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| Status |
Public on Oct 20, 2023 |
| Title |
HUDEP2_GFP_7aa_adar |
| Sample type |
SRA |
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| Source name |
HUDEP-2 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP-2 cells
genotype: TRE-GFP-7aa-ADARcd
treatment: dox 48h
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol. 1ug of total RNA was used for the construction of sequencing libraries.
RNA library for RNA-seq were prepared using RNA Library Prep Kit for Illumina.
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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 |
The RNA-seq data reads were aligned to the grch38_tran index using Hisat2 v2.2.1 to generate a SAM file.
The SAM files were then processed using samtools v1.18 and converted into sorted BAM files.
Duplications were eliminated using picard v2.27.1 .
Variant calling was performed using bcftools v1.5 and retained mutations from A to G in forward-strand transcripts and T to C in reverse-strand transcripts for ADAR, or from C to T in forward-strand transcripts and G to A in reverse-strand transcripts for APOBEC1.
The significant editing sites were identified by comparing them with GFP-ADAR/APOBEC1 using Fisher's exact test, with a p-value less than 0.05.
The results of different linker lengths were merged, and the target genes were identified using map_snp_to_gene from the snpsettest package v0.1.1 .
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes all A-G/C-T sites, containing chr, position, ref number, alt number; csv file includes target genes
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| Submission date |
Oct 18, 2023 |
| Last update date |
Oct 20, 2023 |
| Contact name |
ke yang |
| E-mail(s) |
yangk1024@gmail.com
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| Phone |
18810676200
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| Organization name |
Liangzhu Laboratory, Zhejiang University
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| Lab |
Nan Liu lab
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| Street address |
1369 West Wenyi Road, Hangzhou
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| City |
hangzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
311121 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE245692 |
The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis [ADAR_APOBEC] |
| GSE245697 |
The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis |
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| Relations |
| BioSample |
SAMN37873748 |
| SRA |
SRX22126642 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7847008_GFP_7aa_adar_48h.edit.txt.gz |
94.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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