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| Status |
Public on Aug 02, 2020 |
| Title |
LizardD_A11 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Pogona vitticeps |
| Characteristics |
slice id (cutting angle and slice index): angle9_2_49
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fresh frozen and O.C.T (Tissue-Tek) embedded brains were sectioned and 14 μm thick sections collected on agarose membranes. A metal frame was then placed on the slide and used to make a well, filled with O.C.T and quickly frozen on dry ice. The glass slide was removed and
replaced with a second metal frame and the created well was filled with O.C.T and frozen. In order to mount the sample at a predefined angle we first use a scalpel to remove the sample from the metal frames and then angled using a custom made positioning device. After mounting in the correct angle, he sample was repositioned on the cryostat and 70 μm strips were sliced, collected with a forceps and transferred in a 96-wells plate kept inside the cryostat. The angle of the cryostat sample holder was not changed between samples
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
LizardD_expression.tab.gz
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| Data processing |
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis.
Genome_build: UCSC mm10 for mouse, and for Pogona vitticeps pvi1.1 from http://georges.biomatix.org/genomics-uc, For annotation a synthetic chromosom. composed of al of Pogona vitticepsl transcript models extracted from “Pogona_vitticeps.male.cds" from http://georges.biomatix.org/genomics-uc, extended with 200bp to the 5’ end separated by 20 bp spacers.
Supplementary_files_format_and_content: Tab-delimited file of UMI counts
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| Submission date |
Jun 22, 2020 |
| Last update date |
Aug 02, 2020 |
| Contact name |
Sten Linnarsson |
| Organization name |
Karolinska Institutet
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| Department |
Medical Biochemistry and Biophysics
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| Lab |
Molecular Neurobiology
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| Street address |
Scheeles väg 1
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| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
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| Platform ID |
GPL28731 |
| Series (1) |
| GSE152989 |
A method for spatially resolved tissue transcriptomics applied to the mouse and lizard P. vitticeps brains |
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| Relations |
| BioSample |
SAMN15341479 |
| SRA |
SRX8596910 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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