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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 27, 2015 |
| Title |
RNA-seq Pax5+/- ProB no treatment, rep2 |
| Sample type |
SRA |
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| Source name |
Pax5+/- ProB, no treatment
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6J
genotype/variation: Pax5+/-
cell type: ProB
treatment: none
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| Treatment protocol |
See above.
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| Growth protocol |
ProB-cell isolation / culture protocol: For sorting of Pro B cells, CD16/CD32 (FC) -blocked (93, eBioscience) cells were stained with antibodies against lineage markers CD11b/Mac1 (M1/70), Gr1 (RB6-8C5), TER119 (Ter119), CD3 (17A2, BD Pharmingen), CD11c (N418) and NK1.1 (PK136) and further stained with CD19 (ID3), CD45R/B220 (RA3-6B2), CD43 (S7), IgM (RMM-1) and IgD (11-26. eBioscience, San Diego, CA). Cell sorting was performed on a BD FACSAriaTM (BD Biosciences, San Jose, California) using propidium iodide (PI, Invitrogen, Paisly, UK) as viability marker. For expansion, Pro-B cells were cultured on OP9 stromal cells supplemented with 10ng/mL KIT ligand, 10ng/mL Fms-like tyrosine kinase 3 ligand (FLT3L), and 10ng/mL Interleukin-7 in Optimem supplemented with 10% FCS, Beta-mercaptoethanol, HEPES and Penstrep.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq: RNA was extracted with the Qiagen RNeasy Micro Kit.
RNA-Seq not treated: Total RNA was isolated from four Wt CD19+CD43highIgM- and four Pax5+/-Ebf1+/- pro-B samples using RNeasy MicroKit (Qiagen) according to manufacturer’s recommendations, and sent to UCLA Clinical Microarray Core for library preparation where they used Nugen Ovation Ultra Low DR kit and the libraries were run on the Illumina HiSeq 2500.
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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 |
For RNA-Seq samples, data analysis was performed with Arraystar (DNA STAR). The reads were aligned to mouse reference genome (mm9, NCBI 37) and RPKM normalized. Statistical analysis in Arraystar was performed with Student´s t-test with correction for multiple testing (Benjamini Hochberg). A p-value > 0.05 was considered as statistically significant.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files include BED files. All genomic coordinates are relative to the mm9 mouse assembly.
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| Submission date |
May 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Rajesh Somasundaram |
| E-mail(s) |
rajesh.somasundaram19@gmail.com
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| Phone |
0046708890787
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| Organization name |
Linkoping University
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| Department |
Microbiology and Molecular Medicine
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| Lab |
Lab 1, Floor- 13 Dept of Clinical and Experimental Medicine (IKE)
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| Street address |
Dept of Clinical and Experimental Medicine (IKE)
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| City |
Linkoping |
| ZIP/Postal code |
SE-58185 |
| Country |
Sweden |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE69227 |
Combined heterozygous loss of Ebf1 and Pax5 allows for T-lineage conversion of B-cell progenitors |
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| Relations |
| BioSample |
SAMN03734582 |
| SRA |
SRX1038488 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1695681_ProB_505_Pax5het.bed.gz |
7.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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