|
| Status |
Public on Oct 05, 2020 |
| Title |
LXHWT2 |
| Sample type |
SRA |
| |
|
| Source name |
strain
|
| Organism |
Mycobacterium tuberculosis H37Ra |
| Characteristics |
genotype/variation: H37Ra/WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNeasy Mini Kit (Cat#74106, Qiagen) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium tuberculosis H37Ra whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium tuberculosis H37Ra
Supplementary_files_format_and_content: gene_expression.xls file includes FPKM values for each Sample ...
|
| |
|
| Submission date |
Nov 07, 2019 |
| Last update date |
Oct 05, 2020 |
| Contact name |
Li xiao hui |
| E-mail(s) |
chenliu@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Shizishan Street No. 1, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL27144 |
| Series (1) |
| GSE140113 |
Next Generation Sequencing Facilitates Quantitative Analysis of cmtR-deleted mutant and wild-type strains Transcriptomes in Mycobacterium tuberculosis H37Ra |
|
| Relations |
| BioSample |
SAMN13241021 |
| SRA |
SRX7115494 |
