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| Status |
Public on Oct 10, 2015 |
| Title |
yeast RNA-seq fast BioRep3 |
| Sample type |
SRA |
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| Source name |
yeast sample
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
growth rate: fast
condition: chemostat
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| Growth protocol |
Saccharomyces cerevisiae (EUROSCARF accession number Y11335 BY4742; Mat ALPHA; his3delta1; leu2delta0; lys2delta0; ura3delta0; YJL088w::kanMX4) was grown in defined minimal C-limiting (F1) medium (71) using 10 g.l-1 of glucose as the sole carbon source. The F1 medium was additionally supplemented with 0.5 mM arginine and 1 mM lysine to meet the added auxotrophic requirements of the strain. For biological replication, four cultures were grown in chemostat mode at a dilution rate of 0.1 h-1 and aliquots (15 ml) of the culture were centrifuged (4000 rpm; 4 °C; 10 minutes). The supernatant was discarded, the pellet flash frozen in liquid nitrogen and stored at -80 °C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
All solutions used were prepared with DEPC (diethylpyrocarbonate 0.1% v/v) treated water. Frozen sample aliquots were ground to a fine powder under liquid nitrogen(73). Pestle and mortar were soaked in 10% bleach to destroy residual RNase activity and washed with diethylpyrocarbonate (DEPC) treated water. RNA was extracted using TriZol® reagent according to the methods of Hayes et al.(71) and the final concentration was measured prior to RNA sequencing using a NanoDrop system.
Sequencing libraries were generated using the whole Transcriptome Library Preparation protocol provided with the SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA). Briefly, rRNA depleted samples were fragmented using RNase III, and subsequently cleaned up using the RiboMinus™ Concentration Modules (Life technologies, Carlsbad, CA). Fragmentation was assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using the RNA picochip. Fragmented RNAs were reverse transcribed and size selected on a denaturing polyacrylamide gel selecting for 150-250nt cDNA. cDNA was then amplified and barcoded with SOLiD™ RNA barcoding Kit. Samples were then purified using PureLink™ PCR Micro Kit (Life Technologies, Carlsbad, CA) and assessed on a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) using the High Sensitivity DNA chip.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
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| Data processing |
Sequence reads were mapped to the prebuilt Saccharomyces cerevisiae reference genome obtained from the Bowties website and aligned using Bowtie v1.0.0 with the -m 1 option
Cufflinks version 2.0.0 was run against a the reference GTF file obtained from Saccharomyces Genome Database (SGD), to produce FPKM values per transcript.
Genome_build: Saccharomyces genome obtained from bowtie website.
Supplementary_files_format_and_content: tab delimited text files generated from Cufflinks (version 2), providing FPKM values for each transcript for each sample.
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| Submission date |
Oct 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig Lawless |
| E-mail(s) |
craig.lawless@manchester.ac.uk
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| Organization name |
University of Manchester
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| Department |
Faculty of Life Sciences
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| Lab |
Hubbard Lab
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| Street address |
Dover Street
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| City |
Manchester |
| ZIP/Postal code |
M13 9PT |
| Country |
United Kingdom |
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| Platform ID |
GPL15263 |
| Series (1) |
| GSE73898 |
RNA-seq of chemostat grown yeast (Y11335 BY4742 ) |
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| Relations |
| BioSample |
SAMN04158587 |
| SRA |
SRX1323199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1905478_KL11_fpkm.txt.gz |
245.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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