title: shdj097 | other

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33509.gif

source_name: AML 41

value: AML 41

value: 546 days


title: shfa067 | t(8;21)

status: Public on Jul 11 2010

type: RNA

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62315.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene common reference

extract_protocol: not provided

tag: reference

value: Stratagene common reference

source_name: 03PB813; Sample source=PB; CBF group=t(8;21)

label_protocol: RNA from AML specimens was labeled with Cy5-dUTP using an anchored poly(dT) primer during first strand reverse transcription (Superscript II).  A universal reference RNA (pooled from 11 cell lines) was labeled identically but with Cy3-dUTP

extract_protocol: Normal karyotype acute myeloid leukemia (NK-AML) specimens comprise Ficoll gradient purified mononuclear cells (>80% blasts) from diagnostic peripheral blood or bone marrow.  Total RNA was isolated from stored, frozen mononuclear AML-cell pellets using Trizol reagent, and RNA quality assessed by gel electrophoresis.; Protocol Type = Extract preparation

tag: source

tag: age

tag: overall survival time

value: 873 days

tag: overall survival status

value: dead

tag: genotype

tag: gender

value: female

tag: runx1 mutation


title: shee126 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-07/42877.gif

label_protocol: A universal reference RNA (pooled from 11 cell lines) was labeled identically but with Cy3-dUTP

value: 776 days

value: normal karyotype


title: shdj114 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44176.gif

value: 24 days

value: male


title: shfs112 | other

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60270.gif

value: 511 days

value: other


title: shdj110 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35289.gif

source_name: AML 51

value: AML 51

value: 285 days

value: complex karyotype


title: shdj109 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33651.gif

source_name: AML 8

value: AML 8

value: 237 days


title: shdj072 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33014.gif

source_name: AML 15

value: AML 15

value: 489 days


title: shdj084 | t(9;11)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33167.gif

value: Stratagene common reference

source_name: AML 20

value: AML 20

value: 2653 days

value: alive


title: shgn113 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66435.gif

value: 22 days

value: dead

value: female


title: shdj089 | t(8;21)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33367.gif

source_name: AML 23; Sample source=BM; CBF group=t(8;21)

value: 29 days

value: male


title: shcz209 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32074.gif

source_name: AML 92

value: AML 92

value: 47 days


title: shee228 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44124.gif

value: 48 days

value: normal karyotype


title: shdj107 | inv(16)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33648.gif

source_name: AML 73; Sample source=PB; CBF group=inv(16)

value: 181 days


title: shdj081 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33162.gif

source_name: AML 42

value: AML 42

value: 31 days


title: shcz112 | t(15;17)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32665.gif

source_name: AML 60

value: AML 60

value: 305 days


title: shcz080 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32451.gif

value: Stratagene common reference

source_name: AML 74

value: AML 74

value: 521 days


title: shfs123 | inv(16)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61361.gif

value: 1091 days


title: shgn98 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66261.gif

value: 68 days

value: dead

value: complex karyotype


title: shfs088 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59326.gif

value: 35 days

value: male


title: shfa145 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53883.gif

value: 66 days

value: female


title: shfs180 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63034.gif

value: 301 days

value: normal karyotype


title: shfa126 | inv(16)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62352.gif

source_name: 01KM129; Sample source=BM; CBF group=inv(16)

value: 123 days


title: shdj073 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33015.gif

source_name: AML 61

value: AML 61

value: 184 days


title: shfs111 | inv(16)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60269.gif

source_name: 98PB1096; Sample source=PB; CBF group=inv(16)

value: 175 days


title: shdj100 | other

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33565.gif

value: Stratagene common reference

source_name: AML 71

value: AML 71

value: 633 days

value: other


title: shfs122 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61360.gif

value: 63 days


title: shfs077 | other

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59280.gif

value: 70 days

value: dead


title: shfs080 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59323.gif

value: 553 days

value: complex karyotype


title: shcz081 | t(15;17)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32452.gif

source_name: AML 2

value: AML 2

value: 1740 days

value: alive

value: male


title: shcz076 | other

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32229.gif

source_name: Stratagene common reference

source_name: AML 6

value: AML 6

value: 343 days


title: shcz077 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32233.gif

source_name: AML 108

value: AML 108

value: 684 days

value: normal karyotype

value: female


title: shfs089 | inv(16)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59327.gif

value: Stratagene common reference

source_name: 00PB1811; Sample source=PB; CBF group=inv(16)

value: 1762 days


title: shfs114 | other

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61313.gif

value: 576 days

value: other


title: shcz105 | del(7q)/-7

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35293.gif

source_name: AML 80

value: AML 80

value: 340 days

value: dead


title: shfs048 | inv(16)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62438.gif

source_name: 01PB2546; Sample source=PB; CBF group=inv(16)

value: 870 days


title: shcz228 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32662.gif

source_name: AML 112

value: AML 112

value: 536 days


title: shcz223 | t(15;17)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32555.gif

source_name: AML 99

value: AML 99

value: 2335 days

value: alive


title: shdj113 | del(7q)/-7

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35292.gif

source_name: AML 106

value: AML 106

value: 144 days

value: male


title: shcz227 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32661.gif

source_name: AML 57

value: AML 57

value: 32 days

value: normal karyotype


title: shcz063 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32138.gif

value: Stratagene common reference

source_name: AML 85

value: AML 85

value: 1239 days


title: shcz066 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32214.gif

source_name: AML 78

value: AML 78

value: 25 days

value: complex karyotype


title: shcz088 | t(15;17)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32813.gif

source_name: AML 95

value: AML 95

value: 883 days

value: female


title: shcz110 | inv(16)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32663.gif

source_name: AML 25; Sample source=BM; CBF group=inv(16)

value: 2005 days

value: dead


title: shcz226 | t(9;11)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32660.gif

source_name: AML 88

value: AML 88

value: 339 days


title: shcz075 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32225.gif

source_name: AML 28

value: AML 28

value: 80 days


title: shcz062 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32137.gif

source_name: AML 13

value: AML 13

value: 85 days


title: shcz208 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32073.gif

source_name: Stratagene common reference

value: Stratagene common reference

source_name: AML 36

value: AML 36

value: 380 days

value: normal karyotype

value: male


title: FPET-ABC-E3

status: Public on May 18 2010

city: Pleasanton

first: Rachel

last: Li

state: CA

address: 4300 Hacienda Dr.

country: USA

institute: Roche

description:
Sample_E3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

hyb_protocol: 10ug of Eberwine labeled cRNA or 5ug of WT-Ovation amplified cDNA was applied to U133plus 2 GeneChips (Affymetrix) and hybridized overnight per manufacturer’s recommendations.

scan_protocol: GeneChips were washed, stained and scanned using the Fluidic Station 450 and GeneChip Scanner 3000 (Affymetrix) using manufacturer’s recommendations.

data_processing: Microarray signal was generated using Affymetrix MAS 5.

label: Eberwine biotin method

source_name: formalin-fixed paraffin embedded tissue

label_protocol:
5ug of FF RNA was transcribed into double stranded cDNA (GeneChip One-cycle cDNA Synthesis Kit; Affymetrix) and linearly amplified by the traditional method described by Eberwine (ref) using the GeneChip IVT Labeling Kit (Affymetrix).
10ng of FF or 50ng FFPET RNA was transcribed into double stranded cDNA and linearly amplified using WT-Ovation™ FFPE System (Nugen).
The cDNA was fragmented and biotin labeled using FL-Ovation™ cDNA Biotin Module V2 (Nugen).

growth_protocol:
Tumor containing lymph nodes were excised and shipped on saline soaked gauze directly to the British Columbia Cancer Center for preparation.
Samples were either frozen immediately upon arrival or formalin fixed and embedded in paraffin for archival storage.

extract_protocol:
RNA from freshly frozen biopsied samples was prepared using  Trisol, following manufacturer’s recommendations.
RNA was prepared from the FFPET samples using the RNeasy FFPE kit (Qiagaen #74404) following manufacturers recommendations.

tag: subgroup

value: activated B-cell

tag: tissue

value: B-cell lymphoma

tag: treatment

value: FFPET


title: H1_ES_1

status: Public on Jun 10 2010

city: Boston

first: Hu

state: MA

address: 3 Blackfan Circle

institute: Wyss Institute

description: Gene expression data obtained from human ES

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA (Bioconductor Affy and RMA Packages).

label: biotin

source_name: human ES

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: standard HESC growth conditions as described in Pick et al. (2009).

