|
| Status |
Public on Nov 28, 2019 |
| Title |
293T_Safb1/2_DKO_clone_3 |
| Sample type |
SRA |
| |
|
| Source name |
293T_Safb1/2_DKO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T cell line; DSMZ #ACC635
genotype/variation: Safb1-/-; Safb2-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested, washed once with PBS and total RNA was isolated with the miRNEasy Kit (QIAGEN) according to the manufacturer's recommendation.
Libraries for Illumina sequencing were prepared with the Somagenics RealSeq-AC miRNA library Kit, using 100 ng total RNA as input.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
processed data file:
total reads_293T_all samples.txt
|
| Data processing |
Basecalling by the Illumina Real-Time Analysis (RTA) software
De-multiplexing into sample specific BAM files using Picard tools
Trimming of Sequencing adapter with TrimGalore
Mapping against reference miRNA with HISAT2
Analysis of differential miRNA expression with edgeR
Genome_build: Reference: human miRNAs extracted from the miRBase 22 release
Supplementary_files_format_and_content: tab-delimited text files total reads_Ramos_all samples and total reads_293T_all samples include the number of reads aligned to the respective reference miRNAs; tab-delimited text files Ramos_edgeR_output and 293T_edgeR_output provide logFC, logCPM, F, PValue, FDR and -log10pvalue for the comparison of control vs. Safb1/2 ko cells
|
| |
|
| Submission date |
Nov 27, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Sebastian Herzog |
| E-mail(s) |
Sebastian.Herzog@i-med.ac.at
|
| Organization name |
Medical University of Innsbruck, Biocenter
|
| Department |
Institute of Developmental Immunology
|
| Street address |
Innrain 80-82
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE141098 |
Effects of CRISPR/Cas9-mediated deletion of Safb1 and Safb2 genes on the mature miRNA transcriptome |
|
| Relations |
| BioSample |
SAMN13412077 |
| SRA |
SRX7228347 |
