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This PCR product was then subcloned into pGEMT-Easy and the proper insert verified by EcoR I, Xho I and Sma I digestion.
Quantitative RT-PCR time-course analyses of four of these genes (KLK3, PYGB, TGM2 and SERINC3) (Figure 2 insert) verified both the Illumina expression data and the choice of the 16-hour time point after DHT treatment.
The PCR product was cloned into pGVB2 vector via SacI and NcoI sites and the insert verified by sequencing.
Three colonies were screened for each construct and the presence of insert verified by PCR using a vector specific forward primer and hCNTF gene specific reverse primer (Additional file 1: Figure S2).
At least two inserts were verified by PCR for each 'element' except the Chr 6 element (only one insert verified) and the Chr 3 element (not verified but described by Tubio et al. [ 13]).
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The backend code automatically cuts the sequence down to just the insert, verifies the mutagen tag is present and the genomic sequence starts with 'TA'TA
The fragment was cloned into the pCR®T7 TOPO®-NT vector (Invitrogen Ltd., Paisley, UK) and used to transform E. coli BL21 (DE3) pLysS cells (Invitrogen Ltd., Paisley, UK); colonies were selected and inserts verified by sequencing.
Plasmid DNA was purified from cells with large barcode inserts, verified by digestion with BamH I, and sequenced with primer TAIL-LB LOX71 to determine the barcode sequences.
The Chr8 element showed both transduction and mapping to the native L1 insert of the two inserts verified, one had 3' unique sequence transduced and one was pure L1 3' terminus Transduced sequence, maximum extent of unique sequence observed in inserts verified by PCR (Additional file 2), except for Chr 3 element where read map position is given.
The clone verification was classified into three categories based on the sequencing coverage of the insert, class A: insert is verified from both N and C-terminal ends; class B: insert is verified either from N or C-terminal ends (Additional file 1, Table S1); class C: unverified (or sequence failed).
The presence of the correct sized insert was verified by restriction enzyme digestion (EcoRI), and sequences were obtained from clones with the correct insert by using standard ABI BigDye terminator reactions (Applied Biosystems).
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