|
Status |
Public on Nov 23, 2022 |
Title |
Kasumi-1 cells, FBL knockdown plus empty replicate 2 |
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.
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|
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
shFBL4PCDHrep2
|
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
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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 |
SAMN21593395 |
SRA |
SRX12326480 |