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Status |
Public on Jun 23, 2021 |
Title |
Hepa.ChIAPET_H3K4me3.H8.Dex |
Sample type |
SRA |
|
|
Source name |
Hepatocyte
|
Organism |
Homo sapiens |
Characteristics |
cell type: hiPSC-derived HLCs chip antibody: H3K4me3
|
Treatment protocol |
adipocytes were treated with 1uM dexamethasone for 24h beginning at day 24 for RNA-seq, 6h beginning at day 20 for ChIP-seq, hepatocytes were treated with 1uM dexamethasone for 24h beginning at day 20 for RNA-seq, 6h beginning at day 20 for ChIP-seq, ATAC-seq and ChIA-PET
|
Growth protocol |
hASCs were cultured in DMEM medium. Confluent hASCs were then transferred into adipogenic medium for 14 days. Then, cells were further cultured in maintenance medium another 7 days and 1.5%BSA medium for additional 2 days. hiPSCs were induced differentiation with Definitive Endoderm Kit for 4 days at 30-40% confluence 24 hrs post seeding, then were transferred into RPMI-B27 supplemented with BMP-4 and FGF basic in 5% oxygen/5% CO2 for 5 days, and treated with RPMI-B27 supplemented with recombinant human HGF in 5% oxygen/5% CO2 for 5 days, and were treated with HCM Hepatocyte Culture Medium without EGF and hydrocortisone and supplemented with recombinant human oncostatin M for 5 days in ambient oxygen/5% CO2.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Total RNA was extracted by using Qiagen RNeasey Mini kit. DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier. Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit. Transposed fragments were subjected to library preparation following manufacturer protocol The H3K4me3 in-situ ChIA-PET was performed according to the previously described protocol (Li et al., 2017) RNA libraries were prepared for sequencing by Novogene (CA). ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina. ATAC-seq libraries were sequenced using paired-end, dual-index sequencing on a NextSeq 500 instrument The H3K4me3 in-situ ChIA-PET was performed according to the previously described protocol (Li et al., 2017)
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Library strategy |
ChIA-PET |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
HiSeq X Ten |
|
|
Description |
The bridge linker sequence CGCGATATCTTATCTGACT
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Data processing |
RNA-seq reads were trimmed using fastp v0.19.5 to remove reads with low quality, too short, or too many N. Trimmed reads were then aligned to human reference genome (hg38) using Hisat2 v2.1 with default parameters. Only unique mapped reads extracted by SAMtools v1.9 were considered for downstream analyses. Quantification of gene annotated in GRCh38 v94 from Ensembl database was estimated using StringTie v1.3.4 ChIP-seq raw reads were trimmed using fastp v0.19.5. Trimmed reads were then aligned to human reference genome (hg38) using Bowtie2 v2.3.0 with default parameters. SAMtools v1.9 was used to extract unique mapped reads and remove duplicated reads. Biological replicates from the same individual were pooled together following by peak calling and de novo motif analyses using HOMER v4.9 with default parameters ATAC-seq raw reads were trimmed using fastp v0.19.5. Next, trimmed reads were aligned to human reference genome (hg38) using Bowtie2 v2.3.0 with parameter --very-sensitive. Reads mapped to mitochondria were ignored. SAMtools v1.9 was applied to extract unique mapped reads and remove duplicated reads. Peak calling was performed using Genrich (https://github.com/jsh58/Genrich#contact) ChIA-PET paired-end reads were first removed bridge linker and split into 3 category tags: none-linker containing tags, one-end tags and pair-end tags (PETs). Tags longer than 18 bp were used to mapped to human genome (hg38) by Burrows–Wheeler alignment (BWA) (ref). Duplicated PETs are filtered and uniquely non-redundant PETs were classified into inter-chromosomal PETs, intra-chromosomal PETs (two tags distance >=8 kb) and self-ligated PETs (two tags distance <8 kb). Multiple intra-chromosomal PETs whose respective ends were within 1 kb were then clustered together. PET count of each PET cluster represents the interaction strength. Loops with PETs ≥3 were considered for downstream analysis Genome_build: hg38 Supplementary_files_format_and_content: Normalized abundance measurement was generated using StringTie.Expression profile were extracted using perl script; hic files were generated by ChIAPIPE
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Submission date |
Dec 11, 2020 |
Last update date |
Jun 23, 2021 |
Contact name |
Chunjie Jiang |
E-mail(s) |
chunjie.jiang917@outlook.com
|
Phone |
2153164211
|
Organization name |
University of Pennsylvania
|
Department |
Institute for Diabetes, Obesity, and Metabolism
|
Lab |
Mitchell A. Lazar
|
Street address |
3400 Civic Center Boulevard
|
City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19104 |
Country |
USA |
|
|
Platform ID |
GPL20795 |
Series (1) |
GSE163061 |
Individual-specific functional epigenomics reveals genetic determinants of adverse metabolic effects of glucocorticoids |
|
Relations |
BioSample |
SAMN17059726 |
SRA |
SRX9674372 |