---
tags:
- genomics
- biology
---

Data pulled from https://nascent.colorado.edu/home/

## Querying with DuckDB

```bash
duckdb -csv -c "SELECT * FROM read_csv_auto('~/src/fg/DBNascent/all_samples.csv') WHERE Protocol == 'GRO-seq' AND \"Cell type\" ILIKE '%HeLa%'"
# Write the output to a file
# > hela_groseq.csv
```

| Sample name |     Paper identifier      |  Organism  | Protocol |    Cell type     |                          Treatment                           | Replicate | Read depth | QC score |
|-------------|---------------------------|------------|----------|------------------|--------------------------------------------------------------|-----------|------------|----------|
| ERR769522   | Laitem2015cdk9            | H. sapiens | GRO-seq  | HeLa (cell line) | DRB (30min)                                                  | 1         | 20M        | 4        |
| ERR769523   | Laitem2015cdk9            | H. sapiens | GRO-seq  | HeLa (cell line) | KM05283 (30min)                                              | 1         | 23M        | 4        |
| ERR769524   | Laitem2015cdk9            | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 24M        | 2        |
| ERR769525   | Laitem2015cdk9            | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 2         | 26M        | 2        |
| SRR1342250  | Gardini2014integrator     | H. sapiens | GRO-seq  | HeLa (cell line) | EGF (30min)  , serum starvation (1day)                       | 1         | 58M        | 3        |
| SRR1342251  | Gardini2014integrator     | H. sapiens | GRO-seq  | HeLa (cell line) | EGF (30min)  , doxycycline (4day)  , serum starvation (1day) | 1         | 45M        | 1        |
| SRR1342252  | Gardini2014integrator     | H. sapiens | GRO-seq  | HeLa (cell line) | EGF (30min)  , serum starvation (1day)                       | 2         | 114M       | 4        |
| SRR1342253  | Gardini2014integrator     | H. sapiens | GRO-seq  | HeLa (cell line) | EGF (30min)  , doxycycline (4day)  , serum starvation (1day) | 2         | 71M        | 3        |
| SRR1596500  | Andersson2014nuclear      | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 21M        | 1        |
| SRR1596501  | Andersson2014nuclear      | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 2         | 33M        | 1        |
| SRR2059423  | Zhang2016regulation       | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 56M        | 3        |
| SRR2059424  | Zhang2016regulation       | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 85M        | 3        |
| SRR5109939  | Bouvyliivrand2017analysis | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 22M        | 1        |
| SRR7010982  | Fei2018ndf                | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 64M        | 2        |
| SRR7010983  | Fei2018ndf                | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 76M        | 2        |
| SRR7010984  | Fei2018ndf                | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 2         | 66M        | 2        |
| SRZ10004434 | Bahat2019targeting        | H. sapiens | GRO-seq  | HeLa (cell line) | DMSO (90min)                                                 | 1         | 141M       | 2        |
| SRZ10004438 | Bahat2019targeting        | H. sapiens | GRO-seq  | HeLa (cell line) | DMSO (90min)                                                 | 2         | 124M       | 2        |
| SRZ10004442 | Bahat2019targeting        | H. sapiens | GRO-seq  | HeLa (cell line) | Spt5-Pol II small-molecule inhibitor 21 (90min)              | 1         | 138M       | 2        |
| SRZ1693611  | Duttke2015human           | H. sapiens | GRO-seq  | HeLa (cell line) | NaN                                                          | 1         | 68M        | 4        |