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Sample GSM2256841 Query DataSets for GSM2256841
Status Public on Jun 30, 2018
Title wt R2
Sample type SRA
 
Source name wt cells
Organism Schizosaccharomyces pombe
Characteristics strain: Hu0029 h- ade6-M210 leu1-32 ura4-D18
cell type: whole cells
genotype/variation: wt
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).
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection CAGE
Instrument model Illumina HiSeq 2000
 
Description TC_trimmed_pooled_TPM_chr123.txt
HU0029_meanReplicates_TPM.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
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.
 
Submission date Aug 01, 2016
Last update date May 15, 2019
Contact name Axel Thieffry
E-mail(s) axel.thieffry@gmail.com
Organization name BioPhero-FMC
Department R&D
Street address Lersø Parkallé 42-44
City Copenhagen
State/province Hovedstaden
ZIP/Postal code 2100
Country Denmark
 
Platform ID GPL13988
Series (1)
GSE85046 Transcription start site positioning is not affected by +1 nucleosome depletion
Relations
BioSample SAMN05468362
SRA SRX1993457

Supplementary file Size Download File type/resource
GSM2256841_expression_matrix_tpm_HU0029_R2.txt.gz 768.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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