GSE31039, Histone Modifications in several tissues

Description:

This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq (Robertson et al., 2007) to identify transcription factor binding sites and chromatin modification profiles in many mouse (C57Bl/6) tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.
In specific, the Ren lab examined RNA polymerase II (PolII), co-activator protein p300, the insulator protein CTCF, and two chromatin modification marks H3K4me3 and H3K4me1 due to their demonstrated utilities in identifying promoters, enhancers and insulator elements (Barski et al., 2007; Blow et al., 2010; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005a; Visel et al., 2009). Enrichment of H3K4me3 or PolII signals is a strong indicator of active promoter, while the presence of p300 or H3K4me1 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million monoclonal, uniquely mapped tags.

Overall design

Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell/mouse/).
Enrichment and Library Preparation: Chromatin immunoprecipitation was performed according to Ren Lab ChIP Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf).
Library construction was performed according to Ren Lab Library Protocol (http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf).
Sequencing and Analysis: Samples were sequenced on Illumina Genome Analyzer II Genome Analyzer IIx, and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead et al., 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts.

Source

Samples

Technical Notes

SRA files were downloaded from GEO and processed using the following bash commands:

1. Extract FASTQ from SRA file:
   

   fastq-dump SAMPLE.sra
   

2. Map reads to genome using Bowtie:
   

   bowtie --sam -l 36 -n 3 mm9 -q SAMPLE.fastq > SAMPLE.sam
   

3. Clean the results from unmapped reads:
   

   awk 'BEGIN {FS="\t"} $3 != "\*" {print $0}' SAMPLE.sam > SAMPLE_clean.sam
   

4. Make BAM file:
   

   samtools view -bS -o SAMPLE.bam SAMPLE_clean.sam
   

5. Sort it:
   

   samtools sort SAMPLE.bam SAMPLE_sorted
   

6. Make BED file:
   

   bamToBed -i SAMPLE_sorted.bam > SAMPLE.bed
   

7. Make SGA file:
   

   bed2sga.pl -s mm9 -f FEATURE < SAMPLE.bed | sort -s -k1,1 -k3,3n -k4,4 | compactsga > SAMPLE.sga
   

References

1. GEO series GSE31039 Histone Modifications by ChIP-seq from ENCODE/LICR