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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 01, 2019 |
| Title |
BMSC BM rep1 |
| Sample type |
SRA |
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| Source name |
sorted bmsc
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse bone marrow stem cells
group: BM (GFP-BMSCs collected from the bone marrow of tumor-bearing mice (co-injection of RFP-LLCs and GFP-BMSCs))
strain: C57BL/6
genotype: wide type
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| Extracted molecule |
total RNA |
| Extraction protocol |
BMSCs were sorted, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 |
BGISEQ-500 |
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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.
Explanation for the generation of FPKM and the difference between FPKM and RPKM:
1.RPKM stands for Reads Per Kilobase of transcript per Million mapped reads. In RNA-Seq, the relative expression of a transcript is proportional to the number of cDNA fragments that originate from it. RPKM=(1000000*C)/(N*L/1000), C represents the amount of reads which mapped to the specific transcripts, N represents the amount of reads which mapped to any transcripts. L represents the base amount of the specific transcripts.
2.FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads. FPKM=(1000000*C)/(N*L/1000), C represents the amount of fragment which mapped to the specific transcripts, N represents the amount of fragment which mapped to any transcripts. L represents the base amount of the specific transcripts.
3.In RNA-Seq, the relative expression of a transcript is proportional to the number of cDNA fragments that originate from it. Paired-end RNA-Seq experiments produce two reads per fragment, but that doesn't necessarily mean that both reads will be mappable. For example, the second read is of poor quality. If we were to count reads rather than fragments, we might double-count some fragments but not others, leading to a skewed expression value. Thus, FPKM is calculated by counting fragments, not reads.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Sep 25, 2018 |
| Last update date |
Sep 02, 2019 |
| Contact name |
Buqing Sai |
| E-mail(s) |
[email protected]
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| Organization name |
Buqing Sai
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| Street address |
110 Xiangya Road
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410078 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE120456 |
Cancer-educated mesenchymal stem cells promote pre-metastatic niche formation for disseminated cancer cells via the induction of PMN-MDSC expansion |
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| Relations |
| BioSample |
SAMN10127861 |
| SRA |
SRX4737728 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3401021_treat1.transcript.fpkm.txt.gz |
406.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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