|
| Status |
Public on Apr 05, 2018 |
| Title |
RelA + isoleucine starved rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RelA + isoleucine starved bacterial cells
|
| Organism |
Escherichia coli |
| Characteristics |
strain/background: MG1655relA::HTF
growth condition: isoleucine starved
antibody: M2-anti-FLAG
|
| Treatment protocol |
Non-starved cultures were collected at OD600=0.2 and isoleucine starved cultures were collected after incubation with 500μg/mL L-Valine for 30 min (samples indicated by +val).
|
| Growth protocol |
Bacterial cells were grown in MOPS (morpholinepropanesulfonic acid) minimal medium at 30C supplemented with 0.2% glucose and with all nucleobases (10 µg ml-1 of each).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were subsequently UV-C crosslinked and harvested by centrifugation, washed in ice-cold phosphate-buffered saline (PBS) and snap frozen in liquid nitrogen. The pellets were stored at -80C. The HTF tagged proteins were then purified, linkers ligated to crosslinked RNA, cDNA synthesized and DNA libraries generated as described in Winther et al. 2018.
Libraries were constructed as per Winther et al. 2018.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
CRAC
NG-A1_NNNATTAGC_rela+val1
|
| Data processing |
fastq_quality_filter -q 30 -Q 33 -i<(cat NG-8549_CAT_lib91426_4106_1_1.fastq.bz2 | bunzip2 -c) -o NG-A1.fastq #quality filtering
pyBarcodeFilter.py -f NG-A1.fastq -b barcodes.txt #demultiplex in respect to 5' barcode
cutadapt NG-A1_NNNCACTAGC_cont.fastq -a TGGAATT -m 12 -o cont.trimmed.fastq #trimming of 3' end linker
pyFastqDuplicateRemover.py -f cont.trimmed.fastq -o cont.trimmed.collapsed.fasta #removal of PCR duplicates
bowtie2-build ecoli_masked.fa ecoli bowtie2 -x ecoli -f cont.trimmed.collapsed.fasta > cont.sam #alignment using masked genome file
Genome_build: NC_000913.3
Supplementary_files_format_and_content: *_count_output_reads.gtf: Mapped read coordinates in GTF format.
|
| |
|
| Submission date |
Jan 04, 2018 |
| Last update date |
Apr 05, 2018 |
| Contact name |
Kenn Gerdes |
| E-mail(s) |
kgerdes@bio.ku.dk
|
| Organization name |
University of Copenhagen
|
| Street address |
Ole Maaloesvej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2100 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL16085 |
| Series (1) |
| GSE108758 |
Activation of the stringent response by loading of tRNA-RelA complexes at the ribosomal A-site |
|
| Relations |
| BioSample |
SAMN08292178 |
| SRA |
SRX3532531 |
