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Status |
Public on Aug 25, 2016 |
Title |
Vsx2_2a_B6_S114_R1_001 |
Sample type |
SRA |
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Source name |
Mus musculus retina, P17
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Organism |
Mus musculus |
Characteristics |
tissue: retina genotype: Vsx2-GFP developmental stage: P17
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Extracted molecule |
total RNA |
Extraction protocol |
Dissociated retina were FACS sorted into 96-well plates (single cells) and tubes (bulk libraries) containing lysis buffer Smart-seq2 (Picelli et al., Nature Methods, 2014)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
single cell
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Data processing |
Base calls performed using bcl2fastq2.15 Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values) Genome_build: mm10 Supplementary_files_format_and_content: text files with tab delimiters containing inferred counts and tpm values.
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Submission date |
Apr 13, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Karthik Shekhar |
E-mail(s) |
karthik@broadinstitute.org
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Phone |
217-979-9852
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Organization name |
Broad Institute
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Street address |
415 Main St.
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (2) |
GSE80232 |
Smart-seq2 analysis of P17 FACS sorted retinal cells from the Tg(Chx10-EGFP/cre,-ALPP)2Clc or Vsx2-GFP transgenic line |
GSE81905 |
Single cell RNA-sequencing of retinal bipolar cells |
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Relations |
BioSample |
SAMN04849546 |
SRA |
SRX1702224 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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