The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages

Table 3 Expression changes associated with in vivo versus in vitro culture of T. brucei.

MiTat vs SMB	Gene	Accession	Fold difference
up in SMB	DHH1	Tb10.70.3290	6.2
	procyclin	Tb927.6.450	5.0
	PRA1	Tb10.389.1550	4.1
	procyclin	Tb10.6k15.0030	3.8
	CSNK1D (casein kinase)	Tb927.5.800	3.6
	CAP5.5	Tb927.4.3950	3.5
	Rab1a	Tb927.8.890	3.5
	SNF1-like kinase	Tb10.70.1760	3.5
	cofilin (ADF)	Tb927.3.5180	3.1
	NEK2/6/7 kinase	Tb927.3.3190	3.0
	PI3K (FYVE)	Tb11.01.6980	2.8
	Trs20/sedlin	Tb927.8.5900	2.7
	Ser peptidase (Bem46-like)	Tb09.211.2310	2.7
	Ubiquitin conjugating	Tb11.02.0815	2.6
	AP4 sigma	Tb10.61.2530	2.6
	ARPC5	Tb10.406.0320	2.6
	FYVE Zn finger containing protein	Tb927.4.3380	2.5
	ARPC4	Tb927.2.2900	2.5
	GSK3B kinase	Tb927.7.2420	2.5
	IFT88	Tb11.55.0006	2.3
	RabGAP	Tb10.6k15.1770	2.3
	nuclear transport factor 2	Tb10.70.5500	2.3
	ISG65-like	Tb927.5.410	2.3
	two UIM domains	Tb10.70.1130	2.2
	t-SNARE	Tb11.03.0965	2.2
	Rab7	Tb09.211.2330	2.2
	CBL-interacting protein kinase 9	Tb927.8.870	2.2
	VHS domain containing protein	Tb11.01.2540	2.2
	GTP1/OBG/Hsr1	Tb927.2.4240	2.1
	Hsr1/GTP-binding	Tb927.7.2630	2.1
	MAPK8 kinase	Tb10.70.2070	2.1
	PABP2	Tb09.211.2150	2.1
	calreticulin (lectin)	Tb927.4.5010	2.0
	RanGEF	Tb927.8.7290	2.0
	ARL3A	Tb927.3.3450	2.0
up in MiTat1.1	p67	Tb927.5.1810	2.0
	polyUb	Tb11.01.1680	2.0
	RanGEF	Tb10.6k15.3150	2.9
SMB 4°C vs SMB	Gene	Accession	Fold difference
up in 4°C	CAP5.5	Tb927.4.3950	2.3
	Sec34-like	Tb927.7.2640	2.0

Significantly differentially expressed transcripts for in vivo MITat1.1 bloodstream culture vs in vitro SMB culture, and for SMB treated at 4°C for one hour. Ratios are given on a linear scale. Only ORFs which show at least a two-fold change are shown. Ratios which correspond to a value >1 for the B-statistic in limma analysis are shown in bold.

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