title: Expression data of LM-024

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_024


title: L1513N

status: Public on Aug 26 2011

type: genomic

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

description: Corresponding tumor: L1513

scan_protocol: GeneChip GSC3000 7G Whole-Genome Association System. According to Affymetrix SNP 6.0 standard protocol.

data_processing: Genotyping was performed using the CRLMM algorithm in the Oligo package (Lin, 2008), copy number analysis using the aroma affymetrix package (Bengtsson, 2009), and we constructed LAIR plots to visualize regions of LOH and allelic imbalance (Corver, 2008) in R software (version 2.8). We have used CNCHP log ratio file as an input in Nexus (BioDiscovery, USA) software (version 4.1) and performed HMM based SNP-FASST segmentation for copy number analysis. Copy number inferred after correction with the 5 closest normals.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Ollier patient normal (fresh frozen)

extract_protocol: DNA from fresh frozen tissue was isolated using the Wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.

tag: tissue

value: fresh frozen normal

tag: disease

value: Ollier


title: L2639N

description: This sample is saliva DNA from the patient who had polyostotic chondrosarcoma.

hyb_protocol: According to Affymetrix SNP 6.0 standard protocol.

source_name: Patient normal (polyostotic tumor)

extract_protocol: Saliva DNA was isolated using the Oragene DNA kit (DNA Genotek Inc Ontario, Canada) according to the protocol provided by the supplier and DNA was precipitated using sodium acetate precipitation. DNA concentration was quantified spectrophotometrically using Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA) and the fragment sizes were determined on 1% agarose gel.

value: saliva

tag: sample type

value: control


title: L813

description: According to Affymetrix SNP 6.0 standard protocol.

source_name: Ollier chondrosarcoma grade II

value: chondrosarcoma grade II

tag: tumor location

value: humerus

tag: gender

value: male

tag: age


title: Expression data of LM-023

type: RNA

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

description: TRAINING, LM-P

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

molecule: total RNA

source_name: Colorecal Cancer, Patient_023

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

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturerüfs instructions.

tag: Tissue

value: Colorecal Cancer


title: Expression data of LM-021

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_021


title: L910

description: Another tumor: L206

source_name: Ollier enchondroma

label_protocol: According to Affymetrix SNP 6.0 standard protocol.

value: enchondroma

value: phalanx

value: female


title: Expression data of LM-022

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_022


title: L1980

value: knee


title: L2218

description: Another tumor: L1083

source_name: Ollier chondrosarcoma I

value: chondrosarcoma grade I


title: L2104a

description: Another tumor: L2103b

source_name: Ollier chondrosarcoma grade III

value: chondrosarcoma grade III

value: tibia


title: L2104b

value: femur


title: L206

description: Another tumor: L910


title: Expression data of LM-019

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_019


title: Expression data of LM-020

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_020


title: L1683

value: metacarpal


title: L2205

value: ilium


title: L2463

description: Corresponding normal: L2463N

value: Ollier


title: L1083

description: Another tumor: L2218

source_name: Ollier chondrosarcoma grade I


title: L2258N

description: Patient had an angiosarcoma and we used normal tissue from this patient as a control.

source_name: Patient normal (fresh frozen tissue) used as a control

value: fresh frozen normal


title: Expression data of LM-018

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_018


title: L810

tag: location


title: L2386


title: Expression data of LM-016

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_016


title: L2513

value: pelvis


title: L2103a

description: Another tumor: L2103b


title: Expression data of LM-015

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_015


title: L2103b

description: Another tumor: L2103a.


title: Expression data of LM-017

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_017


title: Expression data of LM-014

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_014


title: Expression data of LM-013

description: TEST, LM-P

source_name: Colorecal Cancer, Patient_013


title: Expression data of LM-012

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_012


title: Expression data of LM-011

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_011


title: L2280

description: Corresponding normal: L2280N

value: acromion


title: Expression data of LM-007

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_007


title: Expression data of LM-008

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_008


title: Expression data of LM-009

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_009


title: L2280N

description: Corresponding tumor: L2280

source_name: Ollier patient normal (blood DNA)

extract_protocol: Blood DNA was isolated as described in Miller SA, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988;16:1215 (PMID 3344216).

value: blood

value: control


title: Expression data of LM-006

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_006

value: Colorecal Cancer


title: Expression data of LM-010

description: TEST, LM-N

source_name: Colorecal Cancer, Patient_010


title: Expression data of LM-005

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_005


title: Expression data of LM-004

description: TRAINING, LM-N

source_name: Colorecal Cancer, Patient_004


title: L1513

description: Corresponding normal: L1513N

source_name: Ollier chondrosarcoma grade I


title: L2221

description: Ccorresponding normal: L2221N


title: Expression data of LM-002

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_002


title: L2221N

description: corresponding tumor: L2221

source_name: Ollier patient normal

value: saliva


title: Expression data of LM-003

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_003


title: L1490N

description: corresponding tumor: L1490


title: L2463N

description: Corresponding tumor is L2463

source_name: Ollier patient normal (fresh frozen)


title: L2099

source_name: Ollier chondrosarcoma grade II

value: chondrosarcoma grade II

value: humerus


title: BrdUIP_hsk1ts_mrc1∆_30ºC_60minHU

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 6µg of DNA was hybridized to Affymetrix S. pombe Tiling 1.0FR Array using Affymetrix recommend component. The arrays were hybridized for 16 hours at 42ºC at 60 rpm using an Affymetrix hybridization oven.

scan_protocol: Standard protocol by Affymetrix

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Input fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.001 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction or BrdU-incorporation region will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

label: Biotin

organism: Schizosaccharomyces pombe

source_name: BrdU IPed from BrdU-incorporated DNA

label_protocol: About 10µg amplified DNA was fragmented to 50bp with DNase I, and the ends of the fragments were labeled with biotin-6N-ddATP by terminal transferase.

growth_protocol: The stains were grown until exponential phase in YES medium and arrest at Metaphase at 20ºC for 5hr or 8hr. The arrested cells were released into subsequential phase at 30ºC for 60min.

extract_protocol:
Growing nda3-KM311 cells (1.0 x 10E9 cells) expressing Thymidine Kinase under control by Adh1 promoter, mrc1∆, and hsk1ts were arrested at metaphase and release in the presence of 200µM BrdU and 25mM HU at 30C for 60min. BrdU was incorporated into nascent DNA during the sub-sequential S-phase. The genomic DNA was extracted and purified by Qiagen Genomic DNA Buffer Set and Genomic-tip. BrdU-incorporated DNA after shearing and denature was immuno-precipitated by anti-bromodeoxyuridine (MBL) and purified by QIAquick PCR Purification Kit (QIAGEN). The catalog Number, Clone and Subclass of Anti-Bromodeoxyuridine (MBL) antibody are MI-11-3, 2B1 and mouse IgG1 respectively.
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).

treatment_protocol: The stains were treated with 200µM BrdU and 25mM Hydroxyurea after Metaphase arrest.

tag: cell type

value: hsk1-89, mrc1∆

tag: cell cycle

value: Early S-phase in HU at 60min after release from metaphase arrst

value: BrdU

tag: antibody

value: Anti-bromodeoxyuridine (MBL)

source_name: Input DNA from Metaphase arrested cells

extract_protocol:
The genomic DNA was extracted and purified from the arrested at M-phase in nda-KM311 cells. The genomic DNA was sheared by sonication.
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).

value: input


title: L1490

description: Corresponding normal: L1490N

source_name: Ollier enchondroma

value: enchondroma

value: phalanx

value: female


title: Expression data of LM-001

description: TRAINING, LM-P

source_name: Colorecal Cancer, Patient_001


title: L2098

value: Ollier


title: L1629

description: Another tumor: L1630

value: unknown

value: male


title: L1687

description: Another tumor: L1686

value: chondrosarcoma grade I


title: BrdUIP_mrc1∆_60minHU

extract_protocol:
Growing nda3-KM311 cells (1.0 x 10E9 cells) expressing Thymidine Kinase under control by Adh1 promoter and mrc1∆ were arrested at metaphase and release in the presence of 200µM BrdU and 25mM HU at 30C for 60min. BrdU was incorporated into nascent DNA during the sub-sequential S-phase. The genomic DNA was extracted and purified by Qiagen Genomic DNA Buffer Set and Genomic-tip. BrdU-incorporated DNA after shearing and denature was immuno-precipitated by anti-bromodeoxyuridine (MBL) and purified by QIAquick PCR Purification Kit (QIAGEN). The catalog Number, Clone and Subclass of Anti-Bromodeoxyuridine (MBL) antibody are MI-11-3, 2B1 and mouse IgG1 respectively.
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).


title: BrdUIP_hsk1ts_30C_60minHU

extract_protocol:
Growing nda3-KM311 cells (1.0 x 10E9 cells) expressing Thymidine Kinase under control by Adh1 promoter and hsk1ts were arrested at metaphase and release in the presence of 200µM BrdU and 25mM HU at 30C for 60min. BrdU was incorporated into nascent DNA during the sub-sequential S-phase. The genomic DNA was extracted and purified by Qiagen Genomic DNA Buffer Set and Genomic-tip. BrdU-incorporated DNA after shearing and denature was immuno-precipitated by anti-bromodeoxyuridine (MBL) and purified by QIAquick PCR Purification Kit (QIAGEN). The catalog Number, Clone and Subclass of Anti-Bromodeoxyuridine (MBL) antibody are MI-11-3, 2B1 and mouse IgG1 respectively.
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).


title: BrdUIP_cds1∆_60minHU

extract_protocol:
Growing nda3-KM311 cells (1.0 x 10E9 cells) expressing Thymidine Kinase under control by Adh1 promoter and cds1∆ were arrested at metaphase and release in the presence of 200µM BrdU and 25mM HU at 30C for 60min. BrdU was incorporated into nascent DNA during the sub-sequential S-phase. The genomic DNA was extracted and purified by Qiagen Genomic DNA Buffer Set and Genomic-tip. BrdU-incorporated DNA after shearing and denature was immuno-precipitated by anti-bromodeoxyuridine (MBL) and purified by QIAquick PCR Purification Kit (QIAGEN). The catalog Number, Clone and Subclass of Anti-Bromodeoxyuridine (MBL) antibody are MI-11-3, 2B1 and mouse IgG1 respectively.
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).


title: L1685

value: chondrosarcom grade I

value: pubic bone


title: 163

source_name: Blood DNA from healthy donor

value: blood

value: healthy

value: control


title: L1978

description:
Corresponding normal: L2278N
Another tumor: L1977

value: foot


title: L1630

description: Another tumor: L1629

value: iliac bone


title: 293_Stop_B_replicate 2

city: Frederick

first: Jun

last: Yang

state: MD

address: P. O. Box B

country: USA

institute: SAIC-Frederick, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek software. RMA normalization with GC content correction.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: vector with nef stop code was transfected into 293 cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HEK293 cells were grown in DMEM medium containing 10% fetal bovine serum.

extract_protocol: Cells were collected in RLT buffer. Total RNA was isolated using Qiagen Rneasy kit. cDNA synthesis and amplification used Ambion  WT expression kit.

treatment_protocol: HEK293 cells were transfected with optimized HIV-1 Nef expressing palsmid and a control non-expressing Nef plasmid using Fugene-HD transfection reagent. Cells were harvested for analysis after 36 h of transfection.

