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Sample GSM6176515 Query DataSets for GSM6176515
Status Public on Jun 09, 2023
Title MCTX-C9-ALS-3_MeRIP
Sample type SRA
 
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).
 
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 SAMN28597141
SRA SRX15414354

Supplementary file Size Download File type/resource
GSM6176515_MCTX-C9-ALS-3_MeRIP_peaks.narrowPeak.gz 3.0 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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