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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 08, 2018 |
| Title |
RNA-seq-FL-ProB-PAX-KO #3 |
| Sample type |
SRA |
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| Source name |
Pax5-/- FL
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL6/J
genotype / variation: Pax5 knock out
cell type: ProB
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| Treatment protocol |
Cultured in Optimem +10% FBS, FL, KL, IL7 on OP9
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| Growth protocol |
[ProB-cell isolation / culture protocol/Facs staining]
Cell culture: Fetal liver cells were purified from wild-type, Ebf1 deficient, or Pax5 deficient fetus, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s recommendations.
Library construction protocol: RNA-Seq Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of single read NextSeq500 sequencing (Illumina, San Diego,CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Analyze-repeats-FL-ProB-WT-EKO-PKO-mm10-count-exons-Condense-genes-with-adjust.txt
Up_PKO_vs_WT.txt
Up_EKO_vs_WT.txt
Down_PKO_vs_WT.txt
Down_EKO_vs_WT.txt
Peak-list-EBF-1-JEM-WT1-peaks-on-genes-sign-UP-wt-vs-EKO.txt
Peak-list-EBF-1-JEM-WT1-peaks-on-genes-sign-down-wt-vs-EKO.txt
Peak-list-Pax-BIO-Peaks-on-genes-sign-up-WT-vs-PKO.txt
Peak-list-Pax-BIO-Peaks-on-Genes-sign-down-WT-vs-PKO.txt
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| Data processing |
RNA-Sequencing and data analysis: Each biological sample was processed and sequenced in triplicate. Libraries were single-end sequenced on a NexSeq500. For analysis of RNA-Seq experiments the reads were aligned to mouse reference genome (mm10 / GRCm38) using TopHat with single read, standard settings. If not indicated, further analyses were performed using the HOMER platform (Heinz et al. 2010). For further analyses we used normalization to 10M mapped reads by the analyzeRepeats.pl command with the option –count exons condeseGenes. For analysis of statistically significance among differently expressed genes, the data was analyzed using analyzeRepeats.pl with the – noadj option followed by the getDiffExpression.pl command using edgeR or DEseq2.
Processed data files format and content: Processed files include txt files of RNA-seq expressionmatrix. All genomic coordinates are relative to mm10 mouse assembly.
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| Submission date |
Dec 06, 2017 |
| Last update date |
Jun 08, 2018 |
| Contact name |
Mikael Sigvardsson |
| E-mail(s) |
mikael.sigvardsson@med.lu.se
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| Organization name |
Lund University
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| Lab |
Sigvardsson
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| Street address |
Sölvegatan 19
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| City |
Lund |
| ZIP/Postal code |
22184 |
| Country |
Sweden |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE92434 |
RNA- and ATAC-seq data of Wt, Ebf1-KO and Pax5-KO FL-ProB-cells. |
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| Relations |
| BioSample |
SAMN08141554 |
| SRA |
SRX3452733 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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