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Sample GSM4795207 Query DataSets for GSM4795207
Status Public on Jul 02, 2021
Title WT_RPS2_STAMP [10X]
Sample type SRA
Source name MDA-MB-231-LM2
Organism Homo sapiens
Characteristics cell type: MDA-MB-231-LM2
treatment: Doxycycline
cell culture: DMEM + 10% FBS
Treatment protocol Mice were maintained on 5% sucrose water with 2mg/mL Doxycycline for 3 days before tumor extraction and dissociation.
Growth protocol MDA-MB-231-LM2 cells were cultured in DMEM + 10% FBS. Cells were split every 3-4 days. For 10X experiments cells were subcutaneously injected in the flank of mice and grown for 6 weeks before tumor dissociation and 10X library preparation.
Extracted molecule total RNA
Extraction protocol 10X Chromium Single Cell 3' polyA v3 Chemistry
10X Chromium Single Cell 3' polyA and feature capture v3 Chemistry
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description cells dissociated from solid tumor
Data processing 10X:
Alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 3.0.2)
MD tags were added to alignments with samtools calmd --threads 15 -rb possorted_genome_bam.bam refdata-cellranger-hg19-3.0.0/fasta/genome.fa > possorted_genome_bam_MD.bam
Reads were split based on the CB:Z tag, resulting in one BAM file per barcode.
Edits were called on each "split-BAM" file using SAILOR ( using default parameters and dbSNP (v147) to remove known SNPs.
Coverage was generated from filtered BAM files (intermediates from SAILOR) for each cell barcode, using the following commands from BedTools (v2.27.1). : bedtools genomecov -split -strand - -g refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt -bg -ibam fwd.bam > bedtools sort -I > bedGraphToBigWig refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt bedtools genomecov -split -strand + -g refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt -bg -ibam rev.bam > bedtools sort -I > bedGraphToBigWig refdata-cellranger-hg19-3.0.0/star/chrNameLength.txt
For each barcode, edit sites were annotated across exons (Gencode v19) and the cumulative C>T depth across each gene was divided by the cumulative depth across C's as obtained from the previous step.
Genome_build: hg19
Supplementary_files_format_and_content: 10X: Edit fractions across barcodes with detectable edits were merged to obtain processed STAMP_edits.txt files for each sample.
Supplementary_files_format_and_content: Featurecounts file for RNA-seq samples
Submission date Sep 18, 2020
Last update date Jul 02, 2021
Contact name Gene Yeo
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platform ID GPL24676
Series (1)
GSE137258 Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
BioSample SAMN16207173
SRA SRX9149658

Supplementary file Size Download File type/resource
GSM4795207_WT_RPS2_STAMP_epkm.txt.gz 4.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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