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Update 10X Conventions
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Jun 08, 2023
by
Cornelius Fischer
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# Project information
*
Project number (PID):
` `
*
Single cell project number (SPID):
` `
-
[ ] no single cell project defined
*
Data analysis by DM
-
[ ] required for QC single-cell team Genomics
-
[ ] required for user
-
[ ] not required (done by CUBI)
-
[ ] not required (done by user)
*
Pipeline selection
-
[ ] cellranger / spaceranger count
-
[ ] cellranger / spaceranger aggr (aggregate anaylsis)
-
[ ] include BAM files
*
Data reciever
-
[ ] all data reciever are listed in NGS overview and PRF
-
[ ] following accounts are data resiever:
[TOC]
# Data analyis information
-
[ ]
**3GEX**
(3' Gene Expression libraries)
-
[ ] Library transfer table (sheet in prf)
-
[
] Library name (with [library names formats
](
Single-Cell-Gene-Expression-Analysis-Request#library-names-formats
)
)
-
[
] index name (see [library Iindex sets
](
Single-Cell-Gene-Expression#gene-expression-library-index-sets
)
)
-
[ ] index sequence (optional)
-
[ ] library type incl. chemistry version
*
organism (see
[
references and probe sets
](
References-and-Probe-sets
)
)
-
[ ] Human
-
[ ] Mouse
-
[ ] other:
-
[ ] transgenic inserts:
-
[
] **3CS** (3' [Feature barcoding
](
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
)
libraries)
-
[
] Feature Reference (required [see
](
Single-Cell-Gene-Expression#feature-reference-csv-file
)
)
-
[ ] TotalSeq-B (with 3GEX)
-
[ ] TotalSeq-A (less common)
-
[
] **CellPlex** (3’ [Cell Multiplexing
](
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi#cmoreference
)
CMOs libraries)
-
[
] Barcode-sample assignment (required, [see
](
Single-Cell-Gene-Expression#barcode-sample-assignment
)
)
## Library names formats:
# Library names formats:
*
PID_SPID_SPNumber (minimum requirenment, e.g. P1234_SP123_004)
*
PID_SPID_SPNumber_LibraryType (required, e.g. P1234_SP123_004_GEX)
*
PID_SPID_SPNumber_LibraryType_LibraryName (optional, e.g. P1234_SP123_004_GEX_Liver01)
#
# Gene expression Library Index Sets
# Gene expression Library Index Sets
*
Dual Index Kit
**TT**
, Set A : 3' Gene Expression (3GEX)
*
Dual Index Kit
**NT**
, Set A : 3' Antibody Capture / Feature barcoding (3CS)
*
Dual Index Kit
**NN**
, Set A : 3' Cell Multiplexing (CellPlex)
#
# Feature Reference CSV file ([example](https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/vdj_v1_hs_pbmc2_5gex_protein/vdj_v1_hs_pbmc2_5gex_protein_feature_ref.csv))
# Feature Reference CSV file ([example](https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/vdj_v1_hs_pbmc2_5gex_protein/vdj_v1_hs_pbmc2_5gex_protein_feature_ref.csv))
```
id,name,read,pattern,sequence,feature_type
...
...
@@ -55,8 +20,7 @@ CD4,CD4_TotalSeqB,R2,5PNNNNNNNNNN(BC),TACCCGTAATAGCGT,Antibody Capture
CD8a,CD8a_TotalSeqB,R2,5PNNNNNNNNNN(BC),ATTGGCACTCAGATG,Antibody Capture
```
## Barcode-sample assignment
# CellPlex barcode-sample assignment
```
sample_id,cmo_ids
...
...
...
...
