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Sample GSM3420781 Query DataSets for GSM3420781
Status Public on Mar 28, 2020
Title YH10_1_BT20_BCL2L14-E4_ETV6_E2_rep1
Sample type SRA
Source name BT20_BCL2L14-E4_ETV6-E2
Organism Homo sapiens
Characteristics cell line: BT20
cell type: human breast cancer cell line
transfection vector: BCL2L14 Exon4 - ETV6 Exon2 fusion variant
Treatment protocol transduction protocol: The BCL2L14-ETV6 fusion or wt ETV6 cDNA containing the full-length ORFs were subcloned into the lentiviral pLenti7.3 vector, and the lentivirus was further transduced to BT20 cell line.
Growth protocol BT20 cells were cultured in EMEM (ATCC) with 10 % fetal bovine serum (Hyclone).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells in individual confluent 10 cm dish, using the standard procedure of Qiagen RNeasy kit. The primary quantitation of the extracted RNA were checked by nanodrop. The integrity and purity of RNA were examined by Agilent 2100.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
The final libraries were normalized by quantification with LightCycler 480 II (Roche Applied Science, Indianapolis, IN, USA) and qualification with Bioanalyzer (Agilent, Palo Alto, CA, USA).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description BCL2L14_Exon4-ETV6_Exon2_s1
Data processing Quality control test on the sequencing data was done with error rate calculation and a Phred Q20 and Q30 score. All samples passed with error rate (%) < 0.03, Q20 > 97%, and Q30 > 92%.
The preprocessed reads (fastq.gz) were mapped into reference genome (GCF_000001405.39_GRCh38.p13_genomic.fna) using Rsubread R package (ver. 1.30.5, Liao et al. 2013).
The transcripts of each sample were assembled based on Transcripts Per Million (TPM) method. The sequence read alignment was annotated with gene IDs by using NCBI gene annotation data, "GCF_000001405.39_GRCh38.p13_genomic.gtf."
The selection of differentially expressed genes (DEGs) among samples was performed based on the TPM log2 values of transcripts. We used Limma R pacakge (ver. 3.36.2, Ritchie et al. 2015).
Genome_build: As reference genome, we downloaded "GCF_000001405.39_GRCh38.p13_genomic.fna" file from NCBI. For gene ID annotation, we downloaded "GCF_000001405.39_GRCh38.p13_genomic.gtf" from NCBI FTP.
Supplementary_files_format_and_content: Tab-delimited text files include TPM log2 values for each Sample.
Submission date Oct 08, 2018
Last update date Jul 21, 2020
Contact name Xiaosong Wang
Organization name University of Pittsburgh
Department Pathology
Lab Cagenome
Street address 5150 Centre Ave
City Pittsburgh
State/province Pennsylvania
ZIP/Postal code 15232
Country USA
Platform ID GPL24676
Series (1)
GSE120919 Genome-wide survey of adjacent gene rearrangements in breast cancer identifies triple-negative specific BCL2L14-ETV6 fusions
Reanalyzed by GSE123917
BioSample SAMN10188664
SRA SRX4809423

Supplementary file Size Download File type/resource
GSM3420781_YH10_1_BT20_BCL2L14-E4_ETV6_E2_rep1_R1.fq.gz_NCBIGTF.featureCounts.txt.gz 202.1 Kb (ftp)(http) TXT
GSM3420781_YH10_1_BT20_BCL2L14-E4_ETV6_E2_rep1_R1.fq.gz_NCBIGTF.tpmlog.txt.gz 364.1 Kb (ftp)(http) TXT
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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