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| Status |
Public on Jun 24, 2022 |
| Title |
IFN2 |
| Sample type |
SRA |
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| Source name |
M17
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| Organism |
Homo sapiens |
| Characteristics |
treatment: IFN_treated
cell line: M17
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| Treatment protocol |
Cells were treated with IFN-γ (NOVUS biologicals, 285-IF-100) at the concentration of 10ng/ml for 24h.
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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 |
total 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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| Description |
rRNA depletion RNA-seq
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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.
Assembly: hg38
Supplementary files format and content: fpkm table
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| Submission date |
Jun 22, 2022 |
| Last update date |
Jun 24, 2022 |
| 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) |
| GSE206720 |
The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in schizophrenia |
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| Relations |
| BioSample |
SAMN29251741 |
| SRA |
SRX15830435 |
| 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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