title: T01-166

description: frozen tissue of primary breast tumors

value: Surv(months):48.263; STATUS (0=alive, 1=dead):0


title: T01-352

status: Public on Nov 07 2005

type: RNA

city: Durham

first: Joseph

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

country: USA

institute: Duke University

description: frozen tissue of primary breast tumors

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: frozen tissue of primary breast tumors

value: Surv(months):45.799; STATUS (0=alive, 1=dead):0


title: T01-476

description: frozen tissue of primary breast tumors

value: Surv(months):42.842; STATUS (0=alive, 1=dead):0


title: T01-537

description: frozen tissue of primary breast tumors

value: Surv(months):44.846; STATUS (0=alive, 1=dead):0


title: T01-387

description: frozen tissue of primary breast tumors

value: Surv(months):47.146; STATUS (0=alive, 1=dead):0


title: T01-156

description: frozen tissue of primary breast tumors

value: Surv(months):49.051; STATUS (0=alive, 1=dead):0


title: T01-154

description: frozen tissue of primary breast tumors

value: Surv(months):44.32; STATUS (0=alive, 1=dead):0


title: T01-202

description: frozen tissue of primary breast tumors

value: Surv(months):47.113; STATUS (0=alive, 1=dead):0


title: T01-366

description: frozen tissue of primary breast tumors

value: Surv(months):46.686; STATUS (0=alive, 1=dead):0


title: T01-204

description: frozen tissue of primary breast tumors

value: Surv(months):47.277; STATUS (0=alive, 1=dead):0


title: T01-194

description: frozen tissue of primary breast tumors

value: Surv(months):39.392; STATUS (0=alive, 1=dead):1


title: T01-469

description: frozen tissue of primary breast tumors

value: Surv(months):42.678; STATUS (0=alive, 1=dead):0


title: T01-357

description: frozen tissue of primary breast tumors

value: Surv(months):47.606; STATUS (0=alive, 1=dead):0


title: T01-452

description: frozen tissue of primary breast tumors

value: Surv(months):44.945; STATUS (0=alive, 1=dead):0


title: T01-428

description: frozen tissue of primary breast tumors

value: Surv(months):43.762; STATUS (0=alive, 1=dead):0


title: T00-454

description: frozen tissue of primary breast tumors

value: Surv(months):10.053; STATUS (0=alive, 1=dead):1


title: T01-356

description: frozen tissue of primary breast tumors

value: Surv(months):39.524; STATUS (0=alive, 1=dead):0


title: T01-384

description: frozen tissue of primary breast tumors

value: Surv(months):43.039; STATUS (0=alive, 1=dead):0


title: T01-47

description: frozen tissue of primary breast tumors

value: Surv(months):21.815; STATUS (0=alive, 1=dead):0


title: T01-407

description: frozen tissue of primary breast tumors

value: Surv(months):45.043; STATUS (0=alive, 1=dead):0


title: T01-461

description: frozen tissue of primary breast tumors

value: Surv(months):44.353; STATUS (0=alive, 1=dead):0


title: T01-468

description: frozen tissue of primary breast tumors

value: Surv(months):42.908; STATUS (0=alive, 1=dead):0


title: T01-378

description: frozen tissue of primary breast tumors

value: Surv(months):45.963; STATUS (0=alive, 1=dead):0


title: T01-158

description: frozen tissue of primary breast tumors

value: Surv(months):49.347; STATUS (0=alive, 1=dead):0


title: T01-145

description: frozen tissue of primary breast tumors

value: Surv(months):48.493; STATUS (0=alive, 1=dead):0


title: HA99-96A

status: Public on Oct 27 2005

city: La Jolla

first: Jennifer

middle: A

last: Hammond

state: CA

address: 10550 N. Torrey Pines Rd.

institute: The Scripps Research Institute

description: Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis.

source_name: Frontal cortex brain tissue from HIVE patient

tag: Tissue

value: brain (frontal cortex)

tag: Disease State

value: HIVE


title: HA99-96B


title: T01-439

description: frozen tissue of primary breast tumors

value: Surv(months):37.749; STATUS (0=alive, 1=dead):0


title: HA01-57B


title: VARIATION_LPS_012

status: Public on Oct 22 2005

city: Seattle

first: Mark

middle: M

last: Wurfel

state: WA

address: 300 9th Ave

department: Pulmonary & Critical Care Medicine

institute: University of Washington

hyb_protocol: AFFYMETRIX

scan_protocol: AFFYMETRIX

data_processing: GCRMA

label: BIOTIN

source_name: whole blood

label_protocol: AFFYMETRIX

extract_protocol: RNEASY

treatment_protocol: LPS 10ng/ml 4HRS 37C

tag: TISSUE

value: WHOLE BLOOD

tag: LPS RESPONSE

value: HIGH


title: HA00-13A


title: VARIATION_LPS_010

value: LOW


title: HA01-149B


title: CA01-103A

source_name: Frontal cortex brain tissue from HIVE-control patient

value: HIVE-control


title: CCC103A


title: VARIATION_LPS_008


title: VARIATION_LPS_011

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

label_protocol: Affymetrix

extract_protocol: RNeasy

treatment_protocol: MEDIA 4HRS 37C


title: HA00-13B


title: VARIATION_LPS_009


title: HA01-149A


title: CA01-103B


title: HA98-146A

description: Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox.  (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis.

label: Biotin

tag: Disease state


title: HA01-57A


title: CCC103B


title: HA98-146B


title: VARIATION_LPS_007


title: HA96-61B


title: VARIATION_LPS_006


title: HA96-61A


title: CA99-43B


title: HA96-37B


title: HA96-112A


title: CA96-116A


title: CA96-116B


title: VARIATION_LPS_003


title: HA96-112B


title: HA96-37A


title: VARIATION_LPS_002

source_name: WHOLE BLOOD

treatment_protocol: LPS 10 NG/ML 4HRS 37C

tag: GENDER

value: MALE


title: IPAH PASMC-2, BMP2-treated

status: Public on Oct 21 2005

first: Carmelle

middle: V

last: Remillard

department: Medicine

institute: University of California San Diego

description:
Isolated human pulmonary artery smooth muscle cells (PASMC) from a patient with idiopathic pulmonary hypertensiion (IPAH) were isolated and treated with vehicle + 200nM BMP-2 for 24 hours. RNA was extracted using a Quiagen RNeasy kit and prepared for microarray using the Bioarray High Yield Kit. Targets were produced using standard Affymetrix procedures from total RNA.
BMP2-treated human IPAH PASMC

source_name: human muscle


title: CA95-198B


title: VARIATION_LPS_005


title: VARIATION_LPS_001

source_name: WHOLE BLOOD NO LPS


title: VARIATION_LPS_004


title: CA97-14B


title: IPAH PASMC-1, untreated

description:
Isolated human pulmonary artery smooth muscle cells (PASMC) from a patient with idiopathic pulmonary hypertension (IPAH) were isolated and treated with vehiclefor 24 hours. RNA was extracted using a Quiagen RNeasy kit and prepared for microarray using the Bioarray High Yield Kit. Targets were produced using standard Affymetrix procedures from total RNA.
Untreated human IPAH PASMC


title: CA95-198A


title: IPAH PASMC-2, untreated


title: IPAH PASMC-1, BMP2-treated


title: Normotensive PASMC-2, BMP2-treated

description:
Isolated human pulmonary artery smooth muscle cells (PASMC) from a non-pulmonary hypertensive patient were isolated and treated with vehicle + 200nM BMP-2 for 24 hours. RNA was extracted using a Quiagen RNeasy kit and prepared for microarray using the Bioarray High Yield Kit. Targets were produced using standard Affymetrix procedures from total RNA.
BMP2-treated normotensive human PASMC


title: PMN_gmcsf_18hr_rep1

status: Public on Oct 07 2005

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

description: Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  time indicates time at which transcript levels were analyzed (hours). treatment indicates whether the polymorphonuclear leukocytes were untreated (ctrl or spon) or treated with 100ng/ml GM-CSF (gmcsf).

