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I want to download the next generation RNA sequencing data in different cell lines. I want the data (alongwith normal) for p53 wild type, p53 knock-out and p53 null cell lines (human colon cancer). From where do I download this data? In fastq format if possible.

Currently, I am going through SRA, to look for the datasets, using their search engine. But the process is extremely tedious.

Also can someone please hint about how to download the data from SRA, in case that's the only way to get data. I'm getting very confused.

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  • $\begingroup$ Welcome to the site. Could you help us explaining if you could manage to download any dataset? Also, what kind of sequencing data do you want: single-cell RNa-seq, long read or bulk RNA-seq? Also if you could clarify if you have some preference for a programming language to automatize the process it would help too $\endgroup$
    – llrs
    Feb 14, 2019 at 14:29
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    $\begingroup$ Hello, What exactly you find tidious? If you search for "p53 AND "Homo sapiens"[orgn:__txid9606]" you get plenty of hits for NULL and WT. For example reads liked to this project. If you want fastq files, you can pull them from ftp server once you know IDs, here is an example: ftp.sra.ebi.ac.uk/vol1/fastq/SRR835/SRR835937 $\endgroup$
    – Kamil S Jaron
    Feb 14, 2019 at 15:30
  • $\begingroup$ Hello, thank you all for such an immediate response. Ilrs, I want RNA seq data obtained from p53 WT, NULL and KO colon cancer cell lines, without any other modifications in the cell. I'm not bothered about programming language for further analysis now. I am actually new to this, and I don't know if I am collecting the right kind of data or not. Kamil, these are shPFKFB4 silenced. I want normal vs experiment data from same experiment if possible. I might be making very silly mistakes, I apologise for the same. Thanks for your help. $\endgroup$
    – Chaitanyaraj Jadeja
    Feb 15, 2019 at 5:56
  • $\begingroup$ Downloading from ENA is simpler: ebi.ac.uk/ena $\endgroup$
    – swbarnes2
    Feb 15, 2019 at 17:47

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I suggest you to try difference resources, including ArrayExpress. A simple search at ArrayExpress returns multiple experiments which might be of your interest. Just a pointer, ArrayExpress is also synced with GEO.

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I agree with Kamil on the downloading method. Moreover, SRA will give you your file in the raw format which is usually a Binary Alignment Map (BAM) or Sequence Alignment Map (SAM) Download SRA toolkit available online, to convert your raw reads to fastq format. Follow the steps using command line. It is a very simple command to convert your SRA file to fastq which uses the fastq-dump command.

Further reading: https://www.ncbi.nlm.nih.gov/books/NBK158900/

Hope it helps!

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  • $\begingroup$ Hello Pawan, my main concern here it to pinpoint the data I require from the database. I am not able to find the data I require. I'm aware about fastq-dump. Thank you for your efforts. $\endgroup$
    – Chaitanyaraj Jadeja
    Feb 15, 2019 at 11:18
  • $\begingroup$ I understand! Since you had asked if it was possible to download in fastq format, i had answered accordingly. Cheers $\endgroup$
    – Pawan Verma
    Feb 15, 2019 at 11:21
  • $\begingroup$ Thanks. Actually, when I'm using fastq-dump, all I see upon execution of command is a bunch of .cache files.Also, as huge files in GB scale take time to download, I would like to know if there is a way where we can track the progress of download? $\endgroup$
    – Chaitanyaraj Jadeja
    Feb 15, 2019 at 11:26
  • $\begingroup$ Can you specify the size of your file? $\endgroup$
    – Pawan Verma
    Feb 15, 2019 at 11:28
  • $\begingroup$ Last file I tried downloading was roughly 12GB. Max download speed on my network is 550kbps. $\endgroup$
    – Chaitanyaraj Jadeja
    Feb 15, 2019 at 11:29

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