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Status |
Public on Feb 05, 2011 |
Title |
[E-MTAB-5] run38_s6 |
Sample type |
SRA |
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Source name |
run38_s6
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Organism |
Schizosaccharomyces pombe |
Characteristics |
material type: whole_organism Sex: mating_type_h_plus/plus strainorline: JB371 genotype: pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ growthcondition: meiosis time: 3 + 4h temperature: 34degree_C media: EMM low nitrogen culture density: 0.5OD
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Extracted molecule |
total RNA |
Extraction protocol |
nucleic_acid_extraction | All cDNA samples used for Illumina sequencing were prepared by first treating ~1 mg of total RNA for 30 min with amplification grade RNase-free DNase (Invitrogen), according to the manufacturers protocols. PolyA enriched RNA was then prepared using an oligo(dT) selection kit (Oligotex Direct mRNA MiniKit, Qiagen). The resulting poly(A)-enriched RNA was then converted to double-stranded cDNA using a cDNA synthesis kit (Superscript choice system for cDNA synthesis, Invitrogen) , primed by an oligo(dT) primer, according to the manufacturers protocols. Random-primed RNA from rapidly proliferating cells was treated with an enzyme that specifically degrades non-capped RNA molecules (mRNA-only, Eukaryotic mRNA isolation kit, Epicentre Biotechnologies) according to the manufacturers protocols. The resulting cDNA was then converted to double-stranded cDNA as above, except that the reaction was primed with random hexamers. RNA samples from the pooled meiotic timepoints were subjected to IVT amplification after undergoing a poly(A) enrichment step as described above. RNA from the oxidative stress condition and prp2 mutant was treated in the same way as the rapidly proliferating samples with oligo(dT)-primed cDNA synthesis after mRNA enrichment.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer |
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Data processing |
Sequence data processing: FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis. Sequencing expression scores: Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp. processed data files: normM21_solexa_logscore_Rchrm1.txt normM21_solexa_logscore_Rchrm2.txt normM21_solexa_logscore_Rchrm3.txt normM22_solexa_logscore_Rchrm1.txt normM22_solexa_logscore_Rchrm2.txt normM22_solexa_logscore_Rchrm3.txt normM23_solexa_logscore_Rchrm1.txt normM23_solexa_logscore_Rchrm2.txt normM23_solexa_logscore_Rchrm3.txt
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Submission date |
Oct 28, 2010 |
Last update date |
Oct 19, 2011 |
Organization |
European Bioinformatics Institute |
E-mail(s) |
miamexpress@ebi.ac.uk
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Lab |
ArrayExpress
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Street address |
Wellcome Trust Genome Campus
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City |
Hinxton |
State/province |
Cambridgeshire |
ZIP/Postal code |
CB10 1SD |
Country |
United Kingdom |
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Platform ID |
GPL9854 |
Series (1) |
GSE25003 |
[E-MTAB-5] Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution |
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Supplementary data files not provided |
Raw data not provided for this record |
Processed data are available on Series record |
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