data_processing: GeneSpring (version 6.1) normalization protocol.  Data Transformation:  Set measurements less than 0.0 to 0.00.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor).  Per Gene:  Normalize to median.

source_name: Human polymorphonuclear (PMN) leukocytes

tag: Human polymorphonuclear leukocytes isolated from blood donated by healthy individuals


title: PMN_gmcsf_24hr_rep2


title: PMN_gmcsf_18hr_rep2


title: PMN_gmcsf_18hr_rep3


title: Normotensive PASMC-1, untreated

description:
Isolated human pulmonary artery smooth muscle cells (PASMC) from a non-pulmonary hypertensive patient were isolated and treated with vehiclefor 24 hours. RNA was extracted using a Quiagen RNeasy kit and prepared for microarray using the Bioarray High Yield Kit. Targets were produced using standard Affymetrix procedures from total RNA.
Untreated normotensive human PASMC


title: PMN_gmcsf_24hr_rep1


title: PMN_gmcsf_24hr_rep3


title: PMN_gmcsf_12hr_rep2


title: CA97-14A


title: PMN_gmcsf_12hr_rep1


title: PMN_gmcsf_12hr_rep3


title: Normotensive PASMC-1, BMP2-treated


title: PMN_gmcsf_6hr_rep1


title: PMN_gmcsf_6hr_rep3


title: PMN_gmcsf_3hr_rep2


title: PMN_gmcsf_6hr_rep2


title: PMN_spon_18hr_rep2


title: PMN_spon_24hr_rep3


title: PMN_spon_12hr_rep1


title: PMN_spon_24hr_rep2


title: PMN_spon_12hr_rep2


title: PMN_spon_24hr_rep1


title: PMN_spon_12hr_rep3


title: PMN_spon_18hr_rep3


title: PMN_spon_18hr_rep1


title: PMN_spon_6hr_rep1


title: PMN_spon_6hr_rep2


title: PMN_spon_6hr_rep3


title: PMN_spon_3hr_rep3


title: PMN_spon_3hr_rep1


title: CA99-43A


title: PMN_spon_3hr_rep2


title: PMN_ctrl_0hr_rep9


title: PMN_ctrl_0hr_rep6


title: PMN_ctrl_0hr_rep7


title: PMN_ctrl_0hr_rep8


title: PMN_ctrl_0hr_rep4


title: PMN_ctrl_0hr_rep2


title: SCARKO d 20

status: Public on Oct 04 2005

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
RNA from 1 testis from three 20 day old Sertoli cell-selective androgen receptor knockout (SCARKO) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor

organism: Mus musculus

source_name: testis


title: PMN_ctrl_0hr_rep1


title: PMN_ctrl_0hr_rep3


title: SCARKO d 12

description:
RNA from 1 testis from three 12 day old Sertoli cell-selective androgen receptor knockout (SCARKO) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: Control d 16

description:
RNA from 1 testis from three 16 day old control (AMHCre) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: PMN_ctrl_0hr_rep5


title: SCARKO d 16

description:
RNA from 1 testis from three 16 day old Sertoli cell-selective androgen receptor knockout (SCARKO) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: Control d 10 (5)

description:
RNA from 1 testis from three 10 day old control (AMHCre) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: SCARKO d 8

description:
RNA from 1 testis from three 8 day old Sertoli cell-selective androgen receptor knockout (SCARKO) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: Control d 12

description:
RNA from 1 testis from three 12 day old control (AMHCre) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: Control d 8

description:
RNA from 1 testis from three 8 day old control (AMHCre) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: PMN_gmcsf_3hr_rep3


title: Skin_PsoriasisFree_N05

status: Public on Oct 01 2005

city: Perth

first: William

middle: D.

last: Kenworthy

address: 90 South Street

department: Centre for Bioinformatics and Biological Computing

country: Australia

institute: Murdoch University

description: Sample was processed using the standard affymetrix protocols.

data_processing: Affymetrix MAS 5.0 software, using normalisation=1 and target=200

label: ENZO kit

source_name: Skin sample from a psoriasis free individual

tag: psoriasis free Japanese individual


title: CLL 21 progressive

status: Public on Sep 14 2005

city: Huddinge

first: Susann

last: Fält

country: Sweden

institute: Karolinska Institutet

description: B-CLL progressive

source_name: Primary lymphocytes


title: CLL 20 progressive

description: B-CLL progressive


title: CLL 17 progressive

description: B-CLL progressive


title: CLL 19 progressive

description: B-CLL progressive


title: CLL 15 progressive

description: B-CLL progressive


title: CLL 16 progressive

description: B-CLL progressive


title: CLL 12 progressive

description: B-CLL progressive


title: CLL 13 progressive

description: B-CLL progressive


title: CLL 14 progressive

description: B-CLL progressive


title: Skin_PsoriasisFree_N02


title: Control_dryseed_Morex_rep2

status: Public on Mar 05 2009

city: Fort Collins

first: Nora

middle: L

last: Lapitan

state: CO

address: Plant Science Bldg

department: Soil and Crop Sciences

institute: Colorado State University

description: Probe synthesis, labeling and hybridization were perfomed according to manufacturer's protocols (Affymetrix, Santa Clara, CA) at the  UCI Microarray Core Facility, Irvine, CA.

hyb_protocol: 10 µg labeled, fragmented cRNA was hybridized at 45°C with rotation for 16 h in an Affymetrix GeneChio Hybridization Oven 320 on Affymetrix Barley1 GeneChip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Different quality control checks were performed including inspection of hybridized images, boxplots and histograms of log2(PM) values, examination of hybridization and PolyA controls.  Based on the results of the quality control screening, some chips were discarded from the analysis.  Twenty-two arrays were retained for further analysis, with two replications per cultivar per time point, with the exception of Harrington day 1, where one of the replicates was discarded. Data analysis was carried out using Bioconductor in R (Gentleman et al. 2004).  Data preprocessing and summarization were performed using Robust Multichip Average (RMA) (Irizarry et al. 2003).

organism: Hordeum vulgare

source_name: Barley seed ungerminated, Morex, Control

label_protocol: The BioArray High-Yield RNA Transcript labeling kit (Enzo Diagnostics) was used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.

growth_protocol: Fifty to 100 g seeds of each variety were micro-malted at Busch Agricultural Resources, LLC, Fort Collins, CO. The micromalting conditions were as follows: steeping at 12°C for 37 h, germination at 12°C for 5 h, 17°C for 65 h, 18°C for 23 h, and kilning stages consisting of  55°C for 10 h, 60°C for 4 h, 68°C for 3 h, 80°C for 2 h and 90°C for 3 h.

extract_protocol: Frozen barley malt was ground and incubated with RNA purification reagent from Invitrogen (Carlsbad, CA) at room temperature for 10 minutes. Total RNA was extracted using Qiagen RNeasy Plant Mini Kit with RNase Free/DNase (Qiagen, Valencia, CA) following the manufacturer's instructions.

treatment_protocol: Samples were frozen in liquid nitrogen and stored at -80°C until use.

