clontracer barcoding pool library dna  (Addgene inc)

Journal: bioRxiv

Article Title: StarTrace: A Multiplex Organoid Avatar Drug Testing Platform for Personalized Medicine

doi: 10.1101/2025.02.12.637574

Figure Lengend Snippet: Isolation of individual DNA barcodes from the ClonTracer barcode virus library and workflow of barcoding and tracking PDOs within a mixture by both NGS and StarTrace PCR. Created in https://BioRender.com

Article Snippet: ClonTracer Barcoding pool Library DNA was purchased from addgene (#67267).

Techniques: Isolation, Virus

Journal: iScience

Article Title: Lineages of embryonic stem cells show non-Markovian state transitions

doi: 10.1016/j.isci.2021.102879

Figure Lengend Snippet: Generation and tracking of ESC lineages (A) FACS plot showing the expression of Nanog and Sox2 in a population of mouse embryonic stem cells. Cells were binned into three states of expression (State 1 = Nanog High Sox2 High, State 2 = Nanog Low Sox2 High, State 3 = Nanog Low Sox2 Low). (B) Experimental Schematic. Lentivirally encoded barcodes were introduced into ESCs in the three States which were expanded into lineages. Cells were cultured over time, during which some ESCs switched between States. At the indicated time points half the culture was sorted into States 1–3 and the representation of each barcode (lineage) assessed in each state through sequencing (see ). Pink circles, Blue circles and Green circles represent State 1, State 2 and State 3, respectively. See for cell numbers assessed. (C) Histogram showing the distribution of lineage sizes (in number of cells) on average across all time points. (D) Stacked bar plot representation showing the proportion each lineage contributed to the overall population across all time points. Each unique color row represents a distinct lineage. The number of lineages observed above background at each time point is indicated; 2,560 lineages were detected in at least one state at all time points. See also and .

Article Snippet: Two mouse embryonic stem cell (ESC) lines were used in this study: V6.5 (gift from the Jaenisch Laboratory, Whitehead Institute, MIT) and V6.5 derived Nanog-GFP/Sox2-mCerulean generated as described below using stably-integrated DNA barcodes ( , Addgene #67267).

Techniques: Expressing, Cell Culture, Sequencing

Journal: iScience

Article Title: Lineages of embryonic stem cells show non-Markovian state transitions

doi: 10.1016/j.isci.2021.102879

Figure Lengend Snippet: High motility ESC lineages skew fate to either neuroectoderm or extraembryonic endoderm upon differentiation (A) Phase contrast microscopy of embryonic stem cell colonies in standard culture, differentiated by 4 days of treatment with retinoic acid. 10X objective images. Scale bar = 25 micrometers. (B) Diagram of experiment. ESC lineages were cultured under standard conditions (serum + LIF) under which cells transition between States 1–3 for 12 days, with sampling on day 0, 6, and 12. On day 12, a cell split was also placed in retinoic acid for differentiation. CD24 high (neuroectoderm) and CD24 low (extraembryonic endoderm) cells were isolated by flow cytometric sorting and the lineages (barcodes) in each population assessed by sequencing. (C) For each lineage, the ratio of its occurrence in CD24 high to CD24 low cells is plotted (CDF). Lineages are separated into deciles of motility across days 0–12. F-test for variance p < 0.01 for all deciles compared against all lineages except for the fifth decile, which was not significant. (D) As in part C, except the top 4 deciles of motility and bottom 4 deciles of motility are grouped to enable visualization. A histogram (left) and CDF plot (right) are shown. F-test for variance p < 0.001 for both groups compared to all lineages.

Article Snippet: Two mouse embryonic stem cell (ESC) lines were used in this study: V6.5 (gift from the Jaenisch Laboratory, Whitehead Institute, MIT) and V6.5 derived Nanog-GFP/Sox2-mCerulean generated as described below using stably-integrated DNA barcodes ( , Addgene #67267).

Techniques: Microscopy, Cell Culture, Sampling, Isolation, Sequencing