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

tag: cell type

value: ES

tag: cell line

value: H1 Human embryonic stem cells


title: H1_ES_2


title: Tlr2-/- to WT_Tlr4/90n [MSAM]

status: Public on Jul 01 2010

type: genomic

city: Houston

first: Richard

last: Kellermayer

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out  according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Mus musculus

source_name: P90 WT

label_protocol: 4ug of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006)

extract_protocol:
tissue isolation protocol: Colonic mucosa was sheared by microscope slide and flash frozen on dry ice.
Total DNA was extracted by standard phenol-chloroform isolation.

tag: genotype/variation

value: wild type

value: 90 postnatal days

value: colonic mucosa

tag: strain

value: Tlr2 knockout


title: Tlr2-/- to WT_Tlr1/90f [MSAM]


title: shcz074 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32221.gif

source_name: AML 43

value: AML 43

value: 2709 days

value: alive

value: female


title: shcz065 | complex karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32141.gif

value: Stratagene common reference

source_name: AML 58

value: AML 58

value: 12 days

value: dead

value: complex karyotype


title: shfs131 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61385.gif

value: 405 days

value: normal karyotype

value: male


title: shcz091 | t(8;21)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32904.gif

source_name: 01KM1838; Sample source=BM; CBF group=t(8;21)

value: 345 days


title: shcz064 | t(8;21)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32140.gif

source_name: AML 62; Sample source=BM; CBF group=t(8;21)

value: 140 days


title: shfs087 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59325.gif

value: 483 days


title: FPET-GCB-D5

description:
Sample_D5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: germinal center B-cell

value: B-cell lymphoma

value: FFPET


title: FPET-GCB-F5

description:
Sample_F5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-D6

description:
Sample_D6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: Abeta treated vs. Control

status: Public on May 30 2010

city: Camperdown

first: Nicole

last: Schonrock

state: New South Wales

address: 100 mallett street

department: Medicine

country: Australia

institute: Brain and Mind Research Institute, University of Sydney

description: RQ value for three Abeta treated samples normalized to three Control treated samples.

hyb_protocol: Not applicable

scan_protocol: TaqMan arrays were run on a 7900HT Thermocycler (Applied Biosystems) using Sequence Detection Systems (SDS) software version 2.3. A single TLDA was used per Abeta or control-treated sample.

data_processing: Manual inspection of all amplification plots was performed and microRNAs were excluded from the analysis if: Ct values were too high (above 35, indicating a miRNA expression too low for accurate detection), if amplification was not achieved in all 6 samples, or if extremely high variation was found. Data analysis was performed using SDS RQ manager v1.2 (Applied Biosystems) using the delta-delta Ct method (Schmittgen TD, 2008, Nat Protocols). The endogenous control, snoRNA234, was used for normalization.

label: multiplexed

source_name: Mouse primary hippocampal neurons, PBS control

label_protocol: Megaplex profiling using rodent TaqMan Low density microRNA microarrays (TLDA) (Applied Biosystems) was used to assay the expression of 380 miRNAs by real time PCR as described by the manufacturer. Briefly, 100ng of total RNA obtained from either Abeta or control-treated primary hippocampal cells was used in the megaplex reverse transcription (RT) reaction containing about 450 miRNA-specific RT primers provided by the manufacturer. No prior miRNA preamplification step was needed. The RT product was mixed with 2x TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems) and loaded onto the TLDA containing the 48-plex PCR reaction mix.

growth_protocol: Primary hippocampal neurons were prepared from 16.5-day-old embryonic C57BL/6 mice (E16.5) as described (Fath T et al, 2009, Nat Protocols). 600 000 cells were plated per dish and cultivated in Neurobasal medium supplemented with 1% (v/v) B27 supplements (Gibco) and 0.25% (v/v) 200 mM L-glutamine (Gibco) to minimize growth of astrocytes and microglia. Neurons were grown for 23 DIV before receiving a 24 hour treatment of either Abeta or PBS.

extract_protocol: total RNA was isolated using the Qiagen miRNeasy Kit (Cat # 217004)

treatment_protocol: Six dishes, each containing 600 000 mouse primary hippocampal neurons were grown for 23 DIV. 3 dished were treated with 5uM amyloid beta (1-42) and 3 dishes were used as an untreated PBS control. Synthetic Abeta peptides (Bachem, Germany) dissolved in PBS were aged by incubation at 37 degrees for 24 hours with shaking at 1000rpm to allow fibril formation. Treatments were carried out for 24 hours before cells were harvested by suspension in Qiazol reagent (Qiagen)

value: primary hippocampal neurons

tag: developmental stage

value: PBS control

source_name: Mouse primary hippocampal neurons, Abeta treated

value: 5uM aged amyloid beta


title: FPET-ABC-G5

description:
Sample_G5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: activated B-cell


title: FPET-GCB-G4

description:
Sample_G4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-Unclassified-H5

description:
Sample_H5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: Unclassified


title: FPET-GCB-F1

description:
Sample_F1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-F4

description:
Sample_F4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-G2

description:
Sample_G2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-B9

description:
Sample_B9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-E8

description:
Sample_E8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-B1

description:
Sample_B1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-B8

description:
Sample_B8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-F6

description:
Sample_F6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: shcz079 | normal karyotype

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32450.gif

value: Stratagene common reference

source_name: AML 76

value: AML 76

value: 256 days

value: female


title: FPET-Unclassified-G8

description:
Sample_G8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-C7

description:
Sample_C7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-G1

description:
Sample_G1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-Unclassified-H3

description:
Sample_H3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-F9

description:
Sample_F9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-D7

description:
Sample_D7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-Unclassified-G7

description:
Sample_G7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-F3

description:
Sample_F3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-B3

description:
Sample_B3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-G3

description:
Sample_G3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-C6

description:
Sample_C6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-C1

description:
Sample_C1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-E1

description:
Sample_E1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-D4

description:
Sample_D4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-E6

description:
Sample_E6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-A1

description:
Sample_A1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-Unclassified-G9

description:
Sample_G9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-Unclassified-H7

description:
Sample_H7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: shcz106 | del(7q)/-7

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35294.gif

source_name: AML 66

value: AML 66

value: 475 days

value: dead


title: FPET-ABC-D1

description:
Sample_D1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-E5

description:
Sample_E5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-C5

description:
Sample_C5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-F2

description:
Sample_F2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-D9

description:
Sample_D9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-E4

description:
Sample_E4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-E9

description:
Sample_E9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-A6

description:
Sample_A6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-C9

description:
Sample_C9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-Unclassified-H2

description:
Sample_H2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-D2

description:
Sample_D2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-B2

description:
Sample_B2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-A3

description:
Sample_A3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-Unclassified-H6

description:
Sample_H6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: H9_ES_2

description: Gene expression data obtained from human ES

value: ES

value: H9 Human embryonic stem cells


title: FPET-ABC-D3

description:
Sample_D3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-A2

description:
Sample_A2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-GCB-E7

description:
Sample_E7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: germinal center B-cell


title: FPET-GCB-B7

description:
Sample_B7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: B-cell lymphoma


title: FPET-Unclassified-H4

description:
Sample_H4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: FFPET


title: FFN-GCB-D2

source_name: fresh/frozen lymphoma tissue

value: fresh/frozen


title: FPET-Unclassified-H1

description:
Sample_H1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-C3

description:
Sample_C3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-B2


title: FPET-Unclassified-G6

description:
Sample_G6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-E2

description:
Sample_E2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FPET-ABC-A5

description:
Sample_A5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-H1


title: FPET-ABC-E2


title: FFN-GCB-D9

description:
Sample_D9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-A3


title: FFN-GCB-E9

description:
Sample_E9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-H4


title: FPET-ABC-A8

description:
Sample_A8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-C3


title: FPET-GCB-A4

description:
Sample_A4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-E7


title: FFN-ABC-A2


title: FFN-ABC-D3


title: FFN-ABC-A8


title: FFN-GCB-A4


title: FFN-GCB-A6

description:
Sample_A6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-A5


title: FFN-GCB-D6

description:
Sample_D6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-G6


title: FFN-GCB-C5

description:
Sample_C5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-G1

description:
Sample_G1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-B1

description:
Sample_B1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-G4

description:
Sample_G4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-D7

description:
Sample_D7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-H6

description:
Sample_H6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-B7

description:
Sample_B7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-E8

description:
Sample_E8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-F9

description:
Sample_F9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-G5

description:
Sample_G5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-F4

description:
Sample_F4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-A1

description:
Sample_A1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-F2

description:
Sample_F2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-B3

description:
Sample_B3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-H2

description:
Sample_H2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-E6

description:
Sample_E6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-E4

description:
Sample_E4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-H7

description:
Sample_H7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-B9

description:
Sample_B9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-E5

description:
Sample_E5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-E3

description:
Sample_E3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-F6

description:
Sample_F6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-C1

description:
Sample_C1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-B8

description:
Sample_B8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-G9

description:
Sample_G9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-C9

description:
Sample_C9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-C7

description:
Sample_C7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-F3

description:
Sample_F3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-F1

description:
Sample_F1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-G7

description:
Sample_G7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-G2

description:
Sample_G2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-E1

description:
Sample_E1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-C6

description:
Sample_C6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-H5

description:
Sample_H5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-G8

description:
Sample_G8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-D5

description:
Sample_D5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-GCB-F5

