|
| Status |
Public on Sep 21, 2022 |
| Title |
e12.5_cko1_input.fq.gz |
| Sample type |
SRA |
| |
|
| Source name |
Forebrain tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: EedcKO
tissue: forebrain
treatment: untreated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
EED DNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. Other DNA libraries were prepared from CUT&Tag protocol and using standard NovaSeq protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
X-ChIP
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 (v.2.4.1).
MACS2 (v.2.2.7.1) was used to call peaks (-g mm -q 0.01 -f BAM) relative to input sample. MAnorm (v.1.2.0) was then used for quantitative comparison of ChIP-Seq data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: wig files were generated using bamcoverage function of DeepTools (v.3.4.0).
Supplementary_files_format_and_content: tab-delimited text files. Peak annotation was performed using ChIPseeker (v.1.22.1) at gene level and promoter regions was defined as +/- 3000bp of TSS
|
| |
|
| Submission date |
Feb 16, 2022 |
| Last update date |
Sep 21, 2022 |
| Contact name |
Zhang shuangfeng |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Street address |
1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE169401 |
Genome-wide maps of chromatin state in E12.5 forebrain tissues |
| GSE169653 |
PRC2/Eed Downregulates Hedgehog Signaling through Activation of Gli3 Expression in Cortical Neurogenesis |
|
| Relations |
| BioSample |
SAMN25999240 |
| SRA |
SRX14205941 |
