|
| Status |
Public on Apr 11, 2019 |
| Title |
POC_snRNAseq_Lane2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK_MEF_Jurkat
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: mixture of HEK,HMECS, and Jurkats
multi-seq reagent: LMO/CMO/None
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C.
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and using a custom MULTI-seq library preparation protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
nuclear polyA RNA
processed data files:
POC_nuc_barcodes.tsv
POC_nuc_genes.tsv
POC_nuc_matrix.mtx
|
| Data processing |
FASTQ files were generated directly from Illumina BCL files using Illumina bcl2fastq version 2.19
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.2 with default parameters (cellranger count).
Read-depth normalization was performed (when appropriate) using 10X Genomics CellRanger version 2.2 with default parameters (cellranger aggr).
Low-quality cell barcodes were excluded as described in the paper.
MULTI-seq barcode alignment and sample classification results were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Genome_build: hg19 (Samples 1-3, 6-12), concatenated mm10-hg19 (Sample 13-14), concatenated mm10-hg19 pre-mRNA (Sample 4-5)
Supplementary_files_format_and_content: Expression Libraries: gene-cell matrices are provided in the format produced by CellRanger. The matrix itself is in matrix market exchange format, with the column (cell barcodes) and row (gene identities) labels given in TSV format as described in the cellranger documentation. MULTI-seq Libraries: MULTI-seq barcode-cell matrices are provided in CSV format.
|
| |
|
| Submission date |
Apr 10, 2019 |
| Last update date |
Apr 14, 2019 |
| Contact name |
Christopher S McGinnis |
| E-mail(s) |
chris.mcginnis@ucsf.edu
|
| Organization name |
University of California, San Francisco
|
| Department |
Pharmaceutical Chemistry
|
| Lab |
Zev Gartner
|
| Street address |
600 16th Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE129578 |
MULTI-seq: Universal sample multiplexing for single-cell RNA sequencing using lipid-tagged indices |
|
| Relations |
| BioSample |
SAMN11388197 |
| SRA |
SRX5676298 |
