
The result was a matrix of normalized FPKM values
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: A tabular file with the normalized FPKM values for each sample

source_name: pancreas

growth_protocol: All animal procedures were approved by local and regional ethics committees (Institutional Animal Care and Use  Committee  and  Ethics  Committee  for  Research  and  Animal Welfare,  Instituto  de Salud  Carlos  III,  Madrid,  Spain)  and  performed  according  to  the  European  Union guidelines

extract_protocol:
Total pancreatic RNA was isolated using guanidine thiocyanate, followed by acid phenol chloroform extraction. RNA quality was assessed on an Agilent 2100 Bioanalyzer.
1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 6.6 to 9.2 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A; for samples Big104, Big90, Big92, Big18, Big277, Big 278, Big33, Big87, Big94, Big113, Big17, Big86) or in Illumina's "TruSeq RNA Sample Preparation v2 Protocol" (Part # 15026494 Rev. C; for samples Big408, Big409, Big410, Big416, Big417, Big423, Big454, Big459, Big461, Big465, Big467 and Big470). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (10 cycles or 8 for samples v2 protocol). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols."

treatment_protocol: A  mild  acute  pancreatitis  was  induced  by  seven  hourly  injections  of  the  CCK analog  caerulein  (Bachem)  at  50 ug/kg.  Briefly,  animals  were  weighted  before  the beginning of the procedure and caerulein was administered i.p. Mice were sacrificed by cervical dislocation 8h, 24h,and 48h after the first injection.

value: pancreas

tag: nr5a2 genotype

value: Saline

tag: mouse background


title: Big90

tag: treatment

value: Caerulin 24h


title: Big461

value: Careulin 48h


title: Big467


title: Big465


title: THMYCN_139076_H3K27Ac

value: TCTGCTGT

tag: chip antibody cat. #


title: Big470


title: Big454


title: Big459


title: Big87


title: Big423

value: Careulin 8h


title: Big86


title: SCG_H3K27Ac

description: Chromatin IP against H3K27ac in superior cervical ganglia from Th-MYCN mice

value: superior cervical ganglia

value: TAGCTTGT


title: Big416


title: Big410


title: Big3


title: Big409


title: Big18


title: Big277


title: Big278


title: BJ LncRNA kd4

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing:
Reads were aligned to the human genome (hg19) using TopHat2
Number of reads mapping to each gene was counted using HTseq and normalized using quantile normalization. Last, floor level of 20.0 was set.
Genome_build: hg19
Supplementary_files_format_and_content: quantile normalized counts

source_name: Immortalized primary fibroblasts

growth_protocol: Immortalized human BJ primary fibroblast cells (by hTERT expression) were cultured in DMEM supplemented with 10% heat-inactivated fetal calf serum (FCS) in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen), following the  manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen)
Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the  manufacturer's instructions.

treatment_protocol: cells treated with 4-OHT for 14 days

tag: cell line

value: BJ cells

tag: condition

value: Activation of RASG12V in BJ cells knocked-down for LncRNA-OIS1 (shRNA#32-9)


title: BJ p53kd

value: Activation of RASG12V in BJ cells knocked-down for p53


title: BJ BRD7 kd

value: Activation of RASG12V in BJ cells knocked-down for BRD7


title: BJ LncRNA kd3

value: Activation of RASG12V in BJ cells knocked-down for LncRNA-OIS1 (shRNA#32-8)


title: BJ.Ctr1

value: BJ Ctr1 (non targeting ShRNA 500) senescence induced by oncogenic RASG12V


title: BJ.Ctr2

value: BJ Ctr1 (non targeting ShRNA 507) senescence induced by oncogenic RASG12V


title: BE2C_H3K27ME3

description: Chromatin IP against BRD4 in BE(2)-C

value: neuroblastoma cell line

value: 10% FBS, DMEM

value: abcam

tag: chip antibody catalog #

value: ACAGTG


title: Big417

value: pancreas


title: Big104

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Tophat5 (version 2.0.4) was used for alignment with the following parameters: --bowtie1, --max-multihits  5, --genome-read-mismatches  1 --segment-mismatches  1 --segment-length 20 --splice-mismatches 0. Gene expression levels were quantified with cufflinks (version 2.0.2) with the following parameters: -N, -u.
Gene expression levels were quantified with cufflinks (version 2.0.2) with the following parameters: -N, -u
Further, gene expression values were normalized for library size with cuffnorm following parameters:  -o  -L --library-norm-method classic-fpkm
The result was a matrix of normalized FPKM values
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: A tabular file with the normalized FPKM values for each sample