description:
Sample_F5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-D4

description:
Sample_D4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-Unclassified-H3

description:
Sample_H3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-E9

description:
Sample_E9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-B7

description:
Sample_B7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-G3

description:
Sample_G3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-A3

description:
Sample_A3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFN-ABC-D1

description:
Sample_D1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-D3

description:
Sample_D3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-E2

description:
Sample_E2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-A2

description:
Sample_A2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-E7

description:
Sample_E7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-C3

description:
Sample_C3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-H4

description:
Sample_H4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-D9

description:
Sample_D9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-A8

description:
Sample_A8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-A5

description:
Sample_A5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-H1

description:
Sample_H1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-B2

description:
Sample_B2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-C1

description:
Sample_C1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-C5

description:
Sample_C5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-A4

description:
Sample_A4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-G6

description:
Sample_G6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-D4

description:
Sample_D4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-B9

description:
Sample_B9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-E3

description:
Sample_E3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-E8

description:
Sample_E8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-E4

description:
Sample_E4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-B8

description:
Sample_B8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-H3

description:
Sample_H3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-F4

description:
Sample_F4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-H7

description:
Sample_H7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-C9

description:
Sample_C9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-F2

description:
Sample_F2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-F5

description:
Sample_F5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-E5

description:
Sample_E5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-F9

description:
Sample_F9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-F3

description:
Sample_F3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-G2

description:
Sample_G2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-G1

description:
Sample_G1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-H2

description:
Sample_H2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-F6

description:
Sample_F6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-D7

description:
Sample_D7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-D6

description:
Sample_D6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-B1

description:
Sample_B1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-D1

description:
Sample_D1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-H5

description:
Sample_H5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: Tumor-her2neg-4

status: Public on Apr 29 2010

city: Galway

first: Paul

last: Geeleher

address: University Road

department: Mathematics

country: Ireland

institute: National University of Ireland, Galway

hyb_protocol: Labelled RNA was hybridized to LNA™ miChip array platforms (Exiqon version 7, containing 453 miRNA sequences) over 16 hours at 54°C using a rotational hybridization chamber. Arrays were subsequently washed in varying stringency washes, rinsed, drained and scanned using a GenePix 4000AL laser scanner (Axon Instruments, Foster City, CA, USA).

scan_protocol: Images generated by the GenePix 4200AL scanner

data_processing: Background subtraction and quantiles normalization were performed in R and Bioconductor using the Limma package.

source_name: lobular

label_protocol: Briefly, 5.5 μg total RNA was 3' ligated to Cy3 dye-linked 2'-deoxyuridine-5'-triphosphate using T4 RNA ligase (catalogue number 2141; Ambion, Woodward, Austin, TX, USA), in the presence of RNase inhibitor (catalogue number 2682; Ambion, Woodward, Austin, TX, USA), ATP (Grade I, catalogue number A2383-1G; Sigma-Aldrich Corp. St. Louis, MO, USA), and polyethylene glycol 50% aqueous solution (PEG 6000, catalogue number 81304; Fluka, Sigma-Aldrich Corp, St. Louis, MO, USA). Following a 12-hour to 16-hour incubation, labelled RNA was washed in ethanol, and precipitated in sodium acetate (3 M) using linear acrylamide.

extract_protocol: Depending on whether samples were destined for microarray or RQ-PCR analysis, slightly modified RNA extraction methods were employed. For the microarray experiment, total RNA was required. Breast tumour tissue (50 to 100 mg) was homogenized using a bench-top homogenizer (Polytron® PT1600E; Kinematica AG, Littau-Luzem, Switzerland) in 1 ml QIAzol lysis reagent (Qiagen, Crawley, UK). Total RNA was isolated from homogenized breast tissue using the RNeasy® Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. For RQ-PCR, miRNA was selectively isolated from approximately 100 mg tissue. Large RNA fractions (> 200 nucleotides) and small RNA fractions (< 200 nucleotides) were isolated separately using the RNeasy Plus Mini Kit and RNeasy MinElute® Cleanup Kit (Qiagen) according to the supplementary protocol: purification of miRNA from animal cells. The concentration and purity of total RNA were assessed using a NanoDrop™ 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). RNA integrity was assessed using the RNA 6000 Nano LabChip Series II Assay with the 2100 Bioanalyzer System (Agilent Technologies, Palo Alto, CA, USA). Electropherograms and gel-like images were evaluated using the Agilent 2100 Expert software (version B.02.03; Agilent Technologies, Palo Alto, CA, USA), which generated the RNA integrity number to ensure that only RNA of good integrity was used in these experiments (RNA integrity number range, 7.6 to 9.5). The miRNA concentration and purity were also assessed by NanoDrop™ 1000 spectrophotometry. Small miRNA-enriched fractions were analysed using the Small RNA Assay on the Agilent 2100 Bioanalyzer.

value: lobular breast cancer

tag: genome/variation


title: FFA-ABC-C7

description:
Sample_C7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-G3

description:
Sample_G3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-G4

description:
Sample_G4
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-G5

description:
Sample_G5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-D5

description:
Sample_D5
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-E1

description:
Sample_E1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-G9

description:
Sample_G9
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-Unclassified-G8

description:
Sample_G8
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-D2

description:
Sample_D2
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-GCB-B3

description:
Sample_B3
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-C6

description:
Sample_C6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: FFA-ABC-E6

description:
Sample_E6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: XX2-B

status: Public on Mar 12 2010

city: Porto

first: Alexandra

middle: M.

last: Lopes

address: R. Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

description: 40,XX from 40,In(X)1H/XPaf x 40,XY

hyb_protocol: 1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 16 hours at 58 degrees celsius.   1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 15 hours at 55 degrees celsius. The microarrays were washed and then stained with streptavidin conjugated to Cy3 fluorescent dye. The staining procedure relies on the affinity of streptavidin to biotin which is incorporated into the UTP residues of the hybridised cRNA sample. Arrays were then washed again and air dried.

scan_protocol: Microarrays were scanned under 532nm laser illumination using a confocal type image system (BeadArray Reader, Illumina California USA).

data_processing: The values for each bead in the array were imported into the Illumina software BeadStudio for preliminary quality checks, summarized according to bead type and then exported into R. Normalization across all arrays was performed on a log scale using the quantile normalization method implemented in the Lumi normalization package from the bioconductor repository (www.bioconductor.org).

source_name: Brain

label_protocol: Biotin-16 UTP of in vitro transcribed RNA. Used Illumina RNA amplification kit (Cat # 1755 Ambion US)

extract_protocol: Total RNA was isolated from homogenized tissues using Trizol reagent and purified using a column based centrifugation method (Qiagen) according to the manufacturer’s instructions.

value: Brain

value: 12 weeks old

tag: genetic background

value: random bred MF1, one single progenitor X chromosome background

value: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XmO3-B

description: 39,XmO from 40,XX x 40,XPafY*

value: 39,XmO from 40,XX x 40,XPafY*


title: FFA-Unclassified-G7

description:
Sample_G7
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: Unclassified


title: XmO1-B

description: 39,XmO from 40,XX x 40,XPafY*

value: female


title: XX1-B

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: FFA-Unclassified-H6

description:
Sample_H6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: XX3-B

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XpO1-B

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY

value: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XmO2-B

description: 39,XmO from 40,XX x 40,XPafY*


title: XpO2-B

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XmO3-M

description: 39,XmO from 40,XX x 40,XPafY*

source_name: Muscle

value: Muscle


title: XmO2-M

description: 39,XmO from 40,XX x 40,XPafY*


title: XpO3-M

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: FFA-GCB-A1

description:
Sample_A1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: XX3-M

