|
| Status |
Public on Jan 14, 2019 |
| Title |
HeyA8_80h_2 |
| Sample type |
SRA |
| |
|
| Source name |
HeyA8
|
| Organism |
Homo sapiens |
| Characteristics |
cells: treated with 80hr of Doxorubicin
passages: 8-15
pull down: Pull down with Pan-AGO peptide (Hauptmann et al., 2015 PNAS
|
| Treatment protocol |
cells were treated where indicated with Doxorubicin (doxo) for 20h, 40h or 80h
|
| Growth protocol |
HeyA8 cells are cultured in RPMI1640 medium supplemented with 10% FBS and 1% L-Glutamine. HCT116 cell lines were cultured in McCoy's 5A medium, supplemented with 10% FBS and 1% L-Glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
AGO1-4 were pulled down from whole cell lysate (Hauptmann et al., 2015 PNAS). The RNA was isolated using Trizol.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
miRNAseq_in_HeyA8_and_HCT116.xlsx
|
| Data processing |
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
The miRNA normalized counts was generated as in Farazi et al., Cancer research 2011 (GEO accession number GSE28884)
Genome_build: hg19
Supplementary_files_format_and_content: format: xlsx content: Normalized counts
|
| |
|
| Submission date |
Mar 02, 2018 |
| Last update date |
Jan 14, 2019 |
| Contact name |
Markus Hafner |
| E-mail(s) |
Markus.hafner@nih.gov
|
| Phone |
3014026956
|
| Organization name |
NIH
|
| Department |
NIAMS
|
| Lab |
Markus Hafner
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE111363 |
Induction of DISE by tumor suppressive microRNAs |
|
| Relations |
| BioSample |
SAMN08631223 |
| SRA |
SRX3758349 |