value: Caerulin 24h


title: BJ LncRNA kd1

value: Activation of RASG12V in BJ cells knocked-down for LncRNA-OIS1 (shRNA#32-2)


title: BJ LncRNA kd2

value: Activation of RASG12V in BJ cells knocked-down for LncRNA-OIS1 (shRNA#32-3)


title: HEK-293TO-si-ZFR-1

city: Bethesda

first: J

middle: Robert

last: Hogg

state: MD

address: 50 South Drive, #2239

department: Biochemistry and Biophysics Center

institute: National Heart, Lung and Blood Institute

data_processing:
Sequencing reads in FASTQ format were aligned to the reference genome hg19 using STAR aligner.
Differential gene expression analysis was performed using the DESEQ2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values and fold expression change.

growth_protocol: HEK-293TO cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml of penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml of L-glutamine at 37°C and 5% CO2. Human monocytic THP-1 cells (ATCC) were maintained in ATCC-formulated RPMI-1640 medium supplemented with 10% FBS (Gibco), 0.05 mM 2-mercaptoethanol (Sigma), and 100 U/mL of Penicillin, 100 μg/mL Streptomycin (Gibco).

extract_protocol:
Qiagen RNeasy Mini RNA isolation kit
One μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq RNA Library Preparation Kit (Illumina).

treatment_protocol: Monocyte-like THP-1 cells were differentiated into macrophage-like cells with 5 ng/mL of phorbol-12-myristate-13-acetate (PMA, Sigma) for 72 hr.

value: Treated with ZFR siRNA

tag: genotype/variation

value: ZFR knockdown


title: HEK-293TO-si-ZFR-2


title: Big408

value: Careulin 8h


title: HEK-293TO-si-NS-3

value: Treated with non-specific siRNA

value: control


title: HEK-293TO-si-NS-2


title: Big17

value: Saline


title: BJ.Ctr

description: BJ.C

value: BJ cells

value: BJ Ctr (non targeting ShRNA 500)


title: Big92


title: HEK-293TO-si-ZFR-3


title: TPO4-TV11-mNG-H2B in vivo STAR+

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

country: United Kingdom

institute: Wellcome Sanger Institute

data_processing:
After trimming of barcodes, reads were aligned to the hg38 transcriptome annotation from UCSC with Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2) version 2.0.4 with reporting alignments tailored for transcript assemblers enabled.
Alligned reads were counted per transcript with the htseq-count script in the HTSeq framework.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files with readcounts per gene

source_name: colon oganoids

growth_protocol: Healthy tissue-derived organoids were maintained as described previously (van de Wetering et al., 2015). The basic culture medium (WENR) contained advanced Dulbecco’s modified Eagles Medium/F12 supplemented with penicillin/streptomycin, 10mM HEPES and 1x Glutamax, 1x B27 [all from Life Technologies], and 1,25mM N-acetylcysteine [Sigma]), supplemented with 10mM Nicotinamide, 500nM A83-01, 3uM SB202190, 10μM Y-27632, 50ng/mL human recombinant EGF (Peprotech), Wnt3A (CM, 50% final volume), RSpondin-1 (CM, 20% final volume), and Noggin (CM, 10% final volume). The TPO-series were maintained as described previously (Drost et al., 2015).

