NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1129517 Query DataSets for GSM1129517
Status Public on Jul 01, 2014
Title dm2
Sample type SRA
 
Source name delta-xap5 delta-pht1 double mutant strain haploid cells
Organism Schizosaccharomyces pombe
Characteristics strain background: ED668
genotype/variation: delta-xap5 delta-pht1 double mutant; h-, ade6-M216, ura4-D18, leu1-32, SPCC1020.12c::KanMx4, SPBC11B10.10c::NatMx4
tissue: exponentially growing haploid cells
Growth protocol cells initially grown in YES medium at 30C overnight and these cultures were used to inoculate cultures in EMM50 at 37C. Exponentially growing cells at 37C in EMM50 were used for RNA extraction with three replicates per each genotype.
Extracted molecule total RNA
Extraction protocol Cell lysis was performed as recommended by Sabatinos and Forsburg (2010, Yeast 23(3): 173-183) in 1 ml Trizol reagent (Invitrogen). RNA was extracted as per the Invitrogen Trizol reagent protocol. Extracted RNA was digested with DNase I (Qiagen) for 30 minutes at room temperature and cleaned up with 3M sodium acetate. rRNA was removed using the Ribo-Zero rRNA removal kit (human/mouse/rat, Epicentre) following the manufacturer’s protocol.
Strand specific cDNA libraries were made with random primers using a protocol by Wang et al. (2011, PloS one 6(10): e26426) after optimizations. Barcodes: WT1 - AACCG, WT2 - ACCAT, WT3 - GCTAT, WT4 - CATAT, xap5m1 - AGCTT, xap5m2 - CATTA, xap5m3 - CCTAG, pht1_1 - AATAG, pht1_2 - TAATG, pht1_3 - GGCTC, dm1 - ACCTA, dm2 - TTAGA, dm3 - GTATT
Samples were multiplexed and 100 bp single reads were sequenced in an Illumina Hi-seq sequencer (Hi-Seq 2000) in two lanes with an average sequence coverage of 11.8 million /library.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Δxap5Δpht1 double mutant strain haploid cells
Sample 12
Data processing All quality control steps were performed using the fastx_tool kit (http://hannonlab.cshl.edu/ fastx toolkit/index.html).
Reads were mapped to the complete S. pombe cDNA (EF2.12) and genomic DNA (from ftp.ensemblgenomes.org) using BWA (ver. 0.5.8c, Li and Durbin 2009, Bioinformatics 25(14): 1754-1760).
Differential expression analysis was performed using edgeR (Robinson et al. 2010)
Genome_build: Ensembl EF2.12 (ftp://ftp.ensemblgenomes.org/pub/fungi/release-12/fasta/schizosaccharomyces_pombe/cdna/Schizosaccharomyces_pombe.EF2.12.cdna.all.fa.gz)
Supplementary_files_format_and_content: Differential expression analyses for sense transcripts, antisense transcripts, all annotated long terminal repeat (LTR) sequences and all intergenic region sequences in Δxap5, Δpht1 and Δxap5Δpht1
 
Submission date Apr 25, 2013
Last update date Nov 16, 2020
Contact name Shajahan Anver
E-mail(s) sanver@ucdavis.edu
Organization name University of California Davis
Department Plant Biology
Lab Harmer Lab
Street address 1002 LSA, One Shields Av
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL13988
Series (2)
GSE46382 Yeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts [RNA-seq]
GSE46506 Yeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts
Relations
BioSample SAMN02056297
SRA SRX271915

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap