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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 07, 2023 |
Title |
twi, pooled CD45+ cells |
Sample type |
SRA |
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Source name |
brain
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Organism |
Mus musculus |
Characteristics |
strain: C57Bl/6 tissue: brain age: Postnatal Day 21 cell type: CD45+ genotype: galc-/- treatment: none
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Extracted molecule |
total RNA |
Extraction protocol |
brain tissues were collected inot RPMI media and enzymatically dissociated using collagenase/dispase and DNAase (1h/37C). Following this, the cellular suspension was filtered (70uM) and then separated on a 70/30 Percoll gradient where leukocytes were collected at tht interphase. CD45+ cells were collected by flowcyotmetry (FACSARIA II, Becton-Dickinson). Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). CD4+ cells were resuspended in a master mix that was loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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Description |
10X Genomics
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Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) Supplementary files format and content: mm10 Supplementary files format and content: Tab-separated values files and matrix files
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Submission date |
May 24, 2023 |
Last update date |
Jun 07, 2023 |
Contact name |
Stephen Crocker |
E-mail(s) |
crocker@uchc.edu
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Phone |
8606798750
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Organization name |
University of Connecticut School of Medicine
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Department |
Neuroscience
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Street address |
263 Farmington Ave.
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City |
Farmington |
State/province |
Connecticut |
ZIP/Postal code |
06030 |
Country |
USA |
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Platform ID |
GPL21493 |
Series (1) |
GSE233320 |
Gene expression profile at single cell level of CD45+ cells isolated from twitcher (twi) mouse brain (postnatal day 21) |
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Relations |
BioSample |
SAMN35345447 |
SRA |
SRX20502035 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7422898_SC17003_barcodes.tsv.gz |
5.8 Kb |
(ftp)(http) |
TSV |
GSM7422898_SC17003_genes.tsv.gz |
212.7 Kb |
(ftp)(http) |
TSV |
GSM7422898_SC17003_matrix.mtx.gz |
5.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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