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Sample GSM3402610 Query DataSets for GSM3402610
Status Public on Jun 01, 2019
Title DAM-mYap1B
Sample type SRA
 
Source name Whole embryos
Organism Oryzias latipes
Characteristics tissue: Whole embryos
developmental stage: Stg 16
genotype/variation: DAM-mYap1B
Extracted molecule genomic DNA
Extraction protocol We followed the protocol reported for medaka (Gutiérrez-Triana et al., 2016). WT zebrafish and medaka embryos were injected with each DAM-TF mRNA and its gDNA fraction was isolated when they reached the 80% epiboly stage. 40 embryos were used for each indipendent DamID replicate. gDNA was fragmented using DpnII restriction enzymes, dephosphorilated with phosphatase alkaline and cleaved at its GATC methylated sites using DpnI. Adapters, produced by hybridazing two oligos, were ligated to both ends for each fragment to build up DNA libraries through a 25-cycle PCR amplification step using a phosphorothioate primer. Each PCR product was run on a 1% agarose gel to check for the presence of a smear in DpnI-treated samples. Each library was amplified then five times before deep sequencing (Illumina HiSeq 2500 sequencing). Remaining DNA templates were removed with T7 exonuclease before sequencing. Three replicates for each sample were used for the iDamID-seq analysis.
DNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Library strategy: DamID-seq
Raw sequencing data was pre-processed using the Cutadapt tool to discard short reads (-m 34 parameter) and the ones corresponding to the adaptors used for deep sequencing.
Reads from zebrafish and medaka proteins were mapped against the GRCz10/danRer10 and the NIG/UT MEDAKA1/oryLat2 genome versions of each breed, respectively, using Bowtie2.
Duplicated reads were removed using Samtools rmdup.
The set of specific DAM-YAP1, DAM-TAZ and DAM-YAP1B peaks as well as their respective control peaks was obtained using the R package iDEAR (available at https://bitbucket.org/juanlmateo/idear).
Each DamID peak was assigned to its closest TSS using bedtools closest. The position of the transcription start site (TSS) of each gene was obtained from ENSEMBL database (Version 89) using the online tool Biomart (www.ensembl.org/biomart).
Motif enrichment analysis was carried out using DREME and AME. GO enrichment analysis was performed using PANTHER.
Genome_build: oryLat2 (medaka) and danRer10 (zebrafish)
Supplementary_files_format_and_content: tab-limited bed files for each DAM-TF sample indicating the number, coordinates and iDEAR score for each specific peak and for each control peak.
 
Submission date Sep 26, 2018
Last update date Jun 01, 2019
Contact name Javier Vázquez-Marín
E-mail(s) jvazmar89@gmail.com, javier.vazquez@cos.uni-heidelberg.de
Organization name Heidelberg University
Department Centre for Organismal Studies (COS)
Street address Im Neuenheimer Feld 230, 5th floor
City Heidelberg
State/province Baden-Württemberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL23308
Series (1)
GSE120531 Identification and functional analysis of yap1b: a new Yap family member in teleosts that evolved a divergent transcriptional activation domain.
Relations
BioSample SAMN10133757
SRA SRX4742255

Supplementary file Size Download File type/resource
GSM3402610_DAM-mYAP1B1.stg16.bw 52.9 Mb (ftp)(http) BW
GSM3402610_DAM-mYAP1B2.stg16.bw 42.2 Mb (ftp)(http) BW
GSM3402610_DAM-mYAP1B3.stg16.bw 43.1 Mb (ftp)(http) BW
GSM3402610_mYAP1B.pos.stg16.bed.gz 41.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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