extract_protocol:
RNA from the FACS sorted organoids was extracted using the RNeasy RNA extraction kit (Qiagen) with DNAseI treatment.
A maximum of 250ng RNA per sample was used for ribosomal RNA depletion using the Ribo-Zero Gold rRNA removal kit (Illumina) followed by an ethanol precipitation. Afterwards the RNA was fragmented for 5 minutes at 95C using 5x fragmentation buffer (200mM tris-acetate, 500mM potassium acetate, 150mM magnesium acetate, pH 8.2). Ethanol precipitation was used to precipitate the fragmented RNA followed by first strand cDNA synthesis with Superscript III (Life Technologies) and second strand cDNA synthesis. Samples were purified using QIAquick MinElute columns (Qiagen) with ERC buffer. A maximum of 2ng cDNA per sample was used for library preparation using the Kapa Hyper Prep Kit (KAPA Biosystems). In short, end repair and A-tailing of the double stranded cDNA was done by incubating the cDNA with end repair and A-tailing buffer and enzyme mix followed by incubation at 20C for 30 minutes and 65C for 30 minutes. Afterwards, unique NEXTflex DNA barcodes (Bioo Scientific) were ligated to the samples by incubation with ligation buffer, DNA ligase, and the NEXTflex DNA barcode (14nM) for 15 minutes at 20C. The barcode ligated samples were purified using a 0.8x SPRI magnetic beads cleanup (Agencourt AMPure XP reagent). The purified samples were incubated for 15 minutes at 37C with USER enzyme (New England Biolabs) to digest the 2nd cDNA strand. Libraries were amplified by adding 2x KAPA HiFi Hotstart ReadyMix and 10x Library Amplification Primer Mix to the purified samples followed by PCR amplification (10 cycles). Amplified libraries were purified using QIAquick MinElute columns (Qiagen) followed by size selection of 300bp using E-Gel SizeSelect Agarose Gels 2% (Thermo Fisher Scientific). Size selected libraries were controlled for correct size selection using the BioAnalyzer (Agilent) and the concentration was measured using the KAPA Library Quantification Kit (KAPA Biosystems).
Sequencing was performed using a Illumina HiSeq 2000 machine and generated 50bp paired-end reads.

treatment_protocol: Organoids were harvested and trypsinized for 1-2 minutes at 37 ⁰C. Trypsin inhibitor in a 1:1 ratio with trypsin blocked the reaction. Cells were washed and spun down at 1200 RPM at 4 ⁰C. Next, the pellet was taken up into culture medium (human CRC or mouse intestinal organoid medium as described above, including 10μM Y-27632 and 2% Matrigel of the final volume) and passed through a 40μm filter. For xenotransplanted samples: Mice were sacrificed four months after transplantation with and the orthotopic tumors were carefully dissected. Tumors were minced in pieces of about 1-2 mm and digested in Collagenase Type II (Thermo Fisher Scientific) for 1h hour at 37 ⁰C while shaking. Next, cells were filtered through a 70 µm cell strainer, washed and spun down at 1200 RPM at 4 ⁰C. Finally, the pellet was collected into culture medium (human CRC as described above, including 10μM Y-27632). To label dead we incubated single cells with 3μM Draq7 (Cell Signaling) for 10 minutes. Viable cells were sorted using the Aria III (Becton Dickinson) and data was analyzed with FACS Diva software.

tag: facs sort

value: STAR positive

tag: cancer mutations

value: APC/TP53/KRAS/SMAD4 mutant

tag: organoid line

value: Normal human colon from patient tissue (P11N) and APC/TP53/KRAS/SMAD4 introduced via CRISPR

tag: xenotransplanted

value: yes


title: TPO4-TV11-mNG-H2B in vivo STAR-

value: STAR negative


title: Big113

value: pancreas


title: TPO4-TV11-mNG-H2B STAR-

value: no


title: TPO4-TV11-mNG-H2B STAR+


title: TPO3-TV11-mNG-H2B STAR-

value: APC/TP53/KRAS mutant

value: Normal human colon from patient tissue (P11N) and APC/TP53/KRAS introduced via CRISPR


