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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 15, 2015 |
| Title |
HCC1419_untreated1 |
| Sample type |
SRA |
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| Source name |
HCC1419
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC1419
treatment: untreated
sample id: par_mg01
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| Growth protocol |
HCC1419 cells (ATCC, CRL-2326, purchased 1/31/11) were grown in RPMI containing 1% penicillin streptomycin (PenStrep) and 10% Gibco certified fetal bovine serum (FBS) (Invitrogen) (RPMI-complete) conditioned with mouse embryonic fibroblasts (MEF). Media was changed every 3 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol + RNEasy cleanup, followed by ribozero rRNA depletion
Strand-specific dUTP followed by TruSeq DNA library prep kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The input Illumina fastq files consisted of paired end reads with each end containing 100 bp, which were reduced to 80x80bp by trimming 20bp from the 3' end of each read to improve mapping of fragments shorter than 100nt.
Fragments that mapped to elements in the repeatMasker human library, using Bowtie2, were removed.
Bowtie2 was used to map the remaining fragments against a version of the human transcriptome derived from the UCSC Known Genes track of the GRCh37hg19 human assembly by using the target generation script supplied with RSEM.
Only mappings with both read ends aligned were kept.
Potential PCR duplicates (mappings of more than one fragment with identical positions for both read ends) were removed with the samtools “rmdup” function, keeping only one of any potential duplicates.
The final set of mapped paired end reads for a sample were converted to transcript and gene expression estimates using RSEM.
For input to DESeq all genes with non-zero counts in any sample were considered.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RSEM expression estimates and DESeq results
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| Submission date |
Oct 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mia Grifford |
| E-mail(s) |
mgrifford@gmail.com
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| Organization name |
UCSC
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| Street address |
1156 High Street
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| City |
San |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE62074 |
Mutation independent activation of the Notch pathway is associated with Lapatinib resistance in Her2+ breast cancer cell lines |
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| Relations |
| BioSample |
SAMN03097371 |
| SRA |
SRX722670 |
| 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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