{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Liangsheng Guo"],"organism":["Lodderomyces elongisporus NRRL YB-4239"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16890"],"description":["One  Lodderomyces elongisporus isolate exhibited small and large colonies when growing on YPD-agar plate. Transcriptomes of one small colony and one large colony were compared to parent"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - We used the phenol-chloroform method to extract Genomic DNA. Cell pellets were suspended in 200µl of lysis buffer, add 100µl of acid washed glass beads, and 0,2ml phenol:chloroform:isoamyl alcohol (25:24:1). Vortex for 30min at 4˚C. Add 200µl TE pH7.5. Centrifuge for 5min at maximum speed. Transfer aqueous layer to a new 1.5ml EP tube. Add 1ml 100% ethanol. Precipitate 1h at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard the supernatant. Add 400µl TE pH 7.5. Add 3ul of RNase A (10mg/ml). Incubate at 37˚C for 30min.  Add 10µl of 3M NaOAc and 1ml of 100% ethanol. Mix by inversion. Precipitate 30min at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard supernatant. Air-dry the pellet overnight. Resuspend in 50µl water.","Library Construction - 1µg Genomic DNA was randomly fragmented by Covaris, followed by fragments selection by Agencourt AMPure XP-Medium kit to an average size of 200~400 bp. Selected fragments were end repaired and 3\\\"adenylate, then the adaptors were ligated to the end of these 3\\\"adenylate fragments. The products were amplified by PCR and purified by the Agencourt AMPure XP-Medium kit. The purified double stranded PCR products were heat denatured to single strand, then circularised by the splint oligo sequence. The single strand circle DNA (ssCirDNA) were formatted as the final library and qualified by QC.","Sequencing - The final qualified libraries were sequenced by BGISEQ-500. ssCir DNA molecule formed a DNA nanoball (DNB) containing more than 300 copies through rolling-cycle replication. The DNBs were loaded into the patterned nano array by using high density DNA nano chip technology. Finally, pair-end 100bp reads were obtained by combinational Probe-Anchor Synthesis (cPAS).","Sample Collection - Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 30˚C overnight. Then several colonies were picked up and suspended in DDW. Cell density was adjusted to 10,000 cells/ml, then 100µl of cell suspension was plated on YPD plates. The plates were incubated at 30˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1 min."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - fastp was used to trim adapter sequences and do quality trimming. Reads containing N >10% (N represents an unresolvable base) were defined as low quality and were discarded. Bases at the 3′-ends with quality lower than 20 were trimmed. If the remaining reads had quality lower than 10, the reads were also removed. If the reads after adapter trimming and quality trimming had length less than 20 bp, the reads were removed."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["BGISEQ-500"],"study_type":["RNA-seq of coding RNA"],"species":["Lodderomyces elongisporus NRRL YB-4239"],"pubmed_authors":["Liangsheng Guo"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome analysis of different sized colonies in Lodderomyces elongisporus","description":"One  Lodderomyces elongisporus isolate exhibited small and large colonies when growing on YPD-agar plate. Transcriptomes of one small colony and one large colony were compared to parent","dates":{"release":"2026-04-24T00:00:00Z","modification":"2026-04-24T01:05:50.952Z","creation":"2026-04-10T13:36:24.141Z"},"accession":"E-MTAB-16890","cross_references":{"ENA":["ERP191996"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}