title: TPO2-TV11-mNG-H2B STAR-

value: APC/TP53 mutant

value: Normal human colon from patient tissue (P11N) and APC/TP53 introduced via CRISPR


title: TPO APC-TV11-mNG-H2B STAR-

value: APC mutant

value: Normal human colon from patient tissue (P11N) and APC introduced via CRISPR


title: TPO APC-TV11-mNG-H2B STAR+


title: TPO2-TV11-mNG-H2B STAR+


title: p16T-TV11-mNG-H2B poly STAR-

value: Patient 16 polyclonal line


title: K562 ZBTB7A ChIP-seq Input 4

source_name: K562 ZBTB7A ChIP-seq Input 4

tag: antibody


title: K562 ZBTB7A ChIP-seq Input 3

source_name: K562 ZBTB7A ChIP-seq Input 3


title: p9T-TV9_#2 mono STAR-

value: Patient 9 monoclonal line


title: p9T-TV9_#2 mono STAR+


title: HEK-293TO-si-NS-1

value: Treated with non-specific siRNA

value: control


title: K562 ZBTB7A ChIP-seq Rep 4

source_name: K562 ZBTB7A ChIP-seq Rep 4

value: ZBTB7A (Santa Cruz Biotechnology Inc, sc-33683 x and eBioscience, 14-3309-82)


title: K562 ZBTB7A ChIP-seq Input 1

source_name: K562 ZBTB7A ChIP-seq Input 1


title: BE2C_RNA_POL2

description: Chromatin IP against RNA Pol 2 in BE(2)-C

value: neuroblastoma cell line

tag: growth condition

value: 10% FBS, DMEM

tag: treated with

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz

tag: input

tag: barcode

value: GCCAAT


title: BE2C_MYCN

description: Chromatin IP against MYCN in BE(2)-C

tag: cell type

value: MYCN

value: abcam

value: GTCCGC


title: BE2C_INPUT

description: Input for BE(2)-C

tag: chip antibody cat. #

value: ACAGTG


title: K562 ZBTB7A ChIP-seq Rep 1

source_name: K562 ZBTB7A ChIP-seq Rep 1

tag: cell line


title: TPO3-TV11-mNG-H2B STAR+

value: STAR positive

value: APC/TP53/KRAS mutant

value: Normal human colon from patient tissue (P11N) and APC/TP53/KRAS introduced via CRISPR

value: no


title: K562 ZBTB7A ChIP-seq Rep 3

source_name: K562 ZBTB7A ChIP-seq Rep 3


title: sox17-1.ESC.p7.rep2.E  (repli-seq)

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

institute: Florida State University

description:
clone replicate 2
K3-E-sox17-1-iPSCs_hg19.txt

data_processing:
Reads are mapped to customized hg19 harboring E-BAC backbone sequences (see chrB-tetP.fa linked as supplementary file on Series record) using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools
Log2 ratio of early to late coverage is calculated in 6kb windows
Log 2 ratio data were quantile normalized using R package preprocessCore
Genome_build: hg19
Supplementary_files_format_and_content: CHR, Start_Position, and replication timing values of each sample

growth_protocol: HeLa-EBNA1 and E-BAC transfected cells were grown in 500mg/ml G418 and 0.2mg/ml hygromycin B, respectively. Raji cells were maintained in RPMI media supplemented with 10% fetal bovine serum.

extract_protocol:
Genome-wide RT profiles were constructed as previously described [45, 46]. Briefly, cells were pulse labeled with BrdU for 2 hours and separated into early and late S-phase fractions by Propidium iodide staining and flow cytometry. BrdU-substituted DNA from 40k early and late S-phase cells was immunoprecipitated by anti-BrdU antibody (Becton Dickinson 347580)
Sequencing libraries were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

treatment_protocol: HeLa-EBNA1or K3-EBNA1 were transfected with E-BACs.

