|
| Status |
Public on Jan 01, 2017 |
| Title |
IgG-3_F_10 |
| Sample type |
SRA |
| |
|
| Source name |
Choroid plexus
|
| Organism |
Mus musculus |
| Characteristics |
strain: 5XFAD
organ: Choroid plexus
selection marker: whole tissue
treatment: IgG control
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice were transcardially perfused with PBS prior to tissue excision. Choroid plexus tissues were isolated under a dissecting microscope (Stemi DV4; Zeiss) from the lateral, third, and fourth ventricles of the brain. Total RNA from the choroid plexus was extracted using the RNA MicroPrep Kit (Zymo Research), and mRNA (1 µg) was converted into cDNA using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science. 3' RNA-seq for digital gene expression quantitation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data in Series supplementary file 20150515_AD.xlsx
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
alignment: bowtie2 with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8) from R2 file.
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
20150515_AD.xlsx - Quantifying RNA expression in genes: analyzeRNA.pl rna mm9 -d <tag directory> -count 3utr -norm 1e7 (HOMER)
20150826_exons_homer.xlsx Quantifying RNA expression in genes: analyzeRNA.pl rna mm9 -d <tag directory> -count exons -norm 1e7 (HOMER)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE75484 |
Effect of PD-1 immune checkpoint in Alzheimer's disease transgenic mice |
|
| Relations |
| BioSample |
SAMN04301497 |
| SRA |
SRX1455855 |
