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Sample GSM5452187 Query DataSets for GSM5452187
Status Public on Dec 31, 2022
Title D08_IWP2
Sample type SRA
 
Source name 3D inner ear organoid
Organism Mus musculus
Characteristics cell type: R1E derived Inner ear organoid
treatment: 0 uM CHIR + 4 uM IWP2
induction day: 8
Extracted molecule total RNA
Extraction protocol Dissociated organoids in TrypLE. Dissociated cells were filtered through 40µM cell strainer follwed by three washes in 2% BSA/DPBS. Finally, suspended in 2%BSA/DPBS.
Single cell 3’ RNA-seq experiment is conducted using the Chromium single cell system (10x Genomics, Inc) and the NovaSeq 6000 sequencer (Illumina, Inc).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The single cell suspension was first counted on the Countess II FL for cell number, cell viability, and cell size. 
Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000.
Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics).
Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA. The resulting library was sequenced using a custom program on Illumina NovaSeq 6000.
CellRanger 3.1.0 was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were analized with the Rpackage Seurat (version 2.3.1) with Rstudio version 1.1.453 and R version 3.5.1
 
Submission date Jul 14, 2021
Last update date Dec 31, 2022
Contact name Pei-Ciao Tang
E-mail(s) peictang@med.miami.edu
Phone 3373260631
Organization name University of Miami
Department Otolayrngology
Street address 1501 NW 10th Avenue, Miami, FL 33136, 926 F2
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
 
Platform ID GPL24247
Series (1)
GSE180062 Wnt signaling promotes cell caudalization and inner ear differentiation in mouse stem cell-derived organoids
Relations
BioSample SAMN20207156
SRA SRX11439001

Supplementary file Size Download File type/resource
GSM5452187_D08_IWP_barcodes.tsv.gz 77.4 Kb (ftp)(http) TSV
GSM5452187_D08_IWP_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM5452187_D08_IWP_matrix.mtx.gz 164.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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