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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 09, 2020 |
| Title |
Tumor budding-2, biological rep2 |
| Sample type |
SRA |
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| Source name |
Tumor budding cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Colorectal cancer
cell type: Tumor budding cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were lysed with TRIzol to isolate the total RNA
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 HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Sep 10, 2019 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Yanrong Liu |
| E-mail(s) |
liuyanrong_2019@outlook.com
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| Organization name |
Tianjin international biomedical joint research institute
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| Street address |
No.220, Tongyan Road
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| City |
Tianjin |
| ZIP/Postal code |
300050 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE137203 |
mRNA expression data of Tumor budding cells and Tumor center cells |
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| Relations |
| BioSample |
SAMN12723075 |
| SRA |
SRX6827654 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4072939_Tumor_budding-2.txt.gz |
135.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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