tag: cell line

tag: vector

value: Stop


title: 293_Stop_C_replicate 1


title: 293_Stop_C_replicate 2


title: Mice fed with control diet

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description:
CT-4
Gene expression data from mice fed with control diet.

hyb_protocol: cRNA was hybridized to Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).

scan_protocol: Affymetrix standard protocol.

data_processing: The MAS5 algorithm was run using GCOS Affymetrix software as follows: the scaling factor using all probe sets was set to 100, the normalize factor was set to 1 and the baseline comparison was done on the control diet hybridization samples.

organism: Mus musculus

source_name: liver tissue, control diet

label_protocol: Biotin-labeled cRNA was synthesized using the GeneChip IVT labelling kit (Affymetrix, Santa Clara, USA).

growth_protocol: Male C57Bl/6J mice (9 weeks old; Charles River, Brussels, Belgium) were housed in groups of four mice per cage at 22°C in a 12h light/dark cycle and given free access to diet and water.

extract_protocol: Total RNA was isolated from liver tissue of fasted and fed mice using the TriPure reagent (Roche, Basel, Switzerland). RNA quality was checked using Bioanalyzer (Agilent). Equal amounts of RNA from each mouse (n = 4 to 7 mice per group) were pooled within each group. Double-stranded cDNA was synthesized from total RNA using the One-cycle cDNA synthesis kit (Affymetrix, Santa Clara, USA).

treatment_protocol: After an acclimatization period of 1 week, the mice were fed a control diet (CT) (D08041805, Research diets, New Brunswick, USA) or an n-3 PUFA-depleted diet (DEF) (D08041806, Research diets, New Brunswick, USA) for 3 months. The CT diet contained the following (percent w/w): casein 20, total carbohydrate 72.4 (including corn starch 44.2, sucrose 10, maltodextrin 13.2, cellulose 5), soybean oil 5, mineral mix 3.5 and vitamin mix 1. The depletion was induced by replacing the soybean oil with sunflower oil, which exhibited a higher n-6/n-3 PUFA ratio. The n-6/n-3 PUFA ratio was 6.9 and 127.2 for the CT diet and the DEF diet, respectively. At the end of the study period, mice (CT, n=6; DEF, n=7) were anesthetized (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively) after a 6h period of fasting. Some mice (CT: n=4 et DEF: n=7) were anesthetized without being starved. Vena cava blood samples were collected in EDTA tubes. After centrifugation (10 min at 1500g), plasma was stored at –80 °C. A fraction of the main liver lobe was fixed-frozen in isopentane and kept at -80°C for histological analysis. The excess tissue material was immediately clamped in liquid N2 and kept at -80°C.

tag: strain

value: liver

tag: treatment

value: control diet


title: L1977

description:
Corresponding normal: L2278N
Another tumor from the same patient: L1978

value: tibia


title: L2278N

description: Patient has L1977 and L1978 tumors.

value: normal blood


title: Mice fed with n-3 PUFA-depleted diet

description:
DEF-4
Gene expression data from mice fed with n-3 PUFA-depleted diet.

source_name: liver tissue, n-3 PUFA-deficient diet

value: n-3 polyunsaturated fatty acids (PUFA)-deficient diet


title: L1251

description:
Corresponding normal: L1253
Another tumor L2220 is from the same patient.

value: Ollier

value: enchondroma

value: phalanx


title: 293_Stop_B_replicate 1


title: L2276N

description: Patient has tumor L1975.

value: male


title: 293_Nef_C_replicate 1

source_name: Nef vector was transfected into 293 cells

value: nef


title: Mice fed with n-3 PUFA-depleted diet and starved before sacrifice

description:
DEF-1
Gene expression data from mice fed with n-3 PUFA-depleted diet and starved before sacrifice.

source_name: liver tissue, n-3 PUFA-deficient diet, starved

value: n-3 polyunsaturated fatty acids (PUFA)-deficient diet followed by starvation


title: L1253N

description: This patient has two tumors L2220 and L1251.


title: L2277N

description: Corresponding tumor from the patient is L1976.


title: Mice fed with control diet and starved before sacrifice

description:
CT-1
Gene expression data from mice fed with control diet and starved before sacrifice.

source_name: liver tissue, control diet, starved

value: control diet followed by starvation


title: 293_Nef_C_replicate 2


title: 293_Stop_A_replicate 1


title: 293_Stop_A_replicate 2


title: 168

value: blood

value: healthy


title: L1976

description: Corresponding normal: L2277N

value: chondrosarcoma grade II


title: L253

source_name: Ollier chondrosarcoma grade I

value: chondrosarcoma grade I


title: 293_Nef_B_replicate 1


title: 293_Nef_A_replicate 2


title: 293_Nef_B_replicate 2


title: 293_Nef_A_replicate 1


title: 294

value: control


title: L2220

description:
Corresponding normal: L1253
Another tumor from the same patient: L1251

value: metacarpal


title: L1975

value: femur


title: Liver_untreated, rep35

status: Public on Aug 25 2011

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

country: Switzerland

institute: F.Hoffmann-La Roche AG

description:
362669A11
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 5 (Roche NimbleGen, Inc.).

organism: Macaca fascicularis

source_name: Untreated fresh-frozen liver, Mauritius

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The 36 liver samples were taken from untreated animals of GLP drug safety studies carried out at a contract research organization in accordance with current animal protection standards.

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). RNA quality and concentration were determined by analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

value: liver

tag: origin

value: Mauritius

value: 2 - 4 years

tag: weight

tag: facility

value: Germany


title: Liver_untreated, rep36

description:
384658A06
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

tag: tissue

value: female


title: 295

description: Affymetrix SNP 6.0 arrays were used.

tag: disease

tag: sample type


title: Liver_untreated, rep34

description:
384662A04
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

tag: gender


title: L286N

description: Corresponding tumor ID is L286 from the same patient.

source_name: Ollier patient normal (frozen tissue)

value: frozen normal tissue

value: Ollier


title: Liver_untreated, rep28

description:
384658A01
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: male

tag: age

value: 3 - 6 years


title: Liver_untreated, rep31

description:
384658A04
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep26

description:
384662A10
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep29

description:
384662A06
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep32

description:
362669A01
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep30

description:
362669A12
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep24

description:
384662A07
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep22

description:
384658A12
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep23

description:
384658A10
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep33

description:
384658A11
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep21

description:
384662A05
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep25

description:
362685A10
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: 161

description: Affymetrix SNP 6.0 arrays were used.


title: Liver_untreated, rep14

description:
362669A08
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

source_name: Untreated fresh-frozen liver, Philippines

value: Philippines

value: 2 - 3 years

value: France


title: Liver_untreated, rep15

description:
384658A09
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep19

description:
362685A01
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep18

description:
362669A02
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep13

description:
362669A03
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep16

description:
362685A04
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep12

description:
362685A07
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep11

description:
362685A08
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

source_name: Untreated fresh-frozen liver, China

value: China

value: Canada


title: Liver_untreated, rep9

description:
362669A10
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: 2.5 years

value: UK


title: 160

description: Affymetrix SNP 6.0 arrays were used.

value: blood

value: healthy

value: control


title: Liver_untreated, rep20

description:
362685A06
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: liver

value: Mauritius


title: Liver_untreated, rep8

description:
362685A11
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: female


title: 153

description: Affymetrix SNP 6.0 arrays were used.


title: 159

description: Affymetrix SNP 6.0 arrays were used.


title: Liver_untreated, rep7

description:
362669A09
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep1

description:
362669A05
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep4

description:
362669A07
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep6

description:
362669A04
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep5

description:
362669A06
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: Liver_untreated, rep2

description:
362685A09
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.


title: B.jap-001-012

city: Buffalo

first: Mark

middle: R.

last: O'Brian

state: NY

address: 140 Farber Hall

department: Biochemistry

institute: State University of New York at Buffalo

description: Biological replicate 3 of 3

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4200AL scanner (Molecular Devices, Sunnyvale, CA). Signal intensities were analyzed using Imagene software (BioDiscovery, El Segundo, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://churchill.jax.org/software/rmaanova.shtml). Expression values from two technical replicates in each array were combined and averaged.

organism: Bradyrhizobium japonicum

source_name: mur Manganese Relete Replication 3

label_protocol: 20 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a QiaQuick PCR Purification Kit (QIAGEN) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Four micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot phenol method

tag: growth condition

value: cultured under manganese replete conditions

source_name: Wt Manganese Deplete Replication 3

value: cultured under manganese deplete conditions


title: Crebbp hetMEF 3

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description: 14.5dpc embryo

hyb_protocol: 3.75 micrograms of biotinylated material was hybridized according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: GCRMA probe summarization and normalization using the Bioconductor gcrma package (http://www.bioconductor.org).

source_name: MEFs from one embryo in litter 3

label_protocol: 12 nanograms of total RNA was amplified and processed to produce biotinylated cDNA targets using the NuGen Ovation Biotin labeling system.

extract_protocol:
Qiagen RNeasy micro kit following manufacturer's protocol.
12ng of total RNA was amplified following the Ovation RNA amplification protocol (FLHSC).

value: Crebbp+/- MEF


title: Liver_untreated, rep3

description:
362685A02
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: male


title: Crebbp hetMEF 1

description: 14.5dpc embryo

source_name: MEFs from one embryo in litter 1


title: B.jap-001-011

description: Biological replicate 2 of 3

source_name: mur Manganese Relete Replication 2

source_name: Wt Manganese Deplete Replication 2


title: Crebbp hetMEF 4

description: 14.5dpc embryo

source_name: MEFs from one embryo in litter 4


title: Liver_untreated, rep17

description:
384662A02
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: Philippines


title: Liver_untreated, rep27

description:
362685A12
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: 2 - 4 years

value: Germany


title: Crebbp hetMEF 2

description: 14.5dpc embryo

source_name: MEFs from one embryo in litter 2


title: L286

description: According to Affymetrix SNP 6.0 standard protocol.

source_name: Ollier chondrosarcoma grade II

value: Ollier

value: chondrosarcoma grade II

tag: tumor location

value: femur


title: Liver_untreated, rep10

description:
384662A11
Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkeys of GLP drug safety studies.

value: China

value: Canada


title: Crebbp wtMEF 4

description: 14.5dpc embryo

tag: cell type

value: Crebbp+/+ MEF


title: S5

description: Matched blood DNA from the same individual is B5.

source_name: Saliva DNA from healthy donor

value: saliva

value: healthy


title: S4

description: Same donor donated blood DNA (B4).


title: B.jap-001-010

description: Biological replicate 1 of 3

source_name: mur Manganese Relete Replication 1

source_name: Wt Manganese Deplete Replication 1


title: B.jap-002-004

description: Biological replicate 2 of 3

source_name: Wt Manganese Replete Replication 2


title: B.jap-001-009

description: Biological replicate 1 of 3

source_name: Wt Manganese Replete Replication 1


title: Crebbp wtMEF 3

description: 14.5dpc embryo


title: Crebbp wtMEF 2

description: 14.5dpc embryo


title: Cdkn1a wtHSC 2

description: 14.5dpc fetal liver HSC

source_name: Sca-1+,Lin-,AA4.1+,c-Kit++ FLHSC from 15 embryos combined

value: Cdkn1a+/+ FLHSC


title: B3

description: From the same healthy donor S3 (saliva sample) as used in the series to compare the blood and saliva DNA.

