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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 04, 2020 |
| Title |
Hepa1-6_Tu_WT-4 |
| Sample type |
SRA |
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| Source name |
mice with tumor challenge
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 18 days after tumor cell injection
genotype/variation: wild type
tissue source: C57BL/6-derived Hepa1-6 hepatoma carcinoma cell
tissue/cell type: syngeneic tumor
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| Treatment protocol |
All isolated cells (Hepa1-6_Tu and Py8119_Tu, G-MDSCs) were washed once with PBS and immediately used for RNA extraction OR DNA extraction.
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| Growth protocol |
Hepa1-6_Tu and Py8119_Tu were derived from C57BL/6-derived Hepa1-6 syngeneic tumor and C57BL/6-derived Py8119 syngeneic tumor. The syngeneic tumors were cut in pre-cooling PBS, and the tissue pieces were ground by mechanical grinding. Filter the cells with a 70um cell strainer. The filtered single cells were washed with PBS twice. Isolation of G-MDSCs was performed with the Myeloid-Derived Suppressor Cell Isolation Kit, mouse (130-094-538, Miltenyi Biotec).
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| Extracted molecule |
total RNA |
| Extraction protocol |
All isolated cells (Hepa1-6_Tu and Py8119_Tu, G-MDSCs) were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The DNA of G-MDSCs were extracted using a DNA extraction kit (56504, QIAamp DNA Investigator Kit).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used to construct the libraries of mRNA-seq. TrueMethyl Seq protocol recommended by Cambridge Epigenetix (CEGX, Cambridge, UK) was used to prepare the libraries for oxidative bisulfite sequencing (OxBS-seq).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw reads of mRNA-seq were first trimmed to remove adapters and low-quality bases by using the trim_galore (v0.4.4_dev) program with parameters: “--paired --illumina”. Trimmed reads were then aligned to the mouse reference genome (mm9) by using the tophat (v2.1.1) program with default parameters. The mouse reference genome and gene annotations were download from the UCSC genome website (http://www.genome.ucsc.edu). The cufflinks (v2.2.1) program to calculate FPKM (Fragments Per Kilobase Million) to estimate the abundance of a given mRNA. The cuffdiff (v2.2.1) program was used to identify differentially expressed genes.
Raw reads of BS-seq and OxBS-seq were trimmed using Trim-Galore to remove low quality bases and adaptor sequences. The trimmed reads were mapped onto the reference genome (mm9) using bsmap (v2.74), followed by removal of PCR duplicates. We extracted methylation signals using methratio.py, a script in the bsmap package (v3.4.2) (40). An R-script was generated to maintain chromosome coordinates consistent for methylation sites between each pair of BS and OxBS samples, allowing to identify 5mC and 5hmC signal in these common sites with the mlml script in methpipe using the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The mRNA-seq processed files containing FPKM value for each gene were genes.fpkm_tracking that was generated by the cuffinks. The OxBS-seq processed files contain methylation level at base-resolution, with five columns: chromosome, position, strand, seq-context, methylated-percentage, and seq-depth.
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| Submission date |
Feb 05, 2020 |
| Last update date |
Aug 04, 2020 |
| Contact name |
Feizhen Wu |
| E-mail(s) |
wufz@fudan.edu.cn
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| Phone |
86-21-54237821
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| Organization name |
Fudan Univ, Shanghai, China
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| Department |
Institutes of Biomedical Sciences
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| Lab |
Epigenetics lab
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| Street address |
Dongan Road 131, Rm 511 Mingdao Building
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE144787 |
TET2 promotes anti-tumor immunity by governing G-MDSCs and CD8+ T cell numbers |
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| Relations |
| BioSample |
SAMN14001999 |
| SRA |
SRX7677794 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4296347_Hepa1-6_Tu_WT-4.fpkm.txt.gz |
780.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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