|
| Status |
Public on Mar 21, 2022 |
| Title |
si2_ALKBH5_elution, repeat 1 |
| Sample type |
SRA |
| |
|
| Source name |
monocyte/macrophage-like cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RAW264.7
treatment: ALKBH5 knockdown si2 followed by P.aeruginosa infection 6h
rna harvest: Enrichment of m6A methylated mRNA with m6A antibody (Abcam, ab208577)
|
| Treatment protocol |
RAW264.7 cells at 4×10^5 cells per mL were infected with 107 P.aeruginosa and harvested at 0, 2, 4, and 6 h post treatment. RAW264.7 cells with ALKBH5 knockdown (ALKBH5 si1: SASI_Mm01_00106232, ALKBH5 si2: SASI_Mm02_00344968, Sigma-Aldrich) were infected with 107 P. aeruginosa 6 hr post infection.
|
| Growth protocol |
RAW 264.7 Cells are maintained in Dulbecco's Modified Eagle's Medium with 10% fetal bovine serum at 37 °C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extraction follows TRI reagent protocol (Thermo-Fisher) and then treated with DNase I to remove DNA contamination. . For m6A MeRIP-seq, the m6A enrichment were performed using m6A antibody (m6A antibody cat#202203, synaptic systems) and m6A-enriched and fragmented RNA was purified using RNeasy Mini Kit as IP.
KAPA Stranded RNA-seq Kit (Illumina) was used for the library preparation of both m6A-IP RNA and input mRNAs. The quality of the completed libraries was performed with Agilent 2100 Bioanalyzer
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Library strategy: meRIP-seq
Illumina bcl2fastq software used for base-calling
reads algined to corresponding genomes (UCSC mm9 for mouse) using TopHat (stranded), converted to sorted BAM using SAMTools, and further processed using exomePeak
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Feb 07, 2022 |
| Last update date |
Mar 21, 2022 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE196270 |
Distinct N6-methyladenosine (m6A) Regulation of Innate Immune Responses During Bacterial Infections II |
| GSE196272 |
Distinct N6-methyladenosine (m6A) Regulation of Innate Immune Responses During Bacterial and Viral Infections |
|
| Relations |
| BioSample |
SAMN25704163 |
| SRA |
SRX14072446 |
