|
| Status |
Public on Apr 17, 2019 |
| Title |
HEK293T_ADAT2_CRISPR(3.1) |
| Sample type |
SRA |
| |
|
| Source name |
Human Embryonic Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T
cell type: Human embryonic kidney cell line
transfection: CRISPR/Cas9 plasmid and an RNA guide strand against human ADAT2
adat2 expression: 50%
replicate: 3
lane: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent, ethanol precipitated and resuspended in DEPC-treated water.
RNA libraries were performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB #E7300S) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CRISPR ADAT2(3.1)
28616
WT transfected with a CRISPR/Cas9 plasmid and an RNA guide strand against human ADAT2 that generated a stable heterozygote cell line having only 50% ADAT2 expression Replicate 3 Lane 1.
RNA-seq (size fractionation) - Fragments between 160bp and 220bp were selected.
processed data file: tRNA_gene_counts_hg38_summarizeOverlaps.xls
|
| Data processing |
Solexa Illumina HiSeq 2000 small RNA-Seq data was aligned against the human reference genome hg38 with Bowtie2 version 2.2.2 using local alignment, allowing for 1 mismatch in the first 28 bases and using default options.
Soft clipped bases were removed from the aligned reads with the bamutils utility from the NGSutils software version 0.5.7.
In order to account for the repetitive nature of tRNA types across the genome, all reads (including those that could map to more than one position) were considered. However, reads aligning to two or more different tRNA types were identified with Bowtie2 and removed from the analyses in order to only use those reads aligning unequivocally to multiple copies of the same tRNA type. Finally, tRNA copies with a coverage depth below 10 reads at the anticodon position were also removed from the analysis.
Per replicate counts (pooled lanes) over hg38 tRNAs (Genomic tRNA database, http://gtrnadb.ucsc.edu , January 2016) were obtained with the summarizeOverlaps function from the GenomicAlignments package, using options mode=Union, ignore.strand=FALSE.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tRNA_gene_counts_hg38_summarizeOverlaps.xls: Excel file contains per sample tRNA gene counts obtained with the SummarizeOverlaps function from the GenomicAlignments package.
|
| |
|
| Submission date |
May 24, 2018 |
| Last update date |
Apr 17, 2019 |
| Contact name |
Oscar Reina Garcia |
| E-mail(s) |
oscar.reina@irbbarcelona.org
|
| Organization name |
IRB Barcelona
|
| Department |
Biostatistics and Bioinformatics
|
| Street address |
C/Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE114904 |
Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments |
|
| Relations |
| BioSample |
SAMN09258359 |
| SRA |
SRX4123203 |
