title: BS-seq_H9_hPGCLC_d8


title: 48 hpf AB tBOOH rep 1

status: Public on Oct 10 2016

type: SRA

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 48 hours post-fertilization (hpf). Replicate 1

library_source: transcriptomic

data_processing:
Raw RNA-Sequencing (RNA-Seq) reads were obtained from HudsonAlpha as 50bp paired-end reads in FASTQ format with approximately 25 million reads per sample. Reads were analyzed for various quality control parameters including: per base sequence quality, per sequence GC content, sequence length distribution and sequence duplication levels and Kmer content using the FastQC tool (Version 0.11.4).
Reads were then aligned to the Ensembl GRCz10 zebrafish reference genome using Tophat2 (Version 2.0.14), which functions based on Bowtie2 alignment software (Version 2.2.5) using a mean inner distance of 300 bp, a maximum intron length of 380,000bp and all other parameters set to default values.
Read counts for each gene were then obtained for the aligned reads using the Htseq-counts tool (Version 0.6.1). The Tophat accepted hits BAM file was analyzed against the Ensembl GTF zebrafish gene annotation reference, with pre-sorting by name through Samtools Sort (Samtools version 0.1.19) within the Htseq-count software. Raw counts data obtained from Htseq-counts were normalized using DESeq2 (Version 1.10.1) in R (version 3.2.3, 64bit platform) using size factors obtained from the total dataset and virtual reference sample based on the data.
Genome_build: GRCz10
Supplementary_files_format_and_content: EXCEL DeSeq2 normalized counts

molecule: total RNA

organism: Danio rerio

growth_protocol: Adults were held in 2:1 female to male groups at a density of ≤ 5 fish/l in aerated, filtered, and re-circulated system water (28.5 °C) and fertilized eggs were obtained from multiple group breedings. Wildtype animals were on the AB background (Zebrafish International Resource Center, Eugene, OR). Fish husbandry protocols were approved by the Bates College Institutional Animal Care and Use Committee (Animal Welfare Assurance Number Number A3320-01) and the University of Michigan Institutional Animal Care and Use Committee (Animal Welfare Assurance Number Number A3114-01). To create a germline nfe2 knockout, a pair of vectors containing TAL effector nucleases (TALENs) targeting exon 3 of nfe2 were generated using the REAL (Restriction Enzyme And Ligation) assembly method. Component plasmids were obtained from Addgene (www.addgene.org/talengineering/talenkit/). Briefly, target sites were selected and TALENs designed using Zifit (http://zifit.partners.org/ZiFiT/), followed by assembly. mRNA was synthesized from the vectors and injected into single cell zebrafish embryos on an AB/TL hybrid background (Shavit et al, in preparation).  The TALEN target sequences are: 5'- TCACCCACCTCTTATGAG-3' and 5'- CATGACTACACGTGGTCA-3'.  A subsequent founder deletion of eight base pairs (GCACATGA) was found via sequencing in exon three starting at nucleotide position 468 from the translational start site; this deletion resulted in a frame shift, causing a change in protein sequence starting at amino acid 111 (M→ D) and the introduction of a premature stop codon 13 amino acids later.  The frameshift was introduced 161 amino acids prior to the Cap'n'collar (CNC) family basic leucine zipper domain that is responsible for DNA binding.

extract_protocol:
Total RNA was isolated from pooled animals using the Aurum Total RNA Mini Kit (BioRad, Hercules, California, USA) following the manufacturer’s protocol. At HudsonAlpha Institute for Biotechnology (Huntsville, AL, USA), the quality of the RNA was checked using Caliper Instrumentation (PerkinElmer, Waltham, MA, USA) and RiboGreen reagents (Invitrogen, Carlsbad, CA, USA).
Directional mRNA libraries with poly(A) selection were made using New England Biolabs (Ipswich, MA, USA) reagents:  NEBNext Poly (A) mRNA Isolation Magnetic Module, NEBNext First Strand Synthesis Module, NEBNext Second Strand Synthesis Module (with dUTP), NEBNext End Repair Module, NEBNext dA Tailing Module, and the NEBNext Quick Ligation Module.  Quality analysis of the libraries was carried out using PicoGreen (Thermo Fisher, Waltham, MA, USA) and Caliper instrumentation (PerkinElmer, Waltham, MA, USA). 50 base pair (bp), paired end, libraries were sequenced using the Illumina HiSeq v4 platform at HudsonAlpha Institute for Biotechnology (Huntsville, AL, USA).

treatment_protocol: Waterborne exposures to either diquat or tBOOH were carried out at three different developmental stages: 2 hours post fertilization (hpf), 48hpf, and 96hpf in 3 pools of 30 embryos per condition. Animals were exposed to no treatment, 20µM diquat or 1mM tBOOH for a 4-hour dosing period in glass scintillation vials in a 20mL volume of 0.3x Danieau’s. For phenotypic analysis, animals were moved to 0.3x Danieau’s for 48 hours post-exposure (hpe) and imaged with a Leica M165 FC stereoscope and DFC310FX camera. For RNA-Seq experiments, animals were moved to 0.3x Danieau’s for 4 hpe before being flash frozen using liquid nitrogen and stored at -80°C.

tag: developmental stage

value: embryo

tag: genotype

value: wildtype


title: BS-seq_H9_hPGCLC_d4_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Library strategy: PBAT
PBAT: Raw sequence reads from PBAT libraries were trimmed to remove poor quality reads and adapter contamination using Trim Galore (v0.4.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.14.4) (Krueger and Andrews, 2011) with the following set of parameters to the mouse reference genome GRCm38 or the human reference genome GRCh37 in paired-end mode: --pbat to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode for Read 1: --pbat; or single-end mode for Read 2: defaults. Reads were then deduplicated and CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
genome build: GRCh37
processed data files format and content: Bismark CpG coverage report files are from paired-end mapping only, are tab-delimited and use 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
PBAT: For small sample amounts (PGCLC samples) post-bisulfite adaptor tagging (PBAT) libraries were prepared directly from cell lysates following recently described protocols (Miura et al., 2012; Smallwood et al., 2014). PBAT libraries were prepared by bisulfite converting Proteinase K digested cell lysates using the EZ DNA Methylation-Direct Kit (Zymo). After cleanup, 1st strand synthesis was performed using 6N-forward oligos at 37°C for 90 minutes. Subsequently, samples were treated with Exonuclease I for 1 hour at 37°C, and DNA was purified using AMPure XP beads (Agencourt). Samples were eluted in 2nd strand synthesis mix with 6N-reverse oligos and incubated at 37°C for 90 minutes. DNA was purified and amplified with KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems). All amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. High-throughput sequencing of all libraries was carried out with a 125 bp paired-end protocol on a HiSeq 2000 instrument (Illumina).
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.

tag: background strain/cell line

tag: cell type

value: PGC-like cells (PGCLCs)

value: Wild-type


title: 2 hpf AB Water rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 2 hours post-fertilization (hpf). Replicate 1


title: Z.fish 64C 6mA-IP-seq (Ab antibody)

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

country: USA

institute: UChicago

data_processing:
Single-ended 50bp reads are mapped by Bowtie 1.0 to Z.fish genome (danRer10) with parameter -M 1  --best –strata.
Peaks are called by MACS2.0 by comparing IP reads with input reads.
Peaks called by MACS2.0 with qvalue < 0.01 are selected as significant peaks.
Genome_build: danRer10
Supplementary_files_format_and_content: bed files are generated by MACS2.0. The genomic loci and scores of peaks are included.

source_name: Z.fish embryo of 64 cell stage

growth_protocol: Zebrafish (Danio rerio) embryos were derived from the Tubingen zebrafish lines. Embryos were incubated in Holtfreter’s solution at 28.5ºC.

extract_protocol:
Phenol/chloroform extraction and DNA precipitation with 1/10 volume of 5 M NaCl and 1 volume of isopropanol were performed. The obtained DNA pellet was dissolved with 3dH2O.
NEBNext® DNA Library Prep Master Mix Set for Illumina® E6040L was used to construct Illumina compatible DNA library.

tag: strain

value: Tubingen

tag: antibody

value: m6A (Abcam, ab151230, lot 4c)

tag: Stage

value: 64-cell stage embryo


title: 2 hpf AB Water rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), water controls. RNA sampled at 2 hours post-fertilization (hpf). Replicate 2


title: BS-seq_H9_hPGCLC_d4_1


title: 2 hpf AB Diquat rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 2 hours post-fertilization (hpf). Replicate 1


title: 2 hpf AB tBOOH rep 1

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 2 hours post-fertilization (hpf). Replicate 1


title: 2 hpf AB Diquat rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 2 hours post-fertilization (hpf). Replicate 3


title: BS-seq_H9_hEpiLC_d4_2

data_processing:
WGBS: Raw sequence reads from WBGS libraries were trimmed to remove poor quality reads and adapter contamination, using Trim Galore (v0.3.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.14.4) (Krueger and Andrews, 2011) with default parameters to the mouse reference genome GRCm38 or the human reference genome GRCh37 in paired-end mode. Reads were then deduplicated and CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (v0.14.4) in paired-end mode.
genome build: GRCh37
processed data files format and content: Bismark CpG coverage report files are from paired-end mapping only, are tab-delimited and use 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol:
WGBS: DNA was isolated using Beckman Coulter's Agencourt RNAdvance Cell v2 kit and used for whole-genome bisulfite (WGBS) libraries (Seisenberger et al., 2012). Briefly, WGBS libraries were prepared by sonicating genomic DNA using a Covaris Sonicator, followed by end-repair, A-tailing and methylated adapter (Illumina) ligation using NEB-Next reagents. Subsequently, libraries were bisulfite treated using EZ DNA Methylation-Direct Kit (Zymo), followed by library amplification with indexed primers using KAPA HiFi Uracil HotStart DNA Polymerase (KAPA Biosystems). All amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. High-throughput sequencing of all libraries was carried out with a 125 bp paired-end protocol on a HiSeq 2000 instrument (Illumina).
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.

