Chipseq sample or test data

Question

[ariel.balter]

I'm trying to find some sample chipseq data (chip and input) to validate some methods and software. These would preferably be 10 MB < x < 50 MB in size. I've googled quite a bit and having a hard time finding search terms that are bringing anything up.

Thanks for any help.

[Sinji]

Encode has a ton of different ChIP-seq datasets, and you could probably just down-sample the fastq files to get smaller file sizes.

[ariel.balter]

Can you point me to some chip/input pairs in that size range? I can't find any.

Answer 1

[Ron]

You can find the chipseq data here https://www.broadinstitute.org/epigenomics/chip-seq-data

[ariel.balter]

How do I tell which is chip and which is input?

Name    Size    Date Modified
[parent directory]      
10035AAXX.8.fastq.gz    65.7 MB 4/16/10, 12:00:00 AM
11070AAXX.8.fastq.gz    95.9 MB 4/16/10, 12:00:00 AM
11071AAXX.1.fastq.gz    118 MB  4/16/10, 12:00:00 AM
11071AAXX.2.fastq.gz    110 MB  4/16/10, 12:00:00 AM
11124AAXX.3.fastq.gz    55.7 MB 4/16/10, 12:00:00 AM
11124AAXX.5.fastq.gz    52.3 MB 4/16/10, 12:00:00 AM
11124AAXX.6.fastq.gz    64.9 MB 4/16/10, 12:00:00 AM
11124AAXX.7.fastq.gz    37.8 MB 4/16/10, 12:00:00 AM
11124AAXX.8.fastq.gz    39.7 MB 4/16/10, 12:00:00 AM
11222AAXX.1.fastq.gz    134 MB  4/16/10, 12:00:00 AM
11222AAXX.2.fastq.gz    134 MB  4/16/10, 12:00:00 AM
12428AAXX.3.fastq.gz    45.0 MB 4/16/10, 12:00:00 AM
12428AAXX.7.fastq.gz    59.1 MB 4/16/10, 12:00:00 AM
12428AAXX.8.fastq.gz    61.6 MB 4/16/10, 12:00:00 AM
12824AAXX.2.fastq.gz    57.0 MB 4/16/10, 12:00:00 AM
12824AAXX.6.fastq.gz    86.2 MB 4/16/10, 12:00:00 AM
13103AAXX.1.fastq.gz    48.4 MB 4/16/10, 12:00:00 AM
13103AAXX.2.fastq.gz    109 MB  4/16/10, 12:00:00 AM
13103AAXX.3.fastq.gz    114 MB  4/16/10, 12:00:00 AM
13103AAXX.4.fastq.gz    110 MB  4/16/10, 12:00:00 AM
13103AAXX.6.fastq.gz    98.0 MB 4/16/10, 12:00:00 AM

[Ron]

If you use the GSM in the linkI mentioned, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM327663 You can download the SRA files,which can be converted to fastq. using SRA toolkit.

Answer 2

[GouthamAtla]

This may be a bit old data set but still could be useful for you, along with the shell script used in the following protocol paper.

A computational pipeline for comparative ChIP-seq analyses Nature Protocols.

http://starklab.org/data/bardet_natprotoc_2011/