|
Status |
Public on Jul 07, 2016 |
Title |
HeLa_CAT13_KD_Rep2 |
Sample type |
SRA |
|
|
Source name |
CAT13 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 candidate RNA
|
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 |
SAMN03074029 |
SRA |
SRX706328 |