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Sample GSM5596402 Query DataSets for GSM5596402
Status Public on Nov 23, 2022
Title Kasumi-1 cells, Control 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: Ctrl 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 shLUCPCDHrep2
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 SAMN21593402
SRA SRX12326488

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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