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Status |
Public on Dec 29, 2019 |
Title |
Cg8-2_set4 (bio-replicate3) |
Sample type |
SRA |
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Source name |
perithecial stage 6
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Organism |
Chaetomium globosum CBS 148.51 |
Characteristics |
strain: CBS 148.51 time points: 144hr morphology: mature asci and ascospore
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Treatment protocol |
Cellophane membranes with fungal tissues were collected at protoperithecial stage (0 time point right before the disturbance), 2, 24, 48, 72, 96, 120, 144 and 168 hr after. Tissue samples were flash frozen in liquid nitrogen and stored at ﹣80 C. All tissues/perithecia that were collected from a single plate were counted as one biological replicate. At least three biological replicates were prepared for each sampled time-point and16 high quality samples were sequenced for transcriptomics.
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Growth protocol |
In order to achieve enough materials for synchronic perithecial development, hyphae of C. globosum were inoculate in 500ml flasks of 200ml liquid CA, and the flask cultures were incubated at 27C on a shaker (100 rpm) under constant light. 10-day liquid cultures were filtered with a sterilized single-layer miracloth (Calbiochem™), and abundant hyphal elements were harvested from the filtrate (Fig. S1). 2 ml filtrate was plated out on cellophane membrane covering solid CA in petri dish (9cm in diameter) and incubated were incubated in a refrigerated incubator (VWR Signature™ Diurnal Growth Chamber), maintained at 27 C under constant white light. Light-colored protoperithecia were spotted in 5 day after inoculation and fully developed perithecia with ripen ascospores were abundant in 8 days after appearance of protoperithecia. A disturbance with spreader was applied to protoperithecia plates to set a synchrony start-time for further perithecial development.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from homogenized tissue with TRI REAGENT (Molecular Research Center) as in Clark et al. (2008). Messenger RNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen). Preparation of cDNA for sequencing followed the Illumina mRNA Sequencing Sample Preparation Guide. Complementary DNA was prepared using N6 primers for samples of all time-points. 22 sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol. The libraries underwent 76 bp paired-end sequencing using Illumina HiSeq 2500 according to Illumina protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
bio-replicate3
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Data processing |
Illumina Casava1.8.2 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts. If, after trimming, the read was shorter than 45-bp, the whole read was discarded. Trimmed reads were aligned to the C. globosum genome (assembly ASM14336v1) from the NCBI using its genome annotation with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results. We used the default settings for all other Tophat options. We tallied reads aligning to exons of genes with the program HTSeq v0.6.1p1. A tally of the number of the reads that overlapped the exons of a gene, was calculated using aligned reads and the gene structure annotation file for the reference genome. Genome_build: ASM14336v1 Supplementary_files_format_and_content: excel file with relative gene abundance as outout by LOX software
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Submission date |
May 14, 2019 |
Last update date |
Dec 29, 2019 |
Contact name |
Francesc Lopez |
E-mail(s) |
francesc.lopez@yale.edu
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Organization name |
Yale University
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Department |
Department of Genetics
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Lab |
YCGA
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Street address |
P.O. Box 27386
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City |
West Haven |
State/province |
CT |
ZIP/Postal code |
06516 |
Country |
USA |
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Platform ID |
GPL26665 |
Series (1) |
GSE131190 |
Comparative study on stage-specific transcriptomics reveals key characters in Chaetomium globosum sexual development |
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Relations |
BioSample |
SAMN11640756 |
SRA |
SRX5830441 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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