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| Status |
Public on May 02, 2018 |
| Title |
shDDX1_rep1 |
| Sample type |
SRA |
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| Source name |
INS-1_shDDX1
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| Organism |
Rattus norvegicus |
| Characteristics |
cell line: INS1
cell type: pancreatic beta cell line
shRNA: DDX1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared directly from the scrambled and shDDX1 INS1 cells using Trizol (Invitrogen, Carlsbad, CA, USA) as per the manufacturer's instructions.
The mRNA was purified by Dynabeads mRNA DIRECT kit (Invitrogen, Carlsbad, CA, USA) from total RNA, fragmented, converted to cDNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Trimmomatic v0.36 was used to trim/filter sequenced reads with default parameters
Sequencing reads were mapped to the rat genome (version Rn5) using Tophat (version 2.0.9) and the default options(Kim et al., 2013). Mapped reads were used with Cufflinks software suite (Trapnell et al., 2012) in combination with rat transcripts annotations from Ensembl database(Aken et al., 2016) version 79 for transcripts assembly.
Genome_build: rn5
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig
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| Submission date |
May 01, 2018 |
| Last update date |
May 03, 2018 |
| Contact name |
Wen Zhong |
| E-mail(s) |
zhongwenhust@gmail.com
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| Organization name |
Institute of Biophysics, Chinese Academy of Sciences
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| Street address |
Datun Road
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE113893 |
DDX1 regulates alternative splicing and insulin secretion in pancreatic β cells |
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| Relations |
| BioSample |
SAMN09006373 |
| SRA |
SRX4016837 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3123061_shDDX1_rep1.bw |
216.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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