Comment[ArrayExpressAccession]	E-MTAB-1835
MAGE-TAB Version	1.1
Investigation Title	CpBV-H4 ChIP-Seq
Comment[Submitted Name]	CpBV-H4 ChIP-Seq
Experiment Description	To address a target gene spectrum of CpBV-H4, we need to analyze total gene expression in response to a specific expression of CpBV-H4 by a transient expression technique.
Experimental Design	in_vivo_design	binding site identification design	genetic modification design	genotype design
Comment[AEExperimentType]	ChIP-seq
Comment[AEExperimentDisplayName]	ChIP-seq of Tribolium castaneum gene expression response to a specific expression of CpBV-H4 by a transient expression technique
Experimental Factor Name	genotype
Experimental Factor Type	genotype
Quality Control Type	biological replicate
Quality Control Term Source REF	EFO
Public Release Date	2013-08-24
Person Last Name	Hepat
Person First Name	Rahul
Person Mid Initials	Pralhad
Person Email	rhepat@gmail.com
Person Phone
Person Address	Department of Bioresource Sciences, Lab of Insect Molecular and Physiology Lab,  Andong National University, Andong 760-749, Korea
Person Affiliation	Lab of Insect Molec Physio College of Natural Sciences,Andong National Univ
Person Roles	submitter
PubMed ID	23926351
Publication Author List	Rahul Hepat; Ji-Joon Song; Daeweon Lee; Yonggyun Kim
Publication Title	A Viral Histone H4 Joins to Eukaryotic Nucleosomes and Alters Host Gene Expression
Publication Status
Protocol Name	P-MTAB-34350	P-MTAB-34351	P-MTAB-34352	P-MTAB-34353	P-MTAB-34354	P-MTAB-34355
Protocol Type	growth protocol	treatment protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol
Protocol Description	T. castaneum was reared in a dry and dark condition (a relative humidity 60 plus/minus 5%) at room temperature (25 plus/minus 10C) with wheat flour (Pareve, USA). Fully grown late instar larvae (5 mm) were used in this study.	A full open reading frame of CpBV-H4 and the truncated CpBV-H4 (without N-terminal 38 amino acids) were cloned into pIB eukaryotic expression vector (Invitrogen, Carlsbad, CA, USA) according to previous studies . The recombinant pIB vector was mixed with Metafectene PRO transfection reagent (Biontex, Planegg, Germany) according to manufacturers instruction. Briefly, 0.5 ug of recombinants were mixed with 3 uL of Metafectene reagent and incubated for 20 min at room temperature to allow DNA-lipid complexes to be formed before injection into hemocoel of late instar larvae of T. castaneum. Glass capillary (World Precision Instruments, Sarasota, FL, USA) injection needles were made using a micropipette puller PN30 (Narishige, Tokyo, Japan). A total 60 nL was injected into the larval hemocoel at the rate 10 nL/sec using a micro-syringe pump controller (WPI) under a microscope (Olympus S730, Tokyo, Japan). After 48 h PI, total RNA was extracted using Trizol reagent (Invitrogen) and followed by reverse transcription using RT-Premix (Bioneer, Daejeon, Korea) with an oligo dT and subsequent RNase H (1 unit/uL) treatment. The synthesized cDNA was used as a template for PCR amplification. Control PCR reaction was performed with RNA extract template, which was used as a template to check absence of DNA contamination.	Briefly, 100 larvae each of Tribolium castaneum injected with recombinant CpBV-H4 and truncated CpBV-H4 were homogenized in PBS on ice, followed by the addition of formaldehyde to a final concentration of 1% and incubation at 37C for 10 min. Chromatin immunoprecipitation assays were performed using a QuikChIP kit (IMGENEX) according to the instruction manual	The precipitated DNA was dissolved in Tris-EDTA buffer and read by an Illumina using paired end sequencing.	The precipitated DNA was analyzed by using Illumina HiSeq 2000. Paired-end sequencing; according to manufacturers protocols Base calls were done by the Illumina software pipeline using RTA 1.13.48.0 and BCL converted using CASAVA 1.8.2 (configureBclToFastq.pl)	Reads were mapped to the Tribolium castaneum genome (Tcas_3.0) using Bowtie (version 0.12.7). Up to 2 mismatches in the seed sequence of each read were allowed; non-unique reads were disarded.Options for bowtie were : -S M-^Vfr M-^Vn 2 M-^Vm 1
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Hardware					Illumina HiSeq 2000
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo
Comment[SecondaryAccession]	ERP003800
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR330016-ERR330017
SDRF File	E-MTAB-1835.sdrf.txt
Publication DOI	10.1128/JVI.01759-13