tag: Genotype

value: Morex


title: SCARKO d 10 (5)

description:
RNA from 1 testis from three 10 day old Sertoli cell-selective androgen receptor knockout (SCARKO) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: CLL 7 stable

description: B-CLL stable


title: CLL 6 stable

description: B-CLL stable


title: CLL 18 progressive

description: B-CLL progressive


title: CLL 9 stable

description: B-CLL stable


title: CLL 11 stable

description: B-CLL stable


title: CLL 5 stable

description: Stable B-CLL


title: CLL 4 stable

description: Stable B-CLL


title: CLL 1 stable

description: Stable B-CLL


title: Th cells_antiCD3+antiCD28+IL4_2h_replicate 2a (U95Av2)

status: Public on Sep 01 2005

city: Turku

first: Riikka

middle: Johanna

last: Lund

address: Tykistökatu 6 A

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku and Åbo Akademi University

source_name: Cord blood CD4+ cells

tag: CD4+ cells isolated from randomly collected cord bloods of healthy neonates, cells pooled from different individuals


title: Th cells_antiCD3+antiCD28+IL4_6h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12_6h_replicate 2a (U95Av2)


title: CLL 2 stable

description: Stable B-CLL


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_6h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_2h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28_2h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_6h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_2h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28_6h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12_2h_replicate 2a


title: Th cells_no treatment_0h_replicate 2a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_48h_replicate 2b (U95Av2)


title: Th cells_antiCD3+antiCD28+IL4_48h_replicate 2b (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_48h_replicate 2b (U95Av2)


title: PMN_gmcsf_3hr_rep1


title: Th cells_antiCD3+antiCD28+IL12_48h_replicate 2b (U95Av2)


title: Th cells_antiCD3+antiCD28+IL4_48h_replicate 1b (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12_48h_replicate 1b (U95Av2)


title: Th cells_no treatment_0h_replicate 2b (U95Av2)


title: Th cells_no treatment_0h_replicate 1b (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_6h_replicate 1a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL4_2h_replicate 1a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_48h_replicate 1b (U95Av2)


title: Th cells_antiCD3+antiCD28_48h_replicate 2b (U95Av2)


title: Th cells_antiCD3+antiCD28+IL4_6h_replicate 1a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_48h_replicate 1b (U95Av2)


title: Th cells_antiCD3+antiCD28_48h_replicate 1b (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12_2h_replicate 1a (U95Av2)


title: Th cells_antiCD3+antiCD28+IL12_6h_replicate 1a (U95Av2)


title: Th cells_antiCD3+antiCD28_2h_replicate 1a (U95Av2)


title: Th cells_antiCD3+antiCD28_6h_replicate 1a (U95Av2)


title: gastric cancer patient28 censored in prospective phase

status: Public on Mar 04 2009

city: Suita

first: ATSUSHI

last: TAKENO

state: Osaka

address: 2-2, Yamadaoka

department: Surgery

country: Japan

institute: Osaka university

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).

data_processing: In each sample, intensity values for both channels (Cy5 and Cy3) were independently transformed using a quantile equalization method, yielding pairs of normalized values of non-exponential scale. We enforced the normalized values to follow an independent hypothetical standard normal distribution, keeping only the rank within a sample and a chennel. The abundance of transcription for each probe was then defined by subtracting the value of Cy5 from that of Cy3, which are free from dye-sensor bias and can be treated just like the log ratio of Cy5 and Cy3.

source_name: 15 Total RNAs mixture from normal gastric mucosa labeled with Cyanine-3 (green).

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

extract_protocol: Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

treatment_protocol: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.

tag: tissue

value: mixture of normal gastric mucosa

value: primary gastric cancer

tag: phenotype

value: gastric cancer with no recurrence


title: n4t8DIF

city: Bethesda

first: James

last: Shelhamer

state: MD

institute: Clinical Center

description: Cells were treated with Interferon gamma (300 Units) and dexamethasone (100 nanomolar) for 8 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.

source_name: Bronchial epithelial cells in primary culture


title: n2t8DIF


title: n3t8DIF


title: Th cells_no treatment_0h_replicate 1a (U95Av2)


title: n1t8IF

description: Cells were treated with Interferon gamma (300 Units) for 8 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.


title: n2t8IF


title: n3t8IF


title: CLL 8 stable

description: B-CLL stable


title: n1t8DIF


title: Th cells_antiCD3+antiCD28+IL12+TGFbeta_2h_replicate 1a (U95Av2)


title: Control d 20

description:
RNA from 1 testis from three 20 day old control (AMHCre) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: n4t8D

description: Cells were treated with dexamethasone, 100 nanomolar, for 8 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_2h_replicate 1a (U95Av2)


title: n3t8D


title: Th cells_antiCD3+antiCD28+IL4+TGFbeta_6h_replicate 1a (U95Av2)


title: n4t8IF


title: n3t8C

description: Cells were treated with control media for 8 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA


title: n4t8C


title: n2t8D


title: n7t24D

description: Cells were treated with dexamethasone, 100 nanomolar, for 24 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.


title: n1t8C


title: n8t24C

description: Cells were treated with control media for 24 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA


title: n7t24IF

description: Cells were treated with Interferon gamma (300 Units) for 24 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.


title: n8t24IF


title: n7t24DIF

description: Cells were treated with Interferon gamma (300 Units) and dexamethasone (100 nanomolar) for 24 hours.  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.


title: n7t24C


title: n6t24D


title: n2t8C


title: n6t24IF


title: n6t24DIF


title: n6t24C


title: CLL 10 stable

description: B-CLL stable


title: n5t24DIF


title: n8t24DIF


title: CLL 3 stable

description: Stable B-CLL


title: n8t24D


title: n1t8D


title: n5t24D


title: n5t24IF


title: n5t24C


title: n4t24D


title: ciprofibrate at 400 mg/kg/day for 15 days biological replicate 3

status: Public on Aug 23 2005

city: Research Triangle Park

first: Neal

middle: F

last: Cariello

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

institute: GlaxoSmithKline

description: liver from animal 23, treated with 400 mg/kg/day ciprofibrate for 15 days

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0 given here for convenience.  Note that data processing reported in the Toxicological Sciences manuscript was done using Rosetta Resolver and the Rosetta Resolver treated versus control group fold-change and p-value are appended to Series entry.

organism: Macaca fascicularis

source_name: animal 23

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 3 grams from the right lateral liver lobe was flash-frozen in liquid nitrogen.  Total RNA isolated using TRIzol.

tag: male liver


title: n4t24DIF


title: n4t24IF


title: ciprofibrate at 400 mg/kg/day for 15 days biological replicate 2

description: liver from animal 21, treated with 400 mg/kg/day ciprofibrate for 15 days

source_name: animal 21


title: ciprofibrate at 150 mg/kg/day for 15 days biological replicate 3

description: liver from animal 50, treated with 150 mg/kg/day ciprofibrate for 15 days

source_name: animal 50


title: ciprofibrate at 150 mg/kg/day for 15 days biological replicate 4

description: liver from animal 62, treated with 150 mg/kg/day ciprofibrate for 15 days

source_name: animal 62


title: ciprofibrate at 150 mg/kg/day for 15 days biological replicate 2

description: liver from animal 32, treated with 150 mg/kg/day ciprofibrate for 15 days

source_name: animal 32


title: ciprofibrate at 400 mg/kg/day for 15 days biological replicate 4

description: liver from animal 29, treated with 400 mg/kg/day ciprofibrate for 15 days

source_name: animal 29


title: ciprofibrate at 150 mg/kg/day for 15 days biological replicate 1

description: liver from animal 25, treated with 150 mg/kg/day ciprofibrate for 15 days

source_name: animal 25


title: ciprofibrate at 30 mg/kg/day for 15 days biological replicate 4

description: liver from animal 52, treated with 30 mg/kg/day ciprofibrate for 15 days

source_name: animal 52


title: ciprofibrate at 400 mg/kg/day for 15 days biological replicate 1

description: liver from animal 16, treated with 400 mg/kg/day ciprofibrate for 15 days

source_name: animal 16


title: n4t24C


title: ciprofibrate at 30 mg/kg/day for 15 days biological replicate 3

description: liver from animal 41, treated with 30 mg/kg/day ciprofibrate for 15 days

source_name: animal 41


title: ciprofibrate at 30 mg/kg/day for 15 days biological replicate 2

description: liver from animal 35, treated with 30 mg/kg/day ciprofibrate for 15 days

source_name: animal 35


title: ciprofibrate at 30 mg/kg/day for 15 days biological replicate 1

description: liver from animal 39, treated with 30 mg/kg/day ciprofibrate for 15 days

source_name: animal 39


title: vehicle control 15 days biological replicate 3

description: liver from animal 59, treated with vehicle only for 15 days

source_name: animal 59


title: ciprofibrate at 3 mg/kg/day for 15 days biological replicate 3

description: liver from animal 63, treated with 3 mg/kg/day ciprofibrate for 15 days

source_name: animal 63


title: ciprofibrate at 3 mg/kg/day for 15 days biological replicate 1

description: liver from animal 14, treated with 3 mg/kg/day ciprofibrate for 15 days

source_name: animal 14


title: ciprofibrate at 3 mg/kg/day for 15 days biological replicate 4

description: liver from animal 37, treated with 3 mg/kg/day ciprofibrate for 15 days

source_name: animal 37


title: gastric cancer patient33 with relapse free in prospective phase

source_name: 15 Total RNAs mixture from normal gastric mucosa labeled with Cyanine-3 (green).

