Hi,
The paper mentions RNA-seq data (used in figure S1) generated for the iPSC-derived NPCs and neurons used in the study. I haven't been able to find this data - has it been deposited on Synapse or anywhere else?
Thanks!
Created by acadiakocher @user230, could you please email me at prashanth.rajarajan@icahn.mssm.edu? I might have some tables to tide you over while I work on getting the raw RNA-seq data uploaded. Thanks! HI @user230, thanks for reaching out. Sorry for the delay but given my clinical responsibilities, I haven't had time to pop into the lab. I will work on this in the next two weeks and let you know on this forum. Thanks for your patience!
@rajarp01 Hi, Prashanth
Sorry to disturb you once again, is it possible to get access to those newly generated RNA-seqs?
It would be great to have even FPKM/TPM tables
Thank you in advance Hello, Acadia. Would you mind sending me your email address to continue the discussion? Hi Prashanth - I'm following up about the RNA-seq and ATAC-seq data generated in your Science paper. Did you end up depositing these datasets? I've found the HiC very useful and would love to access these too. Or if you have a public trackhub (for the ATAC-seq especially), that would be great. Thanks! @rajarp01 Thanks, I appreciate it! Hello, sorry about the delay! Just got back from a trip. Neither the RNA-seq on the specific lines used for Hi-C nor the ATAC-seq data are currently on Synapse. I will work on depositing them here this week and notify you when it is complete. Hi Prashanth - I was interested in the new RNA-seq generated in your paper for the lines that you used for HiC. I'm also interested in the ATAC-seq data you generated, which I haven't been able to find. Is this deposited somewhere? Or is there an accessible genome browser track hub? Thanks! Hello! I think you are talking about the 90+ libraries from hiPSC NPCs and neurons that we used in the PCA plot in Fig S1. If so, that dataset was published earlier as part of this study:
Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains | Nature Communications
https://www.nature.com/articles/s41467-017-02330-5
Hope that helps! We have followed up with the manuscript authors for clarification Yes, that's the paper and I've found the data resource page for it. However, I can only find the HiC data and I'd like to find the RNA-seq data. Are you referring to this manuscript: https://science.sciencemag.org/content/362/6420/eaat4311. There should be a link in the paper to this data resource page: https://www.synapse.org/#!Synapse:syn12979101