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XpO1-M

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XmO3-K

description: 39,XmO from 40,XX x 40,XPafY*

source_name: Kidney

value: Kidney


title: XmO1-M

description: 39,XmO from 40,XX x 40,XPafY*


title: FFA-GCB-A6

description:
Sample_A6
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples


title: XpO2-K

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XpO3-K

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XmO1-K

description: 39,XmO from 40,XX x 40,XPafY*


title: XmO2-K

description: 39,XmO from 40,XX x 40,XPafY*


title: XpO1-L

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY

source_name: Liver

value: Liver


title: XX3-L

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XX1-K

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XmO3-L

description: 39,XmO from 40,XX x 40,XPafY*


title: XpO2-M

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XX2-M

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XpO1-K

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XpO3-B

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: XX1-L

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XX2-K

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: XmO2-L

description: 39,XmO from 40,XX x 40,XPafY*


title: XmO1-L

description: 39,XmO from 40,XX x 40,XPafY*


title: Proliferative zone_12wk5_Biol rep 5

status: Public on Jan 28 2010

city: Stockholm

first: Ola

last: Nilsson

address: Karolinska University Hospital, Q2:08

department: Dept. Woman and Child Health

country: Sweden

institute: Karolinska Institute

description: Proliferative and early hypertrophic zone microdissected from proximal tibiae of animal 5

hyb_protocol: 15 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000

data_processing: Raw data was preprocessed to produce signal values using the MAS5 statistical algorithm.

label: Biotin

organism: Rattus norvegicus

source_name: Proximal tibial growth plate cartilage, Castrated male rats, age 12wks

label_protocol: 50-100ng of total RNA was amplified and labeled using the Two-Cycle Target Labeling and Control Reagents (Affymetrix, P/N 900494) according to Expression Analysis Technical Manual, version 701021 Rev.5 (Affymetrix)

growth_protocol: Rats (not 1wk animals) were castrated at the age of 18 days.

extract_protocol: Total RNA was extracted from microdissected cartilage by guanidinium thiocyanate, proteinase K digestion, phenol-chloroform extraction, isopropanol precipitation, LiCl-precipitation as previously described except that one tenth of every volume was used (Heinrichs C et al. Endocrinology 1994;135:1113-8).

treatment_protocol: Proximal tibiae were excised, trimmed of cortical bone, embedded in OCT, and stored at -80C. 60um frozen sections were fixed, stained and dehydrated before being manually microdissected into individual growth plate zones under a xylene droplet using scalpel blades and hypodermic needles (Nilsson et al J Endocrinol 2007;193:75-84).

tag: castrated

value: Yes

tag: growth plate zone


title: Proliferative zone_12wk2_Biol rep 2

description: Proliferative and early hypertrophic zone microdissected from proximal tibiae of animal 2

tag: age


title: XpO3-L

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: Proliferative zone_12wk4_Biol rep 4

description: Proliferative and early hypertrophic zone microdissected from proximal tibiae of animal 4


title: XX2-L

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: Proliferative zone_12wk1_Biol rep 1

description: Proliferative and early hypertrophic zone microdissected from proximal tibiae of animal 1


title: Proliferative zone_9wk3_Biol rep 3

description: Proliferative and early hypertrophic zone microdissected from proximal tibiae of animal 3

source_name: Proximal tibial growth plate cartilage, Castrated male rats, age 9wks


title: Proliferative zone_12wk3_Biol rep 3

value: Proliferative and early hypertrophic zone


title: XpO2-L

description: 39,XpO from 40,In(X)1H/XPaf x 40,XY


title: Proliferative zone_9wk1_Biol rep 1


title: XX3-K

description: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: Proliferative zone_9wk5_Biol rep 5


title: Proliferative zone_9wk2_Biol rep 2


title: Proliferative zone_3wk4_Biol rep 4

source_name: Proximal tibial growth plate cartilage, Castrated male rats, age 3wks


title: Proliferative zone_9wk4_Biol rep 4


title: Proliferative zone_6wk2_Biol rep 2

source_name: Proximal tibial growth plate cartilage, Castrated male rats, age 6wks


title: Proliferative zone_6wk5_Biol rep 5


title: Proliferative zone_6wk1_Biol rep 1


title: Proliferative zone_3wk5_Biol rep 5


title: Proliferative zone_3wk1_Biol rep 1


title: Proliferative zone_3wk2_Biol rep 2


title: Proliferative zone_3wk3_Biol rep 3


title: Proliferative zone_6wk4_Biol rep 4


title: Proliferative zone_6wk3_Biol rep 3


title: Hypertrophic zone, Biol rep 4

description: Hypertrophic zone microdissected from  proximal tibiae of animal 4

source_name: Proximal tibial growth plate cartilage, Male rats, 7-day-old

value: 1 week

value: No

value: Hypertrophic zone


title: Hypertrophic zone, Biol rep 3

description: Hypertrophic zone microdissected from  proximal tibiae of animal 3


title: Hypertrophic zone, Biol rep 5

description: Hypertrophic zone microdissected from  proximal tibiae of animal 5


title: Hypertrophic zone, Biol rep 2

description: Hypertrophic zone microdissected from  proximal tibiae of animal 2


title: FFA-GCB-F1

description:
Sample_F1
matched diffuse large B-cell lymphoma (i.e. DLBCL) FFPET and fresh/frozen patient samples

value: germinal center B-cell

value: B-cell lymphoma

value: fresh/frozen


title: Proliferative zone, Biol rep 4

description: Proliferative zone microdissected from proximal tibiae of animal 4

value: Proliferative zone


title: Proliferative zone, Biol rep 5

description: Proliferative zone microdissected from proximal tibiae of animal 5


title: Proliferative zone, Biol rep 3

description: Proliferative zone microdissected from proximal tibiae of animal 3


title: Proliferative zone, Biol rep 1

description: Proliferative zone microdissected from proximal tibiae of animal 1


title: Normal_5

status: Public on Jan 05 2010

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression ratios were obtained from human Clear Cell kidney tumor and normal kidney tissues.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 11 entrez gene ID CDF was used.

source_name: Homo Sapiens

label_protocol: 10 ug of Qiagen-purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: subtype

value: normal tissue


title: Normal_9


title: Normal_4


title: Normal_11


title: Normal_12


title: Resting zone, Biol rep 3

description: Resting zone microdissected from proximal tibiae of animal 3

value: Resting zone


title: Resting zone, Biol rep 1

description: Resting zone microdissected from proximal tibiae of animal 1


title: Normal_3


title: Normal_13


title: Normal_8


title: Resting zone, Biol rep 5

description: Resting zone microdissected from proximal tibiae of animal 5


title: Normal_1


title: Resting zone, Biol rep 2

description: Resting zone microdissected from proximal tibiae of animal 2


title: Normal_10


title: Normal_20

hyb_protocol: GeneChips were washed and stained in the Affymetrix hybridization oven 640.


title: Hypertrophic zone, Biol rep 1

description: Hypertrophic zone microdissected from  proximal tibiae of animal 1


title: Normal_19


title: Normal_21


title: Normal_7


title: Normal_2


title: Resting zone, Biol rep 4

description: Resting zone microdissected from proximal tibiae of animal 4


title: Normal_14


title: XX1-M

description: 40,XX from 40,In(X)1H/XPaf x 40,XY

value: 12 weeks old

value: random bred MF1, one single progenitor X chromosome background

value: 40,XX from 40,In(X)1H/XPaf x 40,XY


title: Proliferative zone, Biol rep 2

description: Proliferative zone microdissected from proximal tibiae of animal 2


title: Normal_22


title: Normal_16


title: Normal_18


title: Normal_6


title: Normal_17


title: Normal_15


title: VARI_046T

description:
AFF4
FBXO28
USP24
UTX

value: clear cell


title: VARI_038T


title: VARI_111T


title: SBA_45

status: Public on Oct 07 2009

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: 600ng of tumor and normal DNA were combined with 10 µg Cot-1 DNA and precipitated by adding 2.5 volumes of ice-cold 100% ethanol and 0.1 volume of 3M sodium acetate (pH 5.2). The DNA was collected by centrifugation at 14000 rpm for 30 minutes at 4 °C. The pellet was dissolved in 130 µl hybridization solution and incubated at 73°C for 10 minutes to denature the DNA, followed by 60-120 minute incubation at 37°C. Next, the hybridization mixture was added to the array in a hybridization station (HybArray12TM, Perkin Elmer Life Sciences, Zaventum, Belgium) and incubated for 38 hours at 37°C. After hybridization the slides were washed in six washing steps and dried by centrifugation for 3 minutes at 1000 g.

