|
| Status |
Public on Dec 29, 2023 |
| Title |
P90_CUTNTAG_heaEC_P30Tam_Sox9_OE_r3 |
| Sample type |
SRA |
| |
|
| Source name |
Cardiac ECs
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cardiac ECs
cell line: 3 M
cell type: Cardiac ECs
genotype: Sox9EC-OE
treatment: 1 Month post Tamoxifen
antibody: Millipore, AB5535
|
| Treatment protocol |
animals were injected with Tamoxifen for 5 consecutive days and rested for 1 M before EC isolation
|
| Growth protocol |
Adult mice in mixed cohorts based on sex animals were bred (approximately 5-7 weeks of age) were injected i.p. with Tamoxifen at a dosage of 25 mg/kg×d for 5 consecutive days. With regard to the animal study where endothelial SOX9 ablation was done in pre-existing disease, the Tamoxifen injection was administered on 5 consecutive days following the 10th day after surgery. Cre-/- littermates served as controls and received Tamoxifen in equivalent frequency and dosage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cardiac EC were isolated based on MACS-magnetic MicroBeads technology from Miltenyi Biotec and FACS sorted for CD146 for a 80-90% purity.
Isolated cardiac EC were used for cut and Tag standard protocols. Briefly, cells were incubated with SOX9 primary antibody (Millipore, AB5535), followed by a secondary antibody conjugated to the protein A-Tn5 fusion protein. The transposed DNA was purified and amplified by PCR, and the resulting library was sequenced at 100bp paired end.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Raw fastq files were trimmed with Ngmerge (defaut settings).
Trimmed reads were mapped with Bowtie2 (bowtie2 -p 16 --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700)
sam files were converted to bam files using samtools view (default settings)
Bam files were merged with bamtools merge (v. 2.5.1) (default settings)
bamCoverage was used to create the bw files (-p max -bs 20 --smoothLength 40 --normalizeUsing RPKM )
Assembly: mm10 from UCSC genome
Supplementary files format and content: BigWig files
|
| |
|
| Submission date |
Dec 26, 2023 |
| Last update date |
Dec 29, 2023 |
| Contact name |
Joerg Heineke |
| E-mail(s) |
Joerg.Heineke@medma.uni-heidelberg.de
|
| Organization name |
Medizinische Fakultät Mannheim
|
| Department |
– Department of Cardiovascular Research (HKF)
|
| Street address |
Ludolf-Krehl-Str. 7-11
|
| City |
Mannheim |
| State/province |
Baden Wuttemberg |
| ZIP/Postal code |
68167 |
| Country |
Germany |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE198041 |
Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9 |
| GSE252082 |
Endothelial cells drive organ fibrosis and dysfunction by inducing the transcription factor SOX9 (CUTNTAG) |
|
| Relations |
| BioSample |
SAMN39128066 |
| SRA |
SRX23029064 |