source_name: gastric cancer patient with relapse free in prospective phase


title: ciprofibrate at 3 mg/kg/day for 15 days biological replicate 2

description: liver from animal 33, treated with 3 mg/kg/day ciprofibrate for 15 days

source_name: animal 33


title: vehicle control 15 days biological replicate 2

description: liver from animal 68, treated with vehicle only for 15 days

source_name: animal 68


title: vehicle control 15 days biological replicate 1

description: liver from animal 57, treated with vehicle only for 15 days

source_name: animal 57


title: ciprofibrate at 400 mg/kg/day for 4 days biological replicate 2

description: liver from animal 30, treated with 400 mg/kg/day ciprofibrate for 4 days

source_name: animal 30


title: Subject 3 Pre allergen challenge

status: Public on Aug 01 2005

city: Richmond

first: Larry

middle: A.

last: Sonna

state: VA

address: 2020-I Timbers Hill Road

institute: Gene Expression Consulting

description: Please refer to Lilly et al., Am J Respir Crit Care Med. 2005 Mar 15;171(6):579-86

hyb_protocol: Per Affymetrix protocol

scan_protocol: Per Affymetrix protocol

data_processing: MAS 5.0

source_name: Bronchial epithelium

label_protocol: Per Affymetrix protocol

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: See online supplement to Lilly et al., Am J Respir Crit Care Med. 2005 Mar 15;171(6):579-86


title: Subject 6 Post allergen challenge

tag: Please refer to Lilly et al., Am J Respir Crit Care Med. 2005 Mar 15;171(6):579-86


title: Subject 5 Pre allergen challenge

description:
Please refer to Lilly et al., Am J Respir Crit Care Med. 2005 Mar 15;171(6):579-86

ALSO NOTE: There is no subject #4 in this series (subject 4 was excluded based on clinical criteria)


title: Subject 6 Pre allergen challenge


title: ciprofibrate at 400 mg/kg/day for 4 days biological replicate 1

description: liver from animal 53, treated with 400 mg/kg/day ciprofibrate for 4 days

source_name: animal 53


title: vehicle control 4 days biological replicate 2

description: liver from animal 31, treated with vehicle only for 4 days

source_name: animal 31


title: Subject 2 Pre allergen challenge


title: Subject 5 Post allergen challenge


title: Subject 1 Post allergen challenge


title: vehicle control 4 days biological replicate 1

description: liver from animal 58, treated with vehicle only for 4 days

source_name: animal 58


title: EECs from normal endometrial epithelium tamoxifen(TAM) rep 2

status: Public on Jul 29 2005

city: Beijing

first: Yongfeng

last: Shang

address: 38 Xue Yuan Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University

description: Data - Arrays were scanned with the GeneArray scanner, and raw data were collected and analyzed using Affymetrix MICROARRAY SUITE and DATA MINING TOOLS software. Mann-Whitney pairwise comparisons were performed to identify genes that were differentially expressed. Genes with concordance exceeding 80.6% in EECs from both stage I and stage II samples were considered statistically significant (P < 0.1).

source_name: normal endometrial epithelium


title: EECs from normal endometrial epithelium control rep 2

data_processing: Data - Arrays were scanned with the GeneArray scanner, and raw data were collected and analyzed using Affymetrix MICROARRAY SUITE and DATA MINING TOOLS software.


title: EECs from normal endometrial epithelium control rep 1


title: Subject 2 Post allergen challenge


title: EECs from normal endometrial epithelium oestrogen(E2) rep 1


title: Subject 3 Post allergen challenge


title: EECs from normal endometrial epithelium oestrogen(E2) rep 2


title: EECs from stage II endometrioid carcinomas tamoxifen(TAM) rep 2

source_name: Endometrial epithelial cells


title: EECs from normal endometrial epithelium tamoxifen(TAM) rep 1


title: Subject 1 Pre allergen challenge


title: EECs from stage II endometrioid carcinomas oestrogen(E2) rep 2


title: EECs from stage II endometrioid carcinomas oestrogen(E2) rep 1


title: EECs from stage II endometrioid carcinomas control rep 2

tag: EECs from stage II endometrioid carcinomas (control) rep 2


title: EECs from stage I endometrioid carcinomas tamoxifen(TAM) rep 2


title: EECs from stage I endometrioid carcinomas control rep 2


title: cHL_2

status: Public on Jul 13 2005

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description:
Mononucleated cells were separated from fresh blood samples by density gradient centrifugation. Subsequently, CD3+ T cells were purified by magnetic beads (Miltenyi Biotec, Bergisch-Gladbach, Germany) using the manufacturer’s protocol (purity >95% with comparable CD4+/CD8+ ratios) followed by total RNA isolation from the TRIzol cell extracts (GIBCO, Karlsruhe, Germany). RNA from 3 donors were pooled.
Keywords = Hodgkin’s Lymphoma
Keywords = T cell
Keywords = immune regulation

source_name: CD3+ T cells from patients with classical Hodgkin´s lymphoma (cHl)


title: Control_2

source_name: CD3+ T cells from healthy volunteers


title: cHL_1


title: EECs from stage I endometrioid carcinomas oestrogen(E2) rep 2


title: Control_1


title: Sarc_1

source_name: CD3+ T cells from patients with sarcoidosis


title: Sarc_2


title: 266D6

status: Public on Jul 04 2005

city: Galveston

first: Allan

last: Brasier

state: TX

address: 301 Univ. Blvd

institute: University Texas Medical Branch

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 6h

source_name: HeLa cell


title: 266D0

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 0h


title: 266D3

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 3h


title: 266C6

description: Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 6h


title: 181C0

description: Hela tet off cells expressing IkBa mutant cultured in absence of Dox, TNF stimulated 0h


title: 220D6


title: 266D1

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 1h


title: 220D1


title: 220D0


title: 266C0

description: Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 0h


title: 220C6


title: 266C3

description: Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 3h


title: 220C1

description: Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 1h


title: 181D0


title: 220C3


title: 220C0


title: 181C6

description: Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 6 h


title: 181D6


title: 266C1


title: 180D0

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 0 h


title: 220D3


title: 181D3


title: 181D1


title: 180D1

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 1 h


title: 180C1

description: Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 1 h


title: 180C3

description: Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 3 h


title: 180C0

description: Cells expressing IkBa dominant negative cultured in absence of dox, no TNF stimulation


title: Skinethic OsM treated for 24h

status: Public on Jun 18 2005

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

description: Normal human keratinocytes treated with OsM

hyb_protocol: Standard Banno et al., J Biol Chem 279(31): 32633-32642.

data_processing: MAS5 GCOS

label: Standard Affymetrix protocol

source_name: Skinethic epidermal substitute Keratinocytes

treatment_protocol: Skinethic keratinocytes in the OsM experiment, controls and OsM-treated

tag: Human foreskin epidermal keratinocytes monocultures grown in 3d on air/liquid interface, allowed to differentiate


title: Skinethic OsM treated for 48h

scan_protocol: Standard Banno et al., J Biol Chem 279(31): 32633-32642.


title: 180D6

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 6 h


title: 180D3

description: Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 3 h


title: Skinethic OsM treated for 7days

label_protocol: Standard Banno et al., J Biol Chem 279(31): 32633-32642.


title: Skinethic OsM 48h Control

growth_protocol: Standard Banno et al., J Biol Chem 279(31): 32633-32642.


title: Skinethic OsM 4h Control

extract_protocol: Standard Banno et al., J Biol Chem 279(31): 32633-32642.


