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Series GSE161259 Query DataSets for GSE161259
Status Public on Nov 12, 2020
Title Hi-C ES and neocortex from Bonev et al. 2017
Sample organism Mus musculus
Experiment type Other
Third-party reanalysis
Summary Reanalysis of some Hi-C from Bonev et al. 2017 with HiCUP version 0.6.1
 
Overall design This is a third-party reanalysis of some datasets of GSE96107 to provide a more friendly format
data processing: Fastq were retrieved from SRA. They were processed with HiCUP v0.6.1 specifying DpnII, ^GATC as enzyme. Pairs were extracted with custom python script. The 4 replicates were merged. Pairs were split by chromosome and sorted. All scripts are available at https://github.com/lldelisle/Hi-C_reanalysis_Bonev_2017 .
Genome build: mm10
Files: text file in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2><frag2> <mapq1> <mapq2> with str = strand (0 for forward, anything else for reverse), pos = middle of the fragment.)
 
Contributor(s) Lopez-Delisle L, Duboule D
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 11, 2020
Last update date Feb 22, 2022
Contact name Lucille Lopez-Delisle
E-mail(s) lucille.delisle@epfl.ch
Organization name EPFL
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Relations
Reanalysis of GSM2533818
Reanalysis of GSM2533819
Reanalysis of GSM2533820
Reanalysis of GSM2533821
Reanalysis of GSM2533835
Reanalysis of GSM2533836
Reanalysis of GSM2533837
Reanalysis of GSM2533838
Reanalysis of GSM2533839
Reanalysis of GSM2533840
Reanalysis of GSM2533841
Reanalysis of GSM2533842
Reanalysis of GSE96107

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE161259_ES_chr1.validPairs.csort.txt.gz 3.6 Gb (ftp)(http) TXT
GSE161259_ES_chr10.validPairs.csort.txt.gz 2.4 Gb (ftp)(http) TXT
GSE161259_ES_chr11.validPairs.csort.txt.gz 3.3 Gb (ftp)(http) TXT
GSE161259_ES_chr12.validPairs.csort.txt.gz 2.1 Gb (ftp)(http) TXT
GSE161259_ES_chr13.validPairs.csort.txt.gz 2.1 Gb (ftp)(http) TXT
GSE161259_ES_chr14.validPairs.csort.txt.gz 2.0 Gb (ftp)(http) TXT
GSE161259_ES_chr15.validPairs.csort.txt.gz 2.0 Gb (ftp)(http) TXT
GSE161259_ES_chr16.validPairs.csort.txt.gz 1.8 Gb (ftp)(http) TXT
GSE161259_ES_chr17.validPairs.csort.txt.gz 1.6 Gb (ftp)(http) TXT
GSE161259_ES_chr18.validPairs.csort.txt.gz 1.6 Gb (ftp)(http) TXT
GSE161259_ES_chr19.validPairs.csort.txt.gz 1.2 Gb (ftp)(http) TXT
GSE161259_ES_chr1_GL456210_random.validPairs.csort.txt.gz 1.4 Kb (ftp)(http) TXT
GSE161259_ES_chr1_GL456211_random.validPairs.csort.txt.gz 2.9 Kb (ftp)(http) TXT
GSE161259_ES_chr1_GL456212_random.validPairs.csort.txt.gz 886 b (ftp)(http) TXT
GSE161259_ES_chr1_GL456221_random.validPairs.csort.txt.gz 827 b (ftp)(http) TXT
GSE161259_ES_chr2.validPairs.csort.txt.gz 3.6 Gb (ftp)(http) TXT
GSE161259_ES_chr3.validPairs.csort.txt.gz 2.7 Gb (ftp)(http) TXT
GSE161259_ES_chr4.validPairs.csort.txt.gz 2.9 Gb (ftp)(http) TXT
GSE161259_ES_chr4_GL456216_random.validPairs.csort.txt.gz 116.4 Kb (ftp)(http) TXT
GSE161259_ES_chr4_JH584292_random.validPairs.csort.txt.gz 2.0 Kb (ftp)(http) TXT
GSE161259_ES_chr4_JH584295_random.validPairs.csort.txt.gz 167 b (ftp)(http) TXT
GSE161259_ES_chr5.validPairs.csort.txt.gz 2.8 Gb (ftp)(http) TXT
GSE161259_ES_chr5_JH584299_random.validPairs.csort.txt.gz 1.8 Kb (ftp)(http) TXT
GSE161259_ES_chr6.validPairs.csort.txt.gz 2.7 Gb (ftp)(http) TXT
GSE161259_ES_chr7.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ES_chr8.validPairs.csort.txt.gz 3.1 Gb (ftp)(http) TXT
GSE161259_ES_chr9.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ES_chrM.validPairs.csort.txt.gz 2.3 Mb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456239.validPairs.csort.txt.gz 39.3 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456359.validPairs.csort.txt.gz 8.9 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456360.validPairs.csort.txt.gz 35.4 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456366.validPairs.csort.txt.gz 29.7 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456367.validPairs.csort.txt.gz 10.1 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456368.validPairs.csort.txt.gz 6.6 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456370.validPairs.csort.txt.gz 8.9 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456372.validPairs.csort.txt.gz 1.2 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456378.validPairs.csort.txt.gz 2.6 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456379.validPairs.csort.txt.gz 22.7 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456381.validPairs.csort.txt.gz 9.6 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456382.validPairs.csort.txt.gz 3.7 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456383.validPairs.csort.txt.gz 16.4 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456385.validPairs.csort.txt.gz 11.2 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456387.validPairs.csort.txt.gz 6.5 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456389.validPairs.csort.txt.gz 4.0 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456390.validPairs.csort.txt.gz 13.4 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456392.validPairs.csort.txt.gz 11.0 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456393.validPairs.csort.txt.gz 86.9 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456394.validPairs.csort.txt.gz 7.9 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_GL456396.validPairs.csort.txt.gz 4.6 Kb (ftp)(http) TXT
