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| Status |
Public on Feb 13, 2019 |
| Title |
INS-1 S487A 3 |
| Sample type |
SRA |
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| Source name |
INS-1 S487A
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| Organism |
Rattus norvegicus |
| Characteristics |
cell line: INS-1
cell type: Rat insulinoma cells; Insulin secreting beta cell derived line
passages: 75-80
genotype/variation: overexpressing menin S487A mutant
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| Growth protocol |
INS-1 cells overexpressing menin S487A or S487D mutant were established by transduction with pMX-puro-Flag-Menin derived retroviruses, and cultured in RPMI1640 medium supplemented with 10% FBS, 10 mM HEPES buffer, 2 mM glutamine, 1 mM sodium pyruvate, 50 μM beta-mercaptoethanol and 1% Pen/Strep
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.The purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RINe above 7.0. mRNAs were isolated from Total RNA and fragmented to approximately 200bp. Subsequently, the collected mRNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of TruSeq® RNA LT/HT Sample Prep Kit (Illumina, USA).
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 2500 |
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| Description |
InsM-A-3_RPKM
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| Data processing |
base-calling：bcl2fastq(v2.17)
data filtrting step1：cutadapt（v1.8.1）
data filtrting step2：remove N bases(our program)
data filtrting step3：FASTQ quality filter：fastq_quality_filter（v0.0.13）
alignment genome:tophat(v2.0.13)
quantify gene count:gfold(V1.1.2)
Genome_build: NCBI rn6(GCF_000001895.5_Rnor_6.0)
Supplementary_files_format_and_content: abundance measurements
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| Submission date |
Nov 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bowen Xing |
| E-mail(s) |
bwxing@whu.edu.cn
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| Phone |
86-13005411156
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| Organization name |
Shenzhen University
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| Street address |
Nanhai Street 3688
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE106653 |
GLP-1 signaling suppresses menin's transcriptional block by phosphorylation in beta cells |
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| Relations |
| BioSample |
SAMN07998337 |
| SRA |
SRX3372549 |
| 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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