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| Status |
Public on Oct 01, 2012 |
| Title |
Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development |
| Organism |
Sordaria macrospora |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
RNA-seq analysis of developmental stages from the filamenous ascomycete Sordaria macrospora. Using laser capture microdissection, we separated protoperithecia (young fruiting bodies) from the surrounding hyphae. RNA isolation and amplification from 150 protoperithecia yields enough material for RNA-seq analysis. The resulting data were compared to RNA-seq data from whole mycelial exctracts (total vegetative and total sexual mycelium) to characterize the genome-wide spatial distribution of gene expression during sexual development. We analyzed total vegetative mycelium, total sexual mycelium, and protoperithecia from the wild type as well as protoperithecia from the sterile mutant pro1. Additionally, we used the RNA-seq information to improve the predicted S. macrospora gene models, and annotated UTRs for more than 50 % of the genes.
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| Overall design |
8 samples were sequenced (2 independent biological replicates for the four conditions "wt sex: SM2, SM7", "wt veg: SM1, SM6", "wt proto: SM4, SM5", "pro1 proto: SM8, SM9", each on one Illumina/Solexa lane (GAII or HiSeq, single reads of 36 or 100 bases))
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| Contributor(s) |
Nowrousian M, Teichert I, Wolff G, Kück U |
| Citation(s) |
23016559, 24373411 |
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| Submission date |
Nov 14, 2011 |
| Last update date |
Aug 08, 2019 |
| Contact name |
Minou Nowrousian |
| E-mail(s) |
minou.nowrousian@rub.de
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| Phone |
+49 234 3224588
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| Organization name |
Ruhr-University Bochum
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| Department |
Molecular and Cellular Botany
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| Street address |
Universitaetsstr. 150
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| City |
Bochum |
| ZIP/Postal code |
44780 |
| Country |
Germany |
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| Platforms (2) |
| GPL14880 |
Illumina Genome Analyzer II (Sordaria macrospora) |
| GPL14881 |
Illumina HiSeq 2000 (Sordaria macrospora) |
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| Samples (8)
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| Relations |
| SRA |
SRP009312 |
| BioProject |
PRJNA148727 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE33668_RAW.tar |
14.5 Gb |
(http)(custom) |
TAR (of BAM) |
| GSE33668_Sordaria_macrospora_quantification.txt.gz |
576.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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