Missing Metadata for Brainspan Developmental Transcriptome

Technical
,
1

Hello,
I am a researcher in Dr. Karen Berman’s lab on Psychosis and Cognitive Studies at the National Institute of Mental Health. I am attempting to use Brainspan’s Developmental Transcriptome to gain insight into our lab’s data on schizophrenia.
I loaded Brainspan’s developmental transcriptome data (thanks for such an incredible dataset!) and have been linking the expression values to metadata on the ethnicity, gender, RNA integrity number (RIN), etc. for each sample. These variables are very important covariates for my analysis.
However, I have noticed that 30 out of the 524 samples of which the Brainspan Developmental Transcriptome collected expression values for are missing ethnicity, gender, and RIN metadata. The following samples, organized by Internal ID and brain region, do not have corresponding metadata on Brainspan (found under the documentation section of the website):

H376.IIB.50, DTH
H376.IIB.51, DTH
H376.IIB.52, DTH
H376.IIIB.50, OFC
H376.V.50, CBC and VFC
H376.V.53, all 16 samples
H376.VI.51, all 8 samples
H376.VIII.53, MD

Is there any way that I can find this missing metadata? It would be a shame to not include these values in my analysis.
Thanks,
Teddy Daniel

2

Hi @teddyd,
All information that we have is available in the Donor and Sample Metadata documentation at the link you provided. In particular, for the donors you listed that are missing sample information, you can use the ethnicity, gender, and (for some of them) RIN from page 1. The two exceptions are “H376.V.50” and “H376.VI.51”, which are not available here. In addition, you can get a subset of this information from the RNA-Seq Gencode v10 summarized to genes link on the Download page. Specifically “H376.V.50” is Female and and “H376.VI.51” is Male, but we don’t have ethnicity or RIN info. Finally, this data was collected in collaboration with Dr. Nenad Sestan’s lab, so you might be able to find more information there, although that is unlikely. Best of luck in your analysis!
Best,
Jeremy.

1 Like
3

Thanks so much Jeremy, this is very helpful!