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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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BMC Medical Genomics

ISSN: 1755-8794

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