|
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).
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|
|
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)
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|
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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 |