value: K3-EBNA1 iPSC

tag: s phase fraction

value: Late S fraction


title: sox17-1.ESC.p7.rep2.L  (repli-seq)

value: Early S fraction


title: BE2C_BRD4

description: Chromatin IP against BRD4 in BE(2)-C

value: Bethyl

value: GTGAAA


title: sox17-1.ESC.P56.L  (repli-seq)

description:
pool
K3-E-sox17-1-iPSCs_hg19.txt


title: K562 ZBTB7A ChIP-seq Input 2

source_name: K562 ZBTB7A ChIP-seq Input 2


title: sox17-1.ESC.p7.rep1.L  (repli-seq)

description:
clone replicate 1
K3-E-sox17-1-iPSCs_hg19.txt


title: sox17-1.ESC.p7.rep1.E  (repli-seq)


title: Raji.L  (repli-seq)

value: Raji


title: p16T-TV11-mNG-H2B poly STAR+

value: Patient 16 polyclonal line


title: Raji.E  (repli-seq)


title: FOXA2CDT1 CHIPBS Rep2

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

description: FOXA2 ChIP bisulfite sequencing in FOXA2-CDT1 fusion cells

data_processing:
library strategy: ChIP-BS-Seq
For the analysis of methylation changes associated with FOXA2 binding, we redefined binding sites to maximize overlap with our ChIP-BS-Seq data as bisulfite conversion on small amounts of input DNA results in . To do this, we combined FOXA2 ChIP-seq data from BJFOXA2 cells 4days and 10days post induction. The summit of each peak was determined using MACs, then the region 200bp either side was selected, and overlapping regions merged to generate a list of 113,398 sites. We then intersected these regions with BJ fibroblast WGBS and 4day BJFOXA2 ChIP-BS-Seq datasets and selected only CpGs covered by at least 3 reads in both samples, giving a total of 42,086 sites and 135,785 CpGs. We used these same regions to select matched CpGs covered at ≥3X in the ChIP-BS-Seq data from the BJFOXA2 mimosine treated and released samples (n = 13,494 sites and 18,429 CpGs).  We compared individual CpG and mean FOXA2 binding site methylation, generated CpG count and coverage plots and calculated the distances between the summit and nearest CpG using custom R scripts. For comparison to ATAC seq data (described above), we used HOMER (Heinz et al., 2010) to generate enrichment composite plots for 2kb either side of our peaks.
Genome_build: Hg19
Supplementary_files_format_and_content: Bed files contain regions surrounding FOXA2 peak summits (600bps), methylated CpGs over total CpGs and methylation ratio out of 1000

growth_protocol: Clonal FOXA2 doxycycline inducible cells lines were derived from an immortalized BJ foreskin fibroblast cell line from ATCC (BJ-5ta; CRL-4001).  Cells were cultured in MEM-Alpha (Life technologies: 32561-037) with 10% FBS, 1% pen-strep, .01mg/mL hygromycin B and 5ng/mL bFGF.  Derived BJFOXA2 lines were grown in the same conditions plus .5ug/mL Puromycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
To generate bisulfite converted DNA libraries following ChIP, we used Nugen Ovation UltraLow Methyl-seq Kit (0335-0336).  Bisulfite conversion was performed with EpiTect Bisulfite kit (Qiagen) with carrier DNA.  Libraries were sequenced on a HiSeq 2500 8pmol with 35% PhiX spike in.

treatment_protocol: Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment over night. To induce FOXA2, doxycycline was added at .5ug/mL.

value: BJFOXA2 line

tag: source cell type

value: BJ Fibroblast


title: sox17-1.ESC.P56.E  (repli-seq)

description:
pool
K3-E-sox17-1-iPSCs_hg19.txt


title: K562 ZBTB7A ChIP-seq Rep 2

source_name: K562 ZBTB7A ChIP-seq Rep 2

value: ZBTB7A (Santa Cruz Biotechnology Inc, sc-33683 x and eBioscience, 14-3309-82)


title: BE2C_H3K4ME3

description: Chromatin IP against H3K4me3 in BE(2)-C

value: neuroblastoma cell line

value: 10% FBS, DMEM

value: EMD Millipore

value: CAGATC