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Status |
Public on Apr 19, 2017 |
Title |
ALYREF-RIP-BS-rep1 |
Sample type |
SRA |
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Source name |
Human HeLa cells
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Organism |
Homo sapiens |
Characteristics |
cell line: HeLa rip antibody: ALYREF (Sigma, Cat# A2220, lot# SLBN7698V) age: P7 tissue: carcinoma cervical
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Extracted molecule |
total RNA |
Extraction protocol |
Flag-ALYREF overexpressed cells pellets were resuspended with 2 volume of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/ml RNase inhibitor), and incubated at 4 °C for 30 min with rotation. Then the lysate was centrifuged at 15,000 g for 20 min. The anti-Flag M2 magnetic beads (Sigma, 10 µl per mg lysate) was washed with a 600 ml NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/ml RNase inhibitor) four times and then resuspended in 800 ml ice-cold NT2 buffer. Cell lysate was mixed with M2 beads and incubated at 4 °C for 4 hr with rotation. The beads were washed two times with 1 ml ice-cold NT2 buffer. Then the beads were subject to Micrococal nuclease (NEB) digestion (1:1,000,000 dilution) for 8 min at 37°C. The beads were cooled on ice immediately for 5 min and washed two times with 1 ml ice-cold 1× PNK+EGTA buffer (50 mM Tris-HCl pH 7.5, 20 mM EDTA, 0.05% NP-40, 200 U/ml RNase inhibitor) and two times with 1 ml ice-cold 1× PK buffer (50 mM NaCl, 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.2% SDS, 200 U/ml RNase inhibitor). Then the beads were digested with 200 μl pre-heated (20 min at 50°C) Proteinase K solution (4 mg/ml) for 40 min at 50°C with rotation at 2000 rpm/min. After centrifuge at top speed for 5 min, the supernatant was transferred to a new 1.5 ml tube and isolated the RNAs with equal volume Acid-Phenol: Chloroform, pH 4.5 (Ambion). The RNAs were subjected to RNA-BisSeq. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 in paired-read mode, creating reads with a length of 125 bp.
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
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Description |
RNA-BisSeq for ALYREF RIP in normal HeLa cells rep1.
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Data processing |
Raw Reads were stripped of adaptor sequence and removed low quality bases using Trimmomatic, clean reads were aligned to the hg19 genome assembly using bismark
The m5C sites were called by bismark.
Genome_build: hg19
Supplementary_files_format_and_content: m5C_sites_in_ALYREF-RIP.xls
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Submission date |
Jan 18, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Bao-Fa Sun |
E-mail(s) |
sunbf@big.ac.cn
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Organization name |
Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)
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Street address |
Da-Tun Road
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City |
Beijing |
ZIP/Postal code |
100101 |
Country |
China |
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Platform ID |
GPL16791 |
Series (2) |
GSE93749 |
Single-base resolution methylome of 5-Methylcytosine in human and mouse transcriptome |
GSE93751 |
5-methylcytosine promotes mRNA export |
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Relations |
BioSample |
SAMN06237533 |
SRA |
SRX2499523 |
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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