Sample Files (RNA-Seq)

RNA-Seq_Sample_Files.zip (1.3 GB)

Description

This dataset contains several Illumina paired-end files (FASTQ), a FASTA file containing the genomic sequence of Saccharomyces cerevisiae, a GTF file containing the coordinates of Saccharomyces cerevisiae's genes and a tabulated text file with additional gene annotations (ANN.TXT). All together, these files can be useful to perform a simple RNA-Seq pipeline with three biological replicates per condition.

All files were collected by BioinfoGP for educational purposes.

Reference

The original paper from which these samples were obtained:

Hakkaart X, Liu Y, Hulst M, El Masoudi A, Peuscher E, Pronk J, van Gulik W, Daran-Lapujade P. Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO₂ levels. Biotechnol Bioeng. 2020 Mar;117(3):721-735. doi: 10.1002/bit.27210. Epub 2020 Jan 22. (PubMed) (SRA)

Content

Sample details (paired-end):

File 1 File 2 pH CO₂ Replicate

1M_SRR9336468_1.fastq.gz 1M_SRR9336468_2.fastq.gz 5 0.04% 1

1M_SRR9336469_1.fastq.gz 1M_SRR9336469_2.fastq.gz 5 0.04% 2

1M_SRR9336470_1.fastq.gz 1M_SRR9336470_2.fastq.gz 5 0.04% 3

1M_SRR9336471_1.fastq.gz 1M_SRR9336471_2.fastq.gz 5 50% 1

1M_SRR9336472_1.fastq.gz 1M_SRR9336472_2.fastq.gz 5 50% 2

1M_SRR9336473_1.fastq.gz 1M_SRR9336473_2.fastq.gz 5 50% 3

1M_SRR9336474_1.fastq.gz 1M_SRR9336474_2.fastq.gz 3 0.04% 1

1M_SRR9336475_1.fastq.gz 1M_SRR9336475_2.fastq.gz 3 0.04% 2

1M_SRR9336476_1.fastq.gz 1M_SRR9336476_2.fastq.gz 3 0.04% 3

File 1	File 2	pH	CO₂	Replicate
1M_SRR9336468_1.fastq.gz	1M_SRR9336468_2.fastq.gz	5	0.04%	1
1M_SRR9336469_1.fastq.gz	1M_SRR9336469_2.fastq.gz	5	0.04%	2
1M_SRR9336470_1.fastq.gz	1M_SRR9336470_2.fastq.gz	5	0.04%	3
1M_SRR9336471_1.fastq.gz	1M_SRR9336471_2.fastq.gz	5	50%	1
1M_SRR9336472_1.fastq.gz	1M_SRR9336472_2.fastq.gz	5	50%	2
1M_SRR9336473_1.fastq.gz	1M_SRR9336473_2.fastq.gz	5	50%	3
1M_SRR9336474_1.fastq.gz	1M_SRR9336474_2.fastq.gz	3	0.04%	1
1M_SRR9336475_1.fastq.gz	1M_SRR9336475_2.fastq.gz	3	0.04%	2
1M_SRR9336476_1.fastq.gz	1M_SRR9336476_2.fastq.gz	3	0.04%	3

Genome files:

File Description Format

Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz Genomic sequence (DNA) FASTA

Saccharomyces_cerevisiae.R64-1-1.107.gtf.gz Gene IDs and genomic locations GTF

Saccharomyces_cerevisiae.R64-1-1.107.ann.txt Gene annotations (symbols and descriptions) Text-tabulated

File	Description	Format
Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz	Genomic sequence (DNA)	FASTA
Saccharomyces_cerevisiae.R64-1-1.107.gtf.gz	Gene IDs and genomic locations	GTF
Saccharomyces_cerevisiae.R64-1-1.107.ann.txt	Gene annotations (symbols and descriptions)	Text-tabulated

Notes

To reduce computation times, each FASTQ file was truncated to 1 million reads ("1M_").

Genome files (FASTA and GTF) were obtained from Ensembl database.

Annotations file (Saccharomyces_cerevisiae.R64-1-1.107.ann.txt) was generated with BioMart:

DATABASE: Ensembl Genes 107

DATASET: Saccharomyces cerevisiae genes (R64-1-1)

Filters: None

Attributes (in this order): Gene Stable ID, Gene type, Gene name, Gene description

RNA-Seq_Sample_Files.zip (1.3 GB)