title: beta-TC3 cells, 01-hr treatment, 4.1uM, BRD-K90919562, Replicate1, Batch_08, HTA3_H04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 4.1uM, BRD-K90919562, Replicate3, Batch_04, HTA6_C02

status: Public on Mar 09 2012

type: RNA

city: Cambridge

first: Paul

middle: A

last: Clemons

state: MA

address: 7 Cambridge Center

department: Chemical Biology Program

country: USA

institute: Broad Institute of Harvard and MIT

description: beta-TC3 cells

hyb_protocol: The biotinylated cRNA targets were normalized, fragmented and hybridized to Affymetrix HT Mouse 430 A peg arrays (Affymetrix 901045). The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: Expression data (in the form of CEL files) from eight 96-well Affymetrix HT_MG-430A arrays was background corrected, normalized and summarized with RMA using GenePattern.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: beta-TC3 cells

label_protocol: 1 µg of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688). Total RNA was first reverse transcribed using a T7-Oligo(dT) promoter primer in the first strand cDNA synthesis reaction. Following RNAse H-mediated second strand cDNA synthesis, the double-stranded cDNA was purified and served as a template for an in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for cRNA amplification and biotin labeling.

growth_protocol: Cell lines αTC1 and βTC3 were cultured in low-glucose DMEM supplemented by 10% FBS, 10 U/ml penicillin and 50 µg/ml streptomycin. 24 h prior to compound treatment, 3 mio. cells were plated per well in a 6-well plate in 1 ml medium.

extract_protocol: RNA was prepared using Qiagen RNeasy kits according to the manufacturer’s protocol.

treatment_protocol: Compounds dissolved at 1000-fold the profiling concentration in DMSO were diluted 1:10 with media and 10 µl were added per well. At the indicated time point (1, 6, 24 h, respectively), cells were lysed in 900 µl buffer RLT (Qiagen) by shaking for 30s, and lysates were immediately frozen in liquid nitrogen.

tag: cell line

tag: treatment


title: beta-TC3 cells, 01-hr treatment, 4.1uM, BRD-K90919562, Replicate2, Batch_10, HTA2_G01

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 5uM, BRD-K22912318, Replicate3, Batch_04, HTA6_G08

description: beta-TC3 cells

value: 6 hrs with 5uM, BRD-K22912318


title: beta-TC3 cells, 01-hr treatment, 3.2uM, BRD-K92415738, Replicate3, Batch_04, HTA9_H11

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 3.2uM, BRD-K92415738, Replicate1, Batch_10, HTA2_F01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 5uM, BRD-K22912318, Replicate1, Batch_04, HTA6_B01

description: beta-TC3 cells

value: 1 hr with 5uM, BRD-K22912318


title: beta-TC3 cells, 01-hr treatment, 5uM, BRD-K22912318, Replicate2, Batch_10, HTA2_B06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.4uM, apicidin, Replicate3, Batch_04, HTA6_A12

description: beta-TC3 cells

value: 1 hr with 1.4uM, apicidin


title: beta-TC3 cells, 01-hr treatment, 5uM, BRD-K22912318, Replicate3, Batch_08, HTA3_A08

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.4uM, apicidin, Replicate1, Batch_06, HTA8_E06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 3.7uM, BRD-K62233722, Replicate3, Batch_05, HTA7_A04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 4.3uM, BRD-K17311666, Replicate2, Batch_08, HTA9_F01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 3.2uM, BRD-K92415738, Replicate2, Batch_08, HTA9_H01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 3.7uM, BRD-K62233722, Replicate2, Batch_04, HTA6_A11

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 3.7uM, BRD-K62233722, Replicate1, Batch_06, HTA5_C02

description: beta-TC3 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_10, HTA2_F12

description: alpha-TC1 cells

source_name: alpha-TC1 cells

value: 24 hrs with DMSO-control


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_08, HTA3_C06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_10, HTA2_A03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_04, HTA6_H02

description: alpha-TC1 cells


title: beta-TC3 cells, 01-hr treatment, 1.7uM, chaetocin, Replicate3, Batch_04, HTA6_B05

description: beta-TC3 cells

value: 1 hr with 1.7uM, chaetocins


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_06, HTA5_G08

description: alpha-TC1 cells


title: beta-TC3 cells, 01-hr treatment, 1.7uM, chaetocin, Replicate2, Batch_05, HTA7_B10

description: beta-TC3 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_08, HTA2_B08

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_06, HTA4_C05

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_09, HTA9_A06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_07, HTA3_G11

description: alpha-TC1 cells


title: beta-TC3 cells, 01-hr treatment, 1.4uM, apicidin, Replicate2, Batch_05, HTA7_A08

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 4.3uM, BRD-K17311666, Replicate1, Batch_10, HTA2_A04

description: beta-TC3 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_07, HTA1_B01

description: alpha-TC1 cells


title: beta-TC3 cells, 01-hr treatment, 4.3uM, BRD-K17311666, Replicate3, Batch_04, HTA6_A06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.7uM, chaetocin, Replicate1, Batch_06, HTA4_F07

description: beta-TC3 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_09, HTA2_F03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_05, HTA7_E04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_05, HTA3_G09

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, DMSO-control, Batch_04, HTA7_H03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 2.4uM, PXD101, Replicate3, Batch_09, HTA9_B12

description: alpha-TC1 cells

value: 24 hrs with 2.4uM, PXD101


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD9773, Replicate3, Batch_09, HTA9_A03

description: alpha-TC1 cells

value: 24 hrs with 10uM, BRD9773


title: alpha-TC1 cells, 24-hr treatment, 3uM, BRD-A94377914, Replicate1, Batch_07, HTA4_G09

description: alpha-TC1 cells

value: 24 hrs with 3uM, BRD-A94377914


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD8451, Replicate3, Batch_08, HTA3_D09

description: alpha-TC1 cells

value: 24 hrs with 10uM, BRD8451


title: alpha-TC1 cells, 24-hr treatment, 0.91uM, BRD6929, Replicate2, Batch_09, HTA9_E11

description: alpha-TC1 cells

value: 24 hrs with 0.91uM, BRD6929


title: alpha-TC1 cells, 24-hr treatment, 3uM, BRD-A94377914, Replicate3, Batch_08, HTA9_E08

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, AMI-1, Replicate3, Batch_07, HTA4_A11

description: alpha-TC1 cells

value: 24 hrs with 10uM, AMI-1


title: alpha-TC1 cells, 24-hr treatment, 10uM, AMI-1, Replicate2, Batch_09, HTA3_F12

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD8451, Replicate1, Batch_09, HTA9_G06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 2.4uM, PXD101, Replicate2, Batch_07, HTA4_D08

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, AMI-1, Replicate1, Batch_08, HTA4_C06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD9773, Replicate2, Batch_08, HTA3_B10

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD9773, Replicate1, Batch_07, HTA3_C01

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD5298, Replicate2, Batch_08, HTA8_B10

description: alpha-TC1 cells

value: 24 hrs with 10uM, BRD5298


title: alpha-TC1 cells, 24-hr treatment, 0.91uM, BRD6929, Replicate1, Batch_07, HTA8_C07

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD5298, Replicate3, Batch_09, HTA3_G04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, pyroxamide, Replicate3, Batch_09, HTA9_B04

description: alpha-TC1 cells

value: 24 hrs with 10uM, pyroxamide


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD8451, Replicate2, Batch_07, HTA4_G11

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 3uM, BRD-A94377914, Replicate2, Batch_09, HTA3_G05

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BRD5298, Replicate1, Batch_07, HTA8_H07

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, pyroxamide, Replicate2, Batch_07, HTA9_E01

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.91uM, BRD6929, Replicate3, Batch_08, HTA4_C11

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 2.4uM, PXD101, Replicate1, Batch_08, HTA1_C04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, pyroxamide, Replicate1, Batch_08, HTA8_G02

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, ITF-2357, Replicate3, Batch_08, HTA4_G06

description: alpha-TC1 cells

value: 24 hrs with 10uM, ITF-2357


title: alpha-TC1 cells, 24-hr treatment, 1.5uM, CRA-024781, Replicate2, Batch_09, HTA3_D03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, 5-azadeoxycytidine, Replicate3, Batch_07, HTA4_D06

description: alpha-TC1 cells

value: 24 hrs with 10uM, 5-azadeoxycytidine


title: alpha-TC1 cells, 24-hr treatment, 10uM, RG-0108, Replicate3, Batch_07, HTA8_B12

description: alpha-TC1 cells

value: 24 hrs with 10uM, RG-0108


title: alpha-TC1 cells, 24-hr treatment, 1.5uM, CRA-024781, Replicate1, Batch_07, HTA3_F04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.5uM, CRA-024781, Replicate3, Batch_08, HTA1_C01

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, 5-azadeoxycytidine, Replicate2, Batch_09, HTA9_A05

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BIX-01294, Replicate3, Batch_06, HTA4_A04

description: alpha-TC1 cells

value: 24 hrs with 10uM, BIX-01294


title: alpha-TC1 cells, 24-hr treatment, 10uM, RG-0108, Replicate2, Batch_09, HTA9_H09

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, ITF-2357, Replicate2, Batch_07, HTA8_B05

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, zebuarine, Replicate1, Batch_09, HTA3_A07

description: alpha-TC1 cells

value: 24 hrs with 10uM, zebuarine


title: alpha-TC1 cells, 24-hr treatment, 10uM, 5-azadeoxycytidine, Replicate1, Batch_08, HTA9_C10

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, zebuarine, Replicate2, Batch_08, HTA1_E02

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.22uM, trichostatin A, Replicate3, Batch_06, HTA5_H03

description: alpha-TC1 cells

value: 24 hrs with 0.22uM, trichostatin A


title: alpha-TC1 cells, 24-hr treatment, 10uM, zebuarine, Replicate3, Batch_07, HTA1_A08

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.12uM, HC-toxin, Replicate2, Batch_06, HTA5_G12

description: alpha-TC1 cells

value: 24 hrs with 0.12uM, HC-toxin


title: alpha-TC1 cells, 24-hr treatment, 0.22uM, trichostatin A, Replicate2, Batch_05, HTA1_G07

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.22uM, trichostatin A, Replicate1, Batch_07, HTA1_F06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.12uM, HC-toxin, Replicate1, Batch_07, HTA1_F08

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, BIX-01294, Replicate2, Batch_09, HTA9_D10

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 2uM, scriptaid, Replicate2, Batch_06, HTA5_G10

description: alpha-TC1 cells

value: 24 hrs with 2uM, scriptaid


title: alpha-TC1 cells, 24-hr treatment, 0.015uM, LBH-589, Replicate3, Batch_04, HTA4_A12

description: alpha-TC1 cells

value: 24 hrs with 0.015uM, LBH-589


title: alpha-TC1 cells, 24-hr treatment, 10uM, BIX-01294, Replicate1, Batch_07, HTA1_F04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 2uM, scriptaid, Replicate1, Batch_05, HTA7_E01

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.12uM, HC-toxin, Replicate3, Batch_05, HTA7_D12

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, RG-0108, Replicate1, Batch_08, HTA8_H05

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.015uM, LBH-589, Replicate2, Batch_06, HTA4_E03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 0.015uM, LBH-589, Replicate1, Batch_05, HTA9_G08

