|
| Status |
Public on Jun 23, 2023 |
| Title |
AHR1_Op_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Opaque planktonic cell
|
| Organism |
Candida albicans |
| Characteristics |
aaron hernday_yeast_number: AHY812
cell type: Opaque planktonic cell
genotype: AHR1 homozygous knockout
|
| Growth protocol |
Synthetic Defined with amino acids and Uridine (SD+aa+Uri) was used to grow strains and maintain the white and opaque states at 25⁰C. Stains were streaked out on SD+aa+Uri and grown for 5-10 days. A single colony isolate was then picked and used to inoculate a 5mL overnight liquid culture that was incubated for 12-16 hours. The OD600 was measured and used to make new 45mL back dilute cultures at a calculated OD600 of 0.1. Back diluted cultures were grown to and then collected at an OD600 of 0.7-0.9.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RiboPure™ RNA Purification Kit.
500 ng of total RNA was subjected to library synthesis using Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina kit; 3' Tag Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
AHR1 knockout, Opaque planktonic cell, Replicate1
|
| Data processing |
STAR (Spliced Transcripts Alignment to a Reference) v 2.7.6a
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk with normal parameter settings (k=13; ktrim=r; useshortkmers=t; mink=5; qtrim=r; trimq=10; minlength=20)
rimmed sequence reads were mapped to C_albicans_SC5314_A21 using STAR (parameters: max number of multiple alignments allowed for a read=25; minimum overhang for unannotated junctions=8; minimum overhang for annotated junctions=1; max number of mismatches per pair relative to read length=0.3; minimum intron length=20)
Read count extraction was done using STAR --quantMode. The read counts were normalized by TMM (edgeR)
Assembly: C_albicans_SC5314_A21
Supplementary files format and content: tab-delimited text files include read numbers per gene
|
| |
|
| Submission date |
Nov 07, 2022 |
| Last update date |
Jun 23, 2023 |
| Contact name |
Ruihao Li |
| E-mail(s) |
rli46@ucmerced.edu
|
| Organization name |
University of California, Merced
|
| Department |
QSB/MCB
|
| Lab |
Aaron Hernday lab
|
| Street address |
5200 NORTH LAKE ROAD
|
| City |
MERCED |
| State/province |
CA |
| ZIP/Postal code |
95340 |
| Country |
USA |
| |
|
| Platform ID |
GPL24129 |
| Series (1) |
| GSE217461 |
Inferring gene regulatory networks via transcriptional profiles as associated dynamical attractors |
|
| Relations |
| BioSample |
SAMN31643200 |
| SRA |
SRX18193782 |
