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Sample GSM3753567 Query DataSets for GSM3753567
Status Public on May 07, 2019
Title exp185T
Sample type SRA
 
Source name primary spleen cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: primary spleen cells
molecule type: various proteins
Growth protocol Spleen cells were obtained from C57/Blk6 mice, between 6-8 weeks of age. 16% formaldehyde solution (Thermo Scientific, 28908) was added directly to cells to a final concentration of 1.6% and incubated for 10 min at room temperature to fix the cells. Cells to be analyzed for only protein expression were stored in 1X PBS with 10% DMSO at -80°C until antibody staining.
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 185T.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 GPL16417
Series (1)
GSE130784 Ultra-High Throughput Single Cell Analysis of Proteins and RNAs by Split-pool Synthesis
Relations
BioSample SAMN11583103
SRA SRX5797827

Supplementary file Size Download File type/resource
GSM3753567_185T.txt.tar.gz 1.1 Kb (ftp)(http) TAR
GSM3753567_exp185T_S1_L001_10_3_4_1.JITTERED_forFCS.txt.gz 1.4 Mb (ftp)(http) TXT
GSM3753567_exp185T_S1_L001_10_3_4_1.UNJITTERED_forFCS_normalized_filtered_Chi2Pval_1.0_jittered0.5.txt.gz 3.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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