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| Status |
Public on Jul 10, 2020 |
| Title |
Plate2_Well_E5, AF, ACFs |
| Sample type |
SRA |
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| Source name |
cardiac right atria
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| Organism |
Homo sapiens |
| Characteristics |
cell type: primary atrial fibroblasts
cell culture: No
condition: AF
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| Treatment protocol |
Cells were initially cultured in FBM-3 media (#CC-3131, Lonza, USA) containing 10% FBS and a supplement pack (#CC-4525, Lonza, USA); then starved for ~16 hours and treated with CT in serum-free media for 24 hours.
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| Growth protocol |
Cells were cultured in FBM-3 media (#CC-3131, Lonza, USA) containing 10% FBS and a supplement pack (#CC-4525, Lonza, USA)
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| Extracted molecule |
total RNA |
| Extraction protocol |
On the morning of the experiment, cells were quickly trypsinised, resuspended in ice-cold PBS containing 3% BSA, stained with DAPI and only viable singlets were sorted on a BD FACS Aria Fusion III sorter into 96-well plates containing 4ul SMART-seq2 lysis buffer; cells were kept on ice through the whole procedure. The released RNA was converted to cDNA and then sequence ready libraries essentially as described (https://www.nature.com/articles/nprot. 2014.006), with minor modifications. ThermoFisher Superscript II reverse transcriptase and Roche Kapa PCR enzyme were substituted for Takara Smartscribe reverse transcriptase and SeqAmp PCR enzyme respectively. Twenty PCR cycles were used to amplify cDNA and Illumina Nextera XT kit was used to generate the sequence ready libraries.
75bp single end
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Adapter and quality trimming with cutadapt
Reads aligned to hg38 using STAR aligner
Raw read counts obtained using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: raw_reads_counts_matrix.txt
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| Submission date |
Apr 11, 2020 |
| Last update date |
Jul 10, 2020 |
| Contact name |
Svetlana Reilly |
| Organization name |
University of Oxford
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| Department |
Cardiovascular Medicine, Radcliffe Dept of Medicine
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| Street address |
JOhn Radcliffe Hospita, Headley Way
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| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX9 3DU |
| Country |
United Kingdom |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE148506 |
Single-cell profile of atrial human fibroblasts in cardiac arrhythmia atrial fibrillation (AF) - SmartSeq2 |
| GSE148507 |
Single-cell profile of atrial human fibroblasts in cardiac arrhythmia atrial fibrillation |
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| Relations |
| BioSample |
SAMN14583462 |
| SRA |
SRX8109587 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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