Sample description for high-level modEncode data?
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7.6 years ago
unksci ▴ 180

Is there any sample description for high-level modEncode data (in particular C. elegans transcriptomes)?

I have downloaded the high-level data worm_gene.xlsx from https://www.encodeproject.org/comparative/transcriptome/ which contains spreadsheets with genes vs. samples. While the headers provide a name for the columns, these names consist of a series of abbreviations. While I could make educated guesses (e.g.: based on abbreviations of strains or developmental stages), the column names contain some additional letters and numbers, whose meaning I can not unambiguously decipher without risking to introduce some error into my analysis.

I have contacted the technical support of modENCODE, who also could only partially decipher these column headers. While they forwarded my question to one of the original labs, I have not heard back from them within the last two weeks.

encode modencode annotation • 1.3k views
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7.6 years ago
dyollluap ▴ 310

If you look at modmine it's possible to get the full detailed sample name and link to sample description: http://intermine.modencode.org/release-33/experiment.do?experiment=Transcriptional+profiling+of+C.+elegans+Developmental+Stages+using+RNA-seq

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Thank you. While still not fully unambiguous, you are right that the samples should also occur on intermine, which therefore could limit the possibilities (and it would seem possible to disambiguate the worm_gene.xlsx within 1-2 working days).

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