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Sample GSM6788549 Query DataSets for GSM6788549
Status Public on Dec 08, 2022
Title TD008_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: 36 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
 
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 GPL32911
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 SAMN31836194
SRA SRX18382568

Supplementary file Size Download File type/resource
GSM6788549_AD3.Base.dist.txt.gz 4.0 Kb (ftp)(http) TXT
GSM6788549_AD3.target.fa.gz 2.5 Mb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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