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Sample GSM1433480 Query DataSets for GSM1433480
Status Public on Sep 30, 2015
Title young_C57BL6_STHSC_125
Sample type SRA
 
Source name hematopoietic stem and progenitor cells
Organism Mus musculus
Characteristics strain: C57BL/6
age: 2-3 months old
cell type: short term hematopoietic stem cell
Growth protocol cells were profiled immediately
Extracted molecule total RNA
Extraction protocol for single cells - direct lysis; for populations we used PrepEase (Affymetrix) according to manufacturers protocol.
cDNA from each sample was prepared using the SMARTer cDNA synthesis (Clontech). RNA libraries were prepared for sequencing using Nextera XT (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description young_ST_HSC_125
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx
Data processing Paired-end 25bp reads were mapped to the UCSC mouse transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters. TPM values as defined by RSEM were added a value of 1 (to avoid zeros) and then log2-transformed.
We filtered out cells in which less than 2500 UCSC genes were detected above a log2(TPM+1) threshold of 2. We excluded genes whose log2(TPM+1) was lower than 4 in the aggregared data for each of the 6 populations, and those UCSC genes that were not associated with a HUGO gene Symbol, leaving 7823 genes for the final dataset.
Genome_build: mm9
Supplementary_files_format_and_content: GEO_HSC_single_data.xlsx is an Excel sheet that contain the log-transformed expression levels, log2(TMP+1) of 8422 mouse transcripts in 1429 single cells and in six population averages, including young and old LT-HSCs, ST-HSCs and MPPs. The first row contains cell ID (a unique index for each single cell) or "pop" for the population averages. The second row indicates the type of population (age and cell type) that the cell (or population average) belongs to. The first and second columns include gene symbols and UCSC transcript names, respectively. (The processed data file only represents samples that were of sufficient quality to analyze)
 
Submission date Jul 10, 2014
Last update date May 15, 2019
Contact name Monika Sylwia Kowalczyk
Organization name Broad Institute
Lab Regev Lab
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL13112
Series (1)
GSE59114 Single cell RNA_Seq in aging of hematopoietic stem and progenitor cells
Relations
BioSample SAMN02907108
SRA SRX649685

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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