Northwestern University Feinberg School of Medicine

Eva Gottwein Lab

Data

Manzano et al., Journal of Virology 2013


Detailed Cloning Procedures and Primer Sequences

Detailed Cloning Procedures and Primer Sequences


Gottwein et al., Cell Host & Microbe 2011


Small RNA sequencing data

Small RNA sequencing data from BC-1 (TAB A), BC-3 (TAB B) and BCBL-1 (TAB C) cells. Mature miRNA sequences which made up at least 10% of the sequences derived from the corresponding pre-miRNA are listed. Mature miRNA sequences which made up less than 10% were also included if these miRNA variants were present in miRBase (v16).

PAR-CLIP groups

PAR-CLIP groups derived from BC-1 (TAB A) or BC-3 (TAB B) cells. Groups consist of reads that overlap by at least 1 nt. Columns indicate: the chromosome the cluster is located on (Chromosome), the DNA strand the cluster maps to (Strand), genomic location of the group (Group Start, Group End), GroupID, sequence of the group (Group Sequence), the number of reads that contribute to the group(Read Count), whether the group maps to repetitive elements (Filter), location of the group within the transcript (Transcript location), Ensembl Transcript ID (Transcript ID) and official gene symbol (Gene name). A transcript location designated ">250" indicates that the cluster is less than 250nt 3' to a known polyadenylation site.

PAR-CLIP clusters

PAR-CLIP clusters derived from BC-1 (TAB A) or BC-3 (TAB B) cells. Columns indicate: the chromosome the cluster is located on (Chromosome), DNA strand the cluster maps to (Strand), genomic location of the cluster (Cluster Start, Cluster End), ClusterID, sequence of the cluster (Cluster Sequence), the number of reads that contribute to the cluster (Read Count), the nucleotide of the cluster where the distance between the distributions of converted Ts and non-converted Ts is maximal (Mode Location), Mode Score, the number of locations in the cluster with observed T to C conversions (Conversion Location Count), the total number of T to C conversions in all reads that contribute to the cluster (Conversion Event Count), the total number of nonconverted Ts in all reads that contribute to the cluster (Non-Conversion Event Count), whether the cluster maps to repetitive elements (Filter), location of the cluster within the transcript (Transcript location), Ensembl Transcript ID (Transcript ID) and official gene symbol (Gene name). A transcript location designated ">250" indicates that the cluster is less than 250nt 3' to a known polyadenylation site.

PAR-CLIP clusters with seed matches to expressed miRNAs

PAR-CLIP clusters with seed matches to expressed miRNAs, derived from BC-1 (TAB A) or BC-3 cells (TAB B). Columns indicate: the chromosome the cluster is located on (Chromosome), DNA strand the cluster maps to (Strand), genomic location of the seed match (Site Start, Site End), the miRNA seed sequence with a match on the cluster (Seed Sequence), the type of seed match (Seed Type), ClusterID, sequence of the cluster (Cluster Sequence), the targeting miRNAs (miRNAs), the number of reads that contribute to the cluster (Read Count), the nucleotide of the cluster where the distance between the distributions of converted Ts and non-converted Ts is maximal (Mode Location), Mode Score, the number of locations in the cluster with observed T to C conversions (Conversion Location Count), the total number of T to C conversions in all reads that contribute to the cluster (Conversion Event Count), the total number of nonconverted Ts in all reads that contribute to the cluster (Non-Conversion Event Count), whether the cluster maps to repetitive elements (Filter), location of the cluster within the transcript (Transcript location), Ensembl Transcript ID (Transcript ID) and official gene symbol (Gene name). A transcript location designated ">250" indicates that the cluster is less than 250nt 3' to a known polyadenylation site.