hyb_protocol: According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: The raw signal intensities were obtained with Bluefuse. The unreliable and morphologically corrupted measurement spots were removed from the data. We used the global mode normalization.

source_name: small intestinal adenocarcinoma

extract_protocol: DNA extraction was performed using the the QIAmp DNA Micro Kit (Qiagen).

tag: sex

value: female

tag: tumor site

value: Jejunum

tag: celiac disease

tag: tnm

tag: platform_id type

value: oligo

source_name: male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: sample type

value: Pooled DNA from the blood of 10 normal male individuals


title: SBA_41

label_protocol: According Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

value: Duodenum

value: Yes


title: SBA_36

value: male

value: duodenum

source_name: female reference DNA

value: Pooled DNA from the blood of 10 normal female individuals


title: SBA_39

value: Ileum


title: SBA_37


title: SBA_42


title: SBA_32

value: ILeum

value: No


title: SBA_25


title: SBA_27


title: SBA_26


title: SBA_33


title: SBA_24


title: SBA_23


title: SBA_13


title: SBA_14


title: SBA_17


title: SBA_10


title: SBA_08


title: SBA_20


title: SBA_22


title: SBA_09


title: SBA_05


title: SBA_03


title: SBA_30


title: SBA_44


title: SBA_01


title: SBA_04


title: lung squamous 15

status: Public on Sep 18 2009

city: South San Francisco

first: Li

address: 1 DNA Way

institute: Genentech, Inc

description: characterized as having >60% tumor content

hyb_protocol: Labeled cDNA samples were hybridized to arrays following manufacturer's hybridization protocol (Affymterix); hybridize 17 hours at 45 C at 65 rpm, washing done on Fluidics 450.

scan_protocol: Affymterix Gene Chip Scanner 3000 7G

data_processing: Expression intensities for the “core” probe sets were calculated using quantile normalization and the RMA-Sketch method from Affymetrix’s Power Tools package

source_name: lung squamous

label_protocol: Samples were enzymatically fragmentated and biotinylated using the WT Terminal Labeling Kit (Affymterix).

extract_protocol: Total RNA samples were prepared using AllPrep method (Qiagen). Samples were treated with RiboMinus Reduction Kit (Invitrogen), cDNA synthesis and amplification was performed using the WT Sense Target Lableing Kit  (Affymterix).

tag: sampleID

tag: sourceID

tag: tissue

value: lung cancer

tag: cancer subtype

value: carcinoma squamous cell


title: lung squamous 16


title: lung squamous 22


title: lung squamous 12


title: lung squamous 18


title: lung squamous 20


title: lung squamous 10


title: lung squamous 17


title: lung squamous 14


title: lung squamous 1


title: lung squamous 5


title: lung squamous 19


title: lung squamous 7


title: lung squamous 13


title: lung squamous 8


title: lung squamous 6


title: lung adenocarcinoma 20

source_name: lung adenocarcinoma

value: adenocarcinoma


title: lung adenocarcinoma 21


title: lung squamous 2


title: lung adenocarcinoma 16


title: lung adenocarcinoma 15


title: lung adenocarcinoma 14


title: lung squamous 3


title: lung adenocarcinoma 18


title: lung adenocarcinoma 19


title: lung squamous 11


title: lung squamous 21


title: lung squamous 9


title: lung squamous 4


title: lung adenocarcinoma 13


title: lung adenocarcinoma 11


title: lung adenocarcinoma 12


title: lung adenocarcinoma 10


title: lung adenocarcinoma 8


title: lung adenocarcinoma 9


title: lung adenocarcinoma 3


title: lung adenocarcinoma 17


title: colorectal tumor 26

source_name: colorectal tumor

value: colorectal tumor


title: colorectal tumor 23


title: colorectal tumor 21


title: lung adenocarcinoma 4


title: colorectal tumor 22


title: colorectal tumor 20


title: colorectal tumor 24


title: colorectal tumor 13


title: lung adenocarcinoma 1


title: colorectal tumor 17


title: colorectal tumor 15


title: colorectal tumor 18


title: colorectal tumor 12


title: colorectal tumor 25


title: colorectal tumor 5


title: colorectal tumor 14


title: lung adenocarcinoma 2


title: colorectal tumor 19


title: lung adenocarcinoma 6


title: colorectal tumor 16


title: lung adenocarcinoma 5


title: colorectal tumor 11


title: colorectal tumor 7


title: colorectal tumor 10


title: colorectal tumor 8


title: colorectal tumor 9


title: lung adenocarcinoma 7


title: colorectal tumor 3


title: colorectal tumor 6


title: breast tumor 84

source_name: breast tumor

value: breast tumor

value: Triple negative


title: colorectal tumor 1


title: breast tumor 80

value: HR


title: breast tumor 8


title: breast tumor 9


title: breast tumor 78


title: breast tumor 81


title: breast tumor 83


title: breast tumor 76


title: colorectal tumor 4


title: colorectal tumor 2


title: breast tumor 79


title: breast tumor 74


title: breast tumor 73


title: breast tumor 75


title: breast tumor 7


title: breast tumor 65


title: breast tumor 77


title: breast tumor 68


title: breast tumor 72


title: breast tumor 70


title: breast tumor 62


title: breast tumor 82


title: breast tumor 71


title: breast tumor 61


title: breast tumor 63


title: breast tumor 66


title: breast tumor 6


title: breast tumor 69


title: breast tumor 60


title: breast tumor 64


title: breast tumor 67


title: breast tumor 59


title: breast tumor 52


title: breast tumor 53


title: breast tumor 54


title: breast tumor 42


title: breast tumor 56


title: breast tumor 57


title: breast tumor 44


title: breast tumor 46


title: breast tumor 48


title: breast tumor 43


title: breast tumor 58


title: breast tumor 41


title: breast tumor 49


title: breast tumor 51


title: breast tumor 38


title: breast tumor 50


title: breast tumor 4


title: breast tumor 39


title: breast tumor 45


title: breast tumor 47


title: breast tumor 40


title: breast tumor 32


title: breast tumor 37


title: breast tumor 35


title: breast tumor 36


title: breast tumor 55


title: breast tumor 30


title: breast tumor 29


title: breast tumor 33


title: breast tumor 26


title: breast tumor 3


title: breast tumor 31


title: breast tumor 34


title: 4188223089_D

status: Public on Jul 01 2009

city: Oslo

first: Hege

last: Landmark-Høyvik

address: Montebello

country: Norway

institute: Radiumhospitalet

description:
Variable name definitions:
Fatigued_04: classified as fatigued (1) or non-fatigued (0) in 2004 by the FQ questionnaire
Fatigued_07: classified as fatigued (1) or non-fatigued (0) in 2007 by the FQ questionnaire
HADSdistressed_04: classified as depressed (1) or non-depressed (0) in 2004 by the HADS questionnaire
HADSdistressed_07: classified as depressed (1) or non-depressed (0) in 2007 by the HADS questionnaire

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Quantile normalized of variance stabilized filtered gene expression data

source_name: breast cancer survivors

label_protocol: RNA amplification was performed on a total of 331 samples using 300 ng of total RNA, and the Illumina Totalprep RNA Amplification Kit (Ambion Inc., Texas, USA). The amplification procedure consists of reverse transcription with a T7 promoter and ArrayScript, followed by second-strand synthesis. In vitro transcription with T7 RNA Polymerase using a biotin-NTP mix produced biotinylated cRNA copies of each mRNA in the sample.

extract_protocol: Total RNA for 403 participants were isolated from PAX tubes at AROS Applied Biotechnology (Aarhus, Denmark) by an automated procedure using the column based technologies from Qiagen Inc (Hilden, Germany).

tag: fibrosis status (0=no, 1=yes)

value: whole blood

tag: hybdate

tag: conc.