value: epiblast-like cells (EpiLC)


title: 2 hpf AB tBOOH rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 2 hours post-fertilization (hpf). Replicate 2


title: BS-seq_H9_hEpiLC_d2_2


title: 2 hpf AB Diquat rep 2

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 20 μM Diquat. RNA sampled at 2 hours post-fertilization (hpf). Replicate 2


title: BS-seq_H9_hEpiLC_d4_1


title: BS-seq_H9_hEpiLC_d3_1


title: 2 hpf AB tBOOH rep 3

description: 30 pooled zebrafish wildtype embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 2 hours post-fertilization (hpf). Replicate 3


title: BS-seq_H9_hEpiLC_d2_1


title: BS-seq_H9_hEpiLC_d3_2


title: BS-seq_E14_mPGCLC_d6_1

data_processing:
Library strategy: PBAT
PBAT: Raw sequence reads from PBAT libraries were trimmed to remove poor quality reads and adapter contamination using Trim Galore (v0.4.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.14.4) (Krueger and Andrews, 2011) with the following set of parameters to the mouse reference genome GRCm38 or the human reference genome GRCh37 in paired-end mode: --pbat to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode for Read 1: --pbat; or single-end mode for Read 2: defaults. Reads were then deduplicated and CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
genome build: GRCm38
processed data files format and content: Bismark CpG coverage report files are from paired-end mapping only, are tab-delimited and use 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

organism: Mus musculus


title: BS-seq_E14_mPGCLC_d6_2


title: 48 hpf Nfe2 KO tBOOH rep 2

description: 30 pooled zebrafish Nfe2 knock-out embryos (AB background), exposed to 1 mM tBOOH. RNA sampled at 48 hours post-fertilization (hpf). Replicate 2

value: Nfe2 knock-out


title: BS-seq_E14_mPGCLC_d4_4


title: BS-seq_H9_hEpiLC_d1_1


title: BS-seq_H9_hEpiLC_d1_2


title: BS-seq_E14_mPGCLC_d4_2


title: RNA-seq_hPGCLC d8

data_processing:
RNA-seq: RNA-seq sequences were trimmed using trim_galore (v0.4.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default settings. Trimmed data was separately mapped to the human GRCh37 or mouse GRCm38 genome assemblies using hisat2 (v2.0.5) with options --sp 1000,1000 --no-mixed --no-discordant, and was filtered to remove non-primary alignments or alignments with MAPQ < 20. Mapped RNA-seq data were quantitated using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
genome build: GRCh37
processed data files format and content: Quantitated human RNA-seq RPM file is tab delimited and contains the following 16 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-16) log2 RPM values for each sample

molecule: polyA RNA

source_name: RNA-seq_hPGCLC d8

extract_protocol:
RNA-seq: Total RNA for each sample was extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacturer’s instructions and DNAse treated (Ambion Turbo DNA-free). RNA-seq libraries from small sample amounts (PGCLC samples) were prepared using a modified SMART-Seq2 protocol (Picelli et al., 2014). Briefly, extracted RNA was polyA-enriched using biotinylated oligo-dT primer bound to streptavidin beads (Dynabeads) and reverse transcribed using SuperScript II reverse transcriptase (Invitrogen). cDNA was amplified and libraries were prepared using the Nextera DNA Library preparation kit (Illumina). Libraries were indexed using Illumina Indexes and 75 bp or 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.


title: BS-seq_E14_mPGCLC_d4_3


title: BS-seq_E14_mPGCLC_d4_1


title: RNA-seq_hPGCLC d5

source_name: RNA-seq_hPGCLC d5


title: BS-seq_H9_hPGCLC_d5


title: BS-seq_E14_mEpiLC_d2_3

data_processing:
WGBS: Raw sequence reads from WBGS libraries were trimmed to remove poor quality reads and adapter contamination, using Trim Galore (v0.3.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.14.4) (Krueger and Andrews, 2011) with default parameters to the mouse reference genome GRCm38 or the human reference genome GRCh37 in paired-end mode. Reads were then deduplicated and CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (v0.14.4) in paired-end mode.
genome build: GRCm38
processed data files format and content: Bismark CpG coverage report files are from paired-end mapping only, are tab-delimited and use 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>


title: RNA-seq_hPGCLC d4_2

source_name: RNA-seq_hPGCLC d4_2


title: RNA-seq_hPGCLC d4_1

source_name: RNA-seq_hPGCLC d4_1


title: BS-seq_E14_mEpiLC_d2_2


title: RNA-seq_hEpiLC_d4_3

extract_protocol:
RNA-seq: Total RNA for each sample was extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacturer’s instructions and DNAse treated (Ambion Turbo DNA-free). For RNA-seq, extracted RNA was polyA-enriched and used for library preparation using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions.
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.


title: RNA-seq_hEpiLC_d4_2


title: RNA-seq_hESC_3

value: embryonic stem cells (ESC)


title: RNA-seq_E14_mPGCLC_d6_3

data_processing:
RNA-seq: RNA-seq sequences were trimmed using trim_galore (v0.4.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default settings. Trimmed data was separately mapped to the human GRCh37 or mouse GRCm38 genome assemblies using hisat2 (v2.0.5) with options --sp 1000,1000 --no-mixed --no-discordant, and was filtered to remove non-primary alignments or alignments with MAPQ < 20. Mapped RNA-seq data were quantitated using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
genome build: GRCm38
processed data files format and content: Quantitated mouse RNA-seq RPM file is tab delimited and contains the following 17 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-17) log2 RPM values for each sample


title: RNA-seq_E14_mPGCLC_d6_2


title: RNA-seq_E14_mPGCLC_d6_1


title: RNA-seq_hESC_1


title: RNA-seq_E14_mPGCLC_d4_1


title: Dox E2 RNAPII

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the hg19 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.
Bedtools was used to generate bedGraph file; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: BigWig

source_name: Dox E2, RNAPII ChIP

growth_protocol: MCF7-tet-on-shCtr9 cells were maintained in Dulbecco’s modified medium (DMEM) (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Life Technologies). Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. ChIPed DNA was purified using a Qiagen PCR Purification Kit according to the manufacturer’s protocol
Prior to ChIP-seq library preparation, ChIPed DNA samples were submitted to the Sequencing Facility at University of Wisconsin Madison Biotechnology Center for determining DNA concentration and size distribution, using Qubit Fluorometer (Thermo Fisher Scientific) and Agilent High Sensitivity DNA Kit (Agilent Technologies), respectively. 10 ng of ChIPed DNA from each condition was used to generate ChIP-seq library using the Ovation Ultralow System V2 1-16 Kit (NuGEN Technologies), according to the manufacturer’s protocol. Briefly, the DNA was end-repaired and subsequently ligated to Illumina sequencing adaptors. The ligated DNA was purified using the Agencourt RNAClean XP bead (Beckman Coulter). A subsequent PCR amplification step (15 cycles) added additional linker sequence to the purified fragments to prepare them for annealing to the Genome Analyzer flow-cell. Following PCR amplification, the library was size selected to a narrow range of fragment sizes by separation on a 2% agarose gel (120 V, 1.5 hours) and a band between 300-500 bp was excised. The library was purified from the excised agarose using the Qiagen MiniElute PCR Purification Kit, according to the manufacturer’s protocol. Purified libraries were then submitted to the Sequencing Facility at University of Wisconsin Madison Biotechnology Center for quality control to determine the size, purity, and concentration of the final ChIP-seq libraries. Qualified libraries were submitted to New York Genome Center (NYGC) for deep sequencing using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: Prior to chromatin immunoprecipitation (ChIP) assays, MCF7-tet-on-shCtr9 cells were cultured in DMEM supplemented with 10% FBS in the absence or presence of 500 ng/mL Dox for 4 days, followed by continuing cultured in phenol red-free DMEM supplemented with 5% charcoal-dextran-treated FBS in the absence or presence of 500 ng/mL Dox for another 3 days. Cells were then treated with DMSO or 10 nM E2 for 45 minutes.

tag: cell line

value: ER{alpha}-positive breast cancer cells

tag: culture conditions

value: Dox

tag: treatment

tag: chip antibody

value: Anti-RNAPII (Millipore, 05-623, clone CTD4H8)


title: RNA-seq_hEpiLC_d4_1


title: Dox DMSO RNAPII

source_name: Dox DMSO, RNAPII ChIP

value: DMSO


title: BS-seq_E14_mEpiLC_d2_1


title: RNA-seq_E14_mPGCLC_d4_3


title: RNA-seq_hESC_2


title: RNA-seq_E14_mEpiLC_d2_2


title: RNA-seq_E14_mEpiLC_d2_1


title: Vehicle E2 RNAPII

source_name: Vehicle E2, RNAPII ChIP

value: Vehicle


title: RNA-seq_E14_mEpiLC_d2_3


title: Vehicle DMSO RNAPII

source_name: Vehicle DMSO, RNAPII ChIP


title: RNA-seq_hPGCLC d12

source_name: RNA-seq_hPGCLC d12


title: Dox E2 ER

source_name: Dox E2, ER ChIP

value: Anti-ERα (Santa Cruz, sc-543, clone HC-20)


title: RNA-seq_E14_mESC_2i_2


title: RNA-seq_E14_mESC_2i_1


title: Dox DMSO ER

source_name: Dox DMSO, ER ChIP


title: Vehicle DMSO ER

source_name: Vehicle DMSO, ER ChIP


title: Dox E2 Input

source_name: Dox E2, Input


title: RNA-seq_E14_mPGCLC_d4_2


title: GHZ-40

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description: RNA from 100 intact adult females

data_processing:
Illumina reads generated by Fasteris (Switzerland) on a HiSeq instrument with standard base calling were aligned to T. urticae reference genome (September 29, 2009) with STAR 2.5.0b in two-pass alginment mode; a maximum intron size of 20 kb was used (information from the refrerence annotation was not used for read alignment).
Read counts for genes in the October 29, 2015 annotation were obtained with HTSeq 0.6.0 with "--stranded=yes" and "--feature=exon."
Differential expression evaluated with DESeq2 1.6.3 with "ddsminReplicatesForReplace" set to "Inf", "cooksCutoff" set to "FALSE" and "independentFiltering" set to "FALSE."
Genome_build: September 29, 2009 (genome sequence) and October 29, 2015 (genome annotation). The genome sequence and annotations are publically available from ORCAE (http://bioinformatics.psb.ugent.be/orcae/).
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts and DESeq2 output.

organism: Tetranychus urticae

source_name: Intact adult females, replicate 2

extract_protocol:
RNA extracted with Qiagen RNeasy RNA extraction kit from intact adult females and dissected proterosoma of adult females.
RNA-Seq libraries were prepared for sequencing using the Illumina strand specific protocol.

value: London

tag: tissue

value: Whole body


title: GHZ-39

description: RNA from 100 intact adult females

source_name: Intact adult females, replicate 1


title: Vehicle DMSO Input

source_name: Vehicle DMSO, Input


title: Caco2 Input Replicate 2

status: Public on Oct 09 2016

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

data_processing:
Fastq files were aligned to the hg19 version of the human genome using Bowtie (v 1.0.0) with a seed length of 40 and a maximum number of 3 mismatches allowed in the seed. Only unique reads were used.
Using Homer (v 1.2) software, tag directories were created using the makeTagDirectory command with default settings.
Using Homer (v 1.2) peaks were called using the findPeaks command with an FDR of 0.1%, factor style, input tag directory as the control library, and all other settings as default.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing FOXA2 peaks for each replicate

source_name: Colorectal adenocarcinoma cells

growth_protocol: Caco2 cells were grown in DMEM Low Glucose with 10% FBS.

