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Sample GSM1531751 Query DataSets for GSM1531751
Status Public on Dec 14, 2014
Title pDC_ATAC
Sample type SRA
 
Source name 09_ATAC_pDC_1
Organism Mus musculus
Characteristics cell type: pDC
tissue: Bone marrow
strain: C57BL/6
chip antibody: H3K4me1
Growth protocol Bone marrows were extracted from femora and tibiae of C57BL/6J female mice (6 to 10 weeks old), growth in presence of GM-CSF (for moDC) or Flt3L (for pDC).
Extracted molecule genomic DNA
Extraction protocol Cells were lysed and nuclei were treated with Tn5 transposase enzyme. Nuclei were clean up and treated with Proteinase K.
Tagmenteated DNA was isolated and undergoes two cycles of PCR amplification with indexing Nextra primers
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Description ATAC-seq
Data processing HISEQ split using cassava Y60,I10
alignment using bowtie 1.0.0. command (bowtie -a -m 1 --sam --best --strata -v 2 mm9)
tdf command( igvtools count -w 5 -e 200 )
Genome_build: mm9
 
Submission date Oct 24, 2014
Last update date May 15, 2019
Contact name Ido Amit
E-mail(s) ido.amit@weizmann.ac.il
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
 
Platform ID GPL18480
Series (1)
GSE62703 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (ATAC-Seq)
Relations
BioSample SAMN03142939
SRA SRX742901

Supplementary file Size Download File type/resource
GSM1531751_09_ATAC_pDC_1.tdf 832.3 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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