03 October 2010

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE21512
http://biowhat.ucsd.edu/homer/ - bedGraph mm8 files available

Illumina Genome Analyzer II (Mus musculus)

Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. 
After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library 
fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. 

Alternatively, DNA was phenol/chloroform-extracted from MNase-treated nuclei, and 134-154 bp 
long fragments were extractred from a 2% agarose gel. For MNase-Seq, size-selected mononucleosome-derived 
DNA fragments were ligated to modified adapters that incorporate both the adapter sequence as well as the 
primer landing sites for the flow cell-conjugated primers. 

Alignment: Reads were truncated to 25 bp and aligned to the mouse mm8 genome (NCBI Build 36) using eland. 
Only reads that mapped to a single, unique position were used for downstream analysis.

Peaks were identified using custom software (HOMER, available at http://biowhat.ucsd.edu/homer/). 
For transcription factors, peaks were found by identifying 200 bp regions with tag density exceeding a 
threshold set at a 0.1% false discovery rate (determined by tag randomization). Only peaks with >4x normalized 
tag density relative to control sequencing and >4x normlaized tag density to the sourrounding 10kb of region 
were considered for analysis.

-------------------
GSE21512_README.txt
Genome: mm8
ChIP-Seq Peak File Format (BED):
Column 1: chr
Column 2: start position
Column 3: end position
Column 4: peak name
Column 5: peak score (i.e. peak height)
Column 6: strand (all are +, no applicable for ChIP-Seq peaks)

MNase-Seq Nucleosome positions (BED):
Column 1: chr
Column 2: start position
Column 3: end position
Column 4: nucleosome name
Column 5: number of nucleosomes recorded at that position
Column 6: strand (+/- depending on the strand containing the read used to define the 5' edge of the nucleosome position)

Raw data files:
Raw sequence files were provided as FASTA or FASTQ files when available.
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PUER Cells (PU.1-/- line with PU.1-ER fusion)
=============================================
GSM538796 	PUER-0h-MNase-Seq
GSM538796_Sample33.PUER-MNase-0h.bed.gz 	225.5 Mb
chr10   3002839 3002985 chr10-3002839-0 1       +
chr10   3002755 3002901 chr10-3002901-1 1       -
24,459,966 'nucleosomes'
fastq files:
ftp://ftp.ncbi.nlm.nih.gov/sra/static/SRX019%2FSRX019784/
SRR042041.fastq.bz2	203 MB
SRR042042.fastq.bz2	267 MB
SRR042043.fastq.bz2	256 MB
SRR042044.fastq.bz2	414 MB


GSM538797 	PUER-1h-MNase-Seq
GSM538797_Sample34.PUER-MNase-1h.bed.gz 	266.5 Mb


GSM538012 	PUER-H3K4me1-0h-ChIP-Seq
chip antibody: H3K4me1 (Vendor: Abcam, cat# ab8895, lot# 721955)
GSM538012_Sample30.PUER-H3K4me1-0h.bed.gz 	314.9 Kb  (peak calls)
fastq: ftp://ftp.ncbi.nlm.nih.gov/sra/static/SRX019%2FSRX019775/SRR042031.fastq.bz2	328 MB


GSM538013 	PUER-H3K4me1-1h-ChIP-Seq
chip antibody: H3K4me1 (Vendor: Abcam, cat# ab8895, lot# 721955)
GSM538013_Sample31.PUER-H3K4me1-1h.bed.gz 	307.9 Kb (peak calls)
fastq: ftp://ftp.ncbi.nlm.nih.gov/sra/static/SRX019%2FSRX019776/SRR042032.fastq.bz2	284 MB


GSM538014 	PUER-H3K4me1-24h-ChIP-Seq


GSM537993 	Bcell-input-ChIP-Seq
GSM537993_Sample11.Bcell-input.bed.gz 	1.2 Kb


PUER-PU.1-0h-ChIP-Seq
Chromatin IP against PU.1 in PUER cells after 0h Tamoxifen treatment
chip antibody: PU.1 (Vendor: Santa Cruz, cat# sc-352, lot# F1808)
GSM538000_Sample18.PUER-PU.1-0h.bed.gz 	114.6 Kb