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adjust BSEVA1.0 build instructions for TS cassette cloning
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@hainesm6
hainesm6 committed Aug 28, 2021
1 parent e8e2622 commit 54e1753
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24 changes: 12 additions & 12 deletions basicsynbio/parts_linkers/BASIC_SEVA_collection_v10.gb
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Expand Up @@ -309,11 +309,11 @@ ORIGIN
3841 gttgagcaat atgagcgtag cgagggtcgc cacagcaccg gcggcatgga cgaactgtat
3901 aagggatcct aataa
//
LOCUS BASIC_SEVA_17_TS.1 3984 bp DNA circular UNK 28-AUG-2021
LOCUS BASIC_SEVA_17_TS.10 3984 bp DNA circular UNK 28-AUG-2021
DEFINITION BASIC SEVA vector containing Ampicillin resistance marker and
temperature sensitive pSC101 origin of replication..
ACCESSION BASIC_SEVA_17_TS
VERSION BASIC_SEVA_17_TS.1
VERSION BASIC_SEVA_17_TS.10
KEYWORDS .
SOURCE synthetic construct
ORGANISM synthetic construct
Expand Down Expand Up @@ -895,11 +895,11 @@ ORIGIN
3721 ataccgtggt tgagcaatat gagcgtagcg agggtcgcca cagcaccggc ggcatggacg
3781 aactgtataa gggatcctaa taa
//
LOCUS BASIC_SEVA_27_TS.1 3872 bp DNA circular UNK 28-AUG-2021
LOCUS BASIC_SEVA_27_TS.10 3872 bp DNA circular UNK 28-AUG-2021
DEFINITION BASIC SEVA vector containing Kanamycin resistance marker and
temperature sensitive pSC101 origin of replication..
ACCESSION BASIC_SEVA_27_TS
VERSION BASIC_SEVA_27_TS.1
VERSION BASIC_SEVA_27_TS.10
KEYWORDS .
SOURCE synthetic construct
ORGANISM synthetic construct
Expand Down Expand Up @@ -1467,11 +1467,11 @@ ORIGIN
3541 accgtaaact ggatattacc agccacaacg aggattatac cgtggttgag caatatgagc
3601 gtagcgaggg tcgccacagc accggcggca tggacgaact gtataaggga tcctaataa
//
LOCUS BASIC_SEVA_37_TS.1 3728 bp DNA circular UNK 28-AUG-2021
LOCUS BASIC_SEVA_37_TS.10 3728 bp DNA circular UNK 28-AUG-2021
DEFINITION BASIC SEVA vector containing Chloramphenicol resistance marker and
temperature sensitive pSC101 origin of replication..
ACCESSION BASIC_SEVA_37_TS
VERSION BASIC_SEVA_37_TS.1
VERSION BASIC_SEVA_37_TS.10
KEYWORDS .
SOURCE synthetic construct
ORGANISM synthetic construct
Expand Down Expand Up @@ -2044,11 +2044,11 @@ ORIGIN
3781 aacgaggatt ataccgtggt tgagcaatat gagcgtagcg agggtcgcca cagcaccggc
3841 ggcatggacg aactgtataa gggatcctaa taa
//
LOCUS BASIC_SEVA_47_TS.1 3942 bp DNA circular UNK 28-AUG-2021
LOCUS BASIC_SEVA_47_TS.10 3942 bp DNA circular UNK 28-AUG-2021
DEFINITION BASIC SEVA vector containing Streptomycin resistance marker and
temperature sensitive pSC101 origin of replication..
ACCESSION BASIC_SEVA_47_TS
VERSION BASIC_SEVA_47_TS.1
VERSION BASIC_SEVA_47_TS.10
KEYWORDS .
SOURCE synthetic construct
ORGANISM synthetic construct
Expand Down Expand Up @@ -2645,11 +2645,11 @@ ORIGIN
4081 agcaatatga gcgtagcgag ggtcgccaca gcaccggcgg catggacgaa ctgtataagg
4141 gatcctaata a
//
LOCUS BASIC_SEVA_57_TS.1 4220 bp DNA circular UNK 28-AUG-2021
LOCUS BASIC_SEVA_57_TS.10 4220 bp DNA circular UNK 28-AUG-2021
DEFINITION BASIC SEVA vector containing Tetracycline resistance marker and
temperature sensitive pSC101 origin of replication..
