|
| Status |
Public on Dec 07, 2023 |
| Title |
RubiconKO.rep4 (DISE-033) |
| Sample type |
SRA |
| |
|
| Source name |
5XFADtg/Rubicon ko, brain, mouse #282
|
| Organism |
Mus musculus |
| Characteristics |
genotype: 5XFADtg/Rubicon ko
tissue: brain
fraction: Ago bound RNA
|
| Biomaterial provider |
Douglas Green, St Jude Children's Hospital
|
| Treatment protocol |
RNA was isolated from 250 mg of cortex and hippocampus combined
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lysates were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ 4000 using Illumina provided reagents and protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after). This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Supplementary files format and content: Tab-delimited text file with read, seed (bp 2-7), cell viability based on seed, raw read counts for each sample, and putative source based on blast
|
| |
|
| Submission date |
Sep 11, 2022 |
| Last update date |
Dec 07, 2023 |
| Contact name |
Marcus Peter |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Street address |
303 East Superior Street, Lurie 6-123
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE213121 |
Death Induced by Survival gene Elimination (DISE) is correlated with neurotoxicity in Alzheimer's disease and aging |
| GSE213138 |
Death Induced by Survival gene Elimination (DISE) is correlated with neurotoxicity in Alzheimer's disease and aging |
|
| Relations |
| BioSample |
SAMN30799260 |
| SRA |
SRX17528771 |
