Bulk sequencing datasets for <i>itga4-vcam1b</i> paper
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Bulk RNA-seq @ 5 dpfRunx:mCherry+ HSPCs were sorted via flow cytometry from pooled WT and <i>itga4</i> mutant embryos at 5dpf (immediately after CHT interaction or bypass, respectively).Sorted cell counts (n) as follows: WT samples: n<sub>1</sub>= 7,504, n<sub>2</sub>= 8,556, n<sub>3</sub>= 4,307, n<sub>4</sub>= 26,345 & <i>itga4 </i>mutant samples: n<sub>1</sub>= 3,517, n<sub>2</sub>= 1,610, n<sub>3</sub>= 1,286RNA isolation from sorted cells was prepared in the Tamplin lab before library prep & QC was done at the UW-Madison Gene Expression Center. Sequencing was completed by the UW-Madison Biotech Center and alignment, QC, and preliminary analysis was performed by the UW-Madison Bioinformatics Resource Center before delivery to the Tamplin lab.After preliminary analysis and discussion with the BRC we decided to drop the WT#1 replicate, as they advised it was "at least a putative outlier" (we can provide more information as requested). Both analyses are provided and labeled accordingly (with and without WT#1 replicate).Bulk ATAC-seq @ 5 dpfRunx:mCherry+ HSPCs were sorted via flow cytometry from pooled WT and <i>itga4</i> mutant embryos at 5dpf (immediately after CHT interaction or bypass, respectively).Sorted cell counts (n) as follows: WT samples: n<sub>1</sub>= 1,279, n<sub>2</sub>= 11,056, n<sub>3</sub>= 11,189 & <i>itga4 </i>mutant samples: n<sub>1</sub>= 21,801, n<sub>2</sub>= 330, n<sub>3</sub>= 395Libraries were prepared in the Tamplin lab before QC & sequencing by the UW-Madison Biotech Center and alignment, QC, peak calling, and Homer motif analysis was performed by the UW-Madison Bioinformatics Resource Center before delivery to the Tamplin lab.All replicates clustered within sample sets and had peaks align after analysis by the Bioinformatics Research Core (BRC) at UW-Madison, but reps WT#3 and <i>itga4</i> mut#1 had the deepest/cleanest signal. Therefore, there are some analysis files of just these two in comparison for visualization purposes.Bulk ATAC-seq @ 6-24 mpfRunx:mCherry+ HSPCs were sorted via flow cytometry from dissected WKM of 6 mpf WT, <i>itga4</i> mutant, and <i>vcam1b</i> mutant and 24 mpf WT adult zebrafish.Aging studies are not well established in zebrafish, so for the purpose of this study we label 6 mpf as young adults (relative to 8-10 week old mice) and 24 mpf as old adults (relative to 2 year old mice).Libraries were prepared in the Tamplin lab before QC & sequencing by the UW-Madison Biotech Center and alignment, QC, peak calling, and Homer motif analysis was performed by the UW-Madison Bioinformatics Resource Center before delivery to the Tamplin lab.Preliminary analysis was performed by the Tamplin lab after delivery of the sequencing files, although there was no direct link found to the current results that will be published in this <i>itga4</i>-<i>vcam1b </i>paper. We believe this dataset to be of good quality and will use it for later experiments. If new/further analysis uncovers a link to the current manuscript, we would be happy to include this in the paper.
