|
| Status |
Public on Feb 26, 2019 |
| Title |
mSC_LN_15 |
| Sample type |
SRA |
| |
|
| Source name |
lymph node
|
| Organism |
Mus musculus |
| Characteristics |
library name: TRA00053369
strain: B6
tissue: lymph node
Sex: male
age (weeks): 8
total number of reads: 17293
number of mapped reads: 14934
number of unique reads (umi): 3332
|
| Growth protocol |
Live cells were sorted by flow cytometry from the lymph node, visceral adipose tissue and muscle after cardiotoxin injury (mouse).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lymph nodes were mechanically dissociated. Visceral adipose tissue and muscles were digested with collagenase/dispase to single cell suspensions. mSCs were sorted by flow cytometry as CD45- CD31- Sca-1+ PDGFRα+ PDPN+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
singlecellRNAseq_mSCs_counts.txt
|
| Data processing |
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts
|
| |
|
| Submission date |
Feb 25, 2019 |
| Last update date |
Feb 26, 2019 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
|
| Phone |
617-432-7747
|
| Organization name |
Harvard Medical School
|
| Department |
Microbiology and Immunobiology
|
| Lab |
CBDM
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE127005 |
Single cell transcriptomic analysis (InDrops) of mouse mesenchymal stromal cells (mSCs or FAPs, fibro-adipogenic progenitors) isolated from lymph node, muscle and visceral adipose tissue |
|
| Relations |
| BioSample |
SAMN10998268 |
| SRA |
SRX5418231 |
