|
| Status |
Public on Jun 05, 2018 |
| Title |
B2B_ASCL1_SOX2_DORSO_2_d14 |
| Sample type |
SRA |
| |
|
| Source name |
ASCL1_SOX2_DORSO_2_d14
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: Donor 1
tissue source: brain
cell type: pericytes or pericyte-derived induced neuronal cells
genotype/variation: Ascl1 and Sox2 transduced
timepoint (days post infection): d14
|
| Growth protocol |
Differentiation medium plus dorsomorphin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell isolation by FACS and cDNA generation following SmartSeq2 protocol. (Nat Protoc. 2014 Jan;9(1):171-81. doi: 10.1038/nprot.2014.006. Epub 2014 Jan 2.)
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
B2B_Ascl1Sox2Dorso2d14
Single cell transcriptome from pericytes or pericyte-derived induced neuronal cells
processed data file: data.master.csv
|
| Data processing |
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) or mouse genome (mm10 from UCSC) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.
|
| |
|
| Submission date |
May 08, 2018 |
| Last update date |
Jun 05, 2018 |
| Contact name |
Gray Camp |
| E-mail(s) |
graycamp@gmail.com
|
| Organization name |
Max Planck Institute for Evolutionary Anthropology
|
| Department |
Evolutionary Genetics
|
| Street address |
Deutscher Pl. 6
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE113036 |
Pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program |
|
| Relations |
| BioSample |
SAMN09089736 |
| SRA |
SRX4052474 |
