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Sample GSM7103348 Query DataSets for GSM7103348
Status Public on Feb 28, 2024
Title CHD8+/- ES RNA-seq replicate 1
Sample type SRA
 
Source name Embryonic stem cell
Organism Mus musculus
Characteristics genotype: CHD8 +/-
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 SAMN33798809
SRA SRX19703435

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

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