Nature

SUPPLEMENTARY INFORMATION

A B

doi:10.1038/nature11965

E

C

D

G F

Supplementary Figure 1 - H2B-YFP LRC model and CD24/UEA specificity (A) Images of intestinal epithelium from Cyp1a1-H2B-YFP mice following induction with βNF. (A) 1 week. (B) 3 weeks. (C) 4 weeks. (D) 12 weeks. (E) 1 week after βNF induction a number of YFP+ cells are Paneth cells as identifed by UEA staining (red). (F) Co-expression of Paneth cell markers UEA (red) and lysozyme (green). (G) Section of intestine stained to visualise CD24 (white) and showing crypt specific and apical surface expression. Scale bars: 50µm (C,D), 10µm (A,B,E-G).

W W W. N A T U R E . C O M / N A T U R E | 1

RESEARCH SUPPLEMENTARY INFORMATION

A

CD24 Crypt base label retaining (YFP-LRC) Crypt base non label retaining (LCC) YFP UEA-I Bright field Merge

Ba

UEA-AF647

Bb

2 weeks post βNF induction

Count

YFP-LRC 5%

UEACD24+ gating

Bc

3 weeks post βNF induction

CD24-Pac Blue

Bd

YFP

Count YFP

Count

YFP

Paneth cell (PC)

YFP-LRC 0.5%

4 weeks post βNF induction

YFP-LRC 0%

CD24-Pac Blue

YFP

YFP

C

Gip Chgb Chga Rfx6 Pax6 Vim Notch1 Abca1

Paneth Cell Label Retaining Cell CD24+ Lower Crypt Cells

Chga Abca1 Lgr5

Abcc1 Mctp2 Peg3

Lrig1 Notch1 Dclk1

Peg3 Mmp7 YFP-LRC Paneth YFP-LRC LCC

Supplementary Figure 2 - YFP-LRC, LCC and Paneth cell FACS isolation and microarray data (A) Imagestream data demonstrating the LRCs defined by CD24+/UEA-/YFP+ expression can be purified by FACS and are distinct from non LRC lower crypt base cells (LCC) (CD24+/UEA-/YFP-) and Paneth cells (PC) (CD24+/UEA+/YFP- or CD24+/UEA+/YFP+), latter is illustrated. (B) FACS gating protocol for the isolation of CD24+/UEA-/YFP+ label retaining cells. (Ba) Gating strategy for CD24+/UEA- population isolation. (Bb-Bd) UEA/CD24+/YFP-LRCs at 2,3 and 4 weeks post induction. (C) Heatmaps (z-score transformed) of three-way microarray expression comparison from FACS purified...