list of cells that used in figure 5

Question

list of cells that used in figure 5

bioinformaticss opened this issue 4 years ago · comments

hey @calebweinreb @AllonKleinLab this is a really great work and I enjoyed reading it. In particular, figure 5 provides a good starting point for benchmarking RNA-seq fate prediction tools.

The process to get the cells was described in the paper but it is kind difficult to fully reproduce. And only the list of neutrophil cells in figure 5F are provided. Could you please also provide the complete list of cells that were used in figure 5A/B and 5C?

Thanks in advance and I am looking forward to hearing your replies!

Caleb Weinreb · Answer 1 · Wed Jul 22 2020 03:13:53 GMT+0800 (China Standard Time)

Hi, A link to that list of cells is now on the website. Also, I am attaching a folder with data and a notebook that is sufficient to fully reproduce the benchmarking analysis

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On Mon, Jul 20, 2020 at 6:23 PM bioinformaticss ***@***.***> wrote: hey @calebweinreb <https://github.com/calebweinreb> @AllonKleinLab <https://github.com/AllonKleinLab> this is a really great work and I enjoyed reading it. In particular, figure 5 provides a good starting point for benchmarking RNA-seq fate prediction tools. The process to get the cells was described in the paper but it is kind difficult to fully reproduce. And only the list of neutrophil cells in figure 5F are provided. Could you please also provide the complete list of cells that were used in figure 5A/B and 5C? Thanks in advance and I am looking forward to hearing your replies! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MW5J5EQYAACCBVQILTR4S7VNANCNFSM4PC3QA2Q> .

bioinformaticss · Answer 2 · Wed Jul 22 2020 12:21:10 GMT+0800 (China Standard Time)

thanks a lot for your quick reply! I am looking forward to the folder!

Btw, could you please also provide the names of the 10 genes that were included in fig5D (where only 3 TFs were shown)

Caleb Weinreb · Answer 3 · Fri Jul 24 2020 10:08:01 GMT+0800 (China Standard Time)

Hi, Here is a link to the folder for reproducing Fig. 5 https://www.dropbox.com/sh/zmst7q6tge5zneg/AABmYJwbPDbokPk4nKMOG3FJa?dl=0 The 10 genes were ['Pou2f2', 'Hdac9', 'Mef2c', 'Bcl6', 'Hlx', 'Zfp36', 'Satb1', 'Gata2', 'Ppp1r16b', 'Tle3']

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On Wed, Jul 22, 2020 at 12:21 AM bioinformaticss ***@***.***> wrote: thanks a lot for your quick reply! I am looking forward to the folder! Btw, could you please also provide the names of the 10 genes that were included in fig5D (where only 3 TFs were shown) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MQBJ35H2LQV7IFHL5TR4ZSMHANCNFSM4PC3QA2Q> .

bioinformaticss · Answer 4 · Sat Jul 25 2020 12:55:42 GMT+0800 (China Standard Time)

That is awesome! Thank you for sharing the folder and the gene list.