| 00:34:37 | Angelica Van Goor: | Thank you to the organizers for making this meeting happen despite the (continuing)challenges. |
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| 00:38:53 | PARVAZ SARFARAZ: | thank you |
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| 00:41:16 | Christopher Tuggle: | @PeterHarrison Is there a current effort on a nf-core for scRNAseq or scATACseq? |
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| 00:44:34 | PARVAZ SARFARAZ: | ldont know what you mean |
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| 00:45:12 | PARVAZ SARFARAZ: | peter |
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| 00:50:21 | Christopher Tuggle: | Thanks- will follow up! |
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| 00:53:19 | Hans Cheng: | Nomenclature can be an issue. Are you working with journals to aid the best use? |
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| 00:58:34 | Emily Clark: | **Please post your questions for the speakers here rather than the Q&A box** |
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| 00:59:13 | PARVAZ SARFARAZ: | ok thanks for you gudance🐞 |
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| 01:03:33 | Dan Nonneman: | Ole, why not trophectoderm? |
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| 01:03:35 | Zhihua Jiang: | Hi Ole, do you look at any gene switches from maternal to zygotic transition then? Thanks. |
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| 01:05:53 | Fiona McCarthy: | @OleMadsen Could you please briefly describe the chicken intercross line used? |
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| 01:08:29 | Guillaume Devailly: | @OleMadsen Do you know what are the specificities of the GSM pipeline compared to the nf-core/methylseq pipeline for DNA methylation data ? |
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| 01:13:37 | Emily Clark: | @WesWarren on the subject of alternate assemblies dog is one example of what is currently possible with the genome browser for farmed animals e.g. Ensembl release 105 we updated the main reference to the Labrador reference genome and support alternate annotated assemblies for Boxer, Basenji and Great Dane. As Peter said we’re actively thinking now about how we tackle the explosion of new genomes for all the domestic animal species. |
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| 01:16:08 | Dan Nonneman: | Placenta? |
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| 01:23:28 | Ole Madsen: | @FionaMcCarthy, info about the line can be found here: https://www.ed.ac.uk/roslin/national-avian-research-facility/avian-resources/poultry-lines/advanced-intercross |
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| 01:25:55 | Guillaume Devailly: | @Gabriel It seems theere is only one developmental stage per breed, but it is not the same between breeds. It this counfusion between breeds and developemental stages an issue for the analysis? |
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| 01:26:11 | Ole Madsen: | @GuillaumeDevailly. A few additional downstream analysis/tools have been included, like Methylkit, CGmaptools |
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| 01:27:33 | Ole Madsen: | @ZhihuaJiang. No we do not look at maternal to zygotic transition |
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| 01:30:51 | Ole Madsen: | @DanNonneman. I do not know why we didn't consider trophectoderm, but I agree it will be interesting to look at as well. |
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| 01:31:56 | Annie Robic: | @Gabriel, I am always surprised by the transcriptome of the testis which is always different from other tissues, but why only the testis and not the ovary? |
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| 01:33:26 | Jonah Cullen: | @Gabriel Have you looked at any co-expression networks? |
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| 01:35:38 | Ole Madsen: | @FionaMcCarthy, info about the line can be found here: https://www.ed.ac.uk/roslin/national-avian-research-facility/avian-resources/poultry-lines/advanced-intercross |
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| 01:36:04 | Ole Madsen: | @GuillaumeDevailly. A few additional downstream analysis/tools have been included, like Methylkit, CGmaptools |
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| 01:36:11 | Elisabetta GIUFFRA: | @DanNonneman, to add up: we didn't consider trophectoderm or other early phases: we had to choose among options and one of the ideas was also to complement other data from US on same stages |
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| 01:36:36 | Ole Madsen: | @ZhihuaJiang. No we do not look at maternal to zygotic transition |
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| 01:36:52 | Emily Clark: | @Gabriel and @Annie fetal ovary is highly transcriptionally active relative to juvenile and adult ovary and I think highlights how useful it is to include multiple developmental stages in annotation projects. |
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| 01:58:33 | Emily Clark: | @Dailu sorry to lower your hand please go ahead and type your question for @Matthew in the chat. |
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| 02:07:44 | Ole Madsen: | cool work, Ryan :-) |
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| 02:11:19 | Guillaume Devailly: | @ChrisTuggle Impressive work! Any idea why EuroFAANG projects look so far behind the USDA funded-projects? |
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| 02:13:50 | Emily Clark: | Question from @DominiqueRocha from Q&A box: @C. Tuggle: was the scATAC-seq generated at the same time with scRNA-seq using the multi-omics kit from 10x? |
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| 02:14:48 | Emily Clark: | From @IreneKaplow from Q&A box Thanks for a great talk! You mentioned that there are pig-specific cell types relative to human in PBMCs. Have you investigated whether these help explain differences between pigs and humans. |
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| 02:15:53 | Emily Clark: | **Please use the chat box rather than the Q&A box to post questions 🙂** |
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| 02:17:19 | Shenwen Gu: | thank you |
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| 02:17:29 | Shenwen Gu: | Yes |
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| 02:20:22 | Christopher Tuggle: | Ryan- did you get the chat from Ole? He does methylation data as you probably know. |
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| 02:20:41 | Elisabetta GIUFFRA: | @Chris, nice talk! Are the sc data already available in the FAANG data portal? And also: did you make use of deconvolution pipeines in comparing bulk and sc data from PBMCs? |
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| 02:22:04 | Ryan Corbett: | Ole—thanks! Good to see you (hoping you are party of Host&Panelists and can see this message) |
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| 02:23:25 | Christopher Tuggle: | Thanks Elisabetta! The scRNAseq for PBMC is submitted. The scRNAseq for tissues is being prepared and should be submitted in the next few weeks. We haven’t tried to deconvolution, but plan to do that when we have larger sample sizes |
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| 02:27:45 | Christopher Tuggle: | @HUaijunZHou- can you determine whether your high number of transcripts relative to Ensembl is due to a larger number of tissues, or is your seq deeper? |
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| 02:32:11 | Irene Kaplow: | Do the novel genes have orthologs in non-bovine mammals? |
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| 02:36:04 | Dailu Guan: | Are transcriptomes sequenced by short-read or long-read? If short-read, how it is reliable in identifying splicing? |
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| 02:39:21 | Peter Harrison: | From Dominque Rocha: |
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| 02:39:22 | Peter Harrison: | @HZhou: WGBS is being done for how many tissues? At what targeted raw genome coverage (prior mapping)? |
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| 02:39:35 | Peter Harrison: | @HZhou: WGBS is being done for how many tissues? At what targeted raw genome coverage (prior mapping)? |
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| 02:40:58 | Ishaku Haruna: | Great talk @HZhou |
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| 02:47:24 | Huaijun Zhou: | @Dominque a total of 71 samples from 33 tissues for WGBS with average of 356 million reads. |
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| 02:49:35 | Huaijun Zhou: | @Dailu using short-read sequencing, but independently confirmed by long-read sequencing data. |
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| 02:51:42 | Ying Wang: | @David Do you think Cut&Tag can replace ChIP-Seq assays? |
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| 02:52:25 | Guillaume Devailly: | @DavidHawkins Is there a CUT&Tag equivalent of ChIP-qPCR? What QC do you do (if any) before sequencing the CUT&Tag samples? |
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