 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 31, 2019 |
| Title |
Gene expression 0.5 hours after heme induction_WT |
| Sample type |
SRA |
| |
|
| Source name |
WT_0.5h after heme induction
|
| Organism |
Corynebacterium glutamicum ATCC 13032 |
| Characteristics |
genotype/variation: wild type
medium: CGXII
heme concentration: 4µM
time point: 0.5h
molecule subtype: Total RNA (Ribo-minus)
|
| Treatment protocol |
For the preparation of the RNA, the pellets were resuspended in RTL bufferand the cells disrupted by 3x30 sec silica bead beating, 6000 rt/min. After ultra-centrifugation (150.000xg, 4 °C, 1 h), the RNA was purified using the RNeasy Mini Kit
|
| Growth protocol |
A preculture was inoculated in liquid BHI medium (25 µg/ml kanamycin) from a fresh BHI agar plate and incubated for 8-10 h at 30°C in a rotary shaker. After that, cells were transferred into a second preculture in CGXII medium containing 2 % (w/v) glucose and 0 µM FeSO4 to starve the cells from iron protocatechuic acid (PCA), which was added to the medium, allowed the uptake of trace amounts of iron. From an overnight culture, the main cultures were inoculated (CGXII medium containing 4µM heme) and harvested 0h, 0.5h or 4h after inoculation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany), ribosomal RNA was removed by running twice the workflow of the Ribo-Zero rRNA Removal Kit (Illumina, California, USA)
after fragmentation of RNA, cDNA strand synthesis and indexing was carried out using the TruSeq® Stranded mRNA Library Prep Kit (Illumina, California, USA) according to the supplier’s manual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
time1_wt*_pair*
|
| Data processing |
Reads quality was checked with FASTQC. No trimming was undertaken
Identical reads were collapsed into single records using custom script
Reads were mapped to C. glutamicum genome with Bowtie2. Bowtie2 was ran with the following parameters: bowtie2 -1 [path to the reads, 1st mate] -2 [path to the reads, 2nd mate] -S [path to the mappings] –phred33 –sensitive-local –local –score-min C,90 –rdg 9,5 –rfg 9,5 -a –no-unal -I 40 -X 400 –no-mixed –ignore-quals
Transcript per million values were estimated for the C. glutamicum genes annotated in Baumgart et al., ACS synthetic biology, 2018
Genome_build: BX927147
Supplementary_files_format_and_content: Processed data are in tab separated format. 1st column is gene name, 2nd – expression (in transcripts per million) for the wild type replicates (divided by ‘;’ ), 3rd – expression (in transcripts per million) for the hRRA KO replicates (divided by ‘;’ )
|
| |
|
| Submission date |
Oct 08, 2018 |
| Last update date |
Jan 31, 2019 |
| Contact name |
Andrei Filipchyk |
| E-mail(s) |
a.filipchyk@fz-juelich.de
|
| Phone |
+49 2461 61 2544
|
| Organization name |
FZ-Juelich
|
| Department |
IBG-1
|
| Lab |
Frunzke AG
|
| Street address |
Wilhelm-Johnen-Straße
|
| City |
Juelich |
| ZIP/Postal code |
52428 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25416 |
| Series (1) |
| GSE120924 |
Transcriptome analysis of C. glutamicum wildtype cells and the deletion strain ΔhrrA |
|
| Relations |
| BioSample |
SAMN10216094 |
| SRA |
SRX4810341 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3421588_time1_genecounts.tsv.gz |
41.7 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