tag: rin

tag: yield

tag: speedvac

value: N

tag: conccrnaafteramplification

tag: x

tag: arrayname

tag: patientid


title: 4188223089_C


title: breast tumor 25


title: breast tumor 21


title: breast tumor 28


title: 4188223063_E


title: 4188223067_A


title: breast tumor 15


title: breast tumor 23


title: breast tumor 27


title: breast tumor 24


title: breast tumor 17


title: breast tumor 14


title: breast tumor 18


title: breast tumor 19


title: 4189251003_D


title: breast tumor 13


title: 4176126050_E


title: 4188223068_B

value: Y


title: 4188223089_B


title: 4202996053_C


title: breast tumor 16


title: 4188223068_C


title: 4176126026_E


title: breast tumor 10


title: breast tumor 5


title: 4188223088_D


title: 4203850060_E


title: 4188223090_F


title: breast tumor 12


title: 4203850035_E


title: 4188223089_A


title: 4176126050_C


title: 4157064132_F


title: breast tumor 20


title: breast tumor 22


title: 4188661039_F


title: 4176126026_F


title: 4189251024_A


title: 4203850002_D


title: 4189251010_E


title: 4117151251_F


title: 4189251024_B


title: 4188223062_F


title: 4188223082_F


title: 4189251024_D


title: 4188661036_E


title: 4176126044_B


title: 4188223090_D


title: breast tumor 2


title: 4203850037_D


title: 4203850032_E


title: 4188223062_C


title: 4202996053_F


title: 4203850043_B


title: 4188223082_B


title: breast tumor 1


title: 4157064129_F


title: 4189251008_F


title: 4188223063_A


title: breast tumor 11


title: 4176126050_D


title: 4189251010_F


title: 4188661036_D


title: 4202996013_E


title: 4189251003_B


title: 4188223062_E


title: 4188223068_E


title: 4188661033_E


title: 4203850100_D


title: 4188223089_F


title: 4117151251_B


title: 4188661058_D


title: 4188223090_A


title: 4189251008_D


title: 4176126044_E


title: 4117151261_F


title: 4203850032_D


title: 4176126026_C


title: 4176126050_F


title: 4188223082_D


title: 4203850035_C


title: 4188661058_E


title: 4203850035_D


title: 4203850035_A


title: 4176126025_B


title: 4203850037_A


title: 4188223075_A


title: 4176126026_A


title: 4188223089_E


title: 4189251010_B


title: 4203850083_E


title: 4189251024_C


title: 4203850060_B


title: 4203850045_D


title: 4157064117_A


title: 4203850100_A


title: 4157064158_B


title: 4157064132_B


title: 4203850045_B


title: 4176126024_C


title: 4203850043_E


title: 4203850032_F


title: 4203850068_D


title: 4176126025_A


title: 4157064117_C


title: 4117151250_B


title: 4188223076_E


title: 4176126027_B


title: 4202996013_F


title: 4203850083_D


title: 4188661038_A


title: 4202996013_D


title: 4202996053_E


title: 4117151250_A


title: 4188223063_F


title: 4189251008_A


title: 4117151261_C


title: 4203850005_D


title: 4176126027_F


title: 4189251008_B


title: 4189251024_F


title: 4188223088_F


title: 4188661034_C


title: 4203850005_E


title: 4188223075_C


title: 4117151261_B


title: 4189251008_C


title: 4203850043_D


title: 4176126046_F


title: 4176126027_C


title: 4188223076_F


title: 4188223076_A


title: 4117151261_E


title: 4188223076_D


title: 4189251009_F


title: 4202996016_B


title: 4176126026_B


title: 4203850005_A


title: 4203850060_C


title: 4189251003_F


title: 4157064129_E


title: 4188661033_C


title: 4176126026_D


title: 4188223087_F


title: 4203850002_B


title: 4203850060_A


title: 4188661058_A


title: 4188661039_E


title: 4176126045_D


title: 4176126024_D


title: 4188661039_D


title: 4176126045_F


title: 4189251009_C


title: 4176126044_C


title: 4188223067_D


title: 4188661034_D


title: 4157064133_F


title: 4188223068_A


title: 4203850083_B


title: 4202996016_A


title: 4188661033_B


title: 4189251009_E


title: 4157064133_E


title: 4117151246_E


title: 4189251010_D


title: 4176126045_C


title: 4203850045_F


title: 4157064158_F


title: 4157064158_E


title: 4188661039_C


title: 4117151251_C


title: 4188223088_C


title: 4188661036_A


title: 4188661058_F


title: 4157064133_D


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title: Community-acquired isolate no 5 vs reference strain Mu50 rep1

status: Public on Feb 15 2009

city: Brussels

first: Ricardo

middle: Luis

last: De Mendonca

address: Route de Lennik 808

department: Microbiology

country: Belgium

institute: ULB - Hôpital Erasme

description: Samples were hybridized to StaphVar arrays containing 1326 60mer oligonucleotide probes (Eurogentec, Seraing, Belgium).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 3.5xSSC, SDS 0.1%, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Prior to hybridization, fluorescent labeled DNA fragments were mixed to achieve a final 90µL volume of hybridization solution (3.4XSSC, SDS 0.3% and single stranded salmon sperm DNA 0.01%), denatured for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, microarrays were successively washed in 2XSCC-SDS 0.03% solution (twice) at 60°C, 2XSSC at 60°C, 1XSCC at room temperature and 0.2XSCC, each time for 2 min. They were dried by centrifugation at 800 rpm for 10 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and fluorescence intensities of each spot were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing:
Data processing was achieved as described by Saunders et al (Saunders NA, Underwood A, Kearns AM and Hallas G. 2004. A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus. Microbiology, 3763-3771).

Briefly, for each individual spot, two ratios were calculated:

The first one (VALUE) was calculated by the signal intensity of the spot to the median of negative control signal intensities. Spots were scored as "negative" when the VALUE was less than 3. Spots presenting a ratio superior or equal to 3 were processed further as follows:

The backgrounds were first subtracted from each individual spot for the test and the reference strains. The second one (Ratio_2) was the ratio of test strain intensity to Mu50 intensity (reference strain) normalized against the median ratio obtained for the positive controls (n=4). The spots were scored as "positive" when the Ratio_2 values were above 0.25. In the opposite, spots were scored as "negative" when the Ratio_2 values were below 0.1, and "indeterminate" for Ratio_2 values ranging between 0.1-0.25.

organism: Staphylococcus aureus

source_name: Clinical strain no 5

label_protocol: Prior to labeling, 4 µg of genomic DNA were digested by Sau3AI (New Englands Biolabs, Hitchin, UK) and purified by the MinElute Reaction kit as described by the manufacturer (Qiagen). Fluorescent labeling was performed by random priming with the Bioprime DNA labeling kit (Invitrogen, Merelbeke, Belgium) with a final concentration of non-fluorescent nucleotides of 0.12 mM for dATP, dCTP, dGTP and 0.06 mM for dTTP. To each labeling reaction mixture, fluorescent nucleotide analogs (Cy3-dUTP; Amersham, Gent, Belgium) were added to a final concentration of 0.06 mM. Reactions were stopped by addition of 5 µL of 0.5 M EDTA pH 8.0 and cleaned up with the MinElute Reaction kit as described by the manufacturer (Qiagen).

growth_protocol: Prior to DNA extraction, strains were grown in brain-heart infusion medium at 37°C until optical density at 600 nm reached 1

extract_protocol: Genomic DNA was isolated using DNeasy Tissue Kit according to the manufacturer instructions (Qiagen)

treatment_protocol: No treatment

value: Community acquired methicillin resistant Staphylococcus aureus recovered from a patient in Belgium

source_name: Reference Strain Mu50

label_protocol: Prior to labeling, 4 µg of genomic DNA were digested by Sau3AI (New Englands Biolabs, Hitchin, UK) and purified by the MinElute Reaction kit as described by the manufacturer (Qiagen). Fluorescent labeling was performed by random priming with the Bioprime DNA labeling kit (Invitrogen, Merelbeke, Belgium) with a final concentration of non-fluorescent nucleotides of 0.12 mM for dATP, dCTP, dGTP and 0.06 mM for dTTP. To each labeling reaction mixture, fluorescent nucleotide analogs (Cy5-dUTP; Amersham, Gent, Belgium) were added to a final concentration of 0.06 mM. Reactions were stopped by addition of 5 µL of 0.5 M EDTA pH 8.0 and cleaned up with the MinElute Reaction kit as described by the manufacturer (Qiagen).

