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| Status |
Public on Mar 28, 2020 |
| Title |
YH6_3_BT20_Control_rep3 |
| Sample type |
SRA |
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| Source name |
BT20_Control
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| Organism |
Homo sapiens |
| Characteristics |
cell line: BT20
cell type: human breast cancer cell line
transfection vector: Negative control: only lentiviral pLenti7.3 vector
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| 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.
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| Growth protocol |
BT20 cells were cultured in EMEM (ATCC) with 10 % fetal bovine serum (Hyclone).
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Control_EmptyVector_s3
BT20_Control_rep3
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| 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.
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| Submission date |
Oct 08, 2018 |
| Last update date |
Jul 21, 2020 |
| Contact name |
Xiaosong Wang |
| E-mail(s) |
xiaosongw@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Pathology
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| Lab |
Cagenome
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| Street address |
5150 Centre Ave
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| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15232 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE120919 |
Genome-wide survey of adjacent gene rearrangements in breast cancer identifies triple-negative specific BCL2L14-ETV6 fusions |
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| Relations |
| Reanalyzed by |
GSE123917 |
| BioSample |
SAMN10188674 |
| SRA |
SRX4809413 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3420771_YH6_3_BT20_Control_rep3_R1.fq.gz_NCBIGTF.featureCounts.txt.gz |
201.9 Kb |
(ftp)(http) |
TXT |
| GSM3420771_YH6_3_BT20_Control_rep3_R1.fq.gz_NCBIGTF.tpmlog.txt.gz |
362.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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