source_name: Blood DNA from healthy donor

value: blood


title: B.jap-002-005

description: Biological replicate 3 of 3

source_name: Wt Manganese Replete Replication 3

value: cultured under manganese replete conditions


title: Cdkn1a nullHSC 1

description: 14.5dpc fetal liver HSC

value: Cdkn1a-/- FLHSC


title: Cdkn1a nullHSC 4

description: 14.5dpc fetal liver HSC


title: Cdkn1a nullHSC 3

description: 14.5dpc fetal liver HSC


title: Cdkn1a wtHSC 3

description: 14.5dpc fetal liver HSC


title: Ep300 hetHSC sample 1 replicate 2

description: 14.5dpc fetal liver HSC

value: Ep300+/- FLHSC


title: S3

description: Same donor's blood DNA (Sample B3) was also used in this study to see if matched saliva and blood DNA are comparable or not


title: Ep300 hetHSC sample 2 replicate 1

description: 14.5dpc fetal liver HSC


title: 103 control sample from Affymetrix kit

description: Affymetrix SNP 6.0 arrays were used.

source_name: Blood DNA from 103 control sample

extract_protocol: 103 control sample provided by Affymetrix.


title: Ep300 wtHSC sample 2 replicate 2

description: 14.5dpc fetal liver HSC

value: Ep300+/+ FLHSC


title: B4

description: Same donor also donated S4 saliva DNA sample.


title: Ep300 hetHSC sample 1 replicate 1

description: 14.5dpc fetal liver HSC


title: Crebbp wtMEF 1

description: 14.5dpc embryo


title: Cdkn1a wtHSC 1

description: 14.5dpc fetal liver HSC


title: Ep300 hetHSC sample 2 replicate 2

description: 14.5dpc fetal liver HSC


title: Ep300 wtHSC sample 1 replicate 1

description: 14.5dpc fetal liver HSC


title: Ep300 wtHSC sample 2 replicate 1

description: 14.5dpc fetal liver HSC


title: Cdkn1a nullHSC 2

description: 14.5dpc fetal liver HSC


title: B5

description: Saliva DNA from corresponding individual was also used to compare it with blood DNA.


title: L204

description: Affymetrix SNP 6.0 arrays were used.

source_name: Chondrosarcoma grade I of Ollier patient

value: chondrosarcoma grade I

value: male


title: 158

description: Affymetrix SNP 6.0 arrays were used.

value: control


title: L149N

description: Affymetrix SNP 6.0 arrays were used.

source_name: Ollier patient normal tissue

value: fresh frozen normal tissue

value: Ollier


title: E18th rat embryonic striatal stem cells (EGF+FGF+IGF+LIF)_3

city: KOTA BHARU

first: SOUMYA

last: PATI

address: KUBANG KERIAN

country: Malaysia

institute: UNIVERSITI SAINS MALAYSIA

description:
miRNA expression data from Group E-derived ESSCs
Group E ESSCs
AFMI1112-12.CEL

hyb_protocol: The biotinylated target RNA sample was then hybridized to Affymetrix miRNA arrays for 16 hours at 480C with rotation at 60 rpm according to GeneChip Hybridization. The GeneChip® miRNA Array probeset was used for miRNA profiling.

scan_protocol: The scanned images were inspected for hybridization efficiency and, CEL files generated from AGCC (Affymetrix GeneChip Command Console) were imported into miRNA quality control QC Tool software for determination of data quality.

data_processing:
miRNA array data analysis was performed with the Partek Genomics SuiteTM software.
For evaluation of miRNA expression data, Affymetrix CEL files were imported into the software prior to analysis.
Expression values calculated for rno-miRNAs.

organism: Rattus norvegicus

source_name: Cultured Embryonic progenitors from Striatum (group E)

label_protocol: 1000 ng of total RNA was Poly (A) tailed and ligated to a biotinylated signal molecule using flash tag biotin HSA RNA Labeling Kit.

growth_protocol: ESSCs were cultured in 25 cm2 flasks at a density of 1 X 105 to  3 X 105/ ml in neural basal medium (Stem cell technologies) with the previously discussed growth factor conditions and incubated at 370c, 5% CO2.

extract_protocol: RNA samples were isolated from triplicates of three groups (treatment A, D & E), using Qiagen miRNeasy Mini Kit.

treatment_protocol: Growth factor supplements were replaced as of 50% in every second day and passaging was performed every 4/5th day. In culture, ENP-derived neurospheres were passaged every 5th days into a single cell suspension (P = passage).

value: Sprague Dawley

tag: developmental stage

value: embryonic striatal stem cell

value: EGF+FGF+IGF+LIF


title: E18th rat embryonic striatal stem cells (EGF+FGF+IGF)_3

description:
miRNA expression data from Group D-derived ESSCs
Group D ESSCs
AFMI1112-9.CEL

source_name: Cultured Embryonic progenitors from Striatum (group D)

value: EGF+FGF+IGF


title: E18th rat embryonic striatal stem cells (EGF+FGF+IGF)_2

description:
miRNA expression data from Group D-derived ESSCs
Group D ESSCs
AFMI1112-8.CEL


title: E18th rat embryonic striatal stem cells (EGF+FGF+IGF+LIF)_2

description:
miRNA expression data from Group E-derived ESSCs
Group E ESSCs
AFMI1112-11.CEL


title: L1686

description: Affymetrix SNP 6.0 arrays were used.

source_name: Enchondroma of Ollier patient

value: enchondroma

value: phalanx


title: E18th rat embryonic striatal stem cells (untreated)_2

description:
miRNA expression data from Group A (untreated) ESSCs
Group A ESSCs
AFMI1112-5.CEL

source_name: Cultured Embryonic progenitors from Striatum (group A)

value: untreated


title: E18th rat embryonic striatal stem cells (untreated)_1

description:
miRNA expression data from Group A (untreated) ESSCs
Group A ESSCs
AFMI1112-4.CEL


title: E18th rat embryonic striatal stem cells (EGF+FGF+IGF)_1

description:
miRNA expression data from Group D-derived ESSCs
Group D ESSCs
AFMI1112-7.CEL


title: E18th rat embryonic striatal stem cells (untreated)_3

description:
miRNA expression data from Group A (untreated) ESSCs
Group A ESSCs
AFMI1112-6.CEL


title: E18th rat embryonic striatal stem cells (EGF+FGF+IGF+LIF)_1

description:
miRNA expression data from Group E-derived ESSCs
Group E ESSCs
AFMI1112-10.CEL


title: Crebbp hetHSC sample 1 replicate 1

description: 14.5dpc fetal liver HSC

value: Crebbp+/- FLHSC


title: Ep300 wtHSC sample 1 replicate 2

description: 14.5dpc fetal liver HSC


title: Crebbp wtHSC sample 1 replicate 2

description: 14.5dpc fetal liver HSC

value: Crebbp+/+ FLHSC


title: Crebbp hetHSC sample 2 replicate 2

description: 14.5dpc fetal liver HSC


title: Crebbp hetHSC sample 1 replicate 2

description: 14.5dpc fetal liver HSC


title: Crebbp wtHSC sample 2 replicate 2

description: 14.5dpc fetal liver HSC


title: Crebbp wtHSC sample 1 replicate 1

description: 14.5dpc fetal liver HSC


title: Crebbp wtHSC sample 2 replicate 1

description: 14.5dpc fetal liver HSC


title: Crebbp hetHSC sample 2 replicate 1

description: 14.5dpc fetal liver HSC


title: PRKG2 R678X/+ (unaffected 27) X PRKG2 R678X/R678X (dwarf 28) PMT 70

city: Ames

first: James

middle: M

last: Reecy

state: IA

address: 2255 Kildee Hall, Iowa State University

department: Animal Science

institute: Iowa State University

description: Unaffected vs Dwarf tibia whole growth plate cartilage from Angus cattle aged ~215 days.

hyb_protocol: Cy 3 and Cy 5 dyes were used for differential display of cDNA binding between genotype treatments to the array.  Dye swapping was used for genotype comparisons (not for each individual) to account for differential dye incorporation. A total of four microarrays were hybridized to compare PRKG2R678X/R678X and PRKG2R678X/+ animals using the Genisphere kit.  Microarrays were hybridized using GE Healthcare's Lucidea SlidePro hybridization oven (General Electric Healthcare, Piscataway, NJ) at the Iowa State University DNA facility according to manufacturer protocol.

scan_protocol: Hybridized slides were scanned for visualization of Cy 3 and Cy 5 signal using a Pro Scan Array HT scanner at the microarray facility within the Iowa State University, Plant Sciences Institute.  Slides were scanned at three different laser (photomechanical transfer unit) PMT intensities, 70, 80 and 90 PMT, to account for high and low expression levels of various transcripts (34), as, different genes will appear as expressed or not expressed at the different PMT levels.  Images were analyzed to obtain raw signal intensities and localized background signals with Imagene 5.1 software.

data_processing: Image files were normalized by channel to correct for background, differential dye incorporation using Lowess normalization (43), and heterogeneous variance by median centering and natural log transformation using R statistical software (R 2.5.1) with scripts provided by Dr. Dan Nettleton of Iowa State University.

organism: Bos taurus

source_name: growth plate cartilage, unaffected

label_protocol: Synthesis of cDNA was carried out using SuperscriptII reverse transcriptase (Invitrogen, Carlsbad, CA) along with the Genisphere 3DNA 350 HS kit components (Genisphere, Hatfield, PA).

growth_protocol: Calves were produced by embryo transfer and born in two contemporary groups are roughly the same age (within a few days).

extract_protocol: RNA was isolated from growth plate cartilage using TRIzol (Invitrogen, Carlsbad, CA).  A mass of 0.15 to 0.20 g of growth plate cartilage was placed into a sterile Petri dish with one milliliter (ml) of TRIzol.  Next, each sample was diced into a slurry using a sterile scalpel. Then, samples were homogenized using a rotor stator probe in a total volume of 6 ml TRIzol.  Sample yield was measured by spectrophotometer.  These initial RNA yield values were used to estimate how much purified RNA could be eluted by column purification (Qiagen, Valencia, CA).  Column purified RNA was stored at - 80oC for future use.

treatment_protocol: Koltes et al., 2009 PNAS Nov 17;106(46):19250-5. (PMID: 19887637) identified a mutation in PRKG2 responsible for dwarfism in Angus cattle.  This experiment contrasts growth plate cartilage from two genotype groups- PRKG2 R678X/R678X (dwarf) and PRKG2 R678X/+ (unaffected).  All animals shared the same sire.

tag: genotype

value: PRKG2 R678X/+ (unaffected)

value: female

tag: contemporary group

source_name: growth plate cartilage, dwarf

value: PRKG2 R678X/R678X (dwarf)


title: Primary tumour region 2

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

description: Gene expression from a ccRCC primary site

hyb_protocol: Exon 1.0 ST Cocktail hybridization

scan_protocol: PICR scanner 3000

data_processing: The expression values of the samples were normalized using the oligo R package.

