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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
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
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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