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.1uM, MGCD-0103, Replicate3, Batch_04, HTA6_G01

description: alpha-TC1 cells

value: 24 hrs with 1.1uM, MGCD-0103


title: alpha-TC1 cells, 24-hr treatment, 1.1uM, MGCD-0103, Replicate1, Batch_05, HTA7_E06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, CI-994, Replicate2, Batch_06, HTA5_H10

description: alpha-TC1 cells

value: 24 hrs with 10uM, CI-994


title: alpha-TC1 cells, 24-hr treatment, 2.9uM, MS-275, Replicate3, Batch_05, HTA1_H08

description: alpha-TC1 cells

value: 24 hrs with 2.9uM, MS-275


title: alpha-TC1 cells, 24-hr treatment, 1.1uM, MGCD-0103, Replicate2, Batch_06, HTA9_D04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.4uM, apicidin, Replicate3, Batch_10, HTA2_B01

description: alpha-TC1 cells

value: 24 hrs with 1.4uM, apicidin


title: alpha-TC1 cells, 24-hr treatment, 10uM, CI-994, Replicate1, Batch_04, HTA6_G12

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 2.9uM, MS-275, Replicate2, Batch_06, HTA8_D03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 4.1uM, BRD-K90919562, Replicate1, Batch_04, HTA6_G06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 3.7uM, BRD-K62233722, Replicate2, Batch_06, HTA5_G03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 5uM, BRD-K22912318, Replicate1, Batch_08, HTA8_H03

description: alpha-TC1 cells

value: 24 hrs with 5uM, BRD-K22912318


title: alpha-TC1 cells, 24-hr treatment, 1.3uM, SAHA, Replicate1, Batch_06, HTA5_G02

description: alpha-TC1 cells

value: 24 hrs with 1.3uM, SAHA


title: alpha-TC1 cells, 24-hr treatment, 1.7uM, chaetocin, Replicate4, Batch_06, HTA5_H01

description: alpha-TC1 cells

value: 24 hrs with 1.7uM, chaetocin


title: alpha-TC1 cells, 24-hr treatment, 1.4uM, apicidin, Replicate2, Batch_05, HTA7_E03

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.3uM, SAHA, Replicate2, Batch_05, HTA8_A10

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 5uM, BRD-K22912318, Replicate3, Batch_09, HTA9_B01

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 3.2uM, BRD-K92415738, Replicate2, Batch_09, HTA3_A09

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 3.2uM, BRD-K92415738, Replicate1, Batch_08, HTA1_H09

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.7uM, chaetocin, Replicate3, Batch_10, HTA2_D10

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 4.1uM, BRD-K90919562, Replicate2, Batch_08, HTA9_F06

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 2.9uM, MS-275, Replicate1, Batch_04, HTA6_G02

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.7uM, chaetocin, Replicate1, Batch_05, HTA7_F01

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 3.7uM, BRD-K62233722, Replicate1, Batch_05, HTA1_H07

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 4.1uM, BRD-K90919562, Replicate3, Batch_09, HTA9_B05

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 5uM, BRD-K22912318, Replicate2, Batch_04, HTA7_H04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 4.3uM, BRD-K17311666, Replicate3, Batch_08, HTA9_A04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 10uM, ITF-2357, Replicate1, Batch_10, HTA2_C10

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.4uM, apicidin, Replicate1, Batch_06, HTA1_B11

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 4.3uM, BRD-K17311666, Replicate2, Batch_04, HTA6_G11

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_08, HTA2_B07

description: alpha-TC1 cells

value: 6 hrs with DMSO-control


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_08, HTA3_B03

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_09, HTA9_D02

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_05, HTA7_C04

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 1.7uM, chaetocin, Replicate2, Batch_10, HTA2_A09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_04, HTA8_B01

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD8451, Replicate3, Batch_07, HTA4_D10

description: alpha-TC1 cells

value: 6 hrs with 10uM, BRD8451


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_05, HTA3_G02

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_06, HTA5_D08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_04, HTA6_E08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD5298, Replicate1, Batch_07, HTA1_H04

description: alpha-TC1 cells

value: 6 hrs with 10uM, BRD5298


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_06, HTA4_G05

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD9773, Replicate3, Batch_09, HTA1_C06

description: alpha-TC1 cells

value: 6 hrs with 10uM, BRD9773


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_10, HTA2_G07

description: alpha-TC1 cells


title: alpha-TC1 cells, 24-hr treatment, 4.3uM, BRD-K17311666, Replicate1, Batch_09, HTA9_F02

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 2.4uM, PXD101, Replicate1, Batch_09, HTA8_B09

description: alpha-TC1 cells

value: 6 hrs with 2.4uM, PXD101


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD9773, Replicate2, Batch_07, HTA1_E08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD9773, Replicate1, Batch_08, HTA8_E10

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_07, HTA9_G05

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_09, HTA2_H02

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 2.4uM, PXD101, Replicate3, Batch_08, HTA8_A06

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 2.4uM, PXD101, Replicate2, Batch_07, HTA1_E06

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_07, HTA1_E11

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD8451, Replicate1, Batch_08, HTA1_H05

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD5298, Replicate2, Batch_09, HTA1_D10

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD5298, Replicate3, Batch_08, HTA9_B07

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BRD8451, Replicate2, Batch_09, HTA1_D05

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 3uM, BRD-A94377914, Replicate2, Batch_08, HTA1_B02

description: alpha-TC1 cells

value: 6 hrs with 3uM, BRD-A94377914


title: alpha-TC1 cells, 06-hr treatment, 10uM, AMI-1, Replicate3, Batch_07, HTA4_A08

description: alpha-TC1 cells

value: 6 hrs with 10uM, AMI-1


title: alpha-TC1 cells, 06-hr treatment, 3uM, BRD-A94377914, Replicate3, Batch_09, HTA8_A09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, AMI-1, Replicate2, Batch_09, HTA4_G08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.91uM, BRD6929, Replicate2, Batch_09, HTA3_F09

description: alpha-TC1 cells

value: 6 hrs with 0.91uM, BRD6929


title: alpha-TC1 cells, 06-hr treatment, 1.5uM, CRA-024781, Replicate1, Batch_08, HTA3_H02

description: alpha-TC1 cells

value: 6 hrs with 1.5uM, CRA-024781


title: alpha-TC1 cells, 06-hr treatment, 10uM, ITF-2357, Replicate2, Batch_07, HTA4_C02

description: alpha-TC1 cells

value: 6 hrs with 10uM, ITF-2357


title: alpha-TC1 cells, 06-hr treatment, 1.5uM, CRA-024781, Replicate3, Batch_07, HTA3_A11

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, zebuarine, Replicate3, Batch_07, HTA1_A06

description: alpha-TC1 cells

value: 6 hrs with 10uM, zebuarine


title: alpha-TC1 cells, 06-hr treatment, 10uM, zebuarine, Replicate1, Batch_09, HTA8_H08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, 5-azadeoxycytidine, Replicate3, Batch_10, HTA2_A10

description: alpha-TC1 cells

value: 6 hrs with 10uM, 5-azadeoxycytidine


title: alpha-TC1 cells, 06-hr treatment, 10uM, ITF-2357, Replicate1, Batch_09, HTA1_F10

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BIX-01294, Replicate3, Batch_09, HTA8_A03

description: alpha-TC1 cells

value: 6 hrs with 10uM, BIX-01294


title: alpha-TC1 cells, 06-hr treatment, 10uM, pyroxamide, Replicate3, Batch_08, HTA1_C02

description: alpha-TC1 cells

value: 6 hrs with 10uM, pyroxamide


title: alpha-TC1 cells, 06-hr treatment, 10uM, ITF-2357, Replicate3, Batch_08, HTA9_B08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, RG-0108, Replicate1, Batch_09, HTA8_A07

description: alpha-TC1 cells

value: 6 hrs with 10uM, RG-0108


title: alpha-TC1 cells, 06-hr treatment, 10uM, pyroxamide, Replicate1, Batch_07, HTA1_E01

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, zebuarine, Replicate2, Batch_08, HTA1_A03

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.91uM, BRD6929, Replicate1, Batch_08, HTA4_F03

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, RG-0108, Replicate3, Batch_07, HTA4_E12

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, AMI-1, Replicate1, Batch_08, HTA8_G04

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BIX-01294, Replicate2, Batch_07, HTA4_H10

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, RG-0108, Replicate2, Batch_08, HTA8_D06

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, 5-azadeoxycytidine, Replicate2, Batch_08, HTA8_H01

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.5uM, CRA-024781, Replicate2, Batch_09, HTA9_A01

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, BIX-01294, Replicate1, Batch_06, HTA8_G09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, pyroxamide, Replicate2, Batch_09, HTA1_F09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, 5-azadeoxycytidine, Replicate1, Batch_07, HTA8_D01

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.12uM, HC-toxin, Replicate3, Batch_06, HTA5_D11

description: alpha-TC1 cells

value: 6 hrs with 0.12uM, HC-toxin


title: alpha-TC1 cells, 06-hr treatment, 0.12uM, HC-toxin, Replicate1, Batch_07, HTA3_D11

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.12uM, HC-toxin, Replicate2, Batch_05, HTA4_A03

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.22uM, trichostatin A, Replicate2, Batch_07, HTA8_E08

description: alpha-TC1 cells

value: 6 hrs with 0.22uM, trichostatin A


title: alpha-TC1 cells, 06-hr treatment, 2uM, scriptaid, Replicate2, Batch_06, HTA5_D10

description: alpha-TC1 cells

value: 6 hrs with 2uM, scriptaid


title: alpha-TC1 cells, 06-hr treatment, 0.22uM, trichostatin A, Replicate3, Batch_06, HTA5_D05

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, CI-994, Replicate3, Batch_06, HTA5_C03

description: alpha-TC1 cells

value: 6 hrs with 10uM, CI-994


title: alpha-TC1 cells, 06-hr treatment, 10uM, CI-994, Replicate2, Batch_05, HTA7_C02

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.1uM, MGCD-0103, Replicate2, Batch_06, HTA9_C12

description: alpha-TC1 cells

value: 6 hrs with 1.1uM, MGCD-0103


title: alpha-TC1 cells, 06-hr treatment, 0.015uM, LBH-589, Replicate1, Batch_06, HTA5_C05

description: alpha-TC1 cells

value: 6 hrs with 0.015uM, LBH-589


title: alpha-TC1 cells, 06-hr treatment, 0.22uM, trichostatin A, Replicate1, Batch_05, HTA4_C04

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 2uM, scriptaid, Replicate1, Batch_05, HTA7_C01

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.3uM, SAHA, Replicate2, Batch_06, HTA5_E01

description: alpha-TC1 cells

value: 6 hrs with 1.3uM, SAHA


title: alpha-TC1 cells, 06-hr treatment, 1.1uM, MGCD-0103, Replicate1, Batch_05, HTA7_C05

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 2uM, scriptaid, Replicate3, Batch_04, HTA6_E09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.3uM, SAHA, Replicate3, Batch_04, HTA4_A10

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 10uM, CI-994, Replicate1, Batch_04, HTA3_C12

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.1uM, MGCD-0103, Replicate3, Batch_04, HTA6_E07

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.3uM, SAHA, Replicate1, Batch_05, HTA7_C06

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 4.1uM, BRD-K90919562, Replicate3, Batch_08, HTA1_A04

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.015uM, LBH-589, Replicate3, Batch_05, HTA7_B12

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 2.9uM, MS-275, Replicate3, Batch_04, HTA6_B11

description: alpha-TC1 cells

value: 6 hrs with 2.9uM, MS-275


title: alpha-TC1 cells, 06-hr treatment, 2.9uM, MS-275, Replicate1, Batch_05, HTA4_H09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 2.9uM, MS-275, Replicate2, Batch_06, HTA4_H04

