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| Status |
Public on May 19, 2024 |
| Title |
HUVEC, shCtrl, meRIP-seq [Control1.IP] |
| Sample type |
SRA |
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| Source name |
umbilical cord
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| Organism |
Homo sapiens |
| Characteristics |
tissue: umbilical cord
cell line: HUVEC
genotype: WT
treatment: Normal
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, The integrity of total RNA was assessed using a 2100 Bioanalyzer from Agilent Technologies, while the concentration was determined using a Qubit 2.0 fluorometer with the Qubit RNA assay kit from Invitrogen. For meRIP-seq, RNA was randomly fragmented and incubated overnight with protein A/G beads conjugated to m5C antibodies.
For RNA-seq, sequencing libraries were prepared utilizing the Illumina TruSeq RNA Sample Prep Kit (Illumina, USA), and high-throughput sequencing was performed on an Illumina HiSeq 3000 platform (Illumina, USA). For meRIP-seq, the captured RNA was eluted and extracted using TRIzol reagent. Library construction was performed for both input samples and m5C IP samples. The libraries were assessed using an Agilent 2100 Bioanalyzer (Agilent, USA) and sequenced on a NovaSeq 6000 platform (Illumina, USA). Following quality control and removal of low-quality reads, the clean reads from all libraries were aligned to the reference genome (HG19) using HISAT2 software (v2.0.4).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
HISAT2 software (v2.0.4)
Assembly: Hg 38
Supplementary files format and content: Excexls including differentially expressed genes and differentially methylated mRNA
Library strategy: meRIP-seq
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| Submission date |
May 16, 2024 |
| Last update date |
May 19, 2024 |
| Contact name |
Sipeng Zuo |
| E-mail(s) |
Zsp2019@sjtu.edu.cn
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| Organization name |
Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine
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| Street address |
No. 12, Lane 833, Zhizaoju Road, Huangpu District
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200023 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE267662 |
Histone lactylation-mediated NSUN2 transcriptional activation dictates choroidal neovascularization through promoting AKAP2 mRNA expression [RNA-seq] |
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| Relations |
| BioSample |
SAMN41427275 |
| SRA |
SRX24585315 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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