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Create README.md
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README.md
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---
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tags:
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- genomics
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- biology
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---
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Data pull from https://nascent.colorado.edu/home/
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## Querying with DuckDB
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```bash
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duckdb -csv -c "SELECT * FROM read_csv_auto('~/src/fg/DBNascent/all_samples.csv') WHERE Protocol == 'GRO-seq' AND \"Cell type\" ILIKE '%HeLa%'"
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# Write the output to a file
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# > hela_groseq.csv
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```
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| Sample name | Paper identifier | Organism | Protocol | Cell type | Treatment | Replicate | Read depth | QC score |
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|-------------|---------------------------|------------|----------|------------------|--------------------------------------------------------------|-----------|------------|----------|
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| ERR769522 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | DRB (30min) | 1 | 20M | 4 |
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| ERR769523 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | KM05283 (30min) | 1 | 23M | 4 |
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| ERR769524 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 24M | 2 |
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| ERR769525 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 2 | 26M | 2 |
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| SRR1342250 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , serum starvation (1day) | 1 | 58M | 3 |
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| SRR1342251 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , doxycycline (4day) , serum starvation (1day) | 1 | 45M | 1 |
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| SRR1342252 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , serum starvation (1day) | 2 | 114M | 4 |
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| SRR1342253 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , doxycycline (4day) , serum starvation (1day) | 2 | 71M | 3 |
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| SRR1596500 | Andersson2014nuclear | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 21M | 1 |
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| SRR1596501 | Andersson2014nuclear | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 2 | 33M | 1 |
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| SRR2059423 | Zhang2016regulation | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 56M | 3 |
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| SRR2059424 | Zhang2016regulation | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 85M | 3 |
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| SRR5109939 | Bouvyliivrand2017analysis | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 22M | 1 |
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| SRR7010982 | Fei2018ndf | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 64M | 2 |
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| SRR7010983 | Fei2018ndf | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 76M | 2 |
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| SRR7010984 | Fei2018ndf | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 2 | 66M | 2 |
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| SRZ10004434 | Bahat2019targeting | H. sapiens | GRO-seq | HeLa (cell line) | DMSO (90min) | 1 | 141M | 2 |
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| SRZ10004438 | Bahat2019targeting | H. sapiens | GRO-seq | HeLa (cell line) | DMSO (90min) | 2 | 124M | 2 |
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| SRZ10004442 | Bahat2019targeting | H. sapiens | GRO-seq | HeLa (cell line) | Spt5-Pol II small-molecule inhibitor 21 (90min) | 1 | 138M | 2 |
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| SRZ1693611 | Duttke2015human | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 68M | 4 |
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