ALL RNA-seq publicly available data

Question

[a.james]

Hello All,

I need to do a correlation study with publicly available ALL RNA-seq data samples with in house RNA-seq sample (a single patient sample from different time series), to make the data statistics stronger. I would like to have a bigger patient cohort for my analysis so I was looking for publicly available RNA-seq samples from ALL(Acute lympoblastic Leukemia) patients.

Could any one suggest me with the database or website to find it .?In TGCA database has only AML samples and that too exome-seq

Thank you

[a.james]

Thank you so much for all suggestions, I will look into those.

Answer 1

[Emily]

Have you tried Expression Atlas?

[a.james]

No, I haven't. Thank you!

Answer 2

[matted]

I like DNANexus' SRA search tool since it has easier filtering by species and assay and has good metadata text search.

You can restrict it to studies in human with "RNA-seq" or "transcriptome analysis." Of those, we get:

• 121 studies matching "ALL": here
• Five matching "ALL leukemia": here
• Four matching "acute lymphoblastic leukemia": here

[a.james]

Thank you..! I would like have patient samples from different time series of the disease stage(like from Initial diagnosis to the Complete Remsion) .

Answer 3

[TriS]

NCBI GEO? ICGC?

Answer 4

[EagleEye]

You can use the datasets from here: These are microarray dataset but still you can see the correlation of the genes from your analysis (small dataset) in these dataset [they have Stage 1 (~2000 samples) and Stage II (~1000 samples) patients].