|
| Status |
Public on Feb 26, 2017 |
| Title |
chdC-null 0H rep2 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Growing
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
development stage: Growing
cell type: chdC-null
|
| Treatment protocol |
Cells were developed on nitrocellulose filters until they reached loose-mound stage of development (10H for Ax2, 12H for ChdC null cells)
|
| Growth protocol |
Cells were grown axenicly in HL5 + glucose media (Formedium)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol
Total RNA was isolated and mRNA was enriched using manufacurers protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
RNAseq reads were aligned using Tophat version 1.3.0 and Bowtie version 0.12.7 to the chromosomes 1-6 of the Ax4 dictyostelium genome masking the duplicated region on chromosome 2 (nucleotides 3,015,984 to 3,768,555) and gene models from dictybase.org
FPKM counts were calculated with HTseq and normalized and DEseq
Genome_build: Ax4_May2009
Supplementary_files_format_and_content: Pairwise comparisons with DESeq are uploaded
|
| |
|
| Submission date |
Jun 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Platt |
| Organization name |
University of Oxford
|
| Street address |
Roosevelt Drive
|
| City |
Oxfors |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15643 |
| Series (1) |
| GSE70141 |
Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [RNA-seq] |
|
| Relations |
| BioSample |
SAMN03785401 |
| SRA |
SRX1068252 |
