|
| Status |
Public on Oct 07, 2019 |
| Title |
Enh9E KO-rep3-D0 |
| Sample type |
SRA |
| |
|
| Source name |
E14/TG2A mES cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14/TG2A
genotype/variation: KO
|
| 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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN09847910 |
| SRA |
SRX4563106 |
