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| Status |
Public on Jun 05, 2020 |
| Title |
Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior-to-posterior axis |
| Sample type |
SRA |
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| Source name |
whole embryo
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| Organism |
Danio rerio |
| Characteristics |
strain: Kdrl:mcherry/cd41:eGFP
tissue: embryo
tissue preparation: whole embryo
developmental stage: 28 hours post-fertilization
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| Growth protocol |
Zebrafish were maintained and propagated according to standard laboratory conditions. Kdrl:mcherry/cd41:eGFP reporter fish line was used for tomo-seq at both 28hpf and 40hpf. Fertilized chicken eggs (Bovans Brown) were incubated at 37±1°C in a humidified atmosphere until they reached the appropriate developmental stage. E3 and E4 chicken embryos were used for tomo-seq. C57BL/6 mouse strain was housed according to institutional guidelines, and procedures were performed in compliance with Standards for Care and Use of Laboratory Animals with approval from the Hubrecht Institute ethical review board. E10.5 and E11.5 mouse embryos were used for tomo-seq. Human embryos were obtained from Dr. Chuva de Sousa Lopes laboratory (LUMC, Leiden, Netherlands). The Medical Ethical Committee of the Leiden University Medical Center (P08.087) approved all procedures regarding the collection and use of human embryonic material.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from individual cryosection using TRIzol reagent (Ambion), according to the manufacturer’s manual. RNA extraction, amplification and sequencing libraries were performed as described in {Junker et al., 2014}. Briefly, RNA samples were treated according to the CEL-seq protocol {Hashimshony, 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit (Illumina).
Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina Illumina NextSeq 500 using 75bp paired end sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sample2
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| Data processing |
CEL-seq were mapped with bwa using custom scripts as previously described (Grün et al., Nature Methods, 2014)
Genome_build: mouse: mm10; chicken: galGal4, with improved 3’UTR annotations (see Junker et al., Cell, 2014); zebrafish: Zv9, with improved 3’UTR annotations (see Junker et al., Cell, 2014); human: hg19
Supplementary_files_format_and_content: *.coutc.csv: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. Column names indicate the number of sections/primers, separated by an underscore. For 'ggcells2.coutc.csv' Tab, which belongs to the chicken IAHC sorted cells, the two last columns indicate the number of reads obtained for experiment#1 and experiment#2 (primer#95 and primer#96, respectively). The order of the columns/primers follows the description of the sample from the title. For instance: "Extracted RNA 3-day old chicken embryo from posterior-to-anterior axis": the column 1 = most posterior section while the column 96 = most anterior. This is the case for all the samples listed.
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| Submission date |
Mar 15, 2019 |
| Last update date |
Jun 05, 2020 |
| Contact name |
Catherine Robin |
| E-mail(s) |
c.robin@hubrecht.eu
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| Organization name |
Hubrecht Institute
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL20828 |
| Series (1) |
| GSE128350 |
Multi-species tomo-sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta |
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| Relations |
| BioSample |
SAMN11131027 |
| SRA |
SRX5525690 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3672146_Laurent-sample2_AHFJWGBGXY_S4.coutc.csv.gz |
637.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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