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| Status |
Public on Dec 04, 2014 |
| Title |
RRPC_KO |
| Sample type |
SRA |
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| Source name |
vegetative cells
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| Organism |
Dictyostelium discoideum |
| Characteristics |
strain: Ax2
genotype: knockout of DDB_G0280963 (gene of rrpC)
cell type: vegetative cells
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| Growth protocol |
Ax2 cells and derivates were grown axenically in HL5 liquid medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs (< 200 nts) were extracted from 1 x 107 cells using the NucleoSpin® miRNA Kit (Macherey-Nagel)
RNA samples were poly-A-tailed and the 5’PPP was converted into 5’P before an RNA adaptor was ligated to the 5’-monphosphate of the RNA. A poly-T-oligo was then used as primer for cDNA synthesis and the resulting cDNAs were PCR amplified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.14
Coverage calculation and normalisation
Genome_build: DDB0169550, DDB0215018, DDB0215151, DDB0220052, DDB0232428, DDB0232429, DDB0232430, DDB0232431, DDB0232432, DDB0232433,DDB0237465, DIRS-1 element
Supplementary_files_format_and_content: wiggle
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| Submission date |
Mar 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
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| Organization name |
ZB MED - Information Centre for Life Sciences
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| Department |
Information Services
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| Lab |
Förstner Lab
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| Street address |
Gleueler Str. 60
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| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
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| Platform ID |
GPL15643 |
| Series (1) |
| GSE56111 |
Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1 |
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| Relations |
| BioSample |
SAMN02693852 |
| SRA |
SRX498140 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1356052_RRPC_KO_forward.wig.gz |
4.4 Mb |
(ftp)(http) |
WIG |
| GSM1356052_RRPC_KO_reverse.wig.gz |
4.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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