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Dataset modENCODE_mRNA-Seq_treatments
| General Information | |||
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| Name | modENCODE_mRNA-Seq_treatments | Species | D. melanogaster |
| Dataset type | RNA-Seq transcriptome profiles | FlyBase ID | FBlc0000236 |
| Source & Content | |||
| Consists of |
cDNA short sequencing reads from high-throughput sequencing.
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| Created by | |||
| Available from | |||
| Strain |
Oregon-R-modENCODE
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Stage & tissue | |
| Cell Line |
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Recent Updates
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| Description |
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| Update Feed |
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| FB2013_03 | |||
| FB2013_02 | |||
| All updates | Click here to see a list of all updates to this record from FB2010_08 and on. | ||
Description & Members
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| Description |
Umbrella record for 21 collections that differ by treatment conditions from Oregon-R animals. Consists of 76-100nt strand-specific
paired-end reads; longer reads trimmed so that all aligned reads are 76nt. Transcriptome represented as frequency of reads
along genome (data in wiggle format; see GBrowse presentation). The profiles are represented as uniquely aligned reads.
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| Parent collections |
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| Component collection(s) |
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| Number in collection |
2,674,238,504
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| Comment on number in collection |
Sum of unique reads of component collections; determined by FlyBase.
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| Members |
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Experimental protocol
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| Vector | |||
| Sample preparation |
Polyadenylated RNAs were purified from total RNA extracts via oligo(dT) binding, using standard Illumina protocol. (See specific
treatment collection reports for decriptions of treatment protocols.)
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| Collection preparation |
The poly(A)+ RNA was fragmented using divalent cations under elevated temperature, following by sequential ligation of RNA
linkers to the 5’ and 3’ ends. Next, reverse transcription was performed using a primer complementary to the 3’ linker and
PCR was performed using primers complementary to both linkers. ~ 300 bp fragments were isolated from an agarose gel and gel-purified
again.
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| Mode of assay |
The samples were quantitated using a Nanodrop, and loaded onto a flow cell for cluster generation and sequenced on an Illumina
Genome Analyzer II or HiSeq 2000 using paired end protocols (Illumina).
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| Assay platform |
Illumina Genome Analyzer II (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL9061)
Illumina HiSeq 2000
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| Data analysis |
Bases were called using the most current version of the Illumina processing pipeline. The sequencing was performed using 76
nt reads on the GAIIx and 100 nt reads on the HiSeq2000. Fastq files were generated using the most current version of the
Illumina pipeline software. The HiSeq reads were trimmed from the 3' ends to be 76 nt long, so all aligned reads are 76 nt.
Reads were aligned using Bowtie v0.12.0 to a combined index of the genome and both annotated and predicted splice junctions.
Paired-end alignments were further parsed using Spliced-Paired-end-Aligner (SPA, written by Michael Duff) to identify the
optimal mapping location for mate-pairs.
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Additional data
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More information is available under:
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| Associated files | |||
| Additional sites | |||
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Synonyms & Secondary IDs
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| Reported As | |||
| Symbol Synonym |
Drosophila transcriptome
modENCODE_mRNA-Seq_treatments
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| Secondary FlyBase IDs | |||
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References
( 2 )
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| Personal communication to FlyBase |
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| FlyBase analysis |
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