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| Status |
Public on Jun 30, 2018 |
| Title |
fft2fft3 R2 |
| Sample type |
SRA |
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| Source name |
fft2fft3 cells
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu2000 h- fft2::kan fft3::hph ade6M210 leu1-32 ura4-D18
cell type: whole cells
genotype/variation: fft2fft3 double mutant
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| Growth protocol |
Duplicate liquid cultures were grown in YES media at 30°C and 180 RPM shaking. For all experiments, cells were harvested in mid-log growth (~5×106 cells/ml).
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| Extracted molecule |
total RNA |
| Extraction protocol |
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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
TC_trimmed_pooled_TPM_chr123.txt
HU2000_meanReplicates_TPM.bw
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| 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
Clustering of mapped tags with Bedtools v2.15.0
TPM normalization and trimming of tag clusters by both ends simultaneously until 90 percentile TC expression is reached with in-house script
Genome_build: ASM294v2
Supplementary_files_format_and_content: [.bw] bigwig files generated with Bedtools v2.15.0 where score represents TPM-normalized mapped tags.
Supplementary_files_format_and_content: [R#.txt] Expression matrices are tab-delimited file where first column is identifier for TC (chr:start-end,strand) followed by TPM expression in the sample mentioned as header.
Supplementary_files_format_and_content: [chr123.txt] Trimmed TC file is the full collection of detected TC in all samples along with chromosome, coordinates, id, score (TPM of pooled samples), strand and TC summit coordinates.
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| Submission date |
Aug 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Axel Thieffry |
| E-mail(s) |
axel.thieffry@gmail.com
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| Organization name |
BioPhero-FMC
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| Department |
R&D
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| Street address |
Lersø Parkallé 42-44
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| City |
Copenhagen |
| State/province |
Hovedstaden |
| ZIP/Postal code |
2100 |
| Country |
Denmark |
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| Platform ID |
GPL13988 |
| Series (1) |
| GSE85046 |
Transcription start site positioning is not affected by +1 nucleosome depletion |
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| Relations |
| BioSample |
SAMN05468359 |
| SRA |
SRX1993460 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2256844_expression_matrix_tpm_HU2000_R2.txt.gz |
836.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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