|
| Status |
Public on Sep 30, 2019 |
| Title |
Cre bE 21h repl1 |
| Sample type |
SRA |
| |
|
| Source name |
Liquid cultures
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain genotype: cre-ER
growth conditions: YES-b-Estradiol
strain number in table s2: DHP1235
|
| Growth protocol |
Yeast grown to mid-logarithmic phase
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from 50 mL of exponentially growing cells RNA using TRIzol. DNA was removed by DNase I digestion, using the TURBO DNA-free™ kit. RNA was cleaned using the RNeasy Mini kit. Total RNA quality and concentration was determined using an Agilent Bioanalyzer. Transcripts were purified by polyA-tail selection.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Illumina TruSeq Stranded mRNA Library
|
| Data processing |
Basecalling pipeline at Fasteris: HiSeq Control Software HD 3.4.0.38; RTA 2.7.7; bcl2fastq2.17 v2.17.1.14
Sequenced reads were trimmed for adaptor sequence using FastQ Groomer and mapped to Schizosaccharomyces_pombe_1.1 reference genome using HISAT2 v2.1.0 with strand-specific information (--rna-strandness R) and otherwise default options
Reads were then counted for gene and exon features using htseq-count v0.9.1 in union mode (--mode union), reverse stranded (--stranded Reverse), and a minimum alignment quality of 10 (--minaqual 10)
Variance-mean dependence was estimated from count tables and tested for differential expression based on a negative binomial distribution, using DESeq2 v1.18.1. Pairwise comparison or one-way analysis of variance were run with a parametric fit and genotype as the source of variation (factor: ‘mutant’ or ‘control’)
Genome_build: Schizosaccharomyces_pombe_1.1
Supplementary_files_format_and_content: Tab-delimited txt files wee merged into one Excel spreadsheet, in which each sheet includes Gene ID, Log2 fold-change and normalized P values (P-adj) for each DESeq2 analysis. Tab-delimited text file with raw count data for all samples.
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Sep 30, 2019 |
| Contact name |
Dominique Helmlinger |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Department |
CRBM
|
| Street address |
1919 route de Mende
|
| City |
Montpellier |
| ZIP/Postal code |
34293 |
| Country |
France |
| |
|
| Platform ID |
GPL22682 |
| Series (1) |
| GSE128448 |
Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes |
|
| Relations |
| BioSample |
SAMN11159205 |
| SRA |
SRX5534878 |
