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Table 1 Main features of the samples used in TRAM analyses

From: Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS)

Study ID Sample ID Sample type Platform Microarray Spots References
Pool 'A' (n=43) - DS AMKL (25,955 mapped loci following analysis by TRAM)
A1…A3 (n=3) GSM491372…4 BM Sorted leukemic blasts GPL570 Affymetrix U133 Plus 2.0 54,675 [18]
A4…A25 (n=22) GSM94245, GSM94272…92 BM or PB GPL96 Affymetrix U133A 22,283 [22]
A26…A31 (n=6) GSM417985…90 BM or PB Sorted leukemic blasts GPL570 Affymetrix U133 Plus 2.0 54,675 [17]
A32…A38 (n=7) E-MEXP-72* BMMC or PBMC A-AFFY-33.adf.txt* Affymetrix U133A 22,283 [21]
A39…A43 (n=5) / BMMC or PBMC GPL96 Affymetrix U133A 22,283 [23]
Pool 'B' (n=45) - non-DS AMKL (26,045 mapped loci following analysis by TRAM)
B1-B2 (n=2) GSM491370-1 BM Sorted leukemic blasts GPL570 Affymetrix U133 Plus 2.0 54,675 [18]
B3…B23 (n=21) GSM94221-4-5, GSM94227…32, GSM94234-5-7-8, GSM94240-2-3-8, GSM94256-9, GSM94261-2 BM or PB GPL96 Affymetrix U133A 22,283 [22]
B24…B28 (n=5) GSM39832-5, GSM39842-4, GSM39863 PBMC or BMMC GPL8300 Affymetrix U95 Version 2 12,625 [19]
B29…B35 (n=7) GSM361502…4, GSM361506…8, GSM361510 BM or PB GPL96 Affymetrix U133A 22,283 [24]
B36…B40 (n=5) GSM417991…5 BM or PB Sorted leukemic blasts GPL570 Affymetrix U133 Plus 2.0 54,675 [18]
B41…B45 (n=5) / BMMC or PBMC GPL96 Affymetrix U133A 22,283 [23]
Pool 'C' (n=20) - TMD (25,955 mapped loci following analysis by TRAM)
C1…C3 (n=3) GSM491375…7 BM Sorted leukemic blasts GPL570 Affymetrix U133 Plus 2.0 54,675 [18]
C4…C11 (n=8) GSM94293…9, GSM94300 BM or PB GPL96 Affymetrix U133A 22,283 [22]
C12…C20 (n=9) E-MEXP-72* BMMC or PBMC A-AFFY-33.adf.txt* Affymetrix U133A 22,283 [21]
Pool 'D' (n=19) - MK (26,372 mapped loci following analysis by TRAM)
D1-D2 (n=2) GSM321577-8 MK (BM) (subj = pool) GPL96 Affymetrix U133A 22,283 [45]
D3…D6 (n=4) GSM112277-8, GSM112291-2 MK (PB) (subj = 1, rep. 1) GPL887 Agilent 1A 22,575 [44]
D7-D8 (n=2) GSM15648, GSM8649 MK (BM) (subj = 6) GPL96 Affymetrix U133A 22,283 [42]
D9…D11 (n=3) GSM88014-22-34 MK (PB) (subj = 1) GPL887 Agilent 1A 22,575 [43]
D12…D18 (n=7) GSM609746…52 CB GPL4685 Affymetrix HT-HG_U133A 22,944 [40]
D19 (n=1) E-MEXP-2146* CB A-AFFY-44.adf.txt Affymetrix U133 Plus 2.0 54,675 [41]
Pool 'E' = D12…D19 (n=8) - CB MK (25,577 mapped loci following analysis by TRAM)
  1. Samples selected for the meta-analysis of gene expression profiles in DS AMKL (pool 'A'), non-DS AMKL (pool 'B'), TMD (pool 'C'), and megakaryocytic cells (pool 'D' and 'E'). All Sample IDs and Platforms IDs are related to GEO database, other than codes marked with * (ArrayExpress database). Sample type: BM, bone marrow; PB, peripheral blood; BMMC, bone marrow mononuclear cells; PBMC, peripheral blood mononuclear cells; 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. subj = number of subjects from which the sample was derived (in some cases, where subj = 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; 22k A: Agilent Human oligo 22k A; HG-Focus: Affymetrix Human HG-Focus Target Array.
  2. Details about Sample identifiers and main sample features are listed in Additional file 1 (available at: http://apollo11.isto.unibo.it/suppl).
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