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| Status |
Public on Dec 12, 2019 |
| Title |
AB6893 |
| Sample type |
SRA |
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| Source name |
Total brain
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: Brain
cell type: Immune cells
selection marker: CD45+
source: BDÂ Biosciences
catalog#: 554888
age: 11-14w
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell libraries were prepared as previously described (Keren-Shaul, Nature Protocols, 2019). In brief, mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier (Keren-Shaul, Nature Protocols, 2019).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
paired-end (read2 used to read cell and molecule barcodes only)
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| 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.
Genome_build: hg38
Genome_build: Mmul 8.0.1
Genome_build: calJac3
Genome_build: Oar v3.1
Genome_build: Rnor 6.0
Genome_build: mm10
Genome_build: S.galili v1.0
Genome_build: MesAur1.0
Genome_build: galGal5
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
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| Submission date |
Jul 23, 2019 |
| Last update date |
Dec 13, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
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| Phone |
972-8-9343338
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| Organization name |
Weizmann Institute of Science
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| Department |
Immunology
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| Street address |
234 Herzl st.
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| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
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| Platform ID |
GPL20084 |
| Series (2) |
| GSE134705 |
Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (scRNA-seq) |
| GSE134707 |
Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program |
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| Relations |
| BioSample |
SAMN12342354 |
| SRA |
SRX6581806 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3963903_AB6893.txt.gz |
405.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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