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Sample GSM7373478 Query DataSets for GSM7373478
Status Public on Jun 21, 2023
Title E10.5d TEPC, scRNAseq SmartSeq2
Sample type SRA
 
Source name thymus
Organism Mus musculus
Characteristics tissue: thymus
cell type: thymic epithelial progenitors
genotype: wild type
developmental stage: E10.5 primordia
Extracted molecule polyA RNA
Extraction protocol Individual EPCAM+PLET1+ cells from E10.5 or E12.5 primordia were sorted into 96-well BD Precise WTA Single Cell Encoding Plates. The plates were sealed and stored at -80oC until library preparation. Four plates (376 cells) were collected per timepoint.
Reverse transcription was performed in the presence of ERCC RNA control. The 96 samples from each plate were then pooled and purified with Agencourt® AMPure® XP magnetic beads (clean-up step). Second strand synthesis was carried out and the resulting products cleaned up. Following adaptor ligation and clean-up, ligation products were PCR amplified for 18 cycles overnight, and all subsequent steps were performed in a separate post-amplification area. The amplified products were cleaned up and quantified using Qubit dsDNA HS Assay. 50ng of the products then underwent random primer extension and 12 cycles of further amplification. The amplified libraries were cleaned up and quantified with Qubit assay. The libraries were stored at -80oC until sequencing. The libraries were sequenced on Illumina MiSeq at the Wellcome Centre for Human Genetics in Oxford within 6 months of preparation.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing Preprocessing of the FASTQ files was performed using the BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0. This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
Assembly: GRCm38.p5
Supplementary files format and content: 7Bridges PDF Summary Report = Provides an overview of each sequenced library.
Supplementary files format and content: 7Bridges DBEC Molecular Index Mapping report = Reports the number of unique molecular indices seen associated with each individual transcript per well.
Supplementary files format and content: 7Bridges DBEC Read Mapping report = Reports the number of reads that mapped to a given transcript in each of 96 wells.
Supplementary files format and content: 7Bridges Sample Barcodes (Sample Index) report = Summarizes the number of reads that have been assigned to each well.
Supplementary files format and content: 7Bridges Raw Molecular index counts = Reports the raw counts for each unique molecular index detected for each gene in each well.
Supplementary files format and content: 7Bridges Raw read counts = Reports raw read counts for each gene in each well.
Supplementary files format and content: 7Bridges FastQC Reports = Provides metrics to assess overall quality of the input sequencing reads.
Supplementary files format and content: 7Bridges RSEC Molecular Index Counts = Reports RSEC adjusted MI counts for each gene in each well.
Supplementary files format and content: 7Bridges Status Report = Reports sequencing depth metrics according to gene and well. The summary is in the MI_Detection column in the DBEC Molecular Index Mapping report.
 
Submission date May 17, 2023
Last update date Jul 14, 2023
Contact name Catherine Clare Blackburn
E-mail(s) c.blackburn@ed.ac.uk
Phone +447810223009
Organization name University of Edinburgh
Department School of Biological Sciences
Lab Thymus generation and regeneration
Street address IRR North, 5 Little France Drive
City Edinburgh
ZIP/Postal code EH16 4UU
Country United Kingdom
 
Platform ID GPL16417
Series (1)
GSE232765 Thymic epithelial cell potency and fate in early organogenesis assessed by single cell transcriptional and functional analysis [Smart-Seq2]
Relations
BioSample SAMN35148841
SRA SRX20405363

Supplementary file Size Download File type/resource
GSM7373478_461219_SampleIndex.csv.gz 1.3 Kb (ftp)(http) CSV
GSM7373478_DBEC_MolecularIndexMapping_461219.csv.gz 633.8 Kb (ftp)(http) CSV
GSM7373478_DBEC_ReadMapping_461219.csv.gz 766.1 Kb (ftp)(http) CSV
GSM7373478_RSEC_MolecularIndexCounts_461219.csv.gz 667.5 Kb (ftp)(http) CSV
GSM7373478_StatusReport_461219.csv.gz 899.1 Kb (ftp)(http) CSV
GSM7373478_WTA_SummaryReport_461219.pdf 1.2 Mb (ftp)(http) PDF
GSM7373478_WTCHG_461219_1_fastqc.b64html.txt.gz 241.0 Kb (ftp)(http) TXT
GSM7373478_WTCHG_461219_1_fastqc.zip 374.1 Kb (ftp)(http) ZIP
GSM7373478_WTCHG_461219_2_fastqc.b64html.txt.gz 266.3 Kb (ftp)(http) TXT
GSM7373478_WTCHG_461219_2_fastqc.zip 422.3 Kb (ftp)(http) ZIP
GSM7373478_raw_MolecularIndexCounts_461219.csv.gz 673.2 Kb (ftp)(http) CSV
GSM7373478_raw_ReadCounts_461219.csv.gz 827.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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