Back to Clone Pool Index
Pool:
CP0053 (sgRNA) - Calabrese Set B
- Name:
- CP0053
- Type:
- S. pyogenes Cas9 CRISPRa
- Sub type:
- Single insert
- Taxon:
- Human
- Vectors:
- pXPR_502
- Distinct barcodes:
- 56476
- Addgene ID:
- 92380
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 |
|
|
GRCh38 NCBI |
strict[?]"strict" CHIP filesStrict 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 GRCh38. |
2024-01-30 |
chip [preferred] |
|
|
lax[?]"lax" CHIP filesLax 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 GRCh38. |
2024-01-30 |
chip |
|
|
GRCh38 Ensembl |
strict[?]"strict" CHIP filesStrict 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 GRCh38. |
2024-07-28 |
chip [preferred] |
|
|
lax[?]"lax" CHIP filesLax 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 GRCh38. |
2024-07-28 |
chip |
|
|
GRCh37 NCBI |
strict[?]"strict" CHIP filesStrict 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 GRCh37. |
2022-12-01 |
chip [preferred] |
|
|
lax[?]"lax" CHIP filesLax 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 GRCh37. |
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. |
2019-10-21 |
chip |
| Other Files |
|
|
GRCh37 BED file |
| Track data in the UCSC BED format, with all perfect sgRNA target sequence (Nmer) matches at PAM sites in GRCh37. |
2020-06-17 |
bed |
|
GRCh38 BED file |
| Track data in the UCSC BED format, with all perfect sgRNA target sequence (Nmer) matches at PAM sites in GRCh38. |
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. |
2017-01-06 |
ref |
