We evaluated the Ambion (Silencer Select) and Qiagen (human druggable v3.0 and human whole genome supplement v1.0 sets) siRNA libraries containing 64,781 siRNAs and 70,308 siRNAs, respectively. For annotations NCBI RefSeq release 40 was used.
NEXT-RNAi results
NEXT-RNAi HTML ouputs for the library evaluations are available here:
Input files and settings used
Input FASTA file
- Ambion siRNA sequences: Ambion_siRNA.zip (600KB)
- Qiagen siRNA sequences: Qiagen_siRNA.zip (696KB)
The files contain siRNA sequences used as input for NEXT-RNAi (-i input).
| Code Block | ||||
|---|---|---|---|---|
| ||||
>SI00077350 TCCCGTATAAGTATGTTCC >SI00077336 GAGGACTATACCAACTAGT >SI00077343 CAGACCAAACCGAGGACTA >SI00077357 ACGCCATTATTCAGAACCT >SI00147777 ACCCAGGATATCTCCACCA >SI00147756 CCGGATCCTCAAGGTCTTC >SI00147770 CTCCATATTCTTCTGCATC >SI03092887 CTGAAGCGGCTCATCGAGA |
Targetgroup file (tab-delimited)
TargetGroups_GeneID.tab (1.3MB) defining which RefSeq transcripts belong to the same gene (headers Target and TargetGroup) (TARGETGROUPS option)
| Code Block | ||||
|---|---|---|---|---|
| ||||
Target TargetGroup TargetGroup2 NM_001012993.2 C9orf152 401546 NM_001015.3 RPS11 6205 XM_002348062.1 LOC100291269 100291269 NM_182764.1 ELMO2 63916 NM_133171.3 ELMO2 63916 NM_052854.2 CREB3L1 90993 NM_006029.4 PNMA1 9240 NM_004530.4 MMP2 4313 NM_001127891.1 MMP2 4313 |
Bowtie database/index for off-target evaluation
Bowtie database/index containing annotated RefSeq transcripts (release 40) for specificity calculations (-d input):
human.rnaMOD.tar.gz (114MB)
Feature file with UTR and SNP locations
Tab-delimited feature file containing mappings of UTRs and SNPs (from NCBI dbSNP) to chromosomes that is used to calculate UTR and SNP 'contents' (FEATURE option) of designed reagents: Hs_UTR_SNP.tar.gz (484MB)
| Code Block | ||||
|---|---|---|---|---|
| ||||
ID FeatureName FeatureLoc FeatureStart FeatureEnd UTR_1 UTR 11 11643172 11643172 UTR_2 UTR 11 6741799 6741799 UTR_3 UTR 11 127219 127219 UTR_4 UTR 11 2662385 2662385 UTR_5 UTR 11 45952962 45952962 rs80303196 SNP 6 29985811 29985811 rs80303196 SNP 6 32995534 32995534 rs80303196 SNP 6 29080247 29080247 rs80303196 SNP 6 30038873 30038873 rs80303196 SNP 6 32181031 32181031 |
FASTA file for homology evaluation
Transcriptome FASTA file to evaluate the homology of the designs using Blast (HOMOLOGY and TXNFASTA options):
human.rnaMOD.fna.zip (32MB)
Bowtie database/index for seed match evaluation
To compute the number of siRNA seed matches (seed complement frequency) a Bowtie database/index containing all annotated 3'-UTR sequences (RefSeq release 40) was generated to be used with the SEEDMATCH option (Hs_3UTR.tar.gz (26MB)).
Design criteria
Start of program
Ambion
| Code Block | ||||
|---|---|---|---|---|
| ||||
perl nextrnai.pl -i Ambion_siRNA.fa -s 30000 -r s -d human.rnaMOD -e OLIGO -o options.txt -n Ambion_RefSeq40 |
Qiagen
| Code Block | ||||
|---|---|---|---|---|
| ||||
perl nextrnai.pl -i Qiagen_siRNA.fa -s 30000 -r s -d human.rnaMOD -e OLIGO -o options.txt -n Qiagen_RefSeq40 |
Descriptions for start parameters used are available here.
Options file
| Code Block | ||||
|---|---|---|---|---|
| ||||
SIRNALENGTH=19 EFFICIENCY=SIR,63 BOWTIE=/usr/bin/ SOURCE=CDS TARGETGROUPS=TargetGroups_GeneID.tab BLAT=/usr/bin/ BLATPROGRAM=gfClient BLATHOST=b110-cellarray3 BLATPORT=3500 TXNFASTA=human.rnaMOD.fna GFF=GFF3 GBROWSEBASE=http://www.dkfz.de/signaling/cgi-bin/gbrowse_img/hsrefseq/ GBROWSETRACK=GENE+TXN+ENSEMBLGENESPAN+ENSEMBLGENE AFF=YES LOWCOMPEVAL=/usr/bin/ CANEVAL=6 HOMOLOGY=/usr/bin/,human.rnaMOD.fna,0.1 FEATURE=Hs_UTR_SNP.tab SEEDMATCH=Hs_3UTR |
Descriptions for all options used are available here.