|
| Status |
Public on Nov 23, 2022 |
| Title |
Kasumi-1 cells, FBL knockdown plus empty replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1
cell type: AML cell
treatment: 100 ng/ml doxycycline
expression: FBL knockdown
re-expression: empty reexpression
|
| Growth protocol |
The cells were cultured in RPMI1640 with 20% FBS and 1% Penicillin-Streptomycin. For FBL knockdown, the cells were induced with 100 ng/ml doxycycline.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with mirRNeasy mini kit (NEB).
100 ng total RNA was fragmented by alkaline hydrolysis at 95°C for 12 min. to achieve a fragment length of about 30 nucleotides. Libraries were prepared using the NEBNext® Small RNA library prep kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
shFBL4PCDHrep1
|
| Data processing |
Library strategy: Ribometh-Seq
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina NextSeq 500 or HiScanSQ respectively
Adapter sequences were removed using Cutadapt with a minimum length of 15 nt
Reads were mapped using Bowtie2 to a reference sequence file containing rDNA sequences of U18, U28 and U5.8S and splicosomal RNA U1, U12, U2, U4, U5 and U6
For each position the number of 5’-read ends was counted.
2’O-methyation was calculated as scoreC based on 5’-end frequencies as described before by Birkedal et al., 2015
Genome_build: Annotation of modification sites as well as rRNA & snRNA sequence were downloaded from https://www-snorna.biotoul.fr. Furthermore we considered novel sites reported by Krogh 2016, Jorjani 2016 and Sharma 2017
Supplementary_files_format_and_content: RiboMethSeq_scoreC.txt contains calculated scoreC for annotated modification sites: subunit TAB pos TAB annotation TAB sample_scoreC
|
| |
|
| Submission date |
Sep 24, 2021 |
| Last update date |
Nov 23, 2022 |
| 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 |
GPL18573 |
| Series (2) |
| GSE184724 |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia [ribomethseq_FBL_KD] |
| GSE184728 |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN21593394 |
| SRA |
SRX12326479 |
