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Sample GSM3596086 Query DataSets for GSM3596086
Status Public on Mar 01, 2019
Title mx-HTO
Sample type SRA
Source name HEK-293T, NIH-3T3, PBMCs, MyLa, Sez4
Organisms Homo sapiens; Mus musculus
Characteristics cell type: HEK-293T, NIH-3T3, PBMCs, MyLa, Sez4
antibodies/tag: 12 bases tag: hashtag_1, hashtag_2, hashtag_3, hashtag_A, hashtag_B, hashtag_C, hashtag_D, hashtag_E, hashtag_F, hashtag_G
Treatment protocol K562, NIH-3T3 and peripheral blood mononuclear cells (PBMCs) were stained as described for CITE-seq (Stoeckius et al, 2017)
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.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
Description antibody oligos
processed data file:
mx-HTO-count.csv.gz includes: raw counts for 12 bases HTO
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:
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
Submission date Feb 08, 2019
Last update date Mar 01, 2019
Contact name Eleni Mimitou
Organization name New York Genome Center
Lab Technology Innovation Lab
Street address 101 Avenue of the Americas
City New York
State/province NY
ZIP/Postal code 10013
Country USA
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
BioSample SAMN10897800
SRA SRX5352861

Supplementary file Size Download File type/resource
GSM3596086_mx-HTO-count.csv.gz 167.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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