GSE161259_ES_chrUn_JH584304.validPairs.csort.txt.gz 380.9 Kb (ftp)(http) TXT
GSE161259_ES_chrX.validPairs.csort.txt.gz 1.1 Gb (ftp)(http) TXT
GSE161259_ES_chrX_GL456233_random.validPairs.csort.txt.gz 565.6 Kb (ftp)(http) TXT
GSE161259_ES_chrY.validPairs.csort.txt.gz 4.1 Mb (ftp)(http) TXT
GSE161259_ES_trans.validPairs.csort.txt.gz 12.6 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr1.validPairs.csort.txt.gz 4.1 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr10.validPairs.csort.txt.gz 2.6 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr11.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr12.validPairs.csort.txt.gz 2.2 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr13.validPairs.csort.txt.gz 2.3 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr14.validPairs.csort.txt.gz 2.2 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr15.validPairs.csort.txt.gz 2.0 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr16.validPairs.csort.txt.gz 1.9 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr17.validPairs.csort.txt.gz 1.6 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr18.validPairs.csort.txt.gz 1.7 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr19.validPairs.csort.txt.gz 1.0 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr1_GL456210_random.validPairs.csort.txt.gz 1.5 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chr1_GL456211_random.validPairs.csort.txt.gz 2.9 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chr1_GL456212_random.validPairs.csort.txt.gz 638 b (ftp)(http) TXT
GSE161259_ncx_CN_chr1_GL456221_random.validPairs.csort.txt.gz 973 b (ftp)(http) TXT
GSE161259_ncx_CN_chr2.validPairs.csort.txt.gz 3.8 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr3.validPairs.csort.txt.gz 3.2 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr4.validPairs.csort.txt.gz 3.0 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr4_GL456216_random.validPairs.csort.txt.gz 83.1 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chr4_JH584292_random.validPairs.csort.txt.gz 5.4 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chr4_JH584295_random.validPairs.csort.txt.gz 105 b (ftp)(http) TXT
GSE161259_ncx_CN_chr5.validPairs.csort.txt.gz 2.9 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr5_GL456354_random.validPairs.csort.txt.gz 134 b (ftp)(http) TXT
GSE161259_ncx_CN_chr5_JH584296_random.validPairs.csort.txt.gz 117 b (ftp)(http) TXT
GSE161259_ncx_CN_chr5_JH584299_random.validPairs.csort.txt.gz 1.3 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chr6.validPairs.csort.txt.gz 3.0 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr7.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr8.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chr9.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chrM.validPairs.csort.txt.gz 1.1 Mb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456239.validPairs.csort.txt.gz 72.3 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456359.validPairs.csort.txt.gz 12.0 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456360.validPairs.csort.txt.gz 22.0 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456366.validPairs.csort.txt.gz 16.8 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456367.validPairs.csort.txt.gz 11.8 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456368.validPairs.csort.txt.gz 1.2 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456370.validPairs.csort.txt.gz 30.9 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456372.validPairs.csort.txt.gz 705 b (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456378.validPairs.csort.txt.gz 4.6 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456379.validPairs.csort.txt.gz 33.7 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456381.validPairs.csort.txt.gz 14.3 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456382.validPairs.csort.txt.gz 3.5 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456383.validPairs.csort.txt.gz 25.7 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456385.validPairs.csort.txt.gz 6.5 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456387.validPairs.csort.txt.gz 4.7 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456389.validPairs.csort.txt.gz 7.7 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456390.validPairs.csort.txt.gz 23.4 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456392.validPairs.csort.txt.gz 16.1 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456393.validPairs.csort.txt.gz 83.9 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456394.validPairs.csort.txt.gz 12.7 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_GL456396.validPairs.csort.txt.gz 7.1 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrUn_JH584304.validPairs.csort.txt.gz 452.9 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrX.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_CN_chrX_GL456233_random.validPairs.csort.txt.gz 764.2 Kb (ftp)(http) TXT
