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| Status |
Public on Jan 17, 2018 |
| Title |
358_2: Kras spleen |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
age: 9 weeks
genotype/variation: KrasLA2
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| Treatment protocol |
WT, miR-301a KO, KrasLA2, miR-301aKO-KrasLA2 mice (22-25g, age 9 weeks) were sacrificed and lung and spleen tissue were obtained.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lung and spleen were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Poly(A) RNAs were purified by using the Dynabeads mRNA purification kit and Poly(A) RNAs were fragmented at 94C for 5 min before reverse transcribed to cDNA with random primers. cDNA fragments were blunted and ligated to sequencing adaptors. Libraries were sequenced with the High-Seq 2000 Illumina sequencing platform
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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| Description |
358_2
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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 txt file include RPKM values for each Sample …
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| Submission date |
Jan 16, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Xiaodong Ma |
| E-mail(s) |
sciencema@hotmail.com
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| Phone |
5022955158
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| Organization name |
South China Normal University
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| Street address |
Rm406,Building 29, South China Normal University
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510631 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE109238 |
Next Generation Sequencing Analysis of lung and spleen tissue transcriptomes from Wild Type KrasLA2 and miR-301a-/- Kras mice |
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| Relations |
| BioSample |
SAMN08367688 |
| SRA |
SRX3585255 |
| 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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