title: Skinethic OsM treated for 1h


title: Skinethic OsM treated for 4h


title: OsM treatment 4h control

source_name: Epidermal Keratinocytes

treatment_protocol: ~70% confluent keratinocytes in the OsM experiment, 1h control, untreated

tag: Human foreskin epidermal keratinocytes


title: Skinethic OsM 7day Control


title: OsM treated for 4h


title: OncostatinM 48h Skinethic replicate


title: OsM treated for 48h


title: Skinethic OsM 1h Control


title: OsM treated for 1h


title: 6.K562C_CEL

status: Public on May 25 2005

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description: Total RNA

source_name: K562 erythroleukemia cells (Human)


title: OncostatinM 4h Skinethic replicate


title: 01.NuGEN_Blank_CEL

description: Water Blank, no RNA input

organism: unidentified

source_name: Water Blank


title: OsM treated for 24h


title: OsM treatment 24h control


title: 5.K562B_CEL

description: Total RNA


title: 4.K562A_CEL

description: Total RNA


title: Skinethic OsM 24h Control


title: 3.SHR_CEL

description: Pool of multiple human derived cell line total RNAs

source_name: Stratagene Universal Human Reference Pool RNA


title: mid-passage add-back LIF

status: Public on May 17 2005

city: Madison

first: Jiang

last: Li

state: WI

address: 777 Highland Ave.

department: School of Pharmacy

institute: University of Wisconsin Madison

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the culture with LIF for 35 wks, withdrawn from LIF for 6 wks, and then reexposed to LIF for 3 days.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells

source_name: human cortical neural stem cells


title: 1.SHR_CEL


title: mid-passage withdraw LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the culture with LIF for 35 wks and then withdrawn from LIF for 6 wks.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: Patient 2023 Mannhiem Responder

status: Public on Apr 18 2005

city: Portland

first: Tom

last: Shi

state: OR

institute: OHSU

description:
The sample is a responder to imatinib treatment and belongs in the validation set from Mannheim.  The sample originated from blood or bone marrow from patient with chronic myelogenous leukemia (CML), before imatinib treatment.  Red blood cells were removed by red cell lysis buffer.  Either guanidine-thiocyanate / phenol-cholorform extraction followed by RNeasy (Leipzig), or cesium chloride-gradient purification (Mannheim) were used to extract total RNA from the patient’s white blood cells.  Labeling and hybridization is done by standard Affymetrix protocols.  Scanning is done by HP GeneArray Scanner and image analysis is carried out by Affymetrix Microarray Suite Software, version 5.0.  Robust Multipchip Analysis (RMA) was used for signal quantification, on Bioconductor (http://www.bioconductor.org).
Keywords = chronic myelogenous leukemia
Keywords = imatinib
Keywords = Gleevec
Keywords = cytogenetic responses
Keywords = Affymetrix

source_name: Peripheral blood from patients with chronic myelogenous leukemia before treatment with imatinib


title: 2.SHR_CEL


title: early-passage long-term LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from 25 wks of culture with a long-term presence of LIF.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: Patient 962 Mannhiem Responder

description:
The sample is a responder to imatinib treatment and belongs in the validation set from Mannheim.  The sample originated from blood or bone marrow from patient with chronic myelogenous leukemia (CML), before imatinib treatment.  Red blood cells were removed by red cell lysis buffer.  Either guanidine-thiocyanate / phenol-cholorform extraction followed by RNeasy (Leipzig), or cesium chloride-gradient purification (Mannheim) were used to extract total RNA from the patient’s white blood cells.  Labeling and hybridization is done by standard Affymetrix protocols.  Scanning is done by HP GeneArray Scanner and image analysis is carried out by Affymetrix Microarray Suite Software, version 5.0.  Robust Multipchip Analysis (RMA) was used for signal quantification, on Bioconductor (http://www.bioconductor.org).
Keywords = chronic myelogenous leukemia
Keywords = imatinib
Keywords = cytogenetic responses
Keywords = Gleevec
Keywords = Affymetrix


title: early-passage withdraw LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the culture with LIF for 25 wks and then withdrawn from LIF for 6 wks.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: Patient 1399 Mannhiem Responder


title: OncostatinM treatment

description:
Normal human keratinocytes treated with OsM
1h timepoint control


title: Patient 92239 Mannheim Non-Responder

description:
The sample is a non-responder to imatinib treatment and belongs in the validation set from Mannheim.  The sample originated from blood or bone marrow from patient with chronic myelogenous leukemia (CML), before imatinib treatment.  Red blood cells were removed by red cell lysis buffer.  Either guanidine-thiocyanate / phenol-cholorform extraction followed by RNeasy (Leipzig), or cesium chloride-gradient purification (Mannheim) were used to extract total RNA from the patient’s white blood cells.  Labeling and hybridization is done by standard Affymetrix protocols.  Scanning is done by HP GeneArray Scanner and image analysis is carried out by Affymetrix Microarray Suite Software, version 5.0.  Robust Multipchip Analysis (RMA) was used for signal quantification, on Bioconductor (http://www.bioconductor.org).
Keywords = chronic myelogenous leukemia
Keywords = imatinib
Keywords = Gleevec
Keywords = cytogenetic responses
Keywords = Affymetrix

source_name: Bone marrow from patients with chronic myelogenous leukemia before treatment with imatinib


title: Late-passage add-back LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the culture with LIF for 53 wks, withdrawn from LIF for 6 wks, and then reexposed to LIF for 3 days.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: mid-passage long-term LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the culture with LIF for 35 wks.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: Patient 2025 Mannhiem Responder


title: Late-passage withdraw LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the culture with LIF for 53 wks and then withdrawn from LIF for 6 wks.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: Patient 1229 Mannhiem Responder


title: Patient 1035D Mannhiem Responder


title: Late-passage long-term LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the 53 wks of culture with a long-term presence of LIF.

Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: Patient 201 Mannhiem Responder


title: early-passage add-back LIF

description:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (6-12 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195).  At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (a total of 25 weeks in vitro supplemented with LIF for the final 10 weeks), mid passage (a total of 35 weeks in vitro supplemented with LIF for the final 20 weeks), and late passage (a total of 53 weeks in vitro supplemented with LIF for the final 38 weeks).
This sample is derived from the culture with LIF for 25 wks, withdraw LIF for 6 wks, and then add LIF back for 3 days.
Keywords = leukemia inhibitory factor
Keywords = neural progenitor
Keywords = neural stem cells


title: Patient 11008 Mannhiem Responder

source_name: Peripheral blood or bone marrow from patients with chronic myelogenous leukemia before treatment with imatinib


title: Patient 2210 Mannheim Non-Responder


title: Patient 2115 Mannheim Non-Responder


title: Patient 1844 Mannheim NonResponder


title: Patient 2028 Mannheim Non-Responder


title: Patient 998 Leipzig Responder

description:
The sample is a responder to imatinib treatment and belongs in the training set from Leipzig.  The sample originated from blood or bone marrow from patient with chronic myelogenous leukemia (CML), before imatinib treatment.  Red blood cells were removed by red cell lysis buffer.  Either guanidine-thiocyanate / phenol-cholorform extraction followed by RNeasy (Leipzig), or cesium chloride-gradient purification (Mannheim) were used to extract total RNA from the patient’s white blood cells.  Labeling and hybridization is done by standard Affymetrix protocols.  Scanning is done by HP GeneArray Scanner and image analysis is carried out by Affymetrix Microarray Suite Software, version 5.0.  Robust Multipchip Analysis (RMA) was used for signal quantification, on Bioconductor (http://www.bioconductor.org).
Keywords = chronic myelogenous leukemia
Keywords = imatinib
Keywords = Gleevec
Keywords = cytogenetic responses
Keywords = Affymetrix


title: Patient 1 Mannheim Non-Responder


title: Patient 1169 Leipzig Responder


title: Patient 316 Leipzig Non-Responder

description:
The sample is a non-responder to imatinib treatment and belongs in the training set from Leipzig.  The sample originated from blood or bone marrow from patient with chronic myelogenous leukemia (CML), before imatinib treatment.  Red blood cells were removed by red cell lysis buffer.  Either guanidine-thiocyanate / phenol-cholorform extraction followed by RNeasy (Leipzig), or cesium chloride-gradient purification (Mannheim) were used to extract total RNA from the patient’s white blood cells.  Labeling and hybridization is done by standard Affymetrix protocols.  Scanning is done by HP GeneArray Scanner and image analysis is carried out by Affymetrix Microarray Suite Software, version 5.0.  Robust Multipchip Analysis (RMA) was used for signal quantification, on Bioconductor (http://www.bioconductor.org).
Keywords = chronic myelogenous leukemia
Keywords = imatinib
Keywords = Gleevec
Keywords = cytogenetic responses
Keywords = Affymetrix


