|
| Status |
Public on Dec 12, 2019 |
| Title |
MP_13_fish_1A.M |
| Sample type |
SRA |
| |
|
| Source name |
Total brain
|
| Organism |
Danio rerio |
| Characteristics |
strain: WT
tissue: Brain
selection markers: Ib4+
source: Thermo Fisher
catalog #: I32450
age: 4-5mo
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
10,000 cells from each sample were sorted into lysis/binding buffer (Life Technologies). mRNA was captured with 6.5ul of Dynabeads oligo(dT) (Life Technologies), washed, and eluted at 85C with 10ul of 10 mM Tris-HCl (pH7.5).
We used a derivation of the MARS-seq as described (Jaitin et al. Science 2014), developed for single cell MARS-seq to produce 3' exprssion libraries with a minimum of 3 replicates per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
single end protocol R2 used for 7N barcode + 8N UMI in fastq header
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5 with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Read count by homer (http://homer.salk.edu/homer/ngs/)
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: text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Jul 23, 2019 |
| Last update date |
Dec 13, 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 |
GPL20828 |
| Series (2) |
| GSE134706 |
Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (bulk RNA-seq) |
| GSE134707 |
Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program |
|
| Relations |
| BioSample |
SAMN12342382 |
| SRA |
SRX6581673 |