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.015uM, LBH-589, Replicate2, Batch_04, HTA6_E01

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 4.1uM, BRD-K90919562, Replicate1, Batch_04, HTA6_E10

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 5uM, BRD-K22912318, Replicate2, Batch_10, HTA2_E09

description: alpha-TC1 cells

value: 6 hrs with 5uM, BRD-K22912318


title: alpha-TC1 cells, 06-hr treatment, 3.7uM, BRD-K62233722, Replicate3, Batch_06, HTA5_E02

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 3.2uM, BRD-K92415738, Replicate3, Batch_10, HTA2_B12

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 3.2uM, BRD-K92415738, Replicate1, Batch_08, HTA3_F06

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 4.1uM, BRD-K90919562, Replicate2, Batch_09, HTA8_A08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 5uM, BRD-K22912318, Replicate1, Batch_04, HTA7_H09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.4uM, apicidin, Replicate2, Batch_05, HTA7_C03

description: alpha-TC1 cells

value: 6 hrs with 1.4uM, apicidin


title: alpha-TC1 cells, 06-hr treatment, 5uM, BRD-K22912318, Replicate3, Batch_09, HTA1_G09

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.4uM, apicidin, Replicate3, Batch_06, HTA5_D12

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 3.2uM, BRD-K92415738, Replicate2, Batch_04, HTA6_F11

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 3.7uM, BRD-K62233722, Replicate2, Batch_05, HTA7_B11

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 3.7uM, BRD-K62233722, Replicate1, Batch_04, HTA6_D11

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.7uM, chaetocin, Replicate1, Batch_05, HTA3_G12

description: alpha-TC1 cells

value: 6 hrs with 1.7uM, chaetocin


title: Adipocyte_Hypoxic_24hr_rep1

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

description: Gene expression of human adipocytes incubated in 1% Oxygen for 24hr

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent human whole genome Oligo Arrays (catalogue number G4112F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridisation was performed for 17 h at 65 ºC with 10 rpm rotation. Slides were then washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325), followed by 1 min in Wash Solution 2 that was pre-warmed to 37 ºC (catalogue number 5188-5326) as described in the manufacturer’s manual. Slides were then washed in acetonitrile (Fisher cat# A/0630/PB15) for 1 min followed by 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C US84700251, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%)

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.5.1.1 (protocol GE1_105_Dec08). Downstream data analysis was carried out using GeneSpring

label: Cy 3

organism: Homo sapiens

source_name: human adipocytes

label_protocol: 200ng RNA and 2µl (1:5000 dilution) Agilent One-Color RNA Spike-In RNA were labelled with reagents supplied in the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacturer’s instructions as follows:  Primers were annealed to template by mixing 1.2 µl T7 Promoter Primer, 200ng RNA and 2µl spike in control (in a volume of 11.5µl), denatured at 65ºC for 10min followed by incubation at 4ºC for 5min. First Strand Buffer (to 1X), DTT (to 10mM), dNTP (to 0.5mM), MMLV (1µl) and RNaseOut (0.5 µl) were then added to make up the cDNA synthesis reaction (20µl), which was incubated for 2h at 40 ºC. After 15 min denaturation at 65ºC, the reaction was made up to 80µl with the addition of Cyanine 3-CTP (to 0.3mM), Transcription Buffer (to 1X), DTT (to 10mM), NTP (8µl), PEG (to 4%), RNaseOUT (0.5µl), Inorganic Phosphatase (0.6µl), and T7 RNA Polymerase (0.8µl) and incubated for 2h at 40 ºC to synthesise the fluorescent labelled cRNA.  The labelled cRNA was purified with the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK) according to Manufacturer’s protocol.

growth_protocol: Zen-bio cells were trypsinised from a 75 cm2 flask and plated out at 40,000 cells/cm2 in a 24 well plate, and maintained in a preadipocyte medium (DMEM/Ham’s F12 (1:1, v/v), 10% FCS, 15 mM HEPES, 100 U/ml penicillin, 100 μg/ml streptomycin and 0.25 μg/ml amphotericin B).  Once confluent, differentation was induced by culturing the cells in DMEM/Ham’s F-12 (1:1, v/v), 3% FCS, 0.25 mM isobutyl methylxanthine and 10 μM of a PPARγ agonist, 1 μM dexamethasone, 100 U/ml penicillin, 100 μg/ml streptomycin and 0.25 μg/ml amphotericin B for four days.  Cells were then maintained in DMEM/Ham’s F-12 (1:1, v/v), 3% FCS, 1 μM dexamethasone, 100 U/ml penicillin, 100 μg/ml streptomycin and 0.25 μg/ml amphotericin B.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy kit (Qiagen), and the integrity of the RNA determined by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol: Fully differentiated human adipocytes were incubated under hypoxic conditions (1% O2) using a MIC-101 modular incubator chamber which was flushed with 1% O2/94%N2, 5% CO2, sealed and placed at 37°C for 24h.  Control cells were incubated in a standard incubator (21% 02/5% CO2).

tag: conditions

value: Hypoxic

value: 1% Oxygen for 24hr


title: alpha-TC1 cells, 06-hr treatment, DMSO-control, Batch_10, HTA2_B10

description: alpha-TC1 cells

value: 6 hrs with DMSO-control


title: Adipocyte_Hypoxic_24hr_rep3


title: alpha-TC1 cells, 06-hr treatment, 1.4uM, apicidin, Replicate1, Batch_04, HTA6_F05

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 1.7uM, chaetocin, Replicate3, Batch_06, HTA5_C04

description: alpha-TC1 cells


title: Adipocyte_Hypoxic_24hr_rep4b


title: alpha-TC1 cells, 06-hr treatment, 4.3uM, BRD-K17311666, Replicate2, Batch_04, HTA6_D04

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 4.3uM, BRD-K17311666, Replicate3, Batch_08, HTA3_H06

description: alpha-TC1 cells


title: Adipocyte_Normoxic_24hr_rep2

description: Gene expression of human adipocytes incubated in 21% Oxygen for 24hr

value: Normoxic

value: 21% Oxygen for 24hr


title: Adipocyte_Hypoxic_24hr_rep4a


title: Adipocyte_Normoxic_24hr_rep3


title: alpha-TC1 cells, 06-hr treatment, 1.7uM, chaetocin, Replicate2, Batch_04, HTA7_H10

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 4.3uM, BRD-K17311666, Replicate1, Batch_09, HTA9_C03

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 0.91uM, BRD6929, Replicate3, Batch_07, HTA9_B02

description: alpha-TC1 cells

value: 6 hrs with 0.91uM, BRD6929


title: Adipocyte_Normoxic_24hr_rep4


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_04, HTA6_D01

description: alpha-TC1 cells

value: 1 hr with DMSO-control


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_06, HTA4_B08

description: alpha-TC1 cells


title: alpha-TC1 cells, 06-hr treatment, 3uM, BRD-A94377914, Replicate1, Batch_07, HTA9_D09

description: alpha-TC1 cells

value: 6 hrs with 3uM, BRD-A94377914


title: Expression of SKBR3 cells treated with FOXA1 siRNA for 72hrs #1

city: Columbus

first: Gina

last: Sizemore

state: OH

address: 460 W. 12th Avenue

institute: Ohio State University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization;: (1) local background used, (2) special detrend OFF, (3) adjust background globally OFF, (4) red autoestimate OFF, and (5) green autoestimate OFF. Rosetta Resolver (v.7.2) was used for data analysis.

source_name: SKBR3 cells treated with Non-targeting siRNA for 72hrs

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions.

growth_protocol: All cell lines were obtained from ATCC. MCF7 and MDA-MB-453 cells were grown in DMEM (Mediatech); T47D cells in RPMI 1640 (Gibco); SKBR3 cells in McCoy’s 5A (Sigma). Media was supplemented with 10% FBS and 1% Penicillin-Streptamycin (Invitrogen). Cells were seeded in 100 mm dishes to be 30-50% confluent upon transfection. siRNA targeting firefly luciferase mRNA (siCONTROL Non-targeting siRNA #2, Dharmacon, herein described as NT) or human FOXA1 mRNA (siGENOME M-010319-01 and -04, Dharmacon) were transfected in OPTI-MEM media (Invitrogen) using Lipfectamine 2000 (Invitrogen) to a final concentration of 100 nM. Culture media was changed to complete growth medium after 24 hours. Cells were harvested at 36 or 72 hours post-transfection.

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen), treated with DNAse I (DNA-free, Ambion), and cDNA produced using SuperScript II Reverse Transcriptase (Invitrogen).

tag: tissue

value: breast cancer cell line

value: Non-targeting siRNA for 72hrs

value: FOXA1 siRNA for 72hrs


title: Expression of SKBR3 cells treated with FOXA1 siRNA for 72hrs #3


title: Expression of SKBR3 cells treated with FOXA1 siRNA for 72hrs-ds #1


title: Expression of MB453 cells treated with FOXA1 siRNA for 72hrs #3

source_name: MB453 cells treated with Non-targeting siRNA for 72hrs


title: Adipocyte_Normoxic_24hr_rep1


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_08, HTA3_C11

description: alpha-TC1 cells


title: Expression of SKBR3 cells treated with FOXA1 siRNA for 36hrs

source_name: SKBR3 cells treated with Non-targeting siRNA for 36hrs

value: Non-targeting siRNA for 36hrs

value: FOXA1 siRNA for 36hrs


title: Expression of MB453 cells treated with FOXA1 siRNA for 72hrs #2


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_06, HTA5_A03

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_05, HTA3_E02

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_07, HTA9_A12

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_10, HTA2_C02

description: alpha-TC1 cells


title: Expression of SKBR3 cells treated with FOXA1 siRNA for 72hrs #2


title: Expression of MB453 cells treated with FOXA1 siRNA for 36hrs

source_name: MB453 cells treated with Non-targeting siRNA for 36hrs


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_05, HTA7_G09

description: alpha-TC1 cells


title: Expression of MB453 cells treated with FOXA1 siRNA for 72hrs #1


title: Expression of MB453 cells treated with FOXA1 siRNA for 72hrs-ds #1


title: Expression of T47D cells treated with FOXA1 siRNA for 72hrs-ds #1

source_name: T47D cells treated with Non-targeting siRNA for 72hrs


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_09, HTA2_A01

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_10, HTA2_C01

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_08, HTA2_H08

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_04, HTA8_B08

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_07, HTA1_F02

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, DMSO-control, Batch_09, HTA9_G02

description: alpha-TC1 cells


title: Expression of T47D cells treated with FOXA1 siRNA for 72hrs #2


title: alpha-TC1 cells, 01-hr treatment, 2.4uM, PXD101, Replicate3, Batch_07, HTA3_C04

description: alpha-TC1 cells

value: 1 hr with 2.4uM, PXD101


title: alpha-TC1 cells, 01-hr treatment, 2.4uM, PXD101, Replicate2, Batch_09, HTA1_A02

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD9773, Replicate3, Batch_08, HTA9_A08

description: alpha-TC1 cells

value: 1 hr with 10uM, BRD9773


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD5298, Replicate3, Batch_08, HTA3_D05

description: alpha-TC1 cells

value: 1 hr with 10uM, BRD5298


title: Expression of T47D cells treated with FOXA1 siRNA for 72hrs #1


title: alpha-TC1 cells, 01-hr treatment, 2.4uM, PXD101, Replicate1, Batch_08, HTA9_D08