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the FOXA2 antibody.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.


title: Caco2 HNF1 ChIP-seq Replicate 2

value: HNF1 (Santa-Cruz sc-6554)

tag: style parameter used for peak calling

value: factor

tag: input used for peak calling

value: Caco2 Input Replicate 2


title: Caco2 HNF1 ChIP-seq Replicate 1

value: Caco2 Input Replicate 1


title: Caco2 Input Replicate 1


title: RNA-seq_E14_mESC_2i_3

value: Wild-type


title: Wild type HESCs

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

description: Wild type HESCs

data_processing:
RNA-seq reads were aligned to the genome (hg19) using STAR.
Coverage of C9orf72 second exon (chr9:27566674-27567162) and first intron (chr9:27567163-27573426) were calculated using samtools depth tool.
Genome_build: hg19
Supplementary_files_format_and_content: Comparison of intron retention values in C9orf72 gene in ALS and normal cells. Coverage of C9orf72 second exon and first intron were calculated and normalized to the exon\intron lengths to get average coverage per base. The file includes average coverage valuse for each sample.

source_name: human embryonic stem cells - normal

extract_protocol:
RNA was extracted using TRI Reagent (Sigma). Depletion of rRNA was performed using the Ribominus kit (Invitrogen).
cDNA libraries were generated using the TruSeq RNA sample preparation kit and protocol (Illumina), and stranded, ligation-based libraries were sequenced as previously described (Engreitz et al., 2013) .

value: Human Embryonic Stem Cells (HESCs)

tag: genotype/variation

value: wild type


title: Wild type iPSCs

description: Wild type iPSCs

source_name: human iPS cells - normal

value: Induced Pluripotent Stem Cells (iPSCs)


title: ALS iPSCs patient M rep1

description: ALS C9-iPSCs M1

source_name: human iPS cells - C9/ALS patient

value: C9/ALS patient


title: ALS iPSCs patient H rep2

description: ALS C9-iPSCs H10

source_name: human iPS cells - C9 carrier

value: C9 carrier


title: ALS HESCs rep2

description: SZ-ALS3 HESCs

source_name: human embryonic stem cells - C9 mutant

value: C9 mutation


title: ALS iPSCs patient M rep2

description: ALS C9-iPSCs M9


title: ALS iPSCs patient M rep3

description: ALS C9-iPSCs M10


title: ALS iPSCs patient H rep1

description: ALS C9-iPSCs H8


title: Drd2 mCherry#15

status: Public on Oct 08 2016

city: Boston

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Analysis Software: HCS 1.5.15.1 - RTA 1.13.48, Illumina CASAVA 1.8.2
RUM version 1.11 for alignment and RefSeq for annotation
edgeR for normalization, processing, and analysis
Genome_build: mm9
Supplementary_files_format_and_content: raw counts and TMM-normalized CPM from edgeR

source_name: Acutely dissociated mCherry-expressing neuron from the midbrain Dorsal Raphe Nucleus

extract_protocol:
Transgenic mice were sacrificed, brains were extracted in ice-cold ACSF with activity blockers (TTX, APV, DNQX), 400 µm brain slices containing the Dorsal Raphe were sectioned on a vibratome, slices were digested in protease for an hour, Dorsal Raphe was microdissected with fine scissors, triturated into a single-cell suspension, cells were plated on a dish, and GFP+ and mCherry+ cells were manually sorted using a glass pipette controlled by mouth aspiration under a dissection microscope with fluorescence optics. Sorted single-neurons were deposited in a 250 µm PCR tube containing 50 µl exraction buffer from the PicoPure RNA Isolation Kit (Arcturus), heated for 30 minutes at 42C and stored at -80C until further processing.
Total RNA was purified using the PicoPure RNA Isolation kit (Arcturus), including an on-column DNA digestion step, cDNA was synthesized and amplified using the Ovation RNA-seq V2 kit (Nugen), cDNA was sheared into ~200bp fragments by Covaris sonication, and RNA-seq libraries were prepared using the Ovation Ultralow Library System (Nugen)

value: Dorsal Raphe Nucleus

tag: age

value: postnatal day 73

value: mCherry-expressing

value: neuron


title: Vehicle E2 ER

source_name: Vehicle E2, ER ChIP

value: ER{alpha}-positive breast cancer cells

value: Vehicle

value: Anti-ERα (Santa Cruz, sc-543, clone HC-20)


title: Drd2 mCherry#9

value: postnatal day 115


title: ALS HESCs rep1

description: SZ-ALS1 HESCs


title: Drd2 mCherry#14


title: Drd2 mCherry#5

value: postnatal day 81


title: Drd2 mCherry#6


title: GHZ-41

description: RNA from 100 intact adult females

source_name: Intact adult females, replicate 3

value: London

value: Whole body


title: GHZ-102

description: RNA from proterosoma from 250 adult females

source_name: Dissected proterosoma from adult females

value: Proterosoma


title: Vehicle E2 Input

source_name: Vehicle E2, Input


title: Drd2 mCherry#3


title: Drd2 mCherry#4


title: Dox DMSO Input

source_name: Dox DMSO, Input

value: Dox

value: DMSO


title: Drd2 GFP#18

source_name: Acutely dissociated GFP-expressing neuron from the midbrain Dorsal Raphe Nucleus

value: postnatal day 67

value: GFP-expressing


title: Drd2 GFP#19


title: Drd2 GFP#17


title: Drd2 GFP#10


title: Drd2 GFP#16

value: postnatal day 66


title: Drd2 GFP#14

value: Dorsal Raphe Nucleus


title: Drd2 GFP#15


title: Drd2 GFP#7

value: postnatal day 62


title: Drd2 GFP#9


title: Drd2 GFP#8


title: Drd2 GFP#6


title: WT roots Fe deficient-3

city: Taipei

first: Louis

last: Grillet

address: 128 Sec.2, Academia Rd., Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

data_processing:
Raw data consist of PF reads (Illumina chastity filter).
Demultiplex and base-calling was performed using bcl2fastq 1.8.4 with default settings.
Adapter removal was done using Trimmomatic 0.35 software in single end mode with parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true CROP:101 MINLEN:75
Reads were mapped to the TAIR10 transcriptome using Bowtie 2.0.6 with parameters -k 30 --gbar 101
Rest reads were mapped to the TAIR10 genome using BLAT v34 with parameters -q=rna -t=dna -maxIntron=50000
Read counts and RPKM values of genes were computed using Rackj (http://rackj.sourceforge.net/)
Read counts of compared samples were normalized using the TMM method (edgeR 3.12.1) and the VOOM method (limma 3.26.9)
Normalized read counts were transformed into normalized RPKMs using EXCEL and compared using Z-TEST
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each sample and for each comparison.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown in vitro, horizontally in square Petri dishes, with light intensity of 50 µmol.m-2.s-1, continuous illumination, on ES media (Estelle and Somerville, 1987) containing 1.5% sucrose. Each plate contained 25 seedlings.

extract_protocol: Total RNA was extracted using Qiagen Rneasy plant Minikit. Quality of the samples was estimated with a Bioanalyzer 2100. RIN score ranged from 9.8 to 10 for root samples, and from 8.3 to 8.7 for leaves.

treatment_protocol: Plants were grown for 10 days on full ES media, and transferred to plates containing either full ES media (control) or ES media without Fe and supplemented with 100 µM FerroZine. Samples were collected 72 hours after transfer.

value: Roots

value: Fe-deficient media

value: WT Col-0


title: Drd2 GFP#3

value: neuron


title: Drd2 GFP#5


title: Drd2 GFP#4


title: Drd2 GFP#2


title: Drd2 mCherry#11

value: postnatal day 73

value: mCherry-expressing


title: Drd2 GFP#13


title: WT roots control-3

value: Control ES media


title: WT rosettes Fe deficient-3

value: Whole rosettes


title: WT roots Fe deficient-1


title: WT roots control-2


title: IMA1 OE rosettes - Fe deficient-1

description: EYFP_rosette_control-IMA1_rosette_-Fe.TMM.txt

data_processing:
Raw data consist of PF reads (Illumina chastity filter).
Demultiplex and base-calling was performed using bcl2fastq 1.8.4 with default settings.
Adapter removal was done using Trimmomatic 0.35 software in paired end mode (Keep-to-reads) with parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true CROP:151 MINLEN:75
Reads were mapped to the TAIR10 transcriptome using Bowtie 2.0.6 with parameters -k 30 --gbar 151, only read pairs mapping to the same transcripts were accepted
Rest reads were mapped to the TAIR10 genome using BLAT v34 with parameters -q=rna -t=dna -maxIntron=50000
Read counts and RPKM values of genes were computed using Rackj (http://rackj.sourceforge.net/)
Read counts of compared samples were normalized using the TMM method (edgeR 3.12.1) and the VOOM method (limma 3.26.9)
Normalized read counts were transformed into normalized RPKMs using EXCEL and compared using Z-TEST
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each sample and for each comparison.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy plant Minikit. Quality of the samples was estimated with a Bioanalyzer 2100. RIN score ranged from 9.8 to 10 for root samples, and from 8.3 to 8.7 for leaves.
Libraries were prepared using the TruSeq stranded mRNA LT Sample Prep Kit following manufacturer's instruction.

value: 35spro:IMA1 ORF


title: IMA1 OE rosettes - Fe deficient-2


title: WT rosettes Fe deficient-1


title: WT rosettes Fe deficient-2


title: IMA1 OE rosettes control-2

description: EYFP_rosette_control-IMA1_rosette_control.TMM.txt


title: WT rosettes control-3


title: WT roots Fe deficient-2


title: WT rosettes control-1


title: WT rosettes control-2


title: IMA1 OE roots - Fe deficient-1


title: EYFP OE rosettes control-1

description: EYFP_rosette_control-IMA1_rosette_control.TMM.txt, EYFP_rosette_control-IMA1_rosette_-Fe.TMM.txt

value: 35spro:EYFP (transgenic control)


title: IMA1 OE roots control-1

description: EYFP_root_control-IMA1_root_control.TMM.txt


title: Drd2 GFP#1


title: IMA1 OE roots control-2


title: WT roots control-1


title: 3-fucosyllactose treatment, replicate B

city: Davis

first: Danielle

middle: G

last: Lemay

state: CA

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

data_processing:
Reads were demultiplexed and imported into CLC-Bio Genomics Workbench Version 5.0
Reads were trimmed setting at 2 the maximum of ambiguous base pairs, and deleted if their quality scores were below 0.5.
Edited reads were aligned to fasta files generated at IMG from a draft genome sequence of Bifidobacterium longum SC596
Alignment allowed a maximum of 2 mismatches, and a maximum of 10 matches to other reads. Other settings were considered as default.
The CLC-BIO tools retrieved information regarding the gene length, total and unique gene reads aligning to a specific locus tag, and automatically calculated the RPKM value (Reads Per Kilobase per Million mapped reads) and total read counts.
Genome_build: Bifidobacterium longum SC596
The genome and its annotations (the BLNG identifiers) are on the IMG website at this location:

https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2513237171
Supplementary_files_format_and_content: tab-delimited text files contain abundance measurements as RPKM and counts

organism: Bifidobacterium longum

source_name: bacterial isolate

growth_protocol: B. longum subsp. longum SC596 was grown in mMRS supplemented with either 2% lactose, 2% HMO, 2% LNT, 2% LNnT, 2% 2’FL, or 2% 3FL  in a microplate reader, and cultures were taken at mid-exponential phase OD 0.5-0.6. In the case of HMO, the samples were collected at four different points in the growth curve, approximately OD600nm = 0.2, 0.4, 0.6, and .75. Samples were immediately pelleted at 12000 x g for 1 min and stored in RNA later Ambion.

