|
| Status |
Public on Jan 01, 2022 |
| Title |
WT_pCREB |
| Sample type |
SRA |
| |
|
| Source name |
freshly isolated DBA positive cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
chip antibody: Cell Signaling Technology, #9198
tissue: kidney
cell type: Dolichos biflorus lectin (DBA) positive cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq. Cells were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (200-500 bp) with Sonicator. Immunoprecipitation was performed with indicated antibodies. After elution and reversal cross-linking, DNA was purified for library preparation. For CUT&RUN. Cells were permeabilized with digitonin. DNA were cleaved in situ using a protein A-micrococcal nuclease fusion recruited by an antibody to chromatin associated protein. Then DNA was purified for library preparation.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: CUT&RUN
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Bigwig
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jan 01, 2022 |
| Contact name |
Zhiheng Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Tianjin Medical University
|
| Department |
Tianjin Research Center for Basic Medical Science
|
| Lab |
Gene Expression Laboratory
|
| Street address |
No.22 Qixiangtai Road
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE165416 |
Integrative Low-input Transcriptomic and Cistromic Analyses Identify CREB Target Genes in Cystic Epithelial Cells [CUT&RUN, ChIP-Seq] |
| GSE165418 |
Integrative Low-input Transcriptomic and Cistromic Analyses Identify CREB Target Genes in Cystic Epithelial Cells |
|
| Relations |
| BioSample |
SAMN17527579 |
| SRA |
SRX9930984 |
