|
| Status |
Public on May 25, 2017 |
| Title |
Repeatability No Input rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
none
|
| Organism |
unidentified |
| Characteristics |
sample preparation: none
input: 0 ng
source material manufacturer: none
|
| Growth protocol |
Cell lines were grown in DME with 10% FBS under 5% CO2 in 96-well plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed with 1X PBS, then lysed in 1X Lysis Buffer (BioSpyder Technologies, Inc.) at ~2,000 cells/uL, and stored at -80C.
TempO-Seq targeted expression assay. Addition of adapters by amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: Repeatability Read Counts.xlsx
|
| Data processing |
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Genome_build: Multiple pseudo transcriptomes and hg38 (for GSM2422725 to GSM2422736). Processed data files include the sequences used for alignment in column "Probe_Sequence".
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.
|
| |
|
| Submission date |
Dec 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joanne Yeakley |
| Organization name |
BioSpyder Technologies, Inc.
|
| Street address |
1945 Camino Vida Roble Ste i
|
| City |
Carlsbad |
| State/province |
CA |
| ZIP/Postal code |
92008 |
| Country |
USA |
| |
|
| Platform ID |
GPL22779 |
| Series (1) |
| GSE91395 |
A Trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling |
|
| Relations |
| SRA |
SRX2410954 |
| BioSample |
SAMN06129939 |