extract_protocol:
Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps.
Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles.
Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads).

tag: agent

value: 3-fucosyllactose treatment

value: subsp. longum SC613


title: GFP-ZMYND8

city: Nijmegen

first: Cornelia

middle: Gijsbertha

last: Spruijt

address: Geert Grooteplein 26-28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
Mapping was performed with an in-house Ruby script using BWA alignment to the hg19(build37) genome allowing one mismatch.
Data were filtered on quality and duplicates were removed using samtools.
Peaks were called using MACS 2.0 with the indicated p-value.
ZMYND8_ZMYND8KO was randomly down sampled to have the same number of reads as ZMYND8_v2 using samtools. MBD3_ZMYND8KO is down sampled to have similar read count as MBD3_v1. GFP-GATAD2B is down sampled to have similar read counts as GFP-GATAD2A and GFP-Wtcells.
Genome_build: hg19(build37)
Supplementary_files_format_and_content: Bed files contain filtered, aligned reads and called peaks.

source_name: HeLa Kyoto BAC

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepped using 5ng of ChIP material and the Kapa Hyper Prep Kit for Illumina Sequencing (Kapa Biosystems) according to manufacturer's protocol.

value: GFP (Abcam, ab290)

tag: cross-linking

value: 20 min. Formaldehyde

tag: down sampling


title: 2’fucosyllactose treatment, replicate B

value: 2’fucosyllactose treatment

value: subsp. longum SC611


title: EYFP OE root control-1

description: EYFP_root_control-IMA1_root_control.TMM.txt,EYFP_root_control-IMA1_root_-Fe.TMM.txt

tag: genotype


title: lacto-N-neotetraose treatment, replicate A

description: LNnT-A

value: lacto-N-neotetraose

value: subsp. longum SC608


title: RNAseq_Mock

data_processing:
Sequencing reads were aligned to hg19 using the Genomic Short-read Allignment Program (GSNAP), allowing for one mismatch. Aligned reads were sorted and indexed with the BamTools API 1.0.2 .
Dynamics in gene expression was analysed with cuffdiff tool in the Cufflinks v2.1.1, with the parameters 'frag-bias-correct' and 'multi-read-correct' enabled.
Genome_build: hg19 (build 37)
Supplementary_files_format_and_content: bed

source_name: HeLa FRT-TO Mock-treated

extract_protocol:
Rneasy kit Qiagen
Libraries were prepped using 5ng of cDNA and the Kapa Hyper Prep Kit for Illumina Sequencing (Kapa Biosystems) according to manufacturer's protocol.

treatment_protocol: 48 hour doxycycline treatment

tag: cell line generation

value: CRISPR/Cas9 treatment with guide-RNA targeting GFP


title: lacto-N-neotetraose treatment, replicate B

description: LNnT-B

tag: strain

value: subsp. longum SC609


title: lacto-N-tetraose treatment, replicate B

description: LNT-B

value: lacto-N-tetraose

value: subsp. longum SC607


title: RNAseq_ZMYND8KO

source_name: HeLa FRT-TO ZMYND8KO

value: CRISPR/Cas9 treatment with guide-RNA targeting ZMYND8


title: 2’fucosyllactose treatment, replicate A

value: subsp. longum SC610


title: RNAseq_ZMYND8KO-rescue

source_name: HeLa FRT-TO ZMYND8KO-rescue

value: CRISPR/Cas9 treatment with guide-RNA targeting ZMYND8, followed by flip-in of GFP-ZMYND8


title: GFP-GATAD2B

source_name: HeLa FRT-TO GFP-GATAD2B

tag: antibody

value: 45 min DSG, 10 min Formaldehyde


title: IMA1 OE rosettes control-1

value: Whole rosettes

value: Control ES media

value: 35spro:IMA1 ORF


title: EYFP OE rosettes control-2

value: 35spro:EYFP (transgenic control)


title: GFP-GATAD2A

source_name: HeLa FRT-TO GFP-GATAD2A

value: GFP (Abcam, ab290)


title: pooled HMO, late time point, replicate B

description: HMOlate-B

value: pooled HMO

value: subsp. longum SC605


title: IMA1 OE roots - Fe deficient-2

value: Roots

value: Fe-deficient media


title: pooled HMO, late time point, replicate A

description: HMOlate-A

value: subsp. longum SC604


title: lacto-N-tetraose treatment, replicate A

description: LNT-A

value: subsp. longum SC606


title: GFP-WTcells

source_name: HeLa FRT-TO


title: pooled HMO, mid2 time point, replicate B

value: subsp. longum SC603


title: 3-fucosyllactose treatment, replicate A

value: 3-fucosyllactose treatment

value: subsp. longum SC612


title: MBD3_ZMYND8KO_Hela

source_name: HeLa Kyoto CRISPR ZMYND8 KO

value: MBD3 (Bethyl, A302-528A)


title: EYFP OE root control-2


title: pooled HMO, mid2 time point, replicate A

value: subsp. longum SC602


title: MBD3_v1_Hela

source_name: HeLa Kyoto

value: 45 min DSG, 10 min Formaldehyde


title: ZMYND8_ZMYND8KO_Hela


title: pooled HMO, mid1 time point, replicate A

value: subsp. longum SC600


title: ZMYND8_v2_Hela


title: pooled HMO, mid1 time point, replicate B

value: subsp. longum SC601


title: pooled HMO, early time point, replicate B

description: HMOearly-B

value: subsp. longum SC599


title: ZMYND8_v1_Hela


title: input_HeLa


title: lactose treatment, replicate A

description: LAC-A

value: lactose

value: subsp. longum SC596


title: siControl_input DNA

status: Public on Oct 07 2016

city: Nagasaki

first: TAKEYA

last: NAKAGAWA

address: 1-12-4 sakamoto

department: Biochemistry

country: Japan

institute: Nagasaki unversity

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-Seq reads were aligned to the human hg19 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
peaks were called using Partek Genomic suite version 6.6 with the following setting: Maximum average fragment size 200 no reference window size 100  within a gap distance 100  FDR 0.1  Entire region.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files

source_name: fibrosarcoma

growth_protocol: HT1080 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10 µg/ml gentamicin and 10% fetal calf serum (Thermo Fisher Scinetific).

extract_protocol:
Lysates derived from fixed and sonicated nuclei was immunoprecipitated by  anti-H2ApT120, anti-H2AubK119 and anti-VRK1 antibody.
To add single adenosine, DNA was treated with klewnow exo- (3’ and 5’ exo minus; Illumina). Illumina adaptors were added and subjected to 20 cycles of PCR amplification according to manufacturer's instructions. Purified DNA was subjected to cluster generation and 36 cycles of sequencing on the Illumina cluster station and Genome Analyzer following the manufacturer’s instractions.

treatment_protocol: Transfection was performed by siRNAs targeting human VRK1 or non-targeting siRNA (stealth RNAi, Thermo Fisher Scinetific) using   Lipofectamine® RNAiMAX transfection reagent and opti-MEM serum-free medium ( Thermo Fisher Scinetific)

tag: sirna

value: siControl


title: siVRK1_anti-H2AubK119

tag: cell line


title: lactose treatment, replicate B

description: LAC-B

value: subsp. longum SC597


title: siControl_anti-H2AubK119


title: siControl_anti-VRK1


title: siControl_anti-H2ApT120


title: siVRK1_input DNA


title: siVRK1_anti-H2ApT120


title: H2A T120D #18

data_processing:
Basecalls performed using Illumina MiSeq
RNA-seq reads were aligned to the Mouse mm9 genome assembly using Illumina MiSeq
RPKM were calculated using Partek Genomic suite version 6.6
Genome_build: Mouse mm9

source_name: fibrobrast

growth_protocol: NIH/3T3 cells in which human H2A wild type or T120D mutant was integrated were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10 µg/ml gentamicin and 10% fetal calf serum (Thermo Fisher Scinetific).

extract_protocol:
Total RNA was isolated using ISOGEN II reagent (NIPPON GENE), according to the manufacturer’s protocol.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina)

tag: cell type

value: embryonic fibrobrast cells

tag: expression

value: EGFP-H2A T120D


title: H2A T120D #15


title: H2A T120D #3


title: H2A T120D #6


title: H2A wt

value: EGFP-H2A wild-type


title: MBD3_v2_Hela


title: K562_GATA1_pMPRA1_minP_RNA_3

first: Vijay

last: Sankaran

address: 7 Cambridge Center

institute: Broad Institute

data_processing:
Library strategy: MPRA
(MPRA) Seventy-five GWAS hits associated with RBC traits were obtained from Table 1 in van Der Harst et al. (van der Harst et al., 2012). SNPs in high LD with sentinel GWAS hits were identified from the CEU population of the 1000 Genomes project Phase 1 Version 3 (phase1_release_v3.20101123) using Plink with the following options: “--show-tags --tag-r2 0.8 --tag-kb 500 --list-all” (Genomes Project et al., 2012; Purcell et al., 2007). All SNPs in high LD with rs12150672 were excluded since this resulted in an excessive number of constructs. 145 nucleotide constructs were designed by placing, for each of the 2756 variants, major and minor alleles into the construct such that 1/3, 1/2, and 2/3 of the total length was 5’ of the variant (Table S1). An oligonucleotide library containing the 145 nucleotide genomic regions with fourteen eleven-nucleotide barcodes each, separated by KpnI-XbaI sites and flanked by constant primer sites was obtained from Agilent (LeProust et al., 2010). The oligonucleotide library was then PCR amplified and cloned into the pMPRA1 plasmid backbone (Addgene Plasmid # 49349) with a minP-luc2 (Addgene Plasmid # 49353) insert, as previously described (Melnikov et al., 2014). The resulting plasmid library was introduced into K562 or K562+GATA1 cells using a Nucleofector II Device with Cell Line Kit V (Lonza). 48 hours later, total RNA was harvested and the barcodes were isolated by RT-PCR, as previously described (Melnikov et al., 2014). The barcodes were then sequenced and counted using an Illumina HiSeq 2500 sequencer. A total of 6 replicates were performed for the MPRA screen in K562 cells and 4 replicates in K562+GATA1 cells. Left, middle, and right SWs were designed so that 1/3, 1/2, and 2/3 of the total 145 nucleotide construct was 3’ of the interrogated variant.
(See Ulirsch et al. 2016 for further details)
Genome_build: hg19
Supplementary_files_format_and_content: Construct name and sequence are included in design.txt; construct name and barcodes are included in design_barcodes.txt; processed counts for mRNA and DNA for each construct are included in RBC_MPRA_minP_raw.txt.

