|
| Status |
Public on Jan 21, 2022 |
| Title |
RNIC_2_NICD_TCFWT [Hi-C] |
| Sample type |
SRA |
| |
|
| Source name |
BM LSK (Lin- Sca1+ cKit+)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J; Sv/129
transgene: R26 N1IC lox/+ Mx1Cre
cre: Mx1Cre induction 2ug/g b.w. poly(I:C)
facs sorting: Target population from bone marrow: CD45.2+ eGFP+ Lin- Sca1+ cKit+
group: NICD_TCFWT
replicate: 1
batch: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Low input in situ Hi-C was performed on 150,000 LSKs with Arima-HiC Kit (Arima) according to the manufacturers’ protocols.
DNA fragmentation was performed on Covaris E220 Evolution sonicator (Covaris Cat# 500429) with default settings for 400bp DNA size distribution.
Libraries for sequencing were prepared with Swift Biosciences Accel-NGS 2S Plus DNA Dual Indexing Library Kit (Swift Biosciences Cat# 21024 and #28096). Size selection steps were performed with Agencourt AMPure XP magnetic beads (Beckman Coulter). Library amplification was performed following DNA quantification with Invitrogen Qubit Fluorometer and KAPA Library Quantification Kit (Roche Cat# 07958927001).
sequencing protocol: Prepared libraries were sequenced using the sequencing platforms at Novogene with Illumina NovaSeq 6000 S4 and the 150 bp paired-end reads generating around 700 million paired reads per library.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Hi-C paired-end sequencing reads for each sample were filtered and aligned to the mouse genome (mm10) using the Juicer pipeline (version 1.6) with the restriction site coordinates of the restriction enzymes used in the Arima-HiC kit (cutting at GATC and GANTC). Aligned Hi-C contacts with an alignment score > 30 (MAPQ > 30) from individual replicates were combined using the “mega.sh” script provided with Juicer. Chromatin contact maps from pooled data were created using the “pre” command at custom (2.5 kb and 5 – 25 kb with a 1 kb increase) and default (50, 100, 250, 500 kb, 1, and 2.5 Mb) resolutions.
Chromatin contact domains were identified in KR normalized chromatin contact maps at 5 kb resolution using Arrowhead from Juicer tools version 1.6. (Rao et al. 2014).
Chromatin loops were called at 2.5 and 5 to 25 kb resolutions (with a 1 kb increase) with HiCCUPS from Juicer tools version 1.6 (Rao et al. 2014) using custom parameters for peak size (p), window size (i) and distances for merging nearby pixels to a centroid (d).
For detailed description of methods and parameters, please refer to the material and method section of the main publication.
Genome_build: mm10
Supplementary_files_format_and_content: Contact matrices in 2 resolutions in hic format; TADs in 5Kb resolution in bedpe format, loops in all resolutions in bedpe format.
|
| |
|
| Submission date |
Mar 18, 2021 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Nadine Fournier |
| E-mail(s) |
nadine.fournier@sib.swiss
|
| Organization name |
Agora Cancer Research Center & Swiss Institute of Bioinformatics
|
| Lab |
Translational Data Science Facility
|
| Street address |
Agora Cancer Research Center, Bugon 25A
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1000 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE169120 |
3D chromatin topography of LSK cells with hyperactivated Notch1 and/or Tcf7 knock-out [HiC-seq] |
| GSE169121 |
Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology. |
|
| Relations |
| BioSample |
SAMN18350793 |
| SRA |
SRX10378836 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5179465_RNIC_5000_blocks.bedpe.gz |
201.3 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_inter_30.hic |
9.6 Gb |
(ftp)(http) |
HIC |
| GSM5179465_RNIC_inter_30_2500.hic |
6.1 Gb |
(ftp)(http) |
HIC |
| GSM5179465_RNIC_postprocessed_pixels_10000.bedpe.gz |
654.3 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_11000.bedpe.gz |
687.1 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_12000.bedpe.gz |
676.3 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_13000.bedpe.gz |
689.8 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_14000.bedpe.gz |
676.5 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_15000.bedpe.gz |
661.1 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_16000.bedpe.gz |
655.7 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_17000.bedpe.gz |
663.7 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_18000.bedpe.gz |
649.1 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_19000.bedpe.gz |
649.8 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_20000.bedpe.gz |
615.3 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_21000.bedpe.gz |
646.5 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_22000.bedpe.gz |
628.7 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_23000.bedpe.gz |
629.6 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_24000.bedpe.gz |
606.3 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_2500.bedpe.gz |
143.6 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_25000.bedpe.gz |
594.1 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_5000.bedpe.gz |
534.0 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_6000.bedpe.gz |
607.5 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_7000.bedpe.gz |
656.2 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_8000.bedpe.gz |
661.5 Kb |
(ftp)(http) |
BEDPE |
| GSM5179465_RNIC_postprocessed_pixels_9000.bedpe.gz |
704.7 Kb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