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD9773, Replicate1, Batch_07, HTA8_G06

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD5298, Replicate1, Batch_09, HTA1_G06

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD9773, Replicate2, Batch_09, HTA4_C07

description: alpha-TC1 cells


title: Stressed roots vs Control roots_8d_rep2

city: jinan

first: juren

last: zhang

address: shanda nanlv 27

country: China

institute: shandong university

hyb_protocol: Hybridizations were performed according to the protocols at the website of the Maize Oligonucleotide Array Project.

scan_protocol: Scanned on an LuxScan-10KA (SN100-0094), Images were quantified using GENEPIX 6.0 software (version A.6.0).

data_processing: LOWESS normalized, background subtracted data. TM4 software was used.

organism: Zea mays

source_name: maize Q319 roots treated by low phosphate for 8 days

label_protocol: 1.5 µg of the purified RNA was reverse transcribed, amplified and labeled using Cy5 or Cy3 (Cy3/5™ Mono-Reactive Dye Pack, Cat#PA23001) with the Aminoallyl Message Amp II kit (Ambion, Cat# 1753) according to the manufacturer’s instructions.Unlabelled primers and dyes were removed using Qiagen RNeasy MinElute columns and buffers (Qiagen Cat # 74204).

growth_protocol: Maize (Zea mays L.) inbred line Q319 was used in this study. Seeds of the maize inbred line Q319 were surface sterilized and held at 28°C in darkness. Seedlings (4 days old) were transferred to a sufficient phosphate (SP, 1,000 μM KH2PO4) solution (Ca(NO3)2.4H2O 2 mM, NH4NO3 1.25 mM, KCl 0.1 mM, K2SO4 0.65 mM, MgSO4 0.65 mM, H3BO3 10.0 mM, (NH4)6Mo7O24 0.5 mM, MnSO4 1.0 mM, CuSO4.5H2O 0.1 mM, ZnSO4.7H2O 1.0 mM, Fe-EDTA 0.1 mM), allowed to grow for 4 days (plants with 2–3 leaves), and endosperm was then removed carefully. After 2-3 days of re-culturing in SP nutrient solutions, half of the seedlings were transplanted into a low phosphate (LP, same composition as the SP solution, except that 5 μM KH2PO4 and 1 mM KH2PO4 were replaced with 1 mM KCl) nutrient solution. The plants were grown under a 32°C/25°C (day/night) temperature regime at a photon flux density (PFD) of 700 μmol m-2 s-1 with a 14 h/10 h light/dark cycle in a greenhouse with approximately 65% relative humidity.

extract_protocol: Total RNA was extracted from the frozen samples using the method of McCarty (1986) and purified using Qiagen RNeasy MinElute columns and buffers (Qiagen Cat # 74204).

treatment_protocol: The 1.0-1.5 cm lateral root primordium zone of maize were harvested at 2 days and 8 days, respectively, after transfer into the SP/LP nutrient solutions.Each biological repeat contains segments from 15~20 plants.

value: 1.0-1.5 cm lateral root primordium zone (LRZ)

tag: Stage

value: V4 stage

tag: inbred line

source_name: control maize Q319 roots clutrued in normal conditions


title: Expression of MCF7 cells treated with FOXA1 siRNA for 72hrs #2

source_name: MCF7 cells treated with Non-targeting siRNA for 72hrs


title: Expression of T47D cells treated with FOXA1 siRNA for 36hrs

source_name: T47D cells treated with Non-targeting siRNA for 36hrs


title: Stressed roots vs Control roots_2d_rep5

source_name: maize Q319 roots treated by low phosphate for 2 days


title: Stressed roots vs Control roots_8d_rep4


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD8451, Replicate1, Batch_09, HTA8_D07

description: alpha-TC1 cells

value: 1 hr with 10uM, BRD8451


title: Stressed roots vs Control roots_8d_rep1


title: Stressed roots vs Control roots_8d_rep3


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD5298, Replicate2, Batch_07, HTA1_G04

description: alpha-TC1 cells


title: Expression of MCF7 cells treated with FOXA1 siRNA for 72hrs #3


title: Expression of MCF7 cells treated with FOXA1 siRNA for 72hrs-ds #1


title: Expression of MCF7 cells treated with FOXA1 siRNA for 72hrs #1


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD8451, Replicate3, Batch_08, HTA3_E12

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, BRD8451, Replicate2, Batch_07, HTA4_H01

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 3uM, BRD-A94377914, Replicate3, Batch_08, HTA3_C02

description: alpha-TC1 cells

value: 1 hr with 3uM, BRD-A94377914


title: Expression of MCF7 cells treated with FOXA1 siRNA for 36hrs

source_name: MCF7 cells treated with Non-targeting siRNA for 36hrs


title: Stressed roots vs Control roots_2d_rep4


title: alpha-TC1 cells, 01-hr treatment, 0.91uM, BRD6929, Replicate3, Batch_08, HTA3_D12

description: alpha-TC1 cells

value: 1 hr with 0.91uM, BRD6929


title: alpha-TC1 cells, 01-hr treatment, 3uM, BRD-A94377914, Replicate1, Batch_09, HTA4_D01

description: alpha-TC1 cells


title: Stressed roots vs Control roots_2d_rep3


title: alpha-TC1 cells, 01-hr treatment, 10uM, pyroxamide, Replicate3, Batch_09, HTA4_A01

description: alpha-TC1 cells

value: 1 hr with 10uM, pyroxamide


title: alpha-TC1 cells, 01-hr treatment, 0.91uM, BRD6929, Replicate2, Batch_10, HTA2_D09

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, AMI-1, Replicate1, Batch_09, HTA1_E07

description: alpha-TC1 cells

value: 1 hr with 10uM, AMI-1


title: alpha-TC1 cells, 01-hr treatment, 10uM, pyroxamide, Replicate2, Batch_08, HTA3_H10

description: alpha-TC1 cells


title: Stressed roots vs Control roots_2d_rep2


title: alpha-TC1 cells, 01-hr treatment, 10uM, pyroxamide, Replicate1, Batch_07, HTA9_H08

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, AMI-1, Replicate2, Batch_07, HTA3_F10

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, ITF-2357, Replicate1, Batch_08, HTA4_H03

description: alpha-TC1 cells

value: 1 hr with 10uM, ITF-2357


title: alpha-TC1 cells, 01-hr treatment, 1.5uM, CRA-024781, Replicate3, Batch_07, HTA8_H12

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 0.91uM, BRD6929, Replicate1, Batch_07, HTA8_C01

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 10uM, AMI-1, Replicate3, Batch_08, HTA9_E12

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 3uM, BRD-A94377914, Replicate2, Batch_07, HTA8_F05

description: alpha-TC1 cells


title: PfC Veh Tg-, rep8

city: Groton

first: Phillip

last: Yates

state: CT

address: 440 Eastern Point Rd

institute: Pfizer Inc.

hyb_protocol: Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 Gene Chips for 18 hours, then washed/stained according to manufacturer’s recommendations using the Affymetrix 450 fluidics station.

scan_protocol: Gene chips were scanned using an Affymetrix 3000 array scanner.

data_processing: R/Bioconductor was used to apply the Robust Multi-Array Average (RMA) methodology to generate expression values for the combined samples.

label: Biotin

source_name: Prefrontal Cortex wild type mouse after 28 days of chronic sc Vehicle infusion

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed.

treatment_protocol: Brain regions were microdissected and snap-frozen in microcentrifuge tubes on dry ice

tag: age

value: 4 months

tag: strain

value: B6SJLF1 (F1 cross between C57Bl/6 and SJL)

tag: genotype/variation

value: Tg- (non-transgenic WT littermates)

value: Prefrontal Cortex

tag: treated with

value: Vehicle for 28 days


title: PfC Veh Tg-, rep2


title: PfC Veh Tg-, rep5


title: PfC Veh Tg-, rep6


title: Stressed roots vs Control roots_2d_rep1


title: PfC Veh Tg-, rep7


title: alpha-TC1 cells, 01-hr treatment, 10uM, ITF-2357, Replicate3, Batch_07, HTA9_A07

description: alpha-TC1 cells


title: PfC Veh Tg-, rep3


title: PfC Veh Tg-, rep1


title: leaf_gDNA_Ull2_5_3

type: genomic

city: Austin

first: David

middle: Lee

last: Des Marais

state: TX

address: 1 University Station C0930

department: Integrative Biology

institute: The University of Texas at Austin

description: gDNA hybridizations to explore sequence polymorphisms

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000, GCOS v1.3

data_processing:
Microarray Suite 5, data processed with JMP Genomics, R statistics
RMA background correction, log2 transformation, quantile normalized individual probe data are provided in the supplementary file on the Series record. Analysis of individual probe-level data was performed in order to remove probes from the array that hybridized differently between accessions for related gene expression analysis.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: rosette leaf

label_protocol: Biotin labeling, Invitrogen Bioprime kit, following Borevitz 2005

growth_protocol: standard Arabidopsis growth conditions in a Percival growth chamber - 16L/8D, 21 degrees day, 18 degrees night

extract_protocol: Qiagen Dneasy Plant Mini prep

tag: accession

tag: ecotype

value: rosette leaf


title: alpha-TC1 cells, 01-hr treatment, 10uM, ITF-2357, Replicate2, Batch_10, HTA2_G08

description: alpha-TC1 cells


title: PfC Veh Tg-, rep4


title: leaf_gDNA_Ull2_5_2


title: alpha-TC1 cells, 01-hr treatment, 10uM, 5-azadeoxycytidine, Replicate3, Batch_08, HTA3_C08

description: alpha-TC1 cells

value: 1 hr with 10uM, 5-azadeoxycytidine


title: leaf_gDNA_Ull2_5_1


title: leaf_gDNA_Tamm2_3


title: alpha-TC1 cells, 01-hr treatment, 1.5uM, CRA-024781, Replicate1, Batch_08, HTA9_G12

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 1.5uM, CRA-024781, Replicate2, Batch_09, HTA1_F05

description: alpha-TC1 cells


title: leaf_gDNA_Tamm2_2


title: PfC Veh Tg+, rep8

source_name: Prefrontal Cortex Tg2576 mouse after 28 days of chronic sc Vehicle infusion

value: Tg+ (over-expressing human mutant amyloid precursor protein)


title: alpha-TC1 cells, 01-hr treatment, 10uM, 5-azadeoxycytidine, Replicate1, Batch_07, HTA9_E05

description: alpha-TC1 cells


title: PfC Veh Tg+, rep7


title: PfC Veh Tg+, rep6


title: alpha-TC1 cells, 01-hr treatment, 10uM, RG-0108, Replicate2, Batch_09, HTA1_G10

description: alpha-TC1 cells

value: 1 hr with 10uM, RG-0108


title: IL28B-6_2

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA nomanization by software Partek

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary Human Hepatocytes Were Isolated and Plated on 12 well plates at the University of Pittsburgh in the Laboratory of Dr. Stehphen Strom and provided through the NIH funded Liver Tissue and Cell Distribution System (LTCDS)

