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Sample GSM3753578 Query DataSets for GSM3753578
Status Public on May 07, 2019
Title exp108
Sample type SRA
 
Source name Jurkat cell line and Nalm-6 cell line
Organism Homo sapiens
Characteristics strain: cell lines
cell line: Jurkat and Nalm-6
molecule type: various targeted RNA transcripts
Growth protocol Jurkat cells and Nalm-6 cells were obtained from America Type Tissue Collection (ATCC). Cells at a density of ~1×106/mL were fixed in RPMI medium without serum in 1.6% paraformaldehyde (Electronic Microscopy Sciences) for 10 min at room temperature under gentle agitation. Cells were pelleted and permeabilized with ice-cold methanol for at least 10 min on ice. Once in methanol cells can be stored at −80 °C for several weeks without loss of antibody signal or RNA degradation.
Extracted molecule total RNA
Extraction protocol QIAquick Gel Extraction Kit (Qiagen, 28704).
PCR with Illumina dual index primers
Single cell barcoding by split-pool synthesis via ligation
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description 108.tar.gz
Data processing FLASH-1.2.11 was used to merge the paired end reads.
seqtk-v1.2 was used to convert merged fastq file to fasta format.
The reads were then parsed to identify cell-id and marker-id based on the white-list info in the associated qdata folder, deduplicated based on cell-id and marker-ids and finally chimeric reads were filtered out.
Expression counts were then used to remove putative debris and doublets cells based on the criteria listed in Singlet_settings.txt in the corresponding qdata folder.
Expression counts matrix was then normalized by scaling the counts by row-means and multiplying by a factor of 10.
Genome_build: A github repository for the software used to process the raw-fastqs is available at the following location: https://github.com/bioinform/QBC_Single_Cell_Analysis_NGS
Supplementary_files_format_and_content: Tab separated text files containing jittered expression counts (both normalized and un-normalized) for different markers for each individual cell
The *tar.gz contains various files containing white-list information for cell-barcode ids, anchor-sequence info, marker-sequence info and settings information for removal of cell-debris and cell-doublets. The files in this folder is used to process the raw fastqs for each of the experiment.
 
Submission date May 06, 2019
Last update date May 09, 2019
Contact name Maeve Ohuallachain
E-mail(s) maeve.ohuallachain@roche.com
Organization name ROCHE SEQUENCING SOLUTIONS INC
Street address 4300 Hacienda Drive
City Pleasanton
State/province CALIFORNIA
ZIP/Postal code 94588
Country USA
 
Platform ID GPL15520
Series (1)
GSE130784 Ultra-High Throughput Single Cell Analysis of Proteins and RNAs by Split-pool Synthesis
Relations
BioSample SAMN11583092
SRA SRX5797838

Supplementary file Size Download File type/resource
GSM3753578_108.txt.tar.gz 1.1 Kb (ftp)(http) TAR
GSM3753578_exp108_S1_L001_2_2_99_1.JITTERED_forFCS.txt.gz 252.1 Kb (ftp)(http) TXT
GSM3753578_exp108_S1_L001_2_2_99_1.UNJITTERED_forFCS_normalized_filtered_Chi2Pval_1.0_jittered0.5.txt.gz 715.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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