Hugging Face's logo

Datasets:
CollageBio
/
oligo-datasets

Tasks:
Tabular Regression
Modalities:
Tabular
Text
Formats:
csv
Size:
100K - 1M
Tags:
biology
oligonucleotides
siRNA
ASO
shRNA
HELM
Libraries:
Datasets
pandas
Polars
License:
Dataset card Data Studio Files
xet
 Community
1
phosseini commited on
Commit
4afa948
·
verified ·
1 Parent(s): 174d685

Upload metadata.csv with huggingface_hub

Browse files
Files changed (1) hide show
  1. metadata.csv +13 -26
metadata.csv CHANGED
@@ -1,26 +1,13 @@
1
- name,desc,modality,size,label_desc,model_system,collection,num_targets,task,rec_split,rec_metric,featurizers,source,key
2
- Alharbi_2020_1,2'OMe gapmer screen of TLR8 potentiation,ASO,192,TLR8 level after induction with 100nM ASO as measured by fluorescence as using NF-κB-Luciferase reporter in HEK293-TLR8 cells. Values relative to those obtained after induction with Resiquimod (=1.0),In vitro,Immunomodulation,4,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1093/nar/gkaa523'],TLR7
3
- Alharbi_2020_2,2'OMe gapmer screen of TLR7 inhibition,ASO,192,TLR7 level after induction with 100nM ASO as measured by fluorescence as using NF-κB-Luciferase reporter in HEK293-TLR7 cells. Values relative to those obtained after induction with Resiquimod (=100),In vitro,Immunomodulation,4,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1093/nar/gkaa523'],TLR8
4
- Hagedorn_2022_1,Acute nuerotox of LNA gapmer as measured by calcium oscillation score in cell,ASO,1825,Calcium oscillation score,In vitro,Toxicity,3,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1089/nat.2021.0071'],Neurotox LNA
5
- Hwang_2024_1,A collection of inhibitory activity for different gapmers ASO collected from various patents and publication,ASO,32602,Percentage inhibition of target mRNA relative to untreated controls,In vitro,Activity,18,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMerCounts'],['https://doi.org/10.1016/j.omtn.2024.102186'],ASOptimizer
6
- Ichihara_2007_1,A precurated collection of unmodified siRNA potency data. The dataset can be split into two. Ichihara_2007_1 is a dataset from Huesken_2005 of siRNA screen using GFP reporter assay.,siRNA,2431,Percentage inhibition relative to control using an eCFP-eYFP dual reporter assay.,In vitro,Activity,30,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1093/nar/gkm699'],Huesken
7
- Ichihara_2007_2,A precurated collection of unmodified siRNA potency data. The dataset can be split into two. Ichihara_2007_2 is a dataset from 5 different studies with different assays so its likely the quality is worse than Ichihara_2007_1.,siRNA,419,Percentage inhibition relative to control from various assays as reported by authors of the curated dataset.,In vitro,Activity,12,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1093/nar/gkm699'],Ichihara
8
