|
| Status |
Public on Aug 07, 2014 |
| Title |
JEKO-1 SOX11 siRNA |
| Sample type |
SRA |
| |
|
| Source name |
MCL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: JEKO-1
treatment: SOX11 siRNA
genotype: SOX11 depletion
|
| Treatment protocol |
7 million MCL cells were transfected with 100 uM of either SOX11 siRNA or non-targeting siRNA using the Amaxa system (Kit T, program G016). Cells were collected 48 hours after trasfection and total RNA were extracted as discussed in the extract protocol.
|
| Growth protocol |
The MCL cell lines Granta-519, JEKO-1 and Z138 were grown in a humidified incubator at 37°C and 5% CO2 with RPMI 1640 medium (Cellgro, Herndon, VA) supplemented with 10% fetal bovine serum (FBS; Gemini Bio-Products, Woodland, CA), 2 mM L-glutamine, 100 units/mL of penicillin G and 100 µg/mL of streptomycin (Cellgro, Herndon, VA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were lysed in TRIzol (Life Technology, Cat.# 15596-026 ) and total RNA were extracted with PureLink RNA Mini kit (Life Technology, Cat.# 12183018A) following manufacturer's instructions.
RNA libraries were prepared for sequencing from 100 ng of total RNA using Illumina TruSeq RNA sample (Illumina, # FC-122-1001)preparation kit following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SOX11 depletion
|
| Data processing |
Sequence data generated from the sequencer were run through in house pipeline WASP - 3.0.60. FASTQ files are generated from Illumina QSEQ files, include Sanger (Phred+33) encoded quality scores
Raw FASTQ files were trimmed for adapter sequences using quart.
Alignment to the reference genome was performed using gsnap.
htseq - v0.5.3p3 was used for read quantitation
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg19
Supplementary_files_format_and_content: Excel file containing RPKM values and Gene symbols for each Sample.
|
| |
|
| Submission date |
Nov 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Samir Parekh |
| E-mail(s) |
samir.parekh@MSSM.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Hematology and Medical Oncology
|
| Street address |
1470 Madison Ave, 5th FL, Room 114
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE52148 |
High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma (RNA-Seq) |
| GSE52149 |
High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma |
|
| Relations |
| BioSample |
SAMN02399598 |
| SRA |
SRX373883 |
