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| Status |
Public on Mar 05, 2019 |
| Title |
JKY690 chrIII tDNAD biological replicate 2 |
| Sample type |
SRA |
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| Source name |
JKY690 chrIII tDNAD
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W-303
genotype: MATa ade2-1 trp1-1 ura3-1 chrIII (t0D, t1D, t3D, t4D, t5D, t6D, t7D, t8D+t9D::LEU2), T1+T7::HIS3
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| Treatment protocol |
No treatment
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| Growth protocol |
Cells were grown to early log phase in YPD, spun, washed in PBS and aliquots were flash frozen in liquid nitrogen.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by ACGT Inc., Wheeling IL using the Qiagen Rneasy kit.
Libraries were constructed and sequenced by ACGT Inc., Wheeling IL using the NEXTflex Rapid Directional RNA-Seq kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Total RNA from chIII tDNA D cells biological replicate 2
690b
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| Data processing |
Pseudo-alignment was performed using Kallisto (Bray et al., Nat. Biotechnol., 2016)
Differentially expressed genes were obtained using Sleuth (Pimentel et al., Nature Methods, 2017).
Genome_build: sacCer3
Supplementary_files_format_and_content: abundance.tsv - text file containing the Kallisto estimates of transcript abundances.
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| Submission date |
Oct 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
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| Phone |
301-435-8670
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| Organization name |
National Institutes of Health
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| Department |
NICHD
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| Lab |
David J. Clark Lab
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| Street address |
6 Center Drive, Room 2A14
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21656 |
| Series (2) |
| GSE106248 |
Transfer RNA Genes Affect Chromosome Architecture and Function [RNA-seq] |
| GSE106250 |
Transfer RNA Genes Affect Chromosome Architecture and Function |
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| Relations |
| BioSample |
SAMN07839703 |
| SRA |
SRX3334104 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2832771_690b_abundance.tsv.gz |
89.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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