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Sample GSM3505725 Query DataSets for GSM3505725
Status Public on Apr 29, 2019
Title CHD4_cKO_1 [Chd4_rep1237]
Sample type SRA
 
Source name CHD4_cKO_pro-B cells
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-)
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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)
 
Submission date Dec 07, 2018
Last update date Apr 29, 2019
Contact name James R Hagman
E-mail(s) hagmanj@njhealth.org
Phone 3033981398
Organization name National Jewish Health
Department Biomedical Research
Lab Hagman
Street address 1400 Jackson St
City Denver
State/province Colorado
ZIP/Postal code 80206
Country USA
 
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
Relations
BioSample SAMN10534236
SRA SRX5122637

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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