|
Status |
Public on Jun 12, 2017 |
Title |
AB1742 |
Sample type |
SRA |
|
|
Source name |
Whole brain
|
Organism |
Mus musculus |
Characteristics |
strain: Trem2KO_5XFAD organ: Brain selection marker: CD45-intCD11b-intCD11c+Gr1- treatment: Alzheimer's disease mouse age: 6 months
|
Growth protocol |
Either whole brains, spinal cords, or specific parts of the brain (cortex or cerebellum), not excluding meninges and choroid plexus, were collected from mice following perfusion.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Single-cell suspensions of tissues for all mice, excluding the Trem2 experiment, were achieved using software‐controlled sealed homogenization system (Dispomix; http://www.biocellisolation.com) in PBS, followed by density gradient separation; Pellet was mixed with 40% percoll and centrifuged. Brains of Trem2 mice were processed as previously published (Wang et al., 2015). 3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
polyA+ RNA Trem2_KO_AD_cd11c_plate#2
|
Data processing |
bcl2fastq/2.15.0.4 Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out. Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used. Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well. read2 used to read cell and molecule barcodes only; Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header Genome_build: mm9 Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
|
|
Submission date |
May 16, 2017 |
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 (2) |
GSE98969 |
Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [RNA] |
GSE98971 |
Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease |
|
Relations |
BioSample |
SAMN07134125 |
SRA |
SRX2830061 |