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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 05, 2020 |
| Title |
Atopic1 |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: PBMCs
allergy status: atopic dermatitis
breed: Cocker Spaniel
Sex: male
age (years): 13
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| Extracted molecule |
total RNA |
| Extraction protocol |
Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2015)
Nextera XT Library Preparation Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Drop-seq Core Computation Protocol (version 2.0.0, 9/28/18) with Drop-seq_tools-1-12; Default pipeline and settings unless noted otherwise.
FastqToSam (Picard-tools-2.8.2)
TagBamWithReadSequenceExtended (BASE_RANGE= 1-12, BASE_QUALITY= 10, BARCODED_READ= 1, DISCARD_READ= False, TAG_NAME= XC, NUM_BASES_BELOW_QUALITY= 1)
TagBamWithReadSequenceExtended (BASE_RANGE= 13-20, BASE_QUALITY= 10, BARCODED_READ= 1, DISCARD_READ= True, TAG_NAME= XM, NUM_BASES_BELOW_QUALITY= 1)
FilterBAM (TAG_REJECT= Q)
TrimStartingSequence (SEQUENCE= AAGCAGTGGTATCAACGCAGAGTGAATGGG, MISMATCHES=0, NUM_BASES= 5)
SamToFastq (Picard-tools-2.8.2)
STAR-2.7.0f alignment with CanFam3.1 and CanFam3.1.96 from ensembl
SortSam (SO= queryname) (Picard-tools-2.8.2)
MergeBamAlignment (INCLUDE_SECONDARY_ALIGNMENT= false, PAIRED_RUN= false) (Picard-tools-2.8.2)
TagReadWithGeneExon (TAG= GE)
DigitalExpression (MIN_NUM_GENES_PER_CELL= 10)
Genome_build: CanFam3.1 and CanFam3.1.96 from ensembl
Supplementary_files_format_and_content: .txt (single-cell digital gene expression matrix)
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| Submission date |
Feb 04, 2020 |
| Last update date |
Feb 05, 2020 |
| Contact name |
Elia Tait Wojno |
| Organization name |
University of Washington
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| Department |
Department of Immunology
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| Lab |
Tait Wojno lab
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| Street address |
750 Republican St.
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL21400 |
| Series (1) |
| GSE144730 |
Single-cell RNA sequencing quantitative analysis of PBMC transcriptomes from dogs with atopic dermatitis and healthy dogs |
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| Relations |
| BioSample |
SAMN13979609 |
| SRA |
SRX7670257 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4294449_Atopic1_gene_exon_tagged.dge.txt.gz |
8.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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