Question: Publicly available brain tissue (any part) Histone (H3K27me3 and H3K4me3) ChIP-seq samples
0
gravatar for EagleEye
18 months ago by
EagleEye6.7k
Sweden
EagleEye6.7k wrote:

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.

sequencing chip-seq next-gen • 418 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by EagleEye6.7k
1

There are some from human on ENCODE. Check if they fulfill your criteria.

ADD REPLYlink written 18 months ago by ATpoint40k

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

ADD REPLYlink modified 18 months ago • written 18 months ago by EagleEye6.7k
2
gravatar for genomax
18 months ago by
genomax91k
United States
genomax91k wrote:

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
ADD COMMENTlink modified 18 months ago • written 18 months ago by genomax91k

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.

ADD REPLYlink written 18 months ago by EagleEye6.7k

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

ADD REPLYlink written 18 months ago by genomax91k

I will have a look :)

ADD REPLYlink written 18 months ago by EagleEye6.7k
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