|
| Status |
Public on Feb 10, 2020 |
| Title |
METTL3_Control_nuclearRNA_r1 [HEC-1-A] |
| Sample type |
SRA |
| |
|
| Source name |
HEC-1-A
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: METTL3_Control
|
| Treatment protocol |
6-cm plates of HEC-1-A cells were seeded and controlled to afford the same amount of cells.
|
| Growth protocol |
Cell were grown in McCoy’s 5A medium (Invitrogen) supplemented with 10% FBS (Gibco), and 1% Penicillin-Streptomycin (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The nuclear fraction was separated and total RNA was purified by Trizol. Before purified non-ribosome RNA with RiboMinus transcriptome isolation kit, ERCC RNA spike-in control (Ambion) was added to each sample (0.1 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
non-ribosome RNA
|
| Data processing |
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to human genome and transcriptome (hg38, version 29, 2018-08-30) together with external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters. Annotation files (version 29, 2018-08-30, in gtf format for human) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Read counts for each gene and each sample.
|
| |
|
| Submission date |
Nov 18, 2019 |
| Last update date |
Feb 10, 2020 |
| Contact name |
Xiaoyang Dou |
| E-mail(s) |
[email protected]
|
| Organization name |
Center for Excellence in Molecular Cell Science, CAS
|
| Street address |
320 Yue Yang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE140560 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq_RNA_nuclear] |
| GSE140561 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq] |
|
| Relations |
| BioSample |
SAMN13320050 |
| SRA |
SRX7175472 |
