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| Status |
Public on Nov 13, 2019 |
| Title |
WT_RNA_2 |
| Sample type |
RNA |
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| Source name |
WT
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu0598
genotype: h90
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| Growth protocol |
Cultures were grown at 30°C in YES media to mid-log phase.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using hot acid phenol and chloroform method. Cells were harvested by centrifugation at RT, resuspended in TES buffer (10mM Tris-Cl pH 7.5, 10mMEDTA, 0.5%SDS) and immediately combined with preheated to 65oC Phenol. After incubation (30min-1hour) at 65oC (vortex every 10 min), RNA was phenol-chloroform extracted and purified using RNeasy mini- kit( Qiagen). RNA quality was assessed using Agilent TAPE-station 2200(Agilent).
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| Label |
biotin
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| Label protocol |
Biotin-labeled according to standard Affymetrix protocols.
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| Hybridization protocol |
Hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum.
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| Scan protocol |
Scanned at the Affymetrix core facility at Novum (http://www.bea.ki.se) according to standard Affymetrix protocols.
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| Description |
OK2
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| Data processing |
CEL files were normalized with quantile normalization plus scaling in Tiling Analysis Software (TAS v1.1.02., Affymetrix), 2004 genome assembly, linear scale, target intensity: 100, band width:100.
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1.02 and contain linear values for each probe. F: forward strand, R: reverse strand.Text files contain linear signal scores for RNA levels. Expression_data.csv supplementary result file is generated in Podbat, quantified further in Excel and contains, in order: UniqueID, Systematic name, Chromosome, Left border, Right border, Strand, Description, WT1 (OK1(s)), WT2(OK2(s)), ncRNA111_1(OK3(s)), ncRNA111_2(OK4(s)), Signal to noise ratio (SNR) (aveWT-aveMUT)/(stdevWT+stdevMUT), absolute value SNR, Fold change (aveMUT/aveWT), FOLD Change ( UP(+) DOWN (-))
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| Submission date |
Nov 14, 2016 |
| Last update date |
Nov 13, 2019 |
| Contact name |
Olga Khorosjutina |
| Organization name |
Karolinska Institutet
|
| Department |
Bioscience and nutrition
|
| Lab |
Karl Ekwall
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| Street address |
Hälsovägen7
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| City |
Huddinge |
| ZIP/Postal code |
S-141 83 |
| Country |
Sweden |
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| Platform ID |
GPL7715 |
| Series (1) |
| GSE89825 |
Stepwise chromatin remodeling by two lincRNAs underlies cell fate in fission yeast |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM2390104_OK2__Sp20b_M_v04_.CEL.gz |
10.9 Mb |
(ftp)(http) |
CEL |
| GSM2390104_OK2_forw_signal.bar.gz |
2.7 Mb |
(ftp)(http) |
BAR |
| GSM2390104_OK2_forw_signal.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSM2390104_OK2_rev_signal.bar.gz |
2.7 Mb |
(ftp)(http) |
BAR |
| GSM2390104_OK2_rev_signal.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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