|
| Status |
Public on Nov 26, 2019 |
| Title |
H1437 IKKa knockout xenograft tumor 2_1 |
| Sample type |
SRA |
| |
|
| Source name |
H1437 IKKa knockout xenograft tumor 2
|
| Organism |
Homo sapiens |
| Characteristics |
host strain: NSG (NOD-SCID-IL2Rgamma) mice
tissue: Skin Xenograft Tumor
cell line source: H1437
genotype/variation: IKKa Ko
|
| Growth protocol |
IKKa-Ko or WT tumors were isolated from mice and processed for RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cell RNA sample quality and integrity were verified with an Agilent RNA 6000 nano kit or also by quantifying the relative levels of expression of 28S vs. 18S rRNAs by MOPS denaturing agarose gel electrophoresis. RNA-seq libraries were prepared with the Illumina TruSeq RNA v2 kit using 1 μg of total RNA.
Libraries were checked with the Agilent bioanalyzer DNA1000 chip, quantified with the Qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing. 75 bp Single-End reads were generated with the Illumina NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H1437 IKKa Ko 2_S13_L001
H1437 IKKa Ko 2_L001
|
| Data processing |
Raw Fastq sequencing files were then imported into CLC Biomedical Genomics Workbench version 5.0.1.
The qualities of the samples were assessed and sequences with low quality were trimmed as follows: Quality limit was set to 0.05 and ambiguous limit was set to 2.
Sequences with high quality were then aligned using CLC Biomedical Genomics Workbench using the following parameters: Reference type = Genome annotated with genes and transcripts; reference sequence = homo_sapiens_sequence_hg38; gene track = homo sapiens Ensembl v90 genes; mRNA track = homo sapiens Ensembl v90 mRNA; mismatch cost = 2; insertion cost = 3; deletion cost = 3, length fraction = 0.8; similarity fraction = 0.8; global alignment = no; strand-specific = both; maximum number of hits for a read = 10; count paired reads as two = no and expression value = total counts.
Genome_build: hg38; Ensembl v90 genes
Supplementary_files_format_and_content: counts of each aligned transcript as determined by CLC Biomedical Genomics Bench version 5.0.1.
|
| |
|
| Submission date |
Nov 14, 2019 |
| Last update date |
Nov 26, 2019 |
| Contact name |
David Habiel |
| E-mail(s) |
david.habiel@gmail.com
|
| Organization name |
Cedars-Sinai Medical Center
|
| Street address |
375 Acorn Park Drive,, Apt. 1416
|
| City |
Belmont |
| State/province |
MA |
| ZIP/Postal code |
02478 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE140432 |
CHUK/IKKalpha loss in lung epithelial cells enhances NSCLC growth associated with HIF up-regulation |
|
| Relations |
| BioSample |
SAMN13288656 |
| SRA |
SRX7142103 |
