|
| Status |
Public on Apr 28, 2023 |
| Title |
WT, Control, YTHDF2 IP, r1, RIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
MC38 tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: MC38 tumors
cell type: CD11b+ myeloid cells
genotype: WT
treatment: Control
antibody: anti-mouse YTHDF2 antibody (Abcam, ab220163)
|
| 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,then RIP for YTHDF2 was performed
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit (TaKaRa)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed with Trimmomatic-0.39
Reads on each GENCODE annotated gene were counted using HTSeq
Differentially expressed genes were called using DESeq2 package in R requiring at least 10 read counts in at least three samples with adjusted p-value < 0.05
YTHDF2 target genes were identified as differentially up-regulated genes comparing YTHDF2 IP sample with the corresponding Input samples
Assembly: mm10
Supplementary files format and content: text files include read counts for each Sample
|
| |
|
| Submission date |
Jun 17, 2022 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Xiaoyang Dou |
| E-mail(s) |
xiaoyang.dou@sibcb.ac.cn
|
| 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 |
GPL24247 |
| Series (2) |
| GSE206379 |
YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [RIP-Seq] |
| GSE206387 |
YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells |
|
| Relations |
| BioSample |
SAMN29180180 |
| SRA |
SRX15783112 |
