Question: ALL RNA-seq publicly available data
3
gravatar for a.james
4.0 years ago by
a.james160
Germany
a.james160 wrote:

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

rna-seq • 7.4k views
ADD COMMENTlink modified 4.0 years ago by EagleEye6.2k • written 4.0 years ago by a.james160

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

 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by a.james160
3
gravatar for Emily_Ensembl
4.0 years ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k wrote:

Have you tried Expression Atlas?

ADD COMMENTlink written 4.0 years ago by Emily_Ensembl17k

No, I havent. Thank you.!

ADD REPLYlink written 4.0 years ago by a.james160
2
gravatar for matted
4.0 years ago by
matted7.0k
Boston, United States
matted7.0k wrote:

I like DNANexus's 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
ADD COMMENTlink written 4.0 years ago by matted7.0k

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

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by a.james160
1
gravatar for TriS
4.0 years ago by
TriS3.6k
United States, Buffalo
TriS3.6k wrote:

NCBI GEO? ICGC?

ADD COMMENTlink written 4.0 years ago by TriS3.6k
1
gravatar for EagleEye
4.0 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

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].

http://www.leukemia-gene-atlas.org/LGAtlas/LGAtlas.html

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by EagleEye6.2k
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