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Publicly available brain tissue (any part) Histone (H3K27me3 and H3K4me3) ChIP-seq samples
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21 months ago
EagleEye 6.4k
@EagleEye12958

Hello everyone,

I am looking for H3K4me3 and H3K27me3 ChIP-seq (Illumina) samples for human brain tissue samples (FASTQ, any region of brain). I need greater than 36 bp read length or atleast 50 bp read length samples with proper input (control). I could not find it on Roadmap & ENCODE. Kindly please let me know if there are any samples available.

Thanks.

ChIP-Seq sequencing next-gen • 178 views
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There are some from human on ENCODE. Check if they fulfill your criteria.

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All those samples are either 36 bp read length or embryo samples (looking for adult brain). Anyway thank for the effort :)

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21 months ago
genomax 68k
@genomax

Have you tried SRA-Explorer for a search. Posting small samples below. H3K4me3[All Fields] AND brain[All Fields] AND ("Homo sapiens"[Organism] OR ("Homo sapiens"[Organism] OR human[All Fields]))?

   GSM1821387: H3K4me3 Human Brain Cerebellum HS1; Homo sapiens; ChIP-Seq   SRR2102199  Illumina HiSeq 2000     5378    13 Jan 2016
    GSM1821388: H3K4me3 Human Brain OccipitalPole HS1; Homo sapiens; ChIP-Seq   SRR2102200  Illumina HiSeq 2000     4980    13 Jan 2016
    GSM1821389: H3K4me3 Human Brain PrecentralGyrus HS1; Homo sapiens; ChIP-Seq     SRR2102201  Illumina HiSeq 2000     6395    13 Jan 2016
    GSM1821390: H3K4me3 Human Brain Putamen HS1; Homo sapiens; ChIP-Seq     SRR2102202  Illumina HiSeq 2000     7890    13 Jan 2016

With H3K27me3[All Fields] AND brain[All Fields] AND ("Homo sapiens"[Organism] OR human[All Fields])

H3K27me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC01 (A03488)     SRR2172585  Illumina HiSeq 2000     31599   25 Mar 2016
    H3K27me3 ChIP-Seq analysis of fetal brain tissue from HuFNSC02 (A03496)     SRR2172591  Illumina HiSeq 2000     37130   25 Mar 2016
    H3K27me3 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03504)  SRR2172598  Illumina HiSeq 2000     27016   25 Mar 2016
    H3K27me3 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03504)  SRR2172599  Illumina HiSeq 2000     33818   25 Mar 2016
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Thanks for the information. Looks like SRR2172598 and SRR2172599 are not publicly available (they are protected under dbGAP). Still struggling to get H3K27me3 ChIP-seq.

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There was a much larger list that you may need to look through. I only copied a few entries.

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I will have a look :)

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