|
| Status |
Public on Jun 13, 2023 |
| Title |
A11-lncRNA-3 |
| Sample type |
SRA |
| |
|
| Source name |
81566
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 81566
genotype: AA at rs2027349
cell type: Glutamatergic, NGN2-induced, day-20 neuron
treatment: long non-coding RNA shRNA KD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-Seq, at the day of harvesting the culture media was removed by aspiration and the cells were washed twice using 1 ml PBS each with aspiration. Subsequently, 600 µl of RLT Plus reagent was directly added into each well to homogenise cells in situ. Qiagen RNEasy plus kit was used for the extraction of total RNA according to the manufacturer’s protocol. Extracted RNAs were eluted into 50 µl of RNA-free water and the concentration was determined by nanodrop. Approximately 5 µg total RNA was recovered from each well. Total RNAs isolated by using MirVana kit (Thermofisher) were used in RNA-seq. After QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Subsequently, terminal repair and sequencing adaptor ligation were applied to the templates. The double-stranded cDNA library is completed through size selection and PCR enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Derived from sequence batch #1
|
| Data processing |
All raw sequence reads generated by Illumina HiSeq 2000 had been demultiplexed at Novogene as 2x150 bp reads aiming at 25 M reads;
RNA-seq data was aligned to GRCh38.p12 genome using STAR 2.7.10 and GENCODE v35;
ENSEMBL gene ids were used to serve as the unique gene identifiers. The raw count matrix was constructed by collecting the STAR output matrix of each sample and concatenating into one large tab-delimited text file.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text
|
| |
|
| Submission date |
Jun 12, 2023 |
| Last update date |
Jun 14, 2023 |
| Contact name |
Jubao Duan |
| E-mail(s) |
jduan69@gmail.com
|
| Phone |
(224) 364-7564
|
| Organization name |
NorthShore University HealthSystem
|
| Department |
Center for Psychiatric Genetics
|
| Lab |
Unit of Functional Genomics in Psychiatry
|
| Street address |
1001 University Place
|
| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60201 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE188491 |
Chromatin accessibility mapping for GWAS risk loci reveals compound genetic effects of neurodevelopment and neurodegenerative disorders in human neurons |
|
| Relations |
| BioSample |
SAMN35716338 |
| SRA |
SRX20662026 |
