Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of synovial fibroblast ex vivo cultures or whole joints (J), isolated from arthritic mice (197, DARE) and their corresponding normal (F1, wt) littermates

ABSTRACT: GOAL: Identification of genes and/or pathways involved in the pathogenesis of animal models of Rheumatoid Arthritis (RA). Total RNA samples were extracted from synovial fibroblast ex vivo cultures or whole joints (J), isolated from arthritic mice (197, DARE) and their corresponding normal (F1, wt) littermates. Fluorescent-labeled cRNA probes were utilized to hybridize (in duplicates for 197, indicated by "new") the Affymetrix Mu11K oligonucleotide DNA chipset (A+B). In detail the samples are:

Animal model	Sample source	Sample name
Tg197	Tg197 ex-vivo cultured synoviocyte populations	197
Tg197	Tg197 ex-vivo cultured synoviocyte populations	197new
Tg197	wt ex-vivo cultured synoviocyte populations	F1
Tg197	wt ex-vivo cultured synoviocyte populations	F1new
Tg197	Tg197 whole joints	197J
Tg197	Tg197 whole joints	197Jnew
Tg197	wt whole joints	F1J
Tg197	wt whole joints	F1Jnew
DARE	DARE ex-vivo cultured synoviocyte populations	DARE
DARE	wt ex-vivo cultured synoviocyte populations	wt
DARE	DARE whole joints	DAREJ
DARE	wt whole joints	wtJ

Submitted files carry the extension A or B, corresponding to the subArrays of chipset Mu11K. Arthritic samples were always compared with the corresponding wt sample and not to a common reference chip.

ORGANISM(S): Mus musculus

DISEASE(S): rheumatoid arthritis

SUBMITTER: Maung-Maung Thwin

PROVIDER: E-MEXP-255 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.

Aidinis Vassilis V Carninci Piero P Armaka Maria M Witke Walter W Harokopos Vaggelis V Pavelka Norman N Koczan Dirk D Argyropoulos Christos C Thwin Maung-Maung MM Möller Steffen S Waki Kazunori K Gopalakrishnakone Ponnampalam P Ricciardi-Castagnoli Paola P Thiesen Hans-Jürgen HJ Hayashizaki Yoshihide Y Kollias George G

PLoS genetics 20051028 4

Rheumatoid arthritis is a chronic inflammatory disease with a high prevalence and substantial socioeconomic burden. Despite intense research efforts, its aetiology and pathogenesis remain poorly understood. To identify novel genes and/or cellular pathways involved in the pathogenesis of the disease, we utilized a well-recognized tumour necrosis factor-driven animal model of this disease and performed high-throughput expression profiling with subtractive cDNA libraries and oligonucleotide microar ...[more]

PMID: 16254600

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Project description:Description of Cohort: The California Pacific Medical Center (CPMC) Breast Health Cohort is a cohort study based at CPMC and is linked to the San Francisco Mammography Registry, one of the sites of the NCI-funded Breast Cancer Screening Consortium (U01CA063740). CPMC is a community hospital in San Francisco, which has one of the highest volumes for mammography in San Francisco. Between September 2004 and June 2007, >90,000 mammograms were performed at CPMC. The CPMC breast health cohort collects demographic and risk factor data on women receiving mammography through participation in the San Francisco Mammography Registry, as part of the Breast Cancer Screening Consortium (U01CA063740). The SFMR database collects information from all sources, including a questionnaire on demographic and risk factor information, the clinical results of the breast examination, the measures of breast density by Dr. John Shepherd and the women who agreed to donate a blood sample. By merging these various sources of information we have very efficiently developed a large sample of women who have donated blood and have had a measure of mamographic density. Blood Collection: Dr. Steve Cummings is leading an effort to collect and archive blood samples from women who are receiving mammography screening. All women who are sent for a screening mammogram at CPMC are considered eligible. Since the cohort began collecting blood samples in July 2004 until June 2007, samples have been collected from over 11,000 women. Measurement of Breast Density: Dr. John Shepherd is currently measuring breast density in a large fraction of the cohort using an automated approach with single X-ray absorptiometry. Dr. Shepherd has established a link with the CPMC mammography center that allows him to collect routine digital mammography information. Using the data from the mammogram, Dr. Shepherd and his group have developed the single X-ray absorptiometry (SXA) technique for measuring density which is described in more detail below. The table demonstrates the distribution of demographic variables and some breast cancer risk factors of women who donated blood and had a breast density measurement in the CPMC breast health cohort. Nearly 80% of the participants are Caucasian and most of the women are post-menopausal with a median age of ~52. Since it will be difficult to accrue a large enough sample from each ethnic group, our study will focus only on Caucasian women. Table: Demographic variables, reproductive history and family history of breast cancer among 2962 women participating in the CPMC cohort study who contributed blood samples between 1994-1997. <table border="1"> <tr> <th>Variable</th> <th>Median/Percentage</th> </tr> <tr> <td>Age (Median/IQR)</td> <td align="center">52 (46-59)</td> </tr> <tr> <td>Ethnicity</td> <td></td> </tr> <tr> <td align="right">Caucasian/White</td> <td align="center">0.76</td> </tr> <tr> <td align="right">Asian/Pacific Islander</td> <td align="center">0.141</td> </tr> <tr> <td align="right">Hispanic</td> <td align="center">0.029</td> </tr> <tr> <td align="right">Mixed Race/Ethnicity</td> <td align="center">0.039</td> </tr> <tr> <td align="right">African American/Black</td> <td align="center">0.022</td> </tr> <tr> <td align="right">American Indian</td> <td align="center">0.001</td> </tr> <tr> <td align="right">Other</td> <td align="center">0.009</td> </tr> <tr> <td>First degree relative with breast cancer</td> <td align="center">0.17</td> </tr> <tr> <td>Age at first birth</td> <td></td> </tr> <tr> <td>Nulliparous</td> <td align="center">0.39</td> </tr> <tr> <td align="right">Age<20</td> <td align="center">0.043</td> </tr> <tr> <td align="right">Age>40</td> <td align="center">0.032</td> </tr> <tr> <td align="right">Age<30, ≥20</td> <td align="center">0.251</td> </tr> <tr> <td align="right">Age>30, ≤40</td> <td align="center">0.282</td> </tr> </table> Measurement of Breast Density in Cohort: Measurement of breast density is accomplished using an automated technique for all mammograms obtained by Dr. Shepherd using Single X-Ray absorptiometry (SXA). 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Dataset Information

Transcription profiling of synovial fibroblast ex vivo cultures or whole joints (J), isolated from arthritic mice (197, DARE) and their corresponding normal (F1, wt) littermates

Publications

Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.

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