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| Status |
Public on Nov 23, 2019 |
| Title |
sorted_Hardy_fraction_BC_Ikaros_ZnF4-/- |
| Sample type |
SRA |
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| Source name |
sorted proB cells from primary Bone Marrow (BM)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Ikaros_ZnF4-/-
tissue: bone marrow (BM)
cell type: sorted primary proB cells
developmental stage: Hardy fraction B+C+C'
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| Treatment protocol |
Single cell suspensions were prepared from sorted proB cells from mouse bone marrow (age of mice: 6-7 weeks).
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| Growth protocol |
none - primary cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina TruSeq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
dF4-BC
polyA mRNA enriched from Total RNA
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| Data processing |
Raw data (fastq) was uploaded to the Galaxy website (http://galaxy.psu.edu/) and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Giardine et al., 2005; Trapnell et al., 2009; Blankenberg et al., 2010a; Blankenberg et al., 2010b; Fujita et al., 2010; Goecks et al., 2010).
Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Relative mRNA expression levels (RPKM) (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).
Filtering and calculation of Relative changes in expression levels between samples were analyzed in excel.
Genome_build: mm9 [the July 2007 annotation of mouse (Mus musculus) genome data]
Supplementary_files_format_and_content: Genome coverage visualization files were created with BEDtools and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Supplementary_files_format_and_content: Attached as supplemental file on the Series record are the unfiltered RPKM values for all annotated Refseq genes (as a Tab delimited .txt file)
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| Submission date |
Jul 05, 2012 |
| Last update date |
Nov 24, 2019 |
| Contact name |
Hilde Schjerven |
| Organization name |
UCSF
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| Department |
Laboratory Medicine
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| Street address |
513 Parnassus Ave
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE39123 |
Role of Ikaros in Early B-cell Development: Studies of IkZnF1-/- and IkZnF4-/- mutant mice |
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| Relations |
| SRA |
SRX157752 |
| BioSample |
SAMN01085889 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM956444_dF4_BC.BEDGRAPH.gz |
124.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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