ACCESSION BASIC_SEVA_57_TS
VERSION BASIC_SEVA_57_TS.1
VERSION BASIC_SEVA_57_TS.10
KEYWORDS .
SOURCE synthetic construct
ORGANISM synthetic construct
Expand Down Expand Up @@ -3236,11 +3236,11 @@ ORIGIN
3601 accgtggttg agcaatatga gcgtagcgag ggtcgccaca gcaccggcgg catggacgaa
3661 ctgtataagg gatcctaata a
//
LOCUS BASIC_SEVA_67_TS.1 3750 bp DNA circular UNK 28-AUG-2021
LOCUS BASIC_SEVA_67_TS.10 3750 bp DNA circular UNK 28-AUG-2021
DEFINITION BASIC SEVA vector containing Gentamicin resistance marker and
temperature sensitive pSC101 origin of replication..
ACCESSION BASIC_SEVA_67_TS
VERSION BASIC_SEVA_67_TS.1
VERSION BASIC_SEVA_67_TS.10
KEYWORDS .
SOURCE synthetic construct
ORGANISM synthetic construct
Expand Down
Binary file modified csv_xlsx_files/BASIC_SEVA_collection_v10_echo_scripts.zip
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Binary file modified pdfs/BASIC_SEVA_collection_v10_manual.pdf
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Binary file added pdfs/bs_x7x_ts_instructions.pdf
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78 changes: 47 additions & 31 deletions scripts_nbs/addgene_submission.ipynb
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Expand Up @@ -14,11 +14,11 @@
"\n",
"## Aims and objectives for cell/s below\n",
"\n",
"\n",
"- [x] Import the following objects:\n",
" - [x] pickled BasicLinker `SEVA-BB1`\n",
" - [x] pickled BasicLinker `BSEVA_L1`\n",
" - [x] Selected Oris and AbR markers specified in #130.\n",
" - [x] mScarlet counter selection casettes for associated Oris.\n",
"- [ ] Assemble BS_x7x_TS_CASc with BS_1xx to generate `BS_x7x_TS` and export build instructions. \n",
"- [x] Generate a dictionary mapping between Oris and counter-selection casettes.\n",
"- [ ] Make assemblies and export the following data:\n",
" - [x] Genbank file containing all correctly assembled backbones.\n",
Expand All @@ -28,19 +28,20 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 32,
"source": [
"import basicsynbio as bsb\n",
"from basicsynbio.utils import MARKER_DICT, ORI_DICT\n",
"from pathlib import Path\n",
"import pickle"
"import pickle\n",
"import re"
],
"outputs": [],
"metadata": {}
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 33,
"source": [
"path_to_seqs = Path.cwd().parents[0] / \"sequences\"\n",
"path_to_initial_mods = path_to_seqs / \"genbank_files\" / \"BASIC_SEVA_collection\" / \"initial_mods\"\n",
Expand All @@ -51,28 +52,60 @@
" bsb.import_parts(path_to_initial_mods / \"AbR_markers.gb\",\n",
" \"genbank\"\n",
"))\n",
"oris = list(\n",
" bsb.import_parts(path_to_initial_mods / \"oris.gb\",\n",
"seva_oris = list(\n",
" bsb.import_parts(path_to_initial_mods / \"SEVA_oris.gb\",\n",
" \"genbank\"\n",
"))\n",
"cs_cassettes = list(\n",
" bsb.import_parts(path_to_initial_mods / \"mScarlet_cs_cassettes.gb\",\n",
" \"genbank\"\n",
"))\n",
"bs_x7x_ts_casc = bsb.import_part(path_to_initial_mods / \"bs_x7x_ts_casc.gb\", \"genbank\")"
],