title: Patient 1258 Leipzig Non-Responder


title: Patient 96 Leipzig Responder


title: Patient 67 Leipzig Non-Responder

source_name: Peripheral Blood from patients with chronic myelogenous leukemia before treatment with imatinib


title: Patient 1866 Mannheim Non-Responder


title: RCRL LP FAS

status: Public on Apr 13 2005

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

description:
human SMC resistant to TGF and fas ligand
LP is low passage
FAS is previously selected by fas treatment

source_name: SMC


title: SCRL HP CON

description:
human SMC sensitive to TGF and fas ligand
HP is high passage, CON is unselected for fas ligand


title: Patient 988 Leipzig Responder


title: Patient 70 Leipzig Non-Responder


title: Patient 695 Leipzig Responder


title: RCRL HP FAS

description:
human SMC resistant to TGF and fas ligand
HP is high passage
FAS is previously fas selected


title: Patient 518 Leipzig Responder


title: Patient 40 Leipzig Responder


title: Patient 1290 Leipzig Non-Responder


title: SCRL LP CON

description: human SMC sensitive to TGF and fas ligand


title: Parthenolide-pretreated, 1hr TNFa-treated keratinocytes

status: Public on Apr 06 2005

description:
~70% confluent keratinocytes in the TNFa experiment, parthenolide-pretreated, then 1h treated with TNFa
Keywords = Epidermis Keratinocytes TNFa Inflammation
Keywords = NFkB

source_name: Keratinocytes


title: Parthenolide-pretreated, 24hr TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, parthenolide-pretreated, then 24h treated with TNFa
Keywords = Epidermis Keratinocytes TNFa Inflammation
Keywords = NFkB


title: 24hr TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 24h treated
Keywords = Epidermis Keratinocytes TNFa Inflammation


title: Parthenolide-pretreated, 48hr TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, parthenolide-pretreated, then 48h treated with TNFa
Keywords = Epidermis Keratinocytes TNFa Inflammation
Keywords = NFkB


title: 4hr TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 4h treated
Keywords = Epidermis Keratinocytes TNFa Untreated


title: Repeat 48hr control for TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 48h control, untreated
Keywords = Epidermis Keratinocytes TNFa Untreated


title: Repeat 24hr control for TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 24h control, untreated
Repeated chip

Keywords = Epidermis Keratinocytes TNFa Untreated


title: 48hr control for TNFa-treated keratinocytes


title: 1hr TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 1h treated
Keywords = Epidermis Keratinocytes TNFa Untreated


title: 24hr control for TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 24h control, untreated
Keywords = Epidermis Keratinocytes TNFa Untreated


title: lin-CD34+ II replicate

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description:
HSC CD34+ lineage negative purified from peripheral blood;
To obtain PB HSC cells, 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10   g/kg/d for 5 6 d. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). Haematopoietic stem cell purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.
Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).
MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin  cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34  cell population. Aliquots of sorted Lin  CD34+ and Lin  CD34  cells, were reanalysed by FacScan to assess their purities, which were 98·5 ± 0·7% and 99·8 ± 0·1% respectively.Contamination of CD34+ cells in the CD34  cell population was ruled out by reverse transcription-polymerase chain reaction (RT-PCR) for CD34 mRNA .

Keywords = lin-CD34-
Keywords = HSC
Keywords = hemopoietic stem cells

source_name: lin-CD34+ HSC


title: Repeat 4hr control for TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 4h control, untreated
Repeated chip

Keywords = Epidermis Keratinocytes TNFa Untreated


title: Patient 481 Leipzig Responder

description:
The sample is a responder to imatinib treatment and belongs in the training set from Leipzig.  The sample originated from blood or bone marrow from patient with chronic myelogenous leukemia (CML), before imatinib treatment.  Red blood cells were removed by red cell lysis buffer.  Either guanidine-thiocyanate / phenol-cholorform extraction followed by RNeasy (Leipzig), or cesium chloride-gradient purification (Mannheim) were used to extract total RNA from the patient’s white blood cells.  Labeling and hybridization is done by standard Affymetrix protocols.  Scanning is done by HP GeneArray Scanner and image analysis is carried out by Affymetrix Microarray Suite Software, version 5.0.  Robust Multipchip Analysis (RMA) was used for signal quantification, on Bioconductor (http://www.bioconductor.org).
Keywords = chronic myelogenous leukemia
Keywords = imatinib
Keywords = Gleevec
Keywords = cytogenetic responses
Keywords = Affymetrix


title: Lin-CD34- II replicate

description:
HSC CD34- lineage negative purified from peripheral blood.
To obtain PB HSC cells, 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10   g/kg/d for 5 6 d. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). Haematopoietic stem cell purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.
Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).
MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin  cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34  cell population. Aliquots of sorted Lin  CD34+ and Lin  CD34  cells, were reanalysed by FacScan to assess their purities, which were 98·5 ± 0·7% and 99·8 ± 0·1% respectively.Contamination of CD34+ cells in the CD34  cell population was ruled out by reverse transcription-polymerase chain reaction (RT-PCR) for CD34 mRNA .

Keywords = lin-CD34-
Keywords = HSC
Keywords = hemopoietic stem cells

source_name: Lin-CD34- HSC


title: 4hr control for TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 4h control, untreated
Keywords = Epidermis Keratinocytes TNFa Untreated


title: Repeat 1hr control for TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 1h control, untreated
Repeated chip
Keywords = Epidermis Keratinocytes TNFa Untreated


title: lin-CD34- I replicate

description:
HSC CD34- lineage negative purified from peripheral blood.
To obtain PB HSC cells, 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10   g/kg/d for 5 6 d. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). Haematopoietic stem cell purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.
Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).
MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin  cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34  cell population. Aliquots of sorted Lin  CD34+ and Lin  CD34  cells, were reanalysed by FacScan to assess their purities, which were 98·5 ± 0·7% and 99·8 ± 0·1% respectively.Contamination of CD34+ cells in the CD34  cell population was ruled out by reverse transcription-polymerase chain reaction (RT-PCR) for CD34 mRNA .
Keywords = lin-CD34-
Keywords = HSC
Keywords = hemopoietic stem cells

source_name: lin-CD34- HSC


title: Lin-CD34+ I replicate

description:
HSC CD34+ lineage negative purified from peripheral blood.
To obtain PB HSC cells, 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10   g/kg/d for 5 6 d. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). Haematopoietic stem cell purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.
Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).
MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin  cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34  cell population. Aliquots of sorted Lin  CD34+ and Lin  CD34  cells, were reanalysed by FacScan to assess their purities, which were 98·5 ± 0·7% and 99·8 ± 0·1% respectively.Contamination of CD34+ cells in the CD34  cell population was ruled out by reverse transcription-polymerase chain reaction (RT-PCR) for CD34 mRNA .

Keywords = lin-CD34+
Keywords = HSC
Keywords = hemopoietic stem cells

source_name: Lin-CD34+ HSC


title: 1hr control for TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 1h control, untreated
Keywords = Epidermis Keratinocytes TNFa Untreated


title: lin+CD34+ II replicate

description:
CD34+ lineage positive progenitors cells purified from peripheral blood.
To obtain PB progenitor cells, 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10   g/kg/d for 5 6 d. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). Haematopoietic progenitor purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.
Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).
CD34+ cells were highly purified by MiniMacs high-gradient magnetic separation column (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer's instructions. To assess the percentage of CD34+ elements, aliquots of the CD34+ target cells were restained with an antibody (HPCA-2; IgG1a-fluorescein isothiocyanate [FITC]; Becton Dickinson, San Jose, CA) directed at a different epitope of CD34 antigen than that (QBend10) used with the MiniMacs system. Briefly, CD34+ cells were incubated for 30 minutes in the dark at 4°C with HPCA-2-FITC. Propidium iodide (2 µg/mL) was added for the detection of nonviable cells, which were excluded from analysis. After two washes in PBS/BSA, flow cytometric analysis was performed on a gated population set on scatter properties by using FACScan equipment (Becton Dickinson). A minimum of 10,000 events was collected in list mode on FACScan software.  (Lemoli et al, 1997). The percentages of CD34+ cells in PB samples were 1·6±1%, and 0·9±0·3% of the MNC fraction respectively. After magnetic separation, the percentages of CD34+ in PB samples were 95±5%.

