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| Status |
Public on May 22, 2019 |
| Title |
Ctrl_rep1 |
| Sample type |
SRA |
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| Source name |
pro-B cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 4-6 weeks
tissue: bone marrow
cell type: pro-B
genotype: wild type
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Pro-B cells (Lin–B220+CD43+CD24+BP1–IgM–) were isolated from the bone marrow of Chd4fl/flCd79a-Cre or wild-type littermate controls using the Synergy Sorter (iCyt). Pro-B cells were pooled from one to four mice of each genotype. RNA from these cells (~100,000-200,000 total cells per biological replicate) was isolated using the RNeasy Plus Mini kit and RNeasy MinElute kit (Qiagen), with on-column treatment with RNase-free DNaseI, according to manufacturer’s instructions.
mRNA was captured by two rounds of magnetic Oligo-dT beads. Libraries were prepared with 100 ng of total RNA using the KAPA stranded mRNA-seq kit for the Illumina platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Sequence reads of 30 or more nt were mapped to the mm9 (NCBI build 37) assembly of the mouse genome with the STAR RNA-Seq aligner version 2.4.0a using gene annotation data from Ensembl version 67
For each gene in the Ensembl 67 annotation, reads were counted using the HTSeq software version 0.6.0
Statistical comparisons of the gene expression between the cell types were performed with the DESeq2 package version 1.4.5 for the R statistical software version 3.1.0.
Genome_build: mm9
Supplementary_files_format_and_content: gzipped tar ball of tab-separated text file with raw counts for genes.
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| Submission date |
Jul 25, 2016 |
| Last update date |
May 22, 2019 |
| Contact name |
James R Hagman |
| E-mail(s) |
hagmanj@njhealth.org
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| Phone |
3033981398
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| Organization name |
National Jewish Health
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| Department |
Biomedical Research
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| Lab |
Hagman
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| Street address |
1400 Jackson St
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| City |
Denver |
| State/province |
Colorado |
| ZIP/Postal code |
80206 |
| Country |
USA |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE84806 |
Chromodomain Helicase DNA-binding 4 (CHD4) is required for B cell identity and lineage progression |
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| Relations |
| BioSample |
SAMN05439094 |
| SRA |
SRX1975704 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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