|
| Status |
Public on Dec 09, 2020 |
| Title |
BMDM KO PBS m6A rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow-derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
age: post natal week 6
genotype: Mettl14 f/f; LysM-cre
cell type: bone marrow-derived macrophage
treatment: PBS
rip antibody: anti-m6A (Synaptic Systems; Cat#: 202003; RRID: AB_2279214)
|
| Treatment protocol |
BMDMs were treated by LPS or PBS for 6 hours
|
| Growth protocol |
Bone marrows were isolated from C57BL/6 mice and then cultured in RPMI1640 medium with 30% L929 condition medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
BMDMs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. SMARTer Stranded RNA-seq Kit v2- Pico Input Mammalian (Cat#634411) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing raw data were preprocessed by trim_galore v0.6.5 and then mapped against mm10 reference genome by HISAT2 v2.1.0.
Peak calling was carried out using R package exomePeak.
Downstream analysis and visualization of data were accomplished using R v3.6.
Motif search was performed using HOMER v4.10.0.
The longest isoform was retained if a gene has more than one isoforms.
Genome_build: mm10
Supplementary_files_format_and_content: peak file
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Jie Du |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Chicago
|
| Street address |
900 E. 57th Street
|
| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE153511 |
m6A modification maps of mRNA in bone marrow-derived macrophages (BMDMs) from mouse |
|
| Relations |
| BioSample |
SAMN15400149 |
| SRA |
SRX8634254 |
