NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6777949 Query DataSets for GSM6777949
Status Public on Dec 13, 2023
Title NB2_inputRNA
Sample type SRA
 
Source name Neuroblastoma
Organism Homo sapiens
Characteristics tissue: Neuroblastoma
antibody: none
spike-in organism: Escherichia coli K-12
rna fraction: Total RNA
Extracted molecule total RNA
Extraction protocol Tumor RNA was extracted from frozen tumor samples using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer’s instructions. Tumor samples were analyzed with Applied biosystems CytoScan HD array (Thermo Fisher Scientific, Waltham, MA, USA) according to the experimental procedure previously described (Caren, Kryh et al. 2010, Fransson, Ostensson et al. 2016). The arrays detect both copy number alterations and allele-specific information at high resolution. For primary data analysis, GDAS software (Thermo Fisher Scientific) was used. Chromosome Analysis Suite (ChAS v.3.3; Thermo Fisher Scientific) was used for the generation of genomic profiles and determination of chromosomal aberration, MYCN amplification and ATRX status.
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit V2 (Pico Input Mammalian) from Takara and single end sequenced (1X 75 bp) on illumina NextSeq 550 platform.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model NextSeq 550
 
Description Total RNA used as reference input for m6A detection compared to m6A-RNA immunoprecipitated sample
featureCounts_matrix_NB.tsv
Data processing Raw Illumina short-reads data obtained from SMARTER-Stranded Total RNA-Seq Kit v2 sequencing was processed using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a minimal length threshold of 20bp. Quality control of Illumina short-reads was performed using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with default parameters (-q 20). Trimmed reads were mapped with HISAT2 v2.2.1 (Kim et al. 2019) preserving strand information (-U –rna-strandness R) using the Telomere-to-Telomere (T2T) human reference genome assembly (T2T-CHM13 v1.1) (Nurk et al. 2022) . The Escherichia coli K12 genome was concatenated to the T2T reference assembly for further spike-in normalization. To control the systematic variation across m6A-RIP experiments, the amount of spiked-in bacterial RNA was estimated by counting the total number of reads uniquely mapping to the E. coli K-12 reference genome using Sambamba v0.7.1 (Tarasov et al. 2015). The E. coli spike-in Bacterial counts were further used to calculate scaling factors for each batch of m6A-RIP-seq samples. Duplicate reads were labeled using MarkDuplicates from Picard v2.23.4 (http://broadinstitute.github.io/picard/). Alignments were downsampled according to calculated spike-in scaling factors using DownsampleSam from Picard (--strategy HighAccuracy). Mapping files were separated by strand after duplicate removal using Sambamba v0.7.1.
Assembly: T2T CHM13 v1.1 (Homo sapiens)
Assembly: U00096.2 (Escherichia coli K-12, substr. MG1655)
Supplementary files format and content: bigwig files for coverage on input RNA and m6A-RIP
 
Submission date Dec 02, 2022
Last update date Dec 13, 2023
Contact name Tanmoy Mondal
E-mail(s) tanmoy.mondal@medkem.gu.se
Organization name University of Gothenburg
Department Department of Clinical Chemistry and Transfusion Medicine
Street address Bruna Stråket 16
City Gothenburg
State/province Västra Götaland
ZIP/Postal code 41345
Country Sweden
 
Platform ID GPL21697
Series (2)
GSE219212 m6A RNA modification of TERRA lncRNA drives R-Loop formation and is required for telomere maintenance in ALT tumors [II]
GSE219213 m6A RNA modification of TERRA lncRNA drives R-Loop formation and is required for telomere maintenance in ALT tumors
Relations
BioSample SAMN31989025
SRA SRX18464713

Supplementary file Size Download File type/resource
GSM6777949_NB2_inputRNA_fwd.bw 58.3 Mb (ftp)(http) BW
GSM6777949_NB2_inputRNA_rev.bw 57.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap