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Series GSE120515 Query DataSets for GSE120515
Status Public on Oct 09, 2018
Title Single-cell RNA sequencing in Trypanosoma brucei
Organisms Trypanosoma brucei brucei; other sequences
Experiment type Expression profiling by high throughput sequencing
Summary Trypanosomes were sorted (0 cells, 1 cell, 50 cells) using a FACSaria III (BD Biosciences; precision: single-cell; nozzle: 100 µm). Forward-scatter area (FCS-A) versus side-scatter area (SSC-A) was used to gate the cells. Trypanosomes were sorted in 48-wells plate (Brand) filled with 2.6 µL of lysis buffer (0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water). Immediately after sorting cells were placed on ice for 5 minutes and stored at -80 °C. 50 and single trypanosomes were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) using one fourth of reagents volumes compared to the supplier instructions. PCR amplification was performed using 26 cycles using supplier recommendations. cDNA was purified using XP beads (Beckman Coulter) and recovered in 15 µL of elution buffer (Takara). Libraries were quantified using the Qubit Hs Assay (Life Technologies) and the qualities of the libraries were further monitored using a Bioanalyzer (Agilent). Similar to what has been published previously 19, 1 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using one-quarter of the recommended volumes, 10 minuntes for tagmentation at 55 °C and 1 minute extension time during PCR amplification. Libraries were pooled (96 libraries for NextSeq) and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina's NextSeq 500.
 
Overall design 47 wild-type samples, 1 wild-type negative-control, 47 H3.V-/- H4.V-/- samples, 1 H3.V-/- H4.V-/- negative control
 
Contributor(s) Saliba A, Müller LS, Cosentino RO, Siegel TN
Citation(s) 30333624
Submission date Sep 26, 2018
Last update date Nov 01, 2018
Contact name Konrad U. Förstner
E-mail(s) foerstner@zbmed.de
Organization name ZB MED - Information Centre for Life Sciences
Department Information Services
Lab Förstner Lab
Street address Gleueler Str. 60
City Cologne
State/province North Rhine-Westphalia
ZIP/Postal code 50931
Country Germany
 
Platforms (2)
GPL22141 Illumina NextSeq 500 (Trypanosoma brucei brucei)
GPL24755 Illumina NextSeq 500 (other sequences)
Samples (96)
GSM3402343 wild-type 1 cell N701/S501
GSM3402344 wild-type 1 cell N702/S501
GSM3402345 wild-type 1 cell N703/S501
This SubSeries is part of SuperSeries:
GSE100896 H3.V and H4.V
Relations
BioProject PRJNA495370
SRA SRP164751

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120515_Feature_counts_scRNAseq_set_one.txt.gz 1.6 Kb (ftp)(http) TXT
GSE120515_VSG_raw_counts_scRNAseq_set_one.txt.gz 157.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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