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| Status |
Public on Jun 21, 2023 |
| Title |
FR1_NK_rep3 RNA-seq |
| Sample type |
SRA |
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| Source name |
YT
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| Organism |
Homo sapiens |
| Characteristics |
cell line: YT
cell type: natural-killer-like (NK-like) lymphoid cells
genotype: FR1 expressing
treatment: lentiviral vector infection
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples isolated from CTRL/hnCD16/FR1/FR2 YT cells were treated with DNase using a column assay. High-quality RNA (280/260 and 230/260 both over 1.7, RIN/RQN>9) was subjected to ribosomal RNA depletion followed by library construction.
Sample testing: According to the sample and product requirements, select the corresponding testing method for quality inspection. mRNA isolation: A certain amount of RNA sample was taken, denatured at a suitable temperature to open its secondary structure, and mRNA was enriched using oligo(dT) magnetic beads. mRNA interruption: Add an interruption reagent to the mRNA obtained in the previous step, react at an appropriate temperature for a certain period of time, and fragment the mRNA. cDNA synthesis: Prepare the first-strand synthesis reaction system and set the reaction program to synthesize the first-strand cDNA; prepare the second-strand synthesis reaction system and set the reaction program to synthesize the second-strand cDNA. Prepare the reaction system for end repair, add "A" and adapter ligation, and set the reaction program to repair the double-stranded cDNA end, and add A base at the 3' end; prepare the adapter ligation reaction system, and set the reaction program to make the adapter Ligated with cDNA. PCR Prepare a PCR reaction system and set up a reaction program to amplify the product. Library detection: Select the corresponding detection method according to the product requirements to check the quality of the library. Circularization: After denaturing the PCR product into a single strand, prepare a circularization reaction system and set up a reaction program to obtain a single-stranded circular product and digest the uncircularized linear DNA molecules. On-machine sequencing: The single-stranded circular DNA molecule is replicated by rolling circle to form a DNA nanoball (DNB) containing multiple copies. The obtained DNBs are added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced by combined probe-anchored aggregation technology (cPAS).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
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| Description |
FR12_3
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| Data processing |
Data filtering The raw data obtained by sequencing was filtered using SOAPnuke (v1.5.6)
Differential gene analysis Use HISAT2 (v2.1.0) software to compare the clean data to the reference genome.
Use Bowtie2 (v2.3.4.3) to align the clena data to the reference gene set.
RSEM (v1.3.1) software was used to quantify gene expression, and pheatmap (v1.0.8) was used to draw a cluster heat map of gene expression in different samples.
DESeq2 (v1.4.5) was used for differential gene detection, and the condition was Q value≤0.05 or FDR≤0.001.
Assembly: GCF_000001405.39_GRCh38.p13
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| Submission date |
Jan 24, 2023 |
| Last update date |
Jun 21, 2023 |
| Contact name |
fanyi meng |
| E-mail(s) |
[email protected]
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| Organization name |
peking university
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| Street address |
haidian distinct
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| City |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
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| Platform ID |
GPL29480 |
| Series (1) |
| GSE223656 |
Leveraging CD16 fusion receptors to remodel the immune response for enhancing iPSC-derived NK cell anti-tumor immunotherapy |
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| Relations |
| BioSample |
SAMN32901236 |
| SRA |
SRX19162717 |
| 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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