value: Sequenced Hospital acquired methicillin resistant Staphylococcus aureus


title: Community-acquired isolate no 2 vs reference strain Mu50 rep1

source_name: Clinical strain no 2


title: Community-acquired isolate no 10 vs reference strain Mu50 rep1

source_name: Clinical strain no 10


title: Community-acquired isolate no 5 vs reference strain Mu50 rep2


title: Community-acquired isolate no 2 vs reference strain Mu50 rep2


title: Community-acquired isolate no 13 vs reference strain Mu50 rep1

source_name: Clinical strain no 13


title: 4203850034_D


title: Community-acquired isolate no 7 vs reference strain Mu50 rep2

source_name: Clinical strain no 7


title: Community-acquired isolate no 6 vs reference strain Mu50 rep2

source_name: Clinical strain no 6


title: Community-acquired isolate no 7 vs reference strain Mu50 rep1


title: Community-acquired isolate no 10 vs reference strain Mu50 rep2


title: Community-acquired isolate no 9 vs reference strain Mu50 rep2

source_name: Clinical strain no 9


title: Community-acquired isolate no 6 vs reference strain Mu50 rep1


title: Community-acquired isolate no 3 vs reference strain Mu50 rep2

source_name: Clinical strain no 3


title: Community-acquired isolate no 9 vs reference strain Mu50 rep1


title: Community-acquired isolate no 8 vs reference strain Mu50 rep2

source_name: Clinical strain no 8


title: Community-acquired isolate no 4 vs reference strain Mu50 rep2

source_name: Clinical strain no 4


title: Community-acquired isolate no 3 vs reference strain Mu50 rep1


title: Community-acquired isolate no 1 vs reference strain Mu50 rep2

source_name: Clinical strain no 1


title: Community-acquired isolate no 11 vs reference strain Mu50 rep2

source_name: Clinical strain no 11


title: Community-acquired isolate no 12 vs reference strain Mu50 rep2

source_name: Clinical strain no 12


title: Community-acquired isolate no 13 vs reference strain Mu50 rep2


title: Community-acquired isolate no 11 vs reference strain Mu50 rep1


title: Community-acquired isolate no 4 vs reference strain Mu50 rep1


title: Community-acquired isolate no 1 vs reference strain Mu50 rep1


title: Community-acquired isolate no 12 vs reference strain Mu50 rep1


title: ovarian cancer: O76

status: Public on Feb 09 2009

first: Jan

last: Budczies

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite - Universitaetsmedizin Berlin

description: frozen tissue sample

hyb_protocol: The fragmented cRNA was hybridised to HGU133 arrays at 45 °C in a hybridization oven for 16 hr.

scan_protocol: Chip scanning was done with an Affymetrix Gene Array Scanner G2500A.

data_processing: Signals and detection calls were calculated with the R package affy according to the standard MAS 5.0 protocol of the chip manufacturer.

source_name: ovarian cancer

label_protocol: cDNA was synthesised from 5 µg total RNA by reverse transcription, synthesis of biotin-labeled cRNA was performed using the BioArray High Yield RNA Transcription kit.

extract_protocol: Total cellular RNA was isolated from tumor tissue, using the Qiagen Rneasy Mini Kit.

value: frozen tumor

tag: figo stage

tag: grade

value: III

tag: histological type

value: serous ovca

tag: residual tumor

tag: overall survival time

tag: overall survival event


title: ovarian cancer: O74

description: frozen tissue sample

tag: tissue


title: ovarian cancer: O77

description: frozen tissue sample


title: ovarian cancer: O75

description: frozen tissue sample

value: II


title: ovarian cancer: O79

description: frozen tissue sample


title: ovarian cancer: O73

description: frozen tissue sample

value: undifferentiated ovca


title: ovarian cancer: O70

description: frozen tissue sample


title: ovarian cancer: O80

description: frozen tissue sample


title: ovarian cancer: O72

description: frozen tissue sample


title: ovarian cancer: O68

description: frozen tissue sample


title: ovarian cancer: O71

description: frozen tissue sample


title: ovarian cancer: O69

description: frozen tissue sample


title: ovarian cancer: O66

description: frozen tissue sample


title: ovarian cancer: O67

description: frozen tissue sample


title: ovarian cancer: O64

description: frozen tissue sample


title: ovarian cancer: O65

description: frozen tissue sample


title: ovarian cancer: O63

description: frozen tissue sample


title: ovarian cancer: O61

description: frozen tissue sample


title: ovarian cancer: O62

description: frozen tissue sample


title: ovarian cancer: O55

description: frozen tissue sample


title: ovarian cancer: O54

description: frozen tissue sample


title: ovarian cancer: O57

description: frozen tissue sample


title: ovarian cancer: O58

description: frozen tissue sample

value: sarcomatoid


title: ovarian cancer: O59

description: frozen tissue sample


title: ovarian cancer: O60

description: frozen tissue sample


title: ovarian cancer: O56

description: frozen tissue sample


title: ovarian cancer: O53

description: frozen tissue sample


title: ovarian cancer: O78

description: frozen tissue sample


title: ovarian cancer: O50

description: frozen tissue sample


title: ovarian cancer: O48

description: frozen tissue sample

value: I


title: ovarian cancer: O47

description: frozen tissue sample


title: ovarian cancer: O46

description: frozen tissue sample


title: ovarian cancer: O43

description: frozen tissue sample


title: ovarian cancer: O51

description: frozen tissue sample


title: ovarian cancer: O49

description: frozen tissue sample


title: ovarian cancer: O44

description: frozen tissue sample


title: ovarian cancer: O40

description: frozen tissue sample


title: ovarian cancer: O45

description: frozen tissue sample


title: ovarian cancer: O42

description: frozen tissue sample

value: endometr ovca


title: ovarian cancer: O41

description: frozen tissue sample


title: ovarian cancer: O28

description: frozen tissue sample


title: ovarian cancer: O35

description: frozen tissue sample


title: ovarian cancer: O29

description: frozen tissue sample


title: ovarian cancer: O37

description: frozen tissue sample


title: ovarian cancer: O38

description: frozen tissue sample


title: ovarian cancer: O33

description: frozen tissue sample


title: ovarian cancer: O52

description: frozen tissue sample


title: ovarian cancer: O31

description: frozen tissue sample


title: ovarian cancer: O36

description: frozen tissue sample


title: ovarian cancer: O30

description: frozen tissue sample


title: ovarian cancer: O26

description: frozen tissue sample

value: endometr, clear cell ovca


title: ovarian cancer: O34

description: frozen tissue sample


title: ovarian cancer: O32

description: frozen tissue sample


title: ovarian cancer: O39

description: frozen tissue sample


title: ovarian cancer: O27

description: frozen tissue sample


title: ovarian cancer: O25

description: frozen tissue sample


title: ovarian cancer: O23

description: frozen tissue sample


title: 4157064117_E

tag: fibrosis status (0=no, 1=yes)


title: ovarian cancer: O24

description: frozen tissue sample

value: clear cell ovca


title: ovarian cancer: O22

description: frozen tissue sample


title: ovarian cancer: O21

description: frozen tissue sample


title: ovarian cancer: O20

description: frozen tissue sample


title: ovarian cancer: O17

description: frozen tissue sample


title: ovarian cancer: O16

description: frozen tissue sample


title: ovarian cancer: O19

description: frozen tissue sample


title: ovarian cancer: O15

description: frozen tissue sample


title: Community-acquired isolate no 8 vs reference strain Mu50 rep1

tag: sample type


title: ovarian cancer: O18

description: frozen tissue sample


title: ovarian cancer: O14

description: frozen tissue sample


title: ovarian cancer: O10

description: frozen tissue sample


title: ovarian cancer: O5

description: frozen tissue sample


title: ovarian cancer: O13

description: frozen tissue sample


title: ovarian cancer: O6

description: frozen tissue sample


title: ovarian cancer: O9

description: frozen tissue sample


title: ovarian cancer: O11

description: frozen tissue sample


title: ovarian cancer: O4

description: frozen tissue sample


title: ovarian cancer: O2

description: frozen tissue sample


title: ovarian cancer: O3

description: frozen tissue sample

value: transitional cell ca


title: ovarian cancer: O7

description: frozen tissue sample


title: ovarian cancer: O1

description: frozen tissue sample


title: ovarian cancer: O8

description: frozen tissue sample


title: Carcinoma component of a progressed adenoma (P23C_s55_b16)

status: Public on Oct 15 2008

hyb_protocol: as described by Carvalho et al, Cell Oncol. 2006;28(5-6):283-94.

