|
| Status |
Public on Jan 03, 2014 |
| Title |
chdB-null 0H, rep1rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Growing, chdB-null
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
strain/background: AX2
genotype: chdB-null
development stage: growing (0h)
|
| Treatment protocol |
5H pulsed cells were pulsed with cAMP every 6 min for 5 hours.
|
| Growth protocol |
Cells were grown axenically in HL5 + glucose media (Formedium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol. mRNA was enriched using manufacturer's protocol.
The sequencing library was constructed using the Illumina TruSeq low throughput protocol according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA
This Sample represents 2 replicates.
|
| Data processing |
Basecalls performed using CASAVA version 1.7.
RNA-seq 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: Tab-delimited text files contain FPKM values for each sample.
|
| |
|
| Submission date |
May 23, 2013 |
| 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) |
| GSE47222 |
CHD chromatin remodelers regulate separate gene sets and distinct stages of Dictyostelium development |
|
| Relations |
| SRA |
SRX286264 |
| BioSample |
SAMN02178340 |
