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Sample GSM1576816 Query DataSets for GSM1576816
Status Public on Jun 12, 2015
Title T10_TFIIS4
Sample type RNA
 
Source name T10 time point after TFIIS4 inactivation
Organism Paramecium tetraurelia
Characteristics strain description: 51 new mt8 ∆A ∆ND7
strain: mating type VIII
caryonide: monocaryonide
medium: Escherichia coli WGP
assay physiological state: autogamy competent
Treatment protocol At each time point, 200-600 mL of Paramecium cells were centrifuged at 200 x g for 1 min and total RNA was extracted from unwashed cell pellets.
Growth protocol Silencing media were prepared basically as described in (Galvani and Sperling, 2001) and (Nowak et al., 2011), by inoculating precultures of the appropriate bacterial strains into WGP (wheat grass powder - Pines International Co., Lawrence, USA) medium containing 0.1 mg/mL ampicillin. Following 6–8 hrs of shaking at 37°C, bacterial cultures were diluted six-fold into the same medium containing 0.4 mM IPTG to induce dsRNA synthesis. After overnight induction at 37°C, all silencing media were supplemented with 0.8 µg/mL β-sitosterol (Merck) before use. Paramecium cells were maintained at 27°C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.
Extracted molecule total RNA
Extraction protocol For each sample, total RNA was extracted from ~400,000 Paramecium cells using Trizol.
Label Cy3
Label protocol cDNA synthesis and labeling with Cyanine 3: 300ng of total RNA was used to synthesize cDNA according to the Sigma WGA1 TransPlex Whole Transcriptome Amplification kit protocol.
 
Hybridization protocol Hybridization by NimbleGen company
Scan protocol Scanning by PartnerChip company (MS200 Roche-NimbleGen)
Description mating type VIII is a strain carrying an injection-induced macronuclear deletion of the surface antigen A gene and a silencing-induced macronuclear deletion of the ND7 gene
Population of cells 10 hours after T0 with 100% of autogamy (3% fragmented macs, 97% visible anlagen)
Data processing Images are treated with NimbleScan software from Nimblegen to obtain raw intensities (.RMA.calls) that were then used for analysis with GeneSpring GX11 software.
 
Submission date Jan 05, 2015
Last update date Jun 13, 2015
Contact name Olivier ARNAIZ
Organization name CNRS
Lab I2BC
Street address avenue de la terrasse
City Gif-sur-Yvette
ZIP/Postal code 91198
Country France
 
Platform ID GPL19603
Series (1)
GSE64682 Transcriptome analysis upon TFIIS4 silencing during autogamy time course

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
PTET0001S00000001 784.130833333333
PTET0001S00000002 189.897708333333
PTET0000S00039645 58.9608333333333
PTET0001S00000004 414.441875
PTET0001S00000005 110.49625
PTET0000S00039648 1689.79791666667
PTET0000S00039649 72.6170833333333
PTET0001S00000008 28.143125
PTET0000S00039651 36.2925
PTET0000S00039652 1285.88541666667
PTET0001S00000011 2342.53458333333
PTET0001S00000012 60.4560416666667
PTET0000S00039655 128.009583333333
PTET0000S00039656 93.453125
PTET0000S00039657 305.202083333333
PTET0000S00039658 75.9095833333333
PTET0001S00000017 167.42875
PTET0000S00039660 715.93375
PTET0000S00039661 529.328333333333
PTET0000S00039662 2320.84083333333

Total number of rows: 79083

Table truncated, full table size 2677 Kbytes.




Supplementary file Size Download File type/resource
GSM1576816_T10_TFIIS4_17MB.pair.gz 11.9 Mb (ftp)(http) PAIR
GSM1576816_T10_TFIIS4_17MB_RMA.calls.gz 1.2 Mb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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