|
| Status |
Public on Apr 28, 2023 |
| Title |
Ythdf2 cKO, Control, m6A IP, r2, MeRIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
MC38 tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: MC38 tumors
cell type: CD11b+ myeloid cells
genotype: Ythdf2 cKO
treatment: Control
antibody: EpiMark N6-Methyladenosine Enrichment Kit
|
| Treatment protocol |
MC38 tumors were received irradition (20 Gy, one dose), three days after IR, cells were collected
|
| Growth protocol |
CD11b+ myeloid cells were sorted from MC38 tumors or blood of MC38 tumor-bearing mice
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was harvested using Rneasy mini plus kit (Qiagen), followed by mRNA isolation using Dynabeads™ mRNA Purification Kit,M6A-IP was performed
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit (TaKaRa)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads were trimmed with Trimmomatic-0.39, then aligned to mouse genome and transcriptome (mm10)
Mapped reads were separated by strands with samtools
m6A peaks on each strand were called using MACS (version 2)
Significant peaks with q < 0.01 identified by MACS2 were considered
Peaks identified in at least three biological replicates were merged using bedtools (v.2.26.0)
Assembly: mm10
Supplementary files format and content: text files includes read counts for each Sample, narrowPeak (except for Input sample)
Library strategy: MeRIP-seq
|
| |
|
| Submission date |
Jun 17, 2022 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Chuan He |
| E-mail(s) |
chuanhe@uchicago.edu
|
| Phone |
773-702-5061
|
| Organization name |
University of Chicago
|
| Department |
Department of Chemistry
|
| Street address |
929 E 57th St., GCIS E319
|
| City |
Chicago |
| State/province |
ILLINOIS |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE206384 |
YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [MeRIP-Seq] |
| GSE206387 |
YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells |
|
| Relations |
| BioSample |
SAMN29180692 |
| SRA |
SRX15783392 |
