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Sample GSM3003558 Query DataSets for GSM3003558
Status Public on Aug 01, 2018
Title Zebrafish_Li_KPDS
Sample type SRA
 
Source name whole embryo
Organism Danio rerio
Characteristics tissue: whole embryo
Treatment protocol All samples were untreated, wild type organisms.
Growth protocol Organisms were cultured in standard conditions, withouth any treatment.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted with standard phenol/chloroform extraction as previously described in Chambers et. al 2015 (doi: 10.1038/nbt.3295), except for samples where DNA was purchased from companies (see source and characteristics field).
Genomic DNA samples were sonicated and the library prepared, as in Chambers et al. 2015 (doi: 10.1038/nbt.3295). Libraries were prepared using the TruSeq Nano DNA LT Library Prep Kit (Nano in each sample file name), or with PCR-Free Library Prep Kit (PCRFree or not specified in each sample file name).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description G4-seq protocol
Data processing library strategy: Other (G4-Seq2: modified DNA-Seq)
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: Genome sources;
Homo sapiens (hg19) from http://hgdownload.cse.ucsc.edu/downloads.html/
Mus Musculus (mm10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Danio Rerio (danRer10) from http://hgdownload.cse.ucsc.edu/downloads.html/
Drosophila Melanogaster (dm6) from http://hgdownload.cse.ucsc.edu/downloads.html/
Caenorhabditis elegans (ce10) from http://www.wormbase.org/species/c_elegans/
Saccharomyces cerevisiae (sacCer3) from http://hgdownload.cse.ucsc.edu/downloads.html/
Leishmania major (LmjF_v6.1_all_20131105) from www.genedb.org/Homepage/Lmajor
Trypanosoma Brucei (TriTrypDB-9.0_TbruceiTREU927) from http://www.genedb.org/Homepage/Tbruceibrucei927
Plasmodium falciparum (PlasmoDB-28_Pfalciparum3D7) from http://plasmodb.org/
Arabidopsis thaliana (Arabidopsis_thaliana.TAIR10.31.dna.genome) from https://www.arabidopsis.org/
Escherichia coli (Ecoli_K12) from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/
Rhodobacter sphaeroides from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/. Annotation files sources: Arabidopsis thaliana (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FTAIR10_genome_release%2FTAIR10_gff3)
Caenorhabditis elegans (ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/)
Drosophila Melanogaster (ftp://ftp.ensembl.org/pub/release-87/gff3/drosophila_melanogaster/)
E. coli (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-34/gff3/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655/)
Homo sapiens (USCS annotation for genes: http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html
Gencode annotation for non-coding RNAs: https://www.gencodegenes.org/releases/19.html)
Leishmania major( ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Mus musculus (ftp://ftp.ensembl.org/pub/release-87/gff3/mus_musculus/)
Plasmodium falciparum (http://plasmodb.org/common/downloads/release-28/Pfalciparum3D7/gff/data/)
Rhodobacter sphaeroides (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-30/gff3/bacteria_0_collection/rhodobacter_sphaeroides_2_4_1/)
Saccharomyces cerevisiae (ftp://ftp.ensembl.org/pub/release-87/gff3/saccharomyces_cerevisiae/)
Trypanosoma brucei (ftp://ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT)
Danio rerio (ftp://ftp.ensembl.org/pub/release-87/gff3/danio_rerio/).
Supplementary_files_format_and_content: bedgraphs for coverage and mismatch levels; bed files for scoring G-quadruplexes (separated by strand)
 
Submission date Feb 13, 2018
Last update date Aug 01, 2018
Contact name Giovanni Marsico
E-mail(s) persego@gmail.com
Organization name CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL18413
Series (1)
GSE110582 Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq
Relations
BioSample SAMN08533581
SRA SRX3697632

Supplementary file Size Download File type/resource
GSM3003558_Zebrafish_all_w15_th-1_minus.PDS.bedGraph.gz 459.2 Mb (ftp)(http) BEDGRAPH
GSM3003558_Zebrafish_all_w15_th-1_minus.cov.PDS.bedGraph.gz 410.5 Mb (ftp)(http) BEDGRAPH
GSM3003558_Zebrafish_all_w15_th-1_minus.hits.max.PDS.w50.35.bed.gz 1.5 Mb (ftp)(http) BED
GSM3003558_Zebrafish_all_w15_th-1_plus.PDS.bedGraph.gz 459.2 Mb (ftp)(http) BEDGRAPH
GSM3003558_Zebrafish_all_w15_th-1_plus.cov.PDS.bedGraph.gz 410.6 Mb (ftp)(http) BEDGRAPH
GSM3003558_Zebrafish_all_w15_th-1_plus.hits.max.PDS.w50.35.bed.gz 1.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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