Table 1 Analysis of other datasets 9-12... | American Society of Hematology

Table 1

Analysis of other datasets^9-12 deposited with NCBIGEO

Study	NCBIGEO accession no.	CEL files deposited?	No. of stages	No. of replicates	Pooled or single samples hybridized?	EB source and culture conditions	FACS-sorted	% genes DE	% genes SIG DE
Keller et al⁹ (2006)	GSE4655	No	6	3	Some pooled samples	CD34⁺ progenitors in a novel serum-free system	No	12	3.8
Singleton et al¹¹ (2008)	GSE10584	Yes	3	4	Single samples	CD34⁺ progenitors	No	8	0.1
Peller et al¹⁰ (2009)	GSE12407	Yes	3	2	Single samples	Fibachs	No	0	0.0
Sripichai et al¹² (2009)	GSE7874	Yes	2	5	Single samples	CD34⁺ progenitors cultured for 7 and 14 days + EPO/−SCF	No	47	0.3
Current study	GSE22552	Yes	4	3	Pooled samples	Fibachs	Yes	43	3.8

Study	NCBIGEO accession no.	CEL files deposited?	No. of stages	No. of replicates	Pooled or single samples hybridized?	EB source and culture conditions	FACS-sorted	% genes DE	% genes SIG DE
Keller et al⁹ (2006)	GSE4655	No	6	3	Some pooled samples	CD34⁺ progenitors in a novel serum-free system	No	12	3.8
Singleton et al¹¹ (2008)	GSE10584	Yes	3	4	Single samples	CD34⁺ progenitors	No	8	0.1
Peller et al¹⁰ (2009)	GSE12407	Yes	3	2	Single samples	Fibachs	No	0	0.0
Sripichai et al¹² (2009)	GSE7874	Yes	2	5	Single samples	CD34⁺ progenitors cultured for 7 and 14 days + EPO/−SCF	No	47	0.3
Current study	GSE22552	Yes	4	3	Pooled samples	Fibachs	Yes	43	3.8

The number of replicates and stages of erythroblasts in each study is indicated. RMA (where the CEL files are available) and LIMMA were used to determine the proportion of genes that were: differentially expressed (DE) at the lowest stringency equal to DE1 (B value of at least 2.945, representing a 95% probability that the gene was differentially expressed, and expression levels in all replicates at any stage > 100); significantly differentially expressed (SIG DE) at the highest stringency equal to DE_Sig (minimum average expression threshold of 1000, minimum fold change threshold of 10-fold, only PIDs with a difference of at least 1000 between minimum and maximum average expression were selected).

NCBIGEO indicates National Center for Biotechnology Information Gene Expression Omnibus; and FACS, fluorescence-activated cell sorter.

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