How to get raw data (fastq after sequencer) for data from LINCS?

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4.3 years ago

tomilova.ekaterina.rp • 0

I found datasets of interest to me at LINCS (http://lincsproject.org/LINCS/). I found that the data can be downloaded from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138). However, the GEO contains preprocessed data, and there is no link to download the raw data from the SRA. Was this data loaded into SRA or how else can I get raw data (fastq-files after the sequencer). Thanks!

RNA-Seq database • 851 views

ADD COMMENT • link 4.3 years ago by tomilova.ekaterina.rp • 0

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The platform is GPL20573: Broad Institute Human L1000 epsilon http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573

I do not think this is NGS but some kind of array-based assay so no fastq available.

ADD REPLY • link 4.2 years ago by ATpoint 85k

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Thanks!

For some sets, judging by the description, this is really an array of data, but, for example, for the dataset "iPSC (Exp 1) - ALS, SMA and Control (unaffected) subject-derived iPSC lines - RNA-seq", the data description contains information about the sequencing instrument (Illumina), kit sequencing, sequencing strategy and other information.

http://lincsportal.ccs.miami.edu/datasets/view/LDS-1356#downloaddataset

Therefore, I concluded that the raw data must be somewhere.

ADD REPLY • link 4.2 years ago by tomilova.ekaterina.rp • 0

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