 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 08, 2022 |
| Title |
TD005_after |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Human immunodeficiency virus 1 |
| Characteristics |
tissue: peripheral blood
cell line: Primary cell
cell type: PBMC
genotype: protease/ reverse transcriptase (PR/RT) region sequences
treatment: M10 CAR-T cells
age: 48 years old
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PacBio Sequel instrument (Pacific Biosciences of California, Inc., California, USA)
For each sample, >2ug purified PCR fragments (1kb~10kb) was used for library preparation. Fragmented DNAs were treated with End Prep Enzyme Mix for end repairing, 5’Phosphorylation and 3’dA-tailing in one reaction, followed by a T-A ligation to add universal hairpin adapters to both ends. Then the SMRTbell libraries were validated by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 3.0 Fluorometer. The final SMRTbell libraries were loaded on PacBio Sequel instrument according to manufacturer’s instructions (Pacific Biosciences of California, Inc., California, USA).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Sequel II |
| |
|
| Data processing |
Raw data statistics: Perform statistical analysis on subreads to obtain information such as the number, average length and GC content of subreads sequence.
CCS analysis:Perform Circular Consensus Calling on subreads to obtain high-quality CCS reads by using pbccs software (version 3.3.0), and perform statistical analysis on CCS sequences.
barcode split: Split CCS reads according to barcode by using lima software (version 1.9.0), and statistics the split results.
Statistics of target sequences abundance:If the target area is specified, the target sequence is captured according to the 10nt of upstream and downstream of the target sequence, otherwise, the target sequence refs to the full-length sequences.
Statistics of base distribution: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is extracted and mutation abundance information is counted.
Assembly: HIV-1, complete genome (GenBank: AF033819.3)
Supplementary files format and content: The target sequence is captured according to the 10nt of upstream and downstream of the HIV protease/ reverse transcriptase (PR/RT) region sequences (headers represent the date of sequencing and the sequencing number of the ccs reads)
Supplementary files format and content: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is preserved to bam files
|
| |
|
| Submission date |
Dec 05, 2022 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Zhu YouWei |
| E-mail(s) |
ywzhu22@m.fudan.edu.cn
|
| Phone |
19145632696
|
| Organization name |
Fudan university
|
| Department |
Institutes of Biomedical Sciences
|
| Street address |
130 Dong'an Road
|
| City |
上海 |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL32910 |
| Series (1) |
| GSE220111 |
Anti-HIV-1 CAR-T cells armed with autogenic broadly neutralizing antibody and follicle-homing receptor CXCR5 ar effective against different HIV-1 clades and reduce viral reservoir in HIV-1-infected individuals |
|
| Relations |
| BioSample |
SAMN31836190 |
| SRA |
SRX18382564 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6788545_TD005WKM-M5.Base.dist.txt.gz |
4.0 Kb |
(ftp)(http) |
TXT |
| GSM6788545_TD005WKM-M5.target.fa.gz |
1.3 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