source_name: ccRCC patient1

label_protocol: Affymetrix protocol

extract_protocol: Fresh frozen

value: ccRCC primary tumor

tag: disease state

value: ccRCC


title: Primary tumour region 5


title: PRKG2 R678X/R678X (dwarf 19) X PRKG2 R678X/+ (unaffected 18) PMT90

description: Dwarf vs Unaffected tibia whole growth plate cartilage from Angus cattle aged ~215 days.

value: male


title: PRKG2 R678X/+ (unaffected 27) X PRKG2 R678X/R678X (dwarf 28) PMT 90


title: Methylation profiling in 3A6 MSCs

city: Taipei

first: Chih

middle: Chien

last: Tsai

address: No. 201, Sec. 2, Shih-Pai Road, Taipei 112, Taiwan

country: Taiwan

institute: Taipei Vaterans General Hospital

hyb_protocol: Labeled DNA was hybridized to a human CpG island microarray at 65°C for 40 h.

scan_protocol: Arrays were scanned on the Agilent microarray scanner G2505B (Agilent Technologies, USA). Images were quantified using Feature Extraction 9.1 software (Agilent Technologies, USA).

data_processing: Microarray data were firstly normalized with print-tip loess, followed by background-correction, normalization and analysis by the limma package within the R environment. The methylation level was determined as the ratio of Cy5/Cy3 in each spot.

source_name: HPV E6/E7- and hTERT-transfected mesenchymal stem cells, HpaII/HhaI/BstuI

label_protocol: The HpaII/HhaI/BstuI-digested samples and the McrBC-digested samples were differentially labeled with Cy5- or Cy3-conjugated dUTP using the Agilent Genomic DNA Labeling Kit PLUS.

growth_protocol: KP and 3A6 MSCs were kept in DMEM-LG medium with 10% FBS.

extract_protocol: Genomic DNA was extracted from samples using the Qiagen QIAamp DNA mini kit.

tag: cell line

value: immortalized human mesenchymal stem cells

tag: tissue derivation

value: bone marrow

tag: restriction enzyme

value: HpaII, HhaI, BstuI

tag: transfected gene

value: HPV E6/E7 and hTERT

source_name: HPV E6/E7- and hTERT-transfected mesenchymal stem cells, McrBC

value: McrBC


title: Primary tumour region 1


title: PRKG2 R678X/R678X (dwarf 19) X PRKG2 R678X/+ (unaffected 18) PMT80


title: PRKG2 R678X/+ (unaffected 27) X PRKG2 R678X/R678X (dwarf 28) PMT 80


title: PRKG2 R678X/+ (unaffected 18) X PRKG2 R678X/R678X (dwarf 17) PMT 90


title: Primary tumour region 4


title: Primary tumour region 8


title: Primary tumour region 7


title: Methylation profiling in KP MSCs

description: KP

source_name: HPV E6/E7-transfected mesenchymal stem cells, HpaII/HhaI/BstuI

value: KP

value: HPV E6/E7

source_name: HPV E6/E7-transfected mesenchymal stem cells, McrBC


title: Chestwall metastasis sample b

description: Gene expression from a chestwall metastatic site (sample b)

value: chestwall metastasic tumor from ccRCC


title: Chestwall metastasis sample a

description: Gene expression from a chestwall metastatic site (sample a)


title: EpiSC XAV rep 2

city: los angeles

first: Qilong

last: Ying

state: CA

address: 1425 san pablo st BCC509b

institute: USC

description: Mouse embryonic stem cell, 129

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data analysis was performed using Partek Microarray Software.

source_name: EpiSC treated XAV for 2hrs

label_protocol: standard Affymetrix protocol

growth_protocol: GMEM medium (Sigma) supplemented with 10% fetal bovine serum (FBS) (Hyclone), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma)

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen).

treatment_protocol: CHIR99021 (3 µM), XAV939 (Sigma, 2 µM)

value: EpiSC

tag: genetic background

tag: treatment


title: PRKG2 R678X/+ (unaffected 18) X PRKG2 R678X/R678X (dwarf 17) PMT 80


title: Primary tumour region 3

tag: tissue


title: EpiSC XAV rep 1

description: Mouse embryonic stem cell, 129


title: EpiSC CHIR rep 1

description: Mouse embryonic stem cell, 129

source_name: EpiSC treated CHIR for 2hrs


title: EpiSC CHIR rep 2

description: Mouse embryonic stem cell, 129


title: EpiSC CHIR + XAV rep 3

description: Mouse embryonic stem cell, 129

source_name: EpiSC treated CHIR/XAV for 2hrs


title: EpiSC CHIR + XAV rep 1

description: Mouse embryonic stem cell, 129


title: PRKG2 R678X/R678X (dwarf 29) X PRKG2 R678X/+ (unaffected 27) PMT70


title: EpiSC CHIR + XAV rep 2

description: Mouse embryonic stem cell, 129


title: EpiSC CHIR rep 3

description: Mouse embryonic stem cell, 129


title: EpiSC XAV rep 3

description: Mouse embryonic stem cell, 129


title: PRKG2 R678X/+ (unaffected 18) X PRKG2 R678X/R678X (dwarf 17) PMT 70


title: PRKG2 R678X/R678X (dwarf 19) X PRKG2 R678X/+ (unaffected 18) PMT70


title: PRKG2 R678X/R678X (dwarf 29) X PRKG2 R678X/+ (unaffected 27) PMT80


title: PRKG2 R678X/R678X (dwarf 29) X PRKG2 R678X/+ (unaffected 27) PMT90


title: EpiSC NT rep 3

description: Mouse embryonic stem cell, 129

source_name: EpiSC without treatment

value: untreated


title: EpiSC NT rep 2

description: Mouse embryonic stem cell, 129


title: N/A [EL599]

status: Public on Aug 24 2011

city: Woodbury

first: Yi

last: Su

state: New York

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Lab

description: This experiment was done in dual colour microarray

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

label_protocol: Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.

extract_protocol: Qiagen Genomic DNA Isolation Kit (cat# 51306)

value: Primary Glioblastoma

tag: reference

value: EBV Immortalized Fibroblast Reference


title: N/A [EL601]


title: N/A [IO088]

value: Glioblastoma Cell line


title: N/A [EL547]


title: N/A [EL587]


title: N/A [IO084]


title: N/A [IO078]


title: N/A [EL603]


title: N/A [EL571]


title: N/A [EL553]


title: N/A [JA1211]


title: N/A [EL573]


title: N/A [IO086]


title: N/A [IO094]


title: N/A [EL593]


title: N/A [IO090]


title: N/A [EL581]


title: N/A [EL605]


title: N/A [EL609]


title: N/A [EL617]


title: N/A [EL613]


title: N/A [EL591]


title: N/A [EL545]


title: N/A [EL569]


title: N/A [IO092]


title: N/A [IO076]


title: N/A [IO080]


title: B2 S 4008078 [KN0607]

value: Primary Colon Cancer


title: B2 S 4008653 [KN0752]


title: B2 S 4550b [KN0583]


title: B2 S 2198 [KN0596]


title: B2 S 4007592 [KN0604]


title: B2 S 2159 [KN0595]


title: B2 S 4006814 [KN0598]


title: B2 S 4004872 [KN0581]


title: B2 S 4004829 [KN0580]


title: B2 S 1882 [KN0592]


title: B2 S 4007045 [KN0600]


title: B2 S 2504 [KN0576]


title: B2 S 2057 [KN0593]


title: B2 S 4007270 [KN0601]


title: B2 S 2557 [KN0577]


title: B2 S 4006858 [KN0599]


title: B2 S 4007416 [KN0603]


title: B2 S 4007413 [KN0602]


title: B2 S 2100 [KN0594]


title: B1 S 1858 [KN0573]


title: B2 S 2419 [KN0597]


title: B2 S 1259 [KN0575]


title: B2 S 4007820 [KN0605]


title: B1 S 4005028 [KN0571]


title: B2 S 4005490 [KN0582]


title: B2 S 1004 [KN0585]


title: B2 S 3007 [KN0578]


title: 4652A1 [KN0074]


title: 4644A1 [KN0073]


title: B1 S 4005073 [KN0572]


title: 4471B1 [KN0067]


title: 3960A1 [KN0045]


title: B1 S 2326 [KN0574]


title: 3879A1 [KN0043]


title: 4550B1 [KN0071]


title: 4474B1 [KN0068]


title: 4612A1 [KN0072]


title: B1 S 4007942 [KN0570]


title: 4048A1 [KN0049]


title: 4386A1 [KN0066]


title: 4192A1 [KN0065]


title: EpiSC NT rep 1

description: Mouse embryonic stem cell, 129


title: 3657A1 [KN0042]


title: 4519B1 [KN0070]


title: 4032A1 [KN0048]


title: 3997A1 [KN0047]


title: 294A1 [KN0036]


title: B2 S 4007932 [KN0606]


title: 4112A1 [KN0064]


title: 4504B1 [KN0069]


title: 1761A1 [KN0033]


title: 1704A1 [KN0063]


title: 3522A1 [KN0039]


title: 3975A1 [KN0046]


title: 762A1 [KN0034]


title: 3571A1 [KN0041]


title: 3533A1 [KN0040]


title: 1672B1 [KN0032]


title: 1951 [KN1084]


title: DN000014AB [KN0204]


title: 5855 [KN1085]


title: 1231A1 [KN0030]


title: DN000014B1 [KN0207]


title: 3164 vs 3163 [KN1109]


title: 2469 [KN1086]


title: 4892 [KN1082]


title: 4124 [KN1080]


title: DN000014B9 [KN0211]


title: 2577 [KN1078]


title: 2529 [KN1077]


title: Met D 4009046 [KN0830]


title: Met D 4007072 [KN0822]


title: Met D 4005174 [KN0826]


title: Met D 4030178 [KN0824]


title: DN000014BD [KN0213]


title: Met D 4006972 [KN0823]


title: 1199 [KN1083]


title: Met D 4009161 [KN0828]


title: 4555a [KN1079]


title: DN000014A9 [KN0203]


title: Met D 4007464 [KN0827]


title: Met D 4005687 [KN0829]


title: Met D 4006805 [KN0821]


title: Met D 4008565 [KN0825]


title: Met D 4007670 [KN0818]


title: Met D 4007440 [KN0820]


title: Met D 4008720 [KN0819]


title: Met D 6108 [KN0815]

source_name: Met D 6108


title: Met D 4008747 [KN0812]


title: Met D 4004793 [KN0611]


title: Met D 2433 [KN0817]

source_name: Met D 2433


title: Met D 4007246 [KN0814]


title: V10M [KN0838]

value: Colon Cancer Cell Line


title: Met D 4006261 [KN0613]


title: Met D 4008813 [KN0816]


title: V531 [KN0842]


title: Met D 4009272 [KN0754]


title: Met D 4006274 [KN0748]


title: V429 [KN0840]


title: Met D 6104 [KN0811]

source_name: Met D 6104


title: Met D 4007509 [KN0609]


title: V576 [KN0837]


title: Met D 4004532 [KN0813]


title: Met D 4006587 [KN0612]


title: Met D 4007448 [KN0755]


title: Met D 2406b [KN0749]

source_name: Met D 2406b


title: Met D 4007822 [KN0751]


title: Met D 4007350 [KN0744]


title: Met D 4008460 [KN0746]


title: V456 [KN0841]


