Gene Expression Study of Arachis Hypogaea L.

allȱthreeȱtranscriptsȱandȱindividualȱmappedȱreadsȱinȱ NGS QC Toolkit

.gtfȱfileȱformatȱareȱconsideredȱandȱresultȱofȱCuffdiffȱ

Sequencesȱ filteredȱ withȱ thisȱ toolȱ byȱ removingȱ

reportedȱgeneȱexpressionȱofȱthreeȱsamplesȱwhichȱisȱ

adaptorsȱ andȱ otherȱ contaminatedȱ materialsȱ thenȱ

furtherȱanalyzedȱwithȱCummeRbundȱpackageȱinȱRȱ

qualityȱ ofȱ sequenceȱ alsoȱ checkedȱ andȱ finallyȱ high-

language.

qualityȱ filterȱ sequenceȱ fileȱ consideredȱ forȱ furtherȱ

CummeRbund

analysisȱ(Tableȱ2).

CummeRbundȱisȱanȱRȱpackageȱthatȱisȱdesignedȱtoȱaidȱ Gene Expression results

andȱsimplifyȱtheȱtaskȱofȱanalyzingȱCufflinksȱRNA-Seqȱ

output.ȱ CummeRbundȱ handlesȱ theȱ transformationȱ 1. Overall result

ofȱ Cuffdiffȱ dataȱ intoȱ theȱ Rȱ statisticalȱ computingȱ

Resultsȱ shownȱ inȱ Tableȱ 3ȱ areȱ fromȱ CummeRbundȱ

environment,ȱmakingȱRNA-seqȱexpressionȱanalysisȱ

tool,ȱinȱwhichȱfilesȱfromȱCuffdiffȱtoolȱinsertedȱandȱ

withȱ Cuffdiffȱ moreȱ compatibleȱ withȱ manyȱ otherȱ

afterȱimplementingȱfewȱcommandsȱresultsȱareȱshownȱ

advancedȱstatisticalȱanalysisȱandȱplottingȱpackagesȱ

inȱ Tableȱ 3,ȱ whichȱ showsȱ numbersȱ ofȱ differentiallyȱ

(ColeȱTrapnellȱ et al. 2012).

expressedȱgenesȱinȱthisȱstudy.

Results and Discussion

Table 3. Overview of Gene expression result.

Sequence Comparison

Content

Result

Forȱ geneȱ expressionȱ studyȱ ofȱ Arachis Hypogaea ȱ L.;ȱ

samples

3

threeȱRNA-SeqȱdownloadedȱfromȱNCBIȱdatabaseȱofȱ

genes

27126

SRAȱBioProjectȱIDȱ243319ȱandȱdetailsȱofȱeachȱRNA-

isoforms

35267

SeqȱisȱgivenȱinȱTableȱ1.

TSS

28643

CDS

32744

Table 1. Comparison of three RNA-Seq.

splicing

81378

%GC

relCDS

81048

SRR Number

Spots

Bases

Size

Content

SRR1212866

7.3 M

365.0 Mbp

254.2 M

48.5%

2. Dispersion plot

SRR1212867

7.7 M

383.8 Mbp

268.9 M

49.2%

Figureȱ2ȱshowsȱtheȱDispersionȱplotȱofȱthreeȱRNA-Seqȱ

SRR1212868

7.1 M

355.7 Mbp

240.1 M

44.1%

samples.ȱ Allȱ threeȱ samplesȱ areȱ inȱ differentȱ colors,ȱ

andȱcomparativeȱviewȱcanȱeasilyȱseeȱinȱFigureȱ2.

Table 2. NGS QC Toolkit Result.

Total number of reads

Total number of

Total number of bases

Total number of

Percentage

SRR Number

(High Quality (HQ)

bases (Original

(High Quality (HQ)

reads (Original File)

of HQ reads

Filter file)

File)

Filter file)

SRR1212866

7300624

7216150

365031200

356155344

98.84%

SRR1212867

7676569

7591722

383828450

374677397

98.89%

SRR1212868

7113198

7016388

355659900

346595531

98.64%

297