extract_protocol:
Total RNA was isolated from cell lysates using RNeasy kits (Qiagen). mRNA was extracted from total RNA using MicroPoly(A) kits (Ambion) and treated with DNase I using the Turbo DNA-freekit (Ambion).
First-strand cDNA was synthesized from 400-700 ng mRNA using High Capacity RNA-to-cDNA kits (Applied Biosystems). Tag-Seq sequencing libraries were generated directly from 12% of a cDNA reaction or 50 ng plasmid DNA by 26 cycle PCR using Pfu Ultra HS DNA polymerase 2x master mix (Agilent) and primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG (where XXXXXXXX is a library-specific index sequence). The resultant PCR products were size-selected using 2% agarose E-Gel EX (Invitrogen).

tag: modulation

value: GATA1 overexpression


title: K562_GATA1_pMPRA1_minP_RNA_4


title: pooled HMO, early time point, replicate A

description: HMOearly-A

value: pooled HMO

value: subsp. longum SC598


title: input-of-ChIP-in-Sall4KO+Mutant

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

description:
SAMN02743427
input for ChIP in Sall4 KO cells transfected with mutant Sall4A

data_processing:
Basecalls performed by BGI, Shenzhen
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with only unique mapped reads were kept
Data were filtered using samtools to remove potential PCR duplicates
peaks were called using MACS (v1.4.2)
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 300 bp

growth_protocol: TT2 mouse ESCs were cultured on dishes coated with 0.1% gelatin (Millipore) without feeder cells. The medium contained Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma, D9443), 10% Knockout Serum Replacement (KSR, Life Technologies), 1% dialyzed fetal bovine serum (FBS, Life Technologies), 3.5 mg/ml D-glucose (Amresco), 1× non-essential amino acids (Millipore), 1× β-mercaptoethanol (Millipore), 1,000 U/ml leukaemia inhibitory factor (LIF, Millipore), 105 μg/ml L-leucine (Sigma, L8912), 89 μg/ml L-arginine:HCl (for heavy medium, R10, Cambridge Isotope Laboratories, CNLM-539-0.5; for light medium, R0, Sigma, A8094) and 91 μg/ml L-lysine:HCl (for heavy medium, K8, Cambridge Isotope Laboratories, CNLM-291-0.5; for light medium, K0, Sigma, L8662).

extract_protocol:
Cells for ChIP assays were crosslinked in 1% formaldehyde for 8-10 min at room temperature. The reaction was terminated by adding 2 M glycine to a final concentration of 125 mM. After being washed with PBS, the cells were resuspended in lysis buffer 1 (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630 and 0.25% Triton X-100) and incubated for 10 min on ice. After centrifugation, the cells were resuspended in lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) and incubated for 10 min at room temperature. The chromatin fraction was resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% sodium N-lauroyl sarcosine) and sonicated into 200-400 base-pair (bp) fragments (Bioruptor, Diagenode). Chromatin fragments were immunoprecipitated overnight with antibodies against SALL1, SALL4A and TET1. The protein-antibody complexes were incubated with pre-washed Dynabeads Protein A or G (Life Technologies) for 1 hr. The beads were sequentially washed with the following buffers: once with FA-lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate), twice with FA high salt buffer (500 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate), once with LiCl buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0) and twice with TE buffer (10 mM Tris-HCl, pH 8.0 and 1 mM EDTA). Protein complexes were eluted by incubation with 250 μl of freshly prepared elution buffer (1% SDS and 100 mM sodium bicarbonate) for 15 min at room temperature. The elution step was repeated once, and the eluted fractions were combined.  For ChIP of bio-SALL4A, chromatin fragments were incubated with Dynabeads M-280 Streptavidin (Life Technologies) equilibrated with PBS + 1% BSA. Triton X-100 was added to a final concentration of 1%. Protein-bound beads were washed sequentially with following buffers: 2% SDS twice, FA high salt buffer twice, LiCl buffer (250 mM LiCl, 1% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0) once and TE buffer twice. Protein complexes were eluted by incubating the beads in 300 μl of elution buffer at 65℃ with agitation at 800 rpm overnight.  After crosslinking reversal and RNase A and proteinase K treatment, DNA was extracted with phenol-chloroform and precipitated with ethanol.  For DNA immunoprecipitation assays, genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. The purified genomic DNA was sonicated into 200-400 bp fragments. Adapter-ligated DNA libraries were constructed. DNA fragments were denatured in 0.4 M NaOH by incubation at 95℃ for 10 min and then placed on ice immediately and neutralised by adding an equal volume of 2 M ammonium acetate. Samples (3 μg) of the adapter-ligated DNA libraries were immunoprecipitated with 5 μg of mC or hmC antibodies, and 5 μg of DNA with 0.2 μl of caC anti-serum.  For mRNA deep sequencing analysis, total RNA was isolated by TRIzol Reagent (Life Technologies), and mRNA with a poly (A) tail was purified and subjected to sequencing library construction.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries and 12-16 cycles for DIP-seq libraries).

tag: strain background

value: embryonic stem cells

value: Sall4 delta/-, Flag-SALL4A-MUT transgene

tag: chip antibody


title: TET1-ChIP-in-Sall4KO

description:
SAMN02390148
TET1-ChIPseq in Sall4Δ/- (Sall4 KO) mES cells

source_name: Sall4Δ/- (Sall4 KO) mES cells

value: Sall4 delta/-

value: The antibody against TET1(1749-1902) used in PMID:21514197


title: TET1-ChIP-in-Sall4het

description:
SAMN02390145
TET1-ChIPseq in Sall4flox/- (Sall4 het) mES Cells

source_name: Sall4flox/- (Sall4 het) mES Cells

value: Sall4 flox/-


title: SALL1-ChIP-in-Sall4het

description:
SAMN02390145
SALL1 ChIPseq in Sall4flox/- (Sall4 het) mES Cells

value: SALL1 (Abcam, ab41974)


title: input-of-ChIP-in-Sall4KO+WT

description:
SAMN02743428
input for ChIP in Sall4 KO cells transfected with WT SALL4A

value: Sall4 delta/-, Flag-SALL4A-WT transgene


title: Sall4-ChIP-in-Sall4KO+WT

description:
SAMN02743428
SALL4A ChIP in Sall4 KO cells transfected with WT SALL4A

value: Monoclonal antibody against SALL4A was generated with the immunogenic peptide TSGPNSRDLM in mice at Abmart.


title: Sall4-ChIP-in-Sall4KO+Mutant

description:
SAMN02743427
SALL4A ChIP in Sall4 KO cells transfected with mutant Sall4A


title: SALL1-ChIP-in-Sall4KO

description:
SAMN02390148
SALL1 ChIPseq in Sall4Δ/- (Sall4 KO) mES cells


title: K562_WT_pMPRA1_minP_RNA_6


title: K562_WT_pMPRA1_minP_RNA_5


title: K562_WT_pMPRA1_minP_RNA_4


title: K562_GATA1_pMPRA1_minP_RNA_1


title: K562_GATA1_pMPRA1_minP_RNA_2


title: input-of-DIP-in-sall4KO-shTdg

description: input of DIP in Sall4Δ/- (Sall4 KO) mES cells treated with shRNA of Tdg

value: Sall4 delta/-, Tdg shRNA transgene


title: K562_WT_pMPRA1_minP_RNA_3


title: caC-DIP-in-sall4het-shTdg

description:
caC-DIPSeq
5caC-DIPseq in Sall4flox/- (Sall4 het) mES Cells treated with shRNA of Tdg

value: Sall4 flox/-, Tdg shRNA transgene

value: 5caC (Active Motif, 61226)


title: input-of-DIP-in-sall4het-shTdg

description: input of DIP in Sall4flox/- (Sall4 het) mES Cells treated with shRNA of Tdg


title: input-for-ChIP-in-WT-of-Sall-DKO

description:
SAMN02390146
input for ChIP in WT cells for Sall1/Sall4 DKO

source_name: WT cells for Sall1/Sall4 DKO

value: wild-type


title: K562_WT_pMPRA1_minP_RNA_1


title: K562_WT_pMPRA1_minP_RNA_2


title: Sall1-ChIP-in-WT-of-Sall-DKO

description:
SAMN02390146
Sall1 ChIP in WT cells for Sall1/Sall4 DKO


title: Sall4-ChIP-in-WT-of-Sall-DKO

description:
SAMN02390146
Sall4 ChIP in WT cells for Sall1/Sall4 DKO


title: shRBM38-2_2

data_processing:
RNA-seq was performed by the IDDRC Core Next-Gen Sequencing Facility of Boston Children’s Hospital and Harvard Medical School in collaboration with Axeq Technologies. RNA was extracted at day 16 of culture using the RNEasy® Plus Mini Kit (Qiagen). An on-column DNase (Qiagen) digestion was performed according to the manufacturer's instructions. Approximately 1 μg of RNA from each sample was used to generate cDNA libraries for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA). Sequencing of 101 nucleotide paired-end reads was performed on an Illumina HiSeq 2000 instrument. Adapters were removed with trimmomatic using the following options: “PE -phred33 ILLUMINACLIP:TruSeq2-PE- 2.fa:2:30:10 HEADCROP:5 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:36”. Trimmed reads were aligned to the genome using Tophat2 and expression in FPKM was determined by using the Tuxedo suite as previously described (Trapnell et al., 2012; Ulirsch et al., 2014). RNA-seq from normal human erythropoiesis was obtained and processed as previously described (An et al., 2014; Li et al., 2014; Ulirsch et al., 2014). Percent spliced in (PSI) was determined for exon skipping events using SUPPA (Alamancos et al., 2015) on the gene transfer file (GTF) obtained by using Cuffmerge to create a single set of transcripts from both RNA-seq datasets created here as well as previously for normal human erythropoiesis. Differentially spliced exons were defined as exon skipping events with a >20% change in PSI between conditions (RBM38 sh1 and sh2 v. shLuc and pairwise OrthoE and PolyE v. ProE, eBasoE, and lBasoE). Gviz was used to create sashimi plot visualizations.
(See Ulirsch et al. 2016 for further details)
Genome_build: hg19

source_name: CD34+ hematopoietic cells

extract_protocol:
RNA was extracted at day 16 of culture using the RNEasy Plus Mini Kit (Qiagen)
Approximately 1 ug of RNA from each sample was used to generate cDNA libraries for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA)

value: Erythroid cells

tag: day

value: RBM38 knockdown


title: RNA_AE22.A3-r2

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

country: Italy

institute: Istituto Clinico Humanitas

description: total RNA extracted from EML cell line infected with AML1/ETO cDNA-expressing vector PINCO-GFP

