|
| Status |
Public on May 08, 2015 |
| Title |
wildtype H37Rv experiment 2 replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
H37Rv_rep_1_2014
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: H37Rv
growth condition: aerobic log phase
|
| Growth protocol |
Cultures were grown to log phase (OD 0.5-1) in 7H9 supplemented with OADC, 0.05% Tween-80, and 0.2% glycerol in roller bottles
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were inactivated with RNAlater, disrupted with bead-beating in the presence of Trizol, and total RNA was extracted according to the manufacturer's instructions. RNA was then treated with Dnase and re-purified with RNeasy.
Expression libraries were constructed using either the dUTP method or a ligation-based method to maintain strand specificity. 5' end mapping libraries were constructed by direct ligation of adapters to RNA 5' ends after differential treatment with or without 5' polyphosphatase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
library construction: RNAseq strand-specific expression library
supplementary file: Shell experiment 2 expression RPKM.txt
|
| Data processing |
Data were de-multiplexed and Ssaha2 was used to map and create SAM and BAM files
Read pairs that were not correctly oriented with respect to each other were filtered out, unpaired reads were filtered out, and the region encoding the rRNA was filtered out
For expression libraries, coverage at each genome coordinate on each strand was determined using Samtools and Mpileup. Missing values were replaced with 0.
For expression libraries, RPKMs were calculated from BAM files using Artemis
1st nt identification (5' end mapping libraries only): The first nt of each "read 1" was extracted from BAM files, and 1st nt coverage at each position on each strand was determined.
5' end calling (5' end mapping libraries only): for any position with a 1st nt read depth greater than 10 times the 1st nt read depth at the position 10 nt before OR 10 nt after on the same strand, a 5' end was reported in table "Shell 5 prime end mapping coverage peaks".
Genome_build: NC_000962
Supplementary_files_format_and_content: RPKM files contain RPKM data from RNAseq expression libraries
Supplementary_files_format_and_content: Expression coverage files contain mapped read depth at each genome coordinate from RNAseq expression libraries
Supplementary_files_format_and_content: 5-prime-end peak files contain read depth at each RNA 5' end identified in 5' end mapping libraries
|
| |
|
| Submission date |
Oct 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Scarlet Shell |
| E-mail(s) |
sshell@wpi.edu
|
| Organization name |
Worcester Polytechnic Institute
|
| Department |
Biology and Biotechnology
|
| Lab |
Scarlet Shell
|
| Street address |
60 Prescott St
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19272 |
| Series (1) |
| GSE62152 |
Transcript 5'-end mapping was used to identify transcriptional start sites and RNA processing sites genome-wide in Mycobacterium tuberculosis |
|
| Relations |
| BioSample |
SAMN03098264 |
| SRA |
SRX727249 |
