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| Status |
Public on Feb 06, 2017 |
| Title |
RNA-seq cntrl B-ALL [27572] |
| Sample type |
SRA |
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| Source name |
Bone Marrow
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Trp53-/- NrasG12D/+Retroviral-Myc
cell preparation: Short-time culture
cell sorting strategy: whole Bone Marrow
chip antibody: n.a.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described (Parkhomchuk et al. 2009) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000/2500 system with a read length of 50 nucleotides (single-read) or 100/125 nucleotides (paired-end) according to the manufacturer’s guidelines.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Peaks were determined by using the MACS program version 1.3.6.1 (16) with default parameters, a cutoff of a P value of < 10-10 and a genome size of 2,654,911,517 bp (mm9). The identified peaks were then assigned to target genes as described (12). For comparisons of ChIPseq data, we down-sampled all reads before peak calling to the ChIP-seq experiment with the lowest number of aligned reads.
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (19) with the overlap resolution mode set to ‘union’. The datasets were grouped according to cell type and organism and analyzed using the R package DESeq2 version 1.4.1 (20). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. In detail, the following DESeq2 analyses were performed: all mouse pro B cell samples were analyzed together considering the genotype effects (model design formula: “~ genotype”). Mouse tumor cells and mouse wild-type large pre-B cells were also grouped and analyzed in the same manner, as were human tumor cells and human wild-type pre-B cells.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; text tab delim = TPM values in ASCII text format tab delimited
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| Submission date |
Jul 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria Fischer |
| Organization name |
Research Institute of Molecular Pathology
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| Lab |
Busslinger Group
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE84987 |
Molecular role of the PAX5-ETV6 oncoprotein in promoting B cell acute lymphoblastic leukemia |
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| Relations |
| BioSample |
SAMN05464389 |
| SRA |
SRX1989133 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2255578_TPM_27572.txt.gz |
224.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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