|
| Status |
Public on Jun 09, 2023 |
| Title |
iPSN-Ctrl-3_IP_YTHDF2-RIP |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived neuron
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-derived neuron
genotype: Non-neurologic control
|
| Growth protocol |
iPSCs were maintained in mTeSR media on Matrigel, following the Cedars-Sinai Standard Operating Procedure (SOP, https://www.cedars-sinai.edu/content/dam/cedars-sinai/research/documents/biomanufacturing/complete-ipsc-culturing-protocol-rev-4-2020.pdf). iPSCs were differentiated into spinal neurons using the direct induced motor neuron protocol. All cells were maintained at 37°C with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from cells using TRIzol (Thermo Fisher). Protein-RNA complexes were isolated with YTHDF2 antibody-coated protein G beads. After washing, 1ml TRIZOL was added to the beads to elute the RNAs.
RNAs recovered from RIP and input were subjected to NEBNext Ultra II Directional RNA Library Prep (New England Biolabs) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
|
| |
|
| 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, then aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters. Reads on each GENCODE annotated gene were counted using HTSeq and then differentially expressed genes were called using DESeq2 package.
Reads on each GENCODE annotated gene were counted using HTSeq and then differentially expressed genes were called using DESeq2 package.
Assembly: hg38
Supplementary files format and content: read counts for each sample
|
| |
|
| Submission date |
May 23, 2022 |
| Last update date |
Jun 11, 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 |
GPL24676 |
| Series (2) |
| GSE203578 |
N6-methyladenosine regulates RNA metabolism and neurodegeneration in C9ORF72-ALS/FTD [seq_polyA_RNA-RIP] |
| GSE203581 |
Globally reduced N6-methyladenosine (m6A) in C9ORF72-ALS/FTD dysregulates RNA metabolism and contributes to neurodegeneration |
|
| Relations |
| BioSample |
SAMN28597182 |
| SRA |
SRX15414441 |
