|
| Status |
Public on Feb 28, 2024 |
| Title |
WT ES RNA-seq replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
timepoint: Day0 ESC
|
| Growth protocol |
ES cells were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in ES culture medium with 15% fetal bovine serum (Life Technologies) and antibiotics. ES cell–derived neural progenitor cells were generated by re-plating d 8 and d 14 neural differentiation cultures on low attachment dish in Neural differential medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ES and Neural progenitor cells were lysed with ISOGEN (Nippon gene, 311-02501). RNA were purified with the use of PureLink RNA Mini Kit (Invitrogen). NEBNext Library Quant Kit for Illumina (NEB, E7630L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA_Seq_TPM.txt
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.2.0.
Read counting was performed with the use of featureCounts.
Assembly: mm10
Supplementary files format and content: Counts per transcript
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 v2.4.5
PCR duprication was removed with Picard and bigwig files were generated with bamCoverage (deeptools v3.5.1)
S3norm was used for data normalization and peakcall was conducted using MACS2 bdgpeakcall with parameters -c 4 -l 400.
Assembly: mm10
Supplementary files format and content: BigWig files for Genome Browser
|
| |
|
| Submission date |
Mar 17, 2023 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Taichi Shiraishi |
| E-mail(s) |
taichii0328@gmail.com
|
| Phone |
092-642-6820
|
| Organization name |
Kyushu university
|
| Department |
Medical institute of bioregulation
|
| Lab |
Molecular and cellular biology
|
| Street address |
1-1-3 Maidashi Higashiku Fukuoka
|
| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE227579 |
The complex etiology of autism spectrum disorder due to missense mutations of CHD8 |
|
| Relations |
| BioSample |
SAMN33798811 |
| SRA |
SRX19703433 |
