APA Variant and Reference Libraries
(Pooled Library #1000000214)

• Purpose:

  Libraries made to experimentally validate a residual neural network model's (APARENT2) predictions for 3′-cleavage and polyadenylation from DNA sequence. 100 reference and 100 variant sequences were cloned into a reporter and are available as plasmid libraries. APA profiling data was obtained from RNA-seq of 3 different cell lines (HEK293T, SK-N-SH, and HMC3) with 2 replicates of each library. Polyadenylation cleavage position was determined for mapped reads, and then UMIs were collapsed to determine measured variant log odds ratio of cleavage.

• Vector Backbone:

  APA V2 plasmid backbone.gb (13 KB)

• Depositing Labs: Georg Seelig
• Publication: Linder et al. Genome Biol. 2022 Nov 5;23(1):232. doi: 10.1186/s13059-022-02799-4.

Library Details

• Sequences per library: 100
• Insert Size: 234 nt

Library Shipping

This library is delivered as suspended DNA in microcentrifuge tubes on blue ice. The tubes contents will not necessarily be frozen. For best results, minimize freeze-thaws.

• Volume: ∼25 µL
• Concentration: 25 ng/µL

Resource Information

• Protocols:
  • Library Amplification, Sequencing, and Analysis Protocols (350 KB)
• Depositor Data:
  • Variant Metadata (8 KB)
  • HEK Variant data (97 KB)
  • Primers (9 KB)
• Terms and Licenses:
  • UBMTA
  • Clontech Limited Use Label License

Depositor Comments

Please visit https://www.biorxiv.org/content/10.1101/2022.05.09.491198v1 for bioRxiv preprint.