|
| Status |
Public on Aug 08, 2013 |
| Title |
human_WT_RNAseq_repA |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
antibody: N/A
|
| Treatment protocol |
HCT116 cells were infected with lentivirus harboring either Non-targeting shRNA or ICE1 shRNA in the presence of 8 µg/ml of polybrene (Sigma #H9268) for 24 hours (Target sequence for ICE1 sh1: 5’-ATAAGAGTCGTTTGCGAAATA-3’, Target sequence for ICE1 sh2: 5’-GCCTAATCAAGTATCAGTTAT-3’). The infected cells were selected with 2 µg/ml puromycin for extra 48 h before harvesting the cells for RNA extraction. Total RNA was extracted with Trizol (Invitrogen #15596-018), treated with DNase I (NEB #M03035) for 20 min at room temperature and precipitated with sodium acetate/ethanol in the presence of 1 µg/ml glycogen and dissolved again in RNase-free water.
|
| Growth protocol |
For HCT116 cells, 5x10^7 cells were grown according to previously described protocols (Lee et al., 2006).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2 µg of total RNA was depleted of ribosomal RNA with the Ribo Zero kit (Epicentre #MRZG12324) and libraries were made with the TruSeq RNA sample Pre Kit (Illumina #RS-122-2001).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNAseq after non-targeting-RNAi; Replicate A
|
| Data processing |
Reads were aligned using Ensembl 66 GTF human annotations using TopHat v.1.4.1 and Bowtie v0.12.7. Alignments were not extended. UCSC bedGraph files were created at 10bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.7, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.1 (20110622) using the indicated criteria.
RNA-seq alignments were done using TopHat v1.4.1 Differential expression analysis was done using DESeq corresponding to bioconductor version for R v2.11.1
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
Genome_build: UCSC hg19 and UCSC dm3
|
| |
|
| Submission date |
Jun 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
asg@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE47938 |
Multiple roles for LEC in initiation and elongation phases of snRNA gene transcription |
|
| Relations |
| BioSample |
SAMN02204109 |
| SRA |
SRX306187 |
