Library annotations in metadata - state-fate in vitro

[Kunal Jindal]

Hi @calebweinreb @AllonKleinLab, really great work and thanks for making the data available on github. I had a query about the in vitro state-fate data. Based on your publication, I understand it consists of 3 experiments (2 LK + 1 LSK) and each experiment consists of 5 libraries (1 D2 and 2 each for D4 and D6) leading to 15 total libraries.

However, it looks like the Library column in the metadata contains 35 unique entires?
'LSK_d2_1', 'LSK_d2_2', 'LSK_d4_2_2', 'LSK_d4_1_3', 'LSK_d2_3', 'LSK_d4_2_3', 'LK_d6_2_1', 'LK_d6_2_2', 'LSK_d6_2_2', 'LK_d6_1_1', 'LSK_d4_1_2', 'LSK_d4_2_1', 'LK_d6_1_2', 'LSK_d4_1_1', 'LSK_d6_2_3', 'LSK_d6_1_2', 'LSK_d6_2_1', 'LK_d4_2', 'd4_2_1', 'd4_2_2', 'LSK_d6_1_3', 'LSK_d6_1_1', 'LK_d4_1', 'd6_1_1', 'd6_2_2', 'd2_3', 'd2_2', 'd6_1_2', 'd6_2_3', 'd6_2_1', 'd4_1_2', 'd4_2_4', 'd4_1_1', 'd2_1', 'LK_d2'

Could you please explain how these 35 entires map to the 15 libraries I mentioned? Or am I misunderstanding your experimental design?

Thanks!

[Caleb Weinreb]

Each biological sample is split among several "libraries" in order to combinatorially increase the number of cell barcodes during library preparation. The nomenclature is a little confusing. First of all, you can see that the libraries come in 3 categories with different prefixes. "LSK" denotes the LSK libraries, "LK" denotes one of the LK experiments, and then the labels with no prefix denote the second LK experiment. Each library name from day4 or day6 has three tags separated by underscores (e.g. d4_X_Y). The first tag refers to timepoint. The second tag ("X") refers to one of the two wells in which cells were cultured, and the third tag ("Y") refers to one the splits of the sample (as described above). On day2, the cells have not been split into 2 wells yet, so library names just look like "d2_Y", where again Y refers to one of the splits during library prep.

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On Thu, Aug 20, 2020 at 10:41 PM jindalk ***@***.***> wrote: Hi @calebweinreb <https://github.com/calebweinreb> @AllonKleinLab <https://github.com/AllonKleinLab>, really great work and thanks for making the data available on github. I had a query about the in vitro state-fate data. Based on your publication, I understand it consists of 3 experiments (2 LK + 1 LSK) and each experiment consists of 5 libraries (1 D2 and 2 each for D4 and D6) leading to 15 total libraries. However, it looks like the Library column in the metadata contains 35 unique entires? 'LSK_d2_1', 'LSK_d2_2', 'LSK_d4_2_2', 'LSK_d4_1_3', 'LSK_d2_3', 'LSK_d4_2_3', 'LK_d6_2_1', 'LK_d6_2_2', 'LSK_d6_2_2', 'LK_d6_1_1', 'LSK_d4_1_2', 'LSK_d4_2_1', 'LK_d6_1_2', 'LSK_d4_1_1', 'LSK_d6_2_3', 'LSK_d6_1_2', 'LSK_d6_2_1', 'LK_d4_2', 'd4_2_1', 'd4_2_2', 'LSK_d6_1_3', 'LSK_d6_1_1', 'LK_d4_1', 'd6_1_1', 'd6_2_2', 'd2_3', 'd2_2', 'd6_1_2', 'd6_2_3', 'd6_2_1', 'd4_1_2', 'd4_2_4', 'd4_1_1', 'd2_1', 'LK_d2' Could you please explain how these 35 entires map to the 15 libraries I mentioned? Or am I misunderstanding your experimental design? Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MRRI3R2DCCFTFH7MWLSBXNFDANCNFSM4QGZ6YSQ> .

[Kunal Jindal]

Got it, thanks a lot for the clarification!