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Sample GSM3336354 Query DataSets for GSM3336354
Status Public on Oct 07, 2019
Title WT-rep1-D8
Sample type SRA
Source name E14/TG2A mES day8 neural progenitors
Organism Mus musculus
Characteristics cell line: E14/TG2A
genotype/variation: WT
Treatment protocol For Enh9E KO sample, the cells were generated by using CRISPR-Cas9 system to delete the target enhancer region in E14 mouse embryonic stem cells. For mouse neural differentiation assay, we take advantage of the protocol published previously (DOI:10.1016/j.stemcr.2015.09.010).
Growth protocol Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc; stem cells were cultured under regular condition.
Extracted molecule polyA RNA
Extraction protocol RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; genomic DNA from embryo samples were separated and extracted by modified microChIPseq; RNA from in vitro culture bulk cells were extracted by using Trizol and precipitated by isopropanol.
Libraries of RNA samole were generated by using illumina Nextera XT DNA sample preparation kit; libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of bulk RNA seq were prepared by using NEBNext RNAseq library kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description processed data file: Enh9E_KO-merge.dexseq_clean_refseq.gene.txt
Data processing Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files show the bed files for aligned reads. The "merge.dexseq_clean_refseq.gene.all.xls" file include the expression (FPKM) of all the RefSeq genes for eaach sample.
Submission date Aug 16, 2018
Last update date Oct 07, 2019
Contact name Naihe Jing
Organization name shanghai institute of biochemistry and cell biology
Street address Yueyang Road 320
City Shanghai City
ZIP/Postal code 200031
Country China
Platform ID GPL24247
Series (1)
GSE98101 Spatial-temporal epigenetic landscape of mouse gastrula
BioSample SAMN09847941
SRA SRX4563112

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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