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Sample GSM1531775 Query DataSets for GSM1531775
Status Public on Dec 14, 2014
Title pDC_4 hours PAM
Sample type SRA
Source name Flt3L derived cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone Marrow
treatment: 4 hour 100ng/ml PAM3CSK (PAM)
Treatment protocol (mentioned in the relevant samples)
Growth protocol Samples 1-40: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). Samples 41-50: cells were isolated from the indicated organ, filtered and stained with the indicated antibodies for FACS sorting
Extracted molecule total RNA
Extraction protocol For RNA extraction, cells were harvested in Qiazol lysis solution (Qiagen), and total RNA was extracted using miRNeasy Mini Kit (Qiagen).
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description polyA+ RNA
Data processing Illumina Casava1.8 software used for basecalling.
alignment: TopHat aligner with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Submission date Oct 24, 2014
Last update date May 15, 2019
Contact name Ido Amit
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)
GSE62704 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (RNA-Seq)
BioSample SAMN03142943
SRA SRX742929

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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