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| Status |
Public on Apr 01, 2024 |
| Title |
KO Mycelia Rep 1 [KO1_Myc] |
| Sample type |
SRA |
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| Source name |
Mycelia
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| Organism |
Aspergillus fumigatus |
| Characteristics |
cell type: Mycelia
genotype: ZfpA knockout
treatment: None
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| Growth protocol |
Two flasks of 50mL glucose minimal media each inoculated with 50 million spores and incubated at 37 degrees celcius and 250 rpm for 16hrs
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fungal biomas was harvested and combined from two flasks, flash-frozen in liquid nitrogen, and lyphilized completely. Total RNA was extracted with QIAzol Lysis Reagent (Qiagen) according to manufacture's instruction with additional phenol:chloroform:isoamylalchohol (24:1:1) extraction step before RNA precipitation. Total RNA was further cleaned up using RNeasy Mini Kit with on-column DNase digestion (Qiagen) Library was prepared using TruSeq library preparation protocol with poly-A mRNA enrichment
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ZfpaMutant_TPM_normalized.tsv
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| Data processing |
Given the raw reads (i.e. the .fq.gz files), we clipped the adapter sequences with Trimmomatic (version 0.32, settings 2:30:10:2:keepBothReads LEADING:5 TRAILING:5 MINLEN:36) (Bolger et al. 2014). Subsequently, we counted the transcripts with RSEM (Li & Dewey 2011) using A. fumigatus strain Af293’s reference transcriptome (ftp://ftp.ensemblgenomes.org/pub/fungi/release-49/gff3/aspergillus_fumigatus/Aspergillus_fumigatus.ASM265v1.49.gff3.gz). RSEM produced a transcripts-per-million (TPM) matrix. In this TPM matrix, the rows represent the genes, and the columns represent the samples in that data set. Finally, we log-transformed and quantile normalized the TPM matrix.
Assembly: A. fumigatus strain Af293 reference transcriptome was downloaded from ftp://ftp.ensemblgenomes.org/pub/fungi/release-49/gff3/aspergillus_fumigatus/Aspergillus_fumigatus.ASM265v1.49.gff3.gz .
Supplementary files format and content: The processed data file "ZfpaMutant_TPM_normalized.tsv" is a tab-separated file where the rows represent the genes and the columns represent the samples.
Supplementary files format and content: The processed data file "readcount.csv" is a comma-separated text file that includes the raw counts for each sample.
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| Submission date |
Apr 28, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Nancy Keller |
| E-mail(s) |
npkeller@wisc.edu
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| Organization name |
University of Wisconsin-Madison
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| Department |
Medical Microbiology and Immunology
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| Lab |
Keller Lab
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| Street address |
1550 Linden Drive
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
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| Platform ID |
GPL33056 |
| Series (1) |
| GSE231238 |
RNA-seq data from A. fumigatus strain Af293 with ZfpA wild type, knockout, and overexpression |
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| Relations |
| BioSample |
SAMN34433144 |
| SRA |
SRX20141801 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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