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Sample GSM3990105 Query DataSets for GSM3990105
Status Public on Apr 07, 2020
Title RNAseq of pir2-1 cells
Sample type SRA
 
Source name log. growing cells
Organism Schizosaccharomyces pombe
Characteristics growth stage: log. growing cells
genotype: pir2-1 mutant
Treatment protocol Temperature sensitive mutation of Pir2.
Growth protocol Standard conditions were used for logarithmically growing cultures in rich media (YEA). Cultures were grown at 26C overnight and then shifted to 33C for 5hrs.
Extracted molecule total RNA
Extraction protocol RNA was extracted using hot phenol method.
NEB Ultra Directional RNA Library Prep kit (NEB, E7420S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 4200 TapeStation system (Agilent) and sequenced on the Illumina MiSEQ system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description pir2-1-RNAseq
Data processing Alignment was done using Tophat.
FPKM values were calculated using cufflinks
Genome_build: asm294v2.28
Supplementary_files_format_and_content: Tab delimited text files, from cufflinks
 
Submission date Jul 31, 2019
Last update date Apr 07, 2020
Contact name Shiv Grewal
Phone 2407607553
Organization name NCI
Department LBMB
Lab Shiv Grewal
Street address NCI bldg 37 Rm 6068 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL16192
Series (2)
GSE135159 Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [RNA-Seq]
GSE135161 Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression
Relations
BioSample SAMN12404868
SRA SRX6619816

Supplementary file Size Download File type/resource
GSM3990105_pir2_1_MiSEQ_genes.fpkm_tracking.gz 206.4 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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