TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources

BMC Genomics

Table 1 Samples selected for the biological model used to test TRAM software

TRAM ID	GEO ID	Sample	GEO Platform	Microarray	Spots	Ref.
Pool 'A'
A1	GSM321577	Mk (BM) (n = pool)	GPL96	Affymetrix U133A	22,283	[19]
A2	GSM321578	Mk (BM) (n = pool)	"	"	"	"
A3	GSM112277	Mk (PB) (n = 1, rep. 1)	GPL887	Agilent 1A	22,575	[20]
A4	GSM112278	Mk (PB) (n = 1, rep. 2)	"	"	"	"
A5	GSM15648	Mk (BM) (n = 6)	GPL96	Affymetrix U133A	22,283	[21]
A6	GSM8649	Mk (BM) (n = 6)	"	"	"	"
A7	GSM88022	Mk (PB) (n = 1)	GPL887	Agilent 1A	22,575	[22]
A8	GSM88014	Mk (PB) (n = 1)	"	"	"	"
A9	GSM88034	Mk (PB) (n = 1)	"	"	"	"
Pool 'B'
B1	GSM321567	CD34+ (BM) (n = pool)	GPL96	Affymetrix U133A	22,283	[19]
B2	GSM321568	CD34+ (BM) (n = pool)	"	"	"	"
B3	GSM321569	CD34+ (CB) (n = pool)	"	"	"	"
B4	GSM321570	CD34+ (CB) (n = pool)	"	"	"	"
B5	GSM321571	CD34+ (PB) (n = pool)	"	"	"	"
B6	GSM321572	CD34+ (PB) (n = pool)	"	"	"	"
B7	GSM76923	CD34+ (BM) (n = 5)	GPL96	Affymetrix U133A	22,283	[23]
B8	GSM76924	CD34+ (BM) (n = 5)	"	"	"	"
B9	GSM76925	CD34+ (BM) (n = 5)	"	"	"	"
B10	GSM307288	CD34+ (BM) (n = 6, rep. 1)	GPL7091	Agilent 22 k A	16,391	-
B11	GSM307289	CD34+ (BM) (n = 6, rep. 2)	"	"	"	-
B12	GSM88023	CD34+ (PB) (n = 1)	GPL887	Agilent 1A	22,575	[22]
B13	GSM88003	CD34+ (PB) (n = 1)	"	"	"	"
B14	GSM23407	CD34+ (BM) (n = 1)	GPL201	Affymetrix HG-Focus	8,793	[24]
B15	GSM23410	CD34+ (BM) (n = 1)	"	"	"	"
B16	GSM23411	CD34+ (BM) (n = 1)	"	"	"	"
B17	GSM23408	CD34+ (BM) (n = 1)	"	"	"	"
B18	GSM23409	CD34+ (BM) (n = 1)	"	"	"	"
B19	GSM23406	CD34+ (BM) (n = 1)	"	"	"	"

Sample: Mk, megakaryocytic/megakaryoblast cells, obtained by in vitro differentiation of CD34+ cells; CD34+, undifferentiated CD34+ cells; (BM), (CB) or (PB): CD34+ cells derived from bone marrow, cord blood or peripheral blood, respectively. n = number of subjects from which the sample was derived (in some cases, where n = pool, the exact number of subjects included in a pool was not available). rep. = biological replicate. Microarray: U133A: Affymetrix Human Genome U133A Array; 1A: Agilent-012097 Human 1A Microarray (V2) G4110B; 22 k A: Agilent Human oligo 22 k A; HG-Focus: Affymetrix Human HG-Focus Target Array. When not directly provided, expression value was calculated as the median intensity value of a microarray feature minus the median background value.

ISSN: 1471-2164