GSE107122 Processing Pipeline

RNA-Seq code_examples 4 steps

Publication

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.

Neuron (2024) — PMID 38697111

Dataset

GSE107122

Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook
  1. 1

    FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2 Jan2016, http://mccarrolllab.com/dropseq/)

    scRNA-seq v1.12
  2. 2

    The number of cell barcodes per embryonic age was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.

  3. 3

    2000 Barcodes were selected at E11.5, E13.5 and E17.5 and 5000 Barcodes at E15.5

  4. 4

    Two batches data collected from E15.5 embryos (Batch1 and Batch2) were combined together.

Tools Used

scRNA-seq
Raw Source Text 
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2 Jan2016, http://mccarrolllab.com/dropseq/)
The number of cell barcodes per embryonic age was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
2000 Barcodes were selected at E11.5, E13.5 and E17.5 and 5000 Barcodes at E15.5
Two batches data collected from E15.5 embryos (Batch1 and Batch2) were combined together.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing raw digital gene expression for each embryonic age. Two processed data files are included per age. One containing all data for all cells and one containing only cells predicted as cortical in origin.
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