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| Status |
Public on Jul 25, 2019 |
| Title |
RatIC_NC2_DMSO |
| Sample type |
SRA |
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| Source name |
immune cells
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| Organism |
Rattus norvegicus |
| Characteristics |
timepoint: week 3
preservation protocol: DMSO cryopreservation
strain: Han Wistar
tissue: liver
diet: CSAA
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Livers were sequentially pushed through 500 µm, 200 µm and 70 µm filters and the cells were washed using chilled PBS/0.5 % FCS buffer. Erythrocytes were lysed using RBC Lysis Buffer (Invitrogen, Thermo Fisher Scientific, Waltham, MA) and the cells were resuspended in 15 mL of PBS/0.5 % FCS buffer. The cell suspension was transferred on top of 12 mL of Lymphocyte Separation Medium (Lonza, Basel, Switzerland) and centrifuged for 20 min at 400 g and 4 °C (brake set to 7) to separate the immune cells. Droplet-based single-cell partitioning of washed immune cells was performed using the 10X Genomics Chromium Controller.
Single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3′ Reagent v2 Kit (10X Genomics, Pleasanton, CA) according to the manufacturer´s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Animals were either fed with choline-sufficient, l-amino acid-defined (CSAA) diet or choline-deficient, l-amino acid-defined (CDAA) diet
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| Data processing |
Reads: Read 1: 26 bp (cell barcode and UMI), Index read: 8, Read 2: 98 (sequence read)
Data were processed with Cell Ranger version 2.1.1. Raw base BCL files were demultiplexed using "cellranger mkfastq" and bcl2fastq v2.17.1.14. FASTQ files generated from "cellranger mkfastq" were further processed by "cellranger count" which made use of STAR to align the 98 bp sequence read against Rnor6.0. Filtering for valid cell barcodes and quantification of cell barcodes as well as unique molecular identifiers (UMIs) was also performed using "cellranger count".
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Market Exchange format containing three files: tab-separated values files containing barcodes and annotated genes, respectively, matrix file containing UMI counts and indices for the barcode and gene tsv files
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| Submission date |
Feb 27, 2019 |
| Last update date |
Jul 25, 2019 |
| Contact name |
Christian Thaddaeus Wohnhaas |
| Organization name |
Boehringer Ingelheim
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| Street address |
Birkendorfer Straße 65
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| City |
Biberach |
| ZIP/Postal code |
88397 |
| Country |
Germany |
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| Platform ID |
GPL22396 |
| Series (2) |
| GSE127248 |
DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells [10X Genomics] |
| GSE127249 |
DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells |
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| Relations |
| BioSample |
SAMN11027000 |
| SRA |
SRX5444497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3633092_RatIC_NC2_DMSO.barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSM3633092_RatIC_NC2_DMSO.genes.tsv.gz |
248.6 Kb |
(ftp)(http) |
TSV |
| GSM3633092_RatIC_NC2_DMSO.matrix.mtx.gz |
20.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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