|
| Status |
Public on Oct 12, 2017 |
| Title |
siControl NXF1 RIP Rep-2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa transfected with control siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
culture media: DMEM
antibody: Abcam ab129160 Anti-NXF1 antibody [EPR8009]
strain: ATCC CCL-2
|
| Treatment protocol |
Transfections were carried out using Lipofectamine RNAiMAX according to manufacturers protocol in the absence of antibiotics.
|
| Growth protocol |
HeLa cells (ATCC CCL-2) were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RIP was performed according to literature procedure (Peritz et al., 2006) using polyA selected RNA following treatment with two uique siRNA sequences as biological replicates.
RIP-seq and subcellular RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA kit.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RIP NXF1 Poly(A)
|
| Data processing |
After adaptor trimming with Cutadapt (v1.4.1) and quality control, 50 bp sequence reads were mapped to the human genome (hg19) using TopHat (v.2.0.11) and Bowtie (v1.0.1).
RIP-seq and RNA-seq differential expression was quantified between replicate experiments using Cufflinks (v.2.2.1)
Genome_build: hg19 (human)
Supplementary_files_format_and_content: Differential enrichment in siControl vs siYTHDC1 was assessed in repliacte using Cufflinks (v.2.2.1), including normalization to input samples under each condition.
|
| |
|
| Submission date |
Sep 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ian Roundtree |
| E-mail(s) |
iroundtree@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Department of Chemistry
|
| Lab |
Chuan He Lab
|
| Street address |
929 E 57th Street E307
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE74397 |
N6-methyladenosine-Mediated Nuclear Export of Messenger RNA |
|
| Relations |
| BioSample |
SAMN05770400 |
| SRA |
SRX2162600 |
