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Sample GSM1464971 Query DataSets for GSM1464971
Status Public on Aug 08, 2014
Title CLP
Sample type SRA
 
Source name Common Lymphoid Progenitor (CLP)
Organism Mus musculus
Characteristics strain: C57BL/6
organ: Bone Marrow
selection marker: Lin-, ckit+, Flk2+, Il7R+
treatment: none
cell type: Common Lymphoid Progenitor (CLP)
Treatment protocol Samples were extracted from unrteated, C57BL/6 female wild-type mice.
Growth protocol 12 to 15 weeks-old mice housed at the Weizmann Institute animal facility
Extracted molecule polyA RNA
Extraction protocol Each mouse was euthanized and either leg bones or spleen, or both, removed, homogenized to single cell suspension, red cells removed by selective lysis.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Sample 4
3' RNA-seq for digital gene expression quantitation
Data processing single end protocol ( some samples used read2 to read molecule barcodes only)
Illumina Casava1.8 software used for basecalling.
alignment: bowtie2 with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
Quantifying RNA expression in genes: analyzeRNA.pl rna mm9 -d <tag directory> -norm 1e7 (HOMER)
Genome_build: mm9
Supplementary_files_format_and_content: 1256271tableS2.txt is a tab-delimited expression matrix that includes mRNA molecule count values for each Sample
 
Submission date Aug 05, 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 (2)
GSE60101 Chromatin state dynamics during blood formation (RNA-Seq)
GSE60103 Chromatin state dynamics during blood formation
Relations
Reanalyzed by GSE80797
BioSample SAMN02952063
SRA SRX669485

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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