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Sample GSM2452126 Query DataSets for GSM2452126
Status Public on Jan 31, 2017
Title Drop-Seq analysis of Pooled Arc-ME single-cell suspension_ad lib 60% high fat diet fed_1
Sample type SRA
 
Source name Arcuate Nucleus/Median Eminence
Organism Mus musculus
Characteristics strain: C57BL6/J
tissue: Arcuate-Median Eminence
Sex: M
average age: 47
number of mice pooled: 4
experimental condition: Ad lib fed 60% High fat diet
batch: Batch 4
Extracted molecule total RNA
Extraction protocol Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description HFD
Cell Barcodes are in read 1, gene sequence in read 2,
Data processing Base calls performed with bcl2fastq2.15.0.4
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Cells expressing >800 genes from Samples 1-11 were merged together into a single matrix. Merged DGE file from all 11 samples generated. log(1+10,000*(DGE normalized to total transcripts per cell)) calculated on DGE. This is the Merged_all_020816_DGE.txt.gz file containing 21,421 cell barcodes
Genes showing expression in <50 cells were removed and batch effect correction was performed using the removeBatchEffect function of edgeR
Data was Natural log transformed and cells were clustered using Seurat software (PCA followed by t-SNE and density clustering)
Cell clusters containing markers for more than one other cluster were considered doublets and were removed. Remaining cells are presented in manuscript and contained in Merged_all_020816_BatchCorrected_LNtransformed_doubletsremoved_Data.txt file
Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.
Supplementary_files_format_and_content: Merged_all_020816_DGE.txt: Digital Gene Expression Matrix of raw data
Supplementary_files_format_and_content: Merged_all_020816_BatchCorrected_LNtransformed_doubletsremoved_Data.txt: Digital Gene Expression Matrix, Batch corrected,natural log transformed, cell doublets removed
Supplementary_files_format_and_content: cell_metadata.txt: Metadata for individual cells based on final cluster assignments
 
Submission date Jan 10, 2017
Last update date May 15, 2019
Contact name Linus Tzu-Yen Tsai
E-mail(s) ltsai@bidmc.harvard.edu
Organization name Beth Israel Deaconess Medical Center
Department Medicine, Division of Endocrinology, Diabetes, and Metabolism
Street address 330 Brookline Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19057
Series (1)
GSE93374 A Molecular Census of Arcuate Hypothalamus and Median Eminence Cell Types
Relations
BioSample SAMN06215611
SRA SRX2481512

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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