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 120bp
Transcripts abundance and differentially expressed genes were obtained using Cufflinks 2.2.1 (PMID: 20436464)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression compared to the untreated (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

source_name: EML cell line infected with PINCO-GFP-AML1/ETO_5mM_atRA

growth_protocol: EML cells were grown in IMDM supplemented with horse serum (20%), BHK/MKL conditioned medium (10%), antibiotics, L-glutamine. Cells were kept at 100.000-800.000/Ml of medium

extract_protocol: Total RNA was extracted from 2x10^6 cells using RNAeasy kit (Qiagen). Libraries were prepared from 1-2 µg of RNA, after random primer selection, using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: 5 mM all-trans Retinoic Acid (atRA) for 3 days

value: EML

tag: transfected construct

tag: treatment


title: RNA_EV.A3-r2

description: total RNA extracted from EML cell line infected with control vector PINCO-GFP

source_name: EML cell line infected with control PINCO-GFP_5mM_atRA

value: control PINCO-GFP

value: 5 mM all-trans Retinoic Acid (atRA) for 3 days


title: RNA_EV.A3-r1


title: shRBM38-2_1

extract_protocol:
RNA was extracted at day 16 of culture using the RNEasy Plus Mini Kit (Qiagen)
Approximately 1 ug of DNA from each sample was used to generate cDNA libraries for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA)


title: RNA_AE22.D0-r2

source_name: EML cell line infected with PINCO-GFP-AML1/ETO_no treatment

value: No treatment


title: RNA_AE22.D0-r1


title: RNA_EV.D0-r1

source_name: EML cell line infected with control PINCO-GFP_no treatment


title: RNA_EV.D0-r2


title: caC-DIP-in-sall4KO-shTdg

description:
caC-DIPSeq
5caC-DIPseq in Sall4Δ/- (Sall4 KO) mES cells treated with shRNA of Tdg

value: embryonic stem cells

tag: genotype/variation


title: shLuc_1

value: Luc knockdown (control)


title: RNASeq_s4ko_mut_rescue.rep2

description:
SAMN02743427
mRNA-seq of Sall4-KO+Mutant rescue, rep2

source_name: Sall4 KO cells transfected with mutant Sall4A

value: Sall4 delta/-, Flag-SALL4A-MUT transgene


title: input_of_DIP_in_s1ko

description:
SRX532343
SAMN02741829

source_name: Sall1Δ/- (Sall1 KO) mES cells

value: mouse embryonic stem cells

value: Sall1 delta/- (Sall1 KO)

value: none (input)

tag: sample type

value: input


title: RNASeq-s4ko.rep2

description:
SAMN02390148
mRNA-seq of Sall4-KO cells, rep2

value: Sall4 delta/-


title: hmedip_in_s1het

description:
SRX532340
SAMN02741819

source_name: Sall1flox/- (Sall1 het) mES Cells

value: Sall1flox/- (Sall1 het)

value: 5hmC (Active Motif, 39791)

value: hMeDIP-Seq


title: shLuc_2

value: Erythroid cells


title: RNASeq-WT-TT2

description:
SAMN02374705
mRNA-seq of WT TT2 cells

source_name: WT TT2 mES cells

value: (C57BL/6NCrlj x CBA/JNCrlj)F1

value: wild-type


title: RNASeq-s4het.rep2

description:
SAMN02390145
mRNA-seq of Sall4-het cells, rep2

value: Sall4 flox/-


title: input_of_DIP_in_s1het

description:
SRX532342
SAMN02741819


title: hmedip_in_s1ko

description:
SRX532341
SAMN02741829


title: RNA_AE22.A3-r1

value: EML

value: 5 mM all-trans Retinoic Acid (atRA) for 3 days


title: input-of-DIPSeq-in-sall4ko-plus-WT

description:
SRX372725
SAMN02743428

source_name: Sall4 KO cells transfected with WT SALL4A

value: Sall4 KO transfected with WT SALL4A


title: hmedip-in-sall4KO-plus-mutant

description:
SRX372726
SAMN02743427

value: Sall4 KO transfected with mutant Sall4A


title: hmedip-in-sall4ko-plus-WT

description:
SRX372724
SAMN02743428


title: RNASeq_s4ko_wt_rescue

description:
SRX532349
SAMN02743428

value: RNA-Seq


title: SALL4A-ChIPSeq-in-sall4-KO

description:
SRX372722
SAMN02390148

value: mouse embryonic stem cells

value: Sall4 delta/- (Sall4 KO)

value: The monoclonal antibody against SALL4A was generated with the immunogenic peptide TSGPNSRDLM in mice at Abmart.

value: ChIP-Seq


title: input-of-DIPSeq-in-sall4ko-plus-mutant

description:
SRX372727
SAMN02743427

value: none (input)

value: input


title: hmedip-in-sall4-KO

description:
SRX372720
SAMN02390148

value: 5hmC (Active Motif, 39791)


title: RNASeq_s1_ko

description:
SRX532339
SAMN02741829

value: Sall1 delta/- (Sall1 KO)


title: input-of-ChIPSeq-in-sall4-KO

description:
SRX372723
SAMN02390148


title: RNASeq_s4ko_mut_rescue.rep1

description:
SRX532348
SAMN02743427


title: input-of-DIP-in-sall4-het

description:
SRX372710
SAMN02390145

value: Sall4flox/- (Sall4 het)


title: shRBM38-1_2

value: Erythroid cells

value: RBM38 knockdown


title: hmedip-in-sall4-het

description:
SRX372709
SAMN02390145

value: hMeDIP-Seq


title: shRBM38-1_1


title: SALL4A-ChIPSeq-in-Sall4-het

description:
SRX372707
SAMN02390145


title: RNASeq_s1_het

description:
SRX532338
SAMN02741819

value: Sall1flox/- (Sall1 het)


title: input-of-ChIPSeq-in-sall4-het

description:
SRX372708
SAMN02390145


title: input-of-DIPSeq-in-sall1-sall4-DKO

description:
SRX372719
SAMN02390147

source_name: Sall1-/-/Sall4-/- (DKO) mES Cells

value: Sall1-/-/Sall4-/- (DKO)


title: RNASeq_WT_of_SALL_DKO

description:
SRX532337
SAMN02390146

value: WT cells for Sall1/Sall4 DKO


title: medip-in-sall1-sall4-DKO

description:
SRX372718
SAMN02390147

value: 5mC (Eurogentec, BI-MECY-0100)

value: MeDIP-Seq


title: hmedip-in-sall1-sall4-DKO

description:
SRX372717
SAMN02390147

value: mouse embryonic stem cells


title: RNASeq-s4ko.rep1

description:
SRX532335
SAMN02390148

value: Sall4 delta/- (Sall4 KO)

value: RNA-Seq


title: input-of-DIPSeq-in-sall4-KO

description:
SRX372721
SAMN02390148


title: RNASeq_SALL_DKO

description:
SRX532336
SAMN02390147


title: input-of-DIPSeq-in-WT-of-sall1-sall4-DKO

description:
SRX372706
SAMN02390146

value: wild type


title: medip-in-WT-of-sall1-sall4-DKO

description:
SRX372705
SAMN02390146


title: hmedip-in-WT-of-sall1-sall4-DKO

description:
SRX372704
SAMN02390146


title: RNASeq-s4het.rep1

description:
SRX532334
SAMN02390145

value: none (input)


title: HCT116_C1-27_24h

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: molecule: bru-labeled RNA

data_processing:
Library strategy: Bru-Seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

growth_protocol: HCT116 cells were grown overnight as a monolayer in 10 cm dishes in RPMI 1640 media supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: HCT116 cells were exposed to DMSO, C1-27 or C1-14 for 4 h and GSTO1 siRNA or C1-27 for 24 h, after which, cells were incubated in conditioned media containing 2 mM bromouridine (BrU) at 37C for a 30 min.

tag: concentration

value: 1 μM

tag: treatment time

value: 24 hours

tag: bru labeling time

value: 0.5 hours

tag: time between bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: SALL4A-in-shScr-TT2

description:
SRX370393
SAMN02384824

source_name: TT2 mES cells treated with scrambled shRNA

value: treated with scrambled shRNA

value: The monoclonal antibody against SALL4A was generated with the immunogenic peptide TSGPNSRDLM in mice at Abmart.

value: ChIP-Seq


title: input-of-shScr-TT2

description:
SRX370395
SAMN02384824

value: input


title: input-shTet1-TT2

description:
SRX370398
SAMN02384825

source_name: TT2 mES cells treated with shRNA of Tet1 (shTet1-3387)

value: treated with shRNA of Tet1


title: SALL4A-shTet1-TT2

description:
SRX370396
SAMN02384825


title: HCT116_C1-27_4h

description: molecule: bru-labeled RNA

value: 4 hours


title: HCT116_C1-14_4h

description: molecule: bru-labeled RNA

value: 10 μM


title: caC-DIPSeq-in-shTdg-TT2

description:
SRX372715
SAMN02777978

source_name: TT2 mES cells treated with shRNA of Tdg

value: mouse embryonic stem cells

value: treated with shRNA of Tdg

value: 5caC (Active Motif, 61226)

value: caC-DIPSeq


title: caC-DIPSeq-in-shScr-TT2

description:
SRX372713
SAMN02384824


title: input-of-DIPSeq-in-shScr-TT2

description:
SRX372714
SAMN02384824

value: none (input)


title: input-of-DIPSeq-in-shTdg-TT2

description:
SRX372716
SAMN02777978


title: OS (osmotic shock)

city: Guelph

first: Valeria

middle: Regina

last: Parreira

state: ON

address: 50 Stone Rd E

department: Pathobiology

institute: University of Guelph

data_processing:
Illumina Casava1.8.2. software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. perfringens strain CP4 whole genome using tophat version 2.0.13 with default parameters.
Raw reads counts were generated for each gene using HTSeq software version 0.5.4p1, using the HTSeq counting mode “intersection-nonempty”
Estimates of absolute expression (rpkm, reads per kilobase per million read) were generated using the edgeR function rpkm
Genome_build: C. perfringens CP4 strain
Supplementary_files_format_and_content: text files include RPKM values for each sample

