|
| Status |
Public on Jun 09, 2017 |
| Title |
NR_125939_G1_S2 |
| Sample type |
SRA |
| |
|
| Source name |
A375
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
cell type: Melanoma cells
passages: 5-10
|
| Treatment protocol |
A375 cells were treated with 2uM PLX-4720 for 3 days before RNA-seq
|
| Growth protocol |
A375 cells were cultured in RPMI supplemented with 10% FBS and 1% Pen/Strep
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen 74134) and 1ug of RNA was used for RNA-seq. The 6 candidate lncRNA loci with detectable transcript upregulation were prepped with TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina RS-122-2302) and all other samples were prepped with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530S) and NEBNext PAS mRNA Magnetic Isolation Module (NEB E7490S).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bowtie v0.12.7 index was created based on the human hg19 UCSC genome and known gene and lncRNA transcriptome constructed as described above. Paired-end reads were aligned directly to this index using Bowtie with command line options “-q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 --chunkmbs 512 -p 1 -a -m 200 -S”.
RSEM v1.2.22 was run with default parameters on the alignments created by Bowtie to estimate expression levels (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Jun 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Joung |
| E-mail(s) |
julia@joung.science
|
| Organization name |
Broad Institute
|
| Street address |
75 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE99819 |
Genome-scale Activation Screen Identifies a LncRNA Locus Regulating a Gene Neighborhood [RNA-Seq] |
| GSE99836 |
Genome-scale Activation Screen Identifies a LncRNA Locus Regulating a Gene Neighborhood |
|
| Relations |
| BioSample |
SAMN07205913 |
| SRA |
SRX2896138 |
