|
| Status |
Public on Feb 01, 2016 |
| Title |
TAL1-control RNA-seq, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat cells expressing a Dox-inducible shRNA against TAL1 without Dox addition
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat
treatment: None
|
| Growth protocol |
RPMI 1640 medium supplemented with 10% (v/v) Tet-free FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, 20 µg/ml blasticidin and 1 mg/ml G419
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini extraction kit from Qiagen with the added step of DNAseI digestion
Illumina TruSeq stranded mRNA library kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Replicate 2
TAL1_KD_DESeq_table.txt
TAL1_KD_DESeq2_dds.R
|
| Data processing |
Alignment using Tophat2 (v2.0.12) with default parameters, guided by GTF file from Ensembl release 75
Assignment of reads to transcripts from Ensembl release 75 GTF using htseq-count (v0.6.1p1)
Fold change analysis using DESeq2 to compare two treatment replicates to two control replicates
Results list trimmed to remove transcripts with no associated reads
Raw read counts added to fold change table and exported as text file
DESeqDataSet object exported to file using the R save() command
Genome_build: NCBI 37/hg19
Supplementary_files_format_and_content: Text format table containing differential expression and raw count data. File containing DESeq2 analysis object dumped from R.
|
| |
|
| Submission date |
Aug 24, 2015 |
| Last update date |
May 15, 2019 |
| Organization |
Ottawa Hospital Research Institute |
| Phone |
(613) 737-8899 -73255
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Ottawa Bioinformatics Core Facility
|
| Street address |
501 Smyth Rd.
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE72299 |
Gene expression in TAL1-driven T-cell ALL in response to TAL1-KD, UTX-KD, and GSKJ4 treatment |
| GSE72300 |
T-cell ALL in response to TAL1-KD, UTX-KD, and GSKJ4 treatment |
|
| Relations |
| BioSample |
SAMN04009374 |
| SRA |
SRX1162893 |
