title: TJ3428
organism: Cryptococcus neoformans H99
description: Protocols: Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 37˚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 37˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1min. 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. 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.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2023-05-13T00:14:48Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2023-05-13T00:14:48Z
attributes.tag: External Id
attributes.value: SAMEA112474157
attributes.tag: INSDC center name
attributes.value: Shanghai Tenth People's Hospital
attributes.tag: INSDC first public
attributes.value: 2023-05-13T00:14:48Z
attributes.tag: INSDC last update
attributes.value: 2023-05-13T00:14:48Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-12566:TJ3428
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: genotype
attributes.value: Aneuploid
attributes.tag: sample name
attributes.value: E-MTAB-12566:TJ3428
attributes.tag: scientific_name
attributes.value: Cryptococcus neoformans var. grubii H99