|
| Status |
Public on Oct 15, 2021 |
| Title |
Myocd-LSD1NF_H3K4me2-1 |
| Sample type |
SRA |
| |
|
| Source name |
Aortic SMC
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: Myocd-LSD1NF
cell type: Aortic SMC
cut&tag antibody: Activemotif, H3K4me2, 39141
|
| Growth protocol |
Cell lines were cultured in growth medium (DMEM/F12, Gibco) supplemented with FBS (10%, Corning), L-glutamine (1.6 mM, Gibco) and penicillin-streptomcyin (100 U/ml, Gibco).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA after immunoprecipitation was extracted by CUT&Tag-IT Assay Kit (Active motif) following manufacturer's protocol. 500,000 cells were used for CUT&Tag assay. After binding with Concanavalin A beads, cells were incubated with primary antibody targeting H3K4me2 (Activemotif 39141) or FLAG (Sigma F7425) overnight at 4℃. Samples were then incubated with Guinea Pig anti-Rabbit antibody, CUT&Tag-IT Assembled pA-Tn5 Transposomes. After tagmentation, released DNA was extracted by DNA purification column for library preparation and SPRI Beads clean-up.
DNA library was perpared by illumina Nextera primers provided with CUT&Tag-IT Assay Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
chipseeker_Myocd-LSD1NF_H3K4me2.xlsx
Diffbind_Myocd-LSD1_Myocd-LSD1NF.xlsx
|
| Data processing |
Library strategy: CUT&Tag
CUT&Tag Seq: Paired-end raw reads were aligned to Rn6 using Bowtie2. Tracks were generated by deepTools2 Bamcoverage with normalized counts as bins per million (BPM) and visualized with IGV. Peaks were called using MACS2 callpeak with cut off FDR (q-value) at 0.05. Peaks were annotated by ChIPseeker with rn6.ncbiRefSeq as the annotation source. Differential binding analysis of H3K4m2 enrichment was performed by DiffBind with significant threshold at FDR<0.05.
Genome_build: Rn6
Supplementary_files_format_and_content: bigwig file of each sample
Supplementary_files_format_and_content: Annotated peak files for CUT&Tag seq sample
Supplementary_files_format_and_content: Differential binding peak file comparing Myocd-LSD1 and Myocd-LSD1NF H3K4me2
|
| |
|
| Submission date |
Jun 30, 2021 |
| Last update date |
Oct 15, 2021 |
| Contact name |
Delphine Gomez |
| E-mail(s) |
gomezd@pitt.edu
|
| Phone |
412-383-3269
|
| Organization name |
University of Pittsburgh
|
| Department |
Medicine, division of Cardiology
|
| Lab |
Delphine Gomez Lab
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL19052 |
| Series (2) |
| GSE179217 |
H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [CUT&Tag_H3K4me2_FLAG] |
| GSE179220 |
H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis |
|
| Relations |
| BioSample |
SAMN19971556 |
| SRA |
SRX11318240 |
