Gaffney12, Controls of nucleosome positioning in the human genome.


Paired-end sequenceing of MNase-treated chromatin of seven lymphoblastoid cell lines. Two of the cell lines have been also single-end sequenced for comparison.


Files downloaded from FTP site:
Input file format: SRA


From Human Feb. 2009 (GRCh37/hg19) Assembly

Filename Description Feature GEO-ID
1 GSM907783.sga GM18507 - MNase-seq MNase GSM907783
2 GSM907784.sga GM18508 - MNase-seq MNase GSM907784
3 GSM907785.sga GM18516 - MNase-seq MNase GSM907785
4 GSM907786.sga GM18516 - MNase-seq - Single-end MNase GSM907786
5 GSM907787.sga GM18522 - MNase-seq MNase GSM907787
6 GSM907788.sga GM18522 - MNase-seq - Single-end MNase GSM907788
7 GSM907789.sga GM19193 - MNase-seq MNase GSM907789
8 GSM907790.sga GM19238 - MNase-seq MNase GSM907790
9 GSM907791.sga GM19239 - MNase-seq MNase GSM907791

Technical Notes

Raw data was downloaded from NCBI SRA database (ID SRP012024) and mapped to hg19 genome using Bowtie aligner. The resulting SAM files were converted to BED using SAMtools and BEDtools. Final conversion to SGA files was done using ChIP-Seq.


Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK.
Controls of nucleosome positioning in the human genome. PLoS Genet. 2012;8(11):e1003036. PubMed PMID: 23166509

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