|
| Status |
Public on Nov 01, 2022 |
| Title |
DDX6-AID 0h-1 |
| 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: Before IAA treatment (IAA0h)
|
| 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 |
SAMN27478683 |
| SRA |
SRX14786909 |
