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| Status |
Public on Dec 15, 2015 |
| Title |
EV RNA-seq 2 |
| Sample type |
SRA |
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| Source name |
BY4742 PUF2 null mutants
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
vector: Empty
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| Growth protocol |
Cells were grown to early log phase (0.1 -0.4 OD660) in minimal media.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from 50 ml culture by the hot phenol method, followed by an RNA-cleanup column.
TruSeq Stranded mRNA Sample Preparation Guide Rev E was followed to prepare libraries for sequencing: Poly-A selection, Fragment, Prime, Finish using FPF mix (Frag 6 minutes), cDNA Synthesis, and finally bead purification (Agencourt AMPure XP)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were mapped to the EF4 genome using bowtie2 –local
Reads assigned to genes using HTSeq and the EF4 genomic annotation
Differential gene expression was determined using DESeq2
Genome_build: EF4
Supplementary_files_format_and_content: Processed data files represent the absolute number of reads (not normalized) in each gene, as determined by HTSeq
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| Submission date |
Sep 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Douglas Porter |
| Organization name |
Stanford
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| Department |
Dermatology
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| Lab |
Khavari
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL13821 |
| Series (2) |
| GSE73227 |
The binding specificity and regulatory effect of WT and redesigned Puf2p [RNA-Seq] |
| GSE73274 |
The binding specificity and regulatory effect of WT and redesigned Puf2p |
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| Relations |
| BioSample |
SAMN04099019 |
| SRA |
SRX1267199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1888984_EV-2.txt.gz |
33.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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