|
| Status |
Public on Jun 12, 2017 |
| Title |
AB1449 |
| Sample type |
SRA |
| |
|
| Source name |
Whole brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: 5XFAD
organ: Brain
selection marker: CD45+
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)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
polyA+ RNA
AD6m mouse1 plate#4
|
| 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 |
SAMN07134115 |
| SRA |
SRX2830010 |
