User: bhchiang

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bhchiang0
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Posts by bhchiang

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Converting expected counts to TPM values
... I want to obtain TPM values for MCF-10A RNA-seq. Does anybody know to convert expected counts values to TPM values? Thanks so much! Link to expected counts: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71862 ...
rnaseq expected-counts reads mcf10a tpm written 2.3 years ago by bhchiang0 • updated 2.3 years ago by Kevin Blighe60k
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Comment: C: Looking for DNase-seq of MCF10A cell line
... Got it. I'll give it a shot, thanks. If possible, could you link me to any tutorials you've useful for aligning DNase-seq files? ...
written 2.3 years ago by bhchiang0
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Comment: C: Looking for DNase-seq of MCF10A cell line
... Would it be possible to simply perform CrossOver on the hg38 MCF10A DNase-seq coordinates instead of realigning them? Or will realigning them be more accurate? Thanks! ...
written 2.3 years ago by bhchiang0
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Looking for DNase-seq of MCF10A cell line
... Where can I find data from a DNase-seq assay of the non-cancerous MCF10A breast cell line aligned to the hg19 genome? I've found the following: - MCF10A-ER-Src (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2676283) - MCF10A aligned to hg38 with only one biological replicate (https://www ...
ngs cancer mcf10a dnase-seq breast written 2.3 years ago by bhchiang0
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Comment: C: Where can I find DNase-seq assays of cell line MCF-10A?
... I'm doing something similar to a DNase-seq DNase-seq comparison across cell lines, so I'd prefer both to be DNase-seq. Thanks! ...
written 2.6 years ago by bhchiang0
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Comment: C: Where can I find DNase-seq assays of cell line MCF-10A?
... Most of the assays for MCF-10A are either ChIP-seq or non-DNase-seq assays (`https://www.ncbi.nlm.nih.gov/sra/?term=mcf-10a`). A search for both 'mcf-10a' and 'dnase-seq' yields no results (`https://www.ncbi.nlm.nih.gov/sra/?term=mcf-10a+dnase-seq`). Thanks for your help! ...
written 2.7 years ago by bhchiang0
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Comment: C: Where to find DNase-seq and RNA-seq assays for various cancer lines?
... Thanks for the answer! Do you know how long the application process typically takes or what it involves? Thanks! ...
written 2.7 years ago by bhchiang0
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Where to find DNase-seq and RNA-seq assays for various cancer lines?
... Does anyone know where to find DNase-seq or/and RNA-seq assays of different cancer cell lines (no special treatments). I've tried looking at the SRA, but the assays I could find there are mostly studying the effects of different drugs/treatments on cancer cell lines. Thanks. ...
genome geo dnase-seq rna-seq sequencing written 2.7 years ago by bhchiang0 • updated 2.7 years ago by jared.andrews075.5k

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