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| Status |
Public on May 09, 2023 |
| Title |
HM1-shST3GAL3-2 |
| Sample type |
SRA |
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| Source name |
HM1 cells, ST3GAL3 knockdown
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| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: HM1
cell type: murine ovarian cancer cell
genotype: ST3GAL3 knockdown
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited txt files include TPM values for each sample.
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| Submission date |
Sep 12, 2022 |
| Last update date |
May 11, 2023 |
| Contact name |
Haiou Liu |
| E-mail(s) |
liuhaiou@fudan.edu.cn
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| Phone |
+8613916273769
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| Organization name |
Fudan University
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| Street address |
No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.
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| City |
Shanghai |
| ZIP/Postal code |
200000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE213219 |
Tumor-intrinsic ST3GAL3 Activity Blunts Anti-tumor Immune and Drives Immunotherapy Resistance |
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| Relations |
| BioSample |
SAMN30813964 |
| SRA |
SRX17538794 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6574591_HM1-shST3GAL3-2.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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