title: Met D 4007243 [KN0747]


title: Met D 4030283 [KN0745]


title: V503 [KN0836]


title: Met D 4008824 [KN0750]


title: V400 [KN0834]


title: SW948 [KN0289]


title: V394 [KN0833]


title: CACO2 [KN0003]


title: LS123 [KN0021]


title: SW1116 [KN0017]


title: LS174T [KN0285]


title: Met D 4008382 [KN0753]


title: COLO678 [KN0007]


title: LS103A [KN0024]


title: SW620 [KN0288]


title: R [KN0025]

source_name: R

value: R


title: NsCo0261TA [KN0538]


title: COLO320HSR [KN0005]


title: CHTN0633A [KN0536]


title: COLO320DM [KN0004]


title: SW480 [KN0287]


title: LIM2045 [KN0020]


title: HCT-116 [KN0011]


title: V410 [KN0835]


title: 58A1 [KN0002]


title: LS180 [KN0023]


title: LOVO [KN0019]

source_name: LOVO

value: LOVO


title: COLO206F [KN0006]


title: WiDr [KN0029]

source_name: WiDr

value: WiDr


title: 1874A1 [KN0001]


title: V9M [KN0831]


title: CHTN0515A [KN0535]


title: CHTN0504A [KN0534]


title: HCT-15 [KN0010]


title: CHTN0443A [KN0532]


title: NsCo0267T [KN0506]


title: NsCo0302T [KN0507]


title: CHTN0494A [KN0533]


title: CHTN0447 [KN0494]


title: NsCo0126TA [KN0474]


title: CHTN0581 [KN0495]


title: NsCo0157T [KN0504]


title: NsCo0136T [KN0502]


title: HCC1500 [KN1056]

value: Breast Cancer Cell Line


title: MT-3 [KN1145]


title: EFM-19 [KN1143]


title: MB157 [KN1055]


title: CHTN0397 [KN0493]


title: NsCo0132T [KN0501]


title: CHTN0392 [KN0492]


title: CHTN0616 [KN0498]


title: CHTN0588 [KN0496]


title: NsCo0152T [KN0503]


title: JIMT1 [KN1141]


title: NsCo0284TA [KN0473]


title: HCC202 [KN1087]


title: KPL-1 [KN1140]


title: COLO824 [KN1147]


title: CAL-148 [KN1146]


title: CAL-51 [KN1139]


title: NsCo0125T [KN0499]


title: CHTN0593 [KN0497]


title: MDA-MB-435 [KN1039]


title: CAL-120 [KN1037]


title: HCC38 [KN1042]


title: HCC1569 [KN1040]


title: EVSA-T [KN1038]

source_name: EVSA-T

value: EVSA-T


title: DU4475 [KN1033]


title: BT-474 [KN1030]


title: UACC-893 [KN1031]


title: MCF-7 [KN1018]


title: Hs578T [KN1034]


title: MDA-MB-134-VI [KN1032]


title: MDA-MB-330 [KN1021]


title: ALAB [KN1012]

source_name: ALAB

value: ALAB


title: CRL-2335 [KN1007]


title: BT-549 [KN1015]


title: CRL-2336 [KN1008]


title: MDA-MB-157 [KN1017]


title: MFM-223 [KN1041]


title: CHTN0407A [KN0531]


title: MDA-MB-175-VII [KN1020]


title: UACC-812 [KN1043]


title: BT-20 [KN1013]


title: MDA-MB-436 [KN1024]


title: ZR-75-1 [KN1028]


title: ZR-75-30 [KN1029]


title: BT-483 [KN1014]


title: MDA-MB-361 [KN1022]


title: MDA-MB-468 [KN1026]


title: MDA-MB-415 [KN1023]


title: HCC1187 [KN0485]


title: HCC1395 [KN0486]


title: NsCo0181T [KN0505]


title: HCC1008 [KN0483]


title: T47D [JT321]


title: HCC1599 [KN0487]


title: HCC1937 [KN0488]


title: CRL-2326 [KN0891]


title: HCC1954 [KN0489]


title: CRL-2315 [KN0893]


title: CAMA-1 [JT331]


title: HCC1143 [KN0484]


title: HCC2218 [KN0491]


title: HCC2157 [KN0490]


title: MDA-MB-453 [JT317]


title: SK-BR-3 [JA1185]


title: MSK0043 [KN0730]

value: Primary Prostate Cancer


title: WA5-4 [KN0227]


title: WA19-7 [KN0225]


title: WA21-6 [KN0220]


title: WA5-1 [KN0224]


title: WA4-3 [KN0221]


title: WA16-10 [KN0222]


title: WA16-12 [KN0226]


title: WA20-10 [KN0235]


title: WA18-11 [KN0228]


title: WA4-1 [KN0234]


title: WA13-1 [KN0219]


title: WA17-16 [KN0233]


title: WA20-10 [KN0223]


title: WA5-3 [KN0217]


title: KL00018 [AB674]


title: WA12-2 [KN0218]


title: KL00016 [AB670]


title: JH0021 [TA017]

value: Primary Pancreas Cancer


title: JH0025 [TA021]


title: JH0080 [TA035]


title: JH0033 [TA033]


title: JH0022 [TA019]


title: KL00012 [AB662]


title: PC3 [KO152]

value: Prostate Cancer Cell Line


title: KL00017 [AB672]


title: KL00014 [AB666]


title: DU145 [KO153]


title: LNCAP [KO149]

source_name: LNCAP

value: LNCAP


title: KL00015 [AB668]


title: JH0031 [TA029]


title: KL00013 [AB664]


title: KL00011 [AB660]


title: JH0028 [TA025]


title: JH0030 [TA027]


title: JH0018 [TA011]


title: JH0091 [AB888]


title: JH0032 [CH261]


title: JH0017 [TA009]


title: JH0090 [AB886]


title: JH0024 [CH416]


title: JH0087 [AB882]


title: JH0093 [AB890]


title: JH0086 [AB880]


title: JH0083 [AB769]


title: JH0081 [AB765]


title: JH0034 [AB728]


title: JH0026 [AB718]


title: JH0035 [AB722]


title: JH0027 [AB682]


title: JH0029 [AB720]


title: JH0072 [AB696]


title: JH0074 [AB698]


title: JH0074 [AB700]


title: AGL [KK028]

source_name: AGL


title: A10.7 [KK030]


title: A-13 D [KK013]


title: 2G13B [KK027]


title: JH0023 [AB714]


title: 2G13A [KK026]


title: Xeno 159 [TA012]

source_name: Xeno 159


title: 2G10.4 [KK025]


title: CHTN1789 [CH408]


title: JH0082 [AB767]


title: A-13 B [KK012]


title: ACC0010 [CH380]


title: CHTN1788 [CH410]


title: CHTN1784 [CH406]


title: ACC0011 [CH382]


title: JH0020 [AB680]


title: CHTN1242A [CH340]


title: CHTN1603A [CH325]


title: ACC0013A [CH319]


title: JH0085 [AB779]


title: ACC0001A [CH317]


title: ACC0009A [AB491]


title: JH0016A [AB574]


title: JH0005Aa [AB568]


title: ACC0004A [AB489]


title: JH0007A [CH313]


title: CHTN0155A [AB483]


title: E3GS2.4 [TA144]

value: Pancreas Cancer Cell Line


title: SW1990 [CH404]


title: JH0088 [AB884]


title: JH0071 [AB783]


title: CAPAN2 [CH362]


title: CHTN1548A [AB487]


title: CHTN1065A [AB485]


title: JH0004A [CH311]


title: JH0010A [AB572]


title: Panc10.05 [CH364]


title: JH0083 [TA143]


title: JH0001A [AB566]


title: CHTN1780 [AB785]


title: JH0014A [CH315]


title: Panc08.13 [CH414]


title: CHTN0150A [AB481]


title: CAPAN-1 [CH360]


title: Panc03.27 [CH358]


title: MIA-PaCa-2 [CH354]


title: HGC-25 [CH161]


title: HPAF-II [CH151]

source_name: HPAF-II

value: HPAF-II


title: BXPC-3 [CH157]


title: CHTN1135A [CH342]


title: ASPC-1 [CH352]


title: HPAC [CH336]

source_name: HPAC

value: HPAC


title: PANC-1 [CH155]

value: EBV Immortalized Fibroblast Reference


title: MP0038A [TA068]

value: Primay Ovarian Cancer


title: CHTN0852 [TA095]


title: MP0028A [TA057]


title: SU.86.86 [AB610]


title: ALB0055 [TA074]


title: CHTN0812A [TA090]


title: MP0006A [TA053]


title: CFPAC-1 [CH147]


title: MP0013D [TA055]


title: CHTN0841A [OD335]


title: COLO587 [CH149]


title: Hs700T [CH153]


title: Hs766T [AB493]


title: ALB0057 [TA102]


title: MP0037A [TA063]


title: ALB0052 [TA077]


title: CHTN0798A [OD333]


title: CHTN0866A [OD336]


title: MP0033A [TA062]


title: ALB0058 [AB999]


title: CHTN0796A [OD332]


title: JH0006A [AB570]


title: ALB0054 [AB996]


title: ALB0056 [AB997]


title: ALB0057 [AB998]


title: CHTN0555A [AB985]


title: CHTN0580A [AB989]


title: ALB0046 [AB961]


title: ALB0049 [AB967]


title: CHTN0552A [AB983]


title: ALB0051 [AB971]


title: GCT0002 [AB867]


title: GCT0003 [AB869]


title: ALB0045 [AB959]


title: CHTN0541A [AB981]


title: CHTN0310A [AB977]


title: GCT0004 [AB871]


title: ALB0044 [AB957]


title: ALB0050 [AB969]


title: CHTN0652A [AB991]


title: CHTN0533A [AB979]


title: ALB0043 [AB955]


title: CHTN0653A [AB993]


title: ALB0048 [AB965]


title: CHTN0288A [AB975]


title: CHTN0564A [AB987]


title: ALB0047 [AB963]


title: ALB0042 [AB857]


title: TLRK0028 [AB835]


title: TLRK0027 [AB833]


title: TLRK0045 [AB849]


title: TLRK0034 [AB843]


title: TLRK0046 [AB851]


title: CHTN0756A [AB813]


title: CHTN0769A [AB817]


title: CHTN0787A [AB821]


title: TLRK0021 [AB823]


title: TLRK0025 [AB829]


title: CHTN0778A [AB546]


title: ALB0041 [AB855]


title: CHTN0753A [AB811]


title: CHTN0740A [AB614]


title: CHTN0779A [AB819]


title: CHTN0775A [AB628]


title: TLRK0026 [AB831]


title: TLRK0023 [AB827]


title: TLRK0041 [AB847]


title: TLRK0036 [AB845]


title: CHTN0772A [AB624]


title: CHTN0758A [AB815]


title: CHTN0748A [AB616]


title: CHTN0770A [AB544]


title: TLRK0022 [AB825]


title: TLRK0029 [AB837]


title: CHTN0773A [AB626]


title: GCT0001 [AB865]


title: ALB0053 [AB995]


title: MPanc-96 [CH356]


title: CHTN0745A [AB542]


title: MP0016A [AB540]


title: XU0021A [AB453]


title: MP0010A [AB538]


title: XU0019A [AB451]


title: XU0016A [AB448]