Keywords = lin+CD34+
Keywords = hemopoietic progenitors cells

source_name: lin+CD34+ progenitor cells


title: lin+CD34+ I replicate

description:
CD34+ lineage positive hemopoietic progenitors purified from peripheral blood.
To obtain PB progenitor cells, 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10   g/kg/d for 5 6 d. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). Haematopoietic progenitor purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.
Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).
CD34+ cells were highly purified by MiniMacs high-gradient magnetic separation column (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer's instructions. To assess the percentage of CD34+ elements, aliquots of the CD34+ target cells were restained with an antibody (HPCA-2; IgG1a-fluorescein isothiocyanate [FITC]; Becton Dickinson, San Jose, CA) directed at a different epitope of CD34 antigen than that (QBend10) used with the MiniMacs system. Briefly, CD34+ cells were incubated for 30 minutes in the dark at 4°C with HPCA-2-FITC. Propidium iodide (2 µg/mL) was added for the detection of nonviable cells, which were excluded from analysis. After two washes in PBS/BSA, flow cytometric analysis was performed on a gated population set on scatter properties by using FACScan equipment (Becton Dickinson). A minimum of 10,000 events was collected in list mode on FACScan software.  (Lemoli et al, 1997). The percentages of CD34+ cells in PB samples were 1·6±1%, and 0·9±0·3% of the MNC fraction respectively. After magnetic separation, the percentages of CD34+ in PB samples were 95±5%.

Keywords = lin+CD34+
Keywords = hemopoietic progenitors cells

source_name: lin+CD34+ progenitors cells


title: PEL-8

status: Public on Apr 04 2005

first: Katia

last: Basso

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description: Primary effusion lymphoma cells were isolated and frozen as viable cells. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Primary effusion lymphoma


title: PEL-6


title: PEL-9


title: PEL-4


title: 48hr TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, 48h treated
Keywords = Epidermis Keratinocytes TNFa Inflammation


title: PEL-3


title: PEL-2


title: MCL-22

description: Mantle cell lymphoma biopsy was digested and single cells suspension was frozen as viable cells. CD19-positive cells were later purified by magnetic cell separation. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Mantle cell lymphoma


title: MCL-26


title: PEL-5


title: PEL-1


title: MCL-24


title: MCL-25


title: MCL-19


title: HCL 14 PB

description: CD19-positive cells were purified by magnetic cell separation from mononucleated cells from peripheral blood of hairy cell leukemia patients. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Hairy cell leukemia


title: HCL 15 PB


title: MCL-17


title: HCL 07 PB


title: Parthenolide-pretreated, 4hr TNFa-treated keratinocytes

description:
~70% confluent keratinocytes in the TNFa experiment, parthenolide-pretreated, then 4h treated with TNFa
Keywords = Epidermis Keratinocytes TNFa Inflammation
Keywords = NFkB


title: MCL-16


title: HCL15

description: Hairy cell leukemia bone marrow biopsy. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.


title: HCL12


title: PEL-7


title: HCL02


title: HCL05


title: HCL01


title: HCL 13 PB

description: Mononucleated cells from peripheral blood of hairy cell leukemia patients. The leukemic cells represents approximately 80% of the peripheral blood cells. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.


title: HCL 10


title: HCL 14(A)


title: HCL 09


title: HCL 08


title: HCL 11


title: MCL-18


title: DLCL-33

description: Diffuse large B cell lymphoma biopsy was digested and single cells suspension was frozen as viable cells. CD19 positive cells were later purified by magnetic cell separation. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Diffuse large B cell lymphoma


title: DLCL-4068


title: DLCL-28


title: DLCL31


title: HCL06


title: HCL 04

description: Hairy cell leukemia splenic biopsy was digested and suspension cells were frozen as viable cells. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.


title: DLCL34


title: DLCL-1155


title: DLCL-36


title: DLBCL-IB-7

description: Diffuse Large B cell lymphoma biopsy. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.


title: DLCL-826


title: DLBCL-IB-4


title: DLCL30


title: DLBCL-IB-5


title: DLBCL-IB-8


title: DLBCL-IB-3


title: DLBCL-IB-2


title: DLBCL-IB-6


title: DLBCL-CB-21


title: DLBCL-CB-7


title: DLBCL-CB-9


title: DLBCL-CB-3


title: DLBCL-IB-1


title: DLBCL-CB-20


title: DLBCL-CB-22


title: DLBCL-CB-8


title: DLBCL-CB-5


title: DLBCL-CB-23


title: DLBCL-CB-6


title: DLBCL-CB-4


title: DLBCL-CB-2


title: DLBCL-CB-19


title: DLBCL-CB-17


title: DLBCL-CB-18


title: DLBCL-CB-15


title: DLBCL-CB-16


title: DLBCL-CB-14


title: DLBCL-CB-13


title: DLBCL-CB-1


title: AIDS-DLBCL-IB-1

description: Diffuse Large B cell lymphoma (immunoblastic type) biopsy from HIV+ patient. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Diffuse large B cell lymphoma (immunoblastic type)


title: DLBCL-CB-10


title: AIDS-DLBCL-IB-3


title: DLBCL-CB-12


title: AIDS-DLBCL-CB-4

description: Diffuse Large B cell lymphoma (centroblastic type) biopsy from HIV+ patient. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Diffuse large B cell lymphoma (centroblastic type)


title: AIDS-DLBCL-IB-2


title: AIDS-DLBCL-CB-1


title: DLBCL-CB-11


title: BL-6

description: Burkitt-like lymphoma biopsy. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Burkitt-like lymphoma


title: AIDS-DLBCL-IB-4


title: AIDS-DLBCL-CB-3


title: BL-2


title: BL-5


title: BL-4


title: AIDS-BL-7

description: Burkitt lymphoma biopsy from HIV+ patient. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Burkitt lymphoma biopsy


title: BL-3


title: AIDS-DLBCL-CB-2


title: AIDS-BL-6


title: AIDS-BL-5


title: AIDS-DLBCL-CB-5


title: AIDS-BL-4


title: AIDS-BL-2


title: MM-JJN3

description: Multiple myeloma cell line. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

source_name: JJN3 cell line


title: MM-SKMM1

source_name: SKMM1 cell line


title: Myc.BCvector-5

description: "Lymphoblastoid cell line, conditional EBV mutant by expression of ER-EBNA2 chimeric fusion protein.  It has been engineered with tetracycline repressed expression vector. Cells were coltured in absence of  tetracycline and of estrogen for 24h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol."

source_name: EREB-TC


title: Myc.BCvector-7


title: AIDS-BL-1


title: MM-SKMM2

source_name: SKMM2 cell line


title: Cord 1193

description: CD19-positive B-cells purified by magnetic cell separation from cord blood. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

source_name: Cord blood B-cells


title: B.Myc.11

description: "Lymphoblastoid cell line, conditional EBV mutant by expression of ER-EBNA2 chimeric fusion protein.  It has been engineered with tetracycline repressed MYC expression vector. Cells were coltured in presence of  tetracycline [1ug/ml]  and absence of estrogen for 24h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol."

source_name: EREB-TCMYC


title: Myc.BCvector-4


title: AIDS-BL-3


title: B.Myc.12


title: B.Myc.9


title: MM-F24

source_name: F24 cell line


title: Myc.BCvector-6


title: Cord 1171


title: Myc.BCvector-2


title: B.Myc.8


title: B.Myc.7


title: BL-1


title: B.Myc.5

description: "Lymphoblastoid cell line, conditional EBV mutant by expression of ER-EBNA2 chimeric fusion protein.  It has been engineered with tetracycline repressed MYC expression vector. Cells were coltured in absence of tetracycline and estrogen for 24h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol."