"outputs": [],
"metadata": {}
},
{
"cell_type": "code",
"execution_count": 34,
"source": [
"# Assemble BS_x7x_TS\n",
"linkers = bsb.BASIC_BIOLEGIO_LINKERS[\"v0.1\"]\n",
"bs_x7x_ts_assembly = bsb.BasicAssembly(\n",
" \"BS_x7x_TS\",\n",
" linkers[\"LMP\"],\n",
" bs_x7x_ts_casc,\n",
" linkers[\"LMS\"],\n",
" [marker for marker in abr_markers if marker.id == \"BS_1xx\"][0]\n",
")\n",
"bsb.export_sequences_to_file(\n",
" bs_x7x_ts_assembly,\n",
" path_to_initial_mods / \"bs_x7x_ts.gb\"\n",
")\n",
"bsb.BasicBuild(bs_x7x_ts_assembly)\n",
"oris = seva_oris\n",
"oris.insert(3, bs_x7x_ts_assembly.return_part())"
],
"outputs": [],
"metadata": {}
},
{
"cell_type": "code",
"execution_count": 35,
"source": [
"# Map oris with counter selection cassettes\n",
"ori_cs_cassette_mapping = {\n",
" \"BS_x5x\": \"B407_J23119-RBS34-mScarl\",\n",
" \"BS_x6x\": \"B407_J23119-RBS34-mScarl\",\n",
" \"BS_x7x\": \"B408_J23119-RBS-A12-mSc\",\n",
" \"BS_x7x_TS_CASc\": \"B408_J23119-RBS-A12-mSc\",\n",
" \"BS_x7x_TS\": \"B408_J23119-RBS-A12-mSc\",\n",
" \"BS_x8x\": \"B405_J23106-RBS34-mScarl\",\n",
" \"BS_x9x\": \"B407_J23119-RBS34-mScarl\",\n",
"}\n",
"ori_cs_cassette_mapping = {\n",
" key: cs_cassettes[[cs_cassette.id for cs_cassette in cs_cassettes].index(value)] for key, value in ori_cs_cassette_mapping.items()\n",
"}\n",
"# Make assemblies and export data\n",
"linkers = bsb.BASIC_BIOLEGIO_LINKERS[\"v0.1\"]\n",
"assemblies = []\n",
"for abr_marker in abr_markers:\n",
" for ori in oris: \n",
Expand All @@ -85,10 +118,11 @@
" linkers[\"LMS\"],\n",
" ori_cs_cassette_mapping[ori.id],\n",
" )\n",
" if ori.id == \"BS_x7x_TS_CASc\":\n",
" assembly.id = f\"BASIC_SEVA_{abr_marker.id[-3]}7_TS.1\"\n",
" if ori.id == \"BS_x7x_TS\":\n",
" assembly.id = f\"BASIC_SEVA_{abr_marker.id[-3]}7_TS.10\"\n",
" assembly.description = f\"BASIC SEVA vector containing {MARKER_DICT[abr_marker.id[-3]]} resistance marker and temperature sensitive pSC101 origin of replication.\"\n",
" else:\n",
" assert re.match(\"BS_x\\dx\", ori.id) != None\n",
" assembly.id = f\"BASIC_SEVA_{abr_marker.id[-3] + ori.id[-2]}.10\"\n",
" assembly.description = f\"BASIC SEVA vector containing {MARKER_DICT[abr_marker.id[-3]]} resistance marker and {ORI_DICT[ori.id[-2]]} origin of replication.\"\n",
" assemblies.append(assembly)\n",
Expand All @@ -107,8 +141,7 @@
" build,\n",
" \"/home/hainesm6/github_repos/LondonBiofoundry/basicsynbio/pdfs/BASIC_SEVA_collection_v10_manual.pdf\",\n",
" assemblies_per_clip=20,\n",
")\n",
"\n"
")\n"
],
"outputs": [
{
Expand All @@ -119,24 +152,7 @@
]
},
"metadata": {},
"execution_count": 2
}
],
"metadata": {}
},
{
"cell_type": "code",
"execution_count": 3,
"source": [
"print([abr_marker.id for abr_marker in abr_markers])"
],
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"['BS_1xx', 'BS_2xx', 'BS_3xx', 'BS_4xx', 'BS_5xx', 'BS_6xx']\n"
]
"execution_count": 35
}
],
"metadata": {}
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