Irinalazar
commented
3 years ago Open Irinalazar opened 3 years ago
Irinalazar
commented
3 years ago Irinalazar
commented
3 years ago @dktanwar
Here are the small changes that need to be done for each subfigure:
[x] Fig 2a and 2B: replace "FC" with fold change: I think we agreed to keep in every subfigure "Log2 (underscript) fold change"
[x] Fig 3A and 3B: replace "fold-change" with "fold change"
[x] Fig 4A and 4D: replace "FC" with "fold change" and replace "ATAC" with "ATAC-seq"
[x] Fig 5A and 5B: replace "FC" with "fold change"
[x] Fig 5A and 5B: It's not "sub-family" but "family" in the captio for LINEs and LTRs
[ ] Fig 5A and 5B: to make these 2 heatmaps more informative I suggest to also represent the classes represented in the heatmap in a color coded bar (ERVK, ERVL, ERV1, LINE L1). This way the reader get an idea immediately of what are the predominant LTR and LINE classes changing in accessibility
[x] Fig 5B: position (ATAC-seq) and (RNA-seq) under the Log2 fold change (less wide figure means I can place it better in the page)
[x] Fig 5C: switch order between intergenic and intronic bars so that exonic and @@@intronic are next to eachother (consistent with Fig 1)
[x] Fig 5C: I would add the names of the genes and the names of the L1 loci on this heatmap (we can discuss it tomorrow)
[x] Fig 6A, 6C: replace FC with fold change
This is the plan of the figure panels (main and supplemental) to be included in the developmental paper, following our last data analysis in which we replaced the adult RNA-seq data generated in-house with the PND14 vs PNW8 RNA-seq comparison
Main Figures
**1. Figure 1 Chromatin accessibility dynamics**
General comments: Blue to Red switch for dots in the Volcano plot; Names need to be more descriptive so the reader understands what they mean without having to look at the figure legend, I suggest: "More accessible in adult spg"/"Less accessible in adult spg" - if we unbold them (not necessary) and make the font a bit smaller they fit;
[x] A. Volcano plot of the 3212 differentially accessibile regions (switch color coding of the dots between blue and red for less access vs more access). The rest of the figure remains the same; Please remove the square background and keep it white
[x] B. Distribution of the 3212 DARs across the genome: split gene body in intronic and exonic, similar to how we do it for the transposable elements (TEs); It's relevant to differentiate between intronic and exonic regions in terms of potential regulatory function; Please remove the square background and keep it white; Unbold titles and make the bar chart a bit wider so we can write
[x] C. How are the GO terms sorted again? Should be sorted from highest to lowest adjusted P; same as in B, unbold titles and replace with "More accessible in adult spg"/"Less accessible in adult spg"
[x] D. How are the GO terms sorted again? Should be sorted from highest to lowest adjusted P; same as in B, unbold titles and replace with "More accessible in adult spg"/"Less accessible in adult spg"
2. Figure 2: Transcriptome dynamics
General comments: I am not sure yet if this actually makes sense to be included in a main figure, we can discuss it with Pierre-Luc when we present him with the main figure panels. If he thinks it doesn't make a strong case for our paper, we move it to supplemental.
[x] A. Heatmap of the DEGs from PND8 vs PND15
[x] B. Heatmap of up/down regulated genes between PND14 and PNW8 (decide on a threshold, FPKM > 1 and abs log2FC > 1 so we are coherent with PND8 vs PND15?);
[x] C. fGSEA bar chart of negative and positively enriched GO terms from PND8 vs PND15 - ask Irina for which terms to plot
[x] D. fGSEA bar chart of negative and positively enriched GO terms from PND14 vs PNW8 - ask Irina for which terms to plot
3. Figure 3: Overlap plots and genomic snapshots of representative examples
General remarks: the focus should be on proximal regions, the enriched heatmaps for the distal regions will probably move to Suppl Figures
[x] A. Heatmap of all proximal regions (Category 1-6)
[x] B. Enriched heatmap of Proximal regions (Category 1-4) with ChiP seq, without WGBS
[x] C. Genomic snapshots of representative genes in Category 1: Gfra2
[x] D. Genomic snapshots of representative genes in Category 2: Tbx4
[x] E. genomic snapshots of representative genes in Category 3: Pdgfra
4. Figure 4: TF dynamics across the DARs General comments: I think it makes sense to have this chunk of data here, once we already have introduced the RNA-seq as well and we are done with those comparisons and the literature overlap; switch also here blue with red when it comes to representing the logFC in the dotplots; also the names of the plots unbolded and replace with "More accessible in adult spg"/"Less accessible in adult spg"
[x] A. Dotplot of all TF motifs enriched in more and less accessible regions: please recheck the lists you have used in the previously generated figure, not all TFs are represented there, I think now we can really represent all, pvalue from HOMER and Log2FC from literature RNA-seq; unbold fold changes or p-value names, it's not necessary to have bold names within the plots in general; replace with "More accessible in adult spg"/"Less accessible in adult spg"
[x] B. TF motifs of the most representative examples from the more and less accessible regions
[x] C. Genomic snapshots of RNA expression of several representative TFs so we confirm their RNA downregulation: Fos, Jun, Usf1, Pouf31
[x] D. Dotplots of gene body and intergenic regions in more accessible and less accessible regions; replace plots names with "More accessible in adult spg"/"Less accessible in adult spg"
5. Figure 5: Transposable elements (TEs) accessibility and TF motifs at less accessible LTRs
[x] A. Heatmap of all DA TEs subtypes identified
[x] B. Separate heatmap of the expression changes of only the more accessible TEs
[x] C. Bar chart of the genomic distribution of the DA TEs, with introns separate from exons
[x] D. Genomic snapshots of the Lncenc1 and the other Platr14 and Platr27 RNAseq and ATACseq
[x] E. Dotplots of enriched TFs motifs for less accessible ERVKs, ERVL
6. Figure 6: Transposable elements (TEs) accessibility and TF motifs at more accessible L1s and LTRs
[x] A. Heatmap of the expression of these 22 Olfr genes with upregulated expression between PND14 and PNW8 together with Log2FC of ATAC-seq of the corresponding TE locus.
[x] B. Genomic snapshots of Olfr362 and Olfr1497
[x] C. Dotplots of enriched TF motifs for more accessible L1s, ERV1s and ERV1s