|
| Status |
Public on Apr 06, 2021 |
| Title |
SM4-SFM4_6 |
| Sample type |
SRA |
| |
|
| Source name |
Primary cultured microglia
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Primary cultured microglia
brain area: Subcortical white matter
donor nr: R15031
age: 3
gender: Female
|
| Growth protocol |
Primary microglia were cultured for 8 days in serum and exposed to M-CSF or IL-34, with or without TGF-b (sample1-16). Primary microglia were cultured for 8 days in serum+M-CSF or 4 days in serum followed by a serum-free washout of 4, 11 and 18 days, or cultured in serum-free medium for 22 days (sample21-40). Primary microglia were cultured for 8 days in serum+M-CSF, or cultured in serum for 4 days followed by a serum-free washout for 11 days, or co-cultured with oligodendrocytes and progenitor cells in serum for 4 days followed by a serum-free washout for 11 days (sample 41-52).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was isolated using the RNeasy minikit (Qiagen, Cat#74104) according to manufacturer’s protocol
For sample 1-40 the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat#E7420L) was used to prepare and process the samples, For sample 41-52 The NEBNext Low Input RNA Library Prep Kit (New England Biolabs, Cat#E6420L) for Illumina was used to process the samples
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Clustering and sequencing: Illumina NextSeq 500 was used for sample 1-40, Illumina NextSeq 6000 was used for sample 41-52
Reads were trimmed for adapter sequences using Trimmomatic v0.30
Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12
The Macaca mulatta genomic reference (Macaca_mulatta.Mmul_8.01.dna.toplevel.fa) was used for alignment of the reads for each sample.
The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (Tophat v2.0.14) with default settings.
SAMtools v1.3 package was used to sort and index the BAM files. Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.6.1p1.
Genome_build: Macaca_mulatta.Mmul_8.01.dna.toplevel.fa
Supplementary_files_format_and_content: .count files containing raw gene counts for each sample
Supplementary_files_format_and_content: .tsv files containing FPKM values for each sample
|
| |
|
| Submission date |
Apr 05, 2021 |
| Last update date |
Apr 06, 2021 |
| Contact name |
Raissa Timmerman |
| E-mail(s) |
raissatimmerman@gmail.com
|
| Organization name |
Biomedical Primate Research Centre
|
| Department |
Alternatives
|
| Street address |
Lange Kleiweg 161
|
| City |
Rijswijk |
| ZIP/Postal code |
2288 GJ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE171476 |
Transcriptome analysis reveals the contribution of glia -derived cues for maintenance of microglia identity in rhesus macaques |
|
| Relations |
| BioSample |
SAMN18617193 |
| SRA |
SRX10512787 |
