|
| Status |
Public on Jul 31, 2017 |
| Title |
A375_Ptpn2_NS_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
A375_Ptpn2_NS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
cell type: melanoma
genotype/variation: Ptpn2ko
infected with lentivirus containing sgrna against: Ptpn2sg3
treated with: NS
|
| Treatment protocol |
Cells were treated with either 1000 U/mL IFNb, 100ng/mL IFNg, 10ng/mL TNFa, alone or in combination, or an equivalent volume of vehicle control (PBS + 0.1% BSA) for 48 hours.
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10% heat-inactivated FBS and 2.5% Pen-Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were trypsinized and lysed in QIAGEN RLT buffer and frozen at -80C. RNA was extracted using QIAGEN Rneasy kits according to manufacturer's instructions.
Libraries were constructed using the NEB Ultra-Directional RNA kit using the mRNA capture module, according to manufacturer's instructions.
Directional libraries were barcoded using NEB dual index barcodes and sequenced on the NextSeq (high output flowcell) by pair-end sequencing of 37bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
NextSeq raw data demultiplexed and converted to fastq files using the Illumina software Bcl2fastq v2.17.1.14.
Fastq files were quality-trimmed and illumina adaptors removed using Trimmomatic v0.33
Fastq files were aligned to the relevant genome assembly (mm10 for mouse, hg19 for human) using Bowtie2 v2.2.4.
Feature counts were aggregated into a single data matrix using HTSeq v0.6.1p1.
DESeq2 library size normalization by scale factor of normcounts. Differential expression performed using DESeq2.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Aggregated raw count matrix (output from HTSeq) in tab-delimited .txt file
|
| |
|
| Submission date |
May 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kathleen B Yates |
| Organization name |
Broad Institute
|
| Department |
Cancer Program
|
| Lab |
Manguso
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE99299 |
Cytokine Stimulation of PTPN2-deleted cancer cells |
|
| Relations |
| BioSample |
SAMN07168046 |
| SRA |
SRX2857409 |
