|
| Status |
Public on Oct 21, 2020 |
| Title |
BatchC_C9O_0052_d18 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived motor neurons
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CS52iALS-C9n6
genotype: ALS C9orf72
days of differentiation: 18
capture platform: Illumina Bio-Rad ddSEQ System
library construction kit: Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit
batch: Batch C
genome alignment: hg19
|
| Growth protocol |
Differentiation was performed essentially as described in Maury et al. Nat Biotechnol, 2015
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Live cells were dissociated with 0.25% Trypsin-EDTA, filtered, and counted. Single cell capture was performed using the Illumina Bio-Rad ddSEQ System or 10X Genomics Chromium Controller. Sample specific information can be found in the 'Capture Platform' column in the Samples section.
cDNA libraries were prepared following the manufacturer's instructions using the Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit or 10X Chromium Single Cell 3’ Library & Gel Bead Kit v2. Sample specific information can be found under the 'Library Construction Kit' column in the Samples section.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: BatchC_ddSEQ_UMIcounts.csv
|
| Data processing |
Raw sequencing reads were demultiplexed and processed to FASTQ using Illumina bcl2fastq.
Sample reads were aligned to the transcriptome and uniquely mapped reads were counted and assigned to cell specific barcodes. For ddSEQ libraries, reads were aligned and demultiplexed using Illumina Single-Cell RNA Seq BaseSpace Workflow (v1.0.0) with STAR Aligner (v2.5.2b) and hg19 reference genome. For 10X libraries, reads were aligned and demultiplexed using 10X Genomics Cell Ranger (v2.1.0) with STAR Aligner (v2.5.1) and GRCh38 reference genome.
Cell barcodes used to generate processed UMI counts for each sample are contained in CellBarcodes.csv
Genome_build: hg19 or GRCh38
Supplementary_files_format_and_content: processed UMI counts
|
| |
|
| Submission date |
Sep 27, 2019 |
| Last update date |
Oct 21, 2020 |
| Contact name |
Michael Workman |
| E-mail(s) |
michael.workman@cshs.org
|
| Organization name |
Cedars-Sinai Medical Center
|
| Street address |
8700 Beverly Blvd., AHSP Suite 8405
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE138121 |
scRNAseq of human iPSC-derived motor neurons from control and ALS patients. |
|
| Relations |
| BioSample |
SAMN12863750 |
| SRA |
SRX6917517 |
