|
| Status |
Public on Dec 13, 2016 |
| Title |
cond_2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Asynchonous, log-phase cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell type: Asynchonous, log-phase cells
treatment: plus_estradiol
|
| Treatment protocol |
3 hour incubation with 1 µm beta-estradiol in EtOH or vehicle
|
| Growth protocol |
Log-phase liquid culture in YES at 30˚C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the cells by bead beating with Trizol (Ambion), followed by isopropyl alcohol precipitation and ethanol wash.
To remove ribosomal RNA, we input 1ug of total RNA into the Ribo-Zero™ Magnetic Gold Kit (Yeast) Illumina cat #MRZY1324) followed by a cleanup using Agencourt RNAClean XP beads (Beckman Coulter, cat #A63987) and elution with 19.5 uL of Elute, Prime, Fragment mix from the TruSeq RNA Sample Preparation Kit (Illumina, cat #RS-122-2101). We performed library construction per the vendor’s instructions, starting with the “Incubate RFP” step. We pooled the resulting cDNA libraries and subjected them to paired-end sequencing on an Illumina miSeq --151 base pairs per read.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
We aligned sequencing reads to Ensembl/EF2 S. Pombe assembly and the EF2 transcriptome reference annotation (with GFP added) (Harrow et al. 2012) using TopHat2 (Trapnell, Pachter, and Salzberg 2009) with options -p 4 --library-type fr-firststrand and -M.
We estimated transcript and gene abundances per REPLICATE as well as depletion/ enrichment calls using the Cuffdiff 2 with default options
We made significance calls using Cuffdiff 2
Genome_build: ensemble EF2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample at gene and isoform level in addition to CuffDiff 2 generated p and q values with significance calls
|
| |
|
| Submission date |
Dec 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nick Rhind |
| E-mail(s) |
nick.rhind@umassmed.edu
|
| Phone |
(508) 856-8316
|
| Organization name |
UMass Med School
|
| Department |
Biochemistry and Molecular Pharmalology
|
| Street address |
364 Plantation St.
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL16192 |
| Series (1) |
| GSE92246 |
An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast |
|
| Relations |
| BioSample |
SAMN06131429 |
| SRA |
SRX2414504 |
