|
| Status |
Public on Oct 09, 2018 |
| Title |
ΔH3.V/ΔH4.V_D5 |
| Sample type |
SRA |
| |
|
| Source name |
single cell
|
| Organism |
Trypanosoma brucei brucei |
| Characteristics |
strain: Lister 427 MITat 1.2
genotyope: TetR, T7RNAP, H3.V-/-, H4.V-/-
life cycle stage: bloodstream form
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted and lysed in lysis buffer ((0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water) and RNA was extracted from 1, 10 and 50 cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) with a fourth of the recommended volumes of reagents. PCR amplification was performed for 26 cycles.
Libraries were constructed using a Nextera XT kit (Illumina) according to the manufacturer's instructions, but using only one fourth of the recommended voulmens and 1 ng of cDNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv
|
| Data processing |
NextSeq 500
bcl2fastq v.20.0.422
cutadapt v.1.15
BWA-mem v0.7.16
python 3.6
samtools v1.8
bedtools v2.26.0
picard v2.9.0
Genome_build: Tb427v9
Supplementary_files_format_and_content: Feature counts of all RNA seq data from 1, 10 and 50 cells can be found in Feature_counts_scRNAseq_set_two.tsv. Single-cell samples with appropriate coverage (more than 500 genes captured with at least 10 read counts per gene) were considered for VSG expression analysis and are listed in VSG_raw_counts_scRNAseq_set_two.tsv.
Supplementary_files_format_and_content: txt; scRNA-seq normalization and quantification from scRNA-seq II
|
| |
|
| Submission date |
Oct 09, 2018 |
| Last update date |
Oct 10, 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 |
| |
|
| Platform ID |
GPL22141 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN10224104 |
| SRA |
SRX4820032 |