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

treatment_protocol: RNA was isolated after 6, 12, and 24 h treatment with IFN-α (10 U/mL) or IL28B (25 ng/mL)

value: liver

tag: agent

tag: time


title: IL28B-6_3


title: leaf_gDNA_Tamm2_1


title: alpha-TC1 cells, 01-hr treatment, 10uM, 5-azadeoxycytidine, Replicate2, Batch_09, HTA8_D04

description: alpha-TC1 cells


title: IL28B-6_1


title: IL28B-24_3


title: alpha-TC1 cells, 01-hr treatment, 10uM, RG-0108, Replicate1, Batch_08, HTA9_E10

description: alpha-TC1 cells


title: leaf_gDNA_Omo2_3_3


title: alpha-TC1 cells, 01-hr treatment, 10uM, zebuarine, Replicate3, Batch_08, HTA4_E04

description: alpha-TC1 cells

value: 1 hr with 10uM, zebuarine


title: alpha-TC1 cells, 01-hr treatment, 10uM, zebuarine, Replicate2, Batch_07, HTA1_D12

description: alpha-TC1 cells


title: IL28B-24_2


title: PfC Veh Tg+, rep4


title: alpha-TC1 cells, 01-hr treatment, 10uM, RG-0108, Replicate3, Batch_07, HTA8_B02

description: alpha-TC1 cells


title: Expression of T47D cells treated with FOXA1 siRNA for 72hrs #3

value: breast cancer cell line

value: Non-targeting siRNA for 72hrs

value: FOXA1 siRNA for 72hrs


title: IL28B-24_1


title: PfC Veh Tg+, rep2


title: leaf_gDNA_Omo2_3_1


title: leaf_gDNA_Got22_3


title: IFN-6_3

value: IFN


title: PfC Veh Tg+, rep5


title: alpha-TC1 cells, 01-hr treatment, 10uM, zebuarine, Replicate1, Batch_09, HTA8_H04

description: alpha-TC1 cells


title: PfC PDE9 Tg-, rep8

source_name: Prefrontal Cortex wild type mouse after 28 days of chronic sc PF-04447943 infusion

value: PF-04447943 (PDE9A-inhibitor) for 28 days


title: alpha-TC1 cells, 01-hr treatment, 10uM, BIX-01294, Replicate3, Batch_06, HTA5_E10

description: alpha-TC1 cells

source_name: alpha-TC1 cells

value: 1 hr with 10uM, BIX-01294


title: leaf_gDNA_Omo2_3_2


title: PfC Veh Tg+, rep1

value: 4 months


title: IFN-6_2


title: IFN-6_1


title: alpha-TC1 cells, 01-hr treatment, 10uM, BIX-01294, Replicate2, Batch_05, HTA7_G10

description: alpha-TC1 cells


title: PfC PDE9 Tg-, rep6

value: B6SJLF1 (F1 cross between C57Bl/6 and SJL)


title: PfC PDE9 Tg-, rep7

value: Tg- (non-transgenic WT littermates)


title: leaf_gDNA_Got22_1


title: leaf_gDNA_Got22_2


title: alpha-TC1 cells, 01-hr treatment, 0.12uM, HC-toxin, Replicate3, Batch_07, HTA3_H12

description: alpha-TC1 cells

value: 1 hr with 0.12uM, HC-toxin


title: leaf_gDNA_Eden1_3


title: alpha-TC1 cells, 01-hr treatment, 10uM, BIX-01294, Replicate1, Batch_07, HTA1_G08

description: alpha-TC1 cells


title: IFN-24_2


title: leaf_gDNA_Eden1_2


title: alpha-TC1 cells, 01-hr treatment, 0.12uM, HC-toxin, Replicate2, Batch_05, HTA9_H10

description: alpha-TC1 cells


title: leaf_gDNA_Eden1_1


title: Con_3


title: PfC Veh Tg+, rep3

value: Prefrontal Cortex

value: Vehicle for 28 days


title: IFN-24_1


title: alpha-TC1 cells, 01-hr treatment, 0.12uM, HC-toxin, Replicate1, Batch_06, HTA5_A07

description: alpha-TC1 cells


title: leaf_gDNA_Bil5_3

value: rosette leaf


title: PfC PDE9 Tg-, rep5


title: leaf_gDNA_Bil5_2


title: Con_2


title: Con_1


title: alpha-TC1 cells, 01-hr treatment, 0.22uM, trichostatin A, Replicate3, Batch_06, HTA1_H01

description: alpha-TC1 cells

value: 1 hr with 0.22uM, trichostatin A


title: alpha-TC1 cells, 01-hr treatment, 0.22uM, trichostatin A, Replicate2, Batch_05, HTA9_F05

description: alpha-TC1 cells


title: PfC PDE9 Tg-, rep1


title: PfC PDE9 Tg-, rep4


title: PfC PDE9 Tg-, rep3


title: leaf_gDNA_Bil5_1


title: alpha-TC1 cells, 01-hr treatment, 0.22uM, trichostatin A, Replicate1, Batch_07, HTA3_E05

description: alpha-TC1 cells


title: leaf_gDNA_Ag0_3


title: PfC PDE9 Tg+, rep8

source_name: Prefrontal Cortex Tg2576 mouse after 28 days of chronic sc PF-04447943 infusion

value: Tg+ (over-expressing human mutant amyloid precursor protein)


title: PfC PDE9 Tg+, rep7


title: leaf_gDNA_Ag0_2


title: alpha-TC1 cells, 01-hr treatment, 2uM, scriptaid, Replicate2, Batch_04, HTA6_E05

description: alpha-TC1 cells

value: 1 hr with 2uM, scriptaid


title: PfC PDE9 Tg+, rep5


title: Patient 9, Non-t(12;14) fibroid

city: Rochester

first: Jennelle

last: Hodge

state: MN

address: 200 First Street SW

department: Department of Laboratory Medicine and Pathology

institute: Mayo Clinic

hyb_protocol: Following purification and fragmentation to reduce secondary structure, hybridization in a Model 640 hybridization chamber to GeneChip Human Genome U133 Plus 2.0 oligonucleotide expression microarrays (Affymetrix) occurred overnight at 45oC.  Arrays were washed using a Model 450 Fluidics station with GeneChip Operating Software (Affymetrix).

scan_protocol: Microarrays were scanned using the GeneChip Model 3000 7G

data_processing: Probe set expression values were calculated by GeneChip software using the MAS 5.0 algorithm

source_name: Non-t(12;14) fibroid

label_protocol: Biotinylated according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix GeneChip Expression Analysis Technical Manual revision 4)

extract_protocol: Followed Affymetrix GeneChip Expression Analysis Technical Manual revision 4

value: non-t(12;14) fibroid tumor

tag: gender

value: female


title: Patient 9, t(12;14) fibroid

source_name: t(12;14) fibroid

value: t(12;14) fibroid tumor


title: PfC PDE9 Tg+, rep6


title: leaf_gDNA_Ag0_1


title: Patient 9, Myometrium

source_name: Myometrium

value: myometrium


title: leaf_gDNA_C24_3


title: alpha-TC1 cells, 01-hr treatment, 2uM, scriptaid, Replicate3, Batch_06, HTA5_A04

description: alpha-TC1 cells


title: leaf_gDNA_C24_2


title: Patient 8, Myometrium


title: alpha-TC1 cells, 01-hr treatment, 0.015uM, LBH-589, Replicate2, Batch_06, HTA5_D04

description: alpha-TC1 cells

value: 1 hr with 0.015uM, LBH-589


title: Patient 8, Non-t(12;14) fibroid


title: PfC PDE9 Tg+, rep4

value: PF-04447943 (PDE9A-inhibitor) for 28 days


title: Patient 8, t(12;14) fibroid


title: alpha-TC1 cells, 01-hr treatment, 0.015uM, LBH-589, Replicate1, Batch_05, HTA1_A01

description: alpha-TC1 cells


title: leaf_gDNA_C24_1


title: PfC PDE9 Tg+, rep3


title: leaf_gDNA_SQ8_3

treatment_protocol: no treatment

value: leaf


title: PfC PDE9 Tg+, rep2

value: 4 months


title: alpha-TC1 cells, 01-hr treatment, 2uM, scriptaid, Replicate1, Batch_05, HTA7_G06

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 1.1uM, MGCD-0103, Replicate3, Batch_04, HTA6_C07

description: alpha-TC1 cells

value: 1 hr with 1.1uM, MGCD-0103


title: leaf_gDNA_SQ8_2


title: Patient 7, Myometrium


title: alpha-TC1 cells, 01-hr treatment, 0.015uM, LBH-589, Replicate3, Batch_04, HTA6_D02

description: alpha-TC1 cells


title: Patient 7, Non-t(12;14) fibroid


title: Hipp Veh Tg-, rep8

source_name: Hippocampus wild type mouse after 28 days of chronic sc Vehicle infusion

value: B6SJLF1 (F1 cross between C57Bl/6 and SJL)

value: Tg- (non-transgenic WT littermates)

value: Hippocampus


title: leaf_gDNA_SQ8_1


title: alpha-TC1 cells, 01-hr treatment, 1.1uM, MGCD-0103, Replicate2, Batch_06, HTA5_A06

description: alpha-TC1 cells


title: PfC PDE9 Tg+, rep1

value: Prefrontal Cortex


title: Patient 7, t(12;14) fibroid


title: leaf_gDNA_NFA10_3


title: alpha-TC1 cells, 01-hr treatment, 1.1uM, MGCD-0103, Replicate1, Batch_05, HTA3_H01

description: alpha-TC1 cells


title: Hipp Veh Tg-, rep7

value: Vehicle for 28 days


title: leaf_gDNA_NFA10_2


title: Hipp Veh Tg-, rep6


title: alpha-TC1 cells, 01-hr treatment, 10uM, CI-994, Replicate3, Batch_05, HTA8_A11

description: alpha-TC1 cells

value: 1 hr with 10uM, CI-994


title: leaf_gDNA_NFA10_1


title: Patient 6, Non-t(12;14) fibroid


title: Patient 6, Myometrium


title: alpha-TC1 cells, 01-hr treatment, 10uM, CI-994, Replicate1, Batch_04, HTA6_C09

description: alpha-TC1 cells


title: IFN-24_3

value: liver

value: IFN


title: alpha-TC1 cells, 01-hr treatment, 10uM, CI-994, Replicate2, Batch_06, HTA5_F01

description: alpha-TC1 cells


title: Hipp Veh Tg-, rep5


title: leaf_gDNA_Knox18_3


title: alpha-TC1 cells, 01-hr treatment, 1.3uM, SAHA, Replicate3, Batch_06, HTA5_A09

description: alpha-TC1 cells

value: 1 hr with 1.3uM, SAHA


title: Patient 5, Non-t(12;14) fibroid

value: non-t(12;14) fibroid tumor

value: female


title: alpha-TC1 cells, 01-hr treatment, 1.3uM, SAHA, Replicate2, Batch_05, HTA7_G12

description: alpha-TC1 cells


title: leaf_gDNA_Knox18_1


title: Patient 6, t(12;14) fibroid

value: t(12;14) fibroid tumor


title: Hipp Veh Tg-, rep4


title: Hipp Veh Tg-, rep2


title: Patient 5, t(12;14) fibroid


title: Patient 4, t(12;14) fibroid


title: Hipp Veh Tg-, rep3


title: leaf_gDNA_HR5_3


title: Patient 4, Non-t(12;14) fibroid


title: leaf_gDNA_HR5_2


title: leaf_gDNA_Knox18_2


title: alpha-TC1 cells, 01-hr treatment, 1.3uM, SAHA, Replicate1, Batch_10, HTA2_D05

description: alpha-TC1 cells


title: Hipp Veh Tg+, rep8

source_name: Hippocampus Tg2576 mouse after 28 days of chronic sc Vehicle infusion

value: Tg+ (over-expressing human mutant amyloid precursor protein)


