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| Status |
Public on Oct 22, 2013 |
| Title |
prp4-1_pGAL-IFH |
| Sample type |
SRA |
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| Source name |
Yeast cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: k-HIS3:pGAL1-IFH1, prp4-1
growth conditions: 26ºC YPD OD=0.5
treatment: ~50% down-regulation of IFH1 transcription factor (specific for ribosomal protein genes)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was extracted according to Rio et al., Cold Spring Harb Protoc, 2010 "Method 1"
strand-specific libraries (dUTP/USER) were made from polyA selected mRNA; adaptors, end repair through enrichment steps using Illumina DNA Sample Prep kit V2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
~50% down-regulation of IFH1 transcription factor (specific for ribosomal protein genes)
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads (100bp read1, 58bp read2) were mapped to sacCer3 using tophat, allowing for a maximum intron size of 1200bp, with an estimated mean distance between the read pairs of 85bp (std dev 100bp).
A gtf file of previously known splice sites was supplied to tophat. Tophat's coverage search and segment search intron-finding algorithms were also enabled. In the case of multiply-mapped reads, the single best hit as scored by bowtie was kept.
Expression values (i.e., reads per exon or per gene) are calculated by summing the coverage at each position and dividing by read length.
Genome_build: sacCer3
Supplementary_files_format_and_content: spreadsheet containing summarized gene expression, intron and exon2 read counts, as well as calculated Intron Accumulation Indexes
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| Submission date |
Feb 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lily Shiue |
| E-mail(s) |
[email protected]
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| Phone |
831-459-2612
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| Organization name |
UCSC
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| Department |
MCD Biology
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| Lab |
Ares
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| Street address |
1156 High Street
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| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE44219 |
Competition between pre-mRNAs for a limiting splicing machinery drives global changes in splicing |
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| Relations |
| SRA |
SRX233536 |
| BioSample |
SAMN01919388 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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