|
| Status |
Public on Feb 07, 2013 |
| Title |
HeLa Sh-Scr 3 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa Sh-Scr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: cervical cancer cells
genotype/variation: stably expressing double-strand (ds) interfering RNA against scrambled sequences (sh-Scr)
molecule subtype: small RNA
|
| Treatment protocol |
Sub-confluent HeLa cells were transfected with Nucleolin shRNA (sc-29230-SH) or Control shRNA (sc-3314-SH) plasmids, and stably transfected clones were selected by using 1 µg/ml puromycin.
|
| Growth protocol |
HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% FBS, L-glutamine, and antibiotics (Life Technologies; Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Trizol® (Invitrogen) and libraries for deep sequencing were prepared from 2 µg of total RNA. Specifically 2 µg of total RNA underwent size selection by Flashpage Fractionator (AM110226001 Life Technologies). RNA that was 40bp and under was then quality checked by RNA pico-chip from Agilent.
The Applied Biosystems Total RNA-Seq Kit (cat # 4445374) was used to produce a cDNA library by the following steps. 5’ and 3’ specific adapters undergo hybridization and ligation to the RNA. cDNA was produced by reverse transcription and then purified and size-selected on a gel. The gel slices containing the cDNA library were amplified by PCR with primers specific to the adapter sequences, and then purified and sized selected on a gel. Templated sequencing beads were produced via emulsion PCR with Applied Biosystems’ EZ Bead system. The templated sequencing beads were sequenced on an Applied Biosystems SOLiD 5500 system according to the manufacturer’s protocol (Life Technologies, Foster City).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
40_Hela_ctr3_solid0379_20110818_FRAGBCKal5Fla6mirRNA_solid0379_20110818_FRAGBCKal5Fla6mirRNA_F3_40_Hela_ctr3
|
| Data processing |
Mapping of SOLiD reads was performed using both the small RNA pipeline (Life Technologies) and PASS (Campagna et al., 2009). The small RNA pipeline and PASS were used to extract counts and extensions of miRNA in small RNA reads, from 18 nucleotides in length.
Alignments with up to one mismatch has been recorded when matching to either miRNome (precursor sequences from miRBase) or human genome. Only reads with at least 3 sequenced copies per sample were inputted in the SQL database.
Raw digital expression values (read counts) were obtained by summing the number of reads that mapped to one of the reference databases
Genome_build: human genome hg19 or miRBase release 17.0
Supplementary_files_format_and_content: RPKM data
|
| |
|
| Submission date |
Feb 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Luciano Cascione |
| E-mail(s) |
luciano.cascione@ior.usi.ch
|
| Organization name |
IOR
|
| Department |
Lymphoma & Genomics Research Program
|
| Street address |
Via Chiesa 5
|
| City |
Bellinzona |
| State/province |
Ticino |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13393 |
| Series (2) |
| GSE41973 |
In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation |
| GSE44052 |
In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation [RNA-seq] |
|
| Relations |
| SRA |
SRX227013 |
| BioSample |
SAMN01914923 |
