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Sample GSM956443 Query DataSets for GSM956443
Status Public on Nov 23, 2019
Title sorted_Hardy_fraction_BC_Ikaros_ZnF1-/-
Sample type SRA
Source name sorted proB cells from primary Bone Marrow (BM)
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: Ikaros_ZnF1-/-
tissue: bone marrow (BM)
cell type: sorted primary proB cells
developmental stage: Hardy fraction B+C+C'
Treatment protocol Single cell suspensions were prepared from sorted proB cells from mouse bone marrow (age of mice: 6-7 weeks).
Growth protocol none - primary cells
Extracted molecule total RNA
Extraction protocol Illumina TruSeq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description dF1-BC
polyA mRNA enriched from Total RNA
Data processing Raw data (fastq) was uploaded to the Galaxy website ( 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 ( (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 ( (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)
Submission date Jul 05, 2012
Last update date Nov 24, 2019
Contact name Hilde Schjerven
Organization name UCSF
Department Laboratory Medicine
Street address 513 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
Platform ID GPL13112
Series (1)
GSE39123 Role of Ikaros in Early B-cell Development: Studies of IkZnF1-/- and IkZnF4-/- mutant mice
SRA SRX157751
BioSample SAMN01085888

Supplementary file Size Download File type/resource
GSM956443_dF1_BC.BEDGRAPH.gz 119.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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