|
Status |
Public on Jan 19, 2018 |
Title |
single fibroblast from donor RA9 (RA9_B10) |
Sample type |
SRA |
|
|
Source name |
fibroblasts from athroplasty
|
Organism |
Homo sapiens |
Characteristics |
donor: RA9 disease state: RA age: 67 Sex: Female joint: Elbow flow_fsc-a: 85023 flow_fsc-h: 51852 flow_fsc-w: 107460 flow_ssc-a: 19375 flow_ssc-h: 12748 flow_ssc-w: 99604 flow_thy1: 10255 flow_cd34: 23443 flow_pdpn: 3988 flow_cd31: 14 flow_cd146: 85 flow_live_dead: 92 flow_cdh11: 2020 flow_cd45: -38 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
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|
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)
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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 |
SAMN08380639 |