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| Status |
Public on Aug 26, 2022 |
| Title |
WT1 |
| Sample type |
SRA |
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| Source name |
strain
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| Organism |
Mycobacterium tuberculosis H37Ra |
| Characteristics |
strain: H37Ra
genotype: wild-type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen) following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNA Clean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
HTSeq was firstly applied to count the number of Fragments for each gene after bowtie2 comparison. Then the normalization was completed with TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene is calculated by perl script.
Genome_build: Mycobacterium tuberculosis H37Ra
Supplementary_files_format_and_content: gene_expression.txt file includes FPKM and count values for each Sample.
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| Submission date |
Aug 26, 2019 |
| Last update date |
Aug 26, 2022 |
| Contact name |
Yugang Li |
| E-mail(s) |
xuhui123@web.mail.hzau.edu.cn
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| Organization name |
Huazhong Agricultural University
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| Street address |
shizishan street
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| City |
WuHan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL27144 |
| Series (1) |
| GSE136322 |
Genome-wide maps of gene transcription level in wild-type and mpbR-deleted Mycobacterium tuberculosis H37Ra strains |
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| Relations |
| BioSample |
SAMN12637221 |
| SRA |
SRX6759372 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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