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Sample GSM2410950 Query DataSets for GSM2410950
Status Public on Mar 22, 2017
Title P20_XY_Meioc_wild_type_YTHDC2-RIP-seq_2
Sample type SRA
 
Source name postnatal testis
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: testis
Stage: P20
genotype: wild-type
preclearing: yes
rip antibody: anti-YTHDC2 (Santa Cruz Biotechnology sc-249370)
Extracted molecule total RNA
Extraction protocol For RIP-seq experiments, RNA was precleared with Dynabeads (ThermoFisher Scientific), immunoprecipitated, and isolated via phenol/chloroform extraction.
For RIP-seq experiments, Clontech SMARTer Stranded RNA-Seq Kit with rRNA depeletion was used accorindg to the manufacturer's recommendations.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description YTHDC2-RIP_sample_2
Data processing Sequenced reads were mapped to mm10 using Tophat with parameter -g1
FPKMs were calculated using Cufflinks
For RIP-seq data, counts were obtained from HTSeq and normalized via DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks output, counts from HTSeq, or normalized counts from DESeq2
 
Submission date Nov 30, 2016
Last update date Apr 08, 2024
Contact name Maria M. Mikedis
E-mail(s) maria.mikedis@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Street address 240 Albert Sabin Way
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL16417
Series (2)
GSE90702 Identification of the embryonic germ cell Meioc-/- transcriptome, MEIOC targets in postnatal testis, and YTHDC2 targets in postnatal testis in mouse
GSE96921 Identification of YTHDC2 targets in mouse postnatal testis
Relations
BioSample SAMN06076934
SRA SRX2694313

Supplementary file Size Download File type/resource
GSM2410950_MM135-1a_DESeq2_normalized.counts.txt.gz 121.4 Kb (ftp)(http) TXT
GSM2410950_MM135-1a_HTSeq_counts.txt.gz 88.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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