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Sample GSM4193064 Query DataSets for GSM4193064
Status Public on Nov 27, 2019
Title RNAExp29
Sample type SRA
 
Source name Jurkat cell line and Nalm6 cell line
Organism Homo sapiens
Characteristics cell line: Jurkat cell line and Nalm6 cell line
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
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Library strategy: Single cell barcoding by split-pool synthesis via ligation
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.
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 Nov 26, 2019
Last update date Nov 27, 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 GPL18573
Series (1)
GSE130784 Ultra-High Throughput Single Cell Analysis of Proteins and RNAs by Split-pool Synthesis
Relations
BioSample SAMN13390049
SRA SRX7217827

Supplementary file Size Download File type/resource
GSM4193064_RNAExp29-Jurkat-Nalm6-50k-exo-12cycles_S2_7_3_14_2.JITTERED_forFCS.txt.gz 2.2 Mb (ftp)(http) TXT
GSM4193064_RNAExp29-Jurkat-Nalm6-50k-exo-12cycles_S2_7_3_14_2.UNJITTERED_forFCS_normalized_filtered_Chi2Pval_1.0_jittered0.5.txt.gz 6.7 Mb (ftp)(http) TXT
GSM4193064_RNAExp29.tar.gz 1.9 Kb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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