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Dane transkryptomiczne mikrosporocytów Modrzewia europejskiego

Version 1.0

Majewska, Karolina, 2024, "Dane transkryptomiczne mikrosporocytów Modrzewia europejskiego", https://doi.org/10.18150/OT1YUD, RepOD, V1

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Description

Dane transkrypotmiczne pochodzące z analizy dwóch frakcji komórkowych rożniących się etapem cyklu syntezy i eksportu poliadenylowanych transkryptów.


1. Dane

Przygotowano dane pochodzące z sekwencjonowania nowej generacji dla 30 bibliotek cDNA. Sekwencjonowanie wykonano na sekwenatorze NovaSeq6000 (Illlumina) w trybie PE 150 zasad. Podstawowa analiza bioinformatyczna polegała na przycinaniu i filtrowaniu jakościowym odczytów dla 30 próbek małych cDNA z Modrzewia europejskiego (Larix decidua).  

2. Oprogramowanie

Pierwszym wykonanym etapem było przycięcie surowych odczytów, które zostało wykonane przy użyciu programu Cutadapt v3.0 [1]. Filtrowanie przeprowadzono przy zastosowaniu minimalnej długości odczytów m 15. Kolejno przeprowadzono kontrolę jakości odczytów przy użyciu programu FastQC (version 0.11.8) [2], na podstawie której sporządzono raport podsumowujący stan próbek po wstępnej obróbce. Dodatkowo wykorzystano program MultiQC do stworzenia zbiorczego raportu dla wszystkich sekwencjonowanych próbek.  

3. Zestawienie liczby odczytów:


Nr Nazwa.próbki Iliczba.par.odczytów

1 A1-3 23644147

2 A1-2 20518828

3 A1-1 18232531

4 A2-3 19408284

5 A2-2 16124974

6 A2-1 12465768

7 A3-3 23557627

8 A3-2 17242499

9 A3-1 17477840

10 A4-3 19331991

11 A4-2 19259448

12 A4-1 20835305

13 A5-2 15311792

14 A5-1 17880328

15 A6-3 20233751

16 A6-2 20005771

17 A6-1 19798804

18 A7-3 21397761

19 A7-2 22521336

20 A7-1 23089811

21 A8-3 31130204

22 A8-2 25446819

23 A8-1 20566345

24 A9-3 29593782

25 A9-3 29593782

26 A9-2 27848215

27 A9-1 25099159

28 A10-3 4667178

29 A10-2 13220392

30 A10-1 16472548

4. Zawartość katalogu wynikowego

Katalog z całością wyników zawiera:

  • katalog quality_report zawierający
  • raporty jakości dla analizowanych próbek (katalog fastqc),
  • interaktywny raport przedstawiający wyniki kontrolo jakości wszystkich próbek (multiqc_report).
  • zbiorcze zestawienie statystyk jakościowych dla odczytów filtrowanych (quality_report-html, quality_report-pdf)


 

5. Literatura

  1. Marcel M., Cutadapt removes adapter sequences from high-throughput sequencing reads,EMBnet.journal, [S.l.], v. 17, n. 1, p. pp. 10-12, may. 2011. ISSN 2226-6089.
  2. Andrews, S., FASTQC. A quality control tool for high throughput sequence data, (2010). Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  3. MultiQC: Summarize analysis results for multiple tools and samples in a single report Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller. Bioinformatics (2016)


Subject
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Keyword

transkryptom, poli(A)RNA, mikrosporocyty

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