title: Patient 5, Myometrium

value: myometrium


title: alpha-TC1 cells, 01-hr treatment, 2.9uM, MS-275, Replicate3, Batch_04, HTA6_E06

description: alpha-TC1 cells

value: 1 hr with 2.9uM, MS-275


title: alpha-TC1 cells, 01-hr treatment, 2.9uM, MS-275, Replicate2, Batch_09, HTA9_D11

description: alpha-TC1 cells


title: Hipp Veh Tg-, rep1

value: 4 months


title: Hipp Veh Tg+, rep6


title: alpha-TC1 cells, 01-hr treatment, 2.9uM, MS-275, Replicate1, Batch_06, HTA7_A02

description: alpha-TC1 cells


title: Hipp Veh Tg+, rep7


title: Patient 3, t(12;14) fibroid


title: leaf_gDNA_HR5_1

value: leaf


title: Hipp Veh Tg+, rep5

value: B6SJLF1 (F1 cross between C57Bl/6 and SJL)


title: Hipp Veh Tg+, rep4


title: leaf_gDNA_CIBC17_3


title: alpha-TC1 cells, 01-hr treatment, 4.1uM, BRD-K90919562, Replicate3, Batch_04, HTA6_C03

description: alpha-TC1 cells


title: Patient 4, Myometrium


title: Patient 3, Non-t(12;14) fibroid


title: Patient 3, Myometrium


title: leaf_gDNA_CIBC17_2


title: leaf_gDNA_CIBC17_1


title: alpha-TC1 cells, 01-hr treatment, 4.1uM, BRD-K90919562, Replicate2, Batch_08, HTA9_A09

description: alpha-TC1 cells


title: PfC PDE9 Tg-, rep2

value: Tg- (non-transgenic WT littermates)

value: PF-04447943 (PDE9A-inhibitor) for 28 days


title: leaf_gDNA_Ts1_3


title: Patient 2, t(12;14) fibroid


title: Hipp Veh Tg+, rep3

value: Hippocampus


title: leaf_gDNA_Ts1_2


title: Hipp Veh Tg+, rep2

value: Vehicle for 28 days


title: Patient 2, Non-t(12;14) fibroid


title: alpha-TC1 cells, 01-hr treatment, 3.2uM, BRD-K92415738, Replicate3, Batch_08, HTA1_A07

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 4.1uM, BRD-K90919562, Replicate1, Batch_09, HTA4_H07

description: alpha-TC1 cells


title: leaf_gDNA_Ts1_1


title: leaf_gDNA_Col_3

value: Col


title: Patient 2, Myometrium


title: Hipp Veh Tg+, rep1


title: leaf_gDNA_Col_2


title: Hipp PDE9 Tg-, rep8

source_name: Hippocampus wild type mouse after 28 days of chronic sc PF-04447943 infusion


title: alpha-TC1 cells, 01-hr treatment, 3.2uM, BRD-K92415738, Replicate1, Batch_09, HTA4_D02

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 3.2uM, BRD-K92415738, Replicate2, Batch_04, HTA6_E04

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 5uM, BRD-K22912318, Replicate2, Batch_09, HTA3_E09

description: alpha-TC1 cells

value: 1 hr with 5uM, BRD-K22912318


title: Hipp PDE9 Tg-, rep7


title: alpha-TC1 cells, 01-hr treatment, 5uM, BRD-K22912318, Replicate3, Batch_04, HTA6_E03

description: alpha-TC1 cells


title: leaf_gDNA_Col_1


title: alpha-TC1 cells, 01-hr treatment, 5uM, BRD-K22912318, Replicate1, Batch_08, HTA9_D03

description: alpha-TC1 cells


title: leaf_gDNA_Bur0_3


title: Patient 1, Non-t(12;14) fibroid


title: Hipp PDE9 Tg-, rep5


title: Hipp PDE9 Tg-, rep6


title: Patient 1, t(12;14) fibroid


title: alpha-TC1 cells, 01-hr treatment, 1.4uM, apicidin, Replicate3, Batch_06, HTA5_A08

description: alpha-TC1 cells

value: 1 hr with 1.4uM, apicidin


title: 9QSA_USA300_1hr_Cy3_PIM_1hr_Cy5_14280209_MDS.mev.refIsIA.out

city: Rockville

first: John

last: Braisted

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min. The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry. Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were heated to 95 C degree prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree. Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner.

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Staphylococcus aureus subsp. aureus USA300

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

tag: genotype

value: WT

value: 1 h

value: P1 mutant


title: Hipp PDE9 Tg-, rep3


title: 9QSA_USA300_4hr_Cy3_PIM_4hr_Cy5_14280085_MDS.mev.refIsIA.out

value: 4 h


title: 9QSA_USA300_2hr_Cy3_PIM_2hr_Cy5_14280208_MDS.mev.refIsIA.out

value: 2 h


title: leaf_gDNA_Bur0_2


title: leaf_gDNA_Bur0_1


title: alpha-TC1 cells, 01-hr treatment, 1.4uM, apicidin, Replicate2, Batch_05, HTA7_G08

description: alpha-TC1 cells


title: Hipp PDE9 Tg-, rep4


title: leaf_gDNA_Ws2_3


title: 9QSA_USA300_3hr_Cy3_PIM_3hr_Cy5_14280207_MDS.mev.refIsIA.out

value: 3 h


title: 9QSA_USA300_0hr_Cy3_USA300_4hr_Cy5_14280094_MDS.mev.refIsIA.out

value: 0 h


title: alpha-TC1 cells, 01-hr treatment, 1.4uM, apicidin, Replicate1, Batch_04, HTA6_E11

description: alpha-TC1 cells


title: 9QSA_USA300_0hr_Cy3_USA300_3hr_Cy5_14280093_MDS.mev.refIsIA.out


title: leaf_gDNA_Ws2_2


title: 9QSA_USA300_0hr_Cy3_USA300_2hr_Cy5_14280091_MDS.mev.refIsIA.out


title: Hipp PDE9 Tg-, rep2

value: 4 months


title: alpha-TC1 cells, 01-hr treatment, 3.7uM, BRD-K62233722, Replicate3, Batch_04, HTA6_A01

description: alpha-TC1 cells


title: Hipp PDE9 Tg-, rep1


title: alpha-TC1 cells, 01-hr treatment, 3.7uM, BRD-K62233722, Replicate2, Batch_06, HTA5_A10

description: alpha-TC1 cells


title: Hipp PDE9 Tg+, rep8

source_name: Hippocampus Tg2576 mouse after 28 days of chronic sc PF-04447943 infusion

value: Tg+ (over-expressing human mutant amyloid precursor protein)


title: alpha-TC1 cells, 01-hr treatment, 3.7uM, BRD-K62233722, Replicate1, Batch_05, HTA7_G05

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 1.7uM, chaetocin, Replicate3, Batch_04, HTA6_F03

description: alpha-TC1 cells

value: 1 hr with 1.7uM, chaetocins


title: Hipp PDE9 Tg+, rep6

value: B6SJLF1 (F1 cross between C57Bl/6 and SJL)


title: leaf_gDNA_Ws2_1

value: leaf


title: Hipp PDE9 Tg+, rep7

value: Hippocampus

value: PF-04447943 (PDE9A-inhibitor) for 28 days


title: leaf_gDNA_Ler_3

value: Ler


title: leaf_gDNA_Ler_2


title: 9QSA_USA300_0hr_Cy3_USA300_1hr_Cy5_14280090_MDS.mev.refIsIA.out


title: leaf_gDNA_Ler_1


title: 9QSA_USA300_0hr_Cy3_PIM_0hr_Cy5_14280210_MDS.mev.refIsIA.out


title: 9QSA_PIM_0hr_Cy3_PIM_4hr_Cy5_14280089_MDS.mev.refIsIA.out

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to mid log (60 min).


title: alpha-TC1 cells, 01-hr treatment, 1.7uM, chaetocin, Replicate2, Batch_06, HTA4_H02

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 4.3uM, BRD-K17311666, Replicate3, Batch_08, HTA3_B11

description: alpha-TC1 cells


title: alpha-TC1 cells, 01-hr treatment, 1.7uM, chaetocin, Replicate1, Batch_05, HTA3_H03

description: alpha-TC1 cells


title: 9QSA_PIM_0hr_Cy3_PIM_3hr_Cy5_14280088_MDS.mev.refIsIA.out


title: 9QSA_PIM_0hr_Cy3_PIM_2hr_Cy5_14280087_MDS.mev.refIsIA.out


title: Hipp PDE9 Tg+, rep2


title: Hipp PDE9 Tg+, rep5


title: Patient 1, Myometrium

value: myometrium

value: female


title: alpha-TC1 cells, 01-hr treatment, 4.3uM, BRD-K17311666, Replicate1, Batch_04, HTA6_D03

description: alpha-TC1 cells


title: Hipp PDE9 Tg+, rep3


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T30_RepC

status: Public on Mar 08 2012

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

description: Rifampin treated M. tuberculosis

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide. Resulting images were processed with the Nimblescan software to generate pair files.

data_processing: Data was background subtracted using the average of 30,000 randomers, excluding the highest and lowest 5% of intensities and then normalized to tRNA Rvnt23.

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: M. tuberculosis H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C in a 1.3 L Bioflo 110 fermentor vessel.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Rifampicin was added to a final concentration of 50 ug/ul to stop transcription.  Samples were taken and immediately plunged into a dry ice ethanol bath to arrest mRNA decay, pelleted at 4C, and supe discarded.

tag: replicate

value: C

tag: minutes of mrna decay


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T60_RepB

description: Rifampin treated M. tuberculosis

value: B


title: alpha-TC1 cells, 01-hr treatment, 4.3uM, BRD-K17311666, Replicate2, Batch_09, HTA9_G09

description: alpha-TC1 cells

tag: cell line

tag: treatment


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T60_RepC

description: Rifampin treated M. tuberculosis


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T20_RepC

description: Rifampin treated M. tuberculosis


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T10_RepC

description: Rifampin treated M. tuberculosis


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T10_RepB

description: Rifampin treated M. tuberculosis


title: 9QSA_PIM_0hr_Cy3_PIM_1hr_Cy5_14280086_MDS.mev.refIsIA.out

value: P1 mutant

value: 1 h


title: Hipp PDE9 Tg+, rep1

tag: tissue


title: Hipp PDE9 Tg+, rep4


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T0_RepC

description: Rifampin treated M. tuberculosis


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T20_RepB

description: Rifampin treated M. tuberculosis


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T30_RepB

description: Rifampin treated M. tuberculosis


title: HCT116-1-sponge-sh30a-5p

city: Bochum

first: Stephan

last: Hahn

address: Universitaetsstrasse 150

department: MGO

country: Germany

institute: Ruhr-University Bochum

description: mRNA expression

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using standard setting

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: colon cancer cell line HCT116

label_protocol: 100 ng of total RNA werelabeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with  cyanine-5-CTP (Cy5)

growth_protocol: HCT116 cells were cultured in DMEM-media supplemented with 10% fetal calf serum, 100 U/ml penicillin and 100 μg/ml streptomycin. Cells were maintained in a humidified incubator with 10% CO2 at 37°C.