title: XU0015A [AB447]


title: CHTN0478A [AB397]


title: CHTN0562A [AB401]


title: XU0014A [AB445]


title: XU0007A [AB395]


title: CHTN0957A [AB403]


title: XU0011A [AB431]


title: XU0004A [AB391]


title: XU0012 [AB369]


title: CHTN0561A [AB399]


title: CHTN0577A [AB363]


title: XU0001A [AB387]


title: XU0002A [AB429]


title: XU0009 [AB367]


title: XU0003A [AB389]


title: CHTN0565A [AB361]


title: CHTN0963A [AB365]


title: CHTN0480A [AB425]


title: CHTN0558A [AB330]


title: CHTN0452A [AB329]


title: CHTN0531A [AB427]


title: XU0022A [AB333]


title: CHTN0114A [AB357]


title: ALB0064 [AB1004]


title: XU0006A [AB393]


title: ALB0063 [AB1003]


title: ALB0062 [AB1002]


title: TOV-112D [SE46]

value: Ovarian Cancer Cell Line


title: ALB0061 [AB1001]


title: OVCAR5 [SE24]


title: COLO316 [OD162]


title: SK-OV-3 [AB411]


title: CAOV-4 [AB405]


title: CAOV-3 [OD168]


title: ES-2 [AB407]


title: OVCAR3 [AB409]


title: 79536 [KN1179]

value: Primary Melanoma


title: TOV-21G [KK072]


title: PA-1 [CH412]


title: S02-348934 [KN1180]


title: S03-179402 [KN1181]


title: 3881A1 [KN0190]


title: 795HWA6L [KN0192]


title: 6843A1 [KN0191]


title: S01-16550 [KN1178]


title: CU213 [KN0195]


title: OV-90 [SE47]


title: CI791 [KN0194]


title: CU144 [KN0189]


title: CU78 [KN0188]


title: FLNZ9A4W [KN0186]


title: OVCAR8 [SE25]


title: 6817A1 [KN0185]


title: CU970 [KN0183]


title: OVCAR4 [SE23]


title: SW626 [SE22]


title: ALB0060 [AB1000]


title: CAOV-1 [SE21]


title: SK-MEL-239 [KN1177]

value: Melanoma Cell line


title: 6816A1 [KN0180]


title: 6853A1 [KN0187]


title: CI7668 [KN0182]


title: SK-MEL-208 [KN1174]


title: 1370A1 [KN0179]


title: CU131 [KN0184]


title: CU9094 [KN0177]


title: SK-MEL-200 [KN1173]


title: CU718 [KN0174]


title: CI8528 [KN0176]


title: SK-MEL-196  [KN1170]


title: SK-MEL-199A [KN1171]


title: SK-MEL-199S [KN1172]


title: SK-MEL-238 [KN1176]


title: SK-MEL-187 [KN1169]


title: CU100 [KN0173]


title: CU112 [KN0178]


title: 53127A2 [KN0181]


title: CU698 [KN0175]


title: SK-MEL-217 [KN1175]


title: SK-MEL-105  [KN1165]


title: SK-MEL-118 [KN1166]


title: SK-MEL-100  [KN1164]


title: SK-MEL-178  [KN1168]


title: SK-MEL-085 [KN1163]


title: SK-MEL-130  [KN1167]


title: SK-MEL109 [KN1137]


title: SK-MEL-113 [KN1138]


title: 38654A1D [KN0987]

value: Primary Lung Cancer


title: SK-MEL-12 [KN1134]


title: SK-MEL-022  [KN1162]


title: SK-MEL-23 [KN1135]


title: SKMEL-173 [KN1093]


title: 37011A1C [KN0983]


title: SKMEL-28 [KN1088]


title: SKMEL-30 [KN1092]


title: SKMEL-1 [KN1089]


title: 39458A1E [KN0984]


title: 39630A1E [KN0979]


title: 39926A1C [KN0977]


title: 39061A1H [KN0986]


title: 39160A1D [KN0978]


title: SKMEL-19 [KN1090]


title: 39407A1C [KN0990]


title: SK-MEL-27 [KN1136]


title: 31146A1A [KN0989]


title: 36618A1E [KN0988]


title: 38746A1G [KN0985]


title: SKMEL-103 [KN1094]


title: SKMEL-29 [KN1095]


title: 39830A1C [KN0982]


title: SK-MEL-11 [KN1133]


title: 39824A1A [KN0967]


title: SKMEL-24 [KN1091]


title: 39558A1C [KN0965]


title: 37817A1B [KN0959]


title: CHTN991A [KN0954]


title: 35768A1A [KN0963]


title: 39241A1C [KN0962]


title: 38648A1J [KN0960]


title: 39458A1E [KN0964]


title: 7735A1   [KN0939]


title: 38391A1C [KN0961]


title: 38037A1F [KN0957]


title: 31749A1C [KN0956]


title: CHTN0971 [KN0865]


title: 7733B1   [KN0938]


title: CHTN987A [KN0953]


title: 39443A1C [KN0966]


title: FR00016BBB [KN0890]


title: 2224A1 [KN0952]


title: CHTN0728 [KN0863]


title: CHTN0982 [KN0868]


title: CHTN0985 [KN0869]


title: CHTN0535 [KN0859]


title: CHTN0534 [KN0858]


title: CHTN0980 [KN0867]


title: 4727A1   [KN0937]


title: CHTN0965 [KN0864]


title: CHTN0643 [KN0861]


title: CHTN0516 [KN0857]


title: DN00001597 [KN0932]


title: CHTN0463 [KN0853]


title: CHTN0512 [KN0856]


title: CHTN0492 [KN0855]


title: CHTN0976 [KN0866]


title: CHTN0670 [KN0862]


title: CHTN0450 [KN0852]


title: CHTN0465 [KN0854]


title: CHTN0566 [KN0860]


title: CHTN0260 [KN0847]


title: CHTN0388 [KN0850]


title: CHTN0347 [KN0849]


title: CHTN0235 [KN0846]


title: CHTN0303 [KN0848]


title: 32120 [KN0448]


title: 7352B1 [KN0417]


title: 5857A1 [KN0416]


title: 4169A1 [KN0412]


title: 7734A1 [KN0418]


title: 4222A1 [KN0414]


title: 7A1 [KN0410]


title: 4211A1 [KN0413]


title: 7751B1 [KN0407]


title: 8292A1 [KN0408]


title: CHTN583 [KN0406]


title: CHTN728 [KN0400]


title: CHTN587 [KN0404]


title: CHTN670 [KN0402]


title: CHTN650 [KN0403]


title: 9341A1 [KN0419]


title: CHTN738 [KN0398]


title: CHTN582 [KN0405]


title: CHTN681 [KN0401]


title: 5492A1 [KN0377H]


title: 2224A1 [KN0372]


title: 5436A1 [KN0396]


title: 756A1 [KN0374]


title: 770A1 [KN0361]


title: 1992A1 [KN0362]


title: 5485A1 [KN0367]


title: 4736A1 [KN0355]


title: 705B1 [KN0360]


title: 766A1 [KN0369]


title: 4028A1 [KN0356]


title: 3617A1 [KN0352]


title: 690A1 [KN0373]


title: 1849A1 [KN0358]


title: 1683A1 [KN0353]


title: 4004A1 [KN0354]


title: 450A1 [KN0397]


title: 31A1 [KN0349]


title: 436A1 [KN0341]


title: 263A1 [KN0339]


title: 556B1 [KN0346]


title: 308A1 [KN0348]


title: 4485B1 [KN0347]


title: CHTN0415 [KN0851]


title: 10035B1 [KN0315]


title: 431A1 [KN0340]


title: 4616A1 [KN0351]


title: 3996A1 [KN0336]


title: 106A1 [KN0331]


title: 4A1 [KN0330]


title: DN00001591 [KN0269]


title: DN0000158B [KN0266]


title: DN0000158D [KN0267]


title: 217A1 [KN0338]


title: 3967A1 [KN0333]


title: DN00001593 [KN0270]


title: 3824A1 [KN0335]


title: DN0000159B [KN0274]


title: 371A1 [KN0337]


title: DN00001585 [KN0263]


title: DN0000157F [KN0260]


title: DN0000157D [KN0259]


title: DN00001583 [KN0262]


title: DN00001595 [KN0271]


title: DN00001581 [KN0261]


title: DN00001589 [KN0265]


title: DN0000157B [KN0258]


title: DN00001579 [KN0257]


title: DN00001567 [KN0254]


title: CU0336 [KN0251]


title: DN00001577 [KN0256]


title: DN00001575 [KN0255]


title: CU0602 [KN0249]


title: CU0135 [KN0252]


title: CU0288 [KN0250]


title: DN00001551 [KN0238]


title: DN00001561 [KN0246]


title: DN00001563 [KN0247]


title: DN0000155D [KN0244]


title: CU0250 [KN0248]


title: FR5B33B9B3 [KN0153]


title: 9572A1 [KN0160]


title: DN0000155F [KN0245]


title: DN0000154D [KN0236]


title: DN00001555 [KN0240]


title: 9420A1 [KN0159]


title: DN0000154F [KN0237]


title: DN00001553 [KN0239]


title: FR00016BBB [KN0154]


title: FR00016A74 [KN0151]


title: DN00001557 [KN0241]


title: FR0001CC90 [KN0146]


title: 9419A1 [KN0158]


title: FR00038395 [KN0152]


title: FR000274D6 [KN0142]


title: FR000272A1 [KN0134]


title: FR00033A79 [KN0137]


title: FR0002F4C1 [KN0143]


title: FR5B336AF5 [KN0135]


title: DN00001565 [KN0253]


title: LK2 [KN1272]

value: Lung Cancer Cell Line


title: 6653A1 [KN0120]


title: STC1 [KN1274]


title: 273T [KN1277]


title: 7318B1 [KN0121]


title: 11008E1 [KN0130]


title: RERFLCKJ [KN1273]

source_name: RERFLCKJ

value: RERFLCKJ


title: CDD14BR [KN1270]


title: WI38VA13 [KN1278]


title: DV90 [KN1276]


title: LC1sq [KN1271]


title: HCC827 [KN1267]


title: 9149A1 [KN0122]


title: NCI-H2030 [KN1263]


title: 10024B1 [KN0125]


title: VMRCLCD [KN1279]

source_name: VMRCLCD

value: VMRCLCD


title: NCI-H1793 [KN1259]


title: NCI-H1623 [KN1257]


title: PC9 [KN1265]


title: NCI-H2023 [KN1262]


title: NCI-H1693 [KN1258]


title: HCC15 [KN1268]


title: NCI-H2085 [KN1264]


title: CORL23 [KN1269]


title: HCC78 [KN1266]


title: 11029B1 [KN0129]


title: H889 [KN0971]


title: ABC1 [KN1256]


title: H520 [KN0968]


title: H417 [KN0973]


title: H441 [KN0975]


title: SK-LC-3 [KN0803]


title: H125 [KN0969]


title: NCI-H358 [KN0798]


title: SK-MES-1 [KN0976]


title: NCI-H1299 [KN0800]


title: H1155 [KN0970]


title: NCI-H446 [KN0801]


title: SW900 [KN0802]


title: CALU-1 [KN0797]


title: H1792 [KN0804]


title: H1688 [KN0974]


title: NCI-H820 [KN0799]


title: NCI-H209 [KN0795]


title: NCI-H146 [KN0794]


title: CALU-3 [KN0796]


title: LCLC-103H [KN0787]


title: HLC-1 [KN0972]


title: NCI-H596 [KN0791]


title: BEN [KN0786]

source_name: BEN

value: BEN


title: NCI-H292 [KN0784]


title: NCI-157 [KN0785]


title: NCI-522 [KN0779]


title: A549 [KN0792]


title: CAL-12T [KN0788]


title: NHBE [KN0776]

source_name: NHBE

value: NHBE


title: UMC-11 [KN0783]


title: COLO677 [KN0789]


title: NCI-H187 [KN0778]


title: LCLC-97TMI [KN0780]


title: NCI-H2126 [KN0781]


title: 9812 [KN0775]


title: T cells 72h after pAsc

city: Salt Lake City

first: Gerald

middle: J.