organism: Clostridium perfringens

source_name: Laboratory culture

extract_protocol:
RNAlater was added to chicken intestinal contentes and bacterial cultures and  frozen at -70C. RNA from C. perfringens were isolated using silica column kits.
RNA libraries were prepared using Illumina HiSeq 2500 with TruSeq v3 chemistry

tag: strain

tag: pathogenicity

value: virulent

tag: phenotype

value: netB positive

tag: condition

value: osmotic shock


title: HCT116_DMSO_4h_2

description: molecule: bru-labeled RNA

tag: cell line

value: DMSO

value: 0.5 hours

value: 0 hours


title: PM (poor media)

value: poor media


title: HCT116_siGSTO1_24h

description: molecule: bru-labeled RNA

value: GSTO1 siRNA

value: 10 nM

value: 24 hours

value: Bromouridine (Bru)


title: RM (rich media)

value: rich media


title: hmedip-in-TT2

description:
SRX372711
SAMN02374705

source_name: TT2 mES cells

tag: strain background

tag: cell type

value: mouse embryonic stem cells

value: 5hmC (Active Motif, 39791)

value: hMeDIP-Seq


title: Tet1-ChIPSeq-WT-TT2

description:
SRX372693
SAMN02374705

tag: chip antibody

value: Polyclonal antibody against TET1 was raised in a rabbit.(PMID:21514197)

value: ChIP-Seq


title: IV (in vivo)

source_name: chicken intestinal contents

value: virulent

value: in vivo


title: HCT116_DMSO_4h_1

description: molecule: bru-labeled RNA

value: 4 hours


title: 4h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort) rep3

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

description:
EZ143
4h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort)

data_processing:
Reads were mapped to the zebrafish genome Zv9 by Tophat2.
Refseq annotation was used as known GTF.
bedgrah files for visualization were generated by custom scripts.
reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR.
Genome_build: Zv9
Supplementary_files_format_and_content: bedgraph files for read densities along the genome (RPKM) were generated using custom scripts.

source_name: digestive organs (intestine, liver, pancreas) of 10 zebrafish larvae

growth_protocol: For all experiments, WT (AB background) embryos were collected from natural spawning, staged, and raised in zebrafish embryo media (EM)

extract_protocol:
At the appropriate time points, digestive organs (intestine, liver, pancreas) were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater (Ambion). The samples were stored at -20oC, thawed on ice, and RNA was extracted using an RNAqueous Micro Kit (Ambion) and stored at -80oC.
RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA libraries were constructed from poly(A)-selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 (Illumina) following the LS (low sample throughput) option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.

treatment_protocol: Triplicate samples were independently prepared from pairwise crosses fed either high-fat or low-fat food. 5% egg yolk emulsion (high-fat) feeds and 10% egg white (low-fat) feeds were prepared. For all feeding solutions, a total volume of 20 mL was prepared.

value: AB

tag: tissue

value: intestine, liver, pancreas

tag: age

value: 6.5 dpf


title: SALL1-ChIPSeq-TT2

description:
SRX364003
SAMN02374705

value: SALL1 (Abcam, ab41974)


title: Unfed 6.5 dpf zebrafish larvae (low-fat cohort) rep3

description:
EZ203
Unfed 6.5 dpf zebrafish larvae (low-fat cohort)


title: 4h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort) rep3

description:
EZ243
4h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort)


title: 1h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort) rep3

description:
EZ213
1h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort)


title: input-of-DIP-in-TT2

description:
SRX372712
SAMN02374705

value: none (input)

value: input


title: 4h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort) rep2

description:
EZ242
4h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort)


title: Unfed 6.5 dpf zebrafish larvae (high-fat cohort) rep3

description:
EZ103
Unfed 6.5 dpf zebrafish larvae (high-fat cohort)


title: hMeDIP-in-TT2-shTet1

description:
hMeDIP-Seq
SAMN02384825
hMeDIP in TT2 mES cells treated with shRNA of Tet1

source_name: TT2 mES cells treated with shRNA of Tet1 (shTet1#2)

value: (C57BL/6NCrlj x CBA/JNCrlj)F1

value: embryonic stem cells

tag: genotype/variation

value: Tet1 shRNA transgene


title: input-of-ChIPSeq-TT2

description:
SRX364004
SAMN02374705

value: mouse embryonic stem cells

tag: sample type


title: input-of-DIP-in-TT2-shTet2

description: input of DIP in TT2 mES cells treated with shRNA of Tet2

source_name: TT2 mES cells treated with shRNA of Tet2 (shTet2#3)

value: Tet2 shRNA transgene


title: hMeDIP-in-TT2-shTet2

description:
hMeDIP-Seq
hMeDIP in TT2 mES cells treated with shRNA of Tet2

value: 5hmC (Active Motif, 39791)


title: Unfed 6.5 dpf zebrafish larvae (high-fat cohort) rep2

description:
EZ102
Unfed 6.5 dpf zebrafish larvae (high-fat cohort)


title: 1h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort) rep2

description:
EZ112
1h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort)


title: 1h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort) rep2

description:
EZ212
1h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort)


title: input-of-DIP-in-TT2-shTet1

description:
SAMN02384825
input of DIP in TT2 mES cells treated with shRNA of Tet1


title: input-of-DIP-in-TT2-shScr

description:
SAMN02384824
input of DIP in TT2 mES cells treated with scrambled shRNA

value: scrabled shRNA transgene


title: 4h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort) rep1

description:
EZ241
4h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort)


title: hMeDIP-in-TT2-shScr

description:
hMeDIP-Seq
SAMN02384824
hMeDIP in TT2 mES cells treated with scrambled shRNA


title: input-of-ChIP-in-Sall4het-BirA

description: input of ChIP in Sall4flox/- (Sall4 het) mES Cells with Bio-tagged TET2

value: Sall4 flox/-, FlagBio-tagged TET2 knockin at Tet2 locus


title: 1h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort) rep1

description:
EZ211
1h low-fat fed 6.5 dpf zebrafish larvae (low-fat cohort)


title: bio-Tet2-ChIP-in-Sall4het-BirA

description: TET2 bio-ChIP in Sall4flox/- (Sall4 het) mES Cells with Bio-tagged TET2

value: Dynabeads M-280 Streptavidin (Life Technologies)


title: Unfed 6.5 dpf zebrafish larvae (low-fat cohort) rep2

description:
EZ202
Unfed 6.5 dpf zebrafish larvae (low-fat cohort)


title: input-of-ChIP-in-Sall4KO-BirA

description: input of ChIP in Sall4Δ/- (Sall4 KO) mES cells with Bio-tagged TET2

value: Sall4 delta/-, FlagBio-tagged TET2 knockin at Tet2 locus


title: Unfed 6.5 dpf zebrafish larvae (low-fat cohort) rep1

description:
EZ201
Unfed 6.5 dpf zebrafish larvae (low-fat cohort)


title: bio-Tet2-ChIP-in-Sall4KO-BirA

description: TET2 bio-ChIP in Sall4Δ/- (Sall4 KO) mES cells with Bio-tagged TET2


title: 1h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort) rep3

description:
EZ113
1h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort)


title: 4h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort) rep1

description:
EZ141
4h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort)


title: H3K27ac-ChIP-in-Sall4KO

description:
SAMN02390148
H3K27ac ChIPseq in Sall4Δ/- (Sall4 KO) mES cells

source_name: Sall4Δ/- (Sall4 KO) mES cells

value: Sall4 delta/-

value: Abcam, ab4729


title: pMPRA1_minP_DNA_2

molecule: other

organism: Escherichia coli

source_name: Escherichia coli

tag: description

value: reads of barcodes in the 3'UTR of a reporter gene in a pool of reporter plasmids


title: 4h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort) rep2

description:
EZ142
4h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort)

value: AB

value: intestine, liver, pancreas

value: 6.5 dpf


title: 1h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort) rep1

description:
EZ111
1h high-fat fed 6.5 dpf zebrafish larvae (high-fat cohort)


title: Unfed 6.5 dpf zebrafish larvae (high-fat cohort) rep1

description:
EZ101
Unfed 6.5 dpf zebrafish larvae (high-fat cohort)


title: H3K27ac-ChIP-in-Sall4het

description:
SAMN02390145
H3K27ac ChIPseq in Sall4flox/- (Sall4 het) mES Cells

source_name: Sall4flox/- (Sall4 het) mES Cells

value: Sall4 flox/-


title: input-of-bioTet2-ChIP-in-CloneE1

description: input of bio-TET2 in TT2 mES cells with Biotin-tagged TET2

source_name: TT2 mES cells with Biotin-tagged TET2

value: (C57BL/6NCrlj x CBA/JNCrlj)F1

value: FlagBio-tagged TET2 knockin at Tet2 locus


title: bio-Tet2-ChIP-in-CloneE1

description: ChIP of bio-TET2 in TT2 mES cells with Biotin-tagged TET2

value: embryonic stem cells


title: E12.5 RNA-seq ∆Bor het Rep2

status: Public on Oct 06 2016

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

country: Germany

institute: Berlin Institute of Health

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm9) using the STAR mapper (Dobin et al., 2013) (splice junctions based on RefSeq ;options: ‐‐alignIntronMin 20 ‐‐alignIntronMax 500000 --outFilterMultimapNmax 5 ‐‐outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.1).
The uniquely mapped read counts per gene (annotation based on RefSeq genes) were subsequently transformed to FPKM.
Differential Expression was calculated based on the raw read counts per gene via the DEseq2 package (Love et al 2014; default settings).
To create bigwig files coverage profiles were generated by creating a bedgraph file using bedtools genomecov (-ibam —bg split -scale (normalized per million reads)) (bedtools v2.17.0) and then transformed to bigwig files using the bedgraphtobigwig tool from UCSC (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v287/bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for normalized RNA-seq profiles

source_name: E12.5 limb buds

extract_protocol:
RNA was extracted from snap-frozen tissue by lysis in Trizol and subsequent purification using the Qiagen RNAeasy Mini Kit
polyA enriched RNA-seq libraries were constructed using the Illumina TruSeq RNA V2 Kit according to manufacturer's instructions

