|
| Status |
Public on Nov 28, 2019 |
| Title |
mkt1_1 |
| Sample type |
SRA |
| |
|
| Source name |
mkt1_1
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: EHB2196
genotype: h+ mkt1<delta>::NatR ade6-210 leu1-32 ura4-D18 otr1R(Sph1):ade6+
|
| Growth protocol |
Cells were grown in YES at 32C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 1 × 10e7 cells in exponential growth phase using the Masterpure Yeast RNA Purification Kit (Epicentre) according to manufacturer's instructions.
Libraries were constructed using Illumina TruSeq stranded mRNA library preparation kit according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
h+ mkt1Δ::NatR ade6-210 leu1-32 ura4-D18 otr1R(Sph1):ade6+
processed data file: WT_V_MKT1_FC.txt
|
| Data processing |
Raw reads were filtered for quality and adapter using cutadapt (v1.8.3). Parameters were (-m 50 -q 30 -f fastq -b AGATCGGAAGAGC –B AGATCGGAAGAGC).
Trimmed reads were aligned to the S. pombe reference genome (v2.30) using STAR v2.5.
Read counts were obtained using HTSeq v.0.6.1 with mode 'union'.
Differential expression analysis was then carried out using edgeR (version 3.12.0). Genes with less than 20 reads were discarded from the analysis.
Genome_build: ASM294v2.30
Supplementary_files_format_and_content: Tab-delimited text file including log2FC values for each sample.
|
| |
|
| Submission date |
Aug 01, 2019 |
| Last update date |
Nov 28, 2019 |
| Contact name |
Elizabeth H Bayne |
| Organization name |
University of Edinburgh
|
| Department |
School of Biological Sciences
|
| Street address |
Alexander Crum Brown Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3FF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22682 |
| Series (1) |
| GSE135273 |
Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast [RNA-seq] |
|
| Relations |
| BioSample |
SAMN12423635 |
| SRA |
SRX6639229 |
