|
| Status |
Public on Dec 30, 2020 |
| Title |
LetR siRNA non targeting Rep 31 |
| Sample type |
SRA |
| |
|
| Source name |
LetR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LetR
knockdown: siNT
|
| Treatment protocol |
Experiments were carried out under steroid depleted conditions as cells were washed with PBS and kept in PRF-MEM with 10% CDS-FBS, 1% l-glutamine for 96 hours and media changed every day.
|
| Growth protocol |
MCF7 cells were grown in MEM (10% FCS, 1% L-Glutamine); LetR cells were grown in Phenol-red Free MEM with 10% Charcoal-dextran-stripped FCS, 1% L-glutamine, maintained in G418, Androstenedione and letrozole)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNeasy Kit
Total RNA Sample QC: Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). Purification: mRNA polyA molecules using poly-T oligo-attached magnetic beads. Fragmentation: mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. PCR yield quantified by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. 100bp PE sequencing: BGISEQ 500 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
siRNA control LetR cells
LetRsiNT_rep_3
|
| Data processing |
fastq reads QC: read adapter removal, low quality read filtering using SOAPnuke: version：v1.5.2 parameters: -l 15 -q 0.2 -n 0.05 website: https://github.com/BGI-flexlab/SOAPnuke
read mapping and alignment to GRCH37p.13 reference genome: Bowtie2 Bowtie2 is an ultrafast, memory-efficient short read aligner,indexing the reference with a Burrows-Wheeler index to keep its memory footprint small. :Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml
Gene expression quantification from aligned reads: RSEM : Version: v1.2.12 Parameters: default Website: http://deweylab.biostat.wisc.edu/RSEM
Genome_build: GRCh37 p.13
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected counts and FPKM values for each sample
|
| |
|
| Submission date |
Sep 16, 2020 |
| Last update date |
Sep 28, 2021 |
| Contact name |
Leonie S Young |
| E-mail(s) |
[email protected]
|
| Organization name |
Royal College of Surgeons in Ireland
|
| Street address |
York House, York Street,, Dublin 2
|
| City |
Dublin |
| State/province |
Dublin |
| ZIP/Postal code |
D2 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE158095 |
AIB1 dependent transcriptome in endocrine resistance |
|
| Relations |
| BioSample |
SAMN16189319 |
| SRA |
SRX9139666 |
