|
| Status |
Public on Jan 07, 2015 |
| Title |
hFF_3 |
| Sample type |
SRA |
| |
|
| Source name |
human foreskin fibroblast, scramble siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BJ (ATCC CRL-2522)
cell type: foreskin fibroblast cell line
transfection: scramble siRNA
barcode: ATCACG
lane number: 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from human cell lines was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturers' instructions. RNA quality was assessed using an Agilent Bioanalyzer.
RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions (polyA selection). Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
hFF_scramble3
polyA RNA
|
| Data processing |
All reads aligned with TopHat version 1.4.0 using the following options: "-a 5" against hg19 and annotated UCSC coding transcripts.
Alignments were processed with Cuffdiff version 2.0.0 using default options in the 'non-diff' mode.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: genes.fpkm_tracking: Cuffdiff expression tracking.
Supplementary_files_format_and_content: refAnnotation.UcscAndCabiliEtAl2011lncRNA.hg19.gtf: GTF file including UCSC coding genes and long non-coding RNA from Cabili et al. Genes and Development 2011 (PMID 21890647); Cuffdiff was applied on this reference GTF.
|
| |
|
| Submission date |
Apr 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nataly Moran Cabili |
| E-mail(s) |
nmcabili@fas.harvard.edu
|
| Organization name |
Broad Institute ; Harvard University
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE57049 |
Localization and Abundance Analysis of Human lncRNAs at Single Cell and Single Molecule Resolution |
|
| Relations |
| BioSample |
SAMN02739313 |
| SRA |
SRX528634 |
