|
| Status |
Public on Mar 14, 2018 |
| Title |
H2O2_3 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: h-S 972
tissue: cells
genotype: wt
media: YES
stress: H2O2
|
| Treatment protocol |
Media were YES or EMM. For nitrogen starvation, cells were transferred by vacuum filtration From EMM2 to EMM2 without ammonium chloride and incubated for 16 hours at 30°C. Heat shock was imposed by transferring YEL cultures to 39°C for 15 minutes. Oxidative stress was inflicted by treating YEL cultures with 0.5 mM H2O2 for 15 minutes at 30°C.
|
| Growth protocol |
Triplicate liquid cultures were grown at 30°C to a density of 5 X 10^6 cells/ml
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 108 cells. In brief, cells were harvested by 5 minutes of centrifugation at 3000 rpm. Pellets were resuspended in TES (10 mM TrisHCl pH7.5, 10 mM EDTA and 0.5% SDS) and transferred to 65˚C preheated acidic phenol-chloroform (Sigma P-1944). After 1 hour of incubation at 65˚C with mixing every 10 minutes, RNA was extracted with chloroform-isoamyl alcohol (Sigma C-0549), ethanol precipitated and resuspended in water.
CAGE libraries were prepared as in Takahashi, H., Lassmann, T., Murata, M. & Carninci, P. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 7, 542–561 (2012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
gene_normalized_matrix.tab
gene_count_matrix.tab
TSS_normalized_matrix.tab
TSS_count_matrix.tab
TSSs.bed
YES_H2O2_plus.bw
YES_H2O2_minus.bw
|
| Data processing |
Base-calling with Illumina CASAVA v1.6
Removing of 5' adapters and trimming of read ends (keeping from bp 12 to bp 36) and filtering for Q30 over 50% remaining length with Fastx Toolkit v0.0.13
Mapping with Bowtie v0.12.7
Counting 5'-ends per position and shift positions by 1
Tag clustering, quantification and annotation via CAGEfightR 0.3.
Genome_build: ASM294v2
Supplementary_files_format_and_content: sample-wise bigWig files are number of CAGE tags per basepair, group-wise bigWigs are pooled TPM per basepair; bed files are location of TSSs with score column being pooled TPM; matrix files are counts or normalized TPM for TSSs or Genes.
|
| |
|
| Submission date |
Feb 21, 2018 |
| Last update date |
Mar 14, 2018 |
| Contact name |
Malte Thodberg |
| E-mail(s) |
malte.thodberg@sund.ku.dk
|
| Organization name |
University of Copenhagen
|
| Department |
CBMR
|
| Lab |
Hansen Group
|
| Street address |
Blegdamsvej 3B, Building 7 (Maersk Tower)
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE110976 |
Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. |
|
| Relations |
| BioSample |
SAMN08580027 |
| SRA |
SRX3733265 |
