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| Status |
Public on Mar 01, 2019 |
| Title |
mx-ADT |
| Sample type |
SRA |
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| Source name |
HEK-293T, NIH-3T3, PBMCs, MyLa, Sez4
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: HEK-293T, NIH-3T3, PBMCs, MyLa, Sez4
antibodies/tag: 12 bases tag: hCD29, mCD29
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| Treatment protocol |
K562, NIH-3T3 and peripheral blood mononuclear cells (PBMCs) were stained as described for CITE-seq (Stoeckius et al, 2017)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
‘Stained’ and washed cells were loaded into 10x Genomics single cell 5’ system and processed according to manufacturer’s instructions, and the CITE-seq protocols (Stoeckius et al, 2017). For sgRNA capture a custom RT primer was spiked in during the RT reaction.
library construction was performed with the 10x Genomics single cell 5' (VDJ) product.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
antibody oligos
processed data file:
mx-ADT-count.csv.gz
mx-ADT-count.csv.gz includes: raw counts for 12 bases ADT
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| Data processing |
Library strategy: ECCITE-seq
10x data were processed using cellranger and cellranger vdj pipeline
R1 includes cell barcode, UMI read
R2 is the biological read
ADT data were mapped to a 12 bases or a 15 bases reference ADT list separately using CITE-seq-count
HTO data were mapped to a 12 bases reference HTO list using CITE-seq-count
GDO data were mapped to a 19 bases reference GDO list using CITE-seq-count
ADT, HTO and GDO sequence lists are available at: https://www.biorxiv.org/content/10.1101/466466v1
Genome_build: hg19 for human only samples
Genome_build: samples with both human and mouse cells were mapped to the hg19-mm10 concatenated reference as provided by cell-ranger
Supplementary_files_format_and_content: tab-delimited text file for 10x data; comma-delimited file for ADT, HTO, GDO and clonotype mapping
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| Submission date |
Feb 08, 2019 |
| Last update date |
Mar 01, 2019 |
| Contact name |
Eleni Mimitou |
| E-mail(s) |
emimitou@gmail.com
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| Organization name |
New York Genome Center
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| Lab |
Technology Innovation Lab
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| Street address |
101 Avenue of the Americas
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platform ID |
GPL22245 |
| Series (1) |
| GSE126310 |
Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay |
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| Relations |
| BioSample |
SAMN10897802 |
| SRA |
SRX5352860 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3596085_mx-ADT-count.csv.gz |
120.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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