GSE161259_ncx_CN_chrY.validPairs.csort.txt.gz 31.4 Kb (ftp)(http) TXT
GSE161259_ncx_CN_trans.validPairs.csort.txt.gz 22.7 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr1.validPairs.csort.txt.gz 3.9 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr10.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr11.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr12.validPairs.csort.txt.gz 2.2 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr13.validPairs.csort.txt.gz 2.2 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr14.validPairs.csort.txt.gz 2.1 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr15.validPairs.csort.txt.gz 1.9 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr16.validPairs.csort.txt.gz 1.8 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr17.validPairs.csort.txt.gz 1.6 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr18.validPairs.csort.txt.gz 1.7 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr19.validPairs.csort.txt.gz 1.1 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr1_GL456210_random.validPairs.csort.txt.gz 1.2 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chr1_GL456211_random.validPairs.csort.txt.gz 2.6 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chr1_GL456212_random.validPairs.csort.txt.gz 509 b (ftp)(http) TXT
GSE161259_ncx_NPC_chr1_GL456221_random.validPairs.csort.txt.gz 658 b (ftp)(http) TXT
GSE161259_ncx_NPC_chr2.validPairs.csort.txt.gz 3.8 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr3.validPairs.csort.txt.gz 3.0 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr4.validPairs.csort.txt.gz 2.9 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr4_GL456216_random.validPairs.csort.txt.gz 74.5 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chr4_JH584292_random.validPairs.csort.txt.gz 4.5 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chr5.validPairs.csort.txt.gz 2.9 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr5_JH584299_random.validPairs.csort.txt.gz 1.0 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chr6.validPairs.csort.txt.gz 2.9 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr7.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr8.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chr9.validPairs.csort.txt.gz 2.5 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chrM.validPairs.csort.txt.gz 580.1 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456239.validPairs.csort.txt.gz 59.9 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456359.validPairs.csort.txt.gz 10.8 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456360.validPairs.csort.txt.gz 18.9 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456366.validPairs.csort.txt.gz 15.6 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456367.validPairs.csort.txt.gz 8.8 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456368.validPairs.csort.txt.gz 835 b (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456370.validPairs.csort.txt.gz 25.5 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456372.validPairs.csort.txt.gz 654 b (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456378.validPairs.csort.txt.gz 3.4 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456379.validPairs.csort.txt.gz 24.4 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456381.validPairs.csort.txt.gz 10.1 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456382.validPairs.csort.txt.gz 2.8 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456383.validPairs.csort.txt.gz 20.5 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456385.validPairs.csort.txt.gz 5.3 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456387.validPairs.csort.txt.gz 3.3 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456389.validPairs.csort.txt.gz 5.7 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456390.validPairs.csort.txt.gz 19.1 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456392.validPairs.csort.txt.gz 12.9 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456393.validPairs.csort.txt.gz 61.7 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456394.validPairs.csort.txt.gz 9.5 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_GL456396.validPairs.csort.txt.gz 6.0 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrUn_JH584304.validPairs.csort.txt.gz 385.2 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrX.validPairs.csort.txt.gz 2.2 Gb (ftp)(http) TXT
GSE161259_ncx_NPC_chrX_GL456233_random.validPairs.csort.txt.gz 599.5 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_chrY.validPairs.csort.txt.gz 31.7 Kb (ftp)(http) TXT
GSE161259_ncx_NPC_trans.validPairs.csort.txt.gz 18.2 Gb (ftp)(http) TXT
Processed data are available on Series record
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