|
| Status |
Public on Jul 07, 2016 |
| Title |
HeLa_Bmi1_KD_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bmi1 knockdown
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa F-17
ectopic expression construct: murine FLAG-Bmi1 overexpression
cell treatment: siRNA knockdown by nucleofection + 48hours growth
|
| Treatment protocol |
nucleofection of 20 pmol siRNA
|
| Growth protocol |
1x complete dmem with FBS, gentamycin, 37C, 5% CO2, O2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol, cleanup/DNAse with Zymo clean and concentrate, illumina Truseq to make cDNA
from cDNA or sheared DNA: blunt ends, A-tail, ligate illumina sequencing adapters, PCR with full length/indexed illumina primers
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
knockdown of control mRNA
|
| Data processing |
Basecalls performed using OLB 1.8
RNA-Sequences were aligned to the hg9 transcriptome using tophat 2.4
EdgeR was uset to compute RPKM values
DNA-Sequences were aligned to the hg19 genome using bwa 0.5.9
For one batch of libraries, ("rep2" RNAseq and ChIP samples) high contamination of a single probe made in parallel for another experiment (chr7:15630900-156311000) was observed and the spike was removed in ChIP files
Aligned and filtered sequences were used to compute input normalized read densities using the SPP software (bw files)
Genome_build: hg19
|
| |
|
| Submission date |
Sep 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert E Kingston |
| E-mail(s) |
kingston@molbio.mgh.harvard.edu
|
| Organization name |
MGH/Harvard
|
| Department |
Molbio
|
| Lab |
Kingston
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE61549 |
A long non-coding RNA tunes PRC1 function during human and zebrafish development |
|
| Relations |
| BioSample |
SAMN03074048 |
| SRA |
SRX706348 |
