|
| Status |
Public on Dec 01, 2014 |
| Title |
VCaP [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
VCaP cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Prostate cancer cell line
passages: 5 to 6
|
| Growth protocol |
Prostate cell lines were maintained in appropriate medium. VCaP and VCaP ERa expressing cells were maintained in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin streptomycin. NEAT1 WT and KO MEFs were cultured in 1:1 mixture of DMEM and HamF12 supplemented with 10% FCS and 1% penicillin streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MEF cell lines as well as the VCaP and VCaP ERa cell lines were subjected to RNA extraction using Trizol reagent.
RNA libraries for the MEF cell lines were prepared for sequencing using standard Illumina protocols. In VCaP and VCaP ERa cell lines, Ribo-Zero rRNA removal kit (RZH1046, Epicentre Biotechnologies, Madison, WI) was used to remove ribosomal RNA from 1 ug of total RNA followed by incorporation of deoxy-UTP during second strand cDNA synthesis. Subsequently the uridine containing strand was destroyed and that enabled identification of the transcript orientation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
poly-A-, stranded RNA-sequencing
|
| Data processing |
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were mapped to the genome and a splice junction library based on RefSeq and UCSC knownGenes for MEF and VCaP respectively. Casava 1.8 was used with default parameters. The splice junction library was generated via RSEQtools (Habegger et al. Bioinformatics) using createSpliceJunctionLibrary program. Mm10 or hg18 were used as genome references for MEF and VCAP, respectively.
Reads Per Kilobase of exon per million of library size (RPKM) were calculated using RSEQtools (Habegger et al., Bioinformatics 2011) In short, exons from all isoforms of a gene were merged to create one composite gene model. The number of nucleotides falling in the exons of this composite gene model were counted and normalized by the size of the gene model (per kilobase) and by the size of the library (mapped nucleotides per million)
Genome_build: mm10 for MEFs
Genome_build: hg18 for VCaP experiments
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each sample. For MEF, the corresponding human gene is reported if found. For details see Chakravarty et al. (submitted manuscript: The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression)
|
| |
|
| Submission date |
Feb 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dimple Chakravarty |
| E-mail(s) |
dic2012@med.cornell.edu
|
| Phone |
(646)962-6189
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Pathology
|
| Lab |
BB 1450
|
| Street address |
Belfer Research Building 413 E 69 St., New York
|
| City |
NEW YORK |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE43986 |
The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression [RNA-Seq] |
| GSE43988 |
The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression |
|
| Relations |
| SRA |
SRX222270 |
| BioSample |
SAMN01909117 |
