GPP Web Portal - Pool Details: CP0045

Pool: CP0045 (sgRNA) - Brie Genome 1-4

Name:: CP0045
Type:: S. pyogenes Cas9 CRISPRko
Sub type:: Single insert
Taxon:: Mouse
Vectors:: pXPR_023
Distinct barcodes:: 79633
Addgene ID:: 73632

File Downloads

The files in this table are provided to aid in the analysis of pooled screens. Be aware that these files may go for periods of time without change. However, each file is the most current edition available of its type, generated by a pipeline that runs periodically and assesses if changes are needed.

Refer to this guide for picking the appropriate chip file for your analysis.

Chip Files
Genome Annotation	Match	Description	Last Changed	Download

GRCm38 NCBI	strict[?] "strict" CHIP files Strict CHIP files are generated using the most stringent criteria to determine whether a perturbagen sequence matches the reference target: Strict shRNA CHIP files: Use the full 21mer shRNA target sequence to determine perfect transcriptome matches. Strict sgRNA CHIP files: Use the full 20mer (for S. pyogenes Cas9) or 21mer (for S. aureus Cas9) sgRNA target sequence to assess perfect matches to genomic PAM sites. Only consider matches where the "cut site" is properly contained in or touching (at extreme edge of) a target genomic feature loci. Consider only the "best" feature definition where multiple are available (e.g. TSS annotation from FANTOM and NCBI or Ensembl may differ significantly -- in strict mode, we restrict matches to the single highest confidence annotated locus).	Nmer barcode to gene mapping via strict sgRNA sequence match to NCBI-annotated genes in GRCm38.	2022-12-01	chip [preferred]
	lax[?] "lax" CHIP files Lax CHIP files are generated using less stringent criteria to determine whether a perturbagen sequence matches the reference target: Lax shRNA CHIP files: Use only the initial 19mer of the shRNA target sequence to determine "perfect" transcriptome matches. Lax sgRNA CHIP files: Use only the final 17mer (for S. pyogenes Cas9) or 18mer (for S. aureus Cas9) of the sgRNA target sequence to assess "perfect" matches to genomic PAM sites. Allow 10 bases of "slop" around target genomic feature loci (e.g. intronic sequence not ordinarily considered to be a match to a coding sequence). May consider multiple feature definitions where available (e.g. TSS annotation from FANTOM and NCBI or Ensembl may differ significantly -- in lax mode, a match near either site for a gene would be considered a hit).	Nmer barcode to gene mapping via lax sgRNA sequence match to NCBI-annotated genes in GRCm38.	2022-12-01	chip

GRCm38 Ensembl	strict[?] "strict" CHIP files Strict CHIP files are generated using the most stringent criteria to determine whether a perturbagen sequence matches the reference target: Strict shRNA CHIP files: Use the full 21mer shRNA target sequence to determine perfect transcriptome matches. Strict sgRNA CHIP files: Use the full 20mer (for S. pyogenes Cas9) or 21mer (for S. aureus Cas9) sgRNA target sequence to assess perfect matches to genomic PAM sites. Only consider matches where the "cut site" is properly contained in or touching (at extreme edge of) a target genomic feature loci. Consider only the "best" feature definition where multiple are available (e.g. TSS annotation from FANTOM and NCBI or Ensembl may differ significantly -- in strict mode, we restrict matches to the single highest confidence annotated locus).	Nmer barcode to gene mapping via strict sgRNA sequence match to Ensembl-annotated genes in GRCm38.	2022-12-01	chip [preferred]
	lax[?] "lax" CHIP files Lax CHIP files are generated using less stringent criteria to determine whether a perturbagen sequence matches the reference target: Lax shRNA CHIP files: Use only the initial 19mer of the shRNA target sequence to determine "perfect" transcriptome matches. Lax sgRNA CHIP files: Use only the final 17mer (for S. pyogenes Cas9) or 18mer (for S. aureus Cas9) of the sgRNA target sequence to assess "perfect" matches to genomic PAM sites. Allow 10 bases of "slop" around target genomic feature loci (e.g. intronic sequence not ordinarily considered to be a match to a coding sequence). May consider multiple feature definitions where available (e.g. TSS annotation from FANTOM and NCBI or Ensembl may differ significantly -- in lax mode, a match near either site for a gene would be considered a hit).	Nmer barcode to gene mapping via lax sgRNA sequence match to Ensembl-annotated genes in GRCm38.	2022-12-01	chip

(Original Target)	origtarget[?]The gene that this construct was originally designed to target	Nmer barcode to gene mapping using the construct's originally intended target gene, if known.	2022-03-24	chip
Other Files
File Type		Description	Last Changed	Download

GRCm38 BED file		Track data in the UCSC BED format, with all perfect sgRNA target sequence (Nmer) matches at PAM sites in GRCm38.	2020-06-17	bed
Reference file		Associates all Nmer barcodes in the pool with their construct ID(s), if any. Used for sequence deconvolution, e.g., with PoolQ.	2016-01-20	ref

Pool: CP0045 (sgRNA) - Brie Genome 1-4

File Downloads

"strict" CHIP files

Strict shRNA CHIP files:

Strict sgRNA CHIP files:

"lax" CHIP files

Lax shRNA CHIP files: