Citrus
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ABSTRACT:
REPOSITORIES: ENA
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Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
| 2643590 | ecrin-mdr-crc
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Citrus sinensis tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2011-04-30 | GSE28754 | GEO
Project description:Bowel cancer is the third most common cancer occurring in the UK. Treatment usually involves surgery, often with chemotherapy or radiotherapy. In some cases radiotherapy can be used instead of surgery, especially if surgery may cause a higher risk of symptoms or a colostomy bag. Currently, the medical team collects information on patients’ symptoms before and after treatment by direct questions in a clinic setting. It’s recognised that patient-reported symptoms often differ from doctor-documented symptoms. This leads to inaccuracies in doctors’ descriptions of the effects of cancer or treatment to patients. Patients told us an accurate description of expected symptoms is important when they are choosing their treatment.
Patient-Reported outcomes measures (PROMs) may help us identify what affects the QoL after treatment and develop ways to improve it. The primary aim of the trial is to evaluate whether patients find it acceptable to use electronic data collection to assess their symptoms. Many bowel cancer patients are elderly and they may find electronic data system collection more challenging. The secondary aim is to identify which symptoms impact QoL. This will lead to the development of treatments to manage these symptoms which will be assessed in CITRuS2.
All patients diagnosed with bowel cancer are entered into the colorectal database to determine the effectiveness of cancer treatments and outcomes. Participants will electronically answer questionnaires at study entry and during follow up. The questions are related to health and well-being with a holistic approach. The questions will take approximately 45 minutes to answer the first time and then 15 minutes thereafter. Following consent, participants gain access to their clinical details on the database. Then they can use a computer, laptop, tablet or smart phone to access a webpage and answer questions at monthly intervals over a 2 year period. Email reminders will be sent to prompt log on.
This may help discover how bowel cancer and its treatment affect patients and their lives. This may help doctors describe the effects of treatment more accurately to future patients. It may also help doctors identify which patients need extra help or support through their treatment. Electronic data may allow patterns to be identified that may not be seen by doctors until a later stage. This may enable earlier treatment resulting in less time with symptoms, which could be physically and economically beneficial.
| 2362974 | ecrin-mdr-crc
Project description:The Malaysian Node of the Human Variome Project Database (MyHVPDb) is a country specific database of human variant and gene mutation that was established in 2011. This ethnic specific mutation and variation databases are being continuously updated, recording extensive information over the genetic heterogeneity of the Malaysian ethnic groups. The database comprises of SNP Database and Mutation Database. The SNP database has stored 291718 SNPs that was obtained by genotyping the SNPs of 101 healthy individuals from six Malay sub-ethnic groups which consist of Malay Kelantan, Malay Banjar, Malay Kedah, Malay Jawa, Malay Bugis and Malay Champa.
2015-02-11 | GSE65760 | GEO
Project description:Genome sequencing as part of the Citrus Genomics Project
| PRJNA10879 | ENA
Project description:A microarray containing 62,876 unigenes selected from CitEST database and prepared by Nimblegen Systems was used for identifying candidate resistance genes against P. parasitica at 48 hours after inoculation Four resistant and four susceptible F1 hybrids were selected from the population derived from the cross between Citrus sunki Hort. ex. Tan. and Poncirus trifoliate (L.) Raf cv. Rubidoux, respectively susceptible and resistant to P. parasitica. It was proposed that differentially expressed genes between resistant and susceptible hybrids and their parents provide essential candidates for identifying transcripts involved in disease resistance A total of 62,876 unigenes (18,712 unigenes of Citrus sinensis; 31,583 unigenes of Citrus reticulata and 12,581 unigenes of Poncirus trifoliate) selected from CitEST database assembled from the EST submitted to NCBI (Genebank accession number EY649559 to EY842485) were used to construct genome-wide oligonucleotide cDNA microarrays by Roche NimbleGen Systems using a multi-step approach to select probes with optimal predicted hybridization characteristics. Three probes were selected per unigene, comprising a probe set, and each probe set is represented on the final array by two replicates. All probes were designed as ‘‘perfect match’’ (PM) oligonucleotides (oligos).
2010-02-19 | E-GEOD-20412 | biostudies-arrayexpress
Project description:Single-cell RNA-Seq RNA from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5. The ID of this project in Genentech's ExpressionPlot database is PRJ0007389
2017-03-02 | GSE94641 | GEO
Project description:RNA was purified cancer cell lines. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0013114
2018-10-01 | GSE108464 | GEO