extract_protocol: RNA isolation from cell lines was performed using standard acid guanidinium thiocyanate-phenolchloroform extraction procedure. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

tag: vector


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T60_RepA

description: Rifampin treated M. tuberculosis

value: A


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T20_RepA

description: Rifampin treated M. tuberculosis


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T0_RepB

description: Rifampin treated M. tuberculosis


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T30_RepA

description: Rifampin treated M. tuberculosis


title: HCT116-2-sponge-sh30a-5p

description: mRNA expression


title: HCT116-1-sponge-LV

description: mRNA expression

value: sponge-LV


title: Aerobic_Atc induced DosR-RNAdeg_T0_RepC

description: Rifampin treated M. tuberculosis

source_name: Aerobic_Atc induced DosR-RNAdeg_T0


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T10_RepA

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T20_RepC

description: Rifampin treated M. tuberculosis

source_name: Aerobic_Atc induced DosR-RNAdeg_T20


title: HCT116-3-sponge-LV

description: mRNA expression


title: Aerobic_Uninduced DMSO control DosR-RNAdeg_T0_RepA

description: Rifampin treated M. tuberculosis


title: HCT116-3-sponge-sh30a-5p

description: mRNA expression


title: Aerobic_Atc induced DosR-RNAdeg_T30_RepC

description: Rifampin treated M. tuberculosis

source_name: Aerobic_Atc induced DosR-RNAdeg_T30


title: Aerobic_Atc induced DosR-RNAdeg_T60_RepB

description: Rifampin treated M. tuberculosis

source_name: Aerobic_Atc induced DosR-RNAdeg_T60


title: Aerobic_Atc induced DosR-RNAdeg_T10_RepC

description: Rifampin treated M. tuberculosis

source_name: Aerobic_Atc induced DosR-RNAdeg_T10


title: Aerobic_Atc induced DosR-RNAdeg_T60_RepC

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T20_RepB

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T10_RepB

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T60_RepA

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T5_RepC

description: Rifampin treated M. tuberculosis

tag: hours of mrna decay


title: Aerobic_Atc induced DosR-RNAdeg_T0_RepB

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T30_RepA

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T20_RepA

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T1_RepC

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T2_RepC

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T0_RepA

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T30_RepB

description: Rifampin treated M. tuberculosis


title: HCT116-2-sponge-LV

description: mRNA expression


title: HypoxicStress_RNAdeg_T5_RepA

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T0_RepB

description: Rifampin treated M. tuberculosis


title: Aerobic_Atc induced DosR-RNAdeg_T10_RepA

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T5_RepB

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T1_RepB

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T0_RepC

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T2_RepA

description:
Rifampin treated M. tuberculosis
Bubbles in array


title: HypoxicStress_RNAdeg_T2_RepB

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T1_RepA


title: ColdStress_RNAdeg_T5_RepC

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T1_RepC

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T1_RepB

description: Rifampin treated M. tuberculosis


title: HypoxicStress_RNAdeg_T0_RepA

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T0_RepC

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T2_RepB

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T5_RepB

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T0_RepB

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T2_RepC

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T2_RepA


title: ColdStress_RNAdeg_T0_RepA

description: Rifampin treated M. tuberculosis


title: ColdStress_RNAdeg_T1_RepA


title: ColdStress_RNAdeg_T5_RepA

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T30_repF

description: Rifampin treated M. tuberculosis

value: F


title: Aerobic-RNA-deg_T15_repF

description: Rifampin treated M. tuberculosis


title: Aerobic_mSmeg-RNAdeg_T0_RepB

description: Rifampin treated M. smegmatis

organism: Mycolicibacterium smegmatis MC2 155

growth_protocol: Mycobacterium smegmatis str. MC2 155 was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C in a 1.3 L Bioflo 110 fermentor vessel.


title: Aerobic_mSmeg-RNAdeg_T-5_RepC

description: Rifampin treated M. smegmatis


title: Aerobic-RNA-deg_T20_repF

description: Rifampin treated M. tuberculosis


title: Aerobic_mSmeg-RNAdeg_T5_RepC

description: Rifampin treated M. smegmatis


title: Aerobic_mSmeg-RNAdeg_T0_RepC

description: Rifampin treated M. smegmatis


title: Aerobic_mSmeg-RNAdeg_T-5_RepB

description: Rifampin treated M. smegmatis


title: Aerobic-RNA-deg_T10_repF

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T5_repF

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T30_repE

description: Rifampin treated M. tuberculosis

value: E


title: Aerobic-RNA-deg_T0_repF

description: Rifampin treated M. tuberculosis


title: Aerobic_mSmeg-RNAdeg_T5_RepB

description: Rifampin treated M. smegmatis


title: Aerobic_mSmeg-RNAdeg_T0_RepA

description: Rifampin treated M. smegmatis


title: Aerobic_mSmeg-RNAdeg_T5_RepA

description: Rifampin treated M. smegmatis


title: Aerobic_mSmeg-RNAdeg_T-5_RepA

description: Rifampin treated M. smegmatis


title: Whole blood, individual 10, rep 1, array 4

city: Richmond

first: Karolina

last: Aberg

state: VA

address: 1112 East Clay Street

department: Center for Biomarker Resarch & Personalized Medicine

institute: Virginia Commonwealth University

description: Sample 028

hyb_protocol: DNA was hybridized to the Affymetrix GeneChip® Human Tiling 2.0R array set overnight. The following day, the arrays were washed according to the manufacturer's protocol.

scan_protocol: The arrays were scanned according to the manufacturer's protocol.

data_processing:
The data was background-corrected using the robust multi-array (RMA) procedure, which models the probe intensities as signal plus noise, assuming exponential distribution for the signal and normal distribution for the noise (Irizarry RA, Hobbs B, Collin F et al: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003; 4: 249-264.). Next, we used quantile normalization, which first sorts the probe intensities for each individual array and then averages across all arrays. Finally, to obtain the normalized results for any particular array, we re-order the averages obtained above so as to match the original ordering of the probe intensities on the array (Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003; 19: 185-193.).

Background-corrected and quantile-normalized data is provided for all 30 samples per chromosome. The files are available as supplementary files on the GSE35204 record.

source_name: whole blood, individual 10

label_protocol: Following the manufacturers’ protocols, DNA was fragmented with MseI to a median size of 500 bp and the methylome was enriched for using MethylMiner (Invitrogen, Carlsbad, CA, USA) and further amplified using the Sigma WGA2 kit (Sigma-Aldrich, St. Louis, MO, USA). The amplified methylomes were fragmented using the Affymetrix (Santa Clara, CA, USA) 6.0 fragment reagents and labeled using the Affymetrix WT-ds DNA Terminal labeling kit.

extract_protocol: Genomic DNA was extracted from whole blood and the EBV-LCLs.

value: whole blood

tag: individual


title: EBV-LCL, individual 8, array 4

description: Sample 024

source_name: EBV-LCL, individual 8

tag: cell type

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: EBV-LCL, individual 9, array 4

description: Sample 027

source_name: EBV-LCL, individual 9


title: Whole blood, individual 10, rep 2, array 4

description: Sample 029


title: Whole blood, individual 9, rep 2, array 4

description: Sample 026

source_name: whole blood, individual 9


title: Whole blood, individual 9, rep 1, array 4

description: Sample 025


title: Aerobic-RNA-deg_T15_repE

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T20_repE

description: Rifampin treated M. tuberculosis


title: Whole blood, individual 8, rep 2, array 4

description: Sample 023

source_name: whole blood, individual 8


title: EBV-LCL, individual 10, array 4

description: Sample 030

source_name: EBV-LCL, individual 10


title: Aerobic-RNA-deg_T5_repE

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T0_repE

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T30_repB

description: Rifampin treated M. tuberculosis


title: Whole blood, individual 8, rep 1, array 4

description: Sample 022


title: Aerobic-RNA-deg_T10_repE

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T30_repA

description: Rifampin treated M. tuberculosis


title: EBV-LCL, individual 7, array 4

description: Sample 021

source_name: EBV-LCL, individual 7


title: Whole blood, individual 7, rep 2, array 4

description: Sample 020

source_name: whole blood, individual 7


title: Aerobic-RNA-deg_T20_repB

description: Rifampin treated M. tuberculosis


title: Whole blood, individual 7, rep 1, array 4

description: Sample 019


title: EBV-LCL, individual 6, array 4

description: Sample 018

source_name: EBV-LCL, individual 6


title: Whole blood, individual 6, rep 2, array 4

description: Sample 017

source_name: whole blood, individual 6


title: Aerobic-RNA-deg_T15_repA

description: Rifampin treated M. tuberculosis


title: Whole blood, individual 6, rep 1, array 4

description: Sample 016


title: Aerobic-RNA-deg_T15_repB

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T20_repA

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T10_repB

description: Rifampin treated M. tuberculosis


title: Whole blood, individual 5, rep 1, array 4

description: Sample 013

source_name: whole blood, individual 5


title: EBV-LCL, individual 4, array 4

description: Sample 012

source_name: EBV-LCL, individual 4


title: Aerobic-RNA-deg_T5_repB

description: Rifampin treated M. tuberculosis


title: Aerobic-RNA-deg_T10_repA

description: Rifampin treated M. tuberculosis


title: Whole blood, individual 5, rep 2, array 4

description: Sample 014


title: EBV-LCL, individual 5, array 4

description: Sample 015

source_name: EBV-LCL, individual 5


title: Aerobic-RNA-deg_T5_repA

description: Rifampin treated M. tuberculosis


title: EBV-LCL, individual 3, array 4

description: Sample 009

source_name: EBV-LCL, individual 3


title: Whole blood, individual 3, rep 2, array 4

description: Sample 008

source_name: whole blood, individual 3


title: Whole blood, individual 4, rep 1, array 4

description: Sample 010

source_name: whole blood, individual 4


title: Aerobic-RNA-deg_T0_repA

description: Rifampin treated M. tuberculosis


title: Whole blood, individual 4, rep 2, array 4

description: Sample 011


title: Whole blood, individual 3, rep 1, array 4

description: Sample 007


title: EBV-LCL, individual 1, array 4

description: Sample 003

source_name: EBV-LCL, individual 1


title: Whole blood, individual 2, rep 2, array 4

description: Sample 005

source_name: whole blood, individual 2


title: Whole blood, individual 2, rep 1, array 4

description: Sample 004


title: Whole blood, individual 1, rep 2, array 4

description: Sample 002

source_name: whole blood, individual 1


title: Whole blood, individual 1, rep 1, array 4

description: Sample 001


title: Whole blood, individual 10, rep 2, array 3

description: Sample 029

source_name: whole blood, individual 10


title: EBV-LCL, individual 10, array 3

description: Sample 030


title: Whole blood, individual 10, rep 1, array 3

description: Sample 028


title: Aerobic-RNA-deg_T0_repB

description: Rifampin treated M. tuberculosis


title: EBV-LCL, individual 2, array 4

description: Sample 006

source_name: EBV-LCL, individual 2


title: EBV-LCL, individual 9, array 3

description: Sample 027

source_name: EBV-LCL, individual 9


title: Whole blood, individual 9, rep 2, array 3

description: Sample 026

source_name: whole blood, individual 9


title: Familial colorectal cancer type X_67_rep1

city: Lund

first: Mev

last: Dominguez

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina iScan N240 scanning protocol.

data_processing: Illumina gene expression data were loaded and interpreted in GenomeStudio software (Illumina, San Diego, CA).  Data were normalized using background correction, the cubic spline method and plate scaling. Normalized gene expression data were then exported, and only RefSeq features with a detection  P value of ≤0.01 in at least 80% of the samples (n=122) were used in further analyses. Technical replicates within samples were average combined to create one signature per tumor. Next, data were loaded into MeV v4 (Saeed et al. 2003), where they were log2 transformed and median centered across assays. Significance analysis of microarrays (SAM) was used to identify significantly differentially expressed genes (false-discovery rate, FDR ≤ 5%). Hierarchical clustering and SAM were done in MeV (Saeed et al. 2003).

