|
| Status |
Public on Oct 01, 2012 |
| Title |
Hfq coIP OD2+3h |
| Sample type |
SRA |
| |
|
| Source name |
Hfq coIP OD2+3h
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
genetic variation: SL1344 hfq-3xFLAG
antibody: anti-FLAG
|
| Growth protocol |
Wild-type and Hfq-3xFLAG Salmonella strains were grown in LB. During growth, Equal amount of culture samples were withdrawn at OD600 of 0.15, 0.5, 2.0 and 3h, 6h, 9h after reaching OD2, and overnight culture for coimmunoprecipitation analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was co-immunoprecipitated by anti-FLAG monoclonal antibody from bacterial lysate, treated with DNase I
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNA coimmunoprecipitated with anti-FLAG antibody
|
| Data processing |
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.9.4
Genome_build: SL1344 complete genome: FQ312003.1
Genome_build: SL1344_plasmid1 (pSLT_SL1344): NC_017720.1
Genome_build: SL1344_plasmid2 (pCol1B9_SL1344): NC_017718.1
Genome_build: SL1344_plasmid3 (pRSF1010_SL1344): NC_017719.1
Supplementary_files_format_and_content: Unnormalized read coverages in wiggle format (*_plus.wig = plus strand; *_minus_= _minus_strand.wig)
|
| |
|
| Submission date |
Jun 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
|
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Information Services
|
| Lab |
Förstner Lab
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15732 |
| Series (1) |
|
| Relations |
| SRA |
SRX155644 |
| BioSample |
SAMN01057237 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM951412_IPH_04_3H_in_FQ312003_minus.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
| GSM951412_IPH_04_3H_in_FQ312003_plus.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
| GSM951412_IPH_04_3H_in_SL1344_plasmid1_minus.wig.gz |
20.7 Kb |
(ftp)(http) |
WIG |
| GSM951412_IPH_04_3H_in_SL1344_plasmid1_plus.wig.gz |
29.6 Kb |
(ftp)(http) |
WIG |
| GSM951412_IPH_04_3H_in_SL1344_plasmid2_minus.wig.gz |
14.9 Kb |
(ftp)(http) |
WIG |
| GSM951412_IPH_04_3H_in_SL1344_plasmid2_plus.wig.gz |
25.0 Kb |
(ftp)(http) |
WIG |
| GSM951412_IPH_04_3H_in_SL1344_plasmid3_minus.wig.gz |
7.7 Kb |
(ftp)(http) |
WIG |
| GSM951412_IPH_04_3H_in_SL1344_plasmid3_plus.wig.gz |
6.0 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
