NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2176763 Query DataSets for GSM2176763
Status Public on Aug 15, 2017
Title WT-C3
Sample type SRA
 
Source name Conjugation cells
Organism Tetrahymena thermophila
Characteristics strain: CU428XCU427
genotype: WT
time point: Conjugation 3 hours
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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
 
Submission date May 25, 2016
Last update date May 15, 2019
Contact name Wei Miao
E-mail(s) miaowei@ihb.ac.cn
Organization name Institute of hydrobiology, CAS
Street address donghu south road #7
City wuhan
State/province hubei
ZIP/Postal code 430072
Country China
 
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
Relations
BioSample SAMN05173053
SRA SRX1799004

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