|
| Status |
Public on May 19, 2021 |
| Title |
16_a_3364 |
| Sample type |
SRA |
| |
|
| Source name |
D. discoideum cells
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
genotype: ATG16- mutant
state: vegetative
|
| Treatment protocol |
Total RNA from vegetative D. discoideum cells was isolated
|
| Growth protocol |
D. discoideum cells were grown to log phase and 1 x 107 cells were harvested (500 x g, 5 min, 4°C), followed by two washing steps with 10 ml Soerensen’s phosphate buffer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extraction was carried out using the Qiagen RNeasy® Mini Kit according to the manufacturer’s instructions
Illumina RNASeq library Protocol
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
atg16‾
|
| Data processing |
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline version 1.2.7, based on Ensembl release 33
Sequenced reads mapped to Dictyostelium_discoideum
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Dictyostelium_discoideum 33
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample
|
| |
|
| Submission date |
Nov 24, 2020 |
| Last update date |
May 20, 2021 |
| Contact name |
Ludwig Eichinger |
| E-mail(s) |
ludwig.eichinger@uni-koeln.de
|
| Phone |
+49 221 478 6928
|
| Organization name |
Centre for Biochemistry Medical Faculty University of Cologne
|
| Department |
Biochemistry Medical Faculty
|
| Lab |
Cellular Homeostasis
|
| Street address |
Joseph-Stelzmann-Str. 52
|
| City |
Cologne |
| State/province |
NRW |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15643 |
| Series (1) |
| GSE162070 |
RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16 |
|
| Relations |
| BioSample |
SAMN16881629 |
| SRA |
SRX9567324 |
