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| Status |
Public on Oct 03, 2023 |
| Title |
M17 cells, Miat4 |
| Sample type |
SRA |
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| Source name |
BE(2)-M17
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| Organism |
Homo sapiens |
| Characteristics |
cell line: BE(2)-M17
cell type: neuroblastoma cells
genotype: GOMAFU knockdown
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| Treatment protocol |
Cells were transfected with 100 pmol siRNA, miRNA mimics, or miRNA inhibitors, including Hsa-miR-137 (Ambion, mc10513), has-miR-100 (Ambion, mc10188) and has-anti-miR-137 (Dharmacon, IH-310413-07-0005), using Lipofectamine 2000 (Invitrogen) following manufacturer’s instructions.
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| Growth protocol |
The BE(2)-M17 human neuroblastoma line and SH-SY5Y line (both are from ATCC) were propagated in DMEM/F12 medium containing 10% fetal bovine serum (FBS) (HyClone).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cultured cells were harvested then centrifuged at 1,500 g and cell pellets were used for RNA isolation. Cell pellet was homogenized in TRIzol using a hand-held pestle homogenizer and incubated in TRIzol for at least 5 minutes. Chloroform (1:5 ratio) was added, mixed well and incubated at room temperature for 15 minutes. Samples were then centrifuged at 12,000 g for 15 minutes at 4°C. The top aqueous layer was transferred to a clean tube, and the RNA was precipitated in 3 M NaAc pH 5.2 (10:1 ratio), 4 ml of glycogen (5 mg/ml), 100% isopropanol (1:1 ratio) overnight at -80°C. The next day, the samples were centrifuged at 20,000 g for 20 minutes at 4°C. The resulting RNA pellet was washed once in 75% ethanol, centrifuged at 7,500 g for 10 minutes at 4°C. The washed RNA pellet was dissolved in nuclease-free water. RNA was quantified by NanoDrop and the quality was confirmed by agarose gel.
An amount of 1ug total RNA per sample was processed for library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE, targeting 100M total reads per sample.
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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 |
All total reads were mapped to hg38 by TopHat2 with default parameter followed by gene expression quantification and differential expression analysis using Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: fpkm table
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| Submission date |
Aug 18, 2021 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Bing Yao |
| E-mail(s) |
bing.yao@emory.edu
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| Phone |
3523596473
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| Organization name |
Emory University
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| Department |
Department of Human Genetics
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| Street address |
615 Michael Street
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| City |
Atlanta |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE182370 |
MiR-137 and GOMAFU form a novel non-coding RNA pathway to regulate human neuron differentiation and molecular networks affected in neuropsychiatric diseases |
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| Relations |
| BioSample |
SAMN20849654 |
| SRA |
SRX11811941 |
| 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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