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Status |
Public on Aug 15, 2017 |
Title |
E2FL-1KO_C3 |
Sample type |
SRA |
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Source name |
Conjugation cells
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Organism |
Tetrahymena thermophila |
Characteristics |
strain: CU428XCU427 genotype: E2FL-1 Knock out time point: Conjugation 3 hours
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Growth protocol |
Tetrahymena thermophila cells were grown in SPP medium at 30 oC. For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~16 hrs) and mixed in Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit. Sequencing (Single-end (52X1) for C3 and C6, Paired-end (101x2) FOR C10) was performed using an Illumina HiSeq 2000 sequencer (DNA Sequencing Core of University of Michigan).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
Adaptors of raw reads were trimmed by Trim-Galore (version 0.4.0) mRNA-Seq data processing: Trimmed-reads were mapped to the Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads) using TopHat (version 2.0.9).Genes expression values were quantify to the number of fragments per kilobase of exon per million fragments mapped (FPKM) using Cuffdiff (version 2.1.1). Genome_build: Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads) Supplementary_files_format_and_content: Reads counts table matrix
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Submission date |
May 25, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Wei Miao |
E-mail(s) |
miaowei@ihb.ac.cn
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Organization name |
Institute of hydrobiology, CAS
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Street address |
donghu south road #7
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City |
wuhan |
State/province |
hubei |
ZIP/Postal code |
430072 |
Country |
China |
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Platform ID |
GPL21412 |
Series (1) |
GSE81856 |
mRNA sequencing of WT and e2fl-1∆ cells in conjugation 2, 3, 4, 5, 6 and 7 (C2, C3, C4, C5, C6 and C7) hours of Tetrahymena thermophila |
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Relations |
BioSample |
SAMN05173054 |
SRA |
SRX1799005 |
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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