Datasets produced by the GeneLab Sample Processing Lab are soon to be released from RR-18 retinas (bulk RNAseq and RRBS), and I am helping to start a new Animal AWG sub-group composed of people with bioinformatic experience to help analyze, visualize, and draw conclusions from the data (in conjunction with my other data from RR18). Does anyone have experience with RRBS data analysis? ( Reduced representation bisulfite sequencing)
The data should be released maybe by October, so not super time senstive, yet, but I wanted to let the AWG know
This spaceflight study focuses characterization of acute and delayed risks from exposure to space environment to the eye. The project also aims to determine an antioxidant metalloporphyrin protects against spaceflight environment-induced changes in retinal neurovascular coupling and retinal function. Analysis of retina RNAseq and RRBS from these flight samples will help understand the mechanisms of retina injury from exposure to space environment.
Pinging a few people who either may be interested to join @xmao in analyzing the data from these RR-18 retinas (explanation above ), or know colleagues/bioinformations who may want to join this unique opportunity to help analyze RR-18 data
Hi, @xmao
I am happy to help! I’ve done my BSc diss on collagen associated small proteoglycans and the development of the cornea. I should be ok with the bioinformatic analysis just need to understand the data and the environment. Let me know how I can help!
Kind regards,
Pre
Anyone interested in helping analyze RR-18 retinal RNAseq and RRBS (reducued representation bisultie sequencing) data, and join @xmao Let us know! If you arent yet in the Animal AWG, just let me (Ryan) know
Hi all,
We’ve had some large PI service requests come to GeneLab recently, and those always take precedent over GeneLab generated datasets. So our Methyl-Seq pilot study followed by processing and sequencing of the additional RR-18 samples has been delayed, and is now scheduled to start in spring, 2025. I anticipate that the new raw and processed data will be available in summer, 2025 at the earliest. I will let you know if anything changes.
@xmao,
I encourage you to get started on the submission process for the bulk RNAseq and RRBS data that you already have from the RR-18 mission. Once you submit those data, the Data Processing team will prioritize processing them so that the data can be available to the community sooner rather than later.
Any analysis scripts/pipelines that this group generates with the data you already have should be able to easily be applied to the data from the additional samples when they are available.
I’m happy to contribute to this study but have no prior experience with RRBS data analysis. I’m very much interested in learning and working towards it. Please let me know if there is any option.
The subgroup just met, but the group is still in a holding pattern (won’t meet again likely for a few-several months), until the RR18 LAR +3mo samples are sequenced by GeneLab sample processing lab, then publicly released on OSDR/GL along with the processed data (I believe) using the Methyl-Seq pipeline. The RR-18 datasets for retina (RNAseq & RRBS) in OSDR will be out by late spring/June. Hopefully also the processed data by then too.
RR18 study design (correct me if I’m wrong @xmao):
• Flight (dissected on orbit)
• Flight, then Live Animal Return (dissected 2 days)
• Flight, then Live Animal Return + 3 months (then dissected)
• Ground Control, then Live Animal Return (dissected 2 days to align with flight group)
• Ground Control (dissected aligns with flight orbit group)
• Ground Control then Live Animal Return + 3 months (dissection aligns with flight group)
• Vivarium Control, then Live Animal Return (dissected 2 days to align with flight group)
• Vivarium Control (dissected aligns with flight orbit group)
• Vivarium Control then Live Animal Return + 3 months (dissection aligns with flight group)
), or know colleagues/bioinformations who may want to join this unique opportunity to help analyze RR-18 data