GSE33213, TFBSs and open chromatin in multiple cell lines

Description

Pol-2, CTCF and c-Myc profiles were analysed in several cell lines. These samples are part of the UCSC traks on transcription factor binding sites identified in multiple cell types by ChIP-seq.

Additional information on the cell lines can be found on the ENCODE Common Cell Types page at UCSC.

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 --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -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 (using SamTools):
   

   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 (using ChIP-seq):
   

   bed2sga.pl -s hg18 -f FEATURE < SAMPLE.bed | sort -s -k1,1 -k3,3n -k4,4 | compactsga > SAMPLE.sga
   

References

1. GEO series GSE33213 Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin).