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GEO help: Mouse over screen elements for information. |
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Status |
Public on Apr 29, 2019 |
Title |
CHD4_cKO_1 [Chd4_rep1237] |
Sample type |
SRA |
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Source name |
CHD4_cKO_pro-B cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 age: 4-6 weeks genotype/variation: Chd4 conditional knockout (Chd4fl/flCd79a-CreTg/+) tissue: bone marrow cell type: Pro-B cells (Lin-CD19+c-Kit+IgM-IgD-CD25-)
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Extracted molecule |
polyA RNA |
Extraction protocol |
Pro-B cells (Lin–CD19+c-Kit+IgM–IgD–CD25–) were isolated from the bone marrow of Chd4fl/flCd79a-CreTg/+ or wild-type littermate controls using the Synergy Sorter (iCyt). RNA from these cells (~100,000-200,000 total cells per biological replicate) was isolated using the RNeasy Micro kit (Qiagen), with on-column treatment with RNase-free DNaseI, according to manufacturer’s instructions. RNA analysis, cDNA synthesis and library preparation were performed by the Genomics Core in the Center for Genes, Environment and Health at National Jewish Health. RNA quality was assessed using the Qubit RNA assay (Life Technologies) and Bioanalyzer using the Nano RNA kit (Agilent). mRNA was captured by two rounds of magnetic Oligo-dT beads. Libraries were prepared with 50 ng of total RNA using the KAPA stranded mRNA-seq kit for the Illumina platform. Library quality was assessed using the QubitÒ DNA assay and High Sensitivity Bioanalyzer DNA (Agilent).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
Raw sequence data was demultiplexed and FASTQ files were generated using the Illumina bcl2fastq converter (version 2.17). Nextera TruSight adapters were trimmed with skewer (version 0.2.2), which by default removes reads with a remaining length of less than 18 nt. Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the mm9 (NCBI build 37) assembly of the mouse genome using gene using gene annotations from Ensembl version 67 (http://may2012.archive.ensembl.org/). Reads mapping to each gene of the Ensembl 67 annotation were counted with the featureCounts program from the Subread software package (v1.5.2). Genome_build: mm9 Supplementary_files_format_and_content: counts per gene (Ensembl 67 mouse annotation) for each sample (gzipped output from featureCounts program)
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Submission date |
Dec 07, 2018 |
Last update date |
Apr 29, 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 |
GPL17021 |
Series (2) |
GSE123502 |
CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis [RNA-seq] |
GSE123504 |
CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis |
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Relations |
BioSample |
SAMN10534236 |
SRA |
SRX5122637 |
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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