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| Status |
Public on Jul 25, 2019 |
| Title |
SAM24322048 |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
ligand: GNE-274
concentration: 1uM
time: 24h
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| Treatment protocol |
Cells were treated with either 1 nM E2, or 1 M 4-OH tamoxifen, GDC-0810, fulvestrant, GNE-274 or GDC-0927 for 24 hours
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| Growth protocol |
MCF7, HCC1500, Cama-1, MDA-MB-330, BT-474, EFM-19 and T47D cells were grown in hormone deprivation media for at least 3 days prior to treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from duplicates using Qiagen RNeasy kit as per manufacturer’s protocol and quality control of RNA samples was done to determine their quantity and quality.
Approximately 500 ng of total RNA was used as an input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). In addition, RNA input of 100 ng was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina); The libraries were multiplexed and then sequenced on Illumina HiSeq4000 (Illumina) to generate 30M of single end 50 base pair reads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
RNA sequencing (RNAseq) data were analyzed with HTSeqGenie [Pau and Reeder, R package, 2012] in BioConductor [Huber et al, Nat Methods 2015] as follows: reads were trimmed to 75 bp, filtered for quality and rRNA/adapter contamination, and aligned to the reference genome GRCh38
Gene expression was quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample x gene length x size factor).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tables of read counts for all genes and replicates
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| Submission date |
Jul 31, 2018 |
| Last update date |
Jul 25, 2019 |
| Contact name |
Marc Hafner |
| E-mail(s) |
hafner.marc@gene.com
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| Organization name |
Genentech
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| Department |
Oncology Bioinformatics
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| Street address |
Building 45-1, 1 DNA Way
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE117942 |
RNA-seq of breast cancer cell lines post ligand treatment I |
| GSE117943 |
ATAC-seq, ChIP-seq and RNA-seq of breast cancer cell lines post ligand treatment |
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| Relations |
| BioSample |
SAMN09745217 |
| SRA |
SRX4492963 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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