- Knott_2014_1,"A biased screening of shRNA using the miR-30 scaffold, DSIR algorithm was used to select for sequences likely to be active",shRNA,291551,MinMax-scaled score from the raw score obtained from a high-throughput assay based on sort-seq strategy using fluorescence reporter construct with the target site in the 3UTR of the reporter gene.,In vitro,Activity,17802,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1016/j.molcel.2014.10.025'],Sherwood
9
- MOE_Neurotox_1,Acute neurotox data for MOE modifed ASOs scraped from patent,ASO,2437,Rounded 3h FOB score in mice (7 categories: 0 (safe) > 7(toxic)),In vivo,Acute Neurotoxicity,13,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],"['https://patents.google.com/patent/WO2020172559A1'
10
- 'https://patents.google.com/patent/WO2016168592A2'
11
- 'https://patents.google.com/patent/WO2021021673A1'
12
- 'https://patents.google.com/patent/WO2015153800A2'
13
- 'https://patents.google.com/patent/WO2020205463A1'
14
- 'https://patents.google.com/patent/WO2020006267A1'
15
- 'https://patents.google.com/patent/WO2020023737A1'
16
- 'https://patents.google.com/patent/WO2020243292A1'
17
- 'https://patents.google.com/patent/WO2020106996A1'
18
- 'https://patents.google.com/patent/WO2022026589A1'
19
- 'https://patents.google.com/patent/WO2022165122A1'
20
- 'https://patents.google.com/patent/WO2021174019A1'
21
- 'https://patents.google.com/patent/WO2022032060A2']",Neurotox MOE
22
- Martinelli_2023_1,A curated siRNA potency dataset that contain only sugar and base information.,siRNA,907,Percentage knockdown of the target mRNA,undefined,Activity,1,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1016/j.ygeno.2024.110815'],siRNAmod
23
- McQuisten_2007_1,An ASO-activity dataset collected by IDT from a now defunct ASO database (https://doi.org/10.1093/bioinformatics/16.9.843) and also from patent data. According to the publication each ASO have a full phosphothioate backbone and no chimeric sequences.,ASO,3913,Activity range from 0 (complete target inhibition) to 1 (no difference in target activity when compared to appropriate control). The activity were all measured from either protein product or direct mRNA level.,undefined,Activity,86,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],"['https://doi.org/10.1186/1471-2105-8-184'
24
- 'https://github.com/lackeylela/openASO']",OpenASO
25
- Papargyri_2020_1,A study looking at the relationship between nucleobase and LNA sequence on aso activity and cytotoxicity.,ASO,768,Minmax-scaled average caspase level (N=3) measured in HeLa cells,In vitro,Toxicity,1,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMersCounts'],['https://doi.org/10.1016/j.omtn.2019.12.011'],Cytotox LNA
26
- Shmushkovich_2018_1,Study of cholesterol-conjugated siRNA efficacy using dual luciferase reporter in HeLa cells at 1 μM,siRNA,356,Percentage remaining relative to control of siRNA measured using dual luciferase reporter in HeLa cells at 1 μM,In vitro,Activity,1,Regression,Random,['Spearmanr' 'Pearsonr'],['OneHotEncoder' 'KMerCounts'],['https://doi.org/10.1093/nar/gky745'],Shmushkovich
 
