Question: Large-scale open-source bioinformatics datasets
10
gravatar for Tobias
3.9 years ago by
Tobias140
Tobias140 wrote:

Of course, as a bioinformatician, I am aware of many large-scale open-source bioinformatics datasets, such as

  • the ENCODE consortium www.encodeproject.org, RNA-Seq, ChIP-Seq and so on),
  • the Roadmap Epigenomics consortium www.roadmapepigenomics.org, RNA-Seq, Chip-Seq, Bilsulfite-Seq),
  • the IHEC consortium www.ihec-epigenomes.org, RNA-Seq, Chip-Seq, Bilsulfite-Seq),
  • the TCGA/ICGC consortia www.cancergenome.nih.gov, www.icgc.org, large-scale cancer data, DNA-Seq, RNA-Seq, etc.) and
  • the LINCS consortium www.lincscloud.org/l1000 , gene expression for more than a million of different perurbation experiments).

I am wondering, however, what other wonderful datasets, the are both large and open-source, are currently available. That might include things like RNA-Seq, Chip-Seq, Bisulfite-Seq, whole genome sequencing, WGAS, and many other assays (not necessarily NGS-related, though that is what I am mostly looking for).

Also things like the (neural) connectome of certain species (in any event large data) could be of interest.

There are quite some GEO datasets that at least partially fulfil these requirements, but most are simply having to few data samples in order to be interesting to me.

Your comments are greatly appreciated!

 

rna-seq chip-seq next-gen • 4.9k views
ADD COMMENTlink modified 2.2 years ago by Samuel Lampa1.2k • written 3.9 years ago by Tobias140

To all those who replied: Many thanks for your detailed posts!

ADD REPLYlink written 3.8 years ago by Tobias140

Do you know if there is any other resource providing DNAse-seq and mRNA-seq data, other than ENCODE and Roadmap ?

ADD REPLYlink written 3.3 years ago by Bioinformatist Newbie230
2
gravatar for geek_y
3.9 years ago by
geek_y9.8k
Barcelona
geek_y9.8k wrote:

FANTOM

RegulomeDB ( Not a large scale, but very useful functional database)

1000Genome Project

GoNL

ADD COMMENTlink written 3.9 years ago by geek_y9.8k
1
gravatar for Katie D'Aco
3.9 years ago by
Katie D'Aco1000
Massachusetts
Katie D'Aco1000 wrote:

BioGPS is a good one for expression data

ADD COMMENTlink written 3.9 years ago by Katie D'Aco1000
1
gravatar for Jean-Karim Heriche
3.9 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

Loss of function phenotypes: GenomeRNAi.

ADD COMMENTlink written 3.9 years ago by Jean-Karim Heriche20k
1
gravatar for Prakki Rama
3.9 years ago by
Prakki Rama2.3k
Singapore
Prakki Rama2.3k wrote:
ADD COMMENTlink written 3.9 years ago by Prakki Rama2.3k
1
gravatar for osullivanchristopher
3.9 years ago by
United States
osullivanchristopher180 wrote:

SRA maybe?  http://www.ncbi.nlm.nih.gov/sra 

2.2 Petabases open source, 1.8 Petabases authorized access. (btw, TCGA is authorized access not open access)

 

 

 

 

 

ADD COMMENTlink written 3.9 years ago by osullivanchristopher180
0
gravatar for Samuel Lampa
2.2 years ago by
Samuel Lampa1.2k
Stockholm
Samuel Lampa1.2k wrote:

Human Protein Atlas

ADD COMMENTlink written 2.2 years ago by Samuel Lampa1.2k
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