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Sample GSM5818695 Query DataSets for GSM5818695
Status Public on Jan 17, 2022
Title 374sh3Enpp11
Sample type SRA
 
Source name Enpp1 depleted cell line
Organism Mus musculus
Characteristics cell line: 374
strain: Balb/c
Treatment protocol Cells lines were washed twice with PBS at 4ºC prior RNA purification.
Growth protocol Cells lines were cultured in complete RPMI medium.
Extracted molecule total RNA
Extraction protocol The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
RNA sequencing was performed by adapting the technology of SCRB-Seq (Bagnoli JW et al., Nat Comm, 2018) to allow for the high cost-efficient multiplexed transcriptome characterization. Briefly, cells were collected in cell lysis buffer and poly-(A)+ RNA were purified using the Dynabeads mRNA DIRECT Purification Kit (ThermoFisher Scientific). poly-(A)+ RNA were annealed to a custom primer containing a poly-(T) tract, a Unique Molecule Identifier (UMI), and a sample barcode. Retrotranscription using Template-switching oligonucleotides (TSO) was then used to synthetize and amplify 3’UTR enriched cDNA, resulting in barcoded cDNA fragments. Library preparation was performed using the Nextera XT library preparation protocol which introduces i5-P5 and i7-P7 structure for massive parallel sequencing. Quality control was performed following pre-amplification RT and library preparation to ensure quality and length accuracy, as well as to equilibrate sample pooling. Libraries were then circularized and sequenced using an DNBSeq-G400 sequencer (MGI), using the MGIEasy Circularization Kit (MGI). 5-10 million pair-end reads (100 bp) were sequenced for each sample. Raw sequences were called using Zebra caller (MGI) and demultiplexed using Cutadapt. RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description Triple Negative Breast cancer
Data processing The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to GRCm38 mouse assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode vM25 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.
 
Submission date Jan 14, 2022
Last update date Jan 18, 2022
Contact name Fernando Lecanda
E-mail(s) flecanda@unav.es
Organization name CIMA
Street address Avda. Pio XII 55
City Pamplona
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL28457
Series (2)
GSE193690 Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer [shENPP]
GSE193692 Tumor ENPP1(CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer
Relations
BioSample SAMN24976540
SRA SRX13788354

Supplementary file Size Download File type/resource
GSM5818695_374sh3Enpp11_AAA680_V300056632_L02.counts.txt.gz 3.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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