|
| Status |
Public on Jan 19, 2018 |
| Title |
single fibroblast from donor OA4 (OA4_B7) |
| Sample type |
SRA |
| |
|
| Source name |
fibroblasts from athroplasty
|
| Organism |
Homo sapiens |
| Characteristics |
donor: OA4
disease state: OA
age: 61
Sex: Female
joint: Knee
flow_fsc-a: 143977
flow_fsc-h: 58226
flow_fsc-w: 162053
flow_ssc-a: 27760
flow_ssc-h: 13579
flow_ssc-w: 133979
flow_thy1: 144
flow_cd34: 72
flow_pdpn: 13440
flow_cd31: 32
flow_cd146: 225
flow_live_dead: 238
flow_cdh11: 487
flow_cd45: -1
cd34_protein: -
thy1_protein: -
cdh11_protein: +
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We digested tissues with 4 mg/ml collagenase type 4 (Worthington, NJ), 0.8 mg/ml Dispase II, 0.1 mg/ml DNaseI (Roche) in DMEM at 37°C. After 15 minutes, we collected the supernatant and replaced with fresh enzyme mix. We repeated these procedures every 15 minutes for total 1 hour. We digested tissues with 0.2 mg/ml Liberase TL (Roche), 0.1 mg/ml DNaseI in RPMI at 37°C for 20 minutes to minimize the cleavage of surface markers of lymphocytes during the enzymatic digestion. After lysing red blood cells with ACK-lysing buffer, we stained cells with antibodies, and sorted by FACSAria Fusion (BD) with 100 um nozzle at 20 psi. The cells were stained with antibodies and directly sorted into 5 ul of TCL buffer (QIAGEN) with 1% 2-mercaptoethanol (SIGMA) in 96 well plates.
Smart-Seq2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
singlecell_rnaseq_gene_counts.tsv.gz
singlecell_rnaseq_transcript_counts.tsv.gz
singlecell_rnaseq_gene_tpm.tsv.gz
singlecell_rnaseq_transcript_tpm.tsv.gz
|
| Data processing |
kallisto-0.42.4
Genome_build: Ensembl 83
Supplementary_files_format_and_content: tab-delimited text files with pseudocounts or transcripts per million (TPM) for each transcript or gene reported by kallisto
singlecell_rnaseq_gene_counts.tsv.gz (pseudocounts of each gene)
singlecell_rnaseq_transcript_counts.tsv.gz (pseudocounts of each transcript)
singlecell_rnaseq_gene_tpm.tsv.gz (transcripts per million (TPM) of each gene)
singlecell_rnaseq_transcript_tpm.tsv.gz (transcripts per million (TPM) of each transcript)
|
| |
|
| Submission date |
Jan 19, 2018 |
| Last update date |
Jan 25, 2018 |
| Contact name |
Kamil Slowikowski |
| E-mail(s) |
kslowikowski@mgh.harvard.edu
|
| Organization name |
Massachusetts General Brigham
|
| Lab |
Alexandra-Chloe Villani
|
| Street address |
Mailstop CNY 149-8, 149 13th Street
|
| City |
Charlestown |
| State/province |
Massachusetts |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE109449 |
Single cell RNA-seq analysis of freshly isolated synovial fibroblasts in patients with rheumatoid arthritis or osteoarthritis |
| GSE109450 |
Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis |
|
| Relations |
| BioSample |
SAMN08380513 |
