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| Status |
Public on Aug 28, 2024 |
| Title |
Y79,Mock,RNA-seq,rep3 |
| Sample type |
SRA |
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| Source name |
Y79
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Y79
treatment: Mock
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596026). Take 1 µg of total RNA and perform a reverse transcription experiment using HiScript III RT SuperMix for qPCR (Vazyme, R323-01) to obtain cDNA.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-seq library prep kit following manufacturer's protocols. The Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, TD903) was used for CUT&Tag analysis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
RNA sequencing data were mapped to the GRCh38 reference genome using the STAR aligner, and quantified using featureCounts
CUT&Tag data were also mapped to the GRCh38 genome using Chromap, with peak calling performed using MACS2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: BigWig
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| Submission date |
Dec 20, 2023 |
| Last update date |
Aug 28, 2024 |
| Contact name |
yuhua xiao |
| E-mail(s) |
xiaoyh26@mail2.sysu.edu.cn
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| Phone |
18728192414
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| Organization name |
Sun Yat-sen University
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| Department |
zhongshan Ophthalmic center
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| Street address |
jinsui load
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| City |
guangzhou |
| State/province |
guangdong province |
| ZIP/Postal code |
510627 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE251752 |
PHLDA1-PRDM1 mediates the effect of lentiviral vectors on fate-determination of human retinal progenitor cells |
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| Relations |
| BioSample |
SAMN38983837 |
| SRA |
SRX22985233 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7987329_NC-3_L2_346X46_featurecount.txt.gz |
5.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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