GSM3899341: YH4A; Cryptococcus neoformans var. grubii H99; RNA-Seq - SRA

SRX6098075: GSM3899341: YH4A; Cryptococcus neoformans var. grubii H99; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 13.7M spots, 1.9G bases, 719.2Mb downloads

Submitted by: NCBI (GEO)

Study: Cryptococcus neoformans reactivation in different media and temperatures

PRJNA549871 • SRP201981 • All experiments • All runs

show Abstracthide Abstract

We wanted to find out the transcriptomic response of growth-arrested Cryptococcus yeast cells when initially placed in environments in which they could reactivate or "wake up", focusing on the difference between a rich microbial media (YPD) and a common cell culture media, RPMI + 10% heat-inactivated fetal calf serum. Please contact Edward.Wallace@ed.ac.uk if you use this data and ask for citation information; we are currently (August 2020) working on a publication. Overall design: 36-sample RNA-seq timecourse of reactivation of growth-arrested Cryptococcus neoformans H99 in two media at two temperatures. Two biological samples of cells were pre-grown for 5 days in 10mL YPD. A sample of this was taken as the "0 minute" control timepoint. We then inoculated to OD 0.1 in 4 different cultures of 100mL pre-warmed media: (YPD, RPMI+) x (25C, 37C), and grew for 10, 30, 60, or 120 min. We also obtained a timepoint in more standard growth conditions of YPD, 30C, 180mins.

Sample: YH4A

SAMN12098578 • SRS4998610 • All experiments • All runs

Organism: Cryptococcus neoformans H99

Library:

Instrument: NextSeq 500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: - Fix and freeze yeast culture: - Pre-chill a 50mL tube with 6mL 100% Methanol on dry ice (tightly capped so CO2 does not dissolve in MetOH). - Add 10mL of culture to the chilled MetOH, cap tube, shake to mix, place on dry ice for up to 5 min. - Spin 2 min at ~2500g, pour off supernatant. - Resuspend cell pellet in 1mL ice-cold H2O and transfer to 2mL screw-cap tube. - Spin 1min at 5000g, remove supernatant carefully, and freeze pellet in sealed tube at -80C. - Freeze-dry the pellet in a lyophilizer until dry. - Extract RNA using the RNAeasy plant and fungi kit (Qiagen) RNAtagseq essentially as described in Shishkin et al., Nat. Methods 2015, "Simultaneous generation of many RNA-seq libraries in a single reaction", doi: 10.1038/nmeth.3313. Edits to protocol at https://github.com/ewallace/protocols/blob/master/RNAtagseq.md

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 13.7M spots, 1.9G bases, 719.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR9331479	13,662,665	1.9G	719.2Mb	2020-08-26

ID:: 8151970

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity