|
| Status |
Public on Jan 27, 2023 |
| Title |
MGH66_untreated_Bulk2 [U2] |
| Sample type |
SRA |
| |
|
| Source name |
Antibiotic susceptible clinical isolate
|
| Organism |
Klebsiella pneumoniae |
| Characteristics |
strain: MGH66
treatment: untreated
method: RNAtag-seq
exp_id: Bulk_MGH66
accession no.: GCA_000694555.1
|
| Growth protocol |
37ºC, regular laboratory condition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA extraction for Bulk RNAseq data
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
U2
|
| Data processing |
bcl2fastq2-v2.20.0 was used to generate fastq files
Sequencing reads were trimed and sorted using fastp-0.20.0
Cell barcodes were extracted using UMI-Tools package installed in Python-3.6
Alignment was using BWA
FeatureCounts was used to assign reads to gene, count transcripts and generate counts tables.
Counts matrix from BacDrop experiments were generated using UMI-Tools
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: Counts matrix
|
| |
|
| Submission date |
Jul 16, 2021 |
| Last update date |
Jan 27, 2023 |
| Contact name |
Peijun Ma |
| E-mail(s) |
peijunma@broadinstitute.org
|
| Organization name |
The Broad Institute of MIT and Harvard
|
| Department |
Infectious Disease and Microbiome program
|
| Lab |
Deborah T. Hung
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL28669 |
| Series (1) |
| GSE180237 |
Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states |
|
| Relations |
| BioSample |
SAMN20258265 |
| SRA |
SRX11481985 |
