 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 20, 2023 |
| Title |
HUDEP2_FAM_74aa_adar |
| Sample type |
SRA |
| |
|
| Source name |
HUDEP-2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP-2 cells
genotype: TRE-FAM46C-74aa-ADARcd
treatment: dox 48h
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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
|
| |
|
| Submission date |
Oct 18, 2023 |
| Last update date |
Oct 20, 2023 |
| Contact name |
ke yang |
| E-mail(s) |
yangk1024@gmail.com
|
| Phone |
18810676200
|
| Organization name |
Liangzhu Laboratory, Zhejiang University
|
| Lab |
Nan Liu lab
|
| Street address |
1369 West Wenyi Road, Hangzhou
|
| City |
hangzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
311121 |
| Country |
China |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN37873744 |
| SRA |
SRX22126646 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7847012_FAM_74aa_adar_48h.edit.txt.gz |
81.8 Kb |
(ftp)(http) |
TXT |
| GSM7847012_FAM_74aa_adar_48h_genes.csv.gz |
19.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
