|
Status |
Public on Dec 24, 2016 |
Title |
MPP1 57 rep1 |
Sample type |
SRA |
|
|
Source name |
Multipotent precursors 1
|
Organism |
Mus musculus |
Characteristics |
marker: CD48-CD150+CD135-CD34+ barcodes: GGACTCCT-AAGGAGTA cell count: 2 well id: G05
|
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 MPP1 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 |
SAMN03700545 |
SRA |
SRX1032232 |