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 (PDF, 350 KB)
• Depositor Data:
  • Variant Metadata (TXT, 7.6 KB)
  • HEK Variant Data (XLSX, 97 KB)
  • Primers (XLSX, 37 KB)

Terms and Licenses

Academic/Nonprofit Terms:

• UBMTA
• Takara Bio Limited Use Label License (formerly Clontech)

Industry Terms:

• Not Available to Industry

Trademarks:

• Zeocin® is an InvivoGen trademark.

Depositor Comments

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