last: Spangrude

state: UT

department: Medicine/Hematology

institute: University of Utah

description: Bone marrow progenitor cells in culture with OP9-DL1 with Flt3L and IL7 for 17d, 800 uM pAsc added for final 72h of culture

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer. Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers. Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm. Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each. Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution. The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide. Data captured from the scanned microarray image is saved as a TIF file. TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 10.5.1.1. The software automatically positions a grid and finds the centroid positions of each feature on the microarray. This information is used to perform calculations that include feature intensities, background measurements and statistical analyses. Data generated by the software is recorded as a tab-delimited text file.

data_processing: LogRatio values were LOWESS normalized and filtered to remove control features, non-uniform outliers and feature population outliers. Remaining values were averaged to yield a single value for each microarray probe.

source_name: T cells at 17 days in MEM

label_protocol: The Agilent Two-Color Low RNA Input Linear Amplification Kit is used to generate fluorescently labeled cRNA for two-color microarray hybridizations. Agilent RNA spike-in controls are combined with input total RNA samples (50 to 500 ng). The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT. Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP. Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit. The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: Co-cultures of OP9-DL1 cells and bone marrow-derived progenitor cells were maintained with passage every 3-4 days. For harvest of RNA, stromal cells were depleted from T cells by a 30 min adherance

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: bone marrow

tag: time in culture

value: 17 days

tag: strain

source_name: T cells + pAsc 72h


title: EPLC-272H [KN0774]


title: NCI-H526 [KN0777]


title: LXF-289 [KN0773]


title: SKLU-1 [KN0770]


title: HCC-366 [KN0766]


title: SKLC-13 [KN0769]


title: NCI-322 [KN0793]


title: Stromal Cells 24h after pAsc

description: OP9-DL1 stromal cell response to 800 uM pAsc for 24h

source_name: OP9-DL1 cells in MEM

value: osteoblast

value: continuous

source_name: OP9-DL1 cells + pAsc 24h


title: NCI-H1838 [KN0767]


title: SK-LC-17 [KN0763]


title: NCI-H82 [KN0762]


title: NCI-H1395 [KN0765]


title: NCI-H2122 [KN0761]


title: SCLC-22H [KN0760]


title: epiWAT HF-DR replicate 10

city: Wageningen

first: Evert

last: van Schothorst

address: Marijkeweg 40

department: Human and Animal Physiology

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Cy3-labeled cRNA samples were pooled on an equimolar basis and used as a common reference pool. Individual Cy5-labelled samples were hybridized against the reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 4rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations using a Cy5-dyesaver as published (Anal Biochem 2007_363_315).

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool and log2 transformation.

source_name: epididymal white adipose tissue, high fat diet dietary restricted

label_protocol: 500 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol version 3.1 , as described previously (Am J Clin Nutr 2008; 87:181-189).

extract_protocol: Total RNA was isolated from epididymal WAT as described (Faseb J 2009; 23:1092-1101), quantified using Nanodrop and qualified using Experion Automated Electrophoresis System.

treatment_protocol: Animals were fed a purified high-fat (30 energy% fat) diet. The diet that was used for dietary restriction was in ratio supplemented with a vitamin and mineral premix to guarantee the same level of intake as in the non-restricted group to prevent deficiencies. All three groups received the diet ad-libitum during the three week adaptation phase, after which the t=0  animals were sacrificed. The HF-AL group subsequently remained under the same conditions for 12 weeks, while the HF-DR group received the diet on a restricted basis for 12 weeks.

tag: Sex

value: male

value: adult

value: epididymal white adipose tissue

source_name: epididymal white adipose tissue, reference pool of all samples


title: epiWAT HF-DR replicate 09


title: epiWAT HF-DR replicate 06


title: SCLC-21H [KN0758]

value: EBV Immortalized Fibroblast Reference


title: NCI-H1703 [KN0759]


title: epiWAT HF-AL replicate 12

source_name: epididymal white adipose tissue, high fat diet ad libitum


title: epiWAT HF-DR replicate 07


title: epiWAT HF-DR replicate 11


title: epiWAT HF-DR replicate 04


title: epiWAT HF-DR replicate 08


title: epiWAT HF-DR replicate 05


title: epiWAT HF-AL replicate 10


title: epiWAT HF-DR replicate 02


title: T cells 24h after pAsc

description: Bone marrow progenitor cells in culture with OP9-DL1 with Flt3L and IL7 for 14d, 800 uM pAsc added for final 24h of culture

source_name: T cells at 14 days in MEM

value: 14 days

source_name: T cells + pAsc 24h


title: epiWAT HF-AL replicate 09


title: CHAGO-K-1 [KN0757]


title: epiWAT HF-AL replicate 11


title: H2170 [KN0756]


title: epiWAT HF-DR replicate 03


title: epiWAT HF-AL replicate 08


title: C2C12_myoT_12hr_TGFb_rep2

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Biological replicate 2 of 2. 38B9 cells treated with TGFB for 12 hours

hyb_protocol: Agilent (mouse 4x44k or human 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 825 ng / 1.65 ug cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed.

scan_protocol: Arrays were scanned using an Agilent scanner G2565BA and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1.

data_processing: Data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default two-color gene expression protocol.

source_name: myotubes

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 2 µg total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates. C2C12 myoblasts were grown under typical C2C12 myoblast conditions.  Myotube formation was induced for 48 hours in 2% horse serum and 1x selenium, transferrin and insulin.  38B9 (pro-B) cells were grown under typical conditions in RPMI media with 10% FCS.

value: C2C12 cells

value: TGFb 2.5 ng/ml x 12hr


title: epiWAT HF-DR replicate 01


title: H647 [KN0563]


title: DMS114 [KN0442]


title: 38B9_12hr_TGFb_rep1

description: Biological replicate 1 of 2. 38B9 cells treated with TGFB for 12 hours

source_name: pro-B cell

value: 38B9 cells

value: TGFb 5.0 ng/ml 12hr


title: 38B9_12hr_TGFb_rep2


title: epiWAT HF-AL replicate 07

tag: sex


title: C2C12_myoT_12hr_TGFb_rep1


title: epiWAT HF-AL replicate 06


title: epiWAT HF-AL replicate 05


title: ES_cell_24hr_SB431542_rep2

source_name: mouse ES cells

value: mESC V6.5 cells

value: SB431542 for 24 hours


title: epiWAT HF-AL replicate 01


title: epiWAT HF-AL replicate 03


title: H1437 [KN0438]

tag: cell type

value: Lung Cancer Cell Line


title: H196 [KN0441]


title: epiWAT t=0 replicate 10

source_name: epididymal white adipose tissue, high fat diet, sacrificed after adaptation phase

tag: developmental stage


title: epiWAT HF-AL replicate 02


title: epiWAT t=0 replicate 11


title: epiWAT t=0 replicate 12


title: epiWAT HF-AL replicate 04


title: HCC15 [KN0443]


title: H211 [KN0439]


title: epiWAT t=0 replicate 09


title: H1568 [KN0435]


title: epiWAT t=0 replicate 05


title: epiWAT t=0 replicate 08


title: H1792 [KN0436]


title: epiWAT t=0 replicate 06


title: epiWAT t=0 replicate 07


title: epiWAT t=0 replicate 03


title: H1399 [KN0433]


title: ES_cell_24hr_SB431542_rep1


title: A427 [KN0434]


title: epiWAT t=0 replicate 02


title: H1650 [KN0437]


title: epiWAT t=0 replicate 04


title: epiWAT t=0 replicate 01


title: BW Keio mutant AdiA pH5.5

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

description:
Gene expression data from E.coli K12 at pH5.5 for 15 min
E.coli K12 mutant pH5.5 at 15 mins Adaptation

hyb_protocol: Following labelling , 80pmoles of labelled probe was hybridized for 16 hr at 42C on E.coli whole genome arrays. GeneChips were washed using Adwawash.

scan_protocol: GeneChips were scanned using the Perkin-Elmer Scanarray Scanner 4200.

data_processing: The data were analyzed with Scanarray express microarray analysis system and quantile normalization was used in R package to normalise the data.

organism: Escherichia coli K-12

source_name: BW29113 mutant pH5.5 at 15 mins Adaptation

label_protocol: Labelled cDNA was hybridised on E.coli custom made arrays.

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

tag: E.coli K12 BW29113

tag: Keio mutant


title: BW Keio mutant TrmE pH5.5


title: BW Keio mutant AdiA pH7

description:
Gene expression data from E.coli K12 at pH7 control
E.coli K12 mutant pH7

source_name: BW29113 mutant pH7 (control)


title: BW Keio mutant GadW pH7


title: BW Keio mutant GadW pH5.5


title: MG Keio mutant HNS pH5.5

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

source_name: MG1655 mutant pH5.5 at 15 mins Adaptation

tag: E.coli K12 MG1655


title: MG Keio mutant HNS pH7

source_name: MG1655 mutant pH7 (control)


title: BW Keio mutant TrmE pH7


title: MG wt pH5.5

description:
Gene expression data from E.coli K12 at pH5.5 for 15 min
E.coli K12 pH5.5 wildtype biological rep1

source_name: MG1655 pH5.5 wildtype

tag: wildtype


title: MG wt pH7

description:
Gene expression data from E.coli K12 at pH7 control
E.coli K12 pH7 wildtype biological rep1

source_name: MG1655 pH7 wildtype (control)


title: BW Keio mutant GadX pH5.5


title: BW Keio mutant GadX pH7


title: CPC-N [KN0431]

source_name: CPC-N

tag: cell line

value: CPC-N


title: H2347 [KN0429]


title: BW Keio mutant GrxA pH5.5


title: BW Keio mutant GrxA pH7


title: BW Keio mutant CadA pH5.5


title: H69 [KN0424]


title: H510A [KN0427]


title: H345 [KN0428]


title: HI 0150_Treated

city: Staten Island

first: Mohammed

middle: A.

last: Junaid

address: 1050 Forest Hill Road

department: Developmental Biochemistry

institute: New York State Institute for Basic Research in Developmental Disabilities

description: Agilent Feature Extraction file: 251485036061_S01_GE1_105_Jan09_1_3.txt

hyb_protocol: Fragmentation of the cRNA was done in 55 ul at 65oC for 17 hours according to the manufacturer's instructions. On completion of hybridization, 55 ul of Agilent hybridization was added to the fragmentation mixture and hybridized to Agilent Whole Genome oligonucleotide microarray (G4112F) at 65oC for 17 hours according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately on Agilent G2505B DNA scanner using one-color scan setting for 4x44k slides at 5 um resolution using Green channel at 100%.