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the July 2003 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalised by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.

source_name: colon

label_protocol: as described by Snijders et al, Nat Genetics, volume 29, p 263-4

extract_protocol: as described in Weiss et al, Mol Pathol. 1999 Oct;52(5):243-51.

tag: disease state

tag: site

value: Colorectum

tag: tumor site

value: Left colon

tag: tnm

tag: age

tag: gender

value: F

tag: platform_id type

value: bac

source_name: male Reference DNA

value: A pool of ten normal individuals


title: Carcinoma component of a progressed adenoma (P2C_s14_b14)

value: Rectum


title: Carcinoma component of a progressed adenoma (P22C_s67_b16)

value: M

source_name: female Reference DNA


title: ovarian cancer: O12

description: frozen tissue sample

value: frozen tumor

value: III


title: Carcinoma component of a progressed adenoma (P10C_s23_b16)


title: Carcinoma component of a progressed adenoma (P9C_s21_b16)

value: Right colon


title: Carcinoma component of a progressed adenoma (P8C_s19_b16)


title: Carcinoma component of a progressed adenoma (P14C_s09_b17)


title: Carcinoma (F8C_s67_b21)

extract_protocol: protocol available on www.vumc.nl/microarrays

value: Carcinoma


title: Carcinoma (F10C_s73_b21)

value: Colon


title: Carcinoma component of a progressed adenoma (P18c_s61_b16)


title: Carcinoma component of a progressed adenoma (P36C_s56_b17)

value: Transverse colon


title: Carcinoma component of a progressed adenoma (P27C_s60_b21)


title: Carcinoma component of a progressed adenoma (P35C_s55_b21)


title: Carcinoma (F18C_s63_b17)


title: Carcinoma (F32C_s48_b16)


title: Carcinoma (F58C_s57_b47)

source_name: Female Reference DNA


title: Carcinoma (F5C_s75_b21)


title: Carcinoma (F12C_s42_b16)


title: Carcinoma (F11C_s40_b16)


title: Carcinoma component of a progressed adenoma (P29C_s34_b21)


title: Carcinoma (F27C_s34_b17)


title: Carcinoma (F1C_s63_b21)


title: Carcinoma component of a progressed adenoma (P24C_s21_b17)


title: Day5 EC1118 #2

status: Public on Jul 01 2008

city: Stellenbosch

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

country: South Africa

institute: University of Stellenbosch

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Standard Affymetrix Procedure, MAS5.0

organism: Saccharomyces cerevisiae

source_name: Day5 EC1118

label_protocol: Standard Affymetrix procedure

extract_protocol: Hot-phenol method

tag: strain

tag: replicate

tag: time

value: Day 5 of fermentation


title: Carcinoma (F51C_s48_b47)


title: Day5 VIN13 #3

source_name: Day5 VIN13


title: Day5 EC1118 #3


title: Carcinoma (F39C_s46_b47)


title: Day5 BM45 #3

source_name: Day5 BM45


title: Carcinoma (F29C_s44_b47)


title: Day5 VIN13 #2


title: Carcinoma (F30C_s45_b47)


title: Day5 BM45 #2


title: Carcinoma (F46C_s47_b47)


title: Carcinoma component of a progressed adenoma (P25C_s22_b17)


title: Day14 VIN13 #3

source_name: Day14 VIN13

extract_protocol: Hot-Phenol method

value: Day 14 of fermentation


title: Day2 BM45 #3

source_name: Day2 BM34

value: Day 2 of fermentation


title: Day5 DV10 #1

source_name: Day5 DV10


title: Day2 BM45 #2

source_name: Day2 BM45


title: Day5 EC1118 #1


title: Day2 EC1118 #2

source_name: Day2 EC1118


title: Day5 DV10 #3


title: Day5 DV10 #2


title: Day5 BM45 #1


title: Day5 285 #3

description: Standard Affymetrix Procedure

hyb_protocol: Standard Affymetrix Procedure

scan_protocol: Standard Affymetrix Procedure

label_protocol: Standard Affymetrix Procedure


title: Day5 285 #2

description: Standard Affymetrix Procedure


title: Day2 EC1118 #3


title: Day2 285 #2

description: Standard Affymetrix Procedure


title: Day2 285 #3

description: Standard Affymetrix Procedure


title: Day14 VIN13 #2

extract_protocol: Hot Phenol Method


title: Day5 285 #1

description: Standard Affymetrix Procedure


title: Day2 BM45 #1


title: Day14 285 #2


title: Day14 VIN13 #1


title: Day14 EC1118 #3


title: Day14 285 #1


title: Day14 DV10 #3

source_name: Day14 DV10


title: Day14 BM45 #1

source_name: Day14 BM45


title: Day2 EC1118 #1


title: Day14 EC1118 #1


title: Day2 285 #1

description: Standard Affymetrix Procedure


title: Day14 DV10 #1


title: Day14 DV10 #2


title: Day2 DV10 #3

source_name: Day2 DV10


title: Day14 EC1118 #2


title: Day2 DV10 #1


title: Day2 DV10 #2


title: Ecoli WT -ile rep2

status: Public on Apr 08 2008

city: Norman

first: Tyrrell

last: Conway

state: OK

address: 101 David L. Boren Blvd.

department: Advanced Center for Genome Technology

institute: University of Oklahoma

hyb_protocol: Hybridization was at 60 degrees C for 16 h according to Affymetrix protocol ProkGE_WS2v2-450.

scan_protocol: Affymetrix GCOS scanner software and GeneChip Scanner 3000.

data_processing: RMA with quartile normalization according to method of Irizarry et al, 2003. The raw .cel files were processed in RMA using Bioconductor R package: affy Version:1.8.1 Date:2005-09-03, with the option Filter.genes corresponding to the MG1655 subset of probesets from the arrays, as reflected in the sample files. Replicates were averaged for ratio calculations. Ratio calculations are provided in the supplementary files on the Series record.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli wild-type, isoleucine starved

label_protocol: RNA converted to cDNA by random-hexamer primed first strand synthesis with Superscript II and biotinylated with Roche Enzo kit according to Affymetrix protocol.

growth_protocol: Cells were grown in a fermentor with constant O2 saturation and pH was maintained at 7.4. Growth medium was MOPS+glucose+20 AAs (as described by Wanner 1977).  Replete isoleucine was 400 um; isoleucine starvation was with 60 uM. For wildtype, ile replete control, total RNA was extracted in log phase (OD600 of ~0.4).  For ile starved wt and mutants, total RNA was extracted from cells ~40 min after growth arrest.

extract_protocol: Qiagen RNeasy kit extraction with optional DNase step

treatment_protocol: Cells were allowed to starve for isoleucine in medium containing 60 uM ile.

tag: genotype/variation

value: wild-type


title: Ecoli WT -ile rep1


title: Day2 VIN13 #3

description: Standard Affymetrix Procedure

source_name: VIN13 at day2 of fermentation

extract_protocol: Hot-Phenol Method


title: Ecoli relA -ile rep2

source_name: E. coli relA, isoleucine starved

value: relA spoT


title: Ecoli relA -ile rep1


title: Day2 VIN13 #2

description: Standard Affymetrix Procedure

source_name: VIN13 at day 2 of fermentation


title: Day2 VIN13 #1

description: Standard Affymetrix Procedure

source_name: Industrial yeast strain VIN13 at day 2 of fermentation


title: Ecoli WT +ile rep2

source_name: E. coli wild-type, replete isoleucine, control


title: Ecoli relAspoT -ile rep1

source_name: E. coli relA spoT, isoleucine starved

value: relA


title: Ecoli relAspoT -ile rep2


title: Ecoli WT +ile rep1


title: Cerebral cortex, biological rep 3

status: Public on Feb 24 2008

city: Lawrence

first: Xinkun

last: Wang

state: KS

address: 2099 Constant Ave

department: Genomics Facility

institute: The University of Kansas

description:
total RNA extracted from neurons collected from brain cryosections
Fisher 344/BN F1, 6-month-old

hyb_protocol: standard

scan_protocol: standard

data_processing: Affymetrix MAS 5.0 default processing, all chips scaled to the same target value of 500.

source_name: Cerebral cortex

label_protocol: two-cycle target labeling

extract_protocol: standard

value: Cerebral cortex

tag: biological rep

value: Fisher 344/BN

tag: hybrid


title: Cerebellar granular layer, biological rep 2

source_name: Cerebellar granular layer

value: Cerebellar granular layer


title: Hippocampal CA3, biological rep 3

source_name: Hippocampal CA3

value: Hippocampal CA3


title: Cerebral cortex, biological rep 2


title: Cerebellar granular layer, biological rep 3


title: Hippocampal CA1, biological rep 1

source_name: Hippocampal CA1

value: Hippocampal CA1


title: Cerebral cortex, biological rep 1


title: Hippocampal CA1, biological rep 2


title: Hippocampal CA3, biological rep 1


title: Hippocampal CA1, biological rep 3


title: Hippocampal CA3, biological rep 2