|
Status |
Public on Jun 09, 2023 |
Title |
MCTX-C9-ALS-3_MeRIP |
Sample type |
SRA |
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Source name |
human post-mortem motor cortex
|
Organism |
Homo sapiens |
Characteristics |
tissue: human post-mortem motor cortex genotype: fALS
|
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).
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|
|
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.
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|
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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 |
SAMN28597141 |
SRA |
SRX15414354 |