data_processing: Scanned image was processed using the Feature Extraction Software v10.7.3.1 using default parameters (Protocol: GE1_107_Sep09, Grid: 014850_D_20070207).

source_name: Lymphoblastoid cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA supplemeted with RNA Spike-In mix (Agilent Technologies, Santa Clara, CA) by one-color low-input QuickAmp Plus labeling kit (Agilent Technologies, Santa Clara, CA) as per manufacturer's instructions. The cRNA was purified by RNeasy kit (Qiagen, Valencia, CA), and the incorporation of Cy3 dye and the yield of cRNA was checked by the NanoDrop-1000 spectrophotometer.

growth_protocol: Cells were grown in RPMI-1640 medium (Invitrogen Life Technologies, Carlsbad, CA) supplemented with 15% fetal calf serum and antibiotics penicilin and streptomycin (100 ug/ml). Cells were grown and maintained at 37oC in a humidified incubator with 5% CO2 in air.

extract_protocol: Total RNA was prepared by TRIZOL reagent (Invitrogen Life Technologies, Carlsbad, CA), and further purification was achieved by Qiagen RNeasy kit (Qiagen, Valencia, CA) as per manufacturer's instructions. RNA was quantified by NanoDrop-1000 spectrophotometer and quality was evaluated by E-Gene analyzer (Qiagen, Valencia, CA). All the RNA samples had a 260/280 nm absorption ratio of 2.0, and the amount of 28S band was twice in area and intensity that 18S band.

treatment_protocol: Cells were treated with folic acid (Sigma Chemical Co, St. Louis, MO) at either 0 or 500 ng/ml medium concentration for four days.

value: Lymphoblastoid cells

tag: agent

value: folic acid


title: H661 [KN0425]


title: HI 0961_Treated

description: Agilent Feature Extraction file: 251485036061_S01_GE1_105_Jan09_1_4.txt


title: BW Keio mutant CadA pH7


title: epiWAT HF-DR replicate 12

source_name: epididymal white adipose tissue, high fat diet dietary restricted


title: H838 [KN0423]


title: H727 [KN0421]


title: BW Keio mutant YjbJ pH7


title: BW Keio mutant YjbJ pH5.5


title: BW Keio mutant Spy pH5.5


title: H1563 [KN0422]


title: BW Keio mutant HslJ pH 7


title: BW Keio mutant Spy pH7


title: HI 0961_Untreated

description: Agilent Feature Extraction file: 251485036061_S01_GE1_105_Jan09_1_2.txt

value: control


title: BW Keio mutant AceE pH5.5


title: N/A [JA1219]

value: Primary Glioblastoma


title: BW Keio mutant YcaD pH7


title: BW Keio mutant AceE pH7


title: H460 [KN0420]


title: DN3 KO5

city: Montréal

first: Lothar

last: Vassen

state: Quebec

address: 110, avenue des Pins Ouest

department: Hematopoiesis and Cancer

institute: IRCM

description: Miz1 knockout

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MG-430_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (G7 update).

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: Lin neg., CD44 neg., CD25 pos. thymocytes

label_protocol: 200ng of target RNA was reverse transcribed into cDNA using the Ambion MessageAMP II Biotin Enhanced Kit and in-vitro transcription was performed to generate biotin-labeled cRNA. cRNA was labeled with streptavidin-phycoerythrin.

extract_protocol: TRIzol (GIBCOBRL, Life Technologies) was used to prepare total RNA

tag: genotype

value: Miz1 knockout


title: BW Keio mutant RpoS pH7


title: BW Keio mutant fis pH5.5


title: N/A [JA1217]


title: HI 0150_Untreated

description: Agilent Feature Extraction file: 251485036061_S01_GE1_105_Jan09_1_1.txt


title: BW Keio mutant IhfB pH7


title: BW Keio mutant IhfB pH5.5


title: BW Keio mutant HslJ pH 5.5


title: BW Keio mutant fis pH7


title: BCL6 KO chip 2 untreated

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: GCOS 1.3

source_name: bone marrow, BCL6 KO, untreated

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

tag: age

value: 4 weeks

tag: cell culture

value: BCR-ABL1 transformed myeloid cells

tag: disease state

value: BCR-ABL1-driven CML

tag: genotype/variation

value: BCL6 KO

value: untreated


title: BCL6 KO chip 2 Imatinib treated

description: BCL6 KOCML cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

source_name: bone marrow, BCL6 KO, Imatinib treated

value: Imatinib


title: DN3 WT2

description: wt

value: Lin neg., CD44 neg., CD25 pos. thymocytes

value: wt

tag: genetic background


title: N/A [JA1223]

tag: reference

value: EBV Immortalized Fibroblast Reference


title: N/A [JA1213]


title: BW Keio mutant NarX pH5.5


title: BCL6 KO chip 1 untreated

tag: strain


title: hESCs after 5 days of differentiation sorted fixed SOX17+GATA4+CXCR4+ cells, biological rep3

city: Stanford

first: Yuqiong

last: Pan

address: 300 Pasteur Drive, Alway Bldg. Rm M313

department: Depts of Statistics and Genetics

institute: Stanford University

description:
sample probe group file: HuEx-1_0-st-v2.r2.pgf
sample meta probeset file: HuEx-1_0-st-v2.na24.hg18.probeset.csv

hyb_protocol: Samples were hybridized with Affymetrix Human Exon 1.0 ST Array using Affymetrix hybridization kit materials

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: We computed gene expression indices for all the samples analyzed using the GeneBASE software. We performed background correction, probe selection, and expression index computation on all the samples, followed by quantile normalization of gene level expression values.

source_name: fixed, stained, sorted day 5 differentiated SOX17+GATA4+CXCR4+ hESCs

label_protocol: Samples were enzymatically fragmented and biotin-labeled using GeneChip Whole Transcript Sense Target Labeling Assay Manual (Affymetrix)

growth_protocol: Undifferentiated hES cells (H9 passages 40-55) were maintained on irradiated mouse embryonic fibroblast (MEF) feeders. Definitive endoderm differentiation was induced from hESCs by activin A (R&D Systems Inc.). For differentiation, hESCs were first passaged onto dishes coated with growth factor reduced Matrigel and cultured in hESC media conditioned overnight on primary MEF (CM) for 2 days. Undifferentiated hESCs samples were collected. Differentiation was carried out in RPMI 1640 supplemented with Glutamax, penicillin/streptomycin and varying concentrations of defined FBS. FBS concentrations were 0% for the first 24 h, 0.2% for the second 24 h, and 2.0% for subsequent days of differentiation. Recombinant human activin A was added to the differentiation medium at 100 ng / ml, and cells were treated for 5 days, with medium changed once at day 3.

extract_protocol: All the cells either from sorted populations or from the presorted mixtures were centrifuged at 14,000 rpm, 2 min, 4 0C to get cell pellets. Total mRNA was extracted using the Ambion Recover All nucleic acid extraction kit (optimized for fixed cells) (Applied Biosystems Ambion). Briefly, for each sample, 1.5 g of total RNA was subjected to ribosomal RNA reduction. Following rRNA reduction, double-stranded cDNA was synthesized with random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA was used as a template for amplification with T7 RNA polymerase to create antisense cRNA. Next, random hexamers were used to reverse transcribe the cRNA to produce single-stranded sense strand DNA.

treatment_protocol: Samples were collected after 3 and 5 days of differentiation.  As controls we also collected undifferentiated hESCs before the endoderm differentiation started. Cells were dissociated using 0.05% trypsin-0.53 mM EDTA at 37 0C for 3 min followed by neutralization in hESCs medium with serum. Cells were washed in staining buffer. After cells were fixed by 4% paraformaldehyde (PFA) at 4°C for 15 minutes, they were permeablized, stained with antibodies of combination of nuclear transcription factors or plus cell surface proteins, then isolated by FACS sorting. We utilized the optimized protocol to obtain the intact RNA from these cells after they were processed by the above procedures. The unsorted fixed cells and the sorted unfixed cells were also collected and analyzed  in parallel with these sorted fixed cells.

tag: differentiation stage

value: after 5 days of differentiation

tag: fixed and unfixed

value: fixed cells

tag: sorting marker

value: SOX17 GATA4 CXCR4


title: BW Keio mutant NarX pH7

tag: E.coli K12 BW29113


title: hESCs after 5 days of differentiation sorted unfixed CXCR4+ cells, biological rep1

source_name: unfixed, stained, sorted day 5 differentiated CXCR4+ hESCs

value: unfixed cells


title: hESCs after 5 days of differentiation sorted unfixed CXCR4+ cells, biological rep2


title: BCL6 KO chip 1 Imatinib treated


title: BCL6 WT chip 2 Imatinib/RI-BPI treated

description: BCL6 WT CML cells were incubated with 10 µM STI571 (Imatinib) and 20 µM RI-BPI for 16 hours.

source_name: bone marrow, BCL6 WT, Imatinib/RI-BPI treated

value: BCL6 WT

value: Imatinib/RI-BPI


title: BW Keio mutant CadB pH7

tag: Keio mutant


title: BW Keio mutant CadB pH5.5


title: hESCs after 3 days of differentiation sorted fixed SOX17+GATA4+ cells, biological rep2

source_name: fixed, stained, sorted day 3 differentiated SOX17+GATA4+ hESCs

value: after 3 days of differentiation

value: SOX17 GATA4


title: hESCs after 5 days of differentiation sorted fixed SOX17+GATA4+CXCR4+ cells, biological rep1


title: BW Keio mutant pHoH pH5.5


title: hESCs after 3 days of differentiation sorted fixed SOX17+GATA4+ cells, biological rep1


title: BW Keio mutant pHoQ pH5.5


title: hESCs after 5 days of differentiation sorted fixed SOX17+GATA4+CXCR4+ cells, biological rep2


title: BCL6 WT chip 2 untreated

source_name: bone marrow, BCL6 WT, untreated

value: 4 weeks


title: BCL6 WT chip 1 Imatinib treated

description: BCL6 WT CML cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.

source_name: bone marrow, BCL6 WT, Imatinib treated

value: BCR-ABL1 transformed myeloid cells


title: BCL6 WT chip 1 untreated

value: BCR-ABL1-driven CML


title: BCL6 WT chip 1 Imatinib/RI-BPI treated


title: BW Keio mutant HdeA pH 5.5

source_name: BW29113 mutant pH5.5 at 15 mins Adaptation


title: BW Keio mutant HdeA pH7

source_name: BW29113 mutant pH7 (control)


title: BW Keio mutant pHoP pH5.5


title: BW Keio mutant pHoQ pH7


title: BW Keio mutant pHoH pH7


title: BW Keio mutant GcvP pH5.5


title: hESCs after 5 days of differentiation unsorted fixed, biological rep2

source_name: fixed, stained, unsorted day 5 differentiated hESCs


title: BW Keio mutant pHoP pH7


title: BW Keio mutant GadB pH5.5


title: hESCs after 5 days of differentiation unsorted fixed, biological rep4


title: BW Keio mutant HdeB pH7


title: BW Keio mutant HdeB pH5.5