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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 06, 2019 |
| Title |
Liat 945 (161-MAP) |
| Sample type |
SRA |
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| Source name |
CT26 cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: CT26
mouse strain: BALB/c
tissue: s.c. tumor
tumor extracted: 27 days after implantation
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| Treatment protocol |
After CT26 cells were implanted s.c. (day 0), mice were vaccinatd with either Scr-MAP or 161-MAP (50 ug each, emulsified in Freund's adjuvants) at day 7, 14 and 21.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extrcted from tumors using the Qiacube (Qiagen) with the RNeasy kit (cat. no. 74106). Quality measurements of total RNA were performed using TapeStation (Agilent). RINe values were between 6.5-10.0
Six RNAseq libraries (NEBNext® Ultra™ RNA Library Prep Kit for Illumina, cat no. E7530) were produced according to the manufacturer protcol from 800 ng of total RNA. mRNA pull-up was performed using Magnetic Isolation Module (NEB, cat no. E7490). The six libraries were mixed into a single tube with equal molarity of all samples. The RNAseq data was generated on NextSeq500 mid-output (75bp pair-end reads) kit v2 (Illumina, FC-404-2005).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Quality control was performed using FastQC (v0.11.2) and overrepresented sequences were removed using CUTADAPT tool (v 1.8)
The 75 paired-end reads were aligned to mouse reference genomeand annotation file (Mus_musculus.GRCm38 downloaed from ENSEMBL) using TopHat (v2.0.13), allowing 2 mismatches per read with options - very-sensitive and -GTF. The number of reads per genes was counted using HTseq (0.6.1).
Principal components analysis (PCA), samples' clustering, and differential expressed genes (DEGs), were calculated using Deseq2 (version 1.8.1).
DEGs were further investigated for function and pathway enrichment using Ingenuity Pathway Analysis (IPA) and functional gene and term networks from clustering of enrichment analysis using Bioconductor R package FGNet (V3.2.1).
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample and read counts.
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| Submission date |
Aug 10, 2016 |
| Last update date |
Aug 06, 2019 |
| Contact name |
Michal (Miki) A. Rahat |
| Organization name |
Carmel Medical Center & Technion-Israel Institute of Technology
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| Department |
Immunology, Faculty of Medicine
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| Lab |
Immunotherapy Lab
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| Street address |
7 Michal st.,
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| City |
Haifa |
| ZIP/Postal code |
3436212 |
| Country |
Israel |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE85440 |
Inhibition of Tumor Growth and Metastasis by EMMPRIN Multiple Antigenic Peptide (MAP) Vaccination Is Mediated by Immune Modulation |
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| Relations |
| BioSample |
SAMN05558838 |
| SRA |
SRX2011717 |
| 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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