Comments (5)
Hi,
For our Agilent WES samples we use:
gs://firecloud-tcga-open-access/tutorial/bams/C835.HCC1143_BL.4.bam
I think this is publicly available.
For our ICE WES samples we use a germline blood from the CCLF project's samples:
gs://fc-38a1a377-72c6-4e90-917f-e4bb709b8f2c/CCLF_RCRF1009-Normal-SM-F3R8L/seq_data_v2/CCLF_RCRF1009GL.bam
I'm not sure if this is publicly available, but give it a shot and let me know.
For WGS we use this GTEx sample:
GTEX-111FC-0001-SM-6WBTJ
I think you'd need dbGaP access for this one and get it through the GTEx project.
@jkobject feel free to chime in if I'm missing some information
from depmap_omics.
Thanks for the quick response!
It looks like I am not able to access CCLF
data, but that okay since I'm only interested in the WGS data at the moment.
While trying to figure it out on my own I actually duplicated my question on the DepMap community forum. Sorry about this.
Now having re-read the Ghandi et al (2019) paper again, I see that a pseudo normal (ie panel-of-normal, PoNs) were created via 8,000 TCGA normal samples. Is that the same as the GTEx GTEX-111FC-0001-SM-6WBTJ
you are referring to?
from depmap_omics.
from depmap_omics.
I see. Thank you for clarifying what the psuedo-normal is and where the PoNs originated. For the PoN, are you able to share the sample IDs were and what were the criteria used to select them (besides that they were normal tissue)? I will see if I can request them from GTEx biobank.
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closing this as it can be followed here.
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