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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 14, 2012 |
| Title |
RNA-seq pro-B [8275], 2 |
| Sample type |
SRA |
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| Source name |
Pro-B
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| Organism |
Mus musculus |
| Characteristics |
genotype: Rag2(-/-)
extraction method: 4-5 day culture
tissue: Bone Marrow
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
About 5 ng of ChIP-precipitated DNA, DNA excised from DHS sites or cDNA prepared from mRNA was used as starting material for generating single-end or paired-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol. DNA fragments of the following sizes were selected for the different experiments: 150–250 bp for DHS site mapping, 200–350 bp for ChIP-seq and 150–700 bp for RNA-seq. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested at 37 C for 30 min in 57 μl of 1x TE buffer pH 8 with 5 units of uracil-N-glycosylase (UDG; New England Biolabs) as described (Parkhomchuk et al., 2009) followed by PCR amplification. 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/Solexa Genome Analyzer (GA) IIx systems according to the manufacturer’s guidelines. Sequencing of the paired-end libraries (DHS site mapping) yielded a read length of 76 bp for each end of a DNA fragment, whereas a read length of 36 bp was obtained with single- end libaries (ChIP-seq and RNA-seq).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
8275
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| Data processing |
Sequence reads that passed the Illumina quality filtering were considered for alignment. In case of RNA-seq experiments, reads corresponding to mouse ribosomal RNA (BK000964.1) were removed. The remaining reads were aligned against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al., 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard. RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256.
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain all uniquely aligned reads
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| Submission date |
May 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Meinrad Busslinger |
| E-mail(s) |
busslinger@imp.ac.at
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| Phone |
00431-79730
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| Organization name |
Instutute of Molecular Pathology
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| Street address |
Dr. Bohrgasse 7
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE38046 |
The B cell identity factor Pax5 regulates distinct transcriptional programs in early and late B lymphopoiesis |
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| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX148783 |
| BioSample |
SAMN00996708 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM932911_42GNWAAXX_1_20091123a_8275_20100423_bowtie_clean.bed.gz |
9.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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