|
| Status |
Public on Jan 30, 2023 |
| Title |
Nkx2.5_V2 |
| Sample type |
SRA |
| |
|
| Source name |
ventricle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ventricle
cell type: cardiomyocytes
genotype: NKX2-5fb
chip antibody: M280 Streptavidin Dynabeads
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Homogenized tissues were crosslinked in fresh 1% formaldehyde/PBS for 30 min, quenched with 500 mM glycine. Crosslinked nuclei were sonicated using a QSonica 700. Sonicated chromatin was centrifuged, and the supernatant used for chromatin immunoprecipitation (ChIP) with Invitrogen M280 Streptavidin DynaBeads (Life Technologies). DNA was RNase A and Proteinase K treated the following day and purified using Qiagen MinElute (cat. 28004) for subsequent NGS library synthesis.
Libraries for bioChIP DNA and corresponding input samples were synthesized using KAPA Hyper Prep library kit (#KK8502). Each library was generated according to manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
vCMs_Nkx2-5_ChIP-seq_rep2
|
| Data processing |
Raw reads were aligned by Bowtie v2.3.4.3 against mm10 reference genome. PCR duplicates were removed.
To generate the wig files, we extended the mapped reads to 200 bp and normalized read counts by computing RPKM (the numbers of reads per kilobase of bin per million of reads).
Genome wide quantile normalization among samples was performed using Danpos2 v3.0.0.
Assembly: mm10
Supplementary files format and content: bigWig files
|
| |
|
| Submission date |
Oct 07, 2022 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Xiaoran Zhang |
| E-mail(s) |
xiaoran.zhang@childrens.harvard.edu
|
| Phone |
8574259855
|
| Organization name |
Boston Children's Hospital
|
| Department |
Cardiology
|
| Lab |
Pu lab
|
| Street address |
14 Perkins Square, Apt 11
|
| City |
Jamaica Plain |
| State/province |
MA |
| ZIP/Postal code |
02130 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE215019 |
BioChIP-seq analysis of atrial and ventricular cardiomyocytes |
| GSE215065 |
Regulation of mouse chamber selective enhancers |
|
| Relations |
| BioSample |
SAMN31207865 |
| SRA |
SRX17827793 |