tag: genotype

value: deltaBor

value: limb buds


title: E12.5 RNA-seq wt Rep4

value: WT


title: E12.5 RNA-seq wt Rep3


title: E12.5 RNA-seq ∆Bor het Rep1


title: E12.5 RNA-seq wt Rep2


title: pMPRA1_minP_DNA_1


title: E12.5 RNA-seq ∆Bor hom Rep1


title: E12.5 RNA-seq Dup-L∆Bor Rep4

value: Dup-LdeltaBor


title: E12.5 RNA-seq Dup-L∆Bor Rep2


title: E17.5 RNA-seq wt fingertips

source_name: E17.5 fingertips

value: distal fingertips


title: CHiC E12.5 Dup-S

description: processed data file: Sox9-Dup-S_vs_Sox9-WT-E125_10kb.WashU.txt

data_processing:
Library strategy: HiC-Seq
Base calling with standard Illumina Software
Mapping and filtering of di-tags was performed with the HiCUP pipeline v0.5.8 (http://www.bioinformatics.babraham.ac.uk/projects/hicup/) (parameters: Nofill:1 Format: Sanger  without any size selection). The pipeline used Bowtie2 v2.2.6 for mapping short reads to reference genome (NCBI37/mm9).
Filtered di-tags were further processed with Juicebox command line tools (https://github.com/theaidenlab/juicebox) to bin di-tags (10kb bins) and normalized by KR normalization (Only reads with MAPQ >= 30 were considered). The DNA-capturing step enriches genomic region chr11:109,010,001-114,878,000 on mm9 . Before binning and normalization, di-tags were filtered for the enriched region and mm9 coordinates were shifted by -109,010,000 bp (a custom chromosome file containing only the enriched region on chr11 (length 5,868,000 bp) was used). After binning and normalization, coordinates were shifted back to their original values.
Difference maps were generated based on raw count maps which were scaled individually by dividing each value of the matrix by a factor (sum ‘masked’ triangle matrix/106). The region spanning all tested duplications (chr11:110,772,110-112,514,692) was not considered for the computation of the scaling factor.
For visualization CHi-C maps of count values, difference maps, and log2 ratios were visualized with the WashU epigenome browser (epigenomegateway.wustl.edu/browser/).
Genome_build: mm9
Supplementary_files_format_and_content: CHi-C map in WashU epigenome browser pairwise interaction format

extract_protocol:
Limbs were re-suspended in Trypsin and incubated for 10 minutes at 37°C. Tissues were disrupted by pipetting and single cells were retrieved using cell strainer and fixed for 10 minutes at room temperature in 10ml (2%PFA, 10%FCS, 1XPBS). Final 140mM glycine was added to stop crosslinking. Cells were then lysed for 10’ at 4°C in  lysis buffer (50mM TRIS pH7.5, 150mM NaCl, 5mM EDTA, 0.5%NP-40, 1.15% TX-100 and 1X Proteinase Inhibitor).
Sheared DNA was then ligated to adaptors and 4 amplification cycles were performed prior to SureSelect hybridization. 700ng of adaptor-ligated DNA was hybridized to the custom probes according to Agilent instructions. Hybridized fragments were then amplified (12 cycles) and products were cleaned using AMPure XP beads. Each sample was sequence on an individual Illumina HiSeq lane following a 100bp paired-end mode.

value: Dup-S


title: CHiC E12.5 Dup-C

description: processed data file: Sox9-DupC-E125_vs_Sox9-WT-E125_10kb.WashU.txt

value: Dup-C


title: E12.5 RNA-seq wt Rep1


title: E12.5 RNA-seq Dup-L Rep1

value: Dup-L


title: E12.5 RNA-seq Dup-L∆Bor Rep1


title: E12.5 RNA-seq Dup-C Rep1


title: E12.5 RNA-seq Dup-C Rep2


title: E17.5 RNA-seq Dup-C fingertips


title: CHiC E12.5 ∆Bor

description: processed data file: Sox9-d1-3-E125_vs_Sox9-WT-E125_10kb.WashU.txt

data_processing:
Base calling with standard Illumina Software
Mapping and filtering of di-tags was performed with the HiCUP pipeline v0.5.8 (http://www.bioinformatics.babraham.ac.uk/projects/hicup/) (parameters: Nofill:1 Format: Sanger  without any size selection). The pipeline used Bowtie2 v2.2.6 for mapping short reads to reference genome (NCBI37/mm9).
Filtered di-tags were further processed with Juicebox command line tools (https://github.com/theaidenlab/juicebox) to bin di-tags (10kb bins) and normalized by KR normalization (Only reads with MAPQ >= 30 were considered). The DNA-capturing step enriches genomic region chr11:109,010,001-114,878,000 on mm9 . Before binning and normalization, di-tags were filtered for the enriched region and mm9 coordinates were shifted by -109,010,000 bp (a custom chromosome file containing only the enriched region on chr11 (length 5,868,000 bp) was used). After binning and normalization, coordinates were shifted back to their original values.
Difference maps were generated based on raw count maps which were scaled individually by dividing each value of the matrix by a factor (sum ‘masked’ triangle matrix/106). The region spanning all tested duplications (chr11:110,772,110-112,514,692) was not considered for the computation of the scaling factor.
For visualization CHi-C maps of count values, difference maps, and log2 ratios were visualized with the WashU epigenome browser (epigenomegateway.wustl.edu/browser/).
Genome_build: mm9
Supplementary_files_format_and_content: CHi-C map in WashU epigenome browser pairwise interaction format


title: CHiC E12.5 Dup-L∆Bor

description: processed data file: Sox9-DupL-d1-3-E125_vs_Sox9-DupL-E125_10kb.WashU.txt


title: CHiC E12.5 Dup-L


title: CHiC E12.5 Wt

description:
processed data file: Sox9-Dup-S_vs_Sox9-WT-E125_10kb.WashU.txt
processed data file: Sox9-DupC-E125_vs_Sox9-WT-E125_10kb.WashU.txt
processed data file: Sox9-d1-3-E125_vs_Sox9-WT-E125_10kb.WashU.txt


title: 4C WT Sox9TSS

data_processing:
4C-seq reads were cleaned of the primer sequence and mapped to a corresponding reference (GRCh37/hg19 or NCBI37/mm9) using BWA-MEM (v0.7.12-r1044) with default settings.
4C-seq contacts were analyzed in the murine region chr11:108500000-115000000 and the human region chr17:67000000-75000000.
To calculate read count profiles the viewpoint and adjacent fragments 1.5 kb up- and downstream were removed. A sliding window of 10 fragments was chosen to smooth the data and data was normalized to reads per million mapped reads (RPM).
To compare interaction profiles of different samples, we obtained the log2 fold change for each window of normalized reads.
Genome_build: mm9, hg19

Supplementary_files_format_and_content: bedgraph files of the coverage and the calculated ratios

extract_protocol:
4C-seq libraries were generated from microdissected tissues or cells as described previously (van de Werken et al., 2012). DpnII was used as primary, BfaI as secondary restriction enzymes (Csp6I and NlaIII for human samples). For each viewpoint, a total of 1.6 mg of each library was amplified in 8 or 16 PCR reactions, depending on PCR efficiencies. Samples were multiplexed and sequenced with Ilumina Hi-Seq technology. The following primers were used: Sox9-TSS_1 CCACGAAAGTGTGTTTATATTCT   Sox9-TSS_2 TGGCTATTGTTTGTAAATCTCTT  Kcnj2-TSS_1 CGGTGGTGGAGAGAAAGA   Kcnj2-TSS_2 TCACCAAACAACCTCTACAAA  LacZ_1 TCCGACTTCAACTGTAGGG  LacZ_2 GCAGAGCCATCTATTGCTTA  BOR-Sox9tel_1 TTTGACTCCAAGGACCAGA  BOR-Sox9tel_2 TGTGTAAAGGCGGACAGA  Sox9-TAD_1 AACTGGGTATAGTGTGGAGAGA  Sox9-TAD_2 GGACATCAATGGAACATAGC  BOR-Kcnj/Sox9_1 AATGCTGTGGACATCCTG  BOR-Kcnj/Sox9_2 TCCGTCAAGTTCCATGTG  Kcnj-TAD_1 TCTGTGCCAAATGAACTATTCT  Kcnj-TAD_2 AGCACCATCTGTCCTCCTAT  BOR-Kcnjcen_1 AAGAAGAGGGGCTCAAAAT  BOR-Kcnjcen_2 CTGATTGGCATGGGATAGT  SOX9-TSS_1 TCCAAGTGTGTAAGTTTGTCG  SOX9-TSS_2 AATCTCCTGGACCCCTTC  KCNJ2-TSS_1 TTCAGTGAACGTATTTGTTGAA  KCNJ2-TSS_2 GAGCGTTTGATGTTTTACCA
Samples were multiplexed and sequenced with Ilumina Hi-Seq technology using 100bp paired-end or single end reads according to the manufacturer´s protocol.

tag: viewpoint

value: Sox9 TSS


title: 4C WT KcnjTAD

value: Kcnj TAD


title: 4C WT Sox9TAD

value: Sox9 TAD


title: E12.5 RNA-seq Dup-L∆Bor Rep3


title: 4C WT Kcnj2TSS

value: Kcnj2 TSS


title: Nutlin_S_rep2

city: Göttingen

first: Ina

last: Klusmann

address: Justus-von-Liebig-Weg 11

institute: Institute of Molecular Oncology

data_processing:
demultiplexed to fastq files with CASAVA (version 1.8.2)
Fastq files were mapped to the human reference transcriptome (UCSC hg19) using Tophat (Galaxy Version 0.9)
Read counts for each sample and each gene were aggregated using a htseq-count
DESeq2 (version 1.10.1) was used for measuring differential expression
Genome_build: hg19
Supplementary_files_format_and_content: CSV files

source_name: osteosarcoma cell line

growth_protocol: Cells were cultured in DMEM (Gibco/Life Technologies) supplemented with 10 % fetal calf serum (FCS) and antibiotics

extract_protocol:
Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies).
For RNA-sequencing, the quality of total RNA was determined using the bioanalyzer 2100 from Agilent. All samples analyzed exhibited a RIN>8. Library preparation was conducted using the TruSeq RNA LT SamplePrep Kit (Illumina) starting from 1000 ng of total RNA. Barcodes used for sample preparation were used according to the indications given by the protocol. Accurate library quantitation of cDNA libraries was performed with the QuantiFluor™dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (290-310 bp). cDNA libraries were amplified and sequenced via cBot and HiSeq 2000 from Illumina (SR, 1×50 bp, 6 Gb/sample ca. 30 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA (version 1.8.2).

treatment_protocol: U2OS cells were incubated with thymidine at 2 mM in DMEM/10% FCS for 16 h, then washed and incubated in DMEM/10% FCS for 8 h, and then again incubated with 2 mM thymidine for 16 h (double-thymidine block). Four hours before release from the block (or maintaining the block), 10  M Nutlin (control: DMSO alone) was added. For release, thymidine was removed by washing and incubation with DMEM/10% FCS. When the block was removed, the previous concentration of Nutlin was maintained, followed by further incubation for 4 h before harvest.

value: S-phase cells


title: Nutlin_S_rep1


title: Nutlin_NR_rep2

value: non-released cells


title: DMSO_S_rep1


title: DMSO_AS_rep2

value: asynchronous cells


title: Nutlin_AS_rep1


title: DMSO_AS_rep3


title: Nutlin_AS_rep2


title: Nutlin_NR_rep1