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Sample GSM1956929 Query DataSets for GSM1956929
Status Public on Jan 01, 2017
Title IgG-2_M_14
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 SAMN04301496
SRA SRX1455854

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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