|
| Status |
Public on Jun 09, 2023 |
| Title |
iPSN-Ctrl-2_MeRIP |
| 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 |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using TRIzol (Thermo Fisher). Ribosomal RNAs were further depleted from total RNA by RiboMinus Eukaryote Kit v2 (Thermo Fisher Scientific). m6A-immunoprecipitation (m6A-IP) was performed using the EpiMark N6-Methyladenosine Enrichment Kit (New England Biolabs) following the manufacturer’s protocols.
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit v2 (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, then aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters.
Mapped reads were separated by strands with samtools (version 1.9) and m6A peaks on each strand were called using MACS (version 2) with parameter ‘-nomodel, --keep-dup 5, -g 2.052e9, --tsize 60 -extsize 150’ separately.
Assembly: hg38
Supplementary files format and content: Tab-delimited peak locations together with peak summit, pvalue and qvalue reported by MACS2 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) |
| GSE203580 |
N6-methyladenosine regulates RNA metabolism and neurodegeneration in C9ORF72-ALS/FTD [seq_total_RNA-MeRIP] |
| GSE203581 |
Globally reduced N6-methyladenosine (m6A) in C9ORF72-ALS/FTD dysregulates RNA metabolism and contributes to neurodegeneration |
|
| Relations |
| BioSample |
SAMN28597152 |
| SRA |
SRX15414343 |
