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| Status |
Public on Jun 30, 2023 |
| Title |
tumor tissue, IL-33, 7 |
| Sample type |
SRA |
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| Source name |
tumor tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: tumor tissue
cell line: MFC
cell type: murine gastric cancer cells
genotype: WT
treatment: IL-33
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. Then, map the clean reads to the silva database to remove the rRNA.
Paired-end clean reads were aligned to the reference genome using Hisat2.
Featurecount was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jun 21, 2023 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Keying Che |
| Organization name |
Nanjing Drum Tower Hospital
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| Street address |
321 Zhongshan Road
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| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE235526 |
Macrophages reprogramming improves immunotherapy of IL-33 in peritoneal metastasis of gastric cancer |
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| Relations |
| BioSample |
SAMN35821930 |
| SRA |
SRX20741621 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7504755_IL33-7.txt.gz |
109.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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