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| Status |
Public on Dec 20, 2018 |
| Title |
IP siControl rep1 |
| Sample type |
SRA |
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| Source name |
Embryonic Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Embryonic Kidney
cell line: HEK293T
genotype/variation: wild type
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| Growth protocol |
cells were cultured in DMEM medium (Gibco) supplemented with 10% (vol/vol) FBS (Gibco) and 1% penicillin/streptomycin (Gibco) at 37 °C with 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol (Life technologies) followed by isopropanol precipitation, according to the manufacturer’s instructions (Invitrogen). PolyA+ RNA was purified from total RNA with two sequential rounds of polyA tail purification using oligo(dT)25 Dynabeads (Invitrogen).
RNA library were prepared using NEBNext® UltraTM Directional RNA Library Prep Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw sequencing reads produced from m6A-seq were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for adaptor trimming and quality control. The minimum quality threshold was set to 20, and the minimum length required for reads after trimming was 30 nt.
Processed reads were mapped to human genome (hg19, UCSC Genome Browser) using tophat aligner (v2.0.13) with default parameters.
Peak calling within using MACS2, the effective genome size was set to be 2.7*10e9 under the option of –nomodel and pvalue cutoff 0.01.
Peak annotated by annotatePeaks.pl (Homer V4.8)
Paired-end, adapter-clean reads were mapped to human genome (hg19, UCSC Genome Browser) using Tophat with default parameters. Differentially expressed genes were detected by Cuffdiff (v2.2.1).
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| Submission date |
Sep 20, 2018 |
| Last update date |
Dec 20, 2018 |
| Contact name |
Kai Li |
| E-mail(s) |
li_kai@pku.edu.cn
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| Organization name |
Peking University
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| Department |
School of Life Science
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| Lab |
Yi Lab
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| Street address |
Yi He Yuan Street No.5
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| City |
BeiJing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE120229 |
m6A-seq data analysis of control and PCIF1 knockdown transcriptome |
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| Relations |
| BioSample |
SAMN10095393 |
| SRA |
SRX4720164 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3396437_macs2_m6A_NC1_peaks.txt.gz |
642.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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