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Sample GSM998358 Query DataSets for GSM998358
Status Public on Nov 01, 2012
Title H3K36me3
Sample type SRA
 
Source name Whole embryos
Organism Danio rerio
Characteristics strain: AB
tissue: Whole embryos
developmental stage: Post-MBT (5.3 hpf)
chip antibody: H3K36me3
chip antibody vendor: Diagenode
chip antibody cat. #: 058-050
Growth protocol Embryos for ChIP-seq were collected at 5.3 hpf and chromatin prepared as described (Lindeman et al., 2009).
Extracted molecule genomic DNA
Extraction protocol Immunoprecipitation was performed using H3K36me3 (Diagenode 058-050) and ChiP enriched DNA and input samples prepared for sequencing according to Illumina standard protocol (#11257047 Rev.A).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Data was basecalled with Illumina RTA 1.6 / Bustard 1.6.1 software
Chip-seq reads were aligned to Zv9 using BWA with the following commands: 1) bwa aln -n 2 -t 8 -R 10, 2) bwa samse -n 1
Mapped reads filtered using samtools with the following command: samtools view -S -b -q
Peak calling was performed using CCAT 3.0, with the following settings: fragmentsize = 200, sliding window size = 500, MovingStep = 50, strandsensitive = yes, minCount = 4, minScore = 3
Genome_build: Zv9
 
Submission date Sep 05, 2012
Last update date May 15, 2019
Contact name Håvard Aanes
E-mail(s) havard.aanes@nvh.no
Organization name Norwegian School of Veterinary Science
Department Biochemistry
Street address Ullevålsveien 72
City Oslo
State/province Oslo
ZIP/Postal code 0883
Country Norway
 
Platform ID GPL15583
Series (1)
GSE40629 Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish
Relations
SRA SRX183319
BioSample SAMN01162159

Supplementary file Size Download File type/resource
GSM998358_h3k36me3.tdf 136.7 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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