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Sample GSM3767250 Query DataSets for GSM3767250
Status Public on Dec 29, 2019
Title Cg8-2_set4 (bio-replicate3)
Sample type SRA
 
Source name perithecial stage 6
Organism Chaetomium globosum CBS 148.51
Characteristics strain: CBS 148.51
time points: 144hr
morphology: mature asci and ascospore
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.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description bio-replicate3
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
 
Submission date May 14, 2019
Last update date Dec 29, 2019
Contact name Francesc Lopez
E-mail(s) francesc.lopez@yale.edu
Organization name Yale University
Department Department of Genetics
Lab YCGA
Street address P.O. Box 27386
City West Haven
State/province CT
ZIP/Postal code 06516
Country USA
 
Platform ID GPL26665
Series (1)
GSE131190 Comparative study on stage-specific transcriptomics reveals key characters in Chaetomium globosum sexual development
Relations
BioSample SAMN11640756
SRA SRX5830441

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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