source_name: Colorectal cancer, FCCTX

label_protocol: Ligated products were PCR-amplified and labeled with a universal Cy3-coupled primer, after which single-stranded labeled products were precipitated and then hybridized to WG gene expression BeadChips as previously described (Kuhn et al. 2004).

extract_protocol: Three to five 5 μm sections per FFPE block were used for RNA isolation. RNA deparaffinization, extraction and purification were performed using the High Pure RNA Paraffin Kit (Roche, Castle Hill, Australia) according to the manufacturer's instructions. RNA concentration was determined using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and samples yielding sufficient RNA (200 ng) with 260/280 ratios >1.8 were selected.

value: colorectal cancer

tag: disease state

value: familial colorectal cancer type X (FCCTX)

tag: age

value: male


title: Sporadic Colorectal Cancer MMR proficient tumors_10

source_name: Colorectal cancer, sporadic

value: sporadic colorectal cancer


title: Lynch syndrome_75_rep1

source_name: Colorectal cancer, LS

value: Lynch syndrome


title: Sporadic Colorectal Cancer MMR deficient tumors_4_rep2


title: Lynch syndrome_75_rep2


title: Sporadic Colorectal Cancer MMR deficient tumors_34_rep1


title: Sporadic Colorectal Cancer MMR deficient tumors_106


title: Sporadic Colorectal Cancer MMR deficient tumors_84


title: Lynch syndrome_40_rep2


title: Sporadic Colorectal Cancer MMR deficient tumors_4_rep1


title: Sporadic Colorectal Cancer MMR deficient tumors_59


title: Lynch syndrome_40_rep1


title: Whole blood, individual 8, rep 2, array 3

description: Sample 023

source_name: whole blood, individual 8


title: Sporadic Colorectal Cancer MMR deficient tumors_110


title: EBV-LCL, individual 8, array 3

description: Sample 024

source_name: EBV-LCL, individual 8


title: Sporadic Colorectal Cancer MMR deficient tumors_16


title: Sporadic Colorectal Cancer MMR deficient tumors_81


title: Sporadic Colorectal Cancer MMR deficient tumors_38


title: EBV-LCL, individual 7, array 3

description: Sample 021

source_name: EBV-LCL, individual 7


title: Whole blood, individual 8, rep 1, array 3

description: Sample 022


title: Whole blood, individual 7, rep 2, array 3

description: Sample 020

source_name: whole blood, individual 7


title: Whole blood, individual 7, rep 1, array 3

description: Sample 019


title: EBV-LCL, individual 6, array 3

description: Sample 018

source_name: EBV-LCL, individual 6


title: Whole blood, individual 6, rep 2, array 3

description: Sample 017

source_name: whole blood, individual 6


title: Whole blood, individual 9, rep 1, array 3

description: Sample 025


title: Whole blood, individual 6, rep 1, array 3

description: Sample 016


title: Sporadic Colorectal Cancer MMR deficient tumors_45


title: Sporadic Colorectal Cancer MMR deficient tumors_91


title: Lynch syndrome_111


title: EBV-LCL, individual 4, array 3

description: Sample 012

source_name: EBV-LCL, individual 4


title: Whole blood, individual 5, rep 2, array 3

description: Sample 014

source_name: whole blood, individual 5


title: Lynch syndrome_99


title: Whole blood, individual 4, rep 2, array 3

description: Sample 011

source_name: whole blood, individual 4


title: Lynch syndrome_108


title: Whole blood, individual 5, rep 1, array 3

description: Sample 013


title: EBV-LCL, individual 3, array 3

description: Sample 009

source_name: EBV-LCL, individual 3


title: Whole blood, individual 4, rep 1, array 3

description: Sample 010


title: Lynch syndrome_169


title: Lynch syndrome_198


title: Sporadic Colorectal Cancer MMR deficient tumors_12


title: Whole blood, individual 3, rep 2, array 3

description: Sample 008

source_name: whole blood, individual 3


title: Lynch syndrome_68


title: Lynch syndrome_80


title: Lynch syndrome_159


title: Lynch syndrome_136


title: Sporadic Colorectal Cancer MMR deficient tumors_89


title: EBV-LCL, individual 5, array 3

description: Sample 015

source_name: EBV-LCL, individual 5


title: Whole blood, individual 3, rep 1, array 3

description: Sample 007


title: Lynch syndrome_14


title: Whole blood, individual 2, rep 2, array 3

description: Sample 005

source_name: whole blood, individual 2


title: Whole blood, individual 2, rep 1, array 3

description: Sample 004


title: EBV-LCL, individual 1, array 3

description: Sample 003

source_name: EBV-LCL, individual 1


title: EBV-LCL, individual 2, array 3

description: Sample 006

source_name: EBV-LCL, individual 2


title: Whole blood, individual 1, rep 1, array 3

description: Sample 001

source_name: whole blood, individual 1


title: Lynch syndrome_37

source_name: Colorectal cancer, LS


title: Lynch syndrome_130


title: EBV-LCL, individual 9, array 1

description: Sample 027

source_name: EBV-LCL, individual 9


title: Whole blood, individual 10, rep 2, array 1

description: Sample 029

source_name: whole blood, individual 10


title: EBV-LCL, individual 10, array 1

description: Sample 030

source_name: EBV-LCL, individual 10


title: Whole blood, individual 10, rep 1, array 1

description: Sample 028


title: Whole blood, individual 9, rep 2, array 1

description: Sample 026

source_name: whole blood, individual 9


title: Lynch syndrome_92


title: Lynch syndrome_51


title: EBV-LCL, individual 8, array 1

description: Sample 024

source_name: EBV-LCL, individual 8


title: Lynch syndrome_199


title: Lynch syndrome_172


title: Lynch syndrome_9


title: Familial colorectal cancer type X_35

source_name: Colorectal cancer, FCCTX


title: Lynch syndrome_190


title: Familial colorectal cancer type X_75


title: Lynch syndrome_145


title: Familial colorectal cancer type X_19


title: Familial colorectal cancer type X_64


title: Whole blood, individual 8, rep 2, array 1

description: Sample 023

source_name: whole blood, individual 8


title: Whole blood, individual 1, rep 2, array 3

description: Sample 002


title: Whole blood, individual 9, rep 1, array 1

description: Sample 025


title: Whole blood, individual 8, rep 1, array 1

description: Sample 022


title: Lynch syndrome_187


title: Familial colorectal cancer type X_57


title: Familial colorectal cancer type X_89


title: Lynch syndrome_114


title: Familial colorectal cancer type X_84


title: EBV-LCL, individual 7, array 1

description: Sample 021

source_name: EBV-LCL, individual 7


title: Whole blood, individual 7, rep 2, array 1

description: Sample 020

source_name: whole blood, individual 7


title: EBV-LCL, individual 6, array 1

description: Sample 018

source_name: EBV-LCL, individual 6


title: Whole blood, individual 7, rep 1, array 1

description: Sample 019


title: Whole blood, individual 6, rep 2, array 1

description: Sample 017

source_name: whole blood, individual 6


title: EBV-LCL, individual 5, array 1

description: Sample 015

source_name: EBV-LCL, individual 5


title: Whole blood, individual 5, rep 2, array 1

description: Sample 014

source_name: whole blood, individual 5


title: Whole blood, individual 5, rep 1, array 1

description: Sample 013


title: Whole blood, individual 4, rep 2, array 1

description: Sample 011

source_name: whole blood, individual 4


title: Familial colorectal cancer type X_34


title: Familial colorectal cancer type X_22


title: Familial colorectal cancer type X_27


title: Familial colorectal cancer type X_46


title: Familial colorectal cancer type X_79


title: Familial colorectal cancer type X_10


title: Familial colorectal cancer type X_6_rep1


title: Familial colorectal cancer type X_85


title: Familial colorectal cancer type X_28


title: Familial colorectal cancer type X_39


title: Familial colorectal cancer type X_21


title: Familial colorectal cancer type X_56


title: Whole blood, individual 3, rep 2, array 1

description: Sample 008

source_name: whole blood, individual 3


title: Familial colorectal cancer type X_55_rep1


title: Whole blood, individual 3, rep 1, array 1

description: Sample 007


title: Whole blood, individual 6, rep 1, array 1

description: Sample 016


title: Whole blood, individual 4, rep 1, array 1

description: Sample 010


title: EBV-LCL, individual 4, array 1

description: Sample 012

source_name: EBV-LCL, individual 4


title: EBV-LCL, individual 2, array 1

description: Sample 006

source_name: EBV-LCL, individual 2


title: Sporadic Colorectal Cancer MMR proficient tumors_82

source_name: Colorectal cancer, sporadic


title: Sporadic Colorectal Cancer MMR proficient tumors_35


title: Sporadic Colorectal Cancer MMR proficient tumors_56


title: Whole blood, individual 2, rep 1, array 1

description: Sample 004

source_name: whole blood, individual 2


title: EBV-LCL, individual 3, array 1

description: Sample 009

source_name: EBV-LCL, individual 3


title: Whole blood, individual 1, rep 2, array 1

description: Sample 002

source_name: whole blood, individual 1


title: Sporadic Colorectal Cancer MMR proficient tumors_76


title: Whole blood, individual 1, rep 1, array 1

description: Sample 001


title: Whole blood, individual 10, rep 2, array 2

description: Sample 029

source_name: whole blood, individual 10


title: EBV-LCL, individual 10, array 2

description: Sample 030

source_name: EBV-LCL, individual 10


title: Whole blood, individual 9, rep 2, array 2

description: Sample 026

source_name: whole blood, individual 9


title: Sporadic Colorectal Cancer MMR proficient tumors_79


title: EBV-LCL, individual 9, array 2

description: Sample 027

source_name: EBV-LCL, individual 9


title: Whole blood, individual 9, rep 1, array 2

description: Sample 025


title: EBV-LCL, individual 8, array 2

description: Sample 024

source_name: EBV-LCL, individual 8


title: Whole blood, individual 2, rep 2, array 1

description: Sample 005


title: Sporadic Colorectal Cancer MMR proficient tumors_88


title: Sporadic Colorectal Cancer MMR proficient tumors_36


title: Sporadic Colorectal Cancer MMR proficient tumors_3


title: Sporadic Colorectal Cancer MMR proficient tumors_16


title: Sporadic Colorectal Cancer MMR proficient tumors_2


title: Sporadic Colorectal Cancer MMR deficient tumors_35 rep2


title: Familial colorectal cancer type X_41

source_name: Colorectal cancer, FCCTX


title: Whole blood, individual 8, rep 1, array 2

description: Sample 022

source_name: whole blood, individual 8


title: EBV-LCL, individual 1, array 1

description: Sample 003

source_name: EBV-LCL, individual 1


title: Sporadic Colorectal Cancer MMR proficient tumors_73


title: EBV-LCL, individual 7, array 2

description: Sample 021

source_name: EBV-LCL, individual 7


title: Whole blood, individual 7, rep 2, array 2

description: Sample 020

source_name: whole blood, individual 7


title: EBV-LCL, individual 6, array 2

description: Sample 018

source_name: EBV-LCL, individual 6


title: Whole blood, individual 7, rep 1, array 2

description: Sample 019


title: Sporadic Colorectal Cancer MMR deficient tumors_34_rep2