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Sample GSM6176471 Query DataSets for GSM6176471
Status Public on Jun 09, 2023
Title iPSN-Ctrl-4_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 Chuan He
E-mail(s) chuanhe@uchicago.edu
Phone 773-702-5061
Organization name University of Chicago
Department Department of Chemistry
Street address 929 E 57th St., GCIS E319
City Chicago
State/province ILLINOIS
ZIP/Postal code 60637
Country USA
 
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 SAMN28597181
SRA SRX15414442

Supplementary file Size Download File type/resource
GSM6176471_iPSN-Ctrl-4_IP_YTHDF2-RIP_counts.txt.gz 231.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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