|
Status |
Public on Sep 09, 2016 |
Title |
SCRBseqB_TATGAA |
Sample type |
SRA |
|
|
Source name |
mouse embryonic cell line
|
Organism |
Mus musculus |
Characteristics |
library preparation: SCRB-seq cell line: J1
|
Growth protocol |
J1 mESC were cultured in ground pluripotency states by 2i/LIF culture as described previously.
|
Extracted molecule |
total RNA |
Extraction protocol |
single-cell lysate
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
|
|
Description |
Library preparations were performed with the SCRB-seq protocol from FACS-sorted single cells as described in Soumillon et al. 2014
|
Data processing |
base-calls were performed with Illumina bcl2fastq all cDNA reads were aligned with Star v2.4.0 SCRB-seq and Drop-seq protocol reads were tagged with its mate-pair UMI and cell barcode; unique reads were obtained; more information see README file Smart-seq and Smart-seq2 reads were assigned to genes using Rsubread only cells were considered with at least 1,000,000 reads; doublets discarded and failed libraries filtered by low nearest-neighbor correlation coefficients Genome_build: mm10 Supplementary_files_format_and_content: tab-delimited text file with unique gene-wise counts of cells considered for final analysis: ziegenhain_complete_data.txt
|
|
|
Submission date |
Jun 29, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Christoph Ziegenhain |
E-mail(s) |
ziegenhain@bio.lmu.de
|
Organization name |
Ludwig-Maximilians University Munich
|
Department |
Department Biology II
|
Lab |
Anthropology & Human genomics
|
Street address |
Großhaderner Str. 2
|
City |
Martinsried |
State/province |
Bavaria |
ZIP/Postal code |
82152 |
Country |
Germany |
|
|
Platform ID |
GPL18480 |
Series (1) |
GSE75790 |
Comparative analysis of single-cell RNA sequencing methods |
|
Relations |
BioSample |
SAMN05327279 |
SRA |
SRX1886157 |