|
| Status |
Public on Jul 03, 2019 |
| Title |
ChIP-seq-H3K4me3_III-3-MT |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-CMs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-CMs
day post-differentiation: day 40
genotype/variation: LMNA WT/MT
chip antibody: H3K4me3 (Active Motif 39159)
|
| Treatment protocol |
iPSCs were grown to 90% confluence and subsequently differentiated into beating cardiomyocytes, using a small-molecule-based monolayer method described previously. Ten days after cardiac differentiation, iPSC-CM monolayers were purified using RPMI-1640 without glucose (Life Technologies) with B27 supplement (Life Technologies). Non-glucose culture medium was changed every 2 days. After 5 days, iPSC-CMs were reseeded onto Matrigel-coated plates in a culture medium containing glucose.
|
| Growth protocol |
iPSC lines were maintained in chemically defined medium Essential 8 (E8 medium) (Life Technologies) on Matrigel-coated (BD Bioscience, San Jose, CA) plates at 37°C with 5% (vol/vol) CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and LMNA-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using The Ion Proton™ System protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Parental line III-3
processed data file: H3K4_PT3MT.paired.PE2SE.nodup.tagAlign_x_Input_2_R1.paired.PE2SE.nodup.tagAlign.fc.signal.bw
|
| Data processing |
AQUAS pipeline from the Kundaje lab at Stanford University (https://github.com/kundajelab/chip-seq-pipeline2).
Duplicate reads were removed: MarkDuplicates from Picard Tools (v2.17.3).
LMNA data were analyzed: Enriched Domain Detector (v1.0) with an 11 Kb bin size, gap penalty of 5, and FDR significance threshold of 0.05.
LAD gain, loss, and intersection were found: bedtools (v2.27.1).
Genome_build: human reference genome hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig and bed
|
| |
|
| Submission date |
Aug 21, 2018 |
| Last update date |
Jul 03, 2019 |
| Contact name |
Lei Tian |
| E-mail(s) |
[email protected]
|
| Phone |
6502388262
|
| Organization name |
Stanford's Postdoctoral Scholar programs
|
| Street address |
1215 Welch Rd
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE118884 |
Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy [ChIP-seq] |
| GSE118885 |
Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy |
|
| Relations |
| BioSample |
SAMN09873866 |
| SRA |
SRX4590707 |
