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| Status |
Public on Aug 18, 2014 |
| Title |
HiC crwn4 |
| Sample type |
SRA |
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| Source name |
aerial tissue of 14-day-old seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype/variation: homozygous crwn4-1
age: 14-day-old seedlings
tissue: aerial tissue of seedlings
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiC template DNA was prepared according to Lieberman et al. 2009 with minor changes. For detailed protocol see attached publication
HiC libraries were prepared based on TruSeq DNA Library Preparation Protocol with minor changes. For detailed descriptio see attached publication
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
library strategy: HiC-seq
alignment using bowtie version 0.12.7 with the following parameters: -v 0 -m 1 -a
The aligned read-pairs were used to create an interaction matrix, in which each row (and column) corresponds to one fragment, and values represent the number of read-pairs aligned to the respective fragments.
Matrices were corrected for systematic biases using the approach from Jin et al., 2013
Matrices were binned into larger stretches along the genome (windows of size 10 kb, 25 kb, 50 kb, 100 kb, and 250 kb)
Genome_build: TAIR10
Supplementary_files_format_and_content: .txt formated file, containing pairs of genomic bin numbers and their interaction counts
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| Submission date |
Mar 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Grob |
| E-mail(s) |
sgrob@botinst.uzh.ch
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| Organization name |
University of Zurich
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| Department |
Institute of Plant Biology
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| Lab |
Grossniklaus Lab
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| Street address |
Zollikerstrasse 107
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| City |
Zurich |
| ZIP/Postal code |
8008 |
| Country |
Switzerland |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE55960 |
Chromosomal Architecture of Arabidopsis and its Implication in Transposon Intergration |
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| Relations |
| BioSample |
SAMN02689878 |
| SRA |
SRX494134 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1349331_HiC_crwn4_R1R2_winList_10000.txt.gz |
35.9 Mb |
(ftp)(http) |
TXT |
| GSM1349331_HiC_crwn4_R1R2_winList_100000.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSM1349331_HiC_crwn4_R1R2_winList_200000.txt.gz |
697.7 Kb |
(ftp)(http) |
TXT |
| GSM1349331_HiC_crwn4_R1R2_winList_25000.txt.gz |
19.5 Mb |
(ftp)(http) |
TXT |
| GSM1349331_HiC_crwn4_R1R2_winList_250000.txt.gz |
465.2 Kb |
(ftp)(http) |
TXT |
| GSM1349331_HiC_crwn4_R1R2_winList_50000.txt.gz |
8.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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