|
| Status |
Public on Jun 20, 2017 |
| Title |
Kasumi-1 cell line with shRNA against DDX21 shDDX21 |
| Sample type |
SRA |
| |
|
| Source name |
human leukemia cell line Kasumi-1
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Kasumi-1 cell line with shRNA against DDX21
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Qiagen miRNeasy kit and 500 ng was subject to library preparation using the Illumina Truseq small RNA kit. Molecules with the size of 40-200 nt were purified from a gel before sequencing.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Human AML snoRNA expression
|
| Data processing |
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
CASAVA BclToFastq was used to export fastq files
Illumina adapter sequences were removed using Cutadapt
Reads were mapped using Bowtie2 and further processed to BAM format using samtools
Regions with coverage were called from mapped reads using the bedtools genomeCoverageBed algorithm
Sequences from the extracted regions were compiled to a consensus sequence which was subject to BLAST against a custom small RNA database. Regions with a BLAST hit were further aggregated calculating the mean of the average coverages and further normalized to the total number of mapped reads by the identified hit name.
Genome_build: hg19 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Each processed file contains a column for the identified small nucleolar RNA (snoRNA) elements and the normalized average coverage for the respective sample.
|
| |
|
| Submission date |
Apr 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian Rohde |
| E-mail(s) |
christian.rohde@uni-heidelberg.de
|
| Organization name |
Heidelberg University
|
| Lab |
Molecular Hematology and Oncology
|
| Street address |
Im Neuenheimer Feld 410
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE80523 |
Expression profile of small nucleolar RNA (snoRNA) in acute myeloid leukemia. |
| GSE80602 |
AML1-ETO induces leukemia via C/D box snoRNA/RNPs. |
|
| Relations |
| BioSample |
SAMN04881271 |
| SRA |
SRX1716978 |
