|
| Status |
Public on Apr 26, 2019 |
| Title |
A549 m7G-RIP Input Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
A549 human lung adenocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
sample type: INPUT RNA
|
| Treatment protocol |
Heat-denatured RNA was immunoprecipitated with a specific antibody against m7G (MBL RN017M, Lot.001).
|
| Growth protocol |
A549 cells were cultured in DMEM (Invitrogen), supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in Qiazol (Qiagen) and total RNA was purified using the miRNAeasy mini kit (Qiagen)
Libraries were prepared using the NEBNext SmallRNA kit (NEB) according to the manufacturer’s recommendations
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
profiling strategy:
m7G-RNA Immunoprecipitation
TK_LP_A549_RIP-Seq_RAW_miRNA_counts.txt
|
| Data processing |
Raw sequencing .bcl files were demultiplexed in FASTQ format using Illumina Basespace
Library adaptors were trimmed with Trimmomatic
Reads were mapped to the human genome with Bowtie2
Reads were summarized using featureCounts according to miRbase21 annotation
Genome_build: NCBI GRCh38/hg38
Supplementary_files_format_and_content: Raw miRNA counts in tab-separated value file
|
| |
|
| Submission date |
Mar 21, 2018 |
| Last update date |
Apr 26, 2019 |
| Contact name |
Luca Pandolfini |
| E-mail(s) |
luca.pandolfini@iit.it
|
| Organization name |
Istituto Italiano di Tecnologia - I
|
| Department |
Center for Human Technologies
|
| Street address |
Via Enrico Melen 83, Building B
|
| City |
Genova |
| State/province |
Genova |
| ZIP/Postal code |
16152 |
| Country |
Italy |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE112181 |
m7G methylation by METTL1 regulates let-7 microRNAs [BoRed-Seq & m7G-RIP-Seq A549] |
| GSE112182 |
m7G methylation by METTL1 regulates let-7 microRNAs |
|
| Relations |
| BioSample |
SAMN08769862 |
| SRA |
SRX3829853 |
