|
| Status |
Public on Dec 14, 2022 |
| Title |
167_RAW_Cuttag_CRISPR_GPS2_KO_H3K9ac_rp2 |
| Sample type |
SRA |
| |
|
| Source name |
RAW 264.7
|
| Organism |
Mus musculus |
| Characteristics |
cell type: RAW 264.7 Macrophage
strain: BALB/c
genotype/variation: GPS2 KO
chip antibody: H3K9ac
chip antibody vendor: Sigma
chip antibody cat.: 06-942
|
| Growth protocol |
WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
CUT&Tag
|
| Data processing |
Library strategy: Cut&Tag
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
|
| |
|
| Submission date |
Dec 14, 2021 |
| Last update date |
Dec 14, 2022 |
| Contact name |
Zhiqiang Huang |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Nanjing University
|
| Department |
Medical School
|
| Street address |
Hankou 22
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210093 |
| Country |
China |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE184884 |
GPS2 sensitizes IL4 pathway via the recruitments of KDM1A |
|
| Relations |
| BioSample |
SAMN24038663 |
| SRA |
SRX13437843 |
