|
| Status |
Public on Oct 15, 2016 |
| Title |
S. epidermidis Bioreplicate2 with RppH |
| Sample type |
SRA |
| |
|
| Source name |
exponentially growing culture
|
| Organism |
Staphylococcus epidermidis |
| Characteristics |
growth conditions: 37°C, MH liquid
treatment: with RppH
emote library: EMOTE04
emote barcode: GCTG
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction protocol not provided.
EMOTE, as described in associated paper
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: EMOTE_Sepidermidis_unambiguous.tsv.gz
|
| Data processing |
Library strategy: TSS-EMOTE
FASTQ files for each EMOTE sample is obtained by demultiplexing the original FASTQ file according to the EMOTE-barcode detected in the reads. Demultiplexing is performed by EMOTEconv program, allowing for 1 mismatch in the EMOTE recognition sequence.
EMOTE reads are parsed from the FASTQ files to extract the UMI sequence, and the mapping sequence. This step is performed by EMOTEconv program.
The mapping sequence of each read is aligned to the corresponding bacterial genome using Bowtie. Reads aligning to multiple position on the genome are ignored to keep only unambiguously mapped reads.
For each position on the genome, Emoteconv quantify the number of read whose first base align at this position (N value). In a second it corrects for potential PCR bias by removing duplicated reads (that have the same UMI sequence), and quantify again (Q value).
Supplementary_files_format_and_content: EMOTE_Saureus_unambiguous.tsv.gz: abundance measurements across S. aureus genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Eaerogenes_unambiguous.tsv.gz: abundance measurements across E. aerogenes genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Sepidermidis_unambiguous.tsv.gz: abundance measurements across S. epidermidis genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Abaumannii_unambiguous.tsv.gz: abundance measurements across A. baumannii genome (tab separated text file)
|
| |
|
| Submission date |
Aug 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julien Prados |
| E-mail(s) |
julien.prados@unige.ch
|
| Phone |
+41 22 37 95 396
|
| Organization name |
University of Geneva
|
| Department |
SCMU
|
| Lab |
Bioinformatics Support Platform
|
| Street address |
Rue Michel Servet 1
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21652 |
| Series (1) |
| GSE85110 |
TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens. |
|
| Relations |
| BioSample |
SAMN05505489 |
| SRA |
SRX1995469 |
