|
| Status |
Public on Apr 07, 2020 |
| Title |
DDB_G0272386- 24h |
| Sample type |
SRA |
| |
|
| Source name |
dedifferentiating cells
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
strain: DDB_G0272386-
genotype: DDB_G0272386-
timepoint: 24h
|
| Treatment protocol |
Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA then dedifferentiated in HL5 growth medium as a shaken suspension
|
| Growth protocol |
Before development, cells were grown in HL5 (Formedium, UK).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and flash frozen. Total RNA was extracted by SDS-based lysis, followed by phenol extraction and ethanol preciptiation to remove protein.
100 ng total RNA was used to prepare mRNA libraries using NEBNext mRNA isolation kit and NEBNext Ultra II Directional RNA Library preparation kit. mRNA fragmentation used manufacturer recommended conditions for a 300bp insert size. Library amplification used 13 cycles of PCR. 75bp paired-end reads were generated using an Illumina NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Paired end reads were mapped to the Dictyostelium genome (version obtained from Gareth Bloomfield, masking the duplication on chromosome 2) using Tophat v2.0.9; library type parameter fr-firststrand, -p 4, -g 0
reads for each gene were counted with HtSeqCount v0.5.4p3. -m union -s reverse -a 0
Genome_build: dicty_2.7
Supplementary_files_format_and_content: tab-delimited text file with read counts for all samples
|
| |
|
| Submission date |
Feb 06, 2020 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Jonathan Chubb |
| E-mail(s) |
j.chubb@ucl.ac.uk
|
| Organization name |
University College London
|
| Department |
MRC Laboratory for Molecular Cell Biology
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL26360 |
| Series (2) |
| GSE144891 |
Cell and molecular transitions during efficient dedifferentiation: testing transcription factor mutants |
| GSE144892 |
Cell and molecular transitions during efficient dedifferentiation |
|
| Relations |
| BioSample |
SAMN14052315 |
| SRA |
SRX7691925 |
