Rey 2011, Circadian BMAL1 profiling in liver

Description:

Time series genome-wide map of BMAL1 binding in mouse liver. Time was mesured according to Zeitgeber time (ZT).

Samples:

File name Description Feature GEO-ID
1 BMAL1_ZT02_ChIP-Seq_rep1.sga BMAL1 ZT02 rep1 BMAL1 GSM654880
2 BMAL1_ZT02_ChIP-Seq_rep2.sga BMAL1 ZT02 rep2 BMAL1 GSM654881
3 BMAL1_ZT06_ChIP-Seq_rep1.sga BMAL1 ZT06 rep1 BMAL1 GSM654882
4 BMAL1_ZT06_ChIP-Seq_rep2.sga BMAL1 ZT06 rep2 BMAL1 GSM654883
5 BMAL1_ZT10_ChIP-Seq_rep1.sga BMAL1 ZT10 rep1 BMAL1 GSM654884
6 BMAL1_ZT10_ChIP-Seq_rep2.sga BMAL1 ZT10 rep2 BMAL1 GSM654885
7 BMAL1_ZT14_ChIP-Seq_rep1.sga BMAL1 ZT14 rep1 BMAL1 GSM654886
8 BMAL1_ZT14_ChIP-Seq_rep2.sga BMAL1 ZT14 rep2 BMAL1 GSM654887
9 BMAL1_ZT18_ChIP-Seq_rep1.sga BMAL1 ZT18 rep1 BMAL1 GSM654888
10 BMAL1_ZT18_ChIP-Seq_rep2.sga BMAL1 ZT18 rep2 BMAL1 GSM654889
11 BMAL1_ZT22_ChIP-Seq_rep1.sga BMAL1 ZT22 rep1 BMAL1 GSM654890
12 BMAL1_ZT22_ChIP-Seq_rep2.sga BMAL1 ZT22 rep2 BMAL1 GSM654891
13 Input_DNA.sga Input DNA Input GSM654892

Technical Notes:

SRA files were downloaded from GEO, GEOID: GSE26602, 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:

Rey G, Cesbron F, Rougemont J, Reinke H et al. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol 2011 Feb;9(2):e1000595. PMID: 21364973