How to find the annotation file for GPL16956 platform of Arraystar human lncRNA microarray V3 (Probe Name Version)?

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5.4 years ago

daphneolivia39 ▴ 20

I'm doing annotation of probe id for GPL16956 microarray platform, is anyone know where to find the names of the lncRNAs for the probe id in the platform? I'm lost

annotation lncRNA microarray probe • 2.1k views

ADD COMMENT • link updated 4 months ago by GenoMax 154k • written 5.4 years ago by daphneolivia39 ▴ 20

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please, Did you find any answer for this question as i am stuck in it now!!

ADD REPLY • link 4 months ago by Ahmed Jaber • 0

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You can find the probe sequences in this table: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GPL16956&id=25054&db=GeoDb_blob118

These will need to be mapped to hg19 to get the chromosomal locations. A couple of options for that.

lncRNA annotation file for hg19 is available here: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/GRCh37_mapping/gencode.v48lift37.long_noncoding_RNAs.gtf.gz

Alternatively it may also be possible to use blat to identify the lncRNA from the lncRNA transcript fasta file from GENCODE: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/GRCh37_mapping/gencode.v48lift37.lncRNA_transcripts.fa.gz

ADD REPLY • link 4 months ago by GenoMax 154k

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