|
| Status |
Public on Feb 29, 2020 |
| Title |
WT, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Blastocysts
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
treatment: No treatment
cell type: Blastocysts
strain: C57BL/6
|
| Treatment protocol |
Cells from the treatment group were treated with 200 µM Isoproterenol (Sigma, I2760) for 6 hrs before extracting RNA.
|
| Growth protocol |
Cells were grown in 35mm dishes in DMEM (Fisher, 11-995-073) supplemented with 15% fetal bovine serum (Hyclone), penicillin/streptomycin (Fisher, 15-140-148), Glutamax (Fisher, 35-050-061), NEAA (Fisher, 11-140-050) and β-mercaptoethanol (Sigma, M3148) at 37 degree celcius in a 5% CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Micro kit (Qiagen, 74004) according to manufacturer's specifications. Quality of RNA was assesed using Agilent 2100 Bioanalyzer (NANO).
500 ng of total RNA were used to prepare cDNA library using TruSeq Stranded mRNA Library Prep Kit (Illumina Inc., San Diego, CA, USA) with PolyA selection. The quality of libraries were assessed with Agilent 2200 TapeStation system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
wt_2
|
| Data processing |
Basecalling was performed using illumina's bcl2fastq (v1.8.4).
fastq_screen (v0.5.2) was used to quality check fastq reads for contamination by mapping against multiple genomes.
Trimmomatic (v0.36) was used to trim adapters and low quality bases.
STAR aligner (v2.6.0a) was used to align/map processed reads with reference genome.
Quantification of mapped reads were carried out using featureCounts from Subread package (v1.6.3)
Genome_build: mm10 from UCSC
Supplementary_files_format_and_content: countsPerMillion_filt_TMMnorm.txt is a tab-delimited text file which contains abundance mesurement of genes across the samples. The abundance is in the form of number of reads of genes which are filtered for lowly expressed genes using 'filterByExpr' function from R/Biconductor's EdgeR package and further normalized using Trimmed Mean Value (TMM) method -- to account for composition bias -- before converting them into counts per million to account for the library size difference among samples. The columns represent sample names and rows official gene symbols (NCBI).
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Feb 29, 2020 |
| Contact name |
Sandipkumar Darji |
| E-mail(s) |
sdarji@nki.rfmh.org
|
| Organization name |
Nathan Kline Institute for Psychiatric Research
|
| Department |
Center for Dementia Research
|
| Street address |
140 Old Orangeburg Rd, Bldg 39
|
| City |
Orangeburg |
| State/province |
NY |
| ZIP/Postal code |
10962 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE136894 |
β2-adrenergic agonists rescue lysosome acidification and function in PSEN1 deficiency by reversing defective ER to lysosome delivery of ClC-7 |
|
| Relations |
| BioSample |
SAMN12697734 |
| SRA |
SRX6804082 |
