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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 11, 2023 |
| Title |
HepG2_rep1 |
| Sample type |
SRA |
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| Source name |
human HepG2 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
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| Treatment protocol |
Cells were fixed with PBS containing 1% formaldehyde, and then treated with 1/20 volume of 2.5 M glycine.
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| Growth protocol |
GM12878 and K562 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Life Technologies; 15140). IMR-90 cells were grown in DMEM/F12 + Glutamax (Life Technologies; 10565) supplemented with 5 ng/ml fibroblast growth factor-basic (R&D), 1 μg/ml hydrocortisone hemisuccinate, 50 μg/ml ascorbic acid, 5 μg/ml rhInsulin, 2% fetal bovine serum and 100 U/ml penicillin/streptomycin. Human embryonic stem cells (WA01, Line H1) were obtained from Dr. Hongjie Yao laboratory and cultured according to the protocol from WiCell Research Institute. The hESCs were maintained in mTeSR1 medium (Stem Cell Technologies) in feeder-free conditions on hESC qualified Matrigel (BD Biosciences). mTeSR1 media was changed daily and cells were passaged every 6-8 days with 1 ml of ReLeSR (Stem Cell Technologies). hNPC cells were grown in DMEM/F12 + Glutamax (Life Technologies; 10565) supplemented with 20 ng/ml fibroblast growth factor-basic (R&D), 0.5× N-2, 0.5× B-27, and 100 U/ml penicillin/streptomycin. MEF and HepG2 cells were grown in DMEM containing 10% fetal bovine serum plus 100 U/ml penicillin/streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were treated with micrococcal nuclease and proteinase K. Total RNA was extracted with TRIzol LS.
Total RNA was extracted, and rRNA was depleted with specific probes. After fragmentation, the biotin-marked RNA fragments were enriched with streptavidin magnetic beads, and converted into Illumina HiSeq X10 compatible libraries.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
replicates were merged for processing
EP_and_PP.HepG2.network.xls
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| Data processing |
Library strategy: RIC-seq
Illumina bcl2fastq (v2.16) conversion software used for basecalling.
After sequencing, RIC-seq reads were aligned to the human genome using the RICpipe program with minor revisions. Briefly, RIC-seq reads were first mapped to the reference genome (assembly version: hg19 for human and mm9 for mouse) using the STAR software (v2.5.2b). The parameters were set as: --runMode alignReads --genomeDir index --readFilesIn read.fq --outFileNamePrefix prefix --outReadsUnmapped Fastx --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --limitOutSJcollapsed 10000000 --limitIObufferSize 1500000000 --runThreadN 16 --alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterMatchNminOverLread 0.5 --outFilterScoreMinOverLread 0.5. Next, unmapped reads reported by STAR were aligned again to the reference genome by the bwa program (v0.7.17) with the following parameters: bwa mem -k 12 -T 15. Alignments from STAR and bwa were combined and sent to RICpipe for the subsequent analysis to extract chimeric reads.
Enhancer and promoter intervals for each cell are defined as previously described (Cai et al. Nature, 2020, 582(7812): 432-437.), using ChIP-seq data of H3K4me3, H3K4me1 and H3K27ac downloaded from the ENCODE or GEO database.
Using these defined promoter and enhancer regions, we adopted a Monte Carlo simulation strategy to detect significant enhancer-promoter interactions (P < 0.05, unique chimeric reads ≥ 2) as previously described.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: enhancer-promoter and promoter-promoter interaction networks in Excel format
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| Submission date |
Dec 05, 2021 |
| Last update date |
May 11, 2023 |
| Contact name |
Yuanchao Xue |
| E-mail(s) |
ycxue@ibp.ac.cn
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| Organization name |
Chinese Academy of Sciences
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| Department |
Institute of Biophysics
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| Lab |
Key Laboratory of RNA Biology
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| Street address |
Datun Road #15
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE190214 |
Complementary Alu sequences mediate enhancer-promoter selectivity |
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| Relations |
| BioSample |
SAMN23668661 |
| SRA |
SRX13320630 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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