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| Status |
Public on Nov 26, 2012 |
| Title |
Rrp6D Clr4D |
| Sample type |
SRA |
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| Source name |
Rrp6 and Clr4 double deletion
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: Rrp6D Clr4D
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| Extracted molecule |
total RNA |
| Extraction protocol |
Yeast total RNAs are extracted by using MasterPure Yeast RNA purification kit (epicentre). Fly total RNAs are extracted by using specific buffer(0.5M NaCl, 0.2M Tris-HCl(pH 7.5), 0.01M EDTA, 1% SDS), glass beads, and phenol chloroform.
The protocol is described in [RNA. 2010 Dec;16(12):2537-52].
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
base calls were performed using CASAVA, or ELAND, or BUSTARD for files sequenced on MiSeq, Ilumina Genome Analyser IIx, and HiSeq2000 respectively
The sequence reads were trimmed for adapters and aligned to the S. pombe genome version released on April 2007 using novoalign program.
The parameters for novoalign were as follows: "-m" to treat the data as small RNA and "-a" to automatically trim the adapters
We used custom Python scripts to count number of times each location in the genome was seen in the data on the + and the - strand.
The processed data is uploaded as SGR file. This file is similar to a wig file, first column denotes 'chromosome", second column denotes "position" on the chromosome, and the last column denotes number of times the position was seen in the data.
A negative value on 3rd column denotes the number of times the position was seen when reads mapped to the "-" (minus) strand, and a positive value denotes the number of times the given position was seen when the reads mapped to the "+" (plus) strand.
The counts were nomalized to million mapped reads.
Genome_build: Spombe Genome Released in April 2007
Supplementary_files_format_and_content: The data is uploaded as SGR file where first column denotes the chromosome, second column denotes the position on the chromosome counted from the 5' end on the + strand, and the 3rd column denotes the count (normalized to million mapped reads).
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| Submission date |
Oct 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
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| Organization name |
NCI
|
| Department |
LBMB
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| Lab |
Shiv Grewal
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| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL15167 |
| Series (2) |
| GSE41634 |
RNAi triggered by specialized machinery silences developmental genes and retrotransposons (RNA-Seq) |
| GSE41643 |
RNAi triggered by specialized machinery silences developmental genes and retrotransposons |
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| Relations |
| SRA |
SRX196093 |
| BioSample |
SAMN01766773 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1020599_rrp6d_clr4d_normalized.sgr.gz |
19.9 Mb |
(ftp)(http) |
SGR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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