1
+ key,name,desc,modality,size,label_desc,model_system,collection,num_targets,task,rec_split,rec_metric,featurizers,source
2
+ TLR7,Alharbi_2020_1,2'OMe gapmer screen of TLR8 potentiation,ASO,192,TLR8 level after induction with 100nM ASO as measured by fluorescence as using NF-κB-Luciferase reporter in HEK293-TLR8 cells. Values relative to those obtained after induction with Resiquimod (=1.0),In vitro,Immunomodulation,4,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1093/nar/gkaa523""]"
3
+ TLR8,Alharbi_2020_2,2'OMe gapmer screen of TLR7 inhibition,ASO,192,TLR7 level after induction with 100nM ASO as measured by fluorescence as using NF-κB-Luciferase reporter in HEK293-TLR7 cells. Values relative to those obtained after induction with Resiquimod (=100),In vitro,Immunomodulation,4,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1093/nar/gkaa523""]"
4
+ Neurotox LNA,Hagedorn_2022_1,Acute nuerotox of LNA gapmer as measured by calcium oscillation score in cell,ASO,1825,Calcium oscillation score,In vitro,Toxicity,3,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1089/nat.2021.0071""]"
5
+ ASOptimizer,Hwang_2024_1,A collection of inhibitory activity for different gapmers ASO collected from various patents and publication,ASO,32602,Percentage inhibition of target mRNA relative to untreated controls,In vitro,Activity,18,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMerCounts""]","[""https://doi.org/10.1016/j.omtn.2024.102186""]"
6
+ Huesken,Ichihara_2007_1,A precurated collection of unmodified siRNA potency data. The dataset can be split into two. Ichihara_2007_1 is a dataset from Huesken_2005 of siRNA screen using GFP reporter assay.,siRNA,2431,Percentage inhibition relative to control using an eCFP-eYFP dual reporter assay.,In vitro,Activity,30,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1093/nar/gkm699""]"
7
+ Ichihara,Ichihara_2007_2,A precurated collection of unmodified siRNA potency data. The dataset can be split into two. Ichihara_2007_2 is a dataset from 5 different studies with different assays so its likely the quality is worse than Ichihara_2007_1.,siRNA,419,Percentage inhibition relative to control from various assays as reported by authors of the curated dataset.,In vitro,Activity,12,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1093/nar/gkm699""]"
8
+ Sherwood,Knott_2014_1,"A biased screening of shRNA using the miR-30 scaffold, DSIR algorithm was used to select for sequences likely to be active",shRNA,291551,MinMax-scaled score from the raw score obtained from a high-throughput assay based on sort-seq strategy using fluorescence reporter construct with the target site in the 3UTR of the reporter gene.,In vitro,Activity,17802,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1016/j.molcel.2014.10.025""]"
9
+ Neurotox MOE,MOE_Neurotox_1,Acute neurotox data for MOE modifed ASOs scraped from patent,ASO,2437,Rounded 3h FOB score in mice (7 categories: 0 (safe) > 7(toxic)),In vivo,Acute Neurotoxicity,13,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://patents.google.com/patent/WO2020172559A1"", ""https://patents.google.com/patent/WO2016168592A2"", ""https://patents.google.com/patent/WO2021021673A1"", ""https://patents.google.com/patent/WO2015153800A2"", ""https://patents.google.com/patent/WO2020205463A1"", ""https://patents.google.com/patent/WO2020006267A1"", ""https://patents.google.com/patent/WO2020023737A1"", ""https://patents.google.com/patent/WO2020243292A1"", ""https://patents.google.com/patent/WO2020106996A1"", ""https://patents.google.com/patent/WO2022026589A1"", ""https://patents.google.com/patent/WO2022165122A1"", ""https://patents.google.com/patent/WO2021174019A1"", ""https://patents.google.com/patent/WO2022032060A2""]"
10
+ siRNAmod,Martinelli_2023_1,A curated siRNA potency dataset that contain only sugar and base information.,siRNA,907,Percentage knockdown of the target mRNA,undefined,Activity,1,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1016/j.ygeno.2024.110815""]"
11
+ OpenASO,McQuisten_2007_1,An ASO-activity dataset collected by IDT from a now defunct ASO database (https://doi.org/10.1093/bioinformatics/16.9.843) and also from patent data. According to the publication each ASO have a full phosphothioate backbone and no chimeric sequences.,ASO,3913,Activity range from 0 (complete target inhibition) to 1 (no difference in target activity when compared to appropriate control). The activity were all measured from either protein product or direct mRNA level.,undefined,Activity,86,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1186/1471-2105-8-184"", ""https://github.com/lackeylela/openASO""]"
12
+ Cytotox LNA,Papargyri_2020_1,A study looking at the relationship between nucleobase and LNA sequence on aso activity and cytotoxicity.,ASO,768,Minmax-scaled average caspase level (N=3) measured in HeLa cells,In vitro,Toxicity,1,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMersCounts""]","[""https://doi.org/10.1016/j.omtn.2019.12.011""]"
13
+ Shmushkovich,Shmushkovich_2018_1,Study of cholesterol-conjugated siRNA efficacy using dual luciferase reporter in HeLa cells at 1 μM,siRNA,356,Percentage remaining relative to control of siRNA measured using dual luciferase reporter in HeLa cells at 1 μM,In vitro,Activity,1,Regression,Random,"[""Spearmanr"", ""Pearsonr""]","[""OneHotEncoder"", ""KMerCounts""]","[""https://doi.org/10.1093/nar/gky745""]"