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Status |
Public on Feb 05, 2011 |
Title |
[E-MTAB-75] Cell culture 1 |
Sample type |
SRA |
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Source name |
Cell culture 1
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Organism |
Saccharomyces cerevisiae |
Characteristics |
material type: whole_organism strainorline: BY4742 genotype: MAT_ ura3_0 leu2_0 his3_1 lys2_0
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Growth protocol |
grow | Cells were grown to mid-exponential phase in YPD for a wild type strain (condition 1) and in YPD supplemented with doxycycline (10µg/ml) for 16h for the mutant strain (condition 2).
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Extracted molecule |
total RNA |
Extraction protocol |
nucleic_acid_extraction | Poly(A)+-enriched RNA from the wild type strain was purified using Dynabeads Oligo (dT)25 (Dynal, Invitrogen). RNA from the CUT fraction was obtained by Cbp20 TAP purification. TETRATAGS CONSTRUCTION | 3'Long-SAGE tags were obtained by an improved 3' Long-SAGE technique adapted from Wei et al, PNAS, 2004. The 18nt-long 3' tags resulted from MmeI cleavage were ligated into tetratags. These tetratags correspond to 2 ditags and 3 delimiting linkers. First linkers bears a barcode sequence to distinguish the two conditions.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
454 GS |
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Data processing |
Sequences in FASTA format were analyzed and header from condition 1 (CGCCATCAGCGTCGAC) and condition 2 (CGCCATCAGTCATATG) were identified. Then tag sequences were found by identifiing the linkers positions. Tags were the 18 bp sequences downstream of each linker. The found tags were aligned in genome using BLAST.
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Submission date |
Nov 03, 2010 |
Last update date |
Oct 19, 2011 |
Organization |
European Bioinformatics Institute |
E-mail(s) |
miamexpress@ebi.ac.uk
|
Lab |
ArrayExpress
|
Street address |
Wellcome Trust Genome Campus
|
City |
Hinxton |
State/province |
Cambridgeshire |
ZIP/Postal code |
CB10 1SD |
Country |
United Kingdom |
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|
Platform ID |
GPL11160 |
Series (1) |
GSE25132 |
[E-MTAB-75] Cryptic unstable transcripts in yeast |
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