| Type |
File |
Last Changed |
Target |
Match |
Description |
| 1 |
Reference[?]Reference File Columns:
- Barcode Sequence
- Construct ID
- (Optional) Target Sequence
|
CP0003_reference_20150109.csv |
2015-01-09 |
n/a |
n/a |
Lists all 21mer barcodes contained in the pool, with their associated construct ID(s), if any. Used during initial sequence deconvolution, e.g. with PoolQ. |
| 2 |
CHIP[?]"gene" CHIP File Columns:
- Barcode Sequence
- Gene Symbol
- Gene ID
"trans" CHIP File Columns:
- Barcode Sequence
- Transcript
- Gene Symbol
- Gene ID
|
CP0003_lax_gene_20200722.chip |
2020-07-22 |
gene |
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).
|
21mer barcode to gene mapping via 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).
shRNA target sequence match to gene's transcripts. |
| 3 |
CHIP[?]"gene" CHIP File Columns:
- Barcode Sequence
- Gene Symbol
- Gene ID
"trans" CHIP File Columns:
- Barcode Sequence
- Transcript
- Gene Symbol
- Gene ID
|
CP0003_lax_trans_20200722.chip |
2020-07-22 |
transcript |
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).
|
21mer barcode to transcript mapping via 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).
shRNA target sequence match. |
| 4 |
CHIP[?]"gene" CHIP File Columns:
- Barcode Sequence
- Gene Symbol
- Gene ID
"trans" CHIP File Columns:
- Barcode Sequence
- Transcript
- Gene Symbol
- Gene ID
|
CP0003_origtarget_20140919.chip |
2014-09-19 |
gene |
n/a |
21mer barcode to gene mapping using construct's originally intended target gene, if known. |
| 5 |
CHIP[?]"gene" CHIP File Columns:
- Barcode Sequence
- Gene Symbol
- Gene ID
"trans" CHIP File Columns:
- Barcode Sequence
- Transcript
- Gene Symbol
- Gene ID
|
CP0003_strict_gene_20200722.chip |
2020-07-22 |
gene |
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).
|
(PREFERRED) 21mer barcode to gene mapping via 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).
shRNA target sequence match to gene's transcripts. |
| 6 |
CHIP[?]"gene" CHIP File Columns:
- Barcode Sequence
- Gene Symbol
- Gene ID
"trans" CHIP File Columns:
- Barcode Sequence
- Transcript
- Gene Symbol
- Gene ID
|
CP0003_strict_trans_20200722.chip |
2020-07-22 |
transcript |
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).
|
21mer barcode to transcript mapping via 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).
shRNA target sequence match. |
