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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 27, 2015 |
| Title |
DNA for Ebf1 ChIP-seq WT-ProB no treatment |
| Sample type |
SRA |
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| Source name |
WT ProB, no treatment, input
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6J
genotype/variation: WT
cell type: ProB
treatment: none
chip (antibody): 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 |
genomic DNA |
| Extraction protocol |
ChIP-Seq: Chromatin immunoprecipitation using anti-Ebf1 antibody (Vendor: Millipore, cat# ABE1294, lot# Q2399134).
ChIP-Seq: Samples were sent to UCLA Clinical Microarray Core for library preparation. Covaris M220 was used to shear ChIP-DNA. The library was generated using Nugen Ovation Ultra Low DR kit following standard procedures. Libraries were run on the Illumina HiSeq 2500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
DSG+formaldehyde cross-linked.
This Sample represents 2 replicates.
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| Data processing |
For ChIP-Seq samples, reads were aligned to the mm9 genome using default parameter for Bowtie. Aligned read files from ChIP-seq experiments were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, perform motif- and other analyses in the study.
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 |
SAMN03734569 |
| SRA |
SRX1038475 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1695668_Combined_WT_input.bed.gz |
198.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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