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Sample GSM1689305 Query DataSets for GSM1689305
Status Public on Dec 24, 2016
Title HSC 49 rep1 (Technical replicate)
Sample type SRA
 
Source name Hematopoietic stem cells
Organism Mus musculus
Characteristics marker: CD48-CD150+CD135-CD34-
barcodes: GCTACGCT-AAGGAGTA
cell count: 1
well id: G09
Treatment protocol 18 different populations of mouse BM cells were sorted by FACS AriaII (BD Biosciences) from the Yale cell sorter Core Facility.
Growth protocol Bone Marrow cells were isolated from 6-8 weeks C57BL6 mice
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Smart-seq protocol for single-cell RNA-seq and Pan et al. 2013 protocol for bulk RNA-seq
library preparation was conducted using standard Tru-Seq Illumina kits.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description single-cell RNA-seq in HSC biorep1
Data processing Illumina Casava1.8 software used for basecalling.
RNA-seq reads were mapped to the mouse genome (mm9 from UCSC database) by Tophat (v1.3.3) with “–r 100” option
Gene expression values were then calculated by Cufflinks (v1.2.1), using RefSeq genes as reference annotation with “-G” option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RefSeq gene id, gene symbol, chromosome and FPKM value for each sample
 
Submission date May 18, 2015
Last update date May 15, 2019
Contact name Sherman Weissman
E-mail(s) sherman.weissman@yale.edu
Phone 2037372281
Organization name Yale University
Department Genetics
Lab Sherman Weissman
Street address 1 Gilbert street
City New Haven
State/province CT
ZIP/Postal code 06519
Country USA
 
Platform ID GPL17021
Series (1)
GSE68981 Single Cell Transcriptomics Reveals Multi-Dimensional Heterogeneity in Early Hematopoietic Precursors
Relations
BioSample SAMN03700178
SRA SRX1032032

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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