|
| Status |
Public on Dec 13, 2023 |
| Title |
NB1_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 |
SAMN31989027 |
| SRA |
SRX18464711 |
