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Sample GSM6034889 Query DataSets for GSM6034889
Status Public on Nov 01, 2022
Title DDX6-AID 3h-2
Sample type SRA
 
Source name D6AdP cell line
Organism Mus musculus
Characteristics cell line: D6AdP cell line
cell type: ES cell
genotype: DDX6-AID-mCherry/DDX6-AID-mCherry; DCP1a-EGFP/+; OsTIR1-FLAG Tg
treatment: 3hr after IAA treatment (IAA3hr)
Treatment protocol 500 nM 5-Ph-indole-3-acetic acid (IAA) was added in the maintenance medium.
Growth protocol The D6AdP cell line (ES cells) were maintained in ES medium (Yagi et al., 1993) supplied with PD0325901 and CHIR99021, and Leukemia inhibiting factor in a 37-degree humid incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol The 2 x 105 ES cells were passaged on the Mitomycin-C treated fibroblast feeder cells in each well of the 24 well plate, and treated with IAA for 0, 3, 6 hr.
Total RNA was isolated using the RNAiso Plus (Takara), treated with DNase I (Invitrogen). The quality of collected RNAs was examined using Bioanalyzer (Agilent), and RINs of them were confirmed to be over 8.0. cDNA libraries were prepared from polyA RNAs originally from 500-1000 ng of total RNAs. RNA libraries for RNA-seq were prepared using the Truseq Stranded mRNA Library Prep kit (Illumina) following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Low-quality sequences, adapters were trimmed or removed using fastp (version 0.22.0).
Trimmed reads were were aligned to the Mus musculus genome supported with gene annotation file (the Ensembl GRCm38) using Hisat2 (version 2.2.1)
Only the read counts that uniquely aligned to the exon regions were summarised at the gene level by featureCounts (version 2.0.3).
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each Sample
 
Submission date Apr 08, 2022
Last update date Nov 01, 2022
Contact name Yumiko Saga
E-mail(s) ysaga@nig.ac.jp
Organization name National Institute of Genetics
Department Department of Gene Function and Phenomics
Lab Mammalian Development
Street address 1111 Yata
City Mishima
State/province Shizuoka
ZIP/Postal code 411-8540
Country Japan
 
Platform ID GPL17021
Series (1)
GSE200483 RNA-seq on ES cells where DDX6 was knocked down by the AID method
Relations
BioSample SAMN27478679
SRA SRX14786913

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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