This repository is used to store the code and raw material for the ChIP-seq bioinformatic tutorial of Synechocystis' NtcA published in bio-protocols.
Joaquín Giner-Lamia*, Miguel Hernández-Prieto, M.E. Futschik. "ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803". 2018. bio-protocols
A wiki version of this protocol is available here
The data deposited in this project comes from a series of ChIP-seq experiments to the aims of analyse the regulon of NtcA in conditions of low and high avilability of nitrogen. The analysis of these data can be found at:
Joaquin Giner-Lamia* et al., Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. 2017.Nucleic Acids Res.
Note: Fastq files presents in this repository has been modify to minimize the computational time consuming for the bioinformatic analysis during the protocols. Thus files presents in this repository contains only 1% of total reads presents in the original ChIP-seq files.
The original fastq files are available at Gene Expression Omnibus(GEO) with the accession number: GSE97291.
Joaquin Giner-Lamia* et al., Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. 2017.Nucleic Acids Res.*To whom correspondence should be addressed:jginer[AT]cnb.csic.es
Joaquín Giner-Lamia*, Miguel Hernández-Prieto, M.E. Futschik. "ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803". 2018. bio-protocols*To whom correspondence should be addressed:jginer[AT]cnb.csic.es
Here you can find all the files neccesaries for this tutorial.
N_input.fastq: input sample from Synechocystis cells grown 4 hours in absence of nitrogen.
N_ChIP.fastq: ChIP-seq sample from Synechocystis cells grown 4 hours in absence of nitrogen.
NH4_input.fastq: input sample from Synechocystis cells grown 4 hours in presence of ammonium.
NH4_ChIP.fastq: ChIP-seq sample from Synechocystis cells grown 4 hours in presence of ammonium.
pcc6803.genome.fasta: IGV genome file of Synechocystis created using .fasta and .GFF from the Synechocystis sp. PCC 6803 Refseq genome NC_000911.1
pcc6803.genome.fasta.fai: IGV index genome file of Synechocystis created using .fasta and .GFF from the Synechocystis sp. PCC 6803 Refseq genome NC_000911.1
NC_000911.1.fasta: Synechocystis sp. PCC6803 genome in .fasta format
NC_000911.1.gff: Synechocystis sp. PCC6803 genome in .gff format
Note: while all_files folder contains all the files generated in this tutorial (including intermediate and final files), in the scripts folder users can find all the scripts neccesaries for this tutorial.