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| Status |
Public on Jul 01, 2014 |
| Title |
pht1_3 |
| Sample type |
SRA |
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| Source name |
delta-pht1 mutant strain haploid cells
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain background: ED668
genotype/variation: delta-pht1 mutant; h-, ade6-M216, ura4-D18, leu1-32, SPBC11B10.10c::NatMx4
tissue: exponentially growing haploid cells
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Δpht1 mutant strain haploid cells
Sample 10
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| 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
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| Submission date |
Apr 25, 2013 |
| Last update date |
Nov 16, 2020 |
| Contact name |
Shajahan Anver |
| E-mail(s) |
sanver@ucdavis.edu
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| Organization name |
University of California Davis
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| Department |
Plant Biology
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| Lab |
Harmer Lab
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| Street address |
1002 LSA, One Shields Av
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02056295 |
| SRA |
SRX271913 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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