 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 07, 2023 |
| Title |
HeLa-WT-VACV-tRNA (rep1) |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cells
genotype: WT
infection: WT VACV
fraction: tRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For tRNA-seq, total RNA was extacted with Trizol, deacylated in 50 mM Tris-HCl (pH 9.0) at 37 °C for 45 min and then resolved by 10% polyacrylamide TBE-urea gel (Invitrogen). tRNA (60 to 100 nt) were collected by gel excision and resolved in RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μL SUPERase In) overnight. After ethanol precipitation, tRNA was treated with demethylase (rtStarTM tRNA-optimized First-Strand cDNA Synthesis Kit, ArrayStar) and cleaned up. 1 μg tRNA was used for library construction. For ribo-seq, ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4°C for 1 h. SUPERase inhibitor (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol reagent. RNA was separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and the ribosome protected fractions were excised (25-35 nt).
RNA was dephosphorylated. Poly(A) tailing, 5’ adenylation, adaptor ligation, and library construction were carried out as described in PMID: 36824937.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included. The trimmed reads were aligned to human transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis. TRNA-seq was analyzed following PMID: 33581077.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Apr 19, 2023 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Saori Uematsu |
| E-mail(s) |
su64@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
526 Campus Road, Cornell University
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE230043 |
Human SAMD9 is a Virus-Activatable Anticodon Nuclease Inhibiting Codon-Specific Protein Synthesis |
|
| Relations |
| BioSample |
SAMN34249260 |
| SRA |
SRX20008634 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7184362_Yuanhui_3_tRNA.txt.gz |
730 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
