Hannah Chang's scientific contributions
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Publications (19)
Single-cell gene expression analysis: PCA from Fig 1 recolored for origin in the Sca1 population fraction.
Colors of cells again (as in Fig 1) indicate treatment, but in addition, their provenience from the respective Sca-1 fraction in the progenitor population (d0). Rebellious cells are cells that shift toward the non-intended fate, i.e. EPO-treat...
Quality control of single-cell qCPR.
(A) Inter-chip variability is evaluated using inter-run calibrator (IRC) sample. Each curve represents the distribution of Cq values of each gene across all OpenArray chips. The flat black curve represents the distribution of all genes across all chips. The inter-gene differences are up to 2 orders of magnitude...
Evaluation of qPCR assays.
Table lists all primer pairs and relevant information including IDs and amplicon length. All assays were inventoried. Identical PCR primers were used in the pre-amplification step and the subsequent singleplex qPCR step. In addition, the amplification efficiency and limit of detection (LOD) of the qPCR assays are given. T...
Representation of an OpenArray plate used for single-cell qPCR.
(A) Each OpenArray (Applied Biosystems) is the size of a microscope slide. It holds 48 groups (subarrays, red rectangular) of 64 holes of 33 nl volume in which one PCR reaction occurs. A hydrophilic layer is at the interior surface of each hole and a hydrophobic layer is at the exterio...
Single-cell and 100-cell samples quantification cycles (raw) data.
The quantification cycles (Cq's) for all analyzed single-cells as well as 100-cell-pool control samples are reported. Single cells from untreated EML control cells as well as EML cells treated with EPO, GM-CSF/IL-3 or a combination of all cytokines on d1, d3 and d6 of stimulation. G...
Flow cytometry data for Fig 4 of main text.
FCS-format data files for individual histograms of the two time courses (untreated and IL-3/GM-GM-CSF treated) as shown in Fig 4. Each folder represents a time point for the untreated and the IL-3/GM-CSF treated cells and contains two files for the sample histograms for Sca1 and the PI stained cells, resp...
A certain type of multipotent progenitor cell of the blood can commit to either the white
(myeloid) or the red (erythroid) blood cell lineage, thus making a discrete binary cell fate
decision. To test a theory on fundamental principles of cell fate dynamics (as opposed to
the usually studied molecular mechanisms), we monitored such a fate decision...
The numerical data that underlie the graphs in the figures in the main text.
The relevant data used in the figures are in separate spreadsheets within this file, with the sheet names (tabs) indicating the associated figure.
(XLSX)
Manually curated model of gene regulatory network governing fate decision of CMP.
Network of experimentally verified regulatory interactions of transcription factors involved in multipotency of the CMP state, fate decision and differentiation to the erythroid and myeloid lineages (S1 Table). The canonical GATA1-PU.1 circuit is highlighted in green....
Technical noise associated with single-cell RT-qPCR is significantly smaller than biological cell-cell variability.
(A) Quantification cycles (Cq) of 80 individual EML cells for GATA1 expression is reported. Values are means ± STD for up to 128 technical replicates. (B) Quantification cycles (Cq) of up to 110 technical replicates are presented for...
Gene expression profile of single-cell samples during differentiation.
Expression profiles of 17 transcription factors and control genes (rows) in individual cells (columns) are visualized as a heatmap. Cell columns are arranged for days d1, d3 and d6 with respect to different treatments where grey shades correspond to untreated progenitors (d0), r...
Distinct trajectories of cell differentiation are observed upon stimulation of progenitor cells with cytokines in the PCA state space.
Principal component projections in a total of ~1600 haematopoietic cells including progenitor (black), single-EPO treated (red-shades), single-IL3/GM-CSF treated (blue-shades) and combined-treated (purple-shades) in...
Gene expression in individual cells from the progenitor population and the α, β, and γ subpopulations.
(A-D) Heatmap representation of gene expression profiles for the set of 17 genes of the curated network and 2 endogenous genes as control in total 216 single cells including 72 progenitor cells (panel A) and 48 single cells from each of the three...
Derivation of index IC and pedagogical explanations.
(PDF)
Regulatory interactions in the curated GRN model of binary fate decision in CMP.
Table of the regulatory interactions (either activating (A) or inhibiting (I)) between the genes. For each interaction, the literature is referenced (numbered list in the right panel). All interactions have been reported in for murine hematopoiesis.
(JPG)
Additional support from analysis of public data.
(PDF)
Quantified dissimilarity between transcriptomes from micro-arrays between samples.
Pair-wise dissimilarity between expression profiles (samples) was calculated based on the normalized gene expression levels for 6297 filtered genes (see Material and Methods) with 1–R where R is the Pearson’s correlation coefficient which ranges from 0 to 1, meaning...
Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile. However, how progenitor cells overcome the stability of their robust gene expression configuration (attractor) and exit their state remains elusive. Here we show that commitment of blood progenitor cel...
Citations
... To do this we rely on the fact that in the deterministic (zero noise or large N ) limit, transitions into stable attractor states occur via a bifurcation in the underlying dynamical system [23]. A simple way to determine if a bifurcation is close to occurring from snapshots of single-cell transcriptomes was laid out in [27,28] and along similar lines of reasoning in [29,30], taking advantage of increasing dispersion of cells when they leave destabilized potential minima, while aligning the gene expression values in x. Given a data matrix X where X ij is value of the j th gene in the i th cell the critical transition parameter is ...
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... S10) (53,54), as velocity vectors pointed toward 4-day treated cells. In parallel, we calculated the critical transition index (I c ), a quantitative metric of the high-dimensional state of a system that predicts whether a cell population is undergoing a state transition (higher I c values) or if it has reached some stable attractor state (lower I c values) (55). I c values of SN520 decreased during drug treatment but remained relatively constant in the vehicle control ( Fig. 5B), indicating that pitavastatin had driven the entire PD-GSC population into a predominantly drug-resistant MES subtype attractor state. ...