title: B.Myc.6


title: B.Myc.4


title: B.Myc.3


title: B.Myc.1


title: Mutu type-I

description: Burkitt lymphoma cell line. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol

source_name: MUTU cell line


title: ODH type-III

description: Type III Burkitt lymphoma cell line. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol

source_name: ODH III cell line


title: Mutu type-III

source_name: MUTU III cell line


title: LY8

description: Diffuse large B cell lymphoma cell line. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol

source_name: Ly8 cell line


title: KEM type-I

source_name: KEM cell line


title: B.Myc.10


title: ODH type-I

source_name: ODH cell line


title: 108 40LBCR2

description: Burkitt lymphoma cell line infected with the PINCO vector. Co-Colture for 8 h with NIH3T3 fbroblasts expressing CD40L and treatment with anti-IgM [10 ug/ml]. Treatment was followed by CD19+ magnetic cell sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

source_name: Ramos(pinco) cell line clone #2


title: 105 40LBCR1

source_name: Ramos(pinco) cell line clone #1


title: 104 40LBCR1


title: KEM type-III

source_name: KEM III cell line


title: 102EVBCR2

description: Burkitt lymphoma cell line infected with the PINCO vector. Co-Colture for 8 h with NIH3T3 fbroblasts and treatment with anti-IgM [10 ug/ml]. Treatment was followed by CD19+ magnetic cell sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 103 40LBCR1


title: 106 40LBCR2


title: LY3

source_name: Ly3 cell line


title: 107 40LBCR2


title: B.Myc.2


title: 101EVBCR2


title: 98EVBCR1


title: 99EVBCR1


title: 96cl240L

description: Burkitt lymphoma cell line infected with the PINCO vector. Co-Colture for 8 h with NIH3T3 fbroblasts expressing CD40L and subsequent CD19+ magnetic sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 100EVBCR2


title: 94cl240L


title: 92cl140L


title: 93cl140L


title: 88cl2EV

description: Burkitt lymphoma cell line infected with the PINCO vector. Co-Colture for 8 h with NIH3T3 fbroblasts and subsequent CD19+ magnetic sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 90cl2EV


title: 91cl140L


title: 87cl1EV


title: 89cl2EV


title: 95cl240L


title: 82 EMT B6-A

description: "Lymphoblastoid cell line, conditional EBV mutant by expression of ER-EBNA2 chimeric fusion protein.  It has been engineered with mt-BCL6 conditional expression vector. Cells were treated with CdCl2 [5 uM] for 12 h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol."


title: 80 EMT B6-A


title: 84emt b6-A


title: 77 EMT-A

description: "Lymphoblastoid cell line, conditional EBV mutant by expression of ER-EBNA2 chimeric fusion protein.  It has been engineered with metallothionein conditional expression vector. Cells were treated with CdCl2 [5 uM] for 12 h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol."

source_name: EREBmT


title: 85cl1EV


title: 97EVBCR1


title: 83 EMT B6-A


title: 81 EMT B6-A


title: 86cl1EV


title: 74 EMT-A


title: 75 EMT-A


title: 78 EMT-A


title: 76 EMT-A


title: 79 EMT B6-A


title: 73 EMT-A


title: 66D40L27

description: Burkitt lymphoma cell line engineered for the expression of BCL6 PEST deletion mutant. Co-Colture for 24 h with NIH3T3 fbroblasts expressing CD40L and subsequent CD19+ magnetic sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

source_name: Ramos(pinco BCL6DPEST) cell line clone #27


title: 71D40L30

source_name: Ramos(pinco BCL6DPEST) cell line clone #30


title: 72D40L30


title: 68DEV30

description: Burkitt lymphoma cell line engineered for the expression of BCL6 PEST deletion mutant. Co-Colture for 24 h with NIH3T3 fbroblasts and subsequent CD19+ magnetic sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 67DEV30


title: 69DEV30


title: 70D40L30


title: 64D40L27


title: 65D40L27


title: 62DEV27


title: 63DEV27


title: 5740L1

description: Burkitt lymphoma cell line infected with the PINCO vector. Co-Colture for 24 h with NIH3T3 fbroblasts expressing CD40L and subsequent CD19+ magnetic cell sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 6040L2


title: 58B40L2


title: 61DEV27


title: 5540L1


title: 5940L2


title: 5640L1


title: 50EV1

description: Burkitt lymphoma cell line infected with the PINCO vector. Co-Colture for 24 h with NIH3T3 fbroblasts and subsequent CD19+ magnetic sorting. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 51EV1


title: 52EV2


title: 46UT8h

description: Burkitt lymphoma cell line infected with the PINCO vector and treated  with anti-IgM antibodies [10 ug/ml] for 8 h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 43UT8h

description: Burkitt lymphoma cell line infected with the PINCO vector and coltured for 8 h without simuli. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 53EV2


title: 45UT8h


title: 48UT8h


title: 44UT8h


title: 40DBCR8h

description: BL cell line engineered for the expression of BCL6 PEST deletion mutant. Treatment with anti-IgM antibodies [10 ug/ml] for 8 h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 42DBCR8h


title: 47ut8h


title: 38DUT8h

description: BL cell line engineered for the expression of BCL6 PEST deletion mutant. Coltured without stimuli for 8 h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.


title: 49EV1


title: 41DBCR8h


title: 37DUT8h


title: 39DUT8h


title: 34DUT8h


title: 33DUT8h


title: 36DUT8h


title: 35DUT8h


title: 31DUT8h


title: 27DBCR8h


title: 30DBCR8h


title: 54EV2


title: 28DBCR8h


title: 32DUT8h


title: 24BCR8h


title: 26DBCR8h


title: 22BCR8h


title: 21BCR8h


title: 25DBCR8h


title: 20BCR8h


title: 29DBCR8h


title: 19BCR8h


title: 18UT8h


title: 14UT8h


title: 13UT8h


title: 16UT8h


title: 17UT8h


title: 23BCR8h


title: 8aCD4O24h

description: Burkitt lymphoma cell line stimulated with anti-CD40 antibodies [5ug/ml] from G28-5 hybridomas for 24 h. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

source_name: Ramos cell line


title: 7aCD4O24h


title: 9aCD4O24h


title: V0632

status: Public on Apr 01 2005

city: Vienna

first: Stratowa

last: Christian

address: Dr. Boehringergasse 5-11

department: Dept NCE Lead Discovery

country: Austria

institute: Boehringer Ingelheim Austria

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av3
Sample type is Control sample
Gender is unknown
Chromosomal aberrations is n.a.
IgV mutation status is n.a.

source_name: Peripheral blood lymphocytes


title: 15UT8h


title: V0629

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is Control sample
Gender is unknown
Chromosomal aberrations is n.a.
IgV mutation status is n.a.


title: V0630


title: V0628


title: V0631


title: V0633


title: V0570

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is F
Chromosomal aberrations is 17p
IgV mutation status is unmutated


title: V0627


title: V0527

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is F
Chromosomal aberrations is 13q,12q,t14
IgV mutation status is mutated


title: V0530

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is F
Chromosomal aberrations is none
IgV mutation status is mutated


title: V0529

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is none
IgV mutation status is mutated


title: V0523

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is 13q
IgV mutation status is mutated


title: V0568

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is 11q
IgV mutation status is unmutated


title: V0571

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is 17p
IgV mutation status is unmutated


title: V0522

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is F
Chromosomal aberrations is 13q,6q
IgV mutation status is mutated


title: V0524


title: V0520

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is 13q,11q
IgV mutation status is unmutated


title: V0569


title: V0573

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is 17p
IgV mutation status is mutated


title: V0528

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is none
IgV mutation status is unmutated


title: V0526

description:
Mononuclear cells were isolated using Ficoll gradient. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. The MAS5 algorithm as implemented in the Bioconductor package simpleaffy_2.10 was used to convert raw data to expression values and detection calls.
Chip type is HG-U95Av2
Sample type is B-CLL sample
Gender is M
Chromosomal aberrations is 12q
IgV mutation status is unmutated