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| Status |
Public on Nov 21, 2019 |
| Title |
N134_GFP-miR-LacZ_2 |
| Sample type |
SRA |
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| Source name |
N134_GFP-miR-LacZ
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell line: N134
cell type: pancreatic beta cell tumor
treatment: control
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| Growth protocol |
cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 0.2 mM L-glutamine, and 1% penicillin/streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus mini kit (Qiagen, 74134) and QIAshredder kit (Qiagen, 79654) according to the manufacturer’s protocol.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced with pair-end 51 bps on Illumina HiSeq 4000 sequencer (Illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina CASAVA v1.8.2 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the mouse mm9 reference genome using Tophat v2.0.11.
Differential expression analysis was performed by using Cufflinks v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: excel file including gene name, refseq gene id, expression (FPKM) for each gene in each sample
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| Submission date |
Oct 19, 2019 |
| Last update date |
Nov 21, 2019 |
| Contact name |
Nancy Du |
| E-mail(s) |
nad2012@med.cornell.edu
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| Phone |
2127467312
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| Organization name |
Weill Cornell Medicine
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| Street address |
1300 York Ave
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE139119 |
MicroRNA-431 promotes metastasis of pancreatic neuroendocrine tumors by targeting DAB2IP, a RasGAP tumor suppressor |
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| Relations |
| BioSample |
SAMN13064191 |
| SRA |
SRX7024959 |
| 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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