Dataset Information

Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis

ABSTRACT: Zebrafish organ proteomics was carried out for proteogenomic analysis. High resolution mass spectrometry-based proteomic profiling of 11 adult organs (eye, brain, liver, spleen, intestine-pancreas, ovary, testes, muscle, heart and head) and two developmental stages (embryos 48 and 120 hours post-fertilization) of zebrafish (SAT line) was carried out. Protein extracts were reduced and alkylated (iodoacetamide). Off-loine fractionation was carried out by SDS-PAGE and basic RPLC. MS analysis was cariied on Agilent 6540 Q-TOF. Spleen and Testis samples were also analyzed on Thermo Orbitrap LTQ Velos.

REANALYSED by: PAe004707PAe004706PAe004705PAe004704PAe004372PAe004371PAe004370PAe004369PAe004368PAe004367PAe004366PAe004365PAe004364PAe004363PAe004362PAe004361PAe004360

INSTRUMENT(S): LTQ Orbitrap Velos, 6520 Quadrupole Time-of-Flight LC/MS

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

SUBMITTER: Akhilesh Pandey

PROVIDER: PXD000479 | Pride | 2014-02-26

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	BasicRPLC_Testis1.d.zip	Other
	BasicRPLC_Testis10.d.zip	Other
	BasicRPLC_Testis11.d.zip	Other
	BasicRPLC_Testis12.d.zip	Other
	BasicRPLC_Testis13.d.zip	Other

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Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

Kelkar Dhanashree S DS Provost Elayne E Chaerkady Raghothama R Muthusamy Babylakshmi B Manda Srikanth S SS Subbannayya Tejaswini T Selvan Lakshmi Dhevi N LD Wang Chieh-Huei CH Datta Keshava K KK Woo Sunghee S Dwivedi Sutopa B SB Renuse Santosh S Getnet Derese D Huang Tai-Chung TC Kim Min-Sik MS Pinto Sneha M SM Mitchell Christopher J CJ Madugundu Anil K AK Kumar Praveen P Sharma Jyoti J Advani Jayshree J Dey Gourav G Balakrishnan Lavanya L Syed Nazia N Nanjappa Vishalakshi V Subbannayya Yashwanth Y Goel Renu R Prasad T S Keshava TS Bafna Vineet V Sirdeshmukh Ravi R Gowda Harsha H Wang Charles C Leach Steven D SD Pandey Akhilesh A

Molecular & cellular proteomics : MCP 20140724 11

Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs ...[more]

PMID: 25060758

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Project description:Sense-antisense transcript (SAT) pairs are pairs of transcripts that fully or partially overlap but are transcribed in opposite directions. Although SAT expression occurs in various species, most SAT pairs have not been examined in detail. Because our previous studies revealed some tissue specificity in SAT expression, SAT pairs might be involved in cell differentiation and the maintenance of tissue-specific gene expression programs. To analyze such tissue-specific SAT pairs, we assessed the expression profiles of SATs from 12 tissues of normal mice at a genome-wide scale and found that a considerable number of SAT pairs showed expression patterns unique to testis. This finding prompted us to study the relationship between SAT expression pattern and another epigenetic gene regulatory mechanism, DNA methylation. We conducted a comparative global analysis of the DNA methylation status of CpG island (CGI)-associated SAT loci from various tissues and found that in 99 of the 4911 SAT pairs studied, DNA methylation could cooperatively suppress its downstream “sense” transcription together with the “antisense” transcriptional activity in a tissue-specific manner. The tissue-specific differentially methylated regions (T-DMRs) of these SAT pairs mainly occurred outside of the defined CGIs. In addition, some of these T-DMRs are situated at the 5′ region of the antisense transcripts. This positioning implies a novel mechanism for DNA methylation to regulate gene transcription, in which DNA methylation inhibits an opposing transcriptional activity and therefore maintains stable expression of a tissue-specific gene. Twelve tissues (brain, thymus, heart, lung, liver, spleen, stomach, kidney, small intestine, testis, and placentae [10.5 and 13.5 days postcoitum (dpc)]) of C57BL/6J Jc1 and a mouse fibroblast cell line (SL10) were used for the mouse expression oligo-microarray. The expression array data were obtained by both oligo-dT and random priming methods, except for SL10 (olio-dT only). Twelve tissues (brain, thymus, heart, lung, liver, spleen, stomach, kidney, small intestine, testis, and placentae [10.5 and 13.5 days postcoitum (dpc)]) were used for DIP chip experiments. Nine of twelve tissues were separately analyzed classified on the basis of sex. A technical duplication of DIP chip analysis was performed by using the same genomic DNA of male kidney.